organised tools into directories - made 16M pyfai script work

pyfai-tools/update-geom-from-lab6.py

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+#!/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",
+        "--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(
+        "-i",
+        "--poni",
+        help="path to poni file",
+        type=str,
+    )
+    parser.add_argument(
+        "-p",
+        "--p-group",
+        help="p-group name",
+        type=str,
+    )
+    args = parser.parse_args()
+    # run geom converter
+    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.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.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 ) )