Coverage for python/lsst/source/injection/bin/ingest_injection_catalog.py: 21%

1# This file is part of source_injection. 

2# 

3# Developed for the LSST Data Management System. 

4# This product includes software developed by the LSST Project 

5# (https://www.lsst.org). 

6# See the COPYRIGHT file at the top-level directory of this distribution 

7# for details of code ownership. 

8# 

9# This program is free software: you can redistribute it and/or modify 

10# it under the terms of the GNU General Public License as published by 

11# the Free Software Foundation, either version 3 of the License, or 

12# (at your option) any later version. 

13# 

14# This program is distributed in the hope that it will be useful, 

15# but WITHOUT ANY WARRANTY; without even the implied warranty of 

16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 

17# GNU General Public License for more details. 

18# 

19# You should have received a copy of the GNU General Public License 

20# along with this program. If not, see <https://www.gnu.org/licenses/>. 

21 

22from __future__ import annotations 

23 

24import logging 

25import time 

26from argparse import SUPPRESS, ArgumentParser 

27 

28from astropy.table import Table 

29from lsst.daf.butler import Butler 

30 

31from ..utils.ingest_injection_catalog import ingest_injection_catalog 

32from .source_injection_help_formatter import SourceInjectionHelpFormatter 

33 

34 

35def build_argparser(): 

36 """Build an argument parser for this script.""" 

37 parser = ArgumentParser( 

38 description="""Ingest a source injection catalog into the butler. 

39 

40This script reads an on-disk input catalog or multiple per-band input catalogs 

41and ingests these data into the butler. Catalogs are read in using the astropy 

42Table API. 

43 

44An attempt at auto-identification of the input catalog file format type will be 

45made for each input. A manually specified format can instead be specified for 

46all input catalogs using the ``--format`` option. 

47 

48Each injection catalog must be associated with at least one band, specified 

49immediately after the path to the input catalog. Multiple space-separated bands 

50can be provided for a single input catalog. The injection catalog option may 

51also be called multiple times to ingest multiple per-band catalogs. 

52""", 

53 formatter_class=SourceInjectionHelpFormatter, 

54 epilog="More information is available at https://pipelines.lsst.io.", 

55 add_help=False, 

56 argument_default=SUPPRESS, 

57 ) 

58 parser.add_argument( 

59 "-b", 

60 "--butler-config", 

61 type=str, 

62 help="Location of the butler/registry config file.", 

63 required=True, 

64 metavar="TEXT", 

65 ) 

66 parser.add_argument( 

67 "-i", 

68 "--injection-catalog", 

69 type=str, 

70 help="Location of the input source injection catalog and all associated bands.", 

71 required=True, 

72 metavar=("FILE BAND", "BAND"), 

73 nargs="+", 

74 action="append", 

75 ) 

76 parser.add_argument( 

77 "-o", 

78 "--output-collection", 

79 type=str, 

80 help="Name of the output collection to ingest the injection catalog into.", 

81 required=True, 

82 metavar="COLL", 

83 ) 

84 parser.add_argument( 

85 "-t", 

86 "--dataset-type-name", 

87 type=str, 

88 help="Output dataset type name for the ingested source injection catalog.", 

89 metavar="TEXT", 

90 default="injection_catalog", 

91 ) 

92 parser.add_argument( 

93 "--format", 

94 type=str, 

95 help="Format of the input injection catalog(s), overriding auto-identification.", 

96 metavar="TEXT", 

97 ) 

98 parser.add_argument( 

99 "-h", 

100 "--help", 

101 action="help", 

102 help="Show this help message and exit.", 

103 ) 

104 return parser 

105 

106 

107def main(): 

108 """Use this as the main entry point when calling from the command line.""" 

109 # Set up logging. 

110 tz = time.strftime("%z") 

111 logging.basicConfig( 

112 format="%(levelname)s %(asctime)s.%(msecs)03d" + tz + " - %(message)s", datefmt="%Y-%m-%dT%H:%M:%S" 

113 ) 

114 logger = logging.getLogger(__name__) 

115 logger.setLevel(logging.DEBUG) 

116 

117 args = build_argparser().parse_args() 

118 

119 injection_catalogs = [] 

120 for injection_catalog_schema in args.injection_catalog: 

121 if len(injection_catalog_schema) < 2: 

122 raise RuntimeError("Each injection catalog must be associated with at least one band.") 

123 injection_catalog = injection_catalog_schema.pop(0) 

124 for band in injection_catalog_schema: 

125 injection_catalogs.append((injection_catalog, band)) 

126 

127 writeable_butler = Butler(args.butler_config, writeable=True) 

128 injection_catalog_format = vars(args).get("format", None) 

129 

130 for injection_catalog, band in injection_catalogs: 

131 # The character_as_bytes=False option is preferred, if possible. 

132 try: 

133 table = Table.read(injection_catalog, format=injection_catalog_format, character_as_bytes=False) 

134 except TypeError: 

135 table = Table.read(injection_catalog, format=injection_catalog_format) 

136 

137 _ = ingest_injection_catalog( 

138 writeable_butler=writeable_butler, 

139 table=table, 

140 band=band, 

141 **{ 

142 k: v 

143 for k, v in vars(args).items() 

144 if k not in ["butler_config", "injection_catalog", "format"] 

145 }, 

146 )