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prebuild_JK.m
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%% basic information
% mice = {'JK025','JK027','JK030','JK036','JK037','JK038','JK039','JK041'};
% mice = {'JK052','JK053','JK054','JK056'};
mice = {'JK053'};
videoloc = 'L:\tracked\';
if strcmp(videoloc(end),filesep)
whisker_d = videoloc;
else
whisker_d = ([videoloc filesep]);
end
behavior_base_dir = 'Y:\Whiskernas\JK\SoloData\';
ppm = 17.81;
% 'pxPerMm': 17.81002608 for telecentric lens
% comment out when doing for all of the sessions in the mouse directory
maskmm = 1; % mm from the face to draw the mask
facePosition = 'bottom';
rInMm = 2; % mm from the mask along the whisker to calculate delta kappa
follicleSkip = 'noskip';
remeasureSkip = 'noskip';
%%
%%
%% re-do these
% sessions = {[14,15]}; % for JK039. Did not check JK041 S06~S31
%%
%%
%%
% sessions = {[4,19,22],[3,16,17],[3,21,22],[1,17,18,91],[7],[2],[1,22:25],[3]};
% sessions = {[4,19,22],[3,16,17],[3,21,22],[1,17,18,91],[7],[2],[1,22:25],[3]};
sessions = {[4]};
sessions_pre = {[],[],[],[],[],[],[],[]};
sessions_piezo = {[],[],[],[],[],[],[],[]};
sessions_spont = {[1,2],[],[],[],[],[],[],[]};
all_session = 0; % 1 if using all sessions, 0 if using selected sessions
DoFollicle = 0;
DoRemeasure = 0;
DoWTandWST = 1;
DoWL = 0;
%% Define follicle points and masks
% saves follicle_n_mask.mat file consists of variables 'maskx','masky','width', 'height', and 'follicle_first'
if DoFollicle
if all_session == 1
%% use this code when doing for all of the sessions in the mouse directory
for i = 1 : size(mice,2)
cd(whisker_d)
sn = dir([mice{i},'S*']);
sn_pre = dir([mice{i},'pre*']);
sn_piezo = dir([mice{i},'piezo*']);
sn_spont = dir([mice{i},'spont*']);
if ~isempty(sn)
for j = 1 : length(sn)
if sn(j).isdir
[mouseName, sessionName] = strtok(sn(j).name,'S');
if ~isempty(sessionName)
follicle_n_mask(mouseName,sessionName,videoloc, ppm, maskmm, facePosition, follicleSkip)
end
end
close all
end
end
if ~isempty(sn_pre)
for j = 1 : length(sn_pre)
if sn_pre(j).isdir
[mouseName, sessionName] = strtok(sn_pre(j).name,'pre');
follicle_n_mask(mouseName,sessionName,videoloc, ppm, maskmm, facePosition, follicleSkip)
end
close all
end
end
if ~isempty(sn_piezo)
for j = 1 : length(sn_piezo)
if sn_piezo(j).isdir
[mouseName, sessionName] = strtok(sn_piezo(j).name,'piezo');
follicle_n_mask(mouseName,sessionName,videoloc, ppm, maskmm, facePosition, follicleSkip)
end
close all
end
end
if ~isempty(sn_spont)
for j = 1 : length(sn_spont)
if sn_spont(j).isdir
[mouseName, sessionName] = strtok(sn_spont(j).name,'spont');
follicle_n_mask(mouseName,sessionName,videoloc, ppm, maskmm, facePosition, follicleSkip)
end
close all
end
end
end
else
%% use this code when doing for selected sessions in each mouse directory
for i = 1 : size(mice,2)
cd(whisker_d)
if ~isempty(sessions{i})
for j = 1 : length(sessions{i})
mouseName = mice{i};
sessionName = sprintf('S%02d',sessions{i}(j));
follicle_n_mask(mouseName,sessionName,videoloc, ppm, maskmm, facePosition, follicleSkip)
close all
end
end
if ~isempty(sessions_pre{i})
for j = 1 : length(sessions_pre{i})
mouseName = mice{i};
sessionName = sprintf('pre%d',sessions_pre{i}(j));
follicle_n_mask(mouseName,sessionName,videoloc, ppm, maskmm, facePosition, follicleSkip)
close all
end
end
if ~isempty(sessions_piezo{i})
for j = 1 : length(sessions_piezo{i})
mouseName = mice{i};
sessionName = sprintf('piezo%d',sessions_piezo{i}(j));
follicle_n_mask(mouseName,sessionName,videoloc, ppm, maskmm, facePosition, follicleSkip)
close all
end
end
