Grin bigdata tools

GRINtoolboxGUI.m

@@ -575,9 +575,9 @@
     'Position', [0.53 0.50 0.45 0.20], 'FontSize', 12, 'String', 'Plot Lick',...
     'Callback', @plotLick, 'Enable','off');
 
-tempfun1H = uicontrol('Parent', explorepanelH, 'Units', 'normalized', ...
-    'Position', [0.03 0.25 0.45 0.20], 'FontSize', 12, 'String', 'TBD',...
-    'Callback', @tempfun1, 'Enable','off');
+runPCAh = uicontrol('Parent', explorepanelH, 'Units', 'normalized', ...
+    'Position', [0.03 0.25 0.45 0.20], 'FontSize', 12, 'String', 'PCA',...
+    'Callback', @runPCA, 'Enable','off');
 
 tempfun2H = uicontrol('Parent', explorepanelH, 'Units', 'normalized', ...
     'Position', [0.53 0.25 0.45 0.20], 'FontSize', 12, 'String', 'TBD',...
@@ -2151,6 +2151,14 @@ function plotTileStats(hObject, eventdata)
     end
 
 
+    %keyboard
+    % REMOVE AXES CLUTTER
+    %axh{ii}
+
+
+
+
+
     legpos = {  [0.01,0.95,0.15,0.033], ...
                 [0.01,0.92,0.15,0.033], ...
                 [0.01,0.89,0.15,0.033], ...
@@ -2311,6 +2319,177 @@ function savetilesfun(hObject, eventdata)
 
 
 
+%----------------------------------------------------
+%        RUN PCA
+%----------------------------------------------------
+function runPCA(hObject, eventdata)
+% disableButtons; pause(.02);
+
+
+t1=[];
+t2=[];
+t3=[];
+t4=[];
+
+
+hb = round(blockSize / 2);
+
+PIM = IMG( hb:blockSize:end, hb:blockSize:end, : , : );
+
+size(PIM)
+
+
+CSp = squeeze(PIM(:,:,:,GRINstruct.tf(:,2)));
+
+CSm = squeeze(PIM(:,:,:,GRINstruct.tf(:,1)));
+
+
+size(CSp)
+size(CSm)
+
+
+CSp = CSp(3:7,3:7,:,:);
+CSm = CSm(3:7,3:7,:,:);
+
+szCSp = size(CSp)
+szCSm = size(CSm)
+
+
+CSP = squeeze(reshape(CSp,[],1,szCSp(3),szCSp(4)));
+CSM = squeeze(reshape(CSm,[],1,szCSm(3),szCSm(4)));
+
+size(CSP)
+size(CSM)
+
+CSplus  = CSP;
+CSminus = CSM;
+
+% save('GRINDATA.mat','CSplus','CSminus')
+
+keyboard
+
+size(CSP)
+size(CSM)
+
+
+figure
+imagesc(CSM(:,:,1))
+
+keyboard
+
+%%
+X = [];
+Y = [];
+
+Y = rand(10,100) .* .01;
+
+figure
+plot(Y')
+
+X = X - mean(X);
+
+
+covMX = 1/(n-1) * sum((X - mean(X)) * (X - mean(X))');
+
+
+
+
+
+
+%%
+
+GRINstruct.TreatmentGroups{1}
+size(CSm)
+
+GRINstruct.TreatmentGroups{2}
+size(CSp)
+
+
+
+
+
+% PCAdata = permute(CSM,[3 1 2]);
+PCAdata = CSM;
+
+size(PCAdata)
+
+
+MaxComponents = 10;
+opt = statset('pca');
+opt.MaxIter = 5000;
+
+[PCAScof,PCAval,PCAlat,PCAtsq,PCAexp,PCAmu] = pca( PCAdata ,...
+    'Options',opt,'NumComponents',MaxComponents);
+
+
+
+disp(PCAexp)
+
+
+figure
+plot(PCAScof(:,1:2))
+hold on
+
+figure
+plot(PCAval)
+
+x = repmat((1:size(PCAScof,1))',1,2);
+
+scatter( x(:)  ,  PCAScof(:) )
+
+
+
+clc
+sum(PCASexp(:))
+
+% format shortG
+% PCASval(1:5 , :)
+
+
+
+
+
+
+
+
+
+
+
+
+% [PCAScof,PCASval,PCAlat,PCAtsq,PCASexp,PCAmu] = pca(...
+%     PCAdata,'Options',opt,'Algorithm','svd','NumComponents',Ncomps,'Centered',false);
+
+% PCAStopcof = PCAScof(1,:);
+% PCAScentered = PCASval*PCAScof';
+% PCAStsredu = mahal(PCASval,PCASval);
+% PCAStsqdiscard = PCASts - PCAStsredu;
+
+
+% size(PIM)
+% size(IMG)
+% size(muIMGS)
+% GRINstruct.tf
+% XLSdata
+% blockSize = str2num(imgblockspopupH.String(imgblockspopupH.Value,:));
+% pxl = muIMGS(1:blockSize:end,1:blockSize:end,:,:);
+% pixels = squeeze(reshape(pxl,numel(pxl(:,:,1)),[],size(pxl,3),size(pxl,4)));
+% CSids = unique(GRINstruct.csus);
+% for ii = 1:size(pixels,1)
+%     tiledatX{ii} = 1:size(pixels,2);
+%     tiledatY{ii} = squeeze(pixels(ii,:,:));
+%     pha{ii} = squeeze(pixels(ii,:,:));
+% end
+% ii = 48;
+% PCAdata = squeeze(pixels(ii,:,:))';
+
+
+
+
+
+enableButtons        
+memocon('Run custom function completed!')
+end
+
 
 
 
@@ -4346,6 +4525,8 @@ function enableButtons()
     visualexplorerH.Enable = 'on';
     getAlignH.Enable = 'on';
     setAlignH.Enable = 'on';
+    runPCAh.Enable = 'on';
+
 
     if numel(size(IMG)) > 1 && numel(size(IMG)) < 4;
         openImageJH.Enable = 'on';
@@ -4376,6 +4557,7 @@ function disableButtons()
     visualexplorerH.Enable = 'off';
     getAlignH.Enable = 'off';
     setAlignH.Enable = 'off';
+    runPCAh.Enable = 'off';
 
 end