VariablesToHDF5 Class Reference

Inheritance diagram for VariablesToHDF5:

Collaboration diagram for VariablesToHDF5:

Public Member Functions
def	__init__ (self, listname, variables, filename)
def	initialize (self)
def	event (self)
def	terminate (self)

Protected Attributes
	_filename
	Output filename.
	_listname
	Particle list name.
	_variables
	List of variables.
	_varnames
	variable names
	_var_objects
	variable objects for each variable
	_evtmeta
	Event metadata.
	_plist
	Pointer to the particle list.
	_hdf5file
	The hdf5 file.
	_dtype
	The data type.
	_table
	The pytable.

Detailed Description

Dump variables directly to HDF5

This Module is the equivalent of VariablesToNtuple but creates an hdf5 file
instead of a root file. It is slower as it is implemented in pure python and
should currently be considered a proof of concept.

Definition at line 21 of file b2pandas_utils.py.

Constructor & Destructor Documentation

__init__()

def __init__	(		self,
			listname,
			variables,
			filename
	)

Constructor to initialize the internal state

Arguments:
    listname(str): name of the particle list
    variables(list(str)): list of variables to save for each particle
    filename(str): name of the hdf5 file to be created

Definition at line 30 of file b2pandas_utils.py.

    def __init__(self, listname, variables, filename):
        """Constructor to initialize the internal state
 
        Arguments:
            listname(str): name of the particle list
            variables(list(str)): list of variables to save for each particle
            filename(str): name of the hdf5 file to be created
        """
        super().__init__()
        
        self._filename = filename
        
        self._listname = listname
        
        self._variables = variables
 

Member Function Documentation

event()

def event

(

self

)

Create a new row in the hdf5 file with for each particle in the list

Definition at line 88 of file b2pandas_utils.py.

    def event(self):
        """Create a new row in the hdf5 file with for each particle in the list"""
        buf = np.empty(self._plist.getListSize(), dtype=self._dtype)
        # add some extra columns for bookkeeping
        buf["exp"] = self._evtmeta.getExperiment()
        buf["run"] = self._evtmeta.getRun()
        buf["evt"] = self._evtmeta.getEvent()
        buf["prod"] = self._evtmeta.getProduction()
        buf["ncand"] = len(buf)
        buf["icand"] = np.arange(len(buf))
 
        for row, p in zip(buf, self._plist):
            for name, v in zip(self._varnames, self._var_objects):
                # pyroot proxy not working with callables, we should fix this.
                # For now we need to go back by name and call it.
                # should be `row[v.name] = v.func(p)`
                row[name] = variables.variables.evaluate(v.name, p)
 
        self._table.append(buf)
 

initialize()

def initialize

(

self

)

Create the hdf5 file and list of variable objects to be used during
event processing.

Definition at line 46 of file b2pandas_utils.py.

    def initialize(self):
        """Create the hdf5 file and list of variable objects to be used during
        event processing."""
        # Always avoid the top-level 'import ROOT'.
        import ROOT  # noqa
        
        self._varnames = [
            str(varname) for varname in variables.variables.resolveCollections(
                variables.std_vector(
                    *self._variables))]
        
        self._var_objects = [variables.variables.getVariable(n) for n in self._varnames]
 
        
        self._evtmeta = ROOT.Belle2.PyStoreObj("EventMetaData")
        self._evtmeta.isRequired()
        
        self._plist = ROOT.Belle2.PyStoreObj(self._listname)
        self._plist.isRequired()
 
        
        self._hdf5file = tables.open_file(self._filename, mode="w", title="Belle2 Variables to HDF5")
        if not self._hdf5file:
            basf2.B2ERROR("Cannot create output file")
            return
 
        dtype = [("exp", np.int32), ("run", np.int32), ("evt", np.uint32),
                 ("prod", np.uint32), ("icand", np.uint32), ("ncand", np.uint32)]
        for name in self._varnames:
            # only float variables for now
            dtype.append((name, np.float64))
 
        
        self._dtype = dtype
        filters = tables.Filters(complevel=1, complib='blosc:lz4', fletcher32=False)
        # some variable names are not just A-Za-z0-9 so pytables complains but
        # seems to work. Ignore warning
        with warnings.catch_warnings():
            warnings.simplefilter("ignore")
            
            self._table = self._hdf5file.create_table("/", self._listname, obj=np.zeros(0, dtype), filters=filters)
 

terminate()

def terminate

(

self

)

save and close the output

Definition at line 108 of file b2pandas_utils.py.

    def terminate(self):
        """save and close the output"""
        self._table.flush()
        self._hdf5file.close()
        import ROOT
        ROOT.Belle2.MetadataService.Instance().addHDF5File(self._filename)
 
 

Member Data Documentation

_dtype

_dtype

protected

The data type.

Definition at line 79 of file b2pandas_utils.py.

_evtmeta

_evtmeta

protected

Event metadata.

Definition at line 60 of file b2pandas_utils.py.

_filename

_filename

protected

Output filename.

Definition at line 40 of file b2pandas_utils.py.

_hdf5file

_hdf5file

protected

The hdf5 file.

Definition at line 67 of file b2pandas_utils.py.

_listname

_listname

protected

Particle list name.

Definition at line 42 of file b2pandas_utils.py.

_plist

_plist

protected

Pointer to the particle list.

Definition at line 63 of file b2pandas_utils.py.

_table

_table

protected

The pytable.

Definition at line 86 of file b2pandas_utils.py.

_var_objects

_var_objects

protected

variable objects for each variable

Definition at line 57 of file b2pandas_utils.py.

_variables

_variables

protected

List of variables.

Definition at line 44 of file b2pandas_utils.py.

_varnames

_varnames

protected

variable names

Definition at line 52 of file b2pandas_utils.py.

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The documentation for this class was generated from the following file:

• analysis/scripts/b2pandas_utils.py