if ~isempty(sessions_spont{i})
for j = 1 : length(sessions_spont{i})
mouseName = mice{i};
sessionName = sprintf('spont%d',sessions_spont{i}(j));
follicle_n_mask(mouseName,sessionName,videoloc, ppm, maskmm, facePosition, follicleSkip)
close all
end
end
end
end
end
%%
%%
%%
%%
%% TODO: MAKE MASK CHECKING PROCEDURE
%%
%%
%%
%%
%% Re-measure .measurements file before building whisker arrays
% saves _post.mat file consists of variables 'maskx','masky', 'includef', 'errorlist', 'width', and 'height'
% postmeasurements uses jk_measurements_dir()
if DoRemeasure
if all_session == 1
%% use this code when doing for all of the sessions in the mouse directory
for i = 1 : size(mice,2)
cd(whisker_d)
sn = dir([mice{i},'S*']);
sn_pre = dir([mice{i}, 'pre*']);
sn_piezo = dir([mice{i},'piezo*']);
sn_spont = dir([mice{i},'spont*']);
if ~isempty(sn)
for j = 1 : length(sn)
if sn(j).isdir
[mouseName, sessionName] = strtok(sn(j).name,'S');
if ~isempty(sessionName)
postmeasurements(mouseName,sessionName,videoloc,ppm,remeasureSkip)
end
end
end
end
if ~isempty(sn_pre)
for j = 1 : length(sn_pre)
if sn_pre(j).isdir
[mouseName, sessionName] = strtok(sn_pre(j).name,'pre');
postmeasurements(mouseName,sessionName,videoloc,ppm,remeasureSkip)
end
end
end
if ~isempty(sn_piezo)
for j = 1 : length(sn_piezo)
if sn_piezo(j).isdir
[mouseName, sessionName] = strtok(sn_piezo(j).name,'pizeo');
postmeasurements(mouseName,sessionName,videoloc,ppm,remeasureSkip)
end
end
end
if ~isempty(sn_spont)
for j = 1 : length(sn_spont)
if sn_spont(j).isdir
[mouseName, sessionName] = strtok(sn_spont(j).name,'spont');
postmeasurements(mouseName,sessionName,videoloc,ppm,remeasureSkip)
end
end
end
end
else
%% use this code when doing for selected sessions in each mouse directory
for i = 1 : size(mice,2)
cd(whisker_d)
if ~isempty(sessions{i})
for j = 1 : length(sessions{i})
mouseName = mice{i};
sessionName = sprintf('S%02d',sessions{i}(j));
postmeasurements(mouseName,sessionName,videoloc,ppm,remeasureSkip)
end
end
if ~isempty(sessions_pre{i})
for j = 1 : length(sessions_pre{i})
mouseName = mice{i};
sessionName = sprintf('pre%d',sessions_pre{i}(j));
postmeasurements(mouseName,sessionName,videoloc,ppm,remeasureSkip)
end
end
if ~isempty(sessions_piezo{i})
for j = 1 : length(sessions_piezo{i})
mouseName = mice{i};
sessionName = sprintf('piezo%d',sessions_piezo{i}(j));
postmeasurements(mouseName,sessionName,videoloc,ppm,remeasureSkip)
end
end
if ~isempty(sessions_spont{i})
for j = 1 : length(sessions_spont{i})
mouseName = mice{i};
sessionName = sprintf('spont%d',sessions_spont{i}(j));
postmeasurements(mouseName,sessionName,videoloc,ppm,remeasureSkip)
end
end
end
end
end
%% build WT_2pad, WST_2pad, and WL_2pad
% build WL_2pad after touch plane
if DoWTandWST
cd(whisker_d)
if all_session == 1
for mi = 1 : size(mice,2) % mouse index
cd(whisker_d)
sn = dir([whisker_d, mice{mi},'S*']);
for si = 1 : length(sn)
if sn(si).isdir
[mouseName, sessionName] = strtok(sn(si).name,'S');
behavior_d = [behavior_base_dir mouseName '\'];
if ~isempty(sessionName)
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_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
else
load([behavior_d 'behavior_', mouseName,'.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};
buildWTandWST(mouseName, sessionName, whisker_d, b_session, ppm)
end
end
end
cd(whisker_d)
sn_pre = dir([mice{mi},'pre*']);
for si = 1 : length(sn_pre)
cd(whisker_d)
if sn_pre(si).isdir
[mouseName, sessionName] = strtok(sn_pre(si).name,'pre');
behavior_d = [behavior_base_dir mouseName '\'];
