multimodars 0.2.2__tar.gz → 0.3.0__tar.gz

{multimodars-0.2.2 → multimodars-0.3.0}/.github/ISSUE_TEMPLATE/bug_report.md

@@ -12,27 +12,20 @@ A clear and concise description of what the bug is.
 
 **To Reproduce**
 Steps to reproduce the behavior:
-1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
-4. See error
+1. Load data with '...'
+2. Call function '...'
+3. See error
 
 **Expected behavior**
 A clear and concise description of what you expected to happen.
 
+**Environment (please complete the following information):**
+ - OS: [e.g. Windows, Linux, macOS]
+ - Python version: [e.g. 3.10]
+ - Package version: [e.g. 0.1.0]
+
 **Screenshots**
 If applicable, add screenshots to help explain your problem.
 
-**Desktop (please complete the following information):**
- - OS: [e.g. iOS]
- - Browser [e.g. chrome, safari]
- - Version [e.g. 22]
-
-**Smartphone (please complete the following information):**
- - Device: [e.g. iPhone6]
- - OS: [e.g. iOS8.1]
- - Browser [e.g. stock browser, safari]
- - Version [e.g. 22]
-
 **Additional context**
 Add any other context about the problem here.

{multimodars-0.2.2 → multimodars-0.3.0}/.github/PULL_REQUEST_TEMPLATE.md

@@ -1,7 +1,7 @@
 ## Pull Request Checklist
 
 - [ ] I have added tests that prove the fix is effective or that the feature works.
-- [ ] I ran `pytest` (or `nox` / your CI command) locally and all tests pass.
+- [ ] I ran `pytest` locally and all tests pass.
 - [ ] I updated `CHANGELOG.md` (or NEWS) and bumped the package version if applicable.
 - [ ] I added/updated documentation (README, docstrings, or docs).
 - [ ] This PR is linked to an issue: fixes #<issue-number> (if applicable).

{multimodars-0.2.2 → multimodars-0.3.0}/.github/workflows/CI.yml

@@ -19,6 +19,27 @@ permissions:
   contents: read
 
 jobs:
+  python-compat:
+    name: Python ${{ matrix.python-version }} compatibility
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.11', '3.12', '3.13']
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+      - name: Install Python deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[test]
+      - name: Run Python tests
+        run: pytest
+
   linux:
     runs-on: ${{ matrix.platform.runner }}
     strategy:
@@ -205,7 +226,7 @@ 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-0.3.0/.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-0.3.0/CHANGELOG.md

@@ -0,0 +1,138 @@
+# Changelog multimodars
+
+All notable changes to this project will be documented in this file.
+This project adheres to [Semantic Versioning](https://semver.org/).
+
+## [0.3.0] - 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-0.3.0/CONTRIBUTING.md

