Merge pull request nipy#341 from satra/fix/spmmodel

Fix/spmmodel

CHANGES

@@ -1,3 +1,8 @@
+Since 0.5.2
+===========
+
+* FIX: SPM model generation when output units is in scans
+
 Release 0.5.2 (Mar 14, 2012)
 ============================
 

nipype/algorithms/modelgen.py

@@ -271,6 +271,9 @@ def _generate_standard_design(self, infolist,
             each run
         """
         sessinfo = []
+        output_units = 'secs'
+        if 'output_units' in self.inputs.traits():
+            output_units = self.inputs.output_units
         for i, info in enumerate(infolist):
             sessinfo.insert(i, dict(cond=[]))
             if isdefined(self.inputs.high_pass_filter_cutoff):
@@ -281,11 +284,11 @@ def _generate_standard_design(self, infolist,
                     sessinfo[i]['cond'][cid]['name']  = info.conditions[cid]
                     sessinfo[i]['cond'][cid]['onset'] = scale_timings(info.onsets[cid],
                                                                      self.inputs.input_units,
-                                                                     'secs',
+                                                                     output_units,
                                                                      self.inputs.time_repetition)
                     sessinfo[i]['cond'][cid]['duration'] = scale_timings(info.durations[cid],
                                                                         self.inputs.input_units,
-                                                                        'secs',
+                                                                        output_units,
                                                                         self.inputs.time_repetition)
                     if hasattr(info, 'amplitudes') and info.amplitudes:
                         sessinfo[i]['cond'][cid]['amplitudes']  = info.amplitudes[cid]

nipype/algorithms/tests/test_modelgen.py

@@ -1,5 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
+from copy import deepcopy
 import os
 from shutil import rmtree
 from tempfile import mkdtemp
@@ -44,27 +45,35 @@ def test_modelgen_spm_concat():
     tempdir = mkdtemp()
     filename1 = os.path.join(tempdir, 'test1.nii')
     filename2 = os.path.join(tempdir, 'test2.nii')
-    Nifti1Image(np.random.rand(10, 10, 10, 50), np.eye(4)).to_filename(filename1)
-    Nifti1Image(np.random.rand(10, 10, 10, 50), np.eye(4)).to_filename(filename2)
+    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)
     s = SpecifySPMModel()
     s.inputs.input_units = 'secs'
-    s.inputs.output_units = 'scans'
     s.inputs.concatenate_runs = True
-    setattr(s.inputs, 'output_units', 'scans')
-    yield assert_equal, s.inputs.output_units, 'scans'
+    setattr(s.inputs, 'output_units', 'secs')
+    yield assert_equal, s.inputs.output_units, 'secs'
     s.inputs.functional_runs = [filename1, filename2]
     s.inputs.time_repetition = 6
     s.inputs.high_pass_filter_cutoff = 128.
-    info = [Bunch(conditions=['cond1'], onsets=[[2, 50, 100, 180]], durations=[[1]], amplitudes=None,
-                  pmod=None, regressors=None, regressor_names=None, tmod=None),
-            Bunch(conditions=['cond1'], onsets=[[30, 40, 100, 150]], durations=[[1]], amplitudes=None,
-                  pmod=None, regressors=None, regressor_names=None, tmod=None)]
-    s.inputs.subject_info = info
+    info = [Bunch(conditions=['cond1'], onsets=[[2, 50, 100, 170]], durations=[[1]]),
+            Bunch(conditions=['cond1'], onsets=[[30, 40, 100, 150]], durations=[[1]])]
+    s.inputs.subject_info = deepcopy(info)
     res = s.run()
     yield assert_equal, len(res.outputs.session_info), 1
     yield assert_equal, len(res.outputs.session_info[0]['regress']), 1
+    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, 180.0, 330.0, 340.0, 400.0, 450.0])
+    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])
+    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
+    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])
     rmtree(tempdir)
 
 

nipype/workflows/dmri/fsl/tbss.py

@@ -504,7 +504,7 @@ def create_tbss_non_FA(name='tbss_non_FA'):
         inputnode.distance_map
 
     Outputs::
-    
+
         outputnode.projected_nonFA_file
 
     """

tools/build_interface_docs.py

@@ -42,7 +42,7 @@
                                       'FSL',
                                       'FS',
                                       'Info',
-                                      'SPM',
+                                      '^SPM',
                                       'Tester',
                                       'Spec$',
                                       'Numpy'