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touch_hyperplane_angle.m
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touch_hyperplane_angle.m
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% For 2pad (2-port angle distance), WT, WST, and WL is generated during prebuild_JK.m
%% Setup whisker array builder
behavior_base_dir = 'D:\TPM\JK\soloData\';
whisker_base_dir = 'D:\TPM\JK\tracked\';
mice = {'JK025','JK027','JK030'};
%%%%%%%%%%%%%%%%%%%%%% manual selection
steps = {[10:70],[20:80],[140:200],[140:200]};
%%%%%%%%%%%%%%%%%%%%%% try as short as possible to reduce time next step
sessions = {[1:3,5:18],[1,2,4:7,11,15],[1,2,4:20]};
trial_types = {'rn', 'ln'};
for mi = 1 : length(mice)
mouseName = mice{mi};
sessionNum = sessions{mi};
%%
for sessionInd = 1 : length(sessionNum)
% for sessionInd = 1:3
sessionName = sprintf('S%02d',sessionNum(sessionInd));
behavior_d = [behavior_base_dir mouseName '\'];
whisker_d = [whisker_base_dir mouseName sessionName '\'];
% if exist([whisker_d, 'touch_hp.mat'],'file')
% error('touch_hp.mat exists.')
% end
if exist('b','var')
if strcmp(b{1}.mouseName, mouseName)
disp('using the same behavior file')
else
disp('loading a new behavior file')
load([behavior_d 'behavior.mat']) % loading b of the mouse (all the sessions)
end
else
load([behavior_d 'behavior.mat']) % loading b of the mouse (all the sessions)
end
b_ind = find(cellfun(@(x) strcmp(x.sessionName,sessionName), b));
b_session = b{b_ind};
load_fn = [mouseName sessionName '_post.mat'];
load([whisker_d load_fn]); % loading errorlist
if ~isempty(b_ind) % try only the ones with behavior session
% %%
filelist=dir([whisker_d '*.measurements']);
dirTrialNums=zeros(1,size(filelist,1));
% trialNums=[]; % enter which trial nums to process
% %%
% Assign the trial numbers to existing .measurements files in the directory
% NOTE : This assumes that the .measurements files have leading numbers
% corresponding to trial number in string positions 1:end-13 of the file
% name. These index numbers may need to be changed to match up to the
% numerical code of the trial number. (2016/09/05 JK)
for i=1:length(filelist)
dirTrialNums(i)=str2double(filelist(i).name(1:end-13)); % extract out the trial number from each measurements file present in directory
end
dirTrialNums = setdiff(dirTrialNums,errorlist);
trialNums = sort(dirTrialNums);
trialNums = trialNums(~isnan(trialNums));
trialNums = intersect(trialNums,b{b_ind}.trialNums); % try only the ones with behavior trials
includef=cell(size(trialNums,1),1);
for i = 1: length(trialNums)
includef{i} = num2str(trialNums(i));
end
end
% %% Make whisker-pole touch space for each type of trial, from 10 randomly selected trials (of each type)
% Currently, only dealing with 4 types of trials: 'rc', 'rf', 'lc', 'lf'
% Should make something different for straight pole touch in S00.
