def getFileHandle(self, inputfile):
try:
self._HDF5 = False
if type(inputfile) == numpy.ndarray:
return NumpyStack.NumpyStack(inputfile)
if HDF5SUPPORT:
if h5py.is_hdf5(inputfile):
self._HDF5 = True
try:
# if (len(self._filelist) == 1) && (self.mcaStep > 1)
# it should attempt to avoid loading many times
# the stack into memory in case of multiple processes
return HDF5Stack1D.HDF5Stack1D(self._filelist,
self.selection)
except:
raise
ffile = self.__tryEdf(inputfile)
if ffile is None:
ffile = self.__tryLucia(inputfile)
if ffile is None:
if inputfile[-3:] == "DAT":
ffile = self.__tryAifira(inputfile)
if ffile is None:
if LispixMap.isLispixMapFile(inputfile):
ffile = LispixMap.LispixMap(inputfile, native=False)
if ffile is None:
del ffile
ffile = SpecFileLayer.SpecFileLayer()
ffile.SetSource(inputfile)
return ffile
except:
raise IOError("I do not know what to do with file %s" % inputfile)
def getFileHandle(self, inputfile):
try:
self._HDF5 = False
if HDF5SUPPORT:
if h5py.is_hdf5(inputfile):
self._HDF5 = True
try:
return HDF5Stack1D.HDF5Stack1D(self._filelist,
self.selection)
except:
raise
ffile = self.__tryEdf(inputfile)
if ffile is None:
ffile = self.__tryLucia(inputfile)
if ffile is None:
if inputfile[-3:] == "DAT":
ffile = self.__tryAifira(inputfile)
if ffile is None:
if LispixMap.isLispixMapFile(inputfile):
ffile = LispixMap.LispixMap(inputfile, native=False)
if (ffile is None):
del ffile
ffile = SpecFileLayer.SpecFileLayer()
ffile.SetSource(inputfile)
return ffile
except:
raise IOError("I do not know what to do with file %s" % inputfile)
def processList(self):
self.__ncols = None
self.__nrows = self.filestep
counter = 0
ffile = SpecFileLayer.SpecFileLayer()
for fitfile in self._filelist:
self.onNewFile(fitfile, self._filelist)
ffile.SetSource(fitfile)
fileinfo = ffile.GetSourceInfo()
# nscans = len(fileinfo['KeyList'])
for scankey in fileinfo['KeyList']:
scan,order = scankey.split(".")
info,data = ffile.LoadSource(scankey)
scan_obj = ffile.Source.select(scankey)
if info['NbMca'] > 0:
for i in range(info['NbMca']):
point = int(i/info['NbMcaDet']) + 1
mca = (i % info['NbMcaDet']) + 1
key = "%s.%s.%05d.%d" % (scan,order,point,mca)
if i == 0:
mcainfo,mcadata = ffile.LoadSource(key)
mcadata = scan_obj.mca(i+1)
y0 = numpy.array(mcadata, numpy.float)
if counter == 0:
key0 = "%s key %s" % (os.path.basename(fitfile), key)
self.__ncols = len(y0)
image = numpy.zeros((self.__nrows,self.__ncols), \
numpy.float)
if self.__ncols != len(y0):
print("spectrum has different number of columns")
print("skipping it")
else:
image[counter,:] = y0[:]
if (counter+1) == self.filestep:
if self.filestep > 1:
key1 = "%s key %s" % (os.path.basename(fitfile), key)
title = "%s to %s" % (key0, key1)
else:
title = key0
if 1:
ddict={}
if 'Channel0' in mcainfo:
ddict['MCA start ch'] =\
int(mcainfo['Channel0'])
if 'McaCalib' in mcainfo:
ddict['MCA a'] = mcainfo['McaCalib'][0]
ddict['MCA b'] = mcainfo['McaCalib'][1]
ddict['MCA c'] = mcainfo['McaCalib'][2]
else:
ddict = mcainfo
ddict['Title'] = title
edfname = os.path.join(self.outputdir,title.replace(" ","_")+".edf")
edfout = EdfFile.EdfFile(edfname)
edfout.WriteImage (ddict , image, Append=0)
counter = 0
else:
counter += 1
self.onEnd()
def testSpecMesh(self):
filename = os.path.join(self.path, 'meshscan.dat')
# SpecFileStack: only works with one detector
nDet = 1
info = XrfData.generateSpecMesh(filename, nDet=nDet, same=False)
nDet0, nRows0, nColumns0, nChannels = info['data'].shape
from PyMca5.PyMcaIO import SpecFileStack
stack = SpecFileStack.SpecFileStack(filelist=[filename]).data
self.assertEqual(nDet, nDet0)
self.assertEqual(stack.shape, (1, nRows0 * nColumns0, nChannels))
for i in range(nRows0):
for j in range(nColumns0):
for k in range(1):
# C-order (row-major)
mca = stack[k, i * nColumns0 + j]
numpy.testing.assert_array_equal(mca, info['data'][k, i,
j])
# SpecFileLayer: works with more than one detector
nDet = 2
info = XrfData.generateSpecMesh(filename, nDet=nDet, same=False)
nDet0, nRows0, nColumns0, nChannels = info['data'].shape
nCounters0 = 2
from PyMca5.PyMcaCore import SpecFileLayer
ffile = SpecFileLayer.SpecFileLayer()
ffile.SetSource(filename)
fileinfo = ffile.GetSourceInfo()
scaninfo, counters = ffile.LoadSource('1.1')
scan = ffile.Source.select('1.1')
nCounters, nRows, nColumns = counters.shape
self.assertEqual(scaninfo['NbMcaDet'], nDet)
self.assertEqual(scaninfo['NbMca'], nDet * nColumns * nRows)
self.assertEqual(nColumns, nColumns0)
self.assertEqual(nRows, nRows0)
self.assertEqual(nCounters, nCounters0)
self.assertEqual(nDet, nDet0)
for i in range(nRows):
for j in range(nColumns):
for k in range(nDet):
mca = scan.mca(i * nColumns * nDet + j * nDet + k + 1)
# TODO: bug in specfile (reads one channel less)
numpy.testing.assert_array_equal(mca, info['data'][k, i,
j])
del ffile.Source
def test():
import sys
from PyMca5.PyMcaCore import SpecFileLayer
app = qt.QApplication([])
tab = SpecFileMcaTable()
d = SpecFileLayer.SpecFileLayer()
if len(sys.argv) > 1:
d.SetSource(sys.argv[1])
else:
d.SetSource('03novs060sum.mca')
info, data = d.LoadSource('1.1')
tab.build(info)
tab.setSelectedMca(["1.1"])
tab.show()
app.exec()
def test():
from PyMca5.PyMcaCore import SpecFileLayer
if len(sys.argv) < 3:
print("USAGE: %s <filename> <key>" % sys.argv[0])
sys.exit(0)
d = SpecFileLayer.SpecFileLayer()
d.SetSource(sys.argv[1])
info, data = d.LoadSource(sys.argv[2])
app = qt.QApplication([])
wid = SpecFileDataInfo(info)
wid.show()
app.exec_()