@@ -0,0 +1,164 @@
+#  ✩°｡⋆ Contributing to the project ⋆｡°✩
+
+First off, thank you for considering contributing! **ദ്ദി(˵ •̀ ᴗ - ˵ ) ✧**  
+Whether you’re filing a bug, proposing a new feature, improving documentation, or refactoring code, your help makes this project better for you and the whole community.
+
+## Code of Conduct
+This project adheres to the [Contributor Covenant v2.1](https://www.contributor-covenant.org/version/2/1/code_of_conduct/).  
+By participating, you agree to respect everyone in this community. **˗ˏˋ ♡ ˎˊ˗**
+
+## Table of Contents
+
+1. [Getting Started](#getting-started)  
+2. [I Have a Question](#i-have-a-question)  
+3. [Reporting Bugs](#reporting-bugs)  
+4. [Suggesting Enhancements](#suggesting-enhancements)  
+5. [Your First Code Contribution](#your-first-code-contribution)  
+6. [Pull Request Process](#pull-request-process)  
+7. [Coding Style & Tests](#coding-style--tests)  
+8. [Writing Documentation](#writing-documentation)  
+9. [Where to Get Help](#where-to-get-help)
+
+## Getting started
+1. Fork the repo and clone your fork
+```bash
+git clone https://github.com/yungselm/multimoda-rs.git
+cd multimoda-rs
+```
+2. Create a new branch
+```bash
+git checkout -b feature/sick-feature
+```
+3. install dependencies and run tests
+```bash
+pip install -e
+pytest
+```
+## I have a Question 
+Before opening an issue:
+- Read the [Documentation](https://multimoda-rs.readthedocs.io/en/latest/index.html)
+- Search existing [Issues](https://github.com/yungselm/multimoda-rs/issues?q=is%3Aissue) 
+
+If you still need help:
+- Open a new issue: [Click here](https://github.com/yungselm/multimoda-rs/issues/new/choose)
+- Provide:
+    - A clear, descriptive title
+    - Context: what you're trying to do, expected vs. actual behaviour
+    - Project verion, OS/platform, Python version, and any relevant logs
+
+## Reporting Bugs
+If you find a bug, please help us fix it by opening a [a new issue](https://github.com/yungselm/multimoda-rs/issues/new/choose) and providing:
+- **Title**: A short descriptive title
+- **Steps to reproduce**: Minimal code snippet or sequence to trigger the bug
+- **Expected behaviour** vs **Actual behaviour**
+- **Environment**:
+    - `multimoda-rs` version
+    - Python version
+    - OS and architecture
+
+## Suggesting Enhancements
+Have an idea for a new feature or an improvement to existing behaviour? Open a [feature request issue](https://github.com/yungselm/multimoda-rs/issues/new/choose) and include:
+- **Summary**: A concise description of the enhancement
+- **Motivation**: Why would this be useful? What problem does it solve?
+- **Proposed solution**: How you envision it working (API sketch, example usage, etc.)
+- **Alternatives considered**: Other approaches you've thought about
+
+We appreciate well-scoped proposals with clear use cases.
+
+## Your First Code Contribution
+Not sure where to start? Look for issues labelled [`good first issue`](https://github.com/yungselm/multimoda-rs/issues?q=is%3Aissue+label%3A%22good+first+issue%22) or [`help wanted`](https://github.com/yungselm/multimoda-rs/issues?q=is%3Aissue+label%3A%22help+wanted%22).
+
+**Setup** (Python + Rust hybrid via [maturin](https://github.com/PyO3/maturin)):
+```bash
+# 1. Fork the repo on GitHub, then clone your fork
+git clone https://github.com/<your-username>/multimoda-rs.git
+cd multimoda-rs
+
+# 2. Create and activate a virtual environment
+python -m venv .venv
+source .venv/bin/activate   # Windows: .venv\Scripts\activate
+
+# 3. Install the package in development mode (compiles the Rust extension)
+pip install -e ".[dev]"
+
+# 4. Install pre-commit hooks
+pre-commit install
+
+# 5. Verify everything works
+pytest
+cargo test --lib
+```
+
+## Pull Request Process
+1. **Branch** – create a descriptive branch (`feature/my-feature`, `fix/issue-123`).
+2. **Commit** – write clear, atomic commit messages.
+3. **Tests** – add or update tests to cover your changes; all existing tests must pass.
+4. **Docs** – update docstrings and, if applicable, the RST docs under `docs/`.
+5. **Open the PR** – target the `main` branch. Fill in the PR template with a summary, motivation, and testing notes.
+6. **Review** – address reviewer comments; once approved and CI is green, a maintainer will merge.
+
+PRs that break existing tests or skip the pre-commit hooks will not be merged.
+
+## Coding Style & Tests
+
+### Python
+- **Formatter**: [Black](https://black.readthedocs.io/) (enforced automatically via pre-commit).
+- **Linter**: [Ruff](https://docs.astral.sh/ruff/) with `--fix` (enforced automatically via pre-commit).
+- **Docstrings**: [NumPy docstring style](https://numpydoc.readthedocs.io/en/latest/format.html).
+  Example:
+  ```python
+  def my_function(x: float, y: float) -> float:
+      """Short one-line summary.
+
+      Longer description if needed.
+
+      Parameters
+      ----------
+      x : float
+          Description of x.
+      y : float
+          Description of y.
+
+      Returns
+      -------
+      float
+          Description of the return value.
+      """
+  ```
+- **Type annotations**: use `from __future__ import annotations` at the top of every module and annotate all public functions and methods.
+- **Tests**: place tests under `tests/` and use [pytest](https://docs.pytest.org/). Run with `pytest`.
+
+### Rust
+- **Formatter**: `cargo fmt --all` (enforced automatically via pre-commit).
+- **Tests**: unit tests live alongside the source (`#[cfg(test)]` blocks). Run with `cargo test --lib`.
+
+All checks are wired up via pre-commit and run automatically on every commit. You can also run them manually:
+```bash
+pre-commit run --all-files
+```
+
+## Writing Documentation
+Documentation lives under `docs/` and is built with [Sphinx](https://www.sphinx-doc.org/).
+
+- Public API is documented via **NumPy-style docstrings** (see above) — Sphinx picks these up automatically.
+- Narrative docs (tutorials, how-tos) go in `.rst` files under `docs/`.
+- Build locally with:
+  ```bash
+  cd docs
+  make html
+  # open _build/html/index.html in your browser
+  ```
+- Keep prose clear and concise. Include runnable code examples where possible.
+
+## Where to Get Help
+| Channel | When to use |
+|---------|-------------|
+| [Documentation](https://multimoda-rs.readthedocs.io/en/latest/index.html) | First stop, API reference and tutorials |
+| [GitHub Issues](https://github.com/yungselm/multimoda-rs/issues) | Bug reports and feature requests |
+| [GitHub Discussions](https://github.com/yungselm/multimoda-rs/discussions) | Questions, ideas, and general discussion |
+
+When asking for help, please include your `multimoda-rs` version, Python version, OS, and a minimal reproducible example.
+
+
+**ฅ^>⩊<^ ฅ**
+------------------------------------------------------------------------------------

