def __init__(self,element,options):
'''Initilizes the dataSet by setting baseFileName, start, end, and intilizing plots from an xml
element'''
#set some initial values
self.baseFileName=None
self.start=None
self.end=None
self.axes=[]
self.nNumFiles=None
self.fileIndices=[]
self.hasNonTimeAxis=False
[self.start,self.end,self.baseFileName]=disect_filename.disectFileName(element.attrib["fileRange"])
#get equation of state file if one specified
eosFileElement=element.findall("eosFile")
if len(eosFileElement)>1:
warnings.warn("more than one \"eosFile\" node, ignoring all but first node")
if len(eosFileElement)>0:
self.eosFile=eosFileElement[0].text
else:
self.eosFile=None
#add axes to dataset
axisElements=element.findall("axis")
for axisElement in axisElements:
axis=Axis(axisElement,options)
self.axes.append(axis)
if not axis.bTime:
self.hasNonTimeAxis=True
def main():
#parse command line options
(options, args) = parseOptions()
#get base file name
[start, end, baseFileName] = disect_filename.disectFileName(args[0])
#make sure that all the combined binary files have profiles made
failedFiles = make_profiles.make_fileSet(args[0], options)
#get and sort files
extension = "_pro" + ".txt"
filesExistProfiles = glob.glob(baseFileName + "*" + extension)
files = []
for file in filesExistProfiles:
intOfFile = int(file[len(baseFileName):len(file) - len(extension)])
if intOfFile >= start and intOfFile < end:
files.append(file)
files.sort()
if len(files) < 1:
print __name__+":"+main.__name__+": no files found matching \""+baseFileName\
+"\" in the range "+str(start)+"-"+str(end)
return False
#make list of radial grid velocity, and time
radialGridVelocity = []
times = []
nCount = 0
for file in files:
print "reading profile ", file, " ..."
fileData = datafile.DataFile()
fileData.readFile(file)
nNumZones = len(fileData.fColumnValues)
radialGridVelocity.append(
fileData.fColumnValues[nNumZones - options.zone -
1][options.column - 1])
fileHeader = fileData.sHeader.split()
times.append(float(fileHeader[1]))
nCount = nCount + 1
#print data to file
print "writing to file ..."
outputFileName = options.outputFile + ".txt"
f = open(outputFileName, 'w')
for i in range(0, len(radialGridVelocity) - 1):
line = str(times[i]) + " " + str(radialGridVelocity[i]) + "\n"
f.write(line)
f.close()
success = os.system(paths.SPHERLSanalPath + ' -tl ' + outputFileName)
if success != 0:
print "error computing fourier transform of \"" + outputFileName + "\""
if __name__ == "__main__": #keeps from redundently reporting errors
#report failed files
for file in failedFiles:
print file
def __init__(self,element):
"""Initialize an fileSet from an xml node"""
#define allowed attributes for nodes
self.__setSupportedNodeAttributes()
#warn about unsupported attributes in node
self.__checkSuppotedNodeAttributes(element)
#get file range
self.fileRange=element.get("fileRange")
if self.fileRange==None or self.fileRange=="":
raise Exception("Need a fileRange attribute in fileSet Node")
[self.start,self.end,self.baseFileName]=disect_filename.disectFileName(self.fileRange)
#get timeFile Name
self.timeFile=element.get("timeFile")
#get dataPerFile node
dataPerFile=element.findall("dataPerFile")
#check to see if there are more than one dataPerFile node
if len(dataPerFile)>1:
message="more than one \"dataPerFile\" node found only using first"\
+" node and ignoring the rest"
warnings.warn(message)
#warn about unsupported attributes in node
self.__checkSuppotedNodeAttributes(dataPerFile[0])
#get list of variables to include in file
self.variables=[]
variableElements=dataPerFile[0].findall("variable")
for variableElement in variableElements:
#check that attributes are supported
self.__checkSuppotedNodeAttributes(variableElement)
self.variables.append(variable(variableElement))
#get list of interpolation variables
self.interpVars={}
interpVarElements=element.findall("interpVar")
for interpVarElement in interpVarElements:
#check that attributes of node are supported
self.__checkSuppotedNodeAttributes(interpVarElement)
tmp=interpVarElement.get("name")
if tmp==None or tmp=="":
raise Exception("\"interpVar\" must have a \"name\" attribute set")
self.interpVars[tmp]=interpVar(interpVarElement)
def make_fileSet(fileName,
options,
makeFileFunction=make_profile,
frequency=1):
"""Makes a set of files from SPHERLS output using fileMakingFunction
fileName: is expected to be the name of the inputfile
options: command line options
makeFileFunction: function to be used to create the a new file in the set.
