From 7a7e56519704744010ca46a8227ae2f6a0c517fa Mon Sep 17 00:00:00 2001 From: beale_j Date: Wed, 22 Mar 2023 13:04:37 +0000 Subject: [PATCH] Delete update-geom-from-lab6.py --- update-geom-from-lab6.py | 164 --------------------------------------- 1 file changed, 164 deletions(-) delete mode 100644 update-geom-from-lab6.py diff --git a/update-geom-from-lab6.py b/update-geom-from-lab6.py deleted file mode 100644 index 7bd338a..0000000 --- a/update-geom-from-lab6.py +++ /dev/null @@ -1,164 +0,0 @@ -#!/usr/bin/python - -import pandas as pd -import numpy as np -import regex as re -from scipy import constants -import argparse -from datetime import datetime -date = datetime.today().strftime('%y%m%d') - - -def calculate_new_corner_positions( beam_x, beam_y ): - - # make df of current corner positions - positions = { "current_x" : [ 607, 1646, 607, 1646, 607, 1646, 538, 1577, 538, 1577, 538, 1577, 538, 3212, 514, 3143 ], - "current_y" : [ 0, 69, 550, 619, 1100, 1169, 1650, 1719, 2200, 2269, 2750, 2819, 597, 667, 1636, 1706 ] - } - corner_df = pd.DataFrame( positions ) - - # calculate new corner positions - corner_df[ "new_x" ] = corner_df.current_x.subtract( beam_x ) - corner_df[ "new_y" ] = corner_df.current_y.subtract( beam_y ) - - # drop old positions - corner_df = corner_df[[ "new_x", "new_y" ]] - - return corner_df - -def scrub_poni( path_to_poni_file ): - - # open poni file - poni_file = open( path_to_poni_file, "r" ).read() - - # regex patterns to scrub poni data - clen_m_pattern = r"Distance:\s(\d\.\d*)" - poni1_m_pattern = r"Poni1:\s(\d\.\d*)" - poni2_m_pattern = r"Poni2:\s(\d\.\d*)" - wave_pattern = r"Wavelength:\s(\d\.\d*)e(-\d+)" - - # regex seach - clen = re.search( clen_m_pattern, poni_file ).group( 1 ) - poni1_m = re.search( poni1_m_pattern, poni_file ).group( 1 ) - poni2_m = re.search( poni2_m_pattern, poni_file ).group( 1 ) - wave = re.search( wave_pattern, poni_file ).group( 1, 2 ) - - # calulate proper wavelength - wave = float(wave[0]) * np.float_power( 10, int( wave[1]) ) - - # calculate beam_centre - poni1_p = float( poni1_m ) / 0.000000075 - poni2_p = float( poni2_m ) / 0.000000075 - - # calculate beam energy in eV - eV = ( ( constants.c * constants.h ) / wave ) / constants.electron_volt - - # return poni1 = y, poni2 = x and energy - return poni1_p, poni2_p, eV, round( float( clen )*1000, 5 ) - - -def write_new_positions( path_to_geom, beam_x, beam_y, clen, energy ): - - # open current geometry file - current_geom_file = open( path_to_geom, "r" ).read() - - # calculate new corner positions - corner_df = calculate_new_corner_positions( beam_x, beam_y ) - - # replace current corner positions with new ones - for i in range(0, 16): - - # x and y positions - new_x, new_y = round( corner_df.new_x[i], 3 ), round( corner_df.new_y[i], 3 ) - - # input new x position - current_pattern_x = r"p" + re.escape( str(i) ) + r"/corner_x = -?\d+\.\d+" - new_pattern_x = r"p" + re.escape( str(i) ) + r"/corner_x = " + str( new_x ) - current_geom_file = re.sub( current_pattern_x, new_pattern_x, current_geom_file ) - - # input new y position - current_pattern_y = r"p" + re.escape( str(i) ) + r"/corner_y = -?\d+\.\d+" - new_pattern_y = r"p" + re.escape( str(i) ) + r"/corner_y = " + str( new_y ) - current_geom_file = re.sub( current_pattern_y, new_pattern_y, current_geom_file ) - - # input new clen - current_clen = r"clen = \d\.\d+" - new_clen = r"clen = " + str( clen ) - current_geom_file = re.sub( current_clen, new_clen, current_geom_file ) - - # input new energy - current_energy = r"photon_energy = \d+" - new_energy = r"photon_energy = " + str( energy ) - current_geom_file = re.sub( current_energy, new_energy, current_geom_file ) - - # create geom new file - geom_start = path_to_geom[:-5] - new_geom_name = "{0}_{1}.geom".format( geom_start, date ) - - # write new geom file - f = open( new_geom_name, "w" ) - f.write( current_geom_file ) - f.close() - - # return new_geom_name - return new_geom_name - - -if __name__ == "__main__": - parser = argparse.ArgumentParser() - parser.add_argument( - "-g", - "--path_to_geom", - help="give the path to the cristallina 8M geom file to be updated", - type=str, - default="/sf/cristallina/data/p20558/work/geom/optimised_geom_file/p20558_hewl_op.geom", - ) - parser.add_argument( - "-x", - "--beam_x", - help="beam_x in pixels", - type=float, - default=1603.73 - ) - parser.add_argument( - "-y", - "--beam_y", - help="beam_y in pixels", - type=float, - default=1661.99 - ) - parser.add_argument( - "-c", - "--clen", - help="detector distance in m", - type=int, - default=0.111 - ) - parser.add_argument( - "-e", - "--energy", - help="photon energy", - type=int, - default=12400 - ) - parser.add_argument( - "-p", - "--poni", - help="path to poni file", - type=str, - ) - args = parser.parse_args() - # run geom converter - - # import pdb;pdb.set_trace() - if args.poni is not None: - print( "reading poni file" ) - beam_y, beam_x, eV, clen = scrub_poni( args.poni ) - print( "beam x, beam_y = {0}, {1}\nphoton_energy = {2}\nclen = {3}".format( beam_x, beam_y, eV, clen ) ) - new_geom_name = write_new_positions( args.path_to_geom, beam_x, beam_y, clen, eV ) - print( "updated .geom file with poni calculations\n new .geom = {0}".format( new_geom_name ) ) - else: - print( "manually input positions" ) - print( "beam x, beam_y = {0}, {1}\nphoton_energy = {2}\nclen = {3}".format( args.beam_x, args.beam_y, args.energy, args.clen ) ) - new_geom_name = write_new_positions( args.path_to_geom, args.beam_x, args.beam_y, args.clen, args.energy ) - print( "updated .geom file with poni calculations\nnew .geom = {0}".format( new_geom_name ) ) \ No newline at end of file