imqc(in,out)

function imqc(in,out)
%IMQC runs quality control checks on TIFF images
%
%  IMQC(DRIVER,REPORT_FILE)
%
%  DRIVER is a file listing the TIFF images to be quality controlled (full
%  path and filename should be supplied)
%  REPORT_FILE is the full path and name of a file to which the IMQC report
%  will be written. You should have permission to write to the specified
%  directory. If the filename specified already exists, it will be
%  overwritten.
%
%  This function is not designed to replace visualising the data, but to
%  provide a warning of which files may not be suitable for continued
%  processing.
%
%  Version 1.0
%

%  Adam Leadbetter ([e-mail]) - 2006Nov24

%
%  Try to open the in and out files  -  if we fail on either it is an error
%
  fid  =  fopen(in);
  if(fid  ==  -1)
    error('ImageQualityControl:CannotOpenDriver',...
      'Error: Cannot open the driver file %s',in);
  end
  fir  =  fopen(out,'w');
  if(fir  ==  -1)
    error('ImageQualityControl:CannotOpenReport',...
      'Error: Cannot open the report file %s',out);
  end
  clear in out;
%
%  Process the images
%
  report  =  struct('FileName','',...
      'Error','',...
      'Warning','');
  ImgNam  =  fgetl(fid);
  kk  =  0;
  Counter  =  struct('Processed',0,'Warnings',0,'Errors',0);
  while(ImgNam  ~=  -1)
    kk  =  kk + 1;
    fprintf(1,'\n\tProcessing %s\n',ImgNam);
    report(kk).FileName  =  ImgNam;
%
%  Check that the image exists
%
    fie  =  fopen(ImgNam);
    if(fie  ==  -1)
      fprintf(fir,'\n\tWarning: %s - Could not open image\n',report(kk).FileName);
      fprintf(1,'\n\t\tWarning: Could not open image\n');
      report(kk).Error  =  'CouldNotOpenImageFile';
      Counter.Errors  =  Counter.Errors  +  1;
      ImgNam  =  fgetl(fid);
      continue
    end
    fclose(fie);
%
%  Check we're dealing with a genuine TIFF file
%
    allowed_fmts  =  {'TIF','TIFF','tif','tiff'};
    ImgInfo  =  imfinfo(ImgNam);
    if(~ismember(allowed_fmts,ImgInfo.Format))
      fprintf(fir,'\n\tWarning: %s - Not a TIFF image\n',report(kk).FileName);
      fprintf(1,'\n\t\tWarning: Not a TIFF image\n');
      report(kk).Error  =  'NotTIFF';
      Counter.Errors  =  Counter.Errors  +  1;
      ImgNam  =  fgetl(fid);
      continue
    end
    clear allowed_fmts;
%
%  Load the image & generate the histogram
%
    AA  =  imread(report(kk).FileName);
    if(length(size(AA)) == 3)
      nn  =  2;
      aq  =  size(AA);
      AB  =  AA(:,:,1);
      while(nn  <=  aq(3))
        AB  =  AB  +  AA(:,:,aq(3));
        nn  =  nn + 1;
      end
      AA  =  AB;
      clear aq nn AB;
    end
    try
      [Counts,X]  =  imhist(AA);
    catch
      Counter.Errors  =  Counter.Errors + 1;
      fprintf(1,'\n\t\tWarning: Could not generate an image histogram\n');
      fprintf(fir,'\n\tWarning: %s - Could not generate an image histogram\n',...
        report(kk).FileName);
      report(kk).Error  =  'UnrecognisedImageTypeHistogram';
      ImgNam  =  fgetl(fid);
      continue
    end
%
%  Check for black-out, white-out & one-frequency dominance
%
   if((sum(Counts) * 0.90)  <  (sum(Counts(1:ceil(0.05*length(X))))))
     report(kk).Warning  =  'BlackOut';
     Counter.Warnings  =  Counter.Warnings  +  1;
     fprintf(1,'\n\t\tWarning: May be a black-out\n');
     fprintf(fir,'\n\tWarning: %s May be a black-out\n',report(kk).FileName);
   elseif((sum(Counts) * 0.90)  <  (sum(Counts(floor(0.95*length(X)):end))))
     report(kk).Warning  =  'WhiteOut';
     Counter.Warnings  =  Counter.Warnings  +  1;
     fprintf(1,'\n\t\tWarning: May be a white-out\n');
     fprintf(fir,'\n\tWarning: %s may be a white-out\n',report(kk).FileName);
   elseif(max(Counts)  >  (4*std(Counts)) + median(Counts))  % May need twaeking
     report(kk).Warning  =  'SingleFreqDominant';
     fprintf(1,'\n\tWarning: A single frequency may be dominant\n');
     fprintf(fir,'\n\tWarning: %s - a single frequency may be dominant\n',...
       report(kk).FileName);
   else
     report(kk).Warning  =  [];
   end
%
%  If there's a warning - do a plot
%
    if(~isempty(report(kk).Warning))
      local_imqcplot(AA,ImgNam);
    end
%
%  Get the next image filename
%
    ImgNam  =  fgetl(fid);
    Counter.Processed  =  Counter.Processed  +  1;
  end
  clear fie;
%
%  Tidy up - close the files
%
  fprintf(1,'\n\tFinishing up\n');
  fclose(fid);
  fprintf(fir,'\n\tFiles processed:\t\t%g',Counter.Processed);
  fprintf(fir,'\n\tWarnings found:\t\t%g',Counter.Warnings);
  fprintf(fir,'\n\tImages skipped:\t\t%g\n',Counter.Errors);
  fprintf(fir,'\n\tNormal termination\n');
  fclose(fir);
  fprintf(1,'\n\tReport file written\n');
  fprintf(1,'\n\tFiles processed:\t%g',Counter.Processed);
  fprintf(1,'\n\tWarnings found:\t\t%g',Counter.Warnings);
  fprintf(1,'\n\tImages skipped:\t\t%g\n',Counter.Errors);
  clear fid fir;
  fprintf(1,'\n\tJob done\n');
  
function local_imqcplot(AA,ImgNam)
%LOCAL_IMQCPLOT plots the image quality control window
%
%  AA is the image data acquired by IMREAD
%
%  Version 1.0

%  Adam Leadbetter ([e-mail]) - 2006Nov24
  figure;
  if(find(ImgNam  ==  '\'))
    ImgNam(ImgNam  ==  '\')  =  '/';
  end
  subplot(3,4,[1:3 5:7 9:11]);
  imshow(AA);
  title(ImgNam,'FontWeight','bold','FontSize',14);
  subplot(3,4,8);
  imhist(AA);
  grid on;