def getStack(self, filelist=None, imagestack=None):
if filelist in [None, []]:
filelist, filefilter = self._getStackOfFiles(getfilter=True)
else:
filefilter = ""
if not len(filelist):
return None
if filefilter in ["", "All Files (*)"]:
if HDF5:
if h5py.is_hdf5(filelist[0]):
filefilter = "HDF5"
fileindex = 0
begin = None
end = None
aifirafile = False
if len(filelist):
PyMcaDirs.inputDir = os.path.dirname(filelist[0])
#if we are dealing with HDF5, no more tests needed
if not filefilter.upper().startswith('HDF5'):
f = open(filelist[0], 'rb')
#read 10 characters
if sys.version < '3.0':
line = f.read(10)
else:
try:
line = str(f.read(10).decode())
except UnicodeDecodeError:
#give a dummy value
line = " "
f.close()
omnicfile = False
if filefilter.upper().startswith('HDF5'):
stack = QHDF5Stack1D.QHDF5Stack1D(filelist)
omnicfile = True
elif filefilter.upper().startswith('OPUS-DPT'):
stack = OpusDPTMap.OpusDPTMap(filelist[0])
omnicfile = True
elif filefilter.upper().startswith("AIFIRA"):
stack = AifiraMap.AifiraMap(filelist[0])
omnicfile = True
aifirafile = True
elif filefilter.upper().startswith("SUPAVISIO"):
stack = SupaVisioMap.SupaVisioMap(filelist[0])
omnicfile = True
elif filefilter.upper().startswith("TEXTIMAGE"):
imagestack = True
fileindex = 0
stack = TextImageStack.TextImageStack(imagestack=True)
elif filefilter.upper().startswith("IMAGE") and\
(filelist[0].upper().endswith("TIF") or\
filelist[0].upper().endswith("TIFF")):
stack = TiffStack.TiffStack(imagestack=True)
elif filefilter.upper().startswith("RENISHAW"):
stack = RenishawMap.RenishawMap(filelist[0])
omnicfile = True
elif filefilter == "" and\
(filelist[0].upper().endswith("TIF") or\
filelist[0].upper().endswith("TIFF")):
stack = TiffStack.TiffStack(imagestack=True)
elif filefilter.upper().startswith("IMAGE"):
if imagestack is None:
imagestack = True
fileindex = 0
stack = QStack(imagestack=imagestack)
elif line[0] == "{":
if filelist[0].upper().endswith("RAW"):
if imagestack is None:
imagestack = True
stack = QStack(imagestack=imagestack)
elif line[0:2] in ["II", "MM"]:
if imagestack is None:
imagestack = True
stack = QStack(imagestack=imagestack)
elif line.startswith('Spectral'):
stack = OmnicMap.OmnicMap(filelist[0])
omnicfile = True
elif line.startswith('#\tDate'):
stack = LuciaMap.LuciaMap(filelist[0])
omnicfile = True
elif filelist[0].upper().endswith("RAW.GZ")or\
filelist[0].upper().endswith("EDF.GZ")or\
filelist[0].upper().endswith("CCD.GZ")or\
filelist[0].upper().endswith("RAW.BZ2")or\
filelist[0].upper().endswith("EDF.BZ2")or\
filelist[0].upper().endswith("CCD.BZ2")or\
filelist[0].upper().endswith(".CBF"):
if imagestack is None:
imagestack = True
stack = QStack(imagestack=imagestack)
elif filelist[0].upper().endswith(".RTX"):
stack = RTXMap.RTXMap(filelist[0])
omnicfile = True
elif filelist[0][-4:].upper() in ["PIGE", "PIGE"]:
stack = SupaVisioMap.SupaVisioMap(filelist[0])
omnicfile = True
elif filelist[0][-3:].upper() in ["RBS"]:
stack = SupaVisioMap.SupaVisioMap(filelist[0])
omnicfile = True
elif filelist[0][-3:].upper() in ["SPE"] and\
(line[0] not in ['$', '#']):
#Roper Scientific format
#handle it as MarCCD stack
stack = QStack(imagestack=True)
elif MRCMap.isMRCFile(filelist[0]):
stack = MRCMap.MRCMap(filelist[0])
omnicfile = True
imagestack = True
elif LispixMap.isLispixMapFile(filelist[0]):
stack = LispixMap.LispixMap(filelist[0])
omnicfile = True
elif RenishawMap.isRenishawMapFile(filelist[0]):
