imagesplit.file.metaio_reader module

Utility for reading and writing data to metaio (mhd/mha) files

Author: Tom Doel Copyright UCL 2017

class imagesplit.file.metaio_reader.MetaIoFile(local_file_size, header_filename, file_handle_factory, header_template)

Bases: imagesplit.file.image_file_reader.LinearImageFileReader

A class for reading or writing 3D imaging data to/from a MetaIO file pair (.mhd and .raw).

close()

Close the files associated with this image, if they are not already closed.

close_file()

Close file

classmethod create_read_file(subimage_descriptor, file_handle_factory)

Create a MetaIoFile class for writing

classmethod create_write_file(subimage_descriptor, file_handle_factory)

Create a MetaIoFile class for this filename and template

get_bytes_per_voxel()

Return the number of bytes used to represent a single voxel in this image.

get_dimension_ordering()

Return the preferred dimension ordering for writing data.

Returns an array of 3 element, where each element represents a dimension in the global coordinate system numbered from 1 to 3 and is positive if data are to be written in ascending coordinates (in the global system) or negative if to be written in descending global coordinates along that dimension

classmethod load_and_parse_header(filename)

Reads a MetaIO header file and parses

read_line(start_coords, num_voxels_to_read)

Read consecutive voxels of image data from the raw binary file starting at the specified coordinates.

write_line(start_coords, image_line, rescale_limits)

Write consecutive voxels to the raw binary file.

imagesplit.file.metaio_reader.anatomical_to_cosine(anatomical_orientation_char)

Get Dicom direction cosine for this orientation string

imagesplit.file.metaio_reader.anatomical_to_permutation(anatomical_orientation_string)

Dimension permutation vector corresponding to this orientation string

imagesplit.file.metaio_reader.condensed_to_cosine(condensed_format)

Get mhd direction cosine for this condensed format axis

imagesplit.file.metaio_reader.dimensions_from_orientations(orientation_vector_1, orientation_vector_2)

Get dimension permutation vectors for these orientation vectors

imagesplit.file.metaio_reader.get_condensed_dim_order(header)

Return the condensed dimension order and flip string for this header

imagesplit.file.metaio_reader.get_default_metadata()

Return an OrderedDict containing default mhd file metadata

imagesplit.file.metaio_reader.get_flip_from_orientations(orientation_1, orientation_2, orientation_3, dimension_1, dimension_2, dimension_3)

Get dimension flip vectors for these orientation vectors

imagesplit.file.metaio_reader.load_mhd_header(filename)

Return an OrderedDict containing metadata loaded from an mhd file.

imagesplit.file.metaio_reader.mhd_cosines_to_permutation(direction_cosine_1, direction_cosine_2, direction_cosine_3)

Get dimension permutation vectors for these mhd direction cosines

imagesplit.file.metaio_reader.parse_mhd(header)

Read a metaheader and returns a FileImageDescriptor

imagesplit.file.metaio_reader.permutation_from_orientations(orientation_1, orientation_2)

Get dimension permutation vectors for these orientation vectors

imagesplit.file.metaio_reader.permutation_to_cosine(permutation, flip)

Get mhd direction cosine for this dimension permutation

imagesplit.file.metaio_reader.save_mhd_header(filename, metadata)

Saves a mhd header file to disk using the given metadata