Enh/image io

.github/copilot-instructions.md

@@ -12,8 +12,9 @@
 - Use supported image formats: `.nii`, `.nii.gz`, `.mha`, `.nrrd`.
 - Ensure that the code is syntactically correct and adheres to the project's coding standards.
 - Be sure about the documentation and comments. They should be clear and concise and use the correct Python docstring format.
-- Create commit messages with a detailed description of the changes made, including any bug fixes or new features.
-- Be as much specific as possible in the commit messages, including the files affected and the nature of the changes.
+- Create commit messages with a as much details and description as possible in order to explain all the relevant information about the changes made, including any bug fixes or new features.
+- Be as much specific and complete as possible in the commit messages, including the files affected and the nature of the changes.
+- Organize the commit messages in bullet points for better readability, showing all the relevant information that is needed to explain the changes made.
 - Uses for commit messages prefixes the following pattern:
   - `ENH:` for new features and code enhancements
   - `BUG:` for bug fixes and general corrections

.github/pull_request_template.md

@@ -31,12 +31,12 @@ Please select the relevant option(s):
 - [ ] Code passes linting checks (`task lint-check`)
 - [ ] Code includes appropriate inline documentation
 
-**Note:** According to our [contribution guidelines](docs/contribute.md), please target the `develop` branch for most contributions to ensure proper testing before merging to `main`.
+**Note:** According to our [contribution guidelines](https://asltk.readthedocs.io/en/main/contribute/), please target the `develop` branch for most contributions to ensure proper testing before merging to `main`.
 
 **By submitting this pull request, I confirm:**
-- [ ] I have read and followed the [contribution guidelines](docs/contribute.md)
+- [ ] I have read and followed the [contribution guidelines](https://asltk.readthedocs.io/en/main/contribute/)
 - [ ] I have tested my changes thoroughly
 - [ ] I understand this is an open source project and my contributions may be used by others
-- [ ] I agree to the project's [Code of Conduct](CODE_OF_CONDUCT.md)
+- [ ] I agree to the project's [Code of Conduct](https://github.com/LOAMRI/asltk/blob/main/CODE_OF_CONDUCT.md)
 
 <!-- Thank you for contributing to asltk! 🚀 -->

.github/workflows/bumpversion_publish_workflow.yaml

@@ -28,7 +28,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.10'
 
       - name: Install Poetry
         run: pip install poetry

.github/workflows/ci_develop.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
 
 
     steps:
@@ -54,7 +54,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
 
     steps:
       - name: Clone repo
@@ -106,7 +106,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
 
     steps:
       - name: Clone repo

.github/workflows/ci_main.yaml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
 
 
     steps:
@@ -53,7 +53,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
 
     steps:
       - name: Clone repo
@@ -105,7 +105,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
 
     steps:
       - name: Clone repo

asltk/asldata.py

@@ -1,12 +1,13 @@
 import copy
 import os
 import warnings
+from typing import Union
 
 import numpy as np
 
-from asltk.logging_config import get_logger, log_data_info, log_function_call
+from asltk.logging_config import get_logger, log_data_info
 from asltk.utils.image_manipulation import collect_data_volumes
-from asltk.utils.io import load_image
+from asltk.utils.io import ImageIO
 
 
 class ASLData:
@@ -69,40 +70,53 @@ def __init__(
             if isinstance(kwargs.get('pcasl'), str):
                 pcasl_path = kwargs.get('pcasl')
                 logger.info(f'Loading ASL image from: {pcasl_path}')
-                self._asl_image = load_image(pcasl_path)
+                self._asl_image = ImageIO(image_path=pcasl_path)
                 if self._asl_image is not None:
                     log_data_info(
-                        'ASL image', self._asl_image.shape, pcasl_path
+                        'ASL image',
+                        self._asl_image.get_as_numpy().shape,
+                        pcasl_path,
                     )
             elif isinstance(kwargs.get('pcasl'), np.ndarray):
-                self._asl_image = kwargs.get('pcasl')
-                logger.info('ASL image loaded as numpy array')
+                self._asl_image = ImageIO(image_array=kwargs.get('pcasl'))
+                logger.info('ASL image loaded')
                 log_data_info(
-                    'ASL image', self._asl_image.shape, 'numpy array'
+                    'ASL image', self._asl_image.get_as_numpy().shape
                 )
 
