def isJcampOpusStackFile(filename):
if not JcampFileParser.isJcampFile(filename):
return False
# Parse the first scan
jcamp = JcampFileParser.JcampFileParser(filename, single=True)
scan = jcamp[0]
header = parseFileHeader(scan.fileheader())
if "BLOCKS" in header:
if header["BLOCKS"] > 1:
return True
return False
def isJcampOpusStackFile(filename):
if not JcampFileParser.isJcampFile(filename):
return False
# Parse the first scan
jcamp = JcampFileParser.JcampFileParser(filename, single=True)
scan = jcamp[0]
header = parseFileHeader(scan.fileheader())
if "BLOCKS" in header:
if header["BLOCKS"] > 1:
return True
return False
def Specfile(filename):
if BlissSpecFile.isBlissSpecFile(filename):
return BlissSpecFile.BlissSpecFile(filename)
if sys.version_info < (3, 0):
f = open(filename)
else:
f = open(filename, 'r', errors="ignore")
line0 = f.readline()
if filename.upper().endswith('DTA'):
#TwinMic single column file
line = line0 * 1
line = line.replace('\r', '')
line = line.replace('\n', '')
line = line.replace('\t', ' ')
s = line.split(' ')
if len(s) == 2:
if len(s[-1]) == 0:
try:
float(s[0])
f.close()
output = specfilewrapper(filename, dta=True)
return output
except:
#try to read in other way
pass
# this piece of code checks if we deal with a SPEC file
# Prior to any data, all lines have to be either empty or starting
# by the hash character.
line = line0
while (len(line)):
if len(line) > 1:
if line[0:2] == '#S':
if ('#SIGNALTYPE' in line) or \
('#SPECTRUM' in line):
line = ""
break
elif line[0] not in ['#', ' ', '\r']:
line = ""
break
try:
line = f.readline()
except:
line = ""
break
f.close()
# end of specfile identification
amptek = False
qxas = False
if len(line):
#it is a Specfile
_logger.debug("This looks as a specfile")
output = specfile.Specfile(filename)
elif SPX and ArtaxFileParser.isArtaxFile(filename):
_logger.debug("This looks as an Artax file")
output = ArtaxFileParser.ArtaxFileParser(filename)
else:
_logger.debug("this does not look as a specfile")
if len(line0) > 7:
if line0.startswith('$SPEC_ID') or\
line0.startswith('$DATE_MEA') or\
line0.startswith('$MEAS_TIM') or\
line0.startswith('$Core_ID') or\
line0.startswith('$Section_ID'):
qxas = True
if (not qxas) and line0.startswith('<<'):
amptek = True
if (not qxas) and (
not amptek) and Fit2DChiFileParser.isFit2DChiFile(filename):
return Fit2DChiFileParser.Fit2DChiFileParser(filename)
if (not qxas) and (
not amptek) and APSMEDFileParser.isAPSMEDFile(filename):
return APSMEDFileParser.APSMEDFileParser(filename)
if (not qxas) and (not amptek) and SRSFileParser.isSRSFile(filename):
_logger.debug("SRSFileParser")
return SRSFileParser.SRSFileParser(filename)
if (not qxas) and (
not amptek) and BAXSCSVFileParser.isBAXSCSVFile(filename):
_logger.debug("BAXSCSVFileParser")
return BAXSCSVFileParser.BAXSCSVFileParser(filename)
if (not qxas) and (not amptek) and \
OlympusCSVFileParser.isOlympusCSVFile(filename):
_logger.debug("OlympusCSVFileParser")
return OlympusCSVFileParser.OlympusCSVFileParser(filename)
if (not qxas) and (not amptek) and \
ThermoEMSFileParser.isThermoEMSFile(filename):
_logger.debug("ThermoEMSFileParser")
return ThermoEMSFileParser.ThermoEMSFileParser(filename)
if (not qxas) and (not amptek) and \
JcampFileParser.isJcampFile(filename):
_logger.debug("JcampFileParser")
return JcampFileParser.JcampFileParser(filename)
output = specfilewrapper(filename, amptek=amptek, qxas=qxas)
return output
def Specfile(filename):
f = open(filename)
line0 = f.readline()
if filename.upper().endswith('DTA'):
#TwinMic single column file
line = line0 * 1
line = line.replace('\r', '')
line = line.replace('\n', '')
line = line.replace('\t', ' ')
s = line.split(' ')
if len(s) == 2:
if len(s[-1]) == 0:
try:
float(s[0])
f.close()
output = specfilewrapper(filename, dta=True)
f.close()
return output
except:
#try to read in other way
pass
line = line0
while (len(line)):
if len(line) > 1:
if line[0:2] == '#S':
if ('#SIGNALTYPE' in line) or \
('#SPECTRUM' in line):
line = ""
break
line = f.readline()
f.close()
amptek = False
qxas = False
if len(line):
#it is a Specfile
