@macrostrat/column-views 3.5.0 → 3.6.0

package/CHANGELOG.md

@@ -1,5 +1,30 @@
 # Changelog
 
+## [3.6.0] - 2026-07-28 [_changes_](https://github.com/UW-Macrostrat/web-components/compare/@macrostrat/column-views-v3.5.1...@macrostrat/column-views-v3.6.0)
+
+### Minor Changes
+
+- Remove createStateIsolation and associated exports from
+  `@macrostrat/data-components`; move them to `@macrostrat/scoped-store`.
+
+### Patch Changes
+
+- Updated dependencies
+  - @macrostrat/data-components@1.4.0
+  - @macrostrat/scoped-store@1.0.1
+
+## [3.5.1] - 2026-05-27 [_changes_](https://github.com/UW-Macrostrat/web-components/compare/@macrostrat/column-views-v3.5.0...@macrostrat/column-views-v3.5.1)
+
+### Patch Changes
+
+- Improve code for section merging
+  [14bde559](https://github.com/UW-Macrostrat/web-components/commit/14bde559db68f21beb0e0a58d57db03bf6e68e69)
+- Added a story for correlation diagram creation
+  [67fba54a](https://github.com/UW-Macrostrat/web-components/commit/67fba54a699a925f1bf5595051c9831dc789a4db)
+- Updated dependencies
+  [89bb4be0](https://github.com/UW-Macrostrat/web-components/commit/89bb4be0d6ae6a73ac22d47cb3d9f12964a05e36)
+  - @macrostrat/timescale@3.1.5
+
 ## [3.5.0] - 2026-05-24 [_changes_](https://github.com/UW-Macrostrat/web-components/compare/@macrostrat/column-views-v3.4.2...@macrostrat/column-views-v3.5.0)
 
 ### Minor Changes

package/dist/column-views.css

@@ -1,23 +1,23 @@
-._unit-label-container_7b96n_1 {
+._unit-label-container_eusyg_1 {
   pointer-events: none;
 }
 
-._labeled-unit_7b96n_5 {
+._labeled-unit_eusyg_5 {
   --column-unit-background-internal: var(--column-unit-background-color, var(--column-background-color));
 }
-._labeled-unit_7b96n_5 .unit-overlay {
-  font-size: 10px;
-  font-style: italic;
+._labeled-unit_eusyg_5 .unit-overlay {
+  font-size: var(--column-unit-font-size, 10px);
+  font-style: var(--column-unit-font-style, italic);
   display: flex;
   align-items: center;
   justify-content: center;
 }
-._labeled-unit_7b96n_5 .unit-label {
+._labeled-unit_eusyg_5 .unit-label {
   display: block;
   color: var(--column-text-color);
   text-shadow: 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal), 0px 0px 4px var(--column-unit-background-internal);
 }
-._labeled-unit_7b96n_5 ._background_7b96n_20 {
+._labeled-unit_eusyg_5 ._background_eusyg_20 {
   fill: var(--column-unit-background-internal, transparent);
 }._unit-label_tidbs_1 {
   text-align: center;

package/dist/data-provider/store.cjs

@@ -5,11 +5,11 @@ const h = require("@macrostrat/hyper");
 const compositeScale = require("../prepare-units/composite-scale.cjs");
 const columnComponents = require("@macrostrat/column-components");
 const unitSelection = require("./unit-selection.cjs");
-const dataComponents = require("@macrostrat/data-components");
+const scopedStore = require("@macrostrat/scoped-store");
 const jotai = require("jotai");
 const _interopDefault = (e) => e && e.__esModule ? e : { default: e };
 const h__default = /* @__PURE__ */ _interopDefault(h);
-const scope = dataComponents.createScopedStore();
+const scope = scopedStore.createScopedStore();
 const columnUnitsAtom = jotai.atom();
 const columnUnitsMapAtom = jotai.atom((get) => {
   const units = get(columnUnitsAtom);

