From c1d56ac8e5f4a240f18969816e124f59313432cf Mon Sep 17 00:00:00 2001
From: Jan Caron <j.caron@fz-juelich.de>
Date: Sun, 25 Aug 2013 11:17:14 +0200
Subject: [PATCH] Sphinx and NetCDF4 support implemented, new features for
pyramid objects pyramid: all docstrings in numpydoc (package installed)
format (used by spinx) holoimage: removed error, phase was falsely multiplied
by pi/2 magcreator: removed create_mag_dist_comb, renamed functions for disc
and vortex magdata: Allows creation of empty MagData objects and easy adding
of magnitudes phasemap: Allows units to be set for plots, added 3D plot
phasemapper: Electrostatic component implemented projector: Projection now
includes thickness profile docs: support for html, latex and pdf
(experimental), use "make *" in shell scripts: new structure, deleted some
compare_* functions, added test_methods .hpignore: now also ignores *.c and
_* files (_build used in docs)
---
.hgignore | 2 +
docs/Makefile | 159 +
docs/conf.py | 383 +
docs/index.rst | 23 +
docs/make.bat | 197 +
docs/pyramid.numcore.rst | 12 +
docs/pyramid.rst | 82 +
pyramid/__init__.py | 28 +
pyramid/analytic.py | 174 +-
pyramid/holoimage.py | 112 +-
pyramid/magcreator.py | 288 +-
pyramid/magdata.py | 336 +-
pyramid/numcore/__init__.py | 14 +
pyramid/numcore/phase_mag_real.c | 18750 ----------------
pyramid/numcore/phase_mag_real.pyx | 41 +-
pyramid/phasemap.py | 289 +-
pyramid/phasemapper.py | 417 +-
pyramid/projector.py | 52 +-
pyramid/reconstructor.py | 49 +-
.../{ => compare methods}/compare_methods.py | 13 +-
.../compare_pixel_fields.py | 26 +-
scripts/compare_discs.py | 93 -
.../compare_method_errors_fourier_padding.py | 102 -
scripts/compare_method_errors_res.py | 551 -
scripts/compare_vortices.py | 98 -
.../create_alternating_filaments.py | 23 +-
.../{ => create distributions}/create_logo.py | 3 +-
.../create_multiple_samples.py | 25 +-
.../create_random_pixels.py | 26 +-
.../create_random_slabs.py | 25 +-
.../create_sample.py | 16 +-
.../create_vortex.py | 7 +-
scripts/{ => gui}/gui_create_logo.py | 4 +-
.../ch5-0-evaluation_and_comparison.py | 22 +-
.../paper 1/ch5-1-evaluation_real_space.py | 88 +-
.../paper 1/ch5-2-evaluation_fourier_space.py | 309 +-
.../paper 1/ch5-3-comparison_of_methods.py | 39 +-
scripts/{ => reconstruction}/get_jacobi.py | 15 +-
.../reconstruct_random_pixels.py | 18 +-
scripts/test_methods.py | 74 +
40 files changed, 2447 insertions(+), 20538 deletions(-)
create mode 100644 docs/Makefile
create mode 100644 docs/conf.py
create mode 100644 docs/index.rst
create mode 100644 docs/make.bat
create mode 100644 docs/pyramid.numcore.rst
create mode 100644 docs/pyramid.rst
delete mode 100644 pyramid/numcore/phase_mag_real.c
rename scripts/{ => compare methods}/compare_methods.py (92%)
rename scripts/{ => compare methods}/compare_pixel_fields.py (63%)
delete mode 100644 scripts/compare_discs.py
delete mode 100644 scripts/compare_method_errors_fourier_padding.py
delete mode 100644 scripts/compare_method_errors_res.py
delete mode 100644 scripts/compare_vortices.py
rename scripts/{ => create distributions}/create_alternating_filaments.py (61%)
rename scripts/{ => create distributions}/create_logo.py (91%)
rename scripts/{ => create distributions}/create_multiple_samples.py (68%)
rename scripts/{ => create distributions}/create_random_pixels.py (62%)
rename scripts/{ => create distributions}/create_random_slabs.py (66%)
rename scripts/{ => create distributions}/create_sample.py (75%)
rename scripts/{ => create distributions}/create_vortex.py (85%)
rename scripts/{ => gui}/gui_create_logo.py (94%)
rename scripts/{ => reconstruction}/get_jacobi.py (74%)
rename scripts/{ => reconstruction}/reconstruct_random_pixels.py (74%)
create mode 100644 scripts/test_methods.py
diff --git a/.hgignore b/.hgignore
index ed3c92e..a9ff8eb 100644
--- a/.hgignore
+++ b/.hgignore
@@ -7,6 +7,8 @@ syntax: glob
*.pyd
*.so
*.os
+*.c
+_*
output*
build*
Pyramid.egg-info*
\ No newline at end of file
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..d0ca09c
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,159 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+PAPER =
+BUILDDIR = _build
+
+# Internal variables.
+PAPEROPT_a4 = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+ @echo "Please use \`make <target>' where <target> is one of"
+ @echo " html to make standalone HTML files"
+ @echo " dirhtml to make HTML files named index.html in directories"
+ @echo " singlehtml to make a single large HTML file"
+ @echo " pickle to make pickle files"
+ @echo " json to make JSON files"
+ @echo " htmlhelp to make HTML files and a HTML help project"
+ @echo " qthelp to make HTML files and a qthelp project"
+ @echo " devhelp to make HTML files and a Devhelp project"
+ @echo " epub to make an epub"
+ @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+ @echo " latexpdf to make LaTeX files and run them through pdflatex"
+ @echo " text to make text files"
+ @echo " man to make manual pages"
+ @echo " texinfo to make Texinfo files"
+ @echo " info to make Texinfo files and run them through makeinfo"
+ @echo " gettext to make PO message catalogs"
+ @echo " changes to make an overview of all changed/added/deprecated items"
+ @echo " linkcheck to check all external links for integrity"
+ @echo " doctest to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+ -rm -rf $(BUILDDIR)/*
+
+html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+ $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+ @echo
+ @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+json:
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+ @echo
+ @echo "Build finished; now you can run HTML Help Workshop with the" \
+ ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+ $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+ @echo
+ @echo "Build finished; now you can run "qcollectiongenerator" with the" \
+ ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+ @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pyramid.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pyramid.qhc"
+
+devhelp:
+ $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+ @echo
+ @echo "Build finished."
+ @echo "To view the help file:"
+ @echo "# mkdir -p $$HOME/.local/share/devhelp/pyramid"
+ @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pyramid"
+ @echo "# devhelp"
+
+epub:
+ $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+ @echo
+ @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo
+ @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+ @echo "Run \`make' in that directory to run these through (pdf)latex" \
+ "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through pdflatex..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+ $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+ @echo
+ @echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+ $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+ @echo
+ @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo
+ @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+ @echo "Run \`make' in that directory to run these through makeinfo" \
+ "(use \`make info' here to do that automatically)."
+
+info:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo "Running Texinfo files through makeinfo..."
+ make -C $(BUILDDIR)/texinfo info
+ @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+ $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+ @echo
+ @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+ @echo
+ @echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+ @echo
+ @echo "Link check complete; look for any errors in the above output " \
+ "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+ @echo "Testing of doctests in the sources finished, look at the " \
+ "results in $(BUILDDIR)/doctest/output.txt."
+
+pdf:
+ $(SPHINXBUILD) -b pdf $(ALLSPHINXOPTS) _build/pdf
+ @echo
+ @echo "Build finished. The PDF files are in _build/pdf."
+
\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000..259c097
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,383 @@
+# -*- coding: utf-8 -*-
+#
+# pyramid documentation build configuration file, created by
+# sphinx-quickstart on Tue Aug 20 12:15:35 2013.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+sys.path.insert(0, os.path.abspath('C:\Users\Jan\Home\PhD Thesis\Pyramid'))
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode', 'rst2pdf.pdfbuilder',
+ 'numpydoc']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'pyramid'
+copyright = u'2013, Jan Caron'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = ''
+# The full version, including alpha/beta/rc tags.
+release = ''
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents. If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'pyramiddoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+ ('index', 'pyramid.tex', u'pyramid Documentation',
+ u'Jan Caron', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ ('index', 'pyramid', u'pyramid Documentation',
+ [u'Jan Caron'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output ------------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ ('index', 'pyramid', u'pyramid Documentation',
+ u'Jan Caron', 'pyramid', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+
+# -- Options for Epub output ---------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = u'Pyramid'
+epub_author = u'Jan Caron'
+epub_publisher = u'Jan Caron'
+epub_copyright = u'2013, Jan Caron'
+
+# The language of the text. It defaults to the language option
+# or en if the language is not set.
+#epub_language = ''
+
+# The scheme of the identifier. Typical schemes are ISBN or URL.
+#epub_scheme = ''
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#epub_identifier = ''
+
+# A unique identification for the text.
+#epub_uid = ''
+
+# A tuple containing the cover image and cover page html template filenames.
+#epub_cover = ()
+
+# HTML files that should be inserted before the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_pre_files = []
+
+# HTML files shat should be inserted after the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_post_files = []
+
+# A list of files that should not be packed into the epub file.
+#epub_exclude_files = []
+
+# The depth of the table of contents in toc.ncx.
+#epub_tocdepth = 3
+
+# Allow duplicate toc entries.
+#epub_tocdup = True
+
+# -- Options for PDF output --------------------------------------------------
+# Grouping the document tree into PDF files. List of tuples
+# (source start file, target name, title, author, options).
+#
+# If there is more than one author, separate them with \\.
+# For example: r'Guido van Rossum\\Fred L. Drake, Jr., editor'
+#
+# The options element is a dictionary that lets you override
+# this config per-document.
+# For example,
+# ('index', u'MyProject', u'My Project', u'Author Name',
+# dict(pdf_compressed = True))
+# would mean that specific document would be compressed
+# regardless of the global pdf_compressed setting.
+
+pdf_documents = [
+('index', u'Pyramid', u'Pyramid', u'Jan Caron'),
+]
+
+# A comma-separated list of custom stylesheets. Example:
+pdf_stylesheets = ['sphinx','kerning','a4']
+
+# A list of folders to search for stylesheets. Example:
+pdf_style_path = ['.', '_styles']
+
+# Create a compressed PDF
+# Use True/False or 1/0
+# Example: compressed=True
+#pdf_compressed = False
+
+# A colon-separated list of folders to search for fonts. Example:
+# pdf_font_path = ['/usr/share/fonts', '/usr/share/texmf-dist/fonts/']
+
+# Language to be used for hyphenation support
+#pdf_language = "en_US"
+
+# Mode for literal blocks wider than the frame. Can be
+# overflow, shrink or truncate
+#pdf_fit_mode = "shrink"
+
+# Section level that forces a break page.
+# For example: 1 means top-level sections start in a new page
+# 0 means disabled
+#pdf_break_level = 0
+
+# When a section starts in a new page, force it to be 'even', 'odd',
+# or just use 'any'
+#pdf_breakside = 'any'
+
+# Insert footnotes where they are defined instead of
+# at the end.
+#pdf_inline_footnotes = True
+
+# verbosity level. 0 1 or 2
+#pdf_verbosity = 0
+
+# If false, no index is generated.
+#pdf_use_index = True
+
+# If false, no modindex is generated.
+#pdf_use_modindex = True
+
+# If false, no coverpage is generated.
+#pdf_use_coverpage = True
+
+# Name of the cover page template to use
+#pdf_cover_template = 'sphinxcover.tmpl'
+
+# Documents to append as an appendix to all manuals.
+#pdf_appendices = []
+
+# Enable experimental feature to split table cells. Use it
+# if you get "DelayedTable too big" errors
+#pdf_splittables = False
+
+# Set the default DPI for images
+#pdf_default_dpi = 72
+
+# Enable rst2pdf extension modules (default is only vectorpdf)
+# you need vectorpdf if you want to use sphinx's graphviz support
+#pdf_extensions = ['vectorpdf']
+
+# Page template name for "regular" pages
+#pdf_page_template = 'cutePage'
+
+# Show Table Of Contents at the beginning?
+#pdf_use_toc = True
+
+# How many levels deep should the table of contents be?
+pdf_toc_depth = 9999
+
+# Add section number to section references
+pdf_use_numbered_links = False
+
+# Background images fitting mode
+pdf_fit_background_mode = 'scale'
diff --git a/docs/index.rst b/docs/index.rst
new file mode 100644
index 0000000..9641203
--- /dev/null
+++ b/docs/index.rst
@@ -0,0 +1,23 @@
+.. pyramid documentation master file, created by
+ sphinx-quickstart on Tue Aug 20 12:15:35 2013.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to pyramid's documentation!
+===================================
+
+Contents:
+
+.. toctree::
+ :maxdepth: 4
+
+ pyramid
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 0000000..7a09652
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,197 @@
+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set BUILDDIR=_build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+set I18NSPHINXOPTS=%SPHINXOPTS% .
+if NOT "%PAPER%" == "" (
+ set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+ set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+ :help
+ echo.Please use `make ^<target^>` where ^<target^> is one of
+ echo. html to make standalone HTML files
+ echo. dirhtml to make HTML files named index.html in directories
+ echo. singlehtml to make a single large HTML file
+ echo. pickle to make pickle files
+ echo. json to make JSON files
+ echo. htmlhelp to make HTML files and a HTML help project
+ echo. qthelp to make HTML files and a qthelp project
+ echo. devhelp to make HTML files and a Devhelp project
+ echo. epub to make an epub
+ echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+ echo. text to make text files
+ echo. man to make manual pages
+ echo. texinfo to make Texinfo files
+ echo. gettext to make PO message catalogs
+ echo. changes to make an overview over all changed/added/deprecated items
+ echo. linkcheck to check all external links for integrity
+ echo. doctest to run all doctests embedded in the documentation if enabled
+ goto end
+)
+
+if "%1" == "clean" (
+ for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+ del /q /s %BUILDDIR%\*
+ goto end
+)
+
+if "%1" == "html" (
+ %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+ goto end
+)
+
+if "%1" == "dirhtml" (
+ %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+ goto end
+)
+
+if "%1" == "singlehtml" (
+ %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+ goto end
+)
+
+if "%1" == "pickle" (
+ %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can process the pickle files.
+ goto end
+)
+
+if "%1" == "json" (
+ %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can process the JSON files.
+ goto end
+)
+
+if "%1" == "htmlhelp" (
+ %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+ goto end
+)
+
+if "%1" == "qthelp" (
+ %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+ echo.^> qcollectiongenerator %BUILDDIR%\qthelp\pyramid.qhcp
+ echo.To view the help file:
+ echo.^> assistant -collectionFile %BUILDDIR%\qthelp\pyramid.ghc
+ goto end
+)
+
+if "%1" == "devhelp" (
+ %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished.
+ goto end
+)
+
+if "%1" == "epub" (
+ %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The epub file is in %BUILDDIR%/epub.
+ goto end
+)
+
+if "%1" == "latex" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "text" (
+ %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The text files are in %BUILDDIR%/text.
+ goto end
+)
+
+if "%1" == "man" (
+ %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The manual pages are in %BUILDDIR%/man.
+ goto end
+)
+
+if "%1" == "texinfo" (
+ %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+ goto end
+)
+
+if "%1" == "gettext" (
+ %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+ goto end
+)
+
+if "%1" == "changes" (
+ %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.The overview file is in %BUILDDIR%/changes.
+ goto end
+)
+
+if "%1" == "linkcheck" (
+ %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+ goto end
+)
+
+if "%1" == "doctest" (
+ %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+ goto end
+)
+
+if "%1" == "pdf" (
+ %SPHINXBUILD% -b pdf %ALLSPHINXOPTS% %BUILDDIR%/pdf
+ echo.
+ echo.Build finished. The PDF files are in %BUILDDIR%/pdf
+ goto end
+)
+
+:end
diff --git a/docs/pyramid.numcore.rst b/docs/pyramid.numcore.rst
new file mode 100644
index 0000000..9d3a9c3
--- /dev/null
+++ b/docs/pyramid.numcore.rst
@@ -0,0 +1,12 @@
+numcore Package
+===============
+
+:mod:`numcore` Package
+----------------------
+
+.. automodule:: pyramid.numcore
+ :members:
+ :undoc-members:
+ :show-inheritance:
+ :special-members:
+
diff --git a/docs/pyramid.rst b/docs/pyramid.rst
new file mode 100644
index 0000000..b4ade82
--- /dev/null
+++ b/docs/pyramid.rst
@@ -0,0 +1,82 @@
+pyramid Package
+===============
+
+:mod:`analytic` Module
+----------------------
+
+.. automodule:: pyramid.analytic
+ :members:
+ :undoc-members:
+ :show-inheritance:
+ :special-members:
+
+:mod:`holoimage` Module
+-----------------------
+
+.. automodule:: pyramid.holoimage
+ :members:
+ :undoc-members:
+ :show-inheritance:
+ :special-members:
+
+:mod:`magcreator` Module
+------------------------
+
+.. automodule:: pyramid.magcreator
+ :members:
+ :undoc-members:
+ :show-inheritance:
+ :special-members:
+
+:mod:`magdata` Module
+---------------------
+
+.. automodule:: pyramid.magdata
+ :members:
+ :undoc-members:
+ :show-inheritance:
+ :special-members:
+
+:mod:`phasemap` Module
+----------------------
+
+.. automodule:: pyramid.phasemap
+ :members:
+ :undoc-members:
+ :show-inheritance:
+ :special-members:
+
+:mod:`phasemapper` Module
+-------------------------
+
+.. automodule:: pyramid.phasemapper
+ :members:
+ :undoc-members:
+ :show-inheritance:
+ :special-members:
+
+:mod:`projector` Module
+-----------------------
+
+.. automodule:: pyramid.projector
+ :members:
+ :undoc-members:
+ :show-inheritance:
+ :special-members:
+
+:mod:`reconstructor` Module
+---------------------------
+
+.. automodule:: pyramid.reconstructor
+ :members:
+ :undoc-members:
+ :show-inheritance:
+ :special-members:
+
+Subpackages
+-----------
+
+.. toctree::
+
+ pyramid.numcore
+
diff --git a/pyramid/__init__.py b/pyramid/__init__.py
index e69de29..63782bf 100644
--- a/pyramid/__init__.py
+++ b/pyramid/__init__.py
@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*-
+"""Package for the creation and reconstruction of magnetic distributions and resulting phase maps.
+
+Modules
+-------
+magcreator
+ Create simple magnetic distributions.
+magdata
+ Class for the storage of magnetizatin data.
+projector
+ Create projections of a given magnetization distribution.
+phasemapper
+ Create magnetic and electric phase maps from magnetization data.
+phasemap
+ Class for the storage of phase data.
+analytic
+ Create phase maps for magnetic distributions with analytic solutions.
+holoimage
+ Create holographic contour maps from a given phase map.
+reconstructor
+ Reconstruct magnetic distributions from given phasemaps.
+
+Subpackages
+-----------
+numcore
+ Provides fast numerical functions for core routines.
+
+"""
diff --git a/pyramid/analytic.py b/pyramid/analytic.py
index 89337ce..6035de7 100644
--- a/pyramid/analytic.py
+++ b/pyramid/analytic.py
@@ -1,7 +1,11 @@
# -*- coding: utf-8 -*-
-"""Create simple phasemaps from analytic solutions."""
+"""Create phase maps for magnetic distributions with analytic solutions.
-# TODO: Currently just for projections along the z-axis!
+This module provides methods for the calculation of the magnetic phase for simple geometries for
+which the analytic solutions are known. These can be used for comparison with the phase
+calculated by the functions from the :mod:`~pyramid.phasemapper` module.
+
+"""
import numpy as np
@@ -12,32 +16,45 @@ PHI_0 = -2067.83 # magnetic flux in T*nm²
def phase_mag_slab(dim, res, phi, center, width, b_0=1):
- '''Get the analytic solution for a phase map of a slab of specified dimensions.
- Arguments:
- dim - the dimensions of the grid, shape(z, y, x)
- res - the resolution of the grid (grid spacing) in nm
- phi - the azimuthal angle, describing the direction of the magnetized object
- center - the center of the slab in pixel coordinates, shape(z, y, x)
- width - the width of the slab in pixel coordinates, shape(z, y, x)
- b_0 - magnetic induction corresponding to a magnetization Mo in T (default: 1)
- Returns:
- the analytic solution for the phase map
+ '''Calculate the analytic magnetic phase for a homogeneously magnetized slab.
+
+ Parameters
+ ----------
+ dim : tuple (N=3)
+ The dimensions of the grid `(z, y, x)`.
+ res : float
+ The resolution of the grid (grid spacing) in nm.
+ phi : float
+ The azimuthal angle, describing the direction of the magnetization.
+ center : tuple (N=3)
+ The center of the slab in pixel coordinates `(z, y, x)`.
+ width : tuple (N=3)
+ The width of the slab in pixel coordinates `(z, y, x)`.
+ b_0 : float, optional
+ The magnetic induction corresponding to a magnetization `M`\ :sub:`0` in T.
+ The default is 1.
+
+ Returns
+ -------
+ phase_map : :class:`~numpy.ndarray` (N=2)
+ The phase as a 2-dimensional array.
'''
+
# Function for the phase:
- def phiMag(x, y):
- def F0(x, y):
+ def phi_mag(x, y):
+ def F_0(x, y):
a = np.log(x**2 + y**2 + 1E-30)
b = np.arctan(x / (y+1E-30))
return x*a - 2*x + 2*y*b
- return coeff * Lz * (- np.cos(phi) * (F0(x-x0-Lx/2, y-y0-Ly/2)
- - F0(x-x0+Lx/2, y-y0-Ly/2)
- - F0(x-x0-Lx/2, y-y0+Ly/2)
- + F0(x-x0+Lx/2, y-y0+Ly/2))
- + np.sin(phi) * (F0(y-y0-Ly/2, x-x0-Lx/2)
- - F0(y-y0+Ly/2, x-x0-Lx/2)
- - F0(y-y0-Ly/2, x-x0+Lx/2)
- + F0(y-y0+Ly/2, x-x0+Lx/2)))
+ return coeff * Lz * (- np.cos(phi) * (F_0(x-x0-Lx/2, y-y0-Ly/2)
+ - F_0(x-x0+Lx/2, y-y0-Ly/2)
+ - F_0(x-x0-Lx/2, y-y0+Ly/2)
+ + F_0(x-x0+Lx/2, y-y0+Ly/2))
+ + np.sin(phi) * (F_0(y-y0-Ly/2, x-x0-Lx/2)
+ - F_0(y-y0+Ly/2, x-x0-Lx/2)
+ - F_0(y-y0-Ly/2, x-x0+Lx/2)
+ + F_0(y-y0+Ly/2, x-x0+Lx/2)))
# Process input parameters:
z_dim, y_dim, x_dim = dim
y0 = res * (center[1] + 0.5) # y0, x0 define the center of a pixel,
@@ -49,25 +66,38 @@ def phase_mag_slab(dim, res, phi, center, width, b_0=1):
y = np.linspace(res/2, y_dim*res-res/2, num=y_dim)
xx, yy = np.meshgrid(x, y)
# Return phase:
- return phiMag(xx, yy)
+ return phi_mag(xx, yy)
def phase_mag_disc(dim, res, phi, center, radius, height, b_0=1):
- '''Get the analytic solution for a phase map of a disc of specified dimensions.
- Arguments:
- dim - the dimensions of the grid, shape(z, y, x)
- res - the resolution of the grid (grid spacing) in nm
- phi - the azimuthal angle, describing the direction of the magnetized object
- center - the center of the disc in pixel coordinates, shape(z, y, x)
- radius - the radius of the disc in pixel coordinates (scalar value)
- height - the height of the disc in pixel coordinates (scalar value)
- b_0 - magnetic induction corresponding to a magnetization Mo in T (default: 1)
- Returns:
- the analytic solution for the phase map
+ '''Calculate the analytic magnetic phase for a homogeneously magnetized disc.
+
+ Parameters
+ ----------
+ dim : tuple (N=3)
+ The dimensions of the grid `(z, y, x)`.
+ res : float
+ The resolution of the grid (grid spacing) in nm.
+ phi : float
+ The azimuthal angle, describing the direction of the magnetization.
+ center : tuple (N=3)
+ The center of the disc in pixel coordinates `(z, y, x)`.
+ radius : float
+ The radius of the disc in pixel coordinates.
+ height : float
+ The height of the disc in pixel coordinates.
+ b_0 : float, optional
+ The magnetic induction corresponding to a magnetization `M`\ :sub:`0` in T.
+ The default is 1.
+
+ Returns
+ -------
+ phase_map : :class:`~numpy.ndarray` (N=2)
+ The phase as a 2-dimensional array.
'''
# Function for the phase:
- def phiMag(x, y):
+ def phi_mag(x, y):
r = np.hypot(x - x0, y - y0)
r[center[1], center[2]] = 1E-30
result = coeff * Lz * ((y - y0) * np.cos(phi) - (x - x0) * np.sin(phi))
@@ -85,24 +115,36 @@ def phase_mag_disc(dim, res, phi, center, radius, height, b_0=1):
y = np.linspace(res/2, y_dim*res-res/2, num=y_dim)
xx, yy = np.meshgrid(x, y)
# Return phase:
- return phiMag(xx, yy)
+ return phi_mag(xx, yy)
def phase_mag_sphere(dim, res, phi, center, radius, b_0=1):
- '''Get the analytic solution for a phase map of a sphere of specified dimensions.
- Arguments:
- dim - the dimensions of the grid, shape(z, y, x)
- res - the resolution of the grid (grid spacing) in nm
- phi - the azimuthal angle, describing the direction of the magnetized object
- center - the center of the sphere in pixel coordinates, shape(z, y, x)
- radius - the radius of the sphere in pixel coordinates (scalar value)
- b_0 - magnetic induction corresponding to a magnetization Mo in T (default: 1)
- Returns:
- the analytic solution for the phase map
+ '''Calculate the analytic magnetic phase for a homogeneously magnetized sphere.
+
+ Parameters
+ ----------
+ dim : tuple (N=3)
+ The dimensions of the grid `(z, y, x)`.
+ res : float
+ The resolution of the grid (grid spacing) in nm.
+ phi : float
+ The azimuthal angle, describing the direction of the magnetization.
+ center : tuple (N=3)
+ The center of the sphere in pixel coordinates `(z, y, x)`.
+ radius : float
+ The radius of the sphere in pixel coordinates.
+ b_0 : float, optional
+ The magnetic induction corresponding to a magnetization `M`\ :sub:`0` in T.
+ The default is 1.
+
+ Returns
+ -------
+ phase_map : :class:`~numpy.ndarray` (N=2)
+ The phase as a 2-dimensional array.
'''
# Function for the phase:
- def phiMag(x, y):
+ def phi_mag(x, y):
r = np.hypot(x - x0, y - y0)
r[center[1], center[2]] = 1E-30
result = coeff * R ** 3 / r ** 2 * ((y - y0) * np.cos(phi) - (x - x0) * np.sin(phi))
@@ -119,24 +161,36 @@ def phase_mag_sphere(dim, res, phi, center, radius, b_0=1):
y = np.linspace(res / 2, y_dim * res - res / 2, num=y_dim)
xx, yy = np.meshgrid(x, y)
# Return phase:
- return phiMag(xx, yy)
+ return phi_mag(xx, yy)
def phase_mag_vortex(dim, res, center, radius, height, b_0=1):
- '''Get the analytic solution for a phase map of a sharp vortex disc of specified dimensions.
- Arguments:
- dim - the dimensions of the grid, shape(z, y, x)
- res - the resolution of the grid (grid spacing) in nm
- center - the center of the disc in pixel coordinates, shape(z, y, x)
- radius - the radius of the disc in pixel coordinates (scalar value)
- height - the height of the disc in pixel coordinates (scalar value)
- b_0 - magnetic induction corresponding to a magnetization Mo in T (default: 1)
- Returns:
- the analytic solution for the phase map
+ '''Calculate the analytic magnetic phase for a vortex state disc.
+
+ Parameters
+ ----------
+ dim : tuple (N=3)
+ The dimensions of the grid `(z, y, x)`.
+ res : float
+ The resolution of the grid (grid spacing) in nm.
+ center : tuple (N=3)
+ The center of the disc in pixel coordinates `(z, y, x)`, which is also the vortex center.
+ radius : float
+ The radius of the disc in pixel coordinates.
+ height : float
+ The height of the disc in pixel coordinates.
+ b_0 : float, optional
+ The magnetic induction corresponding to a magnetization `M`\ :sub:`0` in T.
+ The default is 1.
+
+ Returns
+ -------
+ phase_map : :class:`~numpy.ndarray` (N=2)
+ The phase as a 2-dimensional array.
'''
# Function for the phase:
- def phiMag(x, y):
+ def phi_mag(x, y):
r = np.hypot(x - x0, y - y0)
result = coeff * np.where(r <= R, r - R, 0)
return result
@@ -152,4 +206,4 @@ def phase_mag_vortex(dim, res, center, radius, height, b_0=1):
y = np.linspace(res/2, y_dim*res-res/2, num=y_dim)
xx, yy = np.meshgrid(x, y)
# Return phase:
- return phiMag(xx, yy)
+ return phi_mag(xx, yy)
diff --git a/pyramid/holoimage.py b/pyramid/holoimage.py
index cea6f96..014fd3b 100644
--- a/pyramid/holoimage.py
+++ b/pyramid/holoimage.py
@@ -1,14 +1,26 @@
# -*- coding: utf-8 -*-
-"""Display holography images with the gradient direction encoded in color"""
+"""Create holographic contour maps from a given phase map.
+
+This module converts phase maps into holographic contour map. This basically means taking the
+cosine of the (optionally amplified) phase and encoding the direction of the 2-dimensional
+gradient via color. The directional encoding can be seen by using the :func:`~.make_color_wheel`
+function. Use the :func:`~.holoimage` function to create these holographic contour maps. It is
+possible to use these as input for the :func:`~.display` to plot them, or just pass the
+:class:`~pyramid.phasemap.PhaseMap` object to the :func:`~.display_combined` function to plot
+the phase map and the holographic contour map next to each other.
+
+"""
import numpy as np
+from numpy import pi
+
import matplotlib as mpl
import matplotlib.pyplot as plt
-from pyramid.phasemap import PhaseMap
-from numpy import pi
-from PIL import Image
from matplotlib.ticker import NullLocator
+from PIL import Image
+
+from pyramid.phasemap import PhaseMap
CDICT = {'red': [(0.00, 1.0, 0.0),
@@ -33,19 +45,28 @@ HOLO_CMAP = mpl.colors.LinearSegmentedColormap('my_colormap', CDICT, 256)
def holo_image(phase_map, density=1):
- '''Returns a holography image with color-encoded gradient direction.
- Arguments:
- phase_map - a PhaseMap object storing the phase informations
- density - the gain factor for determining the number of contour lines (default: 1)
- Returns:
- holography image
+ '''Create a holographic contour map from a :class:`~pyramid.phasemap.PhaseMap` object.
+
+ Parameters
+ ----------
+ phase_map : :class:`~pyramid.phasemap.PhaseMap`
+ A :class:`~pyramid.phasemap.PhaseMap` object storing the phase information.
+ density : float, optional
+ The gain factor for determining the number of contour lines. The default is 1.
+
+ Returns
+ -------
+ holo_image : :class:`~PIL.image`
+ The resulting holographic contour map with color encoded gradient.
'''
assert isinstance(phase_map, PhaseMap), 'phase_map has to be a PhaseMap object!'
+ # Extract the phase (considering the unit):
+ phase = phase_map.phase
# Calculate the holography image intensity:
- img_holo = (1 + np.cos(density * phase_map.phase * pi/2)) / 2
+ img_holo = (1 + np.cos(density * phase)) / 2
# Calculate the phase gradients, expressed by magnitude and angle:
- phase_grad_y, phase_grad_x = np.gradient(phase_map.phase, phase_map.res, phase_map.res)
+ phase_grad_y, phase_grad_x = np.gradient(phase, phase_map.res, phase_map.res)
phase_angle = (1 - np.arctan2(phase_grad_y, phase_grad_x)/pi) / 2
phase_magnitude = np.hypot(phase_grad_x, phase_grad_y)
phase_magnitude = np.sin(phase_magnitude/phase_magnitude.max() * pi / 2)
@@ -57,11 +78,15 @@ def holo_image(phase_map, density=1):
def make_color_wheel():
- '''Display a color wheel for the gradient direction.
- Arguments:
- None
- Returns:
- None
+ '''Display a color wheel to illustrate the color coding of the gradient direction.
+
+ Parameters
+ ----------
+ None
+
+ Returns
+ -------
+ None
'''
x = np.linspace(-256, 256, num=512)
@@ -84,15 +109,23 @@ def make_color_wheel():
axis.yaxis.set_major_locator(NullLocator())
-def display(holo_image, title='Holography Image', axis=None, interpolation='none'):
- '''Display the color coded holography image resulting from a given phase map.
- Arguments:
- holo_image - holography image created with the holo_image function of this module
- title - the title of the plot (default: 'Holography Image')
- axis - the axis on which to display the plot (default: None, creates new figure)
- interpolation - defines the interpolation method (default: 'none')
- Returns:
- None
+def display(holo_image, title='Holographic Contour Map', axis=None, interpolation='none'):
+ '''Display the color coded holography image.
+
+ Parameters
+ ----------
+ holo_image : :class:`~PIL.image`
+ The resulting holographic contour map with color encoded gradient.
+ title : string, optional
+ The title of the plot. The default is 'Holographic Contour Map'.
+ axis : :class:`~matplotlib.axes.AxesSubplot`, optional
+ Axis on which the graph is plotted. Creates a new figure if none is specified.
+ interpolation : {'none, 'bilinear', 'cubic', 'nearest'}, optional
+ Defines the interpolation method. No interpolation is used in the default case.
+
+ Returns
+ -------
+ None
'''
# If no axis is specified, a new figure is created:
@@ -109,15 +142,24 @@ def display(holo_image, title='Holography Image', axis=None, interpolation='none
axis.set_ylabel('y-axis [px]', fontsize=15)
-def display_combined(phase_map, density, title='Combined Plot', interpolation='none',
- labels=('x-axis [nm]', 'y-axis [nm]', 'phase [rad]')):# TODO DOCSTRING
+def display_combined(phase_map, density=1, title='Combined Plot', interpolation='none'):
'''Display a given phase map and the resulting color coded holography image in one plot.
- Arguments:
- phase_map - the PhaseMap object from which the holography image is calculated
- density - the factor for determining the number of contour lines
- title - the title of the combined plot (default: 'Combined Plot')
- Returns:
- None
+
+ Parameters
+ ----------
+ phase_map : :class:`~pyramid.phasemap.PhaseMap`
+ A :class:`~pyramid.phasemap.PhaseMap` object storing the phase information.
+ density : float, optional
+ The gain factor for determining the number of contour lines. The default is 1.
+ title : string, optional
+ The title of the plot. The default is 'Combined Plot'.
+ interpolation : {'none, 'bilinear', 'cubic', 'nearest'}, optional
+ Defines the interpolation method for the holographic contour map.
+ No interpolation is used in the default case.
+
+ Returns
+ -------
+ None
'''
# Create combined plot and set title:
@@ -129,4 +171,4 @@ def display_combined(phase_map, density, title='Combined Plot', interpolation='n
# Plot phase map:
phase_axis = fig.add_subplot(1, 2, 2, aspect='equal')
fig.subplots_adjust(right=0.85)
- phase_map.display(axis=phase_axis, labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
+ phase_map.display(axis=phase_axis)
diff --git a/pyramid/magcreator.py b/pyramid/magcreator.py
index 7eef6d5..19fc810 100644
--- a/pyramid/magcreator.py
+++ b/pyramid/magcreator.py
@@ -1,5 +1,17 @@
# -*- coding: utf-8 -*-
-"""Create simple LLG Files which describe magnetization in 2D (z-Dim=1)."""
+"""Create simple magnetic distributions.
+
+The :mod:`~.magcreator` module is responsible for the creation of simple distributions of
+magnetic moments. In the :class:`~.Shapes` class, you can find several general shapes for the
+3-dimensional volume that should be magnetized (e.g. slabs, spheres, discs or single pixels).
+These magnetic shapes are then used as input for the creating functions (or you could specify the
+volume yourself as a 3-dimensional boolean matrix or a matrix with values in the range from 0 to 1,
+which modifies the magnetization amplitude). The specified volume can either be magnetized
+homogeneously with the :func:`~.create_mag_dist_homog` function by specifying the magnetization
+direction, or in a vortex state with the :func:`~.create_mag_dist_vortex` by specifying the vortex
+center.
+
+"""
import numpy as np
@@ -8,47 +20,37 @@ from numpy import pi
class Shapes:
- '''Class containing functions for generating shapes.'''
+ '''Class containing functions for generating magnetic shapes.
- @classmethod
- def soft_slab(cls, dim, center, width):
- '''Get the magnetic shape of a slab.
- Arguments:
- dim - the dimensions of the grid, shape(z, y, x)
- center - the center of the slab in pixel coordinates, shape(z, y, x)
- width - the width of the slab in pixel coordinates, shape(z, y, x)
- Returns:
- the magnetic shape as a 3D-array with ones and zeros
+ The :class:`~.Shapes` class is a collection of some mehtods that return a 3-dimensional
+ matrix that represents the magnetized volume and consists of values between 0 and 1.
+ This matrix is used in the functions of the :mod:`~.magcreator` module to create
+ :class:`~pyramid.magdata.MagData` objects which store the magnetic informations.
- '''
- assert np.shape(dim) == (3,), 'Parameter dim has to be a shape of 3 dimensions!'
- assert np.shape(center) == (3,), 'Parameter center has to be a shape of 3 dimensions!'
- assert np.shape(width) == (3,), 'Parameter width has to be a shape of 3 dimensions!'
- z0, y0, x0 = center
- Lz, Ly, Lx = width
- mag_shape = np.zeros(dim)
- for z in range(dim[0]):
- for y in range(dim[1]):
- for x in range(dim[2]):
- mag_shape[z, y, x] = (max(min(x+0.5, x0+Lx/2.)-max(x-0.5, x0-Lx/2.), 0)
- * max(min(y+0.5, y0+Ly/2.)-max(y-0.5, y0-Ly/2.), 0)
- * max(min(z+0.5, z0+Lz/2.)-max(z-0.5, z0-Lz/2.), 0))
- return mag_shape
+ '''
@classmethod
def slab(cls, dim, center, width):
- '''Get the magnetic shape of a slab.
- Arguments:
- dim - the dimensions of the grid, shape(z, y, x)
- center - the center of the slab in pixel coordinates, shape(z, y, x)
- width - the width of the slab in pixel coordinates, shape(z, y, x)
- Returns:
- the magnetic shape as a 3D-array with ones and zeros
+ '''Create the shape of a slab.
+
+ Parameters
+ ----------
+ dim : tuple (N=3)
+ The dimensions of the grid `(z, y, x)`.
+ center : tuple (N=3)
+ The center of the slab in pixel coordinates `(z, y, x)`.
+ width : tuple (N=3)
+ The width of the slab in pixel coordinates `(z, y, x)`.
+
+ Returns
+ -------
+ mag_shape : :class:`~numpy.ndarray` (N=3)
+ The magnetic shape as a 3D-array with values between 1 and 0.
'''
- assert np.shape(dim) == (3,), 'Parameter dim has to be a shape of 3 dimensions!'
- assert np.shape(center) == (3,), 'Parameter center has to be a shape of 3 dimensions!'
- assert np.shape(width) == (3,), 'Parameter width has to be a shape of 3 dimensions!'
+ assert np.shape(dim) == (3,), 'Parameter dim has to be a tuple of length 3!'
+ assert np.shape(center) == (3,), 'Parameter center has to be a tuple of length 3!'
+ assert np.shape(width) == (3,), 'Parameter width has to be a tuple of length 3!'
mag_shape = np.array([[[abs(x - center[2]) <= width[2] / 2
and abs(y - center[1]) <= width[1] / 2
and abs(z - center[0]) <= width[0] / 2
@@ -59,22 +61,32 @@ class Shapes:
@classmethod
def disc(cls, dim, center, radius, height, axis='z'):
- '''Get the magnetic shape of a zylindrical disc in x-, y-, or z-direction.
- Arguments:
- dim - the dimensions of the grid, shape(z, y, x)
- center - the center of the disc in pixel coordinates, shape(z, y, x)
- radius - the radius of the disc in pixel coordinates (scalar value)
- height - the height of the disc in pixel coordinates (scalar value)
- axis - the orientation of the disc axis, (String: 'x', 'y', 'z'), default = 'z'
- Returns:
- the magnetic shape as a 3D-array with ones and zeros
+ '''Create the shape of a zylindrical disc in x-, y-, or z-direction.
+
+ Parameters
+ ----------
+ dim : tuple (N=3)
+ The dimensions of the grid `(z, y, x)`.
+ center : tuple (N=3)
+ The center of the disc in pixel coordinates `(z, y, x)`.
+ radius : float
+ The radius of the disc in pixel coordinates.
+ height : float
+ The height of the disc in pixel coordinates.
+ axis : {'z', 'y', 'x'}, optional
+ The orientation of the disc axis. The default is 'z'.
