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kreshuklab / plant-seg

A tool for cell instance aware segmentation in densely packed 3D volumetric images
https://kreshuklab.github.io/plant-seg/
MIT License
91 stars 31 forks source link

API docs | Docs screenshots | Refactor rescaling | Rearrange widgets #249

Closed lorenzocerrone closed 4 months ago

lorenzocerrone commented 4 months ago

This PR includes

lorenzocerrone commented 4 months ago

Let's merge it as it is now. This PR It's getting to big and too long. I will finish the docs in a next PR

qin-yu commented 4 months ago

Yeah I also think this went over the scope of this PR already. If you don't need me to check anything then just merge it.

lorenzocerrone commented 4 months ago

I would like you to check the new rescaling widget

qin-yu commented 4 months ago

I read the rescaling parts of changes and launched PlantSeg to see it. It looks great, and I think

  1. As long the rescaling functionalities are documented, such as the difference between To voxel size and Set voxel size, then all good
  2. To test these, maybe it's better to also write tests for them? It shouldn't rely on us clicking the widget 7 times to test each functions
  3. It is only a temporary solution to suppress warning with # type: ignore

I can do 2 and 3 if you don't have time for it.

lorenzocerrone commented 4 months ago

Yes it would be great if we you could do 2 and 3. Yeah I will document it all

qin-yu commented 4 months ago

I feel it make sense to have "Set voxel size" here, but it's still confusing before users read the docs. It is a very useful thing to have and I need it, but I don't know where to put either. If you thought about it already then let's just leave it there.

lorenzocerrone commented 4 months ago

I feel it make sense to have "Set voxel size" here, but it's still confusing before users read the docs. It is a very useful thing to have and I need it, but I don't know where to put either. If you thought about it already then let's just leave it there.

The alternative would be to put it in the IO tab as a stand alone widget.

qin-yu commented 4 months ago

I was thinking if we could merge all changes up to ff3d714ad12d06660dde35bf1457e3e7eff1e130 and move the later commits into another PR and work there, but then realised the later commits are kind of related. Since you are done with the planed documentation update in this PR, let's rename and merge it before it includes everything.

Yes it would be great if we you could do 2 and 3. Yeah I will document it all

The alternative would be to put it in the IO tab as a stand alone widget.

I'll do these in the next one.