Open Microscopy Environment

Hi,
Now that I am able to upload my time sequence using a pattern file
(thank you: https://www.openmicroscopy.org/community/viewtopic.php?f=6&t=8616&p=20245&sid=b1f07b48393f60159196ba8650caa023#p20245)
BrowseFacility::getImagesForDatasets will only return the pattern file uploaded for that dataset.
In the filesystem I can see all the associated images that were uploaded to the datadir/ManagedRepository/... but wondered if there was a function available which would return all these images that were uploaded via the pattern file?

Whilst the pattern file allows the user to view the time sequence, I need to be able to offer all the original files for download.

Thanks
Derek

Dear Derek,

Just to clarify: are you hoping for OMERO clients to show the different planes also as separate images with separate thumbnails or, as I suspect, is it more than you want to be able to download the files that were originally uploaded?

Cheers,
Mark

Yes, the latter.
Download the files that were originally uploaded.
Derek

Hi Derek,

in the OMERO sense the "Image" is the whole thing, the image which you created with the pattern file. You can't get the individual parts as single "Image" instances.

If you want to get the paths of the image files in the managed repository: That's not directly implemented in the Java Gateway yet. But you can get these paths via the QueryService, here's an example for how to do that: https://gist.github.com/dominikl/46894a ... e3ab04ae71

If you want download the images files: The 'downloadImage' method in the 'Transferfacility' should be able to do that https://downloads.openmicroscopy.org/om ... ility.html , e.g. something like:

Code: Select all

TransferFacility tf = gateway.getFacility(TransferFacility.class);
tf.downloadImage(ctx, "/home/user/Downloads", imageId);


Kind Regards,
Dominik

Hi Dominik,
That's exactly what I was looking for.
Many thanks.

Derek