Add composite image config and display options by d33bs · Pull Request #222 · cytomining/CytoDataFrame

d33bs · 2026-07-17T22:29:44Z

Description

What kind of change(s) are included?

Documentation (changes docs or other related content)
Bug fix (fixes an issue).
Enhancement (adds functionality).
Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

Please ensure that all boxes are checked before indicating that this pull request is ready for review.

I have read and followed the CONTRIBUTING.md guidelines.
I have searched for existing content to ensure this is not a duplicate.
I have performed a self-review of these additions (including spelling, grammar, and related).
These changes pass all pre-commit checks.
I have added comments to my code to help provide understanding
I have added a test which covers the code changes found within this PR
I have deleted all non-relevant text in this pull request template.

Summary by CodeRabbit

New Features
- Added support for rendering multi-channel single-cell composites from multiple image channels.
- Supports custom composite channel colors, composite naming, and an option to merge all available channels.
- Composite rendering includes segmentation outlines and center markers/points.
Improvements
- Enhanced notebook thumbnail sizing with a minimum width floor and more consistent crop sizing.
- Improved table header styling to keep header text on one line.
Documentation
- Updated README and added/expanded usage examples demonstrating composite channels and display options (including overlays).
Chores
- Updated pre-commit hook revision pins to newer versions.

coderabbitai · 2026-07-17T22:30:03Z

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 4466af5b-cac5-4e4f-a374-1afb398d39d3

📥 Commits

Reviewing files that changed from the base of the PR and between 1a8f2c8 and 491e2e7.

📒 Files selected for processing (2)

src/cytodataframe/frame.py
tests/test_frame.py

🚧 Files skipped from review as they are similar to previous changes (2)

src/cytodataframe/frame.py
tests/test_frame.py

📝 Walkthrough

Walkthrough

CytoDataFrame now renders configurable multi-channel composite crops with optional segmentation overlays, preserves crop geometry across channels, and enforces notebook image sizing. Documentation, tests, and pre-commit hook revisions were also updated.

Changes

Composite rendering

Layer / File(s)	Summary
Composite options and image composition `src/cytodataframe/frame.py`	Adds composite configuration, channel/color resolution, resizing, tinted blending, decoration overlays, width normalization, and composite HTML generation.
Notebook composite integration `src/cytodataframe/frame.py`	Generates composite columns from shared row crop geometry and adds image minimum-width and nowrap header styling.
Composite examples and validation `tests/test_frame.py`, `README.md`, `docs/src/examples/cytodataframe_at_a_glance.py`	Tests composite rendering, channel forms, overlays, layout CSS, and disabled-option behavior; documentation adds composite examples and updates metadata.

Pre-commit hook maintenance

Layer / File(s)	Summary
Pre-commit revision updates `.pre-commit-config.yaml`	Updates pinned revisions for pyproject-fmt, codespell, and Ruff hooks.

Estimated code review effort: 4 (Complex) | ~45 minutes

Sequence Diagram(s)

sequenceDiagram
  participant CytoDataFrame
  participant CompositeRenderer
  participant NotebookHTML
  CytoDataFrame->>CompositeRenderer: Resolve channels and crop geometry
  CompositeRenderer->>CompositeRenderer: Tint, resize, blend, and overlay images
  CompositeRenderer->>NotebookHTML: Add composite HTML image column
  NotebookHTML->>NotebookHTML: Render thumbnails with minimum width

Possibly related PRs

cytomining/CytoDataFrame#216: Updates the shared notebook image crop and HTML rendering path used by composite rendering.

Suggested reviewers: jenna-tomkinson

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly summarizes the main change: adding composite image configuration and display options.
Docstring Coverage	✅ Passed	Docstring coverage is 85.29% which is sufficient. The required threshold is 80.00%.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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…into multi-channel

d33bs · 2026-07-19T21:55:32Z

@coderabbitai review

coderabbitai · 2026-07-19T21:55:50Z

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coderabbitai

Actionable comments posted: 1

🧹 Nitpick comments (1)

src/cytodataframe/frame.py (1)
3504-3510: 📐 Maintainability & Code Quality | 🔵 Trivial | 💤 Low value

Optional: log the swallowed exception before returning "".

A failed composite render is silently converted to an empty cell with no diagnostic trail, and Ruff flags the blind except Exception (BLE001). A debug log keeps the current behavior while making silent-empty composites diagnosable.
♻️ Suggested change
         try:
             return self._image_array_to_html(composite_array)
-        except Exception:
+        except Exception as exc:
+            logger.debug("Failed to render composite image as HTML: %s", exc)
             return ""
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/cytodataframe/frame.py` around lines 3504 - 3510, Update the exception
handler around _image_array_to_html to log the caught exception at debug level
before returning an empty string. Preserve the existing fallback behavior while
replacing the blind exception handling with an explicitly bound exception so
Ruff BLE001 is satisfied.
Source: Linters/SAST tools

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@src/cytodataframe/frame.py`:
- Around line 3095-3101: Normalize numeric width values to CSS pixel strings
before applying the image minimum-width logic in the rendering method containing
_resolve_image_min_width. Ensure configured integer widths such as 300 become
“300px” for both the emitted width style and _resolve_image_min_width, while
preserving existing handling for non-numeric width values.

---

Nitpick comments:
In `@src/cytodataframe/frame.py`:
- Around line 3504-3510: Update the exception handler around
_image_array_to_html to log the caught exception at debug level before returning
an empty string. Preserve the existing fallback behavior while replacing the
blind exception handling with an explicitly bound exception so Ruff BLE001 is
satisfied.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

Push a commit to this branch (recommended)
Create a new PR with the fixes

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: af938fa7-6aea-417b-9f8c-a2d409fcd40f

📥 Commits

Reviewing files that changed from the base of the PR and between 16b7923 and 1a8f2c8.

📒 Files selected for processing (6)

.pre-commit-config.yaml
README.md
docs/src/examples/cytodataframe_at_a_glance.ipynb
docs/src/examples/cytodataframe_at_a_glance.py
src/cytodataframe/frame.py
tests/test_frame.py

jenna-tomkinson · 2026-07-20T19:06:19Z

@d33bs Lucky number 222!

add composite image config and display options

8bd3d61

pre-commit-ci-lite Bot and others added 3 commits July 17, 2026 22:34

[pre-commit.ci lite] apply automatic fixes

9222955

fixes for view widths and general display

34d7a03

Merge branch 'multi-channel' of https://github.com/d33bs/CytoDataFrame …

1a8f2c8

…into multi-channel

coderabbitai Bot reviewed Jul 19, 2026

View reviewed changes

Comment thread src/cytodataframe/frame.py

coderabbitai review changes

491e2e7

d33bs marked this pull request as ready for review July 20, 2026 17:41

d33bs requested a review from jenna-tomkinson as a code owner July 20, 2026 17:41

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Add composite image config and display options#222

Add composite image config and display options#222
d33bs wants to merge 5 commits into
cytomining:mainfrom
d33bs:multi-channel

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