CODEWITHSUNDEEP
javaimagej
raistlin
raistlin

Reputation: 261

Different results with application and code in ImageJ

My problem appeared when I tried to run a picture analysis with ImageJ and try to calculate porosity.

I recorded the macros and run the same procedure in java. The results from these two executions are different and I don't know why. Could you help?

I tried to write the code again using ImageJ API. The two samples I run are shown below:

    ImagePlus imp = new ImagePlus();
    imp = IJ.openImage("path_to_image");
    int measurements = Measurements.AREA + Measurements.MEAN +Measurements.STD_DEV +    Measurements.AREA_FRACTION;
    ResultsTable rt = new ResultsTable();
    Analyzer analyzer = new Analyzer(imp, measurements, rt);
    IJ.setAutoThreshold(imp, "Default");
    System.out.println(rt.MIN);

And with recorded code

    imp = IJ.openImage("path_to_image");
    IJ.run("Set Measurements...", "area mean standard modal min median area_fraction limit redirect=None decimal=3");
    IJ.setAutoThreshold(imp, "Default");
    IJ.run(imp, "Measure", "");

Upvotes: 0

Views: 856

Answers (1)

Jan Eglinger
Jan Eglinger

Reputation: 4090

Your code has several problems:

The code that you recorded seems to be Javascript, not ImageJ macro code, so here are some versions of your script that all take the Blobs sample image (File > Open Samples > Blobs (25K)), set the default threshold and measure the same parameters.

ImageJ1 macro:

run("Blobs (25K)");
setAutoThreshold("Default");
run("Set Measurements...", "area mean standard modal min median area_fraction limit redirect=None decimal=3");
run("Measure");

Javascript:

importClass(Packages.ij.IJ);

imp = IJ.openImage("http://imagej.nih.gov/ij/images/blobs.gif");
IJ.setAutoThreshold(imp, "Default");
IJ.run("Set Measurements...", "area mean standard modal min median area_fraction limit redirect=None decimal=3");
IJ.run(imp, "Measure", "");
imp.show();

Beanshell (which is closest to Java code):

import ij.IJ;

imp = IJ.openImage("http://imagej.nih.gov/ij/images/blobs.gif");
IJ.setAutoThreshold(imp, "Default");
IJ.run("Set Measurements...", "area mean standard modal min median area_fraction limit redirect=None decimal=3");
IJ.run(imp, "Measure", "");
imp.show();

If you want to avoid calls to IJ and use the lower level ImageJ API, this is how it looks in Beanshell:

import ij.ImagePlus;
import ij.IJ;
import ij.measure.Measurements;
import ij.measure.ResultsTable;
import ij.plugin.filter.Analyzer;

ImagePlus imp = IJ.openImage("http://imagej.nih.gov/ij/images/blobs.gif");
// IJ.setAutoThreshold(imp, "Default");
imp.getProcessor().setAutoThreshold("Default");

// IJ.run("Set Measurements...", "area mean standard modal min median area_fraction limit redirect=None decimal=3");
int measurements = Measurements.AREA + Measurements.MEAN + Measurements.MIN_MAX + Measurements.STD_DEV + Measurements.MODE + Measurements.MEDIAN + Measurements.AREA_FRACTION + Measurements.LIMIT;

// IJ.run(imp, "Measure", "");
ResultsTable rt = new ResultsTable();
Analyzer analyzer = new Analyzer(imp, measurements, rt);
analyzer.measure();

Double result = rt.getValue("Min", rt.getCounter() - 1); // get value of interest
IJ.log(result.toString()); // print to log window
// Alternatively, show the full results table
// rt.show("New Results");

Upvotes: 2

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