Handle Extra Files Types not working

[Davíð Þór Bragason]

Dear list,

my plugin opens a special file format. I had a working setup where the
files were opened via HandleExtraFileTypes.class, which I copied to the
plugins directory. After an update a few days ago this no longer works.
Opener gives the following error:

"File is not in a supported format, a reader plugin is not available, or it
was not found"

I am running Fiji ImageJ 2.0.0-rc4/1.49b with Java 1.7. Do I have to set up
HandleExtraFileTypes in a different way now? I understand that one of the
last updates was meant to re-enable .class plugins. Thank you very much for
your help.

Regards,
David

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[dscho]

Hi,

On Sat, 14 Jun 2014, Davíð Þór Bragason wrote:

> my plugin opens a special file format. I had a working setup where the
> files were opened via HandleExtraFileTypes.class, which I copied to the
> plugins directory. After an update a few days ago this no longer works.
> Opener gives the following error:
>
> "File is not in a supported format, a reader plugin is not available, or
> it was not found"
>
> I am running Fiji ImageJ 2.0.0-rc4/1.49b with Java 1.7. Do I have to set
> up HandleExtraFileTypes in a different way now? I understand that one of
> the last updates was meant to re-enable .class plugins. Thank you very
> much for your help.

Since rc-5, the "Find Jar For Class" command (in Plugins/Utilities) should
work again; use it to verify that your HandleExtraFileTypes class can be
found.

In the near future, you might want to turn your reader into a SCIFIO
reader. That way, *many* more users can benefit from your work. It is
pretty easy, just follow the code for the PGM format; I find it pretty
self-explanatory myself:

https://github.com/scifio/scifio/blob/master/scifio/src/main/java/io/scif/formats/PGMFormat.java

Remember, SCIFIO is a stand-alone project for scientific image
input/output, it can be used from *every* Java (*1*) project, without
making said project depend on ImageJ. And you can add support for your
file format by dropping in a .jar file with your reader, no changes in
SCIFIO, HandleExtraFileTypes, or any other central place required.

Ciao,
Johannes

Footnote *1*: SCIFIO can actually also be used from C++, as the ITK
bindings demonstrate: https://github.com/scifio/scifio-itk-bridge

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[Davíð Þór Bragason]

Hello,

HandleExtraFileTypes is working perfectly again. Thank you very much
Johannes for your help. SCIFIO looks very exciting and I will definitely
start using it very soon.
Regards,
David



On Sat, Jun 14, 2014 at 11:30 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Sat, 14 Jun 2014, Davíð Þór Bragason wrote:
>
> > my plugin opens a special file format. I had a working setup where the
> > files were opened via HandleExtraFileTypes.class, which I copied to the
> > plugins directory. After an update a few days ago this no longer works.
> > Opener gives the following error:
> >
> > "File is not in a supported format, a reader plugin is not available, or
> > it was not found"
> >
> > I am running Fiji ImageJ 2.0.0-rc4/1.49b with Java 1.7. Do I have to set
> > up HandleExtraFileTypes in a different way now? I understand that one of
> > the last updates was meant to re-enable .class plugins. Thank you very
> > much for your help.
>
> Since rc-5, the "Find Jar For Class" command (in Plugins/Utilities) should
> work again; use it to verify that your HandleExtraFileTypes class can be
> found.
>
> In the near future, you might want to turn your reader into a SCIFIO
> reader. That way, *many* more users can benefit from your work. It is
> pretty easy, just follow the code for the PGM format; I find it pretty
> self-explanatory myself:
>
>
> https://github.com/scifio/scifio/blob/master/scifio/src/main/java/io/scif/formats/PGMFormat.java
>
> Remember, SCIFIO is a stand-alone project for scientific image
> input/output, it can be used from *every* Java (*1*) project, without
> making said project depend on ImageJ. And you can add support for your
> file format by dropping in a .jar file with your reader, no changes in
> SCIFIO, HandleExtraFileTypes, or any other central place required.
>
> Ciao,
> Johannes
>
> Footnote *1*: SCIFIO can actually also be used from C++, as the ITK
> bindings demonstrate: https://github.com/scifio/scifio-itk-bridge

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[Davíð Þór Bragason]

Unfortunately I have to report that HandleExtraFileTypes is broken again on
my rc-5 installation. I can not find "Find Jar For Class" in
Plugins/Utilities. And HandleExtraFileTypes is now listed in the Plugins
menu, which was not the case before.

