Adding niftyreg

nipype/interfaces/niftyreg/__init__.py

@@ -0,0 +1,15 @@
+# -*- 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 niftyreg module provides classes for interfacing with the `NiftyReg
+<http://sourceforge.net/projects/niftyreg/>`_ command line tools.
+
+Top-level namespace for niftyreg.
+"""
+
+from .base import no_niftyreg, get_custom_path, PositiveInt
+from .reg import RegAladin, RegF3D
+from .regutils import (RegResample, RegJacobian, RegAverage, RegTools,
+                       RegTransform, RegMeasure)

nipype/interfaces/niftyreg/base.py

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+# -*- 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 niftyreg module provides classes for interfacing with `niftyreg
+<http://sourceforge.net/projects/niftyreg/>`_ command line tools.
+
+These are the base tools for working with niftyreg.
+
+Registration tools are found in niftyreg/reg.py
+Every other tool is found in niftyreg/regutils.py
+
+Examples
+--------
+See the docstrings of the individual classes for examples.
+
+"""
+
+from __future__ import (print_function, division, unicode_literals,
+                        absolute_import)
+from builtins import property, super
+from distutils.version import StrictVersion
+import os
+import subprocess
+import warnings
+
+from ..base import CommandLine, isdefined, traits
+from ...utils.filemanip import split_filename
+
+
+warn = warnings.warn
+warnings.filterwarnings('always', category=UserWarning)
+
+
+def get_custom_path(command):
+    try:
+        specific_dir = os.environ['NIFTYREGDIR']
+        command = os.path.join(specific_dir, command)
+        return command
+    except KeyError:
+        return command
+
+
+def no_niftyreg(cmd='reg_f3d'):
+    if True in [os.path.isfile(os.path.join(path, cmd)) and
+                os.access(os.path.join(path, cmd), os.X_OK)
+                for path in os.environ["PATH"].split(os.pathsep)]:
+        return False
+    return True
+
+
+class PositiveInt(traits.BaseInt):
+    # Define the default value
+    default_value = 0
+    # Describe the trait type
+    info_text = 'A positive integer'
+
+    def validate(self, obj, name, value):
+        value = super(PositiveInt, self).validate(obj, name, value)
+        if (value >= 0) == 1:
+            return value
+        self.error(obj, name, value)
+
+
+class NiftyRegCommand(CommandLine):
+    """
+    Base support interface for NiftyReg commands.
+    """
+    _suffix = '_nr'
+    _min_version = '1.5.10'
+
+    def __init__(self, required_version=None, **inputs):
+        super(NiftyRegCommand, self).__init__(**inputs)
+        cur_version = self.get_version()
+        if not cur_version:
+            raise Exception('Niftyreg not found')
+        # Decoding to string:
+        cur_version = cur_version.decode("utf-8")
+        if StrictVersion(cur_version) < StrictVersion(self._min_version):
+            err = 'A later version of Niftyreg is required (%s < %s)'
+            raise ValueError(err % (cur_version, self._min_version))
+        if required_version is not None:
+            if StrictVersion(cur_version) != StrictVersion(required_version):
+                err = 'The version of NiftyReg differs from the required'
+                err += '(%s != %s)'
+                raise ValueError(err % (cur_version, required_version))
+
+    def get_version(self):
+        if no_niftyreg(cmd=self.cmd):
+            return None
+        exec_cmd = ''.join((self.cmd, ' -v'))
+        return subprocess.check_output(exec_cmd, shell=True).strip()
+
+    @property
+    def version(self):
+        return self.get_version()
+
+    def exists(self):
+        if self.get_version() is None:
+            return False
+        return True
+
+    def _gen_fname(self, basename, out_dir=None, suffix=None, ext=None):
+        if basename == '':
+            msg = 'Unable to generate filename for command %s. ' % self.cmd
+            msg += 'basename is not set!'
+            raise ValueError(msg)
+        _, final_bn, final_ext = split_filename(basename)
+        if out_dir is None:
+            out_dir = os.getcwd()
+        if ext is not None:
+            final_ext = ext
+        if suffix is not None:
+            final_bn = ''.join((final_bn, suffix))
+        return os.path.abspath(os.path.join(out_dir, final_bn + final_ext))
+
+    def _gen_filename(self, name):
+        if name == 'out_file':
+            return self._gen_fname(self.inputs.in_file,
+                                   suffix=self._suffix,
+                                   ext='.nii.gz')
+        return None
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        if isdefined(self.inputs.out_file):
+            outputs['out_file'] = self.inputs.out_file
+        else:
+            outputs['out_file'] = self._gen_filename('out_file')
+        return outputs