{multimodars-0.2.2 → multimodars-0.3.0}/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"
@@ -390,15 +384,6 @@ 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"
@@ -726,7 +711,7 @@ dependencies = [
 
 [[package]]
 name = "multimodars"
-version = "0.2.2"
+version = "0.3.0"
 dependencies = [
  "anyhow",
  "approx",
@@ -737,7 +722,6 @@ dependencies = [
  "pyo3",
  "rayon",
  "serde",
- "stl_io",
  "toml",
 ]
 
@@ -1255,16 +1239,6 @@ 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"

{multimodars-0.2.2 → multimodars-0.3.0}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "multimodars"
-version = "0.2.2"
+version = "0.3.0"
 edition = "2021"
 license = "MIT"
 readme = "README.md"
@@ -20,4 +20,3 @@ rayon = "1.7.1"
 crossbeam = "0.8.4"
 anyhow = "1.0.100"
 approx = "0.5"
-stl_io = "0.10.0"

{multimodars-0.2.2 → multimodars-0.3.0}/PKG-INFO

@@ -1,30 +1,35 @@
 Metadata-Version: 2.4
 Name: multimodars
-Version: 0.2.2
+Version: 0.3.0
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Classifier: License :: OSI Approved :: MIT License
 Requires-Dist: numpy>=2.0.0,<3.0.0
 Requires-Dist: trimesh>=4.8.0
-Requires-Dist: pyglet<2
+Requires-Dist: scipy>=1.15.0
 Requires-Dist: sphinx>=8.0,<9.0 ; extra == 'docs'
 Requires-Dist: sphinx-rtd-theme ; extra == 'docs'
 Requires-Dist: sphinx-autodoc-typehints ; extra == 'docs'
 Requires-Dist: myst-parser ; extra == 'docs'
 Requires-Dist: maturin>=1.7,<2.0 ; extra == 'docs'
 Requires-Dist: furo ; extra == 'docs'
+Requires-Dist: pymeshlab>=2023.12 ; extra == 'meshlab'
 Requires-Dist: pytest>=9.0.2 ; extra == 'test'
 Requires-Dist: pytest-cov ; extra == 'test'
 Requires-Dist: ruff ; extra == 'test'
 Requires-Dist: black ; extra == 'test'
+Requires-Dist: mypy ; extra == 'test'
+Requires-Dist: pyglet<2 ; extra == 'viz'
 Provides-Extra: docs
+Provides-Extra: meshlab
 Provides-Extra: test
+Provides-Extra: viz
 License-File: LICENSE
 Summary: A Rust-powered cardiac multi-image modality fusion package
 Author: Anselm W. Stark
 License-Expression: MIT
-Requires-Python: >=3.8
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 Project-URL: Homepage, https://github.com/yungselm/multimoda-rs
 Project-URL: Issues, https://github.com/yungselm/multimoda-rs/issues
@@ -71,7 +76,7 @@ Project-URL: Issues, https://github.com/yungselm/multimoda-rs/issues
 - Centerline Alignment
   - Align registered geometries onto a vessel centerline using three‑point or manual rotation methods.
 - Geometry Utilities
-  - Smooth contours, reorder frames to minimize spatial and index jumps, compute areas and elliptic ratios, find farthest/closest point pairs, and more.
+  - Smooth contours, compute areas and elliptic ratios, find farthest/closest point pairs, and more.
 
