def includeShip(src,viewportId,MMSI,year): begtime=year[-2:]+"010101" endtime=str(int(year)+1)[-2:]+"010100" cmd = "shiptsexist -p -r %s -b%s -e%s -A%s %i" %("f", begtime, endtime, viewportId, MMSI) returnCode,errMsg,outMsg=utilities.execute(cmd) if int(outMsg)==0: return False else: return True
def main(): # setting up option parser parser = OptionParser(usage=usage, version=version) parser.add_option( "-t", "--template", action="store", dest="template", default=None, help="Create default controlfile template" ) (options, args) = parser.parse_args() logger = logging.getLogger("batchTrendReport") if options.template != None: controlFile.generateCf(path.abspath(options.template), cf_template) print "Generated default controlfile" sys.exit() if len(args) != 2: parser.error("Wrong number of arguments") cfPath = path.abspath(args[0]) makroPath = path.abspath(args[1]) if not path.exists(cfPath): logger.error("Control file does not exist") sys.exit(-1) if not path.exists(makroPath): logger.error("Input makro does not exist") sys.exit(-1) domain = pyDomain.domain(os.environ["AVDBNAME"]) substanceIndices = domain.listSubstanceIndices() cf = controlFile.controlFile(cfPath) makro = controlFile.controlFile(makroPath, removeComments=False) outputDir = cf.findExistingPath("outputDir:") users = cf.findStringList("users:") years = cf.findStringList("years:") nyears = len(years) substances = cf.findStringList("substances:") prefix = cf.findString("prefix:") markerTablePath = cp.findExistingPath("markerFile:", optional=True, default=None) if markerTablePath is not None: keys = ["Label", "Geocode", "ActivityCode"] markerTable = dataTable.DataTable( keys=keys, desc=[{"id": "Label", "type": str}, {"id": "Geocode", "type": Str}, {"id": "Activitycode", "type": str}], ) markerTable.read(markerTablePath) substMapping = {} for subst in substances: officialName = cf.findString(subst + ".name:", optional=True, default=None) if officialName is not None: substMapping[subst] = officialName gcMapping = {} for user in users: gc = cf.findString(user + ".gc:") gcMapping[user] = gc # edbs={} # for year in years: # edbs[year]=cf.findStringList("edb."+year+":") for user in users: logger.info("Exporting reports for user %s" % user) # Set the user for each entry in the trend for i in range(nyears): makro.setParam("edb.trend." + str(i) + ".user:"******"edb.reportgeocode:", gcMapping[user]) # for year in years: # makro.setParam("edb.trend.0.name:",year) for subst in substances: logger.info("Substans %s" % subst) substIndex = substanceIndices[subst] # makro.setParam("edb.trend.0.edb:",edbs[year]) makro.setParam("edb.reportsubstancelist:", str(substIndex)) tmp = tempfile.NamedTemporaryFile(suffix=".tmp", dir=path.join(os.environ["DBAS_PATH"], "tmp")) makroRelPath = makro.name.split("/sedb/")[1] cmd = "rusreport " + os.environ["AVDBNAME"] + " " + makroRelPath + " > " + tmp.name returnCode, errMsg, outMsg = execute(cmd) if returnCode != 0: logger.error("Command: " + cmd + " did not finish successfully") logger.error("Std output: " + outMsg) sys.exit() # reportName=path.join(outputDir,prefix+"_"+year+"_sverige_"+subst+".xls") if user != "airviro": reportName = path.join(outputDir, prefix + "_" + user + "_" + subst + ".xls") else: reportName = path.join(outputDir, prefix + "_" + "sverige" + "_" + subst + ".xls") ascii2xls(tmp.name, reportName, substMapping)
def main(): # -----------Setting up and unsing option parser----------------------- parser = OptionParser(usage=usage, version=version) parser.add_option( "-l", "--loglevel", action="store", dest="loglevel", default=2, help="Sets the loglevel (0-3 where 3=full logging)", ) parser.add_option("-o", "--outfile", action="store", dest="outfile", default=None, help="Output file") parser.add_option("--MMSI", action="store", dest="MMSI", default=None, help="Text-file with mmsi to process") parser.add_option("--begin", action="store", dest="begin", default=None, help="Begin processing at 'YYMMDDhhmm'") parser.add_option("--end", action="store", dest="end", default=None, help="End processing at 'YYMMDDhhmm'") (options, args) = parser.parse_args() # --------------------Init logger----------------------- rootLogger = logger.RootLogger(int(options.loglevel)) global log log = rootLogger.getLogger(sys.argv[0]) # -----------------Validating options------------------- if options.MMSI is None: log.error("Need to specify '--MMSI <MMSI>'") return 1 if options.begin is None: log.error("Need to specify '--begin <YYMMDDhh>'") return 1 if options.end is None: log.error("Need to specify '--end <YYMMDDhh>'") return 1 if options.outfile is None: log.error("Needs to specify '-o <output file>'") return 1 output = open(path.abspath(options.outfile), "w") output.write if options.bounds is not None: try: bounds = [int(c) for c in