WIP: Dtitk

nipype/interfaces/dtitk/__init__.py

@@ -0,0 +1,15 @@
+"""The dtitk module provides classes for interfacing with the `Diffusion
+Tensor Imaging Toolkit (DTI-TK)
+<http://dti-tk.sourceforge.net/pmwiki/pmwiki.php>`_ command line tools.
+
+Top-level namespace for dti-tk.
+"""
+
+# from .base import ()
+from .registration import (RigidTask, AffineTask, DiffeoTask,
+                           ComposeXfmTask, diffeoSymTensor3DVolTask,
+                           affSymTensor3DVolTask, affScalarVolTask,
+                           diffeoScalarVolTask)
+from .utils import (TVAdjustOriginTask, TVAdjustVoxSpTask,
+                    SVAdjustVoxSpTask, TVResampleTask, SVResampleTask,
+                    TVtoolTask, BinThreshTask)

nipype/interfaces/dtitk/base.py

@@ -0,0 +1,81 @@
+# -*- 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:
+"""The dtitk module provides classes for interfacing with the `DTITK
+<http://dti-tk.sourceforge.net/pmwiki/pmwiki.php>`_ command line tools.
+
+These are the base tools for working with DTITK.
+Preprocessing tools are found in dtitk/preprocess.py
+Registration tools are found in dtitk/registration.py
+
+Currently these tools are supported:
+
+* Rigid Tensor Registration
+* Affine Tensor Registration
+* Diffeomorphic Tensor Registration
+
+Examples
+--------
+See the docstrings of the individual classes for examples.
+
+"""
+from __future__ import print_function, division, unicode_literals, \
+    absolute_import
+
+import os
+
+from ... import logging
+from ...utils.filemanip import fname_presuffix
+from ..base import CommandLine
+from nipype.interfaces.fsl.base import Info
+
+LOGGER = logging.getLogger('interface')
+
+
+class CommandLineDtitk(CommandLine):
+
+    def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,
+                   ext=None):
+        """Generate a filename based on the given parameters.
+
+        The filename will take the form: cwd/basename<suffix><ext>.
+        If change_ext is True, it will use the extentions specified in
+        <instance>intputs.output_type.
+
+        Parameters
+        ----------
+        basename : str
+            Filename to base the new filename on.
+        cwd : str
+            Path to prefix to the new filename. (default is os.getcwd())
+        suffix : str
+            Suffix to add to the `basename`.  (defaults is '' )
+        change_ext : bool
+            Flag to change the filename extension to the FSL output type.
+            (default True)
+
+        Returns
+        -------
+        fname : str
+            New filename based on given parameters.
+
+        """
+
+        if basename == '':
+            msg = 'Unable to generate filename for command %s. ' % self.cmd
+            msg += 'basename is not set!'
+            raise ValueError(msg)
+        if cwd is None:
+            cwd = os.getcwd()
+        if ext is None:
+            ext = Info.output_type_to_ext(self.inputs.output_type)
+        if change_ext:
+            if suffix:
+                suffix = ''.join((suffix, ext))
+            else:
+                suffix = ext
+        if suffix is None:
+            suffix = ''
+        fname = fname_presuffix(basename, suffix=suffix,
+                                use_ext=False, newpath=cwd)
+        return fname