Measurements Error?

[Nathaniel Ryckman]

Why are these measurement values different?

Programmatically:

name: 0114-0114
area: 2590.0
mean: 15.083397683397683
stdDev: 17.46720135718284
mode: 3
min: 1.0
max: 71.0
xCentroid: 114.0
yCentroid: 796.5
xCenterOfMass: 114.1301131418625
yCenterOfMass: 803.6518711923411
---------------------------------------

Using Menu (Results Table):

Label : 0114-0114
Area : 1855
Mean : 20.41
StdDev: 18.054
Mode : 3
Min: 2
Max: 71
X: 113.961
Y: 799.574
XM: 114.087
YM: 804.086
---------------------------------------



The following is the code I used. I obtained the Results Table measurements (using the imageJ menu) by using the Roi's generated by the program.

int measurements = AREA+MEAN+STD_DEV+MODE+MIN_MAX+
                        CENTROID+CENTER_OF_MASS+PERIMETER+RECT+
                        ELLIPSE+SHAPE_DESCRIPTORS+FERET+INTEGRATED_DENSITY+
                        MEDIAN+SKEWNESS+KURTOSIS+AREA_FRACTION;
                       
RoiManager rm = RoiManager.getInstance();
if(rm == null)
        rm = new RoiManager();
                       
for(int j = 0; j < dapiRois.size(); j++)
{
        o.add(dapiRois.get(j));
        rm.addRoi(dapiRois.get(j));
        imp.setRoi(dapiRois.get(j));
                               
        ImageStatistics stats = ImageStatistics.getStatistics(imp.getProcessor(), measurements, imp.getCalibration());
        IJ.log("name: " + rm.getList().getItem(j));
        IJ.log("area: " + stats.area);
        IJ.log("mean: " + stats.mean);
        IJ.log("stdDev: " + stats.stdDev);
        IJ.log("mode: " + stats.mode);
        IJ.log("min: " + stats.min);
        IJ.log("max: " + stats.max);
        IJ.log("xCentroid: " + stats.xCentroid);
        IJ.log("yCentroid: " + stats.yCentroid);
        IJ.log("xCenterOfMass: " + stats.xCenterOfMass);
        IJ.log("yCenterOfMass: " + stats.yCenterOfMass);
        IJ.log("---------------------------------------");
                               
       
}

imp.setOverlay(o);

[Nathaniel Ryckman]

Just in case anyone wants to know, the imageJ Measure Button uses a pipeline like this:

1) Analyzer class
2) ImagePlus.getStatistics(int mOptions)
3) ImageStatistics

The 2nd step of the pipeline modifies the image processor and its histogram; thus, if you try to only use the 3rd step of the pipeline like this

"ImageStatistics stats = ImageStatistics.getStatistics(imp.getProcessor(), measurements, imp.getCalibration());"
                               

you will possibly get DIFFERENT results than from what you would get if you had pushed the imageJ Measure Button.
 
If you want to simulate the imageJ Measure Button in a custom plugin, ONLY use this command:

"ImageStatistics stats = imp.getStatistics(measurements);"

Nathaniel Ryckman wrote

Why are these measurement values different?

Programmatically:

name: 0114-0114
area: 2590.0
mean: 15.083397683397683
stdDev: 17.46720135718284
mode: 3
min: 1.0
max: 71.0
xCentroid: 114.0
yCentroid: 796.5
xCenterOfMass: 114.1301131418625
yCenterOfMass: 803.6518711923411
---------------------------------------

Using Menu (Results Table):

Label : 0114-0114
Area : 1855
Mean : 20.41
StdDev: 18.054
Mode : 3
Min: 2
Max: 71
X: 113.961
Y: 799.574
XM: 114.087
YM: 804.086
---------------------------------------