[FIX] Improve redirections of X

nipype/algorithms/mesh.py

@@ -78,6 +78,7 @@ class ComputeMeshWarp(BaseInterface):
 
  input_spec = ComputeMeshWarpInputSpec
  output_spec = ComputeMeshWarpOutputSpec
+ _redirect_x = True
 
  def _triangle_area(self, A, B, C):
  A = np.array(A)
@@ -221,6 +222,7 @@ class MeshWarpMaths(BaseInterface):
 
  input_spec = MeshWarpMathsInputSpec
  output_spec = MeshWarpMathsOutputSpec
+ _redirect_x = True
 
  def _run_interface(self, runtime):
  try:

nipype/interfaces/base.py

@@ -61,6 +61,17 @@ def _lock_files():
  ls = [p for p in ls if os.path.isfile(p)]
  return ls
 
+def _unlock_display(ndisplay):
+ lockf = os.path.join('/tmp', '.X%d-lock' % ndisplay)
+ try:
+ os.remove(lockf)
+ except:
+ return False
+
+ return True
+
+
+
 def _search_for_free_display():
  ls = [int(x.split('X')[1].split('-')[0]) for x in _lock_files()]
  min_display_num = 1000
@@ -946,6 +957,36 @@ def _check_version_requirements(self, trait_object, raise_exception=True):
  version, max_ver))
  return unavailable_traits
 
+ def _run_wrapper(self, runtime):
+ sysdisplay = os.getenv('DISPLAY')
+ if self._redirect_x:
+ try:
+ from xvfbwrapper import Xvfb
+ except ImportError:
+ iflogger.error('Xvfb wrapper could not be imported')
+ raise
+
+ vdisp = Xvfb(nolisten='tcp')
+ vdisp.start()
+ vdisp_num = vdisp.vdisplay_num
+
+ iflogger.info('Redirecting X to :%d' % vdisp_num)
+ runtime.environ['DISPLAY'] = ':%d' % vdisp_num
+
+ runtime = self._run_interface(runtime)
+
+ if self._redirect_x:
+ if sysdisplay is None:
+ os.unsetenv('DISPLAY')
+ else:
+ os.environ['DISPLAY'] = sysdisplay
+
+ iflogger.info('Freeing X :%d' % vdisp_num)
+ vdisp.stop()
+ _unlock_display(vdisp_num)
+
+ return runtime
+
  def _run_interface(self, runtime):
  """ Core function that executes interface
  """
@@ -982,34 +1023,7 @@ 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))
- wait_step = 0.2
- wait_time = 0
- while xvfb_proc.poll() is not None:
- if wait_time > config.get('execution', 'xvfb_max_wait'):
- raise Exception('Error: Xvfb did not start')
- time.sleep(wait_step) # give Xvfb time to start
- wait_time += wait_step
-
- runtime.environ['DISPLAY'] = ':%s' % vdisplay_num
-
- runtime = self._run_interface(runtime)
-
- if self._redirect_x:
- xvfb_proc.kill()
- xvfb_proc.wait()
-
+ runtime = self._run_wrapper(runtime)
  outputs = self.aggregate_outputs(runtime)
  runtime.endTime = dt.isoformat(dt.utcnow())
  timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)
@@ -1117,6 +1131,25 @@ def version(self):
  self.__class__.__name__)
  return self._version
 
+ def _exists_in_path(self, cmd, environ):
+ '''
+ Based on a code snippet from
+ http://orip.org/2009/08/python-checking-if-executable-exists-in.html
+ '''
+
+ if 'PATH' in environ:
+ input_environ = environ.get("PATH")
+ else:
+ input_environ = os.environ.get("PATH", "")
+ extensions = os.environ.get("PATHEXT", "").split(os.pathsep)
+ for directory in input_environ.split(os.pathsep):
+ base = os.path.join(directory, cmd)
+ options = [base] + [(base + ext) for ext in extensions]
+ for filename in options:
+ if os.path.exists(filename):
+ return True, filename
+ return False, None
+
 
 class Stream(object):
  """Function to capture stdout and stderr streams with timestamps
@@ -1169,32 +1202,39 @@ def _read(self, drain):
  self._lastidx = len(self._rows)
 
 
-def run_command(runtime, output=None, timeout=0.01):
+def run_command(runtime, output=None, timeout=0.01, redirect_x=False):
  """Run a command, read stdout and stderr, prefix with timestamp.
 
