Replace use of properties with features #425

andy-sweet · 2024-06-10T16:28:49Z

References and relevant issues

Description

This replaces use of properties, property_choices, and current_properties with features and feature_defaults. The motivation for doing this now is to make the latest documentation consistent with existing code and examples on main (here and on napari/napari) for the upcoming v0.5 release. As we also plan to deprecate properties in v0.5 (napari/napari#3911), this documentation update is necessary for that.

jni · 2024-06-11T06:19:12Z

Cool, thanks @andy-sweet! Let me know when you think this is ready for review! 🙏

andy-sweet · 2024-06-11T20:39:16Z

docs/howtos/layers/tracks.md

@@ -121,66 +121,6 @@ napari.run()
 * Graph - check this box to display a previously created graph as explained in
  [](#arguments-of-view_tracks-and-add_tracks).

-## Arguments of `view_tracks` and `add_tracks`


These docs are incomplete and stale for multiple reasons (including properties/features), so I removed this in favor of link to the two functions in the text above.

lmao I came here while trying to resolve merge conflicts with #420 going, "why on earth did this get removed. And no discussion either, wth!"

... Then I found my thumbs-up above 🤣

andy-sweet · 2024-06-11T22:44:48Z

docs/tutorials/annotation/annotate_points.md

@@ -4,8 +4,8 @@

 ```{Admonition} DEPRECATED ATTRIBUTES
 :class: warning
-As of napari 0.5.0, `edge_*` attributes are being renamed to 
-`border_*` attributes. We have yet to update the images and/or videos in 
+As of napari 0.5.0, `edge_*` attributes are being renamed to


The changes in this file mostly come from the corresponding PR over on the pointannotator repo: kevinyamauchi/PointAnnotator#6

I tested the example on that repo with napari's main.

There are also some other name swaps.

andy-sweet · 2024-06-11T22:49:26Z

docs/tutorials/segmentation/annotate_segmentation.md

@@ -100,16 +100,16 @@ def circularity(perimeter, area):
 image = data.coins()[50:-50, 50:-50]
 label_image = segment(image)

-# create the properties dictionary
-properties = regionprops_table(
+# create the features dictionary


The code changes come from napari's examples/annotate_segmentation_with_text.py example and should be consistent now.

Other changes in this file are mostly word swaps.

docs/tutorials/tracking/cell_tracking.md

andy-sweet · 2024-06-11T22:53:28Z

@jni: I have one last compatibility check to do with the btrack cell-tracking example, but other this is ready for review now.

andy-sweet · 2024-06-12T23:23:35Z

@jni: I have one last compatibility check to do with the btrack cell-tracking example, but other this is ready for review now.

Check is done.

brisvag

Other than the specific comment below, I think there's a general overlap between "table" and "dictionary" which might be confusing to new users.

brisvag · 2024-06-13T07:37:04Z

docs/howtos/layers/points.md

+dictionary with two feature columns: `good_point` and `confidence`.
+The table has three rows since there were three coordinates provided in `points`.
+We set the face color as a function of the `confidence` feature by providing the


maybe a bit confusing for folks unfamiliar with pandas to talk about columns/rows in a dictionary.

Ah, indeed, maybe worth saying that this is converted internally to a data frame with two columns and three rows? (I wouldn't specify pandas necessarily, but maybe.)

Agreed this paragraph is mixing things a bit too much. Let me try to fix that.

But I also want to make a distinction between the meaning of features (i.e. it's a table) and the type used to provide or implement it (i.e. a dict or DataFrame). Ideally, we could do that in one place for all layers (see #23).

For now, there's a little effort above to describe what the table is in the "### Using the points features table" section. I'll clean that up a little and will mention that the table can be provided as a dictionary where the values are array-likes of the same length.

I also (tried to) put a link back to the section that describes the dictionary and table/dataframe relationship in both of these similar paragraphs.

jni · 2024-06-13T08:46:45Z

docs/tutorials/segmentation/annotate_segmentation.md

@@ -355,7 +355,7 @@ text_parameters = {
 }
 ```

