108 feature check for name collisions between center and moving modalities

[MarcelRosier]

Review after #133

[Copilot]

Pull Request Overview

Adds a preprocessor check to prevent duplicate modality names and includes a standalone script for manually testing inverse transformations.

• Introduce _check_for_name_conflicts in Preprocessor to raise an error for non-unique modality names.
• Add test_inverse_mapping.py as an example script for verifying inverse mapping behavior.
• Import Counter for name-counting logic and wire up the new check in the constructor.

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
test_inverse_mapping.py	New example script with hardcoded paths to manually test inverse mapping.
brainles_preprocessing/preprocessor.py	Added Counter import, defined _check_for_name_conflicts, and invoked it in __init__.

Comments suppressed due to low confidence (2)

test_inverse_mapping.py:32

• This test script does not include any assertions or automated checks. To turn this into a proper test, wrap calls in a testing framework and assert expected outputs.

back.transform(

brainles_preprocessing/preprocessor.py:110

• The code references self.all_modalities, but there’s no definition of that attribute in this class. You may need to define all_modalities or explicitly combine center_modality and moving_modalities.

        name_counts = Counter(mod.modality_name for mod in self.all_modalities)

[Copilot]

[nitpick] Using absolute, hardcoded paths makes this script brittle and environment-specific. Consider parameterizing paths with fixtures or environment variables for portability.

Suggested change

	f"/home/marcelrosier/preprocessing/example/example_data/TCGA-DU-7294/{abr}_TCGA-DU-7294_brainles/transformations"
	)
	segmentation_path = Path(
	f"/home/marcelrosier/preprocessing/example/example_data/{abr}_TCGA-DU-7294_segmentation.nii.gz"
	)
	flair_img_path = Path(
	"/home/marcelrosier/preprocessing/example/example_data/TCGA-DU-7294/AXIAL_FLAIR_RF2_150_TCGA-DU-7294_TCGA-DU-7294_GE_TCGA-DU-7294_AXIAL_FLAIR_RF2_150_IR_7_fla.nii.gz"
	)
	t1c_img_path = Path(
	"/home/marcelrosier/preprocessing/example/example_data/TCGA-DU-7294/AX_T1_POST_GD_FLAIR_TCGA-DU-7294_TCGA-DU-7294_GE_TCGA-DU-7294_AX_T1_POST_GD_FLAIR_RM_13_t1c.nii.gz"
	os.getenv("TRANSFORMS_DIR", f"./example_data/TCGA-DU-7294/{abr}_TCGA-DU-7294_brainles/transformations")
	)
	segmentation_path = Path(
	os.getenv("SEGMENTATION_PATH", f"./example_data/{abr}_TCGA-DU-7294_segmentation.nii.gz")
	)
	flair_img_path = Path(
	os.getenv("FLAIR_IMG_PATH", "./example_data/TCGA-DU-7294/AXIAL_FLAIR_RF2_150_TCGA-DU-7294_TCGA-DU-7294_GE_TCGA-DU-7294_AXIAL_FLAIR_RF2_150_IR_7_fla.nii.gz")
	)
	t1c_img_path = Path(
	os.getenv("T1C_IMG_PATH", "./example_data/TCGA-DU-7294/AX_T1_POST_GD_FLAIR_TCGA-DU-7294_TCGA-DU-7294_GE_TCGA-DU-7294_AX_T1_POST_GD_FLAIR_RM_13_t1c.nii.gz")

[MarcelRosier]

file should not be in the repo at all, removed

[Copilot]

The warnings module is imported but not used in this file. Consider removing this import to keep dependencies clean.

Suggested change

import warnings

[MarcelRosier]

already done in #133, will be included before merge