% 2017/04/11 JK
steps_hp = cell(1,length(trial_types));
num_points_in_hp = cell(1,length(trial_types));
tt_ind = cell(1,length(trial_types));
wl_array = cell(1,length(trial_types));
touch_hp = cell(1,length(trial_types)); % touch hyperplanes
hp_peaks = cell(1,length(trial_types)); % touch hyperplane peak points. 2 points for each hyperplane
for trial_type_num = 1 : length(trial_types)
% trial_type_num = 1
tt_ind{trial_type_num} = find(cellfun(@(x) strcmp(x.trialType,trial_types{trial_type_num}),b_session.trials));
temp_files = cell(length(tt_ind{trial_type_num}),1);
for j = 1 : length(tt_ind{trial_type_num})
temp_files{j} = num2str(tt_ind{trial_type_num}(j));
end
wl = Whisker.WhiskerTrialLiteArray(whisker_d,'include_files',temp_files);
wl_array{trial_type_num} = wl;
end
%%
for trial_type_num = 1 : length(trial_types)
% for trial_type_num = 4
done_flag = 1;
psi1_polygon_answer = 'Yes'; % for re-drawing of polygon for psi1
while (done_flag)
intersect_3d_total = [];
wl = wl_array{trial_type_num};
for tnum = 1 : length(wl.trials)
try
top_ind = find(~isnan(wl.trials{tnum}.intersect_coord(:,1)));
front_ind = find(~isnan(wl.trials{tnum}.intersect_coord(:,2)));
intersect_ind = intersect(wl.trials{tnum}.pole_available_timepoints,intersect(top_ind,front_ind));
intersect_3d_total = [intersect_3d_total; wl.trials{tnum}.intersect_coord(intersect_ind,1), wl.trials{tnum}.intersect_coord(intersect_ind,2), ones(length(intersect_ind),1)*wl.trials{tnum}.pole_pos];
catch
fprintf('Skipping trial #%d because of index problems \n',tnum);
end
end
intersect_3d_total = unique(round(intersect_3d_total,2),'rows');
psi1_answer = 'Yes'; % for overall psi1 detection
while(strcmp(psi1_answer,'Yes'))
while(strcmp(psi1_polygon_answer,'No'))
h2 = figure('units','normalized','outerposition',[0 0 1 1]); plot(intersect_3d_total(:,1), intersect_3d_total(:,2), 'k.', 'MarkerSize', 0.1), hold on
pre_poly = []; % points of the polygon
i = 1;
temp_point = ginput(1);
while(~isempty(temp_point)) % finish drawing polygon by pressing "enter"
pre_poly = [pre_poly; temp_point];
plot(pre_poly(i,1), pre_poly(i,2), 'bo', 'MarkerSize', 3)
if i > 1
plot(pre_poly(i-1:i,1), pre_poly(i-1:i,2), 'b-')
end
i = i + 1;
temp_point = ginput(1);
end
plot([pre_poly(end,1);pre_poly(1,1)], [pre_poly(end,2);pre_poly(1,2)], 'b-')
psi1_polygon_answer = questdlg('Is the polygon right?', 'Polygon pre-selection', 'Yes', 'No', 'Yes');
switch psi1_polygon_answer
case 'Yes'
close all
in = inpolygon(intersect_3d_total(:,1), intersect_3d_total(:,2), pre_poly(:,1), pre_poly(:,2));
intersect_3d_crop = intersect_3d_total(in,:);
case 'No'
close(h2)
h2 = figure('units','normalized','outerposition',[0 0 1 1]); plot(intersect_3d_total(:,1), intersect_3d_total(:,2), 'k.', 'MarkerSize', 0.1), hold on
end
end
if exist('intersect_3d_crop','var')
intersect_3d = intersect_3d_crop;
clear intersect_3d_crop
else
intersect_3d = intersect_3d_total;
end
h1 = figure; plot3(intersect_3d(:,1), intersect_3d(:,2), intersect_3d(:,3), 'k.', 'MarkerSize', 0.1)
title(wl.trials{1}.trial_type), xlabel('Top-view intersection coord'), ylabel('Front-view intersection coord'), zlabel('Pole position')
%% when interested in certain points in the figure
