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1##################### generated by xml-casa (v2) from flagcmd.xml ################### 

2##################### b8a2611ec7c82cf7a20bc5e22bf736d2 ############################## 

3from __future__ import absolute_import 

4import numpy 

5from casatools.typecheck import CasaValidator as _val_ctor 

6_pc = _val_ctor( ) 

7from casatools.coercetype import coerce as _coerce 

8from casatools.errors import create_error_string 

9from .private.task_flagcmd import flagcmd as _flagcmd_t 

10from casatasks.private.task_logging import start_log as _start_log 

11from casatasks.private.task_logging import end_log as _end_log 

12from casatasks.private.task_logging import except_log as _except_log 

13 

14class _flagcmd: 

15 """ 

16 flagcmd ---- Flagging task based on batches of flag-commands 

17 

18  

19 The flagcmd task will flag the visibility data or calibration 

20 table based on several batch-operations using flag commands. 

21  

22 Flag commands follow the mode and parameter names from the 

23 flagdata task. 

24  

25 The flagcmd task will flag data based on the commands input on 

26 inpmode: 

27 table = input from FLAG_CMD table in MS 

28 list = input from text file or list of strings from inpfile 

29 xml = input from Flag.xml in the MS given by vis 

30  

31 Batch operations include : apply/unapply/list/plot/clear/extract 

32  

33 IMPORTANT: If you use other ways to flag such as interactive 

34 flagging in plotms, the FLAG_CMD will NOT be updated! 

35  

36 NOTE on flagging calibration tables. 

37 ----------------------------------- 

38 We recommend using the flagdata task for flagging cal tabels. When 

39 using flagcmd to flag cal tables, only the 'apply' and 'list' 

40 actions are supported. Because cal tables do not have a FLAG_CMD 

41 sub-table, the default inpmode='table' can only be used if an MS 

42 is given in the 'inpfile' parameter so that flags from the MS are 

43 applied to the cal table. Otherwise, the flag commands must be 

44 given using inpmode='list', either from a file(s) or from a list 

45 of strings. Data selection for calibration tables is limited to 

46 field, scan, antenna, time, spw and observation. 

47  

48  

49 

50 --------- parameter descriptions --------------------------------------------- 

51 

52 vis Name of input visibility file or calibration table. 

53 default: '' (none)  

54  

55 example: vis='uid___A002_X2a5c2f_X54.ms' 

56 inpmode Input mode for flag commands(table/list/xml) 

57 options: 'table','list','xml' 

58 default: 'table' (the input commands from 

59 FLAG_CMD table of the MS) 

60  

61 inpmode='xml' inputs online flags from Flag.xml 

62 file in the MS. This mode has become largely 

63 obsolete with the deprecation of the importevla 

64 task (see the flagcmd task pages in CASA Docs for 

65 more information). This mode will not work for 

66 ALMA MS or cal tables. 

67  

68 NOTE: You can only apply the flags from a list or 

69 xml; you will not be able to unapply 

70 them. Transfer the flag commands to the FLAG_CMD 

71 table if you want to unapply the flags (see 

72 'inpfile' description below). 

73 inpfile Source of flag commands. Subparameter of 

74 inpmode='table/list'. 

75 Path to MS containing FLAG_CMD (table), or name 

76 of an ASCII file, list of files or a list of 

77 Python strings to apply to MS or cal table 

78 (list).  

79 options: [] with flag commands or [] with 

80 filenames or '' with a filename. (String values 

81 must contain quotes around them or the parser 

82 will not work.) 

83 default: '' (read from FLAG_CMD table in the MS 

84 specified via 'vis') 

85  

86 Main use is to read flags from internal FLAG_CMD, 

87 but one use case is to read the flag commands 

88 from an MS given in inpfile and apply them to 

89 another MS or cal table given in vis. 

90 tablerows List of rows of the FLAG_CMD table to read. Subparameter 

91 of inpmode='table/list'. 

92 default: [] (read all rows) 

93  

94 example: [0,1,2,10] 

95  

96 NOTE: currently only takes integer lists, not 

97 parseable strings with ranges. Use the Python 

98 range function to generate ranges, e.g. tablerows 

99 = range(0,30) + range(50,55) instead of 

100 '0~29,50~54' for now. 

101 reason Select flag commands based on REASON(s). Subparameter of 

102 inpmode. 

103 default: 'any' (all flags regardless of reason) 

104  

105 Examples:  

106 reason='FOCUS_ERROR' 

107 reason=['FOCUS_ERROR','SUBREFLECTOR_ERROR'] 

108  

109 If inpfile is a list of files, the reasons given 

110 in this parameter will apply to all the files. 

