scifio and headless fiji under linux

[Daniel Matthews]

Hi

I am using Fiji at the command line in headless mode and running commands using a macro. I am working in a server environment using Ubuntu 14.04 (trusty). The images I am trying to work on our saved in the OME.TIFF format and I am trying to using the "open(path)" macro command with ImageJ2 options enabled.

When I download Fiji in the server it seems as if ImageJ2 options are not enabled by default (I get an error telling me there are no images open). Since I do not have a desktop environment, I use a local machine with the same version of Ubuntu to start Fiji and enable the ImageJ2 options. I then tar and move this version of Fiji to the server. However, when I try to run my macro I get the same "no images open" error message which seems to suggest that the ImageJ2 options are again disabled.

Is there a way to enable ImageJ2 at the command line or in a config file?

Cheers,

Dan.

[ctrueden]

Hi Dan,

> Is there a way to enable ImageJ2 at the command line or in a config
> file?

The preferences are saved in a platform specific way using the Java
Preferences API. Unfortunately, it is not trivial to toggle these values
from the CLI right now.

Could you please file an issue on GitHub with an enhancement request?

https://github.com/imagej/imagej/issues

Thanks,
Curtis


On Mon, Nov 10, 2014 at 5:05 PM, Daniel Matthews <[hidden email]>
wrote:

> Hi
>
> I am using Fiji at the command line in headless mode and running commands
> using a macro. I am working in a server environment using Ubuntu 14.04
> (trusty). The images I am trying to work on our saved in the OME.TIFF
> format
> and I am trying to using the "open(path)" macro command with ImageJ2
> options
> enabled.
>
> When I download Fiji in the server it seems as if ImageJ2 options are not
> enabled by default (I get an error telling me there are no images open).
> Since I do not have a desktop environment, I use a local machine with the
> same version of Ubuntu to start Fiji and enable the ImageJ2 options. I then
> tar and move this version of Fiji to the server. However, when I try to run
> my macro I get the same "no images open" error message which seems to
> suggest that the ImageJ2 options are again disabled.
>
> Is there a way to enable ImageJ2 at the command line or in a config file?
>
> Cheers,
>
> Dan.
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/scifio-and-headless-fiji-under-linux-tp5010369.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[ctrueden]

Hi everyone,

> The preferences are saved in a platform specific way using the Java
> Preferences API. Unfortunately, it is not trivial to toggle these
> values from the CLI right now.

For the archives: the following GitHub issue now tracks this:
   https://github.com/imagej/imagej/issues/102

I posted a couple of quick workarounds there, too.

Regards,
Curtis

On Mon, Nov 17, 2014 at 4:50 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Dan,
>
> > Is there a way to enable ImageJ2 at the command line or in a config
> > file?
>
> The preferences are saved in a platform specific way using the Java
> Preferences API. Unfortunately, it is not trivial to toggle these values
> from the CLI right now.
>
> Could you please file an issue on GitHub with an enhancement request?
>
> https://github.com/imagej/imagej/issues
>
> Thanks,
> Curtis
>
>
> On Mon, Nov 10, 2014 at 5:05 PM, Daniel Matthews <[hidden email]>
> wrote:
>
>> Hi
>>
>> I am using Fiji at the command line in headless mode and running commands
>> using a macro. I am working in a server environment using Ubuntu 14.04
>> (trusty). The images I am trying to work on our saved in the OME.TIFF
>> format
>> and I am trying to using the "open(path)" macro command with ImageJ2
>> options
>> enabled.
>>
>> When I download Fiji in the server it seems as if ImageJ2 options are not
>> enabled by default (I get an error telling me there are no images open).
>> Since I do not have a desktop environment, I use a local machine with the
>> same version of Ubuntu to start Fiji and enable the ImageJ2 options. I
>> then
>> tar and move this version of Fiji to the server. However, when I try to
>> run
>> my macro I get the same "no images open" error message which seems to
>> suggest that the ImageJ2 options are again disabled.
>>
>> Is there a way to enable ImageJ2 at the command line or in a config file?
>>
>> Cheers,
>>
>> Dan.
>>
>>
>>
>> --
>> View this message in context:
>> http://imagej.1557.x6.nabble.com/scifio-and-headless-fiji-under-linux-tp5010369.html
>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>

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