def parseOutput(self, _strFileName):
"""
This method parses the output of dozor
"""
xsDataResultDozor = XSDataResultDozor()
strOutput = EDUtilsFile.readFile(_strFileName)
# Skip the four first lines
listOutput = strOutput.split("\n")[6:]
for strLine in listOutput:
# Remove "|"
listLine = shlex.split(strLine.replace("|", " "))
# print listLine
if listLine != [] and not strLine.startswith("-") and not strLine.startswith("h"):
xsDataImageDozor = XSDataImageDozor()
imageNumber = int(listLine[0])
angle = (
self.startingAngle
+ (imageNumber - self.firstImageNumber) * (self.oscillationRange - self.overlap)
+ self.oscillationRange / 2.0
)
xsDataImageDozor.number = XSDataInteger(imageNumber)
xsDataImageDozor.angle = XSDataAngle(angle)
if listLine[4].startswith("-"):
xsDataImageDozor.spotsNumOf = XSDataInteger(listLine[1])
xsDataImageDozor.spotsIntAver = self.parseDouble(listLine[2])
xsDataImageDozor.spotsResolution = self.parseDouble(listLine[3])
xsDataImageDozor.mainScore = self.parseDouble(listLine[7])
xsDataImageDozor.spotScore = self.parseDouble(listLine[8])
xsDataImageDozor.visibleResolution = self.parseDouble(listLine[9])
else:
xsDataImageDozor.spotsNumOf = XSDataInteger(listLine[1])
xsDataImageDozor.spotsIntAver = self.parseDouble(listLine[2])
xsDataImageDozor.spotsResolution = self.parseDouble(listLine[3])
xsDataImageDozor.powderWilsonScale = self.parseDouble(listLine[4])
xsDataImageDozor.powderWilsonBfactor = self.parseDouble(listLine[5])
xsDataImageDozor.powderWilsonResolution = self.parseDouble(listLine[6])
xsDataImageDozor.powderWilsonCorrelation = self.parseDouble(listLine[7])
xsDataImageDozor.powderWilsonRfactor = self.parseDouble(listLine[8])
xsDataImageDozor.mainScore = self.parseDouble(listLine[9])
xsDataImageDozor.spotScore = self.parseDouble(listLine[10])
xsDataImageDozor.visibleResolution = self.parseDouble(listLine[11])
# Dozor spot file
strWorkingDir = self.getWorkingDirectory()
if strWorkingDir is not None:
strSpotFile = os.path.join(self.getWorkingDirectory(), "%05d.spot" % xsDataImageDozor.number.value)
if os.path.exists(strSpotFile):
xsDataImageDozor.spotFile = XSDataFile(XSDataString(strSpotFile))
# print xsDataImageDozor.marshal()
xsDataResultDozor.addImageDozor(xsDataImageDozor)
elif strLine.startswith("h"):
xsDataResultDozor.halfDoseTime = XSDataDouble(strLine.split("=")[1].split()[0])
return xsDataResultDozor
def parseOutput(self, _strFileName):
"""
This method parses the output of dozor
"""
xsDataResultDozor = XSDataResultDozor()
strOutput = EDUtilsFile.readFile(_strFileName)
# Skip the four first lines
listOutput = strOutput.split("\n")[6:]
strWorkingDir = os.path.dirname(_strFileName)
for strLine in listOutput:
# Remove "|"
listLine = shlex.split(strLine.replace("|", " "))
if len(listLine) > 0 and listLine[0].isdigit():
xsDataImageDozor = XSDataImageDozor()
imageNumber = int(listLine[0])
angle = self.startingAngle + (imageNumber - self.firstImageNumber) * (self.oscillationRange - self.overlap) + self.oscillationRange / 2.0
xsDataImageDozor.number = XSDataInteger(imageNumber)
xsDataImageDozor.angle = XSDataAngle(angle)
xsDataImageDozor.spotsNumOf = XSDataInteger(0)
xsDataImageDozor.spotsIntAver = XSDataDouble(0)
xsDataImageDozor.spotsResolution = XSDataDouble(0)
xsDataImageDozor.mainScore = XSDataDouble(0)
xsDataImageDozor.spotScore = XSDataDouble(0)
xsDataImageDozor.visibleResolution = XSDataDouble(40)
try:
if listLine[4].startswith("-") or len(listLine) < 11:
xsDataImageDozor.spotsNumOf = XSDataInteger(listLine[1])
xsDataImageDozor.spotsIntAver = self.parseDouble(listLine[2])
xsDataImageDozor.spotsResolution = self.parseDouble(listLine[3])
xsDataImageDozor.mainScore = self.parseDouble(listLine[7])
xsDataImageDozor.spotScore = self.parseDouble(listLine[8])
xsDataImageDozor.visibleResolution = self.parseDouble(listLine[9])
else:
xsDataImageDozor.spotsNumOf = XSDataInteger(listLine[1])
