join2bdv.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jun  7 08:27:24 2021

@author: schorb
"""

import mrcfile as mrc
import random
import time
import sys
import os
import mobie
import glob
from multiprocessing import Pool

maxsleep = 90
par_jobs = 1

target='slurm'

outformat='ome.zarr'
chunks = list((64,128,128))
downscale_factors = list(([2,2,2],[2,2,2],[1,2,2],[1,2,2],[2,2,2],[2,2,2]))

indir = '/g/schwab/Tobias/EMPIAR/volumes/'
suffix = sys.argv[1]

# indir = os.path.join(indir,suffix)

# fileslist = os.path.join('/g/schwab/Tobias/MoBIE/',suffix+'_joinfiles.txt')
joinlist = glob.glob(os.path.join('/g/schwab/Tobias/EMPIAR/volumes',suffix.split('_')[0],suffix+'*'))

print('Found ' + str(len(joinlist)) + ' files for type ' + suffix + '.')

outdir = '/g/emcf/schorb/code/centrioles-tomo-datasets'

idx = 0

def mobieconvert(infile):
    # skip empty lines
    if len(infile)<3: return

    sleeptime = int(random.random()*maxsleep)

    base = os.path.basename(infile).split('_join')[0]

    # if os.path.exists(os.path.join(outdir,re.sub('/','_',base)+'.ome.zarr')):
    #     print('Skipping '+base+'. It already exists.')
    #     continue
    #
    # if os.path.exists(outfile):
    #     print('re-doing '+base+'.')
    #     shutil.rmtree(outfile)
    #     #continue
    # idx += 1
    #
    # if idx%blocksize == 0:
    #     time.sleep(break_interval)
    # else:
    #     time.sleep(submit_interval)
    # if not os.path.exists(os.path.join(outdir, 'tomo', 'images',
    #                                    outformat.replace('.', '-').replace('.', '-'),
    #                                    base + '.' + outformat, 's6')):
    if not base in mobie.metadata.read_dataset_metadata(os.path.join(outdir,'tomo'))['sources'].keys():

        print('converting ' + base + ' into MoBIE format after waiting for '+str(sleeptime)+'seconds.')

        time.sleep(sleeptime)

        # get pixel size

        mfile = mrc.mmap(infile, permissive='True')
        tomopx = mfile.voxel_size.x / 10000  # in um
        del (mfile)
        resolution = [tomopx] * 3

        mobie.add_image(infile,
                    "data",
                    outdir,
                    "tomo",
                    base,
                    resolution,
                    downscale_factors,
                    chunks,
                    file_format="ome.zarr",
                    target=target,
                    max_jobs=20,
                    menu_name='tomograms',
                    tmp_folder='/scratch/schorb/mobie/'+base,
                    int_to_uint=True
                    )

    else:
        print('Skipping ' + base + '. Already found converted data.')


with Pool(par_jobs) as p:
    p.map(mobieconvert, joinlist)