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FindCluster_1_PT_S84_m5_mut.m
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FindCluster_1_PT_S84_m5_mut.m
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clear all
dt_path_wt={ '../data/Nuclei_and_Cells_DT_S18_m6_wt/', '../data/Nuclei_and_Cells_DT_S17_m2_wt/',...
'../data/Nuclei_and_Cells_DT_S84_m3_wt/', '../data/Nuclei_and_Cells_DT_S51_m2_wt/',...
'../data/Nuclei_and_Cells_DT_S84_m4_wt/'};
pt_path_wt = { '../data/Nuclei_and_Cells_PT_S18_m6_wt/','../data/Nuclei_and_Cells_PT_S17_m2_wt/',...
'../data/Nuclei_and_Cells_PT_S84_m3_wt/','../data/Nuclei_and_Cells_PT_S51_m2_wt/',...
'../data/Nuclei_and_Cells_PT_S84_m4_wt/'};
dt_path_mut= {'../data/Nuclei_and_Cells_DT_S17_m1_mut/', '../data/Nuclei_and_Cells_DT_S18_m2_mut/' ,...
'../data/Nuclei_and_Cells_DT_S84_m1_mut/', '../data/Nuclei_and_Cells_DT_S84_m5_mut/'};
pt_path_mut = {'../data/Nuclei_and_Cells_PT_S17_m1_mut/', '../data/Nuclei_and_Cells_PT_S18_m2_mut/',...
'../data/Nuclei_and_Cells_PT_S84_m1_mut/', '../data/Nuclei_and_Cells_PT_S84_m5_mut/', };
du_path_wt={'../data/Nuclei_and_Cells_DU_S51_m2_wt/','../data/Nuclei_and_Cells_DU_S84_m2_wt/','../data/Nuclei_and_Cells_DU_S84_m3_wt/'};
allpath={dt_path_wt; pt_path_wt; dt_path_mut; pt_path_mut; du_path_wt};
meanOfAllCelltemp=load('meanOfAllCell.dat');
count=1;
for gi=1:length(allpath)
for gj=1:length(allpath{gi})
GlobalCenter{gi}{gj}=meanOfAllCelltemp(count,1:3);
count=count+1;
end
end
for gi=4%:length(allpath)
bonetype=gi;
for gj=4%1:length(allpath{gi})
path=allpath{gi}{gj};
s=strsplit(path,'Nuclei_and_Cells_');
%ns=strsplit(path,'T_');
input2=strcat('Cluster_Structure_Prediction/',s{2});
if ~exist([input2],'dir')
mkdir([input2]);
end
alignment=load(['./../../',path,'Alignment_matrix.dat']);
vec=alignment(:,1:3);
[numbers,txt,raw] = xlsread(['./../../',path,'Tile_coordinates.xlsx']);
coordinates = zeros(size(txt,1)-3,5);
for i = 4:size(txt,1),
temp = char(txt(i,1));
res = strsplit(temp,'_POS');
coordinates(i-3,1) = str2num(char(res(2)));
coordinates(i-3,2:5) = numbers(i-3,:);
end
tile=coordinates(:,2:end);
input1=strcat('MakeListColumnarStructurePrediction/',s{2});
load([input1,'centroid_and_surface_cells.mat']);
% a1=load(['./../../',path,'all_cells_nuclei.mat']);
% nuc=a1.all_cells_nuclei;
% nuccent=nuc(:,5:7);
a1=load([input1,'NeighboringCell_in_20_micron_cube.dat']);
edges=a1(:,[1,2]); [~,ia]=unique(edges,'rows');
edges=edges(ia,:);
disp('start LCC')
LCCall=LargestConnectedComponents(edges);
%plotClusterFigure(input2,LCCall,centroid,nuc);
end
end
makeClusterTifFiles(input2,tile,coordinates,path,LCCall,unique_tileid,unique_pixel,vec,bonetype,centroid, GlobalCenter{gi}{gj});
function plotClusterFigure(olddirectory,LCCall,centroid,csurfVertices)
directory=strcat(olddirectory,'Figure_matlab/');
if ~exist([directory],'dir')
mkdir([directory]);
end
for k=1:length(LCCall)
LCC=LCCall{k};
if length(LCC)>=4
h=figure;
mu=centroid(LCC,:);
%t=C.coords(LCC,:);
plot3(mu(:,1),mu(:,2),mu(:,3),'bo-');
hold on
for i=1:size(LCC,1)
%plot_cube(t(i,[3,4,1,2,5,6]).*voxelimit);
V=csurfVertices{LCC(i)};
if mod(i,2)==0
plot3(V(:,1),V(:,2),V(:,3),'r.','markersize',0.1);
else
plot3(V(:,1),V(:,2),V(:,3),'g.','markersize',0.1);
end
text(mu(i,1),mu(i,2),mu(i,3),num2str(LCC(i)),'fontsize',16);
hold on
end
saveas(h,[directory,'Fig','_',num2str(k),'_',num2str(length(LCC)),'.fig']);
saveas(h,[directory,'Fig','_',num2str(k),'_',num2str(length(LCC)),'.png']);
close all
end
end
end
function makeClusterTifFiles(olddirectory,tile,coordinates,path,LCCall,unique_tileid,unique_pixel,vec,bonetype,centroid,GlobalCenter)
if (bonetype==3)|(bonetype==1)
tempCentroid=[centroid(:,1:2),-centroid(:,3)];
else
tempCentroid=[centroid(:,1:2),centroid(:,3)];
end
newcentroid=tempCentroid-GlobalCenter;
directory=strcat(olddirectory,'Figure_tif/');
if ~exist([directory],'dir')
mkdir([directory]);
end
for k=1:length(LCCall)
LCC=LCCall{k};
if length(LCC)>=4
tile_frequency_in_col=unique_tileid(LCC,1);
aa=unique(tile_frequency_in_col);
clear freq
for jj=1:length(aa)
freq(jj)=sum(tile_frequency_in_col==aa(jj));
end
freq=freq/sum(freq);
[sa,sb]=max(freq);
complete=0;
if freq(sb)==1
complete=1;
end
fi=aa(sb);
position=coordinates(fi,1);
if ((fi==11) | (fi==7) | (fi==18))
load(strcat('./../../',path,'c_n_pos',num2str(position),' (Characteristics).mat'));
zsize1=double(max(C.coords(:,6)));
zsize2=ceil(abs(tile(fi,4)-tile(fi,3))/0.387);
zsize=max(zsize1,zsize2);
[k,zsize1,zsize2];
I.size= [900, 900, zsize]; I.data_type='uint8';
characteristics = zeros(I.size, I.data_type);
p1=round(min(newcentroid(LCC,3)));
p2=round(max(newcentroid(LCC,3)));
% for j=1:length(LCC)
% if fi==unique_tileid(LCC(j),1)
% i=unique_tileid(LCC(j),2);
% %[i,position,fi,k]
% pos=C.coords(i,:);
% characteristics(pos(1):pos(2),pos(3):pos(4),pos(5):pos(6))= characteristics(pos(1):pos(2),pos(3):pos(4),pos(5):pos(6)) | C.masks{i};
% end
% end
for i=1: size(C.coords,1)
pos=C.coords(i,:);
%centroids = calc_centroids(C.masks(i), C.origins(i,:));
centroids = (calc_centroids_spacing(C.masks(i), C.origins(i,:), C.spacing(i,:)) +repmat([tile(fi,2), -tile(fi,1),tile(fi,3)],1,1))*vec;
for j=1:length(LCC)
if fi==unique_tileid(LCC(j),1)
%k=unique_tileid(LCC(j),2);
%predicted_cent=unique_pixel(LCC(j),:);
predicted_cent = centroid(LCC(j),:);
dist=pdist([predicted_cent;centroids]);
if dist<1
%[k,i,LCC(j),centroids,predicted_cent]
characteristics(pos(1):pos(2),pos(3):pos(4),pos(5):pos(6))= characteristics(pos(1):pos(2),pos(3):pos(4),pos(5):pos(6)) | C.masks{i};
end
end
end
end
tifname=strcat([directory,'/Output_cluster_', 'w_', num2str(complete), '_cid_', num2str(k),'_com_',num2str(length(LCC)), '_til_',num2str(fi),'_pos_', num2str(p1),'-',num2str(p2)],'.tif');
saveTiffFiles(tifname,I,255*characteristics)
end
end
end
end
function LCC=LargestConnectedComponents(edges)
cellIds=unique(edges(:));
for j=1:length(cellIds)
old2new(cellIds(j),1)=j;
new2old(j,1)=cellIds(j);
end
[length(old2new),length(new2old),length(cellIds)];
for i=1:length(edges)
for j=1:2
newedgename(i,j)= old2new(edges(i,j));
end
end
G=graph(newedgename(:,1),newedgename(:,2));
bins=conncomp(G);
% number of connected components
nocomp=unique(bins);
disp(['# of connected components ', num2str(length(nocomp))]);
for i=1:length(nocomp)
numberOfObjectsInConnectedComponents(i)=sum(nocomp(i)==bins);
end
[sa,sb]=sort(numberOfObjectsInConnectedComponents,'descend');
index=1;
for i=1:length(sa)
if sa(i)>1
LCCIds=find(bins==nocomp(sb(i)));
LCC{index}=new2old(LCCIds);
index=index+1;
end
end
end
function saveTiffFiles(tifoutputname,I,characteristics)
t = Tiff(tifoutputname,'w');
tagstruct.ImageLength = I.size(1);
tagstruct.ImageWidth = I.size(2);
tagstruct.SubFileType= Tiff.SubFileType.Page;
tagstruct.SampleFormat = Tiff.SampleFormat.UInt; % uint
tagstruct.Photometric = Tiff.Photometric.MinIsBlack;
tagstruct.BitsPerSample = 8;
tagstruct.SamplesPerPixel = 1;
tagstruct.Compression = Tiff.Compression.PackBits;
tagstruct.PlanarConfiguration = Tiff.PlanarConfiguration.Chunky;
for ii=1:I.size(3)
setTag(t,tagstruct);
write(t,characteristics(:,:,ii));
writeDirectory(t);
end
close(t)
end
function centroids = calc_centroids(masks, origins)
centroids = nan(length(masks),3);
for i = 1 : length(masks)
[x,y,z] = ind2sub(size(masks{i}), find(masks{i}));
centroids(i,:) = (mean([x,y,z],1) + double(origins(i,:) - 1));
end
end
function centroids = calc_centroids_spacing(masks, origins, spacings)
centroids = nan(length(masks),3);
for i = 1 : length(masks)
[x,y,z] = ind2sub(size(masks{i}), find(masks{i}));
centroids(i,:) = (mean([x,y,z],1) + double(origins(i,:) - 1)) .* spacings(i,:);
end
end