Merge pull request #672 from beOn/spm_dicom

Spm dicom

Author: satra

CHANGES

@@ -3,6 +3,7 @@ Next release
 
 * ENH: SelectFiles: a streamlined version of DataGrabber
 * ENH: New interfaces: spm.ResliceToReference, FuzzyOverlap, afni.AFNItoNIFTI
+       spm.DicomImport
 * ENH: W3C PROV support with optional RDF export built into Nipype
 
 * FIX: Deals properly with 3d files in SPM Realign

nipype/interfaces/spm/__init__.py

@@ -10,5 +10,6 @@
 from .model import (Level1Design, EstimateModel, EstimateContrast, Threshold,
                     OneSampleTTestDesign, TwoSampleTTestDesign,
                     PairedTTestDesign, MultipleRegressionDesign)
-from .utils import Analyze2nii, CalcCoregAffine, ApplyTransform, Reslice, ApplyInverseDeformation,ResliceToReference
+from .utils import (Analyze2nii, CalcCoregAffine, ApplyTransform, Reslice,
+                    ApplyInverseDeformation,ResliceToReference,DicomImport)
 

nipype/interfaces/spm/base.py

@@ -413,7 +413,7 @@ def _make_matlab_command(self, contents, postscript=None):
         if self.mlab.inputs.mfile:
             if self.jobname in ['st', 'smooth', 'preproc', 'preproc8',
                                 'fmri_spec', 'fmri_est', 'factorial_design',
-                                'defs']:
+                                'defs', 'dicom']:
                 # parentheses
                 mscript += self._generate_job('jobs{1}.%s{1}.%s(1)' %
                                               (self.jobtype, self.jobname),

nipype/interfaces/spm/preprocess.py

@@ -264,8 +264,9 @@ class CoregisterInputSpec(SPMCommandInputSpec):
                 'nmi' - Normalised Mutual Information,
                 'ecc' - Entropy Correlation Coefficient,
                 'ncc' - Normalised Cross Correlation""")
-    fwhm = traits.Float(field='eoptions.fwhm',
-                        desc='gaussian smoothing kernel width (mm)')
+    fwhm = traits.List(traits.Float(), minlen=2, maxlen=2,
+                       field='eoptions.fwhm',
+                       desc='gaussian smoothing kernel width (mm)')
     separation = traits.List(traits.Float(), field='eoptions.sep',
                              desc='sampling separation in mm')
     tolerance = traits.List(traits.Float(), field='eoptions.tol',

nipype/interfaces/spm/tests/test_utils.py

@@ -59,3 +59,17 @@ def test_reslice():
     expected_interp = 'flags.interp = 1;\n'
     assert_equal(expected_interp in script, True)
     assert_equal('spm_reslice(invols, flags);' in script, True)
+
+def test_dicom_import():
+    dicom = example_data(infile = 'dicomdir/123456-1-1.dcm')
+    di = spmu.DicomImport(matlab_cmd = 'mymatlab')
+    assert_equal(di.inputs.matlab_cmd, 'mymatlab')
+    assert_equal(di.inputs.output_dir_struct, 'flat')
+    assert_equal(di.inputs.output_dir, './converted_dicom/')
+    assert_equal(di.inputs.format, 'nii')
+    assert_equal(di.inputs.icedims, False)
+    assert_raises(TraitError,di.inputs.trait_set,output_dir_struct = 'wrong')
+    assert_raises(TraitError,di.inputs.trait_set,format = 'FAT')
+    assert_raises(TraitError,di.inputs.trait_set,in_files = ['does_sfd_not_32fn_exist.dcm'])
+    di.inputs.in_files = [dicom]
+    assert_equal(di.inputs.in_files, [dicom])

nipype/interfaces/spm/utils.py

@@ -359,3 +359,81 @@ def _list_outputs(self):
             _, fname = os.path.split(filename)
             outputs['out_files'].append(os.path.realpath('w%s' % fname))
         return outputs
+
+class DicomImportInputSpec(SPMCommandInputSpec):
+    in_files = InputMultiPath(
+        File(exists=True),
+        mandatory=True,
+        field='data',
+        desc='dicom files to be converted')
+    output_dir_struct = traits.Enum(
+        'flat', 'series', 'patname', 'patid_date', 'patid', 'date_time',
+        field='root',
+        usedefault=True,
+        desc='directory structure for the output.')
+    output_dir = traits.Str('./',
+        field='outdir',
+        usedefault=True,
+        desc='output directory.')
+    format = traits.Enum(
+        'nii', 'img',
+        field='convopts.format',
+        usedefault=True,
+        desc='output format.')
+    icedims = traits.Bool(False,
+        field='convopts.icedims',
+        usedefault=True,
+        desc='If image sorting fails, one can try using the additional\
+              SIEMENS ICEDims information to create unique filenames.\
+              Use this only if there would be multiple volumes with\
+              exactly the same file names.')
+
+class DicomImportOutputSpec(TraitedSpec):
+    out_files = OutputMultiPath(File(exists=True),
+                                desc='converted files')
+
+class DicomImport(SPMCommand):
+    """ Uses spm to comvert DICOM files to nii or img+hdr.
+
+    Examples
+    --------
+
+    >>> import nipype.interfaces.spm.utils as spmu
+    >>> di = spmu.DicomImport()
+    >>> di.inputs.in_files = ['functional_1.dcm', 'functional_2.dcm']
+    >>> di.run() # doctest: +SKIP
+    """
+
+    input_spec = DicomImportInputSpec
+    output_spec = DicomImportOutputSpec
+
+    _jobtype = 'util'
+    _jobname = 'dicom'
+
+    def _format_arg(self, opt, spec, val):
+        """Convert input to appropriate format for spm
+        """
+        if opt == 'in_files':
+            return np.array(val, dtype=object)
+        if opt == 'output_dir':
+            return np.array([val], dtype=object)
+        if opt == 'output_dir':
+            return os.path.abspath(val)
+        if opt == 'icedims':
+            if val:
+                return 1
+            return 0
+        return super(DicomImport, self)._format_arg(opt, spec, val)
+
+    def _run_interface(self, runtime):
+        od = os.path.abspath(self.inputs.output_dir)
+        if not os.path.isdir(od):
+            os.mkdir(od)
+        return super(DicomImport, self)._run_interface(runtime)
+
+    def _list_outputs(self):
+        from glob import glob
+        outputs = self._outputs().get()
+        od = os.path.abspath(self.inputs.output_dir)
+        outputs['out_files'] = glob(os.path.join(od, '*'))
+        return outputs