brainles-preprocessing 0.6.0__tar.gz → 0.6.1__tar.gz

{brainles_preprocessing-0.6.0 → brainles_preprocessing-0.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: brainles_preprocessing
-Version: 0.6.0
+Version: 0.6.1
 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
@@ -23,6 +23,7 @@ Requires-Dist: antspyx (>=0.5.4,<1.0.0)
 Requires-Dist: auxiliary (>=0.3.1)
 Requires-Dist: brainles_hd_bet (>=0.0.10,<1.0.0)
 Requires-Dist: itk-elastix (>=0.20.0,<0.21.0) ; extra == "all" or extra == "itk-elastix"
+Requires-Dist: loguru (>=0.7.3,<0.8.0)
 Requires-Dist: nibabel (>=3.2.1)
 Requires-Dist: numpy (>=1.23.0,<2.0.0)
 Requires-Dist: pathlib (>=1.0.1,<2.0.0)
@@ -176,11 +177,17 @@ 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).
+We currently provide support for [ANTs](https://github.com/ANTsX/ANTs) (default), [Niftyreg](https://github.com/KCL-BMEIS/niftyreg) (Linux). We also offer basic support for [greedy](https://greedy.readthedocs.io/en/latest/reference.html#greedy-usage) and [elastix](https://pypi.org/project/itk-elastix/0.13.0/).
 
 ### Atlas Reference
-We provide the SRI-24 atlas from this [publication](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915788/).
-However, custom atlases in NIfTI format are supported.
+We provide a range of different atlases, namely:
+-  [SRI24](https://www.nitrc.org/frs/download.php/4502/sri24_anatomy_unstripped_nifti.zip) and its [skull-stripped version](https://www.nitrc.org/frs/download.php/4499/sri24_anatomy_nifti.zip)
+-  A slightly modified SRI24 atlas as found in the BraTS challenges (also with a skull-stripped version)
+-  MNI152: [MNI_ICBM_2009c_Nonlinear_Symmetric](https://nist.mni.mcgill.ca/icbm-152-nonlinear-atlases-2009/)
+-  A slightly modified MNI152 atlas as found in the BraTS challenge 
+
+We also support supplying a custom atlas in NIfTI format
+
 
 ### N4 Bias correction
 We currently provide support for N4 Bias correction based on [SimpleITK](https://simpleitk.org/)

{brainles_preprocessing-0.6.0 → brainles_preprocessing-0.6.1}/README.md

@@ -138,11 +138,17 @@ 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).
+We currently provide support for [ANTs](https://github.com/ANTsX/ANTs) (default), [Niftyreg](https://github.com/KCL-BMEIS/niftyreg) (Linux). We also offer basic support for [greedy](https://greedy.readthedocs.io/en/latest/reference.html#greedy-usage) and [elastix](https://pypi.org/project/itk-elastix/0.13.0/).
 
 ### Atlas Reference
-We provide the SRI-24 atlas from this [publication](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915788/).
-However, custom atlases in NIfTI format are supported.
+We provide a range of different atlases, namely:
+-  [SRI24](https://www.nitrc.org/frs/download.php/4502/sri24_anatomy_unstripped_nifti.zip) and its [skull-stripped version](https://www.nitrc.org/frs/download.php/4499/sri24_anatomy_nifti.zip)
+-  A slightly modified SRI24 atlas as found in the BraTS challenges (also with a skull-stripped version)
+-  MNI152: [MNI_ICBM_2009c_Nonlinear_Symmetric](https://nist.mni.mcgill.ca/icbm-152-nonlinear-atlases-2009/)
+-  A slightly modified MNI152 atlas as found in the BraTS challenge 
+
+We also support supplying a custom atlas in NIfTI format
+
 
 ### N4 Bias correction
 We currently provide support for N4 Bias correction based on [SimpleITK](https://simpleitk.org/)

{brainles_preprocessing-0.6.0 → brainles_preprocessing-0.6.1}/brainles_preprocessing/modality.py

