Added interface to FSL POSSUM/b0calc

Author: oesteban

nipype/interfaces/fsl/__init__.py

@@ -27,3 +27,5 @@
 from .maths import (ChangeDataType, Threshold, MeanImage, ApplyMask,
                     IsotropicSmooth, TemporalFilter, DilateImage, ErodeImage,
                     SpatialFilter, UnaryMaths, BinaryMaths, MultiImageMaths)
+
+from .possum import (B0Calc)

nipype/interfaces/fsl/possum.py

@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+# -*- 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:
+#
+# @Author: oesteban - [email protected]
+# @Date:   2014-07-03 15:27:53
+# @Last Modified by:   oesteban
+# @Last Modified time: 2014-07-03 16:26:09
+"""
+The possum module provides classes for interfacing with `POSSUM
+<http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/POSSUM>`_ command line tools.
+Please, check out the link for pertinent citations using POSSUM.
+
+.. Note:: This was written to work with FSL version 5.0.6.
+
+    Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> os.chdir(datadir)
+
+"""
+
+import os
+import shutil
+import warnings
+
+from nipype.interfaces.fsl.base import FSLCommand, FSLCommandInputSpec, Info
+from nipype.interfaces.base import (TraitedSpec, isdefined, File, Directory,
+                                    InputMultiPath, OutputMultiPath, traits)
+from nipype.utils.filemanip import fname_presuffix, split_filename, copyfile
+
+
+class B0CalcInputSpec(FSLCommandInputSpec):
+    in_file = File(exists=True, mandatory=True, argstr='-i %s', position=0,
+                   desc='filename of input image (usually a tissue/air segmentation)')
+    out_file = File(argstr='-o %s', position=1, name_source=['in_file'],
+                    name_template='%s_b0field', output_name='out_file',
+                    desc='filename of B0 output volume')
+
+
+    x_grad = traits.Float(0.0, argstr='--gx=%0.4f', desc=('Value for zeroth-order x-gradient field '
+                          '(per mm)'))
+    y_grad = traits.Float(0.0, argstr='--gy=%0.4f', desc=('Value for zeroth-order y-gradient field '
+                          '(per mm)'))
+    z_grad = traits.Float(0.0, argstr='--gz=%0.4f', desc=('Value for zeroth-order z-gradient field '
+                          '(per mm)'))
+
+    x_b0 = traits.Float(0.0, argstr='--b0x=%0.2f', desc=('Value for zeroth-order b0 field '
+                        '(x-component), in Tesla'))
+    y_b0 = traits.Float(0.0, argstr='--b0y=%0.2f', desc=('Value for zeroth-order b0 field '
+                        '(y-component), in Tesla'))
+    z_b0 = traits.Float(1.0, argstr='--b0=%0.2f', desc=('Value for zeroth-order b0 field '
+                        '(z-component), in Tesla'))
+
+    delta = traits.Float(-9.45e-6, argstr='-d %e', desc='Delta value (chi_tissue - chi_air)')
+    chi_air = traits.Float(4.0e-7, argstr='--chi0=%e', desc='susceptibility of air')
+    compute_xyz = traits.Bool(False, argstr='--xyz',
+                              desc='calculate and save all 3 field components (i.e. x,y,z)')
+    extendboundary = traits.Float(1.0, argstr='--extendboundary=%0.2f', desc=('Relative proportion to '
+                                  'extend voxels at boundary'))
+    directconv = traits.Bool(False, argstr='--directconv',
+                             desc='use direct (image space) convolution, not FFT')
+
+
+class B0CalcOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='filename of B0 output volume')
+
+
+class B0Calc(FSLCommand):
+    """
+    B0 inhomogeneities occur at interfaces of materials with different magnetic susceptibilities,
+    such as tissue-air interfaces. These differences lead to distortion in the local magnetic field,
+    as Maxwell’s equations need to be satisfied. An example of B0 inhomogneity is the first volume
+    of the 4D volume ```$FSLDIR/data/possum/b0_ppm.nii.gz```.
+
+    Examples ::
+
+    >>> from nipype.interfaces.fsl import B0Calc
+    >>> b0calc = B0Calc()
+    >>> b0calc.inputs.in_file = 'tissue+air_map.nii'
+    >>> b0calc.inputs.z_b0 = 3.0
+    >>> b0calc.cmdline
+    'b0calc -i tissue+air_map.nii -o tissue+air_map_b0field.nii.gz --b0=3.00'
+
+    """
+
+    _cmd = 'b0calc'
+    input_spec = B0CalcInputSpec
+    output_spec = B0CalcOutputSpec
+
+

nipype/interfaces/fsl/tests/test_auto_B0Calc.py

@@ -0,0 +1,65 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.fsl.possum import B0Calc
+
+def test_B0Calc_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    chi_air=dict(argstr='--chi0=%e',
+    ),
+    compute_xyz=dict(argstr='--xyz',
+    ),
+    delta=dict(argstr='-d %e',
+    ),
+    directconv=dict(argstr='--directconv',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    extendboundary=dict(argstr='--extendboundary=%0.2f',
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-i %s',
+    mandatory=True,
+    position=0,
+    ),
+    out_file=dict(argstr='-o %s',
+    name_source=['in_file'],
+    name_template='%s_b0field',
+    output_name='out_file',
+    position=1,
+    ),
+    output_type=dict(),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    x_b0=dict(argstr='--b0x=%0.2f',
+    ),
+    x_grad=dict(argstr='--gx=%0.4f',
+    ),
+    y_b0=dict(argstr='--b0y=%0.2f',
+    ),
+    y_grad=dict(argstr='--gy=%0.4f',
+    ),
+    z_b0=dict(argstr='--b0=%0.2f',
+    ),
+    z_grad=dict(argstr='--gz=%0.4f',
+    ),
+    )
+    inputs = B0Calc.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_B0Calc_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = B0Calc.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+