diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d165e2f2fc38902654eefc8976786029a26792a3..bc5543f5488b64ea4a1e1685cca814dd62303676 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -14,6 +14,8 @@ repos: language: system types: [python] require_serial: true + # Exclude auto-generated Gradio custom component files + exclude: ^packages/niivueviewer/ - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 diff --git a/app.py b/app.py index eb28d04cc42a0574c5fb1f0e52bc5d0bfd49bdb6..2c1a5ae46b77b076c48d85ab740de200acc40cd4 100644 --- a/app.py +++ b/app.py @@ -6,19 +6,11 @@ NOTE: HuggingFace Spaces Docker deployment uses `python -m stroke_deepisles_demo For HF Spaces deployment, see: src/stroke_deepisles_demo/ui/app.py """ -from pathlib import Path - import gradio as gr -# CRITICAL: Allow direct file serving for local assets (niivue.js) -# Must be called BEFORE creating any Blocks -_ASSETS_DIR = Path(__file__).parent / "src" / "stroke_deepisles_demo" / "ui" / "assets" -gr.set_static_paths(paths=[str(_ASSETS_DIR)]) - -from stroke_deepisles_demo.core.config import get_settings # noqa: E402 -from stroke_deepisles_demo.core.logging import get_logger, setup_logging # noqa: E402 -from stroke_deepisles_demo.ui.app import get_demo # noqa: E402 -from stroke_deepisles_demo.ui.viewer import get_niivue_head_html # noqa: E402 +from stroke_deepisles_demo.core.config import get_settings +from stroke_deepisles_demo.core.logging import get_logger, setup_logging +from stroke_deepisles_demo.ui.app import get_demo logger = get_logger(__name__) @@ -33,28 +25,12 @@ if __name__ == "__main__": # Log startup info for debugging logger.info("=" * 60) logger.info("STARTUP: stroke-deepisles-demo (root app.py)") - logger.info("Assets directory: %s", _ASSETS_DIR.resolve()) - logger.info("Assets exists: %s", _ASSETS_DIR.exists()) logger.info("=" * 60) - # CRITICAL FIX (Issue #24): Load NiiVue via head= parameter - # - # The head= parameter injects a + +
+ {#if error} +
{error}
+ {:else if loading} +
Loading viewer...
+ {/if} + +
+ + +``` + +**Key improvements from audit feedback:** +- WebGL2 capability check before initialization +- WebGL context loss/restore handlers +- Proper error UI states +- Loading state management +- Reactive update when value changes + +### Phase 3: Implement Python Backend (2-3 hours) + +```python +# backend/gradio_niivue_viewer/__init__.py +from __future__ import annotations +from typing import Any +from gradio.components.base import Component +from gradio.data_classes import FileData, GradioModel + +class NiiVueViewerData(GradioModel): + background_url: str | None = None + overlay_url: str | None = None + +class NiiVueViewer(Component): + """WebGL NIfTI viewer using NiiVue.""" + + data_model = NiiVueViewerData + + def __init__( + self, + value: NiiVueViewerData | None = None, + *, + label: str | None = None, + height: int = 500, + **kwargs, + ): + self.height = height + super().__init__(value=value, label=label, **kwargs) + + def preprocess(self, payload: NiiVueViewerData | None) -> dict[str, Any] | None: + if payload is None: + return None + return { + "background_url": payload.background_url, + "overlay_url": payload.overlay_url, + } + + def postprocess(self, value: dict[str, Any] | None) -> NiiVueViewerData | None: + if value is None: + return None + return NiiVueViewerData( + background_url=value.get("background_url"), + overlay_url=value.get("overlay_url"), + ) +``` + +### Phase 4: Build and Test (2-3 hours) + +```bash +# Build the component +cd gradio-niivue-viewer +gradio cc build + +# Install locally +pip install -e . + +# Test in demo app +python demo/app.py +``` + +### Phase 5: Integrate into stroke-deepisles-demo (1-2 hours) + +Replace `gr.HTML` with the custom component: + +```python +# Before (broken) +from stroke_deepisles_demo.ui.viewer import create_niivue_html +viewer = gr.HTML(value="", elem_id="niivue-viewer") +# ... then set viewer.value = create_niivue_html(...) + +# After (working) +from gradio_niivue_viewer import NiiVueViewer +viewer = NiiVueViewer(label="Interactive 3D Viewer") +# ... then set viewer.value = {"background_url": dwi_url, "overlay_url": mask_url} +``` + +### Phase 6: HF Spaces Deployment (CRITICAL) + +**This phase is essential.** HF Spaces runs `pip install` only - it does NOT run `npm` or `gradio cc build`. + +#### 6a. Commit build artifacts to git + +```bash +cd packages/gradio-niivue-viewer + +# Build the component (generates frontend/dist/ or templates/) +gradio cc build + +# Force-add build artifacts (they may be gitignored by default) +git add -f gradio_niivue_viewer/templates/ +# Or wherever the build output lands - check with: +# find . -name "*.js" -path "*/dist/*" -o -name "*.css" -path "*/dist/*" + +git commit -m "chore: add compiled frontend assets for HF Spaces deployment" +``` + +**Why:** HF Spaces won't run npm/node build steps. The compiled JS/CSS must be in the repo. + +#### 6b. Update requirements.txt + +Add the local component to the main `requirements.txt`: + +```text +# requirements.txt +gradio>=5.0 +# ... other deps ... + +# Local custom