Merge branch 'master' into bug/FixAntsInitialization

Author: oesteban

CHANGES

@@ -1,7 +1,11 @@
-Release 0.9.2 (January 31, 2014)
-===========
+Next Release
+============
 
 * ENH: New ANTs interface: ApplyTransformsToPoints
+* FIX: MRTrix tracking algorithms were ignoring mask parameters.
+
+Release 0.9.2 (January 31, 2014)
+============
 
 * FIX: DataFinder was broken due to a typo
 * FIX: Order of DataFinder outputs was not guaranteed, it's human sorted now

Vagrantfile

@@ -20,19 +20,19 @@ $script = <<SCRIPT
 # qconf -aattr queue slots "2, [neuro=3]" main.q
 
 # install anaconda
-wget http://repo.continuum.io/miniconda/Miniconda-3.0.0-Linux-x86_64.sh -O miniconda.sh
+wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
 chmod +x miniconda.sh
 ./miniconda.sh -b
 echo "export PATH=$HOME/miniconda/bin:\\$PATH" >> .bashrc
 
 # install nipype dependencies
-$HOME/anaconda/bin/conda update --yes conda
-$HOME/anaconda/bin/conda install --yes pip numpy scipy nose traits networkx
-$HOME/anaconda/bin/conda install --yes dateutil ipython-notebook matplotlib
-$HOME/anaconda/bin/pip install nibabel --use-mirrors
-$HOME/anaconda/bin/pip install https://github.com/RDFLib/rdflib/archive/master.zip
-$HOME/anaconda/bin/pip install https://github.com/satra/prov/archive/enh/rdf.zip
-$HOME/anaconda/bin/pip install https://github.com/nipy/nipype/archive/master.zip
+$HOME/miniconda/bin/conda update --yes conda
+$HOME/miniconda/bin/conda install --yes pip numpy scipy nose traits networkx
+$HOME/miniconda/bin/conda install --yes dateutil ipython-notebook matplotlib
+$HOME/miniconda/bin/pip install nibabel --use-mirrors
+$HOME/miniconda/bin/pip install https://github.com/RDFLib/rdflib/archive/master.zip
+$HOME/miniconda/bin/pip install https://github.com/satra/prov/archive/enh/rdf.zip
+$HOME/miniconda/bin/pip install https://github.com/nipy/nipype/archive/master.zip
 SCRIPT
 
 Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
@@ -42,7 +42,7 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
     engine_config.vm.box = "gridneuro"
     #engine_config.vm.box_url = "http://files.vagrantup.com/precise64.box"
     engine_config.vm.box_url = "https://dl.dropboxusercontent.com/u/363467/precise64_neuro.box"
-    engine_config.vm.network :forwarded_port, guest: 80, host: 8080
+    #engine_config.vm.network :forwarded_port, guest: 80, host: 8080
 
     #engine_config.vm.network :public_network, :bridge => 'en0: Wi-Fi (AirPort)'
     engine_config.vm.network :private_network, ip: "192.168.100.20"

nipype/info.py

@@ -104,6 +104,8 @@ def get_nipype_gitversion():
 NUMPY_MIN_VERSION = '1.3'
 SCIPY_MIN_VERSION = '0.7'
 TRAITS_MIN_VERSION = '4.0'
+DATEUTIL_MIN_VERSION = '1.0'
+NOSE_MIN_VERSION = '1.0'
 
 NAME                = 'nipype'
 MAINTAINER          = "nipype developers"
@@ -122,6 +124,7 @@ def get_nipype_gitversion():
 MICRO               = _version_micro
 ISRELEASE           = _version_extra == ''
 VERSION             = __version__
-REQUIRES            = ["nibabel (>=1.0)", "networkx (>=1.0)", "numpy (>=1.3)",
-                       "scipy (>=0.7)", "traits (>=4.0)"]
+REQUIRES            = ["nibabel>=1.0", "networkx>=1.0", "numpy>=1.3",
+                       "python-dateutil>1.0", "scipy>=0.7", "traits>=4.0",
+                       "nose>=1.0"]
 STATUS              = 'stable'

nipype/interfaces/afni/base.py

@@ -144,7 +144,7 @@ def set_default_output_type(cls, outputtype):
         else:
             raise AttributeError('Invalid AFNI outputtype: %s' % outputtype)
 
-    def _overload_extension(self, value):
+    def _overload_extension(self, value, name=None):
         path, base, _ = split_filename(value)
         return os.path.join(path, base + Info.outputtype_to_ext(self.inputs.outputtype))
 

nipype/interfaces/afni/preprocess.py

@@ -367,7 +367,7 @@ class AutoTcorrelate(AFNICommand):
     output_spec = AFNICommandOutputSpec
     _cmd = '3dAutoTcorrelate'
 
-    def _overload_extension(self, value):
+    def _overload_extension(self, value, name=None):
         path, base, ext = split_filename(value)
         if ext.lower() not in [".1d", ".nii.gz", ".nii"]:
             ext = ext + ".1D"
@@ -1924,7 +1924,7 @@ class AFNItoNIFTI(AFNICommand):
     input_spec = AFNItoNIFTIInputSpec
     output_spec = AFNICommandOutputSpec
 
