brainles-preprocessing 0.6.9__tar.gz → 0.6.11__tar.gz

{brainles_preprocessing-0.6.9 → brainles_preprocessing-0.6.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brainles_preprocessing
-Version: 0.6.9
+Version: 0.6.11
 Summary: Tool for preprocessing tasks in biomedical imaging, with a focus on (but not limited to) multi-modal brain MRI
 License: Apache-2.0
 License-File: LICENSE

brainles_preprocessing-0.6.11/brainles_preprocessing/brain_extraction/__init__.py

@@ -0,0 +1,6 @@
+from .hd_bet import HDBetExtractor
+
+try:
+    from .synthstrip import SynthStripExtractor
+except ImportError:
+    pass

brainles_preprocessing-0.6.11/brainles_preprocessing/brain_extraction/brain_extractor.py

@@ -0,0 +1,69 @@
+# TODO add typing and docs
+from abc import abstractmethod, ABC
+from pathlib import Path
+from typing import Union
+
+from auxiliary.io import read_image, write_image
+
+
+class BrainExtractor(ABC):
+    @abstractmethod
+    def extract(
+        self,
+        input_image_path: Union[str, Path],
+        masked_image_path: Union[str, Path],
+        brain_mask_path: Union[str, Path],
+        **kwargs,
+    ) -> None:
+        """
+        Abstract method to extract the brain from an input image.
+
+        Args:
+            input_image_path (str or Path): Path to the input image.
+            masked_image_path (str or Path): Path where the brain-extracted image will be saved.
+            brain_mask_path (str or Path): Path where the brain mask will be saved.
+            mode (str or Mode): Extraction mode.
+            **kwargs: Additional keyword arguments.
+        """
+        pass
+
+    def apply_mask(
+        self,
+        input_image_path: Union[str, Path],
+        mask_path: Union[str, Path],
+        bet_image_path: Union[str, Path],
+    ) -> None:
+        """
+        Apply a brain mask to an input image.
+
+        Args:
+            input_image_path (str or Path): Path to the input image (NIfTI format).
+            mask_path (str or Path): Path to the brain mask image (NIfTI format).
+            bet_image_path (str or Path): Path to save the resulting masked image (NIfTI format).
+        """
+
+        try:
+            # Read data
+            input_data = read_image(str(input_image_path))
+            mask_data = read_image(str(mask_path))
+        except FileNotFoundError as e:
+            raise FileNotFoundError(f"File not found: {e.filename}") from e
+        except Exception as e:
+            raise RuntimeError(f"Error reading files: {e}") from e
+
+        # Check that the input and mask have the same shape
+        if input_data.shape != mask_data.shape:
+            raise ValueError("Input image and mask must have the same dimensions.")
+
+        # Mask and save it
+        masked_data = input_data * mask_data
+
+        try:
+            write_image(
+                input_array=masked_data,
+                output_path=str(bet_image_path),
+                reference_path=str(input_image_path),
+                create_parent_directory=True,
+            )
+        except Exception as e:
+            raise RuntimeError(f"Error writing output file: {e}") from e

brainles_preprocessing-0.6.9/brainles_preprocessing/brain_extraction/brain_extractor.py → brainles_preprocessing-0.6.11/brainles_preprocessing/brain_extraction/hd_bet.py

@@ -1,11 +1,9 @@
-# TODO add typing and docs
-import shutil
-from abc import ABC, abstractmethod
 from pathlib import Path
 from typing import Optional, Union
+import shutil
 from enum import Enum
 
-from auxiliary.io import read_image, write_image
+from brainles_preprocessing.brain_extraction.brain_extractor import BrainExtractor
 from brainles_hd_bet import run_hd_bet
 
 
@@ -14,69 +12,6 @@ class Mode(Enum):
     ACCURATE = "accurate"
 