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_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
else
load([behavior_d 'behavior_', mouseName,'.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};
buildWTandWST(mouseName, sessionName, whisker_d, b_session, ppm)
end
end
cd(whisker_d)
sn_piezo = dir([mice{mi},'piezo*']);
for si = 1 : length(sn_piezo)
cd(whisker_d)
if sn_piezo(si).isdir
[mouseName, sessionName] = strtok(sn_piezo(si).name,'piezo');
behavior_d = [behavior_base_dir mouseName '\'];
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_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
else
load([behavior_d 'behavior_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
b_ind = find(cellfun(@(x) strcmp(x.sessionName,sessionName), b));
if ~isempty(b_ind)
b_session = b{b_ind};
buildWTandWST(mouseName, sessionName, whisker_d, b_session, ppm)
else
buildWTandWST(mouseName, sessionName, whisker_d, [], ppm)
end
end
end
cd(whisker_d)
sn_spont = dir([mice{mi},'spont*']);
for si = 1 : length(sn_spont)
cd(whisker_d)
if sn_spont(si).isdir
[mouseName, sessionName] = strtok(sn_spont(si).name,'spont');
buildWTandWST(mouseName, sessionName, whisker_d, [], ppm)
end
end
end
else
for mi = 1 : size(mice,2) % mouse index
mouseName = mice{mi};
if ~isempty(sessions{mi})
for j = 1 : length(sessions{mi})
cd(whisker_d)
sessionName = sprintf('S%02d',sessions{mi}(j));
if exist([mouseName, sessionName],'dir')
behavior_d = [behavior_base_dir mouseName '\'];
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_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
else
load([behavior_d 'behavior_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
if strcmp(sessionName, 'S91')
b_ind = find(cellfun(@(x) strcmp(x.sessionName,'S01'), b));
else
b_ind = find(cellfun(@(x) strcmp(x.sessionName,sessionName), b));
end
b_session = b{b_ind};
buildWTandWST(mouseName, sessionName, whisker_d, b_session, ppm)
end
end
end
if ~isempty(sessions_pre{mi})
for j = 1 : length(sessions_pre{mi})
sessionName = sprintf('pre%d',sessions_pre{mi}(j));
cd(whisker_d)
if exist([mouseName, sessionName],'dir')
behavior_d = [behavior_base_dir mouseName '\'];
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_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
else
load([behavior_d 'behavior_', mouseName,'.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};
buildWTandWST(mouseName, sessionName, whisker_d, b_session, ppm)
end
end
end
if ~isempty(sessions_piezo{mi})
for j = 1 : length(sessions_piezo{mi})
sessionName = sprintf('piezo%d',sessions_piezo{mi}(j));
cd(whisker_d)
if exist([mouseName, sessionName],'dir')
behavior_d = [behavior_base_dir mouseName '\'];
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_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
else
load([behavior_d 'behavior_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
if strcmp(sessionName, 'S91')
b_ind = find(cellfun(@(x) strcmp(x.sessionName,'S01'), b));
else
b_ind = find(cellfun(@(x) strcmp(x.sessionName,sessionName), b));
end
b_session = b{b_ind};
buildWTandWST(mouseName, sessionName, whisker_d, b_session, ppm)
end
end
end
if ~isempty(sessions_spont{mi})
for j = 1 : length(sessions_spont{mi})
sessionName = sprintf('spont%d',sessions_spont{mi}(j));
cd(whisker_d)
if exist([mouseName, sessionName],'dir')
buildWTandWST(mouseName, sessionName, whisker_d, [], ppm)
end
end
end
end
end
end
%% Perfrom touch_hyperplane
% it includes frame-by-frame estimation of corresponding motor position, based on _WST files
% touch_hyperplane
%% Build WL (Finally)
% it includes touch frame calculation
if DoWL
