save json labels to trxmat

Artifacts.toml

@@ -21,3 +21,11 @@ lazy = true
 	[[sample_trxmat_file_small.download]]
 	url = "https://gitlab.pasteur.fr/nyx/artefacts/-/raw/master/PlanarLarvae/trx_small.tgz?inline=false"
 	sha256 = "806ac7c2e51d2ed5535e336a44bc33cad4396850318ab771f8c9057ceda9a0d8"
+
+[sample_labels_small]
+git-tree-sha1 = "73e3d5b91e5c8541012d128e094837e1e28239e5"
+lazy = true
+
+	[[sample_labels_small.download]]
+	url = "https://gitlab.pasteur.fr/nyx/artefacts/-/raw/master/PlanarLarvae/labels_small.tgz?inline=false"
+	sha256 = "b6be8a281644726f09ef7ebd0ac3976c388e042838e7258a1d407d1f48abec53"

nyxlabels/remove_behavior_tags.m

+function [trx] = remove_behavior_tags(trx, varargin)
+% REMOVE_BEHAVIOR_TAGS  Remove fields from trx structure array known to be
+%                       behavior tags.
+%
+%   TRX = REMOVE_BEHAVIOR_TAGS(TRX) removes tags such as "run", "run_large"
+%     etc.
+%
+%   TRX = REMOVE_BEHAVIOR_TAGS(TRX, TAG1, TAG2, ...) additionally removes
+%     trailing TAG1, TAG2, ...
+
+std_tags = [ ...
+    "back" "back_large" "back_strong" "back_weak" ...
+    "cast" "cast_large" "cast_strong" "cast_weak" ...
+    "hunch" "hunch_large" "hunch_strong" "hunch_weak" ...
+    "roll" "roll_large" "roll_strong" "roll_weak" ...
+    "run" "run_large" "run_strong" "run_weak" ...
+    "small_motion" ...
+    "stop" "stop_large" "stop_strong" "stop_weak" ...
+    ];
+
+for tag = std_tags
+    if isfield(trx, tag)
+        trx = rmfield(trx, tag);
+    end
+end
+
+for tag = varargin
+    tag = tag{1};
+    trx = rmfield(trx, tag);
+end
+
+end
\ No newline at end of file

nyxlabels/update_trx_with_labels.m

+function [updated_trx] = update_trx_with_labels(trx, labels_file, varargin)
+% UPDATE_TRX_WITH_LABELS  Update trx structure array with json labels.
+%
+%   TRX = UPDATE_TRX_WITH_LABELS(TRX, LABELS_FILE) loads json-encoded
+%     labels from file LABELS_FILE, and add corresponding fields in
+%     structure array TRX.
+%
+%   TRX = UPDATE_TRX_WITH_LABELS(TRX_FILE, LABELS_FILE) loads TRX from file
+%     TRX_FILE.
+%
+%   TRX = UPDATE_TRX_WITH_LABELS(..., "outputfile", OUTPUT_TRX_FILE) saves
+%     the updated TRX to file OUTPUT_TRX_FILE.
+%
+%   TRX = UPDATE_TRX_WITH_LABELS(..., "removetags", 1) removes all known
+%     tags from TRX prior to adding tags from LABELS_FILE.
+%
+%   See also REMOVE_BEHAVIOR_TAGS.
+
+if ~isa(trx, "struct")
+    load(trx, "trx");
+end
+
+args = struct();
+if 2<nargin
+    for n = 3:2:nargin
+        args.(varargin{n-2}) = varargin{n-1};
+    end
+end
+
+if isfield(args, "removetags")
+    if args.removetags
+        trx = remove_behavior_tags(trx);
+    end
+end
+
+data = jsondecode(fileread(labels_file));
+labelnames = data.labels.names;
+
+updated_trx = struct([]);
+% backward indexing trick to preallocate the updated_trx array
+for k = length(trx):-1:1
+    for f = fieldnames(trx)'
+        f = f{1};
+        updated_trx(k,1).(f) = trx(k).(f);
+    end
+    tag = -ones(size(trx(k).t));
+    for label = labelnames'
+        label = label{1};
+        updated_trx(k,1).(label) = tag;
+    end
+end
+
+data = data.data;
+for larva = 1:length(data)
+    labels = data(larva).labels;
+    larvaid = data(larva).id;
+    larva = find([trx.numero_larva_num]==str2num(larvaid));
+    if isempty(larva)
+        disp("skipping larva " + larvaid);
+    else
+    for label = unique(labels)'
+        labelname = labelnames{label};
+        field = updated_trx(larva).(labelname);
+        field(labels==label) = 1;
+        updated_trx(larva).(labelname) = field;
+    end
+    end
+end
+
+if isfield(args, "outputfile")
+    trx = updated_trx;
+    save(args.outputfile, "trx");
+end
+
+end
\ No newline at end of file

src/Trxmat.jl

@@ -210,30 +210,30 @@ function read_behavior_tags(tags, file::TrxMatFile)
 end
 
 behavior_tags = [
-                 :small_motion,
-                 :stop_large,
+                 :back,
+                 :back_large,
+                 :back_strong,
                  :back_weak,
-                 :roll_weak,
+                 :cast,
+                 :cast_large,
+                 :cast_strong,
+                 :cast_weak,
                  :hunch,
-                 :back,
+                 :hunch_large,
+                 :hunch_strong,
                  :hunch_weak,
+                 :roll,
+                 :roll_large,
                  :roll_strong,
-                 :cast_weak,
+                 :roll_weak,
+                 :run,
                  :run_large,
-                 :stop_weak,
+                 :run_strong,
                  :run_weak,
-                 :hunch_strong,
-                 :run,
-                 :cast_large,
-                 :hunch_large,
+                 :small_motion,
+                 :stop_large,
                  :stop_strong,
-                 :back_large,
-                 :roll_large,
-                 :cast_strong,
-                 :roll,
-                 :back_strong,
-                 :cast,
-                 :run_strong,
+                 :stop_weak,
                 ]
 
 read_behavior_tags(file::TrxMatFile) = read_behavior_tags(behavior_tags, file)

test/makedata.jl

@@ -24,6 +24,15 @@ function make_test_data(target="chore_sample_outline")
         elseif target == "sample_trxmat_file"
             artefact = artifact"sample_trxmat_file"
             filename = "trx.mat"
+        elseif target == "sample_trxmat_file_small"
+            artefact = artifact"sample_trxmat_file_small"
+            filename = "trx_small.mat"
+        elseif target == "sample_labels_file_trx_small"
+            artefact = artifact"sample_labels_small"
+            filename = "jbm_tagger.labels"
+        elseif target == "sample_labels_file_nyx_small"
+            artefact = artifact"sample_labels_small"
+            filename = "maggotuba.labels"
         else
             throw(DomainError("unknown artefact: " * target))
         end

test/runtests.jl

@@ -311,7 +311,7 @@ if all_tests || "Trxmat" in ARGS
     data_with_selected_tags = read_trxmat((:tags=>Tags([:hunch, :back, :run, :roll, :cast]),), target″)
     # example from README
     larvastate = first(eachstate(data_with_tags))
-    @test string(larvastate.tags) == "24-element Tag{\"small_motion\", \"run_weak\", \"run\"}"
+    @test string(larvastate.tags) == "24-element Tag{\"run\", \"run_weak\", \"small_motion\"}"
 end
 end