+
+ Returns
+ -------
+ mag_shape : :class:`~numpy.ndarray` (N=3)
+ The magnetic shape as a 3D-array with values between 1 and 0.
'''
- assert np.shape(dim) == (3,), 'Parameter dim has to be a shape of 3 dimensions!'
- assert np.shape(center) == (3,), 'Parameter center has to be a shape of 3 dimensions!'
- assert radius > 0 and np.shape(radius) == (), 'Radius has to be positive scalar value!'
- assert height > 0 and np.shape(height) == (), 'Height has to be positive scalar value!'
- assert axis == 'z' or axis == 'y' or axis == 'x', 'Axis has to be x, y or z (as String)!'
+ assert np.shape(dim) == (3,), 'Parameter dim has to be a a tuple of length 3!'
+ assert np.shape(center) == (3,), 'Parameter center has to be a a tuple of length 3!'
+ assert radius > 0 and np.shape(radius) == (), 'Radius has to be a positive scalar value!'
+ assert height > 0 and np.shape(height) == (), 'Height has to be a positive scalar value!'
+ assert axis == 'z' or axis == 'y' or axis == 'x', 'Axis has to be x, y or z (as a string)!'
if axis == 'z':
mag_shape = np.array([[[np.hypot(x - center[2], y - center[1]) <= radius
and abs(z - center[0]) <= height / 2
@@ -97,20 +109,26 @@ class Shapes:
@classmethod
def sphere(cls, dim, center, radius):
- '''Get the magnetic shape of a sphere.
- Arguments:
- dim - the dimensions of the grid, shape(z, y, x)
- center - the center of the disc in pixel coordinates, shape(z, y, x)
- radius - the radius of the disc in pixel coordinates (scalar value)
- height - the height of the disc in pixel coordinates (scalar value)
- axis - the orientation of the disc axis, (String: 'x', 'y', 'z'), default = 'z'
- Returns:
- the magnetic shape as a 3D-array with ones and zeros
+ '''Create the shape of a sphere.
+
+ Parameters
+ ----------
+ dim : tuple (N=3)
+ The dimensions of the grid `(z, y, x)`.
+ center : tuple (N=3)
+ The center of the sphere in pixel coordinates `(z, y, x)`.
+ radius : float
+ The radius of the sphere in pixel coordinates.
+
+ Returns
+ -------
+ mag_shape : :class:`~numpy.ndarray` (N=3)
+ The magnetic shape as a 3D-array with values between 1 and 0.
'''
- assert np.shape(dim) == (3,), 'Parameter dim has to be a shape of 3 dimensions!'
- assert np.shape(center) == (3,), 'Parameter center has to be a shape of 3 dimensions!'
- assert radius > 0 and np.shape(radius) == (), 'Radius has to be positive scalar value!'
+ assert np.shape(dim) == (3,), 'Parameter dim has to be a a tuple of length 3!'
+ assert np.shape(center) == (3,), 'Parameter center has to be a a tuple of length 3!'
+ assert radius > 0 and np.shape(radius) == (), 'Radius has to be a positive scalar value!'
mag_shape = np.array([[[np.sqrt((x-center[2])**2
+ (y-center[1])**2
+ (z-center[0])**2) <= radius
@@ -121,18 +139,28 @@ class Shapes:
@classmethod
def filament(cls, dim, pos, axis='y'):
- '''Get the magnetic shape of a single filament in x-, y-, or z-direction.
- Arguments:
- dim - the dimensions of the grid, shape(z, y, x)
- pos - the position of the filament in pixel coordinates, shape(coord1, coord2)
- axis - the orientation of the filament axis, (String: 'x', 'y', 'z'), default = 'y'
- Returns:
- the magnetic shape as a 3D-array with ones and zeros
+ '''Create the shape of a filament.
+
+ Parameters
+ ----------
+ dim : tuple (N=3)
+ The dimensions of the grid `(z, y, x)`.
+ pos : tuple (N=2)
+ The position of the filament in pixel coordinates `(coord1, coord2)`.
+ `coord1` and `coord2` stand for the two axes, which are perpendicular to `axis`. For
+ the default case (`axis = y`), it is `(coord1, coord2) = (z, x)`.
+ axis : {'y', 'x', 'z'}, optional
+ The orientation of the filament axis. The default is 'y'.
+
+ Returns
+ -------
+ mag_shape : :class:`~numpy.ndarray` (N=3)
+ The magnetic shape as a 3D-array with values between 1 and 0.
'''
- assert np.shape(dim) == (3,), 'Parameter dim has to be a shape of 3 dimensions!'
- assert np.shape(pos) == (2,), 'Parameter pos has to be a shape of 2 dimensions!'
- assert axis == 'z' or axis == 'y' or axis == 'x', 'Axis has to be x, y or z (as String)!'
+ assert np.shape(dim) == (3,), 'Parameter dim has to be a tuple of length 3!'
+ assert np.shape(pos) == (2,), 'Parameter pos has to be a tuple of length 2!'
+ assert axis == 'z' or axis == 'y' or axis == 'x', 'Axis has to be x, y or z (as a string)!'
mag_shape = np.zeros(dim)
if axis == 'z':
mag_shape[:, pos[0], pos[1]] = 1
@@ -144,31 +172,48 @@ class Shapes:
@classmethod
def pixel(cls, dim, pixel):
- '''Get the magnetic shape of a single magnetized pixel.
- Arguments:
- dim - the dimensions of the grid, shape(z, y, x)
- pixel - the coordinates of the magnetized pixel, shape(z, y, x)
- Returns:
- the magnetic shape as a 3D-array with ones and zeros
+ '''Create the shape of a single pixel.
+
+ Parameters
+ ----------
+ dim : tuple (N=3)
+ The dimensions of the grid `(z, y, x)`.
+ pixel : tuple (N=3)
+ The coordinates of the pixel `(z, y, x)`.
+
+ Returns
+ -------
+ mag_shape : :class:`~numpy.ndarray` (N=3)
+ The magnetic shape as a 3D-array with values between 1 and 0.
'''
- assert np.shape(dim) == (3,), 'Parameter dim has to be a shape of 3 dimensions!'
- assert np.shape(pixel) == (3,), 'Parameter pixel has to be a shape of 3 dimensions!'
+ assert np.shape(dim) == (3,), 'Parameter dim has to be a tuple of length 3!'
+ assert np.shape(pixel) == (3,), 'Parameter pixel has to be a tuple of length 3!'
mag_shape = np.zeros(dim)
mag_shape[pixel] = 1
return mag_shape
-def create_mag_dist(mag_shape, phi, theta=pi/2, magnitude=1):
+def create_mag_dist_homog(mag_shape, phi, theta=pi/2, magnitude=1):
'''Create a 3-dimensional magnetic distribution of a homogeneous magnetized object.
- Arguments:
- mag_shape - the magnetic shapes (numpy arrays, see Shapes.* for examples)
- phi - the azimuthal angle, describing the direction of the magnetized object
- theta - the polar angle, describing the direction of the magnetized object
- (optional, is set to pi/2 if not specified -> z-component is zero)
- magnitude - the relative magnitudes for the magnetic shape (optional, one if not specified)
- Returns:
- the 3D magnetic distribution as a MagData object (see pyramid.magdata for reference)
+
+ Parameters
+ ----------
+ mag_shape : :class:`~numpy.ndarray` (N=3)
+ The magnetic shapes (see Shapes.* for examples).
+ phi : float
+ The azimuthal angle, describing the direction of the magnetized object.
+ theta : float, optional
+ The polar angle, describing the direction of the magnetized object.
+ The default is pi/2, which means, the z-component is zero.
+ magnitude : float, optional
+ The relative magnitude for the magnetic shape. The default is 1.
+
+ Returns
+ -------
+ magnitude : tuple (N=3) of :class:`~numpy.ndarray` (N=3)
+ The magnetic distribution as a tuple of the 3 components in
+ `x`-, `y`- and `z`-direction on the 3-dimensional grid.
'''
dim = np.shape(mag_shape)
@@ -179,56 +224,25 @@ def create_mag_dist(mag_shape, phi, theta=pi/2, magnitude=1):
return z_mag, y_mag, x_mag
-def create_mag_dist_comb(mag_shape_list, phi_list, theta_list=None, magnitude_list=None):
- '''Create a 3-dimensional magnetic distribution from a list of homogeneous magnetized objects.
- Arguments:
- mag_shape_list - a list of magnetic shapes (numpy arrays, see Shapes.* for examples)
- phi_list - a list of azimuthal angles, describing the direction of the
- magnetized object
- theta_list - a list of polar angles, describing the direction of the magnetized object
- (optional, is set to pi/2 if not specified -> z-component is zero)
- magnitude_list - a list of relative magnitudes for the magnetic shapes
- (optional, if not specified, every relative magnitude is set to one)
- Returns:
- the 3D magnetic distribution as a MagData object (see pyramid.magdata for reference)
-
- '''
- # If no relative magnitude is specified, 1 is assumed for every homog. object:
- if magnitude_list is None:
- magnitude_list = np.ones(len(phi_list))
- # If no relative magnitude is specified, 1 is assumed for every homog. object:
- if theta_list is None:
- theta_list = np.ones(len(phi_list)) * pi/2
- # For every shape of a homogeneous object a relative magnitude and angle have to be set:
- assert np.shape(mag_shape_list)[0] == len(phi_list) == len(theta_list) == len(magnitude_list),\
- 'Lists have not the same length!'
- dim = np.shape(mag_shape_list[0]) # Has to be the shape of ALL mag_shapes!
- assert len(dim) == 3, 'Magnetic shapes must describe 3-dimensional distributions!'
- assert np.array([mag_shape_list[i].shape == dim for i in range(len(mag_shape_list))]).all(),\
- 'Magnetic shapes must describe distributions with the same size!'
- # Start with a zero distribution:
- x_mag = np.zeros(dim)
- y_mag = np.zeros(dim)
- z_mag = np.zeros(dim)
- # Add every specified homogeneous object:
- for i in range(np.size(phi_list)):
- mag_object = create_mag_dist(mag_shape_list[i], phi_list[i], magnitude_list[i])
- z_mag += mag_object[0]
- y_mag += mag_object[1]
- x_mag += mag_object[2]
- return z_mag, y_mag, x_mag
-
-
def create_mag_dist_vortex(mag_shape, center=None, magnitude=1):
'''Create a 3-dimensional magnetic distribution of a homogeneous magnetized object.
- Arguments:
- mag_shape - the magnetic shapes (numpy arrays, see Shapes.* for examples)
- center - the vortex center, given in 2D (x,y) or 3D (x,y,z), where z is discarded
- (optional, is set to the center of the field of view if not specified, always
- between two pixels!)
- magnitude - the relative magnitudes for the magnetic shape (optional, one if not specified)
- Returns:
- the 3D magnetic distribution as a MagData object (see pyramid.magdata for reference)
+
+ Parameters
+ ----------
+ mag_shape : :class:`~numpy.ndarray` (N=3)
+ The magnetic shapes (see :class:`.~Shapes` for examples).
+ center : tuple (N=2 or N=3), optional
+ The vortex center, given in 2D `(x, y)` or 3D `(x, y, z)`, where `z` is discarded.
+ Is set to the center of the field of view if not specified.
+ Vortex center has to be between two pixels.
+ magnitude : float, optional
+ The relative magnitude for the magnetic shape. The default is 1.
+
+ Returns
+ -------
+ magnitude : tuple (N=3) of :class:`~numpy.ndarray` (N=3)
+ The magnetic distribution as a tuple of the 3 components in
+ `x`-, `y`- and `z`-direction on the 3-dimensional grid.
'''
dim = np.shape(mag_shape)
@@ -237,7 +251,7 @@ def create_mag_dist_vortex(mag_shape, center=None, magnitude=1):
center = (int(dim[1]/2)-0.5, int(dim[2]/2)-0.5) # center has to be between (!) two pixels
if len(center) == 3: # if a 3D-center is given, just take the x and y components
center = (center[1], center[2])
- assert len(center) == 2, 'Vortex center has to be defined in 3D or 2D!'
+ assert len(center) == 2, 'Vortex center has to be defined in 3D or 2D or not at all!'
x = np.linspace(-center[1], dim[2]-1-center[1], dim[2])
y = np.linspace(-center[0], dim[1]-1-center[0], dim[1])
xx, yy = np.meshgrid(x, y)
diff --git a/pyramid/magdata.py b/pyramid/magdata.py
index 1d172b0..e8d85e2 100644
--- a/pyramid/magdata.py
+++ b/pyramid/magdata.py
@@ -1,62 +1,187 @@
# -*- coding: utf-8 -*-
-"""Class for creating objects to store magnetizatin data."""
+"""Class for the storage of magnetizatin data.
+
+This module provides the :class:`~.MagData` class whose instances can be used to store
+magnetization data for 3 components for a 3-dimensional grid. It is possible to load data from
+NetCDF4 or LLG (.txt) files or to save the data in these formats. Also plotting methods are
+provided. See :class:`~.MagData` for further information.
+
+"""
import numpy as np
-import tables.netcdf3 as nc
+
import matplotlib.pyplot as plt
from matplotlib.ticker import MaxNLocator
+from mayavi import mlab
+
+import netCDF4
+
class MagData:
- '''An object storing magnetization data.'''
+ '''Class for storing magnetization data.
+
+ Represents 3-dimensional magnetic distributions with 3 components which are stored as a
+ tuple of size 3 in `magnitude`. The object can be created empty by omitting the `magnitude`
+ paramter. The `magnitude` can be added later by using the :func:`~.add_magnitude` function.
+ This is useful, if the `magnitude` is more complex and more than one magnetized object should
+ be represented by the :class:`~.MagData` object, which can be added one after another by the
+ :func:`~.add_magnitude` function. The dimensions `dim` of the grid will be set as soon as the
+ magnitude is specified. However, `res` has to be always specified at construction time.
- def __init__(self, res, magnitude): # TODO: electrostatic component!
- '''Constructor for a MagData object for storing magnetization data.
- Arguments:
- res - the resolution of the grid (grid spacing) in nm
- magnitude - the z-, y- and x-component of the magnetization vector for every
- 3D-gridpoint as a tuple
- Returns:
- MagData object
+ Attributes
+ ----------
+ res : float
+ The resolution of the grid (grid spacing in nm)
+ dim : tuple (N=3)
+ Dimensions of the grid.
+ magnitude : tuple (N=3) of :class:`~numpy.ndarray` (N=3)
+ The `z`-, `y`- and `x`-component of the magnetization vector for every 3D-gridpoint
+ as a tuple.
+
+ '''
+
+ def __init__(self, res, magnitude=None):
+ '''Constructor for a :class:`~.MagData` object for storing magnetization data.
+
+ Parameters
+ ----------
+ res : float
+ The resolution of the grid (grid spacing) in nm.
+ magnitude : tuple (N=3) of :class:`~numpy.ndarray` (N=3), optional
+ The `z`-, `y`- and `x`-component of the magnetization vector for every 3D-gridpoint
+ as a tuple. Is zero everywhere if not specified.
+
+ Returns
+ -------
+ mag_data : :class:`~.MagData`
+ The 3D magnetic distribution as a :class:`~.MagData` object.
'''
- dim = np.shape(magnitude[0])
- assert len(dim) == 3, 'Magnitude has to be defined for a 3-dimensional grid!'
- assert np.shape(magnitude[1]) == np.shape(magnitude[2]) == dim, \
- 'Dimensions of the magnitude components do not match!'
+ if magnitude is not None:
+ dim = np.shape(magnitude[0])
+ assert len(dim) == 3, 'Magnitude has to be defined for a 3-dimensional grid!'
+ assert np.shape(magnitude[1]) == np.shape(magnitude[2]) == dim, \
+ 'Dimensions of the magnitude components do not match!'
+ self.magnitude = magnitude
+ self.dim = dim
+ else:
+ self.magnitude = None
+ self.dim = None
self.res = res
- self.dim = dim
- self.magnitude = magnitude
+
+ def add_magnitude(self, magnitude):
+ '''Add a given magnitude to the magnitude of the :class:`~.MagData`.
+
+ Parameters
+ ----------
+ magnitude : tuple (N=3) of :class:`~numpy.ndarray` (N=3)
+ The `z`-, `y`- and `x`-component of the magnetization vector for every 3D-gridpoint
+ as a tuple. If the :class:`~.MagData` object already has a `magnitude`, the added
+ one has to match the dimensions `dim`, otherwise the added magnitude sets `dim`.
+
+ Returns
+ -------
+ None
+
+ '''
+ if self.magnitude is not None: # Add magnitude to existing one
+ assert np.shape(magnitude) == (3,) + self.dim, \
+ 'Added magnitude has to have the same dimensions!'
+ z_mag, y_mag, x_mag = self.magnitude
+ z_new, y_new, x_new = magnitude
+ z_mag += z_new
+ y_mag += y_new
+ x_mag += x_new
+ self.magnitude = (z_mag, y_mag, x_mag)
+ else: # Magnitude is set for the first time and the dimensions are calculated
+ dim = np.shape(magnitude[0])
+ assert len(dim) == 3, 'Magnitude has to be defined for a 3-dimensional grid!'
+ assert np.shape(magnitude[1]) == np.shape(magnitude[2]) == dim, \
+ 'Dimensions of the magnitude components do not match!'
+ self.magnitude = magnitude
+ self.dim = dim
def get_vector(self, mask):
- # TODO: DOCSTRING!
+ '''Returns the magnetic components arranged in a vector, specified by a mask.
+
+ Parameters
+ ----------
+ mask : :class:`~numpy.ndarray` (N=3, boolean)
+ Masks the pixels from which the components should be taken.
+
+ Returns
+ -------
+ vector : :class:`~numpy.ndarray` (N=1)
+ The vector containing magnetization components of the specified pixels.
+ Order is: first all `x`-, then all `y`-, then all `z`-components.
+
+ '''
return np.concatenate([self.magnitude[2][mask],
self.magnitude[1][mask],
self.magnitude[0][mask]])
def set_vector(self, mask, vector):
- # TODO: DOCSTRING!
+ '''Set the magnetic components of the masked pixels to the values specified by `vector`.
+
+ Parameters
+ ----------
+ mask : :class:`~numpy.ndarray` (N=3, boolean)
+ Masks the pixels from which the components should be taken.
+ vector : :class:`~numpy.ndarray` (N=1)
+ The vector containing magnetization components of the specified pixels.
+ Order is: first all `x`-, then all `y-, then all `z`-components.
+
+ Returns
+ -------
+ None
+
+ '''
assert np.size(vector) % 3 == 0, 'Vector has to contain all 3 components for every pixel!'
count = np.size(vector)/3
self.magnitude[2][mask] = vector[:count] # x-component
self.magnitude[1][mask] = vector[count:2*count] # y-component
self.magnitude[0][mask] = vector[2*count:] # z-component
-
+
def get_mask(self, threshold=0):
- # TODO: DOCSTRING!
- z_mask = abs(self.magnitude[0]) > threshold
- x_mask = abs(self.magnitude[1]) > threshold
- y_mask = abs(self.magnitude[2]) > threshold
- return np.logical_or(np.logical_or(x_mask, y_mask), z_mask)
+ '''Mask all pixels where the amplitude of the magnetization lies above `threshold`.
+
+ Parameters
+ ----------
+ threshold : float, optional
+ A pixel only gets masked, if it lies above this threshold . The default is 0.
+
+ Returns
+ -------
+ mask : :class:`~numpy.ndarray` (N=3, boolean)
+ Mask of the pixels where the amplitude of the magnetization lies above `threshold`.
+
+ '''
+ return np.sqrt(np.sum(np.array(self.magnitude)**2, axis=0)) > threshold
def scale_down(self, n=1):
- # TODO: DOCSTRING!
- # Starting magnetic distribution:
- assert n >= 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
+ '''Scale down the magnetic distribution by averaging over two pixels along each axis.
+
+ Parameters
+ ----------
+ n : int, optional
+ Number of times the magnetic distribution is scaled down. The default is 1.
+
+ Returns
+ -------
+ None
+
+ Notes
+ -----
+ Acts in place and changes dimensions and resolution accordingly.
+ Only possible, if each axis length is a power of 2!
+
+ '''
+ assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
assert self.dim[0] % 2**n == 0 and self.dim[1] % 2**n == 0 and self.dim[2] % 2**n == 0, \
- 'For downscaling, every dimension must be a multiple of 2!'
+ 'For downscaling, every dimension must be a multiple of 2!'
for t in range(n):
# Create coarser grid for the magnetization:
z_mag = self.magnitude[0].reshape(self.dim[0]/2, 2, self.dim[1]/2, 2, self.dim[2]/2, 2)
@@ -70,29 +195,40 @@ class MagData:
@classmethod
def load_from_llg(cls, filename):
- '''Construct DataMag object from LLG-file (classmethod).
- Arguments:
- filename - the name of the LLG-file from which to load the data
- Returns.
- MagData object
+ '''Construct :class:`~.MagData` object from LLG-file.
+
+ Parameters
+ ----------
+ filename : string
+ The name of the LLG-file from which to load the data.
+
+ Returns
+ -------
+ mag_data: :class:`~.MagData`
+ A :class:`~.MagData` object containing the loaded data.
'''
- scale = 1.0E-9 / 1.0E-2 # From cm to nm
+ SCALE = 1.0E-9 / 1.0E-2 # From cm to nm
data = np.genfromtxt(filename, skip_header=2)
x_dim, y_dim, z_dim = np.genfromtxt(filename, dtype=int, skip_header=1,
skip_footer=len(data[:, 0]))
- res = (data[1, 0] - data[0, 0]) / scale
+ res = (data[1, 0] - data[0, 0]) / SCALE
# Reshape in Python and Igor is different, Python fills rows first, Igor columns:
x_mag, y_mag, z_mag = [data[:, i].reshape(z_dim, y_dim, x_dim) for i in range(3, 6)]
return MagData(res, (z_mag, y_mag, x_mag))
def save_to_llg(self, filename='magdata_output.txt'):
'''Save magnetization data in a file with LLG-format.
- Arguments:
- filename - the name of the LLG-file in which to store the magnetization data
- (default: 'magdata_output.txt')
- Returns:
- None
+
+ Parameters
+ ----------
+ filename : string, optional
+ The name of the LLG-file in which to store the magnetization data.
+ The default is 'magdata_output.txt'.
+
+ Returns
+ -------
+ None
'''
dim = self.dim
@@ -116,60 +252,82 @@ class MagData:
for cell in row) for row in data))
@classmethod
- def load_from_netcdf(cls, filename):
- '''Construct MagData object from a NetCDF-file (classmethod).
- Arguments:
- filename - name of the file from which to load the data
- Returns:
- PhaseMap object
+ def load_from_netcdf4(cls, filename):
+ '''Construct :class:`~.DataMag` object from NetCDF4-file.
+
+ Parameters
+ ----------
+ filename : string
+ The name of the NetCDF4-file from which to load the data. Standard format is '\*.nc'.
+
+ Returns
+ -------
+ mag_data: :class:`~.MagData`
+ A :class:`~.MagData` object containing the loaded data.
'''
- f = nc.NetCDFFile(filename, 'r')
- res = getattr(f, 'res')
- z_mag = f.variables['z_mag'].getValue()
- y_mag = f.variables['y_mag'].getValue()
- x_mag = f.variables['x_mag'].getValue()
- f.close()
+ mag_file = netCDF4.Dataset(filename, 'r', format='NETCDF4')
+ res = mag_file.res
+ z_mag = mag_file.variables['z_mag'][:]
+ y_mag = mag_file.variables['y_mag'][:]
+ x_mag = mag_file.variables['x_mag'][:]
+ mag_file.close()
return MagData(res, (z_mag, y_mag, x_mag))
- def save_to_netcdf(self, filename='..\output\magdata_output.nc'):
- '''Save magnetization data in a file with NetCDF-format.
- Arguments:
- filename - the name of the file in which to store the phase map data
- (default: 'phasemap_output.txt')
- Returns:
- None
+ def save_to_netcdf4(self, filename='..\output\magdata_output.nc'):
+ '''Save magnetization data in a file with NetCDF4-format.
+
+ Parameters
+ ----------
+ filename : string, optional
+ The name of the NetCDF4-file in which to store the magnetization data.
+ The default is 'magdata_output.nc'.
+
+ Returns
+ -------
+ None
'''
- f = nc.NetCDFFile(filename, 'w')
- setattr(f, 'res', self.res)
- f.createDimension('z_dim', self.dim[0])
- f.createDimension('y_dim', self.dim[1])
- f.createDimension('x_dim', self.dim[2])
- z_mag = f.createVariable('z_mag', 'f', ('z_dim', 'y_dim', 'x_dim'))
- y_mag = f.createVariable('y_mag', 'f', ('z_dim', 'y_dim', 'x_dim'))
- x_mag = f.createVariable('x_mag', 'f', ('z_dim', 'y_dim', 'x_dim'))
+ mag_file = netCDF4.Dataset(filename, 'w', format='NETCDF4')
+ mag_file.res = self.res
+ mag_file.createDimension('z_dim', self.dim[0])
+ mag_file.createDimension('y_dim', self.dim[1])
+ mag_file.createDimension('x_dim', self.dim[2])
+ z_mag = mag_file.createVariable('z_mag', 'f', ('z_dim', 'y_dim', 'x_dim'))
+ y_mag = mag_file.createVariable('y_mag', 'f', ('z_dim', 'y_dim', 'x_dim'))
+ x_mag = mag_file.createVariable('x_mag', 'f', ('z_dim', 'y_dim', 'x_dim'))
z_mag[:] = self.magnitude[0]
y_mag[:] = self.magnitude[1]
x_mag[:] = self.magnitude[2]
- print f
- f.close()
+ print mag_file
+ mag_file.close()
- def quiver_plot(self, title='Magnetic Distribution)', proj_axis='z', ax_slice=None,
- filename=None, axis=None): # TODO!!
+ def quiver_plot(self, title='Magnetic Distribution', filename=None, axis=None,
+ proj_axis='z', ax_slice=None):
'''Plot a slice of the magnetization as a quiver plot.
- Arguments:
- axis - the axis from which a slice is plotted ('x', 'y' or 'z'), default = 'z'
- ax_slice - the slice-index of the specified axis (optional, if not specified, is
- set to the center of the specified axis)
- filename - filename, specifying the location where the image is saved (optional, if
- not specified, image is shown instead)
- Returns:
- None
+
+ Parameters
+ ----------
+ title : string, optional
+ The title for the plot.
+ axis : :class:`~matplotlib.axes.AxesSubplot`, optional
+ Axis on which the graph is plotted. Creates a new figure if none is specified.
+ filename : string, optional
+ The filename, specifying the location where the image is saved. If not specified,
+ the image is shown instead.
+ proj_axis : {'z', 'y', 'x'}, optional
+ The axis, from which a slice is plotted. The default is 'z'.
+ ax_slice : int, optional
+ The slice-index of the axis specified in `proj_axis`. Is set to the center of
+ `proj_axis` if not specified.
+
+ Returns
+ -------
+ None
'''
assert proj_axis == 'z' or proj_axis == 'y' or proj_axis == 'x', \
- 'Axis has to be x, y or z (as string).'
+ 'Axis has to be x, y or z (as string).'
if proj_axis == 'z': # Slice of the xy-plane with z = ax_slice
if ax_slice is None:
ax_slice = int(self.dim[0]/2)
@@ -208,15 +366,17 @@ class MagData:
plt.show()
def quiver_plot3d(self):
- '''3D-Quiver-Plot of the magnetization as vectors.
- Arguments:
- None
- Returns:
- None
+ '''Plot the magnetization as 3D-vectors in a quiverplot.
- '''
- from mayavi import mlab
+ Parameters
+ ----------
+ None
+ Returns
+ -------
+ None
+
+ '''
res = self.res
dim = self.dim
# Create points and vector components as lists:
diff --git a/pyramid/numcore/__init__.py b/pyramid/numcore/__init__.py
index c4a3052..df89b8e 100644
--- a/pyramid/numcore/__init__.py
+++ b/pyramid/numcore/__init__.py
@@ -1 +1,15 @@
+"""Package for numerical core routines which enable fast computations.
+
+Modules
+-------
+phase_mag_real
+ Provides numerical core routines for the real space approach in
+ :func:`~pyramid.phasemapper.phase_mag_real` of module :mod:`~pyramid.phasemapper`.
+
+Notes
+-----
+Packages are written in `pyx`-format for the use with :mod:`~cython`.
+
+"""
+
from phase_mag_real import *
diff --git a/pyramid/numcore/phase_mag_real.c b/pyramid/numcore/phase_mag_real.c
deleted file mode 100644
index 3d391e9..0000000
--- a/pyramid/numcore/phase_mag_real.c
+++ /dev/null
@@ -1,18750 +0,0 @@
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- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
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- #else
- #define CYTHON_RESTRICT
- #endif
-#endif
-#ifdef NAN
-#define __PYX_NAN() ((float) NAN)
-#else
-static CYTHON_INLINE float __PYX_NAN() {
- /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
- a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
- a quiet NaN. */
- float value;
- memset(&value, 0xFF, sizeof(value));
- return value;
-}
-#endif
-
-
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
-#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
-#endif
-
-#ifndef __PYX_EXTERN_C
- #ifdef __cplusplus
- #define __PYX_EXTERN_C extern "C"
- #else
- #define __PYX_EXTERN_C extern
- #endif
-#endif
-
-#if defined(WIN32) || defined(MS_WINDOWS)
-#define _USE_MATH_DEFINES
-#endif
-#include <math.h>
-#define __PYX_HAVE__phase_mag_real
-#define __PYX_HAVE_API__phase_mag_real
-#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "numpy/arrayobject.h"
-#include "numpy/ufuncobject.h"
-#include "pythread.h"
-#include "pystate.h"
-#ifdef _OPENMP
-#include <omp.h>
-#endif /* _OPENMP */
-
-#ifdef PYREX_WITHOUT_ASSERTIONS
-#define CYTHON_WITHOUT_ASSERTIONS
-#endif
-
-#ifndef CYTHON_UNUSED
-# if defined(__GNUC__)
-# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-#endif
-typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
- const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
-#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
-#define __PYX_DEFAULT_STRING_ENCODING ""
-#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
-#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
-#define __Pyx_PyBytes_FromString PyBytes_FromString
-#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char*);
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#else
- #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
-#endif
-#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((char*)s)
-#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((char*)s)
-#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((char*)s)
-#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((char*)s)
-#if PY_MAJOR_VERSION < 3
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
-{
- const Py_UNICODE *u_end = u;
- while (*u_end++) ;
- return u_end - u - 1;
-}
-#else
-#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
-#endif
-#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
-#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
-#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
-#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
-#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-#if CYTHON_COMPILING_IN_CPYTHON
-#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-#else
-#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
-#endif
-#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
-static int __Pyx_sys_getdefaultencoding_not_ascii;
-static int __Pyx_init_sys_getdefaultencoding_params() {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- PyObject* ascii_chars_u = NULL;
- PyObject* ascii_chars_b = NULL;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- if (strcmp(PyBytes_AsString(default_encoding), "ascii") == 0) {
- __Pyx_sys_getdefaultencoding_not_ascii = 0;
- } else {
- const char* default_encoding_c = PyBytes_AS_STRING(default_encoding);
- char ascii_chars[128];
- int c;
- for (c = 0; c < 128; c++) {
- ascii_chars[c] = c;
- }
- __Pyx_sys_getdefaultencoding_not_ascii = 1;
- ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
- if (ascii_chars_u == NULL) goto bad;
- ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
- if (ascii_chars_b == NULL || strncmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
- PyErr_Format(
- PyExc_ValueError,
- "This module compiled with c_string_encoding=ascii, but default encoding '%s' is not a superset of ascii.",
- default_encoding_c);
- goto bad;
- }
- }
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return -1;
-}
-#endif
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
-#else
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
-static char* __PYX_DEFAULT_STRING_ENCODING;
-static int __Pyx_init_sys_getdefaultencoding_params() {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- default_encoding_c = PyBytes_AS_STRING(default_encoding);
- __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
- strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
- Py_DECREF(sys);
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- return -1;
-}
-#endif
-#endif
-
-
-#ifdef __GNUC__
- /* Test for GCC > 2.95 */
- #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
- #define likely(x) __builtin_expect(!!(x), 1)
- #define unlikely(x) __builtin_expect(!!(x), 0)
- #else /* __GNUC__ > 2 ... */
- #define likely(x) (x)
- #define unlikely(x) (x)
- #endif /* __GNUC__ > 2 ... */
-#else /* __GNUC__ */
- #define likely(x) (x)
- #define unlikely(x) (x)
-#endif /* __GNUC__ */
-
-static PyObject *__pyx_m;
-static PyObject *__pyx_d;
-static PyObject *__pyx_b;
-static PyObject *__pyx_empty_tuple;
-static PyObject *__pyx_empty_bytes;
-static int __pyx_lineno;
-static int __pyx_clineno = 0;
-static const char * __pyx_cfilenm= __FILE__;
-static const char *__pyx_filename;
-
-#if !defined(CYTHON_CCOMPLEX)
- #if defined(__cplusplus)
- #define CYTHON_CCOMPLEX 1
- #elif defined(_Complex_I)
- #define CYTHON_CCOMPLEX 1
- #else
- #define CYTHON_CCOMPLEX 0
- #endif
-#endif
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- #include <complex>
- #else
- #include <complex.h>
- #endif
-#endif
-#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__)
- #undef _Complex_I
- #define _Complex_I 1.0fj
-#endif
-
-
-static const char *__pyx_f[] = {
- "phase_mag_real.pyx",
- "numpy.pxd",
- "stringsource",
- "type.pxd",
-};
-struct __pyx_memoryview_obj;
-typedef struct {
- struct __pyx_memoryview_obj *memview;
- char *data;
- Py_ssize_t shape[8];
- Py_ssize_t strides[8];
- Py_ssize_t suboffsets[8];
-} __Pyx_memviewslice;
-
-#define IS_UNSIGNED(type) (((type) -1) > 0)
-struct __Pyx_StructField_;
-#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0)
-typedef struct {
- const char* name; /* for error messages only */
- struct __Pyx_StructField_* fields;
- size_t size; /* sizeof(type) */
- size_t arraysize[8]; /* length of array in each dimension */
- int ndim;
- char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject, c_H_ar */
- char is_unsigned;
- int flags;
-} __Pyx_TypeInfo;
-typedef struct __Pyx_StructField_ {
- __Pyx_TypeInfo* type;
- const char* name;
- size_t offset;
-} __Pyx_StructField;
-typedef struct {
- __Pyx_StructField* field;
- size_t parent_offset;
-} __Pyx_BufFmt_StackElem;
-typedef struct {
- __Pyx_StructField root;
- __Pyx_BufFmt_StackElem* head;
- size_t fmt_offset;
- size_t new_count, enc_count;
- size_t struct_alignment;
- int is_complex;
- char enc_type;
- char new_packmode;
- char enc_packmode;
- char is_valid_array;
-} __Pyx_BufFmt_Context;
-
-#include <pythread.h>
-#ifndef CYTHON_ATOMICS
- #define CYTHON_ATOMICS 1
-#endif
-#define __pyx_atomic_int_type int
-#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 || \
- (__GNUC_MINOR__ == 1 && __GNUC_PATCHLEVEL >= 2)) && \
- !defined(__i386__)
- #define __pyx_atomic_incr_aligned(value, lock) __sync_fetch_and_add(value, 1)
- #define __pyx_atomic_decr_aligned(value, lock) __sync_fetch_and_sub(value, 1)
- #ifdef __PYX_DEBUG_ATOMICS
- #warning "Using GNU atomics"
- #endif
-#elif CYTHON_ATOMICS && MSC_VER
- #include <Windows.h>
- #define __pyx_atomic_int_type LONG
- #define __pyx_atomic_incr_aligned(value, lock) InterlockedIncrement(value)
- #define __pyx_atomic_decr_aligned(value, lock) InterlockedDecrement(value)
- #ifdef __PYX_DEBUG_ATOMICS
- #warning "Using MSVC atomics"
- #endif
-#elif CYTHON_ATOMICS && (defined(__ICC) || defined(__INTEL_COMPILER)) && 0
- #define __pyx_atomic_incr_aligned(value, lock) _InterlockedIncrement(value)
- #define __pyx_atomic_decr_aligned(value, lock) _InterlockedDecrement(value)
- #ifdef __PYX_DEBUG_ATOMICS
- #warning "Using Intel atomics"
- #endif
-#else
- #undef CYTHON_ATOMICS
- #define CYTHON_ATOMICS 0
- #ifdef __PYX_DEBUG_ATOMICS
- #warning "Not using atomics"
- #endif
-#endif
-typedef volatile __pyx_atomic_int_type __pyx_atomic_int;
-#if CYTHON_ATOMICS
- #define __pyx_add_acquisition_count(memview) \
- __pyx_atomic_incr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock)
- #define __pyx_sub_acquisition_count(memview) \
- __pyx_atomic_decr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock)
-#else
- #define __pyx_add_acquisition_count(memview) \
- __pyx_add_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock)
- #define __pyx_sub_acquisition_count(memview) \
- __pyx_sub_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock)
-#endif
-
-
-/* "numpy.pxd":723
- * # in Cython to enable them only on the right systems.
