Mercurial > repos > mzhuang > chess_preprocessor

comparison preprocess_dexela_h5_galaxy.py @ 0:4d2a2268a17a draft

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"planemo upload"
author mzhuang
date Thu, 23 Sep 2021 21:00:48 +0000
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-1:000000000000 0:4d2a2268a17a
1 import argparse
2 import glob
3 import os
4
5 import numpy as np
6
7 import time
8 from datetime import datetime
9
10 from hexrd.imageseries import omega
11 import pp_dexela
12 #from IPython import embed
13
14 # =============================================================================
15 # USER INPUT
16 # =============================================================================
17
18 # panel keys to MATCH INSTRUMENT FILE
19 panel_keys = ['FF1', 'FF2']
20 panel_opts = dict.fromkeys(panel_keys)
21
22 # !!!: hard coded options for each dexela for April 2017
23 panel_opts['FF1'] = [('add-row', 1944), ('add-column', 1296),('flip', 'v'), ]
24 panel_opts['FF2'] = [('add-row', 1944), ('add-column', 1296),('flip', 'h'), ]
25
26 # ==================== End Inputs (should not need to alter below this line)
27
28
29
30 def process_dexelas(file_names, samp_name, scan_number,
31 ostart, ostep, num_frames,
32 panel_opts, threshold):
33 """
34 wrapper for F2 dexela setup
35 """
36 ostop = ostart + num_frames*ostep
37 omw = omega.OmegaWedges(num_frames)
38 omw.addwedge(ostart, ostop, num_frames)
39
40 for file_name in file_names:
41 for key in panel_keys:
42 if key.lower() in file_name:
43 ppd = pp_dexela.PP_Dexela(
44 file_name,
45 omw,
46 panel_opts[key],
47 panel_id=key,
48 frame_start=fstart)
49 # embed()
50 # ppd=add_missing_pixel_gap(ppd)
51
52 #output_name = samp_name + '_' + \
53 # str(scan_number) + '_' + \
54 output_name = file_name.split('/')[-4] + '_' + \
55 file_name.split('/')[-3]+ '_' + \
56 file_name.split('/')[-1].split('.')[0]
57 ppd.save_processed(output_name, threshold)
58 head_tail = os.path.split(file_name)
59 if head_tail[0] is not None:
60 os.system('cp -p ' + './' + output_name + '* ' + head_tail[0] + ' 2>/dev/null')
61 if __name__ == '__main__':
62 #
63 # Run preprocessor
64 #
65
66 parser = argparse.ArgumentParser(
67 description="pre-process double Dexela images from F2")
68
69 parser.add_argument('file_name',
70 help="raw data path on chess daq", type=str)
71
72 #parser.add_argument('base_dir',
73 # help="raw data path on chess daq", type=str)
74 #parser.add_argument('expt_name',
75 # help="experiment name", type=str)
76 #parser.add_argument('samp_name',
77 # help="sample name", type=str)
78 #parser.add_argument('scan_number',
79 # help="ff scan number", type=int)
80
81 parser.add_argument('-n', '--num-frames',
82 help="number of frames to read",
83 type=int, default=1441)
84 parser.add_argument('-s', '--start-frame',
85 help="index of first data frame",
86 type=int, default=4)
87 parser.add_argument('-t', '--threshold',
88 help="threshold for frame caches",
89 type=int, default=50)
90 parser.add_argument('-o', '--ome-start',
91 help="start omega",
92 type=float, default=0.)
93 # parser.add_argument('-d', '--ome-delta',
94 # help="delta omega",
95 # type=float, default=0.2498265093684941)
96
97 parser.add_argument('-e', '--ome-end',
98 help="end omega",
99 type=float, default=360.)
100
101
102 args = parser.parse_args()
103
104 print(args.file_name)
105 # strip args
106 file_name = args.file_name
107 #data_dir = args.base_dir
108 #expt_name = args.expt_name
109 #samp_name = args.samp_name
110 #scan_number = args.scan_number
111 samp_name = file_name.split('/')[-4]
112 scan_number = file_name.split('/')[-3]
113 num_frames = args.num_frames
114 fstart = args.start_frame
115 threshold = args.threshold
116 ostart = args.ome_start
117 oend = args.ome_end
118 ostep = (oend-ostart)/float(num_frames)
119
120 print("== Running preprocessor .... processing " + file_name + " ==")
121 now = datetime.now()
122 print(now.strftime("%m/%d/%Y %H:%M:%S"))
123
124 #file_names = glob.glob(
125 # os.path.join(
126 # data_dir,
127 # expt_name,
128 # samp_name,
129 # str(scan_number),
130 # 'ff',
131 # '*.h5')
132 #)
133 file_names = [file_name]
134 #path = os.path.join(data_dir, expt_name, samp_name, str(scan_number), 'ff', '*.h5')
135 #print("Preprocessor: after getting file_names ...." + path)
136 for f in file_names:
137 print(f)
138
139 check_files_exist = [os.path.exists(file_name) for file_name in file_names]
140 if not np.all(check_files_exist):
141 raise RuntimeError("files don't exist!")
142
143 process_dexelas(file_names, samp_name, scan_number,
144 ostart, ostep, num_frames,
145 panel_opts, threshold)
146 now = datetime.now()
147 print(now.strftime("%m/%d/%Y %H:%M:%S"))
148 print("== End of processing " + file_name + " ==")
149 print(" ")
150 print(" ")
151