returns a list of files that failed being made
"""
#check that we have a file name
if len(fileName) < 1:
raise Exception("Requires an input file")
#get base file name
[start, end, baseFileName] = disect_filename.disectFileName(fileName)
#make sure that all the distributed binary files in this range have been
#converted to combined binary files
failedFiles = combine_bins.combine_bin_files(options.keep, fileName,
options.remakeBins)
#check for combined binary files in iteration range starting with baseFileName
filesExistCombBin = glob.glob(baseFileName +
"[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]")
files = []
for file in filesExistCombBin:
intOfFile = int(file[len(baseFileName):len(file)])
if intOfFile >= start and intOfFile < end:
files.append(file)
files.sort()
if len(files) == 0:
raise NoFilesFound("no combined binary files found in range [" +
str(start) + "-" + str(end) + "]")
nNumFiles = len(files)
nCount = 1
for i in range(0, len(files), frequency):
try:
makeFileFunction(files[i], options, nCount, nNumFiles)
except FileCreateFailed as e:
failedFiles.append(e.message)
nCount += 1
return failedFiles
def main():
#parse command line options
(options,args)=parseOptions()
#get base file name
[start,end,baseFileName]=disect_filename.disectFileName(args[0])
#make sure that all the combined binary files have profiles made
failedFiles=make_profiles.make_fileSet(args[0],options)
#compute the average PKE
averagePKE(start,end,baseFileName,options)
#report failed files
for file in failedFiles:
print file
def cp_files(fileName,newBaseFileName,options):
"""
Copies SPHERLS output files using the BASEFILENAME[startIndex-endIndex] syntax.
This is the same syntax that the other scripts use when working with SPHERLS
output files.
"""
#get base file name
[start,end,baseFileName]=disect_filename.disectFileName(fileName)
#check for distributed binary files in interation range starting with baseFileName
filesExist=glob.glob(baseFileName+"[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]*")
files=[]
for file in filesExist:
intOfFile=-1
#if base part of file name matches the base file name given
if file[0:len(baseFileName)]==baseFileName:
testStr=file[len(baseFileName):len(baseFileName)+8]
endStr=file[len(baseFileName)+8:len(file)]
if testStr.isdigit():
intOfFile=int(testStr)
if intOfFile>=start and intOfFile<end:
if options.cbOnly and endStr=='' or not options.cbOnly:
files.append(file)
if(len(files)==0):
print __name__+":"+cp_files.__name__+": no files found in range "+baseFileName+"["+parts2[0]+"-"+parts2[2]+"]"
return False #nothing to do
#put them in order, might be nice to have them in order? Certainly not required
files.sort()
for file in files:
parts=file.split('_t')
newFileName=newBaseFileName+'_t'+parts[1]
print __name__+":"+cp_files.__name__+": copying file \""+file+"\" to file "+newFileName
#remove the file
cmd='cp '+file+" "+newFileName
os.system(cmd)
return True
def make_2DSlices(keep, fileName, nPlane, nPlaneIndex, remake):
#get base file name
[start, end, baseFileName] = disect_filename.disectFileName(fileName)
#make sure that all the distributed binary files in this range have been converted to combined binary files
combine_bins.combine_bin_files(keep, fileName, False)
#check for combined binary files in interation range starting with baseFileName
filesExistCombBin = glob.glob(baseFileName +
"[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]")
files = []
for file in filesExistCombBin:
intOfFile = int(file[len(baseFileName):len(file)])
if intOfFile >= start and intOfFile < end:
files.append(file)
extension = "_2D"
if nPlane == 0:
extension = extension + "k=" + str(nPlaneIndex) + ".txt"
if nPlane == 1:
extension = extension + "i=" + str(nPlaneIndex) + ".txt"
if nPlane == 2:
extension = extension + "j=" + str(nPlaneIndex) + ".txt"
count = 1
for file in files:
#if this particular 2D slice doesn't already exsist for this binary file create it
if not (os.path.exists(file + extension)) or remake:
#make 2D slice
print __name__+":"+make_2DSlices.__name__+": creating 2D slice from \""+file+"\" "\
+str(count)+"/"+str(len(files))+" ..."
