brainles-preprocessing 0.3.5__tar.gz → 0.3.6__tar.gz

{brainles_preprocessing-0.3.5 → brainles_preprocessing-0.3.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: brainles_preprocessing
-Version: 0.3.5
+Version: 0.3.6
 Summary: Tool for preprocessing tasks in biomedical imaging, with a focus on (but not limited to) multi-modal brain MRI
 License: Apache-2.0
 Keywords: brain tumor,glioma,BraTS,skullstripping,brain extraction
@@ -17,14 +17,12 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Provides-Extra: all
-Provides-Extra: ereg
 Provides-Extra: itk-elastix
 Provides-Extra: picsl-greedy
 Requires-Dist: antspyx (>=0.4.2,<0.5.0)
 Requires-Dist: auxiliary (>=0.0.42)
 Requires-Dist: black (>=22.1.0,<23.0.0)
 Requires-Dist: brainles_hd_bet (>=0.0.10)
-Requires-Dist: ereg (>=0.0.10,<0.0.11) ; extra == "all" or extra == "ereg"
 Requires-Dist: itk-elastix (>=0.20.0,<0.21.0) ; extra == "all" or extra == "itk-elastix"
 Requires-Dist: nibabel (>=3.2.1)
 Requires-Dist: numpy (>=1.23.0,<2.0.0)
@@ -161,7 +159,7 @@ We provide a (WIP) documentation. Have a look [here](https://brainles-preprocess
 Please credit the authors by citing their work.
 
 ### Registration
-We currently provide support for [ANTs](https://github.com/ANTsX/ANTs) (default), [Niftyreg](https://github.com/KCL-BMEIS/niftyreg) (Linux), eReg (experimental)
+We currently provide support for [ANTs](https://github.com/ANTsX/ANTs) (default), [Niftyreg](https://github.com/KCL-BMEIS/niftyreg) (Linux).
 
 ### Atlas Reference
 We provide the SRI-24 atlas from this [publication](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915788/).

{brainles_preprocessing-0.3.5 → brainles_preprocessing-0.3.6}/README.md

@@ -121,7 +121,7 @@ We provide a (WIP) documentation. Have a look [here](https://brainles-preprocess
 Please credit the authors by citing their work.
 
 ### Registration
-We currently provide support for [ANTs](https://github.com/ANTsX/ANTs) (default), [Niftyreg](https://github.com/KCL-BMEIS/niftyreg) (Linux), eReg (experimental)
+We currently provide support for [ANTs](https://github.com/ANTsX/ANTs) (default), [Niftyreg](https://github.com/KCL-BMEIS/niftyreg) (Linux).
 
 ### Atlas Reference
 We provide the SRI-24 atlas from this [publication](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915788/).

brainles_preprocessing-0.3.6/brainles_preprocessing/constants.py

@@ -0,0 +1,25 @@
+from enum import Enum, IntEnum
+
+
+class PreprocessorSteps(IntEnum):
+    INPUT = 0
+    COREGISTERED = 1
+    ATLAS_REGISTERED = 2
+    ATLAS_CORRECTED = 3
+    BET = 4
+    DEFACED = 5
+
+
+class Atlas(str, Enum):
+    BRATS_SRI24 = "brats_sri24.nii"
+    """Slightly modified SRI24 atlas as found in the BraTS challenges"""
+    BRATS_SRI24_SKULLSTRIPPED = "brats_sri24_skullstripped.nii"
+    """Slightly modified SRI24 skull stripped atlas as found in the BraTS challenges"""
+
+    SRI24 = "sri24.nii"
+    """SRI24 atlas from https://www.nitrc.org/frs/download.php/4502/sri24_anatomy_unstripped_nifti.zip"""
+    SRI24_SKULLSTRIPPED = "sri24_skullstripped.nii"
+    """SRI24 skull stripped atlas from https://www.nitrc.org/frs/download.php/4499/sri24_anatomy_nifti.zip"""
+
+    BRATS_MNI152 = "brats_MNI152lin_T1_1mm.nii.gz"
+    """Slightly modified MNI152 atlas as found in the BraTS challenges"""

