131 analysis/req20150821.m
View file
@@ -1,6 +1,10 @@


%% REQ #1
% Video example
% Subplot(121),rearing as a skeleton
% subplot(122),trajectory of rears through the phase space of
% ethologically relavant features

Trial = MTATrial('jg05-20120317');

@@ -209,21 +213,22 @@

%% REQ #3

%% Contour JPDFs
Trial = MTATrial('jg05-20120317');


%% Walking features subspace contours
figTitle = 'req20150821_3_JPDF_WAG_PPC_Scontour'

% DEF Mode: 'ss' -> each state has contour
% 'as' -> primary state has contour, all others states
% are merged.
mode = 'as';


%% Initialize Features
xyz = Trial.load('xyz');

fxyz = xyz.copy;
fxyz.filter('ButFilter',3,.5,'low');

fvel = xyz.vel(1,[1,2]);
fvel.filter('ButFilter',3,2.5,'low');
fvel.data(fvel.data<0) = .1;
fvel.data = log10(fvel.data);
fvel.data = fvel(:,1);

nfet = MTADfet(Trial.spath,Trial.filebase,...
[diff(sqrt(sum((xyz(:,1,[1,2])-fxyz(:,1,[1,2])).^2,3)));0],...
xyz.sampleRate,...
@@ -236,21 +241,15 @@
50,nan).^2))),[2,3,4,1]),'sampleRate',xyz.sampleRate);


tff = MTADxyz('data',...
log10(abs(circ_dist(circshift(fang(:,1,4,1),-20),circshift(fang(:,1,4,1),20)))),...
'sampleRate',xyz.sampleRate);

load(fullfile(Trial.spath,...
[Trial.filebase '-walk_fet_ppc.mat']))



load(fullfile(Trial.spath,...
[Trial.filebase '-walk_fet_ppc.mat']))
man = Trial.xyz.copy;
man.data = mag;
man.filter('ButFilter',3,1.5,'low');



nbinx = 80;
nbiny = 80;
edx = linspace(-8,-1,nbinx);
@@ -268,8 +267,15 @@
hist2(fet(Trial.stc{'a'},:),edx,edy);
caxis([0,250])

sts = 'rwsnm';
stc = 'rwcgm';
switch mode
case 'ss'
sts = {'r','w','s','n','m'};
stc = 'rwcgm';
case 'as'
sts = {'r','a-r'};
stc = 'rc';
end

hedgs = {edx};
hedgs(2) = {edy};
edgs = {edx};
@@ -293,18 +299,22 @@
xlabel('WagPow_{spine lower} (AU)');
ylabel('PPC_{body} (AU)');

saveas(hfig,fullfile('/storage/gravio/figures/req/req20150821',[Trial.filebase '_req20150821_3_JPDF_WAG_PPC_Scontour.eps']),'epsc')
saveas(hfig,fullfile('/storage/gravio/figures/req/req20150821',[Trial.filebase '_req20150821_3_JPDF_WAG_PPC_Scontour.png']),'png')
saveas(hfig,fullfile(hostPath,[Trial.filebase '_' figTitle '_' mode '.eps']),'epsc')
saveas(hfig,fullfile(hostPath,[Trial.filebase '_' figTitle '_' mode '.png']),'png')






% Pitch upperv
%% Rearing feature subspace contours

hostPath = '/gpfs01/sirota/homes/gravio/figures/req/req20150821';
hostPath = '/storage/gravio/figures/req/req20150821';

% TRIAL subset of recording session
Trial = MTATrial('jg05-20120317');

xyz = Trial.load('xyz');
ang = create(MTADang,Trial,xyz);
% FXYZ Filtered Marker Positions {Low Pass 2.5 Hz}
@@ -315,6 +325,15 @@


%% Rear Body pitch vs diff(USpitch)

figTitle = 'req20150821_3_JPDF_Bpitch_dUSpitch_Scontour';

% DEF Mode: 'ss' -> each state has contour
% 'as' -> primary state has contour, all others states
% are merged.
mode = 'as';

% FET assignment
fet = Trial.xyz.copy;
fet.data = ([fang(:,1,4,2),[diff(fang(:,3,4,2));0]*fang.sampleRate]);

@@ -328,8 +347,16 @@
hist2(fet(Trial.stc{'a'},:),edx,edy);
caxis([0,250])

sts = 'rwsnm';
stc = 'rwcgm';
switch mode
case 'ss'
sts = {'r','w','s','n','m'};
stc = 'rwcgm';
case 'as'
sts = {'r','a-r'};
stc = 'rc';
end


hedgs = {edx};
hedgs(2) = {edy};
edgs = {edx};
@@ -340,42 +367,58 @@

hold on,
for i = 1:numel(sts),
ind = Trial.stc{sts(i)};
ind = Trial.stc{sts{i}};
o = hist2(fet(ind,:),hedgs{1},hedgs{2});
F = [.05 .1 .05; .1 .4 .1; .05 .1 .05];
o = conv2(o,F,'same');
contour(X,Y,o',[10,10],'linewidth',2.5,'Color',stc(i))
lbls{i} = ind.label;
end
legend(lbls,'Location','NorthWest');
title('wag_{lower spine}-vs-PPC_{lower_spine}');
xlabel('WagPow_{spine lower} (AU)');
ylabel('PPC_{body} (AU)');


