Added a mechanism for running interfaces that require X without having

one through Xvfb.

Author: chrisgorgo

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 +977,25 @@ def run(self, **inputs):
                         hostname=getfqdn(),
                         version=self.version)
         try:
+            if self._redirect_x:
+                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']
+                os.environ['DISPLAY'] = ':%s' % vdisplay_num
+    
             runtime = self._run_interface(runtime)
+            
+            if self._redirect_x:
+                xvfb_proc.kill()
+                xvfb_proc.wait()
+                os.environ['DISPLAY'] = old_displaynum
+            
             outputs = self.aggregate_outputs(runtime)
             runtime.endTime = dt.isoformat(dt.utcnow())
             timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)
@@ -1344,11 +1383,12 @@ 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/developer.py

@@ -7,7 +7,7 @@
 
 
 class MedicAlgorithmSPECTRE2010InputSpec(CommandLineInputSpec):
-    maxMemoryUsage = traits.Int(desc="Maximum Memory Allowed (in MegaBytes). Increase or decrease this depending on java virtual machine heap size requirements.", argstr="-xDefaultMem %d")
+    maxMemoryUsage = traits.Int(desc="Maximum Memory Allowed (in MegaBytes). Increase or decrease this depending on java virtual machine heap size requirements.", argstr="--maxMemoryUsage %d")
     inInput = File(desc="Input volume to be skullstripped.", exists=True, argstr="--inInput %s")
     inAtlas = File(desc="SPECTRE atlas description file. A text file enumerating atlas files and landmarks.", exists=True, argstr="--inAtlas %s")
     inInitial = traits.Int(desc="Erosion of the inital mask, which is based on the probability mask and the classification., The initial mask is ouput as the d0 volume at the conclusion of SPECTRE.", argstr="--inInitial %d")
@@ -93,6 +93,7 @@ class MedicAlgorithmSPECTRE2010(SEMLikeCommandLine):
     output_spec = MedicAlgorithmSPECTRE2010OutputSpec
     _cmd = "java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010 "
     _outputs_filenames = {'outd0':'outd0.nii','outOriginal':'outOriginal.nii','outMask':'outMask.nii','outSplitHalves':'outSplitHalves.nii','outMidsagittal':'outMidsagittal.nii','outPrior':'outPrior.nii','outFANTASM':'outFANTASM.nii','outSegmentation':'outSegmentation.nii','outStripped':'outStripped.nii'}
+    _redirect_x = True
 
 
 class JistIntensityMp2rageMaskingInputSpec(CommandLineInputSpec):
@@ -133,3 +134,4 @@ class JistIntensityMp2rageMasking(SEMLikeCommandLine):
     output_spec = JistIntensityMp2rageMaskingOutputSpec
     _cmd = "java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.intensity.JistIntensityMp2rageMasking "
     _outputs_filenames = {'outSignal2':'outSignal2.nii','outSignal':'outSignal.nii','outMasked2':'outMasked2.nii','outMasked':'outMasked.nii'}
+    _redirect_x = True

nipype/interfaces/mipav/generate_classes.py

@@ -127,7 +127,7 @@
     modules_list = modules_from_julia
 
     ## SlicerExecutionModel compliant tools that are usually statically built, and don't need the Slicer3 --launcher
-    generate_all_classes(modules_list=modules_list,launcher=["java edu.jhu.ece.iacl.jist.cli.run" ])
+    generate_all_classes(modules_list=modules_list,launcher=["java edu.jhu.ece.iacl.jist.cli.run" ], redirect_x = True)
     ## Tools compliant with SlicerExecutionModel called from the Slicer environment (for shared lib compatibility)
     #launcher = ['/home/raid3/gorgolewski/software/slicer/Slicer', '--launch']
     #generate_all_classes(modules_list=modules_list, launcher=launcher)

nipype/interfaces/slicer/generate_classes.py

@@ -101,7 +101,7 @@ def configuration(parent_package='',top_path=None):
             f.close()
 
 
-def generate_all_classes(modules_list=[], launcher=[]):
+def generate_all_classes(modules_list=[], launcher=[], redirect_x = False):
     """ modules_list contains all the SEM compliant tools that should have wrappers created for them.
         launcher containtains the command line prefix wrapper arugments needed to prepare
         a proper environment for each of the modules.
@@ -111,7 +111,7 @@ def generate_all_classes(modules_list=[], launcher=[]):
         print("=" * 80)
         print("Generating Definition for module {0}".format(module))
         print("^" * 80)
-        package, code, module = generate_class(module, launcher)
+        package, code, module = generate_class(module, launcher, redirect_x = redirect_x)
         cur_package = all_code
         module_name = package.strip().split(" ")[0].split(".")[-1]
         for package in package.strip().split(" ")[0].split(".")[:-1]:
@@ -126,7 +126,7 @@ def generate_all_classes(modules_list=[], launcher=[]):
     crawl_code_struct(all_code, os.getcwd())
 
 
-def generate_class(module, launcher, strip_module_name_prefix=True):
+def generate_class(module, launcher, strip_module_name_prefix=True, redirect_x = False):
     dom = grab_xml(module, launcher)
     if strip_module_name_prefix:
         module_name = module.split(".")[-1]
@@ -293,6 +293,8 @@ def generate_class(module, launcher, strip_module_name_prefix=True):
     output_spec = %module_name%OutputSpec
     _cmd = "%launcher% %name% "
     %output_filenames_code%\n"""
+    template += "    _redirect_x = True\n"
+    
 
     main_class = template.replace('%class_str%', class_string).replace("%module_name%", module_name).replace("%name%", module).replace("%output_filenames_code%", output_filenames_code).replace("%launcher%", " ".join(launcher))