for-loopimagejfiji

FIJI/ImageJ: How to return/update a value from the Results table via for loop?

Cross-posted from Image SC Forum and Reddit

(Edit: I found the problem: my for loop isn’t working because it doesn’t recognize my table as the Results table. Anyone know how to make it do that?)

(Edit 2: Got it to recognize my table by renaming. Next problem is that I can't get the Math>Subtract command to work, even if I just hard code it with a number. It seems like the command is doing nothing at all. Even when I go through the GUI by clicking (which works) while recording and then re-do the recorder commands it doesn't work.)

I am writing a personal macro, and I am stuck on how to get a value from the Results table. Should be a simple fix.

Basically I want to search through the Results table by filename/label and pull out a value. I am using a for loop to query/match filename to label, and then using that index to update a pre-defined variable. But for some reason, the variable is not being updated. I think this is because the loop query is not matching the filename to a row Label.

The core portion of my script is below:

MeanBkgd = 0 // Setting 0 as a default placeholder
for(iRes=0; iRes<nResults; iRes++){
        if (getResultString("Label", iRes) == file) {
            MeanBkgd = getResult("Mean", iRes);
    }   
}
print(MeanBkgd); // Verify stored value
run("Subtract...", "value = MeanBkgd"); // Subtract background from image

Extra details:The macro I am writing is meant to process all of the images in a directory by subtracting out the mean background intensity of each image. In a previous step, I already measured the mean background intensities and saved them as a csv. Here in this macro, I am trying to pair those values back to the original images and then subtract them from the images.

However when I run the code below, the background is not removed from the images because the value of MeanBkgd is never changed from 0 (identified from printing MeanBkgd after the loop). Furthermore, I can guess that the query isn’t matching because it never prints “Match”.

// @File(label = "Input directory", style = "directory") input
// @File(label = "Output directory", style = "directory") output
// @String(label = "File suffix", value = ".zvi") suffix

/*
* Macro to open all images in a folder, append to a stack and set thresholds for each channel
*/

function processFolder(input) { 
    // Setup
    close("*");
    open(input + "/BackgroundLevels.csv");
    list = getFileList(input);
    
    // Process Files by subtracting background
    for (i = 0; i < list.length; i++) {
        if(File.isDirectory(input + list[i]))
            processFolder("" + input + list[i]);
        if(endsWith(list[i], suffix))
            SubtractBackground(input, output, list[i]);
    }
    
    // Combine and Threshold
    run("Concatenate...", "all_open open");
    selectWindow("Untitled");
    setAutoThreshold("Triangle dark no-reset stack");
    getThreshold(lower, upper);
    
    // Output
    print(lower); // Can't concatenate to text because technically an array
    file = File.open(output + "/Threshold.txt");
    print(file, lower);
}

function SubtractBackground(input, output, file) {
    // Open Image
    setBatchMode(false); 
    run("Bio-Formats", "open=[" + input + "/" + file +"] color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
    
    // Set null value
    MeanBkgd = 0;
    
    // Get values from imported Results
    for (iRes=0; iRes < nResults; iRes++) { // What if there are not 1 match (0 or 2+)?
        if (getResultString("Label", iRes) == file) {
            MeanBkgd = getResult("Mean", iRes); 
            print("Match"); // Verify match
        }   
    }
    
    print(MeanBkgd); // Verify stored value
    
    // Subtract background from image
    run("Subtract...", "value = MeanBkgd");
}


processFolder(input);

I adapted this code for finding a value from a Results table from https://stackoverflow.com/a/33723712/14860873

I have also tried treating MeanBkgd as an array and trying to update/append it, but I couldn’t get this to work either. I haven’t found any help online because the ImageJ language is different than other coding languages and less popular.

Anyone have any ideas?

I wonder if the spaces in the Label names could be causing an issue?

Solution

  • The reason the Math > Subtract command isn't working is because the line

    run("Subtract...", "value = MeanBkgd");

    uses the literal term MeanBkgd as the value rather than the variable called MeanBkgd. So if you change it to

    run("Subtract...", "value=" + MeanBkgd);

    the variable will be substituted in the call to Subtract.