Inital commit to add niftyfit interfaces

Author: byvernault

nipype/interfaces/niftyfit/__init__.py

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+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+"""
+The niftyfit module provides classes for interfacing with the `NiftyFit`_
+command line tools.
+
+Top-level namespace for niftyfit.
+"""
+
+from .asl import FitAsl
+from .base import no_niftyfit, get_custom_path
+from .dwi import FitDwi, DwiTool
+from .qt1 import FitQt1

nipype/interfaces/niftyfit/asl.py

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+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+"""
+The ASL module of niftyfit, which wraps the fitting methods in NiftyFit.
+"""
+
+from ..base import TraitedSpec, traits, isdefined, CommandLineInputSpec
+from .base import NiftyFitCommand, get_custom_path
+
+
+class FitAslInputSpec(CommandLineInputSpec):
+    """ Input Spec for FitAsl. """
+    desc = 'Filename of the 4D ASL (control/label) source image (mandatory).'
+    source_file = traits.File(position=1,
+                              exists=True,
+                              argstr='-source %s',
+                              mandatory=True,
+                              desc=desc)
+    pasl = traits.Bool(desc='Fit PASL ASL data [default]', argstr='-pasl')
+    pcasl = traits.Bool(desc='Fit PCASL ASL data', argstr='-pcasl')
+
+    # *** Output options:
+    desc = 'Filename of the Cerebral Blood Flow map (in ml/100g/min).'
+    cbf_file = traits.File(genfile=True, argstr='-cbf %s', desc=desc)
+    desc = 'Filename of the CBF error map.'
+    error_file = traits.File(genfile=True, argstr='-error %s', desc=desc)
+    desc = 'Filename of the synthetic ASL data.'
+    syn_file = traits.File(genfile=True, argstr='-syn %s', desc=desc)
+
+    # *** Input options (see also fit_qt1 for generic T1 fitting):
+    desc = 'Filename of the estimated input T1 map (in ms).'
+    t1map = traits.File(exists=True, argstr='-t1map %s', desc=desc)
+    desc = 'Filename of the estimated input M0 map.'
+    m0map = traits.File(exists=True, argstr='-m0map %s', desc=desc)
+    desc = 'Filename of the estimated input M0 map error.'
+    m0mape = traits.File(exists=True, argstr='-m0mape %s', desc=desc)
+    desc = 'Filename of a [1,2,5]s Inversion Recovery volume (T1/M0 fitting \
+carried out internally).'
+    IRvolume = traits.File(exists=True, argstr='-IRvolume %s', desc=desc)
+    desc = 'Output of [1,2,5]s Inversion Recovery fitting.'
+    IRoutput = traits.File(exists=True, argstr='-IRoutput %s', desc=desc)
+
+    # *** Experimental options (Choose those suitable for the model!):
+    mask = traits.File(position=2,
+                       exists=True,
+                       desc='Filename of image mask.',
+                       argstr='-mask %s')
+    T1a = traits.Float(desc='T1 of arterial component [1650ms].',
+                       argstr='-T1a %f')
+    desc = 'Single plasma/tissue partition coefficient [0.9ml/g].'
+    L = traits.Float(desc=desc, argstr='-L %f')
+    desc = 'Labelling efficiency [0.99 (pasl), 0.85 (pcasl)], ensure any \
+background suppression pulses are included in -eff'
+    eff = traits.Float(desc=desc, argstr='-eff %f')
+    desc = 'Outlier rejection for multi CL volumes (enter z-score threshold \
+(e.g. 2.5)) [off].'
+    out = traits.Float(desc=desc, argstr='-out %f')
+
+    # *** PCASL options (Choose those suitable for the model!):
+    PLD = traits.Float(desc='Post Labelling Delay [2000ms].', argstr='-PLD %f')
+    LDD = traits.Float(desc='Labelling Duration [1800ms].', argstr='-LDD %f')
+    desc = 'Difference in labelling delay per slice [0.0 ms/slice.'
+    dPLD = traits.Float(desc=desc, argstr='-dPLD %f')
+
+    # *** PASL options (Choose those suitable for the model!):
+    Tinv1 = traits.Float(desc='Saturation pulse time [800ms].',
+                         argstr='-Tinv1 %f')
+    Tinv2 = traits.Float(desc='Inversion time [2000ms].', argstr='-Tinv2 %f')
+    desc = 'Difference in inversion time per slice [0ms/slice].'
+    dTinv2 = traits.Float(desc=desc, argstr='-dTinv2 %f')
+
+    # *** Other experimental assumptions:
+
+    # Not programmed yet
+    # desc = 'Slope and intercept for Arterial Transit Time.'
+    # ATT = traits.Float(desc=desc, argstr='-ATT %f')
+
+    gmT1 = traits.Float(desc='T1 of GM [1150ms].', argstr='-gmT1 %f')
+    gmL = traits.Float(desc='Plasma/GM water partition [0.95ml/g].',
+                       argstr='-gmL %f')
+    gmTTT = traits.Float(desc='Time to GM [ATT+0ms].', argstr='-gmTTT %f')
+    wmT1 = traits.Float(desc='T1 of WM [800ms].', argstr='-wmT1 %f')
+    wmL = traits.Float(desc='Plasma/WM water partition [0.82ml/g].',
+                       argstr='-wmL %f')
+    wmTTT = traits.Float(desc='Time to WM [ATT+0ms].', argstr='-wmTTT %f')
+
+    # *** Segmentation options:
+    desc = 'Filename of the 4D segmentation (in ASL space) for L/T1 \
+estimation and PV correction {WM,GM,CSF}.'
+    seg = traits.File(exists=True, argstr='-seg %s', desc=desc)
+    desc = 'Use sigmoid to estimate L from T1: L(T1|gmL,wmL) [Off].'
+    sig = traits.Bool(desc=desc, argstr='-sig')
+    desc = 'Simple PV correction (CBF=vg*CBFg + vw*CBFw, with CBFw=f*CBFg) \
+[0.25].'
+    pv0 = traits.Int(desc=desc, argstr='-pv0 %d')
+    pv2 = traits.Int(desc='In plane PV kernel size [3x3].', argstr='-pv2 %d')
+    pv3 = traits.Tuple(traits.Int, traits.Int, traits.Int,
+                       desc='3D kernel size [3x3x1].',
+                       argstr='-pv3 %d %d %d')
+    desc = 'Multiply CBF by this value (e.g. if CL are mislabelled use -1.0).'
+    mul = traits.Float(desc=desc, argstr='-mul %f')
+    mulgm = traits.Bool(desc='Multiply CBF by segmentation [Off].',
+                        argstr='-sig')
+    desc = 'Set PV threshold for switching off LSQR [O.05].'
+    pvthreshold = traits.Bool(desc=desc, argstr='-pvthreshold')
+    segstyle = traits.Bool(desc='Set CBF as [gm,wm] not [wm,gm].',
+                           argstr='-segstyle')
+
+
+class FitAslOutputSpec(TraitedSpec):
+    """ Output Spec for FitAsl. """
+    desc = 'Filename of the Cerebral Blood Flow map (in ml/100g/min).'
+    cbf_file = traits.File(exists=True, desc=desc)
+    desc = 'Filename of the CBF error map.'
+    error_file = traits.File(exists=True, desc=desc)
+    desc = 'Filename of the synthetic ASL data.'
+    syn_file = traits.File(exists=True, desc=desc)
+
+
+class FitAsl(NiftyFitCommand):
+    """Interface for executable fit_asl from Niftyfit platform.
+
+    Use NiftyFit to perform ASL fitting.
+
+    ASL fitting routines (following EU Cost Action White Paper recommendations)
+    Fits Cerebral Blood Flow maps in the first instance.
+
+    For source code, see https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyFit-Release
+
+    Examples
+    --------
+    >>> from nipype.interfaces.niftyfit import FitAsl
+    >>> node = FitAsl()
+    >>> node.inputs.source_file = "asl.nii.gz"  # doctest: +SKIP
+    >>> node.cmdline  # doctest: +SKIP
+    'fit_asl -source asl.nii -cbf asl_cbf.nii.gz -error asl_error.nii.gz \
+-syn asl_syn.nii.gz'
+
+    """
+    _cmd = get_custom_path('fit_asl')
+    input_spec = FitAslInputSpec
+    output_spec = FitAslOutputSpec
+    _suffix = '_fit_asl'
+
+    def _gen_filename(self, name):
+        if name == 'error_file':
+            return self._gen_fname(self.inputs.source_file,
+                                   suffix='_error', ext='.nii.gz')
+        if name == 'syn_file':
+            return self._gen_fname(self.inputs.source_file,
+                                   suffix='_syn', ext='.nii.gz')
+        if name == 'cbf_file':
+            return self._gen_fname(self.inputs.source_file,
+                                   suffix='_cbf', ext='.nii.gz')
+        return None
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+
+        if isdefined(self.inputs.error_file):
+            outputs['error_file'] = self.inputs.error_file
+        else:
+            outputs['error_file'] = self._gen_filename('error_file')
+
+        if isdefined(self.inputs.syn_file):
+            outputs['syn_file'] = self.inputs.syn_file
+        else:
+            outputs['syn_file'] = self._gen_filename('syn_file')
+
+        if isdefined(self.inputs.cbf_file):
+            outputs['cbf_file'] = self.inputs.cbf_file
+        else:
+            outputs['cbf_file'] = self._gen_filename('cbf_file')
+
+        return outputs