cd(whisker_d)
if all_session == 1
for mi = 1 : size(mice,2) % mouse index
cd(whisker_d)
sn = dir([whisker_d, mice{mi},'S*']);
for si = 1 : length(sn)
if sn(si).isdir
[mouseName, sessionName] = strtok(sn(si).name,'S');
behavior_d = [behavior_base_dir mouseName '\'];
if ~isempty(sessionName)
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_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
else
load([behavior_d 'behavior_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
if strcmp(sessionName, 'S91')
b_ind = find(cellfun(@(x) strcmp(x.sessionName,'S01'), b));
else
b_ind = find(cellfun(@(x) strcmp(x.sessionName,sessionName), b));
end
b_session = b{b_ind};
wd = [whisker_d, mouseName, sessionName];
buildWL(wd, b_session, rInMm)
end
end
end
cd(whisker_d)
sn_pre = dir([mice{mi},'pre*']);
for si = 1 : length(sn_pre)
cd(whisker_d)
if sn_pre(si).isdir
[mouseName, sessionName] = strtok(sn_pre(si).name,'pre');
behavior_d = [behavior_base_dir mouseName '\'];
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_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
else
load([behavior_d 'behavior_', mouseName,'.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};
wd = [whisker_d, mouseName, sessionName];
buildWL(wd, b_session, rInMm)
end
end
cd(whisker_d)
sn_piezo = dir([mice{mi},'piezo*']);
for si = 1 : length(sn_piezo)
cd(whisker_d)
if sn_piezo(si).isdir
[mouseName, sessionName] = strtok(sn_piezo(si).name,'piezo');
wd = [whisker_d, mouseName, sessionName];
buildWL(wd, [], rInMm)
end
end
cd(whisker_d)
sn_spont= dir([mice{mi},'spont*']);
for si = 1 : length(sn_spont)
cd(whisker_d)
if sn_spont(si).isdir
[mouseName, sessionName] = strtok(sn_spont(si).name,'piezo');
wd = [whisker_d, mouseName, sessionName];
buildWL(wd, [], rInMm)
end
end
end
else
for mi = 1 : size(mice,2) % mouse index
mouseName = mice{mi};
if ~isempty(sessions{mi})
for j = 1 : length(sessions{mi})
cd(whisker_d)
sessionName = sprintf('S%02d',sessions{mi}(j));
if exist([mouseName, sessionName],'dir')
behavior_d = [behavior_base_dir mouseName '\'];
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_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
else
load([behavior_d 'behavior_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
if strcmp(sessionName, 'S91')
b_ind = find(cellfun(@(x) strcmp(x.sessionName,'S01'), b));
else
b_ind = find(cellfun(@(x) strcmp(x.sessionName,sessionName), b));
end
b_session = b{b_ind};
wd = [whisker_d, mouseName, sessionName];
buildWL(wd, b_session, rInMm)
end
end
end
if ~isempty(sessions_pre{mi})
for j = 1 : length(sessions_pre{mi})
sessionName = sprintf('pre%d',sessions_pre{mi}(j));
cd(whisker_d)
if exist([mouseName, sessionName],'dir')
behavior_d = [behavior_base_dir mouseName '\'];
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_', mouseName,'.mat']) % loading b of the mouse (all the sessions)
end
else
load([behavior_d 'behavior_', mouseName,'.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};
wd = [whisker_d, mouseName, sessionName];
buildWL(wd, b_session, rInMm)
end
end
end
if ~isempty(sessions_piezo{mi})
for j = 1 : length(sessions_piezo{mi})
sessionName = sprintf('piezo%d',sessions_piezo{mi}(j));
cd(whisker_d)
if exist([mouseName, sessionName],'dir')
wd = [whisker_d, mouseName, sessionName];
buildWL(wd, [], rInMm)
end
end
end
if ~isempty(sessions_spont{mi})
for j = 1 : length(sessions_spont{mi})
sessionName = sprintf('spont%d',sessions_spont{mi}(j));
cd(whisker_d)
if exist([mouseName, sessionName],'dir')
wd = [whisker_d, mouseName, sessionName];
buildWL(wd, [], rInMm)
end
end
end
end
end
end