- *
- * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
- * ctypedef npy_int16 int16_t
- * ctypedef npy_int32 int32_t
- */
-typedef npy_int8 __pyx_t_5numpy_int8_t;
-
-/* "numpy.pxd":724
- *
- * ctypedef npy_int8 int8_t
- * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
- * ctypedef npy_int32 int32_t
- * ctypedef npy_int64 int64_t
- */
-typedef npy_int16 __pyx_t_5numpy_int16_t;
-
-/* "numpy.pxd":725
- * ctypedef npy_int8 int8_t
- * ctypedef npy_int16 int16_t
- * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
- * ctypedef npy_int64 int64_t
- * #ctypedef npy_int96 int96_t
- */
-typedef npy_int32 __pyx_t_5numpy_int32_t;
-
-/* "numpy.pxd":726
- * ctypedef npy_int16 int16_t
- * ctypedef npy_int32 int32_t
- * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
- * #ctypedef npy_int96 int96_t
- * #ctypedef npy_int128 int128_t
- */
-typedef npy_int64 __pyx_t_5numpy_int64_t;
-
-/* "numpy.pxd":730
- * #ctypedef npy_int128 int128_t
- *
- * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
- * ctypedef npy_uint16 uint16_t
- * ctypedef npy_uint32 uint32_t
- */
-typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-
-/* "numpy.pxd":731
- *
- * ctypedef npy_uint8 uint8_t
- * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
- * ctypedef npy_uint32 uint32_t
- * ctypedef npy_uint64 uint64_t
- */
-typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-
-/* "numpy.pxd":732
- * ctypedef npy_uint8 uint8_t
- * ctypedef npy_uint16 uint16_t
- * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
- * ctypedef npy_uint64 uint64_t
- * #ctypedef npy_uint96 uint96_t
- */
-typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-
-/* "numpy.pxd":733
- * ctypedef npy_uint16 uint16_t
- * ctypedef npy_uint32 uint32_t
- * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
- * #ctypedef npy_uint96 uint96_t
- * #ctypedef npy_uint128 uint128_t
- */
-typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-
-/* "numpy.pxd":737
- * #ctypedef npy_uint128 uint128_t
- *
- * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
- * ctypedef npy_float64 float64_t
- * #ctypedef npy_float80 float80_t
- */
-typedef npy_float32 __pyx_t_5numpy_float32_t;
-
-/* "numpy.pxd":738
- *
- * ctypedef npy_float32 float32_t
- * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
- * #ctypedef npy_float80 float80_t
- * #ctypedef npy_float128 float128_t
- */
-typedef npy_float64 __pyx_t_5numpy_float64_t;
-
-/* "numpy.pxd":747
- * # The int types are mapped a bit surprising --
- * # numpy.int corresponds to 'l' and numpy.long to 'q'
- * ctypedef npy_long int_t # <<<<<<<<<<<<<<
- * ctypedef npy_longlong long_t
- * ctypedef npy_longlong longlong_t
- */
-typedef npy_long __pyx_t_5numpy_int_t;
-
-/* "numpy.pxd":748
- * # numpy.int corresponds to 'l' and numpy.long to 'q'
- * ctypedef npy_long int_t
- * ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
- * ctypedef npy_longlong longlong_t
- *
- */
-typedef npy_longlong __pyx_t_5numpy_long_t;
-
-/* "numpy.pxd":749
- * ctypedef npy_long int_t
- * ctypedef npy_longlong long_t
- * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_ulong uint_t
- */
-typedef npy_longlong __pyx_t_5numpy_longlong_t;
-
-/* "numpy.pxd":751
- * ctypedef npy_longlong longlong_t
- *
- * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
- * ctypedef npy_ulonglong ulong_t
- * ctypedef npy_ulonglong ulonglong_t
- */
-typedef npy_ulong __pyx_t_5numpy_uint_t;
-
-/* "numpy.pxd":752
- *
- * ctypedef npy_ulong uint_t
- * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
- * ctypedef npy_ulonglong ulonglong_t
- *
- */
-typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-
-/* "numpy.pxd":753
- * ctypedef npy_ulong uint_t
- * ctypedef npy_ulonglong ulong_t
- * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_intp intp_t
- */
-typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-
-/* "numpy.pxd":755
- * ctypedef npy_ulonglong ulonglong_t
- *
- * ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
- * ctypedef npy_uintp uintp_t
- *
- */
-typedef npy_intp __pyx_t_5numpy_intp_t;
-
-/* "numpy.pxd":756
- *
- * ctypedef npy_intp intp_t
- * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_double float_t
- */
-typedef npy_uintp __pyx_t_5numpy_uintp_t;
-
-/* "numpy.pxd":758
- * ctypedef npy_uintp uintp_t
- *
- * ctypedef npy_double float_t # <<<<<<<<<<<<<<
- * ctypedef npy_double double_t
- * ctypedef npy_longdouble longdouble_t
- */
-typedef npy_double __pyx_t_5numpy_float_t;
-
-/* "numpy.pxd":759
- *
- * ctypedef npy_double float_t
- * ctypedef npy_double double_t # <<<<<<<<<<<<<<
- * ctypedef npy_longdouble longdouble_t
- *
- */
-typedef npy_double __pyx_t_5numpy_double_t;
-
-/* "numpy.pxd":760
- * ctypedef npy_double float_t
- * ctypedef npy_double double_t
- * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_cfloat cfloat_t
- */
-typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- typedef ::std::complex< float > __pyx_t_float_complex;
- #else
- typedef float _Complex __pyx_t_float_complex;
- #endif
-#else
- typedef struct { float real, imag; } __pyx_t_float_complex;
-#endif
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- typedef ::std::complex< double > __pyx_t_double_complex;
- #else
- typedef double _Complex __pyx_t_double_complex;
- #endif
-#else
- typedef struct { double real, imag; } __pyx_t_double_complex;
-#endif
-
-
-/*--- Type declarations ---*/
-struct __pyx_memoryview_obj;
-struct __pyx_array_obj;
-struct __pyx_MemviewEnum_obj;
-struct __pyx_memoryviewslice_obj;
-
-/* "numpy.pxd":762
- * ctypedef npy_longdouble longdouble_t
- *
- * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
- * ctypedef npy_cdouble cdouble_t
- * ctypedef npy_clongdouble clongdouble_t
- */
-typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-
-/* "numpy.pxd":763
- *
- * ctypedef npy_cfloat cfloat_t
- * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
- * ctypedef npy_clongdouble clongdouble_t
- *
- */
-typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-
-/* "numpy.pxd":764
- * ctypedef npy_cfloat cfloat_t
- * ctypedef npy_cdouble cdouble_t
- * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_cdouble complex_t
- */
-typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-
-/* "numpy.pxd":766
- * ctypedef npy_clongdouble clongdouble_t
- *
- * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
- *
- * cdef inline object PyArray_MultiIterNew1(a):
- */
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-static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig);
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-static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
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-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
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-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
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-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *);
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-static void __Pyx_AddTraceback(const char *funcname, int c_line,
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-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
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-/* Module declarations from 'cpython.buffer' */
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-/* Module declarations from 'cpython.ref' */
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-/* Module declarations from 'cpython.type' */
-static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
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-/* Module declarations from 'libc.stdlib' */
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-/* Module declarations from 'numpy' */
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-/* Module declarations from 'numpy' */
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-static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0;
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-static PyTypeObject *__pyx_array_type = 0;
-static PyTypeObject *__pyx_MemviewEnum_type = 0;
-static PyTypeObject *__pyx_memoryviewslice_type = 0;
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-static void copy_strided_to_strided(__Pyx_memviewslice *, __Pyx_memviewslice *, int, size_t); /*proto*/
-static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *, int); /*proto*/
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-static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *, __Pyx_memviewslice *, char, int); /*proto*/
-static int __pyx_memoryview_err_extents(int, Py_ssize_t, Py_ssize_t); /*proto*/
-static int __pyx_memoryview_err_dim(PyObject *, char *, int); /*proto*/
-static int __pyx_memoryview_err(PyObject *, char *); /*proto*/
-static int __pyx_memoryview_copy_contents(__Pyx_memviewslice, __Pyx_memviewslice, int, int, int); /*proto*/
-static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *, int, int); /*proto*/
-static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *, int, int, int); /*proto*/
-static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/
-static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/
-static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/
-static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/
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-/* Implementation of 'phase_mag_real' */
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-static PyObject *__pyx_builtin_RuntimeError;
-static PyObject *__pyx_builtin_MemoryError;
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-static PyObject *__pyx_builtin_Ellipsis;
-static PyObject *__pyx_builtin_TypeError;
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-static PyObject *__pyx_builtin_id;
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-static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
-static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
-static int __pyx_array_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */
-static int __pyx_array_getbuffer_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
-static void __pyx_array_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */
-static PyObject *get_memview_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_array_MemoryView_5array_6__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */
-static PyObject *__pyx_array_MemoryView_5array_8__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */
-static int __pyx_array_MemoryView_5array_10__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */
-static int __pyx_MemviewEnum_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */
-static PyObject *__pyx_MemviewEnum_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */
-static int __pyx_memoryview_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */
-static void __pyx_memoryview_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */
-static int __pyx_memoryview_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */
-static int __pyx_memoryview_getbuffer_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
-static PyObject *__pyx_memoryview_transpose_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview__get__base_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_get_shape_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_get_strides_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_get_suboffsets_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_get_ndim_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_get_itemsize_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_get_nbytes_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_get_size_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static Py_ssize_t __pyx_memoryview_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryview_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
-static void __pyx_memoryviewslice_MemoryView_16_memoryviewslice___dealloc__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_memoryviewslice__get__base_MemoryView_16_memoryviewslice_4base___get__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */
-static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
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-static char __pyx_k_21[] = "Invalid mode, expected 'c' or 'fortran', got %s";
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-static char __pyx_k_25[] = "Can only create a buffer that is contiguous in memory.";
-static char __pyx_k_27[] = "Unable to convert item to object";
-static char __pyx_k_29[] = "Buffer view does not expose strides";
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-static char __pyx_k_32[] = "<MemoryView of %r object>";
-static char __pyx_k_35[] = "Cannot index with type '%s'";
-static char __pyx_k_37[] = "Indirect dimensions not supported";
-static char __pyx_k_39[] = "Index out of bounds (axis %d)";
-static char __pyx_k_40[] = "Step may not be zero (axis %d)";
-static char __pyx_k_41[] = "All dimensions preceding dimension %d must be indexed and not sliced";
-static char __pyx_k_42[] = "Out of bounds on buffer access (axis %d)";
-static char __pyx_k_43[] = "Cannot transpose memoryview with indirect dimensions";
-static char __pyx_k_44[] = "got differing extents in dimension %d (got %d and %d)";
-static char __pyx_k_45[] = "Dimension %d is not direct";
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-static char __pyx_k_50[] = "getbuffer(obj, view, flags)";
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- * if mslice.shape[i] > 1: # <<<<<<<<<<<<<<
- * c_stride = mslice.strides[i]
- * break
- */
- __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1084
- * for i in range(ndim - 1, -1, -1):
- * if mslice.shape[i] > 1:
- * c_stride = mslice.strides[i] # <<<<<<<<<<<<<<
- * break
- *
- */
- __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]);
-
- /* "View.MemoryView":1085
- * if mslice.shape[i] > 1:
- * c_stride = mslice.strides[i]
- * break # <<<<<<<<<<<<<<
- *
- * for i in range(ndim):
- */
- goto __pyx_L4_break;
- goto __pyx_L5;
- }
- __pyx_L5:;
- }
- __pyx_L4_break:;
-
- /* "View.MemoryView":1087
- * break
- *
- * for i in range(ndim): # <<<<<<<<<<<<<<
- * if mslice.shape[i] > 1:
- * f_stride = mslice.strides[i]
- */
- __pyx_t_1 = __pyx_v_ndim;
- for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) {
- __pyx_v_i = __pyx_t_3;
-
- /* "View.MemoryView":1088
- *
- * for i in range(ndim):
- * if mslice.shape[i] > 1: # <<<<<<<<<<<<<<
- * f_stride = mslice.strides[i]
- * break
- */
- __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1089
- * for i in range(ndim):
- * if mslice.shape[i] > 1:
- * f_stride = mslice.strides[i] # <<<<<<<<<<<<<<
- * break
- *
- */
- __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]);
-
- /* "View.MemoryView":1090
- * if mslice.shape[i] > 1:
- * f_stride = mslice.strides[i]
- * break # <<<<<<<<<<<<<<
- *
- * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride):
- */
- goto __pyx_L7_break;
- goto __pyx_L8;
- }
- __pyx_L8:;
- }
- __pyx_L7_break:;
-
- /* "View.MemoryView":1092
- * break
- *
- * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<<
- * return 'C'
- * else:
- */
- __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1093
- *
- * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride):
- * return 'C' # <<<<<<<<<<<<<<
- * else:
- * return 'F'
- */
- __pyx_r = 'C';
- goto __pyx_L0;
- goto __pyx_L9;
- }
- /*else*/ {
-
- /* "View.MemoryView":1095
- * return 'C'
- * else:
- * return 'F' # <<<<<<<<<<<<<<
- *
- * @cython.cdivision(True)
- */
- __pyx_r = 'F';
- goto __pyx_L0;
- }
- __pyx_L9:;
-
- __pyx_r = 0;
- __pyx_L0:;
- return __pyx_r;
-}
-
-/* "View.MemoryView":1098
- *
- * @cython.cdivision(True)
- * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<<
- * char *dst_data, Py_ssize_t *dst_strides,
- * Py_ssize_t *src_shape, Py_ssize_t *dst_shape,
- */
-
-static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v_src_strides, char *__pyx_v_dst_data, Py_ssize_t *__pyx_v_dst_strides, Py_ssize_t *__pyx_v_src_shape, Py_ssize_t *__pyx_v_dst_shape, int __pyx_v_ndim, size_t __pyx_v_itemsize) {
- CYTHON_UNUSED Py_ssize_t __pyx_v_i;
- CYTHON_UNUSED Py_ssize_t __pyx_v_src_extent;
- Py_ssize_t __pyx_v_dst_extent;
- Py_ssize_t __pyx_v_src_stride;
- Py_ssize_t __pyx_v_dst_stride;
- int __pyx_t_1;
- int __pyx_t_2;
- int __pyx_t_3;
- int __pyx_t_4;
- Py_ssize_t __pyx_t_5;
- Py_ssize_t __pyx_t_6;
-
- /* "View.MemoryView":1105
- *
- * cdef Py_ssize_t i
- * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<<
- * cdef Py_ssize_t dst_extent = dst_shape[0]
- * cdef Py_ssize_t src_stride = src_strides[0]
- */
- __pyx_v_src_extent = (__pyx_v_src_shape[0]);
-
- /* "View.MemoryView":1106
- * cdef Py_ssize_t i
- * cdef Py_ssize_t src_extent = src_shape[0]
- * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<<
- * cdef Py_ssize_t src_stride = src_strides[0]
- * cdef Py_ssize_t dst_stride = dst_strides[0]
- */
- __pyx_v_dst_extent = (__pyx_v_dst_shape[0]);
-
- /* "View.MemoryView":1107
- * cdef Py_ssize_t src_extent = src_shape[0]
- * cdef Py_ssize_t dst_extent = dst_shape[0]
- * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<<
- * cdef Py_ssize_t dst_stride = dst_strides[0]
- *
- */
- __pyx_v_src_stride = (__pyx_v_src_strides[0]);
-
- /* "View.MemoryView":1108
- * cdef Py_ssize_t dst_extent = dst_shape[0]
- * cdef Py_ssize_t src_stride = src_strides[0]
- * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<<
- *
- * if ndim == 1:
- */
- __pyx_v_dst_stride = (__pyx_v_dst_strides[0]);
-
- /* "View.MemoryView":1110
- * cdef Py_ssize_t dst_stride = dst_strides[0]
- *
- * if ndim == 1: # <<<<<<<<<<<<<<
- * if (src_stride > 0 and dst_stride > 0 and
- * <size_t> src_stride == itemsize == <size_t> dst_stride):
- */
- __pyx_t_1 = ((__pyx_v_ndim == 1) != 0);
- if (__pyx_t_1) {
-
- /* "View.MemoryView":1111
- *
- * if ndim == 1:
- * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<<
- * <size_t> src_stride == itemsize == <size_t> dst_stride):
- * memcpy(dst_data, src_data, itemsize * dst_extent)
- */
- __pyx_t_1 = ((__pyx_v_src_stride > 0) != 0);
- if (__pyx_t_1) {
- __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1112
- * if ndim == 1:
- * if (src_stride > 0 and dst_stride > 0 and
- * <size_t> src_stride == itemsize == <size_t> dst_stride): # <<<<<<<<<<<<<<
- * memcpy(dst_data, src_data, itemsize * dst_extent)
- * else:
- */
- __pyx_t_3 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize);
- if (__pyx_t_3) {
- __pyx_t_3 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride));
- }
- __pyx_t_4 = (__pyx_t_3 != 0);
- } else {
- __pyx_t_4 = __pyx_t_2;
- }
- __pyx_t_2 = __pyx_t_4;
- } else {
- __pyx_t_2 = __pyx_t_1;
- }
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1113
- * if (src_stride > 0 and dst_stride > 0 and
- * <size_t> src_stride == itemsize == <size_t> dst_stride):
- * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<<
- * else:
- * for i in range(dst_extent):
- */
- memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent));
- goto __pyx_L4;
- }
- /*else*/ {
-
- /* "View.MemoryView":1115
- * memcpy(dst_data, src_data, itemsize * dst_extent)
- * else:
- * for i in range(dst_extent): # <<<<<<<<<<<<<<
- * memcpy(dst_data, src_data, itemsize)
- * src_data += src_stride
- */
- __pyx_t_5 = __pyx_v_dst_extent;
- for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
- __pyx_v_i = __pyx_t_6;
-
- /* "View.MemoryView":1116
- * else:
- * for i in range(dst_extent):
- * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<<
- * src_data += src_stride
- * dst_data += dst_stride
- */
- memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize);
-
- /* "View.MemoryView":1117
- * for i in range(dst_extent):
- * memcpy(dst_data, src_data, itemsize)
- * src_data += src_stride # <<<<<<<<<<<<<<
- * dst_data += dst_stride
- * else:
- */
- __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride);
-
- /* "View.MemoryView":1118
- * memcpy(dst_data, src_data, itemsize)
- * src_data += src_stride
- * dst_data += dst_stride # <<<<<<<<<<<<<<
- * else:
- * for i in range(dst_extent):
- */
- __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride);
- }
- }
- __pyx_L4:;
- goto __pyx_L3;
- }
- /*else*/ {
-
- /* "View.MemoryView":1120
- * dst_data += dst_stride
- * else:
- * for i in range(dst_extent): # <<<<<<<<<<<<<<
- * _copy_strided_to_strided(src_data, src_strides + 1,
- * dst_data, dst_strides + 1,
- */
- __pyx_t_5 = __pyx_v_dst_extent;
- for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
- __pyx_v_i = __pyx_t_6;
-
- /* "View.MemoryView":1124
- * dst_data, dst_strides + 1,
- * src_shape + 1, dst_shape + 1,
- * ndim - 1, itemsize) # <<<<<<<<<<<<<<
- * src_data += src_stride
- * dst_data += dst_stride
- */
- _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize);
-
- /* "View.MemoryView":1125
- * src_shape + 1, dst_shape + 1,
- * ndim - 1, itemsize)
- * src_data += src_stride # <<<<<<<<<<<<<<
- * dst_data += dst_stride
- *
- */
- __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride);
-
- /* "View.MemoryView":1126
- * ndim - 1, itemsize)
- * src_data += src_stride
- * dst_data += dst_stride # <<<<<<<<<<<<<<
- *
- * cdef void copy_strided_to_strided(__Pyx_memviewslice *src,
- */
- __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride);
- }
- }
- __pyx_L3:;
-
-}
-
-/* "View.MemoryView":1128
- * dst_data += dst_stride
- *
- * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<<
- * __Pyx_memviewslice *dst,
- * int ndim, size_t itemsize) nogil:
- */
-
-static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) {
-
- /* "View.MemoryView":1132
- * int ndim, size_t itemsize) nogil:
- * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides,
- * src.shape, dst.shape, ndim, itemsize) # <<<<<<<<<<<<<<
- *
- * @cname('__pyx_memoryview_slice_get_size')
- */
- _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize);
-
-}
-
-/* "View.MemoryView":1135
- *
- * @cname('__pyx_memoryview_slice_get_size')
- * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<<
- * "Return the size of the memory occupied by the slice in number of bytes"
- * cdef int i
- */
-
-static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) {
- int __pyx_v_i;
- Py_ssize_t __pyx_v_size;
- Py_ssize_t __pyx_r;
- Py_ssize_t __pyx_t_1;
- int __pyx_t_2;
- int __pyx_t_3;
-
- /* "View.MemoryView":1138
- * "Return the size of the memory occupied by the slice in number of bytes"
- * cdef int i
- * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<<
- *
- * for i in range(ndim):
- */
- __pyx_t_1 = __pyx_v_src->memview->view.itemsize;
- __pyx_v_size = __pyx_t_1;
-
- /* "View.MemoryView":1140
- * cdef Py_ssize_t size = src.memview.view.itemsize
- *
- * for i in range(ndim): # <<<<<<<<<<<<<<
- * size *= src.shape[i]
- *
- */
- __pyx_t_2 = __pyx_v_ndim;
- for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
- __pyx_v_i = __pyx_t_3;
-
- /* "View.MemoryView":1141
- *
- * for i in range(ndim):
- * size *= src.shape[i] # <<<<<<<<<<<<<<
- *
- * return size
- */
- __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i]));
- }
-
- /* "View.MemoryView":1143
- * size *= src.shape[i]
- *
- * return size # <<<<<<<<<<<<<<
- *
- * @cname('__pyx_fill_contig_strides_array')
- */
- __pyx_r = __pyx_v_size;
- goto __pyx_L0;
-
- __pyx_r = 0;
- __pyx_L0:;
- return __pyx_r;
-}
-
-/* "View.MemoryView":1146
- *
- * @cname('__pyx_fill_contig_strides_array')
- * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<<
- * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride,
- * int ndim, char order) nogil:
- */
-
-static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) {
- int __pyx_v_idx;
- Py_ssize_t __pyx_r;
- int __pyx_t_1;
- int __pyx_t_2;
- int __pyx_t_3;
-
- /* "View.MemoryView":1155
- * cdef int idx
- *
- * if order == 'F': # <<<<<<<<<<<<<<
- * for idx in range(ndim):
- * strides[idx] = stride
- */
- __pyx_t_1 = ((__pyx_v_order == 'F') != 0);
- if (__pyx_t_1) {
-
- /* "View.MemoryView":1156
- *
- * if order == 'F':
- * for idx in range(ndim): # <<<<<<<<<<<<<<
- * strides[idx] = stride
- * stride = stride * shape[idx]
- */
- __pyx_t_2 = __pyx_v_ndim;
- for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
- __pyx_v_idx = __pyx_t_3;
-
- /* "View.MemoryView":1157
- * if order == 'F':
- * for idx in range(ndim):
- * strides[idx] = stride # <<<<<<<<<<<<<<
- * stride = stride * shape[idx]
- * else:
- */
- (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride;
-
- /* "View.MemoryView":1158
- * for idx in range(ndim):
- * strides[idx] = stride
- * stride = stride * shape[idx] # <<<<<<<<<<<<<<
- * else:
- * for idx in range(ndim - 1, -1, -1):
- */
- __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx]));
- }
- goto __pyx_L3;
- }
- /*else*/ {
-
- /* "View.MemoryView":1160
- * stride = stride * shape[idx]
- * else:
- * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<<
- * strides[idx] = stride
- * stride = stride * shape[idx]
- */
- for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) {
- __pyx_v_idx = __pyx_t_2;
-
- /* "View.MemoryView":1161
- * else:
- * for idx in range(ndim - 1, -1, -1):
- * strides[idx] = stride # <<<<<<<<<<<<<<
- * stride = stride * shape[idx]
- *
- */
- (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride;
-
- /* "View.MemoryView":1162
- * for idx in range(ndim - 1, -1, -1):
- * strides[idx] = stride
- * stride = stride * shape[idx] # <<<<<<<<<<<<<<
- *
- * return stride
- */
- __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx]));
- }
- }
- __pyx_L3:;
-
- /* "View.MemoryView":1164
- * stride = stride * shape[idx]
- *
- * return stride # <<<<<<<<<<<<<<
- *
- * @cname('__pyx_memoryview_copy_data_to_temp')
- */
- __pyx_r = __pyx_v_stride;
- goto __pyx_L0;
-
- __pyx_r = 0;
- __pyx_L0:;
- return __pyx_r;
-}
-
-/* "View.MemoryView":1167
- *
- * @cname('__pyx_memoryview_copy_data_to_temp')
- * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<<
- * __Pyx_memviewslice *tmpslice,
- * char order,
- */
-
-static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_tmpslice, char __pyx_v_order, int __pyx_v_ndim) {
- int __pyx_v_i;
- void *__pyx_v_result;
- size_t __pyx_v_itemsize;
- size_t __pyx_v_size;
- void *__pyx_r;
- Py_ssize_t __pyx_t_1;
- int __pyx_t_2;
- int __pyx_t_3;
- struct __pyx_memoryview_obj *__pyx_t_4;
- int __pyx_t_5;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
-
- /* "View.MemoryView":1178
- * cdef void *result
- *
- * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<<
- * cdef size_t size = slice_get_size(src, ndim)
- *
- */
- __pyx_t_1 = __pyx_v_src->memview->view.itemsize;
- __pyx_v_itemsize = __pyx_t_1;
-
- /* "View.MemoryView":1179
- *
- * cdef size_t itemsize = src.memview.view.itemsize
- * cdef size_t size = slice_get_size(src, ndim) # <<<<<<<<<<<<<<
- *
- * result = malloc(size)
- */
- __pyx_v_size = __pyx_memoryview_slice_get_size(__pyx_v_src, __pyx_v_ndim);
-
- /* "View.MemoryView":1181
- * cdef size_t size = slice_get_size(src, ndim)
- *
- * result = malloc(size) # <<<<<<<<<<<<<<
- * if not result:
- * _err(MemoryError, NULL)
- */
- __pyx_v_result = malloc(__pyx_v_size);
-
- /* "View.MemoryView":1182
- *
- * result = malloc(size)
- * if not result: # <<<<<<<<<<<<<<
- * _err(MemoryError, NULL)
- *
- */
- __pyx_t_2 = ((!(__pyx_v_result != 0)) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1183
- * result = malloc(size)
- * if not result:
- * _err(MemoryError, NULL) # <<<<<<<<<<<<<<
- *
- *
- */
- __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
- }
- __pyx_L3:;
-
- /* "View.MemoryView":1186
- *
- *
- * tmpslice.data = <char *> result # <<<<<<<<<<<<<<
- * tmpslice.memview = src.memview
- * for i in range(ndim):
- */
- __pyx_v_tmpslice->data = ((char *)__pyx_v_result);
-
- /* "View.MemoryView":1187
- *
- * tmpslice.data = <char *> result
- * tmpslice.memview = src.memview # <<<<<<<<<<<<<<
- * for i in range(ndim):
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- * broadcast_leading(&src, src_ndim, dst_ndim)
- * elif dst_ndim < src_ndim: # <<<<<<<<<<<<<<
- * broadcast_leading(&dst, dst_ndim, src_ndim)
- *
- */
- __pyx_t_2 = ((__pyx_v_dst_ndim < __pyx_v_src_ndim) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1246
- * broadcast_leading(&src, src_ndim, dst_ndim)
- * elif dst_ndim < src_ndim:
- * broadcast_leading(&dst, dst_ndim, src_ndim) # <<<<<<<<<<<<<<
- *
- * cdef int ndim = max(src_ndim, dst_ndim)
- */
- __pyx_memoryview_broadcast_leading((&__pyx_v_dst), __pyx_v_dst_ndim, __pyx_v_src_ndim);
- goto __pyx_L3;
- }
- __pyx_L3:;
-
- /* "View.MemoryView":1248
- * broadcast_leading(&dst, dst_ndim, src_ndim)
- *
- * cdef int ndim = max(src_ndim, dst_ndim) # <<<<<<<<<<<<<<
- *
- * for i in range(ndim):
- */
- __pyx_t_3 = __pyx_v_dst_ndim;
- __pyx_t_4 = __pyx_v_src_ndim;
- if (((__pyx_t_3 > __pyx_t_4) != 0)) {
- __pyx_t_5 = __pyx_t_3;
- } else {
- __pyx_t_5 = __pyx_t_4;
- }
- __pyx_v_ndim = __pyx_t_5;
-
- /* "View.MemoryView":1250
- * cdef int ndim = max(src_ndim, dst_ndim)
- *
- * for i in range(ndim): # <<<<<<<<<<<<<<
- * if src.shape[i] != dst.shape[i]:
- * if src.shape[i] == 1:
- */
- __pyx_t_5 = __pyx_v_ndim;
- for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_5; __pyx_t_3+=1) {
- __pyx_v_i = __pyx_t_3;
-
- /* "View.MemoryView":1251
- *
- * for i in range(ndim):
- * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<<
- * if src.shape[i] == 1:
- * broadcasting = True
- */
- __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) != (__pyx_v_dst.shape[__pyx_v_i])) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1252
- * for i in range(ndim):
- * if src.shape[i] != dst.shape[i]:
- * if src.shape[i] == 1: # <<<<<<<<<<<<<<
- * broadcasting = True
- * src.strides[i] = 0
- */
- __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) == 1) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1253
- * if src.shape[i] != dst.shape[i]:
- * if src.shape[i] == 1:
- * broadcasting = True # <<<<<<<<<<<<<<
- * src.strides[i] = 0
- * else:
- */
- __pyx_v_broadcasting = 1;
-
- /* "View.MemoryView":1254
- * if src.shape[i] == 1:
- * broadcasting = True
- * src.strides[i] = 0 # <<<<<<<<<<<<<<
- * else:
- * _err_extents(i, dst.shape[i], src.shape[i])
- */
- (__pyx_v_src.strides[__pyx_v_i]) = 0;
- goto __pyx_L7;
- }
- /*else*/ {
-
- /* "View.MemoryView":1256
- * src.strides[i] = 0
- * else:
- * _err_extents(i, dst.shape[i], src.shape[i]) # <<<<<<<<<<<<<<
- *
- * if src.suboffsets[i] >= 0:
- */
- __pyx_t_4 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_L7:;
- goto __pyx_L6;
- }
- __pyx_L6:;
-
- /* "View.MemoryView":1258
- * _err_extents(i, dst.shape[i], src.shape[i])
- *
- * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<<
- * _err_dim(ValueError, "Dimension %d is not direct", i)
- *
- */
- __pyx_t_2 = (((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1259
- *
- * if src.suboffsets[i] >= 0:
- * _err_dim(ValueError, "Dimension %d is not direct", i) # <<<<<<<<<<<<<<
- *
- * if slices_overlap(&src, &dst, ndim, itemsize):
- */
- __pyx_t_4 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, __pyx_k_45, __pyx_v_i); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1259; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
- }
- __pyx_L8:;
- }
-
- /* "View.MemoryView":1261
- * _err_dim(ValueError, "Dimension %d is not direct", i)
- *
- * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<<
- *
- * if not slice_is_contig(&src, order, ndim):
- */
- __pyx_t_2 = (__pyx_slices_overlap((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1263
- * if slices_overlap(&src, &dst, ndim, itemsize):
- *
- * if not slice_is_contig(&src, order, ndim): # <<<<<<<<<<<<<<
- * order = get_best_order(&dst, ndim)
- *
- */
- __pyx_t_2 = ((!(__pyx_memviewslice_is_contig((&__pyx_v_src), __pyx_v_order, __pyx_v_ndim) != 0)) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1264
- *
- * if not slice_is_contig(&src, order, ndim):
- * order = get_best_order(&dst, ndim) # <<<<<<<<<<<<<<
- *
- * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim)
- */
- __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim);
- goto __pyx_L10;
- }
- __pyx_L10:;
-
- /* "View.MemoryView":1266
- * order = get_best_order(&dst, ndim)
- *
- * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) # <<<<<<<<<<<<<<
- * src = tmp
- *
- */
- __pyx_t_6 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_tmpdata = __pyx_t_6;
-
- /* "View.MemoryView":1267
- *
- * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim)
- * src = tmp # <<<<<<<<<<<<<<
- *
- * if not broadcasting:
- */
- __pyx_v_src = __pyx_v_tmp;
- goto __pyx_L9;
- }
- __pyx_L9:;
-
- /* "View.MemoryView":1269
- * src = tmp
- *
- * if not broadcasting: # <<<<<<<<<<<<<<
- *
- *
- */
- __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1272
- *
- *
- * if slice_is_contig(&src, 'C', ndim): # <<<<<<<<<<<<<<
- * direct_copy = slice_is_contig(&dst, 'C', ndim)
- * elif slice_is_contig(&src, 'F', ndim):
- */
- __pyx_t_2 = (__pyx_memviewslice_is_contig((&__pyx_v_src), 'C', __pyx_v_ndim) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1273
- *
- * if slice_is_contig(&src, 'C', ndim):
- * direct_copy = slice_is_contig(&dst, 'C', ndim) # <<<<<<<<<<<<<<
- * elif slice_is_contig(&src, 'F', ndim):
- * direct_copy = slice_is_contig(&dst, 'F', ndim)
- */
- __pyx_v_direct_copy = __pyx_memviewslice_is_contig((&__pyx_v_dst), 'C', __pyx_v_ndim);
- goto __pyx_L12;
- }
-
- /* "View.MemoryView":1274
- * if slice_is_contig(&src, 'C', ndim):
- * direct_copy = slice_is_contig(&dst, 'C', ndim)
- * elif slice_is_contig(&src, 'F', ndim): # <<<<<<<<<<<<<<
- * direct_copy = slice_is_contig(&dst, 'F', ndim)
- *
- */
- __pyx_t_2 = (__pyx_memviewslice_is_contig((&__pyx_v_src), 'F', __pyx_v_ndim) != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1275
- * direct_copy = slice_is_contig(&dst, 'C', ndim)
- * elif slice_is_contig(&src, 'F', ndim):
- * direct_copy = slice_is_contig(&dst, 'F', ndim) # <<<<<<<<<<<<<<
- *
- * if direct_copy:
- */
- __pyx_v_direct_copy = __pyx_memviewslice_is_contig((&__pyx_v_dst), 'F', __pyx_v_ndim);
- goto __pyx_L12;
- }
- __pyx_L12:;
-
- /* "View.MemoryView":1277
- * direct_copy = slice_is_contig(&dst, 'F', ndim)
- *
- * if direct_copy: # <<<<<<<<<<<<<<
- *
- * refcount_copying(&dst, dtype_is_object, ndim, False)
- */
- __pyx_t_2 = (__pyx_v_direct_copy != 0);
- if (__pyx_t_2) {
-
- /* "View.MemoryView":1279
- * if direct_copy:
- *
- * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<<
- * memcpy(dst.data, src.data, slice_get_size(&src, ndim))
- * refcount_copying(&dst, dtype_is_object, ndim, True)
- */
- __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0);
-
- /* "View.MemoryView":1280
- *
- * refcount_copying(&dst, dtype_is_object, ndim, False)
- * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<<
- * refcount_copying(&dst, dtype_is_object, ndim, True)
- * return 0
- */
- memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim));
-
- /* "View.MemoryView":1281
- * refcount_copying(&dst, dtype_is_object, ndim, False)
- * memcpy(dst.data, src.data, slice_get_size(&src, ndim))
- * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<<
- * return 0
- *
- */
- __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1);
-
- /* "View.MemoryView":1282
- * memcpy(dst.data, src.data, slice_get_size(&src, ndim))
- * refcount_copying(&dst, dtype_is_object, ndim, True)
- * return 0 # <<<<<<<<<<<<<<
- *
- * if order == 'F' == get_best_order(&dst, ndim):
- */
- __pyx_r = 0;
- goto __pyx_L0;
- goto __pyx_L13;
- }
- __pyx_L13:;
- goto __pyx_L11;
- }
- __pyx_L11:;
-
- /* "View.MemoryView":1284
- * return 0
- *
- * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<<
- *
- *
- */
- __pyx_t_2 = (__pyx_v_order == 'F');
- if (__pyx_t_2) {
- __pyx_t_2 = ('F' == __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim));
- }
- __pyx_t_7 = (__pyx_t_2 != 0);
- if (__pyx_t_7) {
-
- /* "View.MemoryView":1287
- *
- *
- * transpose_memslice(&src) # <<<<<<<<<<<<<<
- * transpose_memslice(&dst)
- *
- */
- __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "View.MemoryView":1288
- *
- * transpose_memslice(&src)
- * transpose_memslice(&dst) # <<<<<<<<<<<<<<
- *
- * refcount_copying(&dst, dtype_is_object, ndim, False)
- */
- __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L14;
- }
- __pyx_L14:;
-
- /* "View.MemoryView":1290
- * transpose_memslice(&dst)
- *
- * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<<
- * copy_strided_to_strided(&src, &dst, ndim, itemsize)
- * refcount_copying(&dst, dtype_is_object, ndim, True)
- */
- __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0);
-
- /* "View.MemoryView":1291
- *
- * refcount_copying(&dst, dtype_is_object, ndim, False)
- * copy_strided_to_strided(&src, &dst, ndim, itemsize) # <<<<<<<<<<<<<<
- * refcount_copying(&dst, dtype_is_object, ndim, True)
- *
- */
- copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize);
-
- /* "View.MemoryView":1292
- * refcount_copying(&dst, dtype_is_object, ndim, False)
- * copy_strided_to_strided(&src, &dst, ndim, itemsize)
- * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<<
- *
- * free(tmpdata)
- */
- __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1);
-
- /* "View.MemoryView":1294
- * refcount_copying(&dst, dtype_is_object, ndim, True)
- *
- * free(tmpdata) # <<<<<<<<<<<<<<
- * return 0
- *
- */
- free(__pyx_v_tmpdata);
-
- /* "View.MemoryView":1295
- *
- * free(tmpdata)
- * return 0 # <<<<<<<<<<<<<<
- *
- * @cname('__pyx_memoryview_broadcast_leading')
- */
- __pyx_r = 0;
- goto __pyx_L0;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- {
- #ifdef WITH_THREAD
- PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();
- #endif
- __Pyx_AddTraceback("View.MemoryView.memoryview_copy_contents", __pyx_clineno, __pyx_lineno, __pyx_filename);
- #ifdef WITH_THREAD
- PyGILState_Release(__pyx_gilstate_save);
- #endif
- }
- __pyx_r = -1;
- __pyx_L0:;
- return __pyx_r;
-}
-
-/* "View.MemoryView":1298
- *
- * @cname('__pyx_memoryview_broadcast_leading')
- * cdef void broadcast_leading(__Pyx_memviewslice *slice, # <<<<<<<<<<<<<<
- * int ndim,
- * int ndim_other) nogil:
- */
-
-static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_slice, int __pyx_v_ndim, int __pyx_v_ndim_other) {
- int __pyx_v_i;
- int __pyx_v_offset;
- int __pyx_t_1;
- int __pyx_t_2;
-
- /* "View.MemoryView":1302
- * int ndim_other) nogil:
- * cdef int i
- * cdef int offset = ndim_other - ndim # <<<<<<<<<<<<<<
- *
- * for i in range(ndim - 1, -1, -1):
- */
- __pyx_v_offset = (__pyx_v_ndim_other - __pyx_v_ndim);
-
- /* "View.MemoryView":1304
- * cdef int offset = ndim_other - ndim
- *
- * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<<
- * slice.shape[i + offset] = slice.shape[i]
- * slice.strides[i + offset] = slice.strides[i]
- */
- for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) {
- __pyx_v_i = __pyx_t_1;
-
- /* "View.MemoryView":1305
- *
- * for i in range(ndim - 1, -1, -1):
- * slice.shape[i + offset] = slice.shape[i] # <<<<<<<<<<<<<<
- * slice.strides[i + offset] = slice.strides[i]
- * slice.suboffsets[i + offset] = slice.suboffsets[i]
- */
- (__pyx_v_slice->shape[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->shape[__pyx_v_i]);
-
- /* "View.MemoryView":1306
- * for i in range(ndim - 1, -1, -1):
- * slice.shape[i + offset] = slice.shape[i]
- * slice.strides[i + offset] = slice.strides[i] # <<<<<<<<<<<<<<
- * slice.suboffsets[i + offset] = slice.suboffsets[i]
- *
- */
- (__pyx_v_slice->strides[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->strides[__pyx_v_i]);
-
- /* "View.MemoryView":1307
- * slice.shape[i + offset] = slice.shape[i]
- * slice.strides[i + offset] = slice.strides[i]
- * slice.suboffsets[i + offset] = slice.suboffsets[i] # <<<<<<<<<<<<<<
- *
- * for i in range(offset):
- */
- (__pyx_v_slice->suboffsets[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->suboffsets[__pyx_v_i]);
- }
-
- /* "View.MemoryView":1309
- * slice.suboffsets[i + offset] = slice.suboffsets[i]
- *
- * for i in range(offset): # <<<<<<<<<<<<<<
- * slice.shape[i] = 1
- * slice.strides[i] = slice.strides[0]
- */
- __pyx_t_1 = __pyx_v_offset;
- for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
- __pyx_v_i = __pyx_t_2;
-
- /* "View.MemoryView":1310
- *
- * for i in range(offset):
- * slice.shape[i] = 1 # <<<<<<<<<<<<<<
- * slice.strides[i] = slice.strides[0]
- * slice.suboffsets[i] = -1
- */
- (__pyx_v_slice->shape[__pyx_v_i]) = 1;
-
- /* "View.MemoryView":1311
- * for i in range(offset):
- * slice.shape[i] = 1
- * slice.strides[i] = slice.strides[0] # <<<<<<<<<<<<<<
- * slice.suboffsets[i] = -1
- *
- */
- (__pyx_v_slice->strides[__pyx_v_i]) = (__pyx_v_slice->strides[0]);
-
- /* "View.MemoryView":1312
- * slice.shape[i] = 1
- * slice.strides[i] = slice.strides[0]
- * slice.suboffsets[i] = -1 # <<<<<<<<<<<<<<
- *
- *
- */
- (__pyx_v_slice->suboffsets[__pyx_v_i]) = -1;
- }
-
-}
-
-/* "View.MemoryView":1320
- *
- * @cname('__pyx_memoryview_refcount_copying')
- * cdef void refcount_copying(__Pyx_memviewslice *dst, bint dtype_is_object, # <<<<<<<<<<<<<<
- * int ndim, bint inc) nogil:
- *
- */
-
-static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, int __pyx_v_dtype_is_object, int __pyx_v_ndim, int __pyx_v_inc) {
- int __pyx_t_1;
-
- /* "View.MemoryView":1324
- *
- *
- * if dtype_is_object: # <<<<<<<<<<<<<<
- * refcount_objects_in_slice_with_gil(dst.data, dst.shape,
- * dst.strides, ndim, inc)
- */
- __pyx_t_1 = (__pyx_v_dtype_is_object != 0);
- if (__pyx_t_1) {
-
- /* "View.MemoryView":1326
- * if dtype_is_object:
- * refcount_objects_in_slice_with_gil(dst.data, dst.shape,
- * dst.strides, ndim, inc) # <<<<<<<<<<<<<<
- *
- * @cname('__pyx_memoryview_refcount_objects_in_slice_with_gil')
- */
- __pyx_memoryview_refcount_objects_in_slice_with_gil(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_inc);
- goto __pyx_L3;
- }
- __pyx_L3:;
-
-}
-
-/* "View.MemoryView":1329
- *
- * @cname('__pyx_memoryview_refcount_objects_in_slice_with_gil')
- * cdef void refcount_objects_in_slice_with_gil(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<<
- * Py_ssize_t *strides, int ndim,
- * bint inc) with gil:
- */
-
-static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_data, Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, int __pyx_v_ndim, int __pyx_v_inc) {
- __Pyx_RefNannyDeclarations
- #ifdef WITH_THREAD
- PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();
- #endif
- __Pyx_RefNannySetupContext("refcount_objects_in_slice_with_gil", 0);
-
- /* "View.MemoryView":1332
- * Py_ssize_t *strides, int ndim,
- * bint inc) with gil:
- * refcount_objects_in_slice(data, shape, strides, ndim, inc) # <<<<<<<<<<<<<<
- *
- * @cname('__pyx_memoryview_refcount_objects_in_slice')
- */
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-static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, int __pyx_v_ndim, int __pyx_v_inc) {
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- *
- */
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-
-static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, int __pyx_v_ndim, size_t __pyx_v_itemsize, void *__pyx_v_item) {
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- PyObject *o;
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- }
- return o;
-}
-
-static void __pyx_tp_dealloc_memoryview(PyObject *o) {
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- PyObject_GC_UnTrack(o);
- {
- PyObject *etype, *eval, *etb;
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- __pyx_memoryview___dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- Py_CLEAR(p->obj);
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- Py_CLEAR(p->_array_interface);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_memoryview(PyObject *o, visitproc v, void *a) {
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-static int __pyx_tp_clear_memoryview(PyObject *o) {
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-
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-
-static PyObject *__pyx_getprop___pyx_memoryview_size(PyObject *o, CYTHON_UNUSED void *x) {
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- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
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- 0, /*sq_inplace_repeat*/
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- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
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- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
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- __pyx_tp_dealloc_memoryview, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
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- 0, /*tp_as_number*/
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- 0, /*tp_hash*/
- 0, /*tp_call*/
- __pyx_memoryview___str__, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
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- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
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- __pyx_tp_traverse_memoryview, /*tp_traverse*/
- __pyx_tp_clear_memoryview, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_memoryview, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_memoryview, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_memoryview, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
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- p->_format = ((PyObject*)Py_None); Py_INCREF(Py_None);
- if (unlikely(__pyx_array___cinit__(o, a, k) < 0)) {
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- {
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- Py_CLEAR(p->mode);
- Py_CLEAR(p->_format);
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-static int __pyx_tp_traverse_array(PyObject *o, visitproc v, void *a) {
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-static int __pyx_tp_clear_array(PyObject *o) {
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- __pyx_t_1 = __pyx_capsule_create(((void *)(&__pyx_memoryview_getbuffer)), __pyx_k_50); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_memoryviewslice_type->tp_dict, __pyx_n_s____pyx_getbuffer, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- PyType_Modified(__pyx_memoryviewslice_type);
-
- /* "View.MemoryView":1365
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- * size_t itemsize, void *item) nogil:
- */
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- if (__pyx_m) {
- __Pyx_AddTraceback("init phase_mag_real", __pyx_clineno, __pyx_lineno, __pyx_filename);
- Py_DECREF(__pyx_m); __pyx_m = 0;
- } else if (!PyErr_Occurred()) {
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- __Pyx_RefNannyFinishContext();
- #if PY_MAJOR_VERSION < 3
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-static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
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-static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
- PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name);
- if (unlikely(!result)) {
- PyErr_Format(PyExc_NameError,
-#if PY_MAJOR_VERSION >= 3
- "name '%U' is not defined", name);
-#else
- "name '%s' is not defined", PyString_AS_STRING(name));
-#endif
- }
- return result;
-}
-
-static void __Pyx_RaiseArgtupleInvalid(
- const char* func_name,
- int exact,
- Py_ssize_t num_min,
- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
- const char *more_or_less;
- if (num_found < num_min) {
- num_expected = num_min;
- more_or_less = "at least";
- } else {
- num_expected = num_max;
- more_or_less = "at most";
- }
- if (exact) {
- more_or_less = "exactly";
- }
- PyErr_Format(PyExc_TypeError,
- "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
- func_name, more_or_less, num_expected,
- (num_expected == 1) ? "" : "s", num_found);
-}
-
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name,
- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
- #endif
-}
-
-static int __Pyx_ParseOptionalKeywords(
- PyObject *kwds,
- PyObject **argnames[],
- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
- PyObject *key = 0, *value = 0;
- Py_ssize_t pos = 0;
- PyObject*** name;
- PyObject*** first_kw_arg = argnames + num_pos_args;
- while (PyDict_Next(kwds, &pos, &key, &value)) {
- name = first_kw_arg;
- while (*name && (**name != key)) name++;
- if (*name) {
- values[name-argnames] = value;
- continue;
- }
- name = first_kw_arg;
- #if PY_MAJOR_VERSION < 3
- if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
- while (*name) {
- if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
- && _PyString_Eq(**name, key)) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- if ((**argname == key) || (
- (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
- && _PyString_Eq(**argname, key))) {
- goto arg_passed_twice;
- }
- argname++;
- }
- }
- } else
- #endif
- if (likely(PyUnicode_Check(key))) {
- while (*name) {
- int cmp = (**name == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**name, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- int cmp = (**argname == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**argname, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) goto arg_passed_twice;
- argname++;
- }
- }
- } else
- goto invalid_keyword_type;
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
- }
- }
- return 0;
-arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, key);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%s() got an unexpected keyword argument '%s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-static CYTHON_INLINE int __Pyx_IsLittleEndian(void) {
- unsigned int n = 1;
- return *(unsigned char*)(&n) != 0;
-}
-static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx,
- __Pyx_BufFmt_StackElem* stack,
- __Pyx_TypeInfo* type) {
- stack[0].field = &ctx->root;
- stack[0].parent_offset = 0;
- ctx->root.type = type;
- ctx->root.name = "buffer dtype";
- ctx->root.offset = 0;
- ctx->head = stack;
- ctx->head->field = &ctx->root;
- ctx->fmt_offset = 0;
- ctx->head->parent_offset = 0;
- ctx->new_packmode = '@';
- ctx->enc_packmode = '@';
- ctx->new_count = 1;
- ctx->enc_count = 0;
- ctx->enc_type = 0;
- ctx->is_complex = 0;
- ctx->is_valid_array = 0;
- ctx->struct_alignment = 0;
- while (type->typegroup == 'S') {
- ++ctx->head;
- ctx->head->field = type->fields;
- ctx->head->parent_offset = 0;
- type = type->fields->type;
- }
-}
-static int __Pyx_BufFmt_ParseNumber(const char** ts) {
- int count;
- const char* t = *ts;
- if (*t < '0' || *t > '9') {
- return -1;
- } else {
- count = *t++ - '0';
- while (*t >= '0' && *t < '9') {
- count *= 10;
- count += *t++ - '0';
- }
- }
- *ts = t;
- return count;
-}
-static int __Pyx_BufFmt_ExpectNumber(const char **ts) {
- int number = __Pyx_BufFmt_ParseNumber(ts);
- if (number == -1) /* First char was not a digit */
- PyErr_Format(PyExc_ValueError,\
- "Does not understand character buffer dtype format string ('%c')", **ts);
- return number;
-}
-static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) {
- PyErr_Format(PyExc_ValueError,
- "Unexpected format string character: '%c'", ch);
-}
-static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) {
- switch (ch) {
- case 'c': return "'char'";
- case 'b': return "'signed char'";
- case 'B': return "'unsigned char'";
- case 'h': return "'short'";
- case 'H': return "'unsigned short'";
- case 'i': return "'int'";
- case 'I': return "'unsigned int'";
- case 'l': return "'long'";
- case 'L': return "'unsigned long'";
- case 'q': return "'long long'";
- case 'Q': return "'unsigned long long'";
- case 'f': return (is_complex ? "'complex float'" : "'float'");
- case 'd': return (is_complex ? "'complex double'" : "'double'");
- case 'g': return (is_complex ? "'complex long double'" : "'long double'");
- case 'T': return "a struct";
- case 'O': return "Python object";
- case 'P': return "a pointer";
- case 's': case 'p': return "a string";
- case 0: return "end";
- default: return "unparseable format string";
- }
-}
-static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) {
- switch (ch) {
- case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return 2;
- case 'i': case 'I': case 'l': case 'L': return 4;
- case 'q': case 'Q': return 8;
- case 'f': return (is_complex ? 8 : 4);
- case 'd': return (is_complex ? 16 : 8);
- case 'g': {
- PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g')..");
- return 0;
- }
- case 'O': case 'P': return sizeof(void*);
- default:
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
-}
-static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) {
- switch (ch) {
- case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return sizeof(short);
- case 'i': case 'I': return sizeof(int);
- case 'l': case 'L': return sizeof(long);
- #ifdef HAVE_LONG_LONG
- case 'q': case 'Q': return sizeof(PY_LONG_LONG);
- #endif
- case 'f': return sizeof(float) * (is_complex ? 2 : 1);
- case 'd': return sizeof(double) * (is_complex ? 2 : 1);
- case 'g': return sizeof(long double) * (is_complex ? 2 : 1);
- case 'O': case 'P': return sizeof(void*);
- default: {
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
- }
-}
-typedef struct { char c; short x; } __Pyx_st_short;
-typedef struct { char c; int x; } __Pyx_st_int;
-typedef struct { char c; long x; } __Pyx_st_long;
-typedef struct { char c; float x; } __Pyx_st_float;
-typedef struct { char c; double x; } __Pyx_st_double;
-typedef struct { char c; long double x; } __Pyx_st_longdouble;
-typedef struct { char c; void *x; } __Pyx_st_void_p;
-#ifdef HAVE_LONG_LONG
-typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong;
-#endif
-static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) {
- switch (ch) {
- case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short);
- case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int);
- case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long);
-#ifdef HAVE_LONG_LONG
- case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG);
-#endif
- case 'f': return sizeof(__Pyx_st_float) - sizeof(float);
- case 'd': return sizeof(__Pyx_st_double) - sizeof(double);
- case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double);
- case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*);
- default:
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
-}
-/* These are for computing the padding at the end of the struct to align
- on the first member of the struct. This will probably the same as above,
- but we don't have any guarantees.