options.bounds.split(",")] except: parser.error("Could not parse bounds, format should be 'xmin,ymin,xmax,ymax'") if options.exportFile is not None: name, ext = path.splitext(options.exportFile) if ext != ".gz": exportFileName = path.abspath(options.exportFile) + ".gz" else: exportFileName = path.abspath(options.exportFile) export = gzip.open(exportFileName, "wb") log.info("Running keyscan") # Get channels, first data and last date for ships using keyscan cmd = "keyscan -r f -t M -L -x" returnCode, errMsg, outMsg = utilities.execute(cmd) keys = outMsg.split("\n") log.info("Exctracting beginning and end") # split on white-space and remove last row keys = [key.split() for key in keys[:-1]] # Create datetime objects for key in keys: dateStr1 = key[1] dateStr2 = key[2] if dateStr1[-2:] == "60": dateStr1 = dateStr1[:-2] + "59" startTime = datetime.datetime.strptime(dateStr1, "%y%m%d%H%M") startTime += datetime.timedelta(minutes=1) else: startTime = datetime.datetime.strptime(dateStr1, "%y%m%d%H%M") if dateStr2[-2:] == "60": dateStr2 = dateStr2[:-2] + "59" endTime = datetime.datetime.strptime(dateStr2, "%y%m%d%H%M") endTime += datetime.timedelta(minutes=1) else: endTime = datetime.datetime.strptime(dateStr2, "%y%m%d%H%M") key[1] = startTime key[2] = endTime # Convert time-series key to mmsi and create dictionary with mmsi as keys # and (begin,end) tuples as values aisMMSI = {} for key in keys: mmsi = key[0][:3] + key[0][5:11] if len(key[0]) == 12: tsParam = key[0][11] if tsParam == "x": aisMMSI[mmsi] = (key[1], key[2]) if options.mmsiFile is None: mmsiList.append(mmsi) # sort out wanted ships nmissing = 0 missingShips = "" foundShips = 0 skippedShips = 0 for ind, mmsi in enumerate(mmsiList): log.info("Processing MMSI: %s (%i out of %i)" % (mmsi, ind, len(mmsiList))) if mmsi not in aisMMSI.keys(): log.warning("MMSI: %s not found in ais data, skipping" % mmsi) skippedShips += 1 continue if options.interval is not None: beginStr, endStr = options.interval.split(",") try: begin = datetime.datetime.strptime(beginStr, "%y%m%d%H%M") end = datetime.datetime.strptime(endStr, "%y%m%d%H%M") except: parser.error("Interval should be given as 'YYMMDDhhmm,YYMMDDhhmm'") # limit time interval to interval with data if (begin - aisMMSI[mmsi][0]) < datetime.timedelta(minutes=0): begin = aisMMSI[mmsi][0] if (end - aisMMSI[mmsi][1]) > datetime.timedelta(minutes=0): end = aisMMSI[mmsi][1] if end <= begin: continue ts = series.ShipTs(begin=begin, end=end, res=300) ts.read(mmsi) if ts.nvals() == 0: continue else: # Create ts covering all available data ts = series.ShipTs(begin=aisMMSI[mmsi][0], end=aisMMSI[mmsi][1], res=300) ts.read(mmsi) if options.bounds is not None: if not ts.inBounds(bounds[0], bounds[1], bounds[2], bounds[3]): continue output.write( "%s\t%s\t%s\t%i\n" % (mmsi, ts.toDatetime(0).strftime("%y%m%d%H%M"), ts.toDatetime(-1).strftime("%y%m%d%H%M"), ts.nvals()) ) if options.exportFile is not None: export.write(str(ts) + "\n") if options.contentFile is not None: if foundShips == 0: tsDaily = ts.content() else: tsDaily = addTs(tsDaily, ts.content()) if tsDaily.nvals() == 0: pdb.set_trace() foundShips += 1 log.info("Filtered out %i out of %i ships in time-series database" % (foundShips, len(keys))) if skippedShips > 0: log.info("Could not find %i mmsi in the time-series database" % (skippedShips)) if options.contentFile is not None: try: contentFile = open(path.abspath(options.contentFile), "w") except: log.error("Could not open %s for writing" % options.contentFile) contentFile.write("Gap start\tGap end\tNdays\n") gapStart = None for i in range(tsDaily.nvals()): if tsDaily.data[i, 2] == 0: if gapStart is None: gapStart = tsDaily.toDatetime(i) else: if gapStart is not None: gapEnd = tsDaily.toDatetime(i) ndays = (gapEnd - gapStart).days contentFile.write("%s\t%s\t%i\n" % (gapStart.strftime("%y%m%d"), gapEnd.strftime("%y%m%d"), ndays)) gapStart = None contentFile.write("\ntimeseries showing number of unique sighted ships per day\n") contentFile.write("Date\tNships\n") for i in range(tsDaily.nvals()): contentFile.write("%i %i\n" % (tsDaily.data[i, 0], tsDaily.data[i, 2])) contentFile.close()
