TEST: Basic exercise of freesurfer.model.Concatenate

Author: effigies

nipype/interfaces/freesurfer/tests/test_model.py

@@ -0,0 +1,48 @@
+# 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
+import numpy as np
+import nibabel as nib
+
+from nipype.testing import assert_equal
+from nipype.interfaces.freesurfer import model
+
+
+def test_concatenate():
+    tmp_dir = tempfile.mkdtemp()
+    cwd = os.getcwd()
+    os.chdir(tmp_dir)
+    in1 = 'cont1.nii'
+    in2 = 'cont2.nii'
+    out = 'bar.nii'
+
+    data1 = np.zeros((3, 3, 3, 1), dtype=np.float32)
+    data2 = np.ones((3, 3, 3, 5), dtype=np.float32)
+    out_data = np.concatenate((data1, data2), axis=3)
+    mean_data = np.mean(out_data, axis=3)
+
+    nib.Nifti1Image(data1, affine=np.eye(4)).to_filename(in1)
+    nib.Nifti1Image(data2, affine=np.eye(4)).to_filename(in2)
+
+    # Test default behavior
+    res = model.Concatenate(in_files=[in1, in2]).run()
+    yield (assert_equal, res.outputs.concatenated_file,
+           os.path.join(tmp_dir, 'concat_output.nii.gz'))
+    yield (assert_equal, nib.load('concat_output.nii.gz').get_data(), out_data)
+
+    # Test specified concatenated_file
+    res = model.Concatenate(in_files=[in1, in2], concatenated_file=out).run()
+    yield (assert_equal, res.outputs.concatenated_file,
+           os.path.join(tmp_dir, out))
+    yield (assert_equal, nib.load(out).get_data(), out_data)
+
+    # Test a simple statistic
+    res = model.Concatenate(in_files=[in1, in2], concatenated_file=out,
+                            stats='mean').run()
+    yield (assert_equal, nib.load(out).get_data(), mean_data)
+
+    os.chdir(cwd)
+    shutil.rmtree(tmp_dir)