Regards,
David


On Sun, Jun 15, 2014 at 6:16 PM, Davíð Þór Bragason <[hidden email]>
wrote:

> Hello,
>
> HandleExtraFileTypes is working perfectly again. Thank you very much
> Johannes for your help. SCIFIO looks very exciting and I will definitely
> start using it very soon.
> Regards,
> David
>
>
>
> On Sat, Jun 14, 2014 at 11:30 PM, Johannes Schindelin <
> [hidden email]> wrote:
>
>> Hi,
>>
>> On Sat, 14 Jun 2014, Davíð Þór Bragason wrote:
>>
>> > my plugin opens a special file format. I had a working setup where the
>> > files were opened via HandleExtraFileTypes.class, which I copied to the
>> > plugins directory. After an update a few days ago this no longer works.
>> > Opener gives the following error:
>> >
>> > "File is not in a supported format, a reader plugin is not available, or
>> > it was not found"
>> >
>> > I am running Fiji ImageJ 2.0.0-rc4/1.49b with Java 1.7. Do I have to set
>> > up HandleExtraFileTypes in a different way now? I understand that one of
>> > the last updates was meant to re-enable .class plugins. Thank you very
>> > much for your help.
>>
>> Since rc-5, the "Find Jar For Class" command (in Plugins/Utilities) should
>> work again; use it to verify that your HandleExtraFileTypes class can be
>> found.
>>
>> In the near future, you might want to turn your reader into a SCIFIO
>> reader. That way, *many* more users can benefit from your work. It is
>> pretty easy, just follow the code for the PGM format; I find it pretty
>> self-explanatory myself:
>>
>>
>> https://github.com/scifio/scifio/blob/master/scifio/src/main/java/io/scif/formats/PGMFormat.java
>>
>> Remember, SCIFIO is a stand-alone project for scientific image
>> input/output, it can be used from *every* Java (*1*) project, without
>> making said project depend on ImageJ. And you can add support for your
>> file format by dropping in a .jar file with your reader, no changes in
>> SCIFIO, HandleExtraFileTypes, or any other central place required.
>>
>> Ciao,
>> Johannes
>>
>> Footnote *1*: SCIFIO can actually also be used from C++, as the ITK
>> bindings demonstrate: https://github.com/scifio/scifio-itk-bridge
>
>
>

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[dscho]

Hi,

On Tue, 17 Jun 2014, Davíð Þór Bragason wrote:

> Unfortunately I have to report that HandleExtraFileTypes is broken again on
> my rc-5 installation. I can not find "Find Jar For Class" in
> Plugins/Utilities. And HandleExtraFileTypes is now listed in the Plugins
> menu, which was not the case before.

Then I will have to ask you to package it up with Plugins/Utilities/Make
Fiji Package and upload it with Help/Upload Sample Image, because I have
no chance to understand what is going on on your side otherwise.

Ciao,
Johannes

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[Davíð Þór Bragason]

Hi Johannes,

thank you very much for your help. Actually if I do "Export as .jar" from
the Fiji editor and put HandleExtraFileTypes.jar in the plugins directory,
it works fine. However, if I have the .class file in the plugins directory
I get the error. And this is a fresh, up to date Fiji installation, meaning
I have done nothing but copy HandleExtraFileTypes into plugins. And my
addition to HandleExtraFileTypes.java is trivial:

if (name.endsWith(".ret")) {
return tryPlugIn("oximetry.OximetryTest", path);
}

So, this issue is no longer a problem for me. I will be migrating to SCIFIO
soon anyway. Thank you again.

Regards,
David





On Tue, Jun 17, 2014 at 1:02 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Tue, 17 Jun 2014, Davíð Þór Bragason wrote:
>
> > Unfortunately I have to report that HandleExtraFileTypes is broken again
> on
> > my rc-5 installation. I can not find "Find Jar For Class" in
> > Plugins/Utilities. And HandleExtraFileTypes is now listed in the Plugins
> > menu, which was not the case before.
>
> Then I will have to ask you to package it up with Plugins/Utilities/Make
> Fiji Package and upload it with Help/Upload Sample Image, because I have
> no chance to understand what is going on on your side otherwise.
>
> Ciao,
> Johannes

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