{brainles_preprocessing-0.3.5 → brainles_preprocessing-0.3.6}/brainles_preprocessing/preprocessor.py

@@ -12,8 +12,9 @@ from pathlib import Path
 from typing import List, Optional, Union
 import warnings
 
-from brainles_preprocessing.constants import PreprocessorSteps
+from brainles_preprocessing.constants import Atlas, PreprocessorSteps
 from brainles_preprocessing.defacing import Defacer, QuickshearDefacer
+from brainles_preprocessing.utils.zenodo import verify_or_download_atlases
 
 from .brain_extraction.brain_extractor import BrainExtractor, HDBetExtractor
 from .modality import Modality, CenterModality
@@ -50,7 +51,7 @@ class Preprocessor:
         registrator: Registrator = None,
         brain_extractor: Optional[BrainExtractor] = None,
         defacer: Optional[Defacer] = None,
-        atlas_image_path: Union[str, Path] = None,
+        atlas_image_path: Union[str, Path, Atlas] = Atlas.BRATS_SRI24,
         temp_folder: Optional[Union[str, Path]] = None,
         use_gpu: Optional[bool] = None,
         limit_cuda_visible_devices: Optional[str] = None,
@@ -67,10 +68,9 @@ class Preprocessor:
         self.center_modality = center_modality
         self.moving_modalities = moving_modalities
 
-        if atlas_image_path is None:
-            self.atlas_image_path = (
-                Path(__file__).parent / "registration" / "atlas" / "t1_brats_space.nii"
-            )
+        if isinstance(atlas_image_path, Atlas):
+            atlas_folder = verify_or_download_atlases()
+            self.atlas_image_path = atlas_folder / atlas_image_path.value
         else:
             self.atlas_image_path = Path(atlas_image_path)
 

brainles_preprocessing-0.3.6/brainles_preprocessing/registration/__init__.py

@@ -0,0 +1,27 @@
+import warnings
+
+
+try:
+    from .ANTs.ANTs import ANTsRegistrator
+except ImportError:
+    warnings.warn(
+        "ANTS package not found. If you want to use it, please install it using 'pip install antspyx'"
+    )
+
+
+from .niftyreg.niftyreg import NiftyRegRegistrator
+
+
+try:
+    from .elastix.elastix import ElastixRegistrator
+except ImportError:
+    warnings.warn(
+        "itk-elastix package not found. If you want to use it, please install it using 'pip install brainles_preprocessing[itk-elastix]'"
+    )
+
+try:
+    from .greedy.greedy import GreedyRegistrator
+except ImportError:
+    warnings.warn(
+        "picsl_greedy  package not found. If you want to use it, please install it using 'pip install brainles_preprocessing[picsl_greedy]'"
+    )

brainles_preprocessing-0.3.6/brainles_preprocessing/utils/zenodo.py

@@ -0,0 +1,189 @@
+from __future__ import annotations
+
+import shutil
+import sys
+import zipfile
+from io import BytesIO
+from pathlib import Path
+from typing import Dict, List, Tuple
+
+import requests
+from rich.progress import Progress, SpinnerColumn, TextColumn
+
+from brainles_preprocessing.utils.logging_utils import LoggingManager
+
+
+logging_man = LoggingManager(name=__name__)
+logger = logging_man.get_logger()
+
+ZENODO_RECORD_URL = "https://zenodo.org/api/records/15236131"
+ATLASES_FOLDER = Path(__file__).parent.parent / "registration" / "atlases"
+ATLASES_DIR_PATTERN = "atlases_v*.*.*"
+
+
+def verify_or_download_atlases() -> Path:
+    """Check if latest atlases are present and download them otherwise.
+
+    Returns:
+        Path: Path to the atlases folder.
+    """
+
+    zenodo_data = _get_zenodo_metadata_and_archive_url()
+    if zenodo_data:
+        zenodo_metadata, archive_url = zenodo_data
+
+    matching_folders = list(ATLASES_FOLDER.glob(ATLASES_DIR_PATTERN))
+    # Get the latest downloaded atlases
+    latest_downloaded_atlases = _get_latest_version_folder_name(matching_folders)
+
+    if not latest_downloaded_atlases:
+        if not zenodo_data:
+            logger.error(
+                "Atlases not found locally and Zenodo could not be reached. Exiting..."
+            )
+            sys.exit()
+        logger.info(f"Atlases not found locally")
+
+        return _download_atlases(
+            zenodo_metadata=zenodo_metadata,
+            archive_url=archive_url,
+        )
+
+    logger.info(f"Found downloaded local atlases: {latest_downloaded_atlases}")
+
+    if not zenodo_metadata:
+        logger.warning(
+            "Zenodo server could not be reached. Using the latest downloaded atlases."
+        )
+        return ATLASES_FOLDER / latest_downloaded_atlases
+
+    # Compare the latest downloaded atlases with the latest Zenodo version
+    if zenodo_metadata["version"] == latest_downloaded_atlases.split("_v")[1]:
+        logger.info(
+            f"Latest atlases ({zenodo_metadata['version']}) are already present."
+        )
+        return ATLASES_FOLDER / latest_downloaded_atlases
+
+    logger.info(
+        f"New atlases available on Zenodo ({zenodo_metadata['version']}). Deleting old and fetching new atlases..."
+    )
+    # delete old atlases
+    try:
+        shutil.rmtree(
+            ATLASES_FOLDER / latest_downloaded_atlases,
+        )
+    except OSError as e:
+        logger.warning(f"Failed to delete old atlases: {e}")
+    return _download_atlases(zenodo_metadata=zenodo_metadata, archive_url=archive_url)
+
+
+def _get_latest_version_folder_name(folders: List[Path]) -> str | None:
+    """Get the latest (non empty) version folder name from the list of folders.
+
+    Args:
+        folders (List[Path]): List of folders matching the pattern.
+
+    Returns:
+        str | None: Latest version folder name if one exists, else None.
+    """
+    if not folders:
+        return None
+    latest_downloaded_folder = sorted(
+        folders,
+        reverse=True,
+        key=lambda x: tuple(map(int, str(x).split("_v")[1].split("."))),
+    )[0]
+    # check folder is not empty
+    if not list(latest_downloaded_folder.glob("*")):
+        return None
+    return latest_downloaded_folder.name
+
+
+def _get_zenodo_metadata_and_archive_url() -> Tuple[Dict, str] | None:
+    """Get the metadata for the Zenodo record and the files archive url.
+
+    Returns:
+        Tuple: (dict: Metadata for the Zenodo record, str: URL to the archive file)
+    """
+    try:
+        response = requests.get(f"{ZENODO_RECORD_URL}")
+        if response.status_code != 200:
+            logger.error(
+                f"Cant find atlases on Zenodo ({ZENODO_RECORD_URL}). Exiting..."
+            )
+            return None
+        data = response.json()
+        return data["metadata"], data["links"]["archive"]
+
+    except requests.exceptions.RequestException as e:
+        logger.warning(f"Failed to fetch Zenodo metadata: {e}")
+        return None
+
+
+def _download_atlases(zenodo_metadata: Dict, archive_url: str) -> Path:
+    """Download the latest atlases from Zenodo for the requested record and extract them to the target folder.
+
+    Args:
+        zenodo_metadata (Dict): Metadata for the Zenodo record.
+        archive_url (str): URL to the archive file.
+
+    Returns:
+        Path: Path to the atlases folder for the requested record.
+    """
+    record_folder = ATLASES_FOLDER / f"atlases_v{zenodo_metadata['version']}"
+    # ensure folder exists
+    record_folder.mkdir(parents=True, exist_ok=True)
+
+    logger.info(f"Downloading atlases from Zenodo. This might take a while...")
+    # Make a GET request to the URL
+    response = requests.get(archive_url, stream=True)
+    # Ensure the request was successful
+    if response.status_code != 200:
+        raise RuntimeError(
+            f"Failed to download atlases from {archive_url}. Status code: {response.status_code}"
+        )
+
+    _extract_archive(response=response, record_folder=record_folder)
+
+    logger.info(f"Zip file extracted successfully to {record_folder}")
+    return record_folder
+
+
+def _extract_archive(response: requests.Response, record_folder: Path):
+    # Download with progress bar
+    chunk_size = 1024  # 1KB
+    bytes_io = BytesIO()
+
+    with Progress(
+        SpinnerColumn(),
+        TextColumn("[cyan]Downloading atlases..."),
+        TextColumn("[cyan]{task.completed:.2f} MB"),
+        transient=True,
+    ) as progress:
+        task = progress.add_task("", total=None)  # Indeterminate progress
+
+        for data in response.iter_content(chunk_size=chunk_size):
+            bytes_io.write(data)
+            progress.update(
+                task, advance=len(data) / (chunk_size**2)
+            )  # Convert bytes to MB
+
+    # Extract the downloaded zip file to the target folder
+    with zipfile.ZipFile(bytes_io) as zip_ref:
+        zip_ref.extractall(record_folder)
+
+    # check if the extracted file is still a zip
+    for f in record_folder.iterdir():
+        if f.is_file() and f.suffix == ".zip":
+            with zipfile.ZipFile(f) as zip_ref:
+                files = zip_ref.namelist()
+                with Progress(transient=True) as progress:
+                    task = progress.add_task(
+                        "[cyan]Extracting files...", total=len(files)
+                    )
+                    # Iterate over the files and extract them
+                    for i, file in enumerate(files):
+                        zip_ref.extract(file, record_folder)
+                        # Update the progress bar
+                        progress.update(task, completed=i + 1)
+            f.unlink()  # remove zip after extraction

