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[.ShellClassInfo]
IconResource=C:\Users\Jan\Home\PhD Thesis\Pyramid\icon.ico,0
[ViewState]
Mode=
Vid=
FolderType=Generic
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docs/Makefile
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# Makefile for Sphinx documentation
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
# You can set these variables from the command line, and also
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
SOURCEDIR = .
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
# Put it first so that "make" without argument is like "make 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 " 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 $(BUILDDIR)/linkcheck/output.txt."
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
.PHONY: help Makefile
pdf:
$(SPHINXBUILD) -b pdf $(ALLSPHINXOPTS) _build/pdf
@echo
@echo "Build finished. The PDF files are in _build/pdf."
\ No newline at end of file
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
docs/conf.py
View file @ 6e3128b8
# -*- coding: utf-8 -*-
# Configuration file for the Sphinx documentation builder.
#
# 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.
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# http://www.sphinx-doc.org/en/master/config
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'))
# Use command in docs to generate stubs and make html afterwards:
# > sphinx-apidoc -o api ../src/empyre
# > make html
# -- General configuration -----------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.0'
# -- Path setup --------------------------------------------------------------
# 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']
# 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.
#
import os
import sys
sys.path.insert(0, os.path.abspath(os.path.join('..', 'src')))
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# The suffix of source filenames.
source_suffix = '.rst'
# -- Project information -----------------------------------------------------
# The encoding of source files.
#source_encoding = 'utf-8-sig'
project = 'EMPyRe'
copyright = '2020, Jan Caron'
author = 'Jan Caron'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'pyramid'
copyright = u'2013, Jan Caron'
# -- General configuration ---------------------------------------------------
# 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 = ''
# 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',
'numpydoc',
'nbsphinx',
'nbsphinx_link']
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
numpydoc_show_class_members = False
add_module_names = False
# 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'
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# 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
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
# 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 ---------------------------------------------------
# -- 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
html_theme = 'sphinx_rtd_theme'
# 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
# html_static_path = ['_static']
# 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'
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# Show Table Of Contents at the beginning?
#pdf_use_toc = True
# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True
# How many levels deep should the table of contents be?
pdf_toc_depth = 9999
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
html_logo = 'EMPyRe Logo.png'
# Add section number to section references
pdf_use_numbered_links = False
# The name of an image file (relative to this directory) to use as a favicon of
# the doc. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
html_favicon = 'icon.ico'
# Background images fitting mode
pdf_fit_background_mode = 'scale'
# cannot cache unpickable configuration value: 'nbsphinx_custom_formats
# See https://github.com/sphinx-doc/sphinx/issues/12300
suppress_warnings = ["config.cache"]
docs/demos.rst 0 → 100644
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Demos
-----
.. toctree::
demos/demo1
demos/demo2
demos/demo3
docs/demos/demo1.nblink 0 → 100644
View file @ 6e3128b8
{
"path": "../../demos/demo1_first_steps.ipynb"
}
\ No newline at end of file
docs/demos/demo2.nblink 0 → 100644
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{
"path": "../../demos/demo2_handling_3d_fields.ipynb"
}
\ No newline at end of file
docs/demos/demo3.nblink 0 → 100644
View file @ 6e3128b8
{
"path": "../../demos/demo3_io_and_field_manipulation.ipynb"
}
\ No newline at end of file
docs/fields.rst 0 → 100644
View file @ 6e3128b8
The Field container class
=========================
General empyre.fields docu here!
All functions implemented in the subpackages can be accessed directly in the ``empyre.fields`` namespace.
The field module
----------------
.. automodule:: empyre.fields.field
:members:
:show-inheritance:
The shapes module
-----------------
.. automodule:: empyre.fields.shapes
:members:
:show-inheritance:
The vectors module
------------------
.. automodule:: empyre.fields.vectors
:members:
:show-inheritance:
docs/icon.ico 0 → 100644
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docs/icon.ico

