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# Copyright (c) 2016, Science and Technology Facilities Council
# This software is distributed under a BSD licence. See LICENSE.txt.
"""
dtypes
------
numpy dtypes used by the ``mrcfile.py`` library.
The dtypes are defined in a separate module because they do not interact nicely
with the ``from __future__ import unicode_literals`` feature used in the rest
of the package.
"""
# Import Python 3 features for future-proofing
# Deliberately do NOT import unicode_literals due to a bug in numpy dtypes:
# https://github.com/numpy/numpy/issues/2407
from __future__ import absolute_import, division, print_function
import numpy as np
from .utils import normalise_byte_order
HEADER_DTYPE = np.dtype([
('nx', 'i4'), # Number of columns
('ny', 'i4'), # Number of rows
('nz', 'i4'), # Number of sections
('mode', 'i4'), # Mode; indicates type of values stored in data block
('nxstart', 'i4'), # Starting point of sub-image
('nystart', 'i4'),
('nzstart', 'i4'),
('mx', 'i4'), # Grid size in X, Y and Z
('my', 'i4'),
('mz', 'i4'),
('cella', [ # Cell size in angstroms
('x', 'f4'),
('y', 'f4'),
('z', 'f4')
]),
('cellb', [ # Cell angles in degrees
('alpha', 'f4'),
('beta', 'f4'),
('gamma', 'f4')
]),
('mapc', 'i4'), # map column 1=x,2=y,3=z.
('mapr', 'i4'), # map row 1=x,2=y,3=z.
('maps', 'i4'), # map section 1=x,2=y,3=z.
('dmin', 'f4'), # Minimum pixel value
('dmax', 'f4'), # Maximum pixel value
('dmean', 'f4'), # Mean pixel value
('ispg', 'i4'), # space group number
('nsymbt', 'i4'), # number of bytes in extended header
('extra1', 'V8'), # extra space, usage varies by application
('exttyp', 'S4'), # code for the type of extended header
('nversion', 'i4'), # version of the MRC format
('extra2', 'V84'), # extra space, usage varies by application
('origin', [ # Origin of image
('x', 'f4'),
('y', 'f4'),
('z', 'f4')
]),
('map', 'S4'), # Contains 'MAP ' to identify file type
('machst', 'u1', 4), # Machine stamp; identifies byte order
('rms', 'f4'), # RMS deviation of densities from mean density
('nlabl', 'i4'), # Number of labels with useful data
('label', 'S80', 10) # 10 labels of 80 characters
])
VOXEL_SIZE_DTYPE = np.dtype([
('x', 'f4'),
('y', 'f4'),
('z', 'f4')
])
NSTART_DTYPE = np.dtype([
('x', 'i4'),
('y', 'i4'),
('z', 'i4')
])
