Hi Jakob,
I would be surprised if this difference is really because of Linux vs. Mac.
1) Do you have exactly the same files in the relevant directory? Or
differing sets of files? Bio-Formats scans the file system to look for
metadata companion files, etc., and behaves differently depending on what
it finds.
2) Do you have exactly the same options checked in the Bio-Formats Importer
Options dialog? Unfortunately, the programmatic Bio-Formats API will reuse
the last settings selected from that dialog. In particular, if "Group files
with similar names" was checked from your last Importer call, it might
change how the stitching plugin behaves (I am not 100% certain off the top
of my head; would need to double check the Stitching code to be sure.)
3) Maybe a difference in your core ImageJ preferences? You can use the Edit
> Options > Reset... command to be certain they match across the two
systems.
Regards,
Curtis
On Tue, Aug 11, 2015 at 2:42 PM, Jakob M <
[hidden email]> wrote:
> Hi,
>
> I have a problem with the Fiji stitching plugin, but I believe to have
> narrowed it down to being a Bio-Formats import problem on Linux (Ubuntu
> 14.04 LTS). In short, the Bio-Formats import behaves differently on Linux
> and Mac, breaking some of the stitching plugin functionality on Linux
> (stitching works as expected on Mac).
>
> The problem can be reproduced simply as follows:
> Navigating to "File - Import - Bio-Formats" and selecting a file (z-stack
> in my case) opens a dialogue. Accepting the defaults, Fiji opens the
> selected z-stack as an individual file on Mac (even though the "Open Files
> Individually" option is unchecked), while on Linux it opens another
> dialogue, having identified other z-stacks for different time points and
> channels in the same directory. Although this is a nice feature in
> principle, it breaks the stitching plugin functionality for stitching
> z-stacks on Linux, because it tries to open the whole 5D hyperstack when it
> should only be opening a single z-stack.
>
> I can also reproduce the problem when scripting with jython:
> img= Opener.openUsingBioFormats(file)
> returns a z-stack on Mac and tries to read much more on Linux.
>
> I have also tried with different Fiji versions (including the latest
> builds), so that is not the problem. My questions are:
>
> - Why does the Bio-Formats importer return different things on Mac vs.
> Linux?
> - Is there a default option that can be set somewhere to make the Linux
> version behave like the Mac?
> - If that fails, is there a way of making the stitching plugin behave the
> same on Linux and Mac?
>
> Thanks for your help!
> Jakob
>
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