matterviz 0.4.1 → 0.4.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/EmptyState.svelte +10 -4
- package/dist/FilePicker.svelte +48 -60
- package/dist/Icon.svelte +7 -4
- package/dist/MillerIndexInput.svelte +2 -2
- package/dist/api/optimade.js +10 -7
- package/dist/app.css +68 -0
- package/dist/brillouin/BrillouinZone.svelte +90 -91
- package/dist/brillouin/BrillouinZone.svelte.d.ts +5 -7
- package/dist/brillouin/BrillouinZoneControls.svelte +3 -6
- package/dist/brillouin/BrillouinZoneExportPane.svelte +18 -14
- package/dist/brillouin/BrillouinZoneInfoPane.svelte +6 -10
- package/dist/brillouin/BrillouinZoneScene.svelte +46 -68
- package/dist/brillouin/BrillouinZoneScene.svelte.d.ts +1 -1
- package/dist/brillouin/compute.js +10 -16
- package/dist/brillouin/geometry.js +2 -2
- package/dist/chempot-diagram/ChemPotDiagram.svelte +48 -50
- package/dist/chempot-diagram/ChemPotDiagram2D.svelte +61 -169
- package/dist/chempot-diagram/ChemPotDiagram2D.svelte.d.ts +1 -1
- package/dist/chempot-diagram/ChemPotDiagram3D.svelte +559 -755
- package/dist/chempot-diagram/ChemPotDiagram3D.svelte.d.ts +1 -1
- package/dist/chempot-diagram/async-compute.svelte.js +13 -14
- package/dist/chempot-diagram/color.d.ts +21 -1
- package/dist/chempot-diagram/color.js +70 -1
- package/dist/chempot-diagram/compute.d.ts +7 -0
- package/dist/chempot-diagram/compute.js +85 -26
- package/dist/chempot-diagram/controls-state.svelte.js +1 -1
- package/dist/chempot-diagram/export.js +1 -6
- package/dist/chempot-diagram/temperature.js +9 -10
- package/dist/colors/index.d.ts +0 -4
- package/dist/colors/index.js +19 -20
- package/dist/composition/BarChart.svelte +30 -26
- package/dist/composition/BubbleChart.svelte +17 -17
- package/dist/composition/Composition.svelte +10 -19
- package/dist/composition/Formula.svelte +20 -27
- package/dist/composition/FormulaFilter.svelte +115 -184
- package/dist/composition/PieChart.svelte +55 -41
- package/dist/composition/format.js +7 -9
- package/dist/composition/index.d.ts +2 -0
- package/dist/composition/index.js +14 -0
- package/dist/composition/parse.d.ts +2 -2
- package/dist/composition/parse.js +61 -115
- package/dist/constants.d.ts +0 -1
- package/dist/constants.js +17 -26
- package/dist/convex-hull/ConvexHull.svelte +12 -15
- package/dist/convex-hull/ConvexHull.svelte.d.ts +1 -1
- package/dist/convex-hull/ConvexHull2D.svelte +93 -94
- package/dist/convex-hull/ConvexHull2D.svelte.d.ts +1 -1
- package/dist/convex-hull/ConvexHull3D.svelte +127 -186
- package/dist/convex-hull/ConvexHull3D.svelte.d.ts +1 -1
- package/dist/convex-hull/ConvexHull4D.svelte +131 -180
- package/dist/convex-hull/ConvexHull4D.svelte.d.ts +1 -1
- package/dist/convex-hull/ConvexHullChrome.svelte +36 -40
- package/dist/convex-hull/ConvexHullControls.svelte +46 -48
- package/dist/convex-hull/ConvexHullStats.svelte +193 -195
- package/dist/convex-hull/ConvexHullTooltip.svelte +5 -12
- package/dist/convex-hull/GasPressureControls.svelte +5 -12
- package/dist/convex-hull/StructurePopup.svelte +18 -22
- package/dist/convex-hull/StructurePopup.svelte.d.ts +2 -0
- package/dist/convex-hull/TemperatureSlider.svelte +4 -10
- package/dist/convex-hull/canvas-interactions.svelte.js +2 -1
- package/dist/convex-hull/gas-thermodynamics.js +21 -53
- package/dist/convex-hull/helpers.d.ts +8 -10
- package/dist/convex-hull/helpers.js +37 -43
- package/dist/convex-hull/hull-state.svelte.d.ts +1 -1
- package/dist/convex-hull/thermodynamics.js +37 -44
- package/dist/coordination/CoordinationBarPlot.svelte +49 -53
- package/dist/coordination/CoordinationBarPlot.svelte.d.ts +1 -1
- package/dist/coordination/calc-coordination.d.ts +1 -1
- package/dist/coordination/calc-coordination.js +28 -25
- package/dist/element/BohrAtom.svelte +5 -9
- package/dist/element/ElementHeading.svelte +4 -1
- package/dist/element/ElementPhoto.svelte +11 -9
- package/dist/element/ElementStats.svelte +12 -10
- package/dist/element/ElementTile.svelte +44 -67
- package/dist/element/Nucleus.svelte +4 -2
- package/dist/element/data.d.ts +3 -2
- package/dist/element/data.js +5 -1
- package/dist/element/helpers.d.ts +4 -0
- package/dist/element/helpers.js +18 -0
- package/dist/element/index.d.ts +2 -5
- package/dist/element/index.js +4 -19
- package/dist/feedback/DragOverlay.svelte +5 -5
- package/dist/feedback/DragOverlay.svelte.d.ts +2 -2
- package/dist/feedback/StatusMessage.svelte +7 -4
- package/dist/fermi-surface/FermiSlice.svelte +21 -18
- package/dist/fermi-surface/FermiSurface.svelte +35 -44
- package/dist/fermi-surface/FermiSurface.svelte.d.ts +7 -13
- package/dist/fermi-surface/FermiSurfaceControls.svelte +6 -20
- package/dist/fermi-surface/FermiSurfaceControls.svelte.d.ts +1 -1
- package/dist/fermi-surface/FermiSurfaceScene.svelte +64 -136
- package/dist/fermi-surface/FermiSurfaceScene.svelte.d.ts +1 -1
- package/dist/fermi-surface/FermiSurfaceTooltip.svelte +9 -6
- package/dist/fermi-surface/compute.js +25 -58
- package/dist/fermi-surface/parse.js +54 -88
- package/dist/file-viewer/JsonBrowser.svelte +1043 -0
- package/dist/file-viewer/JsonBrowser.svelte.d.ts +9 -0
- package/dist/file-viewer/PlotPanel.svelte +350 -0
- package/dist/file-viewer/PlotPanel.svelte.d.ts +9 -0
- package/dist/file-viewer/TrajectoryWithDos.svelte +30 -0
- package/dist/file-viewer/TrajectoryWithDos.svelte.d.ts +10 -0
- package/dist/file-viewer/detect.d.ts +11 -0
- package/dist/file-viewer/detect.js +381 -0
- package/dist/file-viewer/eligibility.d.ts +4 -0
- package/dist/file-viewer/eligibility.js +53 -0
- package/dist/file-viewer/host-protocol.d.ts +50 -0
- package/dist/file-viewer/host-transfer.d.ts +25 -0
- package/dist/file-viewer/host-transfer.js +42 -0
- package/dist/file-viewer/index.d.ts +5 -0
- package/dist/file-viewer/index.js +5 -0
- package/dist/file-viewer/main.d.ts +44 -0
- package/dist/file-viewer/main.js +535 -0
- package/dist/file-viewer/parse.d.ts +9 -0
- package/dist/file-viewer/parse.js +170 -0
- package/dist/file-viewer/plot-utils.d.ts +24 -0
- package/dist/file-viewer/plot-utils.js +191 -0
- package/dist/file-viewer/types.d.ts +4 -0
- package/dist/file-viewer/types.js +5 -0
- package/dist/heatmap-matrix/HeatmapMatrix.svelte +153 -219
- package/dist/heatmap-matrix/HeatmapMatrix.svelte.d.ts +2 -2
- package/dist/heatmap-matrix/HeatmapMatrixControls.svelte +9 -7
- package/dist/heatmap-matrix/HeatmapMatrixControls.svelte.d.ts +1 -1
