vIQA 2.2.1__tar.gz → 2.2.2__tar.gz

{viqa-2.2.1 → viqa-2.2.2}/.github/ISSUE_TEMPLATE/bug_report.md

@@ -37,6 +37,5 @@ Please search on the [issue tracker](https://github.com/3dct/vIQA/issues) before
 ## Your Environment
 <!--- Include as many relevant details about the environment you experienced the bug in -->
 * Version used:
-* Browser Name and version:
-* Operating System and version (desktop or mobile):
+* Operating System and version:
 * Link to your project:

{viqa-2.2.1 → viqa-2.2.2}/.github/workflows/build_and_push_docker_images.yaml

@@ -33,13 +33,13 @@ jobs:
             description: This is a custom image for volumetric image quality assessment in daskhub.
             source: https://github.com/3dct/vIQA/tree/main/containers/dh-image-quality-notebook/Dockerfile
             documentation: https://github.com/3dct/vIQA/tree/main/containers/dh-image-quality-notebook/README.md
-            prefix: dh
+            prefix: dh-
           - dockerfile: ./containers/jh-image-quality-notebook/Dockerfile
             title: volumetric Image Quality Assessment Notebook - JupyterHub
             description: This is a custom image for volumetric image quality assessment in jupyterhub.
             source: https://github.com/3dct/vIQA/tree/main/containers/jh-image-quality-notebook/Dockerfile
             documentation: https://github.com/3dct/vIQA/tree/main/containers/jh-image-quality-notebook/README.md
-            prefix: jh
+            prefix: jh-
 
     permissions:
       contents: read

{viqa-2.2.1 → viqa-2.2.2}/.github/workflows/release.yaml

@@ -113,7 +113,7 @@ jobs:
 
       - name: Python Semantic Release
         id: release
-        uses: python-semantic-release/python-semantic-release@v9.12.0
+        uses: python-semantic-release/python-semantic-release@v9.21.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           git_committer_name: "github-actions"
@@ -328,7 +328,7 @@ jobs:
             ./dist/*.whl
 
       - name: Publish package distributions to GitHub Releases
-        uses: python-semantic-release/publish-action@v9.12.0
+        uses: python-semantic-release/publish-action@v9.21.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
 

{viqa-2.2.1 → viqa-2.2.2}/.pre-commit-config.yaml

@@ -2,9 +2,9 @@
 # Install pre-commit hooks via
 # pre-commit install
 ci:
-  autofix_prs: false
+  autofix_prs: true
   autoupdate_schedule: 'quarterly'
-  autoupdate_commit_msg: 'chore: pre-commit autoupdate\n\nAutomatically generated by pre-commit.ci'
+  autoupdate_commit_msg: 'chore: pre-commit autoupdate\\n\\nAutomatically generated by pre-commit.ci'
   skip: ['build-docs', 'mypy']
   submodules: true
 repos:
@@ -40,7 +40,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.11.0
+    rev: v0.11.4
     hooks:
       # Run the linter.
       - id: ruff
@@ -50,7 +50,7 @@ repos:
         args: [--config=pyproject.toml]
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.23
+    rev: v0.24.1
     hooks:
       - id: validate-pyproject
         name: Validate pyproject.toml
@@ -61,7 +61,7 @@ repos:
       - id: pyupgrade
 
   - repo: https://github.com/gitleaks/gitleaks
-    rev: v8.22.1
+    rev: v8.24.2
     hooks:
       - id: gitleaks
 
@@ -84,18 +84,18 @@ repos:
         stages: [pre-push]
 
   - repo: https://github.com/rhysd/actionlint
-    rev: v1.7.6
+    rev: v1.7.7
     hooks:
       - id: actionlint
 
   - repo: https://github.com/adrienverge/yamllint
-    rev: v1.35.1
+    rev: v1.37.0
     hooks:
       - id: yamllint
         args: ["--strict", "--config-file=.yamllint.yaml"]
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         files: ^.*\.(py|c|cpp|h|m|md|rst|yml|yaml)$
@@ -106,7 +106,7 @@ repos:
           )
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.14.1
+    rev: v1.15.0
     hooks:
       - id: mypy
         additional_dependencies:

{viqa-2.2.1 → viqa-2.2.2}/CHANGELOG.md

@@ -2,6 +2,43 @@
 
 
 
+## v2.2.2 (2025-04-09)
+
+### Bug fixes
+
+* fix: fix semantic release exclude commit pattern ([`b24070e`](https://github.com/3dct/vIQA/commit/b24070ec67f74d68d0915524d77bfa11a828bcc3))
+
+* fix: fix rois in BatchMetrics.report when exporting images ([`88c8931`](https://github.com/3dct/vIQA/commit/88c89317ae9735685f16953a5b2338e72fe2a74c))
+
+* fix: enable rois in BatchMetrics
+
+closes #11 ([`c2b0ce5`](https://github.com/3dct/vIQA/commit/c2b0ce5102aec6ee9ce9434bfc9d3ea8eabdbc12))
+
+* fix: add check for image dimensions during loading (#15)
+
+* fix: add check for image dimensions during loading
+
+closes #14
+
+* [pre-commit.ci] auto fixes from pre-commit.com hooks
+
+for more information, see https://pre-commit.ci
+
+* refactor: refactor to comply with ruff
+
+* docs(load_data): add Exception to function docstring
+
+---------
+
+Co-authored-by: Lukas Nepelius <p42940@fhooe.at>
+Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
+Co-authored-by: lukasbehammer <lukas.behammer@fh-wels.at> ([`a120ade`](https://github.com/3dct/vIQA/commit/a120adea9a19fa1e19b4f82cbf95232482fa7be4))
+
+### Documentation
+
+* docs: refactor user guide ([`c423f57`](https://github.com/3dct/vIQA/commit/c423f573db92326e4e96f815690ce50866a59a01))
+
+
 ## v2.2.1 (2025-04-02)
 
 ### Bug fixes
@@ -109,12 +146,6 @@ fix csv delimiter sniffing, add support for tsv and txt files during loading of
 
 ## v2.0.0 (2024-10-22)
 
-### Breaking
-
-* refactor!: move utility modules to utils subpackage
-
-BREAKING CHANGE: major refactoring of utility functions ([`d3945b4`](https://github.com/3dct/vIQA/commit/d3945b47b710c471973296c70c93c272cc0f9552))
-
 ### Bug fixes
 
 * fix: convert rgb images to grayscale before binarization ([`f258f96`](https://github.com/3dct/vIQA/commit/f258f96d38efd6acc56fca9f1dcd823987703058))
@@ -169,6 +200,12 @@ update documentation, refactor definition of variable truncate ([`851521b`](http
 
 make sure that an ImageArray is returned via numpy ufunc ([`31524fb`](https://github.com/3dct/vIQA/commit/31524fbff81ff0cf52c9be7dc2e22b116c7dd286))
 
+### Refactoring
+
+* refactor!: move utility modules to utils subpackage
+
+BREAKING CHANGE: major refactoring of utility functions ([`d3945b4`](https://github.com/3dct/vIQA/commit/d3945b47b710c471973296c70c93c272cc0f9552))
+
 
 ## v1.13.0 (2024-09-24)
 
@@ -509,9 +546,8 @@ function writes custom parameters and package version to a .txt file ([`5b8e607`
 
 ## v1.0.0 (2024-08-05)
 
-### Breaking
+### Features
 
 * feat(ImageArray)!: add class for images
 
 subclass of np.ndarray, calculates image statistics ([`40f0d02`](https://github.com/3dct/vIQA/commit/40f0d029ad416747135f79e8716de040335da592))
-

