def open_hdf5(filename):
datadict = {}
a = _pyhl.read_nodelist(filename)
a.selectAll()
a.fetch()
node_names = a.getNodeNames()
items = []
for nodename in node_names.keys():
b = a.getNode(nodename)
items.append((nodename, b, b.type()))
items.sort() # guarantees groups before attributes
h5rad = rave_info.INFO("h5rad", version=H5RAD_VERSION)
groupmapping = {"" : h5rad}
for nodename, node, typ in items:
index = nodename.rindex("/")
parentname, tag = nodename[:index], nodename[index+1:]
# Deal with (ignore) H5IM stubs
#if tag in ["CLASS", "IMAGE_VERSION"]:
if os.path.split(parentname)[1] == 'data':
continue
e = SubElement(groupmapping[parentname], tag)
if typ==1:
groupmapping[nodename] = e # save the nodename to element mapping
elif typ==0:
t = h5type(node.data())
if t == "sequence":
# convert list to string
nodes = []
for n in node.data():
node = n.strip()
node = remove_nulls(str(node))
nodes.append(("'"+node+"'"))
e.text = ", ".join(nodes)
else:
e.text = remove_nulls(str(node.data()))
if t != "string":
e.attrib["type"] = t
elif typ==2:
datadict[nodename] = node.data()
e.attrib["type"] = "dataset"
e.text=nodename
## label = string.replace(parentname, "/", "")
## print parentname, label
## if label.startswith("profile"): # relic from 717 ...
## label = label + "_" + tag
## datadict[label] = node.data()
## e.attrib["type"] = "dataset"
## e.text=label
return h5rad, datadict, items
def Root(tag='h5rad', attrib={"version": H5RAD_VERSION}):
"""
This is the root element: an INFO object with the right version
attribute.
Arguments:
string tag: should always be "h5rad"
dict attrib: should always be the h5rad version
Returns:
an INFO object
"""
return rave_info.INFO(tag=tag, attrib=attrib)
def Root(tag='h5rad', attrib={"version": H5RAD_VERSION}):
"""
This is the root element: an INFO object with the right version
attribute and with a UNIDATA Conventions attribute.
Arguments:
string tag: should always be "h5rad"
dict attrib: should always be the h5rad version
Returns:
an INFO object
"""
this = rave_info.INFO(tag=tag, attrib=attrib)
this.set('/Conventions', rave_defines.ODIM_CONVENTIONS)
return this
def get_metadata(filename):
a = _pyhl.read_nodelist(filename)
a.selectMetadata()
a.fetch()
node_names = a.getNodeNames()
items = []
for nodename in node_names.keys():
b = a.getNode(nodename)
items.append((nodename, b, b.type()))
items.sort() # guarantees groups before attributes
h5rad = rave_info.INFO("h5rad", version=H5RAD_VERSION)
groupmapping = {"" : h5rad}
for nodename, node, typ in items:
index = nodename.rindex("/")
parentname, tag = nodename[:index], nodename[index+1:]
e = SubElement(groupmapping[parentname], tag)
if typ==1:
groupmapping[nodename] = e # save the nodename to element mapping
elif typ==0:
t = h5type(node.data())
if t == "sequence":
# convert list to string
nodes = []
for n in node.data():
node = n.strip()
node = remove_nulls(str(node))
nodes.append(("'"+node+"'"))
e.text = ", ".join(nodes)
else:
e.text = remove_nulls(str(node.data()))
if t != "string":
e.attrib["type"] = t
# Skip typ==2, dataset array
# return only h5rad
return h5rad
def __init__(self, filename=None, **args):
"""
Initializes a RAVE object.
Arguments:
Returns:
"""
self._fcp = None # HDF5 file-creation properties
if filename is not None:
self.open(filename)
else:
import rave_info
self.info = rave_info.INFO("h5rad", version=H5RAD_VERSION)
self.data = {}
self._h5nodes = None # Only used when reading from HDF5 file
self.__file__ = None # Set when reading or writing HDF5 file
if len(args.keys()):
self.new(args)