pymeshmetrics 1.0.0__tar.gz

pymeshmetrics-1.0.0/.gitignore

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pymeshmetrics-1.0.0/MeshMetrics.py

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+"""Deprecated alias for the ``meshmetrics`` package.
+
+Kept as a single module (not a package directory) so it can coexist with
+``meshmetrics/`` on case-insensitive filesystems (Windows, macOS).
+"""
+
+import sys
+import warnings
+
+import meshmetrics
+from meshmetrics.metrics import *  # noqa: F401,F403  (names the old package exposed)
+from meshmetrics import *  # noqa: F401,F403
+from meshmetrics import metrics, utils
+
+warnings.warn(
+    "`import MeshMetrics` is deprecated, use `import meshmetrics` instead.",
+    DeprecationWarning,
+    stacklevel=2,
+)
+
+# keep `from MeshMetrics.utils import ...` / `MeshMetrics.metrics` working
+sys.modules[__name__ + ".metrics"] = metrics
+sys.modules[__name__ + ".utils"] = utils

pymeshmetrics-1.0.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: pymeshmetrics
+Version: 1.0.0
+Summary: Library to compute distance-based performance metrics for image segmentation tasks.
+Project-URL: Homepage, https://github.com/gasperpodobnik/meshmetrics
+Project-URL: Paper, https://doi.org/10.48550/arXiv.2509.05670
+Author: Gasper Podobnik, Tomaz Vrtovec
+License-Expression: Apache-2.0
+License-File: LICENSE
+Requires-Python: >=3.9
+Requires-Dist: numpy
+Requires-Dist: simpleitk
+Requires-Dist: simpleitkutilities
+Requires-Dist: vtk>=9.3
+Provides-Extra: all
+Requires-Dist: meshio; extra == 'all'
+Requires-Dist: trimesh; extra == 'all'
+Provides-Extra: meshio
+Requires-Dist: meshio; extra == 'meshio'
+Provides-Extra: trimesh
+Requires-Dist: trimesh; extra == 'trimesh'
+Description-Content-Type: text/markdown
+
+# MeshMetrics
+> Official Python-based implementation of `MeshMetrics` from [_MeshMetrics: A Precise Implementation of Distance-Based Image Segmentation Metrics_](https://doi.org/10.48550/arXiv.2509.05670), motivated by the implementation pitfalls identified in [_Understanding Implementation Pitfalls of Distance-Based Metrics for Image Segmentation_](https://doi.org/10.48550/arXiv.2410.02630) and [_HDilemma: Are Open-Source Hausdorff Distance Implementations Equivalent?_](https://link.springer.com/chapter/10.1007/978-3-031-72114-4_30)
+
+## About
+`MeshMetrics` is a precise, mesh-based implementation of widely used distance-based metrics for evaluating image segmentation tasks. By leveraging mesh representations of segmentation, `MeshMetrics` ensures precision in distance and boundary element size calculations. For a detailed description and a comparison with other open-source tools supporting distance-based metric calculations, see [our paper](https://doi.org/10.48550/arXiv.2509.05670).
+
+The library supports both 2D and 3D data and works seamlessly with multiple segmentation formats (`numpy.ndarray`, `SimpleITK.Image`, `vtk.vtkPolyData`, `trimesh.Trimesh`, and `meshio.Mesh`). It also allows mixing representations between reference and predicted segmentations - for example, one input can be a mask image (`SimpleITK.Image`), while the other is a surface mesh (`vtk.vtkPolyData`/`trimesh.Trimesh`/`meshio.Mesh`). See the *Advanced usage* section in [`examples.ipynb`](examples.ipynb) for more details.
+
+Available distance-based metrics:
+- **Hausdorff distance** (HD) with $p$-th **percentile variants** (HD<sub>p</sub>)
+- **Mean average surface distance** (MASD)
+- **Average symmetric surface distance** (ASSD)
+- **Normalized surface distance** (NSD)
+- **Boundary intersection over union** (BIoU)
+
+For convenience, `MeshMetrics` also includes implementations of the **Dice similarity coefficient** (DSC) and **intersection over union** (IoU).
+
+![overview](./data/paper_overview.png)
+
+If you use `MeshMetrics` in your work, please cite:
+```
+Podobnik, G., & Vrtovec, T. (2025). MeshMetrics: A Precise Implementation of Distance-Based Image Segmentation Metrics. arXiv preprint arXiv:2509.05670.
