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import glob, sys, os, os.path as path
import numpy as np
import mrcz
from distutils.version import StrictVersion
import shutil
args = sys.argv
directory = '.'
"""
This script is used for updating a directory of older MRCZ files from versions
<= 0.4.1 to the 0.5.0 standard, so that the volume sampling is set to the
default (Mx, My, Mz) = [0, 0, 1].
"""
if len(sys.argv) > 1:
directory = sys.argv[1]
mrcz_files = glob.glob(path.join(directory, '*.mrc'), recursive=False)
mrcz_files.extend(glob.glob(path.join(directory, '*.mrcz'), recursive=False))
backup_dir = path.join(directory, 'backup')
os.makedirs(backup_dir)
for filename in mrcz_files:
shutil.copy(filename, path.join(backup_dir, path.basename(filename)))
data, meta = mrcz.readMRC(filename)
compressor = meta['compressor'] if 'compressor' in meta else None
clevel = meta['clevel'] if 'clevel' in meta else 1
voltage = meta['voltage'] if 'voltage' in meta else 0.0
C3 = meta['C3'] if 'C3' in meta else 0.0
gain = meta['gain'] if 'gain' in meta else 1.0
pixelsize = meta['pixelsize'] if 'pixelsize' in meta else [0.1,0.1,0.1]
pixelunits = meta['pixelunits'] if 'pixelunits' in meta else u'\\AA'
if 'packedBytes' in meta:
meta.pop('packedBytes')
if 'minImage' in meta:
meta.pop('minImage')
if 'maxImage' in meta:
meta.pop('maxImage')
if 'meanImage' in meta:
meta.pop('meanImage')
if 'extendedBytes' in meta:
meta.pop('extendedBytes')
mrcz.writeMRC(data, filename, meta=meta,
pixelsize=pixelsize, pixelunits=pixelunits,
voltage=voltage, C3=C3, gain=gain,
compressor=compressor, clevel=clevel)
# Try and read every file back in.
try:
mrcz.readMRC(filename)
except:
raise ValueError('{} could not be re-read'.format(filename))
print('__All__ originals were backed up to %s, remember to delete them' % path.join(directory, 'backup'))
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