Update SPM interfaces to use the new PackageInfo

Author: oesteban

nipype/interfaces/freesurfer/tests/test_FSSurfaceCommand.py

@@ -29,9 +29,11 @@ def test_FSSurfaceCommand_inputs():
 
 
 @pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed")
-def test_associated_file():
+def test_associated_file(tmpdir):
     fssrc = FreeSurferSource(subjects_dir=fs.Info.subjectsdir(),
                              subject_id='fsaverage', hemi='lh')
+    fssrc.base_dir = tmpdir.strpath
+    fssrc.resource_monitor = False
 
     fsavginfo = fssrc.run().outputs.get()
 

nipype/interfaces/spm/base.py

@@ -29,8 +29,11 @@
 # Local imports
 from ... import logging
 from ...utils import spm_docs as sd, NUMPY_MMAP
-from ..base import (BaseInterface, traits, isdefined, InputMultiPath,
-                    BaseInterfaceInputSpec, Directory, Undefined, ImageFile)
+from ..base import (
+    BaseInterface, traits, isdefined, InputMultiPath,
+    BaseInterfaceInputSpec, Directory, Undefined,
+    ImageFile, PackageInfo
+)
 from ..matlab import MatlabCommand
 from ...external.due import due, Doi, BibTeX
 
@@ -123,12 +126,34 @@ def scans_for_fnames(fnames, keep4d=False, separate_sessions=False):
     return flist
 
 
-class Info(object):
+class Info(PackageInfo):
     """Handles SPM version information
     """
-    @staticmethod
-    def version(matlab_cmd=None, paths=None, use_mcr=None):
-        """Returns the path to the SPM directory in the Matlab path
+    _path = None
+    _name = None
+
+    @classmethod
+    def path(klass, matlab_cmd=None, paths=None, use_mcr=None):
+        if klass._path:
+            return klass._path
+        return klass.getinfo(matlab_cmd, paths, use_mcr)['path']
+
+    @classmethod
+    def version(klass, matlab_cmd=None, paths=None, use_mcr=None):
+        if klass._version:
+            return klass._version
+        return klass.getinfo(matlab_cmd, paths, use_mcr)['release']
+
+    @classmethod
+    def name(klass, matlab_cmd=None, paths=None, use_mcr=None):
+        if klass._name:
+            return klass._name
+        return klass.getinfo(matlab_cmd, paths, use_mcr)['name']
+
+    @classmethod
+    def getinfo(klass, matlab_cmd=None, paths=None, use_mcr=None):
+        """
+        Returns the path to the SPM directory in the Matlab path
         If path not found, returns None.
 
         Parameters
@@ -152,6 +177,13 @@ def version(matlab_cmd=None, paths=None, use_mcr=None):
             returns None of path not found
         """
 
+        if klass._name and klass._path and klass._version:
+            return {
+                'name': klass._name,
+                'path': klass._path,
+                'release': klass._version
+            }
+
         use_mcr = use_mcr or 'FORCE_SPMMCR' in os.environ
         matlab_cmd = ((use_mcr and os.getenv('SPMMCRCMD')) or
                       os.getenv('MATLABCMD') or
@@ -184,13 +216,17 @@ def version(matlab_cmd=None, paths=None, use_mcr=None):
             # No Matlab -- no spm
             logger.debug('%s', e)
             return None
-        else:
-            out = sd._strip_header(out.runtime.stdout)
-            out_dict = {}
-            for part in out.split('|'):
-                key, val = part.split(':')
-                out_dict[key] = val
-            return out_dict
+
+        out = sd._strip_header(out.runtime.stdout)
+        out_dict = {}
+        for part in out.split('|'):
+            key, val = part.split(':')
+            out_dict[key] = val
+
+        klass._version = out_dict['release']
+        klass._path = out_dict['path']
+        klass._name = out_dict['name']
+        return out_dict
 
 
 def no_spm():
@@ -288,13 +324,15 @@ def _matlab_cmd_update(self):
 
     @property
     def version(self):
-        version_dict = Info.version(matlab_cmd=self.inputs.matlab_cmd,
-                                    paths=self.inputs.paths,
-                                    use_mcr=self.inputs.use_mcr)
-        if version_dict:
-            return '.'.join((version_dict['name'].split('SPM')[-1],
-                             version_dict['release']))
-        return version_dict
+        info_dict = Info.getinfo(
+            matlab_cmd=self.inputs.matlab_cmd,
+            paths=self.inputs.paths,
+            use_mcr=self.inputs.use_mcr
+        )
+        if info_dict:
+            return '%s.%s' % (
+                info_dict['name'].split('SPM')[-1],
+                info_dict['release'])
 
     @property
     def jobtype(self):

nipype/interfaces/spm/tests/test_base.py

@@ -16,12 +16,8 @@
 from nipype.interfaces.spm.base import SPMCommandInputSpec
 from nipype.interfaces.base import traits
 
