Replace use of properties with features #425
Conversation
github-actions
bot
added
the
documentation
|
Cool, thanks @andy-sweet! Let me know when you think this is ready for review! 🙏 |
| @@ -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` | |||
There was a problem hiding this comment.
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.
There was a problem hiding this comment.
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 🤣
| @@ -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 | |||
There was a problem hiding this comment.
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.
| @@ -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 | |||
There was a problem hiding this comment.
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.
|
@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
changed the title
Check is done. |
docs/howtos/layers/points.md
Outdated
| 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 |
There was a problem hiding this comment.
maybe a bit confusing for folks unfamiliar with pandas to talk about columns/rows in a dictionary.
There was a problem hiding this comment.
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.)
There was a problem hiding this comment.
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.
There was a problem hiding this comment.
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.
| @@ -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. | |||
There was a problem hiding this comment.
I always forget about this. It's so cool. 😃
There was a problem hiding this comment.
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. 😂
|
I think I addressed the feedback and also fixed a couple of links/cross-references. Please take another quick look before merging! |
|
Thanks for the second look. I'll merge this after the weekend unless anyone objects. |
|
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 |
References and relevant issues
Part of napari/napari#3911
Description
This replaces use of
properties,property_choices, andcurrent_propertieswithfeaturesandfeature_defaults. The motivation for doing this now is to make the latest documentation consistent with existing code and examples onmain(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.