def main(): #-----------Setting up and using the option parser----------------------- parser=OptionParser(usage= usage, version=version) parser.add_option("-v", "--verbose", action="store_true",dest="verbose", help="Verbose output") parser.add_option("-b", "--begin", action="store",dest="begin",default=None, help="Time to start extracting ship tracks") parser.add_option("-e", "--end", action="store",dest="end",default=None, help="Time to end extraction of ship tracks") parser.add_option("-m", "--mmsi", action="store",dest="mmsi",default=None, help="Specify a mmsi") parser.add_option("-o", "--output", action="store",dest="outputFile",default=None, help="To write output in ascii format") (options, args) = parser.parse_args() if options.verbose: loglevel = logging.DEBUG else: loglevel = logging.INFO logging.basicConfig(level=loglevel) log = logging.getLogger(__name__) if options.end is None or options.begin is None: parser.error("Need to specify begin and end time") if options.outputFile is None: parser.error("Need to specify output filename") #Get mmsi for ships with data in the time-inteval using keyscan cmd="keyscan -r f -b %s -e %s" %(options.begin,options.end) returnCode,errMsg,outMsg=utilities.execute(cmd) keys=outMsg.split("\n") keys=[int(key[:3]+key[5:11]) for key in keys[:-1]] keys=utilities.uniqify(keys) #remove doubles ais_stat=AisStat(domain=os.environ.get("AVDBNAME")) ais_stat.read() if options.mmsi is not None: mmsi=int(options.mmsi) if mmsi not in ais_stat.mmsi: log.error("MMSI %s not found in ais_stat.txt" %options.mmsi) sys.exit(1) if mmsi not in keys: log.info("No time-series data for ship in specified time interval") sys.exit(0) mmsiList=[mmsi] else: mmsiList = [mmsi for mmsi in keys if mmsi in ais_stat.mmsi] log.info("%i ships out of %i in time-series db found in ais_stat.txt" %(len(mmsiList), len(keys))) firstShip=True for mmsi in mmsiList: cmd="shiptsget -r f -b %s -e %s %i -S" %(options.begin,options.end,mmsi) returnCode,errMsg,outMsg=utilities.execute(cmd) rows=outMsg.split("\n") geomType=rows.pop(0) attributeNames=rows.pop(0) coords=rows[1::4] data=rows[3::4] if firstShip: dataRows=data coordRows=coords firstShip=False else: dataRows+=data coordRows+=coords output=geomType+"\n" output+=attributeNames+"\n" for i in range(len(coordRows)): output+="#COORD %i 0\n" %(i+1) output+=coordRows[i]+"\n" output+="#DATA %i\n" %(i+1) output+=dataRows[i]+"\n" try: outputFile=open(path.abspath(options.outputFile),"w") except: log.error("Could not open file: %s" %path.abspath(options.outputFile)) sys.exit(1) outputFile.write(output) outputFile.close()
def main(): #-----------Setting up and unsing option parser----------------------- parser=OptionParser(usage= usage, version=version) parser.add_option("-u",'--user', action="store",dest="user", help="Name of target edb user") parser.add_option("-e","--edb", action="store",dest="edb", help="Name of target edb") parser.add_option("-y","--year", action="store",dest="year", help="Cut out for given year") parser.add_option("-f","--file", action="store",dest="file", help="File to get data from") parser.add_option("-l", "--loglevel", action="store",dest="loglevel",default=2, help="Sets the loglevel (0-3 where 3=full logging)") (options, args) = parser.parse_args() #--------------------Init logger----------------------- rootLogger = logger.RootLogger(level=options.loglevel) global log log = rootLogger.getLogger(sys.argv[0]) #-----------------Validating options------------------- if options.user is None: log.error("Need to specify -u <user>") return 1 if options.edb is None: log.error("Need to specify -e <edb>") return 1 if options.year is None: log.error("Need to specify -y <year>") return 1 if options.file is None: log.error("Need to specify -f <file>") return 1 # if len(options.suffix)>4: # log.error("Limit your suffix length to 4 characters") # return 1 if len(options.year)!=4: log.error("Year should be given with four digits") return 1 dmn=Domain() edb=Edb(dmn,options.user,options.edb) subgrpdb=Subgrpdb(edb) rf = codecs.open(options.file,"r","ISO-8859-15") species={} tmp=tempfile.NamedTemporaryFile(suffix=".tmp",dir=dmn.tmpDir()) emisKey={} try: cmd="subdb -0 -o "+tmp.name returnCode,outMsg,errMsg=utilities.execute(cmd) if returnCode!=0: raise IOError("Error while running:\n" + cmd + "\nstdout: "+outMsg+"\nstderr: "+errMsg) f=codecs.open(tmp.name,"r","HP Roman8") # content=f.read() for line in f.read().split('\n'): if line == "": break line=line.split() if line[1] == '""' or line[1] == '"-"': continue emisKey[line[1][1:-1].lower()] = line[0] f.close() except IOError: msg="stdout: "+outMsg+"\nstderr: "+errMsg raise IOError("Could not run: "+cmd+"\n"+msg) for line in rf: if "Average of em" in line: line = line.split("\t") line[-1]=line[-1][:-1] i=0 for spec in line[4:]: i+=1 if len(spec) < 13: continue if spec[13:].lower() == "pm25": species[i]="pm2.5" elif spec[13:].lower() == "bap": species[i]="benzo_a_pyrene" elif spec[13:].lower() == "diox": species[i]="dioxine" elif spec[13:].lower() == "pah": species[i]="pah-4" else: species[i]=spec[13:].lower() continue line = line[:-1].split('\t') if line[3] != options.year: continue name=line[0] i=0 substances={} for emFactor in line[4:]: i+=1 if emFactor == "": continue if species[i] in emisKey: # print "Now doing species "+species[i] index=int(emisKey[species[i]]) emFactor = float(emFactor) if species[i] == "pah-4" or species[i] == "benzo_a_pyrene": emFactor *= 10** -6 if species[i]=="dioxine": emFactor *= 10** -9 if emFactor < 10** -5: unit="g/TJ" emFactor*= 10**6 elif emFactor < 10** -2: unit="kg/TJ" emFactor*= 10**3 elif emFactor < 10: unit="ton/TJ" else: unit="Gg/TJ" emFactor*= 10** -3 substances[index]={"slope":emFactor,"offset":0,"unit":unit} else: print species[i] + " missing" subgrpdb.add_subgrp(name,substances) # subgrpdb.read() subgrpdb.write_to_file("test.txt")
