desktop.ini

-[.ShellClassInfo]
-IconResource=C:\Users\Jan\PhD Thesis\Pyramid\icon.ico,0
-[ViewState]
-Mode=
-Vid=
-FolderType=Generic

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# 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
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# 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

+# Configuration file for the Sphinx documentation builder.
+#
+# 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
+
+
+# Use command in docs to generate stubs and make html afterwards:
+# > sphinx-apidoc -o api ../src/empyre
+# > make html
+
+
+# -- Path setup --------------------------------------------------------------
+
+# 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')))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'EMPyRe'
+copyright = '2020, Jan Caron'
+author = 'Jan Caron'
+
+
+# -- General configuration ---------------------------------------------------
+
+# 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']
+
+numpydoc_show_class_members = False
+add_module_names = False
+
+# 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.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- 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 = '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']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+html_logo = 'EMPyRe Logo.png'
+
+# 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'
+
+# cannot cache unpickable configuration value: 'nbsphinx_custom_formats
+# See https://github.com/sphinx-doc/sphinx/issues/12300
+suppress_warnings = ["config.cache"]

docs/demos.rst

+Demos
+-----
+
+.. toctree::
+    demos/demo1
+    demos/demo2
+    demos/demo3

docs/demos/demo1.nblink

+{
+    "path": "../../demos/demo1_first_steps.ipynb"
+}
\ No newline at end of file

docs/demos/demo2.nblink

+{
+    "path": "../../demos/demo2_handling_3d_fields.ipynb"
+}
\ No newline at end of file

docs/demos/demo3.nblink

+{
+    "path": "../../demos/demo3_io_and_field_manipulation.ipynb"
+}
\ No newline at end of file

docs/fields.rst

+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/index.rst

+.. 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.
+
+EMPyRe - Electron Microscopy Reconstruction
+===========================================
+
+.. include:: ../README.rst
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   fields
+   vis
+   io
+   demos
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/io.rst

+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

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	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.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/vis.rst

+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:

pyproject.toml

+[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",
+]

pyramid/__init__.py

-# -*- coding: utf-8 -*-
-

pyramid/analytic.py

-# -*- coding: utf-8 -*-
-"""Create simple phasemaps from analytic solutions."""
-
-
-import numpy as np
-import matplotlib.pyplot as plt
-from numpy import pi
-
-
-PHI_0 = 2067.83  # magnetic flux in T*nm²
-
-
-def plot_phase(phase, res, name):
-    fig = plt.figure()
-    ax = fig.add_subplot(111, aspect='equal')
-    plt.pcolormesh(phase, cmap='gray')
-    ticks = ax.get_xticks() * res
-    ax.set_xticklabels(ticks.astype(int))
-    ticks = ax.get_yticks() * res
-    ax.set_yticklabels(ticks.astype(int))
-    ax.set_title('Analytical Solution' + name)
-    ax.set_xlabel('x-axis [nm]')
-    ax.set_ylabel('y-axis [nm]')
-    plt.colorbar()
-    plt.show()
-
-
-def phasemap_slab(dim, res, beta, center, width, b_0):
-    '''INPUT VARIABLES'''
-    y_dim, x_dim = dim
-    # y0, x0 have to be in the center of a pixel, hence: cellindex + 0.5
-    y0 = res * (center[0] + 0.5)
-    x0 = res * (center[1] + 0.5)
-    # Ly, Lx have to be odd, because the slab borders should not lie in the
-    # center of a pixel (so L/2 can't be an integer)
-    Ly = res * ( width[0] + (width[0]+1)%2) 
-    Lx = res * ( width[1] + (width[1]+1)%2)   
-    
-    '''COMPUTATION MAGNETIC PHASE SHIFT (REAL SPACE) SLAB'''
-
-    coeff = b_0 * res / ( 4 * PHI_0 )
-     
-    def F0(x,y):
-        a = np.log(x**2 + y**2)
-        b = np.arctan(x / y)
-        return x*a - 2*x + 2*y*b   
-    
-    def phiMag(x,y):
-        return coeff * ( - np.cos(beta) * ( 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(beta) * ( 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) ) )
-             
-    '''CREATE COORDINATE GRIDS'''
-    x = np.linspace(res/2,x_dim*res-res/2,num=x_dim)
-    y = np.linspace(res/2,y_dim*res-res/2,num=y_dim)
-    xx, yy = np.meshgrid(x,y)
-    
-    return phiMag(xx, yy)
-    
-    
-def phasemap_disc(dim, res, beta, center, radius, b_0):
-    '''INPUT VARIABLES'''
-    y_dim, x_dim = dim
-    # y0, x0 have to be in the center of a pixel, hence: cellindex + 0.5
-    y0 = res * (center[0] + 0.5)
-    x0 = res * (center[1] + 0.5)
-    # TODO: Explanation
-    # Ly, Lx have to be odd, because the slab borders should not lie in the
-    # center of a pixel (so L/2 can't be an integer)
-    R  = res * radius
-    
-    '''COMPUTATION MAGNETIC PHASE SHIFT (REAL SPACE) DISC'''
-      
-    coeff = - pi * res * b_0 / ( 2 * PHI_0 )
-    
-#    import pdb; pdb.set_trace()    
-    
-    def phiMag(x,y):
-        r = np.hypot(x-x0, y-y0)
-        r[center[0], center[1]] = 1E-18
-        result = coeff * ((y-y0) * np.cos(beta) - (x-x0) * np.sin(beta))
-        in_or_out = 1 * (r < R) + (R / r) ** 2 * (r > R)
-#        import pdb; pdb.set_trace() 
-        result *= in_or_out
-        return result
-    
-    '''CREATE COORDINATE GRIDS'''
-    x = np.linspace(res/2,x_dim*res-res/2,num=x_dim)
-    y = np.linspace(res/2,y_dim*res-res/2,num=y_dim)
-    xx, yy = np.meshgrid(x,y)
-    
-    return phiMag(xx, yy)
-    
-    
-def phasemap_sphere(dim, res, beta, center, radius, b_0):
-    
-    # TODO: Sphere is equivalent to disc, if only one pixel in z is used!
-    
-    '''INPUT VARIABLES'''
-    y_dim, x_dim = dim
-    y0, x0 = center
-    R = radius
-    
-    '''COMPUTATION MAGNETIC PHASE SHIFT (REAL SPACE) SPHERE''' 
-      
-    coeff = - 2/3 * pi * R**3 * b_0 / PHI_0 * res/R
-      
-    def phiMag(x,y):
-        r = np.sqrt((x-x0) ** 2 + (y-y0) ** 2)      
-        result = coeff  / r**2 * ((y-y0) * np.cos(beta) - (x-x0) * np.sin(beta))
-        in_or_out = 1 * (r > R) + (1 - (1-(r/R)**2)**(3/2)) * (r < R)    
-        result *= in_or_out
-        return result
-    
-    '''CREATE COORDINATE GRIDS'''
-    x = np.linspace(res/2,x_dim*res-res/2,num=x_dim)
-    y = np.linspace(res/2,y_dim*res-res/2,num=y_dim)
-    xx, yy = np.meshgrid(x,y)
-    
-    return phiMag(xx, yy)
\ No newline at end of file