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merged 2 commits into from
Jul 23, 2025
Merged

144 feature optimize logging #149

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7351f75
Add loguru dependency
MarcelRosier Jul 22, 2025
6f6a864
Migrate from custom logging to loguru
MarcelRosier Jul 22, 2025
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3 changes: 1 addition & 2 deletions brainles_preprocessing/modality.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
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
Expand All @@ -17,8 +18,6 @@
from brainles_preprocessing.registration.registrator import Registrator
from brainles_preprocessing.utils.zenodo import verify_or_download_atlases

logger = logging.getLogger(__name__)


class Modality:
"""
Expand Down
175 changes: 89 additions & 86 deletions brainles_preprocessing/preprocessor/atlas_centric_preprocessor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,19 +2,17 @@
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
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):
"""
Expand Down Expand Up @@ -101,97 +99,102 @@ def run(
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
Expand Down
148 changes: 75 additions & 73 deletions brainles_preprocessing/preprocessor/native_space_preprocessor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,10 @@
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):
Expand Down Expand Up @@ -57,81 +55,85 @@ def run(
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
Expand Down
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