##########################################################################
# basf2 (Belle II Analysis Software Framework) #
# Author: The Belle II Collaboration #
# #
# See git log for contributors and copyright holders. #
# This file is licensed under LGPL-3.0, see LICENSE.md. #
##########################################################################
import itertools
from pathlib import Path
import numpy as np
import torch
from .tree_utils import masses_to_classes
from .dataset_utils import populate_avail_samples, preload_root_data
from .edge_features import compute_edge_features
from .normalize_features import normalize_features
from torch_geometric.data import Data, InMemoryDataset
import uproot
def _preload(self):
"""
Creates graph objects and stores them into a python list.
"""
#: Going to use x_files as an array that always exists
self.x_files = sorted(self.root.glob("**/*.root"))
# Select the first N files (useful for testing)
if self.n_files is not None:
if self.n_files > len(self.x_files):
print(
f"WARNING: n_files specified ({self.n_files}) is greater than files in path given ({len(self.x_files)})"
)
self.x_files = self.x_files[: self.n_files]
if len(self.x_files) == 0:
raise RuntimeError(f"No files found in {self.root}")
# Save the features
with uproot.open(self.x_files[0])["Tree"] as t:
#: Features
self.features = [f for f in t.keys() if f.startswith("feat_")]
#: B reco flag
self.B_reco = int(t["isB"].array(library="np")[0])
assert self.B_reco in [0, 1, 2], "B_reco should be 0, 1 or 2, something went wrong"
#: Discarded features
self.discarded = [
f for f in self.features if not f[f.find("_") + 1:] in self.node_features
]
self.features = [
f"feat_{f}" for f in self.node_features if f"feat_{f}" in self.features
]
print(f"Input node features: {self.features}")
print(f"Discarded node features: {self.discarded}")
#: Edge features
self.edge_features = [f"edge_{f}" for f in self.edge_features]
#: Global features
self.global_features = [f"glob_{f}" for f in self.global_features] if self.global_features else []
print(f"Input edge features: {self.edge_features}")
print(f"Input global features: {self.global_features}")
#: Preload data
self.x, self.y = preload_root_data(
self.x_files,
self.features,
self.discarded,
)
#: Need to populate a list of available training samples
self.avail_samples = populate_avail_samples(
self.x,
self.y,
self.B_reco,
)
# Select a subset of available samples if requested
if self.samples and self.samples < len(self.avail_samples):
print(f"Selecting random subset of {self.samples} samples")
self.avail_samples = [
self.avail_samples[i]
for i in np.random.choice(
len(self.avail_samples), self.samples, replace=False
)
]
elif self.samples and (self.samples >= len(self.avail_samples)):
print(
f"WARNING: No. samples specified ({self.samples}) exceeds number of samples loaded ({len(self.avail_samples)})"
)
return len(self.avail_samples)
def _process_graph(self, idx):
"""
Actually builds the graph object.
Args:
idx (int): Index of training example to be processed.
Returns:
torch_geometric.data.Data: Graph object to be used in training.
"""
file_id, evt, p_index = self.avail_samples[idx]
x_item = self.x[file_id]
y_item = self.y[file_id][p_index]
evt_b_index = x_item["b_index"][evt]
evt_leaves = x_item["leaves"][evt]
evt_primary = x_item["primary"][evt]
y_leaves = y_item["LCA_leaves"][evt]
# Use this to correctly reshape LCA (might be able to just use shape of y_leaves?)
n_LCA = y_item["n_LCA"][evt]
# Get the rows of the X inputs to fetch
# This is a boolean numpy array
x_rows = (evt_b_index != -1) if not self.B_reco else evt_b_index == int(p_index)
# Find the unmatched particles
unmatched_rows = evt_b_index == -1
if np.any(unmatched_rows) and self.B_reco:
# Create a random boolean array the same size as the number of leaves
rand_mask = np.random.choice(a=[False, True], size=unmatched_rows.size)
# AND the mask with the unmatched leaves
# This selects a random subset of the unmatched leaves
unmatched_rows = np.logical_and(unmatched_rows, rand_mask)
# Add the unmatched rows to the current decay's rows
x_rows = np.logical_or(x_rows, unmatched_rows)
# Here we actually load the data
# Initialise event's X array
x = np.empty((x_rows.sum(), len(self.features)))
x_dis = np.empty((x_rows.sum(), len(self.discarded)))
# And populate it
for idx, feat in enumerate(self.features):
x[:, idx] = x_item["features"][feat][evt][x_rows]
for idx, feat in enumerate(self.discarded):
x_dis[:, idx] = x_item["discarded"][feat][evt][x_rows]
# Same for edge and global features
x_edges = (
compute_edge_features(
self.edge_features,
self.features + self.discarded,
np.concatenate([x, x_dis], axis=1),
)
if self.edge_features is not []
else []
)
x_global = (