 
-class BrainExtractor:
-    @abstractmethod
-    def extract(
-        self,
-        input_image_path: Union[str, Path],
-        masked_image_path: Union[str, Path],
-        brain_mask_path: Union[str, Path],
-        **kwargs,
-    ) -> None:
-        """
-        Abstract method to extract the brain from an input image.
-
-        Args:
-            input_image_path (str or Path): Path to the input image.
-            masked_image_path (str or Path): Path where the brain-extracted image will be saved.
-            brain_mask_path (str or Path): Path where the brain mask will be saved.
-            mode (str or Mode): Extraction mode.
-            **kwargs: Additional keyword arguments.
-        """
-        pass
-
-    def apply_mask(
-        self,
-        input_image_path: Union[str, Path],
-        mask_path: Union[str, Path],
-        bet_image_path: Union[str, Path],
-    ) -> None:
-        """
-        Apply a brain mask to an input image.
-
-        Args:
-            input_image_path (str or Path): Path to the input image (NIfTI format).
-            mask_path (str or Path): Path to the brain mask image (NIfTI format).
-            bet_image_path (str or Path): Path to save the resulting masked image (NIfTI format).
-        """
-
-        try:
-            # Read data
-            input_data = read_image(str(input_image_path))
-            mask_data = read_image(str(mask_path))
-        except FileNotFoundError as e:
-            raise FileNotFoundError(f"File not found: {e.filename}") from e
-        except Exception as e:
-            raise RuntimeError(f"Error reading files: {e}") from e
-
-        # Check that the input and mask have the same shape
-        if input_data.shape != mask_data.shape:
-            raise ValueError("Input image and mask must have the same dimensions.")
-
-        # Mask and save it
-        masked_data = input_data * mask_data
-
-        try:
-            write_image(
-                input_array=masked_data,
-                output_path=str(bet_image_path),
-                reference_path=str(input_image_path),
-                create_parent_directory=True,
-            )
-        except Exception as e:
-            raise RuntimeError(f"Error writing output file: {e}") from e
-
-
 class HDBetExtractor(BrainExtractor):
     def extract(
         self,

{brainles_preprocessing-0.6.9 → brainles_preprocessing-0.6.11}/brainles_preprocessing/defacing/defacer.py

@@ -22,20 +22,20 @@ class Defacer(ABC):
         # probably be implemented as a property of the the specific modality
         self.masking_value = masking_value
 
-        @abstractmethod
-        def deface(
-            self,
-            input_image_path: Union[str, Path],
-            mask_image_path: Union[str, Path],
-        ) -> None:
-            """
-            Generate a defacing mask provided an input image.
+    @abstractmethod
+    def deface(
+        self,
+        input_image_path: Union[str, Path],
+        mask_image_path: Union[str, Path],
+    ) -> None:
+        """
+        Generate a defacing mask provided an input image.
 
-            Args:
-                input_image_path (str or Path): Path to the input image (NIfTI format).
-                mask_image_path (str or Path): Path to the output mask image (NIfTI format).
-            """
-            pass
+        Args:
+            input_image_path (str or Path): Path to the input image (NIfTI format).
+            mask_image_path (str or Path): Path to save the output mask image (NIfTI format).
+        """
+        pass
 
     def apply_mask(
         self,
@@ -52,6 +52,9 @@ class Defacer(ABC):
             defaced_image_path (str or Path): Path to save the resulting defaced image (NIfTI format).
         """
 
+        input_image_path = Path(input_image_path)
+        mask_path = Path(mask_path)
+
         if not input_image_path.is_file():
             raise FileNotFoundError(
                 f"Input image file does not exist: {input_image_path}"
@@ -72,7 +75,7 @@ class Defacer(ABC):
         if input_data.shape != mask_data.shape:
             raise ValueError("Input image and mask must have the same dimensions.")
 
-        # check whether a global masking value was passed, otherwise choose minimum
+        # Check whether a global masking value was passed, otherwise choose minimum
         if self.masking_value is None:
             current_masking_value = np.min(input_data)
         else:

{brainles_preprocessing-0.6.9 → brainles_preprocessing-0.6.11}/brainles_preprocessing/defacing/quickshear/nipy_quickshear.py

@@ -11,6 +11,7 @@ import sys
 import nibabel as nb
 import numpy as np
 from numpy.typing import NDArray
+from scipy.ndimage import convolve
 
 try:
     from duecredit import BibTeX, due
@@ -83,14 +84,9 @@ def edge_mask(mask):
     brain = mask.any(axis=0)
 
     # Simple edge detection
-    edgemask = (
-        4 * brain
-        - np.roll(brain, 1, 0)
-        - np.roll(brain, -1, 0)
-        - np.roll(brain, 1, 1)
-        - np.roll(brain, -1, 1)
-        != 0
-    )
+    kernel = np.array([[0, -1, 0], [-1, 4, -1], [0, -1, 0]])
+    edgemask = convolve(brain, kernel, mode="constant", cval=0.0) != 0
+
     return edgemask.astype("uint8")
 
