medvol 0.0.2__tar.gz

medvol-0.0.2/LICENSE

@@ -0,0 +1,202 @@
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medvol-0.0.2/MANIFEST.in

@@ -0,0 +1,5 @@
+include LICENSE
+include README.md
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

medvol-0.0.2/PKG-INFO

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+Metadata-Version: 2.1
+Name: medvol
+Version: 0.0.2
+Summary: A wrapper for loading medical 3D image volumes such as NIFTI or NRRD images.
+Author: Karol Gotkowski
+Author-email: karol.gotkowski@dkfz.de
+License: Apache-2.0
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Provides-Extra: testing
+Requires-Dist: tox; extra == "testing"
+Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
+
+# MedVol
+
+[![License Apache Software License 2.0](https://img.shields.io/pypi/l/medvol.svg?color=green)](https://github.com/Karol-G/medvol/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/medvol.svg?color=green)](https://pypi.org/project/medvol)
+[![Python Version](https://img.shields.io/pypi/pyversions/medvol.svg?color=green)](https://python.org)
+
+A wrapper for loading medical 3D image volumes such as NIFTI or NRRD images.
+
+## Installation
+
+You can install `medvol` via [pip](https://pypi.org/project/medvol/):
+
+    pip install medvol
+
+## Example
+
+```python
+from medvol import MedVol
+
+# Load NIFTI image
+image = MedVol("path/to/image.nifti")
+
+# Print some metadata
+print("Spacing: ", image.spacing)
+print("Affine: ", image.affine)
+print("Header: ", image.header)
+
+# Access and modify the image array
+arr = image.array
+arr[0, 0, 0] = 1
+
+# Create a new image with the new array, a new spacing, but copy all remaining metadata
+new_image = MedVol(arr, spacing=[2, 2, 2], copy=image)
+
+# Save the new image as NRRD
+new_image.save("path/to/new_image.nrrd")
+```
+
+
+## Contributing
+
+Contributions are very welcome. Tests can be run with [tox], please ensure
+the coverage at least stays the same before you submit a pull request.
+
+## License
+
+Distributed under the terms of the [Apache Software License 2.0] license,
+"medvol" is free and open source software
+
+## Issues
+
+If you encounter any problems, please file an issue along with a detailed description.
+
+[Cookiecutter]: https://github.com/audreyr/cookiecutter
+[MIT]: http://opensource.org/licenses/MIT
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
+[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
+[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
+[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
+[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
+
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/

medvol-0.0.2/README.md

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+# MedVol
+
+[![License Apache Software License 2.0](https://img.shields.io/pypi/l/medvol.svg?color=green)](https://github.com/Karol-G/medvol/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/medvol.svg?color=green)](https://pypi.org/project/medvol)
+[![Python Version](https://img.shields.io/pypi/pyversions/medvol.svg?color=green)](https://python.org)
+
+A wrapper for loading medical 3D image volumes such as NIFTI or NRRD images.
+
+## Installation
+
+You can install `medvol` via [pip](https://pypi.org/project/medvol/):
+
+    pip install medvol
+
+## Example
+
+```python
+from medvol import MedVol
+
+# Load NIFTI image
+image = MedVol("path/to/image.nifti")
+
+# Print some metadata
+print("Spacing: ", image.spacing)
+print("Affine: ", image.affine)
+print("Header: ", image.header)
+
+# Access and modify the image array
+arr = image.array
+arr[0, 0, 0] = 1
+
+# Create a new image with the new array, a new spacing, but copy all remaining metadata
+new_image = MedVol(arr, spacing=[2, 2, 2], copy=image)
+
+# Save the new image as NRRD
+new_image.save("path/to/new_image.nrrd")
+```
+
+
+## Contributing
+
+Contributions are very welcome. Tests can be run with [tox], please ensure
+the coverage at least stays the same before you submit a pull request.
+
+## License
+
+Distributed under the terms of the [Apache Software License 2.0] license,
+"medvol" is free and open source software
+
+## Issues
+
+If you encounter any problems, please file an issue along with a detailed description.
+
+[Cookiecutter]: https://github.com/audreyr/cookiecutter
+[MIT]: http://opensource.org/licenses/MIT
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
+[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
+[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
+[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
+[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
+
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/

medvol-0.0.2/medvol/__init__.py

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+__version__ = "0.0.2"
+
+from medvol.medvol import MedVol

