Split fsl dti and epi tests

This would fix one of the failed tests

Author: oesteban

nipype/interfaces/fsl/tests/test_dti.py

@@ -68,22 +68,6 @@ def test_dtifit1():
         for metakey, value in metadata.items():
             yield assert_equal, getattr(instance.inputs.traits()[key], metakey), value
 
-@skipif(no_fsl)
-def test_eddy_correct1():
-    input_map = dict(args = dict(argstr='%s',),
-                     environ = dict(),
-                     in_file = dict(argstr='%s',mandatory=True,),
-                     out_file = dict(argstr='%s',),
-                     output_type = dict(),
-                     ref_num = dict(mandatory=True,argstr='%d',),
-                     )
-    instance = fsl.EddyCorrect()
-    for key, metadata in input_map.items():
-        for metakey, value in metadata.items():
-            yield assert_equal, getattr(instance.inputs.traits()[key], metakey), value
-
-
-
 @skipif(no_fsl)
 def test_findthebiggest():
     input_map = dict(args = dict(argstr='%s',),
@@ -232,34 +216,6 @@ def test_bedpostx2():
     yield assert_equal, actualCmdline, desiredCmdline
 
 
-
-# test eddy_correct
-@skipif(no_fsl)
-def test_eddy_correct2():
-    filelist, outdir, cwd = create_files_in_directory()
-    eddy = fsl.EddyCorrect()
-
-    # make sure command gets called
-    yield assert_equal, eddy.cmd, 'eddy_correct'
-
-    # test raising error with mandatory args absent
-    yield assert_raises, ValueError, eddy.run
-
-    # .inputs based parameters setting
-    eddy.inputs.in_file = filelist[0]
-    eddy.inputs.out_file = 'foo_eddc.nii'
-    eddy.inputs.ref_num = 100
-    yield assert_equal, eddy.cmdline, 'eddy_correct %s foo_eddc.nii 100'%filelist[0]
-
-    # .run based parameter setting
-    eddy2 = fsl.EddyCorrect(in_file=filelist[0], out_file='foo_ec.nii', ref_num=20)
-    yield assert_equal, eddy2.cmdline, 'eddy_correct %s foo_ec.nii 20'%filelist[0]
-
-    # test arguments for opt_map
-    # eddy_correct class doesn't have opt_map{}
-    clean_directory(outdir, cwd)
-
-
 # test dtifit
 @skipif(no_fsl)
 def test_dtifit2():

nipype/interfaces/fsl/tests/test_epi.py

@@ -0,0 +1,91 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+import os
+import tempfile
+import shutil
+
+from tempfile import mkdtemp
+from shutil import rmtree
+
+import numpy as np
+
+import nibabel as nb
+
+from nose import with_setup
+
+from nipype.testing import ( assert_equal, assert_not_equal,
+                             assert_raises, skipif, example_data)
+import nipype.interfaces.fsl.epi as fsl
+from nipype.interfaces.fsl import Info, no_fsl
+from nipype.interfaces.base import Undefined
+
+# nosetests --with-doctest path_to/test_fsl.py
+
+@skipif(no_fsl)
+def test_eddy_correct1():
+    input_map = dict(args = dict(argstr='%s',),
+                     environ = dict(),
+                     in_file = dict(argstr='%s',mandatory=True,),
+                     out_file = dict(argstr='%s',),
+                     output_type = dict(),
+                     ref_num = dict(mandatory=True,argstr='%d',),
+                     )
+    instance = fsl.EddyCorrect()
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(instance.inputs.traits()[key], metakey), value
+
+
+def skip_epi_tests():
+    """XXX These tests are skipped until we clean up some of this code
+    """
+    return True
+
+def create_files_in_directory():
+    outdir = os.path.realpath(mkdtemp())
+    cwd = os.getcwd()
+    os.chdir(outdir)
+    filelist = ['a.nii','b.nii']
+    for f in filelist:
+        hdr = nb.Nifti1Header()
+        shape = (3,3,3,4)
+        hdr.set_data_shape(shape)
+        img = np.random.random(shape)
+        nb.save(nb.Nifti1Image(img,np.eye(4),hdr),
+                 os.path.join(outdir,f))
+    return filelist, outdir, cwd
+
+def clean_directory(outdir, old_wd):
+    if os.path.exists(outdir):
+        rmtree(outdir)
+    os.chdir(old_wd)
+
+
+# test eddy_correct
+@skipif(no_fsl)
+def test_eddy_correct2():
+    filelist, outdir, cwd = create_files_in_directory()
+    eddy = fsl.EddyCorrect()
+
+    # make sure command gets called
+    yield assert_equal, eddy.cmd, 'eddy_correct'
+
+    # test raising error with mandatory args absent
+    yield assert_raises, ValueError, eddy.run
+
+    # .inputs based parameters setting
+    eddy.inputs.in_file = filelist[0]
+    eddy.inputs.out_file = 'foo_eddc.nii'
+    eddy.inputs.ref_num = 100
+    yield assert_equal, eddy.cmdline, 'eddy_correct %s foo_eddc.nii 100'%filelist[0]
+
+    # .run based parameter setting
+    eddy2 = fsl.EddyCorrect(in_file=filelist[0], out_file='foo_ec.nii', ref_num=20)
+    yield assert_equal, eddy2.cmdline, 'eddy_correct %s foo_ec.nii 20'%filelist[0]
+
+    # test arguments for opt_map
+    # eddy_correct class doesn't have opt_map{}
+    clean_directory(outdir, cwd)
+
+
+