Adding back base.py for NiftySegCommand because of version control on the software.

Author: byvernault

nipype/interfaces/niftyreg/base.py

@@ -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:

nipype/interfaces/niftyseg/base.py

@@ -0,0 +1,44 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+"""
+The niftyseg module provides classes for interfacing with `niftyseg
+<https://sourceforge.net/projects/niftyseg/>`_ command line tools.
+These are the base tools for working with niftyseg.
+EM Statistical Segmentation tool is found in niftyseg/em.py
+Fill lesions tool is found in niftyseg/lesions.py
+Mathematical operation tool is found in niftyseg/maths.py
+Patch Match tool is found in niftyseg/patchmatch.py
+Statistical operation tool is found in niftyseg/stats.py
+Label Fusion and CalcTopNcc tools are in niftyseg/steps.py
+Examples
+--------
+See the docstrings of the individual classes for examples.
+"""
+
+from nipype.interfaces.niftyreg.base import NiftyRegCommand, no_nifty_package
+import subprocess
+import warnings
+
+
+warn = warnings.warn
+warnings.filterwarnings('always', category=UserWarning)
+
+
+class NiftySegCommand(NiftyRegCommand):
+    """
+    Base support interface for NiftySeg commands.
+    """
+    _suffix = '_ns'
+    _min_version = None
+
+    def __init__(self, **inputs):
+        super(NiftySegCommand, self).__init__(**inputs)
+
+    def get_version(self):
+        if no_nifty_package(cmd=self.cmd):
+            return None
+        # exec_cmd = ''.join((self.cmd, ' --version'))
+        exec_cmd = 'seg_EM --version'
+        # Using seg_EM for version (E.G: seg_stats --version doesn't work)
+        return subprocess.check_output(exec_cmd, shell=True).strip('\n')

nipype/interfaces/niftyseg/em.py

@@ -20,7 +20,8 @@
 
 from ..base import (TraitedSpec, File, traits, CommandLineInputSpec,
                     InputMultiPath)
-from ..niftyreg.base import NiftyRegCommand, get_custom_path
+from .base import NiftySegCommand
+from ..niftyreg.base import get_custom_path
 
 
 class EMInputSpec(CommandLineInputSpec):
@@ -109,7 +110,7 @@ class EMOutputSpec(TraitedSpec):
     out_outlier_file = File(desc='Output outlierness image')
 
 
-class EM(NiftyRegCommand):
+class EM(NiftySegCommand):
     """Interface for executable seg_EM from NiftySeg platform.
 
     seg_EM is a general purpose intensity based image segmentation tool. In

nipype/interfaces/niftyseg/label_fusion.py

@@ -18,7 +18,8 @@
 
 from ..base import (TraitedSpec, File, traits, isdefined, CommandLineInputSpec,
                     NipypeInterfaceError)
-from ..niftyreg.base import get_custom_path, NiftyRegCommand
+from .base import NiftySegCommand
+from ..niftyreg.base import get_custom_path
 from ...utils.filemanip import load_json, save_json, split_filename
 
 
@@ -111,7 +112,7 @@ class LabelFusionOutput(TraitedSpec):
     out_file = File(exists=True, desc='image written after calculations')
 
 
-class LabelFusion(NiftyRegCommand):
+class LabelFusion(NiftySegCommand):
     """Interface for executable seg_LabelFusion from NiftySeg platform using
     type STEPS as classifier Fusion.
 
@@ -288,7 +289,7 @@ class CalcTopNCCOutputSpec(TraitedSpec):
     out_files = traits.Any(File(exists=True))
 
 
-class CalcTopNCC(NiftyRegCommand):
+class CalcTopNCC(NiftySegCommand):
     """Interface for executable seg_CalcTopNCC from NiftySeg platform.
 
