Merge pull request #1304 from carlohamalainen/carlo-minc-interface

ENH: Interfaces for MINC tools.

Author: satra

CHANGES

@@ -10,7 +10,7 @@ Next release
 * ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/1231)
 * API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
 * ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
-
+* ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
 
 Release 0.11.0 (September 15, 2015)
 ============

nipype/interfaces/minc/__init__.py

@@ -0,0 +1,42 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""The minc module provides classes for interfacing with the `MINC
+<http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC>`_ command line tools.  This
+module was written to work with MINC version 2.2.00.
+
+Author: Carlo Hamalainen <[email protected]>
+        http://carlo-hamalainen.net
+"""
+
+
+from .base import (Info)
+
+
+from .minc import (Average,
+                   BBox,
+                   Beast,
+                   BestLinReg,
+                   BigAverage,
+                   Blob,
+                   Blur,
+                   Calc,
+                   Convert,
+                   Copy,
+                   Dump,
+                   Extract,
+                   Gennlxfm,
+                   Math,
+                   NlpFit,
+                   Norm,
+                   Pik,
+                   Resample,
+                   Reshape,
+                   ToEcat,
+                   ToRaw,
+                   Volcentre,
+                   Voliso,
+                   Volpad,
+                   VolSymm,
+                   XfmAvg,
+                   XfmConcat,
+                   XfmInvert, )

nipype/interfaces/minc/base.py

@@ -0,0 +1,142 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""The minc module provides classes for interfacing with the `MINC
+<http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC>`_ command line tools.  This
+module was written to work with MINC version 2.2.00.
+
+Author: Carlo Hamalainen <[email protected]>
+        http://carlo-hamalainen.net
+"""
+
+from ..base import (
+    TraitedSpec,
+    CommandLineInputSpec,
+    CommandLine,
+    StdOutCommandLineInputSpec,
+    StdOutCommandLine,
+    File,
+    Directory,
+    InputMultiPath,
+    OutputMultiPath,
+    traits,
+    isdefined,
+)
+
+import glob
+import os
+import os.path
+import re
+
+import warnings
+warn = warnings.warn
+warnings.filterwarnings('always', category=UserWarning)
+
+
+def check_minc():
+    """Returns True if and only if MINC is installed.'
+    """
+
+    return Info.version() is not None
+
+
+def no_minc():
+    """Returns True if and only if MINC is *not* installed.
+    """
+    return not check_minc()
+
+
+class Info(object):
+    """Handle MINC version information.
+
+    version refers to the version of MINC on the system
+    """
+
+    @staticmethod
+    def version():
+        """Check for minc version on the system
+
+        Parameters
+        ----------
+        None
+
+        Returns
+        -------
+        version : dict
+           Version number as dict or None if MINC not found
+
+        """
+        try:
+            clout = CommandLine(command='mincinfo',
+                                args='-version',
+                                terminal_output='allatonce').run()
+        except IOError:
+            return None
+
+        out = clout.runtime.stdout
+
+        def read_program_version(s):
+            if 'program' in s:
+                return s.split(':')[1].strip()
+            return None
+
+        def read_libminc_version(s):
+            if 'libminc' in s:
+                return s.split(':')[1].strip()
+            return None
+
+        def read_netcdf_version(s):
+            if 'netcdf' in s:
+                return ' '.join(s.split(':')[1:]).strip()
+            return None
+
+        def read_hdf5_version(s):
+            if 'HDF5' in s:
+                return s.split(':')[1].strip()
+            return None
+
+        versions = {'minc': None,
+                    'libminc': None,
+                    'netcdf': None,
+                    'hdf5': None, }
+
+        for l in out.split('\n'):
+            for (name, f) in [('minc', read_program_version),
+                              ('libminc', read_libminc_version),
+                              ('netcdf', read_netcdf_version),
+                              ('hdf5', read_hdf5_version), ]:
+                if f(l) is not None:
+                    versions[name] = f(l)
+
+        return versions
+
+
+def aggregate_filename(files, new_suffix):
+    """
+    Try to work out a sensible name given a set of files that have
+    been combined in some way (e.g. averaged). If we can't work out a
+    sensible prefix, we use the first filename in the list.
+
+    Examples
+    --------
+
+    >>> from nipype.interfaces.minc.base import aggregate_filename
+    >>> f = aggregate_filename(['/tmp/foo1.mnc', '/tmp/foo2.mnc', '/tmp/foo3.mnc'], 'averaged')
+    >>> os.path.split(f)[1] # This has a full path, so just check the filename.
+    'foo_averaged.mnc'
+
+    >>> f = aggregate_filename(['/tmp/foo1.mnc', '/tmp/blah1.mnc'], 'averaged')
+    >>> os.path.split(f)[1] # This has a full path, so just check the filename.
+    'foo1_averaged.mnc'
+
+    """
+
+    path = os.path.split(files[0])[0]
+    names = [os.path.splitext(os.path.split(x)[1])[0] for x in files]
+    common_prefix = os.path.commonprefix(names)
+
+    path = os.getcwd()
+
+    if common_prefix == '':
+        return os.path.abspath(os.path.join(path, os.path.splitext(files[0])[0] + '_' + new_suffix + '.mnc'))
+    else:
+        return os.path.abspath(os.path.join(path, common_prefix + '_' + new_suffix + '.mnc'))