def _readImageListHdf5(self, filenamelist):
if h5py is None:
self._criticalError("Cannot read HDF5 files (h5py is missing)")
return None, None
imagelist = []
imagenames = []
shape = tuple(sorted(self._requiredShape))
def match(dset):
return tuple(sorted(dset.shape)) == shape
for uri in filenamelist:
tmp = uri.split('::')
if len(tmp) == 1:
tmp = uri, None
filename, h5path = tmp
# URI exists?
if h5path:
with HDF5Widget.h5open(filename) as hdf5File:
if h5path not in hdf5File:
h5path = None
# Prompt for missing HDF5 path
if not h5path:
tmp = HDF5Widget.getUri(parent=self._dialogParent,
filename=filename,
message='Select Group or Dataset')
if not tmp:
return None, None
tmp = tmp.split('::')
if len(tmp) == 2:
h5path = tmp[1]
if not h5path:
return None, None
# Add datasets from HDF5 path
with HDF5Widget.h5open(filename) as hdf5File:
# If `h5path` is an instance of NXdata, only the signals
# (including auxilary signals) are considered for `match`.
datasets = NexusUtils.selectDatasets(hdf5File[h5path],
match=match)
if not datasets:
self._criticalError(
"No (valid) datasets were found in '%s::%s'" %
(filename, h5path))
return None, None
elif len({dset.size for dset in datasets}) > 1:
self._criticalError(
"'%s::%s' contains datasets with different sizes. Select datasets separately."
% (filename, h5path))
return None, None
else:
for dset in datasets:
imagename = '/'.join(dset.name.split('/')[-2:])
imagelist.append(dset[()])
imagenames.append(imagename)
if not imagenames:
self._criticalError('No valid data provided')
return imagenames, imagelist
def _loadExternalData(self):
getfilter = True
fileTypeList = ["EDF Files (*edf *ccd *tif)"]
if HDF5:
fileTypeList.append('HDF5 Files (*.h5 *.nxs *.hdf *.hdf5)')
fileTypeList.append('ASCII Files (*)')
fileTypeList.append("EDF Files (*)")
message = "Open data file"
filenamelist, ffilter = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message=message,
getfilter=getfilter,
single=True,
currentfilter=None)
if len(filenamelist) < 1:
return
filename = filenamelist[0]
if ffilter.startswith('HDF5'):
data = HDF5Widget.getDatasetValueDialog(
filename=filename,
message='Select your data set by a double click')
elif ffilter.startswith("EDF"):
edf = EdfFile.EdfFile(filename, "rb")
if edf.GetNumImages() > 1:
# TODO: A dialog showing the different images
# based on the external images browser needed
_logger.warning("WARNING: Taking first image")
data = edf.GetData(0)
edf = None
elif ffilter.startswith("ASCII"):
#data=numpy.loadtxt(filename)
sf = specfilewrapper.Specfile(filename)
targetScan = sf[0]
data = numpy.array(targetScan.data().T, copy=True)
targetScan = None
sf = None
return data
def _loadExternalData(self):
getfilter = True
fileTypeList = ["EDF Files (*edf *ccd *tif)"]
if HDF5:
fileTypeList.append('HDF5 Files (*.h5 *.nxs *.hdf *.hdf5)')
fileTypeList.append('ASCII Files (*)')
fileTypeList.append("EDF Files (*)")
message = "Open data file"
filenamelist, ffilter = PyMcaFileDialogs.getFileList(parent=None,
filetypelist=fileTypeList,
message=message,
getfilter=getfilter,
single=True,
currentfilter=None)
if len(filenamelist) < 1:
return
filename = filenamelist[0]
if ffilter.startswith('HDF5'):
data = HDF5Widget.getDatasetValueDialog(
filename=filename,
message='Select your data set by a double click')
elif ffilter.startswith("EDF"):
edf = EdfFile.EdfFile(filename, "rb")
if edf.GetNumImages() > 1:
# TODO: A dialog showing the different images
# based on the external images browser needed
_logger.warning("WARNING: Taking first image")
data = edf.GetData(0)
edf = None
elif ffilter.startswith("ASCII"):
#data=numpy.loadtxt(filename)
sf = specfilewrapper.Specfile(filename)
targetScan = sf[0]
data = numpy.array(targetScan.data().T, copy=True)
targetScan = None
sf = None
return data