Merge branch 'master' of https://github.com/nipy/nipype.git

Author: chrisgorgo

.travis.yml

@@ -11,12 +11,7 @@ before_install:
   # The next couple lines fix a crash with multiprocessing on Travis
   - sudo rm -rf /dev/shm
   - sudo ln -s /run/shm /dev/shm
-  - sudo apt-get update -qq
-  - sudo apt-get install lsb-release
-  - source /etc/lsb-release
-  - echo ${DISTRIB_CODENAME}
-  - wget -O- http://neuro.debian.net/lists/${DISTRIB_CODENAME}.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
-  - sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9
+  - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
   - sudo apt-get update -qq
   - sudo apt-get install -qq --no-install-recommends fsl afni
   - sudo apt-get install -qq fsl-atlases

CHANGES

@@ -39,6 +39,7 @@ Next release
 * ENH: arrange nodes by topological sort with disconnected subgraphs
 * ENH: uses the nidm iri namespace for uuids
 * ENH: remove old reporting webpage
+* ENH: Added support for Vagrant
 
 * API: 'name' is now a positional argument for Workflow, Node, and MapNode constructors
 * API: SPM now defaults to SPM8 or SPM12b job format

Vagrantfile

@@ -0,0 +1,61 @@
+VAGRANTFILE_API_VERSION = "2"
+
+$script = <<SCRIPT
+
+# Following section commented out as gridengine requires interactive
+# components
+# # Install neurodebian repo
+# bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
+#
+# # Install grid engine
+# sudo apt-get install -qq gridengine-master gridengine-exec gridengine-client gridengine-qmon
+# # Configure: http://wiki.unixh4cks.com/index.php/Setting_up_Sun_Grid_Engine_on_Ubuntu
+# sudo -u sgeadmin qconf -am vagrant
+# qconf -au vagrant users
+# qconf -as neuro
+# qconf -ahgrp @allhosts
+# qconf -aattr hostgroup hostlist neuro @allhosts
+# qconf -aq main.q
+# qconf -aattr queue hostlist @allhosts main.q
+# qconf -aattr queue slots "2, [neuro=3]" main.q
+
+# install anaconda
+wget http://repo.continuum.io/miniconda/Miniconda-2.2.2-Linux-x86_64.sh -O miniconda.sh
+chmod +x miniconda.sh
+./miniconda.sh -b
+echo "export PATH=$HOME/anaconda/bin:\\$PATH" >> .bashrc
+
+# install nipype dependencies
+$HOME/anaconda/bin/conda install --yes pip numpy scipy nose traits networkx
+$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
+SCRIPT
+
+Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
+
+  config.vm.define :engine do |engine_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 :public_network, :bridge => 'en0: Wi-Fi (AirPort)'
+    engine_config.vm.network :private_network, ip: "192.168.100.20"
+    engine_config.vm.hostname = 'neuro'
+    #engine_config.vm.synced_folder "../software", "/software"
+    #engine_config.vm.synced_folder "../data", "/data"
+
+    engine_config.vm.provider :virtualbox do |vb|
+      vb.customize ["modifyvm", :id, "--cpuexecutioncap", "50"]
+      vb.customize ["modifyvm", :id, "--ioapic", "on"]
+      vb.customize ["modifyvm", :id, "--memory", "4096"]
+      vb.customize ["modifyvm", :id, "--cpus", "4"]
+    end
+
+    engine_config.vm.provision "shell", :privileged => false, inline: $script
+  end
+end

doc/links_names.txt

@@ -15,6 +15,7 @@
 .. _nibabel: http://nipy.org/nibabel/
 .. _nipype: http://nipy.org/nipype/
 .. _ConnectomeViewer: http://www.connectomeviewer.org/viewer/
+.. _NeuroDebian: http://neuro.debian.net/
 
 .. Documentation tools
 .. _graphviz: http://www.graphviz.org/
@@ -73,6 +74,8 @@
 .. _pythonxy: http://www.pythonxy.com/
 .. _EPD: http://www.enthought.com/products/epd.php
 .. _Traits: http://code.enthought.com/projects/traits/
+.. _Anaconda: https://store.continuum.io/cshop/anaconda/
+.. _Canopy: https://www.enthought.com/products/canopy/
 
 .. Python imaging projects
 .. _PyMVPA: http://www.pymvpa.org
@@ -98,6 +101,9 @@
 .. _xcode: http://developer.apple.com/TOOLS/xcode
 .. _mingw: http://www.mingw.org
 .. _macports: http://www.macports.org/
+.. _Vagrant: http://www.vagrantup.com/
+.. _Docker: http://www.docker.io/
+.. _Virtualbox: https://www.virtualbox.org/
 
 .. Functional imaging labs
 .. _`functional imaging laboratory`: http://www.fil.ion.ucl.ac.uk

doc/quickstart.rst

@@ -11,6 +11,7 @@ Downloading and installing
    :maxdepth: 1
 
    users/install
+   users/vagrant
 
 Beginner's guide
 ================

doc/users/index.rst

@@ -11,6 +11,7 @@
    :maxdepth: 2
 
    install
+   vagrant
 
    interface_tutorial
    caching_tutorial

doc/users/install.rst

@@ -45,17 +45,12 @@ manager.
 Mac OS X
 ~~~~~~~~
 
-The easiest way to get nipype running on Mac OS X is to install EPD_ and then add
-nibabel and nipype by executing::
+The easiest way to get nipype running on Mac OS X is to install Anaconda_ or
+Canopy_ and then add nibabel and nipype by executing::
 
 	easy_install nibabel
 	easy_install nipype
 
-If you are running a 64 bit version of EPD, you will need to compile
-ETS. Instructions for a 64-bit boot mode are available:
-https://gist.github.com/845545
-
-
 From source
 ~~~~~~~~~~~
 
@@ -131,7 +126,7 @@ Dateutil 1.5 -
 
 .. note::
 
-    Full distributions such as pythonxy_ or EPD_ provide the above packages,
+    Full distributions such as Anaconda_ or Canopy_ provide the above packages,
     except Nibabel_.
 
