RF: CMTK with LibraryBaseInterface

Author: effigies

nipype/interfaces/cmtk/base.py

@@ -0,0 +1,33 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+""" Base interface for cmtk """
+
+from ..base import LibraryBaseInterface
+from ...utils.misc import package_check
+
+
+class CFFBaseInterface(LibraryBaseInterface):
+    _pkg = 'cfflib'
+
+
+# Originally set in convert, nbs, nx, parcellation
+# Set here to be imported, in case anybody depends on its presence
+# Remove in 2.0
+have_cmp = True
+try:
+    package_check('cmp')
+except ImportError:
+    have_cmp = False
+
+have_cfflib = True
+try:
+    package_check('cfflib')
+except ImportError:
+    have_cfflib = False
+
+have_cv = True
+try:
+    package_check('cviewer')
+except ImportError:
+    have_cv = False

nipype/interfaces/cmtk/convert.py

@@ -8,18 +8,10 @@
 import string
 import networkx as nx
 
-from ...utils.misc import package_check
 from ...utils.filemanip import split_filename
-from ..base import (BaseInterface, BaseInterfaceInputSpec, traits, File,
+from ..base import (BaseInterfaceInputSpec, traits, File,
                     TraitedSpec, InputMultiPath, isdefined)
-
-have_cfflib = True
-try:
-    package_check('cfflib')
-except Exception as e:
-    have_cfflib = False
-else:
-    import cfflib as cf
+from .base import CFFBaseInterface, have_cfflib
 
 
 class CFFConverterInputSpec(BaseInterfaceInputSpec):
@@ -67,7 +59,7 @@ class CFFConverterOutputSpec(TraitedSpec):
     connectome_file = File(exists=True, desc='Output connectome file')
 
 
-class CFFConverter(BaseInterface):
+class CFFConverter(CFFBaseInterface):
     """
     Creates a Connectome File Format (CFF) file from input networks, surfaces, volumes, tracts, etcetera....
 
@@ -87,6 +79,7 @@ class CFFConverter(BaseInterface):
     output_spec = CFFConverterOutputSpec
 
     def _run_interface(self, runtime):
+        import cfflib as cf
         a = cf.connectome()
 
         if isdefined(self.inputs.title):
@@ -232,7 +225,7 @@ class MergeCNetworksOutputSpec(TraitedSpec):
         exists=True, desc='Output CFF file with all the networks added')
 
 
-class MergeCNetworks(BaseInterface):
+class MergeCNetworks(CFFBaseInterface):
     """ Merges networks from multiple CFF files into one new CFF file.
 
     Example
@@ -248,6 +241,7 @@ class MergeCNetworks(BaseInterface):
     output_spec = MergeCNetworksOutputSpec
 
     def _run_interface(self, runtime):
+        import cfflib as cf
         extracted_networks = []
 
         for i, con in enumerate(self.inputs.in_files):

nipype/interfaces/cmtk/nbs.py

@@ -10,19 +10,11 @@
 import networkx as nx
 
 from ... import logging
-from ...utils.misc import package_check
-from ..base import (BaseInterface, BaseInterfaceInputSpec, traits, File,
+from ..base import (LibraryBaseInterface, BaseInterfaceInputSpec, traits, File,
                     TraitedSpec, InputMultiPath, OutputMultiPath, isdefined)
+from .base import have_cv
 iflogger = logging.getLogger('interface')
 
-have_cv = True
-try:
-    package_check('cviewer')
-except Exception as e:
-    have_cv = False
-else:
-    import cviewer.libs.pyconto.groupstatistics.nbs as nbs
-
 
 def ntwks_to_matrices(in_files, edge_key):
     first = nx.read_gpickle(in_files[0])
@@ -92,7 +84,7 @@ class NetworkBasedStatisticOutputSpec(TraitedSpec):
         desc='Output network with edges identified by the NBS')
 
 
-class NetworkBasedStatistic(BaseInterface):
+class NetworkBasedStatistic(LibraryBaseInterface):
     """
     Calculates and outputs the average network given a set of input NetworkX gpickle files
 
@@ -111,11 +103,10 @@ class NetworkBasedStatistic(BaseInterface):
     """
     input_spec = NetworkBasedStatisticInputSpec
     output_spec = NetworkBasedStatisticOutputSpec
+    _pkg = 'cviewer'
 
     def _run_interface(self, runtime):
-
-        if not have_cv:
-            raise ImportError("cviewer library is not available")
+        from cviewer.libs.pyconto.groupstatistics import nbs
 
