cryosparc.mrc

cryosparc.mrc#

Classes:

`DT`(value)	MRC data type enumerations
`Header`(nx, ny, nz, datatype, xlen, ylen, ...)	MRC file header

Data:

VOXEL_TYPES

Map from EPU voxelType values to integer data types

Functions:

`read`(file)	Read a .mrc file at the given file into a numpy array.
`write`(file, data, psize)	Write the given ndarray data to a file.

class cryosparc.mrc.DT(value)#: MRC data type enumerations

class cryosparc.mrc.Header(nx: int, ny: int, nz: int, datatype: DT, xlen: float, ylen: float, zlen: float, origin: Tuple[float, float, float], nsymbt: int)#

MRC file header

Attributes:

`datatype`	Integer-representation of MRC data type
`nsymbt`	Number of symbols in the symbol table following the header.
`nx`	Number of pixels in x dimension
`ny`	Number of pixels in y dimension
`nz`	Number of pixels in z dimension
`origin`	Location of image origin
`xlen`	Total size of X axis (e.g., in Angstroms)
`ylen`	Total size of Y axis (e.g., in Angstroms)
`zlen`	Total size of Z axis (e.g., in Angstroms)

datatype: DT#: Integer-representation of MRC data type

nsymbt: int#: Number of symbols in the symbol table following the header. Each symbol is 1024 bytes.

nx: int#: Number of pixels in x dimension

ny: int#: Number of pixels in y dimension

nz: int#: Number of pixels in z dimension

origin: Tuple[float, float, float]#: Location of image origin

xlen: float#: Total size of X axis (e.g., in Angstroms)

ylen: float#: Total size of Y axis (e.g., in Angstroms)

zlen: float#: Total size of Z axis (e.g., in Angstroms)

cryosparc.mrc.VOXEL_TYPES = {'16 BIT FLOAT': DT.FLOAT16, '32 BIT FLOAT': DT.FLOAT32, 'SIGNED 16 BIT INTEGER': DT.INT16, 'UNSIGNED 16 BIT INTEGER': DT.UINT16, 'UNSIGNED 8 BIT INTEGER': DT.UINT8}#: Map from EPU voxelType values to integer data types

cryosparc.mrc.read(file: Union[str, PurePath, IO[bytes]]) → Tuple[Header, NDArray]#

Read a .mrc file at the given file into a numpy array. Returns the MRC header and the resulting array.

Parameters:: file (str | Path | IO) – MRC file path or handle.
Returns:: The MRC header and MRC data as a numpy array.
Return type:: tuple[Header, NDArray]

cryosparc.mrc.write(file: Union[str, PurePath, IO[bytes]], data: NDArray, psize: float)#

Write the given ndarray data to a file. Specify a pixel size for the mrc file as the last argument.

Parameters:

file (str | Path | IO) – File path or handle to write.
data (NDArray) – 2D or 3D numpy array of MRC data.
psize (float) – Pixel size to write into MRC.