Merge pull request #1411 from effigies/mri_concat_fix

FIX: Permit relative path for concatenated_file input to Concatenate()

Author: satra

CHANGES

@@ -1,5 +1,6 @@
 Next release
 ============
+
 * ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
 * FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
 * FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
@@ -26,6 +27,7 @@ Next release
 * FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
 * FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
 * ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
+* FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
 
 Release 0.11.0 (September 15, 2015)
 ============

nipype/interfaces/freesurfer/__init__.py

@@ -2,7 +2,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Top-level namespace for freesurfer."""
 
-from .base import Info, FSCommand
+from .base import Info, FSCommand, no_freesurfer
 from .preprocess import (ParseDICOMDir, UnpackSDICOMDir, MRIConvert, Resample,
                          ReconAll, BBRegister, ApplyVolTransform, Smooth,
                          DICOMConvert, RobustRegister, FitMSParams,

nipype/interfaces/freesurfer/base.py

@@ -117,10 +117,6 @@ def _subjects_dir_update(self):
     def set_default_subjects_dir(cls, subjects_dir):
         cls._subjects_dir = subjects_dir
 
-    @property
-    def version(self):
-        return Info.version()
-
     def run(self, **inputs):
         if 'subjects_dir' in inputs:
             self.inputs.subjects_dir = inputs['subjects_dir']
@@ -220,3 +216,14 @@ def run(self, **inputs):
             self.inputs.num_threads = inputs['num_threads']
         self._num_threads_update()
         return super(FSCommandOpenMP, self).run(**inputs)
+
+
+def no_freesurfer():
+    """Checks if FreeSurfer is NOT installed
+    used with skipif to skip tests that will
+    fail if FreeSurfer is not installed"""
+
+    if Info.version() is None:
+        return True
+    else:
+        return False

nipype/interfaces/freesurfer/model.py

@@ -603,11 +603,11 @@ class Concatenate(FSCommand):
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
-        if not isdefined(self.inputs.concatenated_file):
-            outputs['concatenated_file'] = os.path.join(os.getcwd(),
-                                                        'concat_output.nii.gz')
-        else:
-            outputs['concatenated_file'] = self.inputs.concatenated_file
+
+        fname = self.inputs.concatenated_file
+        if not isdefined(fname):
+            fname = 'concat_output.nii.gz'
+        outputs['concatenated_file'] = os.path.join(os.getcwd(), fname)
         return outputs
 
     def _gen_filename(self, name):

nipype/interfaces/freesurfer/tests/test_model.py

@@ -0,0 +1,61 @@
+# 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, skipif
+from nipype.interfaces.freesurfer import model, no_freesurfer
+import nipype.pipeline.engine as pe
+
+
+@skipif(no_freesurfer)
+def test_concatenate():
+    tmp_dir = tempfile.mkdtemp()
+    cwd = os.getcwd()
+    os.chdir(tmp_dir)
+    in1 = os.path.join(tmp_dir, 'cont1.nii')
+    in2 = os.path.join(tmp_dir, '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 in workflow
+    wf = pe.Workflow('test_concatenate', base_dir=tmp_dir)
+    concat = pe.Node(model.Concatenate(in_files=[in1, in2],
+                                       concatenated_file=out),
+                     name='concat')
+    wf.add_nodes([concat])
+    wf.run()
+    yield (assert_equal, nib.load(os.path.join(tmp_dir, 'test_concatenate',
+                                               'concat', 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)

nipype/interfaces/freesurfer/tests/test_preprocess.py

@@ -5,18 +5,10 @@
 import nibabel as nif
 import numpy as np
 from tempfile import mkdtemp
-from nipype.testing import (assert_equal, assert_false, assert_true,
-                            assert_raises, skipif)
+from nipype.testing import assert_equal, assert_raises, skipif
 import nipype.interfaces.freesurfer as freesurfer
 
 
-def no_freesurfer():
-    if freesurfer.Info().version is None:
-        return True
-    else:
-        return False
-
-
 def create_files_in_directory():
     outdir = os.path.realpath(mkdtemp())
     cwd = os.getcwd()
@@ -38,7 +30,7 @@ def clean_directory(outdir, old_wd):
     os.chdir(old_wd)
 
 
-@skipif(no_freesurfer)
+@skipif(freesurfer.no_freesurfer)
 def test_robustregister():
     filelist, outdir, cwd = create_files_in_directory()
 
@@ -66,7 +58,7 @@ def test_robustregister():
     clean_directory(outdir, cwd)
 
 
-@skipif(no_freesurfer)
+@skipif(freesurfer.no_freesurfer)
 def test_fitmsparams():
     filelist, outdir, cwd = create_files_in_directory()
 
@@ -91,7 +83,7 @@ def test_fitmsparams():
     clean_directory(outdir, cwd)
 
 
-@skipif(no_freesurfer)
+@skipif(freesurfer.no_freesurfer)
 def test_synthesizeflash():
     filelist, outdir, cwd = create_files_in_directory()
 

nipype/interfaces/freesurfer/tests/test_utils.py

@@ -15,13 +15,6 @@
 import nipype.interfaces.freesurfer as fs
 
 
-def no_freesurfer():
-    if fs.Info().version is None:
-        return True
-    else:
-        return False
-
-
 def create_files_in_directory():
     outdir = os.path.realpath(mkdtemp())
     cwd = os.getcwd()
@@ -60,7 +53,7 @@ def clean_directory(outdir, old_wd):
     os.chdir(old_wd)
 
 
-@skipif(no_freesurfer)
+@skipif(fs.no_freesurfer)
 def test_sample2surf():
 
     s2s = fs.SampleToSurface()
@@ -104,7 +97,7 @@ def set_illegal_range():
     clean_directory(cwd, oldwd)
 
 
-@skipif(no_freesurfer)
+@skipif(fs.no_freesurfer)
 def test_surfsmooth():
 
     smooth = fs.SurfaceSmooth()
@@ -139,7 +132,7 @@ def test_surfsmooth():
     clean_directory(cwd, oldwd)
 
 
-@skipif(no_freesurfer)
+@skipif(fs.no_freesurfer)
 def test_surfxfm():
 
     xfm = fs.SurfaceTransform()
@@ -173,7 +166,7 @@ def test_surfxfm():
     clean_directory(cwd, oldwd)
 
 
-@skipif(no_freesurfer)
+@skipif(fs.no_freesurfer)
 def test_surfshots():
 
     fotos = fs.SurfaceSnapshots()