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

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

Answer 1

[Anton Semechko]

Hey, Vincent. Here is an example:

[IM,IM_all]=PubChem_compound_image_stacking_demo;

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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

[Anton Semechko]

To save resulting image as a .tif, use command:

imwrite(IM,'PubChemDemo.tif')

[Vincent Scalfani]

Thanks so much, this is awesome. I can't thank you enough for your time! I tried adjusting the number of columns and rows, but the image then shrinks and becomes too narrow. Do you think there is an easy way to make the thumbnails larger (i.e. less columns)? Also, the insertText function is part of an add-on toolbox, so I had to comment that out. Any ideas for a workaround to label?

[Anton Semechko]

Glad to help, Vincent. You can tune the number of columns by manually setting the variable 'm' to any desired value; the number of rows (specified by 'n') will be adjusted automatically. Example of inserting text into images when Image Processing Toolbox is unavailable can be found here.

[Vincent Scalfani]

thanks!