-    def _overload_extension(self, value):
+    def _overload_extension(self, value, name=None):
         path, base, ext = split_filename(value)
         if ext.lower() not in [".1d", ".nii.gz", ".1D"]:
             ext = ext + ".nii"

nipype/interfaces/base.py

@@ -731,6 +731,7 @@ def _get_trait_desc(self, inputs, name, spec):
         desc = spec.desc
         xor = spec.xor
         requires = spec.requires
+        argstr = spec.argstr
 
         manhelpstr = ['\t%s' % name]
 
@@ -753,6 +754,17 @@ def _get_trait_desc(self, inputs, name, spec):
                                    initial_indent='\t\t',
                                    subsequent_indent='\t\t')
 
+        if argstr:
+            pos = spec.position
+            if pos is not None:
+                manhelpstr += wrap('flag: %s, position: %s' % (argstr, pos), 70,
+                                   initial_indent='\t\t',
+                                   subsequent_indent='\t\t')
+            else:
+                manhelpstr += wrap('flag: %s' % argstr, 70,
+                                   initial_indent='\t\t',
+                                   subsequent_indent='\t\t')
+
         if xor:
             line = '%s' % ', '.join(xor)
             manhelpstr += wrap(line, 70,
@@ -785,7 +797,7 @@ 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)
 
@@ -1480,13 +1492,13 @@ def _filename_from_source(self, name):
             _, _, ext = split_filename(retval)
             if trait_spec.keep_extension and ext:
                 return retval
-            return self._overload_extension(retval)
+            return self._overload_extension(retval, name)
         return retval
 
     def _gen_filename(self, name):
         raise NotImplementedError
 
-    def _overload_extension(self, value):
+    def _overload_extension(self, value, name=None):
         return value
 
     def _list_outputs(self):

nipype/interfaces/camino/__init__.py

@@ -5,10 +5,12 @@
 
 from .connectivity import Conmat
 from .convert import (Image2Voxel, FSL2Scheme, VtkStreamlines, ProcStreamlines,
-                      TractShredder, DT2NIfTI, NIfTIDT2Camino, AnalyzeHeader)
+                      TractShredder, DT2NIfTI, NIfTIDT2Camino, AnalyzeHeader,
+                      Shredder)
 from .dti import (DTIFit, ModelFit, DTLUTGen, PicoPDFs, Track, TrackPICo,
                   TrackBayesDirac, TrackDT, TrackBallStick, TrackBootstrap,
                   ComputeFractionalAnisotropy, ComputeMeanDiffusivity,
                   ComputeTensorTrace,  ComputeEigensystem, DTMetric)
 from .calib import (SFPICOCalibData, SFLUTGen)
-from .odf import (QBallMX, LinRecon, SFPeaks)
+from .odf import (QBallMX, LinRecon, SFPeaks, MESD)
+from .utils import ImageStats

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):
@@ -581,3 +612,54 @@ def _list_outputs(self):
     def _gen_outfilename(self):
         _, name , _ = split_filename(self.inputs.in_file)
         return name + ".hdr"
+
+class ShredderInputSpec(StdOutCommandLineInputSpec):
+    in_file = File(exists=True, argstr='< %s', mandatory=True, position=-2, desc='raw binary data file')
+
+    offset = traits.Int(argstr='%d', units='NA',
+        desc='initial offset of offset bytes', position=1)
+
+    chunksize = traits.Int(argstr='%d', units='NA',
+        desc='reads and outputs a chunk of chunksize bytes', position=2)
+
+    space = traits.Int(argstr='%d', units='NA',
+        desc='skips space bytes', position=3)
+
+class ShredderOutputSpec(TraitedSpec):
+    shredded = File(exists=True, desc='Shredded binary data file')
+
+class Shredder(StdOutCommandLine):
+    """
+    Extracts periodic chunks from a data stream.
+
+    Shredder makes an initial offset of offset bytes. It then reads and outputs
+    chunksize bytes, skips space bytes, and repeats until there is no more input.
+
+    If  the  chunksize  is  negative, chunks of size |chunksize| are read and the
+    byte ordering of each chunk is reversed. The whole chunk will be reversed, so
+    the chunk must be the same size as the data type, otherwise the order of the
+    values in the chunk, as well as their endianness, will be reversed.
+
+    Examples
+    --------
+
+    >>> import nipype.interfaces.camino as cam
+    >>> shred = cam.Shredder()
+    >>> shred.inputs.in_file = 'SubjectA.Bfloat'
+    >>> shred.inputs.offset = 0
+    >>> shred.inputs.chunksize = 1
+    >>> shred.inputs.space = 2
+    >>> shred.run()                  # doctest: +SKIP
+    """
+    _cmd = 'shredder'
+    input_spec=ShredderInputSpec
+    output_spec=ShredderOutputSpec
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['shredded_file'] = os.path.abspath(self._gen_outfilename())
+        return outputs
+
+    def _gen_outfilename(self):
+        _, name , _ = split_filename(self.inputs.in_file)
+        return name + "_shredded"