-try:
-    matlab_cmd = os.environ['MATLABCMD']
-except:
-    matlab_cmd = 'matlab'
-
-mlab.MatlabCommand.set_default_matlab_cmd(matlab_cmd)
+mlab.MatlabCommand.set_default_matlab_cmd(
+    os.getenv('MATLABCMD', 'matlab'))
 
 
 def test_scan_for_fnames(create_files_in_directory):
@@ -35,10 +31,10 @@ def test_scan_for_fnames(create_files_in_directory):
 if not save_time:
     @pytest.mark.skipif(no_spm(), reason="spm is not installed")
     def test_spm_path():
-        spm_path = spm.Info.version()['path']
+        spm_path = spm.Info.path()
         if spm_path is not None:
             assert isinstance(spm_path, (str, bytes))
-            assert 'spm' in spm_path
+            assert 'spm' in spm_path.lower()
 
 
 def test_use_mfile():

nipype/interfaces/spm/tests/test_model.py

@@ -6,12 +6,8 @@
 import nipype.interfaces.spm.model as spm
 import nipype.interfaces.matlab as mlab
 
-try:
-    matlab_cmd = os.environ['MATLABCMD']
-except:
-    matlab_cmd = 'matlab'
-
-mlab.MatlabCommand.set_default_matlab_cmd(matlab_cmd)
+mlab.MatlabCommand.set_default_matlab_cmd(
+    os.getenv('MATLABCMD', 'matlab'))
 
 
 def test_level1design():

nipype/interfaces/spm/tests/test_preprocess.py

@@ -10,12 +10,8 @@
 from nipype.interfaces.spm import no_spm
 import nipype.interfaces.matlab as mlab
 
-try:
-    matlab_cmd = os.environ['MATLABCMD']
-except:
-    matlab_cmd = 'matlab'
-
-mlab.MatlabCommand.set_default_matlab_cmd(matlab_cmd)
+mlab.MatlabCommand.set_default_matlab_cmd(
+    os.getenv('MATLABCMD', 'matlab'))
 
 
 def test_slicetiming():
@@ -88,7 +84,7 @@ def test_normalize12_list_outputs(create_files_in_directory):
 
 @pytest.mark.skipif(no_spm(), reason="spm is not installed")
 def test_segment():
-    if spm.Info.version()['name'] == "SPM12":
+    if spm.Info.name() == "SPM12":
         assert spm.Segment()._jobtype == 'tools'
         assert spm.Segment()._jobname == 'oldseg'
     else:
@@ -98,7 +94,7 @@ def test_segment():
 
 @pytest.mark.skipif(no_spm(), reason="spm is not installed")
 def test_newsegment():
-    if spm.Info.version()['name'] == "SPM12":
+    if spm.Info.name() == "SPM12":
         assert spm.NewSegment()._jobtype == 'spatial'
         assert spm.NewSegment()._jobname == 'preproc'
     else:

nipype/workflows/fmri/spm/preprocess.py

@@ -8,7 +8,6 @@
 from ....interfaces import spm as spm
 from ....interfaces import utility as niu
 from ....pipeline import engine as pe
-from ....interfaces.matlab import no_matlab
 from ...smri.freesurfer.utils import create_getmask_flow
 
 from .... import logging
@@ -141,7 +140,8 @@ def create_vbm_preproc(name='vbmpreproc'):
 
     >>> preproc = create_vbm_preproc()
     >>> preproc.inputs.inputspec.fwhm = 8
-    >>> preproc.inputs.inputspec.structural_files = [os.path.abspath('s1.nii'), os.path.abspath('s3.nii')]
+    >>> preproc.inputs.inputspec.structural_files = [
+    ...     os.path.abspath('s1.nii'), os.path.abspath('s3.nii')]
     >>> preproc.inputs.inputspec.template_prefix = 'Template'
     >>> preproc.run() # doctest: +SKIP
 
@@ -185,7 +185,9 @@ def getclass1images(class_images):
             class1images.extend(session[0])
         return class1images
 
-    workflow.connect(dartel_template, ('segment.native_class_images', getclass1images), norm2mni, 'apply_to_files')
+    workflow.connect(
+        dartel_template, ('segment.native_class_images', getclass1images),
+        norm2mni, 'apply_to_files')
     workflow.connect(inputnode, 'fwhm', norm2mni, 'fwhm')
 
     def compute_icv(class_images):
@@ -217,10 +219,11 @@ def compute_icv(class_images):
                                                        "icv"
                                                        ]),
                          name="outputspec")
-    workflow.connect([(dartel_template, outputnode, [('outputspec.template_file', 'template_file')]),
-                      (norm2mni, outputnode, [("normalized_files", "normalized_files")]),
-                      (calc_icv, outputnode, [("icv", "icv")]),
-                      ])
+    workflow.connect([
+        (dartel_template, outputnode, [('outputspec.template_file', 'template_file')]),
+        (norm2mni, outputnode, [("normalized_files", "normalized_files")]),
+        (calc_icv, outputnode, [("icv", "icv")]),
+    ])
 
     return workflow
 
@@ -233,7 +236,8 @@ def create_DARTEL_template(name='dartel_template'):
     -------
 
