From 9bf8f75f5da4dea25e4611dca3cb1ca635ae676a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fran=C3=A7ois=20Laurent?= <francois.laurent@posteo.net>
Date: Sat, 1 Jul 2023 14:40:41 +0200
Subject: [PATCH] maggotuba time segment extension mechanism made optional
---
Project.toml | 2 +-
src/LarvaDatasets.jl | 8 ++++++--
src/taggingbackends/explorer.py | 7 ++++++-
3 files changed, 13 insertions(+), 4 deletions(-)
diff --git a/Project.toml b/Project.toml
index cc1dc08..672f20b 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
name = "TaggingBackends"
uuid = "e551f703-3b82-4335-b341-d497b48d519b"
authors = ["François Laurent", "Institut Pasteur"]
-version = "0.14"
+version = "0.14.1"
[deps]
Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
diff --git a/src/LarvaDatasets.jl b/src/LarvaDatasets.jl
index babf42d..dc37f42 100644
--- a/src/LarvaDatasets.jl
+++ b/src/LarvaDatasets.jl
@@ -555,6 +555,7 @@ function write_larva_dataset_hdf5(output_dir::String,
includeall="edited",
seed=nothing,
distributed_sampling=true,
+ past_future_extensions=true,
)
if distributed_sampling
new_write_larva_dataset_hdf5(output_dir, input_data;
@@ -570,8 +571,10 @@ function write_larva_dataset_hdf5(output_dir::String,
fixmwt=fixmwt,
frameinterval=frameinterval,
includeall=includeall,
+ past_future_extensions=past_future_extensions,
seed=seed)
else
+ past_future_extensions || throw("not implemented")
legacy_write_larva_dataset_hdf5(output_dir, input_data, window_length;
labels=labels,
labelpointers=labelpointers,
@@ -595,6 +598,7 @@ function new_write_larva_dataset_hdf5(output_dir, input_data;
balance=true,
frameinterval=0.1,
includeall="edited",
+ past_future_extensions=true,
seed=nothing,
kwargs...)
repo = if input_data isa String
@@ -608,7 +612,7 @@ function new_write_larva_dataset_hdf5(output_dir, input_data;
end
@assert !isnothing(frameinterval)
window = TimeWindow(window_length * frameinterval, round(Int, 1 / frameinterval);
- maggotuba_compatibility=true)
+ maggotuba_compatibility=past_future_extensions)
selectors = isnothing(labels) ? getprimarylabels(first(Dataloaders.files(repo))) : labels
min_max_ratio = balance ? 2 : 20
index = if isnothing(includeall)
@@ -627,7 +631,7 @@ function new_write_larva_dataset_hdf5(output_dir, input_data;
total_sample_size = length(loader.index)
classcounts, _ = Dataloaders.groupby(selectors, loader.index.targetcounts)
#
- extended_window_length = 3 * window_length
+ extended_window_length = past_future_extensions ? 3 * window_length : window_length
date = Dates.format(Dates.now(), "yyyy_mm_dd")
win = window_length # shorter name to keep next line within the allowed text width
output_file = "larva_dataset_$(date)_$(win)_$(win)_$(total_sample_size).hdf5"
diff --git a/src/taggingbackends/explorer.py b/src/taggingbackends/explorer.py
index 286dae4..0bbccb6 100644
--- a/src/taggingbackends/explorer.py
+++ b/src/taggingbackends/explorer.py
@@ -485,10 +485,14 @@ run `poetry add {pkg}` from directory: \n
def generate_dataset(self, input_files,
labels=None, window_length=20, sample_size=None, balance=True,
- include_all=None, frame_interval=None, seed=None):
+ include_all=None, frame_interval=None, seed=None,
+ past_future_extensions=None):
"""
Generate a *larva_dataset hdf5* file in data/interim/{instance}/
"""
+ if past_future_extensions is None:
+ past_future_extensions = True
+ logging.warning("Upcoming breaking change: pass argument past_future_extensions=True to BackendExplorer.generate_dataset to maintain current behavior")
return TaggingBackends.LarvaDatasets.write_larva_dataset_hdf5(
str(self.interim_data_dir()),
input_files if isinstance(input_files, list) else str(input_files),
@@ -498,6 +502,7 @@ run `poetry add {pkg}` from directory: \n
balance=balance,
includeall=include_all,
frameinterval=frame_interval,
+ past_future_extensions=past_future_extensions,
seed=seed)
def compile_trxmat_database(self, input_dir,
--
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