66.1 KiB

docs/index.rst
View file @ 6e3128b8
.. pyramid documentation master file, created by
sphinx-quickstart on Tue Aug 20 12:15:35 2013.
.. EMPyRe documentation master file, created by
sphinx-quickstart on Mon Feb 17 14:19:01 2020.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to pyramid's documentation!
===================================
EMPyRe - Electron Microscopy Reconstruction
===========================================
Contents:
.. include:: ../README.rst
.. toctree::
:maxdepth: 4
:maxdepth: 2
:caption: Contents:
pyramid
fields
vis
io
demos
Indices and tables
......@@ -20,4 +24,3 @@ Indices and tables
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
docs/io.rst 0 → 100644
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The io visualization submodule
===============================
General empyre.io docu here!
The io_field module
-------------------
.. automodule:: empyre.io.io_field
:members:
:show-inheritance:
The field_plugins module
------------------------
.. automodule:: empyre.io.field_plugins
:members:
:show-inheritance:
docs/make.bat
View file @ 6e3128b8
@ECHO OFF
pushd %~dp0
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
set SOURCEDIR=.
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
%SPHINXBUILD% >NUL 2>NUL
if errorlevel 9009 (
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.The 'sphinx-build' command was not found. Make sure you have Sphinx
echo.installed, then set the SPHINXBUILD environment variable to point
echo.to the full path of the 'sphinx-build' executable. Alternatively you
echo.may add the Sphinx directory to PATH.
echo.
echo.Build finished. The text files are in %BUILDDIR%/text.
goto end
echo.If you don't have Sphinx installed, grab it from
echo.http://sphinx-doc.org/
exit /b 1
)
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
)
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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
)
:help
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
:end
popd
docs/pyramid.numcore.rst deleted 100644 → 0
View file @ 6e9bc36e
numcore Package
===============
:mod:`numcore` Package
----------------------
.. automodule:: pyramid.numcore
:members:
:undoc-members:
:show-inheritance:
:special-members:
docs/pyramid.rst deleted 100644 → 0
View file @ 6e9bc36e
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
docs/vis.rst 0 → 100644
View file @ 6e3128b8
The vis visualization submodule
===============================
General empyre.vis docu here!
All functions implemented in the subpackages can be accessed directly in the ``empyre.io`` namespace, with the exception
of the ``color`` module, whose methods are accessible via ``empyre.vis.colors``.
Note that the y-axis of all image plots is flipped in comparison to ``matplotlib.pyplot.imshow``, i.e. that the
origin is `'lower'` in this case instead of `'upper'`.
Please note that 3D plots only work in your Jupyter notebook after first installing and then enabling the corresponding
mayavi extension:
.. code-block:: bash
$ jupyter nbextension install --py mayavi --user
$ jupyter nbextension enable mayavi --user --py
If you'd like to utilize 3D plots in your Jupyter Notebook or in the Python Interactive Window
.. code-block:: Python
>>> from mayavi import mlab
>>> mlab.init_notebook('x3d')
The backend, chosen by the `init_notebook` function can be `ipy` (the default, produces static images in Juypter
Notebook and does not work in VSCode), `x3d` (produces interactive plots in Jupyter Noteboo, but seems to not work with
VSCode), or `png` (produces png-images, which work in both Jupyter Notebooks and VSCode).
For more information and a quick introduction visit the `mayavi tips & tricks section <https://docs.enthought.com/mayavi/mayavi/tips.html>`_.
The plot2d module
-----------------
.. automodule:: empyre.vis.plot2d
:members:
:show-inheritance:
The decorators module
---------------------
.. automodule:: empyre.vis.decorators
:members:
:show-inheritance:
The colors module
-----------------
.. automodule:: empyre.vis.colors
:members:
:show-inheritance:
The tools module
----------------
.. automodule:: empyre.vis.tools
:members:
:show-inheritance:
icon.ico deleted 100644 → 0
View file @ 6e9bc36e
icon.ico

132 KiB

pyproject.toml 0 → 100644
View file @ 6e3128b8
[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
[project]
name = "empyre"
dynamic = ["version"]
description = "Electron Microscopy Python Reconstruction"
readme = "README.rst"
license = "GPL-3.0-or-later"
requires-python = ">=3.6"
authors = [
{ name = "Jan Caron", email = "j.caron@fz-juelich.de" },
]
keywords = [
"Electron Microscopy",
"Inverse Problem Solving",
"Model-based Reconstrution",
]
classifiers = [
"Development Status :: 3 - Alpha",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Topic :: Scientific/Engineering",
]
dependencies = [
"matplotlib >= 3.2",
"numpy >= 1.17",
"Pillow",
"scikit-image",
"scipy",
"tqdm",
]
[project.optional-dependencies]
3d = [
"mayavi >= 4.7",
]
all = [
"cmocean",
"pyfftw",
]
colors = [
"cmocean",
]
docs = [
"nbsphinx",
"nbsphinx_link",
"numpydoc",
"pandoc",
"sphinx",
"sphinx_rtd_theme",
]
fftw = [
"pyfftw",
]
io = [
"hyperspy",
"tvtk",
]
tests = [
"coverage",
"pyroma",
"pytest",
"pytest-cov",
"pytest-flake8",
"pytest-runner",
]
[project.urls]
Homepage = "https://iffgit.fz-juelich.de/empyre/empyre"
[tool.hatch.version]
path = "src/empyre/__init__.py"
[tool.hatch.build.targets.sdist]
include = [
"/src",
"/tests",
]