get_extent() refactoring by LucaMarconato · Pull Request #318 · scverse/spatialdata

LucaMarconato · 2023-07-11T11:14:13Z

Starting a PR to rework and move the get_extent() function from @timtreis from spatialdata-plot to spatialdata. This PR is needed for some tiles generation code that @EliHei2 is working on.

codecov · 2023-07-11T11:19:46Z

Codecov Report

Merging #318 (13da8cd) into main (14bf585) will increase coverage by 0.67%.
The diff coverage is 97.20%.

❗ Current head 13da8cd differs from pull request most recent head d6bd822. Consider uploading reports for the commit d6bd822 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #318      +/-   ##
==========================================
+ Coverage   90.61%   91.28%   +0.67%     
==========================================
  Files          36       36              
  Lines        4700     4845     +145     
==========================================
+ Hits         4259     4423     +164     
+ Misses        441      422      -19

Files	Coverage Δ
src/spatialdata/__init__.py	`100.00% <100.00%> (ø)`
src/spatialdata/_core/operations/rasterize.py	`83.41% <100.00%> (ø)`
src/spatialdata/_core/query/spatial_query.py	`92.01% <100.00%> (+0.08%)`	⬆️
src/spatialdata/_types.py	`66.66% <100.00%> (+4.16%)`	⬆️
src/spatialdata/datasets.py	`100.00% <100.00%> (ø)`
src/spatialdata/models/_utils.py	`89.89% <100.00%> (-0.11%)`	⬇️
src/spatialdata/_core/query/_utils.py	`92.00% <92.85%> (+1.09%)`	⬆️
src/spatialdata/_core/data_extent.py	`97.33% <97.27%> (+97.33%)`	⬆️

... and 1 file with indirect coverage changes

LucaMarconato · 2023-07-11T15:23:23Z

Actually it's completed and ready for review. Talked with @timtreis and he may add some extra functionalities/convenience parameters (used in spatialdata-plot) in a follow up PR.

…d version and ignore empty geometries in get_extent(GeoDataFrame)

for more information, see https://pre-commit.ci

…aldata into feature/get_extent

for more information, see https://pre-commit.ci

…aldata into feature/get_extent

src/spatialdata/_core/data_extent.py

LucaMarconato · 2023-08-26T23:37:30Z

@Sonja-Stockhaus thanks for the bugfix and the refactoring! Please let me know when you finish with the additions and the PR is ready for review. You can tag me here/write me in Zulip.

src/spatialdata/_core/data_extent.py

LucaMarconato · 2023-10-09T14:49:02Z

src/spatialdata/_core/data_extent.py

+    # remove potentially empty geometries
+    e_temp = e[e["geometry"].apply(lambda geom: not geom.is_empty)]
+
+    # separate points from (multi-)polygons


This is not needed because we assume that the GeoDataFrame doesn't mix Point with Polygon/MultiPolygon types. I'll removed it to simplify the code.

Very similar to a bugfix @Sonja-Stockhaus implemented in scverse/spatialdata-plot#133. Don't know if I'd delete this

In the PR I kept the removal of empty points, but I have removed the split of shapes and points. It can be easily restored inside the function _get_extent_of_shapes() if you want. We don't expect to need it now, but it would be still ok to have, just to make the code more future proof.

src/spatialdata/models/_utils.py

LucaMarconato · 2023-10-10T14:28:01Z

I applied the code review from Giovanni and added a test for the xy swap bug: #335.

for more information, see https://pre-commit.ci

LucaMarconato · 2023-10-10T15:41:07Z

As you can see, the Python 3.9 tests fail in a0e26ba (#318), but they succeed in 184dd82 (#318). Not sure why it happens, but as a workaround @timtreis suggested to replace the | with Union, and to silence Ruff.

…aldata into feature/get_extent

LucaMarconato added 3 commits July 11, 2023 13:03

intial porting of Tim code

8743a97

intial porting of Tim code

f8dbc18

fix relational query test

02648f4

LucaMarconato added 4 commits July 11, 2023 16:59

get_extent implemented for non-raster types

da09aed

removed old tim code

fb61b26

cleaned up docstrings

5959307

added raster cases

fcc9397

LucaMarconato marked this pull request as ready for review July 11, 2023 15:22

LucaMarconato requested a review from kevinyamauchi July 11, 2023 15:22

LucaMarconato requested a review from timtreis July 13, 2023 16:45

LucaMarconato linked an issue Aug 15, 2023 that may be closed by this pull request

Refactor get_extent() from spatialdata-plot and push upstream #288

Closed

Sonja Stockhaus and others added 7 commits August 20, 2023 14:32

allow computation of extent for only selected elements, similar to ol…

2a1a3b1

…d version and ignore empty geometries in get_extent(GeoDataFrame)