_logger.debug("This looks as a specfile")
output = specfile.Specfile(filename)
elif SPX and filename.upper().endswith("SPX"):
_logger.debug("This looks as an SPX file")
output = SPXFileParser.SPXFileParser(filename)
else:
_logger.debug("this does not look as a specfile")
if len(line0) > 7:
if line0.startswith('$SPEC_ID') or\
line0.startswith('$DATE_MEA') or\
line0.startswith('$MEAS_TIM') or\
line0.startswith('$Core_ID') or\
line0.startswith('$Section_ID'):
qxas = True
if (not qxas) and line0.startswith('<<'):
amptek = True
if (not qxas) and (
not amptek) and Fit2DChiFileParser.isFit2DChiFile(filename):
return Fit2DChiFileParser.Fit2DChiFileParser(filename)
if (not qxas) and (
not amptek) and APSMEDFileParser.isAPSMEDFile(filename):
return APSMEDFileParser.APSMEDFileParser(filename)
if (not qxas) and (not amptek) and SRSFileParser.isSRSFile(filename):
_logger.debug("SRSFileParser")
return SRSFileParser.SRSFileParser(filename)
if (not qxas) and (
not amptek) and BAXSCSVFileParser.isBAXSCSVFile(filename):
_logger.debug("BAXSCSVFileParser")
return BAXSCSVFileParser.BAXSCSVFileParser(filename)
if (not qxas) and (not amptek) and \
OlympusCSVFileParser.isOlympusCSVFile(filename):
_logger.debug("OlympusCSVFileParser")
return OlympusCSVFileParser.OlympusCSVFileParser(filename)
if (not qxas) and (not amptek) and \
ThermoEMSFileParser.isThermoEMSFile(filename):
_logger.debug("ThermoEMSFileParser")
return ThermoEMSFileParser.ThermoEMSFileParser(filename)
if (not qxas) and (not amptek) and \
JcampFileParser.isJcampFile(filename):
_logger.debug("JcampFileParser")
return JcampFileParser.JcampFileParser(filename)
output = specfilewrapper(filename, amptek=amptek, qxas=qxas)
return output
def Specfile(filename):
f = open(filename)
line0 = f.readline()
if filename.upper().endswith('DTA'):
#TwinMic single column file
line = line0 * 1
line = line.replace('\r','')
line = line.replace('\n','')
line = line.replace('\t',' ')
s = line.split(' ')
if len(s) == 2:
if len(s[-1]) == 0:
try:
float(s[0])
f.close()
output = specfilewrapper(filename, dta=True)
f.close()
return output
except:
#try to read in other way
pass
line = line0
while(len(line)):
if len(line) > 1:
if line[0:2] == '#S':
if ('#SIGNALTYPE' in line) or \
('#SPECTRUM' in line):
line = ""
break
line = f.readline()
f.close()
amptek = False
qxas = False
if len(line):
#it is a Specfile
if DEBUG:
print("This looks as a specfile")
output=specfile.Specfile(filename)
elif SPX and filename.upper().endswith("SPX"):
if DEBUG:
print("This looks as an SPX file")
output = SPXFileParser.SPXFileParser(filename)
else:
if DEBUG:
print("this does not look as a specfile")
if len(line0) > 7:
if line0.startswith('$SPEC_ID') or\
line0.startswith('$DATE_MEA') or\
line0.startswith('$MEAS_TIM') or\
line0.startswith('$Core_ID') or\
line0.startswith('$Section_ID'):
qxas = True
if (not qxas) and line0.startswith('<<'):
amptek = True
if (not qxas) and (not amptek) and Fit2DChiFileParser.isFit2DChiFile(filename):
return Fit2DChiFileParser.Fit2DChiFileParser(filename)
if (not qxas) and (not amptek) and APSMEDFileParser.isAPSMEDFile(filename):
return APSMEDFileParser.APSMEDFileParser(filename)
if (not qxas) and (not amptek) and SRSFileParser.isSRSFile(filename):
if DEBUG:
print("SRSFileParser")
return SRSFileParser.SRSFileParser(filename)
if (not qxas) and (not amptek) and BAXSCSVFileParser.isBAXSCSVFile(filename):
if DEBUG:
print("BAXSCSVFileParser")
return BAXSCSVFileParser.BAXSCSVFileParser(filename)
if (not qxas) and (not amptek) and \
OlympusCSVFileParser.isOlympusCSVFile(filename):
if DEBUG:
print("OlympusCSVFileParser")
return OlympusCSVFileParser.OlympusCSVFileParser(filename)
if (not qxas) and (not amptek) and \
ThermoEMSFileParser.isThermoEMSFile(filename):
if DEBUG:
print("ThermoEMSFileParser")
return ThermoEMSFileParser.ThermoEMSFileParser(filename)
if (not qxas) and (not amptek) and \
JcampFileParser.isJcampFile(filename):
if DEBUG:
print("JcampFileParser")
return JcampFileParser.JcampFileParser(filename)
output = specfilewrapper(filename, amptek=amptek, qxas=qxas)
return output