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DOCS: added example notebook to docs page, more docstring updates
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‎docs/notebook_prep.py‎

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import argparse
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import json
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import base64
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from pathlib import Path
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def convert_notebook_attachments(notebook_path: str, output_path: str):
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"""Convert notebook attachments to embedded base64 images."""
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with open(notebook_path, 'r', encoding='utf-8') as f:
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nb = json.load(f)
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for cell in nb.get('cells', []):
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if cell.get('cell_type') == 'markdown' and 'attachments' in cell:
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attachments = cell['attachments']
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source = cell['source']
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# Convert source to list if it's a string
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if isinstance(source, str):
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source = [source]
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new_source = []
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for line in source:
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# Replace attachment references with data URIs
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for att_name, att_data in attachments.items():
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if f'attachment:{att_name}' in line:
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# Get the first available image format
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mime_type = list(att_data.keys())[0]
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data = att_data[mime_type]
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data_uri = f'data:{mime_type};base64,{data}'
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line = line.replace(f'attachment:{att_name}', data_uri)
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new_source.append(line)
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cell['source'] = new_source
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# Remove attachments after conversion
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del cell['attachments']
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# Save the modified notebook
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with open(output_path, 'w', encoding='utf-8') as f:
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json.dump(nb, f, indent=1)
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print(f"Converted notebook saved to: {output_path}")
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# ----------------------------------------------------------------------
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def main() -> None:
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parser = argparse.ArgumentParser()
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parser.add_argument(
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"notebook_path",
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)
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parser.add_argument(
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"output_path",
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)
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args = parser.parse_args()
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convert_notebook_attachments(args.notebook_path, args.output_path)
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if __name__ == "__main__":
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main()

‎docs/requirements.txt‎

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sphinx
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sphinx-rtd-theme
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nbsphinx
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myst-nb

‎docs/source/api/io.rst‎

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* Loading functions:
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* Ptychography data processed by PEAR/Pty-Chi: :func:`pyxalign.io.loaders.pear.load_data_from_pear_format`
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* XRF Data: :func:`pyxalign.io.loaders.pear.load_data_from_xrf_format`
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* XRF Data: :func:`pyxalign.io.loaders.xrf.load_data_from_xrf_format`
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* Loading GUI:
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* Any type of data: :func:`pyxalign.gui.launch_data_loader`
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.. autofunction:: pyxalign.io.loaders.xrf.load_data_from_xrf_format
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.. autoclass:: pyxalign.io.loaders.xrf.XRFLoadOptions
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:members:
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:inherited-members:
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:undoc-members:
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:show-inheritance:
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:member-order: bysource
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.. .. autoclass:: pyxalign.io.loaders.xrf.XRFLoadOptions
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.. :members:
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.. :inherited-members:
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.. :undoc-members:
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.. :show-inheritance:
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.. :member-order: bysource
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.. automodule:: pyxalign.io.loaders.xrf
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:members:
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:inherited-members:
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:undoc-members:
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:show-inheritance:
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:exclude-members: XRFLoadOptions, load_data_from_xrf_format
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:exclude-members: load_data_from_xrf_format
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Data Structures
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^^^^^^^^^^^^^^^^^^^

‎docs/source/conf.py‎

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extensions = [
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"sphinx.ext.autodoc",
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# 'sphinx.ext.autosummary',
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"sphinx.ext.napoleon",
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"sphinx.ext.viewcode",
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"nbsphinx",
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"myst_nb",
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]
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# # Enable autosummary to glsenerate stub pages automatically
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# autosummary_generate = True
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# MyST-NB configuration
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nb_execution_mode = "off" # Don't re-execute notebooks
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nb_render_image_options = {"align": "center"}
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# Enable processing of notebook attachments (pasted images)
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nb_output_stderr = "show"
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nb_merge_streams = True
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# Configure MIME type priorities for different output formats
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nb_mime_priority_overrides = [
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('html', 'image/png', 10),
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('html', 'image/jpeg', 10),
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('html', 'image/svg+xml', 10),
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('html', 'text/html', 20),
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]
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# Ensure MyST parser is configured
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myst_enable_extensions = [
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"colon_fence",
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"deflist",
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"dollarmath",
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"html_image",
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]
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# Configure autodoc to respect __all__
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autodoc_default_options = {
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templates_path = ["_templates"]
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exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
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# -- Options for HTML output -------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
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html_theme = "sphinx_rtd_theme"
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html_static_path = ["_static"]
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‎docs/source/examples/index.rst‎

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Examples
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===========
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Additional examples will be added periodically.
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.. toctree::
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:maxdepth: 1
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simulated_shepp_logan_phantom_alignment_converted

‎docs/source/examples/simulated_shepp_logan_phantom_alignment_converted.ipynb‎

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‎docs/source/index.rst‎

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.. You can adapt this file completely to your liking, but it should at least
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.. contain the root `toctree` directive.
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pyxalign documentation
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pyxalign Documentation
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======================
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.. Add your content using ``reStructuredText`` syntax. See the
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.. `reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
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.. documentation for details.
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hello!
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Welcome to the docs page for **pyxalign**!
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pyxalign is a python package for loading, aligning, and reconstructing 3D volumes for tomography or laminography datasets. pyxalign currently supports ptychography and x-ray flourescence (XRF) datasets.
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To get started with pyxalign, try running an :doc:`example </examples/index>` and consult the :doc:`file loading documentation </api/io>` to learn how to load data from your beamline.
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If you have any questions about pyxalign or if you would like me to add a data loader for your experiment, please email me at hruth@anl.gov.
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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api/index
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examples/index
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install_guide
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‎docs/source/install_guide.rst‎

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.. include:: ../../README.md
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:parser: myst_parser.sphinx_

‎src/pyxalign/data_structures/volume.py‎

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print("There is no volume data to save!")
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with h5py.File(file_path, "w") as F:
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F.create_dataset(name="volume", data=self.data)
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print(f"File saved to: {file_path}")
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def get_tomogram_rotation_angles(

‎src/pyxalign/io/loaders/xrf/api.py‎

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format.
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Args:
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options (pear.options.XRFLoadOptions): Configuration options
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options (xrf.options.XRFLoadOptions): Configuration options
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for loading data.
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Returns:

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