Merge branch 'master' into enh/AntsForFMBworkflow

Conflicts:
	CHANGES

Author: oesteban

.travis.yml

@@ -2,7 +2,6 @@ cache:
   - apt
 language: python
 python:
-  - 2.6
   - 2.7
 env:
   - INSTALL_DEB_DEPENDECIES=true

CHANGES

@@ -3,6 +3,10 @@ Next release
 
 * ENH: Improved FieldMap-Based (FMB) workflow for correction of susceptibility distortions in EPI seqs.
        (https://github.com/nipy/nipype/pull/1019)
+* ENH: Dropped support for now 7 years old Python 2.6 (https://github.com/nipy/nipype/pull/1069)
+* FIX: terminal_output is not mandatory anymore (https://github.com/nipy/nipype/pull/1070)
+* ENH: Added "nipype_cmd" tool for running interfaces from the command line (https://github.com/nipy/nipype/pull/795)
+* FIX: Fixed Camino output naming (https://github.com/nipy/nipype/pull/1061)
 * ENH: Add the average distance to ErrorMap (https://github.com/nipy/nipype/pull/1039)
 * ENH: Inputs with name_source can be now chained in cascade (https://github.com/nipy/nipype/pull/938)
 * ENH: Improve JSON interfaces: default settings when reading and consistent output creation

bin/nipype_cmd

@@ -0,0 +1,8 @@
+#!/usr/bin/env python
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+import sys
+from nipype.utils.nipype_cmd import main
+
+if __name__ == '__main__':
+    main(sys.argv)

doc/users/index.rst

@@ -37,6 +37,7 @@
    saving_workflows
    spmmcr
    mipav
+   nipypecmd
 
 
 

