trame-slicer 0.1.0__tar.gz

trame_slicer-0.1.0/.codespellrc

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+[codespell]
+skip = **/package-lock.json,trame_slicer/resources/*

trame_slicer-0.1.0/.flake8

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+[flake8]
+
+ignore =
+    # Black and flake8 conflict here
+    E203
+    # Just assume black did a good job with the line lengths
+    E501
+
+per-file-ignores =
+    __init__.py: F401, F403

trame_slicer-0.1.0/.gitattributes

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+tests/data/** filter=lfs diff=lfs merge=lfs -text

trame_slicer-0.1.0/.github/workflows/test_and_release.yml

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+name: Test and Release
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      # Install and run pre-commit
+      - run: |
+          pip install pre-commit
+          pre-commit install
+          pre-commit run --all-files
+
+  pytest:
+    if: false # Test running currently deactivated as it requires slicer lib wheel generation for each target
+    name: Pytest ${{ matrix.config.name }}
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.13"]
+        config:
+          - { name: "Linux", os: ubuntu-latest }
+          - { name: "MacOSX", os: macos-latest }
+          - { name: "Windows", os: windows-latest }
+
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install and Run Tests
+        run: |
+          pip install .[dev]
+          pytest -s ./tests
+
+  release:
+    needs: [pre-commit]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push'
+    environment:
+      name: pypi
+      url: https://pypi.org/p/trame-slicer
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+      contents: write # IMPORTANT: mandatory for making GitHub Releases
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Python Semantic Release
+        id: release
+        uses: python-semantic-release/python-semantic-release@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+
+      # https://docs.pypi.org/trusted-publishers/using-a-publisher/
+      - name: Publish package distributions to PyPI
+        if: steps.release.outputs.released == 'true'
+        uses: pypa/gh-action-pypi-publish@release/v1

trame_slicer-0.1.0/.gitignore

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+.DS_Store
+node_modules
+.venv
+
+# local env files
+.env.local
+.env.*.local
+
+# Log files
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+pnpm-debug.log*
+
+# Editor directories and files
+.idea
+.vscode
+*.suo
+*.ntvs*
+*.njsproj
+*.sln
+*.sw?
+tests/data/
+
+__pycache__
+*egg-info
+*pyc
+/dist

trame_slicer-0.1.0/.pre-commit-config.yaml

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+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+exclude: ^.cruft.json|.copier-answers.yml$
+
+repos:
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.19.1"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.*]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v5.0.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+        exclude: "direct_view_factory.py|view_events.py"
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: "v3.4.2"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.9.1"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes", "--line-length", "120"]
+      - id: ruff-format
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.3.0"
+    hooks:
+      - id: codespell
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.10.0.1"
+    hooks:
+      - id: shellcheck
+
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+        exclude: .pre-commit-config.yaml
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.23"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]

