Merge branch 'alexsavio-petpvc'

Author: chrisgorgo

nipype/interfaces/petpvc.py

@@ -0,0 +1,224 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""
+   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)
+
+Nipype interface for PETPVC.
+
+PETPVC is a software from the Nuclear Medicine Department
+of the UCL University Hospital, London, UK.
+
+Its source code is here: https://github.com/UCL/PETPVC
+
+The methods that it implement are explained here:
+K. Erlandsson, I. Buvat, P. H. Pretorius, B. A. Thomas, and B. F. Hutton,
+"A review of partial volume correction techniques for emission tomography
+and their applications in neurology, cardiology and oncology," Phys. Med.
+Biol., vol. 57, no. 21, p. R119, 2012.
+
+There is a publication waiting to be accepted for this software tool.
+
+
+Its command line help shows this:
+
+   -i --input < filename >
+      = PET image file
+   -o --output < filename >
+      = Output file
+   [ -m --mask < filename > ]
+      = Mask image file
+   -p --pvc < keyword >
+      = Desired PVC method
+   -x < X >
+      = The full-width at half maximum in mm along x-axis
+   -y < Y >
+      = The full-width at half maximum in mm along y-axis
+   -z < Z >
+      = The full-width at half maximum in mm along z-axis
+   [ -d --debug ]
+      = Prints debug information
+   [ -n --iter [ Val ] ]
+      = Number of iterations
+        With: Val (Default = 10)
+   [ -k [ Val ] ]
+      = Number of deconvolution iterations
+        With: Val (Default = 10)
+   [ -a --alpha [ aval ] ]
+      = Alpha value
+        With: aval (Default = 1.5)
+   [ -s --stop [ stopval ] ]
+      = Stopping criterion
+        With: stopval (Default = 0.01)
+
+----------------------------------------------
+Technique - keyword
+
+Geometric transfer matrix - "GTM"
+Labbe approach - "LABBE"
+Richardson-Lucy - "RL"
+Van-Cittert - "VC"
+Region-based voxel-wise correction - "RBV"
+RBV with Labbe - "LABBE+RBV"
+RBV with Van-Cittert - "RBV+VC"
+RBV with Richardson-Lucy - "RBV+RL"
+RBV with Labbe and Van-Cittert - "LABBE+RBV+VC"
+RBV with Labbe and Richardson-Lucy- "LABBE+RBV+RL"
+Multi-target correction - "MTC"
+MTC with Labbe - "LABBE+MTC"
+MTC with Van-Cittert - "MTC+VC"
+MTC with Richardson-Lucy - "MTC+RL"
+MTC with Labbe and Van-Cittert - "LABBE+MTC+VC"
+MTC with Labbe and Richardson-Lucy- "LABBE+MTC+RL"
+Iterative Yang - "IY"
+Iterative Yang with Van-Cittert - "IY+VC"
+Iterative Yang with Richardson-Lucy - "IY+RL"
+Muller Gartner - "MG"
+Muller Gartner with Van-Cittert - "MG+VC"
+Muller Gartner with Richardson-Lucy - "MG+RL"
+
+"""
+from __future__ import print_function
+from __future__ import division
+
+import os
+import warnings
+
+from nipype.interfaces.base import (
+    TraitedSpec,
+    CommandLineInputSpec,
+    CommandLine,
+    File,
+    isdefined,
+    traits,
+)
+
+warn = warnings.warn
+
+pvc_methods = ['GTM',
+               'IY',
+               'IY+RL',
+               'IY+VC',
+               'LABBE',
+               'LABBE+MTC',
+               'LABBE+MTC+RL',
+               'LABBE+MTC+VC',
+               'LABBE+RBV',
+               'LABBE+RBV+RL',
+               'LABBE+RBV+VC',
+               'MG',
+               'MG+RL',
+               'MG+VC',
+               'MTC',
+               'MTC+RL',
+               'MTC+VC',
+               'RBV',
+               'RBV+RL',
+               'RBV+VC',
+               'RL',
+               'VC']
+
+
+class PETPVCInputSpec(CommandLineInputSpec):
+    in_file   = File(desc="PET image file", exists=True, mandatory=True, argstr="-i %s")
+    out_file  = File(desc="Output file", genfile=True, hash_files=False, argstr="-o %s")
+    mask_file = File(desc="Mask image file", exists=True, mandatory=True, argstr="-m %s")
+    pvc       = traits.Enum(pvc_methods, desc="Desired PVC method", mandatory=True, argstr="-p %s")
+    fwhm_x    = traits.Float(desc="The full-width at half maximum in mm along x-axis", mandatory=True, argstr="-x %.4f")