     >>> preproc = create_DARTEL_template()
-    >>> preproc.inputs.inputspec.structural_files = [os.path.abspath('s1.nii'), os.path.abspath('s3.nii')]
+    >>> preproc.inputs.inputspec.structural_files = [
+    ...     os.path.abspath('s1.nii'), os.path.abspath('s3.nii')]
     >>> preproc.inputs.inputspec.template_prefix = 'Template'
     >>> preproc.run() # doctest: +SKIP
 
@@ -259,24 +263,34 @@ def create_DARTEL_template(name='dartel_template'):
                          name='segment')
     workflow.connect(inputnode, 'structural_files', segment, 'channel_files')
 
-    version = spm.Info.version()
-    if version:
-        spm_path = version['path']
-        if version['name'] == 'SPM8':
-            tissue1 = ((os.path.join(spm_path, 'toolbox/Seg/TPM.nii'), 1), 2, (True, True), (False, False))
-            tissue2 = ((os.path.join(spm_path, 'toolbox/Seg/TPM.nii'), 2), 2, (True, True), (False, False))
-            tissue3 = ((os.path.join(spm_path, 'toolbox/Seg/TPM.nii'), 3), 2, (True, False), (False, False))
-            tissue4 = ((os.path.join(spm_path, 'toolbox/Seg/TPM.nii'), 4), 3, (False, False), (False, False))
-            tissue5 = ((os.path.join(spm_path, 'toolbox/Seg/TPM.nii'), 5), 4, (False, False), (False, False))
-            tissue6 = ((os.path.join(spm_path, 'toolbox/Seg/TPM.nii'), 6), 2, (False, False), (False, False))
-        elif version['name'] == 'SPM12':
-            spm_path = version['path']
+    spm_info = spm.Info.getinfo()
+    if spm_info:
+        spm_path = spm_info['path']
+        if spm_info['name'] == 'SPM8':
+            tissue1 = ((os.path.join(spm_path, 'toolbox/Seg/TPM.nii'), 1),
+                       2, (True, True), (False, False))
+            tissue2 = ((os.path.join(spm_path, 'toolbox/Seg/TPM.nii'), 2),
+                       2, (True, True), (False, False))
+            tissue3 = ((os.path.join(spm_path, 'toolbox/Seg/TPM.nii'), 3),
+                       2, (True, False), (False, False))
+            tissue4 = ((os.path.join(spm_path, 'toolbox/Seg/TPM.nii'), 4),
+                       3, (False, False), (False, False))
+            tissue5 = ((os.path.join(spm_path, 'toolbox/Seg/TPM.nii'), 5),
+                       4, (False, False), (False, False))
+            tissue6 = ((os.path.join(spm_path, 'toolbox/Seg/TPM.nii'), 6),
+                       2, (False, False), (False, False))
+        elif spm_info['name'] == 'SPM12':
+            spm_path = spm_info['path']
             tissue1 = ((os.path.join(spm_path, 'tpm/TPM.nii'), 1), 1, (True, True), (False, False))
             tissue2 = ((os.path.join(spm_path, 'tpm/TPM.nii'), 2), 1, (True, True), (False, False))
-            tissue3 = ((os.path.join(spm_path, 'tpm/TPM.nii'), 3), 2, (True, False), (False, False))
-            tissue4 = ((os.path.join(spm_path, 'tpm/TPM.nii'), 4), 3, (False, False), (False, False))
-            tissue5 = ((os.path.join(spm_path, 'tpm/TPM.nii'), 5), 4, (False, False), (False, False))
-            tissue6 = ((os.path.join(spm_path, 'tpm/TPM.nii'), 6), 2, (False, False), (False, False))
+            tissue3 = ((os.path.join(spm_path, 'tpm/TPM.nii'), 3),
+                       2, (True, False), (False, False))
+            tissue4 = ((os.path.join(spm_path, 'tpm/TPM.nii'), 4),
+                       3, (False, False), (False, False))
+            tissue5 = ((os.path.join(spm_path, 'tpm/TPM.nii'), 5),
+                       4, (False, False), (False, False))
+            tissue6 = ((os.path.join(spm_path, 'tpm/TPM.nii'), 6),
+                       2, (False, False), (False, False))
         else:
             logger.critical('Unsupported version of SPM')