- */
-typedef struct { short x; char c; } __Pyx_pad_short;
-typedef struct { int x; char c; } __Pyx_pad_int;
-typedef struct { long x; char c; } __Pyx_pad_long;
-typedef struct { float x; char c; } __Pyx_pad_float;
-typedef struct { double x; char c; } __Pyx_pad_double;
-typedef struct { long double x; char c; } __Pyx_pad_longdouble;
-typedef struct { void *x; char c; } __Pyx_pad_void_p;
-#ifdef HAVE_LONG_LONG
-typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong;
-#endif
-static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) {
- switch (ch) {
- case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short);
- case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int);
- case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long);
-#ifdef HAVE_LONG_LONG
- case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG);
-#endif
- case 'f': return sizeof(__Pyx_pad_float) - sizeof(float);
- case 'd': return sizeof(__Pyx_pad_double) - sizeof(double);
- case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double);
- case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*);
- default:
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
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-}
-static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) {
- switch (ch) {
- case 'c':
- return 'H';
- case 'b': case 'h': case 'i':
- case 'l': case 'q': case 's': case 'p':
- return 'I';
- case 'B': case 'H': case 'I': case 'L': case 'Q':
- return 'U';
- case 'f': case 'd': case 'g':
- return (is_complex ? 'C' : 'R');
- case 'O':
- return 'O';
- case 'P':
- return 'P';
- default: {
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
- }
-}
-static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) {
- if (ctx->head == NULL || ctx->head->field == &ctx->root) {
- const char* expected;
- const char* quote;
- if (ctx->head == NULL) {
- expected = "end";
- quote = "";
- } else {
- expected = ctx->head->field->type->name;
- quote = "'";
- }
- PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch, expected %s%s%s but got %s",
- quote, expected, quote,
- __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex));
- } else {
- __Pyx_StructField* field = ctx->head->field;
- __Pyx_StructField* parent = (ctx->head - 1)->field;
- PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'",
- field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex),
- parent->type->name, field->name);
- }
-}
-static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) {
- char group;
- size_t size, offset, arraysize = 1;
- if (ctx->enc_type == 0) return 0;
- if (ctx->head->field->type->arraysize[0]) {
- int i, ndim = 0;
- if (ctx->enc_type == 's' || ctx->enc_type == 'p') {
- ctx->is_valid_array = ctx->head->field->type->ndim == 1;
- ndim = 1;
- if (ctx->enc_count != ctx->head->field->type->arraysize[0]) {
- PyErr_Format(PyExc_ValueError,
- "Expected a dimension of size %zu, got %zu",
- ctx->head->field->type->arraysize[0], ctx->enc_count);
- return -1;
- }
- }
- if (!ctx->is_valid_array) {
- PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d",
- ctx->head->field->type->ndim, ndim);
- return -1;
- }
- for (i = 0; i < ctx->head->field->type->ndim; i++) {
- arraysize *= ctx->head->field->type->arraysize[i];
- }
- ctx->is_valid_array = 0;
- ctx->enc_count = 1;
- }
- group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex);
- do {
- __Pyx_StructField* field = ctx->head->field;
- __Pyx_TypeInfo* type = field->type;
- if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') {
- size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex);
- } else {
- size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex);
- }
- if (ctx->enc_packmode == '@') {
- size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex);
- size_t align_mod_offset;
- if (align_at == 0) return -1;
- align_mod_offset = ctx->fmt_offset % align_at;
- if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset;
- if (ctx->struct_alignment == 0)
- ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type,
- ctx->is_complex);
- }
- if (type->size != size || type->typegroup != group) {
- if (type->typegroup == 'C' && type->fields != NULL) {
- size_t parent_offset = ctx->head->parent_offset + field->offset;
- ++ctx->head;
- ctx->head->field = type->fields;
- ctx->head->parent_offset = parent_offset;
- continue;
- }
- if ((type->typegroup == 'H' || group == 'H') && type->size == size) {
- } else {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return -1;
- }
- }
- offset = ctx->head->parent_offset + field->offset;
- if (ctx->fmt_offset != offset) {
- PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected",
- (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset);
- return -1;
- }
- ctx->fmt_offset += size;
- if (arraysize)
- ctx->fmt_offset += (arraysize - 1) * size;
- --ctx->enc_count; /* Consume from buffer string */
- while (1) {
- if (field == &ctx->root) {
- ctx->head = NULL;
- if (ctx->enc_count != 0) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return -1;
- }
- break; /* breaks both loops as ctx->enc_count == 0 */
- }
- ctx->head->field = ++field;
- if (field->type == NULL) {
- --ctx->head;
- field = ctx->head->field;
- continue;
- } else if (field->type->typegroup == 'S') {
- size_t parent_offset = ctx->head->parent_offset + field->offset;
- if (field->type->fields->type == NULL) continue; /* empty struct */
- field = field->type->fields;
- ++ctx->head;
- ctx->head->field = field;
- ctx->head->parent_offset = parent_offset;
- break;
- } else {
- break;
- }
- }
- } while (ctx->enc_count);
- ctx->enc_type = 0;
- ctx->is_complex = 0;
- return 0;
-}
-static CYTHON_INLINE PyObject *
-__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp)
-{
- const char *ts = *tsp;
- int i = 0, number;
- int ndim = ctx->head->field->type->ndim;
-;
- ++ts;
- if (ctx->new_count != 1) {
- PyErr_SetString(PyExc_ValueError,
- "Cannot handle repeated arrays in format string");
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- while (*ts && *ts != ')') {
- if (isspace(*ts))
- continue;
- number = __Pyx_BufFmt_ExpectNumber(&ts);
- if (number == -1) return NULL;
- if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i])
- return PyErr_Format(PyExc_ValueError,
- "Expected a dimension of size %zu, got %d",
- ctx->head->field->type->arraysize[i], number);
- if (*ts != ',' && *ts != ')')
- return PyErr_Format(PyExc_ValueError,
- "Expected a comma in format string, got '%c'", *ts);
- if (*ts == ',') ts++;
- i++;
- }
- if (i != ndim)
- return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d",
- ctx->head->field->type->ndim, i);
- if (!*ts) {
- PyErr_SetString(PyExc_ValueError,
- "Unexpected end of format string, expected ')'");
- return NULL;
- }
- ctx->is_valid_array = 1;
- ctx->new_count = 1;
- *tsp = ++ts;
- return Py_None;
-}
-static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) {
- int got_Z = 0;
- while (1) {
- switch(*ts) {
- case 0:
- if (ctx->enc_type != 0 && ctx->head == NULL) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- if (ctx->head != NULL) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return NULL;
- }
- return ts;
- case ' ':
- case 10:
- case 13:
- ++ts;
- break;
- case '<':
- if (!__Pyx_IsLittleEndian()) {
- PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler");
- return NULL;
- }
- ctx->new_packmode = '=';
- ++ts;
- break;
- case '>':
- case '!':
- if (__Pyx_IsLittleEndian()) {
- PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler");
- return NULL;
- }
- ctx->new_packmode = '=';
- ++ts;
- break;
- case '=':
- case '@':
- case '^':
- ctx->new_packmode = *ts++;
- break;
- case 'T': /* substruct */
- {
- const char* ts_after_sub;
- size_t i, struct_count = ctx->new_count;
- size_t struct_alignment = ctx->struct_alignment;
- ctx->new_count = 1;
- ++ts;
- if (*ts != '{') {
- PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'");
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_type = 0; /* Erase processed last struct element */
- ctx->enc_count = 0;
- ctx->struct_alignment = 0;
- ++ts;
- ts_after_sub = ts;
- for (i = 0; i != struct_count; ++i) {
- ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts);
- if (!ts_after_sub) return NULL;
- }
- ts = ts_after_sub;
- if (struct_alignment) ctx->struct_alignment = struct_alignment;
- }
- break;
- case '}': /* end of substruct; either repeat or move on */
- {
- size_t alignment = ctx->struct_alignment;
- ++ts;
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_type = 0; /* Erase processed last struct element */
- if (alignment && ctx->fmt_offset % alignment) {
- ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment);
- }
- }
- return ts;
- case 'x':
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->fmt_offset += ctx->new_count;
- ctx->new_count = 1;
- ctx->enc_count = 0;
- ctx->enc_type = 0;
- ctx->enc_packmode = ctx->new_packmode;
- ++ts;
- break;
- case 'Z':
- got_Z = 1;
- ++ts;
- if (*ts != 'f' && *ts != 'd' && *ts != 'g') {
- __Pyx_BufFmt_RaiseUnexpectedChar('Z');
- return NULL;
- } /* fall through */
- case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I':
- case 'l': case 'L': case 'q': case 'Q':
- case 'f': case 'd': case 'g':
- case 'O': case 's': case 'p':
- if (ctx->enc_type == *ts && got_Z == ctx->is_complex &&
- ctx->enc_packmode == ctx->new_packmode) {
- ctx->enc_count += ctx->new_count;
- } else {
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_count = ctx->new_count;
- ctx->enc_packmode = ctx->new_packmode;
- ctx->enc_type = *ts;
- ctx->is_complex = got_Z;
- }
- ++ts;
- ctx->new_count = 1;
- got_Z = 0;
- break;
- case ':':
- ++ts;
- while(*ts != ':') ++ts;
- ++ts;
- break;
- case '(':
- if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL;
- break;
- default:
- {
- int number = __Pyx_BufFmt_ExpectNumber(&ts);
- if (number == -1) return NULL;
- ctx->new_count = (size_t)number;
- }
- }
- }
-}
-static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) {
- buf->buf = NULL;
- buf->obj = NULL;
- buf->strides = __Pyx_zeros;
- buf->shape = __Pyx_zeros;
- buf->suboffsets = __Pyx_minusones;
-}
-static CYTHON_INLINE int __Pyx_GetBufferAndValidate(
- Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags,
- int nd, int cast, __Pyx_BufFmt_StackElem* stack)
-{
- if (obj == Py_None || obj == NULL) {
- __Pyx_ZeroBuffer(buf);
- return 0;
- }
- buf->buf = NULL;
- if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail;
- if (buf->ndim != nd) {
- PyErr_Format(PyExc_ValueError,
- "Buffer has wrong number of dimensions (expected %d, got %d)",
- nd, buf->ndim);
- goto fail;
- }
- if (!cast) {
- __Pyx_BufFmt_Context ctx;
- __Pyx_BufFmt_Init(&ctx, stack, dtype);
- if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail;
- }
- if ((unsigned)buf->itemsize != dtype->size) {
- PyErr_Format(PyExc_ValueError,
- "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)",
- buf->itemsize, (buf->itemsize > 1) ? "s" : "",
- dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : "");
- goto fail;
- }
- if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
- return 0;
-fail:;
- __Pyx_ZeroBuffer(buf);
- return -1;
-}
-static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) {
- if (info->buf == NULL) return;
- if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL;
- __Pyx_ReleaseBuffer(info);
-}
-
-static int
-__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview,
- int ndim,
- __Pyx_memviewslice *memviewslice,
- int memview_is_new_reference)
-{
- __Pyx_RefNannyDeclarations
- int i, retval=-1;
- Py_buffer *buf = &memview->view;
- __Pyx_RefNannySetupContext("init_memviewslice", 0);
- if (!buf) {
- PyErr_SetString(PyExc_ValueError,
- "buf is NULL.");
- goto fail;
- } else if (memviewslice->memview || memviewslice->data) {
- PyErr_SetString(PyExc_ValueError,
- "memviewslice is already initialized!");
- goto fail;
- }
- if (buf->strides) {
- for (i = 0; i < ndim; i++) {
- memviewslice->strides[i] = buf->strides[i];
- }
- } else {
- Py_ssize_t stride = buf->itemsize;
- for (i = ndim - 1; i >= 0; i--) {
- memviewslice->strides[i] = stride;
- stride *= buf->shape[i];
- }
- }
- for (i = 0; i < ndim; i++) {
- memviewslice->shape[i] = buf->shape[i];
- if (buf->suboffsets) {
- memviewslice->suboffsets[i] = buf->suboffsets[i];
- } else {
- memviewslice->suboffsets[i] = -1;
- }
- }
- memviewslice->memview = memview;
- memviewslice->data = (char *)buf->buf;
- if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) {
- Py_INCREF(memview);
- }
- retval = 0;
- goto no_fail;
-fail:
- memviewslice->memview = 0;
- memviewslice->data = 0;
- retval = -1;
-no_fail:
- __Pyx_RefNannyFinishContext();
- return retval;
-}
-static CYTHON_INLINE void __pyx_fatalerror(const char *fmt, ...) {
- va_list vargs;
- char msg[200];
- va_start(vargs, fmt);
-#ifdef HAVE_STDARG_PROTOTYPES
- va_start(vargs, fmt);
-#else
- va_start(vargs);
-#endif
- vsnprintf(msg, 200, fmt, vargs);
- Py_FatalError(msg);
- va_end(vargs);
-}
-static CYTHON_INLINE int
-__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count,
- PyThread_type_lock lock)
-{
- int result;
- PyThread_acquire_lock(lock, 1);
- result = (*acquisition_count)++;
- PyThread_release_lock(lock);
- return result;
-}
-static CYTHON_INLINE int
-__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count,
- PyThread_type_lock lock)
-{
- int result;
- PyThread_acquire_lock(lock, 1);
- result = (*acquisition_count)--;
- PyThread_release_lock(lock);
- return result;
-}
-static CYTHON_INLINE void
-__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno)
-{
- int first_time;
- struct __pyx_memoryview_obj *memview = memslice->memview;
- if (!memview || (PyObject *) memview == Py_None)
- return; /* allow uninitialized memoryview assignment */
- if (__pyx_get_slice_count(memview) < 0)
- __pyx_fatalerror("Acquisition count is %d (line %d)",
- __pyx_get_slice_count(memview), lineno);
- first_time = __pyx_add_acquisition_count(memview) == 0;
- if (first_time) {
- if (have_gil) {
- Py_INCREF((PyObject *) memview);
- } else {
- PyGILState_STATE _gilstate = PyGILState_Ensure();
- Py_INCREF((PyObject *) memview);
- PyGILState_Release(_gilstate);
- }
- }
-}
-static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice,
- int have_gil, int lineno) {
- int last_time;
- struct __pyx_memoryview_obj *memview = memslice->memview;
- if (!memview ) {
- return;
- } else if ((PyObject *) memview == Py_None) {
- memslice->memview = NULL;
- return;
- }
- if (__pyx_get_slice_count(memview) <= 0)
- __pyx_fatalerror("Acquisition count is %d (line %d)",
- __pyx_get_slice_count(memview), lineno);
- last_time = __pyx_sub_acquisition_count(memview) == 1;
- memslice->data = NULL;
- if (last_time) {
- if (have_gil) {
- Py_CLEAR(memslice->memview);
- } else {
- PyGILState_STATE _gilstate = PyGILState_Ensure();
- Py_CLEAR(memslice->memview);
- PyGILState_Release(_gilstate);
- }
- } else {
- memslice->memview = NULL;
- }
-}
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_Restore(type, value, tb);
-#endif
-}
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
-}
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
- Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
- Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- }
- #if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
- #else
- if (PyType_Check(type)) {
- #endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- } else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- } else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
-#if PY_VERSION_HEX >= 0x03030000
- if (cause) {
-#else
- if (cause && cause != Py_None) {
-#endif
- PyObject *fixed_cause;
- if (cause == Py_None) {
- fixed_cause = NULL;
- } else if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- } else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- } else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
- PyErr_Format(PyExc_ValueError,
- "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
- index, (index == 1) ? "" : "s");
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-}
-
-static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* exc_type = tstate->curexc_type;
- if (unlikely(exc_type)) {
- if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
- PyObject *exc_value, *exc_tb;
- exc_value = tstate->curexc_value;
- exc_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- Py_DECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_tb);
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#else
- if (unlikely(PyErr_Occurred())) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#endif
-}
-
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else {
- return __Pyx_IterFinish();
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
- if (unlikely(!type)) {
- PyErr_Format(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (likely(PyObject_TypeCheck(obj, type)))
- return 1;
- PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
- Py_TYPE(obj)->tp_name, type->tp_name);
- return 0;
-}
-
-static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
- const char *name, int exact)
-{
- if (!type) {
- PyErr_Format(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (none_allowed && obj == Py_None) return 1;
- else if (exact) {
- if (Py_TYPE(obj) == type) return 1;
- }
- else {
- if (PyObject_TypeCheck(obj, type)) return 1;
- }
- PyErr_Format(PyExc_TypeError,
- "Argument '%s' has incorrect type (expected %s, got %s)",
- name, type->tp_name, Py_TYPE(obj)->tp_name);
- return 0;
-}
-
-static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) {
-#if CYTHON_COMPILING_IN_CPYTHON
-#if PY_MAJOR_VERSION >= 3
- if (likely(PyUnicode_Check(n)))
-#else
- if (likely(PyString_Check(n)))
-#endif
- return __Pyx_PyObject_GetAttrStr(o, n);
-#endif
- return PyObject_GetAttr(o, n);
-}
-
-static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) {
- PyObject *r = __Pyx_GetAttr(o, n);
- if (!r) {
- if (!PyErr_ExceptionMatches(PyExc_AttributeError))
- goto bad;
- PyErr_Clear();
- r = d;
- Py_INCREF(d);
- }
- return r;
-bad:
- return NULL;
-}
-
-static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) {
- Py_ssize_t q = a / b;
- Py_ssize_t r = a - q*b;
- q -= ((r != 0) & ((r ^ b) < 0));
- return q;
-}
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
-#if CYTHON_COMPILING_IN_PYPY
- return PyObject_RichCompareBool(s1, s2, equals);
-#else
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
- #if CYTHON_PEP393_ENABLED
- if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
- return -1;
- if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_LENGTH(s1) == 1) {
- Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
- Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #else
- if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_SIZE(s1) == 1) {
- Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
- Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #endif
- } else {
- int result = PyUnicode_Compare(s1, s2);
- if ((result == -1) && unlikely(PyErr_Occurred()))
- return -1;
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
- return (equals == Py_NE);
- } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
- return (equals == Py_NE);
- } else {
- int result;
- PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
- if (!py_result)
- return -1;
- result = __Pyx_PyObject_IsTrue(py_result);
- Py_DECREF(py_result);
- return result;
- }
-#endif
-}
-
-static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
- const char* cstring, Py_ssize_t start, Py_ssize_t stop,
- const char* encoding, const char* errors,
- PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) {
- Py_ssize_t length;
- if (unlikely((start < 0) | (stop < 0))) {
- length = strlen(cstring);
- if (start < 0) {
- start += length;
- if (start < 0)
- start = 0;
- }
- if (stop < 0)
- stop += length;
- }
- length = stop - start;
- if (unlikely(length <= 0))
- return PyUnicode_FromUnicode(NULL, 0);
- cstring += start;
- if (decode_func) {
- return decode_func(cstring, length, errors);
- } else {
- return PyUnicode_Decode(cstring, length, encoding, errors);
- }
-}
-
-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
- PyObject *local_type, *local_value, *local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- local_type = tstate->curexc_type;
- local_value = tstate->curexc_value;
- local_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(&local_type, &local_value, &local_tb);
-#endif
- PyErr_NormalizeException(&local_type, &local_value, &local_tb);
-#if CYTHON_COMPILING_IN_CPYTHON
- if (unlikely(tstate->curexc_type))
-#else
- if (unlikely(PyErr_Occurred()))
-#endif
- goto bad;
- #if PY_MAJOR_VERSION >= 3
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
- goto bad;
- #endif
- Py_INCREF(local_type);
- Py_INCREF(local_value);
- Py_INCREF(local_tb);
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = local_type;
- tstate->exc_value = local_value;
- tstate->exc_traceback = local_tb;
- /* Make sure tstate is in a consistent state when we XDECREF
- these objects (DECREF may run arbitrary code). */
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(local_type, local_value, local_tb);
-#endif
- return 0;
-bad:
- *type = 0;
- *value = 0;
- *tb = 0;
- Py_XDECREF(local_type);
- Py_XDECREF(local_value);
- Py_XDECREF(local_tb);
- return -1;
-}
-
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
- PyObject *r;
- if (!j) return NULL;
- r = PyObject_GetItem(o, j);
- Py_DECREF(j);
- return r;
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (is_list || PyList_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
- PyObject *r = PyList_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- }
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- } else {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- return NULL;
- }
- }
- return m->sq_item(o, i);
- }
- }
-#else
- if (is_list || PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-}
-
-static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
- PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
-}
-
-static CYTHON_INLINE long __Pyx_div_long(long a, long b) {
- long q = a / b;
- long r = a - q*b;
- q -= ((r != 0) & ((r ^ b) < 0));
- return q;
-}
-
-static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
- CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) {
- PyObject *old_exc, *old_val, *old_tb;
- PyObject *ctx;
- __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
- #if PY_MAJOR_VERSION < 3
- ctx = PyString_FromString(name);
- #else
- ctx = PyUnicode_FromString(name);
- #endif
- __Pyx_ErrRestore(old_exc, old_val, old_tb);
- if (!ctx) {
- PyErr_WriteUnraisable(Py_None);
- } else {
- PyErr_WriteUnraisable(ctx);
- Py_DECREF(ctx);
- }
-}
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItem(dict, __pyx_n_s____pyx_vtable__, ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-#if PY_MAJOR_VERSION < 3
-static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
- #if PY_VERSION_HEX >= 0x02060000
- if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags);
- #endif
- if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags);
- if (PyObject_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags);
- if (PyObject_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags);
- #if PY_VERSION_HEX < 0x02060000
- if (obj->ob_type->tp_dict) {
- PyObject *getbuffer_cobj = PyObject_GetItem(
- obj->ob_type->tp_dict, __pyx_n_s____pyx_getbuffer);
- if (getbuffer_cobj) {
- getbufferproc func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj);
- Py_DECREF(getbuffer_cobj);
- if (!func)
- goto fail;
- return func(obj, view, flags);
- } else {
- PyErr_Clear();
- }
- }
- #endif
- PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
-#if PY_VERSION_HEX < 0x02060000
-fail:
-#endif
- return -1;
-}
-static void __Pyx_ReleaseBuffer(Py_buffer *view) {
- PyObject *obj = view->obj;
- if (!obj) return;
- #if PY_VERSION_HEX >= 0x02060000
- if (PyObject_CheckBuffer(obj)) {
- PyBuffer_Release(view);
- return;
- }
- #endif
- if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; }
- #if PY_VERSION_HEX < 0x02060000
- if (obj->ob_type->tp_dict) {
- PyObject *releasebuffer_cobj = PyObject_GetItem(
- obj->ob_type->tp_dict, __pyx_n_s____pyx_releasebuffer);
- if (releasebuffer_cobj) {
- releasebufferproc func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj);
- Py_DECREF(releasebuffer_cobj);
- if (!func)
- goto fail;
- func(obj, view);
- return;
- } else {
- PyErr_Clear();
- }
- }
- #endif
- goto nofail;
-#if PY_VERSION_HEX < 0x02060000
-fail:
-#endif
- PyErr_WriteUnraisable(obj);
-nofail:
- Py_DECREF(obj);
- view->obj = NULL;
-}
-#endif /* PY_MAJOR_VERSION < 3 */
-
-
- static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import;
- py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s____import__);
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static int
-__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b)
-{
- int i;
- if (!a || !b)
- return 0;
- if (a == b)
- return 1;
- if (a->size != b->size || a->typegroup != b->typegroup ||
- a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) {
- if (a->typegroup == 'H' || b->typegroup == 'H') {
- return a->size == b->size;
- } else {
- return 0;
- }
- }
- if (a->ndim) {
- for (i = 0; i < a->ndim; i++)
- if (a->arraysize[i] != b->arraysize[i])
- return 0;
- }
- if (a->typegroup == 'S') {
- if (a->flags != b->flags)
- return 0;
- if (a->fields || b->fields) {
- if (!(a->fields && b->fields))
- return 0;
- for (i = 0; a->fields[i].type && b->fields[i].type; i++) {
- __Pyx_StructField *field_a = a->fields + i;
- __Pyx_StructField *field_b = b->fields + i;
- if (field_a->offset != field_b->offset ||
- !__pyx_typeinfo_cmp(field_a->type, field_b->type))
- return 0;
- }
- return !a->fields[i].type && !b->fields[i].type;
- }
- }
- return 1;
-}
-
-static int
-__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec)
-{
- if (buf->shape[dim] <= 1)
- return 1;
- if (buf->strides) {
- if (spec & __Pyx_MEMVIEW_CONTIG) {
- if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) {
- if (buf->strides[dim] != sizeof(void *)) {
- PyErr_Format(PyExc_ValueError,
- "Buffer is not indirectly contiguous "
- "in dimension %d.", dim);
- goto fail;
- }
- } else if (buf->strides[dim] != buf->itemsize) {
- PyErr_SetString(PyExc_ValueError,
- "Buffer and memoryview are not contiguous "
- "in the same dimension.");
- goto fail;
- }
- }
- if (spec & __Pyx_MEMVIEW_FOLLOW) {
- Py_ssize_t stride = buf->strides[dim];
- if (stride < 0)
- stride = -stride;
- if (stride < buf->itemsize) {
- PyErr_SetString(PyExc_ValueError,
- "Buffer and memoryview are not contiguous "
- "in the same dimension.");
- goto fail;
- }
- }
- } else {
- if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) {
- PyErr_Format(PyExc_ValueError,
- "C-contiguous buffer is not contiguous in "
- "dimension %d", dim);
- goto fail;
- } else if (spec & (__Pyx_MEMVIEW_PTR)) {
- PyErr_Format(PyExc_ValueError,
- "C-contiguous buffer is not indirect in "
- "dimension %d", dim);
- goto fail;
- } else if (buf->suboffsets) {
- PyErr_SetString(PyExc_ValueError,
- "Buffer exposes suboffsets but no strides");
- goto fail;
- }
- }
- return 1;
-fail:
- return 0;
-}
-static int
-__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec)
-{
- if (spec & __Pyx_MEMVIEW_DIRECT) {
- if (buf->suboffsets && buf->suboffsets[dim] >= 0) {
- PyErr_Format(PyExc_ValueError,
- "Buffer not compatible with direct access "
- "in dimension %d.", dim);
- goto fail;
- }
- }
- if (spec & __Pyx_MEMVIEW_PTR) {
- if (!buf->suboffsets || (buf->suboffsets && buf->suboffsets[dim] < 0)) {
- PyErr_Format(PyExc_ValueError,
- "Buffer is not indirectly accessisble "
- "in dimension %d.", dim);
- goto fail;
- }
- }
- return 1;
-fail:
- return 0;
-}
-static int
-__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag)
-{
- int i;
- if (c_or_f_flag & __Pyx_IS_F_CONTIG) {
- Py_ssize_t stride = 1;
- for (i = 0; i < ndim; i++) {
- if (stride * buf->itemsize != buf->strides[i] &&
- buf->shape[i] > 1)
- {
- PyErr_SetString(PyExc_ValueError,
- "Buffer not fortran contiguous.");
- goto fail;
- }
- stride = stride * buf->shape[i];
- }
- } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) {
- Py_ssize_t stride = 1;
- for (i = ndim - 1; i >- 1; i--) {
- if (stride * buf->itemsize != buf->strides[i] &&
- buf->shape[i] > 1) {
- PyErr_SetString(PyExc_ValueError,
- "Buffer not C contiguous.");
- goto fail;
- }
- stride = stride * buf->shape[i];
- }
- }
- return 1;
-fail:
- return 0;
-}
-static int __Pyx_ValidateAndInit_memviewslice(
- int *axes_specs,
- int c_or_f_flag,
- int buf_flags,
- int ndim,
- __Pyx_TypeInfo *dtype,
- __Pyx_BufFmt_StackElem stack[],
- __Pyx_memviewslice *memviewslice,
- PyObject *original_obj)
-{
- struct __pyx_memoryview_obj *memview, *new_memview;
- __Pyx_RefNannyDeclarations
- Py_buffer *buf;
- int i, spec = 0, retval = -1;
- __Pyx_BufFmt_Context ctx;
- int from_memoryview = __pyx_memoryview_check(original_obj);
- __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0);
- if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *)
- original_obj)->typeinfo)) {
- memview = (struct __pyx_memoryview_obj *) original_obj;
- new_memview = NULL;
- } else {
- memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new(
- original_obj, buf_flags, 0, dtype);
- new_memview = memview;
- if (unlikely(!memview))
- goto fail;
- }
- buf = &memview->view;
- if (buf->ndim != ndim) {
- PyErr_Format(PyExc_ValueError,
- "Buffer has wrong number of dimensions (expected %d, got %d)",
- ndim, buf->ndim);
- goto fail;
- }
- if (new_memview) {
- __Pyx_BufFmt_Init(&ctx, stack, dtype);
- if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail;
- }
- if ((unsigned) buf->itemsize != dtype->size) {
- PyErr_Format(PyExc_ValueError,
- "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) "
- "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)",
- buf->itemsize,
- (buf->itemsize > 1) ? "s" : "",
- dtype->name,
- dtype->size,
- (dtype->size > 1) ? "s" : "");
- goto fail;
- }
- for (i = 0; i < ndim; i++) {
- spec = axes_specs[i];
- if (!__pyx_check_strides(buf, i, ndim, spec))
- goto fail;
- if (!__pyx_check_suboffsets(buf, i, ndim, spec))
- goto fail;
- }
- if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag))
- goto fail;
- if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice,
- new_memview != NULL) == -1)) {
- goto fail;
- }
- retval = 0;
- goto no_fail;
-fail:
- Py_XDECREF(new_memview);
- retval = -1;
-no_fail:
- __Pyx_RefNannyFinishContext();
- return retval;
-}
-
-static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_double(PyObject *obj) {
- __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } };
- __Pyx_BufFmt_StackElem stack[1];
- int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) };
- int retcode;
- if (obj == Py_None) {
- result.memview = (struct __pyx_memoryview_obj *) Py_None;
- return result;
- }
- retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0,
- PyBUF_RECORDS, 2,
- &__Pyx_TypeInfo_double, stack,
- &result, obj);
- if (unlikely(retcode == -1))
- goto __pyx_fail;
- return result;
-__pyx_fail:
- result.memview = NULL;
- result.data = NULL;
- return result;
-}
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return ::std::complex< float >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return x + y*(__pyx_t_float_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- __pyx_t_float_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-#if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- return (a.real == b.real) && (a.imag == b.imag);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real + b.real;
- z.imag = a.imag + b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrtf(z.real*z.real + z.imag*z.imag);
- #else
- return hypotf(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- float denom = a.real * a.real + a.imag * a.imag;
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- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(a, a);
- case 3:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, a);
- case 4:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
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- r = a.real;
- theta = 0;
- } else {
- r = __Pyx_c_absf(a);
- theta = atan2f(a.imag, a.real);
- }
- lnr = logf(r);
- z_r = expf(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cosf(z_theta);
- z.imag = z_r * sinf(z_theta);
- return z;
- }
- #endif
-#endif
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return ::std::complex< double >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return x + y*(__pyx_t_double_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- __pyx_t_double_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-#if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
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- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
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- return z;
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- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrt(z.real*z.real + z.imag*z.imag);
- #else
- return hypot(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- double denom = a.real * a.real + a.imag * a.imag;
- a.real = a.real / denom;
- a.imag = -a.imag / denom;
- b.real = -b.real;
- }
- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(a, a);
- case 3:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, a);
- case 4:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
- }
- r = a.real;
- theta = 0;
- } else {
- r = __Pyx_c_abs(a);
- theta = atan2(a.imag, a.real);
- }
- lnr = log(r);
- z_r = exp(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cos(z_theta);
- z.imag = z_r * sin(z_theta);
- return z;
- }
- #endif
-#endif
-
-static int
-__pyx_memviewslice_is_contig(const __Pyx_memviewslice *mvs,
- char order, int ndim)
-{
- int i, index, step, start;
- Py_ssize_t itemsize = mvs->memview->view.itemsize;
- if (order == 'F') {
- step = 1;
- start = 0;
- } else {
- step = -1;
- start = ndim - 1;
- }
- for (i = 0; i < ndim; i++) {
- index = start + step * i;
- if (mvs->suboffsets[index] >= 0 || mvs->strides[index] != itemsize)
- return 0;
- itemsize *= mvs->shape[index];
- }
- return 1;
-}
-
-static void
-__pyx_get_array_memory_extents(__Pyx_memviewslice *slice,
- void **out_start, void **out_end,
- int ndim, size_t itemsize)
-{
- char *start, *end;
- int i;
- start = end = slice->data;
- for (i = 0; i < ndim; i++) {
- Py_ssize_t stride = slice->strides[i];
- Py_ssize_t extent = slice->shape[i];
- if (extent == 0) {
- *out_start = *out_end = start;
- return;
- } else {
- if (stride > 0)
- end += stride * (extent - 1);
- else
- start += stride * (extent - 1);
- }
- }
- *out_start = start;
- *out_end = end + itemsize;
-}
-static int
-__pyx_slices_overlap(__Pyx_memviewslice *slice1,
- __Pyx_memviewslice *slice2,
- int ndim, size_t itemsize)
-{
- void *start1, *end1, *start2, *end2;
- __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize);
- __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize);
- return (start1 < end2) && (start2 < end1);
-}
-
-static __Pyx_memviewslice
-__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs,
- const char *mode, int ndim,
- size_t sizeof_dtype, int contig_flag,
- int dtype_is_object)
-{
- __Pyx_RefNannyDeclarations
- int i;
- __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } };
- struct __pyx_memoryview_obj *from_memview = from_mvs->memview;
- Py_buffer *buf = &from_memview->view;
- PyObject *shape_tuple = NULL;
- PyObject *temp_int = NULL;
- struct __pyx_array_obj *array_obj = NULL;
- struct __pyx_memoryview_obj *memview_obj = NULL;
- __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0);
- for (i = 0; i < ndim; i++) {
- if (from_mvs->suboffsets[i] >= 0) {
- PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with "
- "indirect dimensions (axis %d)", i);
- goto fail;
- }
- }
- shape_tuple = PyTuple_New(ndim);
- if (unlikely(!shape_tuple)) {
- goto fail;
- }
- __Pyx_GOTREF(shape_tuple);
- for(i = 0; i < ndim; i++) {
- temp_int = PyInt_FromLong(from_mvs->shape[i]);
- if(unlikely(!temp_int)) {
- goto fail;
- } else {
- PyTuple_SET_ITEM(shape_tuple, i, temp_int);
- temp_int = NULL;
- }
- }
- array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL);
- if (unlikely(!array_obj)) {
- goto fail;
- }
- __Pyx_GOTREF(array_obj);
- memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new(
- (PyObject *) array_obj, contig_flag,
- dtype_is_object,
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- if (unlikely(!memview_obj))
- goto fail;
- if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0))
- goto fail;
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- dtype_is_object) < 0))
- goto fail;
- goto no_fail;
-fail:
- __Pyx_XDECREF(new_mvs.memview);
- new_mvs.memview = NULL;
- new_mvs.data = NULL;
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-{
- PyObject *cobj;
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
- cobj = PyCapsule_New(p, sig, NULL);
-#else
- cobj = PyCObject_FromVoidPtr(p, NULL);
-#endif
- return cobj;
-}
-
-static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->exc_type;
- *value = tstate->exc_value;
- *tb = tstate->exc_traceback;
- Py_XINCREF(*type);
- Py_XINCREF(*value);
- Py_XINCREF(*tb);
-#else
- PyErr_GetExcInfo(type, value, tb);
-#endif
-}
-static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = type;
- tstate->exc_value = value;
- tstate->exc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
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-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
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- long val = __Pyx_PyInt_AsLong(x);
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- if (!unlikely(val == -1 && PyErr_Occurred())) {
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- (is_unsigned && unlikely(val < 0)) ?
