Merge remote-tracking branch 'upstream/master' into fix/spmversion

* upstream/master: (39 commits)
  fixed support for different folder structures in dicom importer
  fix: check if plugin args is None
  sty: autogenerate fix
  fix: make changes for release
  fix: deploy only nipy/nipype master branch
  fix for identifying if one or multiple durations are employed to describe the condition
  corrected line of modelgen and added test for variable concatenated events
  fix
  test
  FIX: Joint Fusion multimodal Interface Fix
  fix parse_inputs for interfaces not defining gradients
  add FSL bvec/bval format explicit to all interfaces
  fix doctests
  add tck2vtk
  add nohash=True on nthreads option
  add auto tests, fix doctests
  fix errors and missing parts
  add tck2connectome interface
  add interface for fs_parc_replace_sgm_first
  fix default file finding
  ...

Author: satra

.travis.yml

@@ -45,4 +45,5 @@ deploy:
     secure: ZaN6Y4hfybPMi1rW3Qe03irCe/3GU4J4BJsjG+tClVN5Fjc3FCJaYU0k4wNd9q2kMjuRDv1efA9BN/5QasJS32oqs6wHvxzIWA18ucel4BBnAAkuviC1vqi/8Hk/DGB6e1gnmZ1Nv58zVLfn0MwlOKmsGDtvGQWc+HbaV2fS5NA=
   on:
     tags: true
+    repo: nipy/nipype
     branch: master

CHANGES

@@ -1,6 +1,7 @@
 Next release
 ============
 
+* ENH: New interfaces for MRTrix3 (https://github.com/nipy/nipype/pull/1126)
 * ENH: New option in afni.3dRefit - zdel, ydel, zdel etc. (https://github.com/nipy/nipype/pull/1079)
 * FIX: ants.Registration composite transform outputs are no longer returned as lists (https://github.com/nipy/nipype/pull/1183)
 * BUG: ANTs Registration interface failed with multi-modal inputs

doc/_templates/sidebar_versions.html

@@ -17,7 +17,7 @@ <h3>{{ _('Versions') }}</h3>
                 <td align="left">Release</td><td align="right">Devel</td>
             </tr>
             <tr>
-                <td align="left">0.10.0</td><td align="right">{{ version }}</td>
+                <td align="left">0.11.0-rc1</td><td align="right">{{ version }}</td>
             </tr>
             <tr>
                 <td align="left"><a href="{{pathto('users/install')}}">Download</a></td>

doc/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions:  `0.9.2 <http://nipy.org/nipype/0.9.2>`_ `0.8 <http://nipy.org/nipype/0.8>`_
+Previous versions:  `0.10.0 <http://nipy.org/nipype/0.10.0>`_ `0.9.2 <http://nipy.org/nipype/0.9.2>`_
 
 .. container:: doc2
 

nipype/algorithms/modelgen.py

@@ -462,6 +462,10 @@ def _concatenate_info(self, infolist):
         # names, onsets, durations, amplitudes, pmod, tmod, regressor_names,
         # regressors
         infoout = infolist[0]
+        for j, val in enumerate(infolist[0].durations):
+            if len(infolist[0].onsets[j]) > 1 and len(val) == 1:
+                infoout.durations[j] = (infolist[0].durations[j] *
+                                        len(infolist[0].onsets[j]))
         for i, info in enumerate(infolist[1:]):
             #info.[conditions, tmod] remain the same
             if info.onsets:
@@ -476,8 +480,15 @@ def _concatenate_info(self, infolist):
                                  sum(nscans[0:(i + 1)])
                         infoout.onsets[j].extend(onsets.tolist())
                 for j, val in enumerate(info.durations):
-                    if len(val) > 1:
+                    if len(info.onsets[j]) > 1 and len(val) == 1:
+                        infoout.durations[j].extend(info.durations[j] *
+                                                    len(info.onsets[j]))
+                    elif len(info.onsets[j]) == len(val):
                         infoout.durations[j].extend(info.durations[j])
+                    else:
+                        raise ValueError('Mismatch in number of onsets and \
+                                         durations for run {0}, condition \
+                                         {1}'.format(i+2, j+1))
                 if hasattr(info, 'amplitudes') and info.amplitudes:
                     for j, val in enumerate(info.amplitudes):
                         infoout.amplitudes[j].extend(info.amplitudes[j])