+    fwhm_y    = traits.Float(desc="The full-width at half maximum in mm along y-axis", mandatory=True, argstr="-y %.4f")
+    fwhm_z    = traits.Float(desc="The full-width at half maximum in mm along z-axis", mandatory=True, argstr="-z %.4f")
+    debug     = traits.Bool (desc="Prints debug information", usedefault=True, default_value=False, argstr="-d")
+    n_iter    = traits.Int  (desc="Number of iterations", default_value=10, argstr="-n %d")
+    n_deconv  = traits.Int  (desc="Number of deconvolution iterations", default_value=10, argstr="-k %d")
+    alpha     = traits.Float(desc="Alpha value", default_value=1.5, argstr="-a %.4f")
+    stop_crit = traits.Float(desc="Stopping criterion", default_value=0.01, argstr="-a %.4f")
+
+
+class PETPVCOutputSpec(TraitedSpec):
+    out_file = File(desc = "Output file")
+
+
+class PETPVC(CommandLine):
+    """ Use PETPVC for partial volume correction of PET images.
+
+    Examples
+    --------
+    >>> from ..testing import example_data
+    >>> #TODO get data for PETPVC
+    >>> pvc = PETPVC()
+    >>> pvc.inputs.in_file   = 'pet.nii.gz'
+    >>> pvc.inputs.mask_file = 'tissues.nii.gz'
+    >>> pvc.inputs.out_file  = 'pet_pvc_rbv.nii.gz'
+    >>> pvc.inputs.pvc = 'RBV'
+    >>> pvc.inputs.fwhm_x = 2.0
+    >>> pvc.inputs.fwhm_y = 2.0
+    >>> pvc.inputs.fwhm_z = 2.0
+    >>> outs = pvc.run() #doctest: +SKIP
+    """
+    input_spec = PETPVCInputSpec
+    output_spec = PETPVCOutputSpec
+    _cmd = 'petpvc'
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = self.inputs.out_file
+        if not isdefined(outputs['out_file']):
+            method_name = self.inputs.pvc.lower()
+            outputs['out_file'] = self._gen_fname(self.inputs.in_file,
+                                                  suffix='_{}_pvc'.format(method_name))
+
+        outputs['out_file'] = os.path.abspath(outputs['out_file'])
+        return outputs
+
+    def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,
+                   ext='.nii.gz'):
+        """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 given `ext`.
+            (Default is False)
+
+        Returns
+        -------
+        fname : str
+            New filename based on given parameters.
+
+        """
+        from nipype.utils.filemanip import fname_presuffix
+
+        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 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
+
+    def _gen_filename(self, name):
+        if name == 'out_file':
+            return self._list_outputs()['out_file']
+        return None

nipype/interfaces/tests/test_auto_PETPVC.py

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+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ...testing import assert_equal
+from ..petpvc import PETPVC
+
+
+def test_PETPVC_inputs():
+    input_map = dict(alpha=dict(argstr='-a %.4f',
+    ),
+    args=dict(argstr='%s',
+    ),
+    debug=dict(argstr='-d',
+    usedefault=True,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    fwhm_x=dict(argstr='-x %.4f',
+    mandatory=True,
+    ),
+    fwhm_y=dict(argstr='-y %.4f',
+    mandatory=True,
+    ),
+    fwhm_z=dict(argstr='-z %.4f',
+    mandatory=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-i %s',
+    mandatory=True,
+    ),
+    mask_file=dict(argstr='-m %s',
+    mandatory=True,
+    ),
+    n_deconv=dict(argstr='-k %d',
+    ),
+    n_iter=dict(argstr='-n %d',
+    ),
+    out_file=dict(argstr='-o %s',
+    genfile=True,
+    hash_files=False,
+    ),
+    pvc=dict(argstr='-p %s',
+    mandatory=True,
+    ),
+    stop_crit=dict(argstr='-a %.4f',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = PETPVC.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+
+def test_PETPVC_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = PETPVC.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value