- package/dist/heatmap-matrix/index.d.ts +5 -0
- package/dist/icons.d.ts +4 -0
- package/dist/icons.js +4 -0
- package/dist/index.d.ts +2 -2
- package/dist/index.js +1 -1
- package/dist/io/ExportPane.svelte +11 -7
- package/dist/io/decompress.d.ts +4 -1
- package/dist/io/decompress.js +24 -36
- package/dist/io/export.d.ts +11 -4
- package/dist/io/export.js +75 -19
- package/dist/io/fetch.d.ts +0 -3
- package/dist/io/fetch.js +0 -11
- package/dist/io/file-drop.js +60 -35
- package/dist/io/index.d.ts +0 -1
- package/dist/io/index.js +2 -9
- package/dist/io/is-binary.d.ts +9 -0
- package/dist/io/is-binary.js +45 -1
- package/dist/io/url-drop.d.ts +2 -0
- package/dist/io/url-drop.js +40 -40
- package/dist/isosurface/Isosurface.svelte +700 -215
- package/dist/isosurface/Isosurface.svelte.d.ts +7 -1
- package/dist/isosurface/IsosurfaceControls.svelte +590 -116
- package/dist/isosurface/IsosurfaceControls.svelte.d.ts +1 -1
- package/dist/isosurface/VolumeSlice.svelte +224 -0
- package/dist/isosurface/VolumeSlice.svelte.d.ts +28 -0
- package/dist/isosurface/coloring.d.ts +20 -0
- package/dist/isosurface/coloring.js +118 -0
- package/dist/isosurface/geometry-worker-types.d.ts +38 -0
- package/dist/isosurface/geometry.worker.d.ts +1 -0
- package/dist/isosurface/geometry.worker.js +59 -0
- package/dist/isosurface/grid.d.ts +10 -0
- package/dist/isosurface/grid.js +31 -0
- package/dist/isosurface/index.d.ts +4 -0
- package/dist/isosurface/index.js +4 -0
- package/dist/isosurface/parse-vaspwave.d.ts +3 -0
- package/dist/isosurface/parse-vaspwave.js +138 -0
- package/dist/isosurface/parse.js +6 -6
- package/dist/isosurface/profile.d.ts +12 -0
- package/dist/isosurface/profile.js +19 -0
- package/dist/isosurface/sampling.d.ts +34 -0
- package/dist/isosurface/sampling.js +408 -0
- package/dist/isosurface/slice-rendering.d.ts +13 -0
- package/dist/isosurface/slice-rendering.js +79 -0
- package/dist/isosurface/slice.d.ts +22 -2
- package/dist/isosurface/slice.js +200 -116
- package/dist/isosurface/types.d.ts +24 -1
- package/dist/isosurface/types.js +120 -8
- package/dist/json-path.d.ts +4 -0
- package/dist/json-path.js +89 -0
- package/dist/labels.d.ts +6 -2
- package/dist/labels.js +44 -14
- package/dist/layout/FullscreenButton.svelte +2 -1
- package/dist/layout/FullscreenToggle.svelte +10 -4
- package/dist/layout/InfoCard.svelte +8 -21
- package/dist/layout/InfoTag.svelte +1 -3
- package/dist/layout/NumberRangeInput.svelte +46 -0
- package/dist/layout/NumberRangeInput.svelte.d.ts +12 -0
- package/dist/layout/PropertyFilter.svelte +2 -6
- package/dist/layout/SettingsSection.svelte +57 -62
- package/dist/layout/SettingsSection.svelte.d.ts +6 -7
- package/dist/layout/SubpageGrid.svelte +3 -1
- package/dist/layout/ViewerChrome.svelte +16 -11
- package/dist/layout/ViewerChrome.svelte.d.ts +2 -1
- package/dist/layout/fullscreen.js +3 -5
- package/dist/layout/fullscreen.svelte.js +1 -2
- package/dist/layout/index.d.ts +1 -0
- package/dist/layout/index.js +1 -0
- package/dist/layout/json-tree/JsonNode.svelte +22 -59
- package/dist/layout/json-tree/JsonTree.svelte +101 -172
- package/dist/layout/json-tree/JsonValue.svelte +9 -32
- package/dist/layout/json-tree/utils.d.ts +0 -3
- package/dist/layout/json-tree/utils.js +50 -188
- package/dist/marching-cubes.d.ts +8 -1
- package/dist/marching-cubes.js +115 -48
- package/dist/math.d.ts +5 -2
- package/dist/math.js +48 -38
- package/dist/overlays/ContextMenu.svelte +19 -34
- package/dist/overlays/CopyButton.svelte +11 -5
- package/dist/overlays/DragControlTab.svelte +6 -1
- package/dist/overlays/DraggablePane.svelte +110 -74
- package/dist/overlays/DraggablePane.svelte.d.ts +2 -1
- package/dist/overlays/GlassChip.svelte +32 -0
- package/dist/overlays/GlassChip.svelte.d.ts +8 -0
- package/dist/overlays/InfoPaneCards.svelte +11 -23
- package/dist/overlays/index.d.ts +7 -0
- package/dist/overlays/index.js +26 -0
- package/dist/overlays/portal.d.ts +2 -0
- package/dist/overlays/portal.js +14 -0
- package/dist/periodic-table/PeriodicTable.svelte +113 -145
- package/dist/periodic-table/PeriodicTable.svelte.d.ts +5 -3
- package/dist/periodic-table/PeriodicTableControls.svelte +37 -115
- package/dist/periodic-table/TableInset.svelte +9 -4
- package/dist/phase-diagram/IsobaricBinaryPhaseDiagram.svelte +68 -105
- package/dist/phase-diagram/IsobaricBinaryPhaseDiagram.svelte.d.ts +6 -8
- package/dist/phase-diagram/PhaseDiagramControls.svelte +70 -94
- package/dist/phase-diagram/PhaseDiagramControls.svelte.d.ts +1 -1
- package/dist/phase-diagram/PhaseDiagramEditorPane.svelte +2 -1
- package/dist/phase-diagram/PhaseDiagramExportPane.svelte +12 -12
- package/dist/phase-diagram/PhaseDiagramTooltip.svelte +54 -58
- package/dist/phase-diagram/TdbInfoPanel.svelte +21 -15
- package/dist/phase-diagram/build-diagram.js +4 -9
- package/dist/phase-diagram/diagram-input.d.ts +1 -2
- package/dist/phase-diagram/parse.js +15 -15
- package/dist/phase-diagram/svg-to-diagram.js +28 -27
- package/dist/phase-diagram/utils.js +2 -3
- package/dist/plot/bar/BarPlot.svelte +461 -426
- package/dist/plot/bar/BarPlot.svelte.d.ts +2 -0
- package/dist/plot/bar/BarPlotControls.svelte +1 -3
- package/dist/plot/bar/BarPlotControls.svelte.d.ts +4 -6
- package/dist/plot/bar/SpacegroupBarPlot.svelte +46 -77
- package/dist/plot/bar/data.d.ts +5 -4
- package/dist/plot/bar/data.js +2 -1
- package/dist/plot/box/BoxPlot.svelte +322 -226
- package/dist/plot/box/BoxPlot.svelte.d.ts +2 -0
- package/dist/plot/box/Violin.svelte.d.ts +1 -0
- package/dist/plot/box/box-plot.js +1 -1
- package/dist/plot/core/auto-place.d.ts +1 -1
- package/dist/plot/core/auto-place.js +2 -2
- package/dist/plot/core/axis-utils.d.ts +12 -7
- package/dist/plot/core/axis-utils.js +48 -48
- package/dist/plot/core/components/AxisLabel.svelte +82 -20
- package/dist/plot/core/components/AxisLabel.svelte.d.ts +1 -0
- package/dist/plot/core/components/ColorBar.svelte +101 -106
- package/dist/plot/core/components/ColorScaleSelect.svelte +1 -1
- package/dist/plot/core/components/FillArea.svelte +10 -17
- package/dist/plot/core/components/HierarchyControls.svelte +249 -0
- package/dist/plot/{sunburst/SunburstControls.svelte.d.ts → core/components/HierarchyControls.svelte.d.ts} +12 -8
- package/dist/plot/core/components/InteractiveAxisLabel.svelte +1 -1
- package/dist/plot/core/components/InteractiveAxisLabel.svelte.d.ts +1 -1
- package/dist/plot/core/components/Line.svelte +18 -9
