Posted by
Mark Hiner-2 on
Aug 14, 2014; 1:35pm
URL: http://imagej.273.s1.nabble.com/SCIFIO-Unusable-tp5009195p5009201.html
Hi Oli,
>SCIFIO is enabled by default and people are not aware of it
It's true, SCIFIO is a beta product and right now it's a step backwards
from classic ImageJ functionality. We enabled it by default because SCIFIO
development is driven completely by user feedback, and we're trying to the
point where it meets the typical user's day-to-day needs as quickly as we
can.
That said, I agree that the significance of the "Use SCIFIO when opening
files" option is not sufficiently conveyed, and it is not clear that users
should try disabling SCIFIO when something goes wrong.
On the plus side, this has led to an internal re-evaluation of our error
handling and reporting system, and we've started discussion on an
interactive troubleshooter plugin that could help identify why images fail
to open (and suggest disabling SCIFIO, for example) - although it's lower
priority than actual bug and performance fixes for SCIFIO right now.
As a temporary improvement I will expand the ImageJ2 options dialog to
provide more of a warning when SCIFIO is enabled, and explain when SCIFIO
should be disabled.
>Though I understand the motivation behind SCIFIO, I find it too rough to
force-enable it every time Fiji gets a major >update at this stage of its
development.
This makes me suspect there may be two bugs that are increasing the
severity of the SCIFIO failures. I opened these issues to investigate:
* SCIFIO should pass control back to ImageJ when it fails
<
https://github.com/imagej/imagej-legacy/issues/78>
* SCIFIO use state shouldn't be toggled after updates
<
https://github.com/imagej/imagej-legacy/issues/79>
>We have multichannel tiffs, lsm files, czi files, zvi files lifs
It would be a great help if you could ensure these are reported on the Fiji
BugZilla
<
http://fiji.sc/bugzilla/buglist.cgi?product=Fiji&resolution=---&list_id=1044>.
There are reports for some of these formats, but I wasn't sure if they were
already from you or your team - especially as some were Bio-Formats
problems (and it sounds like your issues are not).
>So far about once a day we get someone coming over telling us they can no
longer open their files
You can also point people to the bug reporting section
<
http://imagej.net/Bug_reporting_best_practices> of the wiki, which links
to "Report a Bug" use and suggests disabling SCIFIO.
Thanks for the feedback!
- Mark
On Thu, Aug 14, 2014 at 2:53 AM, Burri Olivier <
[hidden email]>
wrote:
> Dear all,
>
> As of right now the SCIFIO library is quite unusable with most of our
> data. We have multichannel tiffs, lsm files, czi files, zvi files lifs and
> so far the only thing that works is to disable it and use the classic LOCI
> formats.
>
> So far about once a day we get someone coming over telling us they can no
> longer open their files and what do you know, SCIFIO is enabled by default
> and people are not aware of it, causing old macros to stop working or just
> being unable to open files.
>
> Though I understand the motivation behind SCIFIO, I find it too rough to
> force-enable it every time Fiji gets a major update at this stage of its
> development.
>
> Best
>
> Oli
>
>
>
>
>
>
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> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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