package/dist/data-provider/store.cjs.map

@@ -1 +1 @@
-{"version":3,"file":"store.cjs","sources":["../../src/data-provider/store.ts"],"sourcesContent":["import {\n  createContext,\n  ReactNode,\n  RefObject,\n  useContext,\n  useMemo,\n} from \"react\";\nimport h from \"@macrostrat/hyper\";\nimport {\n  CompositeColumnScale,\n  createCompositeScale,\n} from \"../prepare-units/composite-scale\";\nimport { ColumnAxisType, ColumnProvider } from \"@macrostrat/column-components\";\nimport type { ExtUnit, PackageLayoutData } from \"../prepare-units\";\nimport {\n  allowUnitSelectionAtom,\n  selectedUnitIDAtom,\n  UnitSelectionCallbacks,\n  UnitSelectionCallbackManager,\n  selectedUnitElementAtom,\n} from \"./unit-selection\";\nimport type { BaseUnit } from \"@macrostrat/api-types\";\nimport {\n  type AtomMap,\n  createScopedStore,\n  StateIsolation,\n} from \"@macrostrat/data-components\";\nimport { atom } from \"jotai\";\nimport { useEffect } from \"react\";\n\nexport const scope: StateIsolation = createScopedStore();\n\nexport const columnUnitsAtom = atom<BaseUnit[]>();\n\nexport const columnUnitsMapAtom = atom<Map<number, BaseUnit> | null>((get) => {\n  const units = get(columnUnitsAtom);\n  if (!units) return null;\n  const unitMap = new Map<number, BaseUnit>();\n  units.forEach((unit) => {\n    unitMap.set(unit.unit_id, unit);\n  });\n  return unitMap;\n});\n\nexport interface ColumnStateProviderProps<\n  T extends BaseUnit,\n> extends Partial<UnitSelectionCallbacks> {\n  children: ReactNode;\n  units: T[];\n  selectedUnit: number | null;\n  allowUnitSelection?: boolean;\n}\n\nexport function MacrostratColumnStateProvider<T extends BaseUnit>({\n  children,\n  units,\n  allowUnitSelection = false,\n  onUnitSelected,\n  selectedUnit,\n}: ColumnStateProviderProps<T>) {\n  /** Top-level provider for Macrostrat column data.\n   * It is either provided by the Column component itself, or\n   * can be hoisted higher in the tree to provide a common data context\n   */\n\n  /* By default, unit selection is disabled. However, if any related props are passed,\n  we enable it.\n  */\n  const _allowSelection = useMemo(() => {\n    if (allowUnitSelection) {\n      return true;\n    }\n    return selectedUnit != null || onUnitSelected != null;\n  }, []);\n\n  const atomMap: AtomMap = [\n    [columnUnitsAtom, units],\n    [allowUnitSelectionAtom, _allowSelection],\n    [selectedUnitIDAtom, selectedUnit],\n  ];\n\n  let selectionHandlers: ReactNode = null;\n  if (_allowSelection) {\n    selectionHandlers = h(UnitSelectionCallbackManager, { onUnitSelected });\n  }\n\n  return h(\n    scope.Provider,\n    {\n      atoms: atomMap,\n      keepUpdated: true,\n      inherit: true,\n    },\n    [selectionHandlers, children],\n  );\n}\n\n/** Interface for imperative handlers that can\n * be invoked outside of the column's react context\n */\nexport interface ColumnRef {\n  scrollSelectedUnitIntoView(): void;\n}\n\nexport interface MacrostratColumnDataContext<T extends BaseUnit> {\n  units: T[];\n  sections: PackageLayoutData[];\n  totalHeight?: number;\n  axisType?: ColumnAxisType;\n  allowUnitSelection?: boolean;\n}\n\nexport interface ColumnDataProviderProps<T extends BaseUnit>\n  extends MacrostratColumnDataContext<T>, ColumnStateProviderProps<T> {\n  children: ReactNode;\n  ref: RefObject<ColumnRef>;\n}\n\nconst MacrostratColumnDataContext =\n  createContext<MacrostratColumnDataContext<any>>(null);\n\nexport function MacrostratColumnDataProvider<T extends BaseUnit>({\n  children,\n  units,\n  sections,\n  totalHeight,\n  axisType,\n  allowUnitSelection,\n  onUnitSelected,\n  selectedUnit,\n  ref,\n}: ColumnDataProviderProps<T>) {\n  /** Internal provider for Macrostrat column data.\n   * As a general rule, we want to provide data and column-axis\n   * height calculations through the context, since these need to\n   * be accessed by any component that lays out information on the\n   * column.\n   *\n   * Cross-axis layout and view configuration (e.g., showing and hiding\n   * of different components or labels) should be handled through passing\n   * props to the components themselves.\n   * */\n\n  const value = useMemo(() => {\n    // For now, change ordinal axis types to age axis types\n    return {\n      units,\n      sections,\n      totalHeight,\n      axisType,\n    };\n  }, [units, sections, totalHeight, axisType]);\n\n  return h(\n    MacrostratColumnStateProvider,\n    {\n      units,\n      allowUnitSelection,\n      onUnitSelected,\n      selectedUnit,\n      ref,\n    },\n    [\n      h(ColumnRefManager, { ref }),\n      h(MacrostratColumnDataContext.Provider, { value }, children),\n    ],\n  );\n}\n\nfunction ColumnRefManager({ ref }: { ref?: RefObject<ColumnRef> }) {\n  const selectedUnitElement = scope.useAtomValue(selectedUnitElementAtom);\n  useEffect(() => {\n    if (ref == null) return;\n    ref.current = {\n      scrollSelectedUnitIntoView(opts?: ScrollIntoViewOptions) {\n        selectedUnitElement?.scrollIntoView(\n          opts ?? {\n            behavior: \"smooth\",\n            block: \"center\",\n            inline: \"nearest\",\n          },\n        );\n      },\n    };\n  }, [ref, selectedUnitElement]);\n\n  return null;\n}\n\nexport function UnitSelectionProvider(props: ColumnStateProviderProps<any>) {\n  /* A basic unit selection provider without column data context.