def main(): #setting up parser parser = argparse.ArgumentParser(description=__doc__) utils.add_standard_command_options(parser) parser.add_argument( "-e","--edbs", action="store",dest="edbList", help="List of 'user/edb' pairs separated by :" ) parser.add_argument( "-L","--labels", action="store", dest="labels", help="List of edb labels separated by :" ) parser.add_argument( "-s","--substances", action="store",dest="substances", help="List of substance names separated by :" ) parser.add_argument( "-t","--title", action="store",dest="title", help="Report title" ) parser.add_argument( "-g","--gc-filter", action="store",dest="gcfilter", help="Filter on Geo codes, separated by :" ) parser.add_argument( "-o","--outfile", action="store",dest="outfile", help="Output filename" ) parser.add_argument( "-f","--format", action="store",dest="format", help="Output in 'excel','csv' or 'raw' " + "(Excel-format requires xlwt python module)" ) parser.add_argument("--substMapping", action="store",dest="substMapping", help="File with tab separated mappings of substance names") parser.add_argument("--markerTable", action="store",dest="markerTable", help="Table of codes to be formatted and commented") parser.add_argument( "macro",metavar="MACRO", help="A macro to use" ) args = parser.parse_args() if args.markerTable is not None: keys=["Year","GC","AC","note_1","note_2"] markerTable = DataTable(keys=keys,desc=[{"id":"Year","type":str},{"id":"GC","type":str},{"id":"AC","type":str},{"id":"note_1","type":str},{"id":"note_2","type":str}]) markerTable.read(args.markerTable) else: markerTable=None substMapping={} if args.substMapping is not None: with codecs.open(args.substMapping,encoding="HP Roman8",mode="r") as f: for line in f: oldName,newName = line.split(":") substMapping[oldName.strip()]=newName.strip() dmn = Domain() if args.gcfilter is not None: args.gcfilter = args.gcfilter.split(":") # Read original macro with codecs.open(args.macro, encoding="HP Roman8", mode="r") as f: originalContent = f.read() # Create a tmp copy of the macro, write content from the original macro macroTempFile = tempfile.NamedTemporaryFile( suffix=".sedb", dir=dmn.tmpDir() ) tmpMacro = codecs.open( macroTempFile.name, encoding="HP Roman8",mode="w" ) tmpMacro.write(originalContent) tmpMacro.flush() # Create a ControlFile obj to simplify reading and modifying macro macro = ControlFile(macroTempFile.name, removeComments=False) ebd = macro.findString("edb.edb:") user = macro.findString("edb.user:"******"edb.reportgeocode:")[-1]) acIndex = int(macro.findString("edb.reportactcode:")[-1]) if args.edbList is None: ebds = [[user, edb]] else: edbs = args.edbList.split(":") edbs = [e.split("/") for e in edbs] nedbs = len(edbs) if args.labels is None: labels = ["No label"] * len(edbs) else: labels = args.labels.split(":") if len(labels) != nedbs: log.error("Number of labels specified should match number of edb:s") sys.exit(1) if args.substances is None: log.error("Need to specify substances") sys.exit(1) else: substances = args.substances.split(":") if args.format not in ('excel','csv','raw'): log.error( "Invalid format specifier : %s, should be one of 'excel'" + ", 'csv' or 'raw'" %args.format ) sys.exit(1) elif args.format == "excel": try: import xlwt except: log.error( "trendReport.py requires python module xlwt to write excel-files") sys.exit(1) # first edb # import pdb; pdb.set_trace() edb = Edb(dmn, edbs[0][0], edbs[0][1]) # assume same code definitions in all edbs to be processed, read from first rsrc = edb.rsrc nrsubstances = len(substances) unitIndex = int(macro.findString("UNIT :")) units = rsrc.search[unitIndex] subdb = Subdb(edb) subdb.read() #decode input title using stdin encoding title=args.title.decode(sys.stdin.encoding) rawOutput = "" rawMeta = u"name: %s\nnrmacros: %i\nnrsub: %i\nunit: %s\n" %( title, nedbs, nrsubstances, units) emissions = [] for ind, edbUser in enumerate(edbs): label = labels[ind] userName = edbUser[0] edbName = edbUser[1] macro.setParam("edb.user:"******"edb.edb:", edbName) macro.setParam("USER :"******"EDB :", edbName) rawMeta += "macro.%i.edbuser: %s\n" %(ind, userName) rawMeta += "macro.%i.edbname: %s\n" %(ind, edbName) rawMeta += "macro.