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1 import argparse
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2 import glob
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3 import os
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4
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5 import numpy as np
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6
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7 import time
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8 from datetime import datetime
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9
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10 from hexrd.imageseries import omega
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11 import pp_dexela
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12 #from IPython import embed
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13
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14 # =============================================================================
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15 # USER INPUT
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16 # =============================================================================
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17
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18 # panel keys to MATCH INSTRUMENT FILE
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19 panel_keys = ['FF1', 'FF2']
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20 panel_opts = dict.fromkeys(panel_keys)
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21
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22 # !!!: hard coded options for each dexela for April 2017
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23 panel_opts['FF1'] = [('add-row', 1944), ('add-column', 1296),('flip', 'v'), ]
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24 panel_opts['FF2'] = [('add-row', 1944), ('add-column', 1296),('flip', 'h'), ]
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25
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26 # ==================== End Inputs (should not need to alter below this line)
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27
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28
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29
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30 def process_dexelas(file_names, samp_name, scan_number,
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31 ostart, ostep, num_frames,
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32 panel_opts, threshold):
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33 """
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34 wrapper for F2 dexela setup
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35 """
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36 ostop = ostart + num_frames*ostep
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37 omw = omega.OmegaWedges(num_frames)
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38 omw.addwedge(ostart, ostop, num_frames)
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39
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40 for file_name in file_names:
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41 for key in panel_keys:
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42 if key.lower() in file_name:
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43 ppd = pp_dexela.PP_Dexela(
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44 file_name,
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45 omw,
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46 panel_opts[key],
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47 panel_id=key,
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48 frame_start=fstart)
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49 # embed()
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50 # ppd=add_missing_pixel_gap(ppd)
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51
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52 #output_name = samp_name + '_' + \
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53 # str(scan_number) + '_' + \
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54 output_name = file_name.split('/')[-4] + '_' + \
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55 file_name.split('/')[-3]+ '_' + \
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56 file_name.split('/')[-1].split('.')[0]
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57 ppd.save_processed(output_name, threshold)
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58 head_tail = os.path.split(file_name)
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59 if head_tail[0] is not None:
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60 os.system('cp -p ' + './' + output_name + '* ' + head_tail[0] + ' 2>/dev/null')
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61 if __name__ == '__main__':
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62 #
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63 # Run preprocessor
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64 #
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65
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66 parser = argparse.ArgumentParser(
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67 description="pre-process double Dexela images from F2")
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68
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69 parser.add_argument('file_name',
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70 help="raw data path on chess daq", type=str)
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71
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72 #parser.add_argument('base_dir',
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73 # help="raw data path on chess daq", type=str)
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74 #parser.add_argument('expt_name',
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75 # help="experiment name", type=str)
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76 #parser.add_argument('samp_name',
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77 # help="sample name", type=str)
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78 #parser.add_argument('scan_number',
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79 # help="ff scan number", type=int)
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80
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81 parser.add_argument('-n', '--num-frames',
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82 help="number of frames to read",
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83 type=int, default=1441)
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84 parser.add_argument('-s', '--start-frame',
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85 help="index of first data frame",
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86 type=int, default=4)
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87 parser.add_argument('-t', '--threshold',
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88 help="threshold for frame caches",
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89 type=int, default=50)
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90 parser.add_argument('-o', '--ome-start',
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91 help="start omega",
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92 type=float, default=0.)
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93 # parser.add_argument('-d', '--ome-delta',
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94 # help="delta omega",
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95 # type=float, default=0.2498265093684941)
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96
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97 parser.add_argument('-e', '--ome-end',
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98 help="end omega",
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99 type=float, default=360.)
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100
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101
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102 args = parser.parse_args()
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103
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104 print(args.file_name)
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105 # strip args
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106 file_name = args.file_name
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107 #data_dir = args.base_dir
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108 #expt_name = args.expt_name
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109 #samp_name = args.samp_name
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110 #scan_number = args.scan_number
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111 samp_name = file_name.split('/')[-4]
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112 scan_number = file_name.split('/')[-3]
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113 num_frames = args.num_frames
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114 fstart = args.start_frame
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115 threshold = args.threshold
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116 ostart = args.ome_start
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117 oend = args.ome_end
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118 ostep = (oend-ostart)/float(num_frames)
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119
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120 print("== Running preprocessor .... processing " + file_name + " ==")
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121 now = datetime.now()
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122 print(now.strftime("%m/%d/%Y %H:%M:%S"))
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123
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124 #file_names = glob.glob(
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125 # os.path.join(
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126 # data_dir,
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127 # expt_name,
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128 # samp_name,
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129 # str(scan_number),
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130 # 'ff',
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131 # '*.h5')
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132 #)
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133 file_names = [file_name]
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134 #path = os.path.join(data_dir, expt_name, samp_name, str(scan_number), 'ff', '*.h5')
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135 #print("Preprocessor: after getting file_names ...." + path)
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136 for f in file_names:
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137 print(f)
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138
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139 check_files_exist = [os.path.exists(file_name) for file_name in file_names]
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140 if not np.all(check_files_exist):
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141 raise RuntimeError("files don't exist!")
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142
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143 process_dexelas(file_names, samp_name, scan_number,
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144 ostart, ostep, num_frames,
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145 panel_opts, threshold)
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146 now = datetime.now()
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147 print(now.strftime("%m/%d/%Y %H:%M:%S"))
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148 print("== End of processing " + file_name + " ==")
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149 print(" ")
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150 print(" ")
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151
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