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-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
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- long val = __Pyx_PyInt_AsLong(x);
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- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
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-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
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- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
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-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
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- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
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- return (char)__Pyx_PyInt_AsLong(x);
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-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
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- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
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- return (short)__Pyx_PyInt_AsLong(x);
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-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
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- long val = __Pyx_PyInt_AsLong(x);
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- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
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- "can't convert negative value to int" :
- "value too large to convert to int");
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-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
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- long val = __Pyx_PyInt_AsLong(x);
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- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
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-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
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- long val = __Pyx_PyInt_AsLong(x);
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- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
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- return (signed short)val;
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- return (signed short)__Pyx_PyInt_AsSignedLong(x);
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-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
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- return (signed int)val;
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- return (signed int)__Pyx_PyInt_AsSignedLong(x);
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-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
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-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
-#include "longintrepr.h"
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-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(unsigned long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (unsigned long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
-#endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(unsigned long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(unsigned long) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(unsigned long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
-#endif
-#endif
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
-#include "longintrepr.h"
-#endif
-#endif
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(unsigned PY_LONG_LONG)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
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- }
-#endif
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- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(unsigned PY_LONG_LONG)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
- }
- }
-#endif
-#endif
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
-#include "longintrepr.h"
-#endif
-#endif
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
-#endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(long) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
-#endif
-#endif
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
-#include "longintrepr.h"
-#endif
-#endif
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(PY_LONG_LONG)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
- }
- }
-#endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(PY_LONG_LONG)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
- }
- }
-#endif
-#endif
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
-#include "longintrepr.h"
-#endif
-#endif
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(signed long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (signed long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
-#endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(signed long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(signed long) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(signed long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
-#endif
-#endif
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
-#include "longintrepr.h"
-#endif
-#endif
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(signed PY_LONG_LONG)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
- }
- }
-#endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-#if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(signed PY_LONG_LONG)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
- }
- }
-#endif
-#endif
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
-#ifndef __PYX_HAVE_RT_ImportType
-#define __PYX_HAVE_RT_ImportType
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%s.%s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%s.%s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {
- return __Pyx_PyUnicode_FromStringAndSize(c_str, strlen(c_str));
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
- Py_ssize_t ignore;
- return __Pyx_PyObject_AsStringAndSize(o, &ignore);
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
- if (
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- __Pyx_sys_getdefaultencoding_not_ascii &&
-#endif
- PyUnicode_Check(o)) {
-#if PY_VERSION_HEX < 0x03030000
- char* defenc_c;
- PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
- if (!defenc) return NULL;
- defenc_c = PyBytes_AS_STRING(defenc);
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- {
- char* end = defenc_c + PyBytes_GET_SIZE(defenc);
- char* c;
- for (c = defenc_c; c < end; c++) {
- if ((unsigned char) (*c) >= 128) {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
- }
- }
-#endif /*__PYX_DEFAULT_STRING_ENCODING_IS_ASCII*/
- *length = PyBytes_GET_SIZE(defenc);
- return defenc_c;
-#else /* PY_VERSION_HEX < 0x03030000 */
- if (PyUnicode_READY(o) == -1) return NULL;
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- if (PyUnicode_IS_ASCII(o)) {
- *length = PyUnicode_GET_DATA_SIZE(o);
- return PyUnicode_AsUTF8(o);
- } else {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
-#else /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
- return PyUnicode_AsUTF8AndSize(o, length);
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
-#endif /* PY_VERSION_HEX < 0x03030000 */
- } else
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT */
- {
- char* result;
- int r = PyBytes_AsStringAndSize(o, &result, length);
- if (r < 0) {
- return NULL;
- } else {
- return result;
- }
- }
-}
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_MAJOR_VERSION < 3
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_MAJOR_VERSION < 3
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_MAJOR_VERSION < 3
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- if ((val != (unsigned PY_LONG_LONG)-1) || !PyErr_Occurred())
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/pyramid/numcore/phase_mag_real.pyx b/pyramid/numcore/phase_mag_real.pyx
index 7f76812..a849783 100644
--- a/pyramid/numcore/phase_mag_real.pyx
+++ b/pyramid/numcore/phase_mag_real.pyx
@@ -1,16 +1,47 @@
+# -*- coding: utf-8 -*-
+"""Numerical core routines for the phase calculation using the real space approach.
+
+Provides a helper function to speed up :func:`~pyramid.phasemapper.phase_mag_real` of module
+:mod:`~pyramid.phasemapper`, by using C-speed for the for-loops and by omitting boundary and
+wraparound checks.
+
+"""
+
+
import numpy as np
import math
+
cimport cython
cimport numpy as np
@cython.boundscheck(False)
@cython.wraparound(False)
-def phase_mag_real_helper(
+def phase_mag_real_core(
unsigned int v_dim, unsigned int u_dim,
- double[:, :] phi_u, double[:, :] phi_v,
- double[:, :] u_mag, double[:, :] v_mag,
+ double[:, :] v_phi, double[:, :] u_phi,
+ double[:, :] v_mag, double[:, :] u_mag,
double[:, :] phase, float threshold):
+ '''Numerical core routine for the phase calculation using the real space approach.
+
+ Parameters
+ ----------
+ v_dim, u_dim : int
+ Dimensions of the projection along the two major axes.
+ v_phi, u_phi : :class:`~numpy.ndarray` (N=2)
+ Lookup tables for the pixel fields oriented in `u`- and `v`-direction.
+ v_mag, u_mag : :class:`~numpy.ndarray` (N=2)
+ Magnetization components in `u`- and `v`-direction.
+ phase : :class:`~numpy.ndarray` (N=2)
+ Matrix in which the resulting magnetic phase map should be stored.
+ threshold : float
+ The `threshold` determines which pixels contribute to the magnetic phase.
+
+ Returns
+ -------
+ None
+
+ '''
cdef unsigned int i, j, p, q, p_c, q_c
cdef double u_m, v_m
for j in range(v_dim):
@@ -22,8 +53,8 @@ def phase_mag_real_helper(
if abs(u_m) > threshold:
for q in range(v_dim):
for p in range(u_dim):
- phase[q, p] += u_m * phi_u[q_c + q, p_c + p]
+ phase[q, p] += u_m * u_phi[q_c + q, p_c + p]
if abs(v_m) > threshold:
for q in range(v_dim):
for p in range(u_dim):
- phase[q, p] -= v_m * phi_v[q_c + q, p_c + p]
+ phase[q, p] -= v_m * v_phi[q_c + q, p_c + p]
diff --git a/pyramid/phasemap.py b/pyramid/phasemap.py
index f2b5a04..12e290c 100644
--- a/pyramid/phasemap.py
+++ b/pyramid/phasemap.py
@@ -1,162 +1,263 @@
# -*- coding: utf-8 -*-
-"""Class for creating objects to store phase maps."""
+"""Class for the storage of phase data.
+
+This module provides the :class:`~.PhaseMap` class whose instances can be used to store
+phase data for a 2-dimensional grid. It is possible to load data from NetCDF4 or LLG (.txt) files
+or to save the data in these formats. Also plotting methods are provided. See :class:`~.PhaseMap`
+for further information.
+
+"""
import numpy as np
+
import matplotlib.pyplot as plt
-import tables.netcdf3 as nc
+from mpl_toolkits.mplot3d import Axes3D
+
+import netCDF4
class PhaseMap:
- '''An object storing magnetization data.'''
+ '''Class for storing phase map data.
+
+ Represents 2-dimensional phase maps. the phase information itself is stored in `phase`.
+ The dimensions `dim` of the grid with resolution `res` will be calculated at construction
+ time, but `res` has to be specified.
+
+ Attributes
+ ----------
+ res : float
+ The resolution of the grid (grid spacing in nm)
+ dim : tuple (N=2)
+ Dimensions of the grid.
+ phase : :class:`~numpy.ndarray` (N=2)
+ Matrix containing the phase shift.
+ unit : {'rad', 'mrad', 'µrad'}, optional
+ Set the unit of the phase map. This is important for the :func:`~.display` function,
+ because the phase is scaled accordingly. Does not change the phase itself, which is
+ always in `rad`.
+
+ '''
+
+ UNITDICT = {'rad': 1E0,
+ 'mrad': 1E3,
+ 'µrad': 1E6}
+
+ def __init__(self, res, phase, unit='rad'):
+ '''Constructor for a :class:`~.PhaseMap` object for storing phase data.
- def __init__(self, res, phase):
- '''Constructor for a MagData object for storing magnetization data.
- Arguments:
- res - the resolution of the grid (grid spacing) in nm
- magnitude - the z-, y- and x-component of the magnetization vector for every
- 3D-gridpoint as a tuple
- Returns:
- MagData object
+ Parameters
+ ----------
+ res : float
+ The resolution of the grid (grid spacing) in nm.
+ phase : :class:`~numpy.ndarray` (N=2)
+ Matrix containing the phase shift.
+ unit : {'rad', 'mrad', 'µrad'}, optional
+ Set the unit of the phase map. This is important for the :func:`~.display` function,
+ because the phase is scaled accordingly. Does not change the phase itself, which is
+ always in `rad`.
+
+ Returns
+ -------
+ phase_map : :class:`~.PhaseMap`
+ The 2D phase shift as a :class:`~.PhaseMap` object.
'''
dim = np.shape(phase)
assert len(dim) == 2, 'Phasemap has to be 2-dimensional!'
self.res = res
self.dim = dim
+ self.unit = unit
self.phase = phase
+ def set_unit(self, unit):
+ '''Set the unit for the phase map.
+
+ Parameters
+ ----------
+ unit : {'rad', 'mrad', 'µrad'}, optional
+ Set the unit of the phase map. This is important for the :func:`~.display` function,
+ because the phase is scaled accordingly. Does not change the phase itself, which is
+ always in `rad`.
+
+ Returns
+ -------
+ None
+
+ '''
+ self.unit = unit
+
@classmethod
def load_from_txt(cls, filename):
- '''Construct PhaseMap object from a human readable txt-file (classmethod).
- Arguments:
- filename - name of the file from which to load the data
- Returns.
- PhaseMap object
+ '''Construct :class:`~.PhaseMap` object from a human readable txt-file.
+
+ Parameters
+ ----------
+ filename : string
+ The name of the file from which to load the data.
+
+ Returns
+ -------
+ phase_map : :class:`~.PhaseMap`
+ A :class:`~.PhaseMap` object containing the loaded data.
'''
- with open(filename, 'r') as f:
- f.readline() # Headerline is not used
- res = int(f.readline()[13:-4])
+ with open(filename, 'r') as phase_file:
+ phase_file.readline() # Headerline is not used
+ res = int(phase_file.readline()[13:-4])
phase = np.loadtxt(filename, delimiter='\t', skiprows=2)
return PhaseMap(res, phase)
def save_to_txt(self, filename='..\output\phasemap_output.txt'):
- '''Save PhaseMap data in a file with txt-format.
- Arguments:
- filename - the name of the file in which to store the phase map data
- (default: 'phasemap_output.txt')
- Returns:
- None
+ '''Save :class:`~.PhaseMap` data in a file with txt-format.
+
+ Parameters
+ ----------
+ filename : string
+ The name of the file in which to store the phase map data.
+ The default is 'phasemap_output.txt'.
+
+ Returns
+ -------
+ None
'''
- with open(filename, 'w') as f:
- f.write('{}\n'.format(filename.replace('.txt', '')))
- f.write('resolution = {} nm\n'.format(self.res))
- np.savetxt(f, self.phase, fmt='%7.6e', delimiter='\t')
+ with open(filename, 'w') as phase_file:
+ phase_file.write('{}\n'.format(filename.replace('.txt', '')))
+ phase_file.write('resolution = {} nm\n'.format(self.res))
+ np.savetxt(phase_file, self.phase, fmt='%7.6e', delimiter='\t')
@classmethod
- def load_from_netcdf(cls, filename):
- '''Construct PhaseMap object from a NetCDF-file (classmethod).
- Arguments:
- filename - name of the file from which to load the data
- Returns:
- PhaseMap object
+ def load_from_netcdf4(cls, filename):
+ '''Construct :class:`~.PhaseMap` object from NetCDF4-file.
+
+ Parameters
+ ----------
+ filename : string
+ The name of the NetCDF4-file from which to load the data. Standard format is '\*.nc'.
+
+ Returns
+ -------
+ phase_map: :class:`~.PhaseMap`
+ A :class:`~.PhaseMap` object containing the loaded data.
'''
- f = nc.NetCDFFile(filename, 'r')
- res = getattr(f, 'res')
- phase = f.variables['phase'].getValue()
- f.close()
+ phase_file = netCDF4.Dataset(filename, 'r', format='NETCDF4')
+ res = phase_file.res
+ phase = phase_file.variables['phase'][:]
+ phase_file.close()
return PhaseMap(res, phase)
- def save_to_netcdf(self, filename='..\output\phasemap_output.nc'):
- '''Save PhaseMap data in a file with NetCDF-format.
- Arguments:
- filename - the name of the file in which to store the phase map data
- (default: 'phasemap_output.txt')
- Returns:
- None
+ def save_to_netcdf4(self, filename='..\output\phasemap_output.nc'):
+ '''Save :class:`~.PhaseMap` data in a file with NetCDF4-format.
+
+ Parameters
+ ----------
+ filename : string, optional
+ The name of the NetCDF4-file in which to store the phase data.
+ The default is 'phasemap_output.nc'.
+
+ Returns
+ -------
+ None
'''
- f = nc.NetCDFFile(filename, 'w')
- setattr(f, 'res', self.res)
- f.createDimension('v_dim', self.dim[0])
- f.createDimension('u_dim', self.dim[1])
- phase = f.createVariable('phase', 'f', ('v_dim', 'u_dim'))
+ phase_file = netCDF4.Dataset(filename, 'w', format='NETCDF4')
+ phase_file.res = self.res
+ phase_file.createDimension('v_dim', self.dim[0])
+ phase_file.createDimension('u_dim', self.dim[1])
+ phase = phase_file.createVariable('phase', 'f', ('v_dim', 'u_dim'))
phase[:] = self.phase
- f.close()
+ print phase_file
+ phase_file.close()
- def display(self, title='Phase Map', labels=('x-axis [nm]', 'y-axis [nm]', 'phase [rad]'),
- cmap='RdBu', limit=None, norm=None, axis=None):
+ def display(self, title='Phase Map', cmap='RdBu', limit=None, norm=None, axis=None):
'''Display the phasemap as a colormesh.
- Arguments:
- title - the title of the plot (default: 'Phase Map')
- axis - the axis on which to display the plot (default: None, a new figure is created)
- cmap - the colormap which is used for the plot (default: 'gray')
- Returns:
- None
-
- ''' # TODO: Docstring!
-
- # TODO: ALWAYS CENTERED around 0
+
+ Parameters
+ ----------
+ title : string, optional
+ The title of the plot. The default is 'Phase Map'.
+ cmap : string, optional
+ The :class:`~matplotlib.colors.Colormap` which is used for the plot as a string.
+ The default is 'RdBu'.
+ limit : float, optional
+ Plotlimit for the phase in both negative and positive direction (symmetric around 0).
+ If not specified, the maximum amplitude the phase is used.
+ norm : :class:`~matplotlib.colors.Normalize` or subclass, optional
+ Norm, which is used to determine the colors to encode the phase information.
+ If not specified, :class:`~matplotlib.colors.Normalize` is automatically used.
+ axis : :class:`~matplotlib.axes.AxesSubplot`, optional
+ Axis on which the graph is plotted. Creates a new figure if none is specified.
+
+ Returns
+ -------
+ None
+
+ '''
+ # Take units into consideration:
+ phase = self.phase * self.UNITDICT[self.unit]
if limit is None:
- limit = np.max(np.abs(self.phase))
-
+ limit = np.max(np.abs(phase))
# If no axis is specified, a new figure is created:
if axis is None:
fig = plt.figure(figsize=(8.5, 7))
axis = fig.add_subplot(1, 1, 1, aspect='equal')
# Plot the phasemap:
- im = axis.pcolormesh(self.phase, cmap=cmap, vmin=-limit, vmax=limit, norm=norm)
+ im = axis.pcolormesh(phase, cmap=cmap, vmin=-limit, vmax=limit, norm=norm)
# Set the axes ticks and labels:
- axis.set_xlim(0, np.shape(self.phase)[1])
- axis.set_ylim(0, np.shape(self.phase)[0])
+ axis.set_xlim(0, np.shape(phase)[1])
+ axis.set_ylim(0, np.shape(phase)[0])
ticks = (axis.get_xticks()*self.res).astype(int)
axis.set_xticklabels(ticks)
ticks = (axis.get_yticks()*self.res).astype(int)
axis.tick_params(axis='both', which='major', labelsize=14)
axis.set_yticklabels(ticks)
axis.set_title(title, fontsize=18)
- axis.set_xlabel(labels[0], fontsize=15)
- axis.set_ylabel(labels[1], fontsize=15)
+ axis.set_xlabel('x [nm]', fontsize=15)
+ axis.set_ylabel('y [nm]', fontsize=15)
# Add colorbar:
fig = plt.gcf()
fig.subplots_adjust(right=0.8)
cbar_ax = fig.add_axes([0.82, 0.15, 0.02, 0.7])
cbar = fig.colorbar(im, cax=cbar_ax)
cbar.ax.tick_params(labelsize=14)
- cbar.set_label(labels[2], fontsize=15)
-
+ cbar.set_label('phase shift [{}]'.format(self.unit), fontsize=15)
+ # Show plot:
plt.show()
- def display3d(self, title='Phase Map', labels=('x-axis [nm]', 'y-axis [nm]', 'phase [rad]'),
- cmap='RdBu', limit=None, norm=None, axis=None):
- '''Display the phasemap as a colormesh.
- Arguments:
- title - the title of the plot (default: 'Phase Map')
- axis - the axis on which to display the plot (default: None, a new figure is created)
- cmap - the colormap which is used for the plot (default: 'gray')
- Returns:
- None
+ def display3d(self, title='Phase Map', cmap='RdBu'):
+ '''Display the phasemap as a 3-D surface with contourplots.
- ''' # TODO: Docstring!
-
- from mpl_toolkits.mplot3d import Axes3D
+ Parameters
+ ----------
+ title : string, optional
+ The title of the plot. The default is 'Phase Map'.
+ cmap : string, optional
+ The :class:`~matplotlib.colors.Colormap` which is used for the plot as a string.
+ The default is 'RdBu'.
- fig = plt.figure()
- ax = Axes3D(fig)#.gca(projection='3d')
+ Returns
+ -------
+ None
+ '''
+ # Take units into consideration:
+ phase = self.phase * self.UNITDICT[self.unit]
+ # Create figure and axis:
+ fig = plt.figure()
+ axis = Axes3D(fig)
+ # Plot surface and contours:
u = range(self.dim[1])
v = range(self.dim[0])
uu, vv = np.meshgrid(u, v)
- ax.plot_surface(uu, vv, self.phase, rstride=4, cstride=4, alpha=0.7, cmap='RdBu',
+ axis.plot_surface(uu, vv, phase, rstride=4, cstride=4, alpha=0.7, cmap=cmap,
linewidth=0, antialiased=False)
- ax.contourf(uu, vv, self.phase, 15, zdir='z', offset=np.min(self.phase), cmap='RdBu')
- ax.view_init(45, -135)
- ax.set_xlabel('x-axis [px]')
- ax.set_ylabel('y-axis [px]')
- ax.set_zlabel('phase [mrad]')
-
+ axis.contourf(uu, vv, phase, 15, zdir='z', offset=np.min(phase), cmap=cmap)
+ axis.view_init(45, -135)
+ axis.set_xlabel('x-axis [px]')
+ axis.set_ylabel('y-axis [px]')
+ axis.set_zlabel('phase shift [{}]'.format(self.unit))
+ # Show Plot:
plt.show()
diff --git a/pyramid/phasemapper.py b/pyramid/phasemapper.py
index 61cffa1..b14cead 100644
--- a/pyramid/phasemapper.py
+++ b/pyramid/phasemapper.py
@@ -1,13 +1,22 @@
# -*- coding: utf-8 -*-
-"""Create and display a phase map from magnetization data."""
+"""Create magnetic and electric phase maps from magnetization data.
+This module executes several forward models to calculate the magnetic or electric phase map from
+a given projection of a 3-dimensional magnetic distribution (see :mod:`~pyramid.projector`).
+For the magnetic phase map, an approach using real space and one using Fourier space is provided.
+The real space approach also calculates the Jacobi matrix, which is used for the reconstruction in
+the :mod:`~pyramid.reconstructor` module. The electrostatic contribution is calculated by using
+the assumption of a mean inner potentail (MIP).
+
+"""
-import numpy as np
-import numcore
+import numpy as np
from numpy import pi
-# Physical constants
+import pyramid.numcore as nc
+
+
PHI_0 = -2067.83 # magnetic flux in T*nm²
H_BAR = 6.626E-34 # Planck constant in J*s
M_E = 9.109E-31 # electron mass in kg
@@ -15,20 +24,31 @@ Q_E = 1.602E-19 # electron charge in C
C = 2.998E8 # speed of light in m/s
-def phase_mag_fourier(res, projection, b_0=1, padding=0):
- '''Calculate phasemap from magnetization data (Fourier space approach).
- Arguments:
- res - the resolution of the grid (grid spacing) in nm
- projection - projection of a magnetic distribution (created with pyramid.projector)
- b_0 - magnetic induction corresponding to a magnetization Mo in T (default: 1)
- padding - factor for zero padding, the default is 0 (no padding), for a factor of n the
- number of pixels is increase by (1+n)**2, padded zeros are cropped at the end
- Returns:
- the phasemap as a 2 dimensional array
+def phase_mag_fourier(res, projection, padding=0, b_0=1):
+ '''Calculate the magnetic phase from magnetization data (Fourier space approach).
+
+ Parameters
+ ----------
+ res : float
+ The resolution of the grid (grid spacing) in nm.
+ projection : tuple (N=3) of :class:`~numpy.ndarray` (N=2)
+ The in-plane projection of the magnetization as a tuple, storing the `u`- and `v`-component
+ of the magnetization and the thickness projection for the resulting 2D-grid.
+ padding : int, optional
+ Factor for the zero padding. The default is 0 (no padding). For a factor of n the number
+ of pixels is increase by ``(1+n)**2``. Padded zeros are cropped at the end.
+ b_0 : float, optional
+ The magnetic induction corresponding to a magnetization `M`\ :sub:`0` in T.
+ The default is 1.
+
+ Returns
+ -------
+ phase : :class:`~numpy.ndarray` (N=2)
+ The phase as a 2-dimensional array.
'''
v_dim, u_dim = np.shape(projection[0])
- v_mag, u_mag = projection
+ v_mag, u_mag = projection[:-1]
# Create zero padded matrices:
u_pad = u_dim/2 * padding
v_pad = v_dim/2 * padding
@@ -52,75 +72,33 @@ def phase_mag_fourier(res, projection, b_0=1, padding=0):
return phase
-def phase_mag_real(res, projection, method, b_0=1, jacobi=None):
- '''Calculate phasemap from magnetization data (real space approach).
- Arguments:
- res - the resolution of the grid (grid spacing) in nm
- projection - projection of a magnetic distribution (created with pyramid.projector)
- method - String, describing the method to use for the pixel field ('slab' or 'disc')
- b_0 - magnetic induction corresponding to a magnetization Mo in T (default: 1)
- jacobi - matrix in which to save the jacobi matrix (default: None, faster computation)
- Returns:
- the phasemap as a 2 dimensional array
-
- '''
- # Function for creating the lookup-tables:
- def phi_lookup(method, n, m, res, b_0):
- if method == 'slab':
- def F_h(n, m):
- a = np.log(res**2 * (n**2 + m**2))
- b = np.arctan(n / m)
- return n*a - 2*n + 2*m*b
- return coeff * 0.5 * (F_h(n-0.5, m-0.5) - F_h(n+0.5, m-0.5)
- - F_h(n-0.5, m+0.5) + F_h(n+0.5, m+0.5))
- elif method == 'disc':
- in_or_out = np.logical_not(np.logical_and(n == 0, m == 0))
- return coeff * m / (n**2 + m**2 + 1E-30) * in_or_out
- # Process input parameters:
- v_dim, u_dim = np.shape(projection[0])
- v_mag, u_mag = projection
- coeff = -b_0 * res**2 / (2*PHI_0)
- # Create lookup-tables for the phase of one pixel:
- u = np.linspace(-(u_dim-1), u_dim-1, num=2*u_dim-1)
- v = np.linspace(-(v_dim-1), v_dim-1, num=2*v_dim-1)
- uu, vv = np.meshgrid(u, v)
- phi_u = phi_lookup(method, uu, vv, res, b_0)
- phi_v = phi_lookup(method, vv, uu, res, b_0)
- # Calculation of the phase:
- phase = np.zeros((v_dim, u_dim))
- threshold = 0
- if jacobi is not None: # With Jacobian matrix (slower)
- jacobi[:] = 0 # Jacobi matrix --> zeros
- ############################### TODO: NUMERICAL CORE #####################################
- for j in range(v_dim):
- for i in range(u_dim):
- phase_u = phi_u[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
- jacobi[:, i+u_dim*j] = phase_u.reshape(-1)
- if abs(u_mag[j, i]) > threshold:
- phase += u_mag[j, i] * phase_u
- phase_v = phi_v[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
- jacobi[:, u_dim*v_dim+i+u_dim*j] = -phase_v.reshape(-1)
- if abs(v_mag[j, i]) > threshold:
- phase -= v_mag[j, i] * phase_v
- ############################### TODO: NUMERICAL CORE #####################################
- else: # Without Jacobi matrix (faster)
- numcore.phase_mag_real_helper(v_dim, u_dim, phi_u, phi_v, u_mag, v_mag, phase, threshold)
- # Return the phase:
- return phase
+def phase_mag_real(res, projection, method='discs', b_0=1, jacobi=None):
+ '''Calculate the magnetic phase from magnetization data (real space approach).
+ Parameters
+ ----------
+ res : float
+ The resolution of the grid (grid spacing) in nm.
+ projection : tuple (N=3) of :class:`~numpy.ndarray` (N=2)
+ The in-plane projection of the magnetization as a tuple, storing the `u`- and `v`-component
+ of the magnetization and the thickness projection for the resulting 2D-grid.
+ method : {'disc', 'slab'}, optional
+ Specifies the elemental geometry to use for the pixel field.
+ The default is 'disc', because of the smaller computational overhead.
+ b_0 : float, optional
+ The magnetic induction corresponding to a magnetization `M`\ :sub:`0` in T.
+ The default is 1.
+ jacobi : :class:`~numpy.ndarray` (N=2), optional
+ Specifies the matrix in which to save the jacobi matrix. The jacobi matrix will not be
+ calculated, if no matrix is specified (default), resulting in a faster computation.
-def phase_mag_real2(res, projection, method, b_0=1, jacobi=None):
- '''Calculate phasemap from magnetization data (real space approach).
- Arguments:
- res - the resolution of the grid (grid spacing) in nm
- projection - projection of a magnetic distribution (created with pyramid.projector)
- method - String, describing the method to use for the pixel field ('slab' or 'disc')
- b_0 - magnetic induction corresponding to a magnetization Mo in T (default: 1)
- jacobi - matrix in which to save the jacobi matrix (default: None, faster computation)
- Returns:
- the phasemap as a 2 dimensional array
+ Returns
+ -------
+ phase : :class:`~numpy.ndarray` (N=2)
+ The phase as a 2-dimensional array.
'''
+
# Function for creating the lookup-tables:
def phi_lookup(method, n, m, res, b_0):
if method == 'slab':
@@ -133,136 +111,203 @@ def phase_mag_real2(res, projection, method, b_0=1, jacobi=None):
elif method == 'disc':
in_or_out = np.logical_not(np.logical_and(n == 0, m == 0))
return coeff * m / (n**2 + m**2 + 1E-30) * in_or_out
+
# Process input parameters:
v_dim, u_dim = np.shape(projection[0])
- v_mag, u_mag = projection
+ v_mag, u_mag = projection[:-1]
coeff = -b_0 * res**2 / (2*PHI_0)
+
# Create lookup-tables for the phase of one pixel:
u = np.linspace(-(u_dim-1), u_dim-1, num=2*u_dim-1)
v = np.linspace(-(v_dim-1), v_dim-1, num=2*v_dim-1)
uu, vv = np.meshgrid(u, v)
- phi_u = phi_lookup(method, uu, vv, res, b_0)
- phi_v = phi_lookup(method, vv, uu, res, b_0)
+ u_phi = phi_lookup(method, uu, vv, res, b_0)
+ v_phi = phi_lookup(method, vv, uu, res, b_0)
+
# Calculation of the phase:
phase = np.zeros((v_dim, u_dim))
threshold = 0
if jacobi is not None: # With Jacobian matrix (slower)
jacobi[:] = 0 # Jacobi matrix --> zeros
- ############################### TODO: NUMERICAL CORE #####################################
for j in range(v_dim):
for i in range(u_dim):
- phase_u = phi_u[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
- jacobi[:, i+u_dim*j] = phase_u.reshape(-1)
+ u_phase = u_phi[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
+ jacobi[:, i+u_dim*j] = u_phase.reshape(-1)
if abs(u_mag[j, i]) > threshold:
- phase += u_mag[j, i] * phase_u
- phase_v = phi_v[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
- jacobi[:, u_dim*v_dim+i+u_dim*j] = -phase_v.reshape(-1)
+ phase += u_mag[j, i] * u_phase
+ v_phase = v_phi[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
+ jacobi[:, u_dim*v_dim+i+u_dim*j] = -v_phase.reshape(-1)
if abs(v_mag[j, i]) > threshold:
- phase -= v_mag[j, i] * phase_v
- ############################### TODO: NUMERICAL CORE #####################################
+ phase -= v_mag[j, i] * v_phase
else: # Without Jacobi matrix (faster)
-# phasecopy = phase.copy()
-# start_time = time.time()
-# numcore.phase_mag_real_helper_1(v_dim, u_dim, phi_u, phi_v,
-# u_mag, v_mag, phasecopy, threshold)
-# print 'with numcore : ', time.time() - start_time
-# start_time = time.time()
- for j in range(v_dim):
- for i in range(u_dim):
- if abs(u_mag[j, i]) > threshold:
- phase += u_mag[j, i] * phi_u[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
- if abs(v_mag[j, i]) > threshold:
- phase -= v_mag[j, i] * phi_v[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
-# print 'without numcore: ', time.time() - start_time
-# print 'num. difference: ', ((phase - phasecopy) ** 2).sum()
+ nc.phase_mag_real_core(v_dim, u_dim, v_phi, u_phi, v_mag, u_mag, phase, threshold)
# Return the phase:
return phase
-def phase_mag_real_alt(res, projection, method, b_0=1, jacobi=None): # TODO: Modify
- '''Calculate phasemap from magnetization data (real space approach).
- Arguments:
- res - the resolution of the grid (grid spacing) in nm
- projection - projection of a magnetic distribution (created with pyramid.projector)
- method - String, describing the method to use for the pixel field ('slab' or 'disc')
- b_0 - magnetic induction corresponding to a magnetization Mo in T (default: 1)
- jacobi - matrix in which to save the jacobi matrix (default: None, faster computation)
- Returns:
- the phasemap as a 2 dimensional array
-
- '''
- # Function for creating the lookup-tables:
- def phi_lookup(method, n, m, res, b_0):
- if method == 'slab':
- def F_h(n, m):
- a = np.log(res**2 * (n**2 + m**2))
- b = np.arctan(n / m)
- return n*a - 2*n + 2*m*b
- return coeff * 0.5 * (F_h(n-0.5, m-0.5) - F_h(n+0.5, m-0.5)
- - F_h(n-0.5, m+0.5) + F_h(n+0.5, m+0.5))
- elif method == 'disc':
- in_or_out = np.logical_not(np.logical_and(n == 0, m == 0))
- return coeff * m / (n**2 + m**2 + 1E-30) * in_or_out
+def phase_elec(res, projection, v_0=1, v_acc=30000):
+ '''Calculate the electric phase from magnetization distributions.
- # Function for the phase contribution of one pixel:
- def phi_mag(i, j):
- return (np.cos(beta[j, i]) * phi_u[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
- - np.sin(beta[j, i]) * phi_v[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i])
+ Parameters
+ ----------
+ res : float
+ The resolution of the grid (grid spacing) in nm.
+ projection : tuple (N=3) of :class:`~numpy.ndarray` (N=2)
+ The in-plane projection of the magnetization as a tuple, storing the u- and v-component
+ of the magnetization and the thickness projection for the resulting 2D-grid.
+ v_0 : float, optional
+ The mean inner potential of the specimen in V. The default is 1.
+ v_acc : float, optional
+ The acceleration voltage of the electron microscope in V. The default is 30000.
- # Function for the derivative of the phase contribution of one pixel:
- def phi_mag_deriv(i, j):
- return -(np.sin(beta[j, i]) * phi_u[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
- + np.cos(beta[j, i]) * phi_v[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i])
+ Returns
+ -------
+ phase : :class:`~numpy.ndarray` (N=2)
+ The phase as a 2-dimensional array.
+ '''
# Process input parameters:
- v_dim, u_dim = np.shape(projection[0])
- v_mag, u_mag = projection
- beta = np.arctan2(v_mag, u_mag)
- mag = np.hypot(u_mag, v_mag)
- coeff = -b_0 * res**2 / (2*PHI_0)
- # Create lookup-tables for the phase of one pixel:
- u = np.linspace(-(u_dim-1), u_dim-1, num=2*u_dim-1)
- v = np.linspace(-(v_dim-1), v_dim-1, num=2*v_dim-1)
- uu, vv = np.meshgrid(u, v)
- phi_u = phi_lookup(method, uu, vv, res, b_0)
- phi_v = phi_lookup(method, vv, uu, res, b_0)
- # Calculation of the phase:
- phase = np.zeros((v_dim, u_dim))
- threshold = 0
- if jacobi is not None: # With Jacobian matrix (slower)
- jacobi[:] = 0 # Jacobi matrix --> zeros
- ############################### TODO: NUMERICAL CORE #####################################
- for j in range(v_dim):
- for i in range(u_dim):
- phase_cache = phi_mag(i, j)
- jacobi[:, i+u_dim*j] = phase_cache.reshape(-1)
- if mag[j, i] > threshold:
- phase += mag[j, i]*phase_cache
- jacobi[:, u_dim*v_dim+i+u_dim*j] = (mag[j, i]*phi_mag_deriv(i, j)).reshape(-1)
- ############################### TODO: NUMERICAL CORE #####################################
- else: # Without Jacobi matrix (faster)
- for j in range(v_dim):
- for i in range(u_dim):
- if abs(mag[j, i]) > threshold:
- phase += mag[j, i] * phi_mag(i, j)
- # Return the phase:
- return phase
-
-
-def phase_elec(mag_data, v_0=1, v_acc=30000):
- # TODO: Docstring
+ lam = H_BAR / np.sqrt(2 * M_E * Q_E * v_acc * (1 + Q_E*v_acc / (2*M_E*C**2)))
+ Ce = 2*pi*Q_E/lam * (Q_E*v_acc + M_E*C**2) / (Q_E*v_acc * (Q_E*v_acc + 2*M_E*C**2))
+ # return phase:
+ return v_0 * Ce * projection[-1] * res*1E-9
- res = mag_data.res
- z_dim, y_dim, x_dim = mag_data.dim
- z_mag, y_mag, x_mag = mag_data.magnitude
- phase = np.logical_or(x_mag, y_mag, z_mag)
-
- lam = H_BAR / np.sqrt(2 * M_E * v_acc * (1 + Q_E*v_acc / (2*M_E*C**2)))
-
- Ce = (2*pi*Q_E/lam * (Q_E*v_acc + M_E*C**2) /
- (Q_E*v_acc * (Q_E*v_acc + 2*M_E*C**2)))
-
- phase *= res * v_0 * Ce
-
- return phase
+#def phase_mag_real2(res, projection, method, b_0=1, jacobi=None):
+# '''Calculate phasemap from magnetization data (real space approach).
+# Arguments:
+# res - the resolution of the grid (grid spacing) in nm
+# projection - projection of a magnetic distribution (created with pyramid.projector)
+# method - string, describing the method to use for the pixel field ('slab' or 'disc')
+# b_0 - magnetic induction corresponding to a magnetization Mo in T (default: 1)
+# jacobi - matrix in which to save the jacobi matrix (default: None, faster computation)
+# Returns:
+# the phasemap as a 2 dimensional array
+#
+# '''
+# # Function for creating the lookup-tables:
+# def phi_lookup(method, n, m, res, b_0):
+# if method == 'slab':
+# def F_h(n, m):
+# a = np.log(res**2 * (n**2 + m**2))
+# b = np.arctan(n / m)
+# return n*a - 2*n + 2*m*b
+# return coeff * 0.5 * (F_h(n-0.5, m-0.5) - F_h(n+0.5, m-0.5)
+# - F_h(n-0.5, m+0.5) + F_h(n+0.5, m+0.5))
+# elif method == 'disc':
+# in_or_out = np.logical_not(np.logical_and(n == 0, m == 0))
+# return coeff * m / (n**2 + m**2 + 1E-30) * in_or_out
+# # Process input parameters:
+# v_dim, u_dim = np.shape(projection[0])
+# v_mag, u_mag = projection
+# coeff = -b_0 * res**2 / (2*PHI_0)
+# # Create lookup-tables for the phase of one pixel:
+# u = np.linspace(-(u_dim-1), u_dim-1, num=2*u_dim-1)
+# v = np.linspace(-(v_dim-1), v_dim-1, num=2*v_dim-1)
+# uu, vv = np.meshgrid(u, v)
+# phi_u = phi_lookup(method, uu, vv, res, b_0)
+# phi_v = phi_lookup(method, vv, uu, res, b_0)
+# # Calculation of the phase:
+# phase = np.zeros((v_dim, u_dim))
+# threshold = 0
+# if jacobi is not None: # With Jacobian matrix (slower)
+# jacobi[:] = 0 # Jacobi matrix --> zeros
+# ############################### TODO: NUMERICAL CORE ####################################
+# for j in range(v_dim):
+# for i in range(u_dim):
+# phase_u = phi_u[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
+# jacobi[:, i+u_dim*j] = phase_u.reshape(-1)
+# if abs(u_mag[j, i]) > threshold:
+# phase += u_mag[j, i] * phase_u
+# phase_v = phi_v[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
+# jacobi[:, u_dim*v_dim+i+u_dim*j] = -phase_v.reshape(-1)
+# if abs(v_mag[j, i]) > threshold:
+# phase -= v_mag[j, i] * phase_v
+# ############################### TODO: NUMERICAL CORE ####################################
+# else: # Without Jacobi matrix (faster)
+## phasecopy = phase.copy()
+## start_time = time.time()
+## numcore.phase_mag_real_helper_1(v_dim, u_dim, phi_u, phi_v,
+## u_mag, v_mag, phasecopy, threshold)
+## print 'with numcore : ', time.time() - start_time
+## start_time = time.time()
+# for j in range(v_dim):
+# for i in range(u_dim):
+# if abs(u_mag[j, i]) > threshold:
+# phase += u_mag[j, i] * phi_u[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
+# if abs(v_mag[j, i]) > threshold:
+# phase -= v_mag[j, i] * phi_v[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
+## print 'without numcore: ', time.time() - start_time
+## print 'num. difference: ', ((phase - phasecopy) ** 2).sum()
+# # Return the phase:
+# return phase
+#
+#
+#def phase_mag_real_alt(res, projection, method, b_0=1, jacobi=None): # TODO: Modify
+# '''Calculate phasemap from magnetization data (real space approach).
