tomodrgn.mrc.MRCHeader

class MRCHeader(header_values: tuple, extended_header: bytes = b'')

Bases: object

Class to parse the header of an MRC file and to write a new MRC header to disk.

Methods

get_apix	Get the pixel size in angstroms per pixel based on header cella_xlen and nx ratio
get_origin	Get the origin of the data coordinate system.
make_default_header	Constructor method to create an MRCHeader object describing a 3-D data array.
parse	Constructor method to create an MRCHeader object from an MRC file name.
update_apix	Update the pixel size in angstrom by adjusting the header cella_xlen, cella_ylen, and cella_zlen
update_origin	Update the origin of the data coordinate system.
write	Write an MRC file header to the specified file handle.

Attributes

dtype_for_mode
field_names
fieldnames_structformats
mode_for_dtype
struct_format_string
struct_formats
total_header_bytes	Calculate the total header length as standard header (1024 bytes) + optional extended header (>= 0)

get_apix() → float

Get the pixel size in angstroms per pixel based on header cella_xlen and nx ratio

Returns:

pixel size in angstroms

get_origin() → tuple[float, float, float]

Get the origin of the data coordinate system.

Returns:

origin in (x, y, z)

classmethod make_default_header(data: ndarray, is_vol: bool = True, angpix: float = 1, origin_x: float = 0, origin_y: float = 0, origin_z: float = 0)

Constructor method to create an MRCHeader object describing a 3-D data array.

Automaticaly calculates and sets:

nx, ny, nz, mode, cella_xlen, cella_ylen, cella_zlen dmin dmax dmean ispg map machst

Assumes default values for:

nxstart = nystart = nzstart := 0, mx := nx, my := ny, mz := nz, cellb_alpha = cellb_beta = cellb_gamma := 90 mapc := 1 mapr := 2 maps := 3 nsymbt := 0 extra1 := b’' * 8 exttyp := b’’ nversion := 0 extra2 := b’' * 84 origin_x = origin_y = origin_z = 0 rms := -1 nlabl := 0 labels := b’' * 84

Parameters:

• data – array of data to be described by this header

• is_vol – whether the data array is a 3-D volume instead of a stack of 2-D images

• angpix – pixel size in angstroms per pixel of the data array

• origin_x – coordinate system origin along x-axis in angstroms, or the phase origin of the transformed image in pixels for MODE 3 or 4 data

• origin_y – coordinate system origin along y-axis in angstroms, or the phase origin of the transformed image in pixels for MODE 3 or 4 data

• origin_z – coordinate system origin along z-axis in angstroms, or the phase origin of the transformed image in pixels for MODE 3 or 4 data

Returns:

MRCHeader object

classmethod parse(fname: str)

Constructor method to create an MRCHeader object from an MRC file name.

Parameters:

fname – path to MRC file on disk

Returns:

MRCHeader object

property total_header_bytes: int

Calculate the total header length as standard header (1024 bytes) + optional extended header (>= 0)

Returns:

total number of bytes in header and extended header

update_apix(angpix: float) → None

Update the pixel size in angstrom by adjusting the header cella_xlen, cella_ylen, and cella_zlen

Parameters:

angpix

Returns:

None

update_origin(origin_x: float, origin_y: float, origin_z: float) → None

Update the origin of the data coordinate system.

Parameters:

• origin_x – new origin along x axis

• origin_y – new origin along y axis

• origin_z – new origin along z axis

Returns:

None

write(fh: BinaryIO) → None

Write an MRC file header to the specified file handle.

Parameters:

fh – filehandle to file on disk opened in binary mode

Returns:

None