Ani branch - #4
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Aug 14, 2026
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- Added UNets and other image models
- Added losses
- Improved docs
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Pull request overview
This PR expands the public API/docs surface for new image models (UNet variants) and additional loss functions, and updates the documentation build outputs/styles. It also adds unit tests for confusion-matrix-based losses and adjusts pytest configuration.
Changes:
- Added API docs pages and API exports for UNet/ReverseHalfUNet + multiple loss/config symbols (including a new
_internalnamespace). - Added unit tests for confusion losses; migrated pytest settings from
pytest.iniintopyproject.toml. - Updated Sphinx docs configuration/templates and introduced custom CSS + regenerated
_buildHTML outputs.
Reviewed changes
Copilot reviewed 88 out of 242 changed files in this pull request and generated 9 comments.
Show a summary per file
| File | Description |
|---|---|
| tools/docs/index.rst | Adds _internal docs to top-level doc index. |
| tools/docs/conf.py | Adjusts linkcode/docstring processing; adds custom CSS. |
| tools/docs/api_docs/im2sim/models/UNet.rst | New API doc page for UNet. |
| tools/docs/api_docs/im2sim/models/ReverseHalfUNet.rst | New API doc page for ReverseHalfUNet. |
| tools/docs/api_docs/im2sim/models.rst | Adds UNet classes to models autosummary. |
| tools/docs/api_docs/im2sim/losses/TverskyLoss.rst | New API doc page for TverskyLoss. |
| tools/docs/api_docs/im2sim/losses/SSIMLoss.rst | New API doc page for SSIMLoss. |
| tools/docs/api_docs/im2sim/losses/IoULoss.rst | New API doc page for IoULoss. |
| tools/docs/api_docs/im2sim/losses/FocalTverskyLoss.rst | New API doc page for FocalTverskyLoss. |
| tools/docs/api_docs/im2sim/losses/F1Loss.rst | New (but currently inconsistent) API doc page for F1Loss. |
| tools/docs/api_docs/im2sim/losses/DiceLoss.rst | New API doc page for DiceLoss. |
| tools/docs/api_docs/im2sim/losses.rst | Populates losses autosummary list. |
| tools/docs/api_docs/im2sim/layers.rst | Removes ImageConvBlock from layers autosummary list. |
| tools/docs/api_docs/im2sim/configs/UNetConfig.rst | New API doc page for UNetConfig. |
| tools/docs/api_docs/im2sim/configs/ReverseHalfUNetConfig.rst | New API doc page for ReverseHalfUNetConfig. |
| tools/docs/api_docs/im2sim/configs/LayerConfig.rst | New API doc page for LayerConfig. |
| tools/docs/api_docs/im2sim/configs.rst | Updates configs autosummary list. |
| tools/docs/api_docs/im2sim/_internal/register_config.rst | New API doc page for _internal.register_config. |
| tools/docs/api_docs/im2sim/_internal/Config.rst | New API doc page for _internal.Config. |
| tools/docs/api_docs/im2sim/_internal.rst | New module page for im2sim._internal. |
| tools/docs/api_docs/im2sim.rst | Adds _internal to im2sim module listing. |
| tools/docs/_templates/_internal/function.rst | New autosummary template for _internal functions. |
| tools/docs/_templates/_internal/class.rst | New autosummary template for _internal classes. |
| tools/docs/_build/html/templates/index.html | Regenerated Sphinx HTML output for templates page. |
| tools/docs/_build/html/sitemap.xml | Adds/updates generated sitemap for HTML builder. |
| tools/docs/_build/html/search.html | Regenerated Sphinx HTML output for search page. |
| tools/docs/_build/html/robots.txt | Adds robots.txt referencing sitemap. |
| tools/docs/_build/html/py-modindex.html | Regenerated Sphinx HTML output for module index. |
| tools/docs/_build/html/index.html | Regenerated Sphinx HTML output for site index. |
| tools/docs/_build/html/guide/recon.html | Regenerated Sphinx HTML output for guide page. |
| tools/docs/_build/html/guide/install.html | Regenerated Sphinx HTML output for guide page. |
| tools/docs/_build/html/guide/faq.html | Regenerated Sphinx HTML output for guide page. |
| tools/docs/_build/html/guide/contribute.html | Regenerated Sphinx HTML output for guide page. |
| tools/docs/_build/html/.buildinfo | Updates Sphinx build metadata. |
| tools/docs/_build/html/_static/tfmri_icon.svg | Adds generated static asset (icon). |
| tools/docs/_build/html/_static/tfmri_icon_96px.png | Adds generated static asset (icon). |