%i.desc: %s\n" %(ind, label) for subst in substances: log.info( "User: %s, edb: %s, substance %s" %( userName, edbName, subst) ) substanceIndex = subdb.substIndex(subst) macro.setParam("ELEMENT :", substanceIndex) macro.write() command = "xrepedb -i " + macro.name log.info("Running xrepedb for substance %s" % subst) # import pdb; pdb.set_trace() (returnCode, errMsg, outMsg) = utilities.execute(command) if returnCode != 0: log.error("Could not run %s\nstdout: %s\nstderr:%s" %( command,outMsg,errMsg)) sys.exit(1) if len(outMsg) < 10: log.error("Invalid output from xrepedb: %s" % outMsg) sys.exit(1) rawOutput += "#MACRO %i \"%s\" \"%s\"\n" % (ind, subst, labels[ind]) rawOutput += outMsg lines = outMsg.split("\n")[:-1] for lineInd, line in enumerate(lines): vals = line.split() ac = vals[1].split(".") gc = vals[3].split(".") if len(ac) == 1: if ac[0] == "<all>": acLev1 = "alla" else: acLev1 = ac[0] acLev2 = "alla" else: acLev1 = ac[0] acLev2 = ac[1] if len(gc) == 1: if gc[0] == "<all>": gcLev1 = "alla" else: gcLev1 = gc[0] gcLev2 = "alla" else: gcLev1 = gc[0] gcLev2 = gc[1] emis = float(vals[4]) if acLev1 == "alla": acLev1Name = "alla" acLev2Name = "alla" else: node = rsrc.ac[acIndex - 1].root.find(acLev1) acLev1Name = node.attrib["name"] if acLev2 == "alla": acLev2Name = "alla" else: node = rsrc.ac[acIndex-1].root.find( acLev1 + "/" + acLev2 ) acLev2Name = node.attrib["name"] if gcLev1 == "alla": gcLev1Name = "alla" gcLev2Name = "alla" else: node = rsrc.gc[gcIndex-1].root.find(gcLev1) gcLev1Name = node.attrib["name"] if gcLev2 == "alla": gcLev2Name = "alla" else: node = rsrc.gc[gcIndex - 1].root.find( gcLev1 + "/" + gcLev2 ) gcLev2Name = node.attrib["name"] if args.gcfilter is not None: if gc[0] not in args.gcfilter: # if args.gcfilter != gcLev1: continue emissions.append({"label": label, "substance": subst, "ac": '.'.join(ac), "gc": '.'.join(gc), "gcLev1": gcLev1Name, "gcLev2": gcLev2Name, "acLev1": acLev1Name, "acLev2": acLev2Name, "acLev1Code": acLev1, "acLev2Code": acLev2, "val": emis, "edbIndex": ind}) #Close tempfile to automatically remove it tmpMacro.close() if args.format == "raw": outfile = codecs.open(args.outfile,"w","HP Roman8") outfile.write(rawMeta) outfile.write(rawOutput) outfile.close() elif args.format == "csv": outfile = open(args.outfile,"w") desc = [ {'id': 'gc', 'type': unicode}, {'id': 'ac', 'type': unicode}, {'id': 'label', 'type': unicode}, {'id': 'user', 'type': unicode}, {'id': 'edb', 'type': unicode} ] for subst in substances: desc.append({'id': subst, 'type': float}) keys = ['gc', 'ac', 'label'] table = DataTable(desc=desc, keys=keys) log.info("Adding emissions to csv-table") for emis in emissions: row = [None] * len(desc) user = edbs[emis['edbIndex']][0] edb = edbs[emis['edbIndex']][1] row[table.colIndex['gc']] = emis['gc'] row[table.colIndex['ac']] = emis['ac'] row[table.colIndex['label']] = emis['label'] row[table.colIndex['user']] = user row[table.colIndex['edb']] = edb row[table.colIndex[emis['substance']]] = emis['val'] # data is appended to the correct row, or a new row is added if the # table keys do not match any existing row log.debug( "Adding row for substance %s, gc %s, ac %s" %( emis['substance'], emis['gc'], emis['ac']) ) table.addRow(row, append=True) table.write(outfile) outfile.close() else: # Create style objects for excel output header1Style = xlwt.easyxf( 'font: name Times New Roman,color-index black, bold on', num_format_str='0.000E+00' ) markerStyle1 = xlwt.easyxf( 'font: name Times New Roman,color-index red, bold off, italic on', num_format_str='0.000E+00') markerStyle2 = xlwt.easyxf( 'font: name Times New Roman,color-index orange, bold off, italic on', num_format_str='0.000E+00') normalStyle = xlwt.easyxf( 'font: name Times New Roman,color-index black, bold off', num_format_str='0.000E+00' ) excelBook = xlwt.Workbook() # Creating info sheet infoWs = excelBook.add_sheet("Info") infoWs.col(0).width = 256*20 infoWs.col(1).width = 256*25 infoWs.col(2).width = 256*20 infoWs.col(3).width = 256*200 infoWs.write(0,0,u"Rapportnamn:",header1Style) infoWs.write(0,1,title,header1Style) infoWs.write(1,0,u"Beskrivning av dataunderlaget",header1Style) infoWs.write(3,0,u"Makron (specificerar utsökningar ur databasen)",header1Style) infoWs.write(4,0,u"Etikett",header1Style) infoWs.write(4,1,u"Ägare till EDB",header1Style) infoWs.write(4,2,u"EDB (emissiondatabas)",header1Style) infoWs.write(4,3,u"Beskrivning",header1Style) for i,edbUser in enumerate(edbs): userName=edbUser[0] edbName=edbUser[1] label=labels[i] infoWs.write(5+i,0,label) infoWs.write(5+i,1,userName) infoWs.write(5+i,2,edbName) #reading edb description file (if it exists) edb=Edb(dmn,userName,edbName) infoWs.write(5+i,3,edb.desc().replace("\n"," ")) #split substances in green house gases and air quality related ghgList=[s for s in substances if s in ghgs] aqList=[s for s in substances if s not in ghgs] #Write air quality headers firstRow=4 #Add two rows for marker