trame_slicer-0.1.0/CHANGELOG.md

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+# CHANGELOG
+
+
+## v0.1.0 (2025-04-14)
+
+### Features
+
+- **api**: Change paths to use slicer package
+  ([`e2639ad`](https://github.com/KitwareMedical/trame-slicer/commit/e2639ad6736203af0a6b6545c78ddca3b8c641ca))
+
+* Change paths to use slicer package for Slicer app compatibility
+
+- **segmentation**: (wip) Add segment editor
+  ([`8702402`](https://github.com/KitwareMedical/trame-slicer/commit/870240271255ca84020d0399653f188340361955))
+
+* Add segmentation editor and paint/erase effect * Add segmentation editor scissor effect * Add
+  examples
+
+- **segmentation**: Refactoring
+  ([`3deb00c`](https://github.com/KitwareMedical/trame-slicer/commit/3deb00c6886b666c51bd22b301f3a02bc02341ad))
+
+* Rename SegmentationEffect to Widget * Rename SegmentationTool to Effect * Rename
+  SegmentationManager to SegmentationEditor * Rename SegmentationEditor to SegmentModifier * Move
+  Segmentation logic to SegmentationEditor * Fix segmentation sanitize when using empty segment *
+  Fix segmentation export to NIFTI file * Move IO to segmentation editor * Fix brush scaling in
+  absolute mode and default to invariant * Fix events sent twice in Slice views * Move events
+  handling in views in dedicated classes * Add SegmentRegionMask responsible for region masking *
+  Fix failing tests * Add support for segmentation Undo / Redo * Add helper for signal / slot
+  connection * Add segmentation button to medical example * Fix brush diameter update when switching
+  views * Add Undo / Redo functionnalities * Update example * Migrate to pyproject.toml * Bump
+  pre-commit rules * Fix pre-commit errors
+
+- **segmentation**: Scissor effect in slice views
+  ([`5b55f3b`](https://github.com/KitwareMedical/trame-slicer/commit/5b55f3be491c7be9702c389b6165112de3d46419))
+
+
+## v0.0.2 (2025-04-08)
+
+### Bug Fixes
+
+- **packaging**: Add missing manifest file
+  ([`51bc005`](https://github.com/KitwareMedical/trame-slicer/commit/51bc0059da861458c0e968b3d37979021f06614f))
+
+* Add missing manifest file to install the trame-slicer resources
+
+- **view**: Fix resize hang on linux
+  ([`27c2a93`](https://github.com/KitwareMedical/trame-slicer/commit/27c2a93736ba01d84590842f0a5ea8b58f95d1c7))
+
+https://github.com/Kitware/trame-rca/pull/18
+
+- **view**: Rollback monitored resize event
+  ([`f2de24e`](https://github.com/KitwareMedical/trame-slicer/commit/f2de24e316ab137dd52735204788e4bb50542e6a))
+
+* Rollback 05e7267a2eea3a953fa5fdc45b401401e898f4e2 which doesn't work for Linux systems.
+
+### Documentation
+
+- Add missing acknowledgments
+  ([`032f400`](https://github.com/KitwareMedical/trame-slicer/commit/032f400c0004369eddb55b19a5174d3b997d3e96))
+
+* Add missing HINT & COSY acknowledgments
+
+### Features
+
+- V0.0.2
+  ([`e0128d6`](https://github.com/KitwareMedical/trame-slicer/commit/e0128d6eebde256bd4c510be1f4d8b1170431ff0))
+
+- **layout**: Add argument to specify layout size
+  ([`4f3c0a4`](https://github.com/KitwareMedical/trame-slicer/commit/4f3c0a4f499f8e58ea3168ad1ce5afe7fb0c329d))
+
+- **rca_view**: Bump RCA version
+  ([`3626778`](https://github.com/KitwareMedical/trame-slicer/commit/3626778b06a9d09fe372218239ca92c80105631a))
+
+* Bump RCA version and change default encoder to Turbo JPEG
+
+- **view**: Update interactor resize event
+  ([`05e7267`](https://github.com/KitwareMedical/trame-slicer/commit/05e7267a2eea3a953fa5fdc45b401401e898f4e2))
+
+* Interactor WindowResizeEvent is scheduled to be deprecated / removed. Update to use ConfigureEvent
+  instead.
+
+- **view_layout**: Add quick access to 3d view properties
+  ([`b1fefcd`](https://github.com/KitwareMedical/trame-slicer/commit/b1fefcdad50c05506b670451a695b66b9856a77a))
+
+- **views**: Add zoom in / out
+  ([`99cf3e9`](https://github.com/KitwareMedical/trame-slicer/commit/99cf3e94724bedee7d8c229620910b038806a2ee))
+
+* Add helper methods to zoom in and out for Slice and 3D views
+
+
+## v0.0.1 (2025-01-30)
+
+### Bug Fixes
+
+- **test**: Fix factory tests
+  ([`159101c`](https://github.com/KitwareMedical/trame-slicer/commit/159101c330c43de9eafdc1cec01dd0c12b98ee82))
+
+- **test**: Fix failing tests with VTK 9.4
+  ([`78916bb`](https://github.com/KitwareMedical/trame-slicer/commit/78916bb596651a4a772f5fe8fa0e9dd5c4e8ee9c))
