Merge branch 'enh/mipav'

Conflicts:
	CHANGES

Author: chrisgorgo

CHANGES

@@ -1,6 +1,7 @@
 Next Release
 ============
 
+* 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
@@ -28,7 +29,8 @@ Next Release
 * 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 nested lists 
+* ENH: MapNode now supports flattening of nested lists 
+* ENH: Support for headless mode using Xvfb
 * FIX: MRTrix tracking algorithms were ignoring mask parameters.
 * FIX: FNIRT registration pathway and associated OpenFMRI example script
 * FIX: spm12b compatibility for Model estimate

doc/devel/interface_specs.rst

@@ -404,6 +404,9 @@ If you used genfile:
 
 And optionally:
 
+* ``_redirect_x``: If set to True it will make Nipype start Xvfb before running the interface and redirect X output to it. This is useful for
+commandlines that spawn a graphical user interface.
+
 * ``_format_arg(name, spec, value)``: For extra formatting of the input values before passing them to generic ``_parse_inputs()`` method.
 
 For example this is the class definition for Flirt, minus the docstring::

doc/users/index.rst

@@ -36,6 +36,7 @@
    model_specification
    saving_workflows
    spmmcr
+   mipav
 
 
 

examples/smri_cbs_skullstripping.py

@@ -0,0 +1,27 @@
+import nipype.interfaces.io as nio           # Data i/o
+import nipype.interfaces.utility as util     # utility
+import nipype.pipeline.engine as pe          # pypeline engine
+import nipype.interfaces.camino as camino
+import nipype.interfaces.fsl as fsl
+import nipype.interfaces.camino2trackvis as cam2trk
+import nipype.algorithms.misc as misc
+import os  
+from nipype.interfaces.mipav.developer import JistIntensityMp2rageMasking, MedicAlgorithmSPECTRE2010
+
+wf = pe.Workflow("skullstripping")
+
+mask = pe.Node(JistIntensityMp2rageMasking(), name="masking")
+mask.inputs.inSecond = "/Users/filo/7t_trt/niftis/sub001/session_1/MP2RAGE_INV2.nii.gz"
+mask.inputs.inQuantitative = "/Users/filo/7t_trt/niftis/sub001/session_1/MP2RAGE_UNI.nii.gz"
+mask.inputs.inT1weighted = "/Users/filo/7t_trt/niftis/sub001/session_1/MP2RAGE_T1.nii.gz"
+mask.inputs.outMasked = True
+mask.inputs.outMasked2 = True
+mask.inputs.outSignal = True
+mask.inputs.outSignal2 = True
+
+skullstrip = pe.Node(MedicAlgorithmSPECTRE2010(), name="skullstrip")
+skullstrip.inputs.outStripped = True
+skullstrip.inputs.xDefaultMem = 6000
+
+wf.connect(mask, 'outMasked', skullstrip, 'inInput')
+wf.run()

nipype/interfaces/base.py

@@ -38,6 +38,7 @@
 from ..utils.provenance import write_provenance
 from .. import config, logging, LooseVersion
 from .. import __version__
+import random, time, fnmatch
 
 nipype_version = LooseVersion(__version__)
 
@@ -46,6 +47,25 @@
 
 __docformat__ = 'restructuredtext'
 
+def _lock_files():
+    tmpdir = '/tmp'
+    pattern = '.X*-lock'
+    names = fnmatch.filter(os.listdir(tmpdir), pattern)
+    ls = [os.path.join(tmpdir, child) for child in names]
+    ls = [p for p in ls if os.path.isfile(p)]
+    return ls
+
+def _search_for_free_display():
+    ls = [int(x.split('X')[1].split('-')[0]) for x in _lock_files()]
+    min_display_num = 1000
+    if len(ls):
+        display_num = max(min_display_num, max(ls) + 1)
+    else:
+        display_num = min_display_num
+    random.seed()
+    display_num += random.randint(0, 100)
+    return display_num
+
 
 def load_template(name):
     """Load a template from the script_templates directory
@@ -701,6 +721,7 @@ class BaseInterface(Interface):
     input_spec = BaseInterfaceInputSpec
     _version = None
     _additional_metadata = []
+    _redirect_x = False
 
     def __init__(self, **inputs):
         if not self.input_spec:
@@ -956,7 +977,30 @@ def run(self, **inputs):
                         hostname=getfqdn(),
                         version=self.version)
         try:
+            if self._redirect_x:
+                exist_val, _ = self._exists_in_path('Xvfb',
+                                                    runtime.environ)
+                if not exist_val:
+                    raise IOError("Xvfb could not be found on host %s" %
+                                  (runtime.hostname))
+                else:
+                    vdisplay_num = _search_for_free_display()
+                    xvfb_cmd = ['Xvfb', ':%d' % vdisplay_num]
+                    xvfb_proc = subprocess.Popen(xvfb_cmd,
+                                                 stdout=open(os.devnull),
+                                                 stderr=open(os.devnull))
+                    time.sleep(0.2)  # give Xvfb time to start
+                    if xvfb_proc.poll() is not None:
+                        raise Exception('Error: Xvfb did not start')
+                    old_displaynum = os.environ['DISPLAY']
+                    runtime.environ['DISPLAY'] = ':%s' % vdisplay_num
+    
             runtime = self._run_interface(runtime)
+            
+            if self._redirect_x:
+                xvfb_proc.kill()
+                xvfb_proc.wait()
+            
             outputs = self.aggregate_outputs(runtime)
             runtime.endTime = dt.isoformat(dt.utcnow())
             timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)
@@ -1344,11 +1388,12 @@ def help(cls, returnhelp=False):
 
     def _get_environ(self):
         out_environ = {}
-        try:
-            display_var = config.get('execution', 'display_variable')
-            out_environ = {'DISPLAY': display_var}
-        except NoOptionError:
-            pass
+        if not self._redirect_x:
+            try:
+                display_var = config.get('execution', 'display_variable')
+                out_environ = {'DISPLAY': display_var}
+            except NoOptionError:
+                pass
         iflogger.debug(out_environ)
         if isdefined(self.inputs.environ):
             out_environ.update(self.inputs.environ)

nipype/interfaces/mipav/__init__.py

@@ -0,0 +1 @@
+from developer import JistLaminarVolumetricLayering, JistBrainMgdmSegmentation, JistLaminarProfileGeometry, JistLaminarProfileCalculator, MedicAlgorithmN3, JistLaminarROIAveraging, MedicAlgorithmLesionToads, JistBrainMp2rageSkullStripping, JistCortexSurfaceMeshInflation, RandomVol, MedicAlgorithmImageCalculator, JistBrainMp2rageDuraEstimation, JistLaminarProfileSampling, MedicAlgorithmMipavReorient, MedicAlgorithmSPECTRE2010, JistBrainPartialVolumeFilter, JistIntensityMp2rageMasking, MedicAlgorithmThresholdToBinaryMask