xsDataImageDozor.spotsIntAver = self.parseDouble(listLine[2])
xsDataImageDozor.spotsResolution = self.parseDouble(listLine[3])
xsDataImageDozor.powderWilsonScale = self.parseDouble(listLine[4])
xsDataImageDozor.powderWilsonBfactor = self.parseDouble(listLine[5])
xsDataImageDozor.powderWilsonResolution = self.parseDouble(listLine[6])
xsDataImageDozor.powderWilsonCorrelation = self.parseDouble(listLine[7])
xsDataImageDozor.powderWilsonRfactor = self.parseDouble(listLine[8])
xsDataImageDozor.mainScore = self.parseDouble(listLine[9])
xsDataImageDozor.spotScore = self.parseDouble(listLine[10])
xsDataImageDozor.visibleResolution = self.parseDouble(listLine[11])
except:
pass
# Dozor spot file
if strWorkingDir is not None:
strSpotFile = os.path.join(strWorkingDir, "%05d.spot" % xsDataImageDozor.number.value)
if os.path.exists(strSpotFile):
xsDataImageDozor.spotFile = XSDataFile(XSDataString(strSpotFile))
# #print xsDataImageDozor.marshal()
xsDataResultDozor.addImageDozor(xsDataImageDozor)
elif strLine.startswith("h"):
xsDataResultDozor.halfDoseTime = XSDataDouble(strLine.split("=")[1].split()[0])
# Check if mtv plot file exists
mtvFileName = "dozor_rd.mtv"
mtvFilePath = os.path.join(strWorkingDir, mtvFileName)
if os.path.exists(mtvFilePath):
xsDataResultDozor.plotmtvFile = XSDataFile(XSDataString(mtvFilePath))
xsDataResultDozor.pngPlots = self.generatePngPlots(mtvFilePath, strWorkingDir)
return xsDataResultDozor
def parseOutput(self, _strFileName):
"""
This method parses the output of dozor
"""
xsDataResultDozor = XSDataResultDozor()
strOutput = EDUtilsFile.readFile(_strFileName)
# Skip the four first lines
listOutput = strOutput.split("\n")[6:]
strWorkingDir = os.path.dirname(_strFileName)
for strLine in listOutput:
# Remove "|"
listLine = shlex.split(strLine.replace("|", " "))
if len(listLine) > 0 and listLine[0].isdigit():
xsDataImageDozor = XSDataImageDozor()
imageNumber = int(listLine[0])
angle = self.startingAngle + (
imageNumber - self.firstImageNumber) * (
self.oscillationRange -
self.overlap) + self.oscillationRange / 2.0
xsDataImageDozor.number = XSDataInteger(imageNumber)
xsDataImageDozor.angle = XSDataAngle(angle)
xsDataImageDozor.spotsNumOf = XSDataInteger(0)
xsDataImageDozor.spotsIntAver = XSDataDouble(0)
xsDataImageDozor.spotsResolution = XSDataDouble(0)
xsDataImageDozor.mainScore = XSDataDouble(0)
xsDataImageDozor.spotScore = XSDataDouble(0)
xsDataImageDozor.visibleResolution = XSDataDouble(40)
try:
if listLine[5].startswith("-") or len(listLine) < 11:
xsDataImageDozor.spotsNumOf = XSDataInteger(
listLine[1])
xsDataImageDozor.spotsIntAver = self.parseDouble(
listLine[2])
xsDataImageDozor.spotsRfactor = self.parseDouble(
listLine[3])
xsDataImageDozor.spotsResolution = self.parseDouble(
listLine[4])
xsDataImageDozor.mainScore = self.parseDouble(
listLine[8])
xsDataImageDozor.spotScore = self.parseDouble(
listLine[9])
xsDataImageDozor.visibleResolution = self.parseDouble(
listLine[10])
else:
xsDataImageDozor.spotsNumOf = XSDataInteger(
listLine[1])
xsDataImageDozor.spotsIntAver = self.parseDouble(
listLine[2])
xsDataImageDozor.spotsRfactor = self.parseDouble(
listLine[3])
xsDataImageDozor.spotsResolution = self.parseDouble(
listLine[4])
xsDataImageDozor.powderWilsonScale = self.parseDouble(
listLine[5])
xsDataImageDozor.powderWilsonBfactor = self.parseDouble(
listLine[6])
xsDataImageDozor.powderWilsonResolution = self.parseDouble(
listLine[7])
xsDataImageDozor.powderWilsonCorrelation = self.parseDouble(
listLine[8])
xsDataImageDozor.powderWilsonRfactor = self.parseDouble(
listLine[9])
xsDataImageDozor.mainScore = self.parseDouble(
listLine[10])
xsDataImageDozor.spotScore = self.parseDouble(
listLine[11])
xsDataImageDozor.visibleResolution = self.parseDouble(
listLine[12])
except:
pass
# Dozor spot file
if strWorkingDir is not None:
strSpotFile = os.path.join(
