FIX: Update mask-regression tests for nipreps#408

Author: oesteban

niworkflows/func/tests/test_util.py

@@ -1,17 +1,47 @@
-""" Testing module for fmriprep.workflows.bold.util """
+"""Testing module for fmriprep.workflows.bold.util."""
 import pytest
 import os
 from pathlib import Path
 
 import numpy as np
 from nipype.pipeline import engine as pe
-from nipype.utils.filemanip import fname_presuffix, copyfile
+from nipype.utils.filemanip import fname_presuffix, copyfile, ensure_list
 from nilearn.image import load_img
 
 from niworkflows.interfaces.masks import ROIsPlot
 
 from ..util import init_bold_reference_wf
 
+# Multi-echo datasets
+bold_datasets = ["""\
+ds000210/sub-06_task-rest_run-01_echo-1_bold.nii.gz
+ds000210/sub-06_task-rest_run-01_echo-2_bold.nii.gz
+ds000210/sub-06_task-rest_run-01_echo-3_bold.nii.gz\
+""".splitlines(), """\
+ds000216/sub-03_task-rest_echo-1_bold.nii.gz
+ds000216/sub-03_task-rest_echo-2_bold.nii.gz
+ds000216/sub-03_task-rest_echo-3_bold.nii.gz
+ds000216/sub-03_task-rest_echo-4_bold.nii.gz""".splitlines()]
+
+# Single-echo datasets
+bold_datasets += """\
+ds000116/sub-12_task-visualoddballwithbuttonresponsetotargetstimuli_run-02_bold.nii.gz
+ds000133/sub-06_ses-post_task-rest_run-01_bold.nii.gz
+ds000140/sub-32_task-heatpainwithregulationandratings_run-02_bold.nii.gz
+ds000157/sub-23_task-passiveimageviewing_bold.nii.gz
+ds000237/sub-03_task-MemorySpan_acq-multiband_run-01_bold.nii.gz
+ds000237/sub-06_task-MemorySpan_acq-multiband_run-01_bold.nii.gz
+ds001240/sub-26_task-localizerimagination_bold.nii.gz
+ds001240/sub-26_task-localizerviewing_bold.nii.gz
+ds001240/sub-26_task-molencoding_run-01_bold.nii.gz
+ds001240/sub-26_task-molencoding_run-02_bold.nii.gz
+ds001240/sub-26_task-molretrieval_run-01_bold.nii.gz
+ds001240/sub-26_task-molretrieval_run-02_bold.nii.gz
+ds001240/sub-26_task-rest_bold.nii.gz
+ds001362/sub-01_task-taskname_run-01_bold.nii.gz""".splitlines()
+
+bold_datasets = [ensure_list(d) for d in bold_datasets]
+
 
 def symmetric_overlap(img1, img2):
     mask1 = load_img(img1).get_fdata() > 0
@@ -32,60 +62,42 @@ def symmetric_overlap(img1, img2):
     "input_fname,expected_fname",
     [
         (
-            os.path.join(os.getenv("FMRIPREP_REGRESSION_SOURCE", ""), base_fname),
+            [os.path.join(os.getenv("FMRIPREP_REGRESSION_SOURCE", ""), bf)
+             for bf in base_fname],
             fname_presuffix(
-                base_fname,
+                base_fname[0].replace("_echo-1", ""),
                 suffix="_mask",
                 use_ext=True,
                 newpath=os.path.join(
                     os.getenv("FMRIPREP_REGRESSION_TARGETS", ""),
-                    os.path.dirname(base_fname),
+                    os.path.dirname(base_fname[0]),
                 ),
             ),
         )
-        for base_fname in """\
-ds000116/sub-12_task-visualoddballwithbuttonresponsetotargetstimuli_run-02_bold.nii.gz
-ds000133/sub-06_ses-post_task-rest_run-01_bold.nii.gz
-ds000140/sub-32_task-heatpainwithregulationandratings_run-02_bold.nii.gz
-ds000157/sub-23_task-passiveimageviewing_bold.nii.gz
-ds000210/sub-06_task-rest_run-01_echo-1_bold.nii.gz
-ds000210/sub-06_task-rest_run-01_echo-2_bold.nii.gz
-ds000210/sub-06_task-rest_run-01_echo-3_bold.nii.gz
-ds000216/sub-03_task-rest_echo-1_bold.nii.gz
-ds000216/sub-03_task-rest_echo-2_bold.nii.gz
-ds000216/sub-03_task-rest_echo-3_bold.nii.gz
-ds000216/sub-03_task-rest_echo-4_bold.nii.gz
-ds000237/sub-03_task-MemorySpan_acq-multiband_run-01_bold.nii.gz
-ds000237/sub-06_task-MemorySpan_acq-multiband_run-01_bold.nii.gz
-ds001240/sub-26_task-localizerimagination_bold.nii.gz
-ds001240/sub-26_task-localizerviewing_bold.nii.gz
-ds001240/sub-26_task-molencoding_run-01_bold.nii.gz
-ds001240/sub-26_task-molencoding_run-02_bold.nii.gz
-ds001240/sub-26_task-molretrieval_run-01_bold.nii.gz
-ds001240/sub-26_task-molretrieval_run-02_bold.nii.gz
-ds001240/sub-26_task-rest_bold.nii.gz
-ds001362/sub-01_task-taskname_run-01_bold.nii.gz""".splitlines()
+        for base_fname in bold_datasets
     ],
 )
 def test_masking(input_fname, expected_fname):
-    basename = Path(input_fname).name
+    basename = Path(input_fname[0]).name
     dsname = Path(expected_fname).parent.name
 
     # Reconstruct base_fname from above
     reports_dir = Path(os.getenv("FMRIPREP_REGRESSION_REPORTS", ""))
     newpath = reports_dir / dsname
 
     name = basename.rstrip("_bold.nii.gz").replace("-", "_")
-    bold_reference_wf = init_bold_reference_wf(omp_nthreads=1, name=name)
-    bold_reference_wf.inputs.inputnode.bold_file = input_fname
+    bold_reference_wf = init_bold_reference_wf(omp_nthreads=1, name=name,
+                                               multiecho=len(input_fname) > 1)
+    bold_reference_wf.inputs.inputnode.bold_file = input_fname[0] if len(input_fname) == 1 \
+        else input_fname
     base_dir = os.getenv("CACHED_WORK_DIRECTORY")
     if base_dir:
         base_dir = Path(base_dir) / dsname
         base_dir.mkdir(parents=True, exist_ok=True)
         bold_reference_wf.base_dir = str(base_dir)
 
     out_fname = fname_presuffix(
-        basename, suffix="_mask.svg", use_ext=False, newpath=str(newpath)
+        Path(expected_fname).name, suffix=".svg", use_ext=False, newpath=str(newpath)
     )
     newpath.mkdir(parents=True, exist_ok=True)
 
@@ -117,7 +129,7 @@ def test_masking(input_fname, expected_fname):
     mask_dir.mkdir(parents=True, exist_ok=True)
     copyfile(
         combine_masks.result.outputs.out_file,
-        fname_presuffix(basename, suffix="_mask", use_ext=True, newpath=str(mask_dir)),
+        str(mask_dir / Path(expected_fname).name),
         copy=True,
     )