use nipype's which in nifty package

Author: oesteban

nipype/interfaces/base.py

@@ -1601,13 +1601,14 @@ def raise_exception(self, runtime):
     def _get_environ(self):
         return getattr(self.inputs, 'environ', {})
 
-    def version_from_command(self, flag='-v'):
-        cmdname = self.cmd.split()[0]
+    def version_from_command(self, flag='-v', cmd=None):
+        if cmd is None:
+            cmd = self.cmd.split()[0]
         env = dict(os.environ)
-        if which(cmdname, env):
+        if which(cmd, env):
             out_environ = self._get_environ()
             env.update(out_environ)
-            proc = sp.Popen(' '.join((cmdname, flag)),
+            proc = sp.Popen(' '.join((cmd, flag)),
                             shell=True,
                             env=env,
                             stdout=sp.PIPE,

nipype/interfaces/niftyfit/base.py

@@ -19,16 +19,11 @@
 """
 
 import os
-import warnings
 
 from ..base import CommandLine
 from ...utils.filemanip import split_filename
 
 
-warn = warnings.warn
-warnings.filterwarnings('always', category=UserWarning)
-
-
 class NiftyFitCommand(CommandLine):
     """
     Base support interface for NiftyFit commands.

nipype/interfaces/niftyfit/tests/test_asl.py

@@ -4,12 +4,18 @@
 
 import pytest
 
-from nipype.interfaces.niftyfit import FitAsl
-from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
-from nipype.testing import example_data
+from ....utils.filemanip import which
+from ....testing import example_data
+from ...niftyreg import get_custom_path
 
+from ..niftyfit import FitAsl
 
-@pytest.mark.skipif(no_nifty_package(cmd='fit_asl'),
+
+def no_nifty_tool(cmd=None):
+    return which(cmd) is None
+
+
+@pytest.mark.skipif(no_nifty_tool(cmd='fit_asl'),
                     reason="niftyfit is not installed")
 def test_fit_asl():
     """ Testing FitAsl interface."""

nipype/interfaces/niftyfit/tests/test_dwi.py

@@ -3,12 +3,18 @@
 
 import pytest
 
-from nipype.interfaces.niftyfit import FitDwi, DwiTool
-from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
-from nipype.testing import example_data
+from ....utils.filemanip import which
+from ....testing import example_data
+from ...niftyreg import get_custom_path
 
+from ..niftyfit import FitDwi, DwiTool
 
-@pytest.mark.skipif(no_nifty_package(cmd='fit_dwi'),
+
+def no_nifty_tool(cmd=None):
+    return which(cmd) is None
+
+
+@pytest.mark.skipif(no_nifty_tool(cmd='fit_dwi'),
                     reason="niftyfit is not installed")
 def test_fit_dwi():
     """ Testing FitDwi interface."""
@@ -56,7 +62,7 @@ def test_fit_dwi():
     assert fit_dwi.cmdline == expected_cmd
 
 
-@pytest.mark.skipif(no_nifty_package(cmd='dwi_tool'),
+@pytest.mark.skipif(no_nifty_tool(cmd='dwi_tool'),
                     reason="niftyfit is not installed")
 def test_dwi_tool():
     """ Testing DwiTool interface."""

nipype/interfaces/niftyfit/tests/test_qt1.py

@@ -4,12 +4,18 @@
 
 import pytest
 
-from nipype.interfaces.niftyfit import FitQt1
-from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
-from nipype.testing import example_data
+from ....utils.filemanip import which
+from ....testing import example_data
+from ...niftyreg import get_custom_path
 
+from ..niftyfit import FitQt1
 
-@pytest.mark.skipif(no_nifty_package(cmd='fit_qt1'),
+
+def no_nifty_tool(cmd=None):
+    return which(cmd) is None
+
+
+@pytest.mark.skipif(no_nifty_tool(cmd='fit_qt1'),
                     reason="niftyfit is not installed")
 def test_fit_qt1():
     """ Testing FitQt1 interface."""

nipype/interfaces/niftyreg/__init__.py

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

nipype/interfaces/niftyreg/base.py

@@ -22,28 +22,18 @@
 from builtins import property, super
 from distutils.version import StrictVersion
 import os
-import shutil
-import subprocess
-from warnings import warn
 
+from ... import logging
 from ..base import CommandLine, CommandLineInputSpec, traits, Undefined
 from ...utils.filemanip import split_filename
 
+iflogger = logging.getLogger('interface')
+
 
 def get_custom_path(command, env_dir='NIFTYREGDIR'):
     return os.path.join(os.getenv(env_dir, ''), command)
 
