Further document use of regionprops function and fix terms. by mkcor · Pull Request #7518 · scikit-image/scikit-image

mkcor · 2024-08-30T14:59:46Z

Description

The main addition here is b0cbf30 + 7617fbd.

Along the way, I proofread the entire docstring. I'm not entirely sure I should have replaced type ndarray with array but I have a vague memory along these lines with @grlee77 ...

I'm pretty confident about all the other changes. @lagru I updated the imports under Examples.

@stefanv I used the term "label image" consistently and according to the conversation we had on Monday.

I made sure regions were referred to as "regions" or "image regions" throughout the text.

For the record, since I cannot apply a second label: I created this PR during the EuroSciPy 2024 sprint following a discussion with @lagru and @stefanv! 🚀

Checklist

A descriptive but concise pull request title
Docstrings for all functions
Unit tests
A gallery example in ./doc/examples for new features
Contribution guide is followed

Release note

For maintainers and optionally contributors, please refer to the instructions on how to document this PR for the release notes.

...

imagesc-bot · 2024-08-30T20:55:20Z

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

https://forum.image.sc/t/handling-coords-output-in-regionprops-table/75770/4

jni · 2024-08-31T07:52:07Z

skimage/measure/_regionprops.py

+    The table is "tidy" [1]_; it is a dictionary mapping property names to
+    value arrays. See Notes section below for details.


I would say:

The return value is a dictionary mapping property names to value arrays. This dictionary can be used as input to pandas.DataFrame to result in a "tidy" [1]_ table with one region per row and one property per column.

I love it, thank you! 0c92394

skimage/measure/_regionprops.py

mkcor · 2024-08-31T12:50:54Z

I'm not entirely sure I should have replaced type ndarray with array but I have a vague memory along these lines with @grlee77 ...

My mistake, ndarray is dominant in our codebase:

$ ack ": ndarray" | wc -l
602
$ ack ": array" | wc -l
254

I'll revert my changes from "ndarray" to "array" then!

Co-authored-by: Juan Nunez-Iglesias <[email protected]>

mkcor · 2025-02-18T21:48:57Z

I'm not entirely sure I should have replaced type ndarray with array but I have a vague memory along these lines with @grlee77 ...

@lagru iirc docstub parses ndarray and array differently...

Co-authored-by: Juan Nunez-Iglesias <[email protected]>

mkcor · 2025-04-08T09:33:51Z

@jni @lagru pinging you for review 🙏

Came back to this because we are currently mentioning regionprops at the GloBIAS + Data Carpentry workshop: We want to include image measurements in the Bioimage analysis with Python lesson-to-be.

lagru · 2025-04-08T11:56:31Z

skimage/measure/_regionprops.py

+    The return value is a dictionary mapping property names to value arrays.
+    This dictionary can be used as input to ``pandas.DataFrame`` to result in
+    a "tidy" [1]_ table with one region per row and one property per column.


This seems a bit redundant with the description in "Returns", no? Since the first line already implies pandas I'd remove this section in favor of highlighting the rest of the docstring.

Suggested change

The return value is a dictionary mapping property names to value arrays.

This dictionary can be used as input to ``pandas.DataFrame`` to result in

a "tidy" [1]_ table with one region per row and one property per column.

(Not a blocker though!)

I agree it's slightly redundant... Would you mind if I replaced "a pandas-compatible table" by "tabular data" in the first line?

I'd like the tidy reference to remain somewhere. It's not present in the Return section currently.

I didn't mean that this is verbatim included in returns. But I thought addressing this aspect in detail would make more sense in the return section where Pandas' DataFrame is already referenced.

lagru · 2025-04-08T11:58:00Z

skimage/measure/_regionprops.py

+    columns; for example, the region centroids of a 3D image end up in three
+    different columns, one per dimension. If you need to do complex
+    computations with the region properties, using
+    :func:`skimage.measure.regionprops` might be more fitting.


This could also go into the "Notes" section but since it's very useful context I'm totally fine with keeping it here. :) Nice improvement!

skimage/measure/_regionprops.py

lagru

Lot's of opportunity for bikeshedding here. 😅 Knowing that, I made a few suggestions on a take it or leave it basis.

The added paragraphs are very nice, the rest doesn't seem like a big game changer to me but I'm fine with it. :)

On second thoughts, probably should give Juan time to chime in as well.

