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#!PYTHONEXE
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"""createMadrigalHdf5FromMatlab.py reads in Matlab file with all information for a CEDAR file
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and creates an output file.
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$Id: createMadrigalHdf5FromMatlab.py 6540 2018-07-05 19:28:51Z brideout $
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"""
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usage = """"python createMadrigalHdf5FromMatlab.py <input_mat_file> [output_Madrigal_file]
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If output_Madrigal_file not given, uses filename set in .mat file
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"""
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# standard python imports
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import os, os.path, sys
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import datetime
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# third party imports
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import scipy.io
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import numpy
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# Madrigal imports
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import madrigal.cedar
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if len(sys.argv) not in (2, 3):
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print(usage)
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sys.exit()
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matlabFile = sys.argv[1]
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# read in all local variables from *.mat file
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mat_dict = scipy.io.loadmat(matlabFile)
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if len(sys.argv) == 2:
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filename = mat_dict['filename'][0]
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else:
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filename = sys.argv[2]
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# convert all parm names with __plus__ to +
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oneDParms = [str(parm[0][0]).replace('__plus__', '+') for parm in mat_dict['oneDParms']]
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independent2DParms = [str(parm[0][0]).replace('__plus__', '+') for parm in mat_dict['independent2DParms']]
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twoDParms = [str(parm[0][0]).replace('__plus__', '+') for parm in mat_dict['twoDParms']]
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arraySplittingParms = [str(parm[0][0]).replace('__plus__', '+') for parm in mat_dict['arraySplittingParms']]
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data = mat_dict['data']
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principleInvestigator = mat_dict['principleInvestigator']
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if len(principleInvestigator):
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principleInvestigator = str(principleInvestigator[0])
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else:
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principleInvestigator = None
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expPurpose = mat_dict['expPurpose']
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if len(expPurpose):
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expPurpose = str(expPurpose[0])
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else:
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expPurpose = None
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expMode = mat_dict['expMode']
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if len(expMode):
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expMode = str(expMode[0])
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else:
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expMode = None
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cycleTime = mat_dict['cycleTime']
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if len(cycleTime):
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cycleTime = float(cycleTime[0])
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else:
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cycleTime = None
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correlativeExp = mat_dict['correlativeExp']
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if len(correlativeExp):
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correlativeExp = str(correlativeExp[0])
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else:
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correlativeExp = None
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sciRemarks = mat_dict['sciRemarks']
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if len(sciRemarks):
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sciRemarks = str(sciRemarks[0])
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else:
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sciRemarks = None
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instRemarks = mat_dict['instRemarks']
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if len(instRemarks):
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instRemarks = str(instRemarks[0])
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else:
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instRemarks = None
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kindatDesc = mat_dict['kindatDesc']
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if len(kindatDesc):
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kindatDesc = str(kindatDesc[0])
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else:
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kindatDesc = None
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analyst = mat_dict['analyst']
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if len(analyst):
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analyst = str(analyst[0])
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else:
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analyst = None
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comments = mat_dict['comments']
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if len(comments):
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comments = str(comments[0])
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else:
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comments = None
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history = mat_dict['history']
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if len(history):
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history = str(history[0])
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else:
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history = None
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skipArray = bool(mat_dict['skipArray'])
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all2DParms = independent2DParms + twoDParms # in python these are combined
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recnoArr = numpy.unique(data[:,0])
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newFile = madrigal.cedar.MadrigalCedarFile(filename, True, skipArray=skipArray)
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# add each record individually
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for recno in recnoArr:
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indices = numpy.where(data[:,0] == recno)[0]
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numRows = len(indices)
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kinst = int(data[indices[0],1])
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kindat = int(data[indices[0],2])
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ut1_unix = data[indices[0],3]
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ut2_unix = data[indices[0],4]
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sDT = datetime.datetime.utcfromtimestamp(ut1_unix)
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eDT = datetime.datetime.utcfromtimestamp(ut2_unix)
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newRec = madrigal.cedar.MadrigalDataRecord(kinst,
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kindat,
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sDT.year,sDT.month,sDT.day,sDT.hour,sDT.minute,sDT.second, 0,
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eDT.year,eDT.month,eDT.day,eDT.hour,eDT.minute,eDT.second, 0,
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oneDParms,
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all2DParms,
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numRows,
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ind2DList=independent2DParms)
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# set 1D parms
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numSkip = 5 # 5 std parms in data to be skipped
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for i, parm in enumerate(oneDParms):
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newRec.set1D(parm, data[indices[0], numSkip+i])
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# set independent parms
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numSkip = 5 + len(oneDParms)
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for i, parm in enumerate(independent2DParms):
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newRec.set2DParmValues(parm, data[indices, numSkip+i])
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# set dependent 2D parms
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numSkip = 5 + len(oneDParms) + len(independent2DParms)
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for i, parm in enumerate(twoDParms):
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newRec.set2DParmValues(parm, data[indices, numSkip+i])
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# done - append record
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newFile.append(newRec)
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# write result
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newFile.write(arraySplittingParms=arraySplittingParms)
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# add catalog and header
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creatorObj = madrigal.cedar.CatalogHeaderCreator(filename)
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creatorObj.createCatalog(principleInvestigator,
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expPurpose,
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expMode,
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cycleTime,
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correlativeExp,
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sciRemarks,
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instRemarks)
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creatorObj.createHeader(kindatDesc,
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analyst,
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comments,
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history)
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creatorObj.write()
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