mc2FromMDOC.py 6.34 KB
Newer Older
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed May 15 09:22:40 2019

@author: adrian
"""

import configparser
import os, sys
from pprint import pprint
import re
import argparse
from datetime import datetime
import getpass

# clusterBaseDir = '/projects/project-nieverge/'
procDir = 'tomoProc'
rawDir = 'raw'
correctedDir = 'corrected'
alignedDir = 'aligned'
tiltStackDir = 'tiltStacks'
subframesDir = 'subframes'
correctAlignSLURM = "/projects/project-nieverge/scripts/cluster/correctAndAlign.slurm"


parser = argparse.ArgumentParser(description = "Generates batch processing scripts for aligning frames with MotionCor2 from MDOC files.")

# parser.add_argument("-f", "--file", help="create overlay for a single file",
parser.add_argument('-i', '--input', nargs='?', default='.', help='Input MDOC file to process.')
parser.add_argument('-d', '--outDir', nargs='?', default='.', help='Optional output directory to write scripts to.')
parser.add_argument('-dp', '--dataPath', nargs='?', default='.', help='Optional override to use if the data is mounted in a different network base path.')
parser.add_argument('-cp', '--clusterPath', nargs='?', default='/projects/project-nieverge/', help='Destination path of the HPC filesystem data directory.')
parser.add_argument('-cv', '--cudaVer', nargs='?', type=int, default=92, help='Override CUDA version. Default 9.2')
parser.add_argument('-ps', '--patchSize', nargs='?', type=int, default=3, help='Override local alignment patch count. Default 3.')
parser.add_argument('-b', '--binning', nargs='?', type=int, default=1, help='Output binning. Default 1 (no binning).')
parser.add_argument('-dw', '--doseWeight', action='store_true', help='Do dose-weighting on alignment.')
parser.add_argument('-v', '--verbose', action='store_true', help='Allow verbose output from motioncor2 during script run.')
parser.add_argument('-kf', '--keepFrames', action='store_true', help='Keep temporary individual aligned frames.')

# parser.add_argument('-c', '--cutoff', nargs='?', type=float, default='1', help='The threshold of how many standard deviations above or below the a line must deviate before it is corrected')
# parser.add_argument('-g', '--graph', action='store_true', help='Store a graph of the corrected and uncorrected line intensities for debug purposes.')

args = parser.parse_args()

def FakeSecHead(fp): yield '[general]\n'; yield from fp

if args.input == '.':
    print("Missing input file");
    print(parser.print_help())
    sys.exit()

parser = configparser.ConfigParser()

with open(args.input) as mdocFile:
    parser.readfp(FakeSecHead(mdocFile))

# getFilename = re.compile()

stackParams = []

for section in parser.sections():
    if not section.startswith("ZValue"):
        continue
    
    tempDict = {}
    for option in parser.options(section):
        tempDict[option] = parser.get(section, option)
        
    tempDict['filename'] = re.search("\\\\([\w.-]+)$", tempDict['subframepath']).group(1)
    for imageParam in ['countsperelectron', 'defocus', 'exposuredose', 'exposuretime', 'intensity', 'pixelspacing', 'priorrecorddose', 'rotationangle', 'stagez', 'targetdefocus', 'tiltangle']:
        tempDict[imageParam] = float(tempDict[imageParam])
    for imageParam in ['binning', 'cameraindex', 'dividedby2', 'magindex', 'magnification', 'numsubframes', 'spotsize']:
        tempDict[imageParam] = int(tempDict[imageParam])
    
    tempDict['frameDose'] = float(tempDict['framedosesandnumber'].split()[0])
    stackParams.append(tempDict)

# Data transfer to cluster
inPath = os.path.splitext(args.input)

# print(inPath)
# pprint(stackParams[0:2])

# find subframes directory

mdocDir = os.path.dirname(args.input)

for (dirpath, dirnames, filenames) in os.walk(mdocDir):
    for filename in filenames:
        if filename == stackParams[0]['filename']:
            subframesDir = os.path.relpath(dirpath, mdocDir)
            print("Found subframes in directory \"%s\"" % (subframesDir))
            break

stackParams = sorted(stackParams, key = lambda i: i['tiltangle']) 
inBaseName = re.search("(\w+)\..*", args.input).group(1)
stackFileName = os.path.join(mdocDir, inBaseName + ".stackFiles")
tiltFileName = os.path.join(mdocDir, inBaseName + ".rawTlt")

with open(stackFileName, "w+") as stackFile:
    for imageParams in stackParams:
        stackFile.write("%s\n" % (os.path.join(alignedDir, imageParams['filename']) ))

with open(tiltFileName, "w+") as tiltFile:
    for imageParams in stackParams:
        tiltFile.write("%f\n" % (imageParams['tiltangle']) )

with open(os.path.join(mdocDir, inBaseName + "_alignFramesMC2.sh"), "w+") as scriptFile:
    scriptFile.write("#!\\bin\\bash\n\n")
    scriptFile.write("# Script file for motioncor2 alignment of tilt series created by mc2FromMDOC.py on %s by %s\n\n" % (datetime.today().strftime('%Y-%m-%d %H:%M'), getpass.getuser()) )                 
                     
    scriptFile.write('cd "$(dirname "$0")"\n')                 
    scriptFile.write("mkdir -p %s\n\n" % (alignedDir))
    
    for imageParams in stackParams:
        if args.doseWeight:
            doseWeightParams = " -Kv 300 -FmDose %f -InitDose %f" % (imageParams['frameDose'], imageParams['priorrecorddose'])
        else:
            doseWeightParams = ""
        if args.verbose:
            verboseString = ""
        else:
            verboseString = " &>/dev/null"
            
        scriptFile.write("echo Aligning frame stack %s \n" % (os.path.join(subframesDir, imageParams['filename']) ))
        scriptFile.write("MotionCor2-cuda%i -InMrc %s -OutMrc %s -Patch %i %i -InFmMotion 1 -Iter 30 -Tilt %f -FtBin %i -PixSize %f%s%s\n\n" %(args.cudaVer, os.path.join(subframesDir, imageParams['filename']), os.path.join(alignedDir, imageParams['filename']), args.patchSize, args.patchSize,  imageParams['tiltangle'], args.binning,  imageParams['pixelspacing'], doseWeightParams, verboseString) )
    scriptFile.write("echo Creating combined tilt series stack %s\n" % (inBaseName + "_mc2.mrc"))    
    scriptFile.write("newstack -fileinlist %s -output %s -tilt %s\n\n" % ( os.path.basename(stackFileName), inBaseName + "_mc2.mrc", os.path.basename(tiltFileName) ))
    
    if not args.keepFrames:
        scriptFile.write("echo Removing temporary aligned files.\n")
        for imageParams in stackParams:
            scriptFile.write("rm %s\n" % (os.path.join(alignedDir, imageParams['filename'])))
        scriptFile.write("rmdir %s\n" % (alignedDir))