Merge branch 'master' into enh/rapidart

* master: (127 commits)
  fix: doctest carriage return
  fix: deprecation warning does not reset trait to Undefined - will set new value
  add support for template files
  API fix for somaworkflow
  PEP8
  Further refactoring
  Reafactoring - less redundant code between SGE and PBS.
  Respect custom execution parameters in graph based models.
  Doctest fix, better error reporting.
  fix: config updated before checking for deprecated options
  put back the n_procs docs
  Udated docs with n_procs for MultiProc
  DOC: Added docstring for MpiCommandLine with example usage.
  DOC: Improve docstring for DataFinder, include example usage.
  fix: adding atlases
  fix: removing recommends
  fix: restore fsl
  fix: remove fsl for now
  fix: variable name
  fix: use neurodebian sources
  ...

Author: satra

.travis.yml

@@ -1,22 +1,21 @@
-# vim ft=yaml
-# travis-ci.org definition for nipy build
-#
-# We pretend to be erlang because we need can't use the python support in
-# travis-ci; it uses virtualenvs, they do not have numpy, scipy, matplotlib,
-# and it is impractical to build them
-language: erlang
-env:
-    - PYTHON=python PYSUF=''
-    # - PYTHON=python3 PYSUF=3 : python3-numpy not currently available
-install:
-    - sudo apt-get install $PYTHON-dev
-    - sudo apt-get install $PYTHON-numpy
-    - sudo apt-get install $PYTHON-scipy
-    - sudo apt-get install $PYTHON-networkx
-    - sudo apt-get install $PYTHON-traits
-    - sudo apt-get install $PYTHON-setuptools
-    - sudo easy_install$PYSUF nibabel # Latest pypi
-    - sudo apt-get install $PYTHON-nose
-script:
-    # Change into an innocuous directory and find tests from installation
-    - make test
+language: python
+python:
+    - "2.7"
+before_install:
+    - deactivate
+    - sudo apt-get update -qq
+    - sudo apt-get install lsb-release
+    - source /etc/lsb-release
+    - wget -O- http://neuro.debian.net/lists/${DISTRIB_CODENAME}.us-nh | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
+    - sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9
+    - sudo apt-get update -qq
+    - sudo apt-get install -qq python-scipy python-nose
+    - sudo apt-get install -qq python-networkx python-traits python-setuptools
+    - sudo apt-get install -qq python-nibabel
+    - sudo apt-get install -qq --no-install-recommends fsl afni
+    - sudo apt-get install -qq fsl-atlases
+    - source /etc/fsl/fsl.sh
+    - virtualenv --system-site-packages ~/virtualenv/this
+    - source ~/virtualenv/this/bin/activate
+install: python setup.py build_ext --inplace
+script: make test

CHANGES

@@ -1,11 +1,14 @@
 Next release
 ============
 
-* ENH: New interfaces: ICC, Meshfix, ants.Register
+* ENH: Add basic support for LSF plugin.
+* ENH: New interfaces: ICC, Meshfix, ants.Register, C3dAffineTool, ants.JacobianDeterminant
 * ENH: New workflows: ants template building (both using 'ANTS' and the new 'antsRegistration')
 * ENH: New examples: how to use ANTS template building workflows (smri_ants_build_tmeplate), 
 	  how to set SGE specific options (smri_ants_build_template_new)
 * ENH: added no_flatten option to Merge
+* ENH: added deprecation metadata to traits
+* ENH: Slicer interfaces were updated to version 4.1
 
