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batch_tomo_reconstruct_par.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Dec 8 2021
Script to run batch imod through the command line using a template from one reconstructed tomogram
v0.7 April 2021 Use exclude views from align.com and tilt.com
TODO: NO TILT SIRT (not really important)
TODO: implement multiprocessing for cluster submission
NOT WORKING YET
is is used specifically for K3 in McGill. Imod 4.11.8
@author: Huy Bui, McGill
"""
import argparse, os, glob, shutil
from multiprocessing import Pool
def run_eraser(baseName, tempCont):
''' Write eraser and run'''
outCom = open(operation + '.com', 'w')
for line in tempCont:
if line.startswith('InputFile'):
outCom.write('InputFile\t{:s}.mrc\n'.format(baseName))
elif line.startswith('OutputFile'):
outCom.write('OutputFile\t{:s}_fixed.mrc\n'.format(baseName))
elif line.startswith('PointModel'):
outCom.write('PointModel\t{:s}_peak.mod\n'.format(baseName))
#elif line.startswith('BinByFactor'):
# outCom.write('BinByFactor\t{:d}.xf\n'.format(binFactor)
else:
outCom.write(line)
outCom.close()
def run_prenewst(baseName, tempCont):
'''Write prenewst and run'''
outCom = open(operation + '.com', 'w')
for line in tempCont:
if line.startswith('InputFile'):
outCom.write('InputFile\t{:s}.mrc\n'.format(baseName))
elif line.startswith('OutputFile'):
outCom.write('OutputFile\t{:s}_preali.mrc\n'.format(baseName))
elif line.startswith('TransformFile'):
outCom.write('TransformFile\t{:s}.prexg\n'.format(baseName))
elif line.endswith('.prexf\n'):
outCom.write('{:s}.prexf\n'.format(baseName))
elif line.endswith('.prexg\n'):
outCom.write('{:s}.prexg\n'.format(baseName))
else:
outCom.write(line)
outCom.close()
def run_newst(baseName, tempCont):
'''Write newst and run'''
outCom = open(operation + '.com', 'w')
for line in tempCont:
if line.startswith('InputFile'):
outCom.write('InputFile\t{:s}.mrc\n'.format(baseName))
elif line.startswith('OutputFile'):
outCom.write('OutputFile\t{:s}_ali.mrc\n'.format(baseName))
elif line.startswith('TransformFile'):
outCom.write('TransformFile\t{:s}.xf\n'.format(baseName))
else:
outCom.write(line)
outCom.close()
def run_align(baseName, tempCont, excludeList):
'''Write align and run'''
outCom = open(operation + '.com', 'w')
for line in tempCont:
if line.startswith('ModelFile'):
outCom.write('ModelFile\t{:s}.fid\n'.format(baseName))
elif line.startswith('ImageFile'):
outCom.write('ImageFile\t{:s}_preali.mrc\n'.format(baseName))
elif line.startswith('OutputModelFile'):
outCom.write('OutputModelFile\t{:s}.3dmod\n'.format(baseName))
elif line.startswith('OutputResidualFile'):
outCom.write('OutputResidualFile\t{:s}.resid\n'.format(baseName))
elif line.startswith('OutputFidXYZFile'):
outCom.write('OutputFidXYZFile\t{:s}fid.xyz\n'.format(baseName))
elif line.startswith('OutputTiltFile'):
outCom.write('OutputTiltFile\t{:s}.tlt\n'.format(baseName))
elif line.startswith('OutputXAxisTiltFile'):
outCom.write('OutputXAxisTiltFile\t{:s}.xtilt\n'.format(baseName))
elif line.startswith('OutputTransformFile'):
outCom.write('OutputTransformFile\t{:s}.tltxf\n'.format(baseName))
elif line.startswith('OutputFilledInModel'):
outCom.write('OutputFilledInModel\t{:s}_nogap.fid\n'.format(baseName))
elif line.startswith('TiltFile'):
outCom.write('TiltFile\t{:s}.rawtlt\n'.format(baseName))
if excludeList != "":
outCom.write('ExcludeList\t{:s}\n'.format(excludeList))
elif line.startswith('InputFile1'):
outCom.write('InputFile1\t{:s}.prexg\n'.format(baseName))
