Merge pull request #1 from nipy/master

Update to current master

Author: blakedewey

.gitignore

@@ -13,3 +13,4 @@
 .settings
 .pydevproject
 .idea/
+/documentation.zip

.travis.yml

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

CHANGES

@@ -1,36 +1,79 @@
 Next release
 ============
 
-* ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made 
+* FIX: Enable absolute path definitions in DCMStack (https://github.com/nipy/nipype/pull/1089,
+       replaced by https://github.com/nipy/nipype/pull/1093)
+* ENH: New mesh.MeshWarpMaths to operate on surface-defined warpings
+       (https://github.com/nipy/nipype/pull/1016)
+* FIX: Refactor P2PDistance, change name to ComputeMeshWarp, add regression tests,
+       fix bug in area weighted distance, and added optimizations
+       (https://github.com/nipy/nipype/pull/1016)
+* ENH: Add an option not to resubmit Nodes that finished running when using SGEGraph (https://github.com/nipy/nipype/pull/1002)
+* FIX: FUGUE is now properly listing outputs. (https://github.com/nipy/nipype/pull/978)
+* 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
+       when writing (https://github.com/nipy/nipype/pull/1047)
+* FIX: AddCSVRow problems when using infields (https://github.com/nipy/nipype/pull/1028)
+* FIX: Removed unused ANTS registration flag (https://github.com/nipy/nipype/pull/999)
+* FIX: Amend create_tbss_non_fa() workflow to match FSL's tbss_non_fa command. (https://github.com/nipy/nipype/pull/1033)
+* FIX: remove unused mandatory flag from spm normalize (https://github.com/nipy/nipype/pull/1048)
+* ENH: Update ANTSCorticalThickness interface (https://github.com/nipy/nipype/pull/1013)
+* FIX: Edge case with sparsemodels and PEP8 cleanup (https://github.com/nipy/nipype/pull/1046)
+* ENH: New io interfaces for JSON files reading/writing (https://github.com/nipy/nipype/pull/1020)
+* ENH: Enhanced openfmri script to support freesurfer linkage (https://github.com/nipy/nipype/pull/1037)
+* BUG: matplotlib is supposed to be optional (https://github.com/nipy/nipype/pull/1003)
+* FIX: Fix split_filename behaviour when path has no file component (https://github.com/nipy/nipype/pull/1035)
+* ENH: Updated FSL dtifit to include option for grad non-linearities (https://github.com/nipy/nipype/pull/1032)
+* ENH: Updated Camino tracking interfaces, which can now use FSL bedpostx output.
+       New options also include choice of tracker, interpolator, stepsize and
+       curveinterval for angle threshold (https://github.com/nipy/nipype/pull/1029)
+* FIX: Interfaces redirecting X crashed if $DISPLAY not defined (https://github.com/nipy/nipype/pull/1027)
+* FIX: Bug crashed 'make api' (https://github.com/nipy/nipype/pull/1026)
+* ENH: Updated antsIntroduction to handle RA and RI registrations (https://github.com/nipy/nipype/pull/1009)
+* ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made
 	   argument formatting consistent. Cleaned ants.segmentation according to PEP8.
 	   (https://github.com/nipy/nipype/pull/990/files)
 * ENH: SPM12 Normalize interface (https://github.com/nipy/nipype/pull/986)
 * FIX: Utility interface test dir (https://github.com/nipy/nipype/pull/986)
 * FIX: IPython engine directory reset after crash (https://github.com/nipy/nipype/pull/987)
 * ENH: Resting state fMRI example with NiPy realignment and no SPM (https://github.com/nipy/nipype/pull/992)
-* FIX: Corrected Freesurfer SegStats _list_outputs to avoid error if summary_file is 
+* FIX: Corrected Freesurfer SegStats _list_outputs to avoid error if summary_file is
 	   undefined (issue #994)(https://https://github.com/nipy/nipype/pull/996)
+* FIX: OpenfMRI support and FSL 5.0.7 changes (https://github.com/nipy/nipype/pull/1006)
+* FIX: Output prefix in SPM Normalize with modulation (https://github.com/nipy/nipype/pull/1023)
+* ENH: Usability improvements in cluster environments (https://github.com/nipy/nipype/pull/1025)
+* ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042)
+* ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044)
+* FIX: typo in nipype.interfaces.freesurfer.utils.py Tkregister2 (https://github.com/nipy/nipype/pull/1083)
+* FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. (https://github.com/nipy/nipype/pull/1086)
 
 Release 0.10.0 (October 10, 2014)
 ============
 
 * ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
        to enable parallel processing of very large images.
 * ENH: Updated FSL interfaces: BEDPOSTX and XFibres, former interfaces are still
-       available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu 
+       available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu
        versions of BEDPOSTX: BEDPOSTXGPU, BEDPOSTX5GPU, and BEDPOSTX4GPU
 * ENH: Added experimental support for MIPAV algorithms thorugh JIST plugins
 * ENH: New dipy interfaces: Denoise, Resample
 * ENH: New Freesurfer interfaces: Tkregister2 (for conversion of fsl style matrices to freesurfer format), MRIPretess
 * ENH: New FSL interfaces: WarpPoints, WarpPointsToStd, EpiReg, ProbTrackX2, WarpUtils, ConvertWarp
 * ENH: New miscelaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
 * ENH: New AFNI interfaces:  Eval, Means, SVMTest, SVMTrain
-* ENH: FUGUE interface has been refactored to use the name_template system, 3 examples 
+* ENH: FUGUE interface has been refactored to use the name_template system, 3 examples
        added to doctests, some bugs solved.
 * API: Interfaces to external packages are no longer available in the top-level
        ``nipype`` namespace, and must be imported directly (e.g.
        ``from nipype.interfaces import fsl``).
-* ENH: Support for elastix via a set of new interfaces: Registration, ApplyWarp, 
+* ENH: Support for elastix via a set of new interfaces: Registration, ApplyWarp,
        AnalyzeWarp, PointsWarp, and EditTransform
 * ENH: New ANTs interface: ApplyTransformsToPoints, LaplacianThickness
 * ENH: New Diffusion Toolkit interface: TrackMerge
@@ -46,7 +89,7 @@ Release 0.10.0 (October 10, 2014)
 * ENH: New color mode for write_graph
 * ENH: You can now force MapNodes to be run serially
 * ENH: Added ANTS based openfmri workflow
-* ENH: MapNode now supports flattening of nested lists 
+* ENH: MapNode now supports flattening of nested lists
 * ENH: Support for headless mode using Xvfb
 * ENH: nipype_display_crash has a debugging mode
 * FIX: MRTrix tracking algorithms were ignoring mask parameters.