 Release 0.6.0 (Jun 30, 2012)
 ============================

doc/devel/interface_specs.rst

@@ -262,7 +262,37 @@ Common
 	can be set to either `True` or `False`. `False` indicates that contents 
 	should be symlinked, while `True` indicates that the contents should be 
 	copied over.
-	
+
+``deprecated``
+    This is metadata for removing or renaming an input field from a spec.::
+
+        class RealignInputSpec(BaseInterfaceInputSpec):
+            jobtype = traits.Enum('estwrite', 'estimate', 'write',
+                                  deprecated='0.8',
+                                  desc='one of: estimate, write, estwrite',
+                                  usedefault=True)
+
+    In the above example this means that the `jobtype` input is deprecated and
+    will be removed in version 0.8. Deprecation should be set to two versions
+    from current release. Raises `TraitError` after package version crosses the
+    deprecation version.
+
+``new_name``
+    For inputs that are being renamed, one can specify the new name of the field.::
+
+        class RealignInputSpec(BaseInterfaceInputSpec):
+            jobtype = traits.Enum('estwrite', 'estimate', 'write',
+                                  deprecated='0.8', new_name='job_type',
+                                  desc='one of: estimate, write, estwrite',
+                                  usedefault=True)
+            job_type = traits.Enum('estwrite', 'estimate', 'write',
+                                  desc='one of: estimate, write, estwrite',
+                                  usedefault=True)
+
+    In the above example, the `jobtype` field is being renamed to `job_type`.
+    When `new_name` is provided it must exist as a trait, otherwise an exception
+    will be raised.
+
 CommandLine
 ^^^^^^^^^^^
 

doc/index.rst

@@ -1,10 +1,3 @@
-.. admonition:: Announcement
-
-   Nipype Connectivity Workshop 2012 in Magdeburg, Germany: Sep 8-9, 2012: 
-   `Information and Registration`__
-
-   __ http://nipype.blogspot.com
-
 .. list-table::
 
  * -  .. image:: images/nipype_architecture_overview2.png

doc/users/plugins.rst

@@ -9,8 +9,8 @@ available plugins allow local and distributed execution of workflows and
 debugging. Each available plugin is described below.
 
 Current plugins are available for Linear, Multiprocessing, IPython_ distributed
-processing platforms and for direct processing on SGE_, PBS_, and Condor_. We
-anticipate future plugins for the Soma_ workflow and LSF_.
+processing platforms and for direct processing on SGE_, PBS_, Condor_, and LSF_. We
+anticipate future plugins for the Soma_ workflow.
 
 .. note::
 
@@ -34,7 +34,7 @@ Optional arguments::
 .. note::
 
    Except for the status_callback, the remaining arguments only apply to the
-   distributed plugins: MultiProc/IPython(X)/SGE/PBS/Condor
+   distributed plugins: MultiProc/IPython(X)/SGE/PBS/Condor/LSF
 
 For example:
 
@@ -71,11 +71,17 @@ a local system.
 
 Optional arguments::
 
-  n_procs :  Number of processes to launch in parallel
+  n_procs :  Number of processes to launch in parallel, if not set number of 
+  processors/threads will be automatically detected
 
 To distribute processing on a multicore machine, simply call::
 
-  workflow.run(plugin='MultiProc', plugin_args={'n_procs' : 2})
+  workflow.run(plugin='MultiProc')
+
+This will use all available CPUs. If on the other hand you would like to restrict
+the number of used resources (to say 2 CPUs), you can call::
+
+  workflow.run(plugin='MultiProc', plugin_args={'n_procs' : 2}
 
 IPython
 -------
@@ -102,7 +108,7 @@ SGE/PBS
 In order to use nipype with SGE_ or PBS_ you simply need to call::
 
        workflow.run(plugin='SGE')
-       workflow.run(plugin='PBS)
+       workflow.run(plugin='PBS')
 
 Optional arguments::
 
@@ -130,6 +136,17 @@ particular node might use more resources than other nodes in a workflow.
 
      node.plugin_args = {'qsub_args': '-l nodes=1:ppn=3', 'overwrite': True}
 
+LSF
+---
+
+Submitting via LSF is almost identical to SGE above:
+
+       workflow.run(plugin='LSF')
+
+Optional arguments::
+
+  template: custom template file to use
+  bsub_args: any other command line args to be passed to bsub.
 