 
-def no_nifty_package(cmd='reg_f3d'):
-    try:
-        return shutil.which(cmd) is None
-    except AttributeError:  # Python < 3.3
-        return not any(
-            [os.path.isfile(os.path.join(path, cmd)) and
-             os.access(os.path.join(path, cmd), os.X_OK)
-             for path in os.environ["PATH"].split(os.pathsep)])
-
-
 class NiftyRegCommandInputSpec(CommandLineInputSpec):
     """Input Spec for niftyreg interfaces."""
     # Set the number of omp thread to use
@@ -65,18 +55,18 @@ 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()
+        _version = self.get_version_from_command()
         if _version:
             _version = _version.decode("utf-8")
             if self._min_version is not None and \
                StrictVersion(_version) < StrictVersion(self._min_version):
                 msg = 'A later version of Niftyreg is required (%s < %s)'
-                warn(msg % (_version, self._min_version))
+                iflogger.warning(msg, _version, self._min_version)
             if required_version is not None:
                 if StrictVersion(_version) != StrictVersion(required_version):
                     msg = 'The version of NiftyReg differs from the required'
                     msg += '(%s != %s)'
-                    warn(msg % (_version, self.required_version))
+                    iflogger.warning(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()
@@ -102,7 +92,7 @@ def _environ_update(self):
             self.inputs.omp_core_val = Undefined
 
     def check_version(self):
-        _version = self.get_version()
+        _version = self.get_version_from_command()
         if not _version:
             raise Exception('Niftyreg not found')
         # Decoding to string:
@@ -116,18 +106,12 @@ def check_version(self):
                 err += '(%s != %s)'
                 raise ValueError(err % (_version, self.required_version))
 
-    def get_version(self):
-        if no_nifty_package(cmd=self.cmd):
-            return None
-        exec_cmd = ''.join((self.cmd, ' -v'))
-        return subprocess.check_output(exec_cmd, shell=True).strip()
-
     @property
     def version(self):
-        return self.get_version()
+        return self.get_version_from_command()
 
     def exists(self):
-        return self.get_version() is not None
+        return self.get_version_from_command() is not None
 
     def _format_arg(self, name, spec, value):
         if name == 'omp_core_val':

nipype/interfaces/niftyreg/reg.py

@@ -20,17 +20,12 @@
                         absolute_import)
 from builtins import staticmethod
 import os
-import warnings
 
 from ..base import TraitedSpec, File, traits, isdefined
 from .base import get_custom_path, NiftyRegCommand, NiftyRegCommandInputSpec
 from ...utils.filemanip import split_filename
 
 
-warn = warnings.warn
-warnings.filterwarnings('always', category=UserWarning)
-
-
 class RegAladinInputSpec(NiftyRegCommandInputSpec):
     """ Input Spec for RegAladin. """
     # Input reference file

nipype/interfaces/niftyreg/regutils.py

@@ -18,18 +18,13 @@
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)
 from builtins import len, open, property, super
-import warnings
 import os
 
 from ..base import TraitedSpec, File, traits, isdefined
 from .base import get_custom_path, NiftyRegCommand, NiftyRegCommandInputSpec
 from ...utils.filemanip import split_filename
 
 
-warn = warnings.warn
-warnings.filterwarnings('always', category=UserWarning)
-
-
 class RegResampleInputSpec(NiftyRegCommandInputSpec):
     """ Input Spec for RegResample. """
     # Input reference file

nipype/interfaces/niftyreg/tests/test_reg.py

@@ -4,13 +4,18 @@
 
 import pytest
 
-from nipype.interfaces.niftyreg import (no_nifty_package, get_custom_path,
-                                        RegAladin, RegF3D)
-from nipype.testing import example_data
+from ....utils.filemanip import which
+from ....testing import example_data
+from ..niftyreg import (
+    get_custom_path, RegAladin, RegF3D)
+
+
+def no_nifty_tool(cmd=None):
+    return which(cmd) is None
 
 
 @pytest.mark.skipif(
-    no_nifty_package(cmd='reg_aladin'),
+    no_nifty_tool(cmd='reg_aladin'),
     reason="niftyreg is not installed. reg_aladin not found.")
 def test_reg_aladin():
     """ tests for reg_aladin interface"""
@@ -48,7 +53,7 @@ def test_reg_aladin():
 
 
 @pytest.mark.skipif(
-    no_nifty_package(cmd='reg_f3d'),
+    no_nifty_tool(cmd='reg_f3d'),
     reason="niftyreg is not installed. reg_f3d not found.")
 def test_reg_f3d():
     """ tests for reg_f3d interface"""