+Podobnik, G., & Vrtovec, T. (2025). Understanding Implementation Pitfalls of Distance-Based Metrics for Image Segmentation. arXiv preprint arXiv:2410.02630.
+```
+
+## Installation
+### System Dependencies
+This package requires `libxrender1` to be installed on your system. Install it via:
+```bash
+sudo apt update && sudo apt install -y libxrender1
+```
+
+### Install `meshmetrics` package
+Install from [PyPI](https://pypi.org/project/pymeshmetrics/) with pip, or add it to your project with [uv](https://docs.astral.sh/uv/):
+```bash
+pip install pymeshmetrics
+uv add pymeshmetrics
+```
+The package is published as `pymeshmetrics` and imported as `meshmetrics`:
+```python
+import meshmetrics
+```
+Optional support for `trimesh` and `meshio` inputs is available via extras: `pip install "pymeshmetrics[all]"` (or `[trimesh]` / `[meshio]`).
+
+To install the latest development version from GitHub:
+```bash
+pip install git+https://github.com/gasperpodobnik/meshmetrics.git
+```
+
+### Development
+Clone the repository and create the environment (including dev tools and all extras):
+```bash
+git clone https://github.com/gasperpodobnik/meshmetrics.git
+cd meshmetrics
+uv sync --all-extras
+uv run pytest
+```
+
+## Usage
+### Quick start
+Compute all metrics for a pair of segmentations in one call:
+```python
+import SimpleITK as sitk
+from meshmetrics import compute_metrics
+
+ref_sitk = sitk.ReadImage("data/example_3d_ref_mask.nii.gz")
+pred_sitk = sitk.ReadImage("data/example_3d_pred_mask.nii.gz")
+
+results = compute_metrics(ref_sitk, pred_sitk, taus=(2.0, 5.0))
+# {'ref_is_empty': False, 'pred_is_empty': False, 'HD_100': ..., 'HD_95': ..., 'MASD': ..., 'ASSD': ...,
+#  'NSD_2.0': ..., 'NSD_5.0': ..., 'BIoU_2.0': ..., 'BIoU_5.0': ..., 'DSC': ..., 'IoU': ...}
+```
+`taus` are the tolerances (in physical units) for NSD and BIoU; they are application-specific, so NSD and BIoU are only computed when `taus` are given. Use `percentiles` to choose the HD variants (default `(100, 95)`) and `metrics` to select a subset, e.g. `metrics=["hd", "nsd"]`. Inputs can be any of the supported types (see below); numpy arrays and pairs of meshes also need `spacing`.
+
+### Step-by-step
+Simple usage example of `MeshMetrics` for 3D segmentation masks is shown below.
+See [`examples.ipynb`](examples.ipynb) notebook for more examples.
+
+```python
+from pathlib import Path
+import SimpleITK as sitk
+from meshmetrics import DistanceMetrics
+
+data_dir = Path("data")
+
+# read binary segmentation masks
+ref_sitk = sitk.ReadImage(str(data_dir / "example_3d_ref_mask.nii.gz"))
+pred_sitk = sitk.ReadImage(str(data_dir / "example_3d_pred_mask.nii.gz"))
+
+# Set parameters
+percentile = 95  # percentile for HD
+tau = 2.0  # tolerance for NSD and BIoU
+
+# Initialize distance metrics class and set inputs
+dist_metrics = DistanceMetrics()
+dist_metrics.set_input(ref=ref_sitk, pred=pred_sitk)
+
+# store flags indicating empty masks
+results = {
+    "ref_is_empty": dist_metrics.ref_is_empty,
+    "pred_is_empty": dist_metrics.pred_is_empty,
+}
+# Hausdorff distance (HD), by default, HD percentile is set to 100 (equivalent to HD)
+results["HD_100"] = dist_metrics.hd()
+# p-th percentile HD (HD_p)
+results[f"HD_{percentile}"] = dist_metrics.hd(percentile=percentile)
+# Mean average surface distance (MASD)
+results["MASD"] = dist_metrics.masd()
+# Average symmetric surface distance (ASSD)
+results["ASSD"] = dist_metrics.assd()
+# Normalized surface distance (NSD) with tau
+results[f"NSD_{tau}"] = dist_metrics.nsd(tau=tau)
+# Boundary intersection over union (BIoU) with tau
+results[f"BIoU_{tau}"] = dist_metrics.biou(tau=tau)
+
+# print metric values
+units = {"HD": "mm", "MASD": "mm", "ASSD": "mm", "NSD": "%", "BIoU": "%"}
+for k, v in results.items():
