Adding changes on niftyreg from branch adding_niftyseg

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
@@ -64,7 +64,8 @@ def __init__(self, required_version=None, **inputs):
         _version = self.get_version()
         if _version:
             _version = _version.decode("utf-8")
-            if StrictVersion(_version) < StrictVersion(self._min_version):
+            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))
             if required_version is not None:
@@ -89,7 +90,7 @@ 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 """