success = os.system(paths.SPHERLSanalPath + ' -s cb ' +
str(nPlane) + ' ' + str(nPlaneIndex) + ' ' +
file)
if success == 0:
pass
else:
#say there was an error and return
print __name__ + ":" + make_2DSlices.__name__ + ": error making 2D slice " + file + extension
return False
else:
print __name__ + ":" + make_2DSlices.__name__ + ": 2D slice \"" + file + extension + "\" already exists"
count += 1
return True
def move_files(fileName, newBaseFileName, options):
#get base file name
[start, end, baseFileName] = disect_filename.disectFileName(fileName)
#check for distributed binary files in interation range starting with baseFileName
filesExist = glob.glob(baseFileName +
"[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]*")
files = []
for file in filesExist:
intOfFile = -1
#if base part of file name matches the base file name given
if file[0:len(baseFileName)] == baseFileName:
testStr = file[len(baseFileName):len(baseFileName) + 8]
endStr = file[len(baseFileName) + 8:len(file)]
if testStr.isdigit():
intOfFile = int(testStr)
if intOfFile >= start and intOfFile < end:
if options.cbOnly and endStr == '' or not options.cbOnly:
files.append(file)
if (len(files) == 0):
print __name__ + ":" + move_files.__name__ + ": no files found in range " + baseFileName + "[" + parts2[
0] + "-" + parts2[2] + "]"
return False #nothing to do
#put them in order, might be nice to have them in order? Certainly not required
files.sort()
for file in files:
parts = file.partition('_t')
newFileName = newBaseFileName + parts[1] + parts[2]
print __name__ + ":" + move_files.__name__ + ": moving file \"" + file + "\" to file " + newFileName
#remove the file
cmd = 'mv ' + file + " " + newFileName
os.system(cmd)
return True
def createSlices(settings,parsed):
#get base file name
[start,end,baseFileName]=disect_filename.disectFileName(settings['inputFileName'])
nCount=0
for plane in settings['planes']:
#make sure that all combined binary files have 2D slices made
if plane['planeType']=="rt":
nPlaneID=0
planeID="k"
if plane['planeType']=="tp":
nPlaneID=1
planeID="i"
if plane['planeType']=="rp":
nPlaneID=2
planeID="j"
if(parsed.eosFile!=""):
cmd = 'mk2DSlice' + ' ' + "\"" + settings['inputFileName'] + "\"" + ' ' + parsed.eosFile + ' ' + str(nPlaneID) + ' ' + str(plane['planeIndex']);
else:
cmd = 'mk2DSlice' + ' ' + "\"" + settings['inputFileName'] + "\"" + str(nPlaneID) + ' ' + str(plane['planeIndex']);
print(cmd)
os.system(cmd);
def combine_bin_files(keep, fileName, remakeBins):
"""Combines distributed binary dump files created by SPHERLS into a single binary file."""
[start, end, baseFileName] = disect_filename.disectFileName(fileName)
#if only doing one file we can make this faster
filesExist = []
if end - start == 1:
filesExist.append(baseFileName + str(start).zfill(8) + "-0")
else:
#check for distributed binary files in iteration range starting with baseFileName
filesExist = glob.glob(baseFileName +
"[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]-0")
files = []
for file in filesExist:
intOfFile = int(file[len(baseFileName):len(file) - 2])
if intOfFile >= start and intOfFile < end:
files.append(file)
if (len(files) == 0):
return [] #nothing to do, return an empty list of failedFiles
files.sort()
failedFiles = []
for i in range(len(files)):
#if combined binary file doesn't already exist with this file name
if not (os.path.exists(files[i][:len(files[i]) - 2])) or remakeBins:
#make combined binary files
if not keep:
print __name__+":"+combine_bin_files.__name__+": combining \""+files[i][:len(files[i])-2]\
+"\" and removing distributed binaries ..."
