make eddy correction tests quicker by trimming the volume

Author: chrisgorgo

nipype/workflows/dmri/fsl/tests/test_epi.py

@@ -19,23 +19,27 @@ def test_create_eddy_correct_pipeline():
     fsl_course_dir = os.path.abspath(os.environ['FSL_COURSE_DATA'])
 
     dwi_file = os.path.join(fsl_course_dir, "fdt1/subj1/data.nii.gz")
+    
+    trim_dwi = pe.Node(fsl.ExtractROI(t_min=0, 
+                                      t_size=3), name="trim_dwi")
+    trim_dwi.inputs.in_file = dwi_file
 
     nipype_eddycorrect = create_eddy_correct_pipeline("nipype_eddycorrect")
-    nipype_eddycorrect.inputs.inputnode.in_file = dwi_file
     nipype_eddycorrect.inputs.inputnode.ref_num = 0
 
     with warnings.catch_warnings():
         warnings.simplefilter("ignore")
         original_eddycorrect = pe.Node(interface=fsl.EddyCorrect(), name="original_eddycorrect")
-    original_eddycorrect.inputs.in_file = dwi_file
     original_eddycorrect.inputs.ref_num = 0
 
     test = pe.Node(util.AssertEqual(), name="eddy_corrected_dwi_test")
 
     pipeline = pe.Workflow(name="test_eddycorrect")
     pipeline.base_dir = tempfile.mkdtemp(prefix="nipype_test_eddycorrect_")
 
-    pipeline.connect([(nipype_eddycorrect, test, [("outputnode.eddy_corrected", "volume1")]),
+    pipeline.connect([(trim_dwi, original_eddycorrect, [("roi_file", "in_file")]),
+                      (trim_dwi, nipype_eddycorrect, [("roi_file", "inputnode.in_file")]),
+                      (nipype_eddycorrect, test, [("outputnode.eddy_corrected", "volume1")]),
                       (original_eddycorrect, test, [("eddy_corrected", "volume2")]),
                       ])