title('State Contours');
xlabel('pitch_{body} (rad)');
ylabel('d(pitch_{upper spine})/dt (rad/s)');

saveas(hfig,fullfile(hostPath,[Trial.filebase '_req20150821_3_JPDF_Bpitch_dUSpitch_Scontour.eps']),'epsc')
saveas(hfig,fullfile(hostPath,[Trial.filebase '_req20150821_3_JPDF_Bpitch_dUSpitch_Scontour.png']),'png')
saveas(hfig,fullfile(hostPath,[Trial.filebase '_' figTitle '_' mode '.eps']),'epsc')
saveas(hfig,fullfile(hostPath,[Trial.filebase '_' figTitle '_' mode '.png']),'png')



%% Rear US pitch vs US log10(abs(diff(ang)))
% REQ 3.2
%
% DEF Mode: 'ss' -> each state has contour
% 'as' -> primary state has contour, all others states
% are merged.

mode = 'ss'; %mode = 'as';
figTitle = 'req20150821_3_JPDF_Bpitch_ladUSpitch_Scontour';
clims = [0,150];
contLim = [20,20];

%% Rear US pitch vs US diff(ang)
fet = Trial.xyz.copy;
fet.data = ([fang(:,3,4,2),log10(abs([diff(fang(:,3,4,2));0]*fang.sampleRate))]);


nbinx = 80;
nbiny = 80;
edx = linspace(-.8,pi/2,nbinx);
edy = linspace(-4,.8,nbiny);

hfig = figure;
hist2(fet(Trial.stc{'a'},:),edx,edy);
caxis([0,250])
caxis(clims)

switch mode
case 'ss';
sts = {'r','w','s','n','m'};
stc = 'rwcgm';
case 'as';
sts = {'r','a-r'};
stc = 'rc';
end


sts = 'rwsnm';
stc = 'rwcgm';
hedgs = {edx};
hedgs(2) = {edy};
edgs = {edx};
@@ -386,23 +429,25 @@

hold on,
for i = 1:numel(sts),
ind = Trial.stc{sts(i)};
ind = Trial.stc{sts{i}};
o = hist2(fet(ind,:),hedgs{1},hedgs{2});
F = [.05 .1 .05; .1 .4 .1; .05 .1 .05];
o = conv2(o,F,'same');
contour(X,Y,o',[20,20],'linewidth',2.5,'Color',stc(i))
contour(X,Y,o',contLim,'linewidth',2.5,'Color',stc(i))
lbls{i} = ind.label;
end
legend(lbls,'Location','southeast');

title('State Contours');
legend(lbls,'Location','southeast');
title({'State Contours', ['(Contour Sample Limit: ' num2str(contLim) ')']});
xlabel('pitch_{upper spine} (rad)');
ylabel('log10(abs(d(pitch_{upper spine})/dt)) (rad/s)');
h = colorbar;
h.Label.String = ['Sample Count (sr: ' num2str(round(Trial.xyz.sampleRate)) ')'];

saveas(hfig,fullfile(hostPath,[Trial.filebase '_req20150821_3_JPDF_USpitch_dUSpitch_Scontour.eps']),'epsc')
saveas(hfig,fullfile(hostPath,[Trial.filebase '_req20150821_3_JPDF_USpitch_dUSpitch_Scontour.png']),'png')

saveas(hfig,fullfile(hostPath,[Trial.filebase '_' figTitle '_' mode '.eps']),'epsc')
saveas(hfig,fullfile(hostPath,[Trial.filebase '_' figTitle '_' mode '.png']),'png')

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

fet = Trial.xyz.copy;
fet.data = [fang(:,1,2,2),fang(:,3,4,2)];
16 utilities/labelBhv_rev1.m
View file
@@ -881,6 +881,21 @@
for i= 1:afet.size(1),
mag(i) = PPC(afet(i,[1:5,7]));
end

msync = Trial.sync.copy;
msync.sync = Trial.sync.copy;

man = MTADfet(Trial.spath,Trial.filebase,...
mag,...
Trial.xyz.sampleRate,...
msync,...
Trial.sync(1),...
[],[],[],'lower_spine_trajectory_yaw_PPC','lsppc','y');
man.save;




save(fullfile(Trial.spath,...
[Trial.filebase '-walk_fet_ppc.mat']),'mag')

@@ -2030,3 +2045,4 @@
caxis([0,200])


feature
9 utilities/syncViconNlx.m
View file
@@ -176,6 +176,15 @@

Session.ufr = MTADufr(Session.spath,Session.filebase);

Session.fet = MTADfet(Session.spath,...
[],...
[],...
[],...
Session.sync.copy,...
Session.sync.data(1),...
[]);


Session.save;
Session.spk.clear;