elif line.startswith('InputFile2'):
outCom.write('InputFile2\t{:s}.tltxf\n'.format(baseName))
elif line.startswith('OutputFile'):
outCom.write('OutputFile\t{:s}_fid.xf\n'.format(baseName))
elif line.startswith('$b3dcopy -p'):
outCom.write('$b3dcopy -p {:s}_fid.xf {:s}.xf\n'.format(baseName, baseName))
outCom.write('$b3dcopy -p {:s}.tlt {:s}_fid.tlt\n'.format(baseName, baseName))
elif 'patch2imod' in line:
outCom.write('$if (-e {:s}.resid) patch2imod -s 10 {:s}.resid {:s}.resmod\n'.format(baseName, baseName, baseName))
else:
outCom.write(line)
outCom.close()
def run_tilt(baseName, tempCont, excludeList):
outCom = open('tilt.com', 'w')
for line in tempCont:
if line.startswith('InputProjections'):
outCom.write('InputProjections\t{:s}_ali.mrc\n'.format(baseName))
elif line.startswith('OutputFile'):
outCom.write('OutputFile\t{:s}_full_rec.mrc\n'.format(baseName))
elif line.startswith('TILTFILE'):
outCom.write('TILTFILE\t{:s}.tlt\n'.format(baseName))
if excludeList != "":
outCom.write('EXCLUDELIST\t{:s}\n'.format(excludeList))
#elif line.startswith('THICKNESS'):
# outCom.write('THICKNESS\t{:s}\n'.format(thickness)
elif line.startswith('XTILTFILE'):
outCom.write('XTILTFILE\t{:s}.xtilt\n'.format(baseName))
else:
outCom.write(line)
outCom.close()
#def run_tilt_for_sirt(baseName, tempCont):
# Not doing anything yet
def run_newst_3dfind(baseName, tempCont):
outCom = open('newst_3dfind.com', 'w')
for line in tempCont:
if line.startswith('InputFile'):
outCom.write('InputFile\t{:s}.mrc\n'.format(baseName))
elif line.startswith('OutputFile'):
outCom.write('OutputFile\t{:s}_3dfind_ali.mrc\n'.format(baseName))
elif line.startswith('TransformFile'):
outCom.write('TransformFile\t{:s}.xf\n'.format(baseName))
else:
outCom.write(line)
outCom.close()
def run_tilt_3dfind(baseName, tempCont, excludeList):
outCom = open('tilt_3dfind.com', 'w')
for line in tempCont:
if line.startswith('InputProjections'):
outCom.write('InputProjections\t{:s}_3dfind_ali.mrc\n'.format(baseName))
elif line.startswith('OutputFile'):
outCom.write('OutputFile\t{:s}_3dfind_rec.mrc\n'.format(baseName))
elif line.startswith('TILTFILE'):
outCom.write('TILTFILE\t{:s}.tlt\n'.format(baseName))
if excludeList != "":
outCom.write('ExcludeList\t{:s}\n'.format(excludeList))
#elif line.startswith('THICKNESS'):
# outCom.write('THICKNESS\t{:s}\n'.format(thickness)
elif line.startswith('XTILTFILE'):
outCom.write('XTILTFILE\t{:s}.xtilt\n'.format(baseName))
else:
outCom.write(line)
outCom.close()
def run_findbeads3d(baseName, tempCont):
outCom = open('findbeads3d.com', 'w')
for line in tempCont:
if line.startswith('InputFile'):
outCom.write('InputFile\t{:s}_3dfind_rec.mrc\n'.format(baseName))
elif line.startswith('OutputFile'):
outCom.write('OutputFile\t{:s}_3dfind.mod\n'.format(baseName))
else:
outCom.write(line)
outCom.close()
def run_tilt_3dfind_reproject(baseName, tempCont):
outCom = open('tilt_3dfind_reproject.com', 'w')
for line in tempCont:
if line.startswith('InputProjections'):
outCom.write('InputProjections\t{:s}_3dfind_ali.mrc\n'.format(baseName))
elif line.startswith('OutputFile'):
outCom.write('OutputFile\t{:s}_erase.fid\n'.format(baseName))
elif line.startswith('TILTFILE'):
outCom.write('TILTFILE\t{:s}.tlt\n'.format(baseName))
elif line.startswith('XTILTFILE'):
outCom.write('XTILTFILE\t{:s}.xtilt\n'.format(baseName))
elif line.startswith('ProjectModel'):
outCom.write('ProjectModel\t{:s}_3dfind.mod\n'.format(baseName))
else:
outCom.write(line)
outCom.close()
def run_golderaser(baseName, tempCont):
outCom = open('golderaser.com', 'w')