# FEI extended header dtype for metadata version 0, as described in the EPU
# manual. Note that the FEI documentation is unclear about the endianness of
# the data in the extended header, except for the bitmask fields which are
# specified as little-endian. To construct mixed-endian dtypes, we initially
# construct a big-endian type, with only the bitmasks little-endian, then we
# swap all fields to little-endian if we need a fully little-endian type.
fei_dtype_dict = [
('Metadata size', '>i4'),
('Metadata version', '>i4'),
('Bitmask 1', '<u4'),
('Timestamp', '>f8'), # Not specified, but suspect this is in days after 1/1/1900
('Microscope type', 'S16'),
('D-Number', 'S16'),
('Application', 'S16'),
('Application version', 'S16'),
('HT', '>f8'),
('Dose', '>f8'),
('Alpha tilt', '>f8'),
('Beta tilt', '>f8'),
('X-Stage', '>f8'),
('Y-Stage', '>f8'),
('Z-Stage', '>f8'),
('Tilt axis angle', '>f8'),
('Dual axis rotation', '>f8'),
('Pixel size X', '>f8'),
('Pixel size Y', '>f8'),
('Unused range', 'S48'),
('Defocus', '>f8'),
('STEM Defocus', '>f8'),
('Applied defocus', '>f8'),
('Instrument mode', '>i4'),
('Projection mode', '>i4'),
('Objective lens mode', 'S16'),
('High magnification mode', 'S16'),
('Probe mode', '>i4'),
('EFTEM On', '?'),
('Magnification', '>f8'),
('Bitmask 2', '<u4'),
('Camera length', '>f8'),
('Spot index', '>i4'),
('Illuminated area', '>f8'),
('Intensity', '>f8'),
('Convergence angle', '>f8'),
('Illumination mode', 'S16'),
('Wide convergence angle range', '?'),
('Slit inserted', '?'),
('Slit width', '>f8'),
('Acceleration voltage offset', '>f8'),
('Drift tube voltage', '>f8'),
('Energy shift', '>f8'),
('Shift offset X', '>f8'),
('Shift offset Y', '>f8'),
('Shift X', '>f8'),
('Shift Y', '>f8'),
('Integration time', '>f8'),
('Binning Width', '>i4'),
('Binning Height', '>i4'),
('Camera name', 'S16'),
('Readout area left', '>i4'),
('Readout area top', '>i4'),
('Readout area right', '>i4'),
('Readout area bottom', '>i4'),
('Ceta noise reduction', '?'),
('Ceta frames summed', '>i4'),
('Direct detector electron counting', '?'),
('Direct detector align frames', '?'),
('Camera param reserved 0', '>i4'),
('Camera param reserved 1', '>i4'),
('Camera param reserved 2', '>i4'),
('Camera param reserved 3', '>i4'),
('Bitmask 3', '<u4'),
('Camera param reserved 4', '>i4'),
('Camera param reserved 5', '>i4'),
('Camera param reserved 6', '>i4'),
('Camera param reserved 7', '>i4'),
('Camera param reserved 8', '>i4'),
('Camera param reserved 9', '>i4'),
('Phase Plate', '?'),
('STEM Detector name', 'S16'),
('Gain', '>f8'),
('Offset', '>f8'),
('STEM param reserved 0', '>i4'),
('STEM param reserved 1', '>i4'),
('STEM param reserved 2', '>i4'),
('STEM param reserved 3', '>i4'),
('STEM param reserved 4', '>i4'),
('Dwell time', '>f8'),
('Frame time', '>f8'),
('Scan size left', '>i4'),
('Scan size top', '>i4'),
('Scan size right', '>i4'),
('Scan size bottom', '>i4'),
('Full scan FOV X', '>f8'),
('Full scan FOV Y', '>f8'),
('Element', 'S16'),
('Energy interval lower', '>f8'),
('Energy interval higher', '>f8'),
('Method', '>i4'),
('Is dose fraction', '?'),
('Fraction number', '>i4'),
('Start frame', '>i4'),
('End frame', '>i4'),
('Input stack filename', 'S80'),
('Bitmask 4', '<u4'),
('Alpha tilt min', '>f8'),
('Alpha tilt max', '>f8')
]
fei1_dtype_big_endian = np.dtype(fei_dtype_dict)
# Additional metadata entries for FEI extended header dtype for metadata version 2,
# as described in https://www.fei-software-center.com/tem-apps/MRC-2014-Specifications/
fei_dtype_dict.extend([
('Scan rotation', '>f8'),
('Diffraction pattern rotation', '>f8'),
('Image rotation', '>f8'),
('Scan mode enumeration', '>i4'),
('Acquisition time stamp', '>i8'),
('Detector commercial name', 'S16'),
('Start tilt angle', '>f8'),
('End tilt angle', '>f8'),
('Tilt per image', '>f8'),
('Tilt speed', '>f8'),
('Beam center X pixel', '>i4'),
('Beam center Y pixel', '>i4'),
('CFEG flash timestamp', '>i8'),
('Phase plate position index', '>i4'),
('Objective aperture name', 'S16')
])
fei2_dtype_big_endian = np.dtype(fei_dtype_dict)
def get_ext_header_dtype(exttyp, byte_order='='):
"""Get a dtype for an extended header.
Args:
exttyp: One of ``b'FEI1'`` or ``b'FEI2'``, which are currently the only
supported extended header types.
byte_order: One of ``=``, ``<`` or ``>``.
Returns:
A :class:`numpy dtype <numpy.dtype>` object for the extended header, or
:data:`None`
Raises:
:exc:`ValueError`: If ``byte_order`` is not one of ``=``, ``<`` or ``>``.
"""
normalised_byte_order = normalise_byte_order(byte_order)
dtype = None
if exttyp == b'FEI1':
dtype = fei1_dtype_big_endian
elif exttyp == b'FEI2':
dtype = fei2_dtype_big_endian
# If returning a little-endian FEI1 or FEI2 dtype, need to swap the byte order
if dtype is not None and normalised_byte_order == '<':
dtype = dtype.newbyteorder('<')
return dtype
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