  The returned runtime contains a merged stdout+stderr log with timestamps
  """
  PIPE = subprocess.PIPE
 
+ cmdline = runtime.cmdline
+ if redirect_x:
+ exist_xvfb, _ = self._exists_in_path('xvfb-run', runtime.environ)
+ if not exist_val:
+ raise RuntimeError('Xvfb was not found, X redirection aborted')
+ cmdline = 'xvfb-run -a ' + cmdline
+
  if output == 'file':
  errfile = os.path.join(runtime.cwd, 'stderr.nipype')
  outfile = os.path.join(runtime.cwd, 'stdout.nipype')
  stderr = open(errfile, 'wt')
  stdout = open(outfile, 'wt')
 
- proc = subprocess.Popen(runtime.cmdline,
+ proc = subprocess.Popen(cmdline,
  stdout=stdout,
  stderr=stderr,
  shell=True,
  cwd=runtime.cwd,
  env=runtime.environ)
  else:
- proc = subprocess.Popen(runtime.cmdline,
-  stdout=PIPE,
-  stderr=PIPE,
-  shell=True,
-  cwd=runtime.cwd,
-  env=runtime.environ)
+ proc = subprocess.Popen(cmdline,
+ stdout=PIPE,
+ stderr=PIPE,
+ shell=True,
+ cwd=runtime.cwd,
+ env=runtime.environ)
  result = {}
  errfile = os.path.join(runtime.cwd, 'stderr.nipype')
  outfile = os.path.join(runtime.cwd, 'stdout.nipype')
@@ -1425,6 +1465,10 @@ def version_from_command(self, flag='-v'):
  o, e = proc.communicate()
  return o
 
+ def _run_wrapper(self, runtime):
+ runtime = self._run_interface(runtime)
+ return runtime
+
  def _run_interface(self, runtime, correct_return_codes=[0]):
  """Execute command via subprocess
 
@@ -1452,32 +1496,14 @@ def _run_interface(self, runtime, correct_return_codes=[0]):
  setattr(runtime, 'command_path', cmd_path)
  setattr(runtime, 'dependencies', get_dependencies(executable_name,
  runtime.environ))
- runtime = run_command(runtime, output=self.inputs.terminal_output)
+ runtime = run_command(runtime, output=self.inputs.terminal_output,
+ redirect_x=self._redirect_x)
  if runtime.returncode is None or \
  runtime.returncode not in correct_return_codes:
  self.raise_exception(runtime)
 
  return runtime
 
- def _exists_in_path(self, cmd, environ):
- '''
- Based on a code snippet from
- http://orip.org/2009/08/python-checking-if-executable-exists-in.html
- '''
-
- if 'PATH' in environ:
- input_environ = environ.get("PATH")
- else:
- input_environ = os.environ.get("PATH", "")
- extensions = os.environ.get("PATHEXT", "").split(os.pathsep)
- for directory in input_environ.split(os.pathsep):
- base = os.path.join(directory, cmd)
- options = [base] + [(base + ext) for ext in extensions]
- for filename in options:
- if os.path.exists(filename):
- return True, filename
- return False, None
-
  def _format_arg(self, name, trait_spec, value):
  """A helper function for _parse_inputs
 

requirements.txt

@@ -5,3 +5,4 @@ traits>=4.0
 python-dateutil>=1.5
 nibabel>=1.0
 nose>=1.0
+xvfbwrapper>=0.2