     Examples

nipype/interfaces/niftyseg/lesions.py

@@ -21,7 +21,8 @@
 import warnings
 
 from ..base import TraitedSpec, File, traits, CommandLineInputSpec
-from ..niftyreg.base import NiftyRegCommand, get_custom_path
+from .base import NiftySegCommand
+from ..niftyreg.base import get_custom_path
 
 
 warn = warnings.warn
@@ -93,7 +94,7 @@ class FillLesionsOutputSpec(TraitedSpec):
     out_file = File(desc="Output segmentation")
 
 
-class FillLesions(NiftyRegCommand):
+class FillLesions(NiftySegCommand):
     """Interface for executable seg_FillLesions from NiftySeg platform.
 
     Fill all the masked lesions with WM intensity average.

nipype/interfaces/niftyseg/maths.py

@@ -22,7 +22,8 @@
 
 from ..base import (TraitedSpec, File, traits, isdefined, CommandLineInputSpec,
                     NipypeInterfaceError)
-from ..niftyreg.base import NiftyRegCommand, get_custom_path
+from .base import NiftySegCommand
+from ..niftyreg.base import get_custom_path
 from ...utils.filemanip import split_filename
 
 
@@ -53,7 +54,7 @@ class MathsOutput(TraitedSpec):
     out_file = File(desc='image written after calculations')
 
 
-class MathsCommand(NiftyRegCommand):
+class MathsCommand(NiftySegCommand):
     """
     Base Command Interface for seg_maths interfaces.
 

nipype/interfaces/niftyseg/patchmatch.py

@@ -15,7 +15,8 @@
 import warnings
 
 from ..base import TraitedSpec, File, traits, CommandLineInputSpec
-from ..niftyreg.base import NiftyRegCommand, get_custom_path
+from .base import NiftySegCommand
+from ..niftyreg.base import get_custom_path
 
 
 warn = warnings.warn
@@ -80,7 +81,7 @@ class PatchMatchOutputSpec(TraitedSpec):
     out_file = File(desc="Output segmentation")
 
 
-class PatchMatch(NiftyRegCommand):
+class PatchMatch(NiftySegCommand):
     """Interface for executable seg_PatchMatch from NiftySeg platform.
 
     The database file is a text file and in each line we have a template

nipype/interfaces/niftyseg/stats.py

@@ -15,7 +15,8 @@
 import numpy as np
 
 from ..base import TraitedSpec, File, traits, CommandLineInputSpec
-from ..niftyreg.base import NiftyRegCommand, get_custom_path
+from .base import NiftySegCommand
+from ..niftyreg.base import get_custom_path
 
 
 class StatsInput(CommandLineInputSpec):
@@ -45,7 +46,7 @@ class StatsOutput(TraitedSpec):
     output = traits.Array(desc='Output array from seg_stats')
 
 
-class StatsCommand(NiftyRegCommand):
+class StatsCommand(NiftySegCommand):
     """
     Base Command Interface for seg_stats interfaces.
 

nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py

@@ -0,0 +1,23 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..base import NiftySegCommand
+
+
+def test_NiftySegCommand_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = NiftySegCommand.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+

nipype/interfaces/niftyseg/tests/test_em_interfaces.py

@@ -3,8 +3,8 @@
 
 import pytest
 
-from nipype.interfaces.niftyreg import no_nifty_package
-from nipype.interfaces.niftyseg import get_custom_path, EM
+from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
+from nipype.interfaces.niftyseg import EM
 from nipype.testing import example_data
 
 
@@ -16,7 +16,8 @@ def test_seg_em():
     seg_em = EM()
 
     # Check if the command is properly defined
-    assert seg_em.cmd == get_custom_path('seg_EM')
+    cmd = get_custom_path('seg_EM', env_dir='NIFTYSEGDIR')
+    assert seg_em.cmd == cmd
 
     # test raising error with mandatory args absent
     with pytest.raises(ValueError):
@@ -30,7 +31,7 @@ def test_seg_em():
     cmd_tmp = '{cmd} -in {in_file} -nopriors 4 -bc_out {bc_out} -out \
 {out_file} -out_outlier {out_outlier}'
     expected_cmd = cmd_tmp.format(
-        cmd=get_custom_path('seg_EM'),
+        cmd=cmd,
         in_file=in_file,
         out_file='im1_em.nii.gz',
         bc_out='im1_bc_em.nii.gz',