+# Arguments:
+# res - the resolution of the grid (grid spacing) in nm
+# projection - projection of a magnetic distribution (created with pyramid.projector)
+# method - string, describing the method to use for the pixel field ('slab' or 'disc')
+# b_0 - magnetic induction corresponding to a magnetization Mo in T (default: 1)
+# jacobi - matrix in which to save the jacobi matrix (default: None, faster computation)
+# Returns:
+# the phasemap as a 2 dimensional array
+#
+# '''
+# # Function for creating the lookup-tables:
+# def phi_lookup(method, n, m, res, b_0):
+# if method == 'slab':
+# def F_h(n, m):
+# a = np.log(res**2 * (n**2 + m**2))
+# b = np.arctan(n / m)
+# return n*a - 2*n + 2*m*b
+# return coeff * 0.5 * (F_h(n-0.5, m-0.5) - F_h(n+0.5, m-0.5)
+# - F_h(n-0.5, m+0.5) + F_h(n+0.5, m+0.5))
+# elif method == 'disc':
+# in_or_out = np.logical_not(np.logical_and(n == 0, m == 0))
+# return coeff * m / (n**2 + m**2 + 1E-30) * in_or_out
+#
+# # Function for the phase contribution of one pixel:
+# def phi_mag(i, j):
+# return (np.cos(beta[j, i]) * phi_u[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
+# - np.sin(beta[j, i]) * phi_v[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i])
+#
+# # Function for the derivative of the phase contribution of one pixel:
+# def phi_mag_deriv(i, j):
+# return -(np.sin(beta[j, i]) * phi_u[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i]
+# + np.cos(beta[j, i]) * phi_v[v_dim-1-j:(2*v_dim-1)-j, u_dim-1-i:(2*u_dim-1)-i])
+#
+# # Process input parameters:
+# v_dim, u_dim = np.shape(projection[0])
+# v_mag, u_mag = projection
+# beta = np.arctan2(v_mag, u_mag)
+# mag = np.hypot(u_mag, v_mag)
+# coeff = -b_0 * res**2 / (2*PHI_0)
+# # Create lookup-tables for the phase of one pixel:
+# u = np.linspace(-(u_dim-1), u_dim-1, num=2*u_dim-1)
+# v = np.linspace(-(v_dim-1), v_dim-1, num=2*v_dim-1)
+# uu, vv = np.meshgrid(u, v)
+# phi_u = phi_lookup(method, uu, vv, res, b_0)
+# phi_v = phi_lookup(method, vv, uu, res, b_0)
+# # Calculation of the phase:
+# phase = np.zeros((v_dim, u_dim))
+# threshold = 0
+# if jacobi is not None: # With Jacobian matrix (slower)
+# jacobi[:] = 0 # Jacobi matrix --> zeros
+# ############################### TODO: NUMERICAL CORE ####################################
+# for j in range(v_dim):
+# for i in range(u_dim):
+# phase_cache = phi_mag(i, j)
+# jacobi[:, i+u_dim*j] = phase_cache.reshape(-1)
+# if mag[j, i] > threshold:
+# phase += mag[j, i]*phase_cache
+# jacobi[:, u_dim*v_dim+i+u_dim*j] = (mag[j, i]*phi_mag_deriv(i, j)).reshape(-1)
+# ############################### TODO: NUMERICAL CORE ####################################
+# else: # Without Jacobi matrix (faster)
+# for j in range(v_dim):
+# for i in range(u_dim):
+# if abs(mag[j, i]) > threshold:
+# phase += mag[j, i] * phi_mag(i, j)
+# # Return the phase:
+# return phase
diff --git a/pyramid/projector.py b/pyramid/projector.py
index 94b6ea4..d0249c2 100644
--- a/pyramid/projector.py
+++ b/pyramid/projector.py
@@ -1,33 +1,51 @@
# -*- coding: utf-8 -*-
-"""Planar projection of the magnetization distribution of a MagData object."""
+"""Create projections of a given magnetization distribution.
+
+This module creates 2-dimensional projections from 3-dimensional magnetic distributions, which
+are stored in :class:`~pyramid.magdata.MagData` objects. Either simple projections along the
+major axes are possible (:func:`~.simple_axis_projection`), or projections along arbitrary
+directions with the use of transfer functions (work in progress).
+
+"""
from pyramid.magdata import MagData
-def simple_axis_projection(mag_data, axis='z'):
- '''Project a magnetization distribution along one of the main axes of the 3D-grid.
- Arguments:
- mag_data - a MagData object storing the magnetization distribution
- axis - the projection direction (String: 'x', 'y', 'z'), default = 'z'
- Returns:
- the in-plane projection of the magnetization as a tuple: (x_mag, y_mag)
- ()
+def simple_axis_projection(mag_data, axis='z', threshold=0):
+ '''
+ Project a magnetization distribution along one of the main axes of the 3D-grid.
+
+ Parameters
+ ----------
+ mag_data : :class:`~pyramid.magdata.MagData`
+ A :class:`~pyramid.magdata.MagData` object storing the magnetization distribution,
+ which should be projected.
+ axis : {'z', 'y', 'x'}, optional
+ The projection direction as a string.
+ threshold : float, optional
+ A pixel only gets masked, if it lies above this threshold. The default is 0.
+
+ Returns
+ -------
+ projection : tuple (N=3) of :class:`~numpy.ndarray` (N=2)
+ The in-plane projection of the magnetization as a tuple, storing the `u`- and `v`-component
+ of the magnetization and the thickness projection for the resulting 2D-grid. The latter
+ has to be multiplied with the resolution for a value in nm.
'''
assert isinstance(mag_data, MagData), 'Parameter mag_data has to be a MagData object!'
- assert axis == 'z' or axis == 'y' or axis == 'x', 'Axis has to be x, y or z (as String)!'
+ assert axis == 'z' or axis == 'y' or axis == 'x', 'Axis has to be x, y or z (as string)!'
if axis == 'z':
projection = (mag_data.magnitude[1].sum(0), # y_mag -> v_mag
- mag_data.magnitude[2].sum(0)) # x_mag -> u_mag
+ mag_data.magnitude[2].sum(0), # x_mag -> u_mag
+ mag_data.get_mask(threshold).sum(0)) # thickness profile
elif axis == 'y':
projection = (mag_data.magnitude[0].sum(1), # z_mag -> v_mag
- mag_data.magnitude[2].sum(1)) # x_mag -> u_mag
+ mag_data.magnitude[2].sum(1), # x_mag -> u_mag
+ mag_data.get_mask(threshold).sum(1)) # thickness profile
elif axis == 'x':
projection = (mag_data.magnitude[0].sum(2), # z_mag -> v_mag
- mag_data.magnitude[1].sum(2)) # y_mag -> u_mag
+ mag_data.magnitude[1].sum(2), # y_mag -> u_mag
+ mag_data.get_mask(threshold).sum(2)) # thickness profile
return projection
-
-# TODO: proper projection algorithm with two angles and such!
-# CAUTION: the res for the projection does not have to be the res of the 3D-magnetization!
-# Just for a first approach
diff --git a/pyramid/reconstructor.py b/pyramid/reconstructor.py
index b16da97..b31d3e5 100644
--- a/pyramid/reconstructor.py
+++ b/pyramid/reconstructor.py
@@ -1,23 +1,50 @@
# -*- coding: utf-8 -*-
-"""Reconstruct magnetic distributions with given phasemaps"""
+"""Reconstruct magnetic distributions from given phasemaps.
+
+This module reconstructs 3-dimensional magnetic distributions (as :class:`~pyramid.magdata.MagData`
+objects) from a given set of phase maps (represented by :class:`~pyramid.phasemap.PhaseMap`
+objects) by using several model based reconstruction algorithms which use the forward model
+provided by :mod:`~pyramid.projector` and :mod:`~pyramid.phasemapper` and a priori knowledge of
+the distribution.
+So far, only a simple least square algorithm for known pixel locations for 2-dimensional problems
+is implemented (:func:`~.reconstruct_simple_leastsq`), but more complex solutions are planned.
+
+"""
import numpy as np
+
+from scipy.optimize import leastsq
+
import pyramid.projector as pj
import pyramid.phasemapper as pm
from pyramid.magdata import MagData
-from scipy.optimize import leastsq
-def reconstruct_simple_leastsq(phase_map, mask, b_0):
- '''Reconstruct a magnetic distribution where the positions of the magnetized voxels are known
- from a single phase_map using the least square method (only works for slice thickness = 1)
- Arguments:
- phase_map - a PhaseMap object, from which to reconstruct the magnetic distribution
- mask - a boolean matrix representing the positions of the magnetized voxels (3D)
- b_0 - magnetic induction corresponding to a magnetization Mo in T (default: 1)
- Returns:
- the reconstructed magnetic distribution (as a MagData object)
+def reconstruct_simple_leastsq(phase_map, mask, b_0=1):
+ '''Reconstruct a magnetic distribution for a 2-D problem with known pixel locations.
+
+ Parameters
+ ----------
+ phase_map : :class:`~pyramid.phasemap.PhaseMap`
+ A :class:`~pyramid.phasemap.PhaseMap` object, representing the phase from which to
+ reconstruct the magnetic distribution.
+ mask : :class:`~numpy.ndarray` (N=3)
+ A boolean matrix (or a matrix consisting of ones and zeros), representing the
+ positions of the magnetized voxels in 3 dimensions.
+ b_0 : float, optional
+ The magnetic induction corresponding to a magnetization `M`\ :sub:`0` in T.
+ The default is 1.
+ Returns
+ -------
+ mag_data : :class:`~pyramid.magdata.MagData`
+ The reconstructed magnetic distribution as a
+ :class:`~pyramid.magdata.MagData` object.
+
+ Notes
+ -----
+ Only works for a single phase_map, if the positions of the magnetized voxels are known and
+ for slice thickness of 1 (constraint for the `z`-dimension).
'''
# Read in parameters:
diff --git a/scripts/compare_methods.py b/scripts/compare methods/compare_methods.py
similarity index 92%
rename from scripts/compare_methods.py
rename to scripts/compare methods/compare_methods.py
index e6677fd..da8fb5d 100644
--- a/scripts/compare_methods.py
+++ b/scripts/compare methods/compare_methods.py
@@ -7,6 +7,7 @@ import time
import pdb
import traceback
import sys
+
import numpy as np
from numpy import pi
@@ -28,21 +29,21 @@ def compare_methods():
'''
# Input parameters:
- b_0 = 1 # in T
+ b_0 = 1.1 # in T
res = 10.0 # in nm
phi = pi/4
padding = 12
density = 1
dim = (16, 128, 128) # in px (z, y, x)
# Create magnetic shape:
- geometry = 'disc'
+ geometry = 'slab'
if geometry == 'slab':
- center = (dim[0]/2-0.5, dim[1]/2-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
+ center = (dim[0]/2-0.5, dim[1]/2-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts at 0!
width = (dim[0]/2, dim[1]/2., dim[2]/2.) # in px (z, y, x)
mag_shape = mc.Shapes.slab(dim, center, width)
phase_ana = an.phase_mag_slab(dim, res, phi, center, width, b_0)
elif geometry == 'disc':
- center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
+ center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts at 0!
radius = dim[1]/4 # in px
height = dim[0]/2 # in px
mag_shape = mc.Shapes.disc(dim, center, radius, height)
@@ -53,13 +54,13 @@ def compare_methods():
mag_shape = mc.Shapes.sphere(dim, center, radius)
phase_ana = an.phase_mag_sphere(dim, res, phi, center, radius, b_0)
# Project the magnetization data:
- mag_data = MagData(res, mc.create_mag_dist(mag_shape, phi))
+ mag_data = MagData(res, mc.create_mag_dist_homog(mag_shape, phi))
mag_data.quiver_plot(ax_slice=int(center[0]))
projection = pj.simple_axis_projection(mag_data)
# Construct phase maps:
phase_map_ana = PhaseMap(res, phase_ana)
start_time = time.time()
- phase_map_fft = PhaseMap(res, pm.phase_mag_fourier(res, projection, b_0, padding))
+ phase_map_fft = PhaseMap(res, pm.phase_mag_fourier(res, projection, padding, b_0))
print 'Time for Fourier space approach: ', time.time() - start_time
start_time = time.time()
phase_map_slab = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab', b_0))
diff --git a/scripts/compare_pixel_fields.py b/scripts/compare methods/compare_pixel_fields.py
similarity index 63%
rename from scripts/compare_pixel_fields.py
rename to scripts/compare methods/compare_pixel_fields.py
index c3bd985..644810f 100644
--- a/scripts/compare_pixel_fields.py
+++ b/scripts/compare methods/compare_pixel_fields.py
@@ -6,6 +6,8 @@
import pdb
import traceback
import sys
+import os
+
from numpy import pi
import pyramid.magcreator as mc
@@ -23,20 +25,24 @@ def compare_pixel_fields():
None
'''
+ directory = '../../output/magnetic distributions'
+ if not os.path.exists(directory):
+ os.makedirs(directory)
# Input parameters:
- res = 10.0 # in nm
+ res = 1.0 # in nm
phi = pi/2 # in rad
- dim = (1, 5, 5)
- pixel = (0, 2, 2)
+ dim = (1, 101, 101)
+ pixel = (0, int(dim[1]/2), int(dim[2]/2))
+ limit = 0.25
# Create magnetic data, project it, get the phase map and display the holography image:
- mag_data = MagData(res, mc.create_mag_dist(mc.Shapes.pixel(dim, pixel), phi))
- mag_data.save_to_llg('../output/mag_dist_single_pixel.txt')
+ mag_data = MagData(res, mc.create_mag_dist_homog(mc.Shapes.pixel(dim, pixel), phi))
+ mag_data.save_to_llg(directory + '/mag_dist_single_pixel.txt')
projection = pj.simple_axis_projection(mag_data)
- phase_map_slab = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))
- phase_map_slab.display('Phase of one Pixel (Slab)')
- phase_map_disc = PhaseMap(res, pm.phase_mag_real(res, projection, 'disc'))
- phase_map_disc.display('Phase of one Pixel (Disc)')
- phase_map_diff = PhaseMap(res, phase_map_disc.phase - phase_map_slab.phase)
+ phase_map_slab = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'), 'mrad')
+ phase_map_slab.display('Phase of one Pixel (Slab)', limit=limit)
+ phase_map_disc = PhaseMap(res, pm.phase_mag_real(res, projection, 'disc'), 'mrad')
+ phase_map_disc.display('Phase of one Pixel (Disc)', limit=limit)
+ phase_map_diff = PhaseMap(res, phase_map_disc.phase - phase_map_slab.phase, 'mrad')
phase_map_diff.display('Phase difference of one Pixel (Disc - Slab)')
if __name__ == "__main__":
diff --git a/scripts/compare_discs.py b/scripts/compare_discs.py
deleted file mode 100644
index 15e031d..0000000
--- a/scripts/compare_discs.py
+++ /dev/null
@@ -1,93 +0,0 @@
-#! python
-# -*- coding: utf-8 -*-
-"""Create the Pyramid-Logo."""
-
-
-import pdb
-import traceback
-import sys
-import numpy as np
-from numpy import pi
-import matplotlib.pyplot as plt
-
-import pyramid.magcreator as mc
-import pyramid.projector as pj
-import pyramid.phasemapper as pm
-import pyramid.holoimage as hi
-from pyramid.magdata import MagData
-from pyramid.phasemap import PhaseMap
-
-
-PHI_0 = -2067.83 # magnetic flux in T*nm²
-
-
-def compare_vortices():
- ''' DOCSTRING''' # TODO: Docstring!
- # Input parameters:
- dim_list = [(16, 256, 256), (8, 128, 128), (4, 64, 64), (2, 32, 32), (1, 16, 16)]
- res_list = [1., 2., 4., 8., 16.] # in nm
- density = 20
- phi = pi/2
-
- x = []
- y = []
-
- # Analytic solution:
- L = dim_list[0][1] # in px/nm
- Lz = 0.5 * dim_list[0][0] # in px/nm
- R = 0.25 * L # in px/nm
- x0 = L / 2 # in px/nm
-
- def F(x):
- coeff = - pi * Lz / (2*PHI_0)
- result = coeff * (- (x - x0) * np.sin(phi))
- result *= np.where(np.abs(x - x0) <= R, 1, (R / (x - x0)) ** 2)
- return result
- x_an = np.linspace(0, L, 1000)
- y_an = F(x_an)
-
- # Starting magnetic distribution:
- dim_start = (2*dim_list[0][0], 2*dim_list[0][1], 2*dim_list[0][2])
- res_start = res_list[0] / 2
- center = (dim_start[0]/2 - 0.5, dim_start[1]/2 - 0.5, dim_start[2]/2 - 0.5)
- radius = 0.25 * dim_start[1]
- height = 0.5 * dim_start[0]
- mag_shape = mc.Shapes.disc(dim_start, center, radius, height)
- mag_data = MagData(res_start, mc.create_mag_dist(mag_shape, phi))
-
- for i, (dim, res) in enumerate(zip(dim_list, res_list)):
- # Create coarser grid for the magnetization:
- print 'dim = ', dim, 'res = ', res
- z_mag = mag_data.magnitude[0].reshape(dim[0], 2, dim[1], 2, dim[2], 2)
- y_mag = mag_data.magnitude[1].reshape(dim[0], 2, dim[1], 2, dim[2], 2)
- x_mag = mag_data.magnitude[2].reshape(dim[0], 2, dim[1], 2, dim[2], 2)
- magnitude = (z_mag.mean(axis=5).mean(axis=3).mean(axis=1),
- y_mag.mean(axis=5).mean(axis=3).mean(axis=1),
- x_mag.mean(axis=5).mean(axis=3).mean(axis=1))
- mag_data = MagData(res, magnitude)
- projection = pj.simple_axis_projection(mag_data)
- phase_map = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))
- hi.display_combined(phase_map, density, 'Vortex State, res = {}'.format(res))
- x.append(np.linspace(0, dim[1]*res, dim[1]))
- y.append(phase_map.phase[dim[1]/2, :])
-
- # Plot:
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.plot(x[0], y[0], 'r',
- x[1], y[1], 'm',
- x[2], y[2], 'y',
- x[3], y[3], 'g',
- x[4], y[4], 'c',
- x_an, y_an, 'k')
- axis.set_xlabel('x [nm]')
- axis.set_ylabel('phase')
-
-
-if __name__ == "__main__":
- try:
- compare_vortices()
- except:
- type, value, tb = sys.exc_info()
- traceback.print_exc()
- pdb.post_mortem(tb)
diff --git a/scripts/compare_method_errors_fourier_padding.py b/scripts/compare_method_errors_fourier_padding.py
deleted file mode 100644
index e393d4a..0000000
--- a/scripts/compare_method_errors_fourier_padding.py
+++ /dev/null
@@ -1,102 +0,0 @@
-#! python
-# -*- coding: utf-8 -*-
-"""Compare the different methods to create phase maps."""
-
-
-import time
-import pdb
-import traceback
-import sys
-import numpy as np
-from numpy import pi
-import matplotlib.pyplot as plt
-
-import pyramid.magcreator as mc
-import pyramid.projector as pj
-import pyramid.phasemapper as pm
-import pyramid.analytic as an
-from pyramid.magdata import MagData
-from pyramid.phasemap import PhaseMap
-import shelve
-
-
-def phase_from_mag():
- '''Calculate and display the phase map from a given magnetization.
- Arguments:
- None
- Returns:
- None
-
- '''
- # Create / Open databank:
- data_shelve = shelve.open('../output/method_errors_shelve')
-
- '''FOURIER PADDING->RMS|DURATION'''
- # Parameters:
- b_0 = 1 # in T
- res = 10.0 # in nm
- dim = (1, 128, 128)
- phi = -pi/2
- padding_list = [0, 0.25, 0.5, 0.75, 1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
- 16, 17, 18, 19, 20, 21, 22]
- geometry = 'disc'
- # Create magnetic shape:
- if geometry == 'slab':
- center = (0, dim[1]/2-0.5, dim[2]/2-0.5) # in px (z, y, x) index starts with 0!
- width = (1, dim[1]/2, dim[2]/2) # in px (z, y, x)
- mag_shape = mc.Shapes.slab(dim, center, width)
- phase_ana = an.phase_mag_slab(dim, res, phi, center, width, b_0)
- elif geometry == 'disc':
- center = (0, dim[1]/2-0.5, dim[2]/2-0.5) # in px (z, y, x) index starts with 0!
- radius = dim[1] / 4 # in px
- height = 1 # in px
- mag_shape = mc.Shapes.disc(dim, center, radius, height)
- phase_ana = an.phase_mag_disc(dim, res, phi, center, radius, b_0)
- # Project the magnetization data:
- mag_data = MagData(res, mc.create_mag_dist(mag_shape, phi))
- projection = pj.simple_axis_projection(mag_data)
- # Create data:
- data = np.zeros((3, len(padding_list)))
- data[0, :] = padding_list
- for (i, padding) in enumerate(padding_list):
- print 'padding =', padding_list[i]
- # Key:
- key = ', '.join(['Padding->RMS|duration', 'Fourier', 'padding={}'.format(padding_list[i]),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry={}'.format(geometry)])
- if key in data_shelve:
- data[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection, b_0, padding_list[i])
- data[2, i] = time.time() - start_time
- phase_diff = phase_ana - phase_num
- PhaseMap(res, phase_diff).display()
- data[1, i] = np.std(phase_diff)
- data_shelve[key] = data[:, i]
- # Plot duration against padding:
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.set_yscale('log')
- axis.plot(data[0], data[1])
- axis.set_title('Fourier Space Approach: Variation of the Padding')
- axis.set_xlabel('padding')
- axis.set_ylabel('RMS')
- # Plot RMS against padding:
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.plot(data[0], data[2])
- axis.set_title('Fourier Space Approach: Variation of the Padding')
- axis.set_xlabel('padding')
- axis.set_ylabel('duration [s]')
- # Close shelve:
- data_shelve.close()
-
-
-if __name__ == "__main__":
- try:
- phase_from_mag()
- except:
- type, value, tb = sys.exc_info()
- traceback.print_exc()
- pdb.post_mortem(tb)
diff --git a/scripts/compare_method_errors_res.py b/scripts/compare_method_errors_res.py
deleted file mode 100644
index 7221cd7..0000000
--- a/scripts/compare_method_errors_res.py
+++ /dev/null
@@ -1,551 +0,0 @@
-#! python
-# -*- coding: utf-8 -*-
-"""Compare the different methods to create phase maps."""
-
-
-import time
-import pdb
-import traceback
-import sys
-import numpy as np
-from numpy import pi
-import matplotlib.pyplot as plt
-
-import pyramid.magcreator as mc
-import pyramid.projector as pj
-import pyramid.phasemapper as pm
-import pyramid.analytic as an
-from pyramid.magdata import MagData
-import shelve
-
-
-def compare_method_errors_res():
- '''Calculate and display the phase map from a given magnetization.
- Arguments:
- None
- Returns:
- None
-
- '''
- # Create / Open databank:
- data_shelve = shelve.open('../output/method_errors_shelve')
-
- '''VARY DIMENSIONS FOR ALL APPROACHES'''
-
- b_0 = 1 # in T
- phi = -pi/4
- dim_list = [(1, 4, 4), (1, 8, 8), (1, 16, 16), (1, 32, 32), (1, 64, 64),
- (1, 128, 128), (1, 256, 256), (1, 512, 512)]
- res_list = [64., 32., 16., 8., 4., 2., 1., 0.5, 0.25] # in nm
-
- '''CREATE DATA ARRAYS'''
-
- data_sl_p_fourier0 = np.zeros((3, len(res_list)))
- data_sl_w_fourier0 = np.zeros((3, len(res_list)))
- data_disc_fourier0 = np.zeros((3, len(res_list)))
- data_vort_fourier0 = np.zeros((3, len(res_list)))
-
- data_sl_p_fourier1 = np.zeros((3, len(res_list)))
- data_sl_w_fourier1 = np.zeros((3, len(res_list)))
- data_disc_fourier1 = np.zeros((3, len(res_list)))
- data_vort_fourier1 = np.zeros((3, len(res_list)))
-
- data_sl_p_fourier20 = np.zeros((3, len(res_list)))
- data_sl_w_fourier20 = np.zeros((3, len(res_list)))
- data_disc_fourier20 = np.zeros((3, len(res_list)))
- data_vort_fourier20 = np.zeros((3, len(res_list)))
-
- data_sl_p_real_s = np.zeros((3, len(res_list)))
- data_sl_w_real_s = np.zeros((3, len(res_list)))
- data_disc_real_s = np.zeros((3, len(res_list)))
- data_vort_real_s = np.zeros((3, len(res_list)))
-
- data_sl_p_real_d = np.zeros((3, len(res_list)))
- data_sl_w_real_d = np.zeros((3, len(res_list)))
- data_disc_real_d = np.zeros((3, len(res_list)))
- data_vort_real_d = np.zeros((3, len(res_list)))
-
- '''CREATE DATA ARRAYS'''
-
- data_sl_p_fourier0[0, :] = res_list
- data_sl_w_fourier0[0, :] = res_list
- data_disc_fourier0[0, :] = res_list
- data_vort_fourier0[0, :] = res_list
-
- data_sl_p_fourier1[0, :] = res_list
- data_sl_w_fourier1[0, :] = res_list
- data_disc_fourier1[0, :] = res_list
- data_vort_fourier1[0, :] = res_list
-
- data_sl_p_fourier20[0, :] = res_list
- data_sl_w_fourier20[0, :] = res_list
- data_disc_fourier20[0, :] = res_list
- data_vort_fourier20[0, :] = res_list
-
- data_sl_p_real_s[0, :] = res_list
- data_sl_w_real_s[0, :] = res_list
- data_disc_real_s[0, :] = res_list
- data_vort_real_s[0, :] = res_list
-
- data_sl_p_real_d[0, :] = res_list
- data_sl_w_real_d[0, :] = res_list
- data_disc_real_d[0, :] = res_list
- data_vort_real_d[0, :] = res_list
-
- for i, (dim, res) in enumerate(zip(dim_list, res_list)):
-
- print 'i =', i, ' dim =', str(dim)
-
- '''ANALYTIC SOLUTIONS'''
- # Slab (perfectly aligned):
- center = (0, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
- width = (1, dim[1]/2, dim[2]/2) # in px (z, y, x)
- mag_shape_sl_p = mc.Shapes.slab(dim, center, width)
- phase_ana_sl_p = an.phase_mag_slab(dim, res, phi, center, width, b_0)
- mag_data_sl_p = MagData(res, mc.create_mag_dist(mag_shape_sl_p, phi))
- projection_sl_p = pj.simple_axis_projection(mag_data_sl_p)
- # Slab (worst case):
- center = (0, dim[1]/2, dim[2]/2) # in px (z, y, x) index starts with 0!
- width = (1, dim[1]/2, dim[2]/2) # in px (z, y, x)
- mag_shape_sl_w = mc.Shapes.slab(dim, center, width)
- phase_ana_sl_w = an.phase_mag_slab(dim, res, phi, center, width, b_0)
- mag_data_sl_w = MagData(res, mc.create_mag_dist(mag_shape_sl_w, phi))
- projection_sl_w = pj.simple_axis_projection(mag_data_sl_w)
- # Disc:
- print center
- center = (0, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
- radius = dim[1]/4 # in px
- height = 1 # in px
- mag_shape_disc = mc.Shapes.disc(dim, center, radius, height)
- phase_ana_disc = an.phase_mag_disc(dim, res, phi, center, radius, height, b_0)
- mag_data_disc = MagData(res, mc.create_mag_dist(mag_shape_disc, phi))
- projection_disc = pj.simple_axis_projection(mag_data_disc)
- # Vortex:
- center_vortex = (center[1], center[2])
- mag_shape_vort = mc.Shapes.disc(dim, center, radius, height)
- phase_ana_vort = an.phase_mag_vortex(dim, res, center, radius, height, b_0)
- mag_data_vort = MagData(res, mc.create_mag_dist_vortex(mag_shape_vort, center_vortex))
- projection_vort = pj.simple_axis_projection(mag_data_vort)
-
- '''FOURIER UNPADDED'''
- padding = 0
- # Slab (perfectly aligned):
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=sl_p'])
- if key in data_shelve:
- data_sl_p_fourier0[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_sl_p, b_0, padding)
- data_sl_p_fourier0[2, i] = time.time() - start_time
- phase_diff = phase_ana_sl_p - phase_num
- data_sl_p_fourier0[1, i] = np.std(phase_diff)
- data_shelve[key] = data_sl_p_fourier0[:, i]
- # Slab (worst case):
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=sl_w'])
- if key in data_shelve:
- data_sl_w_fourier0[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_sl_w, b_0, padding)
- data_sl_w_fourier0[2, i] = time.time() - start_time
- phase_diff = phase_ana_sl_w - phase_num
- data_sl_w_fourier0[1, i] = np.std(phase_diff)
- data_shelve[key] = data_sl_w_fourier0[:, i]
- # Disc:
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=disc'])
- if key in data_shelve:
- data_disc_fourier0[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_disc, b_0, padding)
- data_disc_fourier0[2, i] = time.time() - start_time
- phase_diff = phase_ana_disc - phase_num
- data_disc_fourier0[1, i] = np.std(phase_diff)
- data_shelve[key] = data_disc_fourier0[:, i]
- # Vortex:
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=vortex'])
- if key in data_shelve:
- data_vort_fourier0[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_disc, b_0, padding)
- data_vort_fourier0[2, i] = time.time() - start_time
- phase_diff = phase_ana_vort - phase_num
- data_vort_fourier0[1, i] = np.std(phase_diff)
- data_shelve[key] = data_vort_fourier0[:, i]
-
- '''FOURIER PADDED ONCE'''
- padding = 1
- # Slab (perfectly aligned):
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=sl_p'])
- if key in data_shelve:
- data_sl_p_fourier1[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_sl_p, b_0, padding)
- data_sl_p_fourier1[2, i] = time.time() - start_time
- phase_diff = phase_ana_sl_p - phase_num
- data_sl_p_fourier1[1, i] = np.std(phase_diff)
- data_shelve[key] = data_sl_p_fourier1[:, i]
- # Slab (worst case):
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=sl_w'])
- if key in data_shelve:
- data_sl_w_fourier1[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_sl_w, b_0, padding)
- data_sl_w_fourier1[2, i] = time.time() - start_time
- phase_diff = phase_ana_sl_w - phase_num
- data_sl_w_fourier1[1, i] = np.std(phase_diff)
- data_shelve[key] = data_sl_w_fourier1[:, i]
- # Disc:
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=disc'])
- if key in data_shelve:
- data_disc_fourier1[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_disc, b_0, padding)
- data_disc_fourier1[2, i] = time.time() - start_time
- phase_diff = phase_ana_disc - phase_num
- data_disc_fourier1[1, i] = np.std(phase_diff)
- data_shelve[key] = data_disc_fourier1[:, i]
- # Vortex:
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=vortex'])
- if key in data_shelve:
- data_vort_fourier1[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_disc, b_0, padding)
- data_vort_fourier1[2, i] = time.time() - start_time
- phase_diff = phase_ana_vort - phase_num
- data_vort_fourier1[1, i] = np.std(phase_diff)
- data_shelve[key] = data_vort_fourier1[:, i]
-
- '''FOURIER PADDED 20'''
- if dim[1] <= 128:
- padding = 20
- # Slab (perfectly aligned):
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=sl_p'])
- if key in data_shelve:
- data_sl_p_fourier20[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_sl_p, b_0, padding)
- data_sl_p_fourier20[2, i] = time.time() - start_time
- phase_diff = phase_ana_sl_p - phase_num
- data_sl_p_fourier20[1, i] = np.std(phase_diff)
- data_shelve[key] = data_sl_p_fourier20[:, i]
- # Slab (worst case):
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=sl_w'])
- if key in data_shelve:
- data_sl_w_fourier20[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_sl_w, b_0, padding)
- data_sl_w_fourier20[2, i] = time.time() - start_time
- phase_diff = phase_ana_sl_w - phase_num
- data_sl_w_fourier20[1, i] = np.std(phase_diff)
- data_shelve[key] = data_sl_w_fourier20[:, i]
- # Disc:
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=disc'])
- if key in data_shelve:
- data_disc_fourier20[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_disc, b_0, padding)
- data_disc_fourier20[2, i] = time.time() - start_time
- phase_diff = phase_ana_disc - phase_num
- data_disc_fourier20[1, i] = np.std(phase_diff)
- data_shelve[key] = data_disc_fourier20[:, i]
- # Vortex:
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=vortex'])
- if key in data_shelve:
- data_vort_fourier20[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_disc, b_0, padding)
- data_vort_fourier20[2, i] = time.time() - start_time
- phase_diff = phase_ana_vort - phase_num
- data_vort_fourier20[1, i] = np.std(phase_diff)
- data_shelve[key] = data_vort_fourier20[:, i]
-
- '''REAL SLAB'''
- method = 'slab'
- # Slab (perfectly aligned):
- key = ', '.join(['Resolution->RMS|duration', 'Real', 'method={}'.format(method),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=sl_p'])
- if key in data_shelve:
- data_sl_p_real_s[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_real(res, projection_sl_p, method, b_0)
- data_sl_p_real_s[2, i] = time.time() - start_time
- phase_diff = phase_ana_sl_p - phase_num
- data_sl_p_real_s[1, i] = np.std(phase_diff)
- data_shelve[key] = data_sl_p_real_s[:, i]
- # Slab (worst case):
- key = ', '.join(['Resolution->RMS|duration', 'Real', 'method={}'.format(method),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=sl_w'])
- if key in data_shelve:
- data_sl_w_real_s[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_real(res, projection_sl_w, method, b_0)
- data_sl_w_real_s[2, i] = time.time() - start_time
- phase_diff = phase_ana_sl_w - phase_num
- data_sl_w_real_s[1, i] = np.std(phase_diff)
- data_shelve[key] = data_sl_w_real_s[:, i]
- # Disc:
- key = ', '.join(['Resolution->RMS|duration', 'Real', 'method={}'.format(method),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=disc'])
- if key in data_shelve:
- data_disc_real_s[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_real(res, projection_disc, method, b_0)
- data_disc_real_s[2, i] = time.time() - start_time
- phase_diff = phase_ana_disc - phase_num
- data_disc_real_s[1, i] = np.std(phase_diff)
- data_shelve[key] = data_disc_real_s[:, i]
- # Vortex:
- key = ', '.join(['Resolution->RMS|duration', 'Real', 'method={}'.format(method),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=vortex'])
- if key in data_shelve:
- data_disc_real_s[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_real(res, projection_disc, method, b_0)
- data_vort_real_s[2, i] = time.time() - start_time
- phase_diff = phase_ana_vort - phase_num
- data_vort_real_s[1, i] = np.std(phase_diff)
- data_shelve[key] = data_vort_real_s[:, i]
-
- '''REAL DISC'''
- method = 'disc'
- # Slab (perfectly aligned):
- key = ', '.join(['Resolution->RMS|duration', 'Real', 'method={}'.format(method),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=sl_p'])
- if key in data_shelve:
- data_sl_p_real_d[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_real(res, projection_sl_p, method, b_0)
- data_sl_p_real_d[2, i] = time.time() - start_time
- phase_diff = phase_ana_sl_p - phase_num
- data_sl_p_real_d[1, i] = np.std(phase_diff)
- data_shelve[key] = data_sl_p_real_d[:, i]
- # Slab (worst case):
- key = ', '.join(['Resolution->RMS|duration', 'Real', 'method={}'.format(method),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=sl_w'])
- if key in data_shelve:
- data_sl_w_real_d[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_real(res, projection_sl_w, method, b_0)
- data_sl_w_real_d[2, i] = time.time() - start_time
- phase_diff = phase_ana_sl_w - phase_num
- data_sl_w_real_d[1, i] = np.std(phase_diff)
- data_shelve[key] = data_sl_w_real_d[:, i]
- # Disc:
- key = ', '.join(['Resolution->RMS|duration', 'Real', 'method={}'.format(method),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=disc'])
- if key in data_shelve:
- data_disc_real_d[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_real(res, projection_disc, method, b_0)
- data_disc_real_d[2, i] = time.time() - start_time
- phase_diff = phase_ana_disc - phase_num
- data_disc_real_d[1, i] = np.std(phase_diff)
- data_shelve[key] = data_disc_real_d[:, i]
- # Vortex:
- key = ', '.join(['Resolution->RMS|duration', 'Real', 'method={}'.format(method),
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=vortex'])
- if key in data_shelve:
- data_vort_real_d[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_real(res, projection_disc, method, b_0)
- data_vort_real_d[2, i] = time.time() - start_time
- phase_diff = phase_ana_vort - phase_num
- data_vort_real_d[1, i] = np.std(phase_diff)
- data_shelve[key] = data_vort_real_d[:, i]
-
- # Plot duration against res (perfect slab):
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.set_xscale('log')
- axis.set_yscale('log')
- axis.plot(data_sl_p_fourier0[0], data_sl_p_fourier0[1], 'b+',
- data_sl_p_fourier1[0], data_sl_p_fourier1[1], 'bx',
- data_sl_p_fourier20[0], data_sl_p_fourier20[1], 'b*',
- data_sl_p_real_s[0], data_sl_p_real_s[1], 'rs',
- data_sl_p_real_d[0], data_sl_p_real_d[1], 'ro')
- axis.set_title('Variation of the resolution (perfectly adjusted slab)')
- axis.set_xlabel('res [nm]')
- axis.set_ylabel('RMS')
- # Plot RMS against res (perfect slab):
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.set_xscale('log')
- axis.set_yscale('log')
- axis.plot(data_sl_p_fourier0[0], data_sl_p_fourier0[2], 'b+',
- data_sl_p_fourier1[0], data_sl_p_fourier1[2], 'bx',
- data_sl_p_fourier20[0], data_sl_p_fourier20[2], 'b*',
- data_sl_p_real_s[0], data_sl_p_real_s[2], 'rs',
- data_sl_p_real_d[0], data_sl_p_real_d[2], 'ro')
- axis.set_title('Variation of the resolution (perfectly adjusted slab)')
- axis.set_xlabel('res [nm]')
- axis.set_ylabel('duration [s]')
- # Save to file:
- data_sl_p = np.concatenate((data_sl_p_fourier0,
- data_sl_p_fourier1[1:, :],
- data_sl_p_fourier20[1:, :],
- data_sl_p_real_s[1:, :],
- data_sl_p_real_d[1:, :]))
- np.savetxt('../output/data_slab_perfect.txt', data_sl_p.T)
-
- # Plot duration against res (worst case slab):
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.set_xscale('log')
- axis.set_yscale('log')
- axis.plot(data_sl_w_fourier0[0], data_sl_w_fourier0[1], 'b+',
- data_sl_w_fourier1[0], data_sl_w_fourier1[1], 'bx',
- data_sl_w_fourier20[0], data_sl_w_fourier20[1], 'b*',
- data_sl_w_real_s[0], data_sl_w_real_s[1], 'rs',
- data_sl_w_real_d[0], data_sl_w_real_d[1], 'ro')
- axis.set_title('Variation of the resolution (worst case slab)')
- axis.set_xlabel('res [nm]')
- axis.set_ylabel('RMS')
- # Plot RMS against res (worst case slab):
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.set_xscale('log')
- axis.set_yscale('log')
- axis.plot(data_sl_w_fourier0[0], data_sl_w_fourier0[2], 'b+',
- data_sl_w_fourier1[0], data_sl_w_fourier1[2], 'bx',
- data_sl_w_fourier20[0], data_sl_w_fourier20[2], 'b*',
- data_sl_w_real_s[0], data_sl_w_real_s[2], 'rs',
- data_sl_w_real_d[0], data_sl_w_real_d[2], 'ro')
- axis.set_title('Variation of the resolution (worst case slab)')
- axis.set_xlabel('res [nm]')
- axis.set_ylabel('duration [s]')
- # Save to file:
- data_sl_w = np.concatenate((data_sl_w_fourier0,
- data_sl_w_fourier1[1:, :],
- data_sl_w_fourier20[1:, :],
- data_sl_w_real_s[1:, :],
- data_sl_w_real_d[1:, :]))
- np.savetxt('../output/data_slab_worstcase.txt', data_sl_w.T)
-
- # Plot duration against res (disc):
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.set_xscale('log')
- axis.set_yscale('log')
- axis.plot(data_disc_fourier0[0], data_disc_fourier0[1], 'b+',
- data_disc_fourier1[0], data_disc_fourier1[1], 'bx',
- data_disc_fourier20[0], data_disc_fourier20[1], 'b*',
- data_disc_real_s[0], data_disc_real_s[1], 'rs',
- data_disc_real_d[0], data_disc_real_d[1], 'ro')
- axis.set_title('Variation of the resolution (disc)')
- axis.set_xlabel('res [nm]')
- axis.set_ylabel('RMS')
- # Plot RMS against res (disc):
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.set_xscale('log')
- axis.set_yscale('log')
- axis.plot(data_disc_fourier0[0], data_disc_fourier0[2], 'b+',
- data_disc_fourier1[0], data_disc_fourier1[2], 'bx',
- data_disc_fourier20[0], data_disc_fourier20[2], 'b*',
- data_disc_real_s[0], data_disc_real_s[2], 'rs',
- data_disc_real_d[0], data_disc_real_d[2], 'ro')
- axis.set_title('Variation of the resolution (disc)')
- axis.set_xlabel('res [nm]')
- axis.set_ylabel('duration [s]')
- # Save to file:
- data_disc = np.concatenate((data_disc_fourier0,
- data_disc_fourier1[1:, :],
- data_disc_fourier20[1:, :],
- data_disc_real_s[1:, :],
- data_disc_real_d[1:, :]))
- np.savetxt('../output/data_disc.txt', data_disc.T)
-
- # Plot duration against res (vortex):
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.set_xscale('log')
- axis.set_yscale('log')
- axis.plot(data_vort_fourier0[0], data_vort_fourier0[1], 'b+',
- data_vort_fourier1[0], data_vort_fourier1[1], 'bx',
- data_vort_fourier20[0], data_vort_fourier20[1], 'b*',
- data_vort_real_s[0], data_vort_real_s[1], 'rs',
- data_vort_real_d[0], data_vort_real_d[1], 'ro')
- axis.set_title('Variation of the resolution (vortex)')
- axis.set_xlabel('res [nm]')
- axis.set_ylabel('RMS')
- # Plot RMS against res (vort):
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.set_xscale('log')
- axis.set_yscale('log')
- axis.plot(data_vort_fourier0[0], data_vort_fourier0[2], 'b+',
- data_vort_fourier1[0], data_vort_fourier1[2], 'bx',
- data_vort_fourier20[0], data_vort_fourier20[2], 'b*',
- data_vort_real_s[0], data_vort_real_s[2], 'rs',
- data_vort_real_d[0], data_vort_real_d[2], 'ro')
- axis.set_title('Variation of the resolution (vortex)')
- axis.set_xlabel('res [nm]')
- axis.set_ylabel('duration [s]')
- # Save to file:
- data_vort = np.concatenate((data_vort_fourier0,
- data_vort_fourier1[1:, :],
- data_vort_fourier20[1:, :],
- data_vort_real_s[1:, :],
- data_vort_real_d[1:, :]))
- np.savetxt('../output/data_vortex.txt', data_vort.T)
-
- data_shelve.close()
-
-
-if __name__ == "__main__":
- try:
- compare_method_errors_res()
- except:
- type, value, tb = sys.exc_info()
- traceback.print_exc()
- pdb.post_mortem(tb)
diff --git a/scripts/compare_vortices.py b/scripts/compare_vortices.py
deleted file mode 100644
index 7c01f38..0000000
--- a/scripts/compare_vortices.py
+++ /dev/null
@@ -1,98 +0,0 @@
-#! python
-# -*- coding: utf-8 -*-
-"""Create the Pyramid-Logo."""
