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alexgaffen wants to merge 44 commits intoObayed-Elsayed:mainfrom
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…agnosis report sidebar
…sis completes - Cache analysis results in _analysis_cache so CSV download reuses them - Clear cache on new file uploads (both simple and chunked) - Show fibrosis extent only after full analysis, not from preview
- For JPG/PNG/BMP, skip the /preview endpoint and go straight to /analyze - Reduces backend load by running the fibrosis filter once instead of twice - Images, extent, and classification now appear simultaneously for small files
- Frontend: rejects oversized flat images immediately with a clear error message - Frontend: drop zone now shows file size limits for each format - Backend: safety guard in analyze_single_file() prevents OOM crashes on oversized uploads
- Retrained FCM with K-Means initialization on 468-dim PCA features (fixed_model_params.pkl) All 4 clusters now well-separated (132-649 distance, FPC 0.8100) - Added morphological opening (3x3 ellipse) to remove single-pixel noise from fibrosis mask - Raised jump detection threshold (0.3->0.5%) for more conservative extent calculation - Added brightness normalization (median->160) for consistent stain deconvolution - Adaptive threshold via descending sweep with searchsorted optimization (O(n log n)) - White background excluded from extent denominator (tissue-only ratio) - Per-patch VGG16 classification with worst-class voting (20% quorum) - UI: FCM membership probability bars, right-aligned extent/classification - UI: Disabled image dragging, added mask download button - UI: Renamed CSV button to 'Download CSV Diagnosis' - Extent value font reduced (2rem->1.5rem) for cleaner layout
…rease - Del full_pil, full_mask_pil, preview_pil, img after np.array conversion - Delete uploaded files from disk after processing (os.remove) - Del tile_mask_pil/patch_pil per tile in finally block - gc.collect() every 10 tiles + after freeing full arrays - Remove thumb_pil creation (no longer needed) - Remove worst-class voting, vote_breakdown, thumbnail fallback - Average fuzzy memberships across patches, derive label from argmax - Remove duplicate accumulator declarations - Radar chart: fontSize 12->15 (pct), 9->12 (labels) - Report labels: 0.75rem->0.85rem, spectrum text: 0.68rem->0.78rem - Move pipeline label into top bar - Add fixed_model_params_pca2.pkl
…nd UI polish - Per-pixel area threshold adjustment via magnifier (ArrowLeft/Right) - Accumulating delta with debounce for hold-to-adjust support - Capture-phase key handler to prevent slider from stealing arrow keys - Undo stack (Ctrl+Z) and area reset (Ctrl+R) with backend support - Modified areas mini-map in diagnosis panel (fully opaque colors) - Help overlay with keybinding reference (wider modal) - Ctrl+Z/R binding indicators styled blue - Confirmation overlay when baseline change would reset area edits - Block file uploads during active diagnosis - Cancel diagnosis button with page reload - Hide 'click or drop to change' and disable hover highlight while busy - Fibrosis extent bar and threshold slider track made brighter - Adjusted ratio, area edits badge, and undo button in traffic light green - Backend: rethreshold-area, reset-area, undo-area, delta-map routes
- New classify_from_mask() in nafld.py: runs VGG16+PCA+FCM on the user-refined mask - For large/SVS images: tiles mask, ranks by severity, averages top-5 worst tiles - New /classify-mask/<filename> endpoint in main.py - Frontend: Diagnose button in right panel, radar chart after classification - CSS: classify-prompt, classify-btn, classify-loading, reclassify-btn styles
- CSV: look up analysis cache by filename (file deleted after SVS processing) - Classify scan: two-stage exclusion (>=50% white in original + <1% white in mask) - SSE streaming for classify-mask endpoint with tile progress - Pixel-accurate worst-patch red outlines using real coords - Re-diagnose disabled until mask changes; Analyze Patch Results toggle - Pass classification scores to CSV download when available
… page and login features
…l style, Perisinusoidal->Periportal, CSV requires full diagnosis
…threshold if extent >= 30%
…imation; excluded-pixels overlay
… (preview-excluded, classify-mask-area)
…inate space instead of comparing panel to image coordinates
…Q-key + excluded button when load-balanced to a different worker than the one that ran analyze)
…change 'Excluded' text to 'what was excluded?'
…green tissue during extent calc, black-slate + 1.5s random-pixel reveal on right panel, lens hidden if frame extends outside image, fix img vertical shift in magnifier mode (preview-image absolute), top medical-green slider replaces right-panel scrollbar
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