Development#60
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amirDahari1
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May 28, 2025
amirDahari1
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- Latest figure changes.
- Added backend batch segmentation (just with an added flag - code works with one image as before).
- Links to github from website.
- fixed rgba tiff problem.
- 3 decimal places in website text.
…le on the backend the same way as on the frontend - just take the R channel
changed "background phases" to something more general "image background (e.g. scale bar)"
space removed before )
Feature image stack
Review figure changes
Feature when to test classical
Solves #56
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@rmdocherty after this is merged could you please have this in prod as well? the 3 decimal places are important for me :) |
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Pull Request Overview
This PR implements several development updates spanning both backend and frontend code, addressing image processing improvements, new testing scenarios, and documentation/link updates.
- Updated test cases for CLS estimation and image stack handling
- Enhanced backend processing for RGBA TIFF images and added a batch segmentation flag
- Improved frontend UI text, hyperlink targets, and CI configuration
Reviewed Changes
Copilot reviewed 13 out of 13 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/tests.py | Updated test image dimensions, assertion thresholds, and added image stack tests |
| representativity/server.py | Modified TIFF processing logic and added debug prints |
| representativity/core.py | Introduced new image size constants and refined CLS correction logic |
| paper_figures/model_accuracy.py | Extended prediction interval function with confidence parameter |
| paper_figures/introduction.py | Updated figure labels and file paths for clarity |
| frontend/src/components/imageLogic.tsx | Added guard for empty arrays in phase fraction calculation |
| frontend/src/components/Popups.tsx | Updated links and added extra instructions in popups |
| frontend/src/components/Menu.tsx | Refactored phase fraction display logic and removed precision function |
| frontend/src/components/DragDrop.tsx | Improved drag/drop UI with additional user guidance |
| README.md | Updated preprint link in documentation |
| CITATION.cff | Revised DOI and URL information |
| .github/workflows/tests.yaml | Adjusted branch filter for CI workflows |
Comment on lines
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| if len(arr.shape) == 3 and arr.shape[0] == 1: | ||
| # weird (1, H, W) tiffs | ||
| arr = arr[0, :, :] | ||
| if len(arr.shape) == 3 and arr.shape[-1] == 3: | ||
| # weird (H, W, 3) tiffs | ||
| arr = np.transpose(arr, (-1, 0, 1)) | ||
| if len(arr.shape) == 3 and arr.shape[0] == 3: | ||
| if len(arr.shape) == 3 and (is_rgba or is_rgb): | ||
| arr = arr[:, :, 0] # take only R channel of RGB(A) arrays, like on frontend | ||
| if len(arr.shape) == 3 and (is_rgba or is_rgb): | ||
| # any (3, H, W) tiffs -> (H, W) | ||
| arr = arr[0, :, :] |
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Duplicate condition in preprocess_arr may cause unintended behavior by slicing the array twice in succession. Consider combining the logic to ensure the correct channel is selected once.
not every branch will trigger tests, but adding development
amirDahari1
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Jun 6, 2025
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@rmdocherty just look at this one duplicate if statement in server.py if that was your intention.
This was referenced Jul 25, 2025
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