Posted by
dscho on
Jun 11, 2014; 2:23pm
URL: http://imagej.273.s1.nabble.com/Headless-ImageJ2-rc2-Analyze-Particles-returns-no-result-tp5008127p5008132.html
Hi Paul,
On Wed, 11 Jun 2014, Paul van Schayck wrote:
> I'm running into several problems running ImageJ2-rc2 headless. I'm
> using this command:
>
> ./ImageJ-linux64 --headless -macro scripts/test.ijm
>
> The first one is that the new "Open images using scifio" breaks image opening through open("image.png"):
> java.lang.NullPointerException
> at net.imagej.legacy.IJ1Helper.updateRecentMenu(IJ1Helper.java:307)
Could I ask you to test my fix? If you replaced your
jars/imagej-legacy-*.jar with the version from
http://jenkins.imagej.net/job/ImageJ-legacy/lastSuccessfulBuild/artifact/target/imagej-legacy-0.5.10-SNAPSHOT.jarit should address that problem.
> This can be fixed by disabling the new SCIFIO option.
Note that we are currently stabilizing this code, with the enormous and
outstanding help by the community, such as you!
The idea of using SCIFIO is to make it possible to just File>Open just
about anything and get the correct images. The built-in TIFF reader of
ImageJ 1.x cuts a few corners, which is fast, but fails to open a couple
of valid TIFF files correctly, and it also does not heed extensions such
as OME-TIFF. SCIFIO addresses that.
I have no doubt that with the help of the community, we can make the
support code in ImageJ2 robust so that everybody can gain the benefits of
the SCIFIO library.
> The second one, is that this macro:
>
> open(imagePath);
> run("8-bit");
> setThreshold(1, 255);
> run("Analyze Particles...", "size=300-Infinity circularity=0.40-1.00");
> print(nResults);
>
> Will return 0. No particles seem to be found. Running the same macro not headless:
> ./ImageJ-linux64 -macro scripts/test.ijm
> Will return a number of particles in a log window
Have you tried with
./ImageJ-linux64 -batch scripts/test.ijm
? This is a way to call macros in batch mode that is admittedly not
documented very well... At least that will get you going again if all you
need is to call the script from the command line and let it obtain the
results via stdout.
I just tried to reproduce that headless mode problem and get a different
problem instead. Will keep you posted.
> Thirdly, the option "-macro" seems to be undocumented. Is this the
> preferred way to start macros? How about new scripts (.js or beanshell).
The -macro option is a standard IamgeJ 1.x option, documented
unfortunately only in the developer part of the documentation, far from
regular users' hunting grounds:
http://jenkins.imagej.net/job/ImageJ1-javadoc/javadoc/ij/ImageJ.htmlNote that it is also not *quite* correct: you can pass -batch as last
argument *without* a path, which comes in handy if you want to *evaluate*
an expression -- as opposed to a file containing macro code -- in batch
mode.
So hopefully this addresses two of your questions; I will keep you updated
on the remaining one.
Ciao,
Johannes
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