double-click on headers to generate parametric images - doesn't take into account "rotate" nor"scale" about napari-skimage-regionprops HOT 10 CLOSED

Thanks for the bug report @romainGuiet ! That's easily fixable here by handing over self._layer.affine to new_layer.affine. We should also do this with layer.scale.

If you have time, an could test this, a PR would be very welcome. Otherwise I'll do this in the coming weeks. No problem.

Thanks again for the feedback! 🤩

from napari-skimage-regionprops.

Hi @haesleinhuepf ,

I tried to follow your recommendation to fix it in ( PR #53) but I have absolutely 0 ideas how to test it in napari 😅 . I looked around but could't make a test work so far...

Can you point me to some tutos / documentations about how to test code modification of a napari plugin from VS Code or PYCharm ?

Thank you ,

Romain

from napari-skimage-regionprops.

Awesome thanks for your time @romainGuiet ! 🤩

Can you point me to some tutos / documentations about how to test code modification of a napari plugin from VS Code or PYCharm ?

Not IDE specific, but this page might guide you: https://biapol.github.io/Quantitative_Bio_Image_Analysis_with_Python_2022/day4c_crafting_napari_plugins/04_napari_cookiecutter.html
Also it's very simple: If you navigate in the terminal to the root folder of this repository on your hard drive and call...

pip install -e .

... the plugin will be installed in your active conda environment.
Then, you can test it in napari. Writing automated tests for user-interaction is a research field in itself (not joking) and thus, in this case we need to go for manual testing.

from napari-skimage-regionprops.

HI @haesleinhuepf

Awesome thanks for your time @romainGuiet !

Thank you for making all of these plugins and for the link.

I tried, to:

• make a new env
• pip install napari[all]
• use pip install -e . from the clone&modified folder

but I don't have the menu with Tools > Measurement Tables > Regionprops (nsr)

I tried to install napari-workflow , and still nothing show up.
Finally I tried to opy the code from "_table.py" in a notebook but then it can't find the package napari_tools_menu (while it is installed in this env )

I'm sorry for this newbie technical issues 😅

Cheers

R

from napari-skimage-regionprops.

Hey @romainGuiet ,

no worries. I'm full-time hired to support people who struggle with these kind of things.

• make a new env
• pip install napari[all]
• use pip install -e . from the clone&modified folder

Suspicious! In such cases I tend to immediately erase my conda installation completely and start from scratch as described here: https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/01_introduction/readme.html

I also install almost everything using mamba (read more). Try if this works from your base conda environment and from inside the napari-skimage-regionprops folder:

mamba create --name devbio-napari-env python=3.9 devbio-napari -c conda-forge
conda activate devbio-napari-env
pip install -e .

You're then developing against devbio-napari. The codename of the project is NIJI, because devbio-napari fulfills a similar mission for napari, like Fiji does for ImageJ.

If this doesn't work let's schedule a zoom meeting and troubleshoot together!

Thanks again for your time!

Best,
Robert

from napari-skimage-regionprops.

Hi @haesleinhuepf ,

I installed mambaforge and create a new environment.
I ran pip install -e . (also tried to run the code from a notebook (without import error this time) )
BUT
The image generated from the column header is still not rotated 😑 😅
I saw you merged it, did it work for you ?

BTW in devbio-napari the menu Tools> Measurements tables >, I have Regionprops (scikit-image nsr) but there is also Measurements (n-Simple ITK) and Label statistics (clEsperanto).
They all have similar look out, I guess they are also doing the same thing.
Is that necessary to have all of them ?
I tested all of them and I have the same issue ...

Cheers,

Romain

from napari-skimage-regionprops.

I saw you merged it, did it work for you ?

Will check...

They all have similar look out, I guess they are also doing the same thing.
Is that necessary to have all of them ?

Well not necessarily. I do find it practical to have measurements from multiple libraries in the same menu. In ImageJ, you find the Particle Analyzer, the ROI manager, the 3D ROI Manager and MorpholibJ's measurements in completely different menus

from napari-skimage-regionprops.

Ok, rotate was obviously missing in our changes @romainGuiet . Also just to be clear, I think the napari interface with separate affine, scale and rotate is badly designed. If you plan to develop a 3D viewer with layers, don't do it like this ;-)

from napari-skimage-regionprops.

Ok, rotate was obviously missing in our changes @romainGuiet .

😅 , indeed it was not in the PR (but I had it in my jupyter notebook, I guess I still need to understand how this works)

I modified ˋ_table.pyˋ to add rotate then ˋpip install -e .ˋ and now the rotate works !

in 3D with the scale, it's even more amazing :

from napari-skimage-regionprops.

Hey @romainGuiet ,

I just released napari-skimage-regionprops 0.8.2 which addresses this bug. Would you mind confirming that it works for you now?

pip install napari-skimage-regionprops==0.8.2

Thanks again and welcome in the list of contributors!

Best,
Robert

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