ud

README_SBeA_mapper.md

@@ -13,35 +13,34 @@ Case data: [fig2_data\pose tracking](https://figshare.com/projects/Social_behavi
 ## Run
 ### 1. Seperate multi-animal to single-animal trajectories  
 The first step is a preparation of later steps.
-
+Demo results:  
+![image]()  
+
 Script: [SBeA_step_1.m](https://github.com/YNCris/SBeA_release/blob/main/SBeA_mapper/SBeA_step_1.m)  
 
 Input:  
 *id3d.mat: multi-animal trajectories with identities  
 *-camera-0.avi: one camera view video  
-Demo results:  
-![image]()  
 
 Output:
 *.mat: single-animal trajectories
 *.avi: corresponding videos of single-animal trajectories  
-Demo results:  
-![image]()  
 
 ### 2. Single animal behavior segmentation by Behavior Atlas (BeA)  
+The second step is to decompose the behvior of single animal.  
+Demo results:  
+![image]()  
+
 Script: [SBeA_step_2_mice.m](https://github.com/YNCris/SBeA_release/blob/main/SBeA_mapper/SBeA_step_2_mice.m)  
 
 Input:  
 *id3d.mat: multi-animal trajectories with identities  
 *-camera-0.avi: one camera view video
-Demo results:  
-![image]()  
 
 Output:
 *.mat: single-animal trajectories
 *.avi: corresponding videos of single-animal trajectories
-Demo results:  
-![image]()   
+
 ### 3. 
 Script: [SBeA_step_1.m](https://github.com/YNCris/SBeA_release/blob/main/SBeA_mapper/SBeA_step_1.m)  
 

SBeA_mapper/HBTlog.txt

@@ -20,3 +20,15 @@
 10:02:55: Decomposing completed, time elapse: 208.114seconds
 10:04:03: Decomposing poses, time elapse: 42.705seconds
 10:04:04: Calculating kernel matrix, time elapse: 0.57seconds
+10:10:24: Decomposing movements and ethograms, time elapse: 380.411seconds
+10:10:38: Decomposing completed, time elapse: 437.303seconds
+10:12:02: Decomposing poses, time elapse: 47.762seconds
+10:12:03: Calculating kernel matrix, time elapse: 0.507seconds
+10:15:54: Decomposing movements and ethograms, time elapse: 231.031seconds
+10:16:03: Decomposing completed, time elapse: 288.637seconds
+10:17:27: Decomposing poses, time elapse: 55.063seconds
+10:17:28: Calculating kernel matrix, time elapse: 0.736seconds
+10:18:34: Decomposing movements and ethograms, time elapse: 65.909seconds
+10:18:43: Decomposing completed, time elapse: 131.131seconds
+10:20:44: Decomposing poses, time elapse: 72.282seconds
+10:20:45: Calculating kernel matrix, time elapse: 0.835seconds

SBeA_mapper/tools/demo_results_step_1.asv

@@ -0,0 +1,16 @@
+%{
+    show demo results of step 1
+%}
+clear all
+close all
+%% set path
+rootpath = ['Z:\hanyaning\multi_mice_test\paper\' ...
+    'Nature Methods\test_run\pose tracking'];
+dataname = 'rec11-A1A2-20220803-id3d.mat';
+%% load data
+load([rootpath,'\',dataname])
+%% plot
+traj1 = coords3d(:,1:48);
+traj2 = coords3d(:,49:end);
+
+for k = 1:

SBeA_mapper/tools/demo_results_step_1.m

@@ -0,0 +1,43 @@
+%{
+    show demo results of step 1
+%}
+clear all
+close all
+addpath(genpath(pwd))
+%% set path
+rootpath = ['Z:\hanyaning\multi_mice_test\paper\' ...
+    'Nature Methods\test_run\pose tracking'];
+dataname = 'rec11-A1A2-20220803-id3d.mat';
+%% load data
+load([rootpath,'\',dataname])
+%% plot
+setcolor = cbrewer2('Spectral',11);
+mouse1_c = setcolor(3,:);
+mouse2_c = setcolor(9,:);
+
+traj1 = coords3d(:,1:48);
+traj2 = coords3d(:,49:end);
+
+smo_win = 30;
+line_bias = 150;
+
+for k = 1:48
+    plot(smooth(...
+        traj1(:,k)+k*line_bias-mean(traj1(:,k)),smo_win),...
+        'Color',mouse1_c)
+    hold on
+end
+mice_bias = 300;
+for k = 1:48
+    plot(smooth( ...
+        traj2(:,k)+mice_bias+(k+48)*...
+    line_bias-mean(traj2(:,k)),smo_win),...
+        'Color',mouse2_c)
+    hold on
+end
+hold off
+
+box off
+set(gca,'TickDir','out')
+xlabel('Frames')
+set(gca,'YTick',[])