{brainles_preprocessing-0.3.5 → brainles_preprocessing-0.3.6}/pyproject.toml

@@ -14,7 +14,7 @@ exclude = [
 ]
 
 name = "brainles_preprocessing"
-version = "0.3.5"                                                                                                              # will be overwritten by poetry-dynamic-versioning but needs to be set
+version = "0.3.6"                                                                                                              # 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"
 
@@ -69,14 +69,12 @@ auxiliary = ">=0.0.42"
 rich = "^13.6.0"
 
 # optional registration backends
-ereg = { version = "^0.0.10", optional = true }
 itk-elastix = { version = "^0.20.0", optional = true }
 picsl_greedy = { version = "^0.0.6", optional = true }
 
 
 [tool.poetry.extras]
-all = ["ereg", "itk-elastix", "picsl_greedy"]
-ereg = ["ereg"]
+all = ["itk-elastix", "picsl_greedy"]
 itk-elastix = ["itk-elastix"]
 picsl_greedy = ["picsl_greedy"]
 

brainles_preprocessing-0.3.5/brainles_preprocessing/constants.py

@@ -1,10 +0,0 @@
-from enum import IntEnum
-
-
-class PreprocessorSteps(IntEnum):
-    INPUT = 0
-    COREGISTERED = 1
-    ATLAS_REGISTERED = 2
-    ATLAS_CORRECTED = 3
-    BET = 4
-    DEFACED = 5

brainles_preprocessing-0.3.5/brainles_preprocessing/registration/__init__.py

@@ -1,23 +0,0 @@
-import warnings
-
-
-try:
-    from .ANTs.ANTs import ANTsRegistrator
-except ImportError:
-    warnings.warn(
-        "ANTS package not found. If you want to use it, please install it using 'pip install antspyx'"
-    )
-
-try:
-    from .eReg.eReg import eRegRegistrator
-except ImportError:
-    warnings.warn(
-        "eReg package not found. If you want to use it, please install it using 'pip install brainles_preprocessing[ereg]'"
-    )
-
-
-from .niftyreg.niftyreg import NiftyRegRegistrator
-
-from .elastix.elastix import ElastixRegistrator
-
-from .greedy.greedy import GreedyRegistrator

brainles_preprocessing-0.3.5/brainles_preprocessing/registration/atlas/copyright.md

