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disprecdepth.m
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%% disprecdepth: create display of recordings' depth
%% 5/16/2011 - VP
clear all
%% First getting list of recordings, location on grid, and depth
listprimdir=dir('E:\data\Recordings\Rigel\*A');
listprimdir=listprimdir(12:14);
numfiles1 = length(listprimdir);
listnames=cell(1,numfiles1);
listloc=cell(1,numfiles1);
listdepth=cell(1,numfiles1);
for k = 1:numfiles1
listnames{k}=listprimdir(k).name;
filename=listnames{k};
listloc{k}=filename(4:7);
listdepth{k}=filename(9:13);
rawdepth=listdepth{k};
listdepth{k}=rawdepth(not(isletter(listdepth{k})));
end
convlistloc=listloc;
convlistloc = strrep(convlistloc, 'A', '+');
convlistloc = strrep(convlistloc, 'P', '-');
convlistloc = strrep(convlistloc, 'L', '-');
convlistloc = strrep(convlistloc, 'M', '+');
%% Now, assuming a 15x15 grid (actually a disk), build matrix of recordings locations in depth
recpos=zeros(3,numfiles1);
for k = 1:numfiles1
thisloc=char(convlistloc(k));
recpos(1,k)=str2num(thisloc(1:2))+8; %x position, adding 8 to translate grid's center
recpos(2,k)=str2num(thisloc(3:4))+8; %y position, adding 8 to translate grid's center
recpos(3,k)=str2num(listdepth{k});
end
%% other data
% Create outer disk
center=[8 8 0];
normal=[0 0 0];
radius=7.5;
theta=0:0.01:2*pi;
v=null(normal);
points=repmat(center',1,size(theta,2))+radius*(v(:,1)*cos(theta)+v(:,2)*sin(theta));
% create outer cylinder
[xcyl,ycyl,zcyl] = cylinder(7.5,100);
zcyl(1,:)=ones(1,101);
zcyl(2,:)=ones(1,101).*25000;
%% Create figure
recdepthdisp = figure('Name','Depth and location of recorded neurons',...
'Color',[1 1 1]);
% Create axes
%subplot(1,2,1)
% Create axes
axes1=axes('ZDir','reverse',...
'YTickLabel',{'-6','-4','-2','0','2','4','6'},...
'XTickLabel',{'-6','-4','-2','0','2','4','6'},...
'PlotBoxAspectRatio',[1 1 1.16666666666667],...
'DataAspectRatio',[1 1 2142.85714285714],...
'Color',[0.941176474094391 0.941176474094391 0.941176474094391],...
'CameraViewAngle',5.60116118793687);
xlim(axes1,[0 16]);
ylim(axes1,[0 16]);
view(axes1,[0 90]);
box(axes1,'on');
grid(axes1,'on');
hold(axes1,'all');
% Create scatter3
scatter3(recpos(1,:),recpos(2,:),recpos(3,:),'MarkerFaceColor',[0 0 1],'MarkerEdgeColor',[0 0 1],...
'Marker','.');
hold on
% plot circle
plot3(points(1,:),points(2,:),points(3,:),'LineWidth',2,...
'Color',[0.321568638086319 0.18823529779911 0.18823529779911]);
% plot cylinder
surf(xcyl+8,ycyl+8,zcyl,'Parent',axes1,'LineStyle','none',...
'FaceColor',[0.952941179275513 0.87058824300766 0.733333349227905],...
'FaceAlpha',0.3);
hold off
% Create xlabel
xlabel('mediolateral position','VerticalAlignment','cap',...
'HorizontalAlignment','center');
% Create ylabel
ylabel('anteroposterior position','VerticalAlignment','bottom',...
'Rotation',90,...
'HorizontalAlignment','center');
% Create zlabel
zlabel('Depth','Visible','off','VerticalAlignment','top');
% Create title
title('top view');
%
% axes2=subplot('Position',[0.75 0.25 0.25 0.25])
% axes('ZDir','reverse',...
% 'YTickLabel',{'-6','-4','-2','0','2','4','6'},...
% 'XTickLabel',{'-6','-4','-2','0','2','4','6'},...
% 'PlotBoxAspectRatio',[1 1 0.833333333333333],...
% 'DataAspectRatio',[1 1 2142.85714285714],...
% 'Color',[0.941176474094391 0.941176474094391 0.941176474094391],...
% 'CameraViewAngle',5.60116118793687);
% xlim(axes2,[0 16]);
% ylim(axes2,[0 16]);
% view(axes2,[-34.5 -10.4110419545883]);
% box(axes2,'on');
% grid(axes2,'on');
% hold(axes2,'all');
%
% % Create scatter3
% scatter3(recpos(1,:),recpos(2,:),recpos(3,:),'MarkerFaceColor',[0 0 1],'MarkerEdgeColor',[0 0 1],...
% 'Marker','.');
%
% hold on
% % plot circle
% plot3(points(1,:),points(2,:),points(3,:),'LineWidth',2,...
% 'Color',[0.321568638086319 0.18823529779911 0.18823529779911]);
% % plot cylinder
% surf(xcyl+8,ycyl+8,zcyl,'Parent',axes2,'LineStyle','none',...
% 'FaceColor',[0.952941179275513 0.87058824300766 0.733333349227905],...
% 'FaceAlpha',0.3);
% hold off
% % Create xlabel
% xlabel('mediolateral position','HorizontalAlignment','right');
%
% % Create ylabel
% ylabel('anteroposterior position','HorizontalAlignment','left');
%
% % Create zlabel
% zlabel('Depth');
%
% % Create title
% % title('top view');
%% generated code
%
% function createfigure(X1, Y1, Z1, S1, C1, X2, Y2, Z2, xdata1, ydata1, zdata1)
% %CREATEFIGURE(X1,Y1,Z1,S1,C1,X2,Y2,Z2,XDATA1,YDATA1,ZDATA1)
% % X1: scatter3 x
% % Y1: scatter3 y
% % Z1: scatter3 z
% % S1: scatter3 s
% % C1: scatter3 c
% % X2: vector of x data
% % Y2: vector of y data
% % Z2: vector of z data
% % XDATA1: surface xdata
% % YDATA1: surface ydata
% % ZDATA1: surface zdata
%
% % Auto-generated by MATLAB on 16-May-2011 21:15:42
%
% % Create figure
% figure1 = figure('Renderer','OpenGL',...
% 'Name','Depth and location of recorded neurons',...
% 'Color',[1 1 1]);
%
% % Create subplot
% subplot1 = subplot(2,2,1,'Parent',figure1,'ZDir','reverse',...
% 'YTickLabel',{'','-7','-6','-5','-4','-3','-2','-1','0','1','2','3','4','5','6','7',''},...
% 'YTick',[0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16],...
% 'YMinorTick','on',...
% 'XTickLabel',{'','-7','-6','-5','-4','-3','-2','-1','0','1','2','3','4','5','6','7',''},...
% 'XTick',[0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16],...
% 'PlotBoxAspectRatio',[1 1 1.16666666666667],...
% 'DataAspectRatio',[1 1 2142.85714285714],...
% 'Color',[0.941176474094391 0.941176474094391 0.941176474094391],...
% 'CameraViewAngle',5.60116118793687);
% % Uncomment the following line to preserve the X-limits of the axes
% % xlim(subplot1,[0 16]);
% % Uncomment the following line to preserve the Y-limits of the axes
% % ylim(subplot1,[0 16]);
% box(subplot1,'on');
% grid(subplot1,'on');
% hold(subplot1,'all');
%
% % Create scatter3
% scatter3(X1,Y1,Z1,S1,C1,...
% 'MarkerFaceColor',[0.321568638086319 0.18823529779911 0.18823529779911],...
% 'MarkerEdgeColor',[0.34901961684227 0.200000002980232 0.329411774873734],...
