avoided saving tiff files, now a mat file is saved

CellsortApplyFilter.m

@@ -21,7 +21,7 @@
 %
 
 if (nargin<3)||isempty(flims)
-    nt = tiff_frames(fn);
+    nt = size(data_g, 3)%tiff_frames(fn);
     flims = [1,nt];
 else
     nt = diff(flims)+1;

CellsortChoosePCs.m

@@ -1,4 +1,4 @@
-function [PCuse] = CellsortChoosePCs(fn, mixedfilters)
+function [PCuse] = CellsortChoosePCs(fn, mixedfilters, data_g)
 % [PCuse] = CellsortChoosePCs(fn, mixedfilters)
 %
 % Allows the user to select which principal components will be kept
@@ -19,7 +19,7 @@
 
 fprintf('-------------- CellsortChoosePCs %s -------------- \n', date)
 
-[pixw,pixh] = size(imread(fn,1));
+[pixw,pixh] = size(data_g(:,:,1));
 
 npcs = 20; % Number of PCs to display concurrently
 currpcs = [1:npcs];

CellsortPCA.m

@@ -46,11 +46,9 @@
 
 %-----------------------
 % Check inputs
-if isempty(dir(fn))
-    error('Invalid input file name.')
-end
+numFrames = size(data_g,3);
 if (nargin<2)||(isempty(flims))
-    nt_full = tiff_frames(fn);
+    nt_full = numFrames;
     flims = [1,nt_full];
 end
 
@@ -103,7 +101,7 @@
 
 fncovmat = [outputdir, fname, '_cov_', num2str(flims(1)), ',', num2str(flims(2)), '_', date,'.mat'];
 
-[pixw,pixh] = size(imread(fn,1));
+[pixw,pixh] = size(data_g(:,:,1));
 npix = pixw*pixh;
 
 fprintf('   %d pixels x %d time frames;', npix, nt)
@@ -138,7 +136,7 @@
 end
 mixedfilters = reshape(mixedfilters, pixw,pixh,nPCs);
 
-firstframe_full = imread(fn,1);
+firstframe_full = data_g(:,:,1);%imread(fn,1);
 firstframe = firstframe_full;
 if dsamp_space>1
     firstframe = imresize(firstframe, size(mov(:,:,1)),'bilinear');
@@ -177,7 +175,7 @@
                 end
             end
         else
-            [pixw_dsamp,pixh_dsamp] = size(imresize( imread(fn,1), 1/dsamp_space, 'bilinear' ));
+            [pixw_dsamp,pixh_dsamp] = size(imresize( data_g(:,:,1), 1/dsamp_space, 'bilinear' ));
             npix = pixw_dsamp*pixh_dsamp;
             mov = zeros(pixw_dsamp, pixh_dsamp, nt);
             for jjind=1:length(useframes)
@@ -239,7 +237,7 @@
                 end
             end
         else
-            [pixw_dsamp,pixh_dsamp] = size(imresize( imread(fn,1), 1/dsamp_space, 'bilinear' ));
+            [pixw_dsamp,pixh_dsamp] = size(imresize( data_g(:,:,1), 1/dsamp_space, 'bilinear' ));
             npix = pixw_dsamp*pixh_dsamp;
             mov = zeros(pixw_dsamp, pixh_dsamp, nt);
             for jjind=1:length(useframes)
@@ -324,6 +322,6 @@
         %
         % Modified April 9, 2013 for compatibility with MATLAB 2012b
 
-        j = length(imfinfo(fn));
+        j = size(data_g,3);
     end
 end

CellsortPlotPCspectrum.m

@@ -1,4 +1,4 @@
-function CellsortPlotPCspectrum(fn, CovEvals, PCuse)
+function CellsortPlotPCspectrum(fn, CovEvals, PCuse, data_g)
 % CellsortPlotPCspectrum(fn, CovEvals, PCuse)
 %
 % Plot the principal component (PC) spectrum and compare with the
@@ -18,9 +18,9 @@ function CellsortPlotPCspectrum(fn, CovEvals, PCuse)
     PCuse = [];
 end
 
-[pixw,pixh] = size(imread(fn,1));
+[pixw,pixh] = size(data_g(:,:,1));
 npix = pixw*pixh;
-nt = tiff_frames(fn);
+nt = size(data_g,3);
 
 % Random matrix prediction (Sengupta & Mitra)
 p1 = npix; % Number of pixels

main.m

@@ -16,16 +16,20 @@
 binningFactor = [1 1 2]; %x, y, t
 [data_g, data_r] = CellSortTemporalBinning(data_g, data_r, binningFactor);
 
-fn_green = 'green.tiff';
-fn_red = 'red.tiff';
-CellSortExportTifStack(data_g, fn_green);
-CellSortExportTifStack(data_r, fn_red);
+fn = 'processedData.mat';
+save(fn, 'data_g', 'data_r', '-v7.3');
+% fn_green = 'green.tiff';
+% fn_red = 'red.tiff';
+% CellSortExportTifStack(data_g, fn_green);
+% CellSortExportTifStack(data_r, fn_red);
 %% load files
 %if you haven't used the shiftCorrection you have to load the already processed files
-fn_green = 'green.tiff';
-fn_red = 'red.tiff';
-data_g = readTiff(fn_green);
-data_r = readTiff(fn_red);
+fn_green = 'processedData.mat';
+load(fn);
+% fn_green = 'green.tiff';
+% fn_red = 'red.tiff';
+% data_g = readTiff(fn_green);
+% data_r = readTiff(fn_red);
 %% 1. PCA
 %calculate PCAs
 nPCs = 100;
@@ -37,11 +41,11 @@
 %% 2a. Choose PCs
 %choose PCAs, type f/b in command line to go back or forward. type two number
 %to select the range "1 ENTER 25 ENTER" would select the PCAs from 1 to 25
-[PCuse] = CellsortChoosePCs(fn_green, mixedfilters);
+[PCuse] = CellsortChoosePCs(fn_green, mixedfilters, data_g);
 
 %% 2b. Plot PC spectrum
 %optionally, you can display the PC spectrum..
-CellsortPlotPCspectrum(fn_green, CovEvals, PCuse)
+CellsortPlotPCspectrum(fn_green, CovEvals, PCuse, data_g)
 
 %% 3a. ICA
 %calculate ICAs, set mu to a value between 0 and 1, where 1 means pure
@@ -60,7 +64,7 @@
 dt = 0.1;
 
 figure(2)
-CellsortICAplot('series', ica_filters, ica_sig, movm, tlims, dt, [], [], [1:size(ica_segments,1)]);
+CellsortICAplot('series', ica_filters, ica_sig, movm, tlims, dt, [], [], [1:size(ica_sig,1)]);
 
 %% 4a. Segment contiguous regions within ICs
 %search for indepent segments, you have to adjust these values well: