removing base.py and using niftyreg base.py class/fct. Renaming functions as well

Author: byvernault

nipype/interfaces/niftyreg/__init__.py

@@ -9,7 +9,7 @@
 Top-level namespace for niftyreg.
 """
 
-from .base import no_niftyreg, get_custom_path
+from .base import no_nifty_package, get_custom_path
 from .reg import RegAladin, RegF3D
 from .regutils import (RegResample, RegJacobian, RegAverage, RegTools,
                        RegTransform, RegMeasure)

nipype/interfaces/niftyreg/base.py

@@ -30,11 +30,11 @@
 from ...utils.filemanip import split_filename
 
 
-def get_custom_path(command):
-    return os.path.join(os.getenv('NIFTYREGDIR', ''), command)
+def get_custom_path(command, env_dir='NIFTYREGDIR'):
+    return os.path.join(os.getenv(env_dir, ''), command)
 
 
-def no_niftyreg(cmd='reg_f3d'):
+def no_nifty_package(cmd='reg_f3d'):
     try:
         return shutil.which(cmd) is None
     except AttributeError:  # Python < 3.3
@@ -89,7 +89,7 @@ def check_version(self):
                 raise ValueError(err % (_version, self.required_version))
 
     def get_version(self):
-        if no_niftyreg(cmd=self.cmd):
+        if no_nifty_package(cmd=self.cmd):
             return None
         exec_cmd = ''.join((self.cmd, ' -v'))
         return subprocess.check_output(exec_cmd, shell=True).strip()

nipype/interfaces/niftyreg/tests/test_reg.py

@@ -4,13 +4,13 @@
 
 import pytest
 
-from nipype.interfaces.niftyreg import (no_niftyreg, get_custom_path,
+from nipype.interfaces.niftyreg import (no_nifty_package, get_custom_path,
                                         RegAladin, RegF3D)
 from nipype.testing import example_data
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_aladin'),
+    no_nifty_package(cmd='reg_aladin'),
     reason="niftyreg is not installed. reg_aladin not found.")
 def test_reg_aladin():
     """ tests for reg_aladin interface"""
@@ -48,7 +48,7 @@ def test_reg_aladin():
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_f3d'),
+    no_nifty_package(cmd='reg_f3d'),
     reason="niftyreg is not installed. reg_f3d not found.")
 def test_reg_f3d():
     """ tests for reg_f3d interface"""

nipype/interfaces/niftyreg/tests/test_regutils.py

@@ -2,7 +2,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
-from nipype.interfaces.niftyreg import (no_niftyreg, get_custom_path,
+from nipype.interfaces.niftyreg import (no_nifty_package, get_custom_path,
                                         RegAverage, RegResample, RegJacobian,
                                         RegTools, RegMeasure, RegTransform)
 from nipype.testing import example_data
@@ -11,7 +11,7 @@
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_resample'),
+    no_nifty_package(cmd='reg_resample'),
     reason="niftyreg is not installed. reg_resample not found.")
 def test_reg_resample_res():
     """ tests for reg_resample interface """
@@ -68,7 +68,7 @@ def test_reg_resample_res():
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_jacobian'),
+    no_nifty_package(cmd='reg_jacobian'),
     reason="niftyreg is not installed. reg_jacobian not found.")
 def test_reg_jacobian_jac():
     """ Test interface for RegJacobian """
@@ -132,7 +132,7 @@ def test_reg_jacobian_jac():
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_tools'),
+    no_nifty_package(cmd='reg_tools'),
     reason="niftyreg is not installed. reg_tools not found.")
 def test_reg_tools_mul():
     """ tests for reg_tools interface """
@@ -175,7 +175,7 @@ def test_reg_tools_mul():
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_average'),
+    no_nifty_package(cmd='reg_average'),
     reason="niftyreg is not installed. reg_average not found.")
 def test_reg_average():
     """ tests for reg_average interface """
@@ -318,7 +318,7 @@ def test_reg_average():
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_transform'),
+    no_nifty_package(cmd='reg_transform'),
     reason="niftyreg is not installed. reg_transform not found.")
 def test_reg_transform_def():
     """ tests for reg_transform interface """
@@ -427,7 +427,7 @@ def test_reg_transform_def():
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_measure'),
+    no_nifty_package(cmd='reg_measure'),
     reason="niftyreg is not installed. reg_measure not found.")
 def test_reg_measure():
     """ tests for reg_measure interface """

nipype/interfaces/niftyseg/__init__.py

@@ -8,7 +8,6 @@
 Top-level namespace for niftyseg.
 """
 
