nbmorph 0.1.0__tar.gz

nbmorph-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) [2025] [Marius Causemann]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

nbmorph-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: nbmorph
+Version: 0.1.0
+Summary: A small package with Numba-accelerated morphological operations.
+Author-email: Marius Causemann <mariusca@simula.no>
+License: MIT License
+        
+        Copyright (c) [2025] [Marius Causemann]
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: numba
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: fastmorph; extra == "test"
+Dynamic: license-file
+
+# nbmorph
+
+A small, Numba-accelerated Python package for morphological operations on 3D labeled images.
+
+`nbmorph` provides a set of common morphological operations optimized for performance using Numba. It is designed to work with 3D NumPy arrays representing labeled image data, where different integer labels correspond to different objects.
+
+## Features
+
+* **Numba-accelerated:** Operations are just-in-time compiled with Numba for high performance on CPUs.
+
+* **3D Label Image Support:** All operations are designed for 3D labeled images (integer NumPy arrays).
+
+* **Quasi-Spherical Structuring Elements:** Approximates spherical structuring elements by alternating between box and diamond kernels for dilation and erosion.
+
+* **Core Morphological Operations:**
+
+  * `dilate_labels_spherical`: Expands the boundaries of labeled regions by assigning the mode of the neighborhood to background voxels.
+
+  * `erode_labels_spherical`: Shrinks the boundaries of labeled regions.
+
+  * `open_labels_spherical`: Removes small noise and thin protrusions (erosion followed by dilation).
+
+  * `close_labels_spherical`: Fills small holes within objects (dilation followed by erosion).
+
+  * `smooth_labels_spherical`: Smoothes object boundaries by performing an opening followed by a closing.
+
+![Effect of Morphological Smoothing](img/smoothing_effect.png)
+*Demonstration of the smoothing effect with varying radii and iterations on a sample image.*
+
+
+## Installation
+
+You can install `nbmorph` directly from the source directory using pip:
+
+```
+pip install .
+
+```
+
+
+## Usage
+
+Here is a basic example of how to use `nbmorph` to apply morphological smoothing to a 3D labeled image.
+
+```
+import numpy as np
+import nbmorph
+
+# Create a sample 3D labeled image
+# For example, a 5x5x5 cube of label 1 in a 10x10x10 volume
+labels = np.zeros((10, 10, 10), dtype=np.uint16)
+labels[2:7, 2:7, 2:7] = 1
+
+# Apply morphological smoothing with a radius of 1
+smoothed_labels = nbmorph.smooth_labels_spherical(labels, radius=1)
+
+print("Smoothing complete. The smoothed labels are in the 'smoothed_labels' array.")
+
+```
+
+## Operations
+
+The core functions of the library are:
+
+* `nbmorph.dilate_labels_spherical(labels, radius=1)`
+
+* `nbmorph.erode_labels_spherical(labels, radius=1)`
+
+* `nbmorph.open_labels_spherical(labels, radius=1, iterations=1)`
+
+* `nbmorph.close_labels_spherical(labels, radius=1, iterations=1)`
+
+* `nbmorph.smooth_labels_spherical(labels, radius=1, iterations=1)`
+
+## Testing
+
+Tests are written using `pytest`. To run the tests, first install the test dependencies and then run `pytest`:
+
+```
+pip install .[test]
+pytest
+```
+
+## Benchmarking
+
+A benchmark script is included in the `scripts` directory:
+
+```
+python scripts/benchmark.py
+```
+
+## License
+
+This project is licensed under the MIT License - see the `LICENSE` file for details.

