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