comments if markerTable is not None: firstRow+=2 if len(aqList)>0: aqWs = excelBook.add_sheet(u"Luftföroreningar") aqWs.col(0).width = 256*25 aqWs.col(1).width = 256*30 aqWs.col(2).width = 256*20 aqWs.col(3).width = 256*15 for col in range(nrsubstances*nedbs): aqWs.col(col+4).width=256*15 aqWs.write(0,0,u"Rapportnamn:",header1Style) aqWs.write(0,1,title,header1Style) aqWs.write(1,0,u"Emissioner av luftföroreningar",header1Style) aqWs.write(1,1,u"Enhet: "+units,header1Style) if markerTable is not None: aqWs.write(2,0,u"OBS! Röd kursiv text anger osäkra värden p.g.a. att en stor del av emissionen är fördelad med schabloner inom kommungruppen. Granska underkategorin \"Energiförsörjning via el-värmeverk samt inom industrin\" för att se eventuella misstänkta värden.",markerStyle1) aqWs.write(3,0,u"OBS! Orange kursiv text anger osäkra värden p.g.a. att trenden varierar kraftigt och eventuellt felaktigt, ytterligare verifiering krävs. Granska underkategorin \"Energiförsörjning via el-värmeverk samt inom industrin\" för att se eventuella misstänkta värden.",markerStyle2) aqWs.write(firstRow,0,"Huvudsektor",header1Style) aqWs.write(firstRow,1,"Undersektor",header1Style) aqWs.write(firstRow,2,u"Län",header1Style) aqWs.write(firstRow,3,"Kommun",header1Style) #Write ghg headers if len(ghgList)>0: ghgWs = excelBook.add_sheet(u"Växthusgaser") ghgWs.col(0).width = 256*25 ghgWs.col(1).width = 256*30 ghgWs.col(2).width = 256*20 ghgWs.col(3).width = 256*15 for col in range(nrsubstances*nedbs): ghgWs.col(col+4).width=256*15 ghgWs.write(0,0,u"Rapportnamn:",header1Style) ghgWs.write(0,1,title,header1Style) ghgWs.write(1,0,u"Emissioner av Växthusgaser",header1Style) ghgWs.write(2,0,u"CO2-ekv. efter ämnesnamn innebär att emissionen är uttryckt i CO2-ekvivalenter",header1Style) if markerTable is not None: ghgWs.write(3,0,u"OBS! Röd kursiv text anger osäkra värden p.g.a. att en stor del av emissionen är fördelad med schabloner inom kommungruppen. Granska underkategorin \"Energiförsörjning via el-värmeverk samt inom industrin\" för att se eventuella misstänkta värden.",markerStyle1) ghgWs.write(4,0,u"OBS! Orange kursiv text anger osäkra värden p.g.a. att trenden varierar kraftigt och eventuellt felaktigt, ytterligare verifiering krävs. Granska underkategorin \"Energiförsörjning via el-värmeverk samt inom industrin\" för att se eventuella misstänkta värden.",markerStyle2) ghgWs.write(1,1,u"Enhet: "+units,header1Style) ghgWs.write(firstRow,0,"Huvudsektor",header1Style) ghgWs.write(firstRow,1,"Undersektor",header1Style) ghgWs.write(firstRow,2,u"Län",header1Style) ghgWs.write(firstRow,3,"Kommun",header1Style) def getColInd(nmacros, substances,macroInd,subst): #gets the column index in excel file sInd=substances.index(subst) #Including extra columns to write CO2-equivalents nSubstWithCO2equivalents=0 for s in substances[:sInd+1]: if s in doubleColumns: nSubstWithCO2equivalents+=1 return 4 + macroInd+sInd*nmacros+nSubstWithCO2equivalents*(macroInd+1) #write macro labels and substance headers for air quality sheet for sInd,subst in enumerate(aqList): for i,edbUser in enumerate(edbs): col=getColInd(nedbs,aqList,i,subst) aqWs.write(firstRow-1,col,labels[i],header1Style) #If a substance name is given in mapping this is used, otherwise #The substance bname from the airviro substance list is used aqWs.write(firstRow,col,substMapping.get(subst,subst),header1Style) #write macro labels and substance headers for ghg sheet for sInd,subst in enumerate(ghgList): for i,edbUser in enumerate(edbs): col=getColInd(nedbs,ghgList,i,subst) #If CO2-equivalents are calculated, an extra column is needed if subst in doubleColumns: ghgWs.write(firstRow-1,col-1,labels[i],header1Style) ghgWs.write(firstRow-1,col,labels[i],header1Style) #If CO2-equivalents are calculated, an extra column is needed if subst in doubleColumns: #debug statement #print "writing subst %s in col %i and %i" %(subst,col-1,col) ghgWs.write(firstRow,col-1,substMapping.get(subst,subst),header1Style) ghgWs.write(firstRow,col,substMapping.get(subst,subst)+"CO2-ekv.",header1Style) elif subst in storedAsCO2equivalents: #debug statement #print "writing subst %s in col %i" %(subst,col) ghgWs.write(firstRow,col,substMapping.get(subst,subst)+"CO2-ekv.",header1Style) else: #debug statement #print "writing subst %s in col %i" %(subst,col) ghgWs.write(firstRow,col,substMapping.get(subst,subst),header1Style) #looping over all emissions, writing them to the correct column and row ghgRow=[] aqRow=[] for m in range(nedbs*nrsubstances+4+3*nedbs): ghgRow.append(firstRow+1) for m in range(nedbs*nrsubstances+4): aqRow.append(firstRow+1) for emis in emissions: subst = emis["substance"] emisVal=emis["val"] edbInd=emis["edbIndex"] #Check if gc, ac and year can be found in the error list #debugging marker style if