-The `text` key specifies pattern for the text to be displayed. If `text` is set to the name of a `properties` key, the value for that property will be displayed. napari text also accepts f-string-like syntax, as used here. napari will substitute each pair of curly braces(`{}`) with the values from the property specified inside of the curley braces. For numbers, the precision can be specified in the same style as f-strings. Additionally, napari recognizes standard special characters such as `\n` for new line.
+The `string` key specifies pattern for the text to be displayed. If `string` is set to the name of a `feature` column, the value for that feature will be displayed. napari text also accepts f-string-like syntax, as used here. napari will substitute each pair of curly braces(`{}`) with the values from the feature specified inside of the curly braces. For numbers, the precision can be specified in the same style as f-strings. Additionally, napari recognizes standard special characters such as `\n` for new line.


I always forget about this. It's so cool. 😃

jni

Thanks @andy-sweet, this is excellent! I think @brisvag's minor comment is worth addressing, but I'm also ok with it happening later, so I'm gonna approve this and ready-to-merge it, and if you get to it great and if not we can make an issue. 😂

andy-sweet · 2024-06-13T18:05:49Z

I think I addressed the feedback and also fixed a couple of links/cross-references. Please take another quick look before merging!

brisvag

Love the changes :)

andy-sweet · 2024-06-14T17:42:00Z

Thanks for the second look. I'll merge this after the weekend unless anyone objects.

imagesc-bot · 2024-06-18T17:02:17Z

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/error-while-adding-text-to-napari/76960/5

andy-sweet added 5 commits September 18, 2023 16:32

Initial updates to docs

1f5af0a

Merge branch 'main' into deprecate-properties

c356579

Fix some edge border mistakes

86f4546

Simplify

caa7b14

Remove manual docstring in docs

831a788

andy-sweet added this to the 0.5.0 milestone Jun 10, 2024

github-actions bot added the documentation Improvements or additions to documentation label Jun 10, 2024

github-actions bot assigned andy-sweet Jun 10, 2024

Add references to functions

596d9ca

andy-sweet commented Jun 11, 2024

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andy-sweet mentioned this pull request Jun 11, 2024

Prepare for upcoming napari v0.5 release kevinyamauchi/PointAnnotator#6

Open

andy-sweet added 2 commits June 11, 2024 15:41

Update tutorial from PR

e0b6cde

Fix spacing

b8ce1df

andy-sweet commented Jun 11, 2024

View reviewed changes

Make segmentation consistent with example

165c302

andy-sweet commented Jun 11, 2024

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docs/tutorials/tracking/cell_tracking.md Show resolved Hide resolved

andy-sweet marked this pull request as ready for review June 11, 2024 22:52

andy-sweet changed the title ~~[WIP] Replace use of properties with features~~ Replace use of properties with features Jun 12, 2024

Revert rename of props

fd6df62

brisvag reviewed Jun 13, 2024

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jni reviewed Jun 13, 2024

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jni approved these changes Jun 13, 2024

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jni added the ready to merge label Jun 13, 2024

andy-sweet added 3 commits June 13, 2024 08:34

Fix API links

00ec366

Add high level description of features table

0bfa45d

Add link back to main description

426fde3

andy-sweet added 3 commits June 13, 2024 10:23

Make other paragraph consistent

98032bb

Try to fix links

9eed8ec

Remove dead link

7326789

brisvag approved these changes Jun 14, 2024

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andy-sweet merged commit 1dd9162 into napari:main Jun 17, 2024
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andy-sweet deleted the deprecate-properties branch June 17, 2024 15:37

github-actions bot removed the ready to merge label Jun 17, 2024

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Replace use of properties with features #425

Replace use of properties with features #425

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Replace use of properties with features #425

Replace use of properties with features #425

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References and relevant issues

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