Merge pull request #1515 from satra/ref/deprecate_fmrirealign4d

deprecate fmrirealign4d in version 0.13 and make check fixes

Author: satra

doc/users/resource_sched_profiler.rst

@@ -144,17 +144,17 @@ The pandas_ Python package is required to use this feature.
 	from nipype.pipeline.plugins.callback_log import log_nodes_cb
 	args_dict = {'n_procs' : 8, 'memory_gb' : 10, 'status_callback' : log_nodes_cb}
 	workflow.run(plugin='MultiProc', plugin_args=args_dict)
-	
+
 	# ...workflow finishes and writes callback log to '/home/user/run_stats.log'
-	
+
 	from nipype.utils.draw_gantt_chart import generate_gantt_chart
 	generate_gantt_chart('/home/user/run_stats.log', cores=8)
 	# ...creates gantt chart in '/home/user/run_stats.log.html'
 
 The ``generate_gantt_chart`` function will create an html file that can be viewed
 in a browser. Below is an example of the gantt chart displayed in a web browser.
 Note that when the cursor is hovered over any particular node bubble or resource
-bubble, some additional information is shown in a pop-up. 
+bubble, some additional information is shown in a pop-up.
 
  * -  .. image:: images/gantt_chart.png
          :width: 100 %

nipype/interfaces/afni/preprocess.py

@@ -543,7 +543,7 @@ class DegreeCentralityInputSpec(CentralityInputSpec):
                             argstr='-sparsity %f')
 
     oned_file = traits.Str(desc='output filepath to text dump of correlation matrix',
-                           argstr='-out1D %s', mandatory=False)
+                           argstr='-out1D %s')
 
 
 class DegreeCentralityOutputSpec(AFNICommandOutputSpec):
@@ -567,7 +567,7 @@ class DegreeCentrality(AFNICommand):
     ========
 
     >>> from nipype.interfaces import afni as afni
-    >>> degree = afni.DegreeCentrality()           
+    >>> degree = afni.DegreeCentrality()
     >>> degree.inputs.in_file = 'functional.nii'
     >>> degree.inputs.mask = 'mask.nii'
     >>> degree.inputs.sparsity = 1 # keep the top one percent of connections
@@ -1889,11 +1889,15 @@ class SegInputSpec(CommandLineInputSpec):
                    exists=True,
                    copyfile=True)
 
-    mask = traits.Str(desc='only non-zero voxels in mask are analyzed. mask can either be a dataset or the string \'AUTO\' which would use AFNI\'s automask function to create the mask.',
-                   argstr='-mask %s',
-                   position=-2,
-                   mandatory=True,
-                   exists=True)
+    mask = traits.Either(traits.Enum('AUTO'),
+                         File(exists=True),
+                         desc=('only non-zero voxels in mask are analyzed. '
+                               'mask can either be a dataset or the string '
+                               '"AUTO" which would use AFNI\'s automask '
+                               'function to create the mask.'),
+                         argstr='-mask %s',
+                         position=-2,
+                         mandatory=True)
 
     blur_meth = traits.Enum('BFT', 'BIM',
                             argstr='-blur_meth %s',

nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py

@@ -24,7 +24,6 @@ def test_DegreeCentrality_inputs():
     mask=dict(argstr='-mask %s',
     ),
     oned_file=dict(argstr='-out1D %s',
-    mandatory=False,
     ),
     out_file=dict(argstr='-prefix %s',
     name_source=['in_file'],

nipype/interfaces/afni/tests/test_auto_Seg.py

@@ -30,7 +30,6 @@ def test_Seg_inputs():
     main_N=dict(argstr='-main_N %d',
     ),
     mask=dict(argstr='-mask %s',
-    exists=True,
     mandatory=True,
     position=-2,
     ),

nipype/interfaces/base.py

@@ -1197,7 +1197,7 @@ def _read(self, drain):
 # Get number of threads for process
 def _get_num_threads(proc):
     """Function to get the number of threads a process is using
-    NOTE: If 
+    NOTE: If
 
     Parameters
     ----------

nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py

@@ -54,6 +54,10 @@ def test_MRIsConvert_inputs():
     ),
     terminal_output=dict(nohash=True,
     ),
+    to_scanner=dict(argstr='--to-scanner',
+    ),
+    to_tkr=dict(argstr='--to-tkr',
+    ),
     vertex=dict(argstr='-v',
     ),
     xyz_ascii=dict(argstr='-a',

nipype/interfaces/freesurfer/utils.py

@@ -857,7 +857,7 @@ class MRIsConvertInputSpec(FSTraitedSpec):
                                "ICO: .ico, .tri GEO: .geo STL: .stl VTK: .vtk GIFTI: .gii MGH surface-encoded 'volume': .mgh, .mgz")
     to_scanner = traits.Bool(argstr="--to-scanner",
                              desc="convert coordinates from native FS (tkr) coords to scanner coords")
-    to_tkr = traits.Bool(agrstr="--to-tkr",
+    to_tkr = traits.Bool(argstr="--to-tkr",
                          desc="convert coordinates from scanner coords to native FS (tkr) coords")
 
 

nipype/interfaces/fsl/tests/test_Level1Design.py

@@ -0,0 +1,21 @@
+import os
+from nose.tools import assert_true
+from ...base import Undefined
+from ..model import Level1Design
+
+
+def test_level1design():
+    l = Level1Design()
+    runinfo = dict(cond=[{'name': 'test_condition', 'onset': [0, 10],
+                          'duration':[10, 10]}],regress=[])
+    runidx = 0
+    contrasts = Undefined
+    usetd = False
+    do_tempfilter = False
+    for key, val in [('hrf', 3), ('dgamma', 3), ('gamma', 2), ('none', 0)]:
+        output_num, output_txt = Level1Design._create_ev_files(l, os.getcwd(),
+                                                               runinfo, runidx,
+                                                               usetd, contrasts,
+                                                               do_tempfilter,
+                                                               key)
+        yield assert_true, "set fmri(convolve1) {0}".format(val) in output_txt

nipype/interfaces/fsl/tests/test_Level1Design_functions.py

@@ -146,6 +146,11 @@ class FmriRealign4d(BaseInterface):
     output_spec = FmriRealign4dOutputSpec
     keywords = ['slice timing', 'motion correction']
 
+    def __init__(self, **inputs):
+        DeprecationWarning(('Will be deprecated in release 0.13. Please use'
+                            'SpaceTimeRealigner'))
+        BaseInterface.__init__(self, **inputs)
+
     def _run_interface(self, runtime):
         from nipy.algorithms.registration import FmriRealign4d as FR4d
         all_ims = [load_image(fname) for fname in self.inputs.in_file]