multimodars 0.2.3__tar.gz → 0.3.1__tar.gz

{multimodars-0.2.3 → multimodars-0.3.1}/.github/workflows/CI.yml

@@ -19,6 +19,31 @@ permissions:
   contents: read
 
 jobs:
+  notebook-tests:
+    name: Notebook tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: 3.12.x
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+      - name: Install system dependencies
+        # pymeshlab loads MeshLab filter plugins as shared libraries at import time via
+        # load_default_plugins(). On bare Linux runners this requires libopengl0 to be
+        # present; without it the call silently fails (PyMeshLabException is caught in
+        # pymeshlab's __init__.py) and MeshSet is left with no filter methods, causing
+        # AttributeError on any filter call such as meshing_close_holes().
+        run: sudo apt-get install -y libopengl0
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e '.[meshlab]'
+          pip install --group dev
+      - name: Run notebook tests
+        run: pytest --nbmake docs/notebooks/
+
   python-compat:
     name: Python ${{ matrix.python-version }} compatibility
     runs-on: ubuntu-latest
@@ -27,8 +52,8 @@ jobs:
       matrix:
         python-version: ['3.10', '3.11', '3.12', '3.13']
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install Rust
@@ -36,7 +61,8 @@ jobs:
       - name: Install Python deps
         run: |
           python -m pip install --upgrade pip
-          pip install -e .[test]
+          pip install -e .
+          pip install --group test
       - name: Run Python tests
         run: pytest
 
@@ -50,16 +76,17 @@ jobs:
           - runner: ubuntu-latest
             target: aarch64
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: 3.12.x
 
       - name: Install Python deps
         run: |
           python -m pip install --upgrade pip
-          pip install -e .[test,docs,maturin]
+          pip install -e .
+          pip install --group test
 
       - name: run Python tests
         run: pytest
@@ -102,14 +129,15 @@ jobs:
           - runner: ubuntu-latest
             target: armv7
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
         with:
           python-version: 3.12.x
       - name: Install Python deps
         run: |
           python -m pip install --upgrade pip
-          pip install -e .[test,docs,maturin]
+          pip install -e .
+          pip install --group test
       - name: run Python tests
         run: pytest
       - name: Format Python code
@@ -139,15 +167,16 @@ jobs:
           - runner: windows-latest
             target: x64
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
         with:
           python-version: 3.12.x
           architecture: ${{ matrix.platform.target }}
       - name: Install Python deps
         run: |
           python -m pip install --upgrade pip
-          pip install -e .[test,docs,maturin]
+          pip install -e .
+          pip install --group test
       - name: run Python tests
         run: pytest
       - name: Format Python code
@@ -179,14 +208,15 @@ jobs:
             target: aarch64
             arch: arm64
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
         with:
           python-version: 3.12.x
       - name: Install Python deps
         run: |
           python -m pip install --upgrade pip
-          pip install -e .[test,docs,maturin]
+          pip install -e .
+          pip install --group test
       - name: run Python tests
         run: pytest
       - name: Format Python code
@@ -210,7 +240,7 @@ jobs:
   sdist:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Build sdist
         uses: PyO3/maturin-action@v1
         with:
@@ -226,7 +256,7 @@ jobs:
     name: Release
     runs-on: ubuntu-latest
     if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
-    needs: [linux, musllinux, windows, macos, sdist]
+    needs: [linux, musllinux, windows, macos, sdist, python-compat]
     permissions:
       id-token: write
       contents: write

