Standalone python script by will-moore · Pull Request #669 · ome/omero-figure

will-moore · 2026-02-23T17:03:28Z

As part of the work to support figure usage and PDF/TIFF generation with OME-Zarr data (without using OMERO),
this PR focusses on the Figure_To_Pdf.py (see #619 for front-end changes).

We want to be able to use the same PDF/TIFF generation code both in OMERO and as a stand-alone script (in a python environment that doesn't have omero-py installed, but has zarr, dask etc instead).

Basic idea is that you go to a stand-alone OMERO.figure app (from #619) e.g. https://will-moore.github.io/omero-figure/?file=https://gist.githubusercontent.com/will-moore/75a7f0de5be0f7b4202d5f0229cadcc9/raw/8d9681c70354189420c1c0adfe1f442dd1caac3e/ngff_images_figure.json and File > Save to download the figure.json file.
NB: LUTs not yet supported for Zarrs

Then, you run below (also added this to README):

# All images in figure are zarr images
# so we don't need omero-py - `[export]` install will include reportlab and markdown

$ conda create --name figure_export python=3.12
$ conda activate figure_export

# Once on pypi, this will just be: pip install omero-figure[export]
$ pip install "omero-figure[export] @ git+https://github.com/ome/omero-figure.git@refs/pull/669/head"
...
Successfully installed charset-normalizer-3.4.6 click-8.3.1 cloudpickle-3.1.2 dask-2026.1.2 donfig-0.8.1.post1 
fsspec-2026.2.0 google-crc32c-1.8.0 locket-1.0.0 numcodecs-0.16.5 numpy-2.4.3 omero-figure-7.4.2.dev0 
packaging-26.0 partd-1.4.2 pillow-12.1.1 pyyaml-6.0.3 reportlab-4.4.10 toolz-1.1.0 typing-extensions-4.15.0 zarr-3.1.5

$ figure_export figure_json/OME-Zarr_demo.json OME-Zarr_demo.pdf

TODO:

Support LUTs for zarrs (or ignore)?

…cript

…mero-web

jburel · 2026-03-23T09:36:57Z

./setup.py:85:80: E501 line too long (86 > 79 characters)

will-moore · 2026-03-23T09:46:57Z

@pwalczysko This PR wasn't included in merge-ci today, but you can still test the pip install workflow above to test locally, Thanks

pwalczysko · 2026-03-23T11:54:59Z

wfm, but it feels strange to test it only on the one single json which is mentioned in teh header of the PR. Would this work also on a Figure which was created in OMERO with all the images as Zarrs ?

pwalczysko · 2026-03-23T11:55:19Z

wfm, but it feels strange to test it only on the one single json which is mentioned in teh header of the PR. Would this work also on a Figure which was created in OMERO with all the images as Zarrs ?

Answer is: Yes, this is possible. Created a json out of the (purely zarr-containing) figure https://merge-ci.openmicroscopy.org/web/figure/file/8175. Then run the cmd

figure_export test-omero.json OME-Zarr_demo.pdf # this did not overwrite the already existing OME-Zarr_demo.pdf
ls -lah | grep .pdf
...

-rw-r--r--    1 pwalczysko  staff   1.1M 23 Mar 11:47 OME-Zarr_demo_page_02.pdf
-rw-r--r--    1 pwalczysko  staff   1.1M 23 Mar 11:48 OME-Zarr_demo_page_03.pdf
-rw-r--r--@   1 pwalczysko  staff    72M 23 Mar 11:36 OME-Zarr_demo.pdf

Basically, the pdf once created is not overwritten if another json is fed into the cmd figure_export.....
Instead, some new pdfs with similar names are (silently) created. This is highly unusual.

pwalczysko

Please address the comment ^^^ thank you

will-moore · 2026-03-23T21:39:11Z

@pwalczysko Done:

$ figure_export ngff_images_figure.json TEST_labels2.pdf 
input:  ngff_images_figure.json
output: TEST_labels2.pdf
Output file TEST_labels2.pdf already exists; Exiting.

pwalczysko · 2026-03-24T12:40:25Z

Tried to test what happens if I use LUTs in a figure.
Figure: https://merge-ci.openmicroscopy.org/web/figure/file/8175

Exported the colorbar.json from the figure ^^^ and then run the below which errored.

Error

figure_export colorbar.json  testcolobar-aha.pdf
input:  colorbar.json
output: testcolobar-aha.pdf
render_zarr_to_pil: URL https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0036/20633.ome.zarr/I/6/0
Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/bin/figure_export", line 6, in <module>
    sys.exit(figure_export())
             ^^^^^^^^^^^^^^^
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/lib/python3.12/site-packages/omero_figure/cli.py", line 57, in figure_export
    export_figure(None, script_args)
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/lib/python3.12/site-packages/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py", line 3428, in export_figure
    return fig_export.build_figure()
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/lib/python3.12/site-packages/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py", line 1257, in build_figure
    self.add_panels_to_page(panels_json, page)
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/lib/python3.12/site-packages/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py", line 2752, in add_panels_to_page
    pil_img = self.draw_panel(panel, page, i)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/lib/python3.12/site-packages/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py", line 2571, in draw_panel
    pil_img = self.get_panel_image(panel, orig_name)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/lib/python3.12/site-packages/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py", line 2483, in get_panel_image
    scale, pil_img = self.render_zarr_to_pil(panel)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/lib/python3.12/site-packages/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py", line 2434, in render_zarr_to_pil
    r = int(hex_color[0:2], 16)
        ^^^^^^^^^^^^^^^^^^^^^^^
ValueError: invalid literal for int() with base 16: 'ra'

