Delete distance-refinement.py
This commit is contained in:
@@ -1,155 +0,0 @@
|
|||||||
|
|
||||||
|
|
||||||
# modules
|
|
||||||
import pandas as pd
|
|
||||||
import subprocess
|
|
||||||
import os, errno
|
|
||||||
import regex as re
|
|
||||||
import numpy as np
|
|
||||||
|
|
||||||
def h5_sample( lst, sample ):
|
|
||||||
|
|
||||||
# create sample of images from run
|
|
||||||
# read h5.lst - note - removes // from imade column
|
|
||||||
cols = [ "h5", "image" ]
|
|
||||||
sample_df = pd.read_csv( lst, sep="\s//", engine="python", names=cols )
|
|
||||||
|
|
||||||
# take defined sample
|
|
||||||
sample_df = sample_df.sample( sample )
|
|
||||||
|
|
||||||
# sort list
|
|
||||||
sample_df = sample_df.sort_index()
|
|
||||||
|
|
||||||
# re-add // to image columm
|
|
||||||
sample_df[ "image" ] = "//" + sample_df.image.astype(str)
|
|
||||||
|
|
||||||
# write sample to file
|
|
||||||
sample_file = "h5_{0}_sample.lst".format( sample )
|
|
||||||
sample_df.to_csv( sample_file, sep=" ", index=False, header=False )
|
|
||||||
|
|
||||||
# return sample file name
|
|
||||||
return sample_file
|
|
||||||
|
|
||||||
def geom_amend( lab6_geom_file, clen ):
|
|
||||||
|
|
||||||
# read lab6 geom
|
|
||||||
lab6_geom = open( lab6_geom_file, "r" )
|
|
||||||
|
|
||||||
# use regex to find clen and replace with new
|
|
||||||
# clen example => clen = 0.1217
|
|
||||||
clen_geom = re.sub( "clen = 0\.\d+", "clen = {0}".format( clen ), lab6_geom.read() )
|
|
||||||
|
|
||||||
# close lab6 geom file
|
|
||||||
lab6_geom.close()
|
|
||||||
|
|
||||||
# write new clen_geom to file
|
|
||||||
clen_geom_file = "{0}.geom".format( clen )
|
|
||||||
geom = open( clen_geom_file, "w" )
|
|
||||||
geom.write( clen_geom )
|
|
||||||
geom.close()
|
|
||||||
|
|
||||||
# return clen_geom file name
|
|
||||||
return clen_geom_file
|
|
||||||
|
|
||||||
def write_crystfel_run( clen, sample_h5_file, clen_geom_file, cell_file ):
|
|
||||||
|
|
||||||
# crystfel file name
|
|
||||||
cryst_run_file = "{0}_cryst_run.sh".format( clen )
|
|
||||||
|
|
||||||
# write file
|
|
||||||
run_sh = open( cryst_run_file, "w" )
|
|
||||||
run_sh.write( "#!/bin/sh\n\n" )
|
|
||||||
run_sh.write( "module purge\n" )
|
|
||||||
run_sh.write( "module load crystfel/0.10.2\n" )
|
|
||||||
# run_sh.write( "module use MX unstable\n" )
|
|
||||||
# run_sh.write( "module load gcc/4.8.5 hdf5_serial/1.10.3 xds/20210205 DirAx/1.17 pinkindexer/2021.08\n" )
|
|
||||||
# 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" )
|
|
||||||
run_sh.write( "indexamajig -i {0} \\\n".format( sample_h5_file ) )
|
|
||||||
run_sh.write( " --output={0}.stream \\\n".format( clen ) )
|
|
||||||
run_sh.write( " --geometry={0}\\\n".format( clen_geom_file ) )
|
|
||||||
run_sh.write( " --pdb={0} \\\n".format( cell_file ) )
|
|
||||||
run_sh.write( " --indexing=xgandalf-latt-cell --peaks=peakfinder8 \\\n" )
|
|
||||||
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" )
|
|
||||||
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" )
|
|
||||||
run_sh.close()
|
|
||||||
|
|
||||||
# make file executable
|
|
||||||
subprocess.call( [ "chmod", "+x", "{0}".format( cryst_run_file ) ] )
|
|
||||||
|
|
||||||
# return crystfel file name
|
|
