def getObject3DInstance(config=None):
#for the time being a former configuration
#for serializing purposes is not implemented
#I do the import here for the case PyMca is not installed
#because the modules could be instanstiated without using
#this method
try:
from PyMca5.PyMcaIO import EDFStack
from PyMca5.PyMcaIO import TiffStack
except ImportError:
import EDFStack
import TiffStack
fileTypeList = [
'EDF Z Stack (*edf *ccd)', 'EDF X Stack (*edf *ccd)',
'TIFF Stack (*tif *tiff)'
]
old = PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs * 1
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = False
fileList, filterUsed = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message="Please select the object file(s)",
mode="OPEN",
getfilter=True)
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = old
if not len(fileList):
return None
if filterUsed == fileTypeList[0]:
fileindex = 2
else:
fileindex = 1
#file index is irrelevant in case of an actual 3D stack.
filename = fileList[0]
legend = os.path.basename(filename)
if filterUsed == fileTypeList[2]:
#TIFF
stack = TiffStack.TiffStack(dtype=numpy.float32, imagestack=False)
stack.loadFileList(fileList, fileindex=1)
elif len(fileList) == 1:
stack = EDFStack.EDFStack(dtype=numpy.float32, imagestack=False)
stack.loadIndexedStack(filename, fileindex=fileindex)
else:
stack = EDFStack.EDFStack(dtype=numpy.float32, imagestack=False)
stack.loadFileList(fileList, fileindex=fileindex)
if stack is None:
raise IOError("Problem reading stack.")
object3D = Object3DStack(name=legend)
object3D.setStack(stack)
return object3D
def get4DStack():
"""
Open a stack of image files in EDF or TIFF format, and return
the data with metadata.
:returns: legend, data, xScale, yScale, fileindex
Legend and data are both ``None`` in case of failure.
Scales are 2-tuples (originX, deltaX).
fileindex indicates the dimension/axis in the data corresponding to
the Z-axis.
:raise IOError: If the data could not be read
"""
fileTypeList = [
'EDF Z Stack (*edf *ccd)', 'EDF X Stack (*edf *ccd)',
'TIFF Stack (*tif *tiff)'
]
old = PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs * 1
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = False
fileList, filterUsed = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message="Please select the object file(s)",
mode="OPEN",
getfilter=True)
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = old
if not fileList:
return None, None
if filterUsed.startswith('EDF Z'):
fileindex = 2
else:
fileindex = 1
filename = fileList[0]
legend = os.path.basename(filename)
if filterUsed.startswith('TIFF'):
stack = TiffStack.TiffStack(dtype=numpy.float32, imagestack=False)
stack.loadFileList(fileList, fileindex=1)
else:
stack = EDFStack.EDFStack(dtype=numpy.float32, imagestack=False)
if len(fileList) == 1:
stack.loadIndexedStack(filename, fileindex=fileindex)
else:
stack.loadFileList(fileList, fileindex=fileindex)
if stack is None:
raise IOError("Problem reading stack.")
xScale = stack.info.get("xScale")
yScale = stack.info.get("yScale")
return legend, stack.data, xScale, yScale, fileindex
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