-
-
-import pdb
-import traceback
-import sys
-import numpy as np
-from numpy import pi
-import matplotlib.pyplot as plt
-
-import pyramid.magcreator as mc
-import pyramid.projector as pj
-import pyramid.phasemapper as pm
-import pyramid.holoimage as hi
-from pyramid.magdata import MagData
-from pyramid.phasemap import PhaseMap
-
-
-PHI_0 = -2067.83 # magnetic flux in T*nm²
-
-
-def compare_vortices():
- '''Calculate and display the Pyramid-Logo.
- Arguments:
- None
- Returns:
- None
-
- '''
- # Input parameters:
- dim_list = [(16, 256, 256), (8, 128, 128), (4, 64, 64), (2, 32, 32), (1, 16, 16)]
- res_list = [1., 2., 4., 8., 16.] # in nm
- density = 20
-
- x = []
- y = []
-
- # Starting magnetic distribution:
- dim_start = (2*dim_list[0][0], 2*dim_list[0][1], 2*dim_list[0][2])
- res_start = res_list[0] / 2
- center = (dim_start[0]/2 - 0.5, dim_start[1]/2 - 0.5, dim_start[2]/2 - 0.5)
- radius = 0.25 * dim_start[1]
- height = 0.5 * dim_start[0]
- mag_shape = mc.Shapes.disc(dim_start, center, radius, height)
- mag_data = MagData(res_start, mc.create_mag_dist_vortex(mag_shape))
-
- # Analytic solution:
- L = dim_list[0][1] # in px/nm
- Lz = 0.5 * dim_list[0][0] # in px/nm
- R = 0.25 * L # in px/nm
- x0 = L / 2 # in px/nm
-
- def F(x):
- coeff = pi*Lz/PHI_0
- result = coeff * np.where(np.abs(x - x0) <= R, (np.abs(x-x0)-R), 0)
- return result
- x_an = np.linspace(0, L, 1001)
- y_an = F(x_an)
-
- for i, (dim, res) in enumerate(zip(dim_list, res_list)):
- # Create coarser grid for the magnetization:
- print 'dim = ', dim, 'res = ', res
- z_mag = mag_data.magnitude[0].reshape(dim[0], 2, dim[1], 2, dim[2], 2)
- y_mag = mag_data.magnitude[1].reshape(dim[0], 2, dim[1], 2, dim[2], 2)
- x_mag = mag_data.magnitude[2].reshape(dim[0], 2, dim[1], 2, dim[2], 2)
- magnitude = (z_mag.mean(axis=5).mean(axis=3).mean(axis=1),
- y_mag.mean(axis=5).mean(axis=3).mean(axis=1),
- x_mag.mean(axis=5).mean(axis=3).mean(axis=1))
- mag_data = MagData(res, magnitude)
- #mag_data.quiver_plot()
- projection = pj.simple_axis_projection(mag_data)
- phase_map = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))
- hi.display_combined(phase_map, density, 'Vortex State, res = {}'.format(res))
- x.append(np.linspace(0, dim[1]*res, dim[1]))
- y.append(phase_map.phase[dim[1]/2, :])
-
- # Plot:
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.plot(x[0], y[0], 'r',
- x[1], y[1], 'm',
- x[2], y[2], 'y',
- x[3], y[3], 'g',
- x[4], y[4], 'c',
- x_an, y_an, 'k')
- axis.set_xlabel('x [nm]')
- axis.set_ylabel('phase')
-
-
-if __name__ == "__main__":
- try:
- compare_vortices()
- except:
- type, value, tb = sys.exc_info()
- traceback.print_exc()
- pdb.post_mortem(tb)
diff --git a/scripts/create_alternating_filaments.py b/scripts/create distributions/create_alternating_filaments.py
similarity index 61%
rename from scripts/create_alternating_filaments.py
rename to scripts/create distributions/create_alternating_filaments.py
index a07706a..3c40730 100644
--- a/scripts/create_alternating_filaments.py
+++ b/scripts/create distributions/create_alternating_filaments.py
@@ -6,7 +6,8 @@
import pdb
import traceback
import sys
-import numpy as np
+import os
+
from numpy import pi
import pyramid.magcreator as mc
@@ -21,25 +22,27 @@ def create_alternating_filaments():
None
'''
+ directory = '../../output/magnetic distributions'
+ if not os.path.exists(directory):
+ os.makedirs(directory)
# Input parameters:
- filename = '../output/mag_dist_alt_filaments.txt'
+ filename = directory + '/mag_dist_alt_filaments.txt'
dim = (1, 21, 21) # in px (z, y, x)
res = 10.0 # in nm
phi = pi/2
spacing = 5
- # Create lists for magnetic objects:
+ # Create empty MagData object:
+ mag_data = MagData(res)
count = int((dim[1]-1) / spacing) + 1
- mag_shape_list = np.zeros((count,) + dim)
- phi_list = np.zeros(count)
for i in range(count):
pos = i * spacing
- mag_shape_list[i] = mc.Shapes.filament(dim, (0, pos))
- phi_list[i] = (1-2*(int(pos/spacing) % 2)) * phi
- # Create magnetic distribution
- magnitude = mc.create_mag_dist_comb(mag_shape_list, phi_list)
- mag_data = MagData(res, magnitude)
+ mag_shape = mc.Shapes.filament(dim, (0, pos))
+ mag_data.add_magnitude(mc.create_mag_dist_homog(mag_shape, phi))
+ phi *= -1 # Switch the angle
+ # Plot magnetic distribution
mag_data.quiver_plot()
mag_data.save_to_llg(filename)
+# print np.max(mag_data.magnitude)
if __name__ == "__main__":
diff --git a/scripts/create_logo.py b/scripts/create distributions/create_logo.py
similarity index 91%
rename from scripts/create_logo.py
rename to scripts/create distributions/create_logo.py
index bf763f0..f800275 100644
--- a/scripts/create_logo.py
+++ b/scripts/create distributions/create_logo.py
@@ -6,6 +6,7 @@
import pdb
import traceback
import sys
+
import numpy as np
from numpy import pi
@@ -40,7 +41,7 @@ def create_logo():
right = np.fliplr(left)
mag_shape[0, ...] = np.logical_and(np.logical_and(left, right), bottom)
# Create magnetic data, project it, get the phase map and display the holography image:
- mag_data = MagData(res, mc.create_mag_dist(mag_shape, phi))
+ mag_data = MagData(res, mc.create_mag_dist_homog(mag_shape, phi))
mag_data.quiver_plot()
projection = pj.simple_axis_projection(mag_data)
phase_map = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))
diff --git a/scripts/create_multiple_samples.py b/scripts/create distributions/create_multiple_samples.py
similarity index 68%
rename from scripts/create_multiple_samples.py
rename to scripts/create distributions/create_multiple_samples.py
index c353aed..9590e78 100644
--- a/scripts/create_multiple_samples.py
+++ b/scripts/create distributions/create_multiple_samples.py
@@ -1,11 +1,12 @@
# -*- coding: utf-8 -*-
"""Create random magnetic distributions."""
-import random as rnd
+
import pdb
import traceback
import sys
-import numpy as np
+import os
+
from numpy import pi
import pyramid.magcreator as mc
@@ -24,7 +25,11 @@ def create_multiple_samples():
None
'''
- filename = '../output/mag_dist_multiple_samples.txt'
+ directory = '../../output/magnetic distributions'
+ if not os.path.exists(directory):
+ os.makedirs(directory)
+ # Input parameters:
+ filename = directory + '/mag_dist_multiple_samples.txt'
res = 10.0 # nm
dim = (64, 128, 128)
# Slab:
@@ -40,13 +45,13 @@ def create_multiple_samples():
center = (32, 96, 64) # in px (z, y, x), index starts with 0!
radius = 24 # in px
mag_shape_sphere = mc.Shapes.sphere(dim, center, radius)
- # Create lists for magnetic objects:
- mag_shape_list = [mag_shape_slab, mag_shape_disc, mag_shape_sphere]
- phi_list = [pi/4, pi/2, pi]
- # Create magnetic distribution:
- magnitude = mc.create_mag_dist_comb(mag_shape_list, phi_list)
- mag_data = MagData(res, magnitude)
- mag_data.quiver_plot('z', dim[0]/2)
+ # Create empty MagData object and add magnetized objects:
+ mag_data = MagData(res)
+ mag_data.add_magnitude(mc.create_mag_dist_homog(mag_shape_slab, pi/4))
+ mag_data.add_magnitude(mc.create_mag_dist_homog(mag_shape_disc, pi/2))
+ mag_data.add_magnitude(mc.create_mag_dist_homog(mag_shape_sphere, pi))
+ # Plot the magnetic distribution, phase map and holographic contour map:
+ mag_data.quiver_plot()
mag_data.save_to_llg(filename)
projection = pj.simple_axis_projection(mag_data)
phase_map = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))
diff --git a/scripts/create_random_pixels.py b/scripts/create distributions/create_random_pixels.py
similarity index 62%
rename from scripts/create_random_pixels.py
rename to scripts/create distributions/create_random_pixels.py
index a52e686..e6eea7a 100644
--- a/scripts/create_random_pixels.py
+++ b/scripts/create distributions/create_random_pixels.py
@@ -5,6 +5,8 @@ import random as rnd
import pdb
import traceback
import sys
+import os
+
import numpy as np
from numpy import pi
@@ -24,25 +26,27 @@ def create_random_pixels():
None
'''
+ directory = '../../output/magnetic distributions'
+ if not os.path.exists(directory):
+ os.makedirs(directory)
+ # Input parameters:
+ filename = directory + '/mag_dist_random_pixels.txt'
# Input parameters:
count = 10
dim = (1, 128, 128)
res = 10 # in nm
rnd.seed(12)
- # Create lists for magnetic objects:
- mag_shape_list = np.zeros((count,) + dim)
- phi_list = np.zeros(count)
- magnitude_list = np.zeros(count)
+ # Create empty MagData object and add pixels:
+ mag_data = MagData(res)
for i in range(count):
pixel = (rnd.randrange(dim[0]), rnd.randrange(dim[1]), rnd.randrange(dim[2]))
- mag_shape_list[i, ...] = mc.Shapes.pixel(dim, pixel)
- phi_list[i] = 2 * pi * rnd.random()
- magnitude_list[i] = 1 # TODO: rnd.random()
- # Create magnetic distribution:
- magnitude = mc.create_mag_dist_comb(mag_shape_list, phi_list, magnitude_list)
- mag_data = MagData(res, magnitude)
+ mag_shape = mc.Shapes.pixel(dim, pixel)
+ phi = 2 * pi * rnd.random()
+ magnitude = 1 # TODO: rnd.random()
+ mag_data.add_magnitude(mc.create_mag_dist_homog(mag_shape, phi, magnitude=magnitude))
+ # Plot magnetic distribution, phase map and holographic contour map:
mag_data.quiver_plot()
- mag_data.save_to_llg('../output/mag_dist_random_pixels.txt')
+ mag_data.save_to_llg(filename)
projection = pj.simple_axis_projection(mag_data)
phase_map = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))
hi.display(hi.holo_image(phase_map, 10))
diff --git a/scripts/create_random_slabs.py b/scripts/create distributions/create_random_slabs.py
similarity index 66%
rename from scripts/create_random_slabs.py
rename to scripts/create distributions/create_random_slabs.py
index 03960f2..c54b27c 100644
--- a/scripts/create_random_slabs.py
+++ b/scripts/create distributions/create_random_slabs.py
@@ -5,6 +5,8 @@ import random as rnd
import pdb
import traceback
import sys
+import os
+
import numpy as np
from numpy import pi
@@ -24,29 +26,30 @@ def create_random_slabs():
None
'''
+ directory = '../../output/magnetic distributions'
+ if not os.path.exists(directory):
+ os.makedirs(directory)
# Input parameters:
+ filename = directory + '/mag_dist_random_pixels.txt'
count = 10
dim = (1, 128, 128)
res = 10 # in nm
rnd.seed(42)
w_max = 10
- # Create lists for magnetic objects:
- mag_shape_list = np.zeros((count,) + dim)
- phi_list = np.zeros(count)
- magnitude_list = np.zeros(count)
+ # Create empty MagData object and add slabs:
+ mag_data = MagData(res)
for i in range(count):
width = (1, rnd.randint(1, w_max), rnd.randint(1, w_max))
center = (rnd.randrange(int(width[0]/2), dim[0]-int(width[0]/2)),
rnd.randrange(int(width[1]/2), dim[1]-int(width[1]/2)),
rnd.randrange(int(width[2]/2), dim[2]-int(width[2]/2)))
- mag_shape_list[i, ...] = mc.Shapes.slab(dim, center, width)
- phi_list[i] = 2 * pi * rnd.random()
- magnitude_list[i] = 1 # TODO: rnd.random()
- # Create magnetic distribution:
- magnitude = mc.create_mag_dist_comb(mag_shape_list, phi_list, magnitude_list)
- mag_data = MagData(res, magnitude)
+ mag_shape = mc.Shapes.slab(dim, center, width)
+ phi = 2 * pi * rnd.random()
+ magnitude = 1 # TODO: rnd.random()
+ mag_data.add_magnitude(mc.create_mag_dist_homog(mag_shape, phi, magnitude=magnitude))
+ # Plot magnetic distribution, phase map and holographic contour map:
mag_data.quiver_plot()
- mag_data.save_to_llg('../output/mag_dist_random_slabs.txt')
+ mag_data.save_to_llg(filename)
projection = pj.simple_axis_projection(mag_data)
phase_map = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))
hi.display(hi.holo_image(phase_map, 10))
diff --git a/scripts/create_sample.py b/scripts/create distributions/create_sample.py
similarity index 75%
rename from scripts/create_sample.py
rename to scripts/create distributions/create_sample.py
index 1ee772e..e2471c6 100644
--- a/scripts/create_sample.py
+++ b/scripts/create distributions/create_sample.py
@@ -5,6 +5,8 @@
import pdb
import traceback
import sys
+import os
+
from numpy import pi
import pyramid.magcreator as mc
@@ -19,14 +21,18 @@ def create_sample():
None
'''
+
+ directory = '../../output/magnetic distributions'
+ if not os.path.exists(directory):
+ os.makedirs(directory)
# Input parameters:
- key = 'slab'
- filename = '../output/mag_dist_' + key + '.txt'
- dim = (1, 128, 128) # in px (z, y, x)
+ key = 'sphere'
+ filename = directory + '/mag_dist_' + key + '.txt'
+ dim = (128, 128, 128) # in px (z, y, x)
res = 10.0 # in nm
phi = pi/4
# Geometry parameters:
- center = (0, 64, 64) # in px (z, y, x), index starts with 0!
+ center = (64, 64, 64) # in px (z, y, x), index starts with 0!
width = (1, 50, 50) # in px (z, y, x)
radius = 25 # in px
height = 1 # in px
@@ -44,7 +50,7 @@ def create_sample():
elif key == 'pixel':
mag_shape = mc.Shapes.pixel(dim, pixel)
# Create magnetic distribution
- magnitude = mc.create_mag_dist(mag_shape, phi)
+ magnitude = mc.create_mag_dist_homog(mag_shape, phi)
mag_data = MagData(res, magnitude)
mag_data.quiver_plot()
mag_data.save_to_llg(filename)
diff --git a/scripts/create_vortex.py b/scripts/create distributions/create_vortex.py
similarity index 85%
rename from scripts/create_vortex.py
rename to scripts/create distributions/create_vortex.py
index 4fa8ad6..e96ea13 100644
--- a/scripts/create_vortex.py
+++ b/scripts/create distributions/create_vortex.py
@@ -5,6 +5,8 @@
import pdb
import traceback
import sys
+import os
+
import matplotlib.pyplot as plt
import pyramid.magcreator as mc
@@ -23,8 +25,11 @@ def create_vortex():
None
'''
+ directory = '../../output/magnetic distributions'
+ if not os.path.exists(directory):
+ os.makedirs(directory)
# Input parameters:
- filename = '../output/mag_dist_vortex.txt'
+ filename = directory + '/mag_dist_vortex.txt'
res = 10.0 # in nm
density = 1
dim = (1, 128, 128)
diff --git a/scripts/gui_create_logo.py b/scripts/gui/gui_create_logo.py
similarity index 94%
rename from scripts/gui_create_logo.py
rename to scripts/gui/gui_create_logo.py
index 45432c2..c7b7e52 100644
--- a/scripts/gui_create_logo.py
+++ b/scripts/gui/gui_create_logo.py
@@ -59,7 +59,7 @@ class CreateLogoWidget(QtGui.QWidget, Ui_CreateLogoWidget):
# Call parent constructor
QtGui.QWidget.__init__(self)
self.setupUi(self)
- self.ui = uic.loadUi('gui/create_logo.ui')
+ self.ui = uic.loadUi('create_logo.ui')
# self.setCentralWidget(self.ui)
# Connect Widgets with locally defined functions:
self.connect(self.logoPushButton, QtCore.SIGNAL('clicked()'), self.buttonPushed)
@@ -120,7 +120,7 @@ def create_logo(dim, axis):
right = np.fliplr(left)
mag_shape[0, ...] = np.logical_and(np.logical_and(left, right), bottom)
# Create magnetic data, project it, get the phase map and display the holography image:
- mag_data = MagData(res, mc.create_mag_dist(mag_shape, phi))
+ mag_data = MagData(res, mc.create_mag_dist_homog(mag_shape, phi))
projection = pj.simple_axis_projection(mag_data)
phase_map = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))
hi.display(hi.holo_image(phase_map, density), 'PYRAMID - LOGO', axis)
diff --git a/scripts/paper 1/ch5-0-evaluation_and_comparison.py b/scripts/paper 1/ch5-0-evaluation_and_comparison.py
index f9f6773..7c12cb5 100644
--- a/scripts/paper 1/ch5-0-evaluation_and_comparison.py
+++ b/scripts/paper 1/ch5-0-evaluation_and_comparison.py
@@ -4,6 +4,8 @@ Created on Fri Jul 26 14:37:20 2013
@author: Jan
"""
+
+
import sys
import traceback
import pdb
@@ -20,7 +22,7 @@ import matplotlib.pyplot as plt
def run():
-
+
print '\nACCESS SHELVE'
# Create / Open databank:
directory = '../../output/paper 1'
@@ -42,41 +44,41 @@ def run():
phi = pi/2
dim = (32, 256, 256) # in px (z, y, x)
# Create magnetic shape:
- center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
+ center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts at 0!
radius = dim[1]/4 # in px
height = dim[0]/2 # in px
mag_shape = mc.Shapes.disc(dim, center, radius, height)
print '--CREATE MAGN. DISTR. OF HOMOG. MAG. DISC'
- mag_data_disc = MagData(res, mc.create_mag_dist(mag_shape, phi))
+ mag_data_disc = MagData(res, mc.create_mag_dist_homog(mag_shape, phi))
mag_data_disc.scale_down(3)
print '--CREATE MAGN. DISTR. OF VORTEX STATE DISC'
mag_data_vort = MagData(res, mc.create_mag_dist_vortex(mag_shape, center))
mag_data_vort.scale_down(3)
- # Mayavi-Plots
- mag_data_disc.quiver_plot3d()
+ # Mayavi-Plots:
+ mag_data_disc.quiver_plot3d()
mag_data_vort.quiver_plot3d()
print '--SHELVE MAGNETIC DISTRIBUTIONS'
data_shelve[key] = (mag_data_disc, mag_data_vort)
-
+
print '--PLOT/SAVE MAGNETIC DISTRIBUTIONS'
fig, axes = plt.subplots(1, 2, figsize=(16, 7))
fig.suptitle('Magnetic Distributions', fontsize=20)
# Plot MagData (Disc):
- mag_data_disc.quiver_plot('Homog. magn. disc', axis = axes[0])
+ mag_data_disc.quiver_plot('Homog. magn. disc', axis=axes[0])
axes[0].set_aspect('equal')
# Plot MagData (Disc):
- mag_data_vort.quiver_plot('Vortex state disc', axis = axes[1])
+ mag_data_vort.quiver_plot('Vortex state disc', axis=axes[1])
axes[1].set_aspect('equal')
# Save Plots:
plt.figtext(0.15, 0.15, 'a)', fontsize=30)
plt.figtext(0.57, 0.15, 'b)', fontsize=30)
plt.savefig(directory + '/ch5-0-magnetic_distributions.png', bbox_inches='tight')
-
+
###############################################################################################
print 'CLOSING SHELVE\n'
# Close shelve:
data_shelve.close()
-
+
###############################################################################################
if __name__ == "__main__":
diff --git a/scripts/paper 1/ch5-1-evaluation_real_space.py b/scripts/paper 1/ch5-1-evaluation_real_space.py
index 430b9b3..2bf7b23 100644
--- a/scripts/paper 1/ch5-1-evaluation_real_space.py
+++ b/scripts/paper 1/ch5-1-evaluation_real_space.py
@@ -4,6 +4,8 @@ Created on Fri Jul 26 14:37:30 2013
@author: Jan
"""
+
+
import pdb
import traceback
import sys
@@ -48,6 +50,7 @@ def run():
res = 0.125 # in nm
phi = pi/2
dim = (128, 1024, 1024) # in px (z, y, x)
+ density = 100
# Create magnetic shape:
center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
radius = dim[1]/4 # in px
@@ -56,18 +59,18 @@ def run():
# Get analytic solution:
phase_ana_disc = an.phase_mag_disc(dim, res, phi, center, radius, height)
phase_ana_vort = an.phase_mag_vortex(dim, res, center, radius, height)
- phase_map_ana_disc = PhaseMap(res, phase_ana_disc*1E3) # in mrad -> *1000
- phase_map_ana_vort = PhaseMap(res, phase_ana_vort*1E3) # in mrad -> *1000
+ phase_map_ana_disc = PhaseMap(res, phase_ana_disc)
+ phase_map_ana_vort = PhaseMap(res, phase_ana_vort)
print '--PLOT/SAVE ANALYTIC SOLUTIONS'
- hi.display_combined(phase_map_ana_disc, 0.1, 'Analytic solution: hom. magn. disc', 'bilinear',
- labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
+ hi.display_combined(phase_map_ana_disc, density,
+ 'Analytic solution: hom. magn. disc', 'bilinear')
axis = plt.gcf().add_subplot(1, 2, 2, aspect='equal')
axis.axhline(y=512, linewidth=3, linestyle='--', color='r')
plt.figtext(0.15, 0.2, 'a)', fontsize=30, color='w')
plt.figtext(0.52, 0.2, 'b)', fontsize=30)
plt.savefig(directory + '/ch5-1-analytic_solution_disc.png', bbox_inches='tight')
- hi.display_combined(phase_map_ana_vort, 0.1, 'Analytic solution: vortex state', 'bilinear',
- labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
+ hi.display_combined(phase_map_ana_vort, density,
+ 'Analytic solution: vortex state', 'bilinear')
axis = plt.gcf().add_subplot(1, 2, 2, aspect='equal')
axis.axhline(y=512, linewidth=3, linestyle='--', color='r')
plt.figtext(0.15, 0.2, 'c)', fontsize=30, color='w')
@@ -80,17 +83,17 @@ def run():
###############################################################################################
print 'CH5-1 PHASE SLICES REAL SPACE'
-
+
# Input parameters:
res = 0.25 # in nm
phi = pi/2
- density = 0.1 # Because phase is in mrad -> amplification by 100 (0.001 * 100 = 0.1)
+ density = 100
dim = (64, 512, 512) # in px (z, y, x)
# Create magnetic shape:
center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
radius = dim[1]/4 # in px
height = dim[0]/2 # in px
-
+
key = 'ch5-1-phase_slices_real'
if key in data_shelve:
print '--LOAD MAGNETIC DISTRIBUTION'
@@ -98,7 +101,7 @@ def run():
else:
print '--CREATE MAGNETIC DISTRIBUTION'
mag_shape = mc.Shapes.disc(dim, center, radius, height)
-
+
print '--CREATE PHASE SLICES HOMOG. MAGN. DISC'
# Arrays for plotting:
x_d = []
@@ -109,32 +112,31 @@ def run():
Lz = 0.5 * dim[0] * res # in px/nm
R = 0.25 * L # in px/nm
x0 = L / 2 # in px/nm
-
+
def F_disc(x):
coeff = - pi * Lz / (2*PHI_0) * 1E3 # in mrad -> *1000
result = coeff * (- (x - x0) * np.sin(phi))
result *= np.where(np.abs(x - x0) <= R, 1, (R / (x - x0)) ** 2)
return result
-
+
x_d.append(np.linspace(0, L, 5000))
y_d.append(F_disc(x_d[0]))
dy_d.append(np.zeros_like(x_d[0]))
# Create MagData (Disc):
- mag_data_disc = MagData(res, mc.create_mag_dist(mag_shape, phi))
+ mag_data_disc = MagData(res, mc.create_mag_dist_homog(mag_shape, phi))
for i in range(5):
mag_data_disc.scale_down()
print '----res =', mag_data_disc.res, 'nm', 'dim =', mag_data_disc.dim
projection = pj.simple_axis_projection(mag_data_disc)
- phase_map = PhaseMap(mag_data_disc.res,
- pm.phase_mag_real(mag_data_disc.res, projection, 'slab') * 1E3)
- hi.display_combined(phase_map, density, 'Disc, res = {} nm'.format(mag_data_disc.res),
- labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
- x_d.append(np.linspace(mag_data_disc.res * 0.5,
- mag_data_disc.res * (mag_data_disc.dim[1]-0.5),
+ phase_map = PhaseMap(mag_data_disc.res,
+ pm.phase_mag_real(mag_data_disc.res, projection, 'slab'))
+ hi.display_combined(phase_map, density, 'Disc, res = {} nm'.format(mag_data_disc.res))
+ x_d.append(np.linspace(mag_data_disc.res * 0.5,
+ mag_data_disc.res * (mag_data_disc.dim[1]-0.5),
mag_data_disc.dim[1]))
slice_pos = int(mag_data_disc.dim[1]/2)
- y_d.append(phase_map.phase[slice_pos, :])
- dy_d.append(phase_map.phase[slice_pos, :] - F_disc(x_d[-1]))
+ y_d.append(phase_map.phase[slice_pos, :]*1E3) # *1E3: rad to mrad
+ dy_d.append(phase_map.phase[slice_pos, :]*1E3 - F_disc(x_d[-1])) # *1E3: rad to mrad
print '--CREATE PHASE SLICES VORTEX STATE DISC'
x_v = []
@@ -145,12 +147,12 @@ def run():
Lz = 0.5 * dim[0] * res # in px/nm
R = 0.25 * L # in px/nm
x0 = L / 2 # in px/nm
-
+
def F_vort(x):
coeff = pi*Lz/PHI_0 * 1E3 # in mrad -> *1000
result = coeff * np.where(np.abs(x - x0) <= R, (np.abs(x-x0)-R), 0)
return result
-
+
x_v.append(np.linspace(0, L, 5001))
y_v.append(F_vort(x_v[0]))
dy_v.append(np.zeros_like(x_v[0]))
@@ -160,16 +162,15 @@ def run():
mag_data_vort.scale_down()
print '----res =', mag_data_vort.res, 'nm', 'dim =', mag_data_vort.dim
projection = pj.simple_axis_projection(mag_data_vort)
- phase_map = PhaseMap(mag_data_vort.res,
- pm.phase_mag_real(mag_data_vort.res, projection, 'slab') * 1E3)
- hi.display_combined(phase_map, density, 'Disc, res = {} nm'.format(mag_data_vort.res),
- labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
- x_v.append(np.linspace(mag_data_vort.res * 0.5,
- mag_data_vort.res * (mag_data_vort.dim[1]-0.5),
+ phase_map = PhaseMap(mag_data_vort.res,
+ pm.phase_mag_real(mag_data_vort.res, projection, 'slab'))
+ hi.display_combined(phase_map, density, 'Disc, res = {} nm'.format(mag_data_vort.res))
+ x_v.append(np.linspace(mag_data_vort.res * 0.5,
+ mag_data_vort.res * (mag_data_vort.dim[1]-0.5),
mag_data_vort.dim[1]))
slice_pos = int(mag_data_vort.dim[1]/2)
- y_v.append(phase_map.phase[int(mag_data_vort.dim[1]/2), :])
- dy_v.append(phase_map.phase[slice_pos, :] - F_vort(x_v[-1]))
+ y_v.append(phase_map.phase[slice_pos, :]*1E3) # *1E3: rad to mrad
+ dy_v.append(phase_map.phase[slice_pos, :]*1E3 - F_vort(x_v[-1])) # *1E3: rad to mrad
# Shelve x, y and dy:
print '--SAVE PHASE SLICES'
@@ -197,7 +198,7 @@ def run():
zoom = (23.5, 160, 15, 40)
rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
axes[0].add_patch(rect)
- axes[0].arrow(zoom[0]+zoom[2], zoom[1]+zoom[3]/2, 36, 0, length_includes_head=True,
+ axes[0].arrow(zoom[0]+zoom[2], zoom[1]+zoom[3]/2, 36, 0, length_includes_head=True,
head_width=10, head_length=4, fc='k', ec='k')
# Plot zoom inset:
ins_axis_d = plt.axes([0.33, 0.57, 0.14, 0.3])
@@ -210,7 +211,7 @@ def run():
ins_axis_d.tick_params(axis='both', which='major', labelsize=14)
ins_axis_d.set_xlim(zoom[0], zoom[0]+zoom[2])
ins_axis_d.set_ylim(zoom[1], zoom[1]+zoom[3])
- ins_axis_d.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
+ ins_axis_d.xaxis.set_major_locator(MaxNLocator(nbins=4, integer=True))
ins_axis_d.yaxis.set_major_locator(MaxNLocator(nbins=3))
print '--PLOT/SAVE PHASE SLICES VORTEX STATE DISC'
@@ -232,7 +233,7 @@ def run():
zoom = (59, 340, 10, 55)
rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
axes[1].add_patch(rect)
- axes[1].arrow(zoom[0]+zoom[2]/2, zoom[1], 0, -193, length_includes_head=True,
+ axes[1].arrow(zoom[0]+zoom[2]/2, zoom[1], 0, -193, length_includes_head=True,
head_width=2, head_length=20, fc='k', ec='k')
# Plot zoom inset:
ins_axis_v = plt.axes([0.695, 0.15, 0.075, 0.3])
@@ -245,14 +246,14 @@ def run():
ins_axis_v.tick_params(axis='both', which='major', labelsize=14)
ins_axis_v.set_xlim(zoom[0], zoom[0]+zoom[2])
ins_axis_v.set_ylim(zoom[1], zoom[1]+zoom[3])
- ins_axis_v.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
+ ins_axis_v.xaxis.set_major_locator(MaxNLocator(nbins=4, integer=True))
ins_axis_v.yaxis.set_major_locator(MaxNLocator(nbins=4))
-
+
plt.show()
plt.figtext(0.15, 0.13, 'a)', fontsize=30)
plt.figtext(0.57, 0.13, 'b)', fontsize=30)
plt.savefig(directory + '/ch5-1-phase_slice_comparison.png', bbox_inches='tight')
-
+
# Create figure:
fig, axes = plt.subplots(1, 2, figsize=(16, 7))
fig.suptitle('Central phase slice errors', fontsize=20)
@@ -290,7 +291,7 @@ def run():
plt.figtext(0.15, 0.13, 'a)', fontsize=30)
plt.figtext(0.57, 0.13, 'b)', fontsize=30)
plt.savefig(directory + '/ch5-1-phase_slice_errors.png', bbox_inches='tight')
-
+
###############################################################################################
print 'CH5-1 PHASE DIFFERENCES REAL SPACE'
@@ -316,7 +317,7 @@ def run():
height_big = dim_big[0]/2 # in px
mag_shape = mc.Shapes.disc(dim_big, center_big, radius_big, height_big)
# Create MagData (4 times the size):
- mag_data_disc = MagData(res_big, mc.create_mag_dist(mag_shape, phi))
+ mag_data_disc = MagData(res_big, mc.create_mag_dist_homog(mag_shape, phi))
mag_data_vort = MagData(res_big, mc.create_mag_dist_vortex(mag_shape, center_big))
# Scale mag_data, resolution and dimensions:
mag_data_disc.scale_down()
@@ -337,11 +338,11 @@ def run():
norm = BoundaryNorm(bounds, RdBu.N)
# Calculations (Disc):
phase_num_disc = pm.phase_mag_real(res, projection_disc, 'slab')
- phase_diff_disc = PhaseMap(res, (phase_num_disc-phase_ana_disc)*1E3) # in mrad -> *1000)
+ phase_diff_disc = PhaseMap(res, (phase_num_disc-phase_ana_disc), 'mrad')
RMS_disc = np.sqrt(np.mean(phase_diff_disc.phase**2))
# Calculations (Vortex):
phase_num_vort = pm.phase_mag_real(res, projection_vort, 'slab')
- phase_diff_vort = PhaseMap(res, (phase_num_vort-phase_ana_vort)*1E3) # in mrad -> *1000
+ phase_diff_vort = PhaseMap(res, (phase_num_vort-phase_ana_vort), 'mrad')
RMS_vort = np.sqrt(np.mean(phase_diff_vort.phase**2))
print '--PLOT/SAVE PHASE DIFFERENCES'
@@ -349,12 +350,10 @@ def run():
fig.suptitle('Difference of the real space approach from the analytical solution', fontsize=20)
# Plot MagData (Disc):
phase_diff_disc.display('Homog. magn. disc, RMS = {:3.2f} mrad'.format(RMS_disc),
- labels=('x-axis [nm]', 'y-axis [nm]', '$\Delta$phase [mrad]'),
limit=np.max(bounds), norm=norm, axis=axes[0])
axes[0].set_aspect('equal')
# Plot MagData (Disc):
phase_diff_vort.display('Vortex state disc, RMS = {:3.2f} mrad'.format(RMS_vort),
- labels=('x-axis [nm]', 'y-axis [nm]', '$\Delta$phase [mrad]'),
limit=np.max(bounds), norm=norm, axis=axes[1])
axes[1].set_aspect('equal')
# Save Plots:
@@ -366,7 +365,7 @@ def run():
print 'CLOSING SHELVE\n'
# Close shelve:
data_shelve.close()
-
+
###############################################################################################
@@ -377,4 +376,3 @@ if __name__ == "__main__":
type, value, tb = sys.exc_info()
traceback.print_exc()
pdb.post_mortem(tb)
-
diff --git a/scripts/paper 1/ch5-2-evaluation_fourier_space.py b/scripts/paper 1/ch5-2-evaluation_fourier_space.py
index b103fd9..13f4e2f 100644
--- a/scripts/paper 1/ch5-2-evaluation_fourier_space.py
+++ b/scripts/paper 1/ch5-2-evaluation_fourier_space.py
@@ -1,5 +1,9 @@
# -*- coding: utf-8 -*-
-"""Compare the different methods to create phase maps."""