 

{brainles_preprocessing-0.6.9 → brainles_preprocessing-0.6.11}/brainles_preprocessing/preprocessor/preprocessor.py

@@ -11,10 +11,8 @@ from typing import List, Optional, Union
 
 from loguru import logger
 
-from brainles_preprocessing.brain_extraction.brain_extractor import (
-    BrainExtractor,
-    HDBetExtractor,
-)
+from brainles_preprocessing.brain_extraction.brain_extractor import BrainExtractor
+from brainles_preprocessing.brain_extraction.hd_bet import HDBetExtractor
 from brainles_preprocessing.constants import PreprocessorSteps
 from brainles_preprocessing.defacing import Defacer, QuickshearDefacer
 from brainles_preprocessing.modality import CenterModality, Modality

{brainles_preprocessing-0.6.9 → brainles_preprocessing-0.6.11}/brainles_preprocessing/registration/__init__.py

@@ -1,6 +1,5 @@
 import warnings
 
-
 try:
     from .ANTs.ANTs import ANTsRegistrator
 except ImportError:
@@ -11,7 +10,6 @@ except ImportError:
 
 from .niftyreg.niftyreg import NiftyRegRegistrator
 
-
 try:
     from .elastix.elastix import ElastixRegistrator
 except ImportError:

{brainles_preprocessing-0.6.9 → brainles_preprocessing-0.6.11}/brainles_preprocessing/utils/zenodo.py

@@ -4,7 +4,7 @@ import shutil
 import zipfile
 from io import BytesIO
 from pathlib import Path
-from typing import Dict, List, Tuple
+from typing import ClassVar, Dict, List, Tuple
 
 import requests
 from loguru import logger
@@ -56,6 +56,9 @@ class ZenodoException(Exception):
 class ZenodoRecord:
     BASE_URL = "https://zenodo.org/api/records"
 
+    # Process-level cache: maps (record_id, target_dir) -> resolved Path
+    _cache: ClassVar[Dict[Tuple[str, str], Path]] = {}
+
     def __init__(
         self,
         record_id: str,
@@ -66,8 +69,34 @@ class ZenodoRecord:
         self.target_dir = target_dir
         self.label = label
 
+    @classmethod
+    def clear_cache(cls) -> None:
+        """Clear the process-level fetch cache. Primarily intended for testing."""
+        cls._cache.clear()
+
+    def _cache_key(self) -> Tuple[str, str]:
+        return (self.record_id, str(self.target_dir))
+
     def fetch(self) -> Path:
-        """Fetch the latest version of the record from Zenodo or from local storage."""
+        """Fetch the latest version of the record from Zenodo or from local storage.
+
+        Results are cached for the lifetime of the process so that repeated calls
+        (e.g. when processing many subjects in a loop) do not trigger redundant
+        Zenodo API requests.
+        """
+        key = self._cache_key()
+
+        cached = ZenodoRecord._cache.get(key)
+        if cached is not None:
+            logger.debug(f"Using cached {self.label} path: {cached}")
+            return cached
+
+        result = self._fetch_uncached()
+        ZenodoRecord._cache[key] = result
+        return result
+
+    def _fetch_uncached(self) -> Path:
+        """Perform the actual Zenodo check / download without consulting the cache."""
         zenodo_response = self._get_metadata_and_archive_url()
 
         pattern = self._glob_pattern()

{brainles_preprocessing-0.6.9 → brainles_preprocessing-0.6.11}/pyproject.toml

@@ -14,7 +14,7 @@ exclude = [
 ]
 
 name = "brainles_preprocessing"
-version = "0.6.9"                                                                                                              # will be overwritten by poetry-dynamic-versioning but needs to be set
+version = "0.6.11"                                                                                                              # will be overwritten by poetry-dynamic-versioning but needs to be set
 description = "Tool for preprocessing tasks in biomedical imaging, with a focus on (but not limited to) multi-modal brain MRI"
 license = "Apache-2.0"
 

brainles_preprocessing-0.6.9/brainles_preprocessing/brain_extraction/__init__.py

@@ -1 +0,0 @@
-from .brain_extractor import HDBetExtractor