def _multiframe_to_block(multiframe_dicom): """ Generate a full datablock containing all stacks """ # Calculate the amount of stacks and slices in the stack number_of_stack_slices = int(common.get_ss_value(multiframe_dicom[Tag(0x2001, 0x105f)][0][Tag(0x2001, 0x102d)])) number_of_stacks = int(int(multiframe_dicom.NumberOfFrames) / number_of_stack_slices) # We create a numpy array size_x = multiframe_dicom.pixel_array.shape[2] size_y = multiframe_dicom.pixel_array.shape[1] size_z = number_of_stack_slices size_t = number_of_stacks # get the format format_string = common.get_numpy_type(multiframe_dicom) # get header info needed for ordering frame_info = multiframe_dicom[0x5200, 0x9230] data_4d = numpy.zeros((size_z, size_y, size_x, size_t), dtype=format_string) # loop over each slice and insert in datablock t_location_index = _get_t_position_index(multiframe_dicom) for slice_index in range(0, size_t * size_z): z_location = frame_info[slice_index].FrameContentSequence[0].InStackPositionNumber - 1 if t_location_index is None: t_location = frame_info[slice_index].FrameContentSequence[0].TemporalPositionIndex - 1 else: t_location = frame_info[slice_index].FrameContentSequence[0].DimensionIndexValues[t_location_index] - 1 block_data = multiframe_dicom.pixel_array[slice_index, :, :] # apply scaling rescale_intercept = frame_info[slice_index].PixelValueTransformationSequence[0].RescaleIntercept rescale_slope = frame_info[slice_index].PixelValueTransformationSequence[0].RescaleSlope block_data = common.do_scaling(block_data, rescale_slope, rescale_intercept) # switch to float if needed if block_data.dtype != data_4d.dtype: data_4d = data_4d.astype(block_data.dtype) data_4d[z_location, :, :, t_location] = block_data full_block = numpy.zeros((size_x, size_y, size_z, size_t), dtype=data_4d.dtype) # loop over each stack and reorganize the data for t_index in range(0, size_t): # transpose the block so the directions are correct data_3d = numpy.transpose(data_4d[:, :, :, t_index], (2, 1, 0)) # add the block the the full data full_block[:, :, :, t_index] = data_3d return full_block