% ttype = 4;
% zvalue = 90050;
% tnum = find(cellfun(@(x) abs(x.pole_pos - zvalue) < 10, wl_array{ttype}.trials))
% wl_array{ttype}.trials{tnum(1)}.trackerFileName
% figure, plot3(wl_array{ttype}.trials{tnum(1)}.intersect_coord(:,1), wl_array{ttype}.trials{tnum(1)}.intersect_coord(:,2), 1:length(wl_array{ttype}.trials{tnum(1)}.intersect_coord(:,1)))
% xlabel('Top-view intersection coord'), ylabel('Front-view intersection coord'), zlabel('Frame #')
%% Calculate psi1 % takes ~ 15 sec
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Manual selection
ind_opt = 1; % optimal peak index. Starting from 1
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
disp('Calculating psi1')
max_zeros = 0;
angle_steps_pre = 0:180;
stds_pre = zeros(length(angle_steps_pre),1);
for i = 1 : length(angle_steps_pre)
A = viewmtx(angle_steps_pre(i),0);
x4d = [intersect_3d, ones(size(intersect_3d,1),1)]';
x2d = A*x4d;
x2d_pix = [floor(x2d(1,:));floor(x2d(2,:)/100)];
x2d_dim = [max(x2d_pix(2,:)) - min(x2d_pix(2,:)) + 1, max(x2d_pix(1,:)) - min(x2d_pix(1,:)) + 1];
x2d_proj = zeros(x2d_dim);
j_offset = min(x2d_pix(1,:)) - 1;
i_offset = min(x2d_pix(2,:)) - 1;
for j = 1 : length(x2d_pix)
x2d_proj(x2d_pix(2,j) - i_offset, x2d_pix(1,j) - j_offset) = x2d_proj(x2d_pix(2,j) - i_offset, x2d_pix(1,j) - j_offset) + 1;
end
stds_pre(i) = std(x2d_proj(find(x2d_proj(:))));
% stds_pre(i) = std(x2d_proj(:));
end
[P, I] = findpeaks(smooth(smooth(stds_pre)),'sortstr','descend');
answer = 'No';
while(strcmp(answer,'No'))
max_psi1_pre = angle_steps_pre(I(ind_opt));
h2 = figure; subplot(1,2,1), plot(1:length(stds_pre), smooth(smooth(stds_pre,5))), hold on, plot(I(ind_opt),stds_pre(I(ind_opt)),'ro')
subplot(1,2,2), plot(1:length(stds_pre), stds_pre)
max_std = 0;
psi1 = 0;
angle_steps = max_psi1_pre-4.99:0.01:max_psi1_pre+4.99;
stds = zeros(length(angle_steps),1);
x2d_final = zeros(size(x2d_proj));
for i = 1:length(angle_steps)
A = viewmtx(angle_steps(i),0);
x4d = [intersect_3d, ones(size(intersect_3d,1),1)]';
x2d = A*x4d;
x2d_pix = [floor(x2d(1,:));floor(x2d(2,:)/100)];
x2d_dim = [max(x2d_pix(2,:)) - min(x2d_pix(2,:)) + 1, max(x2d_pix(1,:)) - min(x2d_pix(1,:)) + 1];
x2d_proj = zeros(x2d_dim);
j_offset = min(x2d_pix(1,:)) - 1;
i_offset = min(x2d_pix(2,:)) - 1;
for j = 1 : length(x2d_pix)
x2d_proj(x2d_pix(2,j) - i_offset, x2d_pix(1,j) - j_offset) = x2d_proj(x2d_pix(2,j) - i_offset, x2d_pix(1,j) - j_offset) + 1;
end
temp_std = std(x2d_proj(find(x2d_proj(:))));
% temp_std = std(x2d_proj(:));
stds(i) = temp_std;
if temp_std > max_std
max_std = temp_std;
psi1 = angle_steps(i);
x2d_final = x2d_proj;
end
end
psi1 = psi1-90;
subplot(1,2,2), plot(1:length(stds), stds)
A = viewmtx(psi1+90,0);
x4d = [intersect_3d, ones(size(intersect_3d,1),1)]';
x2d = A*x4d;
h3 = figure; plot(x2d(1,:), x2d(2,:),'k.', 'MarkerSize',3)
questTitle='whisker-pole intersection coordinate scatter'; start(timer('StartDelay',1,'TimerFcn',@(o,e)set(findall(0,'Tag',questTitle),'WindowStyle','normal')));
answer = questdlg('Is psi1 correct?', questTitle, 'Yes', 'No', 'Yes');
switch answer
case 'Yes'
close all
psi1_answer = 'No'; % get out of this large while loop
case 'No'
close(h2), close(h3)
ind_opt = ind_opt + 1;
if length(I) >= ind_opt
