implements larvatagger.jl#110

LICENSE

 MIT License
 
-Copyright (c) 2022 François Laurent, Institut Pasteur
+Copyright (c) 2022-2023 François Laurent, Institut Pasteur
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

src/LarvaDatasets.jl

@@ -266,9 +266,11 @@ function thresholdedcounts(counts; majorityweight=20)
 end
 
 function write_larva_dataset_hdf5(path, counts, files, refs, nsteps_before, nsteps_after;
-        fixmwt=false, frameinterval=nothing, includeall=nothing,
+        fixmwt=false, frameinterval=nothing, includeall=nothing, seed=nothing,
     )
     fixmwt && @warn "`fixmwt=true` is no longer supported"
+    @debug "Seeding the random number generator" seed
+    isnothing(seed) || Random.seed!(seed)
     # this method mutates argument `refs`
     T = eltype(keys(counts))
     refs′= Tuple{Int, Int, Int, T}[]
@@ -480,7 +482,8 @@ end
 """
     write_larva_dataset_hdf5(output_directory, input_files, window_length=20)
     write_larva_dataset_hdf5(...; labels=nothing, labelpointers=nothing)
-    write_larva_dataset_hdf5(...; sample_size=nothing, balance=true, chunks=false, shallow=false)
+    write_larva_dataset_hdf5(...; sample_size=nothing, balance=true, seed=nothing)
+    write_larva_dataset_hdf5(...; chunks=false, shallow=false)
     write_larva_dataset_hdf5(...; file_filter, timestep_filter)
 
 Sample series of 5-point spines from data files and save them in a hdf5 file,
@@ -542,7 +545,8 @@ function write_larva_dataset_hdf5(output_dir::String,
         balance=true,
         fixmwt=false,
         frameinterval=nothing,
-        includeall="edited")
+        includeall="edited",
+        seed=nothing)
     files = if input_data isa String
         repository = input_data
         labelledfiles(repository, chunks; selection_rule=file_filter, shallow=shallow)
@@ -601,7 +605,7 @@ function write_larva_dataset_hdf5(output_dir::String,
     write_larva_dataset_hdf5(output_file,
                              sample_sizes, files, refs, nsteps_before, nsteps_after;
                              fixmwt=fixmwt, frameinterval=frameinterval,
-                             includeall=includeall)
+                             includeall=includeall, seed=seed)
 
     h5open(output_file, "cw") do h5
         attributes(h5["samples"])["len_traj"] = window_length

src/taggingbackends/explorer.py

@@ -474,7 +474,7 @@ 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):
+            include_all=None, frame_interval=None, seed=None):
         """
         Generate a *larva_dataset hdf5* file in data/interim/{instance}/
         """
@@ -486,7 +486,8 @@ run `poetry add {pkg}` from directory: \n
                 sample_size=sample_size,
                 balance=balance,
                 includeall=include_all,
-                frameinterval=frame_interval)
+                frameinterval=frame_interval,
+                seed=seed)
 
     def compile_trxmat_database(self, input_dir,
             labels=None, window_length=20, sample_size=None, reuse_h5files=False):

src/taggingbackends/main.py

@@ -12,6 +12,7 @@ Usage:  tagging-backend [train|predict] --model-instance <name>
         tagging-backend train ... --pretrained-model-instance <name>
         tagging-backend train ... --include-all <secondary-label>
         tagging-backend train ... --skip-make-dataset --skip-build-features
+        tagging-backend train ... --seed <seed>
         tagging-backend predict ... --make-dataset --build-features
         tagging-backend predict ... --sandbox <token>
         tagging-backend --help
@@ -99,6 +100,7 @@ def main(fun=None):
         balancing_strategy = 'auto'
         include_all = None
         class_weights = None
+        seed = None
         unknown_args = {}
         k = 2
         while k < len(sys.argv):
@@ -150,6 +152,9 @@ def main(fun=None):
             elif sys.argv[k] == "--include-all":
                 k = k + 1
                 include_all = sys.argv[k]
+            elif sys.argv[k] == "--seed":
+                k = k + 1
+                seed = sys.argv[k]
             else:
                 unknown_args[sys.argv[k].lstrip('-').replace('-', '_')] = sys.argv[k+1]
                 k = k + 1
@@ -187,6 +192,8 @@ def main(fun=None):
                 logging.info("option --reuse-h5files is ignored in the absence of --trxmat-only")
             if include_all:
                 make_dataset_kwargs["include_all"] = include_all
+            if seed is not None:
+                make_dataset_kwargs["seed"] = seed
             backend._run_script(backend.make_dataset, **make_dataset_kwargs)
         if build_features:
             backend._run_script(backend.build_features)
@@ -198,6 +205,8 @@ def main(fun=None):
                 train_kwargs["pretrained_model_instance"] = pretrained_model_instance
             if class_weights:
                 train_kwargs['class_weights'] = class_weights
+            if seed is not None:
+                train_kwargs['seed'] = seed
             backend._run_script(backend.train_model, trailing=unknown_args, **train_kwargs)
     else:
         # called by make_dataset, build_features, train_model and predict_model