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 = Object3DFileDialogs.Object3DDirs.nativeFileDialogs * 1
Object3DFileDialogs.Object3DDirs.nativeFileDialogs = False
fileList, filterUsed = Object3DFileDialogs.getFileList(None, fileTypeList,
"Please select the object file(s)",
"OPEN",
True)
Object3DFileDialogs.Object3DDirs.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 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 = Object3DFileDialogs.Object3DDirs.nativeFileDialogs * 1
Object3DFileDialogs.Object3DDirs.nativeFileDialogs = False
fileList, filterUsed = Object3DFileDialogs.getFileList(
None, fileTypeList, "Please select the object file(s)", "OPEN", True)
Object3DFileDialogs.Object3DDirs.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 getObject3DInstance(config=None):
fileTypeList = [
'Picture Files (*jpg *jpeg *tif *tiff *png)', 'EDF Files (*edf)',
'EDF Files (*ccd)', 'ADSC Files (*img)', 'EDF Files (*)'
]
fileList, filterUsed = Object3DFileDialogs.getFileList(
None,
filetypelist=fileTypeList,
message="Please select one object data file",
mode="OPEN",
getfilter=True)
if not len(fileList):
return
fname = fileList[0]
if filterUsed.split()[0] == "Picture":
qimage = qt.QImage(fname)
if qimage.isNull():
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read file %s as an image" % fname)
msg.exec_()
return
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setQImage(qimage)
return object3D
if filterUsed.split()[0] in ["EDF", "ADSC"]:
edf = EdfFile.EdfFile(fname)
data = edf.GetData(0)
if True:
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setImageData(data)
else:
(image, size, minmax) = spslut.transform(data, (1, 0),
(spslut.LINEAR, 3.0),
"RGBX", spslut.TEMP, 1,
(0, 1), (0, 255), 1)
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setPixmap(image,
size[0],
size[1],
xmirror=False,
ymirror=False)
return object3D
return None
def getObject3DInstance(config=None):
fileTypeList = ['Picture Files (*jpg *jpeg *tif *tiff *png)',
'EDF Files (*edf)',
'EDF Files (*ccd)',
'ADSC Files (*img)',
'EDF Files (*)']
fileList, filterUsed = Object3DFileDialogs.getFileList(None,
filetypelist=fileTypeList,
message="Please select one object data file",
mode="OPEN",
getfilter=True)
if not len(fileList):
return
fname = fileList[0]
if filterUsed.split()[0] == "Picture":
qimage = qt.QImage(fname)
if qimage.isNull():
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read file %s as an image" % fname)
msg.exec_()
return
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setQImage(qimage)
return object3D
if filterUsed.split()[0] in ["EDF", "ADSC"]:
edf = EdfFile.EdfFile(fname)
data = edf.GetData(0)
if True:
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setImageData(data)
else:
(image,size,minmax)= spslut.transform(data, (1,0),
(spslut.LINEAR,3.0),
"RGBX", spslut.TEMP,
1,
(0, 1),
(0, 255), 1)
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setPixmap(image, size[0], size[1], xmirror = False, ymirror = False)
return object3D
return None
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 EdfFile
except ImportError:
import EdfFile
fileTypeList = [
'EDF Files (*edf)', 'EDF Files (*ccd)', 'ADSC Files (*img)',
'EDF Files (*)'
]
old = Object3DFileDialogs.Object3DDirs.nativeFileDialogs * 1
Object3DFileDialogs.Object3DDirs.nativeFileDialogs = False
fileList, filterUsed = Object3DFileDialogs.getFileList(
None,
filetypelist=fileTypeList,
message="Please select one object data file",
mode="OPEN",
getfilter=True)
Object3DFileDialogs.Object3DDirs.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)
edf = EdfFile.EdfFile(filename, access='rb')
data = edf.GetData(0).astype(numpy.float32)
object3D = Object3DMesh(os.path.basename(filename))
object3D.setData(data, z=data[:])
return object3D
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 EdfFile
except ImportError:
import EdfFile
fileTypeList = ['EDF Files (*edf)',
'EDF Files (*ccd)',
'ADSC Files (*img)',
'EDF Files (*)']
old = Object3DFileDialogs.Object3DDirs.nativeFileDialogs * 1
Object3DFileDialogs.Object3DDirs.nativeFileDialogs = False
fileList, filterUsed = Object3DFileDialogs.getFileList(None,
filetypelist=fileTypeList,
message="Please select one object data file",
mode="OPEN",
getfilter=True)
Object3DFileDialogs.Object3DDirs.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)
edf = EdfFile.EdfFile(filename, access='rb')
data = edf.GetData(0).astype(numpy.float32)
object3D = Object3DMesh(os.path.basename(filename))
object3D.setData(data, z=data[:])
return object3D
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
except ImportError:
import EDFStack
fileTypeList = ['Chimera Stack (*cmp)',
'Chimera Stack (*)']
old = Object3DFileDialogs.Object3DDirs.nativeFileDialogs * 1
#Object3DFileDialogs.Object3DDirs.nativeFileDialogs = False
fileList, filterUsed = Object3DFileDialogs.getFileList(None, fileTypeList,
"Please select the object file(s)",
"OPEN",
True)
Object3DFileDialogs.Object3DDirs.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)
f = h5py.File(filename)
stack = f['Image']['data'].value
f = None
if stack is None:
raise IOError("Problem reading stack.")
object3D = ChimeraStack(name=legend)
object3D.setStack(stack)
return object3D