doc/users/install.rst

@@ -107,7 +107,7 @@ recommendations.
 Must Have
 ~~~~~~~~~
 
-Python_ 2.6 - 2.7
+Python_ 2.7
 
 Nibabel_ 1.0 - 1.4
   Neuroimaging file i/o library

doc/users/nipypecmd.rst

@@ -0,0 +1,68 @@
+.. _nipypecmd:
+
+============================================================
+Running Nipype Interfaces from the command line (nipype_cmd)
+============================================================
+
+The primary use of Nipype_ is to build automated non-interactive pipelines.
+However, sometimes there is a need to run some interfaces quickly from the command line.
+This is especially useful when running Interfaces wrapping code that does not have 
+command line equivalents (nipy or SPM). Being able to run Nipype interfaces opens new
+possibilities such as inclusion of SPM processing steps in bash scripts.
+
+To run Nipype Interafces you need to use the nipype_cmd tool that should already be installed.
+The tool allows you to list Interfaces available in a certain package:
+
+.. testcode::
+	
+	
+	$nipype_cmd nipype.interfaces.nipy
+
+	Available Interfaces:
+	    SpaceTimeRealigner
+	    Similarity
+	    ComputeMask
+	    FitGLM
+	    EstimateContrast
+	    FmriRealign4d
+		
+After selecting a particular Interface you can learn what inputs it requires:
+
+.. testcode::
+	
+	
+	$nipype_cmd nipype.interfaces.nipy ComputeMask --help
+	
+	usage:nipype_cmd nipype.interfaces.nipy ComputeMask [-h] [--M M] [--cc CC]
+	                                                     [--ignore_exception IGNORE_EXCEPTION]
+	                                                     [--m M]
+	                                                     [--reference_volume REFERENCE_VOLUME]
+	                                                     mean_volume
+
+	Run ComputeMask
+
+	positional arguments:
+	  mean_volume           mean EPI image, used to compute the threshold for the
+	                        mask
+
+	optional arguments:
+	  -h, --help            show this help message and exit
+	  --M M                 upper fraction of the histogram to be discarded
+	  --cc CC               Keep only the largest connected component
+	  --ignore_exception IGNORE_EXCEPTION
+	                        Print an error message instead of throwing an
+	                        exception in case the interface fails to run
+	  --m M                 lower fraction of the histogram to be discarded
+	  --reference_volume REFERENCE_VOLUME
+	                        reference volume used to compute the mask. If none is
+	                        give, the mean volume is used.
+							
+Finally you can run run the Interface:
+
+.. testcode::
+	
+	$nipype_cmd nipype.interfaces.nipy ComputeMask mean.nii.gz
+
+All that from the command line without having to start python interpreter manually.
+
+.. include:: ../links_names.txt

examples/fmri_ants_openfmri.py

@@ -241,7 +241,7 @@ def create_reg_workflow(name='registration'):
 
     warpmean = pe.Node(ants.ApplyTransforms(),
                        name='warpmean')
-    warpmean.inputs.input_image_type = 3
+    warpmean.inputs.input_image_type = 0
     warpmean.inputs.interpolation = 'Linear'
     warpmean.inputs.invert_transform_flags = [False, False]
     warpmean.inputs.terminal_output = 'file'
@@ -257,7 +257,7 @@ def create_reg_workflow(name='registration'):
     warpall = pe.MapNode(ants.ApplyTransforms(),
                          iterfield=['input_image'],
                          name='warpall')
-    warpall.inputs.input_image_type = 3
+    warpall.inputs.input_image_type = 0
     warpall.inputs.interpolation = 'Linear'
     warpall.inputs.invert_transform_flags = [False, False]
     warpall.inputs.terminal_output = 'file'
@@ -449,7 +449,7 @@ def create_fs_reg_workflow(name='registration'):
     Transform the mean image. First to anatomical and then to target
     """
     warpmean = Node(ants.ApplyTransforms(), name='warpmean')
-    warpmean.inputs.input_image_type = 3
+    warpmean.inputs.input_image_type = 0
     warpmean.inputs.interpolation = 'Linear'
     warpmean.inputs.invert_transform_flags = [False, False]
     warpmean.inputs.terminal_output = 'file'
@@ -464,7 +464,7 @@ def create_fs_reg_workflow(name='registration'):
     warpall = pe.MapNode(ants.ApplyTransforms(),
                          iterfield=['input_image'],
                          name='warpall')
-    warpall.inputs.input_image_type = 3
+    warpall.inputs.input_image_type = 0
     warpall.inputs.interpolation = 'Linear'
     warpall.inputs.invert_transform_flags = [False, False]
     warpall.inputs.terminal_output = 'file'

nipype/algorithms/metrics.py

@@ -572,7 +572,7 @@ def _run_interface(self, runtime):
         nb.Nifti1Image(errmap.astype(np.float32), nii_ref.get_affine(),
                        hdr).to_filename(self._out_file)
 
-        return runtime 
+        return runtime
 
     def _list_outputs(self):
         outputs = self.output_spec().get()

nipype/algorithms/tests/test_auto_ErrorMap.py

@@ -32,7 +32,7 @@ def test_errormap():
 	errmap.inputs.in_ref = os.path.join(tempdir, 'alan.nii.gz')
 	errmap.out_map = os.path.join(tempdir, 'out_map.nii.gz')
 	result = errmap.run()
-	yield assert_equal, result.outputs.distance, 1.125 
+	yield assert_equal, result.outputs.distance, 1.125
 
 	# Square metric
 	errmap.inputs.metric = 'sqeuclidean'
@@ -42,9 +42,9 @@ def test_errormap():
 	# Linear metric
 	errmap.inputs.metric = 'euclidean'
 	result = errmap.run()
-	yield assert_equal, result.outputs.distance, 0.875 
+	yield assert_equal, result.outputs.distance, 0.875
 
-	# Masked 
+	# Masked
 	errmap.inputs.mask = os.path.join(tempdir, 'mask.nii.gz')
 	result = errmap.run()
 	yield assert_equal, result.outputs.distance, 1.0

nipype/algorithms/tests/test_auto_Overlap.py

@@ -16,8 +16,7 @@ def test_AFNICommand_inputs():
     name_template='%s_afni',
     ),
     outputtype=dict(),
-    terminal_output=dict(mandatory=True,
-    nohash=True,
+    terminal_output=dict(nohash=True,
     ),
     )
     inputs = AFNICommand.input_spec()

nipype/algorithms/tests/test_errormap.py

@@ -21,8 +21,7 @@ def test_AFNItoNIFTI_inputs():
     name_template='%s.nii',
     ),
     outputtype=dict(),
-    terminal_output=dict(mandatory=True,
-    nohash=True,
+    terminal_output=dict(nohash=True,
     ),
     )
     inputs = AFNItoNIFTI.input_spec()

nipype/interfaces/afni/tests/test_auto_AFNICommand.py

@@ -83,8 +83,7 @@ def test_Allineate_inputs():
     ),
     source_mask=dict(argstr='-source_mask %s',
     ),
-    terminal_output=dict(mandatory=True,
-    nohash=True,
+    terminal_output=dict(nohash=True,
     ),
     two_best=dict(argstr='-twobest %d',
     ),

nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py

@@ -33,8 +33,7 @@ def test_AutoTcorrelate_inputs():
     outputtype=dict(),
     polort=dict(argstr='-polort %d',
     ),
-    terminal_output=dict(mandatory=True,
-    nohash=True,
+    terminal_output=dict(nohash=True,
     ),
     )
     inputs = AutoTcorrelate.input_spec()

nipype/interfaces/afni/tests/test_auto_Allineate.py

@@ -23,8 +23,7 @@ def test_Autobox_inputs():
     outputtype=dict(),
     padding=dict(argstr='-npad %d',
     ),
-    terminal_output=dict(mandatory=True,
-    nohash=True,
+    terminal_output=dict(nohash=True,
     ),
     )
     inputs = Autobox.input_spec()

nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py

@@ -31,8 +31,7 @@ def test_Automask_inputs():
     name_template='%s_mask',
     ),
     outputtype=dict(),
-    terminal_output=dict(mandatory=True,
-    nohash=True,
+    terminal_output=dict(nohash=True,
     ),
     )
     inputs = Automask.input_spec()

nipype/interfaces/afni/tests/test_auto_Autobox.py

@@ -54,8 +54,7 @@ def test_Bandpass_inputs():
     position=1,
     ),
     outputtype=dict(),
-    terminal_output=dict(mandatory=True,
-    nohash=True,
+    terminal_output=dict(nohash=True,
     ),
     tr=dict(argstr='-dt %f',
     ),

nipype/interfaces/afni/tests/test_auto_Automask.py

@@ -38,8 +38,7 @@ def test_BlurInMask_inputs():
     outputtype=dict(),
     preserve=dict(argstr='-preserve',
     ),
-    terminal_output=dict(mandatory=True,
-    nohash=True,
+    terminal_output=dict(nohash=True,
     ),
     )
     inputs = BlurInMask.input_spec()

nipype/interfaces/afni/tests/test_auto_Bandpass.py

@@ -26,8 +26,7 @@ def test_BrickStat_inputs():
     name_template='%s_afni',
     ),
     outputtype=dict(),
-    terminal_output=dict(mandatory=True,
-    nohash=True,
+    terminal_output=dict(nohash=True,
     ),
     )
     inputs = BrickStat.input_spec()

nipype/interfaces/afni/tests/test_auto_BlurInMask.py

@@ -37,8 +37,7 @@ def test_Calc_inputs():
     ),
     stop_idx=dict(requires=['start_idx'],
     ),
-    terminal_output=dict(mandatory=True,
-    nohash=True,
+    terminal_output=dict(nohash=True,
     ),
     )
     inputs = Calc.input_spec()

nipype/interfaces/afni/tests/test_auto_BrickStat.py

@@ -21,8 +21,7 @@ def test_Copy_inputs():
     name_template='%s_copy',
     ),
     outputtype=dict(),
-    terminal_output=dict(mandatory=True,
-    nohash=True,
+    terminal_output=dict(nohash=True,
     ),
     )
     inputs = Copy.input_spec()

nipype/interfaces/afni/tests/test_auto_Calc.py

@@ -21,8 +21,7 @@ def test_Despike_inputs():
     name_template='%s_despike',
     ),
     outputtype=dict(),
-    terminal_output=dict(mandatory=True,
-    nohash=True,
+    terminal_output=dict(nohash=True,
     ),
     )
     inputs = Despike.input_spec()

nipype/interfaces/afni/tests/test_auto_Copy.py

@@ -21,8 +21,7 @@ def test_Detrend_inputs():
     name_template='%s_detrend',
     ),
     outputtype=dict(),
-    terminal_output=dict(mandatory=True,
-    nohash=True,
+    terminal_output=dict(nohash=True,
     ),
     )
     inputs = Detrend.input_spec()