Mercurial > repos > mzhuang > chess_preprocessor

comparison preprocess_dexela_h5_filesystem.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 import time
7 from datetime import datetime
8
9 from hexrd.imageseries import omega
10 import pp_dexela
11 #from IPython import embed
12
13 # =============================================================================
14 # USER INPUT
15 # =============================================================================
16
17 # panel keys to MATCH INSTRUMENT FILE
18 panel_keys = ['FF1', 'FF2']
19 panel_opts = dict.fromkeys(panel_keys)
20
21 # !!!: hard coded options for each dexela for April 2017
22 panel_opts['FF1'] = [('add-row', 1944), ('add-column', 1296),('flip', 'v'), ]
23 panel_opts['FF2'] = [('add-row', 1944), ('add-column', 1296),('flip', 'h'), ]
24
25 # ==================== End Inputs (should not need to alter below this line)
26
27
28
29 def process_dexelas(file_names, samp_name, scan_number,
30 ostart, ostep, num_frames,
31 panel_opts, threshold):
32 """
33 wrapper for F2 dexela setup
34 """
35 ostop = ostart + num_frames*ostep
36 omw = omega.OmegaWedges(num_frames)
37 omw.addwedge(ostart, ostop, num_frames)
38
39 for file_name in file_names:
40 for key in panel_keys:
41 if key.lower() in file_name:
42 ppd = pp_dexela.PP_Dexela(
43 file_name,
44 omw,
45 panel_opts[key],
46 panel_id=key,
47 frame_start=fstart)
48 # embed()
49 # ppd=add_missing_pixel_gap(ppd)
50
51 output_name = samp_name + '_' + \
52 str(scan_number) + '_' + \
53 file_name.split('/')[-1].split('.')[0]
54 ppd.save_processed(output_name, threshold)
55 head_tail = os.path.split(file_name)
56 if head_tail[0] is not None:
57 os.system('cp -p ' + './' + output_name + '* ' + head_tail[0] + ' 2>/dev/null')
58
59 if __name__ == '__main__':
60 #
61 # Run preprocessor
62 #
63 print("Running preprocessor....")
64 parser = argparse.ArgumentParser(
65 description="pre-process double Dexela images from F2")
66
67 parser.add_argument('base_dir',
68 help="raw data path on chess daq", type=str)
69 parser.add_argument('expt_name',
70 help="experiment name", type=str)
71 parser.add_argument('samp_name',
72 help="sample name", type=str)
73 parser.add_argument('scan_number',
74 help="ff scan number", type=int)
75
76 parser.add_argument('-n', '--num-frames',
77 help="number of frames to read",
78 type=int, default=1441)
79 parser.add_argument('-s', '--start-frame',
80 help="index of first data frame",
81 type=int, default=4)
82 parser.add_argument('-t', '--threshold',
83 help="threshold for frame caches",
84 type=int, default=50)
85 parser.add_argument('-o', '--ome-start',
86 help="start omega",
87 type=float, default=0.)
88 # parser.add_argument('-d', '--ome-delta',
89 # help="delta omega",
90 # type=float, default=0.2498265093684941)
91
92 parser.add_argument('-e', '--ome-end',
93 help="end omega",
94 type=float, default=360.)
95
96
97 args = parser.parse_args()
98
99 # strip args
100 data_dir = args.base_dir
101 expt_name = args.expt_name
102 samp_name = args.samp_name
103 scan_number = args.scan_number
104 num_frames = args.num_frames
105 fstart = args.start_frame
106 threshold = args.threshold
107 ostart = args.ome_start
108 oend = args.ome_end
109 ostep = (oend-ostart)/float(num_frames)
110
111 print("== Running preprocessor .... processing ")
112 now = datetime.now()
113 print(now.strftime("%m/%d/%Y %H:%M:%S"))
114
115 file_names = glob.glob(
116 os.path.join(
117 data_dir,
118 expt_name,
119 samp_name,
120 str(scan_number),
121 'ff',
122 '*.h5')
123 )
124 path = os.path.join(data_dir, expt_name, samp_name, str(scan_number), 'ff', '*.h5')
125 print("path = " + path)
126 for f in file_names:
127 print(f)
128
129 check_files_exist = [os.path.exists(file_name) for file_name in file_names]
130 if not np.all(check_files_exist):
131 raise RuntimeError("files don't exist!")
132
133 process_dexelas(file_names, samp_name, scan_number,
134 ostart, ostep, num_frames,
135 panel_opts, threshold)
136 now = datetime.now()
137 print(now.strftime("%m/%d/%Y %H:%M:%S"))
138 print("== End of processing " + " ==")
139 print(" ")
140