nipype/algorithms/tests/test_modelgen.py

@@ -61,6 +61,7 @@ def test_modelgen_spm_concat():
     filename2 = os.path.join(tempdir, 'test2.nii')
     Nifti1Image(np.random.rand(10, 10, 10, 30), np.eye(4)).to_filename(filename1)
     Nifti1Image(np.random.rand(10, 10, 10, 30), np.eye(4)).to_filename(filename2)
+    # Test case when only one duration is passed, as being the same for all onsets.
     s = SpecifySPMModel()
     s.inputs.input_units = 'secs'
     s.inputs.concatenate_runs = True
@@ -78,23 +79,41 @@ def test_modelgen_spm_concat():
     yield assert_equal, np.sum(res.outputs.session_info[0]['regress'][0]['val']), 30
     yield assert_equal, len(res.outputs.session_info[0]['cond']), 1
     yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0, 210.0, 220.0, 280.0, 330.0])
+    yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([1., 1., 1., 1., 1., 1., 1., 1.])
+    # Test case of scans as output units instead of seconds
     setattr(s.inputs, 'output_units', 'scans')
     yield assert_equal, s.inputs.output_units, 'scans'
     s.inputs.subject_info = deepcopy(info)
     res = s.run()
     yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0, 210.0, 220.0, 280.0, 330.0])/6
+    # Test case for no concatenation with seconds as output units
     s.inputs.concatenate_runs = False
     s.inputs.subject_info = deepcopy(info)
     s.inputs.output_units = 'secs'
     res = s.run()
     yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0])
+    # Test case for variable number of events in separate runs, sometimes unique.
+    filename3 = os.path.join(tempdir, 'test3.nii')
+    Nifti1Image(np.random.rand(10, 10, 10, 30), np.eye(4)).to_filename(filename3)
+    s.inputs.functional_runs = [filename1, filename2, filename3]
     info = [Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2]], durations=[[1, 1], [1]]),
-            Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2, 4]], durations=[[1, 1], [1, 1]])]
+            Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2, 4]], durations=[[1, 1], [1, 1]]),
+            Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2]], durations=[[1, 1], [1]])]
     s.inputs.subject_info = deepcopy(info)
     res = s.run()
     yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([1., 1.])
     yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][1]['duration']), np.array([1.,])
     yield assert_almost_equal, np.array(res.outputs.session_info[1]['cond'][1]['duration']), np.array([1., 1.])
+    yield assert_almost_equal, np.array(res.outputs.session_info[2]['cond'][1]['duration']), np.array([1.,])
+    # Test case for variable number of events in concatenated runs, sometimes unique.
+    s.inputs.concatenate_runs = True
+    info = [Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2]], durations=[[1, 1], [1]]),
+            Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2, 4]], durations=[[1, 1], [1, 1]]),
+            Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2]], durations=[[1, 1], [1]])]
+    s.inputs.subject_info = deepcopy(info)
+    res = s.run()
+    yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([1., 1., 1., 1., 1., 1.])
+    yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][1]['duration']), np.array([1., 1., 1., 1.])
     rmtree(tempdir)
 
 

nipype/info.py

@@ -10,7 +10,7 @@
 _version_major = 0
 _version_minor = 11
 _version_micro = 0
-_version_extra = 'dev'
+_version_extra = 'rc1'
 
 def get_nipype_gitversion():
     """Nipype version as reported by the last commit in git

nipype/interfaces/ants/base.py

@@ -83,3 +83,8 @@ def set_default_num_threads(cls, num_threads):
         <instance>.inputs.num_threads
         """
         cls._num_threads = num_threads
+
+    def _format_xarray(self, val):
+        """ Convienence method for converting [1,2,3] -> 1x2x3 """
+        val = 'x'.join([str(x) for x in val])
+        return val

nipype/interfaces/ants/registration.py

@@ -284,13 +284,11 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
     interpolation = traits.Enum(
         'Linear', 'NearestNeighbor', 'CosineWindowedSinc', 'WelchWindowedSinc',
         'HammingWindowedSinc', 'LanczosWindowedSinc', 'BSpline',
-        # 'MultiLabel',
-        # 'Gaussian',
-        # 'BSpline',
-        argstr='%s', usedefault=True)
         # MultiLabel[<sigma=imageSpacing>,<alpha=4.0>]
         # Gaussian[<sigma=imageSpacing>,<alpha=1.0>]
         # BSpline[<order=3>]
+        argstr='%s', usedefault=True)
+
     write_composite_transform = traits.Bool(
         argstr='--write-composite-transform %d',
         default=False, usedefault=True, desc='')
@@ -616,7 +614,7 @@ def _get_outputfilenames(self, inverse=False):
         output_filename = None
         if not inverse:
             if isdefined(self.inputs.output_warped_image) and \
-                self.inputs.output_warped_image:
+                    self.inputs.output_warped_image:
                 output_filename = self.inputs.output_warped_image
                 if isinstance(output_filename, bool):
                     output_filename = '%s_Warped.nii.gz' % self.inputs.output_transform_prefix
@@ -625,7 +623,7 @@ def _get_outputfilenames(self, inverse=False):
             return output_filename
         inv_output_filename = None
         if isdefined(self.inputs.output_inverse_warped_image) and \
-            self.inputs.output_inverse_warped_image:
+                self.inputs.output_inverse_warped_image:
             inv_output_filename = self.inputs.output_inverse_warped_image
             if isinstance(inv_output_filename, bool):
                 inv_output_filename = '%s_InverseWarped.nii.gz' % self.inputs.output_transform_prefix