+"""
+Created on Fri Jul 26 14:37:30 2013
+
+@author: Jan
+"""
import time
@@ -25,7 +29,6 @@ import matplotlib.pyplot as plt
from matplotlib.colors import BoundaryNorm
from matplotlib.ticker import MaxNLocator
from matplotlib.cm import RdBu
-from matplotlib.patches import Rectangle
PHI_0 = -2067.83 # magnetic flux in T*nm²
@@ -42,17 +45,17 @@ def run():
###############################################################################################
print 'CH5-1 PHASE SLICES FOURIER SPACE'
-
+
# Input parameters:
res = 0.25 # in nm
phi = pi/2
- density = 0.1 # Because phase is in mrad -> amplification by 100 (0.001 * 100 = 0.1)
+ density = 100
dim = (64, 512, 512) # in px (z, y, x)
# Create magnetic shape:
center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
radius = dim[1]/4 # in px
height = dim[0]/2 # in px
-
+
key = 'ch5-2-phase_slices_fourier'
if key in data_shelve:
print '--LOAD MAGNETIC DISTRIBUTION'
@@ -60,7 +63,7 @@ def run():
else:
print '--CREATE MAGNETIC DISTRIBUTION'
mag_shape = mc.Shapes.disc(dim, center, radius, height)
-
+
print '--CREATE PHASE SLICES HOMOG. MAGN. DISC'
# Arrays for plotting:
x_d = []
@@ -73,42 +76,42 @@ def run():
Lz = 0.5 * dim[0] * res # in px/nm
R = 0.25 * L # in px/nm
x0 = L / 2 # in px/nm
-
+
def F_disc(x):
coeff = - pi * Lz / (2*PHI_0) * 1E3 # in mrad -> *1000
result = coeff * (- (x - x0) * np.sin(phi))
result *= np.where(np.abs(x - x0) <= R, 1, (R / (x - x0)) ** 2)
return result
-
+
x_d.append(np.linspace(0, L, 5000))
y_d0.append(F_disc(x_d[0]))
y_d10.append(F_disc(x_d[0]))
dy_d0.append(np.zeros_like(x_d[0]))
dy_d10.append(np.zeros_like(x_d[0]))
# Create MagData (Disc):
- mag_data_disc = MagData(res, mc.create_mag_dist(mag_shape, phi))
+ mag_data_disc = MagData(res, mc.create_mag_dist_homog(mag_shape, phi))
for i in range(5):
mag_data_disc.scale_down()
print '----res =', mag_data_disc.res, 'nm', 'dim =', mag_data_disc.dim
projection = pj.simple_axis_projection(mag_data_disc)
- phase_map0 = PhaseMap(mag_data_disc.res,
+ phase_map0 = PhaseMap(mag_data_disc.res,
pm.phase_mag_fourier(mag_data_disc.res, projection,
- padding=0) * 1E3)
- phase_map10 = PhaseMap(mag_data_disc.res,
+ padding=0), 'mrad')
+ phase_map10 = PhaseMap(mag_data_disc.res,
pm.phase_mag_fourier(mag_data_disc.res, projection,
- padding=10) * 1E3)
- hi.display_combined(phase_map0, density, 'Disc, res = {} nm'.format(mag_data_disc.res),
- labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
- hi.display_combined(phase_map10, density, 'Disc, res = {} nm'.format(mag_data_disc.res),
- labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
- x_d.append(np.linspace(mag_data_disc.res * 0.5,
- mag_data_disc.res * (mag_data_disc.dim[1]-0.5),
+ padding=10), 'mrad')
+ hi.display_combined(phase_map0, density,
+ 'Disc, res = {} nm'.format(mag_data_disc.res))
+ hi.display_combined(phase_map10, density,
+ 'Disc, res = {} nm'.format(mag_data_disc.res))
+ x_d.append(np.linspace(mag_data_disc.res * 0.5,
+ mag_data_disc.res * (mag_data_disc.dim[1]-0.5),
mag_data_disc.dim[1]))
slice_pos = int(mag_data_disc.dim[1]/2)
- y_d0.append(phase_map0.phase[slice_pos, :])
- y_d10.append(phase_map10.phase[slice_pos, :])
- dy_d0.append(phase_map0.phase[slice_pos, :] - F_disc(x_d[-1]))
- dy_d10.append(phase_map10.phase[slice_pos, :] - F_disc(x_d[-1]))
+ y_d0.append(phase_map0.phase[slice_pos, :]*1E3) # *1E3: rad to mrad
+ y_d10.append(phase_map10.phase[slice_pos, :]*1E3) # *1E3: rad to mrad
+ dy_d0.append(phase_map0.phase[slice_pos, :]*1E3 - F_disc(x_d[-1])) # *1E3: in mrad
+ dy_d10.append(phase_map10.phase[slice_pos, :]*1E3 - F_disc(x_d[-1])) # *1E3: in mrad
print '--CREATE PHASE SLICES VORTEX STATE DISC'
x_v = []
@@ -121,12 +124,12 @@ def run():
Lz = 0.5 * dim[0] * res # in px/nm
R = 0.25 * L # in px/nm
x0 = L / 2 # in px/nm
-
+
def F_vort(x):
coeff = pi*Lz/PHI_0 * 1E3 # in mrad -> *1000
result = coeff * np.where(np.abs(x - x0) <= R, (np.abs(x-x0)-R), 0)
return result
-
+
x_v.append(np.linspace(0, L, 5000))
y_v0.append(F_vort(x_v[0]))
y_v10.append(F_vort(x_v[0]))
@@ -138,24 +141,24 @@ def run():
mag_data_vort.scale_down()
print '----res =', mag_data_vort.res, 'nm', 'dim =', mag_data_vort.dim
projection = pj.simple_axis_projection(mag_data_vort)
- phase_map0 = PhaseMap(mag_data_vort.res,
+ phase_map0 = PhaseMap(mag_data_vort.res,
pm.phase_mag_fourier(mag_data_vort.res, projection,
- padding=0) * 1E3)
- phase_map10 = PhaseMap(mag_data_vort.res,
+ padding=0), 'mrad')
+ phase_map10 = PhaseMap(mag_data_vort.res,
pm.phase_mag_fourier(mag_data_vort.res, projection,
- padding=10) * 1E3)
- hi.display_combined(phase_map0, density, 'Disc, res = {} nm'.format(mag_data_vort.res),
- labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
- hi.display_combined(phase_map10, density, 'Disc, res = {} nm'.format(mag_data_vort.res),
- labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
- x_v.append(np.linspace(mag_data_vort.res * 0.5,
- mag_data_vort.res * (mag_data_vort.dim[1]-0.5),
+ padding=10), 'mrad')
+ hi.display_combined(phase_map0, density,
+ 'Disc, res = {} nm'.format(mag_data_vort.res))
+ hi.display_combined(phase_map10, density,
+ 'Disc, res = {} nm'.format(mag_data_vort.res))
+ x_v.append(np.linspace(mag_data_vort.res * 0.5,
+ mag_data_vort.res * (mag_data_vort.dim[1]-0.5),
mag_data_vort.dim[1]))
slice_pos = int(mag_data_vort.dim[1]/2)
- y_v0.append(phase_map0.phase[slice_pos, :])
- y_v10.append(phase_map10.phase[slice_pos, :])
- dy_v0.append(phase_map0.phase[slice_pos, :] - F_vort(x_v[-1]))
- dy_v10.append(phase_map10.phase[slice_pos, :] - F_vort(x_v[-1]))
+ y_v0.append(phase_map0.phase[slice_pos, :]*1E3) # *1E3: rad to mrad
+ y_v10.append(phase_map10.phase[slice_pos, :]*1E3) # *1E3: rad to mrad
+ dy_v0.append(phase_map0.phase[slice_pos, :]*1E3 - F_vort(x_v[-1])) # *1E3: in mrad
+ dy_v10.append(phase_map10.phase[slice_pos, :]*1E3 - F_vort(x_v[-1])) # *1E3: in mrad
# Shelve x, y and dy:
print '--SAVE PHASE SLICES'
@@ -179,25 +182,25 @@ def run():
axes[0].set_ylabel('phase [mrad]', fontsize=15)
axes[0].set_xlim(0, 128)
axes[0].set_ylim(-220, 220)
- # Plot Zoombox and Arrow:
- zoom = (23.5, 160, 15, 40)
- rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
- axes[0].add_patch(rect)
- axes[0].arrow(zoom[0]+zoom[2], zoom[1]+zoom[3]/2, 36, 0, length_includes_head=True,
- head_width=10, head_length=4, fc='k', ec='k')
- # Plot zoom inset:
- ins_axis_d = plt.axes([0.33, 0.57, 0.14, 0.3])
- ins_axis_d.plot(x_d[0], y_d0[0], '-k', linewidth=1.5, label='analytic')
- ins_axis_d.plot(x_d[1], y_d0[1], '-r', linewidth=1.5, label='0.5 nm')
- ins_axis_d.plot(x_d[2], y_d0[2], '-m', linewidth=1.5, label='1 nm')
- ins_axis_d.plot(x_d[3], y_d0[3], '-y', linewidth=1.5, label='2 nm')
- ins_axis_d.plot(x_d[4], y_d0[4], '-g', linewidth=1.5, label='4 nm')
- ins_axis_d.plot(x_d[5], y_d0[5], '-c', linewidth=1.5, label='8 nm')
- ins_axis_d.tick_params(axis='both', which='major', labelsize=14)
- ins_axis_d.set_xlim(zoom[0], zoom[0]+zoom[2])
- ins_axis_d.set_ylim(zoom[1], zoom[1]+zoom[3])
- ins_axis_d.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
- ins_axis_d.yaxis.set_major_locator(MaxNLocator(nbins=3))
+# # Plot Zoombox and Arrow:
+# zoom = (23.5, 160, 15, 40)
+# rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
+# axes[0].add_patch(rect)
+# axes[0].arrow(zoom[0]+zoom[2], zoom[1]+zoom[3]/2, 36, 0, length_includes_head=True,
+# head_width=10, head_length=4, fc='k', ec='k')
+# # Plot zoom inset:
+# ins_axis_d = plt.axes([0.33, 0.57, 0.14, 0.3])
+# ins_axis_d.plot(x_d[0], y_d0[0], '-k', linewidth=1.5, label='analytic')
+# ins_axis_d.plot(x_d[1], y_d0[1], '-r', linewidth=1.5, label='0.5 nm')
+# ins_axis_d.plot(x_d[2], y_d0[2], '-m', linewidth=1.5, label='1 nm')
+# ins_axis_d.plot(x_d[3], y_d0[3], '-y', linewidth=1.5, label='2 nm')
+# ins_axis_d.plot(x_d[4], y_d0[4], '-g', linewidth=1.5, label='4 nm')
+# ins_axis_d.plot(x_d[5], y_d0[5], '-c', linewidth=1.5, label='8 nm')
+# ins_axis_d.tick_params(axis='both', which='major', labelsize=14)
+# ins_axis_d.set_xlim(zoom[0], zoom[0]+zoom[2])
+# ins_axis_d.set_ylim(zoom[1], zoom[1]+zoom[3])
+# ins_axis_d.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
+# ins_axis_d.yaxis.set_major_locator(MaxNLocator(nbins=3))
print '--PLOT/SAVE PHASE SLICES VORTEX STATE DISC PADDING = 0'
# Plot phase slices:
@@ -214,25 +217,25 @@ def run():
axes[1].set_xlim(0, 128)
axes[1].yaxis.set_major_locator(MaxNLocator(nbins=6))
axes[1].legend()
- # Plot Zoombox and Arrow:
- zoom = (59, 340, 10, 55)
- rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
- axes[1].add_patch(rect)
- axes[1].arrow(zoom[0]+zoom[2]/2, zoom[1], 0, -193, length_includes_head=True,
- head_width=2, head_length=20, fc='k', ec='k')
- # Plot zoom inset:
- ins_axis_v = plt.axes([0.695, 0.15, 0.075, 0.3])
- ins_axis_v.plot(x_v[0], y_v0[0], '-k', linewidth=1.5, label='analytic')
- ins_axis_v.plot(x_v[1], y_v0[1], '-r', linewidth=1.5, label='0.5 nm')
- ins_axis_v.plot(x_v[2], y_v0[2], '-m', linewidth=1.5, label='1 nm')
- ins_axis_v.plot(x_v[3], y_v0[3], '-y', linewidth=1.5, label='2 nm')
- ins_axis_v.plot(x_v[4], y_v0[4], '-g', linewidth=1.5, label='4 nm')
- ins_axis_v.plot(x_v[5], y_v0[5], '-c', linewidth=1.5, label='8 nm')
- ins_axis_v.tick_params(axis='both', which='major', labelsize=14)
- ins_axis_v.set_xlim(zoom[0], zoom[0]+zoom[2])
- ins_axis_v.set_ylim(zoom[1], zoom[1]+zoom[3])
- ins_axis_v.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
- ins_axis_v.yaxis.set_major_locator(MaxNLocator(nbins=4))
+# # Plot Zoombox and Arrow:
+# zoom = (59, 340, 10, 55)
+# rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
+# axes[1].add_patch(rect)
+# axes[1].arrow(zoom[0]+zoom[2]/2, zoom[1], 0, -193, length_includes_head=True,
+# head_width=2, head_length=20, fc='k', ec='k')
+# # Plot zoom inset:
+# ins_axis_v = plt.axes([0.695, 0.15, 0.075, 0.3])
+# ins_axis_v.plot(x_v[0], y_v0[0], '-k', linewidth=1.5, label='analytic')
+# ins_axis_v.plot(x_v[1], y_v0[1], '-r', linewidth=1.5, label='0.5 nm')
+# ins_axis_v.plot(x_v[2], y_v0[2], '-m', linewidth=1.5, label='1 nm')
+# ins_axis_v.plot(x_v[3], y_v0[3], '-y', linewidth=1.5, label='2 nm')
+# ins_axis_v.plot(x_v[4], y_v0[4], '-g', linewidth=1.5, label='4 nm')
+# ins_axis_v.plot(x_v[5], y_v0[5], '-c', linewidth=1.5, label='8 nm')
+# ins_axis_v.tick_params(axis='both', which='major', labelsize=14)
+# ins_axis_v.set_xlim(zoom[0], zoom[0]+zoom[2])
+# ins_axis_v.set_ylim(zoom[1], zoom[1]+zoom[3])
+# ins_axis_v.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
+# ins_axis_v.yaxis.set_major_locator(MaxNLocator(nbins=4))
plt.show()
plt.figtext(0.15, 0.13, 'a)', fontsize=30)
@@ -257,25 +260,25 @@ def run():
axes[0].set_ylabel('phase [mrad]', fontsize=15)
axes[0].set_xlim(0, 128)
axes[0].set_ylim(-220, 220)
- # Plot Zoombox and Arrow:
- zoom = (23.5, 160, 15, 40)
- rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
- axes[0].add_patch(rect)
- axes[0].arrow(zoom[0]+zoom[2], zoom[1]+zoom[3]/2, 36, 0, length_includes_head=True,
- head_width=10, head_length=4, fc='k', ec='k')
- # Plot zoom inset:
- ins_axis_d = plt.axes([0.33, 0.57, 0.14, 0.3])
- ins_axis_d.plot(x_d[0], y_d10[0], '-k', linewidth=1.5, label='analytic')
- ins_axis_d.plot(x_d[1], y_d10[1], '-r', linewidth=1.5, label='0.5 nm')
- ins_axis_d.plot(x_d[2], y_d10[2], '-m', linewidth=1.5, label='1 nm')
- ins_axis_d.plot(x_d[3], y_d10[3], '-y', linewidth=1.5, label='2 nm')
- ins_axis_d.plot(x_d[4], y_d10[4], '-g', linewidth=1.5, label='4 nm')
- ins_axis_d.plot(x_d[5], y_d10[5], '-c', linewidth=1.5, label='8 nm')
- ins_axis_d.tick_params(axis='both', which='major', labelsize=14)
- ins_axis_d.set_xlim(zoom[0], zoom[0]+zoom[2])
- ins_axis_d.set_ylim(zoom[1], zoom[1]+zoom[3])
- ins_axis_d.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
- ins_axis_d.yaxis.set_major_locator(MaxNLocator(nbins=3))
+# # Plot Zoombox and Arrow:
+# zoom = (23.5, 160, 15, 40)
+# rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
+# axes[0].add_patch(rect)
+# axes[0].arrow(zoom[0]+zoom[2], zoom[1]+zoom[3]/2, 36, 0, length_includes_head=True,
+# head_width=10, head_length=4, fc='k', ec='k')
+# # Plot zoom inset:
+# ins_axis_d = plt.axes([0.33, 0.57, 0.14, 0.3])
+# ins_axis_d.plot(x_d[0], y_d10[0], '-k', linewidth=1.5, label='analytic')
+# ins_axis_d.plot(x_d[1], y_d10[1], '-r', linewidth=1.5, label='0.5 nm')
+# ins_axis_d.plot(x_d[2], y_d10[2], '-m', linewidth=1.5, label='1 nm')
+# ins_axis_d.plot(x_d[3], y_d10[3], '-y', linewidth=1.5, label='2 nm')
+# ins_axis_d.plot(x_d[4], y_d10[4], '-g', linewidth=1.5, label='4 nm')
+# ins_axis_d.plot(x_d[5], y_d10[5], '-c', linewidth=1.5, label='8 nm')
+# ins_axis_d.tick_params(axis='both', which='major', labelsize=14)
+# ins_axis_d.set_xlim(zoom[0], zoom[0]+zoom[2])
+# ins_axis_d.set_ylim(zoom[1], zoom[1]+zoom[3])
+# ins_axis_d.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
+# ins_axis_d.yaxis.set_major_locator(MaxNLocator(nbins=3))
print '--PLOT/SAVE PHASE SLICES VORTEX STATE DISC PADDING = 10'
# Plot phase slices:
@@ -292,29 +295,29 @@ def run():
axes[1].set_xlim(0, 128)
axes[1].yaxis.set_major_locator(MaxNLocator(nbins=6))
axes[1].legend()
- # Plot Zoombox and Arrow:
- zoom = (59, 340, 10, 55)
- rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
- axes[1].add_patch(rect)
- axes[1].arrow(zoom[0]+zoom[2]/2, zoom[1], 0, -193, length_includes_head=True,
- head_width=2, head_length=20, fc='k', ec='k')
- # Plot zoom inset:
- ins_axis_v = plt.axes([0.695, 0.15, 0.075, 0.3])
- ins_axis_v.plot(x_v[0], y_v10[0], '-k', linewidth=1.5, label='analytic')
- ins_axis_v.plot(x_v[1], y_v10[1], '-r', linewidth=1.5, label='0.5 nm')
- ins_axis_v.plot(x_v[2], y_v10[2], '-m', linewidth=1.5, label='1 nm')
- ins_axis_v.plot(x_v[3], y_v10[3], '-y', linewidth=1.5, label='2 nm')
- ins_axis_v.plot(x_v[4], y_v10[4], '-g', linewidth=1.5, label='4 nm')
- ins_axis_v.plot(x_v[5], y_v10[5], '-c', linewidth=1.5, label='8 nm')
- ins_axis_v.tick_params(axis='both', which='major', labelsize=14)
- ins_axis_v.set_xlim(zoom[0], zoom[0]+zoom[2])
- ins_axis_v.set_ylim(zoom[1], zoom[1]+zoom[3])
- ins_axis_v.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
- ins_axis_v.yaxis.set_major_locator(MaxNLocator(nbins=4))
+# # Plot Zoombox and Arrow:
+# zoom = (59, 340, 10, 55)
+# rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
+# axes[1].add_patch(rect)
+# axes[1].arrow(zoom[0]+zoom[2]/2, zoom[1], 0, -193, length_includes_head=True,
+# head_width=2, head_length=20, fc='k', ec='k')
+# # Plot zoom inset:
+# ins_axis_v = plt.axes([0.695, 0.15, 0.075, 0.3])
+# ins_axis_v.plot(x_v[0], y_v10[0], '-k', linewidth=1.5, label='analytic')
+# ins_axis_v.plot(x_v[1], y_v10[1], '-r', linewidth=1.5, label='0.5 nm')
+# ins_axis_v.plot(x_v[2], y_v10[2], '-m', linewidth=1.5, label='1 nm')
+# ins_axis_v.plot(x_v[3], y_v10[3], '-y', linewidth=1.5, label='2 nm')
+# ins_axis_v.plot(x_v[4], y_v10[4], '-g', linewidth=1.5, label='4 nm')
+# ins_axis_v.plot(x_v[5], y_v10[5], '-c', linewidth=1.5, label='8 nm')
+# ins_axis_v.tick_params(axis='both', which='major', labelsize=14)
+# ins_axis_v.set_xlim(zoom[0], zoom[0]+zoom[2])
+# ins_axis_v.set_ylim(zoom[1], zoom[1]+zoom[3])
+# ins_axis_v.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
+# ins_axis_v.yaxis.set_major_locator(MaxNLocator(nbins=4))
plt.show()
- plt.figtext(0.15, 0.13, 'a)', fontsize=30)
- plt.figtext(0.57, 0.13, 'b)', fontsize=30)
+ plt.figtext(0.15, 0.13, 'c)', fontsize=30)
+ plt.figtext(0.57, 0.13, 'd)', fontsize=30)
plt.savefig(directory + '/ch5-1-phase_slice_padding_10.png', bbox_inches='tight')
# Create figure:
@@ -418,7 +421,7 @@ def run():
height_big = dim_big[0]/2 # in px
mag_shape = mc.Shapes.disc(dim_big, center_big, radius_big, height_big)
# Create MagData (4 times the size):
- mag_data_disc = MagData(res_big, mc.create_mag_dist(mag_shape, phi))
+ mag_data_disc = MagData(res_big, mc.create_mag_dist_homog(mag_shape, phi))
mag_data_vort = MagData(res_big, mc.create_mag_dist_vortex(mag_shape, center_big))
# Scale mag_data, resolution and dimensions:
mag_data_disc.scale_down()
@@ -436,60 +439,52 @@ def run():
phase_ana_vort = an.phase_mag_vortex(dim, res, center, radius, height)
# Create figure:
- fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
fig.suptitle('Difference of the real space approach from the analytical solution', fontsize=20)
# Create norm for the plots:
bounds = np.array([-100, -50, -25, -5, 0, 5, 25, 50, 100])
norm = BoundaryNorm(bounds, RdBu.N)
# Disc:
phase_num_disc = pm.phase_mag_fourier(res, projection_disc, padding=0)
- phase_diff_disc = PhaseMap(res, (phase_num_disc-phase_ana_disc)*1E3) # in mrad -> *1000)
+ phase_diff_disc = PhaseMap(res, (phase_num_disc-phase_ana_disc), 'mrad')
RMS_disc = np.sqrt(np.mean(phase_diff_disc.phase**2))
phase_diff_disc.display('Homog. magn. disc, RMS = {:3.2f} mrad'.format(RMS_disc),
- axis=axes[0], labels=('x-axis [nm]', 'y-axis [nm]',
- '$\Delta$phase [mrad] (padding = 0)'),
- limit=np.max(bounds), norm=norm)
+ axis=axes[0], limit=np.max(bounds), norm=norm)
axes[0].set_aspect('equal')
# Vortex:
phase_num_vort = pm.phase_mag_fourier(res, projection_vort, padding=0)
- phase_diff_vort = PhaseMap(res, (phase_num_vort-phase_ana_vort)*1E3) # in mrad -> *1000
+ phase_diff_vort = PhaseMap(res, (phase_num_vort-phase_ana_vort), 'mrad')
RMS_vort = np.sqrt(np.mean(phase_diff_vort.phase**2))
phase_diff_vort.display('Vortex state disc, RMS = {:3.2f} mrad'.format(RMS_vort),
- axis=axes[1], labels=('x-axis [nm]', 'y-axis [nm]',
- '$\Delta$phase [mrad] (padding = 0)'),
- limit=np.max(bounds), norm=norm)
+ axis=axes[1], limit=np.max(bounds), norm=norm)
axes[1].set_aspect('equal')
-
+
plt.show()
plt.figtext(0.15, 0.2, 'a)', fontsize=30)
plt.figtext(0.52, 0.2, 'b)', fontsize=30)
plt.savefig(directory + '/ch5-2-fourier_phase_differe_no_padding.png', bbox_inches='tight')
# Create figure:
- fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
fig.suptitle('Difference of the real space approach from the analytical solution', fontsize=20)
# Create norm for the plots:
bounds = np.array([-3, -0.5, -0.25, -0.1, 0, 0.1, 0.25, 0.5, 3])
norm = BoundaryNorm(bounds, RdBu.N)
# Disc:
phase_num_disc = pm.phase_mag_fourier(res, projection_disc, padding=10)
- phase_diff_disc = PhaseMap(res, (phase_num_disc-phase_ana_disc)*1E3) # in mrad -> *1000)
+ phase_diff_disc = PhaseMap(res, (phase_num_disc-phase_ana_disc), 'mrad')
RMS_disc = np.sqrt(np.mean(phase_diff_disc.phase**2))
phase_diff_disc.display('Homog. magn. disc, RMS = {:3.2f} mrad'.format(RMS_disc),
- axis=axes[0], labels=('x-axis [nm]', 'y-axis [nm]',
- '$\Delta$phase [mrad] (padding = 10)'),
- limit=np.max(bounds), norm=norm)
+ axis=axes[0], limit=np.max(bounds), norm=norm)
axes[0].set_aspect('equal')
# Vortex:
phase_num_vort = pm.phase_mag_fourier(res, projection_vort, padding=10)
- phase_diff_vort = PhaseMap(res, (phase_num_vort-phase_ana_vort)*1E3) # in mrad -> *1000
+ phase_diff_vort = PhaseMap(res, (phase_num_vort-phase_ana_vort), 'mrad')
RMS_vort = np.sqrt(np.mean(phase_diff_vort.phase**2))
phase_diff_vort.display('Vortex state disc, RMS = {:3.2f} mrad'.format(RMS_vort),
- axis=axes[1], labels=('x-axis [nm]', 'y-axis [nm]',
- '$\Delta$phase [mrad] (padding = 10)'),
- limit=np.max(bounds), norm=norm)
+ axis=axes[1], limit=np.max(bounds), norm=norm)
axes[1].set_aspect('equal')
-
+
plt.show()
plt.figtext(0.15, 0.2, 'c)', fontsize=30)
plt.figtext(0.52, 0.2, 'd)', fontsize=30)
@@ -505,7 +500,7 @@ def run():
center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
radius = dim[1]/4 # in px
height = dim[0]/2 # in px
-
+
key = 'ch5-2-fourier_padding_mag_dist'
if key in data_shelve:
print '--LOAD MAGNETIC DISTRIBUTIONS'
@@ -520,7 +515,7 @@ def run():
height_big = dim_big[0]/2 # in px
mag_shape = mc.Shapes.disc(dim_big, center_big, radius_big, height_big)
# Create MagData (4 times the size):
- mag_data_disc = MagData(res_big, mc.create_mag_dist(mag_shape, phi))
+ mag_data_disc = MagData(res_big, mc.create_mag_dist_homog(mag_shape, phi))
mag_data_vort = MagData(res_big, mc.create_mag_dist_vortex(mag_shape, center_big))
# Scale mag_data, resolution and dimensions:
mag_data_disc.scale_down()
@@ -552,15 +547,15 @@ def run():
start_time = time.time()
phase_num_disc = pm.phase_mag_fourier(res, projection_disc, padding=padding_list[i])
data_disc[2, i] = time.time() - start_time
- phase_diff = (phase_num_disc-phase_ana_disc) * 1E3 # in mrad -> *1000)
- phase_map_diff = PhaseMap(res, phase_diff)
- phase_map_diff.display(labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
- data_disc[1, i] = np.sqrt(np.mean(phase_diff**2))
+ phase_diff = (phase_num_disc-phase_ana_disc)
+ phase_map_diff = PhaseMap(res, phase_diff, 'mrad')
+ phase_map_diff.display()
+ data_disc[1, i] = np.sqrt(np.mean(phase_map_diff.phase**2))*1E3 # *1E3: rad to mraddd
data_shelve[key] = data_disc[:, i]
print '--PLOT/SAVE PADDING SERIES OF HOMOG. MAGN. DISC'
# Create figure:
- fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
fig.suptitle('Variation of the padding (homog. magn. disc)', fontsize=20)
# Plot RMS against padding:
axes[0].axhline(y=0.18, linestyle='--', color='g', label='RMS [mrad] (real space)')
@@ -569,7 +564,7 @@ def run():
axes[0].set_ylabel('RMS [mrad]', fontsize=15)
axes[0].set_xlim(-0.5, 16.5)
axes[0].set_ylim(-5, 45)
- axes[0].xaxis.set_major_locator(MaxNLocator(nbins=10, integer= True))
+ axes[0].xaxis.set_major_locator(MaxNLocator(nbins=10, integer=True))
axes[0].tick_params(axis='both', which='major', labelsize=14)
axes[0].legend()
# Plot zoom inset:
@@ -586,10 +581,10 @@ def run():
axes[1].set_ylabel('duration [s]', fontsize=15)
axes[1].set_xlim(-0.5, 16.5)
axes[1].set_ylim(-0.05, 1.5)
- axes[1].xaxis.set_major_locator(MaxNLocator(nbins=10, integer= True))
+ axes[1].xaxis.set_major_locator(MaxNLocator(nbins=10, integer=True))
axes[1].yaxis.set_major_locator(MaxNLocator(nbins=10))
axes[1].tick_params(axis='both', which='major', labelsize=14)
-
+
plt.show()
plt.figtext(0.15, 0.13, 'a)', fontsize=30)
plt.figtext(0.57, 0.17, 'b)', fontsize=30)
@@ -608,15 +603,15 @@ def run():
start_time = time.time()
phase_num_vort = pm.phase_mag_fourier(res, projection_vort, padding=padding_list[i])
data_vort[2, i] = time.time() - start_time
- phase_diff = (phase_num_vort-phase_ana_vort) * 1E3 # in mrad -> *1000)
- phase_map_diff = PhaseMap(res, phase_diff)
- phase_map_diff.display(labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
- data_vort[1, i] = np.sqrt(np.mean(phase_diff**2))
+ phase_diff = (phase_num_vort-phase_ana_vort)
+ phase_map_diff = PhaseMap(res, phase_diff, 'mrad')
+ phase_map_diff.display()
+ data_vort[1, i] = np.sqrt(np.mean(phase_map_diff.phase**2))*1E3 # *1E3: rad to mrad
data_shelve[key] = data_vort[:, i]
print '--PLOT/SAVE PADDING SERIES OF VORTEX STATE DISC'
# Create figure:
- fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
fig.suptitle('Variation of the padding (Vortex state disc)', fontsize=20)
# Plot RMS against padding:
axes[0].axhline(y=0.22, linestyle='--', color='g', label='RMS [mrad] (real space)')
@@ -626,7 +621,7 @@ def run():
axes[0].set_xlim(-0.5, 16.5)
axes[0].set_ylim(-5, 45)
axes[0].tick_params(axis='both', which='major', labelsize=14)
- axes[0].xaxis.set_major_locator(MaxNLocator(nbins=10, integer= True))
+ axes[0].xaxis.set_major_locator(MaxNLocator(nbins=10, integer=True))
axes[0].legend()
# Plot zoom inset:
ins_axis_v = plt.axes([0.2, 0.35, 0.25, 0.4])
@@ -642,10 +637,10 @@ def run():
axes[1].set_ylabel('duration [s]', fontsize=15)
axes[1].set_xlim(-0.5, 16.5)
axes[1].set_ylim(-0.05, 1.5)
- axes[1].xaxis.set_major_locator(MaxNLocator(nbins=10, integer= True))
+ axes[1].xaxis.set_major_locator(MaxNLocator(nbins=10, integer=True))
axes[1].yaxis.set_major_locator(MaxNLocator(nbins=10))
axes[1].tick_params(axis='both', which='major', labelsize=14)
-
+
plt.show()
plt.figtext(0.15, 0.13, 'c)', fontsize=30)
plt.figtext(0.57, 0.17, 'd)', fontsize=30)
@@ -655,7 +650,7 @@ def run():
print 'CLOSING SHELVE\n'
# Close shelve:
data_shelve.close()
-
+
###############################################################################################
diff --git a/scripts/paper 1/ch5-3-comparison_of_methods.py b/scripts/paper 1/ch5-3-comparison_of_methods.py
index d5b886a..7ba6609 100644
--- a/scripts/paper 1/ch5-3-comparison_of_methods.py
+++ b/scripts/paper 1/ch5-3-comparison_of_methods.py
@@ -1,6 +1,10 @@
#! python
# -*- coding: utf-8 -*-
-"""Compare the different methods to create phase maps."""
+"""
+Created on Fri Jul 26 14:37:30 2013
+
+@author: Jan
+"""
import time
@@ -8,6 +12,7 @@ import pdb
import traceback
import sys
import os
+
import numpy as np
from numpy import pi
@@ -33,8 +38,8 @@ def run():
###############################################################################################
print 'CH5-3 METHOD COMPARISON'
-
- key = 'ch5-3-compare_method_data'
+
+ key = 'ch5-3-method_comparison'
if key in data_shelve:
print '--LOAD METHOD DATA'
(data_disc_fourier0, data_vort_fourier0,
@@ -44,23 +49,23 @@ def run():
data_disc_real_d, data_vort_real_d) = data_shelve[key]
else:
# Input parameters:
- steps = 6
+ steps = 6
res = 0.25 # in nm
phi = pi/2
dim = (64, 512, 512) # in px (z, y, x)
- center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
+ center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts at 0!
radius = dim[1]/4 # in px
height = dim[0]/2 # in px
-
+
print '--CREATE MAGNETIC SHAPE'
mag_shape = mc.Shapes.disc(dim, center, radius, height)
# Create MagData (4 times the size):
print '--CREATE MAG. DIST. HOMOG. MAGN. DISC'
- mag_data_disc = MagData(res, mc.create_mag_dist(mag_shape, phi))
+ mag_data_disc = MagData(res, mc.create_mag_dist_homog(mag_shape, phi))
print '--CREATE MAG. DIST. VORTEX STATE DISC'
mag_data_vort = MagData(res, mc.create_mag_dist_vortex(mag_shape, center))
-
- # Create Data Arrays
+
+ # Create Data Arrays:
res_list = [res*2**i for i in np.linspace(1, steps, steps)]
data_disc_fourier0 = np.vstack((res_list, np.zeros((2, steps))))
data_vort_fourier0 = np.vstack((res_list, np.zeros((2, steps))))
@@ -79,12 +84,12 @@ def run():
mag_data_vort.scale_down()
dim = mag_data_disc.dim
res = mag_data_disc.res
- center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
+ center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px, index starts at 0!
radius = dim[1]/4 # in px
height = dim[0]/2 # in px
-
+
print '--res =', res, 'nm', 'dim =', dim
-
+
print '----CALCULATE RMS/DURATION HOMOG. MAGN. DISC'
# Create projections along z-axis:
projection_disc = pj.simple_axis_projection(mag_data_disc)
@@ -172,16 +177,16 @@ def run():
print '------time (vortex, real disc) =', data_vort_real_d[2, i]
phase_diff_vort = (phase_ana_vort-phase_num_vort) * 1E3 # in mrad -> *1000
data_vort_real_d[1, i] = np.sqrt(np.mean(phase_diff_vort**2))
-
+
print '--SHELVE METHOD DATA'
data_shelve[key] = (data_disc_fourier0, data_vort_fourier0,
data_disc_fourier1, data_vort_fourier1,
data_disc_fourier10, data_vort_fourier10,
data_disc_real_s, data_vort_real_s,
data_disc_real_d, data_vort_real_d)
-
+
print '--PLOT/SAVE METHOD DATA'
-
+
# Plot using shared rows and colums:
fig, axes = plt.subplots(2, 2, sharex='col', sharey='row', figsize=(12, 8))
fig.tight_layout(rect=(0.05, 0.05, 0.95, 0.95))
@@ -243,7 +248,7 @@ def run():
axes[0, 1].tick_params(axis='both', which='major', labelsize=14)
axes[0, 1].xaxis.set_major_locator(IndexLocator(base=4, offset=-0.5))
axes[0, 1].legend(loc=1)
-
+
# Save figure as .png:
plt.show()
plt.figtext(0.45, 0.85, 'a)', fontsize=30)
@@ -256,7 +261,7 @@ def run():
print 'CLOSING SHELVE\n'
# Close shelve:
data_shelve.close()
-
+
###############################################################################################
diff --git a/scripts/get_jacobi.py b/scripts/reconstruction/get_jacobi.py
similarity index 74%
rename from scripts/get_jacobi.py
rename to scripts/reconstruction/get_jacobi.py
index 779fb4a..f3369d5 100644
--- a/scripts/get_jacobi.py
+++ b/scripts/reconstruction/get_jacobi.py
@@ -9,13 +9,16 @@ import time
import pdb
import traceback
import sys
+import os
+
import numpy as np
+from numpy import pi
+
import pyramid.magcreator as mc
import pyramid.projector as pj
import pyramid.phasemapper as pm
from pyramid.magdata import MagData
from pyramid.phasemap import PhaseMap
-from numpy import pi
def get_jacobi():
@@ -26,16 +29,20 @@ def get_jacobi():
None
'''
+ directory = '../../output/reconstruction'
+ if not os.path.exists(directory):
+ os.makedirs(directory)
+ filename = directory + '/jacobi.npy'
# TODO: Input via GUI
b_0 = 1.0 # in T
dim = (1, 3, 3) # in px (y,x)
res = 10.0 # in nm
phi = pi/4
- center = (0, 1, 1) # in px (y,x) index starts with 0!
+ center = (0, int(dim[1]/2), int(dim[2]/2)) # in px (y,x) index starts with 0!
width = (0, 1, 1) # in px (y,x)
- mag_data = MagData(res, mc.create_mag_dist(mc.Shapes.slab(dim, center, width), phi))
+ mag_data = MagData(res, mc.create_mag_dist_homog(mc.Shapes.slab(dim, center, width), phi))
projection = pj.simple_axis_projection(mag_data)
'''NUMERICAL SOLUTION'''
@@ -45,7 +52,7 @@ def get_jacobi():
phase_map = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab', b_0, jacobi=jacobi))
toc = time.clock()
phase_map.display()
- np.savetxt('../output/jacobi.npy', jacobi)
+ np.savetxt(filename, jacobi)
print 'Time for Real Space Approach with Jacobi-Matrix (Slab): ' + str(toc - tic)
return jacobi
diff --git a/scripts/reconstruct_random_pixels.py b/scripts/reconstruction/reconstruct_random_pixels.py
similarity index 74%
rename from scripts/reconstruct_random_pixels.py
rename to scripts/reconstruction/reconstruct_random_pixels.py
index c4d62a6..710293e 100644
--- a/scripts/reconstruct_random_pixels.py
+++ b/scripts/reconstruction/reconstruct_random_pixels.py
@@ -33,20 +33,16 @@ def reconstruct_random_distribution():
res = 10.0 # in nm
rnd.seed(18)
- # Create lists for magnetic objects:
- mag_shape_list = np.zeros((n_pixel,) + dim)
- phi_list = np.zeros(n_pixel)
- magnitude_list = np.zeros(n_pixel)
+ # Create empty MagData object and add random pixels:
+ mag_data = MagData(res)
for i in range(n_pixel):
pixel = (rnd.randrange(dim[0]), rnd.randrange(dim[1]), rnd.randrange(dim[2]))
- mag_shape_list[i, ...] = mc.Shapes.pixel(dim, pixel)
- phi_list[i] = 2 * pi * rnd.random()
- magnitude_list[i] = rnd.random()
- # Create magnetic distribution:
- magnitude = mc.create_mag_dist_comb(mag_shape_list, phi_list, magnitude_list)
- mag_data = MagData(res, magnitude)
+ mag_shape = mc.Shapes.pixel(dim, pixel)
+ phi = 2 * pi * rnd.random()
+ magnitude = rnd.random()
+ mag_data.add_magnitude(mc.create_mag_dist_homog(mag_shape, phi, magnitude))
+ # Plot magnetic distribution, phase map and holographic contour map:
mag_data.quiver_plot()
- # Display phase map and holography image:
projection = pj.simple_axis_projection(mag_data)
phase_map = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab', b_0))
hi.display_combined(phase_map, 10, 'Generated Distribution')
diff --git a/scripts/test_methods.py b/scripts/test_methods.py
new file mode 100644
index 0000000..9c407a8
--- /dev/null
+++ b/scripts/test_methods.py
@@ -0,0 +1,74 @@
+#! python
+# -*- coding: utf-8 -*-
+"""Compare the different methods to create phase maps."""
+
+import pdb
+import traceback
+import sys
+
+from numpy import pi
+
+import pyramid.magcreator as mc
+import pyramid.projector as pj
+import pyramid.phasemapper as pm
+import pyramid.holoimage as hi
+from pyramid.magdata import MagData
+from pyramid.phasemap import PhaseMap
+
+
+def compare_methods():
+ '''Calculate and display the phase map from a given magnetization.
+ Arguments:
+ None
+ Returns:
+ None
+
+ '''
+# # Input parameters:
+# res = 10.0 # in nm
+# phi = pi/4
+# density = 1
+# dim = (64, 64, 64) # in px (z, y, x)
+# # Create magnetic shape:
+# geometry = 'sphere'
+# if geometry == 'slab':
+# center = (dim[0]/2-0.5, dim[1]/2-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts at 0!
+# width = (dim[0]/2, dim[1]/2., dim[2]/2.) # in px (z, y, x)
+# mag_shape = mc.Shapes.slab(dim, center, width)
+# elif geometry == 'disc':
+# center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts at 0!
+# radius = dim[1]/4 # in px
+# height = dim[0]/2 # in px
+# mag_shape = mc.Shapes.disc(dim, center, radius, height)
+# elif geometry == 'sphere':
+# center = (32, 32, 32) # in px (z, y, x) index starts with 0!
+# radius = 16 # in px
+# mag_shape = mc.Shapes.sphere(dim, center, radius)
+# # Project the magnetization data:
+# mag_data = MagData(res, mc.create_mag_dist_homog(mag_shape, phi))
+
+ density = 0.3
+
+ mag_data = MagData.load_from_llg('../output/magnetic distributions/mag_dist_sphere.txt')
+ res = mag_data.res
+ mag_data.quiver_plot()
+# mag_data.quiver_plot3d()
+ projection = pj.simple_axis_projection(mag_data)
+ # Construct phase maps:
+ phase_map_mag = PhaseMap(res, pm.phase_mag_fourier(res, projection, padding=1))
+ phase_map_elec = PhaseMap(res, pm.phase_elec(res, projection, v_0 = 3))
+ # Display the combinated plots with phasemap and holography image:
+ hi.display_combined(phase_map_mag, density, title='Magnetic Phase')
+ hi.display_combined(phase_map_elec, density, title='Electric Phase')
+
+ phase_map = PhaseMap(res, phase_map_mag.phase+phase_map_elec.phase)
+ hi.display_combined(phase_map, density)
+
+
+if __name__ == "__main__":
+ try:
+ compare_methods()
+ except:
+ type, value, tb = sys.exc_info()
+ traceback.print_exc()
+ pdb.post_mortem(tb)
--
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