         if kwargs.get('m0') is not None:
+            average_m0 = kwargs.get('average_m0', False)
+
             if isinstance(kwargs.get('m0'), str):
                 m0_path = kwargs.get('m0')
                 logger.info(f'Loading M0 image from: {m0_path}')
-                self._m0_image = load_image(m0_path)
+                self._m0_image = ImageIO(
+                    image_path=m0_path, average_m0=average_m0
+                )
 
                 # Check if M0 image is 4D and warn if so
                 if (
                     self._m0_image is not None
-                    and len(self._m0_image.shape) > 3
+                    and len(self._m0_image.get_as_numpy().shape) > 3
                 ):
                     warnings.warn('M0 image has more than 3 dimensions.')
 
                 if self._m0_image is not None:
-                    log_data_info('M0 image', self._m0_image.shape, m0_path)
+                    log_data_info(
+                        'M0 image',
+                        self._m0_image.get_as_numpy().shape,
+                        m0_path,
+                    )
             elif isinstance(kwargs.get('m0'), np.ndarray):
-                self._m0_image = kwargs.get('m0')
+                self._m0_image = ImageIO(
+                    image_array=kwargs.get('m0'), average_m0=average_m0
+                )
                 logger.info('M0 image loaded as numpy array')
-                log_data_info('M0 image', self._m0_image.shape, 'numpy array')
-
-        if kwargs.get('average_m0', False):
-            self._m0_image = np.mean(self._m0_image, axis=0)
+                log_data_info(
+                    'M0 image',
+                    self._m0_image.get_as_numpy().shape,
+                    'numpy array',
+                )
 
         self._parameters['ld'] = (
             [] if kwargs.get('ld_values') is None else kwargs.get('ld_values')
@@ -133,8 +147,8 @@ def __init__(
 
         logger.debug('ASLData object created successfully')
 
-    def set_image(self, image, spec: str):
-        """Insert a image necessary to define de ASL data processing.
+    def set_image(self, image: Union[str, np.ndarray], spec: str, **kwargs):
+        """Insert an image necessary to define the ASL data processing.
 
         The `spec` parameters specifies what is the type of image to be used in
         ASL processing step. Choose one of the options: `m0` for the M0 volume,
@@ -152,7 +166,7 @@ def set_image(self, image, spec: str):
             >>> data = ASLData()
             >>> path_m0 = './tests/files/m0.nii.gz' # M0 file with shape (5,35,35)
             >>> data.set_image(path_m0, spec='m0')
-            >>> data('m0').shape
+            >>> data('m0').get_as_numpy().shape
             (5, 35, 35)
 
         Args:
@@ -161,10 +175,18 @@ def set_image(self, image, spec: str):
         """
         if isinstance(image, str) and os.path.exists(image):
             if spec == 'm0':
-                self._m0_image = load_image(image)
+                self._m0_image = ImageIO(image, **kwargs)
             elif spec == 'pcasl':
-                self._asl_image = load_image(image)
+                self._asl_image = ImageIO(image, **kwargs)
         elif isinstance(image, np.ndarray):
+            warnings.warn(
+                'Using numpy array as image input does not preserve metadata or image properties.'
+            )
+            if spec == 'm0':
+                self._m0_image = ImageIO(image_array=image, **kwargs)
+            elif spec == 'pcasl':
+                self._asl_image = ImageIO(image_array=image, **kwargs)
+        elif isinstance(image, ImageIO):
             if spec == 'm0':
                 self._m0_image = image
             elif spec == 'pcasl':
@@ -277,9 +299,11 @@ def __call__(self, spec: str):
         Examples:
             >>> data = ASLData(pcasl='./tests/files/t1-mri.nrrd')
             >>> type(data('pcasl'))
+            <class 'asltk.utils.io.ImageIO'>
+            >>> type(data('pcasl').get_as_numpy())
             <class 'numpy.ndarray'>
 
