def append_member_to_h5(self, h5like_name, obj):
"""Add one group or one dataset to :attr:`h5f`"""
h5_name = self.h5path + h5like_name.lstrip("/")
if is_softlink(obj):
# links to be created after all groups and datasets
h5_target = self.h5path + obj.path.lstrip("/")
self._links.append((h5_name, h5_target))
elif is_dataset(obj):
_logger.debug("Saving dataset: " + h5_name)
member_initially_exists = h5_name in self._h5f
if self.overwrite_data and member_initially_exists:
_logger.warning("Overwriting dataset: " + h5_name)
del self._h5f[h5_name]
if self.overwrite_data or not member_initially_exists:
if fabioh5 is not None and \
isinstance(obj, fabioh5.FrameData) and \
len(obj.shape) > 2:
# special case of multiframe data
# write frame by frame to save memory usage low
ds = self._h5f.create_dataset(h5_name,
shape=obj.shape,
dtype=obj.dtype,
**self.create_dataset_args)
for i, frame in enumerate(obj):
ds[i] = frame
else:
# fancy arguments don't apply to small dataset
if obj.size < self.min_size:
ds = self._h5f.create_dataset(h5_name, data=obj.value)
else:
ds = self._h5f.create_dataset(h5_name, data=obj.value,
**self.create_dataset_args)
else:
ds = self._h5f[h5_name]
# add HDF5 attributes
for key in obj.attrs:
if self.overwrite_data or key not in ds.attrs:
ds.attrs.create(key,
_attr_utf8(obj.attrs[key]))
if not self.overwrite_data and member_initially_exists:
_logger.warning("Not overwriting existing dataset: " + h5_name)
elif is_group(obj):
if h5_name not in self._h5f:
_logger.debug("Creating group: " + h5_name)
grp = self._h5f.create_group(h5_name)
else:
grp = self._h5f[h5_name]
# add HDF5 attributes
for key in obj.attrs:
if self.overwrite_data or key not in grp.attrs:
grp.attrs.create(key,
_attr_utf8(obj.attrs[key]))
def isDataset(item):
if isinstance(item, Dataset):
return True
elif is_dataset(item):
return True
else:
return False
def append_member_to_h5(self, h5like_name, obj):
"""Add one group or one dataset to :attr:`h5f`"""
h5_name = self.h5path + h5like_name.lstrip("/")
if is_softlink(obj):
# links to be created after all groups and datasets
h5_target = self.h5path + obj.path.lstrip("/")
self._links.append((h5_name, h5_target))
elif is_dataset(obj):
_logger.debug("Saving dataset: " + h5_name)
member_initially_exists = h5_name in self._h5f
if self.overwrite_data and member_initially_exists:
_logger.warning("Overwriting dataset: " + h5_name)
del self._h5f[h5_name]
if self.overwrite_data or not member_initially_exists:
if fabioh5 is not None and \
isinstance(obj, fabioh5.FrameData) and \
len(obj.shape) > 2:
# special case of multiframe data
# write frame by frame to save memory usage low
ds = self._h5f.create_dataset(h5_name,
shape=obj.shape,
dtype=obj.dtype,
**self.create_dataset_args)
for i, frame in enumerate(obj):
ds[i] = frame
else:
# fancy arguments don't apply to small dataset
if obj.size < self.min_size:
ds = self._h5f.create_dataset(h5_name, data=obj.value)
else:
ds = self._h5f.create_dataset(
h5_name,
data=obj.value,
**self.create_dataset_args)
else:
ds = self._h5f[h5_name]
# add HDF5 attributes
for key in obj.attrs:
if self.overwrite_data or key not in ds.attrs:
ds.attrs.create(key, _attr_utf8(obj.attrs[key]))
if not self.overwrite_data and member_initially_exists:
_logger.warning("Not overwriting existing dataset: " + h5_name)
elif is_group(obj):
if h5_name not in self._h5f:
_logger.debug("Creating group: " + h5_name)
grp = self._h5f.create_group(h5_name)
else:
grp = self._h5f[h5_name]
# add HDF5 attributes
for key in obj.attrs:
if self.overwrite_data or key not in grp.attrs:
grp.attrs.create(key, _attr_utf8(obj.attrs[key]))
def _loadFromFile(self):
stack = self.getStackDataObject()
if stack is None:
return
mcaIndex = stack.info.get('McaIndex')
if not (mcaIndex in [0, -1, 2]):
raise IndexError("1D index must be 0, 2, or -1")
# test io dependencies
if h5py is None:
filefilter = []
else:
filefilter = ['HDF5 (*.h5 *.nxs *.hdf *.hdf5)']
filefilter.append('CSV (*.csv *.txt)')
if silx_open is not None:
filefilter.append('Any (*)')
filename, ffilter = PyMcaFileDialogs.\
getFileList(parent=None,
filetypelist=filefilter,
message='Load',
mode='OPEN',
single=True,
getfilter=True,
currentfilter=filefilter[0])
if len(filename):
if DEBUG:
print("file name = %s file filter = %s" % (filename, ffilter))
else:
if DEBUG:
print("nothing selected")
return
filename = filename[0]
positioners = {}
if not ffilter.startswith('CSV'):
h5GroupName = getGroupNameDialog(filename)
if h5GroupName is None:
return
with h5open(filename) as h5f:
h5Group = h5f[h5GroupName]
positioners = {}
for dsname in h5Group:
# links and subgroups just ignored for the time being
if not is_dataset(h5Group[dsname]):
continue
positioners[dsname] = h5Group[dsname][()]
else:
sf = specfilewrapper.Specfile(filename)
scan = sf[0]
labels = scan.alllabels()
data = scan.data()
scan = None
sf = None
for i, label in enumerate(labels):
positioners[label] = data[i, :]
self._stackWindow.setPositioners(positioners)