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)

bin/nipype_display_crash

@@ -74,7 +74,6 @@ if __name__ == "__main__":
                         default=None,
                         help='Directory to run the node in' + defstr)
     args = parser.parse_args()
-    print args.debug, args.ipydebug
     debug = 'ipython' if args.ipydebug else args.debug
     if debug == 'ipython':
         import sys

doc/devel/interface_specs.rst

@@ -358,6 +358,9 @@ CommandLine
 ``name_source``
     Indicates the list of input fields from which the value of the current File
     output variable will be drawn. This input field must be the name of a File.
+    Chaining is allowed, meaning that an input field can point to another as
+    ``name_source``, which also points as ``name_source`` to a third field.
+    In this situation, the templates for substitutions are also accumulated.
 
 ``name_template``
     By default a ``%s_generated`` template is used to create the output

doc/devel/software_using_nipype.rst

@@ -28,6 +28,11 @@ Forward
 
 `Forward <http://cyclotronresearchcentre.github.io/forward/>`_ is set of tools simplifying the preparation of accurate electromagnetic head models for EEG forward modeling. It uses Nipype Workflows and Interfaces.
 
+Limbo
+-----
+
+`Limbo <https://github.com/Gilles86/in_limbo>`_ is a toolbox for finding brain regions that are neither significantly active nor inactive, but rather “in limbo”. It was build using custom Nipype Interfaces and Workflows.
+
 Lyman
 -----
 
@@ -38,6 +43,11 @@ Medimsight
 
 `Medimsight <https://www.medimsight.com>`_ is a commercial service medical imaging cloud platform. It uses Nipype to interface with various neuroimaging software.
 
+MIA
+---
+
+`MIA <http://mia.sourceforge.net>`_ MIA is a a toolkit for gray scale medical image analysis. It provides Nipype interfaces for easy integration with other software.
+
 Mindboggle
 ----------
 

doc/quickstart.rst

@@ -16,7 +16,7 @@ Downloading and installing
 Beginner's guide
 ================
 
-Beginner's tutorials (IPython Notebooks). `Availible here`__
+Beginner's tutorials (IPython Notebooks). `Available here`__
 
 Michael Notter's Nipype guide. `Available here`__
 

doc/users/config_file.rst

@@ -120,6 +120,11 @@ Execution
     characters will be replaced by their hash. (possible values: ``true`` and
 	``false``; default value: ``true``)
 
+*poll_sleep_duration*
+    This controls how long the job submission loop will sleep between submitting
+    all pending jobs and checking for job completion. To be nice to cluster
+    schedulers the default is set to 60 seconds.
+
 Example
 ~~~~~~~
 

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

doc/users/plugins.rst

@@ -136,27 +136,54 @@ particular node might use more resources than other nodes in a workflow.
   this local configuration::
 
      node.plugin_args = {'qsub_args': '-l nodes=1:ppn=3', 'overwrite': True}
+	 
+SGEGraph
+~~~~~~~~
+SGEGraph_ is a exuction plugin working with Sun Grid Engine that allows for
+submitting entire graph of dependent jobs at once. This way Nipype does not 
+need to run a monitoring process - SGE takes care of this.
+
+.. note::
+
+  When rerunning unfinished workflows using SGEGraph you may decide not to 
+  submit jobs for Nodes that previously finished running. This can speed up
+  execution, but new or modified inputs that would previously trigger a Node
+  to rerun will be ignored. The following option turns on this functionality::
+
+     workflow.run(plugin='SGEGraph', plugin_args = {'dont_resubmit_completed_jobs': True})
 
 LSF
 ---
 
-Submitting via LSF is almost identical to SGE above:
+Submitting via LSF is almost identical to SGE above above except for the optional arguments field::
 
-       workflow.run(plugin='LSF')
+    workflow.run(plugin='LSF')
 
 Optional arguments::
 
   template: custom template file to use
   bsub_args: any other command line args to be passed to bsub.
 
+SLURM
+-----
+
+Submitting via SLURM is almost identical to SGE above except for the optional arguments field:
+
+       workflow.run(plugin='SLURM')
+
+Optional arguments::
+
+  template: custom template file to use
+  sbatch_args: any other command line args to be passed to bsub.
+
 HTCondor
 --------
 
 DAGMan
 ~~~~~~
 
 With its DAGMan_ component HTCondor_ (previously Condor) allows for submitting
-entire graphs of dependent jobs at once. With the ``CondorDAGMan`` plug-in
+entire graphs of dependent jobs at once (similar to SGEGraph_). With the ``CondorDAGMan`` plug-in
 Nipype can utilize this functionality to submit complete workflows directly and
 in a single step.  Consequently, and in contrast to other plug-ins, workflow
 execution returns almost instantaneously -- Nipype is only used to generate the