def parse_vge(header):
"""Parse vge header file"""
file_section = header.get('VolumeSection0\\_FileSection0')
image_size_string = file_section['filesize']
image_size = [int(i) for i in image_size_string.split()]
volume_section = header.get('VolumeSection0')
voxel_size_string = volume_section['volumeresolution']
voxel_size = [float(i) for i in voxel_size_string.split()]
file_format = file_section['filefileformat']
if file_format != "VolumeFileFormat_Raw":
raise ValueError("Unknown file format " + file_format)
msb = True # True
file_format = FileFormats.VOL_FORMAT
dim_order = dim_order_from_header(header)
data_type = DataType.name_from_vge(file_section['filedatatype'])
compression = None
header_dict = header
return (FileImageDescriptor(file_format=file_format,
dim_order=dim_order,
data_type=data_type,
image_size=image_size,
msb=msb,
compression=compression,
voxel_size=voxel_size), header_dict)
def parse_mhd(header):
"""Read a metaheader and returns a FileImageDescriptor"""
file_format = "mhd"
dim_order = get_dim_order(header)
data_type = DataType.name_from_metaio(header["ElementType"])
image_size = header["DimSize"]
msb = header["BinaryDataByteOrderMSB"]
compression = None
return (FileImageDescriptor(file_format=file_format,
dim_order=dim_order,
data_type=data_type,
image_size=image_size,
msb=msb,
compression=compression), header)
def create_write_file(cls, subimage_descriptor, file_handle_factory):
"""Create a MetaIoFile class for this filename and template"""
header_template = cls._create_meta_header(subimage_descriptor)
# header_template = copy.deepcopy(subimage_descriptor.template)
local_file_size = subimage_descriptor.get_local_size()
local_origin = subimage_descriptor.get_local_origin()
if subimage_descriptor.data_type:
header_template["ElementType"] = \
DataType.metaio_from_name(subimage_descriptor.data_type)
header_template["DimSize"] = local_file_size
header_template["Origin"] = local_origin
filename = subimage_descriptor.filename
return cls(local_file_size, filename, file_handle_factory,
header_template)
def _create_meta_header(cls, subimage_descriptor):
local_file_size = subimage_descriptor.get_local_size()
local_origin = subimage_descriptor.get_local_origin()
local_voxel_size = subimage_descriptor.get_local_voxel_size()
transform_matrix = condensed_to_cosine(
subimage_descriptor.axis.to_condensed_format())
header = get_default_metadata()
header["ObjectType"] = 'Image'
header["NDims"] = np.size(local_file_size)
header["BinaryData"] = 'True'
header["BinaryDataByteOrderMSB"] = subimage_descriptor.msb
header["CompressedData"] = 'False'
header["TransformMatrix"] = transform_matrix
header["ElementSize"] = local_voxel_size
header["DimSize"] = local_file_size
header["ElementType"] = \
DataType.metaio_from_name(subimage_descriptor.data_type)
header["Origin"] = local_origin
return header
def test_metaio_from_name(self):
self.assertEqual(DataType.metaio_from_name("short"), "MET_SHORT")
def test_name_from_metaio(self):
self.assertEqual(DataType.name_from_metaio("MET_SHORT"), "short")