[pre-commit.ci] auto fixes from pre-commit.com hooks

0fab1a0

for more information, see https://pre-commit.ci

change typehints

ad21245

Merge branch 'feature/get_extent' of https://github.com/scverse/spati…

3c05d63

…aldata into feature/get_extent

[pre-commit.ci] auto fixes from pre-commit.com hooks

d9bdd94

for more information, see https://pre-commit.ci

fix swapped x and y for MultiscaleImage in visium_associated_xenium_io

8761190

Merge branch 'feature/get_extent' of https://github.com/scverse/spati…

cdd8d88

…aldata into feature/get_extent

Sonja-Stockhaus reviewed Aug 26, 2023

View reviewed changes

src/spatialdata/_core/data_extent.py Outdated Show resolved Hide resolved

LucaMarconato commented Aug 26, 2023

View reviewed changes

src/spatialdata/_core/data_extent.py Outdated Show resolved Hide resolved

remove unnecessary arguments

a5870ba

Sonja-Stockhaus linked an issue Aug 29, 2023 that may be closed by this pull request

get_extent switches x and y #335

Closed

update typehints

ffdd842

timtreis mentioned this pull request Sep 5, 2023

Refactored transformations implementation scverse/spatialdata-plot#162

Merged

timtreis added 3 commits September 6, 2023 14:47

Merge branch 'main' into feature/get_extent

b570b27

fixed test

7da099b

Aliged typehint to code

3d47833

LucaMarconato added 2 commits October 9, 2023 15:46

wip test

00ddb62

Merge branch 'feature/get_extent' into fix/rotation_bug

f879c8b

LucaMarconato commented Oct 9, 2023

View reviewed changes

src/spatialdata/models/_utils.py Outdated Show resolved Hide resolved

LucaMarconato and others added 9 commits October 9, 2023 19:40

wip tests for the rotation get_extent bug

f26d988

tests passing, pre-commit failing

f5378c3

1 test not passing

0bf2353

test passing

b9a1fc4

removed plots

3ddc378

Merge branch 'main' into feature/get_extent

b229099

removed commented code

b15827c

Fixes bug with extent of rotated data (#373)

1395fb5

applied code review, added test for xy swap bug

a08e413

LucaMarconato added 3 commits October 10, 2023 16:38

trying to fix test with python 3.9

b30b712

Merge branch 'fix/rotation_bug' into feature/get_extent

62284ee

test bug due to typing_extentions?

7050161

LucaMarconato mentioned this pull request Oct 10, 2023

(Debug failing tests) fix/rotation_bug #375

Closed

LucaMarconato and others added 3 commits October 10, 2023 17:35

restore newer typing_extensions

a0e26ba

removed | in favor of Union in single dispatch

184dd82

[pre-commit.ci] auto fixes from pre-commit.com hooks

f3d2874

for more information, see https://pre-commit.ci

LucaMarconato added 4 commits October 10, 2023 17:41

ignored ruff Union

a4368fb

Merge branch 'feature/get_extent' of https://github.com/scverse/spati…

19e8d84

…aldata into feature/get_extent

explained why we ignore ruff

13da8cd

renamed variable

d6bd822

LucaMarconato merged commit cf925c5 into main Oct 10, 2023

LucaMarconato deleted the feature/get_extent branch October 10, 2023 15:49

LucaMarconato mentioned this pull request Oct 10, 2023

transform() function rotates shapes incorrectly -> incorrect extend #353

Closed

giovp mentioned this pull request Nov 27, 2023

refactor data loader #299

Merged

6 tasks

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

get_extent() refactoring#318

get_extent() refactoring#318
LucaMarconato merged 51 commits intomainfrom
feature/get_extent

LucaMarconato commented Jul 11, 2023 •

edited

Loading

Uh oh!

codecov bot commented Jul 11, 2023 •

edited

Loading

Uh oh!

LucaMarconato commented Jul 11, 2023 •

edited

Loading

Uh oh!

Uh oh!

LucaMarconato commented Aug 26, 2023 •

edited

Loading

Uh oh!

Uh oh!

LucaMarconato Oct 9, 2023 •

edited

Loading

Uh oh!

timtreis Oct 9, 2023

Uh oh!

LucaMarconato Oct 9, 2023

Uh oh!

Uh oh!

LucaMarconato commented Oct 10, 2023

Uh oh!

LucaMarconato commented Oct 10, 2023

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Conversation

LucaMarconato commented Jul 11, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

codecov bot commented Jul 11, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

LucaMarconato commented Jul 11, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Uh oh!

LucaMarconato commented Aug 26, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Uh oh!

LucaMarconato Oct 9, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

timtreis Oct 9, 2023

Choose a reason for hiding this comment

Uh oh!

LucaMarconato Oct 9, 2023

Choose a reason for hiding this comment

Uh oh!

Uh oh!

LucaMarconato commented Oct 10, 2023

Uh oh!

LucaMarconato commented Oct 10, 2023

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

LucaMarconato commented Jul 11, 2023 •

edited

Loading

codecov bot commented Jul 11, 2023 •

edited

Loading

LucaMarconato commented Jul 11, 2023 •

edited

Loading

LucaMarconato commented Aug 26, 2023 •

edited

Loading

LucaMarconato Oct 9, 2023 •

edited

Loading