 Strong Recommendations

doc/users/vagrant.rst

@@ -0,0 +1,52 @@
+.. _debug:
+
+======================
+Running Nipype in a VM
+======================
+
+.. tip::
+
+   Creating the Vagrant VM as described below requires an active internet
+   connection.
+
+Container technologies (Vagrant_, Docker_) allow creating and manipulating
+lightweight virtual environments. The Nipype_ source now contains a Vagrantfile
+to launch a Vagrant_ VM.
+
+Requirements:
+
+* Vagrant_
+* Virtualbox_
+
+After you have installed Vagrant and Virtualbox, you simply need to download the
+latest Nipype source and unzip/tar/compress it. Go into your terminal and switch
+to the nipype source directory. Make sure the Vagrantfile is in the directory.
+Now you can execute::
+
+  vagrant up
+
+This will launch and provision the virtual machine.
+
+The default virtual machine is built using Ubuntu Precise 64, linked to the
+NeuroDebian_ source repo and contains a 2 node Grid Engine for cluster
+execution.
+
+The machine has a default IP address of `192.168.100.20` . From the vagrant
+startup directory you can log into the machine using::
+
+  vagrant ssh
+
+Now you can install your favorite software using::
+
+  sudo apt-get install fsl afni
+
+Also note that the directory in which you call `vagrant up` will be mounted
+under `/vagrant` inside the virtual machine. You can also copy the Vagrantfile
+or modify it in order to mount a different directory/directories.
+
+Please read through Vagrant_ documentation on other features. The python
+environment is built using a `miniconda <http://repo.continuum.io/miniconda/>`_
+distribution. Hence `conda` can be used to do your python package management
+inside the VM.
+
+.. include:: ../links_names.txt

nipype/interfaces/afni/preprocess.py

@@ -19,7 +19,8 @@
 from nipype.utils.filemanip import fname_presuffix
 from .base import AFNICommand, AFNICommandInputSpec,\
     AFNICommandOutputSpec
-from nipype.interfaces.base import CommandLineInputSpec, CommandLine
+from nipype.interfaces.base import CommandLineInputSpec, CommandLine,\
+    OutputMultiPath
 
 warn = warnings.warn
 warnings.filterwarnings('always', category=UserWarning)
@@ -1443,7 +1444,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
         return outputs
 
 
-class ROIStatsInputSpec(AFNICommandInputSpec):
+class ROIStatsInputSpec(CommandLineInputSpec):
     in_file = File(desc='input file to 3dROIstats',
                    argstr='%s',
                    position=-1,
@@ -1465,12 +1466,18 @@ class ROIStatsInputSpec(AFNICommandInputSpec):
                         argstr='-quiet',
                         position=1)
 
+    terminal_output = traits.Enum('allatonce',
+                                  desc=('Control terminal output:'
+                                        '`allatonce` - waits till command is '
+                                        'finished to display output'),
+                                  nohash=True, mandatory=True, usedefault=True)
+
 
 class ROIStatsOutputSpec(TraitedSpec):
-    stats = File(desc='output', exists=True)
+    stats =  File(desc='output tab separated values file', exists=True)
 
 
-class ROIStats(AFNICommand):
+class ROIStats(CommandLine):
     """Display statistics over masked regions
 
     For complete details, see the `3dROIstats Documentation.
@@ -1492,37 +1499,13 @@ class ROIStats(AFNICommand):
     output_spec = ROIStatsOutputSpec
 
     def aggregate_outputs(self, runtime=None, needed_outputs=None):
-
         outputs = self._outputs()
+        output_filename = "roi_stats.csv"
+        f = open(output_filename, "w")
+        f.write(runtime.stdout)
+        f.close()
 
-        outfile = os.path.join(os.getcwd(), 'stat_result.json')
-
-        if runtime is None:
-            try:
-                stats = load_json(outfile)['stat']
-            except IOError:
-                return self.run().outputs
-        else:
-            stats = []
-            for line in runtime.stdout.split('\n'):
-                if line:
-                    values = line.split()
-                    if len(values) > 1:
-                        stats.append([float(val) for val in values])
-                    else:
-                        stats.extend([float(val) for val in values])
-
-            if len(stats) == 1:
-                stats = stats[0]
-            of = os.path.join(os.getcwd(), 'TS.1D')
-            f = open(of, 'w')
-
-            for st in stats:
-                f.write(str(st) + '\n')
-            f.close()
-            save_json(outfile, dict(stat=of))
-        outputs.stats = of
-
+        outputs.stats = os.path.abspath(output_filename)
         return outputs
 
 

nipype/interfaces/afni/tests/test_auto_ROIStats.py

@@ -5,21 +5,17 @@ def test_ROIStats_inputs():
     input_map = dict(ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    out_file=dict(name_source=['in_file'],
-    name_template='%s_afni',
-    argstr='-prefix %s',
-    ),
     args=dict(argstr='%s',
     ),
     mask=dict(position=3,
     argstr='-mask %s',
     ),
-    outputtype=dict(),
     quiet=dict(position=1,
     argstr='-quiet',
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,
+    usedefault=True,
     ),
     environ=dict(nohash=True,
     usedefault=True,