markerTable is not None: TableRowInd=markerTable.rowIndices([labels[edbInd], emis["gc"], emis["ac"], "ja","*"]) if len(TableRowInd) >0: valueStyle=markerStyle1 else: TableRowInd=markerTable.rowIndices([labels[edbInd], emis["gc"], emis["ac"], "*","ja"]) if len(TableRowInd)>0: valueStyle=markerStyle2 else: valueStyle=normalStyle else: valueStyle=normalStyle if subst in ghgList: col=getColInd(nedbs,ghgList,edbInd,subst) row=ghgRow[col] if ghgRow[0]<=+row: ghgWs.write(row,0,emis["acLev1"],normalStyle) ghgWs.write(row,1,emis["acLev2"],normalStyle) ghgWs.write(row,2,emis["gcLev1"],normalStyle) ghgWs.write(row,3,emis["gcLev2"],normalStyle) ghgRow[0]+=1 #converts the emission to CO2-ekquivalents if subst in doubleColumns: ghgWs.write(row,col-1,float(emisVal),valueStyle) ghgWs.write(row,col,float(emisVal)*float(ekvFactors[subst]),valueStyle) else: ghgWs.write(row,col,float(emisVal),valueStyle) ghgRow[col]+=1 else: col=getColInd(nedbs,aqList,edbInd,subst) row=aqRow[col] if aqRow[0]<=+row: aqWs.write(row,0,emis["acLev1"],normalStyle) aqWs.write(row,1,emis["acLev2"],normalStyle) aqWs.write(row,2,emis["gcLev1"],normalStyle) aqWs.write(row,3,emis["gcLev2"],normalStyle) aqRow[0]+=1 aqWs.write(row,col,float(emisVal),valueStyle) aqRow[col]+=1 excelBook.save(args.outfile) log.info("Finished!")
def main(): #-----------Setting up and unsing option parser----------------------- parser=OptionParser(usage= usage, version=version) parser.add_option("-l", "--loglevel", action="store",dest="loglevel",default=2, help="Sets the loglevel (0-3 where 3=full logging)") parser.add_option("-u", "--user", action="store", dest="user", default=None, help="Specify user manually") parser.add_option("-e", "--edb", action="store", dest="edb", default=None, help="Name of target edb") parser.add_option("-t", "--template", action="store",dest="cf",default=None, help="Generate default controlfile") parser.add_option("-f", "--force", action="store_true",dest="force",default=False, help="To start the process without confirming the domain") (options, args) = parser.parse_args() # Setup logging logging.configure(terminal_level=logging.DEBUG) log = logging.getLogger(__name__) if options.cf!=None: generateCf(path.abspath(options.cf)) log.info("Wrote default controlfile") sys.exit() if len(args)!=1: parser.error("Incorrect number of arguments") if options.edb ==None: parser.error("Need to specify edb using flag -e") if options.user ==None: parser.error("Need to specify user using flag -u") dmn = Domain() if not options.force: answer=raw_input("Chosen dbase is: "+dmn.name+",continue(y/n)?") if answer!="y": sys.exit("Interrupted by user") if not dmn.edbExistForUser(options.edb,options.user): log.error("Edb "+options.edb+" does not exist for user "+ options.user+" in domain "+dmn.name) sys.exit() #---Creating edb and rsrc objects------------------ edb=Edb(dmn,options.user,options.edb) rsrc=Rsrc(edb.rsrcPath()) #Opening controlfile #---retrieving data from control file---- cf=ControlFile(fileName=path.abspath(args[0])) substances=cf.findStringList("substances:") outputDir=cf.findExistingPath("outputDir:") acIndex=cf.findInt("acIndex:") macroFileName=path.abspath(cf.findExistingPath("xrepedbMacro:")) fromProj=cf.findString("fromProj:") toProj=cf.findString("toProj:") try: fromProj=transcoord.proj4Dict[fromProj] except KeyError: log.error("Projection %s not found in proj4Dictin transCoord.py" %fromProj) try: toProj=transcoord.proj4Dict[toProj] except KeyError: log.error("Projection %s not found in proj4Dictin transCoord.py" %toProj) formats = cf.findStringList("formats:") units = cf.findString("units:") writeGrids=cf.findBoolean("writeGrids:",optional=True,default=True) edb_xll=cf.findInt("edb_xll:") edb_yll=cf.findInt("edb_yll:") edb_ncols=cf.findInt("edb_ncols:") edb_nrows=cf.findInt("edb_nrows:") edb_cellsize=cf.findFloat("edb_cellsize:") if fromProj!=toProj: out_xll=cf.findFloat("out_xll:") out_yll=cf.findFloat("out_yll:") out_ncols=cf.findInt("out_ncols:") out_nrows=cf.findInt("out_nrows:") out_cellsize=cf.findFloat("out_cellsize:") #----------------------------------------- #Finds index to search units unitIndex=None for key,unit in rsrc.search.iteritems(): if isinstance(key,int): if rsrc.search[key]==units: unitIndex=key break if unitIndex is None: log.error("Search units: %s not defined in edb.rsrc" %units) sys.exit() macro = ControlFile(fileName=macroFileName,removeComments=False) #preparing export macro macro.setParam("general.database:",dmn.name) xmin=edb_xll xmax=edb_xll+edb_ncols*edb_cellsize ymin=edb_yll ymax=edb_yll+edb_nrows*edb_cellsize macro.setParam("edb.mapopt.bounds:", "%i %i %i %i" %(xmin, xmax, ymin, ymax)) macro.setParam("edb.user:"******"edb.edb:",edb.name) macro.setParam("REGION :","%i %i %i %i" %(xmin, xmax, ymin, ymax)) macro.setParam("USER :"******"EDB :",edb.name) macro.setParam("GRID :", "%i %i %i %i %i %i" %(edb_xll,edb_yll,edb_ncols,edb_nrows,edb_cellsize,edb_cellsize)) macro.setParam("edb.unit:",unitIndex) macro.setParam("UNIT :",unitIndex) # macro.setParam("NOACTCODE :",acIndex) macro.setParam("NOACTCODE :",len(rsrc.ac)) #Get activity code tree acTree=codeemistree.CodeEmisTree("Activity codes",units=units) acTree.readActivityCodes(rsrc.path,acIndex) substDict=dmn.listSubstanceIndices() edbRast = Raster(Xll=edb_xll,Yll=edb_yll,Ncols=edb_ncols, Nrows=edb_nrows,Cellsize=edb_cellsize, Nodata=-9999,init=0) if fromProj!