medvol-0.0.2/medvol/medvol.py

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+import SimpleITK as sitk
+from dataclasses import dataclass, field
+from typing import Dict, Optional, Union
+import numpy as np
+
+
+@dataclass
+class MedVol:
+    array: Union[np.ndarray, str]
+    spacing: Optional[np.ndarray] = None
+    origin: Optional[np.ndarray] = None
+    direction: Optional[np.ndarray] = None
+    header: Optional[Dict] = None
+    copy: Optional['MedVol'] = field(default=None, repr=False)
+
+    def __post_init__(self):
+        # Validate array: Must be a 3D array
+        if not ((isinstance(self.array, np.ndarray) and self.array.ndim == 3) or isinstance(self.array, str)):
+            raise ValueError("array must be a 3D numpy array or a filepath string")
+        
+        if isinstance(self.array, str):
+            self._load(self.array)
+
+        # Validate spacing: Must be None or a 1D array with three floats
+        if self.spacing is not None:
+            if not (isinstance(self.spacing, np.ndarray) and self.spacing.shape == (3,) and np.issubdtype(self.spacing.dtype, np.floating)):
+                raise ValueError("spacing must be None or a 1D numpy array with three floats")
+
+        # Validate origin: Must be None or a 1D array with three floats
+        if self.origin is not None:
+            if not (isinstance(self.origin, np.ndarray) and self.origin.shape == (3,) and np.issubdtype(self.origin.dtype, np.floating)):
+                raise ValueError("origin must be None or a 1D numpy array with three floats")
+
+        # Validate direction: Must be None or a 3x3 array of floats
+        if self.direction is not None:
+            if not (isinstance(self.direction, np.ndarray) and self.direction.shape == (3, 3) and np.issubdtype(self.direction.dtype, np.floating)):
+                raise ValueError("direction must be None or a 3x3 numpy array of floats")
+
+        # Validate header: Must be None or a dictionary
+        if self.header is not None and not isinstance(self.header, dict):
+            raise ValueError("header must be None or a dictionary")
+        
+        # If copy is set, copy fields from the other Nifti instance
+        if self.copy is not None:
+            self._copy_fields_from(self.copy)
+
+    @property
+    def affine(self) -> np.ndarray:
+        if self.spacing is None or self.origin is None or self.direction is None:
+            raise ValueError("spacing, origin, and direction must all be set to compute the affine.")
+        
+        affine = np.eye(4)
+        affine[:3, :3] = self.direction @ np.diag(self.spacing)
+        affine[:3, 3] = self.origin
+        return affine
+
+    def _copy_fields_from(self, other: 'MedVol'):
+        if self.spacing is None:
+            self.spacing = other.spacing
+        if self.origin is None:
+            self.origin = other.origin
+        if self.direction is None:
+            self.direction = other.direction
+        if self.header is None:
+            self.header = other.header
+
+    def _load(self, filepath):
+        image_sitk = sitk.ReadImage(filepath)
+        self.array = sitk.GetArrayFromImage(image_sitk)
+        self.spacing = np.array(image_sitk.GetSpacing()[::-1])
+        self.origin = np.array(image_sitk.GetOrigin()[::-1])
+        self.direction = np.array(image_sitk.GetDirection()[::-1]).reshape(3, 3)
+        self.header = {key: image_sitk.GetMetaData(key) for key in image_sitk.GetMetaDataKeys()}
+
+    def save(self, filepath):
+        image_sitk = sitk.GetImageFromArray(self.array)
+        image_sitk.SetSpacing(self.spacing.tolist()[::-1])
+        image_sitk.SetOrigin(self.origin.tolist()[::-1])
+        image_sitk.SetDirection(self.direction.flatten().tolist()[::-1])
+        for key, value in self.header.items():
+            image_sitk.SetMetaData(key, value) 
+        sitk.WriteImage(image_sitk, filepath)