nbmorph-0.1.0/README.md

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+# nbmorph
+
+A small, Numba-accelerated Python package for morphological operations on 3D labeled images.
+
+`nbmorph` provides a set of common morphological operations optimized for performance using Numba. It is designed to work with 3D NumPy arrays representing labeled image data, where different integer labels correspond to different objects.
+
+## Features
+
+* **Numba-accelerated:** Operations are just-in-time compiled with Numba for high performance on CPUs.
+
+* **3D Label Image Support:** All operations are designed for 3D labeled images (integer NumPy arrays).
+
+* **Quasi-Spherical Structuring Elements:** Approximates spherical structuring elements by alternating between box and diamond kernels for dilation and erosion.
+
+* **Core Morphological Operations:**
+
+  * `dilate_labels_spherical`: Expands the boundaries of labeled regions by assigning the mode of the neighborhood to background voxels.
+
+  * `erode_labels_spherical`: Shrinks the boundaries of labeled regions.
+
+  * `open_labels_spherical`: Removes small noise and thin protrusions (erosion followed by dilation).
+
+  * `close_labels_spherical`: Fills small holes within objects (dilation followed by erosion).
+
+  * `smooth_labels_spherical`: Smoothes object boundaries by performing an opening followed by a closing.
+
+![Effect of Morphological Smoothing](img/smoothing_effect.png)
+*Demonstration of the smoothing effect with varying radii and iterations on a sample image.*
+
+
+## Installation
+
+You can install `nbmorph` directly from the source directory using pip:
+
+```
+pip install .
+
+```
+
+
+## Usage
+
+Here is a basic example of how to use `nbmorph` to apply morphological smoothing to a 3D labeled image.
+
+```
+import numpy as np
+import nbmorph
+
+# Create a sample 3D labeled image
+# For example, a 5x5x5 cube of label 1 in a 10x10x10 volume
+labels = np.zeros((10, 10, 10), dtype=np.uint16)
+labels[2:7, 2:7, 2:7] = 1
+
+# Apply morphological smoothing with a radius of 1
+smoothed_labels = nbmorph.smooth_labels_spherical(labels, radius=1)
+
+print("Smoothing complete. The smoothed labels are in the 'smoothed_labels' array.")
+
+```
+
+## Operations
+
+The core functions of the library are:
+
+* `nbmorph.dilate_labels_spherical(labels, radius=1)`
+
+* `nbmorph.erode_labels_spherical(labels, radius=1)`
+
+* `nbmorph.open_labels_spherical(labels, radius=1, iterations=1)`
+
+* `nbmorph.close_labels_spherical(labels, radius=1, iterations=1)`
+
+* `nbmorph.smooth_labels_spherical(labels, radius=1, iterations=1)`
+
+## Testing
+
+Tests are written using `pytest`. To run the tests, first install the test dependencies and then run `pytest`:
+
+```
+pip install .[test]
+pytest
+```
+
+## Benchmarking
+
+A benchmark script is included in the `scripts` directory:
+
+```
+python scripts/benchmark.py
+```
+
+## License
+
+This project is licensed under the MIT License - see the `LICENSE` file for details.

nbmorph-0.1.0/pyproject.toml

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+# pyproject.toml
+
+[project]
+name = "nbmorph"
+version = "0.1.0"
+authors = [
+  { name="Marius Causemann", email="mariusca@simula.no" },
+]
+description = "A small package with Numba-accelerated morphological operations."
+readme = "README.md"
+license = { file="LICENSE" }
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Image Processing",
+]
+dependencies = [
+    "numpy",
+    "numba",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest", "pytest-cov", "fastmorph",
+]
+
+[tool.coverage.run]
+branch = false
+
+[tool.coverage.report]
+ignore_errors = true
+

nbmorph-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

nbmorph-0.1.0/src/nbmorph/__init__.py

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+from .morphology import (
+    dilate_labels_spherical,
+    erode_labels_spherical,
+    open_labels_spherical,
+    close_labels_spherical,
+    smooth_labels_spherical,
+)
+from .mode import onlyzero_mode_box,onlyzero_mode_diamond, fast_mode
+from .minmax import minimum_box, maximum_box, minimum_diamond, maximum_diamond
+from .zero_edges import zero_label_edges_box, zero_label_edges_diamond
+from .utils import cycle
+
+# Define the package version
+__version__ = "0.1.0"