-from .base import no_niftyseg, get_custom_path
 from .em import EM
 from .label_fusion import LabelFusion, CalcTopNCC
 from .lesions import FillLesions

nipype/interfaces/niftyseg/base.py

@@ -20,7 +20,7 @@
 
 from ..base import (TraitedSpec, File, traits, CommandLineInputSpec,
                     InputMultiPath)
-from .base import NiftySegCommand, get_custom_path
+from ..niftyreg.base import NiftyRegCommand, get_custom_path
 
 
 class EMInputSpec(CommandLineInputSpec):
@@ -47,10 +47,9 @@ class EMInputSpec(CommandLineInputSpec):
                     desc='4D file containing the priors',
                     xor=['no_prior', 'priors'])
 
-    desc = 'List of priors filepaths.'
     priors = InputMultiPath(argstr='%s',
                             mandatory=True,
-                            desc=desc,
+                            desc='List of priors filepaths.',
                             xor=['no_prior', 'prior_4D'])
 
     # iterations
@@ -110,7 +109,7 @@ class EMOutputSpec(TraitedSpec):
     out_outlier_file = File(desc='Output outlierness image')
 
 
-class EM(NiftySegCommand):
+class EM(NiftyRegCommand):
     """Interface for executable seg_EM from NiftySeg platform.
 
     seg_EM is a general purpose intensity based image segmentation tool. In
@@ -132,7 +131,7 @@ class EM(NiftySegCommand):
 -out im1_em.nii.gz -out_outlier im1_outlier_em.nii.gz'
 
     """
-    _cmd = get_custom_path('seg_EM')
+    _cmd = get_custom_path('seg_EM', env_dir='NIFTYSEGDIR')
     _suffix = '_em'
     input_spec = EMInputSpec
     output_spec = EMOutputSpec

nipype/interfaces/niftyseg/em.py

@@ -18,7 +18,7 @@
 
 from ..base import (TraitedSpec, File, traits, isdefined, CommandLineInputSpec,
                     NipypeInterfaceError)
-from .base import NiftySegCommand, get_custom_path
+from ..niftyreg.base import get_custom_path, NiftyRegCommand
 from ...utils.filemanip import load_json, save_json, split_filename
 
 
@@ -111,7 +111,7 @@ class LabelFusionOutput(TraitedSpec):
     out_file = File(exists=True, desc='image written after calculations')
 
 
-class LabelFusion(NiftySegCommand):
+class LabelFusion(NiftyRegCommand):
     """Interface for executable seg_LabelFusion from NiftySeg platform using
     type STEPS as classifier Fusion.
 
@@ -151,7 +151,7 @@ class LabelFusion(NiftySegCommand):
 im1_steps.nii'
 
     """
-    _cmd = get_custom_path('seg_LabFusion')
+    _cmd = get_custom_path('seg_LabFusion', env_dir='NIFTYSEGDIR')
     input_spec = LabelFusionInput
     output_spec = LabelFusionOutput
     _suffix = '_label_fused'
@@ -197,7 +197,7 @@ def get_staple_args(self, ranking):
             return None
 
         if ranking == 'ALL':
-            return '-%s' % ranking
+            return '-ALL'
 
         if not isdefined(self.inputs.template_file):
             err = "LabelFusion requires a value for input 'tramplate_file' \
@@ -288,7 +288,7 @@ class CalcTopNCCOutputSpec(TraitedSpec):
     out_files = traits.Any(File(exists=True))
 
 
-class CalcTopNCC(NiftySegCommand):
+class CalcTopNCC(NiftyRegCommand):
     """Interface for executable seg_CalcTopNCC from NiftySeg platform.
 