| tools/docs/_build/html/_static/tfmri_icon_48px.png | Adds generated static asset (icon). |
| tools/docs/_build/html/_static/tfmri_icon_32px.png | Adds generated static asset (icon). |
| tools/docs/_build/html/_static/tfmri_icon_24px.png | Adds generated static asset (icon). |
| tools/docs/_build/html/_static/sphinx_highlight.js | Adds generated/static JS asset. |
| tools/docs/_build/html/_static/print.css | Adds generated/static CSS asset. |
| tools/docs/_build/html/_static/plus.png | Adds generated/static icon asset. |
| tools/docs/_build/html/_static/minus.png | Adds generated/static icon asset. |
| tools/docs/_build/html/_static/language_data.js | Adds generated/static JS asset. |
| tools/docs/_build/html/_static/file.png | Adds generated/static icon asset. |
| tools/docs/_build/html/_static/download_icon_white.svg | Adds generated/static icon asset. |
| tools/docs/_build/html/_static/download_icon_white_32px.png | Adds generated/static icon asset. |
| tools/docs/_build/html/_static/documentation_options.js | Updates Sphinx options (builder now html). |
| tools/docs/_build/html/_static/doctools.js | Adds generated/static JS asset. |
| tools/docs/_build/html/_static/custom.css | Adds generated/static custom CSS. |
| tools/docs/_build/html/_sources/tutorials.rst.txt | Adds generated source for tutorials page. |
| tools/docs/_build/html/_sources/templates/index.rst.txt | Adds generated source for templates index. |
| tools/docs/_build/html/_sources/index.rst.txt | Updates generated source index. |
| tools/docs/_build/html/_sources/guide/recon.ipynb.txt | Adds generated notebook source. |
| tools/docs/_build/html/_sources/guide/optim.ipynb.txt | Adds generated notebook source. |
| tools/docs/_build/html/_sources/guide/linalg.ipynb.txt | Adds generated notebook source. |
| tools/docs/_build/html/_sources/guide/install.rst.txt | Adds generated guide source. |
| tools/docs/_build/html/_sources/guide/faq.rst.txt | Adds generated guide source. |
| tools/docs/_build/html/_sources/guide/contribute.ipynb.txt | Adds generated notebook source. |
| tools/docs/_build/html/_sources/guide.rst.txt | Adds generated guide index source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/plot.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/ops/normtorange.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/ops.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/models/UNet.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/models/ReverseHalfUNet.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/models/HalfUNet.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/models.rst.txt | Updates generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/losses/TverskyLoss.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/losses/SSIMLoss.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/losses/IoULoss.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/losses/FocalTverskyLoss.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/losses/F1Loss.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/losses/DiceLoss.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/losses.rst.txt | Updates generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/layers/SqueezeExcite.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/layers/ImageConvBlock.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/layers/GraphResDecoderBlock.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/layers/GraphConvResBlock.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/layers/GraphConvBlock.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/layers/GhostConv.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/layers/EfficientChannelAttn.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/layers/DepthwiseSeparableConv.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/layers/DepthwiseConv.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/layers/DefaultGraphNorm.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/layers/ConditionedSqueezeExcite.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/layers.rst.txt | Updates generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/data.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/configs/UNetConfig.