=toProj: outRastTemplate = Raster(Xll=out_xll,Yll=out_yll,Ncols=out_ncols, Nrows=out_nrows,Cellsize=out_cellsize, Nodata=-9999) else: outRastTemplate=Raster() outRastTemplate.assign(edbRast) for node in acTree.root.getiterator(): if node.tag=="root" or node.tag=="Record": continue ac=node.tag log.debug("Activity code: "+ac) #Finds row index for activity codes in macro #Add a row with the current ac #If there are many ac already given, these are #replaced by the current ac macroLines=macro.content.split("\n") actCodeInd=None geoCodeInd=None for lineInd,line in enumerate(macroLines): if "NOACTCODE" in line: actCodeInd=lineInd if "NOGEOCODE" in line: geoCodeInd=lineInd if len(ac.split('.')) >= rsrc.ac[acIndex-1].depth: macroLines=macroLines[:actCodeInd+1]+["none"]*(acIndex-1)+[ac]+["none"]*(len(rsrc.ac)-acIndex)+macroLines[geoCodeInd:] else: macroLines=macroLines[:actCodeInd+1]+["none"]*(acIndex-1)+[ac+'.']+["none"]*(len(rsrc.ac)-acIndex)+macroLines[geoCodeInd:] macro.content="\n".join(macroLines) macro.write() #boolean raster marking where there is data for any of the substances if 'CLRTAP' in formats: dataMarker = Raster(Xll=out_xll,Yll=out_yll,Ncols=out_ncols, Nrows=out_nrows,Cellsize=out_cellsize, Nodata=-9999,init=0) rasterDict={} substancesWithData=[] for substance in substances: log.debug("Substance %s" %substance) substanceIndex=substDict[substance] macro.setParam("ELEMENT :",substanceIndex) macro.write() command="xrepedb -i "+macro.name (returnCode,errMsg,outMsg)=utilities.execute(command) tmp=outMsg.split()[10:-2] tmp.sort() if tmp[0] == '0.000000E+00' and tmp[-1] == '0.000000E+00': print "ERROR: The field for "+substance+" is empty!" continue # pdb.set_trace() emisRast=string2rast(outMsg,edbRast) emisSum=emisRast.sum() outRast=Raster() outRast.assign(outRastTemplate) rec=ET.SubElement(node,"Record") rec.attrib["substance"]=substance rec.attrib["emission"]=str(emisSum) if emisSum>0 and writeGrids: if substance not in substancesWithData: substancesWithData.append(substance) if fromProj!=toProj: exportRast = transcoord.transformEmisRaster(emisRast,outRast,fromProj,toProj,tmpDir=dmn.tmpDir()) else: exportRast=emisRast if 'CLRTAP' in formats: dataMarker.data = numpy.where(exportRast.data > 0, 1, dataMarker.data) rasterDict[substance]=exportRast categoryDirPath = path.join(outputDir, ac) if not path.isdir(categoryDirPath): os.mkdir(categoryDirPath) if 'ESRI Ascii grid' in formats: fileName = path.join(categoryDirPath, substance+ ".asc") exportRast.write(fileName) log.debug("Grid for " + substance + "written to outputDir for category: " + ac) summaryTable=acTree.createTable(writeAll=True) summaryTable.sortRows() tableFile=open(path.join(outputDir,"summaryTable.txt"),'w') summaryTable.write(tableFile) if len(rasterDict)>0 and 'CLRTAP' in formats: #creating substance header in the same order as the substances in the template header = "i\tj\t" #headerList=["SO2","NOx","NH3","NMVOC","CO","TSP","PM10","PM25","Pb ","Cd","Hg","As","Cr","Cu","Ni","Se","Zn","Aldrin","Chlordane","Chlordecone","Dieldrin","Endrin","Heptachlor","Hexabromobiphenyl","Mirex","Toxaphene","HCH","DDT","PCB","DIOX","PAH","HCB","PCP","SCCP"] for s in substancesWithData: header += s + "\t" #remove the tab after the last column and add a newline instead header = header[: - 1]+ "\n" #Creating file for EMEP-data fileName = "CLRTAP_" + ac + ".txt" categoryDirPath = path.join(outputDir, ac) if not path.isdir(categoryDirPath): os.mkdir(categoryDirPath) fid = open(path.join(categoryDirPath, fileName), 'w') fid.writelines(header) sum=0 #Writing indexes and data for all non-zero elements for row in range(dataMarker.nrows): for col in range(dataMarker.ncols): if dataMarker.data[row, col] > 0: (i, j) = dataMarker.getCentreCoords(row, col) fid.write(str(i) + "\t" + str(j) + "\t") for substWithData in substancesWithData[:-1]: fid.write(str(rasterDict[substWithData].data[row, col]) + "\t") sum+=rasterDict[substWithData].data[row, col] fid.write(str(rasterDict[substancesWithData[-1]].data[row, col]) + "\n") sum+=rasterDict[substancesWithData[-1]].data[row, col] fid.close() log.info("wrote emissions to clrtap-file: " + path.join(categoryDirPath, fileName)) log.info("Finished")