Merge pull request #1913 from mmodat/adding_niftyreg

Adding niftyreg

Author: satra

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
+from .reg import RegAladin, RegF3D
+from .regutils import (RegResample, RegJacobian, RegAverage, RegTools,
+                       RegTransform, RegMeasure)

nipype/interfaces/niftyreg/base.py

@@ -0,0 +1,128 @@
+# -*- 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 shutil
+import subprocess
+from warnings import warn
+
+from ..base import CommandLine, isdefined, CommandLineInputSpec, traits
+from ...utils.filemanip import split_filename
+
+
+def get_custom_path(command):
+    return os.path.join(os.getenv('NIFTYREGDIR', ''), command)
+
+
+def no_niftyreg(cmd='reg_f3d'):
+    try:
+        return shutil.which(cmd) is None
+    except AttributeError:  # Python < 3.3
+        return not any(
+            [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)])
+
+
+class NiftyRegCommandInputSpec(CommandLineInputSpec):
+    """Input Spec for niftyreg interfaces."""
+    # Set the number of omp thread to use
+    omp_core_val = traits.Int(desc='Number of openmp thread to use',
+                              argstr='-omp %i')
+
+
+class NiftyRegCommand(CommandLine):
+    """
+    Base support interface for NiftyReg commands.
+    """
+    _suffix = '_nr'
+    _min_version = '1.5.30'
+
+    def __init__(self, required_version=None, **inputs):
+        super(NiftyRegCommand, self).__init__(**inputs)
+        self.required_version = required_version
+        _version = self.get_version()
+        if _version:
+            _version = _version.decode("utf-8")
+            if StrictVersion(_version) < StrictVersion(self._min_version):
+                msg = 'A later version of Niftyreg is required (%s < %s)'
+                warn(msg % (_version, self._min_version))
+            if required_version is not None:
+                if StrictVersion(_version) != StrictVersion(required_version):
+                    msg = 'The version of NiftyReg differs from the required'
+                    msg += '(%s != %s)'
+                    warn(msg % (_version, self.required_version))
+
+    def check_version(self):
+        _version = self.get_version()
+        if not _version:
+            raise Exception('Niftyreg not found')
+        # Decoding to string:
+        _version = _version.decode("utf-8")
+        if StrictVersion(_version) < StrictVersion(self._min_version):
+            err = 'A later version of Niftyreg is required (%s < %s)'
+            raise ValueError(err % (_version, self._min_version))
+        if self.required_version:
+            if StrictVersion(_version) != StrictVersion(self.required_version):
+                err = 'The version of NiftyReg differs from the required'
+                err += '(%s != %s)'
+                raise ValueError(err % (_version, self.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):
+        return self.get_version() is not None
+
+    def _run_interface(self, runtime):
+        # Update num threads estimate from OMP_NUM_THREADS env var
+        # Default to 1 if not set
+        if not isdefined(self.inputs.environ['OMP_NUM_THREADS']):
+            self.inputs.environ['OMP_NUM_THREADS'] = self.num_threads
+        return super(NiftyRegCommand, self)._run_interface(runtime)
+
+    def _format_arg(self, name, spec, value):
+        if name == 'omp_core_val':
+            self.numthreads = value
+        return super(NiftyRegCommand, self)._format_arg(name, spec, value)
+
+    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))