else:
print __name__ + ":" + combine_bin_files.__name__ + ": combining \"" + files[
i][:len(files[i]) - 2] + "\" ..."
success = os.system(paths.SPHERLSanalPath + ' -c dbcb ' +
files[i][:len(files[i]) - 2])
if success == 0:
if not keep:
#remove distributed binary files
os.system('rm -f ' + files[i][:len(files[i]) - 2] + '-*')
else:
#say there was an error and quit
failedFiles.append(__name__ + ":" +
combine_bin_files.__name__ +
": error combining binary file " +
files[i][:len(files[i]) - 2])
else:
if not keep:
print __name__+":"+combine_bin_files.__name__+": combined binary \""\
+files[i][:len(files[i])-2]+"\" already exists, removing distributed binaries ..."
#remove distributed binary files
os.system('rm -f ' + files[i][:len(files[i]) - 2] + '-*')
else:
print __name__+":"+combine_bin_files.__name__+": combined binary \""\
+files[i][:len(files[i])-2]+"\" already exists"
if __name__ == "__main__": #keeps from redundently reporting errors
#report problem files
for failedFile in failedFiles:
print failedFile
return failedFiles
def __init__(self, element):
"""Initialize an fileSet from an xml node"""
#define allowed attributes for nodes
self.__setSupportedNodeAttributes()
#warn about unsupported attributes in node
self.__checkSuppotedNodeAttributes(element)
#get file range
self.fileRange = element.get("fileRange")
if self.fileRange == None or self.fileRange == "":
raise Exception(
"Need a \"fileRange\" attribute in \"fileSet\" Node")
[self.start, self.end,
self.baseFileName] = disect_filename.disectFileName(self.fileRange)
#get timeFile Name
self.timeFile = element.get("timeFile")
if self.timeFile == None:
self.timeFile = "timeFile.hdf"
#get frequency
self.frequency = 1
self.frequency = int(element.get("frequency"))
#get output path
self.outputPath = element.get("outputPath")
if self.outputPath == None or self.outputPath == "":
raise Exception(
"Need a \"outputPath\" attribute in \"fileSet\" Node")
#get radialCutZone element text
elementRadialCutZone = element.findall("radialCutZone")
if len(elementRadialCutZone) > 1:
warnings.warn(
"more than one \"radialCutZone\" node ignoring all but first node"
)
elif len(elementRadialCutZone) == 1:
self.__checkSuppotedNodeAttributes(elementRadialCutZone[0])
if elementRadialCutZone[0].text != None or elementRadialCutZone[
0].text != "":
self.radialCutZone = int(elementRadialCutZone[0].text)
else:
raise Exception(
"must have a \"radialCutZone\" node in a \"fileSet\" node with an integer value"
)
#get includeBoundaries element text
elementIncludeBoundaries = element.findall("includeBoundaries")
if len(elementIncludeBoundaries) > 1:
warnings.warn(
"more than one \"includeBoundaries\" node ignoring all but first node"
)
elif len(elementIncludeBoundaries) == 1:
self.__checkSuppotedNodeAttributes(elementIncludeBoundaries[0])
if elementIncludeBoundaries[0] != None:
if elementIncludeBoundaries[0].text in [
"true", "yes", "y", "t", "1"
]:
self.includeBoundaries = True
elif elementIncludeBoundaries[0].text in [
"false", "no", "n", "n", "0"
]:
self.includeBoundaries = False
else:
raise Exception(
"\"includeBoundaries\" node expects \"true\" or \"false\""
)
else:
raise Exception(
"must have a \"includeBoundaries\" node in a \"fileSet\" node")
#get numRInterp element text
elementnumRInterp = element.findall("numRInterp")
if len(elementnumRInterp) > 1:
warnings.warn(
"more than one \"numRInterp\" node ignoring all but first node"
)
elif len(elementnumRInterp) == 1:
self.__checkSuppotedNodeAttributes(elementnumRInterp[0])
if elementnumRInterp[0].text != None or elementnumRInterp[0] != "":
self.numRInterp = int(elementnumRInterp[0].text)
else:
raise Exception(
"must have a \"numRInterp\" node in a \"fileSet\" node with an integer value"
)
'''
def __init__(self, element):
#get file of bolo metric corrections
boloCorrElements = element.findall("boloCorr")
if len(boloCorrElements) > 1:
warnings.warn(
"more than one \"boloCorr\" node in \"lightCurve\" node" +
", ignoring all but first node")
if len(boloCorrElements) > 0:
self.boloCorrFile = boloCorrElements[0].text
else:
raise Exception(
"Must have one \"boloCorr\" input file per \"lightCurve\" node"
)
#get column for bolometric correction
try:
self.columnBC = int(boloCorrElements[0].get("columnBC"))
except Exception as e:
raise Exception(
e.message +
"\n Must have a \"columnBC\" attribute set to the column number for"
+
" the bolometric correction. The first column in the file is column 0"
)
#get column for bolometric correction
if boloCorrElements[0].get("withAcceleration").lower() in [
"true", "yes", "y", "1", "t"
]:
self.withAcceleration = True
else:
self.withAcceleration = False
#get input set
inputFilesElements = element.findall("inputFiles")
if len(inputFilesElements) > 1:
warnings.warn(
"more than one \"inputFiles\" node in \"lightCurve\" node" +
", ignoring all but first node")
if len(inputFilesElements) > 0:
self.inputFileRange = inputFilesElements[0].text
else:
raise Exception(
"Must have one \"inputFiles\" node per \"lightCurve\" node")
#get frequency
if inputFilesElements[0].get("frequency") != None:
try:
self.frequency = int(inputFilesElements[0].get("frequency"))
except ValueError as e:
raise Exception(
e.message +
"\n \"frequency\" attribute in \"inputFiles\" node must be an "
+ "integer")
else:
self.frequency = 1
#split up file set string
[self.start, self.end, self.baseFileName
] = disect_filename.disectFileName(self.inputFileRange)
#get equation of state file if one specified
eosFileElement = element.findall("eosFile")
if len(eosFileElement) > 1:
warnings.warn(
"more than one \"eosFile\" node, ignoring all but first node")
if len(eosFileElement) > 0:
self.eosFile = eosFileElement[0].text
else:
self.eosFile = None
#get get number of zones in from the surface, 0=surface
zonesFromSurfElement = element.findall("zonesFromSurf")
if len(zonesFromSurfElement) > 1:
warnings.warn(
"more than one \"zonesFromSurf\" node, ignoring all but first node"
)
if len(zonesFromSurfElement) > 0:
try:
self.zonesFromSurf = int(zonesFromSurfElement[0].text)
except ValueError as e:
raise Exception(
e.message +
"\nExpecting an integer for \"zonesFromSurf\" node")
else:
self.zonesFromSurf = 0
#get outputFile
outputFileElements = element.findall("outputFile")
if len(outputFileElements) > 1:
warnings.warn(
"more than one \"outputFile\" node in \"lightCurve\" node" +
", ignoring all but first node")
if len(outputFileElements) > 0:
self.outputFile = outputFileElements[0].text
else:
raise Exception(
"Must have one \"outputFile\" node per \"lightCurve\" node")
#get period
periodElements = element.findall("period")
if len(periodElements) > 1:
warnings.warn(
"more than one \"period\" node in \"lightCurve\" node" +
", ignoring all but first node")
if len(periodElements) > 0:
self.period = float(periodElements[0].text)
else:
self.period = None
def main():
#parse command line options
(options, args) = parseOptions()
import matplotlib
if not options.show:
matplotlib.use('Agg') #needed for saving figures
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
#get base file name
fileName = args[0]
[start, end, baseFileName] = disect_filename.disectFileName(fileName)
#make sure that all the combined binary files have profiles made
make_profiles.make_profiles(options.keep, fileName, options.remake,
options.remakeBins)
#get and sort files
extension = "_pro" + ".txt"
filesExistProfiles = glob.glob(baseFileName + "*" + extension)
files = []
for file in filesExistProfiles:
intOfFile = int(file[len(baseFileName):len(file) - len(extension)])
if intOfFile >= start and intOfFile < end:
files.append(file)
files.sort()
#get surface velocity for all files in range, and find max/min of value to plotting
surfaceLuminosity = []
fileTimes = []
nCount = 0
max = -1e60
min = 1e60
nColumn = 55
nZonesFromSurface = 3
for file in files:
print "reading in profile ", file, " ..."
