Mercurial > repos > rv43 > plot_smb_tiff

annotate plot_smb_tiff.py @ 4:0ffa2fbc7546 draft default tip

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213-dirty
author rv43
date Mon, 20 Mar 2023 17:12:07 +0000
parents 6be076b081c4
children
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9f331fb5be2c planemo upload for repository https://github.com/rolfverberg/galaxytools commit ec74ae97e0ca220d04cb668baa656358abf190e9
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1 #!/usr/bin/env python3
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3 import logging
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4
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5 import argparse
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6 import matplotlib.pyplot as plt
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7 import os
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8 #from re import compile as re_compile
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9 import sys
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11 def __main__():
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13 # Parse command line arguments
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14 parser = argparse.ArgumentParser(
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15 description='Plot an image for the SMB schema')
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16 parser.add_argument('-o', '--output_file',
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17 required=True,
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18 type=pathlib.Path,
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19 help='''Full or relative path to the output file.''')
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20 parser.add_argument('--cycle',
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21 required=True,
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22 help='''Run cycle.''')
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23 parser.add_argument('--station',
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24 required=True,
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25 choices=['id1a3', 'id3a'],
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26 help='''Beamline station.''')
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27 parser.add_argument('--btr',
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28 required=True,
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29 help='''BTR.''')
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30 parser.add_argument('--sample',
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31 required=True,
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32 help='''Sample name.''')
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33 parser.add_argument('--scan_number',
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34 default=-1,
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35 type=int,
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36 help='SPEC scan number')
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37 parser.add_argument('--image_index',
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38 default=0,
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39 type=int,
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40 help='Image index relative the first')
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41 parser.add_argument('-l', '--log',
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42 # type=argparse.FileType('w'),
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43 default=sys.stdout,
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44 help='Logging stream or filename')
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45 parser.add_argument('--log_level',
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46 choices=logging._nameToLevel.keys(),
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47 default='INFO',
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48 help='''Specify a preferred logging level.''')
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49 args = parser.parse_args()
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50
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51 # Set log configuration
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52 # When logging to file, the stdout log level defaults to WARNING
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53 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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54 level = logging.getLevelName(args.log_level)
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55 if args.log is sys.stdout:
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56 logging.basicConfig(format=logging_format, level=level, force=True,
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57 handlers=[logging.StreamHandler()])
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58 else:
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59 if isinstance(args.log, str):
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60 logging.basicConfig(filename=f'{args.log}', filemode='w',
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61 format=logging_format, level=level, force=True)
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62 elif isinstance(args.log, io.TextIOWrapper):
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63 logging.basicConfig(filemode='w', format=logging_format, level=level,
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64 stream=args.log, force=True)
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65 else:
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66 raise(ValueError(f'Invalid argument --log: {args.log}'))
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67 stream_handler = logging.StreamHandler()
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68 logging.getLogger().addHandler(stream_handler)
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69 stream_handler.setLevel(logging.WARNING)
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70 stream_handler.setFormatter(logging.Formatter(logging_format))
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71
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72 # Log command line arguments
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73 logging.info(f'cycle = {args.cycle}')
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74 logging.info(f'station = {args.station}')
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75 logging.info(f'btr = {args.btr}')
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76 logging.info(f'sample = {args.sample}')
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77 logging.info(f'scan_number = {args.scan_number}')
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78 logging.info(f'image_index = {args.image_index}')
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79 logging.debug(f'log = {args.log}')
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80 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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81
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82 # Check input parameters
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83 if args.image_index < 0:
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84 raise ValueError(f'Invalid "image_index" parameter ({args.image_index})')
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85
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86 # Check work directory
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87 workdir = f'/nfs/chess/{args.station}/{args.cycle}/{args.btr}/{args.sample}'
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88 logging.info(f'workdir = {workdir}')
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89 if not os.path.isdir(workdir):
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90 raise ValueError('Invalid work directory: {workdir}')
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91
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92 # Get all available scan_numbers
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93 scan_numbers = [int(v) for v in os.listdir(workdir) if v.isdigit() and
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94 os.path.isdir(f'{workdir}/{v}')]
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95
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96 if args.scan_number == -1:
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97 # Pick lowest scan_number with image files
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98 image_file = None
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99 for scan_number in sorted(scan_numbers):
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100 if 'nf' in os.listdir(f'{workdir}/{scan_number}'):
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101 # indexRegex = re_compile(r'\d+')
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102 path = f'{workdir}/{scan_number}/nf'
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103 # image_files = [f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f)) and
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104 # f.endswith(".tif") and indexRegex.search(f)]
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105 image_files = [f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f))
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106 and f.endswith(".tif")]
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107 if len(image_files):
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108 image_file = f'{path}/{image_files[0]}'
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109 break
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110 else:
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111 # Pick requested image file
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112 scan_number = args.scan_number
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113 if not os.path.isdir(f'{workdir}/{scan_number}'):
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114 raise ValueError('Invalid scan_number (non-existing directory {workdir}/{scan_number})')
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115 path = f'{workdir}/{scan_number}/nf'
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116 if 'nf' not in os.listdir(f'{workdir}/{scan_number}'):
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117 raise ValueError('Unable to find directory {path}')
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118 image_files = [f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f))
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119 and f.endswith(".tif")]
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120 if args.image_index >= len(image_files):
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121 raise ValueError('Unable to open the {args.image_index}th image file in {path}')
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122 image_file = f'{path}/{image_files[args.image_index]}'
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123
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124 # Plot image to file
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125 if image_file is None:
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126 raise ValueError('Unable to find a valid image')
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127 data = plt.imread(image_file)
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128 title = 'image_files[0]'
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129 plt.figure(title)
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130 plt.imshow(data)
3
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131 plt.savefig(args.output_file)
0
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132 plt.close(fig=title)
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133
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134 if __name__ == "__main__":
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135 __main__()
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136