/
compute_tsne_features.m
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/
compute_tsne_features.m
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function analysisstruct = compute_tsne_features(MLmatobj,mocapstruct,analysisparams)
%subselect features to make a tsne map
% ---------------------------
% (C) Jesse D Marshall 2020
% Harvard University
analysisstruct=struct();
numfiles = size(MLmatobj,2);
%mocapstruct_reduced_agg = cell(1,max(chgpsin));
tsnefeat_name = cell(0,1);
agg_feat = [];
a6_agg = [];
a6_agg_nooffset = [];
filelength_total = 0;
fileuseind =[];
featnames_use = {'dyadic_spectrograms_score_wl_appendages_euc','dyadic_spectrograms_score_wl_appendages',...
'appendage_pca_score_lengths','appendage_pca_score','appendage_pca_score_euc'};
featnumber = [15,15,10,10,10];
%% collect features
agg_feat_indiv = [];
a_vec =cell(1,5);
for kz=1:numel(featnames_use)
try
ahere = MLmatobj.(featnames_use{kz});
catch ME
ahere = MLmatobj.(featnames_use{kz});
end
a_vec{kz} = ahere{8}(:,1:min(size(ahere{8},2),featnumber(kz)));
for rr = 1:size( a_vec{kz} ,2)
tsnefeat_name{end+1} = strcat(featnames_use{kz},'__',num2str(rr));
end
%issue with a hanging index too long/short
agg_feat_indiv = cat(2,agg_feat_indiv,a_vec{kz});
end
%% do the move frames etc here to match the normal
frameshere_temp = MLmatobj.frames_appendage_gps;
framesuse = intersect(frameshere_temp{8},mocapstruct.move_frames);
framesuse = framesuse(1:end-1);%in the old code but not sure why
framesuse_sub = framesuse(1:analysisparams.tsnegranularity:numel(framesuse));
a6 = framesuse_sub;
[~,framesuse_aggfeat] = intersect(frameshere_temp{8},mocapstruct.move_frames);
framesuse_aggfeat = framesuse_aggfeat(1:end-1);
framesuse_aggfeat = framesuse_aggfeat(1:analysisparams.tsnegranularity:numel(framesuse));
a6_agg = cat(1,a6_agg,bsxfun(@plus,reshape(a6,[],1),filelength_total));
a6_agg_nooffset = cat(1,a6_agg_nooffset,reshape(a6,[],1));
filelength_total = filelength_total+size(mocapstruct.aligned_mean_position,1);
fileuseind = cat(1,fileuseind,1*ones(numel(a6),1));
%% some weird bug for one animal plus the initial case
if numel(agg_feat)==0
agg_feat = cat(1,agg_feat,agg_feat_indiv(framesuse_aggfeat,:));
else
if size(agg_feat_indiv,2) ==size(agg_feat,2)
agg_feat = cat(1,agg_feat,agg_feat_indiv(framesuse_aggfeat,:));
else
fprintf('weird error where one appendage file is the wrong size \n')
size(agg_feat)
size(agg_feat_indiv)
agg_feat = cat(1,agg_feat,zeros(numel(framesuse_aggfeat),size(agg_feat,2)));
end
end
analysisstruct.tsnefeat_name = tsnefeat_name;
frames_track = reshape(1:size(agg_feat,1),[],1);
jt_features = agg_feat(frames_track,:);
analysisstruct.frames_with_good_tracking{1} = a6_agg(frames_track);
analysisstruct.frames_tracking_appendages = (frames_track);
analysisstruct.subset_of_points_to_plot_tsne_capped{1} = 1:numel(frames_track);
analysisstruct.subset_of_points_to_plot_tsne_move{1} = 1:numel(frames_track);
analysisstruct.condition_inds = ones(1,numel(frames_track));
a6_agg_nooffset = a6_agg_nooffset(frames_track);
fileuseind_restriced = fileuseind(frames_track);
%% save raw and various parameters
jt_features_raw = agg_feat(frames_track,:);
jt_features_mean = nanmean(jt_features,1);
jt_features_std = nanstd(jt_features,[],1);
jt_features = bsxfun(@rdivide,bsxfun(@minus,jt_features,...
nanmean(jt_features,1)),nanstd(jt_features,[],1));
analysisstruct.jt_features =jt_features;
analysisstruct.jt_features_raw =jt_features_raw;
analysisstruct.jt_features_mean =jt_features_mean;
analysisstruct.jt_features_std =jt_features_std;
agg_feat = [];
%% load in the mocapstruct
fprintf('loading mocap \n');
analysisstruct.file_sizes{1} = [];
frames_with_good_tracking_sub = a6_agg_nooffset;
markernames = fieldnames(mocapstruct.markers_preproc);
aligned_markers_temp = mocapstruct.markers_aligned_preproc;
preproc_markers_temp = mocapstruct.markers_preproc;
if isfield(mocapstruct,'analog')
analog_markers_temp = mocapstruct.analog;
end
analysisstruct.file_sizes{1} = cat(1,analysisstruct.file_sizes{1}, size(aligned_markers_temp,1));
fieldscopy = {'markernames','fps','links','markercolor','modular_cluster_properties','bad_frames_agg'};
for fhere= 1:numel(fieldscopy)
mocapstruct_reduced_agg.(fieldscopy{fhere}) = mocapstruct.(fieldscopy{fhere});
end
if isfield(mocapstruct,'mocapfiletimes' )
mocapstruct_reduced_agg.('mocapfiletimes') = mocapstruct.('mocapfiletimes');
else
mocapstruct_reduced_agg.('mocapfiletimes') = [];
end
for rr = 1:numel(markernames)
mocapstruct_reduced_agg.markers_preproc.(markernames{rr}) = ...
preproc_markers_temp.(markernames{rr})(frames_with_good_tracking_sub ,:);
mocapstruct_reduced_agg.markers_aligned_preproc.(markernames{rr}) =...
aligned_markers_temp.(markernames{rr})(frames_with_good_tracking_sub ,:);
end
analysisstruct.mocapstruct_reduced_agg{1} = mocapstruct_reduced_agg;
analysisstruct.coarse_annotation_mat = [];