# gridDataFormats --- python modules to read and write gridded data
# Copyright (c) 2009-2021 Oliver Beckstein <[email protected]>
# Released under the GNU Lesser General Public License, version 3 or later.
#
""":mod:`mrc` --- the MRC/CCP4 volumetric data format
===================================================
.. versionadded:: 0.7.0
Reading of MRC/CCP4 volumetric files (`MRC2014 file format`_) using
the mrcfile_ library [Burnley2017]_.
.. _mrcfile: https://mrcfile.readthedocs.io/
.. _`MRC2014 file format`: http://www.ccpem.ac.uk/mrc_format/mrc2014.php
References
----------
.. [Burnley2017] Burnley T, Palmer C and Winn M (2017) Recent
developments in the CCP-EM software suite. *Acta
Cryst.* D73:469-477. doi: `10.1107/S2059798317007859`_
.. _`10.1107/S2059798317007859`: https://doi.org/10.1107/S2059798317007859
Classes
-------
"""
import numpy as np
import mrcfile
[docs]
class MRC(object):
"""Represent a MRC/CCP4 file.
Load `MRC/CCP4 2014 <MRC2014 file format>`_ 3D volumetric data with
the mrcfile_ library.
Parameters
----------
filename : str (optional)
input file (or stream), can be compressed
Raises
------
ValueError
If the unit cell is not orthorhombic or if the data
are not volumetric.
Attributes
----------
header : numpy.recarray
Header data from the MRC file as a numpy record array.
array : numpy.ndarray
Data as a 3-dimensional array where axis 0 corresponds to X,
axis 1 to Y, and axis 2 to Z. This order is always enforced,
regardless of the order in the mrc file.
delta : numpy.ndarray
Diagonal matrix with the voxel size in X, Y, and Z direction
(taken from the :attr:`mrcfile.mrcfile.voxel_size` attribute)
origin : numpy.ndarray
numpy array with coordinates of the coordinate system origin
(computed from :attr:`header.origin`, the offsets
:attr:`header.origin.nxstart`, :attr:`header.origin.nystart`,
:attr:`header.origin.nzstart` and the spacing :attr:`delta`)
rank : int
The integer 3, denoting that only 3D maps are read.
Notes
-----
* Only volumetric (3D) densities are read.
* Only orthorhombic unitcells supported (other raise :exc:`ValueError`)
* Only reading is currently supported.
.. versionadded:: 0.7.0
"""
def __init__(self, filename=None):
self.filename = filename
if filename is not None:
self.read(filename)
[docs]
def read(self, filename):
"""Populate the instance from the MRC/CCP4 file *filename*."""
if filename is not None:
self.filename = filename
with mrcfile.open(filename) as mrc:
if not mrc.is_volume(): #pragma: no cover
raise ValueError(
"MRC file {} is not a volumetric density.".format(filename))
self.header = h = mrc.header.copy()
# check for being orthorhombic
if not np.allclose([h.cellb.alpha, h.cellb.beta, h.cellb.gamma],
[90, 90, 90]):
raise ValueError("Only orthorhombic unitcells are currently "
"supported, not "
"alpha={0}, beta={1}, gamma={2}".format(
h.cellb.alpha, h.cellb.beta, h.cellb.gamma))
# mrc.data[z, y, x] indexed: convert to x,y,z as used in GridDataFormats
# together with the axes orientation information in mapc/mapr/maps.
# mapc, mapr, maps = 1, 2, 3 for Fortran-ordering and 3, 2, 1 for C-ordering.
# Other combinations are possible. We reorder the data for the general case
# by sorting mapc, mapr, maps in ascending order, i.e., to obtain x,y,z.
# mrcfile provides the data in zyx shape (without regard to map*) so we first
# transpose it to xyz and then reorient with axes_c_order.
#
# All other "xyz" quantitities are also reordered.
axes_order = np.hstack([h.mapc, h.mapr, h.maps])
axes_c_order = np.argsort(axes_order)
transpose_order = np.argsort(axes_order[::-1])
self.array = np.transpose(mrc.data, axes=transpose_order)
self.delta = np.diag(np.array([mrc.voxel_size.x, mrc.voxel_size.y, mrc.voxel_size.z]))
# the grid is shifted to the MRC origin by offset
# (assume orthorhombic)
offsets = np.hstack([h.nxstart, h.nystart, h.nzstart])[axes_c_order] * np.diag(self.delta)
# GridData origin is centre of cell at x=col=0, y=row=0 z=seg=0
self.origin = np.hstack([h.origin.x, h.origin.y, h.origin.z]) + offsets
self.rank = 3
@property
def shape(self):
"""Shape of the :attr:`array`"""
return self.array.shape
@property
def edges(self):
"""Edges of the grid cells, origin at centre of 0,0,0 grid cell.
Only works for regular, orthonormal grids.
"""
# TODO: Add triclinic cell support.
return [self.delta[d, d] * np.arange(self.shape[d] + 1) +
self.origin[d] - 0.5 * self.delta[d, d]
for d in range(self.rank)]
[docs]
def histogramdd(self):
"""Return array data as (edges,grid), i.e. a numpy nD histogram."""
return (self.array, self.edges)