# This is dangerous. Any .txt file with four
# columns would be accepted as a Renishaw Map
# by other hand, I do not know how to handle
# that case as a stack.
stack = RenishawMap.RenishawMap(filelist[0])
omnicfile = True
else:
stack = QSpecFileStack()
if len(filelist) == 1:
if not omnicfile:
try:
stack.loadIndexedStack(filelist[0],
begin,
end,
fileindex=fileindex)
except:
msg = qt.QMessageBox()
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("%s" % sys.exc_info()[1])
if QTVERSION < '4.0.0':
msg.exec_loop()
else:
msg.exec_()
if DEBUG:
raise
elif len(filelist):
if not omnicfile:
try:
stack.loadFileList(filelist, fileindex=fileindex)
except:
msg = qt.QMessageBox()
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("%s" % sys.exc_info()[1])
if QTVERSION < '4.0.0':
msg.exec_loop()
else:
msg.exec_()
if DEBUG:
raise
if aifirafile:
masterStack = DataObject.DataObject()
masterStack.info = copy.deepcopy(stack.info)
masterStack.data = stack.data[:, :, 0:1024]
masterStack.info['Dim_2'] = int(masterStack.info['Dim_2'] / 2)
slaveStack = DataObject.DataObject()
slaveStack.info = copy.deepcopy(stack.info)
slaveStack.data = stack.data[:, :, 1024:]
slaveStack.info['Dim_2'] = int(slaveStack.info['Dim_2'] / 2)
return [masterStack, slaveStack]
else:
return stack
def getStackFromPattern(self,
filepattern,
begin,
end,
increment=None,
imagestack=None,
fileindex=0):
#get the first filename
filename = filepattern % tuple(begin)
if not os.path.exists(filename):
raise IOError("Filename %s does not exist." % filename)
#get the file list
args = self.getFileListFromPattern(filepattern,
begin,
end,
increment=increment)
#get the file type
f = open(args[0], 'rb')
#read 10 characters
line = f.read(10)
f.close()
specfile = False
marCCD = False
if line.startswith("II") or line.startswith("MM"):
marCCD = True
if line[0] == "\n":
line = line[1:]
if (line[0] == "{") or marCCD:
if imagestack is None:
if marCCD:
imagestack = True
if imagestack:
#prevent any modification
fileindex = 0
if filepattern is not None:
#this dows not seem to put any trouble
#(because of no redimensioning attempt)
if False and (len(begin) != 1):
raise IOError("EDF stack redimensioning not supported yet")
stack = QStack(imagestack=imagestack)
elif line.startswith('Spectral'):
stack = OmnicMap.OmnicMap(args[0])
elif line.startswith('#\tDate:'):
stack = LuciaMap.LuciaMap(args[0])
elif args[0][-4:].upper() in ["PIGE", "PIXE"]:
stack = SupaVisioMap.SupaVisioMap(args[0])
elif args[0][-3:].upper() in ["RBS"]:
stack = SupaVisioMap.SupaVisioMap(args[0])
elif args[0][-3:].lower() in [".h5", "nxs", "hdf"]:
if not HDF5:
raise IOError(\
"No HDF5 support while trying to read an HDF5 file")
stack = QHDF5Stack1D.QHDF5Stack1D(args)
elif args[0].upper().endswith("RAW.GZ")or\
args[0].upper().endswith("EDF.GZ")or\
args[0].upper().endswith("CCD.GZ")or\
args[0].upper().endswith("RAW.BZ2")or\
args[0].upper().endswith("EDF.BZ2")or\
args[0].upper().endswith("CCD.BZ2"):
if imagestack is None:
imagestack = True
stack = QStack(imagestack=imagestack)
else:
if HDF5:
if h5py.is_hdf5(args[0]):
stack = QHDF5Stack1D.QHDF5Stack1D(args)
else:
stack = QSpecFileStack()
specfile = True
else:
stack = QSpecFileStack()
specfile = True
if specfile and (len(begin) == 2):
if increment is None:
increment = [1] * len(begin)
shape = (len(range(begin[0], end[0] + 1, increment[0])),
len(range(begin[1], end[1] + 1, increment[1])))
stack.loadFileList(args, fileindex=fileindex, shape=shape)
else:
stack.loadFileList(args, fileindex=fileindex)
return stack