component (editable install) +-e ./packages/gradio-niivue-viewer +``` + +**Alternative:** If the component is at repo root: +```text +-e . +``` + +#### 6c. Verify .gitignore doesn't exclude build artifacts + +Check that `packages/gradio-niivue-viewer/.gitignore` doesn't exclude: +- `gradio_niivue_viewer/templates/` +- `frontend/dist/` +- Any compiled `.js` or `.css` files needed at runtime + +If they're excluded, either: +1. Remove those lines from `.gitignore`, OR +2. Use `git add -f` to force-add them + +#### 6d. Test deployment flow + +```bash +# Simulate what HF Spaces does +pip install -r requirements.txt +python -m stroke_deepisles_demo.ui.app + +# Should work WITHOUT running gradio cc build +``` + +--- + +## Existing References + +### Working WebGL Custom Components + +1. **[gradio-litmodel3d](https://pypi.org/project/gradio-litmodel3d/)** + - WebGL Model3D viewer with HDR lighting + - Source: https://github.com/gradio-app/gradio/tree/main/demo/model3d_component + - Proof that WebGL works in Custom Components + +2. **[gradio-molecule3d](https://pypi.org/project/gradio-molecule3d/)** + - 3D molecule viewer + - Uses Three.js (WebGL) + +### Gradio Documentation + +- [Custom Components in 5 Minutes](https://www.gradio.app/guides/custom-components-in-five-minutes) +- [Gradio Components Documentation](https://www.gradio.app/docs/gradio/components) +- [Custom Component Gallery](https://www.gradio.app/custom-components/gallery) + +### NiiVue Resources + +- [NiiVue GitHub](https://github.com/niivue/niivue) +- [NiiVue npm](https://www.npmjs.com/package/@niivue/niivue) +- [NiiVue Examples](https://niivue.com/docs/) + +--- + +## Acceptance Criteria + +### Must Have (MVP) + +- [ ] Component loads NIfTI volumes from Gradio file URLs +- [ ] Component displays background image (DWI) +- [ ] Component displays overlay mask (segmentation) with colormap +- [ ] Component works on HuggingFace Spaces +- [ ] No "Loading..." hang - failures are graceful +- [ ] All existing tests pass + +### Nice to Have (Future) + +- [ ] Crosshair controls +- [ ] Slice orientation toggle (axial/coronal/sagittal) +- [ ] Opacity slider for overlay +- [ ] Pan/zoom/rotate controls +- [ ] Screenshot/export functionality +- [ ] Publish to PyPI for community use + +--- + +## Risk Assessment + +| Risk | Mitigation | +|------|------------| +| Svelte/TypeScript learning curve | Follow gradio-litmodel3d example closely | +| NiiVue WebGL2 browser support | Explicit WebGL2 check in Svelte + graceful error UI | +| Build system complexity | Use gradio cc tooling, don't customize | +| HF Spaces static file serving | Component bundles NiiVue, no external deps | +| **Build artifacts not in git** | Phase 6a: Force-add compiled assets with `git add -f` | +| **requirements.txt missing component** | Phase 6b: Add `-e ./packages/gradio-niivue-viewer` | + +--- + +## Alternatives Considered + +### Alternative 1: Keep Hacking gr.HTML +- **Effort:** Low +- **Success probability:** 0% (CONFIRMED FAILED) +- **Why rejected:** We tried 6 approaches over 2 days. ALL failed. This is not a viable path. + +### Alternative 2: Static HTML Space (No Gradio) +- **Effort:** High (rebuild entire UI) +- **Success probability:** 99% +- **Why rejected:** Lose Gradio's file upload, dropdowns, layout features. Too much work. + +### Alternative 3: Remove 3D Viewer (2D Only) +- **Effort:** Low +- **Success probability:** 100% +- **Why rejected:** Loses key feature. Static Report tab already works, but 3D is valuable. + +--- + +## Decision + +**Proceed with Gradio Custom Component approach.** + +This is the official Gradio-recommended solution. It's more work than hacking `gr.HTML`, but it's the architecturally correct approach with 90% success probability vs 30%. + +--- + +## Testing Matrix + +### Level 1: Local Build Verification + +```bash +cd packages/gradio-niivue-viewer + +# Build component +gradio cc build + +# Install locally +pip install -e . + +# Run demo app +python demo/app.py +# → Verify: App loads, no console errors, viewer renders +``` + +**Pass criteria:** +- [ ] `gradio cc build` completes without errors +- [ ] Demo app launches at localhost:7860 +- [ ] No JavaScript console errors +- [ ] Canvas renders (black background visible) + +### Level 2: Volume Loading Test + +```python +# demo/app.py +import gradio as gr +from gradio_niivue_viewer import NiiVueViewer + +def load_sample(): + # Use a known good NIfTI file + return { + "background_url": "/gradio_api/file=/path/to/sample.nii.gz", + "overlay_url": None + } + +with gr.Blocks() as demo: + viewer = NiiVueViewer() + btn = gr.Button("Load Sample") + btn.click(load_sample, outputs=viewer) + +demo.launch() +``` + +**Pass criteria:** +- [ ] NIfTI file loads without errors +- [ ] Multiplanar view displays correctly +- [ ] Overlay mask renders with red colormap (when provided) + +### Level 3: HF Spaces Dry Run + +Deploy to a **private/throwaway Space** before production: + +```bash +# Create test space +huggingface-cli repo create test-niivue-viewer --type space --private + +# Push and test +git push hf-test main +``` + +**Pass criteria:** +- [ ] Space shows "Running" (not stuck on "Loading...") +- [ ] Viewer initializes (no hydration deadlock) +- [ ] Volume loading works via Gradio file serving +- [ ] WebGL2 error shown gracefully if unsupported + +### Level 4: Integration Test + +Replace `gr.HTML` in stroke-deepisles-demo: + +```python +# src/stroke_deepisles_demo/ui/components.py +from gradio_niivue_viewer import NiiVueViewer + +def create_results_display(): + # ... + niivue_viewer = NiiVueViewer(label="Interactive 3D Viewer") + # ... +``` + +**Pass criteria:** +- [ ] Existing 136 tests still pass +- [ ] Segmentation pipeline works end-to-end +- [ ] Viewer displays DWI + mask overlay +- [ ] No "Loading..." hang on HF Spaces + +--- + +## Next Steps + +1. [x] Senior review of this spec (AUDIT_REPORT_2025_12_10.md) +2. [x] Red team review - all gaps addressed (build artifacts, npm install, null handling) +3. [ ] Create `packages/gradio-niivue-viewer/` subdirectory +4. [ ] Scaffold component with `gradio cc create` +5. [ ] Install NiiVue: `cd frontend && npm install @niivue/niivue@0.65.0` +6. [ ] Implement Svelte frontend (with WebGL2 checks + null value handling) +7. [ ] Implement Python backend +8. [ ] Level 1 test: Local build verification +9. [ ] Level 2 test: Volume loading +10. [ ] Level 3 test: HF Spaces dry run +11. [ ] Level 4 test: Integration +12. [ ] **CRITICAL**: Commit build artifacts to git +13. [ ] **CRITICAL**: Update requirements.txt with `-e ./packages/gradio-niivue-viewer` +14. [ ] (Optional) Publish to PyPI + +--- + +## Appendix: Why WebGL + `gr.HTML` Doesn't Work + +From the ROOT_CAUSE_ANALYSIS.md and GRADIO_WEBGL_ANALYSIS.md research: + +1. **Gradio CAN do WebGL** - proven by `gradio-litmodel3d` custom component +2. **But NOT via `gr.HTML`** - the `js_on_load` + `import()` pattern blocks Svelte hydration +3. **Our A/B test proved it** - disabling `js_on_load` makes the app load perfectly +4. **Gradio closed NIfTI support** (Issue #4511) - "Not planned for core" +5. **Gradio closed WebGL canvas** (Issue #7649) - "Not planned for core" +6. **gr.HTML strips script tags** - Security feature, can't bypass +7. **HF Spaces CSP blocks external CDNs** - Must vendor or bundle dependencies +8. **Gradio maintainer recommendation**: Custom Components + +The pattern is clear: **The `gr.HTML` + `js_on_load` + async `import()` pattern is fundamentally broken.** The Custom Component is the officially supported path for WebGL content. diff --git a/docs/specs/29-codebase-status-audit.md b/docs/specs/29-codebase-status-audit.md new file mode 100644 index 0000000000000000000000000000000000000000..ed4fc4886c977ab39ae36cb208f8ad5f57bdb3bf --- /dev/null +++ b/docs/specs/29-codebase-status-audit.md @@ -0,0 +1,276 @@ +# Spec #29: Codebase Status Audit (Issue #24 NiiVue/WebGL) + +**Date:** 2025-12-10 +**Status:** ALL `gr.HTML` HACKS CONFIRMED FAILED (Dec 10, 2025) +**Purpose:** Top-down analysis of current frontend/NiiVue implementation state after multiple hotfix attempts + +--- + +## Executive Summary: The `gr.HTML` + `js_on_load` + `import()` Pattern is Broken + +After 6 iterations of attempted hotfixes for Issue #24 (HF Spaces "Loading..." forever), **every `gr.HTML`-based approach has failed**: + +| Attempt | Result | +|---------|--------| +| CDN import | FAILED - CSP blocked | +| Vendored + js_on_load import() | FAILED - Blocks Svelte hydration | +| head_paths | FAILED - Same hydration issue | +| head= with import() | **FAILED** - Confirmed Dec 10 | + +**Root Cause (PROVEN):** Async `import()` inside `js_on_load` blocks Gradio's Svelte hydration. Our A/B test confirmed: disabling `js_on_load` makes the app load. + +**Clarification:** Gradio CAN do WebGL via Custom Components (`gradio-litmodel3d` proves this). The issue is the `gr.HTML` approach, not Gradio itself. + +**The correct solution is Gradio Custom Component (spec #28).** + +--- + +## Current Frontend Architecture + +### File Inventory + +| File | Purpose | Lines | Status | +|------|---------|-------|--------| +| `ui/viewer.py` | NiiVue HTML/JS generation | 643 | **BLOATED** - contains 5 approaches | +| `ui/app.py` | Main Gradio app | 313 | Clean | +| `ui/components.py` | UI components | 94 | Clean | +| `app.py` (root) | Local dev entry | 61 | Clean | +| `ui/assets/niivue.js` | Vendored NiiVue v0.65.0 | 2.9MB | **NECESSARY** | + +### What's in `viewer.py` Right Now + +| Component | Lines | Status | Notes | +|-----------|-------|--------|-------| +| `NIIVUE_VERSION` | 30 | OK | Version tracking | +| `_ASSET_DIR`, `_NIIVUE_JS_PATH` | 31-32 | OK | Path constants | +| `NIIVUE_JS_URL` | 36 | **UNUSED** | Computed but not actually used | +| Module-level logging | 39-42 | **SLOP** | 4 log statements at import time | +| `get_niivue_head_html()` | 45-77 | **PROBLEMATIC** | Still uses `await import()` | +| `get_niivue_loader_path()` | 80-109 | **DEPRECATED** | Marked deprecated but still exists | +| `nifti_to_gradio_url()` | 112-142 | OK | Issue #19 fix, working | +| `get_slice_at_max_lesion()` | 145-187 | OK | Matplotlib helper | +| `render_3panel_view()` | 190-281 | OK | Matplotlib 3-panel | +| `render_slice_comparison()` | 284-380 | OK | Matplotlib comparison | +| `create_niivue_html()` | 383-434 | OK | HTML generation | +| `NIIVUE_ON_LOAD_JS` | 449-538 | **MOSTLY OK** | No import(), uses window.Niivue | +| `NIIVUE_UPDATE_JS` | 546-642 | **MOSTLY OK** | No import(), uses window.Niivue | + +--- + +## The Core Problem: `get_niivue_head_html()` Still Uses `import()` + +The current "fix" in `get_niivue_head_html()` does this: + +```javascript +// viewer.py:63-76 + +``` + +**This is the EXACT same `await import()` pattern that breaks on HF Spaces.