@@ -5,6 +5,7 @@ from pathlib import Path
 from typing import Dict, Optional, Union
 
 from auxiliary.io import read_image, write_image
+from loguru import logger
 
 from brainles_preprocessing.brain_extraction.brain_extractor import BrainExtractor
 from brainles_preprocessing.constants import Atlas, PreprocessorSteps
@@ -17,8 +18,6 @@ from brainles_preprocessing.registration import (  # TODO: this will throw warni
 from brainles_preprocessing.registration.registrator import Registrator
 from brainles_preprocessing.utils.zenodo import verify_or_download_atlases
 
-logger = logging.getLogger(__name__)
-
 
 class Modality:
     """

{brainles_preprocessing-0.6.0 → brainles_preprocessing-0.6.1}/brainles_preprocessing/preprocessor/atlas_centric_preprocessor.py

@@ -2,6 +2,8 @@ import shutil
 from pathlib import Path
 from typing import List, Optional, Union
 
+from loguru import logger
+
 from brainles_preprocessing.brain_extraction.brain_extractor import BrainExtractor
 from brainles_preprocessing.constants import Atlas, PreprocessorSteps
 from brainles_preprocessing.defacing import Defacer, QuickshearDefacer
@@ -9,12 +11,8 @@ from brainles_preprocessing.modality import CenterModality, Modality
 from brainles_preprocessing.n4_bias_correction import N4BiasCorrector
 from brainles_preprocessing.preprocessor.preprocessor import BasePreprocessor
 from brainles_preprocessing.registration.registrator import Registrator
-from brainles_preprocessing.utils.logging_utils import LoggingManager
 from brainles_preprocessing.utils.zenodo import verify_or_download_atlases
 
-logging_man = LoggingManager(name=__name__)
-logger = logging_man.get_logger()
-
 
 class AtlasCentricPreprocessor(BasePreprocessor):
     """
@@ -101,97 +99,102 @@ class AtlasCentricPreprocessor(BasePreprocessor):
         Results are saved in the specified directories, allowing for modular and configurable output storage.
         """
 
-        logging_man._set_log_file(log_file)
-        logger.info(f"{' Starting preprocessing ':=^80}")
-        logger.info(f"Logs are saved to {logging_man.log_file_handler.baseFilename}")
-        modality_names = ", ".join(
-            [modality.modality_name for modality in self.moving_modalities]
-        )
-        logger.info(
-            f"Received center modality: {self.center_modality.modality_name} "
-            f"and moving modalities: {modality_names}"
-        )
-
-        # Co-register moving modalities to center modality
-        logger.info(f"{' Starting Coregistration ':-^80}")
-        self.run_coregistration(
-            save_dir_coregistration=save_dir_coregistration,
-        )
-        logger.info(
-            f"Coregistration complete. Output saved to {save_dir_coregistration}"
-        )
-
-        # Register center modality to atlas
-        logger.info(f"{' Starting atlas registration ':-^80}")
-        self.run_atlas_registration(
-            save_dir_atlas_registration=save_dir_atlas_registration,
-        )
-        logger.info(
-            f"Transformations complete. Output saved to {save_dir_atlas_registration}"
-        )
+        logger_id = self._add_log_file_handler(log_file)
+        try:
+            logger.info(f"{' Starting preprocessing ':=^80}")
+            modality_names = ", ".join(
+                [modality.modality_name for modality in self.moving_modalities]
+            )
+            logger.info(
+                f"Received center modality: {self.center_modality.modality_name} "
+                f"and moving modalities: {modality_names}"
+            )
 
-        # Optional: additional correction in atlas space
-        logger.info(f"{' Checking optional atlas correction ':-^80}")
-        self.run_atlas_correction(
-            save_dir_atlas_correction=save_dir_atlas_correction,
-        )
+            # Co-register moving modalities to center modality
+            logger.info(f"{' Starting Coregistration ':-^80}")
+            self.run_coregistration(
+                save_dir_coregistration=save_dir_coregistration,
+            )
+            logger.info(
+                f"Coregistration complete. Output saved to {save_dir_coregistration}"
+            )
 