continue
else
psi1_answer = questdlg('Do you want to change your polygon drawing?', 'psi1 polygon', 'Yes', 'No', 'Yes');
if strcmp(psi1_answer,'Yes')
answer = 'Yes'; % to get out of innner while loop
psi1_polygon_answer = 'No';
else
error(['No observable psi1 at ' sessionName ' of ' mouseName])
end
end
end
end
end
%% Manual check of the view
% A = viewmtx(I(6)+5,0);
% x4d = [intersect_3d, ones(size(intersect_3d,1),1)]';
% x2d = A*x4d;
% h3 = figure; plot(x2d(1,:), x2d(2,:),'k.', 'MarkerSize',3)
%% Psi2
%%%%%%%%%%%%%%%%%%%%%%%%%%%% Manual selection
answer1 = 'No'; answer2 = 'Yes';
disp('Calculating psi2')
x2d_flip = flip(x2d_final,1);
while(strcmp(answer1,'No'))
h2 = figure('units','normalized','outerposition',[0 0 1 1]); imagesc(x2d_flip), hold on
BW = zeros(size(x2d_flip)) + 1;
while(strcmp(answer2,'No')) % Draw polygon to select regions for radon transform
psi2_poly = [];
i = 1;
temp_point = ginput(1);
while(~isempty(temp_point)) % finish drawing polygon by pressing "enter"
psi2_poly = [psi2_poly;temp_point];
plot(psi2_poly(i,1), psi2_poly(i,2), 'yo', 'MarkerSize', 3)
if i > 1
plot(psi2_poly(i-1:i,1), psi2_poly(i-1:i,2), 'y-')
end
i = i + 1;
temp_point = ginput(1);
end
plot([psi2_poly(end,1);psi2_poly(1,1)], [psi2_poly(end,2);psi2_poly(1,2)], 'y-')
answer2 = questdlg('Is the polygon right?', 'Polygon pre-selection', 'Yes', 'No', 'Yes');
switch answer2
case 'Yes'
close all
[sub_1, sub_2] = ind2sub(size(x2d_flip),1:length(x2d_flip(:)));
in = inpolygon(sub_2, sub_1, round(psi2_poly(:,1)), round(psi2_poly(:,2)));
BW = zeros(size(x2d_flip));
BW(in) = 1;
case 'No'
close(h2)
h2 = figure('units','normalized','outerposition',[0 0 1 1]); imagesc(x2d_flip), hold on
end
end
x2d_edge = x2d_flip .* BW;
figure, imagesc(x2d_edge)
%%
theta = 0:0.01:180;
R = radon(x2d_edge, theta);
[~, max_ind] = max(std(R));
psi2 = (max_ind-1)*0.01;
psi2 = atand(tand(psi2)/100); % psi2 adjusted because it was calculated with pole position divided by 100
linex = zeros(3,2);
x2d_flip_1strow = x2d_flip(1,:);
[~, linex(1,1)] = max(x2d_flip_1strow); x2d_flip_1strow(max(1,linex(1,1)-5):min(size(x2d_flip,2),linex(1,1)+5)) = 0;
[~, linex(2,1)] = max(x2d_flip_1strow); x2d_flip_1strow(max(1,linex(2,1)-5):min(size(x2d_flip,2),linex(2,1)+5)) = 0;
[~, linex(3,1)] = max(x2d_flip_1strow);
for i = 1 : 3
linex(i,2) = linex(i,1) + tand((max_ind-1)*0.01)*size(x2d_flip,1);
end
liney = [1 size(x2d_flip,1);1 size(x2d_flip,1);1 size(x2d_flip,1)];
figure('units','normalized','outerposition',[0 0 1 1]),
subplot(121), imagesc(R), xlabel('Angle = 0:0.01:180'), ylabel('Projected values'), axis square
subplot(122), imagesc(x2d_flip, [0 1000]), axis square, hold on,
for i = 1 : 3
line(linex(i,:),liney(i,:), 'LineWidth', 3, 'Color', [1 1 1])
end
questTitle='whisker-pole intersection coordinate side-view'; start(timer('StartDelay',1,'TimerFcn',@(o,e)set(findall(0,'Tag',questTitle),'WindowStyle','normal')));
answer1 = questdlg('Is psi2 correct?', questTitle, 'Yes', 'No', 'Yes');
switch answer1
case 'Yes'
close all
case 'No'
answer3 = questdlg('Do you want to select the polygon again?', ' ', 'Yes', 'No', 'Yes');
close all
switch answer3
case 'Yes'
answer2 = 'No';
case 'No'
error(['No optimal psi2 found in ' sessionName ' of ' mouseName])