{viqa-2.2.1 → viqa-2.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vIQA
-Version: 2.2.1
+Version: 2.2.2
 Summary: A Python package for volumetric image quality assessment.
 Keywords: IQA,image quality assessment,volumetric data,image comparison,CT,computed tomography
 Author-Email: Lukas Behammer <lukas.behammer@fh-wels.at>
@@ -50,7 +50,7 @@ Requires-Dist: sphinx_github_changelog>=1.4.0; extra == "docs"
 Requires-Dist: sphinx-last-updated-by-git>=0.3.8; extra == "docs"
 Requires-Dist: viqa[tests]; extra == "docs"
 Provides-Extra: cd
-Requires-Dist: python-semantic-release==9.12.0; extra == "cd"
+Requires-Dist: python-semantic-release==9.21.0; extra == "cd"
 Requires-Dist: cibuildwheel==2.19.2; extra == "cd"
 Provides-Extra: build
 Requires-Dist: meson-python>=0.16.0; extra == "build"

{viqa-2.2.1 → viqa-2.2.2}/containers/dh-image-quality-notebook/Dockerfile

@@ -17,7 +17,7 @@ USER ${NB_UID}
 RUN pip install viqa
 RUN pip install jupyter_app_launcher
 RUN pip install jupyterlab-git
-RUN pip install pexpect>4.8.0
+RUN pip install pexpect==4.9.0
 
 COPY notebooks /usr/share/jupyter/jupyter_app_launcher/notebooks
 COPY containers/config/jp_app_launcher/jp_app_launcher.yaml /usr/share/jupyter/jupyter_app_launcher/jp_app_launcher.yaml

{viqa-2.2.1 → viqa-2.2.2}/containers/jh-image-quality-notebook/Dockerfile

@@ -17,7 +17,7 @@ USER ${NB_UID}
 RUN pip install viqa
 RUN pip install jupyter_app_launcher
 RUN pip install jupyterlab-git
-RUN pip install pexpect>4.8.0
+RUN pip install pexpect==4.9.0
 
 COPY notebooks /usr/share/jupyter/jupyter_app_launcher/notebooks
 COPY containers/config/jp_app_launcher/jp_app_launcher.yaml /usr/share/jupyter/jupyter_app_launcher/jp_app_launcher.yaml

{viqa-2.2.1 → viqa-2.2.2}/docs/source/user_guide.rst

@@ -111,4 +111,4 @@ Possible, but worse (recommended only if you want to calculate a single metric):
     The current recommended usage files are the Jupyter Notebooks on the `Github page`_.
     Additional information can be found in the documentation of the individual metrics under :doc:`api_reference`.
 
-.. _Github page: https://github.com/3dct/vIQA
+    .. _Github page: https://github.com/3dct/vIQA

{viqa-2.2.1 → viqa-2.2.2}/pyproject.toml

@@ -68,7 +68,7 @@ docs = [
     "viqa[tests]",
 ]
 cd = [
-    "python-semantic-release ==9.12.0",
+    "python-semantic-release ==9.21.0",
     "cibuildwheel ==2.19.2",
 ]
 build = [
@@ -254,6 +254,8 @@ changelog_file = "CHANGELOG.md"
 exclude_commit_patterns = [
     ".*\\n\\nAutomatically generated by python-semantic-release",
     "chore: pre-commit autoupdate\n\nAutomatically generated by pre-commit.ci",
+    "chore: pre-commit autoupdate\\n\\nAutomatically generated by pre-commit.ci",
+    "\\[pre-commit\\.ci\\].*",
     "chore(?:\\([^)]*?\\))?: .+",
     "ci(?:\\([^)]*?\\))?: .+",
     "refactor(?:\\([^)]*?\\))?: .+",

{viqa-2.2.1 → viqa-2.2.2}/requirements/cd.txt

@@ -1,4 +1,4 @@
 # Generated via tools/generate_requirements.py and pre-commit hook.
 # Do not edit this file; modify pyproject.toml instead.
-python-semantic-release ==9.12.0
+python-semantic-release ==9.21.0
 cibuildwheel ==2.19.2