-        # Optional: N4 bias correction
-        logger.info(f"{' Checking optional N4 bias correction ':-^80}")
-        self.run_n4_bias_correction(
-            save_dir_n4_bias_correction=save_dir_n4_bias_correction,
-        )
+            # Register center modality to atlas
+            logger.info(f"{' Starting atlas registration ':-^80}")
+            self.run_atlas_registration(
+                save_dir_atlas_registration=save_dir_atlas_registration,
+            )
+            logger.info(
+                f"Transformations complete. Output saved to {save_dir_atlas_registration}"
+            )
 
-        # Now we save images that are not skullstripped (current image = atlas registered or atlas registered + corrected)
-        logger.info("Saving non skull-stripped images...")
-        for modality in self.all_modalities:
-            if modality.raw_skull_output_path:
-                modality.save_current_image(
-                    modality.raw_skull_output_path,
-                    normalization=False,
-                )
-            if modality.normalized_skull_output_path:
-                modality.save_current_image(
-                    modality.normalized_skull_output_path,
-                    normalization=True,
-                )
+            # Optional: additional correction in atlas space
+            logger.info(f"{' Checking optional atlas correction ':-^80}")
+            self.run_atlas_correction(
+                save_dir_atlas_correction=save_dir_atlas_correction,
+            )
 
-        # Optional: Brain extraction
-        logger.info(f"{' Checking optional brain extraction ':-^80}")
-        self.run_brain_extraction(
-            save_dir_brain_extraction=save_dir_brain_extraction,
-        )
+            # Optional: N4 bias correction
+            logger.info(f"{' Checking optional N4 bias correction ':-^80}")
+            self.run_n4_bias_correction(
+                save_dir_n4_bias_correction=save_dir_n4_bias_correction,
+            )
 
-        # Defacing
-        logger.info(f"{' Checking optional defacing ':-^80}")
-        self.run_defacing(
-            save_dir_defacing=save_dir_defacing,
-        )
+            # Now we save images that are not skullstripped (current image = atlas registered or atlas registered + corrected)
+            logger.info("Saving non skull-stripped images...")
+            for modality in self.all_modalities:
+                if modality.raw_skull_output_path:
+                    modality.save_current_image(
+                        modality.raw_skull_output_path,
+                        normalization=False,
+                    )
+                if modality.normalized_skull_output_path:
+                    modality.save_current_image(
+                        modality.normalized_skull_output_path,
+                        normalization=True,
+                    )
+
+            # Optional: Brain extraction
+            logger.info(f"{' Checking optional brain extraction ':-^80}")
+            self.run_brain_extraction(
+                save_dir_brain_extraction=save_dir_brain_extraction,
+            )
 
-        # move to separate method
-        if save_dir_transformations:
-            save_dir_transformations = Path(save_dir_transformations)
+            # Defacing
+            logger.info(f"{' Checking optional defacing ':-^80}")
+            self.run_defacing(
+                save_dir_defacing=save_dir_defacing,
+            )
 
-            # Save transformation matrices
-            logger.info(f"Saving transformation matrices to {save_dir_transformations}")
-            for modality in self.all_modalities:
+            # move to separate method
+            if save_dir_transformations:
+                save_dir_transformations = Path(save_dir_transformations)
 
-                modality_transformations_dir = (
-                    save_dir_transformations / modality.modality_name
+                # Save transformation matrices
+                logger.info(
+                    f"Saving transformation matrices to {save_dir_transformations}"
                 )
-                modality_transformations_dir.mkdir(exist_ok=True, parents=True)
-                for step, path in modality.transformation_paths.items():
-                    if path is not None:
-                        shutil.copyfile(
-                            src=str(path.absolute()),
-                            dst=str(
-                                modality_transformations_dir
-                                / f"{step.value}_{path.name}"
-                            ),
-                        )
-
-        # End
-        logger.info(f"{' Preprocessing complete ':=^80}")
+                for modality in self.all_modalities:
+
+                    modality_transformations_dir = (
+                        save_dir_transformations / modality.modality_name
+                    )
+                    modality_transformations_dir.mkdir(exist_ok=True, parents=True)
+                    for step, path in modality.transformation_paths.items():
+                        if path is not None:
+                            shutil.copyfile(
+                                src=str(path.absolute()),
+                                dst=str(
+                                    modality_transformations_dir
+                                    / f"{step.value}_{path.name}"
+                                ),
+                            )
+
+            # End
+            logger.info(f"{' Preprocessing complete ':=^80}")
+        finally:
+            # Remove log file handler if it was added
+            logger.remove(logger_id)
 
