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/analytic.py

-# -*- coding: utf-8 -*-
-"""Create simple phasemaps from analytic solutions."""
-
-# TODO: Currently just for projections along the z-axis!
-
-
-import numpy as np
-from numpy import pi
-
-
-PHI_0 = -2067.83  # magnetic flux in T*nm²
-
-
-def phase_mag_slab(dim, res, beta, 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)
-        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
-
-    '''
-    # Function for the phase:
-    def phiMag(x,  y):
-        def F0(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(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)))
-    # Process input parameters:
-    z_dim, y_dim, x_dim = dim
-    y0 = res * (center[1] + 0.5)  # y0, x0 have to be in the center of a pixel,
-    x0 = res * (center[2] + 0.5)  # hence: cellindex + 0.5
-    Lz, Ly, Lx = res * width[0], res * width[1], res * width[2]
-    coeff = b_0 / (4*PHI_0)
-    # Create grid:
-    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 phase:
-    return phiMag(xx, yy)
-
-
-def phase_mag_disc(dim, res, beta, 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)
-        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
-
-    '''
-    # Function for the phase:
-    def phiMag(x, y):
-        r = np.hypot(x - x0, y - y0)
-        r[center[1], center[2]] = 1E-30
-        result = coeff * Lz * ((y - y0) * np.cos(beta) - (x - x0) * np.sin(beta))
-        result *= np.where(r <= R, 1, (R / r) ** 2)
-        return result
-    # Process input parameters:
-    z_dim, y_dim, x_dim = dim
-    y0 = res * (center[1] + 0.5)  # y0, x0 have to be in the center of a pixel,
-    x0 = res * (center[2] + 0.5)  # hence: cellindex + 0.5
-    Lz = res * height
-    R = res * radius
-    coeff = - pi * b_0 / (2*PHI_0)
-    # Create grid:
-    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 phase:
-    return phiMag(xx, yy)
-
-
-def phase_mag_sphere(dim, res, beta, 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)
-        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
-
-    '''
-    # Function for the phase:
-    def phiMag(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(beta) - (x - x0) * np.sin(beta))
-        result *= np.where(r > R, 1, (1 - (1 - (r / R) ** 2) ** (3. / 2.)))
-        return result
-    # Process input parameters:
-    z_dim, y_dim, x_dim = dim
-    y0 = res * (center[1] + 0.5)  # y0, x0 have to be in the center of a pixel,
-    x0 = res * (center[2] + 0.5)  # hence: cellindex + 0.5
-    R = res * radius
-    coeff = - 2./3. * pi * b_0 / PHI_0
-    # Create grid:
-    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 phase:
-    return phiMag(xx, yy)

pyramid/holoimage.py

-# -*- coding: utf-8 -*-
-"""Display holography images with the gradient direction encoded in color"""
-
-
-import numpy as np
-import matplotlib as mpl
-import matplotlib.pyplot as plt
-from pyramid.phasemap import PhaseMap
-from numpy import pi
-from PIL import Image
-
-
-CDICT = {'red':   [(0.00, 1.0, 0.0),
-                   (0.25, 1.0, 1.0),
-                   (0.50, 1.0, 1.0),
-                   (0.75, 0.0, 0.0),
-                   (1.00, 0.0, 1.0)],
-
-         'green': [(0.00, 0.0, 0.0),
-                   (0.25, 0.0, 0.0),
-                   (0.50, 1.0, 1.0),
-                   (0.75, 1.0, 1.0),
-                   (1.00, 0.0, 1.0)],
-
-         'blue':  [(0.00, 1.0, 1.0),
-                   (0.25, 0.0, 0.0),
-                   (0.50, 0.0, 0.0),
-                   (0.75, 0.0, 0.0),
-                   (1.00, 1.0, 1.0)]}
-
-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
-
-    '''
-    assert isinstance(phase_map, PhaseMap), 'phase_map has to be a PhaseMap object!'
-    # Calculate the holography image intensity:
-    img_holo = (1 + np.cos(density * phase_map.phase * pi/2)) / 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_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)
-    # Color code the angle and create the holography image:
-    rgba = HOLO_CMAP(phase_angle)
-    rgb = (255.999 * img_holo.T * phase_magnitude.T * rgba[:, :, :3].T).T.astype(np.uint8)
-    holo_image = Image.fromarray(rgb)
-    return holo_image
-
-
-def make_color_wheel():
-    '''Display a color wheel for the gradient direction.
-    Arguments:
-        None
-    Returns:
-        None
-
-    '''
-    x = np.linspace(-256, 256, num=512)
-    y = np.linspace(-256, 256, num=512)
-    xx, yy = np.meshgrid(x, y)
-    r = np.sqrt(xx ** 2 + yy ** 2)
-    # Create the wheel:
-    color_wheel_magnitude = (1 - np.cos(r * pi/360)) / 2
-    color_wheel_magnitude *= 0 * (r > 256) + 1 * (r <= 256)
-    color_wheel_angle = (1 - np.arctan2(xx, -yy)/pi) / 2
-    # Color code the angle and create the holography image:
-    rgba = HOLO_CMAP(color_wheel_angle)
-    rgb = (255.999 * color_wheel_magnitude.T * rgba[:, :, :3].T).T.astype(np.uint8)
-    color_wheel = Image.fromarray(rgb)
-    # Plot the color wheel:
-    fig = plt.figure()
-    ax = fig.add_subplot(111, aspect='equal')
-    ax.imshow(color_wheel)
-    ax.set_title('Color Wheel')
-    ax.set_xlabel('x-axis')
-    ax.set_ylabel('y-axis')
-
-
-def display(holo_image, title='Holography Image', axis=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, a new figure is created)
-    Returns:
-        None
-
-    '''
-    # If no axis is specified, a new figure is created:
-    if axis is None:
-        fig = plt.figure()
-        axis = fig.add_subplot(1, 1, 1, aspect='equal')
-    # Plot the image and set axes:
-    axis.imshow(holo_image)
-    axis.set_title(title)
-    axis.set_xlabel('x-axis')
-    axis.set_ylabel('y-axis')
-
-
-def display_combined(phase_map, density, title='Combined Plot'):
-    '''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
-
-    '''
-    # Create combined plot and set title:
-    fig = plt.figure(figsize=(14, 7))
-    fig.suptitle(title, fontsize=20)
-    # Plot holography image:
-    holo_axis = fig.add_subplot(1, 2, 1, aspect='equal')
-    display(holo_image(phase_map, density), axis=holo_axis)
-    # Plot phase map:
-    phase_axis = fig.add_subplot(1, 2, 2, aspect='equal')
-    phase_map.display(axis=phase_axis)