% 'Parent',subplot1);
%
% % Create plot3
% plot3(X2,Y2,Z2,'Parent',subplot1,'LineWidth',2,...
% 'Color',[0.321568638086319 0.18823529779911 0.18823529779911]);
%
% % Create surf
% surf(xdata1,ydata1,zdata1,'Parent',subplot1,'LineStyle','none',...
% 'FaceColor',[0.952941179275513 0.87058824300766 0.733333349227905],...
% 'FaceAlpha',0.3);
%
% % Create xlabel
% xlabel('lateromedial','FontName','Tahoma');
%
% % Create ylabel
% ylabel('anteroposterior','FontName','Tahoma');
%
% % Create zlabel
% zlabel('Depth','Visible','off','VerticalAlignment','top');
%
% % Create title
% title('top view','FontWeight','demi','FontName','Tahoma');
%
% % Create axes
% axes1 = axes('Parent',figure1,'ZDir','reverse',...
% 'YTickLabel',{'','-7','-6','-5','-4','-3','-2','-1','0','1','2','3','4','5','6','7',''},...
% 'YTick',[0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16],...
% 'YMinorTick','on',...
% 'XTickLabel',{'','-7','-6','-5','-4','-3','-2','-1','0','1','2','3','4','5','6','7',''},...
% 'XTick',[0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16],...
% 'Position',[0.546595380667234 0.608327005220698 0.334659090909091 0.341162790697675],...
% 'PlotBoxAspectRatio',[1 1 0.729166666666668],...
% 'DataAspectRatio',[1 1 2142.85714285714],...
% 'Color',[0.941176474094391 0.941176474094391 0.941176474094391],...
% 'CameraViewAngle',5.60116118793687);
% % Uncomment the following line to preserve the X-limits of the axes
% % xlim(axes1,[0 16]);
% % Uncomment the following line to preserve the Y-limits of the axes
% % ylim(axes1,[0 16]);
% view(axes1,[-90 0]);
% box(axes1,'on');
% grid(axes1,'on');
% hold(axes1,'all');
%
% % Create scatter3
% scatter3(X1,Y1,Z1,S1,C1,...
% 'MarkerFaceColor',[0.321568638086319 0.18823529779911 0.18823529779911],...
% 'MarkerEdgeColor',[0.34901961684227 0.200000002980232 0.329411774873734],...
% 'Parent',axes1);
%
% % Create plot3
% plot3(X2,Y2,Z2,'Parent',axes1,'LineWidth',2,...
% 'Color',[0.321568638086319 0.18823529779911 0.18823529779911]);
%
% % Create surf
% surf(xdata1,ydata1,zdata1,'Parent',axes1,'LineStyle','none',...
% 'FaceColor',[0.952941179275513 0.87058824300766 0.733333349227905],...
% 'FaceAlpha',0.3);
%
% % Create xlabel
% xlabel('lateromedial','Visible','off','HorizontalAlignment','center',...
% 'FontName','Tahoma');
%
% % Create ylabel
% ylabel('anteroposterior','VerticalAlignment','cap',...
% 'HorizontalAlignment','center',...
% 'FontName','Tahoma');
%
% % Create zlabel
% zlabel('Depth (mm)','VerticalAlignment','top');
%
% % Create title
% title('anteroposterior profile','FontWeight','demi','FontName','Tahoma');
%
% % Create axes
% axes2 = axes('Parent',figure1,'ZDir','reverse',...
% 'YTickLabel',{'','-7','-6','-5','-4','-3','-2','-1','0','1','2','3','4','5','6','7',''},...
% 'YTick',[0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16],...
% 'YMinorTick','on',...
% 'XTickLabel',{'','-7','-6','-5','-4','-3','-2','-1','0','1','2','3','4','5','6','7',''},...
% 'XTick',[0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16],...
% 'Position',[0.129144568006843 0.0613882297104895 0.334659090909091 0.341162790697675],...