{multimodars-0.2.3 → multimodars-0.3.1}/.gitignore

@@ -5,7 +5,19 @@
 /paper/old
 .VSCodeCounter
 /test
-/examples
+examples/__pycache__/
+examples/logs/
+examples/data/output/
+examples/data/test/
+examples/data/logs/
+# generated/intermediate STL outputs in data root
+examples/data/all.stl
+examples/data/all_wall.stl
+examples/data/fixed_mesh.stl
+examples/data/prefixed_mesh.stl
+examples/data/lca.stl
+examples/data/rca.stl
+examples/data/aorta.stl
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

multimodars-0.3.1/.pre-commit-config.yaml

@@ -0,0 +1,52 @@
+repos:
+  - repo: local
+    hooks:
+      # - id: pytest
+      #   name: Run pytest
+      #   entry: pytest
+      #   language: system
+      #   types: [python]
+      #   pass_filenames: false
+        
+      - id: rust-fmt
+        name: Rust format
+        entry: cargo fmt --all
+        language: system
+        types: [rust]
+        pass_filenames: false
+
+      - id: rust-clippy
+        name: Rust clippy
+        entry: cargo clippy --all-targets --all-features -- -D warnings
+        language: system
+        types: [rust]
+        pass_filenames: false
+
+      # - id: rust-test
+      #   name: Rust unit tests
+      #   entry: cargo test --lib # --quiet
+      #   language: system
+      #   types: [rust]
+      #   pass_filenames: false
+
+      - id: python-black
+        name: Black formatting
+        entry: black
+        language: system
+        types: [python]
+        require_serial: true
+        args: [--quiet, --target-version, py312]
+
+      - id: python-ruff
+        name: Ruff linting
+        entry: ruff check
+        language: system
+        types: [python]
+        args: [--fix]
+
+      - id: python-mypy
+        name: Mypy type checking
+        entry: mypy multimodars --ignore-missing-imports
+        language: system
+        types: [python]
+        pass_filenames: false

