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subplot with multiple images - Pulling images from API into one figure

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Hello, I have some working code where I search for chemical structures (compounds) via the PubChem API, and then loop through the retrieved PubChem Compound identifiers and display the PNG images of them. What I would like to do is not create a separate figure for each image, but rather use something like subplot to create a grid (3 columns wide). This way, all of the compound images are in one figure. I am not having much luck. Your help would be much appreciated. Here is the code I wrote below:
% Search for chemical structures by Identity (same connectivity, SC) as Ingenol
api = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/';
SC_url = [api 'fastidentity/cid/442042/cids/JSON?identity_type=same_connectivity'];
SC = webread(SC_url);
SC = num2cell(SC.IdentifierList.CID)
% Retrieve PNG images of same connectivity CIDs in SC dataset.
% loop through CIDs and define web api url
for r = 1:length(SC)
SC_CID = SC{r};
SC_CID_url = [api 'cid/' num2str(SC_CID) '/PNG'];
try
% retrieve CID PNG image and display
[SC_CID_img,map] = imread(SC_CID_url);
figure;
imshow(SC_CID_img,map)
drawnow;
title(num2str(SC_CID));
% be polite to PubChem server
n = 1;
pause(n);
catch
disp('CID image not found')
disp('Execution will continue')
end
end

Accepted Answer

Anton Semechko
Anton Semechko on 5 Jul 2018
Hey, Vincent. Here is an example:
[IM,IM_all]=PubChem_compound_image_stacking_demo;
------------------------------------------------------------------------------------------------------------------------------------------
function [IM,IM_all]=PubChem_compound_image_stacking_demo
% Search for chemical structures by Identity (same connectivity, SC) as Ingenol
api = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/';
SC_url = [api 'fastidentity/cid/442042/cids/JSON?identity_type=same_connectivity'];
SC = webread(SC_url);
SC = num2cell(SC.IdentifierList.CID);
% Retrieve PNG images of same connectivity CIDs in SC dataset.
% loop through CIDs and define web api url
N=numel(SC);
[IM,CID,flag]=deal(cell(N,1),zeros(N,1),true(N,1));
for i = 1:N
SC_CID = SC{i};
SC_CID_url = [api 'cid/' num2str(SC_CID) '/PNG'];
try
% retrieve CID PNG image and display
[IM{i},map] = imread(SC_CID_url);
CID(i)=SC_CID;
IM{i}=uint8(255*ind2rgb(IM{i},map));
flag(i)=false;
% be polite to PubChem server
pause(1)
fprintf('image %2u\\%2u dowloaded\n',i,N)
catch
fprintf(2,'CID image # %u not found\n',SC_CID);
end
end
% All available images
IM(flag)=[];
CID(flag)=[];
% Sort images according to CID; all images are assumed to have equal dimensions
N=numel(IM);
[CID,id_srt]=sort(CID);
IM=IM(id_srt);
siz=size(IM{1});
% Arrange images into a rectangular array, so that images are ordered
% according to CID from top to bottom, left to right
m=floor(sqrt(N)); % number of colums
n=ceil(N/m); % number of rows
cnt=0;
IM_all=cell(n,m);
for i=1:n % row
for j=1:m % column
% Get the image
cnt=cnt+1;
if cnt<=N
im=IM{cnt};
IM{cnt}=[];
if cnt==1
bkg_col=im(1,1,:);
im_bkg=repmat(bkg_col,[siz(1:2) 1]);
bkg_col=bkg_col(:)';
end
% annotate
im=insertText(im,[siz(2)/2 round(0.92*siz(1))],num2str(CID(cnt)),'AnchorPoint','center','BoxColor',bkg_col,'FontSize',25);
else
im=im_bkg;
end
% Make border
im(1:2,:,:)=0;
im(:,1:2,:)=0;
if j==m, im(:,(siz(2)-1):siz(2),:)=0; end
if i==n, im((siz(1)-1):siz(1),:,:)=0; end
IM_all{i,j}=im;
end
end
IM=cell2mat(IM_all);
% Visualize
figure('color','w')
imshow(IM)
if nargout<1, clear IM IM_all; end
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