     def run_atlas_registration(
         self, save_dir_atlas_registration: Optional[Union[str, Path]] = None

{brainles_preprocessing-0.6.0 → brainles_preprocessing-0.6.1}/brainles_preprocessing/preprocessor/native_space_preprocessor.py

@@ -2,12 +2,10 @@ import shutil
 from pathlib import Path
 from typing import Optional, Union
 
+from loguru import logger
+
 from brainles_preprocessing.defacing import QuickshearDefacer
 from brainles_preprocessing.preprocessor.preprocessor import BasePreprocessor
-from brainles_preprocessing.utils.logging_utils import LoggingManager
-
-logging_man = LoggingManager(name=__name__)
-logger = logging_man.get_logger()
 
 
 class NativeSpacePreprocessor(BasePreprocessor):
@@ -57,81 +55,85 @@ class NativeSpacePreprocessor(BasePreprocessor):
         Results are saved in the specified directories, allowing for modular and configurable output storage.
         """
 
-        logging_man._set_log_file(log_file)
-        logger.info(f"{' Starting preprocessing ':=^80}")
-        logger.info(f"Logs are saved to {logging_man.log_file_handler.baseFilename}")
-        modality_names = ", ".join(
-            [modality.modality_name for modality in self.moving_modalities]
-        )
-        logger.info(
-            f"Received center modality: {self.center_modality.modality_name} "
-            f"and moving modalities: {modality_names}"
-        )
-
-        # Co-register moving modalities to center modality
-        logger.info(f"{' Starting Coregistration ':-^80}")
-        self.run_coregistration(
-            save_dir_coregistration=save_dir_coregistration,
-        )
-        logger.info(
-            f"Coregistration complete. Output saved to {save_dir_coregistration}"
-        )
-        # Optional: N4 bias correction
-        logger.info(f"{' Checking optional N4 bias correction ':-^80}")
-        self.run_n4_bias_correction(
-            save_dir_n4_bias_correction=save_dir_n4_bias_correction,
-        )
-
-        # Now we save images that are not skullstripped (current image = atlas registered or atlas registered + corrected)
-        logger.info("Saving non skull-stripped images...")
-        for modality in self.all_modalities:
-            if modality.raw_skull_output_path:
-                modality.save_current_image(
-                    modality.raw_skull_output_path,
-                    normalization=False,
-                )
-            if modality.normalized_skull_output_path:
-                modality.save_current_image(
-                    modality.normalized_skull_output_path,
-                    normalization=True,
-                )
+        logger_id = self._add_log_file_handler(log_file)
+        try:
+            logger.info(f"{' Starting preprocessing ':=^80}")
+            modality_names = ", ".join(
+                [modality.modality_name for modality in self.moving_modalities]
+            )
+            logger.info(
+                f"Received center modality: {self.center_modality.modality_name} "
+                f"and moving modalities: {modality_names}"
+            )
 
-        # Optional: Brain extraction
-        logger.info(f"{' Checking optional brain extraction ':-^80}")
-        self.run_brain_extraction(
-            save_dir_brain_extraction=save_dir_brain_extraction,
-        )
+            # Co-register moving modalities to center modality
+            logger.info(f"{' Starting Coregistration ':-^80}")
+            self.run_coregistration(
+                save_dir_coregistration=save_dir_coregistration,
+            )
+            logger.info(
+                f"Coregistration complete. Output saved to {save_dir_coregistration}"
+            )
+            # Optional: N4 bias correction
+            logger.info(f"{' Checking optional N4 bias correction ':-^80}")
+            self.run_n4_bias_correction(
+                save_dir_n4_bias_correction=save_dir_n4_bias_correction,
+            )
 