end
end
end
%% Calculate touch hyperplanes
disp('Sweeping the hyperplane')
maxdist = ceil(sqrt(max(intersect_3d_total(:,1).^2) + max(intersect_3d_total(:,2).^2)));
xmin = -maxdist; xmax = maxdist; zmin_data = min(intersect_3d_total(:,3)); zmax_data = max(intersect_3d_total(:,3)); zdiff = zmax_data - zmin_data; zmax = zmax_data + zdiff; zmin = zmin_data - zdiff;
ymin_data = min(intersect_3d_total(:,2)); ymax_data = max(intersect_3d_total(:,2));
z = zmin:zmax;
xyz = zeros((length(z))*(xmax-xmin+1),3);
for i = xmin:xmax
xyz((i-xmin)*length(z)+1 : (i-xmin+1)*length(z),:) = [ones(length(z),1)*i, zeros(length(z),1), z'];
end
[xyz_psi1, ~, ~] = AxelRot(xyz',psi1,[0 0 1], 0); % rotate psi1 degrees counterclockwise around z axis
zcenter = floor(mean([zmax_data, zmin_data]));
x0 = [0 0 zcenter];
u = [1 tand(psi1) 0];
[xyz_psi2, ~, ~] = AxelRot(xyz_psi1, psi2, u, x0);
xyz_psi2(:,xyz_psi2(3,:) < zmin_data) = [];
xyz_psi2(:,xyz_psi2(3,:) > zmax_data) = [];
xyz_psi2(:,xyz_psi2(2,:) < ymin_data) = [];
xyz_psi2(:,xyz_psi2(2,:) > ymax_data) = [];
figure, plot3(intersect_3d_total(:,1),intersect_3d_total(:,2), intersect_3d_total(:,3),'k.', 'MarkerSize',3), xlabel('top'), ylabel('front'), zlabel('pos'), hold on
plot3(xyz_psi2(1,:), xyz_psi2(2,:), xyz_psi2(3,:), 'r.', 'MarkerSize',3)
%% ~ 0.5 min (depending on the length of "steps" and the size of xyz_psi2)
hp_decision = 'No';
while(strcmp(hp_decision,'No'))
intersect_pix = round(intersect_3d_total);
num_points = zeros(length(steps{trial_type_num}),1);
parfor i = 1:length(steps{trial_type_num}) % this is time consuming...
hp = round(xyz_psi2);
hp(1,:) = hp(1,:)+steps{trial_type_num}(i);
num_points(i) = sum(ismember(intersect_pix, hp','rows'));
end
h1 = figure; plot(steps{trial_type_num},num_points(:), 'k-', 'LineWidth', 3), xlabel('translocation (pix)'), ylabel('# intersection')
options.WindowStyle = 'normal';
questTitle='Touch hyperplane peaks'; start(timer('StartDelay',1,'TimerFcn',@(o,e)set(findall(0,'Tag',questTitle),'WindowStyle','normal')));
answer = questdlg('Does the result look correct?', questTitle, 'Yes', 'No', 'Yes');
peak_answer = 'Yes';
while(strcmp(peak_answer,'Yes'))
if strcmp(answer,'Yes')
datacursormode(h1,'on')
hp_peak_ans = inputdlg({'Left peak','Right peak'},'What are the peak points?',1,{'',''},options);
hp_peaks{trial_type_num} = [str2num(hp_peak_ans{1}) str2num(hp_peak_ans{2})];
% Final confirmation
% project the peak hyperplanes and all coordinates onto psi1 psi2 view
h2 = figure('units','normalized','outerposition',[0 0 1 1]);
A = viewmtx(psi1,90-psi2);
intersect_4d = [intersect_3d_total, ones(size(intersect_3d_total,1),1)]';
intersect_2d = A*intersect_4d;
intersect_2d = unique(round(intersect_2d(1:2,:)',2),'rows');
th_4d1 = [xyz_psi2(1,:) + hp_peaks{trial_type_num}(1);xyz_psi2(2:3,:);ones(1,size(xyz_psi2,2))];
th_2d1 = A*th_4d1;
th_2d1 = unique(th_2d1(1:2,:)','rows');
th_4d2 = [xyz_psi2(1,:) + hp_peaks{trial_type_num}(2);xyz_psi2(2:3,:);ones(1,size(xyz_psi2,2))];
th_2d2 = A*th_4d2;
th_2d2 = unique(th_2d2(1:2,:)','rows');
scatter(intersect_2d(:,1),intersect_2d(:,2),'k.'), hold on, scatter(th_2d1(:,1), th_2d1(:,2),'r.'), scatter(th_2d2(:,1), th_2d2(:,2),'r.')