fileData = datafile.DataFile()
fileData.readFile(file)
surfaceLuminosity.append(
fileData.fColumnValues[len(fileData.fColumnValues) -
nZonesFromSurface - 1][nColumn])
fileHeader = fileData.sHeader.split()
fileTimes.append(float(fileHeader[1]))
nCount = nCount + 1
if max < fileData.fColumnValues[
len(fileData.fColumnValues) - nZonesFromSurface -
1][nColumn] and fileData.fColumnValues[
len(fileData.fColumnValues) - nZonesFromSurface -
1][nColumn] != None:
max = fileData.fColumnValues[len(fileData.fColumnValues) -
nZonesFromSurface - 1][nColumn]
if min > fileData.fColumnValues[
len(fileData.fColumnValues) - nZonesFromSurface -
1][nColumn] and fileData.fColumnValues[
len(fileData.fColumnValues) - nZonesFromSurface -
1][nColumn] != None:
min = fileData.fColumnValues[len(fileData.fColumnValues) -
nZonesFromSurface - 1][nColumn]
#make plots
nCount = 0
fig = plt.figure(figsize=(13, 8))
ax1 = plt.subplot2grid((3, 3), (0, 0), colspan=3, rowspan=3)
if not options.noGrid:
ax1.grid()
plotString = '-'
if options.noLines:
plotString = 'o'
if options.points:
plotString = plotString + 'o'
if options.ymin != None:
min = options.ymin
if options.ymax != None:
max = options.ymax
print "min=", min, " max=", max
ax1.plot(fileTimes, surfaceLuminosity, plotString)
plt.ylim(min, max)
ax1.set_xlabel("t [s]")
ax1.set_ylabel("L [L_sun]")
ax1.set_title("Ligh Curve")
if options.show:
plt.show()
else:
sOutFileName = options.outputFile + "." + options.format
print __name__ + ":" + main.__name__ + ": creating plot \"" + sOutFileName + "\" from file " + file + "..."
fig.savefig(sOutFileName, format=options.format,
transparent=False) #save to file
ax1.cla() #clear plot
def main():
#parse command line options
(options,args)=parseOptions()
#get XML settings
currentSettings=Settings()
currentSettings.parseXML(args[0])
#get base file name
[start,end,baseFileName]=disect_filename.disectFileName(currentSettings.files)
#make sure that all the combined binary files have profiles made
failedFiles=make_profiles.make_profiles(options.keep,currentSettings.files,options.remake,False)
#get period ranges and times for each period from PKE file
[periodRange,time]=getPeriodRanges(baseFileName,start,end,options)
dWSum=[]
dWSumError=[]
dClosestToTurn=[]
#get all possible file names
extension="_pro"+".txt"
filesExistProfiles=glob.glob(baseFileName+"*"+extension)
filesExistProfiles.sort()
#check for the t=0 model
if currentSettings.workPlotSettings.temperatureProfileFile!=None:#if set use user set value
firstFile=currentSettings.workPlotSettings.temperatureProfileFile
else:
firstFile=baseFileName+"00000000"
failedFiles2=make_profiles.make_profiles(options.keep,firstFile,options.remake,False)
if not os.path.isfile(firstFile+extension):
warnings.warn("didn't find profile or dump at \""+firstFile+extension+
"\" using, \""+filesExistProfiles[0]+"\" instead.")
