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@NicolasGensollen
NicolasGensollen committed Dec 5, 2024
1 parent c76f001 commit 4e234ca
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72 changes: 55 additions & 17 deletions clinica/utils/testing_utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@

from clinica.pipelines.dwi.utils import DWIDataset

from .spm import SPMTissue, get_spm_tissue_from_index

__all__ = [
"build_test_image_cubic_object",
"build_bids_directory",
Expand Down Expand Up @@ -223,7 +225,7 @@ def _build_subjects(directory: Path, configuration: dict) -> None:
_build_t1(directory, sub, ses, configuration)
if pipeline_name == "t1_volume_tissue_segmentation":
_build_t1_volume_tissue_segmentation(
directory, sub, ses, configuration
directory, sub, ses, pipeline_config
)


Expand All @@ -235,22 +237,58 @@ def _build_t1_volume_tissue_segmentation(
directory / "subjects" / sub / ses / "t1" / "spm" / "segmentation"
)
segmentation_folder.mkdir(parents=True, exist_ok=True)
folders = ["dartel_input", "native_space", "normalized_space"]
for folder in folders:
(segmentation_folder / folder).mkdir(exist_ok=True)
for tissue in ("csf", "graymatter", "whitematter"):
common_filename_part = f"{sub}_{ses}_T1w_segm-{tissue}"
for folder, filename_end in zip(
folders,
[
"dartelinput.nii.gz",
"probability.nii.gz",
"space-Ixi549Space_modulated-off_probability.nii.gz",
],
):
(
segmentation_folder / folder / f"{common_filename_part}_{filename_end}"
).touch()
common_filename_part = f"{sub}_{ses}_T1w_segm-"
_build_t1_volume_tissue_segmentation_native_space(
segmentation_folder, common_filename_part, config
)
_build_t1_volume_tissue_segmentation_dartel_input(
segmentation_folder, common_filename_part, config
)
_build_t1_volume_tissue_segmentation_normalized_space(
segmentation_folder, common_filename_part, config
)


def _extract_tissues_from_config(config: dict, key: str) -> list[SPMTissue]:
if (tissue_classes := config.get(key, None)) is not None:
return [get_spm_tissue_from_index(i) for i in tissue_classes]
return [tissue for tissue in SPMTissue]


def _build_t1_volume_tissue_segmentation_native_space(
segmentation_folder: Path, common_filename_part: str, config: dict
) -> None:
(segmentation_folder / "native_space").mkdir(exist_ok=True)
for tissue in _extract_tissues_from_config(config, "tissue_classes"):
(
segmentation_folder
/ "native_space"
/ f"{common_filename_part}{tissue.value}_probability.nii.gz"
).touch()


def _build_t1_volume_tissue_segmentation_dartel_input(
segmentation_folder: Path, common_filename_part: str, config: dict
) -> None:
(segmentation_folder / "dartel_input").mkdir(exist_ok=True)
for tissue in _extract_tissues_from_config(config, "dartel_tissues"):
(
segmentation_folder
/ "dartel_input"
/ f"{common_filename_part}{tissue.value}_dartelinput.nii.gz"
).touch()


def _build_t1_volume_tissue_segmentation_normalized_space(
segmentation_folder: Path, common_filename_part: str, config: dict
) -> None:
(segmentation_folder / "normalized_space").mkdir(exist_ok=True)
for tissue in _extract_tissues_from_config(config, "tissue_classes"):
(
segmentation_folder
/ "normalized_space"
/ f"{common_filename_part}{tissue.value}_space-Ixi549Space_modulated-off_probability.nii.gz"
).touch()