Imho it is fine not to support LUTs (simple colorbar was working fine, I think the error is rather about the LUTs).
But do not let the user experience the error

will-moore · 2026-03-24T16:37:08Z

@pwalczysko OK, so I've ignored LUTs for now, and added a NB note to the README about it.

pwalczysko

figure_export colorbar.json  testcolobar-aha.pdf    
input:  colorbar.json
output: testcolobar-aha.pdf
render_zarr_to_pil: URL https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0036/20633.ome.zarr/I/6/0
Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/bin/figure_export", line 6, in <module>
    sys.exit(figure_export())
             ^^^^^^^^^^^^^^^
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/lib/python3.12/site-packages/omero_figure/cli.py", line 57, in figure_export
    export_figure(None, script_args)
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/lib/python3.12/site-packages/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py", line 3431, in export_figure
    return fig_export.build_figure()
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/lib/python3.12/site-packages/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py", line 1257, in build_figure
    self.add_panels_to_page(panels_json, page)
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/lib/python3.12/site-packages/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py", line 2763, in add_panels_to_page
    self.draw_colorbar(panel, page)
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/lib/python3.12/site-packages/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py", line 2002, in draw_colorbar
    color_ramp = self.get_color_ramp(channel)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pwalczysko/opt/anaconda3/envs/figure_export/lib/python3.12/site-packages/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py", line 1935, in get_color_ramp
    script_service = self.conn.getScriptService()
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^

The error above is different than previously. I have reinstalled omero-figure in my env. The non-colorbar figure is working fine.

Co-authored-by: pwalczysko <p.walczysko@dundee.ac.uk>

will-moore · 2026-03-25T09:48:26Z

@pwalczysko Thanks for that - LUTs now also grey in colorbars, removed extra line, and also fixed handling of "inactive" channels for Zarr.

pwalczysko · 2026-03-25T18:31:51Z

Tested again, with LUTs, colorbar and fresh ROIs. lgtm, thanks

pwalczysko

Just a second. I have realized you are overwriting the existing script in this PR ?

I have uploaded the Figure_to_pdf.py script from this PR to merge-ci.

Then I have exported the figure (the old way) and see that there is a discrepancy between the generated pdf and the Figure https://merge-ci.openmicroscopy.org/web/figure/file/8175/

Possibly this is expected, but I would like us to have a look, thanks.

will-moore · 2026-03-25T21:49:34Z

@pwalczysko The issue you're seeing there is the lack of support for rendering LUT channels of OME-Zarr images, so it's greyscale in the image.
I guess it's confusing because the colorbar is rendered correctly because you are connected to OMERO.

pwalczysko · 2026-03-26T10:46:09Z

Tested couple of more figures on merge-ci, mostly non-zarr, but also zarr, with ROIs and LuTs as well as switched-off channels.

pwalczysko

lgtm

will-moore added 2 commits February 23, 2026 16:57

Allow Figure_To_Pdf.py to run without omero

37f4d56

Add local pilfonts to scripts folder

f309995

will-moore mentioned this pull request Feb 23, 2026

OME-Zarr and standalone app #668

Open

revert removing omero-web requirement

1c7ff8d

This was referenced Feb 26, 2026

Export script handles OME-zarr images #662

Merged

Standalone app #666

Merged

will-moore added 7 commits March 4, 2026 14:31

Add outputPathName option for standalone export script

28f3988

Update README with standalone export script info

1af65fb

Merge remote-tracking branch 'origin/master' into standalone_python_s…

90e2961

…cript

pip install [export] to include script dependencies, or [omero] for o…

d7b6b60

…mero-web

Add __init__.py files to make figure_scripts into importable package

6682109

Add figure_export cli command

e6fc213

Add fsspec[http] to export dependencies

7f1f623

will-moore marked this pull request as ready for review March 17, 2026 21:03

will-moore added 2 commits March 17, 2026 21:18

Update README with export instructions

fe95184

Flake8 fixes and add copyright to cli.py

0affd4b

will-moore force-pushed the standalone_python_script branch from 567f85c to 0affd4b Compare March 18, 2026 11:24

will-moore added 2 commits March 18, 2026 11:32

Add NB: to figure export in README

4deda5b

Add 'markdown' to export dependencies

03bd800

flake8 fix

0fbdafd

will-moore requested a review from pwalczysko March 23, 2026 09:45

pwalczysko requested changes Mar 23, 2026

View reviewed changes

figure export command checks for output file exists

5e455c6

Ignore luts for OME-Zarr images in export script

96624c7

Add note to README about lack of LUTs support for figure export

d629a36

pwalczysko reviewed Mar 24, 2026

View reviewed changes

Comment thread README.rst Outdated

pwalczysko requested changes Mar 24, 2026

View reviewed changes

will-moore and others added 4 commits March 24, 2026 20:42

Update README.rst

10b6914

Co-authored-by: pwalczysko <p.walczysko@dundee.ac.uk>

Use grey instead of LUT for colorbar if no conn

28e72e5

Fix: Zarr rendering ignores inactive channels

254b60a

Remove blank line in README

ab007ae

flake8 fix

8453017

pwalczysko approved these changes Mar 25, 2026

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pwalczysko requested changes Mar 25, 2026

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pwalczysko approved these changes Mar 26, 2026

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will-moore merged commit 91c9a46 into ome:master Mar 26, 2026
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