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permission issues on CI machines
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@NicolasGensollen
NicolasGensollen committed Aug 6, 2024
1 parent a81b4bb commit ad77d3b
Showing 1 changed file with 131 additions and 92 deletions.
223 changes: 131 additions & 92 deletions test/instantiation/test_instantiate_all_pipelines.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,20 +119,24 @@ def run_register_dartel(base_dir: Path, output_dir: Path, working_dir: Path) ->
).build()


def test_instantiate_t1_volume_parcellation(cmdopt):
def test_instantiate_t1_volume_parcellation(cmdopt, tmp_path):
from clinica.pipelines.t1_volume_parcellation.t1_volume_parcellation_pipeline import (
T1VolumeParcellation,
)

input_dir = Path(cmdopt["input"])
root = input_dir / "T1VolumeParcellation"
parameters = {"group_label": "UnitTest"}
pipeline = T1VolumeParcellation(
caps_directory=fspath(root / "in" / "caps"),
tsv_file=fspath(root / "in" / "subjects.tsv"),
parameters=parameters,
base_dir = Path(cmdopt["input"])
working_dir = Path(cmdopt["wd"])
input_dir, tmp_dir, ref_dir = configure_paths(
base_dir, tmp_path, "T1VolumeParcellation"
)
pipeline.build()
# Copy the CAPS folder in temp folder in order to have writing privileges
shutil.copytree(str(input_dir / "caps"), str(tmp_dir / "caps"))
T1VolumeParcellation(
caps_directory=fspath(tmp_dir / "caps"),
tsv_file=fspath(input_dir / "subjects.tsv"),
base_dir=fspath(working_dir),
parameters={"group_label": "UnitTest"},
).build()


def test_instantiate_dwi_preprocessing_using_t1(cmdopt, tmp_path):
Expand Down Expand Up @@ -183,25 +187,33 @@ def test_instantiate_dwi_preprocessing_using_phase_diff_field_map(cmdopt, tmp_pa
).build()


def test_instantiate_dwi_dti(cmdopt):
def test_instantiate_dwi_dti(cmdopt, tmp_path):
from clinica.pipelines.dwi.dti.pipeline import DwiDti

input_dir = Path(cmdopt["input"])
root = input_dir / "DWIDTI"
base_dir = Path(cmdopt["input"])
working_dir = Path(cmdopt["wd"])
input_dir, tmp_dir, ref_dir = configure_paths(base_dir, tmp_path, "DWIDTI")
# Copy the CAPS folder in temp folder in order to have writing privileges
shutil.copytree(str(input_dir / "caps"), str(tmp_dir / "caps"))
DwiDti(
caps_directory=fspath(root / "in" / "caps"),
tsv_file=fspath(root / "in" / "subjects.tsv"),
caps_directory=fspath(tmp_dir / "caps"),
tsv_file=fspath(input_dir / "subjects.tsv"),
base_dir=fspath(working_dir),
).build()


def test_instantiate_dwi_connectome(cmdopt):
def test_instantiate_dwi_connectome(cmdopt, tmp_path):
from clinica.pipelines.dwi.connectome.pipeline import DwiConnectome

input_dir = Path(cmdopt["input"])
root = input_dir / "DWIConnectome"
base_dir = Path(cmdopt["input"])
working_dir = Path(cmdopt["wd"])
input_dir, tmp_dir, ref_dir = configure_paths(base_dir, tmp_path, "DWIConnectome")
# Copy the CAPS folder in temp folder in order to have writing privileges
shutil.copytree(str(input_dir / "caps"), str(tmp_dir / "caps"))
DwiConnectome(
caps_directory=fspath(root / "in" / "caps"),
tsv_file=fspath(root / "in" / "subjects.tsv"),
caps_directory=fspath(tmp_dir / "caps"),
tsv_file=fspath(input_dir / "subjects.tsv"),
base_dir=fspath(working_dir),
parameters={"n_tracks": 1000},
).build()