+
+- **test**: Fix missing test dependency
+  ([`b690082`](https://github.com/KitwareMedical/trame-slicer/commit/b6900827f1e9aa06959f619c085c85b3acd9ce9b))
+
+- **views**: Fix 2D view resize
+  ([`ffb1131`](https://github.com/KitwareMedical/trame-slicer/commit/ffb1131f025cc625a02a9d56fda5a22be6713793))
+
+- **views**: Fix rendering for 2D Slices
+  ([`95ac535`](https://github.com/KitwareMedical/trame-slicer/commit/95ac5350c92947a4b95acc6f367956efbf3a31df))
+
+### Chores
+
+- Mark test data folder as LFS
+  ([`f21db41`](https://github.com/KitwareMedical/trame-slicer/commit/f21db41db36f8d6232e47ddaf48158f67c54bc34))
+
+- Remove outdated rendering pool
+  ([`356e942`](https://github.com/KitwareMedical/trame-slicer/commit/356e942448498cc5c397f54e5095004eb994dfca))
+
+- Remove test data from repository
+  ([`6f7e145`](https://github.com/KitwareMedical/trame-slicer/commit/6f7e145d70474bbd78129b2c742f795678496ddb))
+
+### Documentation
+
+- Update library documentation
+  ([`f2a5234`](https://github.com/KitwareMedical/trame-slicer/commit/f2a52345eabecf78048b6f7051eb4e46c1fff022))
+
+- Update readme and contributing
+  ([`7ec1c6a`](https://github.com/KitwareMedical/trame-slicer/commit/7ec1c6a505fc24256a5a4c61b6f828aab045db36))
+
+### Features
+
+- **api**: Change imports for Slicer application compatibility
+  ([`6f43b9e`](https://github.com/KitwareMedical/trame-slicer/commit/6f43b9e2dd2b40661a0e79133926d64f4bb59dea))
+
+- **api**: Change view API to use factories for displayable manager creation
+  ([`4c9f6a4`](https://github.com/KitwareMedical/trame-slicer/commit/4c9f6a42fafeec6dce2abcd1a4265828fd831d0e))
+
+- **api**: Improve trame Slicer folder structure
+  ([`2c33ed2`](https://github.com/KitwareMedical/trame-slicer/commit/2c33ed2d76d7957a018c1cc4d293a1e333050759))
+
+- **api**: Move files to git project root
+  ([`4864f5b`](https://github.com/KitwareMedical/trame-slicer/commit/4864f5bd4c3f5281ec2d361f6d3ecf4a3b32ff8e))
+
+- **api**: Rename library to trame-slicer
+  ([`e79f9a2`](https://github.com/KitwareMedical/trame-slicer/commit/e79f9a26e93be32377e87f6d4417f8ac24597610))
+
+* Rename library to trame-slicer for future usage consistency * SlicerTrame is reserved for Slicer
+  integrated trame-slicer extension
+
+- **core**: Add custom share directory
+  ([`9f26de6`](https://github.com/KitwareMedical/trame-slicer/commit/9f26de6a7b0db8048626b3d313e62d6150193455))
+
+- **core**: Add file loading from front end
+  ([`634708c`](https://github.com/KitwareMedical/trame-slicer/commit/634708c8af04bf4f442d1165190b06ec9eed06e9))
+
+* Add file loading from front end * Automatically display the first volume * Fix Trame / Slicer
+  synchronization for 2D sliders and 3D view reset * Add background color property to view
+  definitions * Fix 2D view orientation to match volume orientation
+
+- **core**: Add markups handling
+  ([`d74153a`](https://github.com/KitwareMedical/trame-slicer/commit/d74153ac735437f51eaa7f62b881a1d9fa8dc810))
+
+- **core**: Add slice 3D view visibility
+  ([`5032996`](https://github.com/KitwareMedical/trame-slicer/commit/5032996e3c79838a5c6818d8bee46b4549cef866))
+
+* Add Slice 3D view visibility * Add helper functions in io_manager * Move resources to dedicated
+  folder * Initialize additional logic * Bump minimum required trame-rca version to supporting mouse
+  hover
+
+- **core**: Add volume rendering shift helpers
+  ([`550953f`](https://github.com/KitwareMedical/trame-slicer/commit/550953f3aed077ee35e70cd6cfd2e6f47a298c46))
+
+* Add VolumeProperty class responsible for VR shift logic * Add VolumeRendering vr shift logic * Add
+  3D Slicer resources for preset icons
+
+- **example**: Create demo content with simplistic UI
+  ([`b96a875`](https://github.com/KitwareMedical/trame-slicer/commit/b96a875d7c2a43075ca92c4488c9964a4680d145))
+
+- **example**: Split medical view example
+  ([`cff98d3`](https://github.com/KitwareMedical/trame-slicer/commit/cff98d30d21dbc7b37a72e382696b907d6788bb5))
+
+* Split medical viewer example code into modularized widgets * Add example for the VR Slider * Add
+  smoke test for medical viewer example
+
+- **io-manager**: Add explicit options to save / load models without coordinate change