{viqa-2.2.1 → viqa-2.2.2}/src/viqa/__init__.py

@@ -5,7 +5,7 @@ The package provides a set of metrics to assess the quality of volumetric images
 It can be used for 2D and 3D images.
 """
 
-__version__ = "2.2.1"
+__version__ = "2.2.2"
 __author__ = "Lukas Behammer"
 __all__ = [
     "FSIM",

{viqa-2.2.1 → viqa-2.2.2}/src/viqa/multiple.py

@@ -155,6 +155,11 @@ class BatchMetrics(_MultipleInterface):
         List of metric instances. Each instance must be of type :py:class:`Metric`.
     metrics_parameters : list
         List of dictionaries containing the parameters for the metrics.
+    rois : list[list[tuple]], optional
+        A list of lists of tuples. Each tuple has the start and
+        end coordinates of the ROI in the format (x_start, x_end). Each tuple is
+        for one coordinate. Each entry of the outer list is
+        for one image pair.
 
     Raises
     ------
@@ -164,6 +169,7 @@ class BatchMetrics(_MultipleInterface):
         If the parameters list contains non-dictionary objects
         If the pairs file does not contain the columns 'reference_image' and
         'modified_image'.
+        If the length of the pairs and ROIs is not equal.
 
     Notes
     -----
@@ -192,13 +198,19 @@ class BatchMetrics(_MultipleInterface):
         >>> batch.export_results(file_path='path/to/results', file_name='results.csv')
     """
 
-    def __init__(self, file_dir, pairs_file, metrics, metrics_parameters):
+    def __init__(self, file_dir, pairs_file, metrics, metrics_parameters, rois=None):
         """Construct method."""
         super().__init__(metrics, metrics_parameters)
 
         self.file_dir = file_dir
         self.pairs_file = pairs_file
         self.pairs = _read_pairs(self.pairs_file)
+        if rois and len(self.pairs) != len(rois):
+            raise ValueError(
+                "The number of pairs and ROIs must be equal. "
+                f"Got {len(self.pairs)} pairs and {len(rois)} ROIs."
+            )
+        self.rois = rois
 
     def calculate(self, **kwargs):
         """Calculate the metrics in batch mode.
@@ -213,6 +225,9 @@ class BatchMetrics(_MultipleInterface):
         scaling_order : int, default=1
             Order of the spline interpolation used for image resizing. Default is 1.
             Passed to :py:func:`skimage.transform.resize`.
+        roi : list[tuple], optional
+            Region of interest to use for the calculation of all images. Overrides the
+            `rois` Class attribute.
 
         Returns
         -------
@@ -223,7 +238,17 @@ class BatchMetrics(_MultipleInterface):
         -----
         UserWarning
             If the images are the same as in the previous pair.
+            If the Class attribute `rois` is overwritten by the `roi` parameter.
         """
+        # Remove roi parameter from kwargs to avoid conflicts with loading
+        # Set None if not given to use either no roi or the class attribute rois
+        roi = kwargs.pop("roi", None)
+        self.global_roi = roi
+        if self.rois is not None and roi is not None:
+            warn(
+                "Class attribute `rois` is overwritten by the `roi` parameter.",
+                UserWarning,
+            )
         scaling_order = kwargs.pop("scaling_order", 1)
         reference_img = None
         prev_ref_path = None
@@ -239,7 +264,6 @@ class BatchMetrics(_MultipleInterface):
                 warn("Skipping calculation for identical image pair.", UserWarning)
                 continue
             # Load the images only once if it is the same for multiple pairs
-            roi = kwargs.pop("roi", None)  # Remove roi parameter to avoid conflicts
             if reference_path != prev_ref_path:
                 reference_img = load_data(reference_path, **kwargs)
                 prev_ref_path = reference_path
@@ -253,6 +277,9 @@ class BatchMetrics(_MultipleInterface):
             else:
                 prev_result_modified = metric_results
 