Expand Down Expand Up @@ -252,22 +264,25 @@ def test_instantiate_pet_linear(cmdopt, tmp_path):
def test_instantiate_statistics_surface(cmdopt, tmp_path):
from clinica.pipelines.statistics_surface.pipeline import StatisticsSurface

input_dir = Path(cmdopt["input"])
root = input_dir / "StatisticsSurface"
parameters = {
"group_label": "UnitTest",
"orig_input_data": "t1-freesurfer",
"glm_type": "group_comparison",
"contrast": "group",
"covariates": "age sex",
}
pipeline = StatisticsSurface(
caps_directory=root / "in" / "caps",
base_dir=tmp_path,
tsv_file=root / "in" / "subjects.tsv",
parameters=parameters,
base_dir = Path(cmdopt["input"])
working_dir = Path(cmdopt["wd"])
input_dir, tmp_dir, ref_dir = configure_paths(
base_dir, tmp_path, "StatisticsSurface"
)
pipeline.build()
# Copy the CAPS folder in temp folder in order to have writing privileges
shutil.copytree(str(input_dir / "caps"), str(tmp_dir / "caps"))
StatisticsSurface(
caps_directory=fspath(tmp_dir / "caps"),
tsv_file=fspath(input_dir / "subjects.tsv"),
base_dir=fspath(working_dir),
parameters={
"group_label": "UnitTest",
"orig_input_data": "t1-freesurfer",
"glm_type": "group_comparison",
"contrast": "group",
"covariates": "age sex",
},
).build()


def test_instantiate_pet_surface_cross_sectional(cmdopt, tmp_path):
Expand Down Expand Up @@ -396,48 +411,63 @@ def test_instantiate_workflows_ml(cmdopt, tmp_path):
raise ValueError("An error occurred...")


def test_instantiate_spatial_svm(cmdopt):
def test_instantiate_spatial_svm(cmdopt, tmp_path):
from clinica.pipelines.machine_learning_spatial_svm.spatial_svm_pipeline import (
SpatialSVM,
)

input_dir = Path(cmdopt["input"])
root = input_dir / "SpatialSVM"
parameters = {"group_label": "ADNIbl", "orig_input_data_ml": "t1-volume"}
pipeline = SpatialSVM(
caps_directory=fspath(root / "in" / "caps"),
tsv_file=fspath(root / "in" / "subjects.tsv"),
parameters=parameters,
)
pipeline.build()
base_dir = Path(cmdopt["input"])
working_dir = Path(cmdopt["wd"])
input_dir, tmp_dir, ref_dir = configure_paths(base_dir, tmp_path, "SpatialSVM")
# Copy the CAPS folder in temp folder in order to have writing privileges
shutil.copytree(str(input_dir / "caps"), str(tmp_dir / "caps"))
SpatialSVM(
caps_directory=fspath(tmp_dir / "caps"),
tsv_file=fspath(input_dir / "subjects.tsv"),
base_dir=fspath(working_dir),
parameters={
"group_label": "ADNIbl",
"orig_input_data_ml": "t1-volume",
},
).build()


def test_instantiate_t1_freesurfer_template(cmdopt):
def test_instantiate_t1_freesurfer_template(cmdopt, tmp_path):
from clinica.pipelines.anatomical.freesurfer.longitudinal.template.pipeline import (
T1FreeSurferTemplate,
)

input_dir = Path(cmdopt["input"])
root = input_dir / "T1FreeSurferTemplate"
pipeline = T1FreeSurferTemplate(
caps_directory=fspath(root / "in" / "caps"),
tsv_file=fspath(root / "in" / "subjects.tsv"),
base_dir = Path(cmdopt["input"])
working_dir = Path(cmdopt["wd"])
input_dir, tmp_dir, ref_dir = configure_paths(
base_dir, tmp_path, "T1FreeSurferTemplate"
)
pipeline.build()
# Copy the CAPS folder in temp folder in order to have writing privileges
shutil.copytree(str(input_dir / "caps"), str(tmp_dir / "caps"))
T1FreeSurferTemplate(
caps_directory=fspath(tmp_dir / "caps"),
tsv_file=fspath(input_dir / "subjects.tsv"),
base_dir=fspath(working_dir),
).build()


def test_instantiate_t1_freesurfer_longitudinal_correction(cmdopt):
def test_instantiate_t1_freesurfer_longitudinal_correction(cmdopt, tmp_path):
from clinica.pipelines.anatomical.freesurfer.longitudinal.correction.pipeline import (
T1FreeSurferLongitudinalCorrection,
)

input_dir = Path(cmdopt["input"])
root = input_dir / "T1FreeSurferLongitudinalCorrection"
pipeline = T1FreeSurferLongitudinalCorrection(
caps_directory=fspath(root / "in" / "caps"),
tsv_file=fspath(root / "in" / "subjects.tsv"),
base_dir = Path(cmdopt["input"])
working_dir = Path(cmdopt["wd"])
input_dir, tmp_dir, ref_dir = configure_paths(
base_dir, tmp_path, "T1FreeSurferLongitudinalCorrection"
)
pipeline.build()
# Copy the CAPS folder in temp folder in order to have writing privileges
shutil.copytree(str(input_dir / "caps"), str(tmp_dir / "caps"))
T1FreeSurferLongitudinalCorrection(
caps_directory=fspath(tmp_dir / "caps"),
tsv_file=fspath(input_dir / "subjects.tsv"),
base_dir=fspath(working_dir),
).build()