np.array(
[
[
x_item["global"][feat + f"_{p_index}"][evt]
for feat in self.global_features
]
]
)
if self.global_features != []
else []
)
x_leaves = evt_leaves[x_rows]
# Set nans to zero, this is a surrogate value, may change in future
np.nan_to_num(x, copy=False)
np.nan_to_num(x_edges, copy=False)
np.nan_to_num(x_global, copy=False)
# Normalize any features that should be
if self.normalize is not None:
normalize_features(
self.normalize,
self.features,
x,
self.edge_features,
x_edges,
self.global_features,
x_global,
)
# Reorder LCA
# Get LCA indices in order that the leaves appear in reconstructed particles
# Secondaries aren't in the LCA leaves list so they get a 0
locs = np.array(
[
np.where(y_leaves == i)[0].item() if (i in y_leaves) else 0
for i in x_leaves
]
)
# Get the LCA in the correct subset order
# If we're not allowing secondaries this is all we need
# If we are this will contain duplicates (since secondary locs are set to 0)
# We can't load the firs locs directly (i.e. y_item[locs, :]) because locs is (intentionally) unsorted
y_edge = y_item["LCA"][evt].reshape((n_LCA, n_LCA)).astype(int)
# Get the true mcPDG pf FSPs
y_mass = masses_to_classes(x_item["mc_pdg"][evt][x_rows])
# Get the specificed row/cols, this inserts dummy rows/cols for secondaries
y_edge = y_edge[locs, :][:, locs]
# if self.allow_secondaries:
# Set everything that's not primary (unmatched and secondaries) rows.cols to 0
# Note we only consider the subset of leaves that made it into x_rows
y_edge = np.where(evt_primary[x_rows], y_edge, 0) # Set the rows
y_edge = np.where(evt_primary[x_rows][:, None], y_edge, 0) # Set the columns
# Set diagonal to -1 (actually not necessary but ok...)
np.fill_diagonal(y_edge, -1)
n_nodes = x.shape[0]
# Target edge tensor: shape [E]
edge_y = torch.tensor(
y_edge[np.eye(n_nodes) == 0],
dtype=torch.long
)
# Fill tensor with edge indices: shape [N*(N-1), 2] == [E, 2]
edge_index = torch.tensor(
list(itertools.permutations(range(n_nodes), 2)),
dtype=torch.long,
)
# Target global tensor: shape [B, F_g]
u_y = torch.tensor(
[[1]], dtype=torch.float
)
# Target node tensor: shape [N]
x_y = torch.tensor(y_mass, dtype=torch.long)
g = Data(
x=torch.tensor(x, dtype=torch.float),
edge_index=edge_index.t().contiguous(),
edge_attr=torch.tensor(x_edges, dtype=torch.float),
u=torch.tensor(x_global, dtype=torch.float),
x_y=x_y,
edge_y=edge_y,
u_y=u_y,
)
return g
[docs]
class GraphDataSet(InMemoryDataset):
"""
Dataset handler for converting Belle II data to PyTorch geometric InMemoryDataset.
The ROOT format expects the tree in every file to be named ``Tree``,
and all node features to have the format ``feat_FEATNAME``.
.. note:: This expects the files under root to have the structure ``root/**/<file_name>.root``
where the root path is different for train and val.
The ``**/`` is to handle subdirectories, e.g. ``sub00``.
Args:
root (str): Path to ROOT files.
n_files (int): Load only ``n_files`` files.
samples (int): Load only ``samples`` events.
features (list): List of node features names.
edge_features (list): List of edge features names.
global_features (list): List of global features names.
normalize (bool): Whether to normalize input features.
"""
def __init__(
self,
root,
n_files=None,
samples=None,
features=[],
edge_features=[],
global_features=[],
normalize=None,
**kwargs,
):
"""
Initialization.
"""
assert isinstance(
features, list
), f'Argument "features" must be a list and not {type(features)}'
assert len(features) > 0, "You need to use at least one node feature"
#: Root path
self.root = Path(root)
#: Normalize
self.normalize = normalize
#: Number of files
self.n_files = n_files
#: Node features
self.node_features = features
#: Edge features
self.edge_features = edge_features
#: Global features
self.global_features = global_features
#: Samples
self.samples = samples
# Delete processed files, in case
file_path = Path(self.root, "processed")
files = list(file_path.glob("*.pt"))
for f in files:
f.unlink(missing_ok=True)
# Needs to be called after having assigned all attributes
super().__init__(root, None, None, None)
#: Data and Slices
self.data, self.slices = torch.load(self.processed_paths[0])
@property
def processed_file_names(self):
"""
Name of processed file.
"""
return ["processed_data.pt"]
def process(self):
"""
Processes the data to create graph objects and stores them in ``root/processed/processed_data.pt``
where the root path is different for train and val.
Called internally by PyTorch.
"""
num_samples = _preload(self)
data_list = [_process_graph(self, i) for i in range(num_samples)]
data, slices = self.collate(data_list)
torch.save((data, slices), self.processed_paths[0])
del self.x, self.y, self.avail_samples, data_list, data, slices