Co-authored-by: Lars Grüter <[email protected]>

Co-authored-by: Juan Nunez-Iglesias <[email protected]>

mkcor · 2025-04-11T12:59:01Z

skimage/measure/_regionprops.py

    spacing=None,
 ):
-    """Compute image properties and return them as a pandas-compatible table.
+    """Compute region properties and return them as a pandas-compatible table.


Suggested change

"""Compute region properties and return them as a pandas-compatible table.

"""Compute region properties and return them as tabular data.

* origin/main: Deprecate estimate method in favor of class constructor (scikit-image#7771) Temporary fix for Visual Studio & Clang incompatibility in Windows image (scikit-image#7835) Address deprecations in Pillow 11.3 (scikit-image#7828) Remove unused & obsolete `legacy_datasets`, `legacy_registry` vars (scikit-image#7677) Draft migration guide for skimage2 (scikit-image#7785) Do not report failure in wheels sub-recipe (scikit-image#7806) Use consistent wording in property description. (scikit-image#7804) Add intensity_median to regionprops (scikit-image#7745) CI: Update pypa/gh-action-pypi-publish to v1.12.4 for attestations on PyPI (scikit-image#7793) Document output dtype for transform.resize. (scikit-image#7792) Use `cibuildwheel` to build WASM/Pyodide wheels for `scikit-image`, push nightlies to Anaconda.org (scikit-image#7440) DOC: Include missing gain parameter in adjust_gamma equation (scikit-image#7763) Temporarily pin to `pyodide-build==0.30.0`, and ensure that the correct xbuildenvs are used (scikit-image#7788) Deprecate old names & attributes in RegionProperties (scikit-image#7778) Pin JasonEtco/create-an-issue action to SHA for v2.9.2 (scikit-image#7787) Make doctest-plus work with spin (scikit-image#7786) Report failures on main via issue (scikit-image#7752) Use `workers` instead of alternate parameter names (scikit-image#7302) Fix f-string in otsu plot (scikit-image#7780) Further document use of regionprops function and fix terms. (scikit-image#7518)

mkcor added 4 commits August 30, 2024 14:52

Proofread docstrings for related docstrings

c56e4ce

Proofread docstring of regionprops function

2559113

Update doctest

cdac16b

Detail use of regionprops vs regionprops_table

b0cbf30

mkcor added the 📄 type: Documentation Updates, fixes and additions to documentation label Aug 30, 2024

mkcor added 2 commits August 31, 2024 09:41

Add reference to tidy data

1db7a17

Document difference between the two regionprops functions

5030275

jni reviewed Aug 31, 2024

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Clarify meaning of pixel-area

9f06925

jni reviewed Aug 31, 2024

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mkcor and others added 3 commits August 31, 2024 17:35

Revert changes from ndarray to array

2d6daea

Improve description

0c92394

Co-authored-by: Juan Nunez-Iglesias <[email protected]>

Reword description

a639075

Co-authored-by: Juan Nunez-Iglesias <[email protected]>

mkcor mentioned this pull request Nov 19, 2024

Generate typing stubs with docstub #7546

Closed

3 tasks

Merge branch 'main' into improve-regionprops-docs

5244437

Address code review

7617fbd

Co-authored-by: Juan Nunez-Iglesias <[email protected]>

mkcor requested review from jni and lagru February 18, 2025 21:58

Merge branch 'main' into improve-regionprops-docs

8440370

lagru reviewed Apr 8, 2025

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lagru previously approved these changes Apr 8, 2025

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Apply suggestions from code review

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Co-authored-by: Lars Grüter <[email protected]>

jni approved these changes Apr 11, 2025

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Update skimage/measure/_regionprops.py

47500ae

Co-authored-by: Juan Nunez-Iglesias <[email protected]>

mkcor commented Apr 11, 2025

View reviewed changes

jni added this to the 0.26 milestone Apr 25, 2025

jni merged commit d480b0e into scikit-image:main Apr 25, 2025
23 checks passed

mkcor mentioned this pull request Jul 16, 2025

Documentation for measure.regionprops property 'image_intensity' is misleading #7840

Open

		The table is "tidy" [1]_; it is a dictionary mapping property names to
		value arrays. See Notes section below for details.

	The return value is a dictionary mapping property names to value arrays.
	This dictionary can be used as input to ``pandas.DataFrame`` to result in
	a "tidy" [1]_ table with one region per row and one property per column.

	"""Compute region properties and return them as a pandas-compatible table.
	"""Compute region properties and return them as tabular data.

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mkcor commented Aug 30, 2024 •

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