Merge pull request #3 from nipy/master

nipype update

Author: stymy

nipype/interfaces/base.py

@@ -785,7 +785,7 @@ def _inputs_help(cls):
 
         opthelpstr = ['', '\t[Optional]']
         for name, spec in sorted(inputs.traits(transient=None).items()):
-            if spec in mandatory_items:
+            if name in mandatory_items:
                 continue
             opthelpstr += cls._get_trait_desc(inputs, name, spec)
 

nipype/interfaces/camino/convert.py

@@ -7,10 +7,12 @@
 
 """
 import os
+import glob
 
 from nipype.interfaces.base import (CommandLineInputSpec, CommandLine, traits,
                                     TraitedSpec, File, StdOutCommandLine,
-                                    StdOutCommandLineInputSpec, isdefined)
+                                    OutputMultiPath, StdOutCommandLineInputSpec,
+                                    isdefined)
 from nipype.utils.filemanip import split_filename
 
 class Image2VoxelInputSpec(StdOutCommandLineInputSpec):
@@ -226,16 +228,21 @@ class ProcStreamlinesInputSpec(StdOutCommandLineInputSpec):
     outputtracts = traits.Bool(argstr='-outputtracts', desc="Output streamlines in raw binary format.")
 
     outputroot = File(exists=False, argstr='-outputroot %s',
-                    desc='root directory for output')
+                    desc='Prepended onto all output file names.')
 
     gzip = traits.Bool(argstr='-gzip', desc="save the output image in gzip format")
-    outputcp = traits.Bool(argstr='-outputcp', desc="output the connection probability map (Analyze image, float)")
-    outputsc = traits.Bool(argstr='-outputsc', desc="output the connection probability map (raw streamlines, int)")
-    outputacm = traits.Bool(argstr='-outputacm', desc="output all tracts in a single connection probability map (Analyze image)")
-    outputcbs = traits.Bool(argstr='-outputcbs', desc="outputs connectivity-based segmentation maps; requires target outputfile")
+    outputcp = traits.Bool(argstr='-outputcp', desc="output the connection probability map (Analyze image, float)",
+                           requires=['outputroot','seedfile'])
+    outputsc = traits.Bool(argstr='-outputsc', desc="output the connection probability map (raw streamlines, int)",
+                           requires=['outputroot','seedfile'])
+    outputacm = traits.Bool(argstr='-outputacm', desc="output all tracts in a single connection probability map (Analyze image)",
+                            requires=['outputroot','seedfile'])
+    outputcbs = traits.Bool(argstr='-outputcbs', desc="outputs connectivity-based segmentation maps; requires target outputfile",
+                            requires=['outputroot','targetfile','seedfile'])
 
 class ProcStreamlinesOutputSpec(TraitedSpec):
     proc = File(exists=True, desc='Processed Streamlines')
+    outputroot_files = OutputMultiPath(File(exists=True))
 
 class ProcStreamlines(StdOutCommandLine):
     """
@@ -256,9 +263,33 @@ class ProcStreamlines(StdOutCommandLine):
     input_spec=ProcStreamlinesInputSpec
     output_spec=ProcStreamlinesOutputSpec
 
+    def _format_arg(self, name, spec, value):
+        if name == 'outputroot':
+            return spec.argstr % self._get_actual_outputroot(value)
+        return super(ProcStreamlines, self)._format_arg(name, spec, value)
+
+    def _run_interface(self, runtime):
+        outputroot = self.inputs.outputroot
+        if isdefined(outputroot):
+            actual_outputroot = self._get_actual_outputroot(outputroot)
+            base, filename, ext = split_filename(actual_outputroot)
+            if not os.path.exists(base):
+                os.makedirs(base)
+            new_runtime = super(ProcStreamlines, self)._run_interface(runtime)
+            self.outputroot_files = glob.glob(os.path.join(os.getcwd(),actual_outputroot+'*'))
+            return new_runtime
+        else:
+            new_runtime = super(ProcStreamlines, self)._run_interface(runtime)
+            return new_runtime
+
+    def _get_actual_outputroot(self, outputroot):
+        actual_outputroot = os.path.join('procstream_outfiles', outputroot)
+        return actual_outputroot
+
     def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs['proc'] = os.path.abspath(self._gen_outfilename())
+        outputs['outputroot_files'] = self.outputroot_files
         return outputs
 
     def _gen_outfilename(self):

nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py

@@ -56,14 +56,18 @@ def test_ProcStreamlines_inputs():
     position=-1,
     ),
     outputacm=dict(argstr='-outputacm',
+    requires=['outputroot', 'seedfile'],
     ),
     outputcbs=dict(argstr='-outputcbs',
+    requires=['outputroot', 'targetfile', 'seedfile'],
     ),
     outputcp=dict(argstr='-outputcp',
+    requires=['outputroot', 'seedfile'],
     ),
     outputroot=dict(argstr='-outputroot %s',
     ),
     outputsc=dict(argstr='-outputsc',
+    requires=['outputroot', 'seedfile'],
     ),
     outputtracts=dict(argstr='-outputtracts',
     ),
@@ -103,7 +107,8 @@ def test_ProcStreamlines_inputs():
             yield assert_equal, getattr(inputs.traits()[key], metakey), value
 
 def test_ProcStreamlines_outputs():
-    output_map = dict(proc=dict(),
+    output_map = dict(outputroot_files=dict(),
+    proc=dict(),
     )
     outputs = ProcStreamlines.output_spec()
 

nipype/interfaces/fsl/dti.py

@@ -46,7 +46,7 @@ class DTIFitInputSpec(FSLCommandInputSpec):
     save_tensor = traits.Bool(desc='save the elements of the tensor',
                         argstr='--save_tensor')
     sse = traits.Bool(desc='output sum of squared errors', argstr='--sse')
-    cni = File(exists=True, desc='input counfound regressors', argstr='-cni %s')
+    cni = File(exists=True, desc='input counfound regressors', argstr='--cni=%s')
     little_bit = traits.Bool(desc='only process small area of brain',
                              argstr='--littlebit')
 

nipype/interfaces/fsl/model.py

@@ -1272,7 +1272,8 @@ def _list_outputs(self):
 class MELODICInputSpec(FSLCommandInputSpec):
     in_files = InputMultiPath(
         File(exists=True), argstr="-i %s", mandatory=True, position=0,
-        desc="input file names (either single file name or a list)")
+        desc="input file names (either single file name or a list)",
+        sep=",")
     out_dir = Directory(
         argstr="-o %s", desc="output directory name", genfile=True)
     mask = File(exists=True, argstr="-m %s",

nipype/interfaces/fsl/tests/test_auto_DTIFit.py

@@ -17,7 +17,7 @@ def test_DTIFit_inputs():
     mandatory=True,
     position=3,
     ),
-    cni=dict(argstr='-cni %s',
+    cni=dict(argstr='--cni=%s',
     ),
     dwi=dict(argstr='-k %s',
     mandatory=True,

nipype/interfaces/fsl/tests/test_auto_MELODIC.py

@@ -32,6 +32,7 @@ def test_MELODIC_inputs():
     in_files=dict(argstr='-i %s',
     mandatory=True,
     position=0,
+    sep=',',
     ),
     log_power=dict(argstr='--logPower',
     ),

nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py

@@ -94,7 +94,7 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     step_size=dict(argstr='-step %s',
     units='mm',
     ),
-    stop=dict(argstr='-gzip',
+    stop=dict(argstr='-stop',
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,

nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py

@@ -92,7 +92,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs():
     step_size=dict(argstr='-step %s',
     units='mm',
     ),
-    stop=dict(argstr='-gzip',
+    stop=dict(argstr='-stop',
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,

nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py

@@ -90,7 +90,7 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs():
     step_size=dict(argstr='-step %s',
     units='mm',
     ),
-    stop=dict(argstr='-gzip',
+    stop=dict(argstr='-stop',
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,

nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py

@@ -90,7 +90,7 @@ def test_StreamlineTrack_inputs():
     step_size=dict(argstr='-step %s',
     units='mm',
     ),
-    stop=dict(argstr='-gzip',
+    stop=dict(argstr='-stop',
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,

nipype/interfaces/mrtrix/tracking.py

@@ -99,7 +99,7 @@ class StreamlineTrackInputSpec(CommandLineInputSpec):
     inputmodel = traits.Enum('DT_STREAM', 'SD_PROB', 'SD_STREAM',
         argstr='%s', desc='input model type', usedefault=True, position=-3)
 
-    stop = traits.Bool(argstr='-gzip', desc="stop track as soon as it enters any of the include regions.")
+    stop = traits.Bool(argstr='-stop', desc="stop track as soon as it enters any of the include regions.")
     do_not_precompute = traits.Bool(argstr='-noprecomputed', desc="Turns off precomputation of the legendre polynomial values. Warning: this will slow down the algorithm by a factor of approximately 4.")
     unidirectional = traits.Bool(argstr='-unidirectional', desc="Track from the seed point in one direction only (default is to track in both directions).")
     no_mask_interpolation = traits.Bool(argstr='-nomaskinterp', desc="Turns off trilinear interpolation of mask images.")