def _build_t1_linear(directory: Path, sub: str, ses: str, config: dict) -> None:
Expand Down
61 changes: 47 additions & 14 deletions ...ts/pipelines/t1_volume_tissue_segmentation/test_t1_volume_tissue_segmentation_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,7 @@ def test_t1_volume_tissue_segmentation_get_processed_visits_empty(tmp_path, mock
def test_t1_volume_tissue_segmentation_get_processed_visits(tmp_path, mocker):
"""Test the get_processed_visits for T1VolumeTissueSegmentation.
We build the following CAPS dataset:
We build a CAPS dataset with the following structure:
caps2
├── dataset_description.json
Expand All @@ -98,19 +98,20 @@ def test_t1_volume_tissue_segmentation_get_processed_visits(tmp_path, mocker):
└── spm
└── segmentation
├── dartel_input
│ ├── sub-01_ses-M000_T1w_segm-csf_dartelinput.nii.gz
│ ├── sub-01_ses-M000_T1w_segm-graymatter_dartelinput.nii.gz
│ └── sub-01_ses-M000_T1w_segm-whitematter_dartelinput.nii.gz
│ └── sub-01_ses-M000_T1w_segm-XXXXXXXX_dartelinput.nii.gz
├── native_space
│ ├── sub-01_ses-M000_T1w_segm-csf_probability.nii.gz
│ ├── sub-01_ses-M000_T1w_segm-graymatter_probability.nii.gz
│ └── sub-01_ses-M000_T1w_segm-whitematter_probability.nii.gz
│ └── sub-01_ses-M000_T1w_segm-YYYYYYYY_probability.nii.gz
└── normalized_space
├── sub-01_ses-M000_T1w_segm-csf_space-Ixi549Space_modulated-off_probability.nii.gz
├── sub-01_ses-M000_T1w_segm-graymatter_space-Ixi549Space_modulated-off_probability.nii.gz
└── sub-01_ses-M000_T1w_segm-whitematter_space-Ixi549Space_modulated-off_probability.nii.gz
... same for other subjects and sessions.
Verify that removing files for a given visit will remove it from the "processed" visits.
└── sub-01_ses-M000_T1w_segm-YYYYYYYY_space-Ixi549Space_modulated-off_probability.nii.gz
And this for several subjects and sessions.
We can control the values for XXXXX and YYYYY through the lists of tissues that we pass
to the CAPS generator (XXXX is controlled by 'dartel_tissues', while YYYY is controlled by 'tissue_classes').
The purpose of this test is to verify that, depending on what the user wants in terms of tissues,
the pipeline correctly identifies the already processed visits as the ones having ALL images for
the tissues of interest. If there is at least one image missing, then the visit will be processed
again (and therefore won't be listed in the list of "processed" visits).
"""
from clinica.pipelines.t1_volume_tissue_segmentation.t1_volume_tissue_segmentation_pipeline import (
T1VolumeTissueSegmentation,
Expand All @@ -127,7 +128,12 @@ def test_t1_volume_tissue_segmentation_get_processed_visits(tmp_path, mocker):
caps = build_caps_directory(
tmp_path / "caps",
{
"pipelines": {"t1_volume_tissue_segmentation": {}},
"pipelines": {
"t1_volume_tissue_segmentation": {
"tissue_classes": (1, 2, 3, 4),
"dartel_tissues": (2, 4, 5, 6),
}
},
"subjects": {
"sub-01": ["ses-M006"],
"sub-02": ["ses-M000", "ses-M012"],
Expand All @@ -138,15 +144,41 @@ def test_t1_volume_tissue_segmentation_get_processed_visits(tmp_path, mocker):
bids_directory=str(bids),
caps_directory=str(caps),
parameters={
"tissue_classes": (1, 2, 3),
"tissue_classes": (1, 2, 5, 6),
"dartel_tissues": (2, 4, 6),
},
)
# No visit considered already processed since we are asking for tissues 1, 2, 5, and 6
# and the CAPS folder only contains tissues 1, 2, 3, and 4
assert pipeline.get_processed_visits() == []

pipeline = T1VolumeTissueSegmentation(
bids_directory=str(bids),
caps_directory=str(caps),
parameters={
"tissue_classes": (1, 2, 3, 4),
"dartel_tissues": (1, 2, 3),
},
)
# No visit considered already processed since we are asking for dartel tissues 1, 2, and 3
# and the CAPS folder only contains tissues 2, 4, 5, and 6 (1 and 3 are missing...)
assert pipeline.get_processed_visits() == []

pipeline = T1VolumeTissueSegmentation(
bids_directory=str(bids),
caps_directory=str(caps),
parameters={
"tissue_classes": (1, 2, 3),
"dartel_tissues": (2, 4, 5),
},
)
# All visits are considered processed since we are asking for tissues that are present in the CAPS folder
assert pipeline.get_processed_visits() == [
Visit("sub-01", "ses-M006"),
Visit("sub-02", "ses-M000"),
Visit("sub-02", "ses-M012"),
]

# Delete the folder "dartel_input" altogether for subject 02 session M000 (but keep the other folders)
shutil.rmtree(
tmp_path
Expand All @@ -164,6 +196,7 @@ def test_t1_volume_tissue_segmentation_get_processed_visits(tmp_path, mocker):
Visit("sub-01", "ses-M006"),
Visit("sub-02", "ses-M012"),
]

# Delete a single file in the "native_space" folder for subject 01 session M006 (keep other files and folders)
(
tmp_path
Expand Down

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