+    unit = units.get(k.split("_")[0], "")
+    f = 100.0 if unit == "%" else 1.0
+    print(f"{k}: {v*f:.2f} {unit}")
+
+# ----------------------------------------
+# If using `numpy.ndarray` representations, note that the spacing must be
+# reordered when converting a `SimpleITK.Image` object to a `numpy.ndarray`
+ref_np = sitk.GetArrayFromImage(ref_sitk).astype(bool)
+pred_np = sitk.GetArrayFromImage(pred_sitk).astype(bool)
+
+# spacing should resemble the order of numpy array axes
+spacing = ref_sitk.GetSpacing()[::-1]
+
+dist_metrics = DistanceMetrics()
+dist_metrics.set_input(ref=ref_np, pred=pred_np, spacing=spacing)
+# ... follow the same procedure as before
+```

pymeshmetrics-1.0.0/README.md

@@ -0,0 +1,135 @@
+# MeshMetrics
+> Official Python-based implementation of `MeshMetrics` from [_MeshMetrics: A Precise Implementation of Distance-Based Image Segmentation Metrics_](https://doi.org/10.48550/arXiv.2509.05670), motivated by the implementation pitfalls identified in [_Understanding Implementation Pitfalls of Distance-Based Metrics for Image Segmentation_](https://doi.org/10.48550/arXiv.2410.02630) and [_HDilemma: Are Open-Source Hausdorff Distance Implementations Equivalent?_](https://link.springer.com/chapter/10.1007/978-3-031-72114-4_30)
+
+## About
+`MeshMetrics` is a precise, mesh-based implementation of widely used distance-based metrics for evaluating image segmentation tasks. By leveraging mesh representations of segmentation, `MeshMetrics` ensures precision in distance and boundary element size calculations. For a detailed description and a comparison with other open-source tools supporting distance-based metric calculations, see [our paper](https://doi.org/10.48550/arXiv.2509.05670).
+
+The library supports both 2D and 3D data and works seamlessly with multiple segmentation formats (`numpy.ndarray`, `SimpleITK.Image`, `vtk.vtkPolyData`, `trimesh.Trimesh`, and `meshio.Mesh`). It also allows mixing representations between reference and predicted segmentations - for example, one input can be a mask image (`SimpleITK.Image`), while the other is a surface mesh (`vtk.vtkPolyData`/`trimesh.Trimesh`/`meshio.Mesh`). See the *Advanced usage* section in [`examples.ipynb`](examples.ipynb) for more details.
+
+Available distance-based metrics:
+- **Hausdorff distance** (HD) with $p$-th **percentile variants** (HD<sub>p</sub>)
+- **Mean average surface distance** (MASD)
+- **Average symmetric surface distance** (ASSD)
+- **Normalized surface distance** (NSD)
+- **Boundary intersection over union** (BIoU)
+
+For convenience, `MeshMetrics` also includes implementations of the **Dice similarity coefficient** (DSC) and **intersection over union** (IoU).
+
+![overview](./data/paper_overview.png)
+
+If you use `MeshMetrics` in your work, please cite:
+```
+Podobnik, G., & Vrtovec, T. (2025). MeshMetrics: A Precise Implementation of Distance-Based Image Segmentation Metrics. arXiv preprint arXiv:2509.05670.
+Podobnik, G., & Vrtovec, T. (2025). Understanding Implementation Pitfalls of Distance-Based Metrics for Image Segmentation. arXiv preprint arXiv:2410.02630.
+```
+
+## Installation
+### System Dependencies
+This package requires `libxrender1` to be installed on your system. Install it via:
+```bash
+sudo apt update && sudo apt install -y libxrender1
+```
+
+### Install `meshmetrics` package
+Install from [PyPI](https://pypi.org/project/pymeshmetrics/) with pip, or add it to your project with [uv](https://docs.astral.sh/uv/):
+```bash
+pip install pymeshmetrics
+uv add pymeshmetrics
+```
+The package is published as `pymeshmetrics` and imported as `meshmetrics`:
+```python
+import meshmetrics
+```
+Optional support for `trimesh` and `meshio` inputs is available via extras: `pip install "pymeshmetrics[all]"` (or `[trimesh]` / `[meshio]`).