 ## Installation
 
@@ -106,7 +111,8 @@ maturin develop
 
 
 ## Quickstart Example
-Download the example data from the latest release and place it in your working directory. A Jupyter Notebook with step-by-step examples is available at `examples/ivus_to_centerline.ipynb`.
+Download [examples.zip](https://github.com/yungselm/multimoda-rs/releases/latest/download/examples.zip) (SHA256: `d11ebc7607f43ab4571fb51c9ac9178caac57774cf5d97f4f068ace4eb070fee`) from the latest release and place it in your working directory. A Jupyter Notebook with step-by-step examples is available at `examples/ivus_to_centerline.ipynb`.
+Provided you extraced examples to the project root you can just copy paste the below example to ensure proper setup:
 
 ```python
 import multimodars as mm
@@ -114,8 +120,8 @@ import numpy as np
 
 # IVUS pullbacks: full alignment of rest/stress & diastole/systole
 rest, stress, dia, sys, _ = mm.from_file_full(
-    input_path_a="ivus_rest",
-    input_path_b="ivus_stress",
+    input_path_a="examples/data/ivus_rest",
+    input_path_b="examples/data/ivus_stress",
     label="full",
     step_rotation_deg=0.1,
     range_rotation_deg=90,
@@ -128,12 +134,12 @@ rest, stress, dia, sys, _ = mm.from_file_full(
     output_path_b="output/stress",
     output_path_c="output/diastole",
     output_path_d="output/systole",
-    interpolation_steps=28,
+    interpolation_steps=0,
     contour_types=[mm.PyContourType.Lumen, mm.PyContourType.Catheter, mm.PyContourType.Wall]
 )
 
 # Load raw centerline and align geometry onto it
-cl_raw = np.genfromtxt("centerline_raw.csv", delimiter=",")
+cl_raw = np.genfromtxt("examples/data/centerline_raw.csv", delimiter=",")
 centerline = mm.numpy_to_centerline(cl_raw)
 
 aligned_pair, cl_resampled = mm.align_three_point(

{multimodars-0.2.2 → multimodars-0.3.0}/README.md

@@ -40,7 +40,7 @@
 - Centerline Alignment
   - Align registered geometries onto a vessel centerline using three‑point or manual rotation methods.
 - Geometry Utilities
-  - Smooth contours, reorder frames to minimize spatial and index jumps, compute areas and elliptic ratios, find farthest/closest point pairs, and more.
+  - Smooth contours, compute areas and elliptic ratios, find farthest/closest point pairs, and more.
 
 ## Installation
 
@@ -75,7 +75,8 @@ maturin develop
 
 
 ## Quickstart Example
-Download the example data from the latest release and place it in your working directory. A Jupyter Notebook with step-by-step examples is available at `examples/ivus_to_centerline.ipynb`.
+Download [examples.zip](https://github.com/yungselm/multimoda-rs/releases/latest/download/examples.zip) (SHA256: `d11ebc7607f43ab4571fb51c9ac9178caac57774cf5d97f4f068ace4eb070fee`) from the latest release and place it in your working directory. A Jupyter Notebook with step-by-step examples is available at `examples/ivus_to_centerline.ipynb`.
+Provided you extraced examples to the project root you can just copy paste the below example to ensure proper setup:
 
 ```python
 import multimodars as mm
@@ -83,8 +84,8 @@ import numpy as np
 
 # IVUS pullbacks: full alignment of rest/stress & diastole/systole
 rest, stress, dia, sys, _ = mm.from_file_full(
-    input_path_a="ivus_rest",
-    input_path_b="ivus_stress",
+    input_path_a="examples/data/ivus_rest",
+    input_path_b="examples/data/ivus_stress",
     label="full",
     step_rotation_deg=0.1,
     range_rotation_deg=90,
@@ -97,12 +98,12 @@ rest, stress, dia, sys, _ = mm.from_file_full(
     output_path_b="output/stress",
     output_path_c="output/diastole",
     output_path_d="output/systole",
-    interpolation_steps=28,
+    interpolation_steps=0,
     contour_types=[mm.PyContourType.Lumen, mm.PyContourType.Catheter, mm.PyContourType.Wall]
 )
 
 # Load raw centerline and align geometry onto it
-cl_raw = np.genfromtxt("centerline_raw.csv", delimiter=",")
+cl_raw = np.genfromtxt("examples/data/centerline_raw.csv", delimiter=",")
 centerline = mm.numpy_to_centerline(cl_raw)
 
 aligned_pair, cl_resampled = mm.align_three_point(