strWorkingDir,
"%05d.spot" % xsDataImageDozor.number.value)
if os.path.exists(strSpotFile):
xsDataImageDozor.spotFile = XSDataFile(
XSDataString(strSpotFile))
# #print xsDataImageDozor.marshal()
xsDataResultDozor.addImageDozor(xsDataImageDozor)
elif strLine.startswith("h"):
xsDataResultDozor.halfDoseTime = XSDataDouble(
strLine.split("=")[1].split()[0])
# Check if mtv plot file exists
mtvFileName = "dozor_rd.mtv"
mtvFilePath = os.path.join(strWorkingDir, mtvFileName)
if os.path.exists(mtvFilePath):
xsDataResultDozor.plotmtvFile = XSDataFile(
XSDataString(mtvFilePath))
xsDataResultDozor.pngPlots = self.generatePngPlots(
mtvFilePath, strWorkingDir)
return xsDataResultDozor
def parseOutput(self, _strFileName):
"""
This method parses the output of dozor
"""
xsDataResultDozor = XSDataResultDozor()
strOutput = EDUtilsFile.readFile(_strFileName)
# Skip the four first lines
self.DEBUG('***** Dozor raw output ***** ')
self.DEBUG(strOutput)
listOutput = strOutput.split("\n")[14:]
for strLine in listOutput:
xsDataImageDozor = XSDataImageDozor()
# Remove "|"
listLine = shlex.split(strLine.replace("|", " "))
#print listLine
if listLine != [] and not listLine[0].startswith("-"):
xsDataImageDozor.number = XSDataInteger(listLine[0])
# Fix for xaloc-ALBA
#if listLine[5].startswith("-") or len(listLine) < 11:
if len(listLine) < 11:
xsDataImageDozor.spots_num_of = XSDataInteger(listLine[1])
xsDataImageDozor.spots_int_aver = self.parseDouble(listLine[2])
try:
xsDataImageDozor.spots_resolution = self.parseDouble(listLine[3])
except IndexError as e:
xsDataImageDozor.spots_resolution = XSDataDouble(0.0)
xsDataImageDozor.score = XSDataDouble(0.0) #self.parseDouble(listLine[4])
else:
xsDataImageDozor.spots_num_of = XSDataInteger(listLine[1])
xsDataImageDozor.spots_int_aver = self.parseDouble(listLine[2])
xsDataImageDozor.spots_resolution = self.parseDouble(listLine[3])
xsDataImageDozor.powder_wilson_scale = self.parseDouble(listLine[4])
xsDataImageDozor.powder_wilson_bfactor = self.parseDouble(listLine[5])
xsDataImageDozor.powder_wilson_resolution = self.parseDouble(listLine[6])
xsDataImageDozor.powder_wilson_correlation = self.parseDouble(listLine[7])
xsDataImageDozor.powder_wilson_rfactor = self.parseDouble(listLine[8])
xsDataImageDozor.score = self.parseDouble(listLine[9])
# print xsDataImageDozor.marshal()
xsDataResultDozor.addImageDozor(xsDataImageDozor)
return xsDataResultDozor
def parseOutput(self, _strFileName):
"""
This method parses the output of dozor
"""
xsDataResultDozor = XSDataResultDozor()
strOutput = EDUtilsFile.readFile(_strFileName)
# Skip the four first lines
listOutput = strOutput.split("\n")[6:]
for strLine in listOutput:
xsDataImageDozor = XSDataImageDozor()
# Remove "|"
listLine = shlex.split(strLine.replace("|", " "))
# print listLine
if listLine != []:
xsDataImageDozor.number = XSDataInteger(listLine[0])
if listLine[4].startswith("-"):
xsDataImageDozor.spots_num_of = XSDataInteger(listLine[1])
xsDataImageDozor.spots_int_aver = self.parseDouble(listLine[2])
xsDataImageDozor.spots_resolution = self.parseDouble(listLine[3])
xsDataImageDozor.score = self.parseDouble(listLine[7])
else:
xsDataImageDozor.spots_num_of = XSDataInteger(listLine[1])
xsDataImageDozor.spots_int_aver = self.parseDouble(listLine[2])
xsDataImageDozor.spots_resolution = self.parseDouble(listLine[3])
xsDataImageDozor.powder_wilson_scale = self.parseDouble(listLine[4])
xsDataImageDozor.powder_wilson_bfactor = self.parseDouble(listLine[5])
xsDataImageDozor.powder_wilson_resolution = self.parseDouble(listLine[6])
xsDataImageDozor.powder_wilson_correlation = self.parseDouble(listLine[7])
xsDataImageDozor.powder_wilson_rfactor = self.parseDouble(listLine[8])
xsDataImageDozor.score = self.parseDouble(listLine[9])
# print xsDataImageDozor.marshal()
xsDataResultDozor.addImageDozor(xsDataImageDozor)
return xsDataResultDozor