Fixing the base interface _run_interface function for NiftyRegCommand

nipype/interfaces/niftyreg/base.py

@@ -26,7 +26,7 @@
 import subprocess
 from warnings import warn
 
-from ..base import CommandLine, isdefined, CommandLineInputSpec, traits
+from ..base import CommandLine, CommandLineInputSpec, traits, Undefined
 from ...utils.filemanip import split_filename
 
 
@@ -47,8 +47,9 @@ def no_nifty_package(cmd='reg_f3d'):
 class NiftyRegCommandInputSpec(CommandLineInputSpec):
  """Input Spec for niftyreg interfaces."""
  # Set the number of omp thread to use
- omp_core_val = traits.Int(desc='Number of openmp thread to use',
- argstr='-omp %i')
+ omp_core_val = traits.Int(int(os.environ.get('OMP_NUM_THREADS', '1')),
+ desc='Number of openmp thread to use',
+ argstr='-omp %i', usedefault=True)
 
 
 class NiftyRegCommand(CommandLine):
@@ -58,7 +59,10 @@ class NiftyRegCommand(CommandLine):
  _suffix = '_nr'
  _min_version = '1.5.30'
 
+ input_spec = NiftyRegCommandInputSpec
+
  def __init__(self, required_version=None, **inputs):
+ self.num_threads = 1
  super(NiftyRegCommand, self).__init__(**inputs)
  self.required_version = required_version
  _version = self.get_version()
@@ -73,6 +77,29 @@ def __init__(self, required_version=None, **inputs):
  msg = 'The version of NiftyReg differs from the required'
  msg += '(%s != %s)'
  warn(msg % (_version, self.required_version))
+ self.inputs.on_trait_change(self._omp_update, 'omp_core_val')
+ self.inputs.on_trait_change(self._environ_update, 'environ')
+ self._omp_update()
+
+ def _omp_update(self):
+ if self.inputs.omp_core_val:
+ self.inputs.environ['OMP_NUM_THREADS'] = \
+ str(self.inputs.omp_core_val)
+ self.num_threads = self.inputs.omp_core_val
+ else:
+ if 'OMP_NUM_THREADS' in self.inputs.environ:
+ del self.inputs.environ['OMP_NUM_THREADS']
+ self.num_threads = 1
+
+ def _environ_update(self):
+ if self.inputs.environ:
+ if 'OMP_NUM_THREADS' in self.inputs.environ:
+ self.inputs.omp_core_val = \
+ int(self.inputs.environ['OMP_NUM_THREADS'])
+ else:
+ self.inputs.omp_core_val = Undefined
+ else:
+ self.inputs.omp_core_val = Undefined
 
  def check_version(self):
  _version = self.get_version()
@@ -102,13 +129,6 @@ def version(self):
  def exists(self):
  return self.get_version() is not None
 
- def _run_interface(self, runtime):
- # Update num threads estimate from OMP_NUM_THREADS env var
- # Default to 1 if not set
- if not isdefined(self.inputs.environ['OMP_NUM_THREADS']):
- self.inputs.environ['OMP_NUM_THREADS'] = self.num_threads
- return super(NiftyRegCommand, self)._run_interface(runtime)
-
  def _format_arg(self, name, spec, value):
  if name == 'omp_core_val':
  self.numthreads = value

nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py

@@ -12,6 +12,9 @@ def test_NiftyRegCommand_inputs():
  ignore_exception=dict(nohash=True,
  usedefault=True,
  ),
+ omp_core_val=dict(argstr='-omp %i',
+ usedefault=True,
+ ),
  terminal_output=dict(nohash=True,
  ),
  )

nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py

@@ -46,6 +46,7 @@ def test_RegAladin_inputs():
  nosym_flag=dict(argstr='-noSym',
  ),
  omp_core_val=dict(argstr='-omp %i',
+ usedefault=True,
  ),
  platform_val=dict(argstr='-platf %i',
  ),

nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py

@@ -43,6 +43,7 @@ def test_RegAverage_inputs():
  usedefault=True,
  ),
  omp_core_val=dict(argstr='-omp %i',
+ usedefault=True,
  ),
  out_file=dict(argstr='%s',
  genfile=True,

nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py

@@ -76,6 +76,7 @@ def test_RegF3D_inputs():
  noz_flag=dict(argstr='-noz',
  ),
  omp_core_val=dict(argstr='-omp %i',
+ usedefault=True,
  ),
  pad_val=dict(argstr='-pad %f',
  ),

nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py

@@ -13,6 +13,7 @@ def test_RegJacobian_inputs():
  usedefault=True,
  ),
  omp_core_val=dict(argstr='-omp %i',
+ usedefault=True,
  ),
  out_file=dict(argstr='%s',
  name_source=['trans_file'],

nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py

@@ -19,6 +19,7 @@ def test_RegMeasure_inputs():
  mandatory=True,
  ),
  omp_core_val=dict(argstr='-omp %i',
+ usedefault=True,
  ),
  out_file=dict(argstr='-out %s',
  name_source=['flo_file'],

nipype/interfaces/niftyreg/tests/test_auto_RegResample.py

@@ -18,6 +18,7 @@ def test_RegResample_inputs():
  inter_val=dict(argstr='-inter %d',
  ),
  omp_core_val=dict(argstr='-omp %i',
+ usedefault=True,
  ),
  out_file=dict(argstr='%s',
  name_source=['flo_file'],

nipype/interfaces/niftyreg/tests/test_auto_RegTools.py

@@ -34,6 +34,7 @@ def test_RegTools_inputs():
  noscl_flag=dict(argstr='-noscl',
  ),
  omp_core_val=dict(argstr='-omp %i',
+ usedefault=True,
  ),
  out_file=dict(argstr='-out %s',
  name_source=['in_file'],

nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py

@@ -57,6 +57,7 @@ def test_RegTransform_inputs():
  xor=['def_input', 'disp_input', 'flow_input', 'comp_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', 'half_input', 'aff_2_rig_input', 'flirt_2_nr_input'],
  ),
  omp_core_val=dict(argstr='-omp %i',
+ usedefault=True,
  ),
  out_file=dict(argstr='%s',
  genfile=True,

nipype/interfaces/niftyreg/tests/test_regutils.py

@@ -190,6 +190,7 @@ def test_reg_average():
  two_file = example_data('im2.nii')
  three_file = example_data('im3.nii')
  nr_average.inputs.avg_files = [one_file, two_file, three_file]
+ nr_average.inputs.omp_core_val = 1
  generated_cmd = nr_average.cmdline
 
  # Read the reg_average_cmd
@@ -198,10 +199,10 @@ def test_reg_average():
  argv = f_obj.read()
  os.remove(reg_average_cmd)
 
- expected_argv = '%s %s -avg %s %s %s' % (get_custom_path('reg_average'),
-  os.path.join(os.getcwd(),
-   'avg_out.nii.gz'),
-  one_file, two_file, three_file)
+ expected_argv = '%s %s -avg %s %s %s -omp 1' % (
+ get_custom_path('reg_average'),
+ os.path.join(os.getcwd(), 'avg_out.nii.gz'),
+ one_file, two_file, three_file)
 
  assert argv.decode('utf-8') == expected_argv
 
@@ -217,6 +218,7 @@ def test_reg_average():
  two_file = example_data('ants_Affine.txt')
  three_file = example_data('elastix.txt')
  nr_average_2.inputs.avg_files = [one_file, two_file, three_file]
+ nr_average_2.inputs.omp_core_val = 1
  generated_cmd = nr_average_2.cmdline
 
  # Read the reg_average_cmd
@@ -225,10 +227,10 @@ def test_reg_average():
  argv = f_obj.read()
  os.remove(reg_average_cmd)
 