** + +The only difference from our previous attempts: +- Before: `await import()` in `js_on_load` +- Now: `await import()` in `head=` script + +**Why this might not matter:** The A/B test proved that `js_on_load` with async code breaks Gradio. Moving the `import()` to `head=` might help, but it's still executing async code that could fail silently and leave `window.Niivue` undefined. + +--- + +## What's Necessary vs What's Slop + +### NECESSARY (Keep) + +| Item | Why | +|------|-----| +| `ui/assets/niivue.js` | HF Spaces CSP blocks CDN imports | +| `gr.set_static_paths()` | Required for Gradio 6.x file serving | +| `nifti_to_gradio_url()` | Issue #19 fix, working | +| `create_niivue_html()` | Generates viewer HTML | +| `NIIVUE_ON_LOAD_JS` | Initializes viewer (doesn't import) | +| `NIIVUE_UPDATE_JS` | Re-initializes after updates | +| Matplotlib functions | Working 2D fallback | +| `allowed_paths` in launch() | Runtime file access | + +### SLOP (Should Remove/Refactor) + +| Item | Why It's Slop | +|------|---------------| +| `NIIVUE_JS_URL` module-level computation | Computed but unused in production | +| Module-level logging (lines 39-42) | Noisy startup logs, not useful | +| `get_niivue_loader_path()` | Deprecated, generates file we don't need | +| `get_niivue_head_html()` with import() | Still uses broken pattern | +| Multiple diagnostic docs | Overlapping, contradictory, stale | + +### UNCERTAIN (Depends on head= fix working) + +| Item | Status | +|------|--------| +| `head=get_niivue_head_html()` in launch() | **30% chance this works** | + +--- + +## Documentation Status + +### docs/specs/ Files + +| File | Status | Issue | +|------|--------|-------| +| `00-context.md` | **ACCURATE** | None | +| `28-gradio-custom-component-niivue.md` | **ACCURATE** | Just written | +| `AUDIT_JS_LOADING_ISSUES.md` | **OUTDATED** | Says `set_static_paths` is blocker, but we've moved past that | +| `DIAGNOSTIC_HF_LOADING.md` | **OUTDATED** | Lists hypotheses we've since disproven | +| `ROOT_CAUSE_ANALYSIS.md` | **PARTIALLY OUTDATED** | Says "IN PROGRESS", discusses head= as solution | +| `GRADIO_WEBGL_ANALYSIS.md` | **ACCURATE** | Core analysis, identifies real problem | + +### docs/TECHNICAL_DEBT.md + +| Status | Issue | +|--------|-------| +| **OUTDATED** | Claims "Ironclad/Production-Ready" but doesn't mention P0 NiiVue/WebGL blocker | + +--- + +## Recommended Cleanup Actions + +### Immediate (If head= fix fails) + +1. **Delete deprecated code:** + - Remove `get_niivue_loader_path()` + - Remove module-level logging + - Clean up `NIIVUE_JS_URL` if unused + +2. **Archive old diagnostic docs:** + - Move `AUDIT_JS_LOADING_ISSUES.md` to `archive/` + - Move `DIAGNOSTIC_HF_LOADING.md` to `archive/` + - Update `ROOT_CAUSE_ANALYSIS.md` status + +3. **Update TECHNICAL_DEBT.md:** + - Add P0 section for NiiVue/WebGL blocker + - Link to spec #28 (Custom Component) + +### Long-term (After decision on path forward) + +1. **If Custom Component route:** + - Remove all `head=` NiiVue loading code + - Remove `get_niivue_head_html()` + - Simplify `viewer.py` to just Matplotlib functions + - NiiVue loading becomes the component's responsibility + +2. **If 2D fallback route:** + - Remove entire NiiVue integration + - Remove `ui/assets/niivue.js` (2.9MB) + - Remove `NIIVUE_ON_LOAD_JS`, `NIIVUE_UPDATE_JS` + - Keep only Matplotlib rendering + +--- + +## Honest Assessment + +### What We've Tried (6+ iterations) + +1. **CDN import** → Blocked by CSP +2. **Vendored + dynamic import in js_on_load** → Blocks Svelte hydration +3. **head_paths with loader HTML** → Complex, didn't work +4. **head= with inline import()** → Current state, **probably won't work** +5. **Various set_static_paths/allowed_paths combos** → File serving works, JS loading doesn't + +### The Pattern + +Every attempt has been a variation of: +> "Load NiiVue via some JavaScript mechanism within Gradio" + +Every attempt has failed because: +> **Gradio was not designed for custom WebGL content** + +### The Correct Solution + +**Stop fighting Gradio's architecture. Use a Gradio Custom Component.** + +This is: +- What Gradio maintainers recommend (Issues #4511, #7649) +- How existing WebGL components work (gradio-litmodel3d) +- 90% success probability vs 30% for more hacks + +See spec #28 for implementation details. + +--- + +## Current Entry Point Flow + +``` +HF Spaces Docker + ↓ +CMD ["python", "-m", "stroke_deepisles_demo.ui.app"] + ↓ +ui/app.py __main__ block + ↓ +gr.set_static_paths([_ASSETS_DIR]) # Enable file serving + ↓ +get_demo() # Creates Blocks with js_on_load components + ↓ +demo.launch( + head=get_niivue_head_html(), # <-- Injects + +
