Unrecognized command: Rotate...

[Nestor Milyaev]

I have a weird problem: I use THE SAME vanilla version of Fiji as of
07/05/2012 on my local machine and the server.
I run the following script (rotate.ijm):
==========
filename = getArgument();
print("Processing file: "+ filename);
open(filename);
run("Rotate... ", "angle=52 grid=1 interpolation=Bilinear stack");
run("Image Sequence... ", "format=TIFF name=303MaleDualA digits=3
save=/tmp/tiff/");
==========
the script is run an .lsm file, like
fiji-linux64 -macro rotate.ijm 303A.lsm -batch.

On my machine it runs fine and rotated lsm is exploded as a series of
tiffs under /tmp/tiff folder.

On the server, it says "Unrecognized command: Rotate..." and breaks

I tried upgrading fiji but that does not help.

can anyone help?

[Albert Cardona]

2012/5/18 Nestor Milyaev <nestor....@gmail.com>:

Notice a white space after the three dots: run("Rotate... "

Just remove it.

Albert

[Jean-Yves Tinevez]

No it is the right one. The command without the space applies to ROIs.
The error is somewhere else...

[Johannes Schindelin]

Hi Nestor,

It would be nice to know what ImageJ version you run. Somehow I doubt that
you have identical versions of ij.jar in your setups.

Ciao,
Johannes

[Nestor Milyaev]

Thank you all for your kind help.

Firstly, it's IJ 1.46. How do I find out the Fiji version? As I said,
it's version of 07/05/2012.

Removing the trailing space in "Rotate..." might work - I have not
tried it.

I've upgraded both versions of Fiji. It turns out the syntax for
Rotate has changed:
before >>

run("Rotate... ", "angle=52 grid=1 interpolation=Bilinear stack");

after>>
run("TransformJ Rotate", "z-angle=52 y-angle=0 x-angle=0
interpolation=linear background=0.0 adjust");

That seem to fix it and works on both now.

All the best,

Nestor

On May 18, 7:37 pm, Johannes Schindelin <Johannes.Schinde...@gmx.de>
wrote:

[Nestor Milyaev]

Dear all,

I run a simple script to explode an .lsm file as a series of tiffs
(attached). I run it as follows:
fiji-linux64 -macro lsm2tiff.ijm 303MaleDualA -batch

There is a .lsm file in the 303MaleDualA/lsm folder.

When run from a command line it works fine. However when I run it from a
java application it throws the following error:

Processing folder: 303MaleDualA/lsm/
Processing: 303MaleDualA.lsm
opening: 303MaleDualA/lsm//303MaleDualA.lsm => 303MaleDualA/lsm/tiff/
filename 303MaleDualA.lsm
open file ok
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at ij.Command.runPlugIn(Command.java:146)
at ij.Command.runCommand(Command.java:95)
at ij.Executer.run(Executer.java:64)
at ij.IJ.run(IJ.java:251)
at ij.macro.Functions.doRun(Functions.java:579)
at ij.macro.Functions.doFunction(Functions.java:82)
at ij.macro.Interpreter.doStatement(Interpreter.java:214)
at ij.macro.Interpreter.doBlock(Interpreter.java:537)
at ij.macro.Interpreter.doStatement(Interpreter.java:250)
at ij.macro.Interpreter.doIf(Interpreter.java:894)
at ij.macro.Interpreter.doStatement(Interpreter.java:226)
at ij.macro.Interpreter.doBlock(Interpreter.java:537)
at ij.macro.Interpreter.doStatement(Interpreter.java:250)
at ij.macro.Interpreter.doFor(Interpreter.java:483)
at ij.macro.Interpreter.doStatement(Interpreter.java:232)
at ij.macro.Interpreter.doStatements(Interpreter.java:202)
at ij.macro.Interpreter.run(Interpreter.java:103)
at ij.macro.Interpreter.run(Interpreter.java:73)
at ij.macro.Interpreter.run(Interpreter.java:84)
at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:105)
at ij.plugin.Macro_Runner.runMacroFile(Macro_Runner.java:90)
at ij.IJ.runMacroFile(IJ.java:119)
at ij.ImageJ.main(ImageJ.java:670)
at fiji.Main.main(Main.java:105)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at imagej.ClassLauncher.launch(ClassLauncher.java:220)
at imagej.ClassLauncher.run(ClassLauncher.java:158)
at imagej.ClassLauncher.main(ClassLauncher.java:71)
Caused by: java.lang.VerifyError: (class: ij/gui/GenericDialog,
method: showHelp signature: ()V) Incompatible argument to function
at ij.plugin.StackWriter.run(StackWriter.java:54)
at ij.IJ.runPlugIn(IJ.java:158)
... 35 more

The permissions on all the files inside the 303MaleDualA folder is 777.

I run imageJ v. 1.46o, java 1.6.0 (64bit), updated Fiji today (however
it did not work before either).

I believe the problem was not there running Fiji v. of 07/05/2012 (ij1.46n)

Any idea what is going wrong?

Many thanks,

Nestor


--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[Johannes Schindelin]

Hi Nestor,

On Thu, 24 May 2012, Nestor Milyaev wrote:

> I run a simple script to explode an .lsm file as a series of tiffs (attached).
> I run it as follows:
> fiji-linux64 -macro lsm2tiff.ijm 303MaleDualA -batch

Just a suspicion: if you add the --headless option to this call, do you
see the same problem as with your "Java application" (whatever that is) then?

Ciao,
Johannes

[Nestor Milyaev]

Hi Johannes,

Thanks for taking trouble replying.

Unfortunately that does not work either. I have downoladed vanilla Fiji
IJA v. 1.45b and that worked...

I'm still puzzled by what the updates do to Fiji...

Thanks,

Nestor

[Johannes Schindelin]

Hi Nestor,

On Thu, 24 May 2012, Nestor Milyaev wrote:

> Caused by: java.lang.VerifyError: (class: ij/gui/GenericDialog, method:
> showHelp signature: ()V) Incompatible argument to function
> at ij.plugin.StackWriter.run(StackWriter.java:54)
> at ij.IJ.runPlugIn(IJ.java:158)
> ... 35 more

I finally managed to dig into this and I think I solved it in commit
https://github.com/fiji/fiji/commit/93f65e5ca76c2462dbbb1a43b7a93679ed582a47

The fiji-compat.jar I uploaded after making the fix should resolve your
issues.

Ciao,
Johannes

[Nestor Milyaev]

Thanks all, figured it out now - the new Fiji version uses different
syntax:

run("TransformJ Rotate",'"z-angle='+z+' y-angle='+y+' x-angle='+x+'
interpolation=linear background=0.0 adjust"');

Thanks a lot!

Nestor
On Jun 5, 10:11 pm, Johannes Schindelin <Johannes.Schinde...@gmx.de>
wrote:

> Hi Nestor,
>
> On Thu, 24 May 2012, Nestor Milyaev wrote:
> >  Caused by: java.lang.VerifyError: (class: ij/gui/GenericDialog, method:
> > showHelp signature: ()V) Incompatible argument to function
> >      at ij.plugin.StackWriter.run(StackWriter.java:54)
> >      at ij.IJ.runPlugIn(IJ.java:158)
> >      ... 35 more
>

> I finally managed to dig into this and I think I solved it in commithttps://github.com/fiji/fiji/commit/93f65e5ca76c2462dbbb1a43b7a93679e...