generate_coordinate_mapping

nighres.registration.generate_coordinate_mapping(reference_image, source_image=None, transform_matrix=None, invert_matrix=False, save_data=False, overwrite=False, output_dir=None, file_name=None)[source]

Generate coordiante mapping

Generate a coordinate mapping for the image(s) and linear transformation as used in CBSTools registration and transformation routines.

Parameters:
  • reference_image (niimg) – Image to generate a coordinate mapping from, listing its X,Y,Z coordinates
  • source_image (niimg, optional) – In case the mapping is from a source and target in different coordinate spaces, this image represents the source space
  • transform_matrix (niimg, optional) – Whether to use a MIPAV formatted transformation matrix to define the mapping
  • invert_matrix (bool) – Whether or not to invert the transformation, if given
  • save_data (bool) – Save output data to file (default is False)
  • overwrite (bool) – Overwrite existing results (default is False)
  • output_dir (str, optional) – Path to desired output directory, will be created if it doesn’t exist
  • file_name (str, optional) – Desired base name for output files with file extension (suffixes will be added)
Returns:

Dictionary collecting outputs under the following keys (suffix of output files in brackets)

  • result (niimg): Coordinate mapping of the reference image (_coord-map)
Return type:

dict

Notes

Port of the CBSTools Java module by Pierre-Louis Bazin. Currently the transformation amtrix follows the MIPAV conventions.