Label mesh rendering, skeleton shaders, cross-section cameras, and recolor crossfades - #4
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davidackerman wants to merge 25 commits into
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Label mesh rendering, skeleton shaders, cross-section cameras, and recolor crossfades#4davidackerman wants to merge 25 commits into
davidackerman wants to merge 25 commits into
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This reverts commit c765e79.
Label meshing (mesh_from_labels): - Read + mesh the ROI block-by-block (parallel) and weld seams, so a sparse but huge bbox doesn't materialize the whole box at once. Auto-engages by planned read size vs. a memory threshold that respects the job's cgroup limit (LSF/containers), not just the node's free RAM. - target_vertices caps what we LOAD (planner never meshes finer than the budget); decimate_fraction then reduces below it, per segment so instance colors survive. fast-simplification added as the decimation backend. - Removed the confusing simplify_factor knob entirely (smooth + decimate only). Per-keyframe 3D background: - Capture Neuroglancer projectionBackgroundColor per keyframe on bake/update, interpolate it across transitions, and apply/animate it per frame in both the PNG render and the .blend export. - Propagate it across keyframes via the "Update current frame" prompt, mirroring the change back into each keyframe's stored ng_state so the NG link round-trips. UI: render controls regrouped into labeled rows (movie/render/mesh/scene) and the timeline bar into move/keyframe/output; "quality"->"detail"; decimate dropdown; opacity slider relabeled (all layers). README + tests updated.
Per-keyframe `waypoint` flag: the camera passes through the keyframe at speed instead of easing to a stop (and any hold is ignored), so a run of waypoints reads as one continuous flow. Easing is derived per-segment from endpoint type — stop->stop ease-in-out, stop->wp ease-in, wp->stop ease-out, wp->wp linear — which also generalizes the director's smooth-ends curve. Timelines with no waypoints are unchanged. Toggle lives in the transition-edit popover; persisted via DurationReq.
Evaluate the NG skeleton shader subset (uicontrol floats, prop_*() attributes, math/vec* functions, emitRGB/RGBA) directly so tube colors match custom NG colormaps, not just the older piecewise-smoothstep pattern. Threads shader text into the mesh geometry cache key so a shader edit invalidates baked tube colors.
…amera NG's 2D panels (xy/xz/yz and oblique cross-sections) are orthographic, not the 3D panel's perspective view. Convert the captured NG state into an orthographic Blender camera (position, cross-section plane, and a pixel-accurate ortho scale derived from the captured viewport size), thread projection/ortho_scale_nm through camera interpolation so 2D-to- 2D transitions behave like NG movie states, and upgrade older saved 2D keyframes at render time without mutating the project file. Also fixes slice contrast: the display window is now scaled from the source dtype instead of the crop's observed max (a dark/bright crop no longer skews brighter/darker than NG), a bare shaderControls "range" (no "window") is honored, and contrast limits now survive interpolation between keyframes instead of being dropped.
Meshes are now matched by layer name and split by segment membership: segments common to both keyframes stay continuously visible, removed ids fade out, and added ids fade in. This fixes common segments blinking when a layer's selected id set changes size across a transition. When several same-source layers recolor overlapping segments mid- transition, render them as one merged mesh with two baked vertex-color sets (Col/Col2) crossfaded by a material mix factor, instead of stacking independently-fading duplicate meshes — coincident transparent surfaces could fail to resolve in Cycles and hide geometry behind them for the whole crossfade.
Exploratory scripts comparing zmesh vs. voxel-surface vs. blockwise- decimated ER meshes and clip/cap methods, following the repo's existing spikes/ convention for throwaway experiments.
203MB of binary PLY/PNG comparison output shouldn't be tracked.
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@stuarteberg
Summary
Continuation of the label-mesh-rendering branch (renamed from
feature/label-mesh-rendering, previously PR #3, closed when the branch was renamed). Adds:prop_*()attributes, math/vec*functions,emitRGB/RGBA) so tube colors match custom NG colormaps, not just the older piecewise-smoothstep pattern.shaderControls.range(nowindow) is honored, and contrast limits now survive interpolation between keyframes.spikes/).