def _loadFromFile(self):
stack = self.getStackDataObject()
if stack is None:
return
mcaIndex = stack.info.get('McaIndex')
if not (mcaIndex in [0, -1, 2]):
raise IndexError("1D index must be 0, 2, or -1")
# test io dependencies
if h5py is None:
filefilter = []
else:
filefilter = ['HDF5 (*.h5 *.nxs *.hdf *.hdf5)']
filefilter.append('CSV (*.csv *.txt)')
if silx_open is not None:
filefilter.append('Any (*)')
filename, ffilter = PyMcaFileDialogs.\
getFileList(parent=None,
filetypelist=filefilter,
message='Load',
mode='OPEN',
single=True,
getfilter=True,
currentfilter=filefilter[0])
if len(filename):
_logger.debug("file name = %s file filter = %s", filename, ffilter)
else:
_logger.debug("nothing selected")
return
filename = filename[0]
positioners = {}
if not ffilter.startswith('CSV'):
h5GroupName = getGroupNameDialog(filename)
if h5GroupName is None:
return
with h5open(filename) as h5f:
h5Group = h5f[h5GroupName]
positioners = {}
for dsname in h5Group:
# links and subgroups just ignored for the time being
if not is_dataset(h5Group[dsname]):
continue
positioners[dsname] = h5Group[dsname][()]
else:
sf = specfilewrapper.Specfile(filename)
scan = sf[0]
labels = scan.alllabels()
data = scan.data()
scan = None
sf = None
for i, label in enumerate(labels):
positioners[label] = data[i, :]
self._stackWindow.setPositioners(positioners)
def validate_auxiliary_signals(group, signal_name, auxiliary_signals_names):
"""Check data dimensionality and size. Return False if invalid."""
issues = []
for asn in auxiliary_signals_names:
if asn not in group or not is_dataset(group[asn]):
issues.append("Cannot find auxiliary signal dataset '%s'" % asn)
elif group[signal_name].shape != group[asn].shape:
issues.append("Auxiliary signal dataset '%s' does not" % asn +
" have the same shape as the main signal.")
return issues
def validate_auxiliary_signals(group, signal_name, auxiliary_signals_names):
"""Check data dimensionality and size. Return False if invalid."""
issues = []
for asn in auxiliary_signals_names:
if asn not in group or not is_dataset(group[asn]):
issues.append(
"Cannot find auxiliary signal dataset '%s'" % asn)
elif group[signal_name].shape != group[asn].shape:
issues.append("Auxiliary signal dataset '%s' does not" % asn +
" have the same shape as the main signal.")
return issues
def append_member_to_h5(self, h5like_name, obj):
"""Add one group or one dataset to :attr:`h5f`"""
h5_name = self.h5path + h5like_name.lstrip("/")
if is_softlink(obj):
# links to be created after all groups and datasets
h5_target = self.h5path + obj.path.lstrip("/")
self._links.append((h5_name, h5_target))
elif is_dataset(obj):
_logger.debug("Saving dataset: " + h5_name)
member_initially_exists = h5_name in self._h5f
if self.overwrite_data and member_initially_exists:
_logger.warn("Overwriting dataset: " + h5_name)
del self._h5f[h5_name]
if self.overwrite_data or not member_initially_exists:
# fancy arguments don't apply to small dataset
if obj.size < self.min_size:
ds = self._h5f.create_dataset(h5_name, data=obj.value)
else:
ds = self._h5f.create_dataset(h5_name, data=obj.value,
**self.create_dataset_args)
else:
ds = self._h5f[h5_name]
# add HDF5 attributes
for key in obj.attrs:
if self.overwrite_data or key not in ds.attrs:
ds.attrs.create(key,
_attr_utf8(obj.attrs[key]))
if not self.overwrite_data and member_initially_exists:
_logger.warn("Not overwriting existing dataset: " + h5_name)
elif is_group(obj):
if h5_name not in self._h5f:
_logger.debug("Creating group: " + h5_name)
grp = self._h5f.create_group(h5_name)
else:
grp = self._h5f[h5_name]
# add HDF5 attributes
for key in obj.attrs:
if self.overwrite_data or key not in grp.attrs:
grp.attrs.create(key,
_attr_utf8(obj.attrs[key]))
def visit_function(name, obj):
if is_dataset(obj):
append = False
forget = False
namebased = False
for key, value in obj.attrs.items():
if key == "interpretation":
if value in ["spectrum", b"spectrum"]:
append = True
else:
forget = True
if (not append) and (not forget):
#support (risky) name based solutions too.
# the dataset name starts with MCA or
# the parent group starts with MCA
if posixpath.basename(name).lower().startswith("mca") or \
posixpath.basename(posixpath.dirname(name)).lower().startswith("mca"):
append = True
namebased = True
if append:
# an actual MCA spectrum will have more than one channel
if (not namebased) and ("measurement" in name):
# ALBA sets the interpretation attribute to spectrum
# to every counter in the measurement group
if len(obj.shape) == 1:
# I have to figure out if in fact it is just a
# misuse of the interpretation attribute
posnames = getScannedPositioners(h5file, path)
for motor in posnames:
if h5file[motor].size == obj.size:
append = False
if append:
# perform some name filtering
if posixpath.basename(obj.name).lower() in ignore:
append = False
if append:
# the measurement group
if len(obj.shape) > 0:
if obj.shape[-1] > 1:
if dataset:
datasetList.append(obj)
else:
datasetList.append(obj.name)