multimodars-0.3.1/CHANGELOG.md

@@ -0,0 +1,167 @@
+# Changelog multimodars
+
+All notable changes to this project will be documented in this file.
+This project adheres to [Semantic Versioning](https://semver.org/).
+
+## [0.3.1] - 2026-05-04
+
+### Added
+- Example data and Jupyter notebooks are now included directly in the repository under
+  `examples/` — no longer distributed as a release attachment. Both tutorials link to
+  the `examples/` directory and cross-reference the rendered notebook pages.
+- CCTA and intravascular Jupyter notebooks (`docs/notebooks/`) are now rendered and served
+  in the documentation via `myst-nb`, accessible as `:doc:` references from the tutorials.
+- Detailed explanation of the rolling-sphere and ray-casting labeling algorithms added to
+  the CCTA tutorial, including annotated figures.
+
+### Changed
+- README condensed: developer-setup section added, key workflow images included, installation
+  and quickstart sections tightened.
+- `plotly` added as a documentation dependency for interactive notebook figures.
+- Improved all print statements in the whole package.
+
+### Fixed
+- CI pipeline now correctly installs optional dependency groups required for the full test
+  suite.
+- Notebook tests no longer fail with `AttributeError: MeshSet has no attribute
+  'meshing_close_holes'` on bare Linux runners. pymeshlab silently skips plugin loading when
+  `libopengl0` is absent, leaving `MeshSet` with no filter methods; the CI now installs
+  `libopengl0` before the notebook test job runs.
+
+### Performance
+- Rust labeling step migrated to `par_iter()` for parallel vertex classification, reducing
+  wall time on large meshes.
+
+## [0.3.0] - 2026-04-30
+
+### Added
+- `stitch_ccta_to_intravascular()`: fuses an aligned intravascular `PyGeometry` with a CCTA
+  trimesh by triangulating a patch between the open boundary ring of the CCTA mesh and the
+  proximal/distal contour of the intravascular geometry. Supports two boundary-ring alignment
+  modes (`"nearest_iv"` and `"highest_z"`) for proximal and distal ends independently.
+- `fix_and_remesh_stitched_mesh()`: repairs the stitched surface (non-manifold edges/vertices,
+  open holes) and applies isotropic remeshing via `pymeshlab`. Requires the optional
+  `multimodars[meshlab]` extra.
+- `manual_hole_fill()`: flat-fills remaining open holes in a trimesh after automatic repair.
+- `remove_labeled_points_from_mesh()`: deletes one or more labeled vertex regions from the mesh, remaps faces, and returns the open boundary ring as `"boundary_points"` for downstream stitching.
+- `keep_labeled_points_from_mesh()`: retains only the vertices of a specified labeled region,
+  discarding all others.
+- `sync_results_to_mesh()`: refreshes all coordinate lists in the results dictionary after
+  `scale_region_centerline_morphing()` moves vertices, keeping labels consistent with the
+  updated mesh.
+- `find_aortic_wall_scaling()`: computes the optimal radial scaling factor for the aortic wall
+  region by minimising the distance to the first intravascular frame whose lumen elliptic ratio
+  drops below 1.3 (transition from intramural to free-segment lumen).
+- `export_section_stl()`: exports the full mesh or a labeled sub-region (`"all"`, `"aorta"`,
+  `"rca"`, `"lca"`) as an STL file.
+- `plot_results_key()`: opens an interactive 3-D trimesh scene visualising selected labeled
+  regions with colour coding (yellow = aorta, blue = RCA, green = LCA, red = removed/intramural,
+  cyan = proximal, magenta = distal, orange = anomalous).
+- Tests for all new CCTA functions.
+- `mypy` added to pre-commit hooks for static type checking.
+
+### Changed
+- Rust-side CCTA STL reader (`src/ccta/io/input.rs`) removed; mesh I/O is now handled
+  entirely via Python `trimesh`, eliminating the `stl_io` dependency.
+- `pymeshlab` and `pyglet` are now optional dependencies; the core package installs without
+  them. Install extras with `pip install 'multimodars[meshlab]'`.
+- Debug-plot helpers moved to a dedicated `ccta.debug_plots` module.
+- CCTA Python module refactored into focused sub-modules (`labeling`, `manipulating`,
+  `fixing_functions`, `debug_plots`).
+- Parameter order updated in several CCTA API calls for consistency.
+- `diastole` argument removed from functions where it was not used.
+- Labeling of aorta boundary points improved to avoid incorrect assignment at mesh edges.
+- Type stubs updated and extended to cover all new public functions.
+- Clippy lints applied across the Rust codebase (non-breaking).
+
+### Fixed
+- 3-D area and elliptic ratio calculation corrected for non-planar contours.
+- Mesh face normals corrected after stitching to ensure consistent outward orientation.
+
+### Documentation
+- CCTA tutorial completely rewritten to cover the full stitching workflow:
+  `remove_labeled_points_from_mesh` → `stitch_ccta_to_intravascular` →
+  `fix_and_remesh_stitched_mesh` → Taubin smoothing → `export_section_stl` → re-labeling.
+- Intravascular tutorial reviewed and completed: section numbering corrected (1–7),
+  CSV-vs-numpy workflow note added, column descriptions with units added to data tables,
+  Sphinx cross-references added throughout, `translate()` tuple-argument bug fixed.
+
+
+## [0.2.3] - 2026-03-06
+
+### Added
+- Type stubs for the Rust-implemented interface (via maturin)
+- `PyFrame.get_frame_at_z`: retrieve a frame by its z position
+- `PyFrame.get_frame_at_index`: retrieve a frame by its index
+- `PyFrame.replace_frame`: replace an existing frame with another
+
+### Changed
+- CI pipeline now tests against Python 3.10 through 3.13
+- Updated documentation to reflect the current interface and Python version requirements
+- Added direct download links to example data in the README and documentation
+- Migrated to modern NumPy-style type annotations throughout the Python codebase
+- All imports are now top-level across all Python modules
+
+## [0.2.2] - 2026-03-03
+
+### Changed
+- Uploaded new example data
+- Updated docs to match the new example data
+
+## [0.2.1] - 2026-01-12
+
+### Changed
+- Automatic version update based on Cargo.toml
+
+## [0.2.0] - 2026-01-11
+
+### Added
+- Functionality to read in CCTA .stl files and label them according to centerline object
+- Functionality to label the CCTA geometry additionally by an aligned intravascular aligned geometry.
+- Functionality to better align intravascular geometry to a centerline using additionally the CCTA vertices `align_combined`
+- Functionality to radially scale different regions radially to their corresponding centerline
+- Algorihtm for finding the best radial scaling factor for distal and proximal region compared to the aligned geometry
+- Algorithm for finding the best radial scaling factor for the aorta to minimize the distance between "wall" of `PyGeometry` object and the identified intramural vertices
+
+### Changed
+- Updated documentation to include a tutorial for the new functionality
+- Reduced the amount of testing data to reduce size of the package
+- Removed the examples folder from the repository and coupled to release (.zip file)
+
+## [0.1.2] - 2025-11-21
+
+### Changed 
+- intravascular::processing::align_within::fill_holes() now does not panic with gaps > 2
+  frames, but instead still fixes the holes and returns a warning to the user to check integrity of the data.
+
+## [0.1.1] - 2025-11-17
+
+### Changed
+- Update documentation to match new functionality
+
+## [0.1.0] - 2025-11-17
+
+### Added
+- Fill-holes functionality: when a geometry has a large gap between frames,
+  up to two frames will be inserted to improve continuity.
+- Geometry integrity tests: after aligning frames within a geometry,
+  several integrity checks are performed before continuing the pipeline.
+- `InputData`: the entire pipeline can be driven from an `InputData` object
+  that includes coordinates for different contours.
+- Enum for contour types: `Lumen`, `EEM`, `sidebranch`, `calcification`,
+  `wall`, `catheter`.
+- `PyFrame` struct: each frame can hold multiple contour types which are
+  processed in parallel.
+
+### Changed
+- Full architecture refactor:
+  - Raw data is read and ordered into a `Geometry` struct.
+  - The `Geometry` struct undergoes integrity checks to ensure data quality.
+  - Alignment is performed first *within* geometries, then *between* geometries.
+  - Modules are loosely coupled to improve maintainability.
+- Parallelization model updated: each geometry is processed in parallel;
+  within-geometry alignment runs first, then between-geometry alignment runs in parallel.
+- Multiple bug fixes in the alignment algorithms.
+
+### Fixed
+- Various stability and indexing bugs discovered during alignment testing.