-        # Defacing
-        logger.info(f"{' Checking optional defacing ':-^80}")
-        self.run_defacing(
-            save_dir_defacing=save_dir_defacing,
-        )
+            # Now we save images that are not skullstripped (current image = atlas registered or atlas registered + corrected)
+            logger.info("Saving non skull-stripped images...")
+            for modality in self.all_modalities:
+                if modality.raw_skull_output_path:
+                    modality.save_current_image(
+                        modality.raw_skull_output_path,
+                        normalization=False,
+                    )
+                if modality.normalized_skull_output_path:
+                    modality.save_current_image(
+                        modality.normalized_skull_output_path,
+                        normalization=True,
+                    )
+
+            # Optional: Brain extraction
+            logger.info(f"{' Checking optional brain extraction ':-^80}")
+            self.run_brain_extraction(
+                save_dir_brain_extraction=save_dir_brain_extraction,
+            )
 
-        # move to separate method
-        if save_dir_transformations:
-            save_dir_transformations = Path(save_dir_transformations)
+            # Defacing
+            logger.info(f"{' Checking optional defacing ':-^80}")
+            self.run_defacing(
+                save_dir_defacing=save_dir_defacing,
+            )
 
-            # Save transformation matrices
-            logger.info(f"Saving transformation matrices to {save_dir_transformations}")
-            for modality in self.all_modalities:
+            # move to separate method
+            if save_dir_transformations:
+                save_dir_transformations = Path(save_dir_transformations)
 
-                modality_transformations_dir = (
-                    save_dir_transformations / modality.modality_name
+                # Save transformation matrices
+                logger.info(
+                    f"Saving transformation matrices to {save_dir_transformations}"
                 )
-                modality_transformations_dir.mkdir(exist_ok=True, parents=True)
-                for step, path in modality.transformation_paths.items():
-                    if path is not None:
-                        shutil.copyfile(
-                            src=str(path.absolute()),
-                            dst=str(
-                                modality_transformations_dir
-                                / f"{step.value}_{path.name}"
-                            ),
-                        )
-
-        # End
-        logger.info(f"{' Preprocessing complete ':=^80}")
+                for modality in self.all_modalities:
+
+                    modality_transformations_dir = (
+                        save_dir_transformations / modality.modality_name
+                    )
+                    modality_transformations_dir.mkdir(exist_ok=True, parents=True)
+                    for step, path in modality.transformation_paths.items():
+                        if path is not None:
+                            shutil.copyfile(
+                                src=str(path.absolute()),
+                                dst=str(
+                                    modality_transformations_dir
+                                    / f"{step.value}_{path.name}"
+                                ),
+                            )
+
+            # End
+            logger.info(f"{' Preprocessing complete ':=^80}")
+        finally:
+            logger.remove(logger_id)
 
     def run_defacing(
         self, save_dir_defacing: Optional[Union[str, Path]] = None

{brainles_preprocessing-0.6.0 → brainles_preprocessing-0.6.1}/brainles_preprocessing/preprocessor/preprocessor.py

@@ -5,10 +5,12 @@ import tempfile
 import warnings
 from abc import ABC, abstractmethod
 from collections import Counter
-from functools import wraps
+from datetime import datetime
 from pathlib import Path
 from typing import List, Optional, Union
 
+from loguru import logger
+
 from brainles_preprocessing.brain_extraction.brain_extractor import (
     BrainExtractor,
     HDBetExtractor,
@@ -23,10 +25,6 @@ from brainles_preprocessing.n4_bias_correction import (
 from brainles_preprocessing.registration import ANTsRegistrator
 from brainles_preprocessing.registration.registrator import Registrator
 from brainles_preprocessing.utils.citation_reminder import citation_reminder
-from brainles_preprocessing.utils.logging_utils import LoggingManager
-
-logging_man = LoggingManager(name=__name__)
-logger = logging_man.get_logger()
 
 
 class BasePreprocessor(ABC):
@@ -46,6 +44,28 @@ class BasePreprocessor(ABC):
 