- package/dist/plot/core/components/Line.svelte.d.ts +2 -0
- package/dist/plot/core/components/PlotAxis.svelte +40 -17
- package/dist/plot/core/components/PlotControls.svelte +65 -41
- package/dist/plot/core/components/PlotLegend.svelte +31 -35
- package/dist/plot/core/components/PlotMarginals.svelte +616 -0
- package/dist/plot/core/components/PlotMarginals.svelte.d.ts +15 -0
- package/dist/plot/core/components/PlotTooltip.svelte +1 -1
- package/dist/plot/core/components/PortalSelect.svelte +4 -8
- package/dist/plot/core/components/ReferenceLine.svelte +27 -24
- package/dist/plot/core/components/ReferenceLine3D.svelte +54 -57
- package/dist/plot/core/components/ReferencePlane.svelte +7 -8
- package/dist/plot/core/components/ZeroLines.svelte +4 -8
- package/dist/plot/core/components/ZoomRect.svelte +1 -2
- package/dist/plot/core/components/index.d.ts +1 -0
- package/dist/plot/core/components/index.js +1 -0
- package/dist/plot/core/data-cleaning-signal.d.ts +46 -0
- package/dist/plot/core/data-cleaning-signal.js +467 -0
- package/dist/plot/core/data-cleaning.d.ts +2 -42
- package/dist/plot/core/data-cleaning.js +27 -474
- package/dist/plot/core/data-transform.d.ts +1 -2
- package/dist/plot/core/data-transform.js +9 -15
- package/dist/plot/core/fill-utils.d.ts +3 -1
- package/dist/plot/core/fill-utils.js +28 -6
- package/dist/plot/core/index.d.ts +1 -0
- package/dist/plot/core/index.js +1 -0
- package/dist/plot/core/interactions.js +0 -2
- package/dist/plot/core/layout.d.ts +15 -6
- package/dist/plot/core/layout.js +57 -38
- package/dist/plot/core/marginals.d.ts +170 -0
- package/dist/plot/core/marginals.js +436 -0
- package/dist/plot/core/pan-zoom.svelte.d.ts +2 -4
- package/dist/plot/core/pan-zoom.svelte.js +34 -17
- package/dist/plot/core/placed-tween.svelte.d.ts +3 -0
- package/dist/plot/core/placed-tween.svelte.js +68 -21
- package/dist/plot/core/reference-line.js +1 -1
- package/dist/plot/core/scales.d.ts +23 -0
- package/dist/plot/core/scales.js +39 -13
- package/dist/plot/core/svg.js +0 -1
- package/dist/plot/core/types/fills.d.ts +101 -0
- package/dist/plot/core/types/fills.js +15 -0
- package/dist/plot/core/types/plot-3d.d.ts +87 -0
- package/dist/plot/core/types/plot-3d.js +4 -0
- package/dist/plot/core/types/reference-lines.d.ts +140 -0
- package/dist/plot/core/types/reference-lines.js +9 -0
- package/dist/plot/core/types.d.ts +29 -324
- package/dist/plot/core/types.js +23 -20
- package/dist/plot/core/utils/hierarchy-chart.d.ts +52 -0
- package/dist/plot/core/utils/hierarchy-chart.js +191 -0
- package/dist/plot/core/utils/hierarchy-labels.d.ts +20 -0
- package/dist/plot/core/utils/hierarchy-labels.js +100 -0
- package/dist/plot/core/utils/label-placement.js +2 -2
- package/dist/plot/histogram/Histogram.svelte +314 -340
- package/dist/plot/histogram/Histogram.svelte.d.ts +7 -7
- package/dist/plot/histogram/HistogramControls.svelte +30 -28
- package/dist/plot/histogram/histogram.d.ts +31 -0
- package/dist/plot/histogram/histogram.js +70 -0
- package/dist/plot/histogram/index.d.ts +1 -0
- package/dist/plot/histogram/index.js +1 -0
- package/dist/plot/index.d.ts +1 -0
- package/dist/plot/index.js +1 -0
- package/dist/plot/sankey/Sankey.svelte +78 -69
- package/dist/plot/sankey/Sankey.svelte.d.ts +2 -2
- package/dist/plot/sankey/SankeyControls.svelte +22 -16
- package/dist/plot/sankey/sankey.js +13 -9
- package/dist/plot/scatter/BinnedScatterPlot.svelte +311 -141
- package/dist/plot/scatter/BinnedScatterPlot.svelte.d.ts +7 -0
- package/dist/plot/scatter/ElementScatter.svelte +4 -1
- package/dist/plot/scatter/ScatterPlot.svelte +517 -410
- package/dist/plot/scatter/ScatterPlot.svelte.d.ts +2 -0
- package/dist/plot/scatter/ScatterPlotControls.svelte +18 -19
- package/dist/plot/scatter/ScatterPlotControls.svelte.d.ts +1 -1
- package/dist/plot/scatter/ScatterPoint.svelte +16 -9
- package/dist/plot/scatter/adaptive-density.d.ts +1 -1
- package/dist/plot/scatter/adaptive-density.js +36 -20
- package/dist/plot/scatter/binned-scatter-types.d.ts +3 -2
- package/dist/plot/scatter/binned-scatter-types.js +6 -1
- package/dist/plot/scatter/scatter-data.d.ts +1 -1
- package/dist/plot/scatter/scatter-data.js +8 -7
- package/dist/plot/scatter-3d/ScatterPlot3D.svelte +25 -34
- package/dist/plot/scatter-3d/ScatterPlot3D.svelte.d.ts +2 -2
- package/dist/plot/scatter-3d/ScatterPlot3DControls.svelte +8 -5
- package/dist/plot/scatter-3d/ScatterPlot3DScene.svelte +113 -116
- package/dist/plot/scatter-3d/ScatterPlot3DScene.svelte.d.ts +2 -2
- package/dist/plot/scatter-3d/Surface3D.svelte +4 -13
- package/dist/plot/sunburst/Sunburst.svelte +269 -347
- package/dist/plot/sunburst/Sunburst.svelte.d.ts +2 -2
- package/dist/plot/sunburst/index.d.ts +1 -1
- package/dist/plot/sunburst/index.js +2 -1
- package/dist/plot/sunburst/render.d.ts +2 -2
- package/dist/plot/sunburst/render.js +47 -22
- package/dist/plot/sunburst/sunburst.d.ts +5 -1
- package/dist/plot/sunburst/sunburst.js +10 -3
- package/dist/plot/treemap/Treemap.svelte +1022 -0
- package/dist/plot/treemap/Treemap.svelte.d.ts +90 -0
- package/dist/plot/treemap/index.d.ts +4 -0
- package/dist/plot/treemap/index.js +4 -0
- package/dist/plot/treemap/labels.d.ts +38 -0
- package/dist/plot/treemap/labels.js +80 -0
- package/dist/plot/treemap/treemap.d.ts +28 -0
- package/dist/plot/treemap/treemap.js +102 -0
- package/dist/rdf/RdfPlot.svelte +37 -59
- package/dist/rdf/RdfPlot.svelte.d.ts +1 -1
- package/dist/rdf/calc-rdf.js +63 -52
- package/dist/rdf/index.d.ts +0 -1
- package/dist/sanitize.js +85 -27
- package/dist/scene/SceneCamera.svelte +1 -1
- package/dist/scene/SceneCamera.svelte.d.ts +1 -1
- package/dist/scene/bind-renderer.svelte.js +14 -6
- package/dist/scene/index.d.ts +1 -2
- package/dist/scene/index.js +1 -1
- package/dist/scene/{props.js → props.svelte.js} +15 -1
- package/dist/settings.d.ts +19 -9
- package/dist/settings.js +229 -525
- package/dist/spectral/Bands.svelte +207 -221
- package/dist/spectral/BandsAndDos.svelte +11 -9
- package/dist/spectral/BrillouinBandsDos.svelte +19 -42
- package/dist/spectral/Dos.svelte +92 -93
- package/dist/spectral/helpers.d.ts +3 -3
- package/dist/spectral/helpers.js +65 -140
- package/dist/state.svelte.js +5 -18
- package/dist/structure/Arrow.svelte +5 -18
- package/dist/structure/ArrowInstances.svelte +160 -0
- package/dist/structure/ArrowInstances.svelte.d.ts +16 -0