-            >>> np.min(data('pcasl'))
+            >>> np.min(data('pcasl').get_as_numpy())
             0
 
         Returns:
@@ -327,7 +351,7 @@ def _check_ld_pld_sizes(self, ld, pld):
             )
 
     def _check_m0_dimension(self):
-        if len(self._m0_image.shape) > 3:
+        if len(self._m0_image.get_as_numpy().shape) > 3:
             warnings.warn(
                 'M0 image has more than 3 dimensions. '
                 'This may cause issues in processing. '

asltk/aux_methods.py

@@ -4,15 +4,38 @@
 import numpy as np
 
 from asltk.smooth import isotropic_gaussian, isotropic_median
+from asltk.utils.io import ImageIO
 
 
-def _check_mask_values(mask, label, ref_shape):
-    # Check wheter mask input is an numpy array
-    if not isinstance(mask, np.ndarray):
-        raise TypeError(f'mask is not an numpy array. Type {type(mask)}')
+def _check_mask_values(mask: ImageIO, label, ref_shape):
+    """Validate mask array for brain mask processing.
+
+    This function performs comprehensive validation of brain mask data to ensure
+    it meets the requirements for ASL processing. It checks data type, binary
+    format compliance, label presence, and dimensional compatibility.
+
+    Args:
+        mask (np.ndarray): The brain mask image to validate.
+        label (int or float): The label value to search for in the mask.
+        ref_shape (tuple): The reference shape that the mask should match.
+
+    Raises:
+        TypeError: If mask is not a numpy array or dimensions don't match.
+        ValueError: If the specified label value is not found in the mask.
+
+    Warnings:
+        UserWarning: If mask contains more than 2 unique values (not strictly binary).
+    """
+    # Check wheter mask input is an ImageIO object
+    if not isinstance(mask, ImageIO):
+        raise TypeError(
+            f'mask is not an ImageIO object. Type {type(mask)} is not allowed.'
+        )
+
+    mask_array = mask.get_as_numpy()
 
     # Check whether the mask provided is a binary image
-    unique_values = np.unique(mask)
+    unique_values = np.unique(mask_array)
     if unique_values.size > 2:
         warnings.warn(
             'Mask image is not a binary image. Any value > 0 will be assumed as brain label.',
@@ -29,18 +52,18 @@ def _check_mask_values(mask, label, ref_shape):
         raise ValueError('Label value is not found in the mask provided.')
 
     # Check whether the dimensions between mask and input volume matches
-    mask_shape = mask.shape
+    mask_shape = mask_array.shape
     if mask_shape != ref_shape:
         raise TypeError(
             f'Image mask dimension does not match with input 3D volume. Mask shape {mask_shape} not equal to {ref_shape}'
         )
 
 
 def _apply_smoothing_to_maps(
-    maps: Dict[str, np.ndarray],
+    maps: Dict[str, ImageIO],
     smoothing: Optional[str] = None,
     smoothing_params: Optional[Dict[str, Any]] = None,
-) -> Dict[str, np.ndarray]:
+) -> Dict[str, ImageIO]:
     """Apply smoothing filter to all maps in the dictionary.
 
     This function applies the specified smoothing filter to all map arrays
@@ -117,7 +140,7 @@ def _apply_smoothing_to_maps(
     # Apply smoothing to all maps
     smoothed_maps = {}
     for key, map_array in maps.items():
-        if isinstance(map_array, np.ndarray):
+        if isinstance(map_array, ImageIO):
             try:
                 smoothed_maps[key] = smooth_func(map_array, **smoothing_params)
             except Exception as e: