/usr/share/pyshared/PyMca/specfilewrapper.py is in pymca 4.5.0-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# Copyright (C) 2004-2012 European Synchrotron Radiation Facility
#
# This file is part of the PyMCA X-ray Fluorescence Toolkit developed at
# the ESRF by the Beamline Instrumentation Software Support (BLISS) group.
#
# This toolkit is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# PyMCA is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# PyMCA; if not, write to the Free Software Foundation, Inc., 59 Temple Place,
# Suite 330, Boston, MA 02111-1307, USA.
#
# PyMCA follows the dual licensing model of Trolltech's Qt and Riverbank's PyQt
# and cannot be used as a free plugin for a non-free program.
#
# Please contact the ESRF industrial unit (industry@esrf.fr) if this license
# is a problem for you.
#############################################################################*/
import os
import sys
import numpy
import numpy.oldnumeric as Numeric
import re
try:
from PyMca import specfile
except ImportError:
import specfile
from PyMca import Fit2DChiFileParser
from PyMca import APSMEDFileParser
from PyMca import SRSFileParser
try:
from PyMca import SPXFileParser
SPX = True
except:
SPX = False
DEBUG = 0
if sys.version >= '2.6':
def safe_str(bytesObject):
try:
return str(bytesObject, 'utf-8')
except UnicodeDecodeError:
try:
return str(bytesObject, 'latin-1')
except:
try:
return str(bytesObject, 'utf-16')
except:
return str(bytesObject)
else:
def safe_str(*var, **kw):
return str(var[0])
#python 2.5 does not have bytes function
def bytes(*var, **kw):
return var[0]
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:
v = 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':
break
line = f.readline()
f.close()
amptek = False
qxas = False
if len(line):
#it is a Specfile
output=specfile.Specfile(filename)
elif SPX and filename.upper().endswith("SPX"):
#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('$MEAS_TIM'):
qxas = True
if (not qxas) and line0.startswith('<<'):
amptek = True
if (not qxas) and (not amptek) and Fit2DChiFileParser.isFit2DChiFile(filename):
return Fit2DChiFileParser.Fit2DChiFileParser(filename)
if (not qxas) and (not amptek) and APSMEDFileParser.isAPSMEDFile(filename):
return APSMEDFileParser.APSMEDFileParser(filename)
if (not qxas) and (not amptek) and SRSFileParser.isSRSFile(filename):
return SRSFileParser.SRSFileParser(filename)
output=specfilewrapper(filename, amptek=amptek, qxas = qxas)
return output
class specfilewrapper:
def __init__(self,filename,amptek=None, qxas = None, dta = None):
if amptek is None: amptek = False
if qxas is None: qxas = False
if dta is None: dta = False
self.amptek = amptek
self.qxas = qxas
self.dta = dta
self.header = []
if self.dta:
#TwinMic .dta files with only one spectrum
if 0:
f = open(filename, 'rb')
raw_content = f.read()
f.close()
expr = '([-+]?\d+)\t\r\n'
self.data = [float(i) for i in re.split(expr,raw_content) if i != '']
self.data = numpy.array(self.data, numpy.float32)
else:
self.data = numpy.fromfile(filename,
dtype=numpy.float32,
sep='\t\r\n')
self.header = ['#S1 %s' % os.path.basename(filename)]
self.data.shape = -1, 1
self.scandata=[myscandata(self.data,'MCA','1.1',scanheader=self.header)]
return
if self.qxas:
f = open(filename)
else:
f = BufferedFile(filename)
line = f.readline()
outdata = []
ncol0 = -1
nlines= 0
if amptek:
if sys.version < '3.0':
while "<<DATA>>" not in line:
self.header.append(line.replace("\n",""))
line = f.readline()
else:
while bytes("<<DATA>>", 'utf-8') not in line:
self.header.append(safe_str(line.replace(bytes("\n", 'utf-8'),
bytes("", 'utf-8'))))
line = f.readline()
elif qxas:
line.replace("\n","")
line.replace("\x00","")
self._qxasHeader = {}
self._qxasHeader['S'] = '#S1 '+ " Unlabelled Spectrum"
while 1:
self.header.append(line)
if line.startswith('$SPEC_ID:'):
line = f.readline().replace("\n","")
line.replace("\x00","")
self.header.append(line)
self._qxasHeader['S'] = '#S1 '+ line
if line.startswith('$DATE_MEA'):
line = f.readline().replace("\n","")
self.header.append(line)
self._qxasHeader['D'] = line
if line.startswith('$MEAS_TIM'):
line = f.readline().replace("\n","")
self.header.append(line)
tmpList = [float(i) for i in line.split()]
if len(tmpList) == 1:
preset = tmpList[0]
elapsed = preset
else:
preset, elapsed = tmpList[0:2]
self._qxasHeader['@CTIME'] = ['#@CTIME %f %f %f' % (preset, preset, elapsed)]
if line.startswith('$MCA_CAL'):
try:
line = f.readline().replace("\n","")
self.header.append(line)
if line.startswith('$'):
continue
line = f.readline().replace("\n","")
self.header.append(line)
if line.startswith('$'):
continue
coefficients = [float(i) for i in line.split()]
if len(coefficients) == 2:
coefficients.append(0.0)
self._qxasHeader['@CALIB']= ['#@CALIB %f %f %f' %\
(coefficients[0], coefficients[1], coefficients[2])]
except:
pass
if line.startswith('$DATA:'):
line = f.readline().replace("\n","")
self.header.append(line)
start, stop = [int(i) for i in line.split()]
self._qxasHeader['@CHANN'] = ['#@CHANN %d %d %d 1' % (stop-start+1, start, stop)]
break
line = f.readline().replace("\n","")
if qxas:
outdata = [float(x) for x in f.read().split()]
nlines = len(outdata)
f.close()
self.data=Numeric.resize(Numeric.array(outdata).astype(Numeric.Float),(nlines,1))
else:
if sys.version < '3.0':
line = line.replace(","," ")
line = line.replace(";"," ")
line = line.replace("\t"," ")
line = line.replace("\r","\n")
line = line.replace('"',"")
line = line.replace('\n\n',"\n")
else:
tmpBytes = bytes(" ",'utf-8')
line = line.replace(bytes(",",'utf-8'), tmpBytes)
line = line.replace(bytes(";",'utf-8'), tmpBytes)
line = line.replace(bytes("\t",'utf-8'), tmpBytes)
tmpBytes = bytes("\n",'utf-8')
line = line.replace(bytes("\r","utf-8"), tmpBytes)
line = line.replace(bytes('"',"utf-8"), bytes("", "utf-8"))
line = line.replace(bytes('\n\n',"utf-8"), tmpBytes)
while(len(line)):
values = line.split()
if len(values):
try:
reals = [float(x) for x in values]
ncols = len(reals)
if ncol0 < 0:ncol0 = ncols
if ncols == ncol0:
outdata.append(reals)
nlines += 1
except:
if len(line) > 1:
if sys.version < '3.0':
self.header.append(line.replace("\n",""))
else:
self.header.append(safe_str(line.replace(\
bytes("\n",'utf-8'),\
bytes("", 'utf-8'))))
else:
if len(line) > 1:
if sys.version < '3.0':
self.header.append(line.replace("\n",""))
else:
self.header.append(safe_str(line.replace(bytes("\n",'utf-8'),
bytes("", 'utf-8'))))
line = f.readline()
if sys.version < '3.0':
line = line.replace(","," ")
line = line.replace(";"," ")
line = line.replace("\t"," ")
line = line.replace("\r","\n")
line = line.replace('"',"")
line = line.replace('\n\n',"\n")
else:
tmpBytes = bytes(" ",'utf-8')
line = line.replace(bytes(",",'utf-8'), tmpBytes)
line = line.replace(bytes(";",'utf-8'), tmpBytes)
line = line.replace(bytes("\t",'utf-8'), tmpBytes)
tmpBytes = bytes("\n",'utf-8')
line = line.replace(bytes("\r","utf-8"), tmpBytes)
line = line.replace(bytes('"',"utf-8"), bytes("", "utf-8"))
line = line.replace(bytes('\n\n',"utf-8"), tmpBytes)
f.close()
self.data=Numeric.resize(Numeric.array(outdata).astype(Numeric.Float),(nlines,ncol0))
if self.amptek:
self.scandata=[myscandata(self.data,'MCA','1.1',scanheader=self.header)]
elif self.qxas:
self.scandata=[myscandata(self.data,'MCA','1.1',scanheader=self.header, qxas=self._qxasHeader)]
else:
labels = None
if len(self.header) > 0:
if len(self.header[0]) > 0:
labels = self.header[0].split(" ")
if len(labels) != ncol0:
labels = None
self.scandata=[myscandata(self.data,'SCAN','1.1', labels=labels),myscandata(self.data,'MCA','2.1')]
def list(self):
if self.amptek or self.qxas or self.dta:
return "1:1"
else:
return "1:2"
def __getitem__(self,item):
return self.scandata[item]
def select(self,i):
n=i.split(".")
return self.__getitem__(int(n[0])-1)
def scanno(self):
if self.amptek or self.qxas:
return 1
else:
return 2
class myscandata:
def __init__(self,data,scantype=None,identification=None, scanheader=None, qxas=None, labels=None):
if identification is None:identification='1.1'
if scantype is None:scantype='SCAN'
self.qxas = qxas
self.scanheader = scanheader
#print Numeric.shape(data)
(rows, cols) = Numeric.shape(data)
if scantype == 'SCAN':
self.__data = Numeric.zeros((rows, cols +1 ), Numeric.Float)
self.__data[:,0] = Numeric.arange(rows) * 1.0
self.__data[:,1:] = data * 1
self.__cols = cols + 1
self.labels = ['Point']
else:
self.__data = data
self.__cols = cols
self.labels = []
self.scantype = scantype
self.rows = rows
if labels is None:
for i in range(cols):
self.labels.append('Column %d' % i)
else:
for label in labels:
self.labels.append('%s' % label)
n = identification.split(".")
self.__number = int(n[0])
self.__order = int(n[1])
def alllabels(self):
if self.scantype == 'SCAN':
return self.labels
else:
return []
def allmotorpos(self):
return []
def cols(self):
return self.__cols
def command(self):
if DEBUG:
print("command called")
if self.qxas is not None:
if 'S' in self.qxas:
text = self.qxas['S']
elif self.scanheader is not None:
if len(self.scanheader):
text = self.scanheader[0]
return text
def data(self):
return Numeric.transpose(self.__data)
def datacol(self,col):
return self.__data[:,col]
def dataline(self,line):
return self.__data[line,:]
def date(self):
text = 'sometime'
if self.qxas is not None:
if 'D' in self.qxas:
return self.qxas['D']
elif self.scanheader is not None:
for line in self.scanheader:
if 'START_TIME' in line:
text = "%s" % line
break
return text
def fileheader(self):
if DEBUG:
print("file header called")
labels = '#L '
for label in self.labels:
labels += ' '+label
if self.scantype == 'SCAN':
return ['#S1 Unknown command','#N %d' % len(self.labels), labels]
else:
if self.scanheader is None:
return ['#S1 Unknown command']
else:
if DEBUG:
print("returning ",self.scanheader)
return self.scanheader
def header(self,key):
if self.qxas is not None:
if key in self.qxas:
return self.qxas[key]
elif key == "" or key == " ":
return self.fileheader()
if key == 'S': return self.fileheader()[0]
elif key == 'N':return self.fileheader()[-2]
elif key == 'L':return self.fileheader()[-1]
elif key == '@CALIB':
output = []
if self.scanheader is None: return output
if self.scanheader[0][0:2] == '<<':
#amptek
try:
amptekCalibrationLines = []
amptekInCalibrationLines = False
for line in self.scanheader:
if '<<CALIBRATION>>' in line:
amptekInCalibrationLines = True
continue
if line.startswith('<<'):
amptekInCalibrationLines = False
continue
if amptekInCalibrationLines and\
('LABEL' not in line):
amptekCalibrationLines.append(line)
n = len(amptekCalibrationLines)
if n == 0 :
return output
if n == 1:
#one point calibration
x0,y0 = 0.0, 0.0
values = amptekCalibrationLines[0].split()
x1,y1 = map(float,values)
gain = (y1-y0)/(x1-x0)
zero = y0 - gain * x0
elif n == 2:
#two point calibration
values = amptekCalibrationLines[0].split()
x0,y0 = map(float,values)
values = amptekCalibrationLines[1].split()
x1,y1 = map(float,values)
gain = (y1-y0)/(x1-x0)
zero = y0 - gain * x0
else:
x = numpy.zeros((n,), numpy.float)
y = numpy.zeros((n,), numpy.float)
for i in range(n):
values = amptekCalibrationLines[i].split()
x[i], y[i] = map(float,values)
Sxy = numpy.dot(x, y.T)
Sxx = numpy.dot(x, x.T)
Sx = x.sum()
Sy = y.sum()
d = n * Sxx - Sx * Sx
zero = (Sxx * Sy - Sx * Sxy)/d
gain = (n * Sxy - Sx * Sy)/d
output = ['#@CALIB %g %g 0' % (zero, gain)]
except:
pass
return output
elif key == "" or key == " ":return self.fileheader()
else:
#print "requested key = ",key
return []
def order(self):
return self.__order
def number(self):
return self.__number
def lines(self):
if self.scantype == 'SCAN':
return self.rows
else:
return 0
def nbmca(self):
if self.scantype == 'SCAN':
return 0
else:
return self.__cols
def mca(self,number):
return self.__data[:,number-1]
class BufferedFile(object):
def __init__(self, filename):
f = open(filename, 'rb')
self.__buffer = f.read()
f.close()
if sys.version < '3.0':
self.__buffer=self.__buffer.replace("\r", "\n")
self.__buffer=self.__buffer.replace("\n\n", "\n")
self.__buffer = self.__buffer.split("\n")
else:
tmp = bytes("\n", 'utf-8')
self.__buffer=self.__buffer.replace(bytes("\r", 'utf-8'), tmp)
self.__buffer=self.__buffer.replace(bytes("\n\n", 'utf-8'), tmp)
self.__buffer = self.__buffer.split(tmp)
self.__currentLine = 0
if sys.version < '3.0':
def readline(self):
if self.__currentLine >= len(self.__buffer):
return ""
line = self.__buffer[self.__currentLine] + "\n"
self.__currentLine += 1
return line
else:
def readline(self):
if self.__currentLine >= len(self.__buffer):
return bytes("", 'utf-8')
line = self.__buffer[self.__currentLine] + bytes("\n", 'utf-8')
self.__currentLine += 1
return line
def close(self):
self.__currentLine = 0
return
if __name__ == "__main__":
filename = sys.argv[1]
print(filename)
sf=Specfile(filename)
sf.list()
print(sf[0].alllabels())
print(dir(sf[0]))
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