- package/dist/structure/AtomLegend.svelte +120 -85
- package/dist/structure/AtomLegend.svelte.d.ts +2 -3
- package/dist/structure/Bond.svelte +31 -23
- package/dist/structure/CanvasTooltip.svelte +15 -3
- package/dist/structure/CellSelect.svelte +45 -35
- package/dist/structure/Cylinder.svelte +24 -40
- package/dist/structure/InstancedAtoms.svelte +114 -0
- package/dist/structure/InstancedAtoms.svelte.d.ts +15 -0
- package/dist/structure/Lattice.svelte +85 -149
- package/dist/structure/SiteLabels.svelte +122 -0
- package/dist/structure/SiteLabels.svelte.d.ts +18 -0
- package/dist/structure/Structure.svelte +636 -504
- package/dist/structure/Structure.svelte.d.ts +4 -2
- package/dist/structure/StructureCarousel.svelte +637 -0
- package/dist/structure/StructureCarousel.svelte.d.ts +19 -0
- package/dist/structure/StructureControls.svelte +165 -425
- package/dist/structure/StructureControls.svelte.d.ts +1 -1
- package/dist/structure/StructureExportPane.svelte +17 -21
- package/dist/structure/StructureInfoPane.svelte +128 -133
- package/dist/structure/StructureInfoPane.svelte.d.ts +1 -1
- package/dist/structure/StructureScene.svelte +535 -578
- package/dist/structure/StructureScene.svelte.d.ts +6 -2
- package/dist/structure/StructureViewport.svelte +451 -0
- package/dist/structure/StructureViewport.svelte.d.ts +65 -0
- package/dist/structure/atom-label-placement.d.ts +16 -12
- package/dist/structure/atom-label-placement.js +70 -37
- package/dist/structure/atom-properties.d.ts +2 -0
- package/dist/structure/atom-properties.js +105 -38
- package/dist/structure/bond-order-perception.js +3 -8
- package/dist/structure/bonding.d.ts +9 -3
- package/dist/structure/bonding.js +95 -46
- package/dist/structure/edit-history.d.ts +6 -0
- package/dist/structure/edit-history.js +27 -0
- package/dist/structure/export.d.ts +1 -0
- package/dist/structure/export.js +89 -105
- package/dist/structure/format-detect.d.ts +1 -0
- package/dist/structure/format-detect.js +20 -0
- package/dist/structure/geometry.d.ts +9 -0
- package/dist/structure/geometry.js +27 -0
- package/dist/structure/index.d.ts +16 -1
- package/dist/structure/index.js +15 -10
- package/dist/structure/measure.d.ts +1 -1
- package/dist/structure/measure.js +6 -12
- package/dist/structure/parse.d.ts +2 -1
- package/dist/structure/parse.js +272 -313
- package/dist/structure/partial-occupancy.js +10 -5
- package/dist/structure/pbc.js +85 -107
- package/dist/structure/polyhedra.d.ts +0 -1
- package/dist/structure/polyhedra.js +7 -21
- package/dist/structure/prop-groups.d.ts +85 -0
- package/dist/structure/prop-groups.js +18 -0
- package/dist/structure/supercell.d.ts +1 -2
- package/dist/structure/supercell.js +7 -13
- package/dist/symmetry/SymmetryElements.svelte +11 -15
- package/dist/symmetry/SymmetryStats.svelte +55 -71
- package/dist/symmetry/WyckoffTable.svelte +10 -28
- package/dist/symmetry/cell-transform.js +6 -14
- package/dist/symmetry/index.d.ts +1 -0
- package/dist/symmetry/index.js +13 -10
- package/dist/symmetry/spacegroups.js +3 -2
- package/dist/table/HeatmapTable.svelte +1142 -447
- package/dist/table/HeatmapTable.svelte.d.ts +12 -2
- package/dist/table/ToggleMenu.svelte +168 -53
- package/dist/table/ToggleMenu.svelte.d.ts +1 -1
- package/dist/table/index.d.ts +21 -6
- package/dist/table/index.js +34 -21
- package/dist/theme/ThemeControl.svelte +16 -8
- package/dist/theme/embedded.d.ts +18 -0
- package/dist/theme/embedded.js +206 -0
- package/dist/theme/index.d.ts +5 -5
- package/dist/theme/index.js +5 -12
- package/dist/theme/themes.mjs +44 -66
- package/dist/tooltip/KCoords.svelte +4 -1
- package/dist/tooltip/TooltipContent.svelte +3 -6
- package/dist/tooltip/TooltipContent.svelte.d.ts +1 -1
- package/dist/tooltip/index.d.ts +8 -1
- package/dist/trajectory/Trajectory.svelte +613 -386
- package/dist/trajectory/Trajectory.svelte.d.ts +1 -1
- package/dist/trajectory/TrajectoryError.svelte +12 -74
- package/dist/trajectory/TrajectoryExportPane.svelte +14 -32
- package/dist/trajectory/TrajectoryInfoPane.svelte +127 -164
- package/dist/trajectory/TrajectoryInfoPane.svelte.d.ts +2 -1
- package/dist/trajectory/extract.js +61 -49
- package/dist/trajectory/format-detect.d.ts +2 -0
- package/dist/trajectory/format-detect.js +17 -13
- package/dist/trajectory/frame-reader.d.ts +2 -0
- package/dist/trajectory/frame-reader.js +35 -32
- package/dist/trajectory/helpers.d.ts +2 -0
- package/dist/trajectory/helpers.js +34 -56
- package/dist/trajectory/index.d.ts +1 -0
- package/dist/trajectory/index.js +5 -8
- package/dist/trajectory/parse/ase.js +1 -1
- package/dist/trajectory/parse/h5-utils.d.ts +13 -0
- package/dist/trajectory/parse/h5-utils.js +109 -0
- package/dist/trajectory/parse/hdf5.d.ts +1 -1
- package/dist/trajectory/parse/hdf5.js +116 -106
- package/dist/trajectory/parse/index.d.ts +6 -6
- package/dist/trajectory/parse/index.js +25 -33
- package/dist/trajectory/parse/lammps.js +8 -12
- package/dist/trajectory/parse/vasp.js +10 -7
- package/dist/trajectory/parse/vaspout-electronic.d.ts +13 -0
- package/dist/trajectory/parse/vaspout-electronic.js +207 -0
- package/dist/trajectory/parse/vaspout-h5.d.ts +4 -0
- package/dist/trajectory/parse/vaspout-h5.js +281 -0
- package/dist/trajectory/parse/xyz.js +59 -9
- package/dist/trajectory/plotting.d.ts +8 -9
- package/dist/trajectory/plotting.js +113 -64
- package/dist/utils.d.ts +3 -0
- package/dist/utils.js +7 -0
- package/dist/xrd/XrdPlot.svelte +79 -118
- package/dist/xrd/broadening.js +2 -1
- package/dist/xrd/calc-xrd.js +24 -62
- package/dist/xrd/parse.d.ts +0 -1
- package/dist/xrd/parse.js +69 -95
- package/package.json +94 -34
- package/readme.md +6 -5
- package/dist/api/mp.d.ts +0 -6
- package/dist/api/mp.js +0 -22
- package/dist/plot/sunburst/SunburstControls.svelte +0 -200
- package/dist/scene/types.d.ts +0 -26
- package/dist/tooltip/types.d.ts +0 -8
- package/dist/trajectory/constants.d.ts +0 -6
- package/dist/trajectory/constants.js +0 -11
- /package/dist/{scene/types.js → file-viewer/host-protocol.js} +0 -0
- /package/dist/{tooltip/types.js → isosurface/geometry-worker-types.js} +0 -0
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// Data cleaning utilities for plot data
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//
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// Enforces physical bounds, handles invalid values, and cleans multi-dimensional datasets.
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// Signal-processing primitives (variance, instability detection, smoothing, outlier removal)
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// live in ./data-cleaning-signal and are re-exported here so the public API is unchanged.
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import { apply_gaussian_smearing } from '../../spectral/helpers';
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const DEFAULT_OSCILLATION_THRESHOLD = 3.0;
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const DEFAULT_POLYNOMIAL_ORDER = 2;
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// --- Core Detection Functions ---
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// Compute rolling variance using Welford's online algorithm - O(n)
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// Returns variance for each point based on surrounding window
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export function compute_local_variance(values, window_size) {
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const len = values.length;
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if (len === 0)
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return [];
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if (len === 1)
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return [0];
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const half_window = Math.floor(window_size / 2);
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const result = Array(len);
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// Single pass for each index, no slice allocation (avoids O(n × window) allocations)
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for (let idx = 0; idx < len; idx++) {
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const start = Math.max(0, idx - half_window);
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const end = Math.min(len, idx + half_window + 1);
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// Welford's online variance calculation
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let [mean, m2, count] = [0, 0, 0];
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for (let jdx = start; jdx < end; jdx++) {
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const val = values[jdx];
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continue;
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count++;
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const delta = val - mean;
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mean += delta / count;
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const delta2 = val - mean;
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m2 += delta * delta2;
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}
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result[idx] = count > 1 ? m2 / (count - 1) : 0;
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}
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return result;
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}
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// Compute first-order finite differences (discrete derivative)
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function compute_derivatives(values) {
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return [];
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const derivs = Array(values.length - 1);
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for (let idx = 0; idx < values.length - 1; idx++) {
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derivs[idx] = values[idx + 1] - values[idx];
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}
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return derivs;
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}
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// Detect derivative variance spikes (method 1)
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// Returns onset index where derivative variance exceeds threshold
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function detect_derivative_variance(values, window_size, threshold_multiplier) {
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const derivs = compute_derivatives(values);
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if (derivs.length < window_size) {
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return { onset_index: -1, score: 0 };
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}
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const local_var = compute_local_variance(derivs, window_size);
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// Compute baseline variance from first stable portion
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const baseline_end = Math.min(Math.floor(derivs.length / 4), 50);
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const baseline_vars = local_var.slice(0, Math.max(baseline_end, window_size));
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const baseline_median = median(baseline_vars.filter((val) => val > 0));
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if (baseline_median === 0) {
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return { onset_index: -1, score: 0 };
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}
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// Find first point where variance exceeds threshold
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let max_score = 0;
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for (let idx = baseline_end; idx < local_var.length; idx++) {
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const ratio = local_var[idx] / baseline_median;
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if (ratio > threshold_multiplier) {
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return { onset_index: idx + 1, score: ratio }; // +1 to convert from deriv index to value index
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return { onset_index: -1, score: max_score };
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}
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// Detect exponential amplitude growth (method 2)
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// Looks for values growing exponentially from their mean
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function detect_amplitude_growth(values, window_size) {
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}
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// Compute running amplitude (deviation from local mean)
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const amplitudes = [];
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const half_window = Math.floor(window_size / 2);
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const start = idx - half_window;
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const end = idx + half_window + 1;
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const window_len = end - start;
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// Compute local mean without slice allocation
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let sum = 0;
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sum += values[jdx];
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const local_mean = sum / window_len;
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// Find max deviation without slice allocation
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let max_deviation = 0;
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const deviation = Math.abs(values[jdx] - local_mean);
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amplitudes.push(max_deviation);
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}
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// Detect exponential growth by checking if amplitude ratio increases
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const baseline_amp = median(amplitudes.slice(0, Math.floor(amplitudes.length / 4)));
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}
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let max_score = 0;
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for (let idx = Math.floor(amplitudes.length / 4); idx < amplitudes.length; idx++) {
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const ratio = amplitudes[idx] / baseline_amp;
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if (ratio > max_score)
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max_score = ratio;
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// Exponential growth threshold: amplitude 10x baseline
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if (ratio > 10) {
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return { onset_index: idx + half_window, score: ratio / 10 };
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}
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return { onset_index: -1, score: max_score / 10 };
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}
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// Count derivative sign changes per window (method 3)
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// Detects high-frequency oscillations
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function detect_sign_change_frequency(values, window_size, max_changes_per_window = 3) {
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const derivs = compute_derivatives(values);
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if (derivs.length < window_size * 2) {
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return { onset_index: -1, score: 0 };
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}
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// Count sign changes in sliding windows
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const half_window = Math.floor(window_size / 2);
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let max_score = 0;
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for (let idx = half_window; idx < derivs.length - half_window; idx++) {
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const start = idx - half_window;
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const end = idx + half_window + 1;
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let sign_changes = 0;
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// Count sign changes without slice allocation
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for (let jdx = start + 1; jdx < end; jdx++) {
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if (derivs[jdx] * derivs[jdx - 1] < 0) {
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sign_changes++;
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}
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}
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const normalized_score = sign_changes / max_changes_per_window;
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if (normalized_score > max_score)
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max_score = normalized_score;
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if (sign_changes > max_changes_per_window) {
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return { onset_index: idx + 1, score: normalized_score };
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}
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}
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return { onset_index: -1, score: max_score };
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}
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// Combined detection with configurable weights
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export function detect_instability(x_values, y_values, config = {}) {
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const window_size = config.window_size ?? DEFAULT_WINDOW_SIZE;
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const threshold = config.oscillation_threshold ?? DEFAULT_OSCILLATION_THRESHOLD;
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const weights = {
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derivative_variance: config.oscillation_weights?.derivative_variance ?? 1.0,
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amplitude_growth: config.oscillation_weights?.amplitude_growth ?? 1.0,
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sign_changes: config.oscillation_weights?.sign_changes ?? 1.0,
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};
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// Filter out invalid values for detection
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const valid_indices = [];
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const valid_y = [];
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for (let idx = 0; idx < y_values.length; idx++) {
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if (Number.isFinite(y_values[idx])) {
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valid_indices.push(idx);
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}
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}
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if (valid_y.length < window_size * 2) {
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const method_scores = { derivative_variance: 0, amplitude_growth: 0, sign_changes: 0 };
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const detected = false;
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return { detected, onset_index: -1, onset_x: NaN, combined_score: 0, method_scores };
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}
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// Run all three detection methods
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const deriv_result = detect_derivative_variance(valid_y, window_size, threshold);
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const amp_result = detect_amplitude_growth(valid_y, window_size);
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const sign_result = detect_sign_change_frequency(valid_y, window_size);
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const method_scores = {
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derivative_variance: deriv_result.score,
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amplitude_growth: amp_result.score,
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sign_changes: sign_result.score,
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};
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// Compute weighted combined score
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const total_weight = weights.derivative_variance + weights.amplitude_growth + weights.sign_changes;
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const combined_score = total_weight > 0
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? (weights.derivative_variance * deriv_result.score +
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weights.amplitude_growth * amp_result.score +
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weights.sign_changes * sign_result.score) /
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total_weight
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: 0;
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// Find earliest onset across all methods that exceeded threshold
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const onset_candidates = [
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{
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idx: deriv_result.onset_index,
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score: deriv_result.score * weights.derivative_variance,
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},
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{ idx: amp_result.onset_index, score: amp_result.score * weights.amplitude_growth },
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{ idx: sign_result.onset_index, score: sign_result.score * weights.sign_changes },
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const detected = combined_score >= threshold || onset_index >= 0;
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// --- Smoothing Functions ---
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let [sum, count] = [0, 0];
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result[idx] = count > 0 ? sum / count : values[idx];
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}
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return result;
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}
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// Savitzky-Golay filter coefficients for polynomial smoothing
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// Uses least-squares polynomial fitting in each window
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function compute_savgol_coefficients(window, order) {
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const size = 2 * half + 1;
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const vandermonde = [];
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for (let power = 0; power <= order; power++) {
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|
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row.push(idx ** power);
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}
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|
-
vandermonde.push(row);
|
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|
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}
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|
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// Compute (V^T V)^-1 V^T using simple pseudoinverse
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|
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// For smoothing, we only need the first row (constant term coefficients)
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|
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|
-
const vtv = multiply_matrices(transpose(vandermonde), vandermonde);
|
|
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|
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const vtv_inv = invert_matrix(vtv);
|
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|
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if (!vtv_inv) {
|
|
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|
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|
|
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|
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|
|
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|
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}
|
|
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|
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const vt = transpose(vandermonde);
|
|
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|
-
const coeffs_matrix = multiply_matrices(vtv_inv, vt);
|
|
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|
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// First row gives smoothing coefficients
|
|
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|
-
return coeffs_matrix[0];
|
|
262
|
-
}
|
|
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|
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// Savitzky-Golay filter (derivative-preserving) - O(n * window)
|
|
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|
-
export function smooth_savitzky_golay(values, window, polynomial_order = DEFAULT_POLYNOMIAL_ORDER) {
|
|
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|
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|
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|
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return [];
|
|
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|
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|
|
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|
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|
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|
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actual_window = Math.max(actual_window, polynomial_order + 2);
|
|
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|
-
actual_window = Math.min(actual_window, values.length);
|
|
271
|
-
if (actual_window < 3)
|
|
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|
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return [...values];
|
|
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|
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const coeffs = compute_savgol_coefficients(actual_window, polynomial_order);
|
|
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|
-
const half = Math.floor(actual_window / 2);
|
|
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|
-
const result = Array(values.length);
|
|
276
|
-
// Cache coefficient sum to avoid O(n × window) redundant reductions in loop
|
|
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|
-
const coeffs_sum = coeffs.reduce((sum, coeff) => sum + coeff, 0);
|
|
278
|
-
for (let idx = 0; idx < values.length; idx++) {
|
|
279
|
-
let [sum, weight_sum] = [0, 0];
|
|
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|
-
for (let jdx = 0; jdx < actual_window; jdx++) {
|
|
281
|
-
const data_idx = idx - half + jdx;
|
|
282
|
-
if (data_idx >= 0 && data_idx < values.length && Number.isFinite(values[data_idx])) {
|
|
283
|
-
sum += coeffs[jdx] * values[data_idx];
|
|
284
|
-
weight_sum += coeffs[jdx];
|
|
285
|
-
}
|
|
286
|
-
}
|
|
287
|
-
result[idx] = weight_sum !== 0 ? (sum / weight_sum) * coeffs_sum : values[idx];
|
|
288
|
-
}
|
|
289
|
-
return result;
|
|
290
|
-
}
|
|
6
|
+
import { detect_instability, remove_local_outliers, smooth_moving_average, smooth_savitzky_golay, } from './data-cleaning-signal';
|
|
7
|
+
export * from './data-cleaning-signal';
|
|
291
8
|
// Apply smoothing based on config
|
|
292
9
|
function apply_smoothing(x_values, y_values, config) {
|
|
293
10
|
if (config.type === `moving_avg`) {
|
|
294
11
|
return smooth_moving_average(y_values, config.window);
|
|
295
12
|
}
|
|
296
13
|
else if (config.type === `savgol`) {
|
|
297
|
-
|
|
14
|
+
// pass polynomial_order through: when it's undefined, smooth_savitzky_golay's
|
|
15
|
+
// default parameter applies (JS defaults also kick in for an explicit undefined)
|
|
16
|
+
return smooth_savitzky_golay(y_values, config.window, config.polynomial_order);
|
|
298
17
|
}
|
|
299
18
|
else if (config.type === `gaussian`) {
|
|
300
19
|
return apply_gaussian_smearing(x_values, y_values, config.sigma);
|
|
301
20
|
}
|
|
302
21
|
return y_values;
|
|
303
22
|
}
|
|
304
|
-
// --- Local Outlier Detection ---
|
|
305
|
-
// Default values for local outlier detection
|
|
306
|
-
const DEFAULT_LOCAL_WINDOW_HALF = 7;
|
|
307
|
-
const DEFAULT_LOCAL_MAD_THRESHOLD = 2.0;
|
|
308
|
-
const DEFAULT_LOCAL_MAX_ITERATIONS = 5;
|
|
309
|
-
// Compute local median within a window, excluding the center point
|
|
310
|
-
// This allows detecting if the center point is an outlier relative to its neighbors
|
|
311
|
-
function compute_local_median_excluding_center(values, center_idx, window_half) {
|
|
312
|
-
const window_values = [];
|
|
313
|
-
const start = Math.max(0, center_idx - window_half);
|
|
314
|
-
const end = Math.min(values.length - 1, center_idx + window_half);
|
|
315
|
-
for (let idx = start; idx <= end; idx++) {
|
|
316
|
-
if (idx !== center_idx && Number.isFinite(values[idx])) {
|
|
317
|
-
window_values.push(values[idx]);
|
|
318
|
-
}
|
|
319
|
-
}
|
|
320
|
-
if (window_values.length === 0)
|
|
321
|
-
return values[center_idx];
|
|
322
|
-
return median(window_values);
|
|
323
|
-
}
|
|
324
|
-
// Compute local MAD (median absolute deviation) within a window, excluding center
|
|
325
|
-
function compute_local_mad_excluding_center(values, center_idx, window_half, local_median) {
|
|
326
|
-
const abs_devs = [];
|
|
327
|
-
const start = Math.max(0, center_idx - window_half);
|
|
328
|
-
const end = Math.min(values.length - 1, center_idx + window_half);
|
|
329
|
-
for (let idx = start; idx <= end; idx++) {
|
|
330
|
-
if (idx !== center_idx && Number.isFinite(values[idx])) {
|
|
331
|
-
abs_devs.push(Math.abs(values[idx] - local_median));
|
|
332
|
-
}
|
|
333
|
-
}
|
|
334
|
-
if (abs_devs.length === 0)
|
|
335
|
-
return 0;
|
|
336
|
-
return median(abs_devs);
|
|
337
|
-
}
|
|
338
|
-
// Remove local outliers using iterative sliding window MAD-based detection
|
|
339
|
-
// Detects points that deviate significantly from their local neighborhood
|
|
340
|
-
// Returns only the indices to keep, preserving good data before AND after bad regions
|
|
341
|
-
export function remove_local_outliers(y_values, config = {}) {
|
|
342
|
-
const window_half = config.window_half ?? DEFAULT_LOCAL_WINDOW_HALF;
|
|
343
|
-
const mad_threshold = config.mad_threshold ?? DEFAULT_LOCAL_MAD_THRESHOLD;
|
|
344
|
-
const max_iterations = config.max_iterations ?? DEFAULT_LOCAL_MAX_ITERATIONS;
|
|
345
|
-
const len = y_values.length;
|
|
346
|
-
if (len === 0) {
|
|
347
|
-
return { kept_indices: [], removed_indices: [], iterations_used: 0 };
|
|
348
|
-
}
|
|
349
|
-
// Need enough neighbors for meaningful local statistics
|
|
350
|
-
const min_points_needed = window_half * 2 + 1;
|
|
351
|
-
if (len < min_points_needed) {
|
|
352
|
-
return {
|
|
353
|
-
kept_indices: Array.from({ length: len }, (_, idx) => idx),
|
|
354
|
-
removed_indices: [],
|
|
355
|
-
iterations_used: 0,
|
|
356
|
-
};
|
|
357
|
-
}
|
|
358
|
-
let kept_mask = Array(len).fill(true);
|
|
359
|
-
let iterations_used = 0;
|
|
360
|
-
for (let iter = 0; iter < max_iterations; iter++) {
|
|
361
|
-
let removed_any = false;
|
|
362
|
-
const new_kept_mask = [...kept_mask];
|
|
363
|
-
// Note: Local statistics are computed from original values, not filtered values.
|
|
364
|
-
// This prevents cascading removals where one outlier's removal dramatically
|
|
365
|
-
// shifts statistics and causes false positives on neighboring points.
|
|
366
|
-
for (let idx = 0; idx < len; idx++) {
|
|
367
|
-
if (!kept_mask[idx])
|
|
368
|
-
continue; // Already removed
|
|
369
|
-
if (!Number.isFinite(y_values[idx]))
|
|
370
|
-
continue; // Skip invalid values
|
|
371
|
-
const local_median = compute_local_median_excluding_center(y_values, idx, window_half);
|
|
372
|
-
const local_mad = compute_local_mad_excluding_center(y_values, idx, window_half, local_median);
|
|
373
|
-
// Cannot compute robust threshold if MAD is zero (all neighbors identical)
|
|
374
|
-
if (local_mad === 0)
|
|
375
|
-
continue;
|
|
376
|
-
const threshold = local_mad * mad_threshold;
|
|
377
|
-
const deviation = Math.abs(y_values[idx] - local_median);
|
|
378
|
-
if (deviation > threshold) {
|
|
379
|
-
new_kept_mask[idx] = false;
|
|
380
|
-
removed_any = true;
|
|
381
|
-
}
|
|
382
|
-
}
|
|
383
|
-
kept_mask = new_kept_mask;
|
|
384
|
-
iterations_used = iter + 1;
|
|
385
|
-
if (!removed_any)
|
|
386
|
-
break;
|
|
387
|
-
}
|
|
388
|
-
const kept_indices = [];
|
|
389
|
-
const removed_indices = [];
|
|
390
|
-
for (let idx = 0; idx < len; idx++) {
|
|
391
|
-
if (kept_mask[idx]) {
|
|
392
|
-
kept_indices.push(idx);
|
|
393
|
-
}
|
|
394
|
-
else {
|
|
395
|
-
removed_indices.push(idx);
|
|
396
|
-
}
|
|
397
|
-
}
|
|
398
|
-
return { kept_indices, removed_indices, iterations_used };
|
|
399
|
-
}
|
|
400
23
|
// --- Helper Functions ---
|
|
401
24
|
// Handle NaN/Infinity based on mode
|
|
402
25
|
export function handle_invalid_values(values, mode) {
|
|
@@ -461,20 +84,19 @@ export function apply_bounds(x_values, y_values, bounds) {
|
|
|
461
84
|
for (let idx = 0; idx < result.length; idx++) {
|
|
462
85
|
const x_val = x_values[idx];
|
|
463
86
|
const y_val = result[idx];
|
|
464
|
-
|
|
465
|
-
|
|
466
|
-
|
|
467
|
-
|
|
468
|
-
|
|
469
|
-
|
|
470
|
-
|
|
471
|
-
if (violated) {
|
|
87
|
+
// Resolve bounds once per point; is_in_bounds would redundantly re-resolve them
|
|
88
|
+
// (costly when min/max are functions of x). NaN compares false on both checks
|
|
89
|
+
// and thus counts as in-bounds, matching is_in_bounds semantics.
|
|
90
|
+
const { min: min_bound, max: max_bound } = resolve_physical_bounds(x_val, bounds);
|
|
91
|
+
const below_min = min_bound !== undefined && y_val < min_bound;
|
|
92
|
+
const above_max = max_bound !== undefined && y_val > max_bound;
|
|
93
|
+
if (below_min || above_max) {
|
|
472
94
|
violations++;
|
|
473
95
|
const mode = bounds.mode ?? `clamp`;
|
|
474
96
|
if (mode === `clamp`) {
|
|
475
|
-
if (
|
|
97
|
+
if (below_min)
|
|
476
98
|
result[idx] = min_bound;
|
|
477
|
-
if (
|
|
99
|
+
if (above_max)
|
|
478
100
|
result[idx] = max_bound;
|
|
479
101
|
}
|
|
480
102
|
else if (mode === `filter`) {
|
|
@@ -497,10 +119,17 @@ export function sync_metadata(metadata, kept_indices) {
|
|
|
497
119
|
}
|
|
498
120
|
// Filter arrays by kept indices
|
|
499
121
|
const filter_by_indices = (arr, kept_indices) => kept_indices.map((idx) => arr[idx]);
|
|
500
|
-
//
|
|
122
|
+
// Resolve static or x-dependent min/max bounds at a given x value
|
|
123
|
+
function resolve_physical_bounds(x_val, bounds) {
|
|
124
|
+
return {
|
|
125
|
+
min: typeof bounds.min === `function` ? bounds.min(x_val) : bounds.min,
|
|
126
|
+
max: typeof bounds.max === `function` ? bounds.max(x_val) : bounds.max,
|
|
127
|
+
};
|
|
128
|
+
}
|
|
129
|
+
// Check if value is within bounds (static or x-dependent).
|
|
130
|
+
// NB: NaN values compare false on both checks and therefore count as in-bounds.
|
|
501
131
|
function is_in_bounds(val, x_val, bounds) {
|
|
502
|
-
const
|
|
503
|
-
const max = typeof bounds.max === `function` ? bounds.max(x_val) : bounds.max;
|
|
132
|
+
const { min, max } = resolve_physical_bounds(x_val, bounds);
|
|
504
133
|
if (min !== undefined && val < min)
|
|
505
134
|
return false;
|
|
506
135
|
if (max !== undefined && val > max)
|
|
@@ -775,79 +404,3 @@ export function clean_trajectory_props(props, config = {}) {
|
|
|
775
404
|
}
|
|
776
405
|
return { props: result_props, quality: quality_reports };
|
|
777
406
|
}
|
|
778
|
-
// --- Utility Functions ---
|
|
779
|
-
function median(values) {
|
|
780
|
-
if (values.length === 0)
|
|
781
|
-
return 0;
|
|
782
|
-
const sorted = [...values].sort((a, b) => a - b);
|
|
783
|
-
const mid = Math.floor(sorted.length / 2);
|
|
784
|
-
return sorted.length % 2 !== 0 ? sorted[mid] : (sorted[mid - 1] + sorted[mid]) / 2;
|
|
785
|
-
}
|
|
786
|
-
// Simple matrix operations for Savitzky-Golay
|
|
787
|
-
function transpose(matrix) {
|
|
788
|
-
if (matrix.length === 0)
|
|
789
|
-
return [];
|
|
790
|
-
const rows = matrix.length;
|
|
791
|
-
const cols = matrix[0].length;
|
|
792
|
-
const result = Array.from({ length: cols }, () => Array(rows).fill(0));
|
|
793
|
-
for (let row = 0; row < rows; row++) {
|
|
794
|
-
for (let col = 0; col < cols; col++) {
|
|
795
|
-
result[col][row] = matrix[row][col];
|
|
796
|
-
}
|
|
797
|
-
}
|
|
798
|
-
return result;
|
|
799
|
-
}
|
|
800
|
-
function multiply_matrices(matrix_a, matrix_b) {
|
|
801
|
-
const rows_a = matrix_a.length;
|
|
802
|
-
const cols_a = matrix_a[0]?.length ?? 0;
|
|
803
|
-
const cols_b = matrix_b[0]?.length ?? 0;
|
|
804
|
-
const result = Array.from({ length: rows_a }, () => Array(cols_b).fill(0));
|
|
805
|
-
for (let row = 0; row < rows_a; row++) {
|
|
806
|
-
for (let col = 0; col < cols_b; col++) {
|
|
807
|
-
for (let idx_k = 0; idx_k < cols_a; idx_k++) {
|
|
808
|
-
result[row][col] += matrix_a[row][idx_k] * matrix_b[idx_k][col];
|
|
809
|
-
}
|
|
810
|
-
}
|
|
811
|
-
}
|
|
812
|
-
return result;
|
|
813
|
-
}
|
|
814
|
-
function invert_matrix(matrix) {
|
|
815
|
-
const size = matrix.length;
|
|
816
|
-
if (size === 0 || matrix[0].length !== size)
|
|
817
|
-
return null;
|
|
818
|
-
// Create augmented matrix [A | I]
|
|
819
|
-
const aug = matrix.map((row, idx) => [
|
|
820
|
-
...row,
|
|
821
|
-
...Array.from({ length: size }, (_, jdx) => (idx === jdx ? 1 : 0)),
|
|
822
|
-
]);
|
|
823
|
-
// Gaussian elimination with partial pivoting
|
|
824
|
-
for (let col = 0; col < size; col++) {
|
|
825
|
-
// Find pivot
|
|
826
|
-
let max_row = col;
|
|
827
|
-
for (let row = col + 1; row < size; row++) {
|
|
828
|
-
if (Math.abs(aug[row][col]) > Math.abs(aug[max_row][col])) {
|
|
829
|
-
max_row = row;
|
|
830
|
-
}
|
|
831
|
-
}
|
|
832
|
-
if (Math.abs(aug[max_row][col]) < 1e-10) {
|
|
833
|
-
return null; // Singular
|
|
834
|
-
} // Swap rows
|
|
835
|
-
;
|
|
836
|
-
[aug[col], aug[max_row]] = [aug[max_row], aug[col]];
|
|
837
|
-
// Eliminate column
|
|
838
|
-
const pivot = aug[col][col];
|
|
839
|
-
for (let jdx = 0; jdx < 2 * size; jdx++) {
|
|
840
|
-
aug[col][jdx] /= pivot;
|
|
841
|
-
}
|
|
842
|
-
for (let row = 0; row < size; row++) {
|
|
843
|
-
if (row !== col) {
|
|
844
|
-
const factor = aug[row][col];
|
|
845
|
-
for (let jdx = 0; jdx < 2 * size; jdx++) {
|
|
846
|
-
aug[row][jdx] -= factor * aug[col][jdx];
|
|
847
|
-
}
|
|
848
|
-
}
|
|
849
|
-
}
|
|
850
|
-
}
|
|
851
|
-
// Extract inverse
|
|
852
|
-
return aug.map((row) => row.slice(size));
|
|
853
|
-
}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import type { D3SymbolName } from '../../labels';
|
|
2
|
-
import type { DataSeries
|
|
2
|
+
import type { DataSeries } from '..';
|
|
3
3
|
export declare const get_series_color: (series_idx: number) => string;
|
|
4
4
|
export declare const get_series_symbol: (series_idx: number) => D3SymbolName;
|
|
5
5
|
export declare const extract_series_color: (series_data: DataSeries) => string;
|
|
@@ -12,5 +12,4 @@ export declare const prepare_legend_data: (series: DataSeries[]) => {
|
|
|
12
12
|
symbol_color: string;
|
|
13
13
|
};
|
|
14
14
|
}[];
|
|
15
|
-
export declare const create_data_points: (series: DataSeries[], filter_fn?: (series: DataSeries) => boolean) => Point[];
|
|
16
15
|
export declare function process_prop<T>(prop: T[] | T | undefined | null, idx: number): T | undefined;
|
|
@@ -6,11 +6,15 @@ export const get_series_color = (series_idx) => DEFAULT_SERIES_COLORS[series_idx
|
|
|
6
6
|
export const get_series_symbol = (series_idx) => DEFAULT_SERIES_SYMBOLS[series_idx % DEFAULT_SERIES_SYMBOLS.length];
|
|
7
7
|
// Extract the primary color from a series data object.
|
|
8
8
|
// Checks line stroke, then point fill (handling arrays), with fallback to default blue.
|
|
9
|
-
export const extract_series_color = (series_data) =>
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
9
|
+
export const extract_series_color = (series_data) => {
|
|
10
|
+
const color = series_data.line_style?.stroke ??
|
|
11
|
+
(Array.isArray(series_data.point_style)
|
|
12
|
+
? series_data.point_style[0]?.fill
|
|
13
|
+
: series_data.point_style?.fill);
|
|
14
|
+
if (color)
|
|
15
|
+
return color;
|
|
16
|
+
return DEFAULTS.scatter.point.color;
|
|
17
|
+
};
|
|
14
18
|
// Prepare legend data from series array
|
|
15
19
|
export const prepare_legend_data = (series) => series.map((series_data, series_idx) => ({
|
|
16
20
|
series_idx,
|
|
@@ -24,16 +28,6 @@ export const prepare_legend_data = (series) => series.map((series_data, series_i
|
|
|
24
28
|
symbol_color: extract_series_color(series_data),
|
|
25
29
|
},
|
|
26
30
|
}));
|
|
27
|
-
// Create data points from series for analysis
|
|
28
|
-
export const create_data_points = (series, filter_fn) => series
|
|
29
|
-
.filter(filter_fn ?? ((srs) => srs.visible ?? true))
|
|
30
|
-
.flatMap(({ x: xs, y: ys }, series_idx) => {
|
|
31
|
-
const length = Math.min(xs.length, ys.length);
|
|
32
|
-
if (xs.length !== ys.length) {
|
|
33
|
-
console.warn(`length mismatch in series ${series_idx}: x.length=${xs.length} vs y.length=${ys.length}`);
|
|
34
|
-
}
|
|
35
|
-
return xs.slice(0, length).map((x, idx) => ({ x, y: ys[idx] }));
|
|
36
|
-
});
|
|
37
31
|
// Process array or scalar properties for indexed access.
|
|
38
32
|
// If prop is an array, returns the element at the given index.
|
|
39
33
|
// If prop is a scalar, returns the scalar (applied to all indices).
|
|
@@ -1,5 +1,6 @@
|
|
|
1
1
|
import type { Vec2 } from '../../math';
|
|
2
|
-
import type {
|
|
2
|
+
import type { CurveFactory } from 'd3-shape';
|
|
3
|
+
import type { DataSeries, ErrorBand, FillBoundary, FillCurveType, FillGradient, FillRegion, LineCurve } from './types';
|
|
3
4
|
export declare const LOG_EPSILON = 1e-10;
|
|
4
5
|
export interface Pt {
|
|
5
6
|
x: number;
|
|
@@ -28,6 +29,7 @@ interface DomainContext {
|
|
|
28
29
|
}
|
|
29
30
|
export declare function resolve_boundary_points(boundary: FillBoundary, series: readonly DataSeries[], domains: DomainContext, companion?: Pt[] | null): ResolvedBoundary | null;
|
|
30
31
|
export declare function compute_fill_segments(region: FillRegion, series: readonly DataSeries[], domains: DomainContext): FillSegment[];
|
|
32
|
+
export declare const line_curve_factory: (curve: LineCurve | undefined) => CurveFactory;
|
|
31
33
|
export declare function generate_fill_path(upper: readonly Pt[], lower: readonly Pt[], upper_curve?: FillCurveType, lower_curve?: FillCurveType): string;
|
|
32
34
|
export declare function convert_error_band_to_fill_region(error_band: ErrorBand, series: readonly DataSeries[], default_color?: string): FillRegion | null;
|
|
33
35
|
export declare const is_fill_gradient: (fill: string | FillGradient | undefined) => fill is FillGradient;
|