From b318e195f6b0b75ce373ce5e35e7d75043265b67 Mon Sep 17 00:00:00 2001
From: Rasmus Oersoe <rahn@outlook.dk>
Date: Sat, 3 Feb 2024 19:10:52 +0100
Subject: [PATCH 1/2] bugfix + minkowski mypy
---
src/graphnet/models/graphs/edges/minkowski.py | 11 +++---
src/graphnet/models/standard_model.py | 39 +++++++++++++------
2 files changed, 34 insertions(+), 16 deletions(-)
diff --git a/src/graphnet/models/graphs/edges/minkowski.py b/src/graphnet/models/graphs/edges/minkowski.py
index 5d1134ec5..2526de1cb 100644
--- a/src/graphnet/models/graphs/edges/minkowski.py
+++ b/src/graphnet/models/graphs/edges/minkowski.py
@@ -69,12 +69,13 @@ class MinkowskiKNNEdges(EdgeDefinition):
row = []
col = []
for batch in range(x.shape[0]):
+ x_masked = x[batch][mask[batch]]
distance_mat = compute_minkowski_distance_mat(
- x_masked := x[batch][mask[batch]],
- x_masked,
- self.c,
- self.space_coords,
- self.time_coord,
+ x=x_masked,
+ y=x_masked,
+ c=self.c,
+ space_coords=self.space_coords,
+ time_coord=self.time_coord,
)
num_points = x_masked.shape[0]
num_edges = min(self.nb_nearest_neighbours, num_points)
diff --git a/src/graphnet/models/standard_model.py b/src/graphnet/models/standard_model.py
index 663664996..098f63d98 100644
--- a/src/graphnet/models/standard_model.py
+++ b/src/graphnet/models/standard_model.py
@@ -410,6 +410,9 @@ class StandardModel(Model):
f"number of output columns ({predictions.shape[1]}) don't match."
)
+ # Check if predictions are on event- or pulse-level
+ pulse_level_predictions = len(predictions) > len(dataloader.dataset)
+
# Get additional attributes
attributes: Dict[str, List[np.ndarray]] = OrderedDict(
[(attr, []) for attr in additional_attributes]
@@ -423,25 +426,39 @@ class StandardModel(Model):
# Check if node level predictions
# If true, additional attributes are repeated
# to make dimensions fit
- if len(predictions) != len(dataloader.dataset):
+ if pulse_level_predictions:
if len(attribute) < np.sum(
batch.n_pulses.detach().cpu().numpy()
):
attribute = np.repeat(
attribute, batch.n_pulses.detach().cpu().numpy()
)
- try:
- assert len(attribute) == len(batch.x)
- except AssertionError:
- self.warning_once(
- "Could not automatically adjust length"
- f"of additional attribute {attr} to match length of"
- f"predictions. Make sure {attr} is a graph-level or"
- "node-level attribute. Attribute skipped."
- )
- pass
attributes[attr].extend(attribute)
+ # Confirm that attributes match length of predictions
+ skip_attributes = []
+ for attr in attributes.keys():
+ try:
+ assert len(attributes[attr]) == len(predictions)
+ except AssertionError:
+ self.warning_once(
+ "Could not automatically adjust length"
+ f" of additional attribute '{attr}' to match length of"
+ f" predictions.This error can be caused by heavy"
+ " disagreement between number of examples in the"
+ " dataset vs. actual events in the dataloader, e.g. "
+ " heavy filtering of events in `collate_fn` passed to"
+ " `dataloader`. This can also be caused by requesting"
+ " pulse-level attributes for `Task`s that produce"
+ " event-level predictions. Attribute skipped."
+ )
+ skip_attributes.append(attr)
+
+ # Remove bad attributes
+ for attr in skip_attributes:
+ attributes.pop(attr)
+ additional_attributes.remove(attr)
+
data = np.concatenate(
[predictions]
+ [
--
GitLab
From 36a2384ff06afabec9fc143ef3d548672b398761 Mon Sep 17 00:00:00 2001
From: Rasmus Oersoe <rahn@outlook.dk>
Date: Sat, 3 Feb 2024 19:52:56 +0100
Subject: [PATCH 2/2] check requirement links
---
requirements/torch_cpu.txt | 2 +-
requirements/torch_gpu.txt | 2 +-
requirements/torch_macos.txt | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/requirements/torch_cpu.txt b/requirements/torch_cpu.txt
index 59e273288..babb4fb8e 100644
--- a/requirements/torch_cpu.txt
+++ b/requirements/torch_cpu.txt
@@ -1,2 +1,2 @@
--find-links https://download.pytorch.org/whl/cpu
---find-links https://data.pyg.org/whl/torch-2.1.0+cpu.html
\ No newline at end of file
+--find-links https://data.pyg.org/whl/torch-2.2.0+cpu.html
\ No newline at end of file
diff --git a/requirements/torch_gpu.txt b/requirements/torch_gpu.txt
index 1f1abba3f..ddcb85038 100644
--- a/requirements/torch_gpu.txt
+++ b/requirements/torch_gpu.txt
@@ -1,4 +1,4 @@
# Contains packages requirements for GPU installation
--find-links https://download.pytorch.org/whl/torch_stable.html
torch==2.1.0+cu118
---find-links https://data.pyg.org/whl/torch-2.1.0+cu118.html
+--find-links https://data.pyg.org/whl/torch-2.2.0+cu118.html
diff --git a/requirements/torch_macos.txt b/requirements/torch_macos.txt
index 3e9d75df4..2b5009a8e 100644
--- a/requirements/torch_macos.txt
+++ b/requirements/torch_macos.txt
@@ -1,2 +1,2 @@
--find-links https://download.pytorch.org/whl/torch_stable.html
---find-links https://data.pyg.org/whl/torch-2.1.0+cpu.html
\ No newline at end of file
+--find-links https://data.pyg.org/whl/torch-2.2.0+cpu.html
\ No newline at end of file
--
GitLab