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Port of the mayavi aligner to the WebGL viewer: the functional reference volume stays on its own voxel grid, the pial and white matter surfaces are moved into its space by rotations and translations only, and they are cut off at the displayed slices so that their outline shows on each slice. - cortex/webgl/aligner.py: tornado server (reference mosaic, CTM pack, page, save endpoint), the world frame (voxel grid in mm permuted to RAS) and the JSAligner handle with tagged calls and frame waits - resources/js/aligner.js, aligner.html, resources/css/aligner.css: coronal, axial, sagittal and 3D views, cursor and slice navigation, mesh translation and rotation by mouse and keyboard with undo, colormap with range, brightness, contrast, gamma and flip, mesh color and opacity, a mode painting the volume onto the surface, saving - shaderlib.js: aligner_volume and aligner_mesh shader builders - menu.js: color picker controls - cortex.align.webgl_manual, [webgl_aligner] config defaults, docs and tests Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0115CeZYMxr1wvRSL2V8meKZ
The browser aligner refused to open a transform that had cached masks. It now opens, and deletes those masks when it saves: they were cut out of the reference volume through the alignment being replaced, nothing else invalidates them, and db.save_xfm refuses to write over a transform that still has them. - cortex/webgl/aligner.py: cached_masks and clear_masks, called from the save handler before db.save_xfm; the save response names what it deleted, and the page config lists the masks - the page warns, on opening a transform that has masks, that saving deletes them and that data masked with them has to be masked again - view_only stays an explicit choice rather than something masks force Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0115CeZYMxr1wvRSL2V8meKZ
The browser aligner replaces it, and it had not worked since mayavi stopped running on anything newer than Ubuntu 14.04. - drop cortex/mayavi_aligner.py, cortex.align.mayavi_manual and the [mayavi_aligner] config section - drop the mayavi sections of docs/align.rst and their screenshots, and point docs/transforms.rst at the browser aligner - the mayavi imports elsewhere (segmentation, surface display in freesurfer and database) are untouched, as are the mypy overrides they need Also make the aligner tests redirect the transform's mask paths into a directory of their own, so they neither depend on nor delete the masks another test file leaves in the bundled filestore. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0115CeZYMxr1wvRSL2V8meKZ
- WASD moves the mesh in the view under the mouse, like the arrow keys, in both cases with shift for the fine step - the colormap dropdown draws a strip of each colormap beside its name, through select2, the library the viewer's colormap picker uses; a css block in the shared template lets the aligner's stylesheet load last, since the viewer hides the select2 control it now needs - a transform field above the save button names what the alignment is saved under, so it can be saved as a new transform, leaving the one it was loaded from and its masks alone; the name is checked before it reaches the filesystem - an asterisk on the save button and in the title marks an alignment that differs from the one last saved - cortex.align.webgl_manual spells out every option rather than taking **kwargs menu.js keeps the controller of a button action, so its label can change. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0115CeZYMxr1wvRSL2V8meKZ
A `layout` control chooses where the surface is shown. "4 panels" is the layout as it was. "panels + surface" keeps the three slices showing their planes and outlines and turns the corner the 3D view occupies into the viewer, so the mesh can be nudged in the slices while the data on the surface follows. "surface" gives that viewer the whole window, framed on the surface the way the viewer opens on one. Both carry the reference data through the alignment as it stands, saved or not, and redraw as the mesh moves, so an alignment can be judged from the pattern the data makes on the cortex before it is committed. Also corrects the documented mouse buttons of the 3D view: its controls are the viewer's, which pan on the middle button and zoom on the right. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0115CeZYMxr1wvRSL2V8meKZ
- replace the `view` and `layout` dropdowns with one `display` control: 3 ortho + 3D slices, 3 ortho + 3D brain, or the data on the surface - draw the data view's surfaces in the anatomy's own frame with the morph targets of the CTM pack, so they inflate and flatten there while the alignment only moves where the volume is sampled - add `unfold` and `pivot`, and cull the medial wall while the flatmap shows - take the keyboard back from the panel when the mouse enters a view, and start with a view under the keys - keep the open colormap list within the window, which was scrolling the page sideways when it reached past the right edge Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0115CeZYMxr1wvRSL2V8meKZ
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@claude review |
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Claude finished @mvdoc's task in 1m 52s —— View job Review of #739 — the WebGL aligner
This is a substantial, well-documented replacement of the mayavi aligner. The docstrings are thorough and the test suite ( 1. 2. 3. 4. Unguarded Everything else — the coordinate-frame math ( No code changes were made — this was a review-only request, per the instructions ("review" → provide feedback, don't implement). |
- WebApp binds the loopback interface unless a caller asks otherwise; the viewer opens up to every interface only when domain_name names one - the aligner's save endpoint takes only posts carrying the token of the page it served, so nothing else reaching the port can write a transform - JSAligner.save waits for the save to land and returns the server's message, raising when it was refused - get_client hands the handle its server, which the documented open_browser=False flow needs for the tagged-reply loop - guard a zero vmin/vmax span in the aligner shader - drop get_local_client, which called an attribute WebApp does not have - add an edit history to the panel: a row per edit since load, with how far it moved and turned the surfaces; clicking one puts that alignment back - confirm closing the page while the alignment differs from the saved one Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0115CeZYMxr1wvRSL2V8meKZ
I had claude re-implement the mayavi aligner in webgl.
cortex.align.webgl_maual(<surface>, <transform>)gives a webgl viewer that can edit transforms.Updated to show the data also on the surface in real-time as you move the transform.
Controls:
WASD or RMB to translate, QE to rotate, hold shift to move in 1/10th size increments
Aligner_.TZfs.aligner-test.-.Vivaldi.2026-09-19.13-28-07.webm