         THRESH = self.inputs.threshold
         K = self.inputs.number_of_permutations

nipype/interfaces/cmtk/nx.py

@@ -14,20 +14,12 @@
 
 from ... import logging
 from ...utils.filemanip import split_filename
-from ...utils.misc import package_check
 from ..base import (BaseInterface, BaseInterfaceInputSpec, traits, File,
                     TraitedSpec, InputMultiPath, OutputMultiPath, isdefined)
+from .base import have_cmp
 
 iflogger = logging.getLogger('interface')
 
-have_cmp = True
-try:
-    package_check('cmp')
-except Exception as e:
-    have_cmp = False
-else:
-    import cmp
-
 
 def read_unknown_ntwk(ntwk):
     if not isinstance(ntwk, nx.classes.graph.Graph):

nipype/interfaces/cmtk/parcellation.py

@@ -8,29 +8,21 @@
 import os
 import os.path as op
 import shutil
-import warnings
 
 import numpy as np
 import nibabel as nb
 import networkx as nx
 
 from ... import logging
-from ...utils.misc import package_check
 from ..base import (BaseInterface, BaseInterfaceInputSpec, traits, File,
                     TraitedSpec, Directory, isdefined)
+from .base import have_cmp
 iflogger = logging.getLogger('interface')
 
-have_cmp = True
-try:
-    package_check('cmp')
-except Exception as e:
-    have_cmp = False
-else:
-    import cmp
-    from cmp.util import runCmd
-
 
 def create_annot_label(subject_id, subjects_dir, fs_dir, parcellation_name):
+    import cmp
+    from cmp.util import runCmd
     iflogger.info("Create the cortical labels necessary for our ROIs")
     iflogger.info("=================================================")
     fs_label_dir = op.join(op.join(subjects_dir, subject_id), 'label')
@@ -174,6 +166,8 @@ def create_annot_label(subject_id, subjects_dir, fs_dir, parcellation_name):
 def create_roi(subject_id, subjects_dir, fs_dir, parcellation_name, dilation):
     """ Creates the ROI_%s.nii.gz files using the given parcellation information
     from networks. Iteratively create volume. """
+    import cmp
+    from cmp.util import runCmd
     iflogger.info("Create the ROIs:")
     output_dir = op.abspath(op.curdir)
     fs_dir = op.join(subjects_dir, subject_id)
@@ -306,6 +300,8 @@ def create_roi(subject_id, subjects_dir, fs_dir, parcellation_name, dilation):
 
 
 def create_wm_mask(subject_id, subjects_dir, fs_dir, parcellation_name):
+    import cmp
+    import scipy.ndimage.morphology as nd
     iflogger.info("Create white matter mask")
     fs_dir = op.join(subjects_dir, subject_id)
     cmp_config = cmp.configuration.PipelineConfiguration()
@@ -328,11 +324,6 @@ def create_wm_mask(subject_id, subjects_dir, fs_dir, parcellation_name):
     aseg = nb.load(op.join(fs_dir, 'mri', 'aseg.nii.gz'))
     asegd = aseg.get_data()
 
-    try:
-        import scipy.ndimage.morphology as nd
-    except ImportError:
-        raise Exception('Need scipy for binary erosion of white matter mask')
-
     # need binary erosion function
     imerode = nd.binary_erosion
 
@@ -438,6 +429,7 @@ def create_wm_mask(subject_id, subjects_dir, fs_dir, parcellation_name):
 
 def crop_and_move_datasets(subject_id, subjects_dir, fs_dir, parcellation_name,
                            out_roi_file, dilation):
+    from cmp.util import runCmd
     fs_dir = op.join(subjects_dir, subject_id)
     cmp_config = cmp.configuration.PipelineConfiguration()
     cmp_config.parcellation_scheme = "Lausanne2008"
@@ -549,7 +541,7 @@ class ParcellateOutputSpec(TraitedSpec):
     )
 
 
-class Parcellate(BaseInterface):
+class Parcellate(LibraryBaseInterface):
     """Subdivides segmented ROI file into smaller subregions
 
     This interface implements the same procedure as in the ConnectomeMapper's
@@ -571,6 +563,8 @@ class Parcellate(BaseInterface):
 
     input_spec = ParcellateInputSpec
     output_spec = ParcellateOutputSpec
+    _pkg = 'cmp'
+    imports = ('scipy', )
 
     def _run_interface(self, runtime):
         if self.inputs.subjects_dir: