Merge branch 'master' of https://gitlab.psi.ch/beale_j/crmx-tools
There appeared to be an issue between the repo and branch. Not sure what.
This commit is contained in:
Beale John Henry
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# modules
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import pandas as pd
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import subprocess
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import os, errno
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import regex as re
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import numpy as np
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def h5_sample( lst, sample ):
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# create sample of images from run
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# read h5.lst - note - removes // from imade column
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cols = [ "h5", "image" ]
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sample_df = pd.read_csv( lst, sep="\s//", engine="python", names=cols )
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# take defined sample
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sample_df = sample_df.sample( sample )
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# sort list
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sample_df = sample_df.sort_index()
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# re-add // to image columm
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sample_df[ "image" ] = "//" + sample_df.image.astype(str)
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# write sample to file
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sample_file = "h5_{0}_sample.lst".format( sample )
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sample_df.to_csv( sample_file, sep=" ", index=False, header=False )
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# return sample file name
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return sample_file
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def geom_amend( lab6_geom_file, clen ):
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# read lab6 geom
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lab6_geom = open( lab6_geom_file, "r" )
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# use regex to find clen and replace with new
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# clen example => clen = 0.1217
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clen_geom = re.sub( "clen = 0\.\d+", "clen = {0}".format( clen ), lab6_geom.read() )
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# close lab6 geom file
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lab6_geom.close()
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# write new clen_geom to file
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clen_geom_file = "{0}.geom".format( clen )
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geom = open( clen_geom_file, "w" )
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geom.write( clen_geom )
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geom.close()
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# return clen_geom file name
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return clen_geom_file
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def write_crystfel_run( clen, sample_h5_file, clen_geom_file, cell_file ):
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# crystfel file name
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cryst_run_file = "{0}_cryst_run.sh".format( clen )
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# write file
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run_sh = open( cryst_run_file, "w" )
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run_sh.write( "#!/bin/sh\n\n" )
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run_sh.write( "module purge\n" )
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run_sh.write( "module load crystfel/0.10.2\n" )
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# run_sh.write( "module use MX unstable\n" )
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# run_sh.write( "module load gcc/4.8.5 hdf5_serial/1.10.3 xds/20210205 DirAx/1.17 pinkindexer/2021.08\n" )
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# run_sh.write( "module load xgandalf/2021.08 fdip/2021.08 mosflm/7.3.0 crystfel/0.10.0 HDF5_bitshuffle/2018.05 HDF5_LZ4/2018.05 ccp4\n\n" )
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run_sh.write( "indexamajig -i {0} \\\n".format( sample_h5_file ) )
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run_sh.write( " --output={0}.stream \\\n".format( clen ) )
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run_sh.write( " --geometry={0}\\\n".format( clen_geom_file ) )
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run_sh.write( " --pdb={0} \\\n".format( cell_file ) )
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run_sh.write( " --indexing=xgandalf-latt-cell --peaks=peakfinder8 \\\n" )
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run_sh.write( " --integration=rings-grad --tolerance=10.0,10.0,10.0,2,3,2 --threshold=10 --min-snr=5 --int-radius=2,3,6 \\\n" )
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run_sh.write( " -j 36 --no-multi --no-retry --check-peaks --max-res=3000 --min-pix-count=1 --local-bg-radius=4 --min-res=85\n\n" )
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run_sh.close()
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# make file executable
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subprocess.call( [ "chmod", "+x", "{0}".format( cryst_run_file ) ] )
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# return crystfel file name
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return cryst_run_file
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def main( lst, sample, lab6_geom_file, centre_clen, cell_file, steps, scan_name, step_size ):
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# set current working directory
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cwd = os.getcwd()
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# make sample list
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print( "making {0} sample of images".format( sample ) )
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sample_h5 = h5_sample( lst, sample)
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sample_h5_file = "{0}/{1}".format( cwd, sample_h5 )
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print( "done" )
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# make list of clen steps above and below the central clen
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print( "make clen array around {0}".format( centre_clen ) )
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step_range = step_size*steps
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bottom_step = centre_clen-step_range/2
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top_step = bottom_step+step_range
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step_range = np.arange( bottom_step, top_step, step_size )
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step_range = step_range.round( 4 ) # important - otherwise np gives your .99999999 instead of 1 somethimes
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print( "done" )
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# make directorys for results
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print( "begin CrystFEL anaylsis of different clens" )
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# loop to cycle through clen steps
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for clen in step_range:
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# move back to cwd
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os.chdir( cwd )
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print( "processing clen = {0}".format( clen ) )
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# define process directory
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proc_dir = "{0}/{1}/{2}".format( cwd, scan_name, clen )
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# make process directory
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try:
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os.makedirs( proc_dir )
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except OSError as e:
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if e.errno != errno.EEXIST:
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raise
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# move to process directory
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os.chdir( proc_dir )
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# make geom file
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print( "amend .geom file" )
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clen_geom_file = geom_amend( lab6_geom_file, clen )
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print( "done" )
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# make crystfel run file
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print( "make crystfel file" )
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cryst_run_file = write_crystfel_run( clen, sample_h5_file, clen_geom_file, cell_file )
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print( "done" )
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# run crystfel file
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print( "run crystFEL" )
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#subprocess.call( [ "./{0}".format( cryst_run_file ) ] )
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subprocess.call( [ "sbatch", "-p", "day", "--cpus-per-task=32", "--", "./{0}".format( cryst_run_file ) ] )
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print( "done" )
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#subprocess.call( [ "sbatch", "-p", "day", "--cpus-per-task=32", "--", "run{0}.sh".format( run.zfill(4) ) ] )
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# variables
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sample = 500
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lst = "/sf/cristallina/data/p20590/work/process/jhb/detector_refinement/acq0001.JF17T16V01.dark.lst"
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lab6_geom_file = "/sf/cristallina/data/p20590/work/process/jhb/detector_refinement/8M_p-op_c-op_p20590.geom"
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centre_clen = 0.122 # in m
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cell_file = "/sf/cristallina/data/p20590/work/process/jhb/detector_refinement/hewl.cell"
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steps = 10
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scan_name = "fine_scan"
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step_size = 0.0005 # m - 0.001 = coarse scan, 0.0005 = fine
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main( lst, sample, lab6_geom_file, centre_clen, cell_file, steps, scan_name, step_size )
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