Open Microscopy Environment

Hi,

The 'Export PDF' function in Figure is failing and gives an error:

Traceback (most recent call last):
File "./script", line 2315, in <module>
run_script()
File "./script", line 2301, in run_script
file_annotation = export_figure(conn, script_params)
File "./script", line 2257, in export_figure
return fig_export.build_figure()
File "./script", line 962, in build_figure
self.add_panels_to_page(panels_json, image_ids, page)
File "./script", line 1767, in add_panels_to_page
image, pil_img = self.draw_panel(panel, page, i)
File "./script", line 1589, in draw_panel
pil_img = self.get_panel_image(image, panel, orig_name)
File "./script", line 1487, in get_panel_image
pil_img = self.get_panel_big_image(image, panel)
File "./script", line 1442, in get_panel_big_image
viewport_region, max_width)
File "./script", line 1361, in render_big_image_region
scale, level = self.get_zoom_level_scale(image, region, max_width)
File "./script", line 1337, in get_zoom_level_scale
max_level = len(zm_levels.keys()) - 1
AttributeError: 'NoneType' object has no attribute 'keys'

I've upgraded to Figure 4.02. Could the old version be cached somewhere perhaps?

Thanks,

Matt.

Hi Matt,

Couple of things I'd check:

Did you install the new export script as part of the upgrade?

See "Upgrade the figure export script" at https://figure.openmicroscopy.org/ for more on that.

Are all the OMERO.web prerequisites up to date?

You can check the OMERO.web install docs that relate to the installation method you used, for example, https://docs.openmicroscopy.org/omero/5 ... -omero-web

Cheers,

Kenny

Thanks Kenny. I've followed the instructions on those pages but i'm still getting the same error.

No worries. It was worth a try.

Is the figure export working for other figures/images, or is this an issue just with a particular image set?

And did it work for that same set of images before the upgrade (if it's possible to know that)?

Thanks,

Kenny

The problem seems to be with our .dm4 files. I think we had trouble with them before the upgrade too but if I remember they didn't open in Figure at all.

Thanks,

Matt.

Could you please send us a sample via http://qa.openmicroscopy.org.uk/qa/upload/ if it's <2GB?

Many thanks,

Kenny

Thanks. I uploaded a sample .dm4 yesterday morning.

Hi Matt, just to confirm that we received the dm4 file you uploaded and will have it tested shortly, apologies for the delay.

David Gault

Hi Matt,

thanks for uploading the sample file. I have been able to reproduce the issue on one of our testing server.

As far as I can tell the scope of this error is limited to the case of large floating-point images. OMERO has a known limitation while handling this type of data as it is currently unable to generate pyramidal levels if those are not present in the original file format.

At present, the OMERO.figure export script is expecting subresolution levels to render large images and generate the PDF. I opened a developer issue to start discussing the various options.

Best,
Sebastien

Thanks for looking at this.