{multimodars-0.2.3 → multimodars-0.3.1}/Cargo.lock

@@ -161,12 +161,6 @@ version = "1.23.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "5c76a5792e44e4abe34d3abf15636779261d45a7450612059293d1d2cfc63422"
 
-[[package]]
-name = "byteorder"
-version = "1.5.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
-
 [[package]]
 name = "byteorder-lite"
 version = "0.1.0"
@@ -197,6 +191,19 @@ version = "1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3d7b894f5411737b7867f4827955924d7c254fc9f4d91a6aad6b097804b1018b"
 
+[[package]]
+name = "console"
+version = "0.15.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "054ccb5b10f9f2cbf51eb355ca1d05c2d279ce1804688d0db74b4733a5aeafd8"
+dependencies = [
+ "encode_unicode",
+ "libc",
+ "once_cell",
+ "unicode-width",
+ "windows-sys",
+]
+
 [[package]]
 name = "core2"
 version = "0.4.0"
@@ -304,6 +311,12 @@ version = "1.15.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "48c757948c5ede0e46177b7add2e67155f70e33c07fea8284df6576da70b3719"
 
+[[package]]
+name = "encode_unicode"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "34aa73646ffb006b8f5147f3dc182bd4bcb190227ce861fc4a4844bf8e3cb2c0"
+
 [[package]]
 name = "equator"
 version = "0.4.2"
@@ -390,15 +403,6 @@ dependencies = [
  "miniz_oxide",
 ]
 
-[[package]]
-name = "float-cmp"
-version = "0.10.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b09cf3155332e944990140d967ff5eceb70df778b34f77d8075db46e4704e6d8"
-dependencies = [
- "num-traits",
-]
-
 [[package]]
 name = "getrandom"
 version = "0.3.4"
@@ -590,6 +594,19 @@ dependencies = [
  "hashbrown",
 ]
 
+[[package]]
+name = "indicatif"
+version = "0.17.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "183b3088984b400f4cfac3620d5e076c84da5364016b4f49473de574b2586235"
+dependencies = [
+ "console",
+ "number_prefix",
+ "portable-atomic",
+ "unicode-width",
+ "web-time",
+]
+
 [[package]]
 name = "indoc"
 version = "2.0.6"
@@ -632,6 +649,16 @@ dependencies = [
  "libc",
 ]
 