def test_instantiate_t1_linear(cmdopt, tmp_path):
Expand All @@ -446,57 +476,66 @@ def test_instantiate_t1_linear(cmdopt, tmp_path):
base_dir = Path(cmdopt["input"])
working_dir = Path(cmdopt["wd"])
input_dir, tmp_dir, ref_dir = configure_paths(base_dir, tmp_path, "T1Linear")
pipeline = AnatLinear(
AnatLinear(
bids_directory=fspath(input_dir / "bids"),
caps_directory=fspath(tmp_dir / "caps"),
tsv_file=fspath(input_dir / "subjects.tsv"),
base_dir=fspath(working_dir),
name="t1-linear",
parameters={"uncropped_image": False},
)
pipeline.build()
).build()


def test_instantiate_statistics_volume(cmdopt):
def test_instantiate_statistics_volume(cmdopt, tmp_path):
from clinica.pipelines.statistics_volume.statistics_volume_pipeline import (
StatisticsVolume,
)

input_dir = Path(cmdopt["input"])
root = input_dir / "StatisticsVolume"
parameters = {
"group_label": "UnitTest",
"orig_input_data_volume": "pet-volume",
"contrast": "group",
"acq_label": Tracer.FDG,
"use_pvc_data": False,
"suvr_reference_region": SUVRReferenceRegion.PONS,
}
pipeline = StatisticsVolume(
caps_directory=fspath(root / "in" / "caps"),
tsv_file=fspath(root / "in" / "group-UnitTest_covariates.tsv"),
parameters=parameters,
base_dir = Path(cmdopt["input"])
working_dir = Path(cmdopt["wd"])
input_dir, tmp_dir, ref_dir = configure_paths(
base_dir, tmp_path, "StatisticsVolume"
)
pipeline.build()
# Copy the CAPS folder in temp folder in order to have writing privileges
shutil.copytree(str(input_dir / "caps"), str(tmp_dir / "caps"))

StatisticsVolume(
caps_directory=fspath(tmp_dir / "caps"),
tsv_file=fspath(input_dir / "group-UnitTest_covariates.tsv"),
base_dir=fspath(working_dir),
parameters={
"group_label": "UnitTest",
"orig_input_data_volume": "pet-volume",
"contrast": "group",
"acq_label": Tracer.FDG,
"use_pvc_data": False,
"suvr_reference_region": SUVRReferenceRegion.PONS,
},
).build()


def test_instantiate_statistics_volume_correction(cmdopt):
def test_instantiate_statistics_volume_correction(cmdopt, tmp_path):
from clinica.pipelines.statistics_volume_correction.statistics_volume_correction_pipeline import (
StatisticsVolumeCorrection,
)

input_dir = Path(cmdopt["input"])
root = input_dir / "StatisticsVolumeCorrection"
parameters = {
"t_map": "group-UnitTest_AD-lt-CN_measure-fdg_fwhm-8_TStatistics.nii",
"height_threshold": 3.2422,
"FWEp": 4.928,
"FDRp": 4.693,
"FWEc": 206987,
"FDRc": 206987,
"n_cuts": 15,
}
pipeline = StatisticsVolumeCorrection(
caps_directory=fspath(root / "in" / "caps"), parameters=parameters
base_dir = Path(cmdopt["input"])
working_dir = Path(cmdopt["wd"])
input_dir, tmp_dir, ref_dir = configure_paths(
base_dir, tmp_path, "StatisticsVolumeCorrection"
)
pipeline.build()
# Copy the CAPS folder in temp folder in order to have writing privileges
shutil.copytree(str(input_dir / "caps"), str(tmp_dir / "caps"))
StatisticsVolumeCorrection(
caps_directory=fspath(tmp_dir / "caps"),
base_dir=fspath(working_dir),
parameters={
"t_map": "group-UnitTest_AD-lt-CN_measure-fdg_fwhm-8_TStatistics.nii",
"height_threshold": 3.2422,
"FWEp": 4.928,
"FDRp": 4.693,
"FWEc": 206987,
"FDRc": 206987,
"n_cuts": 15,
},
).build()

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