 Condor
 ------

examples/dmri_connectivity_advanced.py

@@ -56,12 +56,13 @@
 import nipype.interfaces.cmtk as cmtk
 import nipype.interfaces.dipy as dipy
 import inspect
-import os.path as op                      # system functions
+import os, os.path as op                      # system functions
 from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
 from nipype.workflows.dmri.camino.connectivity_mapping import select_aparc_annot
 from nipype.utils.misc import package_check
 import warnings
 from nipype.workflows.dmri.connectivity.nx import create_networkx_pipeline, create_cmats_to_csv_pipeline
+from nipype.workflows.smri.freesurfer import create_tessellation_flow
 
 try:
     package_check('cmp')
@@ -82,6 +83,9 @@
 fs.FSCommand.set_default_subjects_dir(subjects_dir)
 fsl.FSLCommand.set_default_output_type('NIFTI')
 
+fs_dir = os.environ['FREESURFER_HOME']
+lookup_file = op.join(fs_dir,'FreeSurferColorLUT.txt')
+
 """
 This needs to point to the fdt folder you can find after extracting
 
@@ -328,7 +332,7 @@
 
 CFFConverter = pe.Node(interface=cmtk.CFFConverter(), name="CFFConverter")
 CFFConverter.inputs.script_files = op.abspath(inspect.getfile(inspect.currentframe()))
-giftiSurfaces = pe.Node(interface=util.Merge(8), name="GiftiSurfaces")
+giftiSurfaces = pe.Node(interface=util.Merge(9), name="GiftiSurfaces")
 giftiLabels = pe.Node(interface=util.Merge(2), name="GiftiLabels")
 niftiVolumes = pe.Node(interface=util.Merge(3), name="NiftiVolumes")
 fiberDataArrays = pe.Node(interface=util.Merge(4), name="FiberDataArrays")
@@ -344,6 +348,9 @@
 NxStatsCFFConverter = pe.Node(interface=cmtk.CFFConverter(), name="NxStatsCFFConverter")
 NxStatsCFFConverter.inputs.script_files = op.abspath(inspect.getfile(inspect.currentframe()))
 
+tessflow = create_tessellation_flow(name='tessflow', out_format='gii')
+tessflow.inputs.inputspec.lookup_file = lookup_file
+
 """
 Connecting the workflow
 =======================
@@ -371,6 +378,9 @@
 mapping.connect([(inputnode, FreeSurferSourceRH,[("subjects_dir","subjects_dir")])])
 mapping.connect([(inputnode, FreeSurferSourceRH,[("subject_id","subject_id")])])
 
+mapping.connect([(inputnode, tessflow,[("subjects_dir","inputspec.subjects_dir")])])
+mapping.connect([(inputnode, tessflow,[("subject_id","inputspec.subject_id")])])
+
 mapping.connect([(inputnode, parcellate,[("subjects_dir","subjects_dir")])])
 mapping.connect([(inputnode, parcellate,[("subject_id","subject_id")])])
 mapping.connect([(parcellate, mri_convert_ROI_scale500,[('roi_file','in_file')])])
@@ -516,6 +526,7 @@
 mapping.connect([(mris_convertRHinflated, giftiSurfaces,[("converted","in6")])])
 mapping.connect([(mris_convertLHsphere, giftiSurfaces,[("converted","in7")])])
 mapping.connect([(mris_convertRHsphere, giftiSurfaces,[("converted","in8")])])
+mapping.connect([(tessflow, giftiSurfaces,[("outputspec.meshes","in9")])])
 
 mapping.connect([(mris_convertLHlabels, giftiLabels,[("converted","in1")])])
 mapping.connect([(mris_convertRHlabels, giftiLabels,[("converted","in2")])])

examples/dmri_group_connectivity_mrtrix.py

@@ -140,12 +140,6 @@
 
     l1pipeline = create_group_connectivity_pipeline(group_list, group_id, data_dir, subjects_dir, output_dir, info)
 
-    # This is used to demonstrate the ease through which different parameters can be set for each group.
-    if group_id == 'parkinsons':
-        l1pipeline.inputs.connectivity.mapping.threshold_FA.absolute_threshold_value = 0.5
-    else:
-        l1pipeline.inputs.connectivity.mapping.threshold_FA.absolute_threshold_value = 0.7
-
     # Here with invert the b-vectors in the Y direction and set the maximum harmonic order of the
     # spherical deconvolution step
     l1pipeline.inputs.connectivity.mapping.fsl2mrtrix.invert_y = True