     """
 
+    def _add_log_file_handler(self, log_file: Optional[Path | str]) -> int:
+        """
+        Add a log file handler to the logger.
+
+        Args:
+            log_file (Optional[Path | str]): Path to the log file. If None, a default log file will be created (brainles_preprocessing_{timestamp}.log).
+
+        Returns:
+            int: The logger id
+        """
+        log_file = Path(
+            log_file
+            if log_file
+            else f"brainles_preprocessing_{datetime.now().strftime('%Y-%m-%d_T%H-%M-%S.%f')}.log"
+        )
+        logger_id = logger.add(log_file, level="DEBUG", catch=True)
+        logger.info(
+            f"Logging console logs and further debug information to: {log_file.absolute()}"
+        )
+
+        return logger_id
+
     @citation_reminder
     def __init__(
         self,
@@ -59,7 +79,6 @@ class BasePreprocessor(ABC):
         use_gpu: Optional[bool] = None,
         limit_cuda_visible_devices: Optional[str] = None,
     ):
-        logging_man._setup_logger()
 
         if not isinstance(center_modality, CenterModality):
             warnings.warn(
@@ -146,18 +165,6 @@ class BasePreprocessor(ABC):
         except (subprocess.CalledProcessError, FileNotFoundError):
             return False
 
-    def ensure_remove_log_file_handler(func):
-        @wraps(func)
-        def wrapper(*args, **kwargs):
-            try:
-                return func(*args, **kwargs)
-            finally:
-                self = args[0]
-                if isinstance(self, BasePreprocessor):
-                    logging_man.remove_log_file_handler()
-
-        return wrapper
-
     @property
     def all_modalities(self) -> List[Modality]:
         """
@@ -173,7 +180,6 @@ class BasePreprocessor(ABC):
         return any(modality.requires_deface for modality in self.all_modalities)
 
     @abstractmethod
-    @ensure_remove_log_file_handler
     def run(self, *args, **kwargs):
         """
         Execute the preprocessing pipeline, encompassing

{brainles_preprocessing-0.6.0 → brainles_preprocessing-0.6.1}/brainles_preprocessing/transform.py

@@ -1,12 +1,10 @@
 from pathlib import Path
 from typing import Optional, Union
 
+from loguru import logger
+
 from brainles_preprocessing.registration import ANTsRegistrator
 from brainles_preprocessing.registration.registrator import Registrator
-from brainles_preprocessing.utils.logging_utils import LoggingManager
-
-logging_man = LoggingManager(name=__name__)
-logger = logging_man.get_logger()
 
 
 class Transform:

{brainles_preprocessing-0.6.0 → brainles_preprocessing-0.6.1}/brainles_preprocessing/utils/zenodo.py

@@ -8,14 +8,9 @@ from pathlib import Path
 from typing import Dict, List, Tuple
 
 import requests
+from loguru import logger
 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*.*.*"

{brainles_preprocessing-0.6.0 → brainles_preprocessing-0.6.1}/pyproject.toml

@@ -14,7 +14,7 @@ exclude = [
 ]
 
 name = "brainles_preprocessing"
-version = "0.6.0"                                                                                                              # will be overwritten by poetry-dynamic-versioning but needs to be set
+version = "0.6.1"                                                                                                              # 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"
 
@@ -72,6 +72,7 @@ rich = "^13.6.0"
 # optional registration backends
 itk-elastix = { version = "^0.20.0", optional = true }
 picsl_greedy = { version = "^0.0.6", optional = true }
+loguru = "^0.7.3"
 
 
 [tool.poetry.extras]

brainles_preprocessing-0.6.0/brainles_preprocessing/utils/logging_utils.py

@@ -1,131 +0,0 @@
-import sys
-import signal
-import logging
-import traceback
-
-from datetime import datetime
-from pathlib import Path
-from typing import Optional, Union
-
-
-class LoggingManager:
-    """
-    Manages logging configurations for the application or library.
-    """
-
-    def __init__(self, name: str, log_file_path: Optional[Union[str, Path]] = None):
-        self.name = name
-        self.log_file_path = log_file_path
-
-        # Create and configure the custom logger
-        self.logger = logging.getLogger(self.name)
-        self.log_file_handler = None
-
-        # Disable log propagation
-        self.logger.propagate = False
-
-        # Set up the logger
-        self._setup_logger()
-
-        # Set up the logger file if provided
-        if log_file_path:
-            self._set_log_file(log_file_path)
-
-    def get_logger(self) -> logging.Logger:
-        """
-        Returns the logger instance.
-        """
-        return self.logger
-
-    def _setup_logger(self):
-        """
-        Sets up the custom logger and overwrites system hooks to add logging for exceptions and signals.
-        """
-        # Configure the custom logger if it hasn't been configured yet
-        if not self.logger.handlers:
-            self.logger.setLevel(logging.INFO)
-            formatter = logging.Formatter(
-                "[%(levelname)s | %(name)s] %(asctime)s: %(message)s",
-                "%Y-%m-%dT%H:%M:%S%z",
-            )
-
-            # Add a console handler
-            console_handler = logging.StreamHandler()
-            console_handler.setFormatter(formatter)
-            self.logger.addHandler(console_handler)
-
-        # Overwrite system hooks to log exceptions and signals (caution advised)
-        sys.excepthook = self.exception_handler
-        signal.signal(signal.SIGINT, self.signal_handler)
-        signal.signal(signal.SIGTERM, self.signal_handler)
-
-    def _set_log_file(self, log_file: str = None) -> None:
-        """
-        Sets the log file handler for the logger.
-
-        Args:
-            log_file (str | Path, optional): Log file path. If not provided, a timestamped log file is created.
-        """
-
-        # Remove existing log file handler if present
-        if self.log_file_handler:
-            self.remove_log_file_handler()
-
-        # Ensure parent directories exist
-        log_file = Path(
-            log_file
-            if log_file
-            else f"brainles_preprocessing_{datetime.now().strftime('%Y-%m-%d_T%H-%M-%S.%f')}.log"
-        )
-        log_file.parent.mkdir(parents=True, exist_ok=True)
-
-        # Create and add the file handler
-        self.log_file_handler = logging.FileHandler(str(log_file))
-        self.log_file_handler.setFormatter(
-            logging.Formatter(
-                "[%(levelname)-8s | %(name)s | %(module)-15s | L%(lineno)-5d] %(asctime)s: %(message)s",
-                "%Y-%m-%dT%H:%M:%S%z",
-            )
-        )
-        self.logger.addHandler(self.log_file_handler)
-        self.log_file_path = log_file
-
-    def remove_log_file_handler(self) -> None:
-        """
-        Removes the log file handler from the logger.
-        """
-        if self.log_file_handler:
-            self.logger.removeHandler(self.log_file_handler)
-            self.log_file_handler.close()
-            self.log_file_handler = None
-            self.log_file_path = None
-
-    # overwrite system hooks to log exceptions and signals (SIGINT, SIGTERM)
-    #! NOTE: This will note work in Jupyter Notebooks, (Without extra setup) see https://stackoverflow.com/a/70469055:
-    def exception_handler(self, exception_type, value, tb):
-        """Handle exceptions
-
-        Args:
-            exception_type (Exception): Exception type
-            exception (Exception): Exception
-            traceback (Traceback): Traceback
-        """
-        self.logger.error(
-            "".join(traceback.format_exception(exception_type, value, tb))
-        )
-
-        if issubclass(exception_type, SystemExit):
-            # add specific code if exception was a system exit
-            sys.exit(value.code)
-
-    def signal_handler(self, sig, frame):
-        """
-        Handles signals by logging them and exiting.
-
-        Args:
-            sig (int): Signal number
-            frame (FrameType): Current stack frame
-        """
-        signame = signal.Signals(sig).name
-        self.logger.error(f"Received signal {sig} ({signame}), exiting...")
-        sys.exit(0)