+
+To install the latest development version from GitHub:
+```bash
+pip install git+https://github.com/gasperpodobnik/meshmetrics.git
+```
+
+### Development
+Clone the repository and create the environment (including dev tools and all extras):
+```bash
+git clone https://github.com/gasperpodobnik/meshmetrics.git
+cd meshmetrics
+uv sync --all-extras
+uv run pytest
+```
+
+## Usage
+### Quick start
+Compute all metrics for a pair of segmentations in one call:
+```python
+import SimpleITK as sitk
+from meshmetrics import compute_metrics
+
+ref_sitk = sitk.ReadImage("data/example_3d_ref_mask.nii.gz")
+pred_sitk = sitk.ReadImage("data/example_3d_pred_mask.nii.gz")
+
+results = compute_metrics(ref_sitk, pred_sitk, taus=(2.0, 5.0))
+# {'ref_is_empty': False, 'pred_is_empty': False, 'HD_100': ..., 'HD_95': ..., 'MASD': ..., 'ASSD': ...,
+#  'NSD_2.0': ..., 'NSD_5.0': ..., 'BIoU_2.0': ..., 'BIoU_5.0': ..., 'DSC': ..., 'IoU': ...}
+```
+`taus` are the tolerances (in physical units) for NSD and BIoU; they are application-specific, so NSD and BIoU are only computed when `taus` are given. Use `percentiles` to choose the HD variants (default `(100, 95)`) and `metrics` to select a subset, e.g. `metrics=["hd", "nsd"]`. Inputs can be any of the supported types (see below); numpy arrays and pairs of meshes also need `spacing`.
+
+### Step-by-step
+Simple usage example of `MeshMetrics` for 3D segmentation masks is shown below.
+See [`examples.ipynb`](examples.ipynb) notebook for more examples.
+
+```python
+from pathlib import Path
+import SimpleITK as sitk
+from meshmetrics import DistanceMetrics
+
+data_dir = Path("data")
+
+# read binary segmentation masks
+ref_sitk = sitk.ReadImage(str(data_dir / "example_3d_ref_mask.nii.gz"))
+pred_sitk = sitk.ReadImage(str(data_dir / "example_3d_pred_mask.nii.gz"))
+
+# Set parameters
+percentile = 95  # percentile for HD
+tau = 2.0  # tolerance for NSD and BIoU
+
+# Initialize distance metrics class and set inputs
+dist_metrics = DistanceMetrics()
+dist_metrics.set_input(ref=ref_sitk, pred=pred_sitk)
+
+# store flags indicating empty masks
+results = {
+    "ref_is_empty": dist_metrics.ref_is_empty,
+    "pred_is_empty": dist_metrics.pred_is_empty,
+}
+# Hausdorff distance (HD), by default, HD percentile is set to 100 (equivalent to HD)
+results["HD_100"] = dist_metrics.hd()
+# p-th percentile HD (HD_p)
+results[f"HD_{percentile}"] = dist_metrics.hd(percentile=percentile)
+# Mean average surface distance (MASD)
+results["MASD"] = dist_metrics.masd()
+# Average symmetric surface distance (ASSD)
+results["ASSD"] = dist_metrics.assd()
+# Normalized surface distance (NSD) with tau
+results[f"NSD_{tau}"] = dist_metrics.nsd(tau=tau)
+# Boundary intersection over union (BIoU) with tau
+results[f"BIoU_{tau}"] = dist_metrics.biou(tau=tau)
+
+# print metric values
+units = {"HD": "mm", "MASD": "mm", "ASSD": "mm", "NSD": "%", "BIoU": "%"}
+for k, v in results.items():
+    unit = units.get(k.split("_")[0], "")
+    f = 100.0 if unit == "%" else 1.0
+    print(f"{k}: {v*f:.2f} {unit}")
+
+# ----------------------------------------
+# If using `numpy.ndarray` representations, note that the spacing must be
+# reordered when converting a `SimpleITK.Image` object to a `numpy.ndarray`
+ref_np = sitk.GetArrayFromImage(ref_sitk).astype(bool)
+pred_np = sitk.GetArrayFromImage(pred_sitk).astype(bool)
+
+# spacing should resemble the order of numpy array axes
+spacing = ref_sitk.GetSpacing()[::-1]
+
+dist_metrics = DistanceMetrics()
+dist_metrics.set_input(ref=ref_np, pred=pred_np, spacing=spacing)
+# ... follow the same procedure as before
+```