fslcomplex interface + fix line removed inadvertently

Author: bpinsard

nipype/interfaces/fsl/preprocess.py

@@ -199,7 +199,7 @@ class FASTInputSpec(FSLCommandInputSpec):
                           argstr='%s', position=-1, mandatory=True)
     out_basename = File(desc='base name of output files',
                         argstr='-o %s')  # uses in_file name as basename if none given
-
+    number_classes = traits.Range(low=1, high=10, argstr='-n %d',
                                   desc='number of tissue-type classes')
     output_biasfield = traits.Bool(desc='output estimated bias field',
                                    argstr='-b')

nipype/interfaces/fsl/utils.py

@@ -1236,3 +1236,129 @@ def _list_outputs(self):
         else:
             outputs['out_file'] = os.path.abspath(self.inputs.out_file)
         return outputs
+
+
+class ComplexInputSpec(FSLCommandInputSpec):
+    complex_in_file = File(exists=True, argstr="%s", position=2)
+    complex_in_file2 = File(exists=True, argstr="%s", position=3)
+
+    real_in_file = File(exists=True, argstr="%s", position=2)
+    imaginary_in_file = File(exists=True, argstr="%s", position=3)
+    magnitude_in_file = File(exists=True, argstr="%s", position=2)
+    phase_in_file = File(exists=True, argstr='%s', position=3)
+
+    _ofs = ['complex_out_file',
+            'magnitude_out_file','phase_out_file',
+            'real_out_file','imaginary_out_file']
+    _conversion = ['real_polar','real_cartesian',
+                   'complex_cartesian','complex_polar',
+                   'complex_split','complex_merge',]
+
+    complex_out_file = File(genfile=True, argstr="%s", position=-3, 
+                            xor=_ofs+_conversion[:2])
+    magnitude_out_file = File(genfile=True, argstr="%s", position=-4,
+                              xor=_ofs[:1]+_ofs[3:]+_conversion[1:])
+    phase_out_file = File(genfile=True, argstr="%s", position=-3,
+                          xor=_ofs[:1]+_ofs[3:]+_conversion[1:])
+    real_out_file = File(genfile=True, argstr="%s", position=-4,
+                         xor=_ofs[:3]+_conversion[:1]+_conversion[2:])
+    imaginary_out_file = File(genfile=True, argstr="%s", position=-3,
+                              xor=_ofs[:3]+_conversion[:1]+_conversion[2:])
+
+    start_vol = traits.Int(position=-2, argstr='%d')
+    end_vol = traits.Int(position=-1, argstr='%d')
+
+    real_polar = traits.Bool(
+        argstr = '-realpolar', xor = _conversion, position=1,)
+#        requires=['complex_in_file','magnitude_out_file','phase_out_file'])
+    real_cartesian = traits.Bool(
+        argstr = '-realcartesian', xor = _conversion, position=1,)
+#        requires=['complex_in_file','real_out_file','imaginary_out_file'])
+    complex_cartesian = traits.Bool(
+        argstr = '-complex', xor = _conversion, position=1,)
+#        requires=['real_in_file','imaginary_in_file','complex_out_file'])
+    complex_polar = traits.Bool(
+        argstr = '-complexpolar', xor = _conversion, position=1,)
+#        requires=['magnitude_in_file','phase_in_file',
+#                  'magnitude_out_file','phase_out_file'])
+    complex_split = traits.Bool(
+        argstr = '-complexsplit', xor = _conversion, position=1,)
+#        requires=['complex_in_file','complex_out_file'])
+    complex_merge = traits.Bool(
+        argstr = '-complexmerge', xor = _conversion + ['start_vol','end_vol'],
+        position=1,)
+#        requires=['complex_in_file','complex_in_file2','complex_out_file'])
+
+class ComplexOuputSpec(TraitedSpec):
+    magnitude_out_file = File()
+    phase_out_file = File()
+    real_out_file = File()
+    imaginary_out_file = File()
+    complex_out_file = File()
+    
+    
+class Complex(FSLCommand):
+    """fslcomplex is a tool for converting complex data
+    Examples
+    --------
+    >>> complex = Complex()
+    >>> complex.inputs.complex_in_file = "complex.nii"
+    >>> res = complex.run() # doctest: +SKIP
+
+    """
+    _cmd = 'fslcomplex'
+    input_spec = ComplexInputSpec
+    output_spec = ComplexOuputSpec
+
+    def _parse_inputs(self, skip=None):
+        if skip == None:
+            skip = []
+        if self.inputs.real_cartesian:
+            skip += self.inputs._ofs[:3]
+        elif self.inputs.real_polar:
+            skip += self.inputs._ofs[:1]+self.inputs._ofs[3:]
+        else:
+            skip += self.inputs._ofs[1:]
+        return super(Complex,self)._parse_inputs(skip)
+
+    def _gen_filename(self, name):
+        if name == 'complex_out_file':
+            if self.inputs.complex_cartesian:
+                in_file = self.inputs.real_in_file
+            elif self.inputs.complex_polar:
+                in_file = self.inputs.magnitude_in_file
+            elif self.inputs.complex_split or self.inputs.complex_merge:
+                in_file = self.inputs.complex_in_file
+            else:
+                return None
+            return self._gen_fname(in_file, suffix="_cplx")
+        elif name =='magnitude_out_file':
+            return self._gen_fname(self.inputs.complex_in_file, suffix="_mag")
+        elif name =='phase_out_file':
+            return self._gen_fname(self.inputs.complex_in_file,suffix="_phase")
+        elif name =='real_out_file':
+            return self._gen_fname(self.inputs.complex_in_file, suffix="_real")
+        elif name =='imaginary_out_file':
+            return self._gen_fname(self.inputs.complex_in_file, suffix="_imag")
+        return None
+
+    def _get_output(self,name):
+        output = getattr(self.inputs,name)
+        if not isdefined(output):
+            output = self._gen_filename(name)
+        return os.path.abspath(output)
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        if self.inputs.complex_cartesian or self.inputs.complex_polar or \
+                self.inputs.complex_split or self.inputs.complex_merge:
+            outputs['complex_out_file'] = self._get_output('complex_out_file')
+        elif self.inputs.real_cartesian:
+            outputs['real_out_file'] = self._get_output('real_out_file')
+            outputs['imaginary_out_file'] = self._get_output('imaginary_out_file')
+        elif self.inputs.real_polar:
+            outputs['magnitude_out_file'] = self._get_output('magnitude_out_file')
+            outputs['phase_out_file'] = self._get_output('phase_out_file')
+        return outputs
+
+