def openFile(self, filename, weakreference=False):
gc.collect()
for item in self.rootItem:
if item.file.filename == filename:
ddict = {}
ddict['event'] = "fileUpdated"
ddict['filename'] = filename
self.sigFileUpdated.emit(ddict)
return item.file
phynxFile = h5open(filename)
if weakreference:
def phynxFileInstanceDistroyed(weakrefObject):
idx = self.rootItem._identifiers.index(id(weakrefObject))
child = self.rootItem._children[idx]
child.clearChildren()
del self._idMap[id(child)]
self.rootItem.deleteChild(child)
if not self.rootItem.hasChildren:
self.clear()
return
refProxy = weakref.proxy(phynxFile, phynxFileInstanceDistroyed)
self.rootItem.appendChild(refProxy)
else:
self.rootItem.appendChild(phynxFile)
ddict = {}
ddict['event'] = "fileAppended"
ddict['filename'] = filename
self.sigFileAppended.emit(ddict)
return phynxFile
def openFile(self, filename, weakreference=False):
gc.collect()
for item in self.rootItem:
if item.file.filename == filename:
ddict = {}
ddict['event'] = "fileUpdated"
ddict['filename'] = filename
self.sigFileUpdated.emit(ddict)
return item.file
phynxFile = h5open(filename)
if weakreference:
def phynxFileInstanceDistroyed(weakrefObject):
idx = self.rootItem._identifiers.index(id(weakrefObject))
child = self.rootItem._children[idx]
child.clearChildren()
del self._idMap[id(child)]
self.rootItem.deleteChild(child)
if not self.rootItem.hasChildren:
self.clear()
return
refProxy = weakref.proxy(phynxFile, phynxFileInstanceDistroyed)
self.rootItem.appendChild(refProxy)
else:
self.rootItem.appendChild(phynxFile)
ddict = {}
ddict['event'] = "fileAppended"
ddict['filename'] = filename
self.sigFileAppended.emit(ddict)
return phynxFile
def getDatasetDialog(filename=None, value=False, message=None):
# function kept for backward compatibility, in case someone
# uses it with value=False outside PyMca5
if value:
return getDatasetValueDialog(filename, message)
hdf5Dialog = Hdf5SelectionDialog(None, filename, message, "dataset")
ret = hdf5Dialog.exec_()
if not ret:
return None
selectedHdf5Uri = hdf5Dialog.selectedItemUri
hdf5File = h5open(filename)
return hdf5File[selectedHdf5Uri.split("::")[-1]]
def getDatasetDialog(filename=None, value=False, message=None, parent=None):
# function kept for backward compatibility, in case someone
# uses it with value=False outside PyMca5
if value:
return getDatasetValueDialog(filename=filename, message=message,
parent=parent)
hdf5Dialog = Hdf5SelectionDialog(parent, filename, message, "dataset")
ret = hdf5Dialog.exec_()
if not ret:
return None
selectedHdf5Uri = hdf5Dialog.selectedItemUri
hdf5File = h5open(filename)
return hdf5File[selectedHdf5Uri.split("::")[-1]]
def getDatasetValueDialog(filename=None, message=None, parent=None):
"""Open a dialog to select a dataset in a HDF5 file.
Return the value of the dataset.
If the dataset selection was cancelled, None is returned.
:param str filename: HDF5 file path. If None, a file dialog
is used to select the file.
:param str message: Message used as window title for dialog
:return: HDF5 dataset as numpy array, or None
"""
hdf5Dialog = Hdf5SelectionDialog(parent, filename, message, "dataset")
ret = hdf5Dialog.exec_()
if not ret:
return None
selectedHdf5Uri = hdf5Dialog.selectedItemUri
with h5open(filename) as hdf5File:
hdf5Item = hdf5File[selectedHdf5Uri.split("::")[-1]]
data = hdf5Item[()]
return data
def getDatasetValueDialog(filename=None, message=None, parent=None):
"""Open a dialog to select a dataset in a HDF5 file.
