NaN value in log window

[Oskar Jäckel]

Dear all,

We are working on segmented images of microfossils (gray value particle on a
black background) and are trying to measure a couple of parameters regarding
the outline of the particle. There is always one particle on the image.
The macro is as follow:
                   …
setThreshold(50, 255);
                  run("Convert to Mask");
                   run("Create Selection");
                    run("Revert");
                   setThreshold(10, 254);
                   getSelectionCoordinates(selX, selY);
                   run("Select None");
                   makeSelection("polygon", selX, selY);
                   run("Set Measurements...", "area mean standard modal min
perimeter bounding fit circularity feret's integrated median skewness
kurtosis display redirect=None decimal=3");
                  run("Measure");
perim=getResult("Perim.");
print(perim);
…

We used to work with imageJ 1.38n where we could read the result table
without problem. Since we have upgraded the software to the version 1.44p,
we always get a normal result table with values for each column but when we
want to read them and print each of them, this give NaN (e.g.
perim=getResult("Perim."); print(perim);) except for the area value…
Is there a solution to go about it? Is it a bug?

In any case, thanks in advance for your help.

Oskar Jäckel & France E. Girault
Uppsala University & ETH Zurich


--
Oskar Jäckel
Department of Earth Sciences - Paleobiology
Uppsala University
Villavägen 16
752 36 Uppsala
Sweden


Phone: [phone]
email: [hidden email]

[Nathaniel Ryckman]

An easy fix would be to download the original version that you had previously used.

http://rsbweb.nih.gov/ij/download/

I would recommend that anyone who is relying on imageJ create a backup of the version of imageJ that they are using.

Backwards compatibility is not always guaranteed...

As for what's causing the problem, it's hard to tell without running a few programming experiments. My initial guess is that your selection commands are not working properly.

Oskar Jäckel wrote

Dear all,

We are working on segmented images of microfossils (gray value particle on a
black background) and are trying to measure a couple of parameters regarding
the outline of the particle. There is always one particle on the image.
The macro is as follow:
                   …
setThreshold(50, 255);
                  run("Convert to Mask");
                   run("Create Selection");
                    run("Revert");
                   setThreshold(10, 254);
                   getSelectionCoordinates(selX, selY);
                   run("Select None");
                   makeSelection("polygon", selX, selY);
                   run("Set Measurements...", "area mean standard modal min
perimeter bounding fit circularity feret's integrated median skewness
kurtosis display redirect=None decimal=3");
                  run("Measure");
perim=getResult("Perim.");
print(perim);
…

We used to work with imageJ 1.38n where we could read the result table
without problem. Since we have upgraded the software to the version 1.44p,
we always get a normal result table with values for each column but when we
want to read them and print each of them, this give NaN (e.g.
perim=getResult("Perim."); print(perim);) except for the area value…
Is there a solution to go about it? Is it a bug?

In any case, thanks in advance for your help.

Oskar Jäckel & France E. Girault
Uppsala University & ETH Zurich


--
Oskar Jäckel
Department of Earth Sciences - Paleobiology
Uppsala University
Villavägen 16
752 36 Uppsala
Sweden


Phone: [phone]
email: [hidden email]