[ome-users] ImageProcessorReader.setId performance

[Mohammad Samarah]

We are using loci_tools.jar to read radiographs in RVG format and extract a
thumbnail JPEG image. All works as expected, however if the image in
question is in a directory whose parent directory contains several thousands
subfolders, then the ImageProcesserReader takes minutes to complete the
setId() method. Please see attached code. The same image placed in a folder
with its parent directory having much fewer subfolders works with no delay.
This behavior can also be seen when using loci_tools.jar UI to open the same
image. The issue does not seem to be related to the image itself but rather
the fact that the containing folder is a child of a directory with thousands
of subfolders. Could you please point us to how we can resolve this issue.

Many thanks for your help,

--
M. Samarah
msamarah at alumni.fit.edu

 
private ImagePlus readDicomImage(String imagePath)
    {
        ImagePlus imp            = null;
        ImagePlus colorizedImage = null;
        
        ImageProcessorReader r = new ImageProcessorReader(new
ChannelSeparator(LociPrefs.makeImageReader()));
        try
        {
            log_message("INFO: Examining file " + imagePath);

            // the next line takes 10 to 20 minutes to complete when parent
folder contains 4000+ subfolders. It takes no time when parent folder has
100 subfolders
            r.setId(imagePath);

            log_message("INFO: Setting file path " + imagePath);
            int num = r.getImageCount();
            log_message("INFO: Image count is" + num);
            int width = r.getSizeX();
            int height = r.getSizeY();
            log_message("INFO: Image Width %d Height %d", width, height);
            ImageStack stack = new ImageStack(width, height);
            log_message("INFO: After constructing image stack");
            byte[][][] lookupTable = new byte[r.getSizeC()][][];
            log_message("INFO: After Allocating memmory for image");
            for (int i=0; i<num; i++)
            {
                ImageProcessor ip = r.openProcessors(i)[0];
                stack.addSlice("" + (i + 1), ip);
                int channel = r.getZCTCoords(i)[1];
                lookupTable[channel] = r.get8BitLookupTable();
            }
            log_message("INFO: After constructing lookup table");
            log_message("INFO:Constructing image");
            imp = new ImagePlus("Dicom", stack);
               
            colorizedImage = applyLookupTables(r, imp, lookupTable);
            r.close();

        }
        catch(Exception exc)
        {
           log_message("ERROR an error occurred: " + exc.getMessage());
        }
       return colorizedImage;
    }

Example: Takes 10 to 20 minutes on an 8 core machine with 24GB of memory to
complete setId method
> Data <folder>
>> 0001 <folder>
>> 0002 <folder>
>> 0003 <folder>
>> ...
>> 1000 <folder>
>> 1001 <folder>
>>> File R1.RVG
>> ...
>> 4000 <folder>

Example: Works with no delay
> Data <folder>
>> 0001 <folder>
>> 0002 <folder>
>> 0003 <folder>
>> ...
>> 0050 <folder>
>> 0051 <folder>
>>> File R1.RVG
>> ...
>> 00080 <folder>



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