Return the value of the dataset.
If the dataset selection was cancelled, None is returned.
:param str filename: HDF5 file path. If None, a file dialog
is used to select the file.
:param str message: Message used as window title for dialog
:return: HDF5 dataset as numpy array, or None
"""
hdf5Dialog = Hdf5SelectionDialog(parent, filename, message,
"dataset")
ret = hdf5Dialog.exec_()
if not ret:
return None
selectedHdf5Uri = hdf5Dialog.selectedItemUri
with h5open(filename) as hdf5File:
hdf5Item = hdf5File[selectedHdf5Uri.split("::")[-1]]
data = hdf5Item[()]
return data
def exec_(self):
with h5open(self.filename) as hdf5File:
self.fileModel.appendPhynxFile(hdf5File, weakreference=True)
ret = qt.QDialog.exec_(self)
return ret
def h5todict(h5file, path="/", exclude_names=None):
"""Read a HDF5 file and return a nested dictionary with the complete file
structure and all data.
Example of usage::
from silx.io.dictdump import h5todict
# initialize dict with file header and scan header
header94 = h5todict("oleg.dat",
"/94.1/instrument/specfile")
# add positioners subdict
header94["positioners"] = h5todict("oleg.dat",
"/94.1/instrument/positioners")
# add scan data without mca data
header94["detector data"] = h5todict("oleg.dat",
"/94.1/measurement",
exclude_names="mca_")
.. note:: This function requires `h5py <http://www.h5py.org/>`_ to be
installed.
.. note:: If you write a dictionary to a HDF5 file with
:func:`dicttoh5` and then read it back with :func:`h5todict`, data
types are not preserved. All values are cast to numpy arrays before
being written to file, and they are read back as numpy arrays (or
scalars). In some cases, you may find that a list of heterogeneous
data types is converted to a numpy array of strings.
:param h5file: File name or :class:`h5py.File` object or spech5 file or
fabioh5 file.
:param str path: Name of HDF5 group to use as dictionary root level,
to read only a sub-group in the file
:param list[str] exclude_names: Groups and datasets whose name contains
a string in this list will be ignored. Default is None (ignore nothing)
:return: Nested dictionary
"""
if h5py_missing:
raise h5py_import_error
if not is_file(h5file):
h5f = h5open(h5file)
else:
h5f = h5file
ddict = {}
for key in h5f[path]:
if _name_contains_string_in_list(key, exclude_names):
continue
if is_group(h5f[path + "/" + key]):
ddict[key] = h5todict(h5f,
path + "/" + key,
exclude_names=exclude_names)
else:
# Convert HDF5 dataset to numpy array
ddict[key] = h5f[path + "/" + key][...]
if not is_file(h5file):
# close file, if we opened it
h5f.close()
return ddict
def exec_(self):
with h5open(self.filename) as hdf5File:
self.fileModel.appendPhynxFile(hdf5File, weakreference=True)
ret = qt.QDialog.exec_(self)
return ret
indices.sort()
if len(indices):
scanned = [measurement[key].name for idx, key in indices]
return scanned
if __name__ == "__main__":
import sys
import h5py
try:
sourcename=sys.argv[1]
except:
print("Usage: NexusTools <file> <key>")
sys.exit()
try:
from silx.io import open as h5open
h5 = h5open(sourcename)
except:
h5 = h5py.File(sourcename, 'r')
entries = getNXClassGroups(h5, "/", ["NXentry", b"NXentry"], single=False)
if not len(entries):
entries = [item for name, item in h5["/"].items() if isGroup(item)]
for entry in entries:
print("Entry name = %s" % entry.name)
if "title" in entry:
print("Entry title = %s" % entry["title"][()])
measurement = getMeasurementGroup(h5, entry.name)
if measurement is None:
print("No measurement")
else:
print("Measurement name = %s " % measurement.name)
instrument = getInstrumentGroup(h5, entry.name)
