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", "");

Solution

Your code has several problems:

To get measurements from an Analyzer, you need to run its measure() method
You are printing rt.MIN which is a constant used to define the default headings corresponding to the measurements, see the source code. Instead, you should use ResultsTable#getValueAsDouble(int column, int row) or getValue(String column, int row) to get your value of interest.
Apparently you want to measure the minimum value. You should include Measurements.MIN_MAX into your measurements variable to do so.

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");