+  ([`cd57308`](https://github.com/KitwareMedical/trame-slicer/commit/cd57308ad714c365af703992779a4cd4dc7bce86))
+
+- **segmentation**: Add segmentation
+  ([`5226c1e`](https://github.com/KitwareMedical/trame-slicer/commit/5226c1edf226639c17cf8372c6d1b8bb3a9f47ac))
+
+* Add segmentation handling in the POC
+
+- **views**: Add additional support for RCA encoding formats
+  ([`887a5d2`](https://github.com/KitwareMedical/trame-slicer/commit/887a5d2082a6f4d7b8c8fb41eab0763652cc2103))
+
+- **views**: Add component responsible for the layout
+  ([`ca92047`](https://github.com/KitwareMedical/trame-slicer/commit/ca92047e8be4d86f9fdb6dc2e3996e4e505c1278))
+
+* Refactor code structure for more clarity * Apply precommit rules * Add LayoutGrid component for
+  displaying the view layout * Add ViewManager responsible for instantiating the views * Removed
+  outdated classes and code
+
+- **views**: Add mouse hover support
+  ([`99552f9`](https://github.com/KitwareMedical/trame-slicer/commit/99552f9a0eefc0be23cc29d2785c06ff213807fb))
+
+* Add mouse hover support * Fix double mouse release bug
+
+- **views**: Add Slice and 3D view interaction
+  ([`43861be`](https://github.com/KitwareMedical/trame-slicer/commit/43861bedf7d24232ea2760dbaff1bad0b629b421))
+
+* Bump VTK version to 9.3 for serialization support * Add 2D Slice interaction * Add 3D View
+  interaction in Remote Controlled Area * Add trame-vtklocal as dependency for local rendering * Add
+  trame-rca as dependency for remote rendering
+
+- **views**: Add Slice offset interaction
+  ([`acf6b8f`](https://github.com/KitwareMedical/trame-slicer/commit/acf6b8f78bcd8a606cccee0f392d89a9f719e15c))
+
+- **views**: Add View factory and hook with Slicer / Trame
+  ([`f99b427`](https://github.com/KitwareMedical/trame-slicer/commit/f99b427ae21276199a65e29bf3a6afd510345663))
+
+- **views**: Add view orientation marker / rulers
+  ([`93dacc1`](https://github.com/KitwareMedical/trame-slicer/commit/93dacc1c5b232031418c4dc43d7db08531a97a56))
+
+* Add helper function to activate orientation marker and ruler
+
+- **views**: Add Volume Rendering
+  ([`0b79e02`](https://github.com/KitwareMedical/trame-slicer/commit/0b79e029b52605bc0096db1d162eeb5eb76a68d5))
+
+- **views**: Add Volume Rendering and 2D interaction refresh
+  ([`b6cea3c`](https://github.com/KitwareMedical/trame-slicer/commit/b6cea3cc1537c3dc396768d1ca68963eda2c9442))
+
+* Add strategy responsible for scheduled rendering * Add volume rendering in POC application * Add
+  default scheduled rendering to direct rendering in unit tests
+
+- **views**: Add WebP RCA encoding
+  ([`a90173b`](https://github.com/KitwareMedical/trame-slicer/commit/a90173b5cbcba2a8f7669d027d30a1c2e24050e9))
+
+- **views**: Factorize trame-rca utils components
+  ([`8a62d35`](https://github.com/KitwareMedical/trame-slicer/commit/8a62d35ef36c4e549972eef77c4b68ff1c2ceb00))
+
+* Factorize RCA components to use trame-rca utils implementation
+
+- **views**: First working version of layout display
+  ([`de91828`](https://github.com/KitwareMedical/trame-slicer/commit/de91828aa2a91da41ad42155c298c833f53cdff7))
+
+* Change expected layout dict to dict of layout * Add fit to view to abstract view * Add rotate view
+  to 3D view * Add option to fit to content when showing volume
+
+- **views**: Improve rendering reactivity
+  ([`44dd219`](https://github.com/KitwareMedical/trame-slicer/commit/44dd219b55b0a212ccf61af22db7b7460a0a3672))
+
+* Improve rendering reactivity by implementing encoding and push as subprocesses
+
+- **views**: Improve view creation and connectivity
+  ([`9a07d6b`](https://github.com/KitwareMedical/trame-slicer/commit/9a07d6b358c8a2725256415847977d130b633c72))
+
+* Add DisplayManager responsible for showing nodes depending on views * Update SlicerApp * Update
+  TrameApp to reflect changes * Add IOManager responsible for loading volumes / models and
+  segmentations * Add tests for loading DCM volume * Move test data to dedicated folder
+
+- **views**: Make RCA overlay configurable
+  ([`578e7c1`](https://github.com/KitwareMedical/trame-slicer/commit/578e7c1bde0d64a93be6d1c54b66364be3beb3e5))
+
+* Allow injecting UI creation for the RCA views * Remove custom CSS for the vertical sliders * Add
+  helpers to configure Vuetify sliders and connect them to Slicer views