- expected_argv = '%s %s -avg %s %s %s' % (get_custom_path('reg_average'),
-  os.path.join(os.getcwd(),
-   'avg_out.txt'),
-  one_file, two_file, three_file)
+ expected_argv = '%s %s -avg %s %s %s -omp 1' % (
+ get_custom_path('reg_average'),
+ os.path.join(os.getcwd(), 'avg_out.txt'),
+ one_file, two_file, three_file)
 
  assert argv.decode('utf-8') == expected_argv
 
@@ -238,6 +240,7 @@ def test_reg_average():
  two_file = example_data('ants_Affine.txt')
  three_file = example_data('elastix.txt')
  nr_average_3.inputs.avg_lts_files = [one_file, two_file, three_file]
+ nr_average_3.inputs.omp_core_val = 1
  generated_cmd = nr_average_3.cmdline
 
  # Read the reg_average_cmd
@@ -246,7 +249,7 @@ def test_reg_average():
  argv = f_obj.read()
  os.remove(reg_average_cmd)
 
- expected_argv = ('%s %s -avg_lts %s %s %s'
+ expected_argv = ('%s %s -avg_lts %s %s %s -omp 1'
  % (get_custom_path('reg_average'),
  os.path.join(os.getcwd(), 'avg_out.txt'),
  one_file, two_file, three_file))
@@ -266,6 +269,7 @@ def test_reg_average():
  trans2_file, two_file,
  trans3_file, three_file]
  nr_average_4.inputs.avg_ref_file = ref_file
+ nr_average_4.inputs.omp_core_val = 1
  generated_cmd = nr_average_4.cmdline
 
  # Read the reg_average_cmd
@@ -274,12 +278,12 @@ def test_reg_average():
  argv = f_obj.read()
  os.remove(reg_average_cmd)
 
- expected_argv = ('%s %s -avg_tran %s %s %s %s %s %s %s'
+ expected_argv = ('%s %s -avg_tran %s -omp 1 %s %s %s %s %s %s'
  % (get_custom_path('reg_average'),
  os.path.join(os.getcwd(), 'avg_out.nii.gz'),
  ref_file, trans1_file, one_file, trans2_file, two_file,
  trans3_file, three_file))
-
+ 
  assert argv.decode('utf-8') == expected_argv
 
  # Test Reg Average: demean3
@@ -298,6 +302,7 @@ def test_reg_average():
  aff2_file, trans2_file, two_file,
  aff3_file, trans3_file, three_file]
  nr_average_5.inputs.demean3_ref_file = ref_file
+ nr_average_5.inputs.omp_core_val = 1
  generated_cmd = nr_average_5.cmdline
 
  # Read the reg_average_cmd
@@ -306,7 +311,7 @@ def test_reg_average():
  argv = f_obj.read()
  os.remove(reg_average_cmd)
 
- expected_argv = ('%s %s -demean3 %s %s %s %s %s %s %s %s %s %s'
+ expected_argv = ('%s %s -demean3 %s -omp 1 %s %s %s %s %s %s %s %s %s'
  % (get_custom_path('reg_average'),
  os.path.join(os.getcwd(), 'avg_out.nii.gz'),
  ref_file,

nipype/interfaces/niftyseg/base.py

@@ -16,7 +16,8 @@
 See the docstrings of the individual classes for examples.
 """
 
-from nipype.interfaces.niftyreg.base import NiftyRegCommand, no_nifty_package
+from nipype.interfaces.niftyreg.base import no_nifty_package
+from nipype.interfaces.niftyfit.base import NiftyFitCommand
 import subprocess
 import warnings
 
@@ -25,7 +26,7 @@
 warnings.filterwarnings('always', category=UserWarning)
 
 
-class NiftySegCommand(NiftyRegCommand):
+class NiftySegCommand(NiftyFitCommand):
  """
  Base support interface for NiftySeg commands.
  """