Fiji Main Window does not open when started from command line

[Sebastian Rhode-4]

Hi guys,

I tried to start fiji from the command line with

c:\Users\Public\Documents\Fiji>ImageJ-win64.exe -macro XYZ.ijm

When I press enter I see the Fiji symbol appear and my toolbars and the
Fiji control panel opens up. But the Fiji main windows never does? And the
macro is not excuted as well? When I open the macro manually and run it it
is excuted correctly. Any idea, what the problem might be?

But when I try:

c:\Users\Public\Documents\Fiji>ImageJ-win64.exe

Fiji opens correctly and the main window is visible.

Sebi


Macro XYZ.ijm:

name = "c:\\Users\\M1SRH\\Documents\\Experiment-29.czi"

run("Bio-Formats Importer", "open=[" + name + "] autoscale
color_mode=Default open_all_series view=Hyperstack stack_order=XYCZT");
getDimensions(width,height,channels,slices,frames);
run("Z Project...", "start=1 stop=" + slices + " projection=[Max
Intensity]");
run("Fire"); // apply special LUT

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi SebI,

That is strange. Try following the instructions at
http://imagej.net/Troubleshooting, especially the bit about launching in
debug mode. Might shed some light on the issue.

Regards,
Curtis
On Oct 26, 2015 7:53 AM, "Sebastian Rhode" <[hidden email]> wrote:

> Hi guys,
>
> I tried to start fiji from the command line with
>
> c:\Users\Public\Documents\Fiji>ImageJ-win64.exe -macro XYZ.ijm
>
> When I press enter I see the Fiji symbol appear and my toolbars and the
> Fiji control panel opens up. But the Fiji main windows never does? And the
> macro is not excuted as well? When I open the macro manually and run it it
> is excuted correctly. Any idea, what the problem might be?
>
> But when I try:
>
> c:\Users\Public\Documents\Fiji>ImageJ-win64.exe
>
> Fiji opens correctly and the main window is visible.
>
> Sebi
>
>
> Macro XYZ.ijm:
>
> name = "c:\\Users\\M1SRH\\Documents\\Experiment-29.czi"
>
> run("Bio-Formats Importer", "open=[" + name + "] autoscale
> color_mode=Default open_all_series view=Hyperstack stack_order=XYCZT");
> getDimensions(width,height,channels,slices,frames);
> run("Z Project...", "start=1 stop=" + slices + " projection=[Max
> Intensity]");
> run("Fire"); // apply special LUT
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Sebastian Rhode-5]

Hi Curtis,

I downloaded a fresh Fiji with JRE for Win64 bit and I tried the same again with the --debug option.

The output can be downlodaed from:

https://dl.dropboxusercontent.com/u/623476/Fiji_Command_Line_Issue.txt

The same behavior, no Fiji window ...

Sebi

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Sebi,

> The same behavior, no Fiji window ...

Sorry for the very long delay in following up. Did you ever resolve this
issue?

I checked out the log you posted, and I don't see anything suspicious. It
actually gets very far along.

What do you get when you print a thread dump after all the debugging output
is done printing?
   http://imagej.net/Troubleshooting#If_ImageJ_freezes_or_hangs

Anything enlightening in the stack traces?

Does it happen with all macros, or only your XYZ.ijm?

Regards,
Curtis

On Tue, Oct 27, 2015 at 9:56 AM, Sebastian Rhode <
[hidden email]> wrote:

> Hi Curtis,
>
> I downloaded a fresh Fiji with JRE for Win64 bit and I tried the same
> again with the --debug option.
>
> The output can be downlodaed from:
>
> https://dl.dropboxusercontent.com/u/623476/Fiji_Command_Line_Issue.txt
>
> The same behavior, no Fiji window ...
>
> Sebi
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html