+ {#if value} + + {/if} +
+ + diff --git a/packages/niivueviewer/frontend/Index.svelte b/packages/niivueviewer/frontend/Index.svelte new file mode 100644 index 0000000000000000000000000000000000000000..3652843dc8923bd88e93d54e4df0a1648189b2d2 --- /dev/null +++ b/packages/niivueviewer/frontend/Index.svelte @@ -0,0 +1,145 @@ + + + + {#if loading_status} + + {/if} + +
+ +
+ + + diff --git a/packages/niivueviewer/frontend/gradio.config.js b/packages/niivueviewer/frontend/gradio.config.js new file mode 100644 index 0000000000000000000000000000000000000000..c096bf5a1d34c2632f358b80cd61347deb1291c0 --- /dev/null +++ b/packages/niivueviewer/frontend/gradio.config.js @@ -0,0 +1,9 @@ +export default { + plugins: [], + svelte: { + preprocess: [], + }, + build: { + target: "modules", + }, +}; diff --git a/packages/niivueviewer/frontend/package-lock.json b/packages/niivueviewer/frontend/package-lock.json new file mode 100644 index 0000000000000000000000000000000000000000..439b4a0d8df358815a868b6d1f2a0417fbdce978 --- /dev/null +++ b/packages/niivueviewer/frontend/package-lock.json @@ -0,0 +1,5967 @@ +{ + "name": "gradio_niivueviewer", + "version": "0.24.0", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "name": "gradio_niivueviewer", + "version": "0.24.0", + "license": "ISC", + "dependencies": { + "@gradio/atoms": "0.19.0", + 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+++ b/packages/niivueviewer/frontend/package.json @@ -0,0 +1,57 @@ +{ + "name": "gradio_niivueviewer", + "version": "0.24.0", + "description": "Gradio UI packages", + "type": "module", + "author": "", + "license": "ISC", + "private": false, + "dependencies": { + "@gradio/atoms": "0.19.0", + "@gradio/client": "2.0.0", + "@gradio/icons": "0.15.0", + "@gradio/statustracker": "0.12.0", + "@gradio/upload": "0.17.2", + "@gradio/utils": "0.10.4", + "@niivue/niivue": "0.65.0", + "cropperjs": "^2.0.1", + "lazy-brush": "^2.0.2", + "resize-observer-polyfill": "^1.5.1" + }, + "devDependencies": { + "@gradio/preview": "0.15.1" + }, + "main_changeset": true, + "main": "./Index.svelte", + "exports": { + "./package.json": "./package.json", + ".": { + "gradio": "./Index.svelte", + "svelte": "./dist/Index.svelte", + "types": "./dist/Index.svelte.d.ts" + }, + "./example": { + "gradio": "./Example.svelte", + "svelte": "./dist/Example.svelte", + "types": "./dist/Example.svelte.d.ts" + }, + "./base": { + "gradio": "./shared/ImagePreview.svelte", + "svelte": "./dist/shared/ImagePreview.svelte", + "types": "./dist/shared/ImagePreview.svelte.d.ts" + }, + "./shared": { + "gradio": "./shared/index.ts", + "svelte": "./dist/shared/index.js", + "types": "./dist/shared/index.d.ts" + } + }, + "peerDependencies": { + "svelte": "^5.43.4" + }, + "repository": { + "type": "git", + "url": "git+https://github.com/gradio-app/gradio.git", + "directory": "js/image" + } +} diff --git a/packages/niivueviewer/frontend/shared/Image.svelte b/packages/niivueviewer/frontend/shared/Image.svelte new file mode 100644 index 0000000000000000000000000000000000000000..834056a71ad01b2d491a18487320c9dffe24dc5c --- /dev/null +++ b/packages/niivueviewer/frontend/shared/Image.svelte @@ -0,0 +1,28 @@ + + + + + + diff --git a/packages/niivueviewer/frontend/shared/ImagePreview.svelte b/packages/niivueviewer/frontend/shared/ImagePreview.svelte new file mode 100644 index 0000000000000000000000000000000000000000..ff36b070342b09fd0c52a0c673bb491ba1dbc1bb --- /dev/null +++ b/packages/niivueviewer/frontend/shared/ImagePreview.svelte @@ -0,0 +1,147 @@ + + + +{#if value == null || !value?.url} + +{:else} +
+ + {#if buttons === null ? true : buttons.includes("fullscreen")} + + {/if} + + {#if buttons === null ? true : buttons.includes("download")} + + + + {/if} + {#if buttons === null ? true : buttons.includes("share")} + { + if (!value) return ""; + let url = await uploadToHuggingFace(value, "url"); + return ``; + }} + {value} + /> + {/if} + + +
+{/if} + + diff --git a/packages/niivueviewer/frontend/shared/ImageUploader.svelte b/packages/niivueviewer/frontend/shared/ImageUploader.svelte new file mode 100644 index 0000000000000000000000000000000000000000..3c862d2aa8fd8d5c4be7d438b60380913e25b5d2 --- /dev/null +++ b/packages/niivueviewer/frontend/shared/ImageUploader.svelte @@ -0,0 +1,305 @@ + + + + +
+ + {#if value?.url && !active_streaming} + {#if show_fullscreen_button} + + {/if} + + {/if} + + +
1} + style:width={value ? "auto" : "100%"} + on:dragover={on_drag_over} + on:drop={on_drop} + > + + {#if active_source === "webcam" && !streaming && pending} + + {:else if active_source === "webcam" && (streaming || (!streaming && !value))} + handle_save(e.detail, "change")} + on:stream={(e) => handle_save(e.detail, "stream")} + on:error + on:drag + on:upload={(e) => handle_save(e.detail, "upload")} + on:close_stream + {stream_state} + mirror_webcam={webcam_options.mirror} + {stream_every} + {streaming} + mode="image" + include_audio={false} + {i18n} + {upload} + {time_limit} + webcam_constraints={webcam_options.constraints} + /> + {:else if value !== null && !streaming} + + +