+            if roi is None and self.rois is not None:
+                roi = self.rois[pair_num]
+
             metric_results = _calc(
                 self.metrics,
                 self.metrics_parameters,
@@ -326,9 +353,12 @@ class BatchMetrics(_MultipleInterface):
                 ),
             )
         if image:
+            roi = self.global_roi
             for pair_num, pair in enumerate(tqdm(self.pairs)):
                 img_r = os.path.join(self.file_dir, pair["reference_image"])
                 img_m = os.path.join(self.file_dir, pair["modified_image"])
+                if self.global_roi is None and self.rois is not None:
+                    roi = self.rois[pair_num]
                 export_image(
                     results=self.results[str(pair_num)],
                     img_r=img_r,
@@ -343,6 +373,7 @@ class BatchMetrics(_MultipleInterface):
                     x=x,
                     y=y,
                     z=z,
+                    roi=roi,
                 )
 
     def export_results(self, file_path=".", file_name="results.csv"):

{viqa-2.2.1 → viqa-2.2.2}/src/viqa/utils/export.py

@@ -47,7 +47,7 @@ from warnings import warn
 import matplotlib.pyplot as plt
 import numpy as np
 
-from .loading import _check_imgs, _resize_image, load_data
+from .loading import _check_imgs, _resize_image, crop_image, load_data
 
 
 def export_results(metrics, output_path, filename, return_dict=False):
@@ -208,6 +208,7 @@ def export_image(
         warn("No results to plot. Only the images are plotted.", UserWarning)
 
     dpi = kwargs.pop("dpi", 300)
+    roi = kwargs.pop("roi", None)
 
     img_r = load_data(img_r)
     img_m = load_data(img_m)
@@ -216,6 +217,9 @@ def export_image(
         raise ValueError("Images must have the same number of dimensions.")
     scaling_order = kwargs.pop("scaling_order", 1)
     img_m = _resize_image(img_r, img_m, scaling_order=scaling_order)
+    if roi is not None:
+        img_r = crop_image(img_r, *roi)
+        img_m = crop_image(img_m, *roi)
     img_r, img_m = _check_imgs(img_r, img_m)
 
     if img_r.ndim == 2 or (img_r.ndim == 3 and img_r.shape[-1] == 3):

{viqa-2.2.1 → viqa-2.2.2}/src/viqa/utils/loading.py

@@ -655,7 +655,8 @@ def load_data(
     ------
     ValueError
         If input type is not supported \n
-        If ``data_range=None`` and ``normalize=True``
+        If ``data_range=None`` and ``normalize=True`` \n
+        If number of dimensions not 2 or 3
 
     Warns
     -----
@@ -738,6 +739,21 @@ def load_data(
                 "Input type not supported"
             )  # Raise exception if input type is not supported
 
+    if batch:
+        # TODO: Deprecate in version 4.0.0
+        for img_num, img in enumerate(img_arr):
+            if len(img.shape) > 3 or len(img.shape) < 2:
+                raise ValueError(
+                    f"Number of dimensions of input image should be 2 or 3, got "
+                    f"{len(img.shape)} for image number {img_num} in img_arr."
+                )
+    elif not isinstance(img_arr, list):
+        if len(img_arr.shape) > 3 or len(img_arr.shape) < 2:
+            raise ValueError(
+                f"Number of dimensions of input image should be 2 or 3, got "
+                f"{len(img_arr.shape)}."
+            )
+
     # Normalize data
     if normalize and data_range:
         # TODO: Deprecate in version 4.0.0
@@ -929,7 +945,7 @@ def crop_image(
         crop_shape = np.array((x[1] - x[0], y[1] - y[0], z[1] - z[0]))
         if (crop_shape < img_shape).all():  # If cropping is smaller than original image
             img_crop = img[x[0] : x[1], y[0] : y[1], z[0] : z[1]]
-        elif crop_shape == img_shape:  # If image is already cropped
+        elif (crop_shape == img_shape).all():  # If image is already cropped
             warn("Image is already cropped.", RuntimeWarning)
             img_crop = img
         else:  # If cropping is larger than original image