feat: Spatial Mode User Story 1 #805

kaloster · 2024-03-04T18:58:29Z

Added all features based on cellxgene POC and adjusted to explorer
Added feature flag
Added default imageUnderlay switch when viewing spatial embedding
Changed to webp format for image underlay

To test:

Pull branch and add the test database (either locally or via the direct S3 URI (to be added by Seve)
Run explorer
Visit the frontend and add the feature flag query param -
http://localhost:3000/d/ba344978-e1aa-40db-a611-b952c10df148.cxg?spatial=true

Still to do in separate PRs:

Add different spatial embedding resolutions to embedding drawer
Add proper typing where any
Unit and e2e tests

Screen.Recording.2024-03-04.at.3.48.37.PM.mov

codecov · 2024-03-04T19:15:06Z

Codecov Report

Attention: Patch coverage is 40.47619% with 50 lines in your changes are missing coverage. Please review.

Project coverage is 76.57%. Comparing base (d2e1ea2) to head (1bc470c).

Files	Patch %	Lines
server/common/rest.py	21.21%	26 Missing ⚠️
server/dataset/dataset.py	50.00%	17 Missing ⚠️
server/dataset/cxg_dataset.py	16.66%	5 Missing ⚠️
server/app/api/v3.py	80.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #805      +/-   ##
==========================================
- Coverage   77.47%   76.57%   -0.90%     
==========================================
  Files          88       88              
  Lines        6856     6994     +138     
==========================================
+ Hits         5312     5356      +44     
- Misses       1544     1638      +94

Flag	Coverage Δ
frontend	`76.57% <40.47%> (-0.90%)`	⬇️
javascript	`76.57% <40.47%> (-0.90%)`	⬇️
unitTest	`76.57% <40.47%> (-0.90%)`	⬇️

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client/src/actions/index.ts

client/src/components/graph/graph.tsx

kaloster · 2024-03-04T21:04:34Z

client/src/components/menubar/index.tsx

+
+    if (!prevConditionMet && currentConditionMet) {
+      dispatch({
+        type: "toggle image underlay",


Toggle image underlay on update if Spatial embedding exists and currently selected

client/src/actions/index.ts

client/src/components/graph/drawSpatialImageRegl.ts

client/__tests__/e2e/e2e.test.ts

client/__tests__/e2e/playwright.global.setup.ts

client/src/components/graph/graph.tsx

tihuan · 2024-03-06T23:00:09Z

server/requirements.txt

@@ -15,6 +15,7 @@ gunicorn[gevent]==20.0.4
 numba==0.56.4
 numpy==1.23.5
 pandas==1.5.3
+pillow==9.5.0


what is this new package for? Thanks!

This is PIL/Pillow used to generate the spatial image in the backend based on the RGB array and return in any image format, in our case webp

tihuan

Just reviewed the PR 🙏 ✨

All looks super good and I could only offer tiny nits 😆

Thanks again for the wonderful work, Ronen!

Since we're aiming to merge the PR on Friday, no rush to address it today. I know it's late in EST 👍

Have a great evening!

client/src/components/embedding/index.tsx

client/src/components/graph/drawSpatialImageRegl.ts

client/src/components/graph/graph.tsx

client/src/components/menubar/index.tsx

seve · 2024-03-07T00:34:47Z

client/src/reducers/imageUnderlay.ts

@@ -0,0 +1,24 @@
+import { Action } from "redux";


this can probably just be moved to controls

client/__tests__/e2e/e2e.test.ts

client/src/components/graph/graph.tsx

tihuan · 2024-03-07T22:24:15Z

@seve just wanted to double check that this is no longer an issue:

#805 (comment)

Thank you!

client/__tests__/e2e/e2e.test.ts

tihuan · 2024-03-12T15:07:11Z

client/src/components/graph/graph.tsx

    /*
        Map an XY coordinate from cell/point domain to screen range.  Inverse
        of mapScreenToPoint()
        */
    const { camera, projectionTF, modelTF, viewport } = this.state;
-    const cameraTF = camera!.view();
+    const cameraTF = camera?.view() || undefined;


since we have optional chaining already, we don't have to do || defined, since TS transpiles camera?.view() to camera ? camera.view() : camera in JS automatically

kaloster added 5 commits March 4, 2024 13:57

feat: Spatial Mode User Story 1

3ba6b66

feat: feature flag

9e56881

feat: feature flag

66c6136

fix: pillow dep

f36c03c

fix: pillow dep

a2e09e7

kaloster commented Mar 4, 2024

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fix: pillow dep

920bcc7

kaloster marked this pull request as ready for review March 4, 2024 19:21

fix: lint

dfc5608

kaloster requested review from tihuan and seve March 4, 2024 21:02

kaloster commented Mar 4, 2024

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kaloster and others added 9 commits March 5, 2024 09:35

Merge branch 'main' into kaloster/spatial-user-story-1

379411d

chore: better error message

2178d7e

typing

167849a

per timmy

d497b2f

add feature flag to endpoints

f5b4122

chore: better error message

27288e2

chore: lint fix

e24ceba

update tests

4a5bb84

fix smoke tests

b6feb89

tihuan reviewed Mar 6, 2024

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tihuan reviewed Mar 6, 2024

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seve suggested changes Mar 7, 2024

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kaloster and others added 3 commits March 6, 2024 19:44

Timmy's review

8564cce

Merge branch 'main' into kaloster/spatial-user-story-1

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per Seve

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seve reviewed Mar 7, 2024

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kaloster and others added 2 commits March 8, 2024 09:16

Merge branch 'main' into kaloster/spatial-user-story-1

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further consideration

a807ac1

kaloster requested review from seve and tihuan March 8, 2024 17:01

seve approved these changes Mar 8, 2024

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Merge branch 'main' into kaloster/spatial-user-story-1

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kaloster merged commit df7d42d into main Mar 8, 2024
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kaloster deleted the kaloster/spatial-user-story-1 branch March 8, 2024 21:50

tihuan reviewed Mar 12, 2024

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czi-github-helper bot mentioned this pull request Jun 20, 2024

chore(main): release 1.0.0 #995

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feat: Spatial Mode User Story 1 #805

feat: Spatial Mode User Story 1 #805

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feat: Spatial Mode User Story 1 #805

feat: Spatial Mode User Story 1 #805

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