||||||
return cryst_run_file
|
|
||||||
|
|
||||||
def main( lst, sample, lab6_geom_file, centre_clen, cell_file, steps, scan_name, step_size ):
|
|
||||||
|
|
||||||
# set current working directory
|
|
||||||
cwd = os.getcwd()
|
|
||||||
|
|
||||||
# make sample list
|
|
||||||
print( "making {0} sample of images".format( sample ) )
|
|
||||||
sample_h5 = h5_sample( lst, sample)
|
|
||||||
sample_h5_file = "{0}/{1}".format( cwd, sample_h5 )
|
|
||||||
print( "done" )
|
|
||||||
|
|
||||||
# make list of clen steps above and below the central clen
|
|
||||||
print( "make clen array around {0}".format( centre_clen ) )
|
|
||||||
step_range = step_size*steps
|
|
||||||
bottom_step = centre_clen-step_range/2
|
|
||||||
top_step = bottom_step+step_range
|
|
||||||
step_range = np.arange( bottom_step, top_step, step_size )
|
|
||||||
step_range = step_range.round( 4 ) # important - otherwise np gives your .99999999 instead of 1 somethimes
|
|
||||||
print( "done" )
|
|
||||||
|
|
||||||
# make directorys for results
|
|
||||||
print( "begin CrystFEL anaylsis of different clens" )
|
|
||||||
|
|
||||||
# loop to cycle through clen steps
|
|
||||||
for clen in step_range:
|
|
||||||
|
|
||||||
# move back to cwd
|
|
||||||
os.chdir( cwd )
|
|
||||||
|
|
||||||
print( "processing clen = {0}".format( clen ) )
|
|
||||||
# define process directory
|
|
||||||
proc_dir = "{0}/{1}/{2}".format( cwd, scan_name, clen )
|
|
||||||
|
|
||||||
# make process directory
|
|
||||||
try:
|
|
||||||
os.makedirs( proc_dir )
|
|
||||||
except OSError as e:
|
|
||||||
if e.errno != errno.EEXIST:
|
|
||||||
raise
|
|
||||||
|
|
||||||
# move to process directory
|
|
||||||
os.chdir( proc_dir )
|
|
||||||
|
|
||||||
# make geom file
|
|
||||||
print( "amend .geom file" )
|
|
||||||
clen_geom_file = geom_amend( lab6_geom_file, clen )
|
|
||||||
print( "done" )
|
|
||||||
|
|
||||||
# make crystfel run file
|
|
||||||
print( "make crystfel file" )
|
|
||||||
cryst_run_file = write_crystfel_run( clen, sample_h5_file, clen_geom_file, cell_file )
|
|
||||||
print( "done" )
|
|
||||||
|
|
||||||
# run crystfel file
|
|
||||||
print( "run crystFEL" )
|
|
||||||
#subprocess.call( [ "./{0}".format( cryst_run_file ) ] )
|
|
||||||
subprocess.call( [ "sbatch", "-p", "day", "--cpus-per-task=32", "--", "./{0}".format( cryst_run_file ) ] )
|
|
||||||
print( "done" )
|
|
||||||
|
|
||||||
#subprocess.call( [ "sbatch", "-p", "day", "--cpus-per-task=32", "--", "run{0}.sh".format( run.zfill(4) ) ] )
|
|
||||||
|
|
||||||
# variables
|
|
||||||
sample = 500
|
|
||||||
lst = "/sf/cristallina/data/p20590/work/process/jhb/detector_refinement/acq0001.JF17T16V01.dark.lst"
|
|
||||||
lab6_geom_file = "/sf/cristallina/data/p20590/work/process/jhb/detector_refinement/8M_p-op_c-op_p20590.geom"
|
|
||||||
centre_clen = 0.122 # in m
|
|
||||||
cell_file = "/sf/cristallina/data/p20590/work/process/jhb/detector_refinement/hewl.cell"
|
|
||||||
steps = 10
|
|
||||||
scan_name = "fine_scan"
|
|
||||||
step_size = 0.0005 # m - 0.001 = coarse scan, 0.0005 = fine
|
|
||||||
|
|
||||||
main( lst, sample, lab6_geom_file, centre_clen, cell_file, steps, scan_name, step_size )
|
|
||||||
|
|
||||||
|
|
||||||
Reference in New Issue
Block a user