exportToHdf.py
138 lines
| 4.8 KiB
| text/x-python
|
PythonLexer
| r0 | #!PYTHONEXE | |||
| #$Id: exportToHdf.py 7355 2021-03-31 20:25:01Z brideout $ | ||||
| usage = """ | ||||
| exportToHdf.py is a script used to convert a Cedar file to hdf5 format. | ||||
| Required arguments: | ||||
| --cedarFilename - full path of existing Madrigal file. | ||||
| --hdf5Filename - full path of hdf5 file to write. | ||||
| Optional arguments - set these to add layouts, parameters or filters. Default is to use cachedFiles.ini: | ||||
| --independentSpatialParms - a comma separated list of parameters as mnemonics | ||||
| that represent independent spatial variables. Causes array layout to be added to | ||||
| output Hdf5 file. If not given, uses $MADROOT/cachedFiles.ini | ||||
| --arraySplittingParms - a comma separated list of parameters as mnemonics used to split | ||||
| arrays into subarrays. For example, beamcode would split data with separate beamcodes | ||||
| into separate arrays. The number of separate arrays will be up to the product of the number of | ||||
| unique values found for each parameter, with the restriction that combinations with no records will | ||||
| not create a separate array. . If not given, uses $MADROOT/cachedFiles.ini | ||||
| --extraParameters - These parameters will be added to the output file if | ||||
| they are not already in the input file. Comma-delimited. Default is no | ||||
| extra parameter | ||||
| --filter - Filter argument as in isprint command as string (eg, 'ti.500,2000') Only one allowed. | ||||
| Default is no filtering | ||||
| --status - use to set status of file. Default is 1 (default). Use -1 to get from fileTab (error raised | ||||
| if not available) | ||||
| Example: | ||||
| exportToHdf --cedarFilename=/opt/madrigal/experiments/1998/mlh/20jan98/mil20100112.001 | ||||
| --hdf5Filename=/home/user/data/mil20100112.hdf5 | ||||
| --independentSpatialParms=range | ||||
| --arraySplittingParms=kinst,pl,mdtyp | ||||
| --extraParameters=ti,te | ||||
| --filter=ti,500,1000 | ||||
| """ | ||||
| import sys | ||||
| import os, os.path | ||||
| import getopt | ||||
| import traceback | ||||
| import madrigal.data | ||||
| # parse command line | ||||
| arglist = 'h' | ||||
| longarglist = ['cedarFilename=', | ||||
| 'hdf5Filename=', | ||||
| 'independentSpatialParms=', | ||||
| 'arraySplittingParms=', | ||||
| 'extraParameters=', | ||||
| 'filter=', | ||||
| 'status=' | ||||
| 'help'] | ||||
| optlist, args = getopt.getopt(sys.argv[1:], arglist, longarglist) | ||||
| # set default values | ||||
| cedarFilename = None | ||||
| hdf5Filename = None | ||||
| independentSpatialParms = None | ||||
| arraySplittingParms = None | ||||
| extraParameters = [] | ||||
| filter = None | ||||
| status = '1' | ||||
| for opt in optlist: | ||||
| if opt[0] == '--cedarFilename': | ||||
| cedarFilename = opt[1] | ||||
| elif opt[0] == '--hdf5Filename': | ||||
| hdf5Filename = opt[1] | ||||
| elif opt[0] == '--independentSpatialParms': | ||||
| independentSpatialParms = opt[1].split(',') | ||||
| elif opt[0] == '--arraySplittingParms': | ||||
| arraySplittingParms = opt[1].split(',') | ||||
| elif opt[0] == '--extraParameters': | ||||
| extraParameters = opt[1].split(',') | ||||
| elif opt[0] == '--filter': | ||||
| filter = opt[1] | ||||
| elif opt[0] == '--status': | ||||
| status = opt[1] | ||||
| if status == '-1': | ||||
| status = None | ||||
| elif opt[0] in ('-h', '--help'): | ||||
| print(usage) | ||||
| sys.exit(0) | ||||
| else: | ||||
| raise ValueError('Illegal option %s\n%s' % (opt[0], usage)) | ||||
| # check that all required arguments passed in | ||||
| if cedarFilename == None: | ||||
| print('--cedarFilename argument required - must be full path of existing madrigal file') | ||||
| print(usage) | ||||
| sys.exit(-1) | ||||
| if hdf5Filename == None: | ||||
| print('--hdf5Filename argument required - must be full path of hdf5 file to write') | ||||
| sys.exit(-1) | ||||
| fileObj = madrigal.data.MadrigalFile(cedarFilename) | ||||
| # read the cachedFiles.ini to see if information needed | ||||
| kinst = fileObj.getKinstList()[0] | ||||
| kindat = fileObj.getKindatList()[0] | ||||
| x,y,x = fileObj._parseCachedIni(kinst, kindat) | ||||
| iniExtraParms, altFormatDict, skipArray = fileObj._parseCachedIni(kinst, kindat) | ||||
| iniSpatialParms = [] | ||||
| iniSplittingParms=[] | ||||
| if 'array' in altFormatDict: | ||||
| value = altFormatDict['array'] | ||||
| if type(value) in (bytes, str): | ||||
| iniSpatialParms = [value] | ||||
| elif len(value) == 2 and type(value[0]) in (tuple, list): | ||||
| iniSpatialParms = value[0] | ||||
| iniSplittingParms = value[1] | ||||
| else: | ||||
| iniSpatialParms = value | ||||
| if independentSpatialParms is None: | ||||
| independentSpatialParms = iniSpatialParms | ||||
| if arraySplittingParms is None: | ||||
| arraySplittingParms = iniSplittingParms | ||||
| fileObj.exportToHdf(output = hdf5Filename, | ||||
| independentSpatialParms = independentSpatialParms, | ||||
| arraySplittingParms = arraySplittingParms, | ||||
| extraParameters = extraParameters, | ||||
| filter = filter, skipArray = skipArray, status=status) | ||||
| print() | ||||
| print('The file %s has been converted to hdf5 format: %s' % (cedarFilename, hdf5Filename)) | ||||