+[[package]]
+name = "js-sys"
+version = "0.3.82"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b011eec8cc36da2aab2d5cff675ec18454fad408585853910a202391cf9f8e65"
+dependencies = [
+ "once_cell",
+ "wasm-bindgen",
+]
+
 [[package]]
 name = "lebe"
 version = "0.5.3"
@@ -726,18 +753,18 @@ dependencies = [
 
 [[package]]
 name = "multimodars"
-version = "0.2.3"
+version = "0.3.1"
 dependencies = [
  "anyhow",
  "approx",
  "crossbeam",
  "csv",
  "image",
+ "indicatif",
  "nalgebra",
  "pyo3",
  "rayon",
  "serde",
- "stl_io",
  "toml",
 ]
 
@@ -864,6 +891,12 @@ dependencies = [
  "autocfg",
 ]
 
+[[package]]
+name = "number_prefix"
+version = "0.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3"
+
 [[package]]
 name = "once_cell"
 version = "1.21.3"
@@ -1255,16 +1288,6 @@ version = "1.2.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6ce2be8dc25455e1f91df71bfa12ad37d7af1092ae736f3a6cd0e37bc7810596"
 
-[[package]]
-name = "stl_io"
-version = "0.10.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "da63e75b86345156b191c021b3ce2a13b973941ecdb8c70d6f00cbbfe0076ed7"
-dependencies = [
- "byteorder",
- "float-cmp",
-]
-
 [[package]]
 name = "syn"
 version = "2.0.104"
@@ -1367,6 +1390,12 @@ version = "1.0.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "5a5f39404a5da50712a4c1eecf25e90dd62b613502b7e925fd4e4d19b5c96512"
 
+[[package]]
+name = "unicode-width"
+version = "0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b4ac048d71ede7ee76d585517add45da530660ef4390e49b098733c6e897f254"
+
 [[package]]
 name = "unindent"
 version = "0.2.4"
@@ -1438,6 +1467,16 @@ dependencies = [
  "unicode-ident",
 ]
 
+[[package]]
+name = "web-time"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5a6580f308b1fad9207618087a65c04e7a10bc77e02c8e84e9b00dd4b12fa0bb"
+dependencies = [
+ "js-sys",
+ "wasm-bindgen",
+]
+
 [[package]]
 name = "weezl"
 version = "0.1.11"
@@ -1454,6 +1493,79 @@ dependencies = [
  "safe_arch",
 ]
 
+[[package]]
+name = "windows-sys"
+version = "0.59.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b"
+dependencies = [
+ "windows-targets",
+]
+
+[[package]]
+name = "windows-targets"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973"
+dependencies = [
+ "windows_aarch64_gnullvm",
+ "windows_aarch64_msvc",
+ "windows_i686_gnu",
+ "windows_i686_gnullvm",
+ "windows_i686_msvc",
+ "windows_x86_64_gnu",
+ "windows_x86_64_gnullvm",
+ "windows_x86_64_msvc",
+]
+
+[[package]]
+name = "windows_aarch64_gnullvm"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3"
+
+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469"
+
+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b"
+
+[[package]]
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+checksum = "0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66"
+
+[[package]]
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+checksum = "240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66"
+
+[[package]]
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+checksum = "147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78"
+
+[[package]]
+name = "windows_x86_64_gnullvm"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d"
+
+[[package]]
+name = "windows_x86_64_msvc"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec"
+
 [[package]]
 name = "winnow"
 version = "0.7.13"

{multimodars-0.2.3 → multimodars-0.3.1}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "multimodars"
-version = "0.2.3"
+version = "0.3.1"
 edition = "2021"
 license = "MIT"
 readme = "README.md"
@@ -20,4 +20,4 @@ rayon = "1.7.1"
 crossbeam = "0.8.4"
 anyhow = "1.0.100"
 approx = "0.5"
-stl_io = "0.10.0"
+indicatif = "0.17"