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 __init__(self, filename):
DataObject.DataObject.__init__(self)
fileParser = JcampFileParser.JcampFileParser(filename, single=False)
scan = fileParser[0]
fileHeader = scan.fileheader()
firstHeaderInfo = parseFileHeader(fileHeader)
if scan.nbmca() == 0:
scan = fileParser[1]
nBlocks = firstHeaderInfo["BLOCKS"]
nbmca = scan.nbmca()
# take the last mca of the scan
lastMca = scan.mca(nbmca)
nChannels = lastMca.size
calib = scan.header('@CALIB')[0]
if len(calib):
calib = [float(x) for x in calib.split()[1:]]
else:
calib = [0.0, 1.0, 0.0]
chann = scan.header('@CHANN')[0]
if len(chann):
ctxt = chann.split()
if len(ctxt) == 5:
chann = float(ctxt[2])
else:
chann = 0.0
else:
chann = 0.0
# assume all mca have the same size, calibration, ...
data = numpy.zeros((1, nBlocks, nChannels), dtype=numpy.float32)
nScans = fileParser.scanno()
mcaIndex = 0
for i in range(nScans):
scan = fileParser[i]
if scan.nbmca():
mcaData = scan.mca(scan.nbmca())
data[0, mcaIndex] = mcaData
mcaIndex += 1
# make use of the collected information
# shape
xShape = firstHeaderInfo.get("$MAP_POINTS_IN_X", None)
yShape = firstHeaderInfo.get("$MAP_POINTS_IN_Y", None)
if (xShape is not None) and (yShape is not None):
if xShape * yShape == nBlocks:
data.shape = yShape, xShape, nChannels
else:
print("PRODUCT DOES NOT MATCH NUMBER OF BLOCKS")
#scales
xScale = [0.0, 1.0]
yScale = [0.0, 1.0]
xScale[0] = firstHeaderInfo.get("$MAP_ORIGIN_X", 0.0)
xScale[1] = firstHeaderInfo.get("$MAP_DELTA_X", 1.0)
yScale[0] = firstHeaderInfo.get("$MAP_ORIGIN_Y", 0.0)
yScale[1] = firstHeaderInfo.get("$MAP_DELTA_Y", 1.0)
self.sourceName = filename
self.info = {}
self.info["SourceType"] = SOURCE_TYPE
self.info["SourceName"] = self.sourceName
shape = self.data.shape
for i in range(len(shape)):
key = 'Dim_%d' % (i + 1, )
self.info[key] = shape[i]
self.info["NumberOfFiles"] = 1
self.info["McaIndex"] = 2
self.info["McaCalib"] = calib
self.info["Channel0"] = chann
self.info["xScale"] = xScale
self.info["yScale"] = yScale
self.data = data
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