medvol-0.0.2/medvol.egg-info/PKG-INFO

@@ -0,0 +1,91 @@
+Metadata-Version: 2.1
+Name: medvol
+Version: 0.0.2
+Summary: A wrapper for loading medical 3D image volumes such as NIFTI or NRRD images.
+Author: Karol Gotkowski
+Author-email: karol.gotkowski@dkfz.de
+License: Apache-2.0
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Provides-Extra: testing
+Requires-Dist: tox; extra == "testing"
+Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
+
+# MedVol
+
+[![License Apache Software License 2.0](https://img.shields.io/pypi/l/medvol.svg?color=green)](https://github.com/Karol-G/medvol/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/medvol.svg?color=green)](https://pypi.org/project/medvol)
+[![Python Version](https://img.shields.io/pypi/pyversions/medvol.svg?color=green)](https://python.org)
+
+A wrapper for loading medical 3D image volumes such as NIFTI or NRRD images.
+
+## Installation
+
+You can install `medvol` via [pip](https://pypi.org/project/medvol/):
+
+    pip install medvol
+
+## Example
+
+```python
+from medvol import MedVol
+
+# Load NIFTI image
+image = MedVol("path/to/image.nifti")
+
+# Print some metadata
+print("Spacing: ", image.spacing)
+print("Affine: ", image.affine)
+print("Header: ", image.header)
+
+# Access and modify the image array
+arr = image.array
+arr[0, 0, 0] = 1
+
+# Create a new image with the new array, a new spacing, but copy all remaining metadata
+new_image = MedVol(arr, spacing=[2, 2, 2], copy=image)
+
+# Save the new image as NRRD
+new_image.save("path/to/new_image.nrrd")
+```
+
+
+## Contributing
+
+Contributions are very welcome. Tests can be run with [tox], please ensure
+the coverage at least stays the same before you submit a pull request.
+
+## License
+
+Distributed under the terms of the [Apache Software License 2.0] license,
+"medvol" is free and open source software
+
+## Issues
+
+If you encounter any problems, please file an issue along with a detailed description.
+
+[Cookiecutter]: https://github.com/audreyr/cookiecutter
+[MIT]: http://opensource.org/licenses/MIT
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
+[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
+[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
+[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
+[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
+
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/

medvol-0.0.2/medvol.egg-info/SOURCES.txt

@@ -0,0 +1,12 @@
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+setup.cfg
+medvol/__init__.py
+medvol/medvol.py
+medvol.egg-info/PKG-INFO
+medvol.egg-info/SOURCES.txt
+medvol.egg-info/dependency_links.txt
+medvol.egg-info/requires.txt
+medvol.egg-info/top_level.txt

medvol-0.0.2/medvol.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

medvol-0.0.2/medvol.egg-info/requires.txt

@@ -0,0 +1,6 @@
+numpy
+
+[testing]
+tox
+pytest
+pytest-cov

medvol-0.0.2/medvol.egg-info/top_level.txt

@@ -0,0 +1 @@
+medvol

medvol-0.0.2/pyproject.toml

@@ -0,0 +1,56 @@
+[build-system]
+requires = ["setuptools>=42.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+
+
+[tool.black]
+line-length = 79
+target-version = ['py38', 'py39', 'py310']
+
+
+[tool.ruff]
+line-length = 79
+select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "BLE", # flake8-blind-exception
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    "C4", # flake8-comprehensions
+    "ISC", # flake8-implicit-str-concat
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "SIM", # flake8-simplify
+]
+ignore = [
+    "E501", # line too long. let black handle this
+    "UP006", "UP007", # type annotation. As using magicgui require runtime type annotation then we disable this.
+    "SIM117", # flake8-simplify - some of merged with statements are not looking great with black, reanble after drop python 3.9
+]
+
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    ".pants.d",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+    "*vendored*",
+    "*_vendor*",
+]
+
+target-version = "py38"
+fix = true

medvol-0.0.2/setup.cfg

@@ -0,0 +1,43 @@
+[metadata]
+name = medvol
+version = attr: medvol.__version__
+description = A wrapper for loading medical 3D image volumes such as NIFTI or NRRD images.
+long_description = file: README.md
+long_description_content_type = text/markdown
+author = Karol Gotkowski
+author_email = karol.gotkowski@dkfz.de
+license = Apache-2.0
+license_files = LICENSE
+classifiers = 
+	Development Status :: 2 - Pre-Alpha
+	Intended Audience :: Developers
+	License :: OSI Approved :: Apache Software License
+	Operating System :: OS Independent
+	Programming Language :: Python
+	Programming Language :: Python :: 3
+	Programming Language :: Python :: 3 :: Only
+	Programming Language :: Python :: 3.8
+	Programming Language :: Python :: 3.9
+	Programming Language :: Python :: 3.10
+	Topic :: Scientific/Engineering :: Image Processing
+
+[options]
+packages = find:
+install_requires = 
+	numpy
+python_requires = >=3.8
+include_package_data = True
+
+[options.extras_require]
+testing = 
+	tox
+	pytest  # https://docs.pytest.org/en/latest/contents.html
+	pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
+
+[options.package_data]
+* = *.yaml
+
+[egg_info]
+tag_build = 
+tag_date = 0
+