From a2a3c5a5e03b41c7cac275ea42f9bb50471bead0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fran=C3=A7ois=20Laurent?= <francois.laurent@posteo.net>
Date: Tue, 3 May 2022 21:17:27 +0200
Subject: [PATCH] contributes to
https://gitlab.pasteur.fr/nyx/TaggingBackends/-/issues/1
---
pyproject.toml | 4 ++--
src/maggotuba/models/predict_model.py | 14 ++++++++------
2 files changed, 10 insertions(+), 8 deletions(-)
diff --git a/pyproject.toml b/pyproject.toml
index 1507981..8ebdc6f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,7 +2,7 @@
name = "MaggotUBA-adapter"
version = "0.1.0"
description = "Interface between MaggotUBA and the Nyx tagging UI"
-authors = ["François Laurent <francois.laurent@posteo.net>"]
+authors = ["François Laurent"]
license = "MIT"
packages = [
{ include = "maggotuba", from = "src" },
@@ -10,7 +10,7 @@ packages = [
[tool.poetry.dependencies]
python = "^3.8,<3.11"
-taggingbackends = {git = "https://gitlab.pasteur.fr/nyx/TaggingBackends", rev = "main"}
+taggingbackends = {git = "https://gitlab.pasteur.fr/nyx/TaggingBackends", rev = "dev"}
structured-temporal-convolution = {git = "git@gitlab.pasteur.fr:les-larves/structured-temporal-convolution.git", branch="dev-branch"}
torch = "^1.11.0"
numpy = "^1.19.3"
diff --git a/src/maggotuba/models/predict_model.py b/src/maggotuba/models/predict_model.py
index 3c636da..a6f0742 100644
--- a/src/maggotuba/models/predict_model.py
+++ b/src/maggotuba/models/predict_model.py
@@ -60,7 +60,7 @@ def predict_model(backend):
config_file = [file for file in model_files if file.name.endswith("config.json")]
model = RandomForest(config_file[-1]).load()
# assign labels
- labels = Labels()
+ labels = Labels(tracking=input_files)
if isinstance(data, dict):
ref_length = np.mean(np.concatenate([
model.body_length(spines) for spines in data.values()
@@ -84,12 +84,14 @@ def predict_model(backend):
labels[run, larva] = dict(zip(t[mask], predictions))
# save the predicted labels to file
if metadata:
- labels[run]['metadata'] = metadata
+ labels.metadata = metadata
else:
- labels[run]['metadata'] = {'filename': file.name}
- labels.metadata['labels'] = ["run", "bend", "stop", "hunch", "back", "roll"]
- labels.metadata['label_colors'] = ["#000000", "#ff0000", "#00ff00",
- "#0000ff", "#00ffff", "#ffff00"]
+ labels.metadata = {'filename': file.name}
+ labels.labelspec = {
+ "names": ["run", "bend", "stop", "hunch", "back", "roll"],
+ "colors": ["#000000", "#ff0000", "#00ff00", "#0000ff",
+ "#00ffff", "#ffff00"]
+ }
labels.dump(backend.processed_data_dir() / "predicted.labels")
--
GitLab