Esempio n. 1
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def tractography_from_trackvis_file(filename):
    tracts_and_data, header = trackvis.read(filename, points_space='rasmm')

    tracts, scalars, properties = izip(*tracts_and_data)

    scalar_names = [n for n in header['scalar_name'] if len(n) > 0]

    #scalar_names_unique = []
    #scalar_names_subcomp = {}
    #for sn in scalar_names:
    #    if re.match('.*_[0-9]{2}', sn):
    #        prefix = sn[:sn.rfind('_')]
    #        if prefix not in scalar_names_unique:
    #            scalar_names_unique.append(prefix)
    #            scalar_names_subcomp[prefix] = int(sn[-2:])
    #        scalar_names_subcomp[prefix] = max(sn[-2:], scalar_names_subcomp[prefix])
    #    else:
    #        scalar_names_unique.append(sn)

    tracts_data = {}
    for i, sn in enumerate(scalar_names):
        tracts_data[sn] = [scalar[:, i][:, None] for scalar in scalars]

    affine = header['vox_to_ras']
    image_dims = header['dim']

    tr = Tractography(tracts, tracts_data)
    tr.affine = affine
    tr.image_dims = image_dims

    return tr
def tractography_from_vtk_files(vtk_file_names):
    tr = Tractography()

    if isinstance(vtk_file_names, str):
        vtk_file_names = [vtk_file_names]

    for file_name in vtk_file_names:
        tracts = read_vtkPolyData(file_name)
        tr.append(tracts.tracts(), tracts.tracts_data())

    return tr
Esempio n. 3
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def tractography_from_vtk_files(vtk_file_names):
    tr = Tractography()

    if isinstance(vtk_file_names, str):
        vtk_file_names = [vtk_file_names]

    for file_name in vtk_file_names:
        tracts = read_vtkPolyData(file_name)
        tr.append(tracts.tracts(), tracts.tracts_data())

    return tr
def vtkPolyData_to_tracts(polydata, return_tractography_object=True):
    r'''
    Reads a VTKPolyData object and outputs a tracts/tracts_data pair

    Parameters
    ----------
    polydata : vtkPolyData
        VTKPolyData Object

    Returns
    -------
    tracts : list of float array N_ix3
        Each element of the list is a tract represented as point array,
        the length of the i-th tract is N_i
    tract_data : dict of <data name>= list of float array of N_ixM
        Each element in the list corresponds to a tract,
        N_i is the length of the i-th tract and M is the
        number of components of that data type.
    '''

    result = {}
    result['lines'] = ns.vtk_to_numpy(polydata.GetLines().GetData())
    result['points'] = ns.vtk_to_numpy(polydata.GetPoints().GetData())
    result['numberOfLines'] = polydata.GetNumberOfLines()

    data = {}
    if polydata.GetPointData().GetScalars():
        data['ActiveScalars'] = polydata.GetPointData().GetScalars().GetName()
    if polydata.GetPointData().GetVectors():
        data['ActiveVectors'] = polydata.GetPointData().GetVectors().GetName()
    if polydata.GetPointData().GetTensors():
        data['ActiveTensors'] = polydata.GetPointData().GetTensors().GetName()

    for i in xrange(polydata.GetPointData().GetNumberOfArrays()):
        array = polydata.GetPointData().GetArray(i)
        np_array = ns.vtk_to_numpy(array)
        if np_array.ndim == 1:
            np_array = np_array.reshape(len(np_array), 1)
        data[polydata.GetPointData().GetArrayName(i)] = np_array

    result['pointData'] = data

    tracts, data = vtkPolyData_dictionary_to_tracts_and_data(result)
    if return_tractography_object:
        tr = Tractography()
        tr.append(tracts, data)
        return tr
    else:
        return tracts, data
Esempio n. 5
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def vtkPolyData_to_tracts(polydata, return_tractography_object=True):
    r'''
    Reads a VTKPolyData object and outputs a tracts/tracts_data pair

    Parameters
    ----------
    polydata : vtkPolyData
        VTKPolyData Object

    Returns
    -------
    tracts : list of float array N_ix3
        Each element of the list is a tract represented as point array,
        the length of the i-th tract is N_i
    tract_data : dict of <data name>= list of float array of N_ixM
        Each element in the list corresponds to a tract,
        N_i is the length of the i-th tract and M is the
        number of components of that data type.
    '''

    result = {}
    result['lines'] = ns.vtk_to_numpy(polydata.GetLines().GetData())
    result['points'] = ns.vtk_to_numpy(polydata.GetPoints().GetData())
    result['numberOfLines'] = polydata.GetNumberOfLines()

    data = {}
    if polydata.GetPointData().GetScalars():
        data['ActiveScalars'] = polydata.GetPointData().GetScalars().GetName()
    if polydata.GetPointData().GetVectors():
        data['ActiveVectors'] = polydata.GetPointData().GetVectors().GetName()
    if polydata.GetPointData().GetTensors():
        data['ActiveTensors'] = polydata.GetPointData().GetTensors().GetName()

    for i in xrange(polydata.GetPointData().GetNumberOfArrays()):
        array = polydata.GetPointData().GetArray(i)
        np_array = ns.vtk_to_numpy(array)
        if np_array.ndim == 1:
            np_array = np_array.reshape(len(np_array), 1)
        data[polydata.GetPointData().GetArrayName(i)] = np_array

    result['pointData'] = data

    tracts, data = vtkPolyData_dictionary_to_tracts_and_data(result)
    if return_tractography_object:
        tr = Tractography()
        tr.append(tracts, data)
        return tr
    else:
        return tracts, data
def tractography_from_vtkPolyData(polydata):
    tractography = Tractography()

    tractography._originalFibers = []
    tractography._tractData = {}
    tractography._originalLines = []
    tractography._originalData = {}
    tractography._tracts = []

    lines, lines_ids, point_data = vtkPolyData_to_lines(polydata)

    tractography._tracts = lines
    tractography._tractData = point_data

    tractography._originalFibers = np.vstack(lines)
    tractography._originalLines = lines_ids
    tractography._originalData = dict(
        ((key, np.vstack(value)) for key, value in tractography._tractData))
Esempio n. 7
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def tractography_from_vtkPolyData(polydata):
    tractography = Tractography()

    tractography._originalFibers = []
    tractography._tractData = {}
    tractography._originalLines = []
    tractography._originalData = {}
    tractography._tracts = []

    lines, lines_ids, point_data = vtkPolyData_to_lines(polydata)

    tractography._tracts = lines
    tractography._tractData = point_data

    tractography._originalFibers = np.vstack(lines)
    tractography._originalLines = lines_ids
    tractography._originalData = dict((
        (key, np.vstack(value))
        for key, value in tractography._tractData
    ))