options.WindowStyle = 'normal';
questTitle='Final Confirmation'; start(timer('StartDelay',1,'TimerFcn',@(o,e)set(findall(0,'Tag',questTitle),'WindowStyle','normal')));
answer2 = questdlg('Is the result REALLY correct?', questTitle, 'Yes', 'No', 'Yes');
switch answer2
case 'Yes'
close all
peak_answer = 'No'; % get out of peak while
hp_decision = 'Yes';
done_flag = 0; % the whole precedure is finally done. get out of while(done_flag) loop.
case 'No'
answer3 = questdlg('Do you want to change the steps?', 'Touch hyperplane sweep steps', 'Yes', 'No', 'Yes');
switch answer3
case 'Yes'
step_boundary_cell = inputdlg({'First step','Last step'},'What are the sweep boundaries?',1,{'',''},options);
steps{trial_type_num} = str2double(step_boundary_cell{1}):str2double(step_boundary_cell{2});
peak_answer = 'No'; % get out of peak while
close all
case 'No'
peak_answer = questdlg('Do you want to change the peak points?', 'Touch hyperplane peaks', 'Yes', 'No', 'Yes');
if strcmp(peak_answer,'Yes')
close(h2);
else
psi1_return_answer = questdlg('Do you want to select polygon for psi1?', 'Return to psi1 polygon', 'Yes', 'No', 'Yes');
if strcmp(psi1_return_answer, 'Yes')
close all
psi1_polygon_answer = 'No';
peak_answer = 'No';
hp_decision = 'Yes';
else
error(['No optimal hyperplanes peaks found in ' sessionName ' of ' mouseName])
end
end
end
end
else % answer = 'No' to question 'Does the result look correct?'
answer3 = questdlg('Do you want to change the steps?', 'Touch hyperplane sweep steps', 'Yes', 'No', 'Yes');
switch answer3
case 'Yes'
step_boundary_cell = inputdlg({'First step','Last step'},'What are the sweep boundaries?',1,{'',''},options);
steps{trial_type_num} = str2double(step_boundary_cell{1}):str2double(step_boundary_cell{2});
peak_answer = 'No';
close all
case 'No'
psi1_return_answer = questdlg('Do you want to select polygon for psi1?', 'Return to psi1 polygon', 'Yes', 'No', 'Yes');
if strcmp(psi1_return_answer, 'Yes')
close all
psi1_polygon_answer = 'No';
peak_answer = 'No';
hp_decision = 'Yes';
else
error(['No optimal hyperplanes peaks found in ' sessionName ' of ' mouseName])
end
end
end
end
end
end
%% save parameters
steps_hp{trial_type_num} = steps;
num_points_in_hp{trial_type_num} = num_points;
touch_hp{trial_type_num} = xyz_psi2; % Don't round them! (at least at this saving process)
fprintf('%s %s trial type #%d processed\n',mouseName, sessionName,trial_type_num)
end
%%
save([whisker_d mouseName sessionName '_touch_hp.mat'],'touch_hp','num_points_in_hp','steps_hp','hp_peaks','trial_types', 'psi1', 'psi2')
fprintf('%s %s hp_peaks saved\n', mouseName, sessionName)
end
end