Merge pull request #1781 from alexsavio/fix/createnifti

Fix small bug/typo in misc.CreateNifti

Author: satra

nipype/algorithms/misc.py

@@ -247,7 +247,7 @@ def _run_interface(self, runtime):
         else:
             affine = None
 
-        with open(self.inputs.header_file, 'rb') as data_file:
+        with open(self.inputs.data_file, 'rb') as data_file:
             data = hdr.data_from_fileobj(data_file)
 
         img = nb.Nifti1Image(data, affine, hdr)

nipype/algorithms/tests/test_misc.py

@@ -0,0 +1,34 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+import pytest
+import os
+
+import nibabel as nb
+
+from nipype.algorithms import misc
+from nipype.utils.filemanip import fname_presuffix
+from nipype.testing.fixtures import create_analyze_pair_file_in_directory
+
+
+def test_CreateNifti(create_analyze_pair_file_in_directory):
+
+    filelist, outdir = create_analyze_pair_file_in_directory
+
+    create_nifti = misc.CreateNifti()
+
+    # test raising error with mandatory args absent
+    with pytest.raises(ValueError):
+        create_nifti.run()
+
+    # .inputs based parameters setting
+    create_nifti.inputs.header_file = filelist[0]
+    create_nifti.inputs.data_file = fname_presuffix(filelist[0],
+                                                    '',
+                                                    '.img',
+                                                    use_ext=False)
+
+    result = create_nifti.run()
+
+    assert os.path.exists(result.outputs.nifti_file)
+    assert nb.load(result.outputs.nifti_file)

nipype/testing/fixtures.py

@@ -15,6 +15,15 @@
 from nipype.interfaces.fsl.base import FSLCommand
 
 
+def analyze_pair_image_files(outdir, filelist, shape):
+    for f in filelist:
+        hdr = nb.Nifti1Header()
+        hdr.set_data_shape(shape)
+        img = np.random.random(shape)
+        analyze = nb.AnalyzeImage(img, np.eye(4), hdr)
+        analyze.to_filename(os.path.join(outdir, f))
+
+
 def nifti_image_files(outdir, filelist, shape):
     for f in filelist:
         hdr = nb.Nifti1Header()
@@ -39,6 +48,21 @@ def change_directory():
     return (filelist, outdir)
 
 
+@pytest.fixture()
+def create_analyze_pair_file_in_directory(request, tmpdir):
+    outdir = str(tmpdir)
+    cwd = os.getcwd()
+    os.chdir(outdir)
+    filelist = ['a.hdr']
+    analyze_pair_image_files(outdir, filelist, shape=(3, 3, 3, 4))
+
+    def change_directory():
+        os.chdir(cwd)
+
+    request.addfinalizer(change_directory)
+    return (filelist, outdir)
+
+
 @pytest.fixture()
 def create_files_in_directory_plus_dummy_file(request, tmpdir):
     outdir = str(tmpdir)