@@ -1,11 +0,0 @@
-Copyright (C) 1993-2004 Louis Collins, McConnell Brain
-Imaging Centre, Montreal Neurological Institute, McGill University.
-Permission to use, copy, modify, and distribute this software and
-its documentation for any purpose and without fee is hereby granted,
-provided that the above copyright notice appear in all copies.  The
-authors and McGill University make no representations about the
-suitability of this software for any purpose.  It is provided "as
-is" without express or implied warranty.  The authors are not
-responsible for any data loss, equipment damage, property loss, or
-injury to subjects or patients resulting from the use or misuse of
-this software package. 

brainles_preprocessing-0.3.5/brainles_preprocessing/registration/eReg/eReg.py

@@ -1,100 +0,0 @@
-# TODO add typing and docs
-import os
-
-from ereg.registration import RegistrationClass
-
-from brainles_preprocessing.registration.registrator import Registrator
-
-
-class eRegRegistrator(Registrator):
-    def __init__(
-        self,
-        # TODO define default
-        configuration_file: str | None = None,
-    ):
-        """
-        # TODO
-        """
-        self.configuration_file = configuration_file
-
-    def register(
-        self,
-        fixed_image_path: str,
-        moving_image_path: str,
-        transformed_image_path: str,
-        matrix_path: str,
-        log_file_path: str = None,
-    ) -> None:
-        """
-        Register images using eReg.
-
-        Args:
-            fixed_image_path (str): Path to the fixed image.
-            moving_image_path (str): Path to the moving image.
-            transformed_image_path (str): Path to the transformed image (output).
-            matrix_path (str): Path to the transformation matrix (output).
-            log_file_path (str): Path to the log file.
-        """
-        # TODO do we need to handle kwargs?
-        registrator = RegistrationClass(
-            configuration_file=self.configuration_file,
-        )
-
-        matrix_path = _add_mat_suffix(matrix_path)
-
-        registrator.register(
-            target_image=fixed_image_path,
-            moving_image=moving_image_path,
-            output_image=transformed_image_path,
-            transform_file=matrix_path,
-            log_file=log_file_path,
-        )
-
-    def transform(
-        self,
-        fixed_image_path: str,
-        moving_image_path: str,
-        transformed_image_path: str,
-        matrix_path: str,
-        log_file_path: str = None,
-    ) -> None:
-        """
-        Apply a transformation using eReg.
-
-        Args:
-            fixed_image_path (str): Path to the fixed image.
-            moving_image_path (str): Path to the moving image.
-            transformed_image_path (str): Path to the transformed image (output).
-            matrix_path (str): Path to the transformation matrix.
-            log_file_path (str): Path to the log file.
-        """
-        # TODO do we need to handle kwargs?
-        registrator = RegistrationClass(
-            configuration_file=self.configuration_file,
-        )
-
-        matrix_path = _add_mat_suffix(matrix_path)
-
-        registrator.resample_image(
-            target_image=fixed_image_path,
-            moving_image=moving_image_path,
-            output_image=transformed_image_path,
-            transform_file=matrix_path,
-            log_file=log_file_path,
-        )
-
-
-def _add_mat_suffix(filename: str) -> str:
-    """
-    Adds a ".mat" suffix to the filename if it doesn't have any extension.
-
-    Parameters:
-        filename (str): The filename to check and potentially modify.
-
-    Returns:
-        str: The filename with ".mat" suffix added if needed.
-    """
-    base, ext = os.path.splitext(filename)
-    if not ext:
-        filename += ".mat"
-    return filename