trame_slicer-0.1.0/CONTRIBUTING.md

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+# Contributing to trame-slicer
+
+1. Clone the repository using `git clone`
+1. Install the dev dependencies via `pip install pre-commit`
+1. Run `pre-commit install` to set up pre-commit hooks
+1. Make changes to the code, and commit your changes to a separate branch
+1. Create a fork of the repository on GitHub
+1. Push your branch to your fork, and open a pull request
+
+## Testing
+
+The library testing rely on the trame-slicer test data. To setup your testing
+environment :
+
+1. Download the [trame-slicer-test-data]{.title-ref} zip file available in this
+   repository\'s release page
+1. Unzip the file content to the [tests/data]{.title-ref} folder
+1. Install the test requirements using pip using the
+   [tests/requirements.txt]{.title-ref} file
+1. Run the tests using the pytest module `python -m pytest tests`
+
+## Interactivity
+
+Some tests allow for interactive interaction with the views and can be activated
+by using the following arguments :
+
+`python -m pytest tests --render_interactive=<interaction_time_limit_s>`
+
+The interactivity time limit will apply to tests using a trame server in an
+asyncio tasks. Interactivity for VTK render window logic will require manually
+closing the windows to stop the interaction.
+
+## Commit messages
+
+trame-slicer follows trame\'s commit message convention to be compatible with
+it\'s CI features including the auto semantic release.
+
+## Tips
+
+1. When first creating a new project, it is helpful to run
+   `pre-commit run --all-files` to ensure all files pass the pre-commit checks.
+1. A quick way to fix `black` issues is by installing black
+   (`pip install black`) and running the `black` command at the root of your
+   repository.
+1. Sometimes, `black` and `flake8` do not agree. Add options to your `.flake8`
+   file to fix these things. See the
+   [flake8 configuration docs](https://flake8.pycqa.org/en/latest/user/configuration.html)
+   for more details.
+1. A quick way to fix `codespell` issues is by installing codespell
+   (`pip install codespell`) and running the `codespell -w` command at the root
+   of your directory.
+1. The
+   [.codespellrc file](https://github.com/codespell-project/codespell#using-a-config-file)
+   can be used fix any other codespell issues, such as ignoring certain files,
+   directories, words, or regular expressions.

trame_slicer-0.1.0/LICENSE

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+Apache Software License 2.0
+
+Copyright (c) 2024, Kitware SAS
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

trame_slicer-0.1.0/MANIFEST.in

@@ -0,0 +1,4 @@
+recursive-include trame_slicer/resources *
+recursive-exclude tests *
+recursive-exclude examples *
+recursive-exclude */__pycache__ *