     Examples
@@ -303,7 +303,7 @@ class CalcTopNCC(NiftySegCommand):
     'seg_CalcTopNCC -target im1.nii -templates 2 im2.nii im3.nii -n 1'
 
     """
-    _cmd = get_custom_path('seg_CalcTopNCC')
+    _cmd = get_custom_path('seg_CalcTopNCC', env_dir='NIFTYSEGDIR')
     _suffix = '_topNCC'
     input_spec = CalcTopNCCInputSpec
     output_spec = CalcTopNCCOutputSpec
@@ -312,7 +312,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
         outputs = self._outputs()
         # local caching for backward compatibility
         outfile = os.path.join(os.getcwd(), 'CalcTopNCC.json')
-        if runtime is None:
+        if runtime is None or not runtime.stdout:
             try:
                 out_files = load_json(outfile)['files']
             except IOError:

nipype/interfaces/niftyseg/label_fusion.py

@@ -21,7 +21,7 @@
 import warnings
 
 from ..base import TraitedSpec, File, traits, CommandLineInputSpec
-from .base import NiftySegCommand, get_custom_path
+from ..niftyreg.base import NiftyRegCommand, get_custom_path
 
 
 warn = warnings.warn
@@ -93,7 +93,7 @@ class FillLesionsOutputSpec(TraitedSpec):
     out_file = File(desc="Output segmentation")
 
 
-class FillLesions(NiftySegCommand):
+class FillLesions(NiftyRegCommand):
     """Interface for executable seg_FillLesions from NiftySeg platform.
 
     Fill all the masked lesions with WM intensity average.
@@ -112,6 +112,6 @@ class FillLesions(NiftySegCommand):
     'seg_FillLesions -i im1.nii -l im2.nii -o im1_lesions_filled.nii.gz'
 
     """
-    _cmd = get_custom_path('seg_FillLesions')
+    _cmd = get_custom_path('seg_FillLesions', env_dir='NIFTYSEGDIR')
     input_spec = FillLesionsInputSpec
     output_spec = FillLesionsOutputSpec

nipype/interfaces/niftyseg/lesions.py

@@ -22,7 +22,7 @@
 
 from ..base import (TraitedSpec, File, traits, isdefined, CommandLineInputSpec,
                     NipypeInterfaceError)
-from .base import NiftySegCommand, get_custom_path
+from ..niftyreg.base import NiftyRegCommand, get_custom_path
 from ...utils.filemanip import split_filename
 
 
@@ -40,10 +40,9 @@ class MathsInput(CommandLineInputSpec):
                     argstr='%s',
                     desc='image to write')
 
-    _dtypes = ['float', 'char', 'int', 'short', 'double', 'input']
-
     desc = 'datatype to use for output (default uses input type)'
-    output_datatype = traits.Enum(*_dtypes,
+    output_datatype = traits.Enum('float', 'char', 'int', 'short',
+                                  'double', 'input',
                                   position=-3,
                                   argstr='-odt %s',
                                   desc=desc)
@@ -54,7 +53,7 @@ class MathsOutput(TraitedSpec):
     out_file = File(desc='image written after calculations')
 
 
-class MathsCommand(NiftySegCommand):
+class MathsCommand(NiftyRegCommand):
     """
     Base Command Interface for seg_maths interfaces.
 
@@ -71,7 +70,7 @@ class MathsCommand(NiftySegCommand):
     into several 3D images, to estimating the maximum, minimum and average
     over all time-points, etc.
     """
-    _cmd = get_custom_path('seg_maths')
+    _cmd = get_custom_path('seg_maths', env_dir='NIFTYSEGDIR')
     input_spec = MathsInput
     output_spec = MathsOutput
     _suffix = '_maths'