% 'PlotBoxAspectRatio',[1 1 0.729166666666668],...
% 'DataAspectRatio',[1 1 2142.85714285714],...
% 'Color',[0.941176474094391 0.941176474094391 0.941176474094391],...
% 'CameraViewAngle',5.60116118793687);
% % Uncomment the following line to preserve the X-limits of the axes
% % xlim(axes2,[0 16]);
% % Uncomment the following line to preserve the Y-limits of the axes
% % ylim(axes2,[0 16]);
% view(axes2,[0 0]);
% box(axes2,'on');
% grid(axes2,'on');
% hold(axes2,'all');
%
% % Create scatter3
% scatter3(X1,Y1,Z1,S1,C1,...
% 'MarkerFaceColor',[0.321568638086319 0.18823529779911 0.18823529779911],...
% 'MarkerEdgeColor',[0.34901961684227 0.200000002980232 0.329411774873734],...
% 'Parent',axes2);
%
% % Create plot3
% plot3(X2,Y2,Z2,'Parent',axes2,'LineWidth',2,...
% 'Color',[0.321568638086319 0.18823529779911 0.18823529779911]);
%
% % Create surf
% surf(xdata1,ydata1,zdata1,'Parent',axes2,'LineStyle','none',...
% 'FaceColor',[0.952941179275513 0.87058824300766 0.733333349227905],...
% 'FaceAlpha',0.3);
%
% % Create xlabel
% xlabel('lateromedial','VerticalAlignment','cap',...
% 'HorizontalAlignment','center',...
% 'FontName','Tahoma');
%
% % Create ylabel
% ylabel('anteroposterior','Visible','off','HorizontalAlignment','center',...
% 'FontName','Tahoma');
%
% % Create zlabel
% zlabel('Depth (mm)','VerticalAlignment','top');
%
% % Create title
% title('lateromedial profile','FontWeight','demi','FontName','Tahoma');
%
% % Create axes
% axes3 = axes('Parent',figure1,'ZDir','reverse',...
% 'YTickLabel',{'','-7','-6','-5','-4','-3','-2','-1','0','1','2','3','4','5','6','7',''},...
% 'YTick',[0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16],...
% 'YMinorTick','on',...
% 'XTickLabel',{'','-7','-6','-5','-4','-3','-2','-1','0','1','2','3','4','5','6','7',''},...
% 'XTick',[0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16],...
% 'Position',[0.584260051325919 0.146938775510204 0.285714285714286 0.220408163265306],...
% 'PlotBoxAspectRatio',[1 1 0.875000000000001],...
% 'DataAspectRatio',[1 1 2142.85714285714],...
% 'Color',[0.941176474094391 0.941176474094391 0.941176474094391],...
% 'CameraViewAngle',5.60116118793687);
% % Uncomment the following line to preserve the X-limits of the axes
% % xlim(axes3,[0 16]);
% % Uncomment the following line to preserve the Y-limits of the axes
% % ylim(axes3,[0 16]);
% view(axes3,[-20 36]);
% box(axes3,'on');
% grid(axes3,'on');
% hold(axes3,'all');
%
% % Create scatter3
% scatter3(X1,Y1,Z1,S1,C1,...
% 'MarkerFaceColor',[0.321568638086319 0.18823529779911 0.18823529779911],...
% 'MarkerEdgeColor',[0.34901961684227 0.200000002980232 0.329411774873734],...
% 'Parent',axes3);
%
% % Create plot3
% plot3(X2,Y2,Z2,'Parent',axes3,'LineWidth',2,...
% 'Color',[0.321568638086319 0.18823529779911 0.18823529779911]);
%
% % Create surf
% surf(xdata1,ydata1,zdata1,'Parent',axes3,'LineStyle','none',...
% 'FaceColor',[0.952941179275513 0.87058824300766 0.733333349227905],...
% 'FaceAlpha',0.3);
%
% % Create zlabel
% zlabel('Depth (mm)','VerticalAlignment','top');
% end