firstFile=filesExistProfiles[0]
else:
firstFile+=extension
fileData=datafile.DataFile()
fileData.readFile(firstFile)
Log10T=fileData.fColumnValues[0:len(fileData.fColumnValues)-1,currentSettings.tColumn]
Log10T=np.array(Log10T,dtype=np.float64)#force double precision
Log10T=np.log10(Log10T)
#find out how close to the surface to go
nEndZone=len(fileData.fColumnValues)-1
for j in range(len(fileData.fColumnValues)-1):#position
if Log10T[j]<currentSettings.workPlotSettings.minTemp:
nEndZone=j
break
for n in range(len(periodRange)):
#get and sort files
files=[]
for file in filesExistProfiles:
intOfFile=int(file[len(baseFileName):len(file)-len(extension)])
if intOfFile>=periodRange[n][0] and intOfFile<periodRange[n][1]:
files.append(file)
#check to make sure we have a start and end for the period
if periodRange[n][1]==None:
raise Exception("file range index range "+str(start)+"-"+str(end)+" should contain at least"
+" one period as indicated by PKE peaks, but does not.")
if len(files)<3:
raise Exception("need more than 3 files to compute the work, likely alot more with file"
+" indices in the range ("+str(periodRange[n][0])+","+str(periodRange[n][1])+")")
#for first model dump
fileData=datafile.DataFile()
print "reading file ",files[0]," ..."
fileData.readFile(files[0])
#read in p, and 1/rho for first file
p=np.zeros( (len(fileData.fColumnValues)-1,len(files)+1) )
rhoInvert=np.zeros( (len(fileData.fColumnValues)-1,len(files)+1) )
deltaM=np.zeros( (len(fileData.fColumnValues)-1,len(files)+1) )
temperature=np.zeros( (len(fileData.fColumnValues)-1,len(files)+1) )
maxP=np.empty(len(fileData.fColumnValues)-1)
maxP.fill(-1.0*sys.float_info.max)
minP=np.empty(len(fileData.fColumnValues)-1)
minP.fill(sys.float_info.max)
for i in range(len(fileData.fColumnValues)-1):
p[i][0]=fileData.fColumnValues[i][currentSettings.pColumn]
p[i][len(files)]=fileData.fColumnValues[i][currentSettings.pColumn]
if currentSettings.AV:
p[i][0]+=fileData.fColumnValues[i][currentSettings.QColumn]
p[i][len(files)]+=fileData.fColumnValues[i][currentSettings.QColumn]
#get max P
if p[i][0]>=maxP[i]:
maxP[i]=p[i][0]
#get min P
if p[i][0]<=minP[i]:
maxP[i]=p[i][0]
rhoInvert[i][0]=1.0/fileData.fColumnValues[i][currentSettings.rhoColumn]
rhoInvert[i][len(files)]=1.0/fileData.fColumnValues[i][currentSettings.rhoColumn]
deltaM[i][0]=fileData.fColumnValues[i][currentSettings.deltaMColumn]
deltaM[i][len(files)]=fileData.fColumnValues[i][currentSettings.deltaMColumn]
temperature[i][0]=fileData.fColumnValues[i][currentSettings.tColumn]
temperature[i][len(files)]=fileData.fColumnValues[i][currentSettings.tColumn]
#read all files in for current period
for i in range(1,len(files)):#for each dump
print "reading file ",files[i]," ..."
fileData.readFile(files[i])
#check headers for used columns
if fileData.sColumnNames[currentSettings.pColumn]!=currentSettings.pColumnHeader:
warings.warn("file \""+files[i]+" has pressure column header as \""\
+fileData.sColumnNames[currentSettings.pColumn]+" expected something like \""\
+currentSettings.pColumnHeader+"\".")
if currentSettings.AV:
if fileData.sColumnNames[currentSettings.QColumn]!=currentSettings.QColumnHeader:
warnings.warn("file \""+files[i]+" has A.V. column header as \""\
+fileData.sColumnNames[currentSettings.QColumn]+" expected something like \""\
+currentSettings.QColumnHeader+"\".")
if fileData.sColumnNames[currentSettings.rhoColumn]!=currentSettings.rhoColumnHeader:
warnings.warn("file \""+files[i]+" has density column header as \""\
+fileData.sColumnNames[currentSettings.rhoColumn]+" expected something like \""\
+currentSettings.rhoColumnHeader+"\".")
if fileData.sColumnNames[currentSettings.deltaMColumn]!=currentSettings.deltaMColumnHeader:
warnings.warn("file \""+files[i]+" has delta M_r column header as \""\
+fileData.sColumnNames[currentSettings.deltaMColumn]+" expected something like \""\
+currentSettings.deltaMColumnHeader+"\".")