for line in tempCont:
if line.startswith('InputFile'):
outCom.write('InputFile\t{:s}_ali.mrc\n'.format(baseName))
elif line.startswith('OutputFile'):
outCom.write('OutputFile\t{:s}_erase_ali.mrc\n'.format(baseName))
elif line.startswith('ModelFile'):
outCom.write('ModelFile\t{:s}_erase.fid\n'.format(baseName))
else:
outCom.write(line)
outCom.close()
def run_trimvol(baseName, tempCont):
outCom = open('trimvol.com', 'w')
outCom.write('$trimvol -f -rx {:s}_full_rec.mrc {:s}_rec.mrc'.format(baseName, baseName))
outCom.close()
if __name__=='__main__':
parser = argparse.ArgumentParser(description='Batch tomo reconstruct using IMOD')
parser.add_argument('--i', help='Input Tilt Series',required=True)
parser.add_argument('--operation', help='Imod operation (newst/tilt/newst_3dfind/tilt_3dfind/findbeads3d/tilt_3dfind_reproject/golderaser/trimvol)',required=True)
#parser.add_argument('--bin', help='Bin factor',required=True)
parser.add_argument('--template', help='Template file from 1 reconstruction',required=True)
parser.add_argument('--noproc', help='Number of processors',required=False, default=1)
parser.add_argument('--excludeList', help='ExcludeList',required=False, default="")
#parser.add_argument('--xsize', help='X size of image',required=True)
#parser.add_argument('--ysize', help='Y size of image',required=True)
print('Only tested with 4.11 only')
args = parser.parse_args()
tempfile = open(args.template, 'r')
tempCont = tempfile.readlines()
operation = args.operation
currentDir = os.getcwd()
# Parallel
# Init multiprocessing.Pool()
#pool = mp.Pool(nocpu)
tsList = glob.glob(args.i)
for tiltseries in tsList:
tsName = os.path.basename(tiltseries)
if not tiltseries.endswith('.mrc'):
print('---> Processing ' + tiltseries + ': ERROR! Only mrc file supported')
break
baseName = tsName.replace('.mrc','')
tsPath = os.path.dirname(tiltseries)
print('---> Processing ' + tiltseries + ' ...')
print('Change dir to ' + tsPath)
os.chdir(tsPath)
if operation == 'eraser':
run_eraser(baseName, tempCont)
os.system('submfg eraser.com')
shutil.move(baseName + '.mrc', baseName + '_orig.mrc')
print('mv ' + baseName + '_fixed.mrc ' + baseName + '.mrc')
shutil.move(baseName + '_fixed.mrc', baseName + '.mrc')
elif operation == 'prenewst':
run_prenewst(baseName, tempCont)
os.system('submfg prenewst.com')
elif operation == 'align':
run_align(baseName, tempCont, args.excludeList)
os.system('submfg align.com')
elif operation == 'newst':
run_newst(baseName, tempCont)
os.system('submfg newst.com')
elif operation == 'tilt':
run_tilt(baseName, tempCont, args.excludeList)
os.system('submfg tilt.com')
elif operation == 'newst_3dfind':
run_newst_3dfind(baseName, tempCont)
os.system('submfg newst_3dfind.com')
elif operation == 'tilt_3dfind':
run_tilt_3dfind(baseName, tempCont, args.excludeList)
os.system('submfg tilt_3dfind.com')
elif operation == 'findbeads3d':
run_findbeads3d(baseName, tempCont)
os.system('submfg findbeads3d.com')
elif operation == 'tilt_3dfind_reproject':
run_tilt_3dfind_reproject(baseName, tempCont)
os.system('submfg tilt_3dfind_reproject.com')
elif operation == 'golderaser':
run_golderaser(baseName, tempCont)
os.system('submfg golderaser.com')
shutil.move(baseName + '_ali.mrc', baseName + '_ali.mrc~')
print('mv ' + baseName + '_erase_ali.mrc ' + baseName + '_ali.mrc')
shutil.move(baseName + '_erase_ali.mrc', baseName + '_ali.mrc')
elif operation == 'trimvol':
run_trimvol(baseName, tempCont)
os.system('submfg trimvol.com')
else:
print('Unknown option')
exit(1)
os.chdir(currentDir)