fmridisplay overhaul: stateful controller, unified colour pipeline, visualization walkthrough#87
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…fixes
Interactive controller
- Auto-launch on construction (gated off in -batch / 'nocontroller'); restores
the current figure so it never hijacks montage/surface rendering; opens
top-right to avoid overlap.
- Threshold slider fixes: normalised [0 1] scale for raw |x| (uislider is
unreliable on tiny ranges), double-cast (data-derived thresholds are single),
numeric entry field, out-of-range shows an empty map.
- Split-colormap legend: 4 numeric labels + gap, live-updating with cmaprange.
- Colour bar renders via uiimage (fills the cell); larger legend font.
- Echoed code + title use the caller's real workspace variable name.
Layouts / entry points
- New fmridisplay.multiview method exposing all canlab_results_fmridisplay
compositions (compact/compact2/full/multirow/hcp/freesurfer/subcortex/...).
- canlab_results_fmridisplay reuses a passed-in object: composes onto it if it
has no montages, else just adds blobs (long-standing reuse preserved).
- fmridisplay.montage default routes through multiview('compact') (sag+axial
combo, matching fmri_data.montage) and echoes the equivalent call.
- montage pulls existing blob layers onto a newly added montage; surface
multi-keyword path (foursurfaces_hcp, ...) routes through addbrain.
Uniform colour scaling
- Shared canlab_default_cmaprange: robust per-arm percentile default used by
montages, render_on_surface, and the surface path (no more min/max vs
percentile divergence).
Consistency / robustness fixes
- Shared canlab_is_uifigure: never draw slices/surfaces into the controller
uifigure (open a fresh figure instead) across all entry points.
- removeblobs clears surface-only layers (no montage blobhandles).
- Multi-image objects handled without errors: montage() lays out a per-image
(multirow) display (fixed existing_axes expansion for a single placeholder
axis with many slices); addblobs() uses the first image only.
- Hide the per-axes "..." interaction toolbar on montage slices and rendered
surfaces (canlab_hide_axes_toolbar).
Tests
- Add regression tests: existing_axes expansion, multi-image montage/addblobs,
multiview compose+pull-in; update the split-legend label test. 47/47 pass.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013ZJacdhhByLGXqGHH9YQeo
…lormap
Unify montage value->colour with the surface path by building the central
canlab_colormap for EVERY mode, not just split/single. Previously solid,
continuous ('colormap' LUT) and indexed ('indexmap'/atlas) blobs used legacy
inline render_blobs paths that bypassed canlab_colormap; the indexmap path was
also buggy (broken sub2ind assignment). Now:
- render_blobs builds central_cm for split, single, solid, continuous and
indexed, and colours every slice via central_map_slice (one code path).
- canlab_colormap.map is NaN/Inf-robust for indexed and continuous, matching
the legacy guards, since blob slices contain out-of-blob NaN voxels.
Montage and surface of the same data now produce identical value->colour
mappings across all colour modes (verified max|dRGB|=0), and the buggy indexmap
rendering is removed.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Route indexed (indexmap/atlas) layers through the central canlab_colormap everywhere, so montage, surface, and the controller legend all agree: - canlab_colormap.from_render_args now builds an 'indexed' colormap for indexmap layers (was falling through to the default mango split). - controller: indexed layers show an 'indexed (atlas)' label, the region's solid colour as the swatch/stripe (not the whole palette), and blank the meaningless numeric range labels. - render_layer_surfaces: index/atlas surfaces render through the same true-colour central-colormap path as every other mode (nearest-neighbour sampling to preserve integer indices), replacing the render_on_surface legacy indexmap branch. Verified: surface vertex colours equal cmap(region_index) exactly (d=0) and match the montage; split/single/solid/continuous unaffected. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Multi-page markdown walkthrough of CanlabCore visualization methods: getting started, montages, surfaces, colormaps, the fmridisplay controller GUI with command-line equivalents, and atlases/regions. Includes per-section figure generators (_gen/) and embedded figures. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…ogs, master script
Applies the 8 approved revisions to the visualization walkthrough (docs only):
- §1: OO-API intro (methods return manipulable fmridisplay objects); add
canlab_orthviews (SPM-free) + pointer to the canlab_niivue web viewer.
- §2.6: custom montage via fmridisplay.montage (orientation/slice_range/spacing).
- §3.4/§3.6: addbrain help pointers + full surface & composite catalog.
- §5.4: montage-set and surface-layout catalog.
- §6: atlas object help, atlas-type table, Neuroimaging_Pattern_Masks dependency.
- Clean surface figures without colorbar legends; new 01_canlab_orthviews.png
and 02_custom_montage.png.
- Add master script _gen/visualization_walkthrough.m (one section per page,
regenerates all figures; ran clean in R2026a); referenced from §1 and index.
- Remove temporary _gen/gen_revise.m; fix R2026a func(){:} syntax in docs.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…ADME doc sections - Object_methods.md "Visualizing images and results": add a callout linking the new visualization_walkthrough/index.md as the hands-on starting point. - README.md: reorganize the documentation list into "In this repository" vs "Online", adding the visualization walkthrough, workflows, and markdown tutorials sections alongside the existing Object methods reference. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Summary
Overhauls the
fmridisplaydisplay stack and adds a full multi-page visualization walkthrough. Two themes:1. Display engine + colour pipeline
@fmridisplay/controller.m,multiview.m): layers remember their source data and options, so montages and surfaces re-threshold/recolour/re-render live from one handle object. Every GUI control has a one-line command-line twin.render_blobs.m,canlab_colormap.m,canlab_default_cmaprange.m): all montage modes (split / single / solid / continuous / indexed) build a singlecentral_cmand colour throughcentral_map_slice; the buggy indexmapsub2indpath and legacy continuousmap_functionpath are removed. Result:max|dRGB| = 0across montage modes, and surface indexmap vertex colours equalcmap(region_index)exactly.render_layer_surfaces.m,render_on_surface.m): all modes incl. indexed/atlas route through the truecolor path with'interp','nearest'for indexed; controller/surface legend handling for indexed atlases fixed.addblobs/removeblobs/surface/montagemethod updates,canlab_results_fmridisplayoptions, uifigure helpers (canlab_is_uifigure,canlab_hide_axes_toolbar), and expandedcanlab_test_fmridisplay_handlecoverage.2. Visualization walkthrough (
docs/visualization_walkthrough/)A hands-on, six-page guide pairing runnable code with the figure it produces, covering montages, 3-D surfaces, the interactive controller, colormaps, and atlases:
index.md,01_getting_started…06_atlases_and_regions.canlab_orthviews+ a pointer to thecanlab_niivueweb viewer; OO-API intro; custom montages viafmridisplay.montage; full catalogs of surfaces, composites, and montage-sets; atlas object help and theNeuroimaging_Pattern_Masksdependency._gen/visualization_walkthrough.m— one section per page (1.1 … 6.5) — regenerates every figure; per-pagegen_0*.mgenerators kept for single-page regen. Verified: runs end-to-end clean in MATLAB R2026a.Also removes stray Dropbox conflict temp files under
Unit_tests/walkthroughs/private/and minor typo/codespell fixes.Test plan
canlab_test_fmridisplay_handle(extended) passes._gen/visualization_walkthrough.mruns end-to-end in R2026a, regenerating all figures with no errors.max|dRGB| = 0across split/single/solid/continuous montage modes; surface indexmap vertex colours matchcmap(region_index)(d=0).🤖 Generated with Claude Code