+ +
+ {/if} +
+ {#if sources.length > 1 || sources.includes("clipboard")} + + {/if} +
+ + diff --git a/packages/niivueviewer/frontend/shared/Webcam.svelte b/packages/niivueviewer/frontend/shared/Webcam.svelte new file mode 100644 index 0000000000000000000000000000000000000000..af2c7438a31aa5bae758418c20e9a8714d2d22ce --- /dev/null +++ b/packages/niivueviewer/frontend/shared/Webcam.svelte @@ -0,0 +1,486 @@ + + +
+ + + +
+ + diff --git a/packages/niivueviewer/frontend/shared/WebcamPermissions.svelte b/packages/niivueviewer/frontend/shared/WebcamPermissions.svelte new file mode 100644 index 0000000000000000000000000000000000000000..1efc4cb9243fc130320acc24629573a6edd1a169 --- /dev/null +++ b/packages/niivueviewer/frontend/shared/WebcamPermissions.svelte @@ -0,0 +1,46 @@ + + + + + diff --git a/packages/niivueviewer/frontend/shared/index.ts b/packages/niivueviewer/frontend/shared/index.ts new file mode 100644 index 0000000000000000000000000000000000000000..4b2f5408b760a6e27b2490270323821a87d0c698 --- /dev/null +++ b/packages/niivueviewer/frontend/shared/index.ts @@ -0,0 +1,2 @@ +export { default as Image } from "./Image.svelte"; +export { default as StaticImage } from "./ImagePreview.svelte"; diff --git a/packages/niivueviewer/frontend/shared/stream_utils.ts b/packages/niivueviewer/frontend/shared/stream_utils.ts new file mode 100644 index 0000000000000000000000000000000000000000..bba1b4de0f90c5fae3aec102fc283bd280362397 --- /dev/null +++ b/packages/niivueviewer/frontend/shared/stream_utils.ts @@ -0,0 +1,50 @@ +export function get_devices(): Promise { + return navigator.mediaDevices.enumerateDevices(); +} + +export function handle_error(error: string): void { + throw new Error(error); +} + +export function set_local_stream( + local_stream: MediaStream | null, + video_source: HTMLVideoElement +): void { + video_source.srcObject = local_stream; + video_source.muted = true; + video_source.play(); +} + +export async function get_video_stream( + include_audio: boolean, + video_source: HTMLVideoElement, + webcam_constraints: { [key: string]: any } | null, + device_id?: string +): Promise { + const constraints: MediaStreamConstraints = { + video: device_id + ? { deviceId: { exact: device_id }, ...webcam_constraints?.video } + : webcam_constraints?.video || { + width: { ideal: 1920 }, + height: { ideal: 1440 } + }, + audio: include_audio && (webcam_constraints?.audio ?? true) // Defaults to true if not specified + }; + + return navigator.mediaDevices + .getUserMedia(constraints) + .then((local_stream: MediaStream) => { + set_local_stream(local_stream, video_source); + return local_stream; + }); +} + +export function set_available_devices( + devices: MediaDeviceInfo[] +): MediaDeviceInfo[] { + const cameras = devices.filter( + (device: MediaDeviceInfo) => device.kind === "videoinput" + ); + + return cameras; +} diff --git a/packages/niivueviewer/frontend/shared/types.ts b/packages/niivueviewer/frontend/shared/types.ts new file mode 100644 index 0000000000000000000000000000000000000000..061520f2d2b635d435e425f8006e7435ebdf3f39 --- /dev/null +++ b/packages/niivueviewer/frontend/shared/types.ts @@ -0,0 +1,42 @@ +import type { LoadingStatus } from "@gradio/statustracker"; +import type { FileData } from "@gradio/client"; + +export interface Base64File { + url: string; + alt_text: string; +} + +export interface WebcamOptions { + mirror: boolean; + constraints: MediaStreamConstraints; +} + +export interface ImageProps { + _selectable: boolean; + sources: ("clipboard" | "webcam" | "upload")[]; + height: number; + width: number; + webcam_options: WebcamOptions; + value: FileData | null; + buttons: string[]; + pending: boolean; + streaming: boolean; + stream_every: number; + input_ready: boolean; + placeholder: string; + watermark: FileData | null; +} + +export interface ImageEvents { + clear: void; + change: any; + stream: any; + select: any; + upload: any; + input: any; + clear_status: LoadingStatus; + share: any; + error: any; + close_stream: void; + edit: void; +} diff --git a/packages/niivueviewer/frontend/shared/utils.ts b/packages/niivueviewer/frontend/shared/utils.ts new file mode 100644 index 0000000000000000000000000000000000000000..1911367a8884ea8c5468cf5fff062cd887197586 --- /dev/null +++ b/packages/niivueviewer/frontend/shared/utils.ts @@ -0,0 +1,29 @@ +export const get_coordinates_of_clicked_image = ( + evt: MouseEvent +): [number, number] | null => { + let image; + if (evt.currentTarget instanceof Element) { + image = evt.currentTarget.querySelector("img") as HTMLImageElement; + } else { + return [NaN, NaN]; + } + + const imageRect = image.getBoundingClientRect(); + const xScale = image.naturalWidth / imageRect.width; + const yScale = image.naturalHeight / imageRect.height; + if (xScale > yScale) { + const displayed_height = image.naturalHeight / xScale; + const y_offset = (imageRect.height - displayed_height) / 2; + var x = Math.round((evt.clientX - imageRect.left) * xScale); + var