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/configs/ReverseHalfUNetConfig.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/configs/LayerConfig.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/configs/ImageConvBlockConfig.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/configs/HalfUNetConfig.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/configs.rst.txt | Updates generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/_internal/register_config.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/_internal/Config.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim/_internal.rst.txt | Adds generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs/im2sim.rst.txt | Updates generated API-doc source. |
| tools/docs/_build/html/_sources/api_docs.rst.txt | Adds generated API-doc index source. |
| tools/docs/_build/dirhtml/sitemap.xml | Removes old dirhtml sitemap output. |
| tools/docs/_build/dirhtml/guide/linalg/index.html | Removes old dirhtml build output page. |
| tools/assets/custom.css | Adds custom CSS for docs theme/header layout. |
| tests/unit/losses/test_confusion_losses.py | Adds unit tests validating confusion-loss implementations. |
| pytest.ini | Removes pytest.ini in favor of pyproject configuration. |
| pyproject.toml | Adds pytest pythonpath + warning filters under pyproject config. |
| my_config.yaml | Adds example config file for model setup. |
| im2sim/src/utils/api_util.py | Refactors API export/import utilities and submodule metadata. |
| im2sim/src/losses/init.py | Exposes new losses submodules. |
| im2sim/src/layers/module_config.py | Updates config serialization/deserialization and _internal exports. |
| im2sim/src/layers/layer_util.py | Updates layer registration helpers and activation handling. |
| im2sim/src/layers/graph_blocks.py | Minor formatting/whitespace updates. |
| im2sim/src/layers/init.py | Exposes new unet module in layers package. |
| im2sim/src/data/transforms.py | Reformats imports. |
| im2sim/src/data/ops.py | Adds API export for normtorange and minor formatting. |
| im2sim/src/data/core.py | Minor formatting/whitespace updates. |
| im2sim/src/data/init.py | Exposes collate in data public surface. |
| im2sim/src/init.py | Normalizes submodule imports/aliases. |
| im2sim/_api/models/init.py | Exports ReverseHalfUNet and UNet in public API. |
| im2sim/_api/losses/init.py | Exports new confusion losses + SSIMLoss in public API. |
| im2sim/_api/layers/init.py | Reorders/adjusts exported layer symbols. |
| im2sim/_api/configs/init.py | Exports new configs (LayerConfig, UNet configs). |
| im2sim/_api/_internal/init.py | Adds _internal namespace exports. |
| im2sim/init.py | Imports _internal namespace at top level. |
| .github/workflows/build_package.yml | Adds CI test job (ruff + pytest) on PRs and main. |
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| url = 'https://github.com/mrphys/im2sim' | ||
| # Add version blob. | ||
| url += '/blob/v' + release | ||
| # url += '/blob/v' + release | ||
| # Add file. | ||
| url += '/' + file |
| @@ -0,0 +1,5 @@ | |||
| im2sim._internal.{{ objname | escape | underline }}================= | |||
| @@ -0,0 +1,7 @@ | |||
| im2sim._internal.{{ objname | escape | underline }}================= | |||
| @@ -0,0 +1,8 @@ | |||
| im2sim.models.UNet | |||
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| import numpy as np | ||
| import numpy as np |
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| spec = importlib.machinery.ModuleSpec( | ||
| f"tensorflow_mri.{namespace}", APILoader(namespace=namespace) | ||
| ) | ||
| module = importlib.util.module_from_spec(spec) |
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| { | ||
| "__class__": "ReverseHalfUNetConfig", | ||
| "hidden_channels": 64, | ||
| "n_levels": 3, | ||
| "pool_cfg": [ |
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| im2sim.losses.F1Loss | ||
| ==================== | ||
|
|
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| .. currentmodule:: im2sim.losses | ||
|
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| """Process autodoc docstrings.""" | ||
| text = process_docstring_text('\n'.join(lines)) | ||
| lines[:] = text.splitlines() | ||
| return | ||
| # if what != 'class': |
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