170 lines
5.7 KiB
Python
170 lines
5.7 KiB
Python
#!/usr/bin/python
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import pandas as pd
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import numpy as np
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import regex as re
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from scipy import constants
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import argparse
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from datetime import datetime
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date = datetime.today().strftime('%y%m%d')
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def calculate_new_corner_positions( beam_x, beam_y ):
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# make df of current corner positions
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positions = { "current_x" : [ 607, 1646, 607, 1646, 607, 1646, 538, 1577, 538, 1577, 538, 1577, 538, 3212, 514, 3143 ],
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"current_y" : [ 0, 69, 550, 619, 1100, 1169, 1650, 1719, 2200, 2269, 2750, 2819, 597, 667, 1636, 1706 ]
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}
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corner_df = pd.DataFrame( positions )
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# calculate new corner positions
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corner_df[ "new_x" ] = corner_df.current_x.subtract( beam_x )
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corner_df[ "new_y" ] = corner_df.current_y.subtract( beam_y )
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# drop old positions
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corner_df = corner_df[[ "new_x", "new_y" ]]
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return corner_df
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def scrub_poni( path_to_poni_file ):
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# open poni file
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poni_file = open( path_to_poni_file, "r" ).read()
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# regex patterns to scrub poni data
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clen_m_pattern = r"Distance:\s(\d\.\d*)"
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poni1_m_pattern = r"Poni1:\s(\d\.\d*)"
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poni2_m_pattern = r"Poni2:\s(\d\.\d*)"
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wave_pattern = r"Wavelength:\s(\d\.\d*)e(-\d+)"
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# regex seach
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clen = re.search( clen_m_pattern, poni_file ).group( 1 )
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poni1_m = re.search( poni1_m_pattern, poni_file ).group( 1 )
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poni2_m = re.search( poni2_m_pattern, poni_file ).group( 1 )
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wave = re.search( wave_pattern, poni_file ).group( 1, 2 )
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# calulate proper wavelength
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wave = float(wave[0]) * np.float_power( 10, int( wave[1]) )
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# calculate beam_centre
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poni1_p = float( poni1_m ) / 0.000000075
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poni2_p = float( poni2_m ) / 0.000000075
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# calculate beam energy in eV
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eV = ( ( constants.c * constants.h ) / wave ) / constants.electron_volt
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# return poni1 = y, poni2 = x and energy
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return poni1_p, poni2_p, eV, round( float( clen )*1000, 5 )
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def write_new_positions( path_to_geom, beam_x, beam_y, clen, energy, p_group ):
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# open current geometry file
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current_geom_file = open( path_to_geom, "r" ).read()
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# calculate new corner positions
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corner_df = calculate_new_corner_positions( beam_x, beam_y )
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# replace current corner positions with new ones
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for i in range(0, 16):
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# x and y positions
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new_x, new_y = round( corner_df.new_x[i], 3 ), round( corner_df.new_y[i], 3 )
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# input new x position
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current_pattern_x = r"p" + re.escape( str(i) ) + r"/corner_x = -?\d+\.\d+"
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new_pattern_x = r"p" + re.escape( str(i) ) + r"/corner_x = " + str( new_x )
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current_geom_file = re.sub( current_pattern_x, new_pattern_x, current_geom_file )
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# input new y position
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current_pattern_y = r"p" + re.escape( str(i) ) + r"/corner_y = -?\d+\.\d+"
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new_pattern_y = r"p" + re.escape( str(i) ) + r"/corner_y = " + str( new_y )
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current_geom_file = re.sub( current_pattern_y, new_pattern_y, current_geom_file )
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# input new clen
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current_clen = r"clen = \d\.\d+"
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new_clen = r"clen = " + str( clen )
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current_geom_file = re.sub( current_clen, new_clen, current_geom_file )
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# input new energy
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current_energy = r"photon_energy = \d+"
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new_energy = r"photon_energy = " + str( energy )
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current_geom_file = re.sub( current_energy, new_energy, current_geom_file )
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# create geom new file
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geom_start = path_to_geom[:-5]
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new_geom_name = "crmx8M_{0}_{1}.geom".format( p_group, date )
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# write new geom file
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f = open( new_geom_name, "w" )
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f.write( current_geom_file )
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f.close()
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# return new_geom_name
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return new_geom_name
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if __name__ == "__main__":
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parser = argparse.ArgumentParser()
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parser.add_argument(
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"-g",
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"--geom",
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help="give the path to the cristallina 8M geom file to be updated",
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type=str,
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default="/sf/cristallina/applications/mx/crmx-tools/geom_files/crmx8M_230322.geom",
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)
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parser.add_argument(
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"-x",
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"--beam_x",
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help="beam_x in pixels",
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type=float,
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default=1603.73
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)
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parser.add_argument(
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"-y",
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"--beam_y",
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help="beam_y in pixels",
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type=float,
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default=1661.99
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)
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parser.add_argument(
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"-c",
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"--clen",
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help="detector distance in m",
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type=int,
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default=0.111
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)
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parser.add_argument(
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"-e",
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"--energy",
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help="photon energy",
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type=int,
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default=12400
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)
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parser.add_argument(
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"-i",
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"--poni",
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help="path to poni file",
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type=str,
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)
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parser.add_argument(
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"-p",
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"--p_group",
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help="p-group name",
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type=str,
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)
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args = parser.parse_args()
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# run geom converter
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if args.p_group is None:
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print( "you must specify a p-group that the .geom file is associated with\n\nfor example -p p20560" )
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elif args.poni is not None:
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print( "reading poni file" )
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beam_y, beam_x, eV, clen = scrub_poni( args.poni )
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print( "beam x, beam_y = {0}, {1}\nphoton_energy = {2}\nclen = {3}".format( beam_x, beam_y, eV, clen ) )
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new_geom_name = write_new_positions( args.geom, beam_x, beam_y, clen, eV, args.p_group )
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print( "updated .geom file with poni calculations\n new .geom = {0}".format( new_geom_name ) )
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else:
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print( "manually input positions" )
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print( "beam x, beam_y = {0}, {1}\nphoton_energy = {2}\nclen = {3}".format( args.beam_x, args.beam_y, args.energy, args.clen ) )
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new_geom_name = write_new_positions( args.geom, args.beam_x, args.beam_y, args.clen, args.energy, args.p_group )
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print( "updated .geom file with poni calculations\nnew .geom = {0}".format( new_geom_name ) ) |