111  

112 NOTE: what is within the string is literally 

113 matched, e.g. reason='' matches only blank 

114 reasons, and reason 

115 ='FOCUS_ERROR,SUBREFLECTOR_ERROR' matches this 

116 compound reason string only 

117 useapplied Select commands whose rows have APPLIED column set to 

118 True. Subparameter of inpmode='table'. 

119 options: True,False 

120 default: False  

121  

122 If useapplied=True it will read in both applied 

123 and unapplied flags. 

124  

125 IMPORTANT: The APPLIED column is set to True 

126 after a flag command is applied to the MS. In 

127 order to re-apply the same flag command, this 

128 parameter should be set to True. 

129 tbuff Time buffer (sec) to pad flags. Subparameter of 

130 inpmode='xml'. 

131 default: 0.0 

132 ants Allowed flag antenna names to select by. Subparameter of 

133 inpmode='xml'. 

134 action Action to perform in MS and/or in inpfile 

135 options: apply/unapply/list/plot/clear/extract 

136 default: 'apply' 

137  

138 Examples: 

139 -- action='apply': This operation will apply 

140 the commands chosen by inpmode. If 

141 inpmode='table' and inpfile='' then the 

142 APPLIED column in FLAG_CMD will be set to 

143 True. 

144 -- action='unapply': unapply flags in MS. (Not 

145 available for cal tables). This operation will 

146 unapply the commands chosen by inpmode='table' 

147 ONLY. After unapplying the commands, the task 

148 will update the APPLIED column to False. 

149 -- action='list': list and/or save flag 

150 commands. This operation will list the 

151 commands chosen by inpmode on the screen and 

152 save them to the MS or to a file without 

153 applying. It will save the commands to outfile 

154 if the parameter savepars is set to True. If 

155 outfile is None, it will save the commands to 

156 the MS given in 'vis'. 

157 -- action='plot': plot flags (ant 

158 vs. time). (Not available for cal 

159 tables). This operation will plot the flags 

160 chosen by inpmode to a matplotlib gui or to a 

161 file. These will be sorted by antenna 

162 vs. time. Most useful for showing the online 

163 flags. 

164 -- action='clear': clear flags from FLAG_CMD 

165 in the MS. (Not available for cal tables) This 

166 operation will delete the selected flag rows 

167 from the internal FLAG_CMD table of the MS. 

168 -- action='extract': extract internal flag 

169 dictionary. (Not available for cal tables) 

170 This option will return the internal flagging 

171 dictionary to python. There is no extant 

172 description of the format of this dictionary, 

173 as it is an internal device used by the 

174 flagcmd task. This action is provided for the 

175 convenience of advanced users. 

176  

177 WARNING: choosing this action='clear' will 

178 disregard anything you set in inpmode and will 

179 always work on the FLAG_CMD table in vis. This can 

180 be used to totally delete rows from the FLAG_CMD 

181 table, when setting clearall=True. 

182 flagbackup Automatically backup the FLAG column before 

183 execution. Subparameter of action='apply/unapply'. 

184 options: True,False 

185 default: True 

186 clearall Delete all rows from FLAG_CMD. Subparameter of 

187 action='clear'. 

188 default: False (will not clear) 

189 rowlist FLAG_CMD rows to clear. Subparameter of action='clear'. 

190 default: [] (all flags in table) 

191  

192 example: [0,1,2,10] 

193  

194 WARNING: this can be dangerous, and you must set 

195 clearall=True to use this!!! This will delete 

196 the specified rows from the internal FLAG_CMD 

197 table for vis regardless of what mode is set to 

198 (useful for when you import from xml or file), 

199 and decide to redo it). This action will NOT 

200 unapply the commands. 

201  

202 NOTE: currently only takes integer lists, not 

203 parseable strings with ranges. Use the Python 

204 range function to generate ranges, e.g. rowlist = 

205 range(0,30) + range(50,55) instead of 

206 '0~29,50~54' for now. 

207 plotfile Name of output file to save plot 

208 default: '' (plot to matplotlib window) 

209  

210 WARNING: will only reliably plot individual flags 

211 per antenna and timerange (e.g. direct from xml) 

212 savepars Save the flag commands to the FLAG_CMD table of the MS or 

213 to an output text file. 

214 options: True/False  

215 default: False 

216 outfile Name of output file to save commands. Subparameter of 

217 savepars=True. 

218 default: ' '; it will save the commands in the 

219 FLAG_CMD table of the MS. 

220  

221 example: outfile='flags.txt' will save the 

222 parameters in a text file. 

223 overwrite Overwrite an existing file given in 'outfile' to save the 

224 flag commands. Subparameter of savepars=True. 

225 options: True/False 

226 default: True; it will remove the existing file 

227 given in 'outfile' and save the current flag 

228 commands to a new file with the same name. When 

229 set to False, the task will exit with an error 

230 message if the file exist. 

231 RETURNS void 

232 

233 --------- examples ----------------------------------------------------------- 

234 

235  

236  

237 For more information, see the task pages of flagcmd in CASA Docs: 

238  

239 https://casa.nrao.edu/casadocs/ 

240 

241 

242 """ 

243 

244 _info_group_ = """flagging""" 

245 _info_desc_ = """Flagging task based on batches of flag-commands""" 

246 

247 def __call__( self, vis='', inpmode='table', inpfile='', tablerows=[ ], reason='any', useapplied=False, tbuff=float(0.0), ants='', action='apply', flagbackup=True, clearall=False, rowlist=[ ], plotfile='', savepars=False, outfile='', overwrite=True ): 

248 schema = {'vis': {'type': 'cReqPath', 'coerce': _coerce.expand_path}, 'inpmode': {'type': 'cStr', 'coerce': _coerce.to_str, 'allowed': [ 'table', 'list', 'xml' ]}, 'inpfile': {'anyof': [{'type': 'cStr', 'coerce': _coerce.to_str}, {'type': 'cStrVec', 'coerce': [_coerce.to_list,_coerce.to_strvec]}]}, 'tablerows': {'type': 'cIntVec', 'coerce': [_coerce.to_list,_coerce.to_intvec]}, 'reason': {'anyof': [{'type': 'cStr', 'coerce': _coerce.to_str}, {'type': 'cStrVec', 'coerce': [_coerce.to_list,_coerce.to_strvec]}]}, 'useapplied': {'type': 'cBool'}, 'tbuff': {'type': 'cFloat', 'coerce': _coerce.to_float}, 'ants': {'type': 'cStr', 'coerce': _coerce.to_str}, 'action': {'type': 'cStr', 'coerce': _coerce.to_str, 'allowed': [ 'apply', 'clear', 'plot', 'list', 'extract', 'unapply' ]}, 'flagbackup': {'type': 'cBool'}, 'clearall': {'type': 'cBool'}, 'rowlist': {'type': 'cIntVec', 'coerce': [_coerce.to_list,_coerce.to_intvec]}, 'plotfile': {'type': 'cStr', 'coerce': _coerce.to_str}, 'savepars': {'type': 'cBool'}, 'outfile': {'type': 'cStr', 'coerce': _coerce.to_str}, 'overwrite': {'type': 'cBool'}} 

249 doc = {'vis': vis, 'inpmode': inpmode, 'inpfile': inpfile, 'tablerows': tablerows, 'reason': reason, 'useapplied': useapplied, 'tbuff': tbuff, 'ants': ants, 'action': action, 'flagbackup': flagbackup, 'clearall': clearall, 'rowlist': rowlist, 'plotfile': plotfile, 'savepars': savepars, 'outfile': outfile, 'overwrite': overwrite} 

250 assert _pc.validate(doc,schema), create_error_string(_pc.errors) 

251 _logging_state_ = _start_log( 'flagcmd', [ 'vis=' + repr(_pc.document['vis']), 'inpmode=' + repr(_pc.document['inpmode']), 'inpfile=' + repr(_pc.document['inpfile']), 'tablerows=' + repr(_pc.document['tablerows']), 'reason=' + repr(_pc.document['reason']), 'useapplied=' + repr(_pc.document['useapplied']), 'tbuff=' + repr(_pc.document['tbuff']), 'ants=' + repr(_pc.document['ants']), 'action=' + repr(_pc.document['action']), 'flagbackup=' + repr(_pc.document['flagbackup']), 'clearall=' + repr(_pc.document['clearall']), 'rowlist=' + repr(_pc.document['rowlist']), 'plotfile=' + repr(_pc.document['plotfile']), 'savepars=' + repr(_pc.document['savepars']), 'outfile=' + repr(_pc.document['outfile']), 'overwrite=' + repr(_pc.document['overwrite']) ] ) 

252 task_result = None 

253 try: 

254 task_result = _flagcmd_t( _pc.document['vis'], _pc.document['inpmode'], _pc.document['inpfile'], _pc.document['tablerows'], _pc.document['reason'], _pc.document['useapplied'], _pc.document['tbuff'], _pc.document['ants'], _pc.document['action'], _pc.document['flagbackup'], _pc.document['clearall'], _pc.document['rowlist'], _pc.document['plotfile'], _pc.document['savepars'], _pc.document['outfile'], _pc.document['overwrite'] ) 

255 except Exception as exc: 

256 _except_log('flagcmd', exc) 

257 raise 

258 finally: 

259 task_result = _end_log( _logging_state_, 'flagcmd', task_result ) 

260 return task_result 

261 

262flagcmd = _flagcmd( ) 

263