plotIndividualsegment.m

clear all;

filename = '9cells_3ch_0bn_0pn_1e-06pd_1.0ef';
load(['simData/sim_' filename '_denoised.mat'])
load(['simData/sim_' filename '_6conn_denoised_ws0.01_isplit0.5_20_augmented0.1_merge2_sAff10.mat'])
load(['simData/sim_' filename '_index.mat'])
bbVol = overallRawVolume;
bbVol(bbVol<0)=0;
for kk = 1:size(bbVol, 4); 
    rawStack = bbVol(:,:,:,kk); 
    rawStack = rawStack - min(rawStack(:)); 
    rawStack = rawStack / max(rawStack(:)); 
    bbVol(:,:,:,kk) = rawStack; 
end; 
clear rawStack;
clusterCount                                 = max(index);
segmentation = zeros(stackSize); 
for kka=1:clusterCount; 
    thisCluster = find(index==kka); 
    for kkb=1:numel(thisCluster); 
        segmentation(svCells{thisCluster(kkb)}) = kka; 
    end; 
end;
voxelCount                                   = numel(segmentation);
xTileCount                                   = round(sqrt((clusterCount+1)/3) * 1) +2;
yTileCount                                   = ceil((clusterCount+1)/xTileCount);
compx                                        = size(segmentation,1)+size(segmentation,3);
compy                                        = size(segmentation,2)+size(segmentation,3);
bigIm                                        = ones( (size(segmentation,1)+1)*xTileCount-1, (size(segmentation,2)+1)*yTileCount-1, size(bbVol,4));
xTile                                        = 1;
yTile                                        = 1;
bigIm(1:size(segmentation,1), 1:size(segmentation,2), :) = squeeze(max(bbVol, [], 3));
for kk=1:clusterCount
  [xTile, yTile]                             = ind2sub([xTileCount yTileCount], kk+1);
  tmp2                                       = find(segmentation==kk);
  for mm = 1:3
    tmp1                                     = zeros(size(segmentation));
    tmp1(tmp2)                               = bbVol(tmp2+(mm-1)*voxelCount);
    bigIm((xTile-1)*(size(segmentation,1)+1)+1:xTile*(size(segmentation,1)+1)-1, (yTile-1)*(size(segmentation,2)+1)+1:yTile*(size(segmentation,2)+1)-1, mm) = max(tmp1, [], 3);
  end
end
imwrite(bigIm(:,:,1:3),['simData/bigim_' filename '.png'])