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 __tryEdf(self, inputfile):
try:
ffile = EdfFileLayer.EdfFileLayer(fastedf=0)
ffile.SetSource(inputfile)
fileinfo = ffile.GetSourceInfo()
if fileinfo['KeyList'] == []:
ffile = None
elif len(self._filelist) == 1:
#Is it a Diamond stack?
if len(fileinfo['KeyList']) > 1:
info, data = ffile.LoadSource(fileinfo['KeyList'][0])
shape = data.shape
if len(shape) == 2:
if min(shape) == 1:
#It is a Diamond Stack
ffile = EDFStack.EDFStack(inputfile)
return ffile
except:
return None
def testEdfMap(self):
filename = os.path.join(self.path, 'xrfmap.edf')
nDet = 2
info = XrfData.generateEdfMap(filename, nDet=nDet, same=False)
nDet0, nRows0, nColumns0, nChannels = info['data'].shape
from PyMca5.PyMcaIO import EDFStack
files = [
os.path.join(self.path,
'xrfmap_xia{:02d}_0001_0000_{:04d}.edf'.format(k, i))
for i in range(nRows0) for k in range(nDet0)
]
stack = EDFStack.EDFStack(filelist=sorted(files)).data
self.assertEqual(nDet, nDet0)
self.assertEqual(stack.shape, (nDet0 * nRows0, nColumns0, nChannels))
for i in range(nRows0):
for j in range(nColumns0):
for k in range(nDet):
mca = stack[i + k * nRows0, j]
numpy.testing.assert_array_equal(mca, info['data'][k, i,
j])
if opt in '--begin':
begin = int(arg)
elif opt in '--end':
end = int(arg)
elif opt in '--fileindex':
fileindex = int(arg)
app = qt.QApplication(sys.argv)
window = SceneGLWindow.SceneGLWindow()
window.show()
if len(sys.argv) == 1:
object3D = getObject3DInstance()
if object3D is not None:
window.addObject(object3D)
else:
if len(sys.argv) > 1:
stack = EDFStack.EDFStack(dtype=numpy.float32, imagestack=False)
filename = args[0]
else:
stack = EDFStack.EDFStack(dtype=numpy.float32, imagestack=False)
filename = r"..\COTTE\ch09\ch09__mca_0005_0000_0070.edf"
if os.path.exists(filename):
print("fileindex = ", fileindex)
stack.loadIndexedStack(filename, begin=begin, end=end, fileindex=fileindex)
object3D = Object3DStack()
object3D.setStack(stack)
stack = 0
else:
print("filename %s does not exists" % filename)
sys.exit(1)
time.sleep(1)
print("START ADDING")