y = Math.round((evt.clientY - imageRect.top - y_offset) * xScale); + } else { + const displayed_width = image.naturalWidth / yScale; + const x_offset = (imageRect.width - displayed_width) / 2; + var x = Math.round((evt.clientX - imageRect.left - x_offset) * yScale); + var y = Math.round((evt.clientY - imageRect.top) * yScale); + } + if (x < 0 || x >= image.naturalWidth || y < 0 || y >= image.naturalHeight) { + return null; + } + return [x, y]; +}; diff --git a/packages/niivueviewer/frontend/tsconfig.json b/packages/niivueviewer/frontend/tsconfig.json new file mode 100644 index 0000000000000000000000000000000000000000..04273573e42fee3c99beacec3faf9ab94320148a --- /dev/null +++ b/packages/niivueviewer/frontend/tsconfig.json @@ -0,0 +1,14 @@ +{ + "compilerOptions": { + "allowJs": true, + "checkJs": true, + "esModuleInterop": true, + "forceConsistentCasingInFileNames": true, + "resolveJsonModule": true, + "skipLibCheck": true, + "sourceMap": true, + "strict": true, + "verbatimModuleSyntax": true + }, + "exclude": ["node_modules", "dist", "./gradio.config.js"] +} diff --git a/packages/niivueviewer/pyproject.toml b/packages/niivueviewer/pyproject.toml new file mode 100644 index 0000000000000000000000000000000000000000..a3a24a60a44bdd9b3693d459c0a80b260231d83d --- /dev/null +++ b/packages/niivueviewer/pyproject.toml @@ -0,0 +1,48 @@ +[build-system] +requires = [ + "hatchling", + "hatch-requirements-txt", + "hatch-fancy-pypi-readme>=22.5.0", +] +build-backend = "hatchling.build" + +[project] +name = "gradio_niivueviewer" +version = "0.0.1" +description = "A Gradio custom component for 3D medical imaging visualization using NiiVue (WebGL)." +readme = "README.md" +license = "apache-2.0" +requires-python = ">=3.10" +authors = [{ name = "Stroke DeepIsles Demo", email = "demo@example.com" }] +keywords = [ + "gradio-custom-component", + "gradio-template-Image", + "niivue", + "nifti", + "medical-imaging", + "webgl", + "visualization" +] +# Add dependencies here +dependencies = ["gradio>=6.0,<7.0"] +classifiers = [ + 'Development Status :: 3 - Alpha', + 'Operating System :: OS Independent', + 'Programming Language :: Python :: 3', + 'Programming Language :: Python :: 3 :: Only', + 'Programming Language :: Python :: 3.10', + 'Programming Language :: Python :: 3.11', + 'Topic :: Scientific/Engineering', + 'Topic :: Scientific/Engineering :: Artificial Intelligence', + 'Topic :: Scientific/Engineering :: Visualization', + 'Topic :: Scientific/Engineering :: Medical Science Apps.', +] + +[project.optional-dependencies] +dev = ["build", "twine"] + +[tool.hatch.build] +artifacts = ["/backend/gradio_niivueviewer/templates", "*.pyi"] + +[tool.hatch.build.targets.wheel] +packages = ["/backend/gradio_niivueviewer"] diff --git a/pyproject.toml b/pyproject.toml index 96d65cd21df360feaa66b2842c64f5216b8b2355..04e0095637d8c6475ffe23aa0a6751144c9bb3fd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,6 +35,9 @@ dependencies = [ "gradio>=6.0.0,<7.0.0", "matplotlib>=3.8.0", + # Custom component for NiiVue WebGL viewer (local package) + "gradio_niivueviewer", + # Networking "requests>=2.0.0", ] @@ -65,6 +68,9 @@ allow-direct-references = true [tool.hatch.build.targets.wheel] packages = ["src/stroke_deepisles_demo"] +[tool.uv.sources] +gradio_niivueviewer = { path = "packages/niivueviewer", editable = true } + # ───────────────────────────────────────────────────────────────── # Tool configurations # ───────────────────────────────────────────────────────────────── @@ -73,6 +79,8 @@ packages = ["src/stroke_deepisles_demo"] target-version = "py312" line-length = 100 src = ["src", "tests"] +# Exclude auto-generated files from Gradio custom component +exclude = ["packages/niivueviewer/demo/space.py"] [tool.ruff.lint] select = [ @@ -103,11 +111,14 @@ warn_return_any = true warn_unused_ignores = true disallow_untyped_defs = true plugins = ["pydantic.mypy"] +# Exclude auto-generated Gradio custom component demo files +exclude = "packages/niivueviewer/" [[tool.mypy.overrides]] module = [ "nibabel.*", "gradio.*", + "gradio_niivueviewer.*", "datasets.*", "niivue.*", "numpy.*", diff --git a/requirements.txt b/requirements.txt index 02d9dc6cce447db50c51eb1aa674339ee14432ee..3e84dfa115b749c13293ad0188b26fc8c73ba648 100644 --- a/requirements.txt +++ b/requirements.txt @@ -23,3 +23,6 @@ matplotlib>=3.8.0 # Networking requests>=2.0.0 + +# Custom Components +./packages/niivueviewer diff --git a/src/stroke_deepisles_demo/ui/app.py b/src/stroke_deepisles_demo/ui/app.py index b59c769cb177049a5f576fe8d585a6c3d089545f..4589815fbfc27bb470d283f9497c01cbf9b748f8 100644 --- a/src/stroke_deepisles_demo/ui/app.py +++ b/src/stroke_deepisles_demo/ui/app.py @@ -9,25 +9,16 @@ from typing import Any import gradio as gr from matplotlib.figure import Figure # noqa: TC002 -# CRITICAL: Allow direct file serving for local assets (niivue.js) -# This fixes the P0 "Loading..." bug on HF Spaces (Issue #11649) -# Must be called BEFORE creating any Blocks - hence imports after this call -_ASSETS_DIR = Path(__file__).parent / "assets" -gr.set_static_paths(paths=[str(_ASSETS_DIR)]) - -from stroke_deepisles_demo.core.logging import get_logger # noqa: E402 -from stroke_deepisles_demo.data import list_case_ids # noqa: E402 -from stroke_deepisles_demo.metrics import compute_volume_ml # noqa: E402 -from stroke_deepisles_demo.pipeline import run_pipeline_on_case # noqa: E402 -from stroke_deepisles_demo.ui.components import ( # noqa: E402 +from stroke_deepisles_demo.core.logging import get_logger +from stroke_deepisles_demo.data import list_case_ids +from stroke_deepisles_demo.metrics import compute_volume_ml +from stroke_deepisles_demo.pipeline import run_pipeline_on_case +from stroke_deepisles_demo.ui.components import ( create_case_selector, create_results_display, create_settings_accordion, ) -from stroke_deepisles_demo.ui.viewer import ( # noqa: E402 - NIIVUE_UPDATE_JS, - create_niivue_html, - get_niivue_head_html, +from stroke_deepisles_demo.ui.viewer import ( nifti_to_gradio_url, render_3panel_view, render_slice_comparison, @@ -80,7 +71,15 @@ def run_segmentation( fast_mode: bool, show_ground_truth: bool, previous_results_dir: str | None, -) -> tuple[str, Figure | None, Figure | None, dict[str, Any], str | None, str, str | None]: +) -> tuple[ + dict[str, str | None] | None, + Figure | None, + Figure | None, + dict[str, Any], + str | None, + str, + str | None, +]: """ Run segmentation and return results for display. @@ -91,12 +90,12 @@ def run_segmentation( previous_results_dir: Path to previous results (from gr.State, for cleanup) Returns: - Tuple of (niivue_html, slice_fig, ortho_fig, metrics_dict, download_path, status_msg, new_results_dir) + Tuple of (niivue_data, slice_fig, ortho_fig, metrics_dict, download_path, status_msg, new_results_dir) The new_results_dir is returned to update the gr.State for next cleanup. """ if not case_id: return ( - "", + None, None, None, {}, @@ -130,11 +129,7 @@ def run_segmentation( if result.prediction_mask.exists(): mask_url = nifti_to_gradio_url(result.prediction_mask) - niivue_html = create_niivue_html( - dwi_url, - mask_url, - height=500, - ) + niivue_data = {"background_url": dwi_url, "overlay_url": mask_url} # 2. Static Visualizations (Matplotlib) gt_path = result.ground_truth if show_ground_truth else None @@ -180,7 +175,7 @@ def run_segmentation( # Return new results_dir to update gr.State for next cleanup return ( - niivue_html, + niivue_data, slice_fig, ortho_fig, metrics, @@ -191,7 +186,7 @@ def run_segmentation( except Exception as e: logger.exception("Error running segmentation") - return "", None, None, {}, None, f"Error: {e!s}", previous_results_dir + return None, None, None, {}, None, f"Error: {e!s}", previous_results_dir def create_app() -> gr.Blocks: @@ -251,10 +246,8 @@ def create_app() -> gr.Blocks: status, previous_results_state, # Update state with new results_dir ], - ).then( - fn=None, # JS-only handler to re-initialize NiiVue after HTML update - js=NIIVUE_UPDATE_JS, ) + # Note: No need for .then(js=...) anymore, the custom component updates reactively. # Trigger data loading after UI renders (prevents startup timeout) demo.load(initialize_case_selector, outputs=[case_selector]) @@ -284,29 +277,13 @@ if __name__ == "__main__": # Log startup info for debugging HF Spaces issues logger.info("=" * 60) logger.info("STARTUP: stroke-deepisles-demo") - logger.info("Assets directory: %s", _ASSETS_DIR.resolve()) - logger.info("Assets exists: %s", _ASSETS_DIR.exists()) logger.info("=" * 60) - # CRITICAL FIX (Issue #24): Load NiiVue via head= parameter - # - # The head= parameter injects a -""" - - -def get_niivue_loader_path() -> Path: - """ - DEPRECATED: Use get_niivue_head_html() with the `head` parameter instead. - - Get path to the NiiVue loader HTML file, creating it if needed. - This file-based approach is kept for backwards compatibility but - the direct `head` parameter approach is preferred. - - Returns: - Path to the niivue-loader.html file - """ - loader_path = _ASSET_DIR / "niivue-loader.html" - loader_content = get_niivue_head_html() - - try: - if loader_path.exists(): - existing_content = loader_path.read_text() - if existing_content == loader_content: - return loader_path - - loader_path.write_text(loader_content) - logger.debug("Generated NiiVue loader at %s", loader_path) - except OSError as e: - logger.warning("Could not write loader file at %s: %s", loader_path, e) - if not loader_path.exists(): - raise RuntimeError( - f"NiiVue loader file not found and cannot be created: {loader_path}" - ) from e - - return loader_path - def nifti_to_gradio_url(nifti_path: Path) -> str: """ @@ -378,265 +295,3 @@ def render_slice_comparison( fig.tight_layout() return fig - - -def create_niivue_html( - volume_url: str, - mask_url: str | None = None, - *, - height: int = 400, -) -> str: - """ - Create HTML for NiiVue viewer (static content only). - - This function generates an HTML snippet with data attributes containing - volume URLs. The actual NiiVue initialization is handled by js_on_load - in the gr.HTML component (see NIIVUE_ON_LOAD_JS). - - IMPORTANT (Issue #24): - - Gradio's gr.HTML strips