nipype/interfaces/niftyfit/base.py

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+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+"""
+The niftyfit module provide an interface with the niftyfit software
+developed in TIG, UCL.
+
+Software available at:
+https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyFit-Release
+
+Version used for this version of the interfaces (git):
+
+commit c6232e4c4223c3d19f7a32906409da5af36299a2
+Date:   Fri Jan 6 13:34:02 2017 +0000
+
+Examples
+--------
+See the docstrings of the individual classes for examples.
+"""
+
+import os
+import warnings
+
+from ..base import CommandLine
+from ...utils.filemanip import split_filename
+
+
+warn = warnings.warn
+warnings.filterwarnings('always', category=UserWarning)
+
+
+def get_custom_path(command):
+    """Get path of niftyfit."""
+    try:
+        specific_dir = os.environ['NIFTYFITDIR']
+        command = os.path.join(specific_dir, command)
+        return command
+    except KeyError:
+        return command
+
+
+def no_niftyfit(cmd='fit_dwi'):
+    """Check if niftyfit is installed."""
+    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 NiftyFitCommand(CommandLine):
+    """
+    Base support interface for NiftyFit commands.
+    """
+    _suffix = '_nf'
+
+    def __init__(self, **inputs):
+        """ Init method calling super. No version to be checked."""
+        super(NiftyFitCommand, self).__init__(**inputs)
+
+    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))