for j in range(len(fileData.fColumnValues)-1):#for each zone
p[j][i]=fileData.fColumnValues[j][currentSettings.pColumn]
if currentSettings.AV:
p[j][i]+=fileData.fColumnValues[j][currentSettings.QColumn]
#get max P
if p[j][i]>=maxP[j]:
maxP[j]=p[j][i]
#get min P
if p[j][i]<=minP[j]:
maxP[j]=p[j][i]
deltaM[j][i]=fileData.fColumnValues[j][currentSettings.deltaMColumn]
rhoInvert[j][i]=1.0/fileData.fColumnValues[j][currentSettings.rhoColumn]
#compute work
dW=np.zeros(len(fileData.fColumnValues)-1)
for i in range(1,len(files)+1):#time
for j in range(0,nEndZone):#position
dW[j]+=(0.5*(rhoInvert[j][i]-rhoInvert[j][i-1])*(p[j][i]+p[j][i-1]))*deltaM[j][i]
dWMax=0.0
dWMin=0.0
dWError=np.zeros(len(fileData.fColumnValues)-1)
dClosenessToEdge=np.zeros(len(fileData.fColumnValues)-1)
dWSum.append(0.0)
dClosestToTurnThisPeriod=sys.float_info.max
for j in range(0,nEndZone):#position
dWSum[n]+=dW[j]
#
y1=p[j][len(files)]
y0=p[j][len(files)-1]
ym1=p[j][len(files)-2]
x1=rhoInvert[j][len(files)]
x0=rhoInvert[j][len(files)-1]
xm1=rhoInvert[j][len(files)-2]
deltaX=(x1-x0)
y1py0=y1+y0
tiny=1e-300#fixes the case where things don't move, e.g. near the core
m=(y0-ym1)/((x0-xm1)+tiny)
y1p=y0+m*deltaX
y1ppy0=y1p+y0
#how far off is our guess from assuming a linear extrapolation
dW1=0.5*deltaX*y1py0#work from setting first point equal to last point
dW1p=0.5*deltaX*y1ppy0#work from linear extrapolation
dWError[j]=abs(dW1-dW1p)*deltaM[j][len(files)]
dWMax+=dW[j]+dWError[j]
dWMin+=dW[j]-dWError[j]
#how close to a turn is the start/end position
dtotal=maxP[j]-minP[i]
dmax=max(abs(p[j][0]-maxP[j]),abs(p[j][0]-minP[j]))
distanceFromEdge=dmax/dtotal#will be 1/2 if near middle, will be near 0 if near edge
#keep value of closest start/end position to turn
if distanceFromEdge<dClosestToTurnThisPeriod:
dClosestToTurnThisPeriod=distanceFromEdge
dClosestToTurn.append(dClosestToTurnThisPeriod)
dWSumError.append((dWMax-dWMin)*0.5)
#make plots of P and 1/rho for each zone
fig=plt.figure(figsize=(13,8))
ax1 = plt.subplot2grid((3,3), (0,0),colspan=3,rowspan=3)
if currentSettings.plotPdVCurves:
for j in range(currentSettings.PdVPlotSettings.startZone,len(fileData.fColumnValues)-1):
#print rhoInvert[j]
make_PdV_plot(rhoInvert[j],p[j],j,n,fig,ax1,currentSettings.PdVPlotSettings)
#make work plot
make_Work_plot(Log10T,dW,dWError,fig,ax1
,currentSettings.workPlotSettings,n,time[n],"Log10(T)")
make_Work_plot(range(len(fileData.fColumnValues)-1),dW,dWError,fig,ax1
,currentSettings.workPlotSettings,n,time[n],"zone #")
#print out total work done by model
f=open("work_per_period.txt",'w')
f.write("period time[s] work[ergs] work_uncertianty[ergs] relative_distance_from_turn\n")
for i in range(len(dWSum)):
f.write(str(i)+" "+str(time[i])+" "+str(dWSum[i])+" "+str(dWSumError[i])+" "
+str(dClosestToTurn[i])+"\n")
f.close()