\n  Mostly for use with the CorrelationChart component.\n   */\n  return h(MacrostratColumnStateProvider, {\n    ...props,\n    allowUnitSelection: true,\n  });\n}\n\nexport function useMacrostratColumnData() {\n  const ctx = useContext(MacrostratColumnDataContext);\n  if (!ctx) {\n    throw new Error(\n      \"useMacrostratColumnData must be used within a MacrostratColumnDataProvider\",\n    );\n  }\n  return ctx;\n}\n\nexport function useMacrostratUnits() {\n  return scope.useAtomValue(columnUnitsAtom);\n}\n\nexport function useColumnUnitsMap(): Map<number, ExtUnit> | null {\n  try {\n    return scope.useAtomValue(columnUnitsMapAtom) as Map<number, ExtUnit>;\n  } catch {\n    return null;\n  }\n}\n\nexport function useCompositeScale(): CompositeColumnScale {\n  const ctx = useMacrostratColumnData();\n  return useMemo(\n    () => createCompositeScale(ctx.sections, true),\n    [ctx.sections],\n  );\n}\n\nexport function MacrostratColumnProvider(props) {\n  /** A column provider specialized the Macrostrat API. 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+{"version":3,"file":"store.cjs","sources":["../../src/data-provider/store.ts"],"sourcesContent":["import {\n  createContext,\n  ReactNode,\n  RefObject,\n  useContext,\n  useMemo,\n} from \"react\";\nimport h from \"@macrostrat/hyper\";\nimport {\n  CompositeColumnScale,\n  createCompositeScale,\n} from \"../prepare-units/composite-scale\";\nimport { ColumnAxisType, ColumnProvider } from \"@macrostrat/column-components\";\nimport type { ExtUnit, PackageLayoutData } from \"../prepare-units\";\nimport {\n  allowUnitSelectionAtom,\n  selectedUnitIDAtom,\n  UnitSelectionCallbacks,\n  UnitSelectionCallbackManager,\n  selectedUnitElementAtom,\n} from \"./unit-selection\";\nimport type { BaseUnit } from \"@macrostrat/api-types\";\nimport {\n  type AtomMap,\n  createScopedStore,\n  StateIsolation,\n} from \"@macrostrat/scoped-store\";\nimport { atom } from \"jotai\";\nimport { useEffect } from \"react\";\n\nexport const scope: StateIsolation = createScopedStore();\n\nexport const columnUnitsAtom = atom<BaseUnit[]>();\n\nexport const columnUnitsMapAtom = atom<Map<number, BaseUnit> | null>((get) => {\n  const units = get(columnUnitsAtom);\n  if (!units) return null;\n  const unitMap = new Map<number, BaseUnit>();\n  units.forEach((unit) => {\n    unitMap.set(unit.unit_id, unit);\n  });\n  return unitMap;\n});\n\nexport interface ColumnStateProviderProps<\n  T extends BaseUnit,\n> extends Partial<UnitSelectionCallbacks> {\n  children: ReactNode;\n  units: T[];\n  selectedUnit: number | null;\n  allowUnitSelection?: boolean;\n}\n\nexport function MacrostratColumnStateProvider<T extends BaseUnit>({\n  children,\n  units,\n  allowUnitSelection = false,\n  onUnitSelected,\n  selectedUnit,\n}: ColumnStateProviderProps<T>) {\n  /** Top-level provider for Macrostrat column data.\n   * It is either provided by the Column component itself, or\n   * can be hoisted higher in the tree to provide a common data context\n   */\n\n  /* By default, unit selection is disabled. However, if any related props are passed,\n  we enable it.\n  */\n  const _allowSelection = useMemo(() => {\n    if (allowUnitSelection) {\n      return true;\n    }\n    return selectedUnit != null || onUnitSelected != null;\n  }, []);\n\n  const atomMap: AtomMap = [\n    [columnUnitsAtom, units],\n    [allowUnitSelectionAtom, _allowSelection],\n    [selectedUnitIDAtom, selectedUnit],\n  ];\n\n  let selectionHandlers: ReactNode = null;\n  if (_allowSelection) {\n    selectionHandlers = h(UnitSelectionCallbackManager, { onUnitSelected });\n  }\n\n  return h(\n    scope.Provider,\n    {\n      atoms: atomMap,\n      keepUpdated: true,\n      inherit: true,\n    },\n    [selectionHandlers, children],\n  );\n}\n\n/** Interface for imperative handlers that can\n * be invoked outside of the column's react context\n */\nexport interface ColumnRef {\n  scrollSelectedUnitIntoView(): void;\n}\n\nexport interface MacrostratColumnDataContext<T extends BaseUnit> {\n  units: T[];\n  sections: PackageLayoutData[];\n  totalHeight?: number;\n  axisType?: ColumnAxisType;\n  allowUnitSelection?: boolean;\n}\n\nexport interface ColumnDataProviderProps<T extends BaseUnit>\n  extends MacrostratColumnDataContext<T>, ColumnStateProviderProps<T> {\n  children: ReactNode;\n  ref: RefObject<ColumnRef>;\n}\n\nconst MacrostratColumnDataContext =\n  createContext<MacrostratColumnDataContext<any>>(null);\n\nexport function MacrostratColumnDataProvider<T extends BaseUnit>({\n  children,\n  units,\n  sections,\n  totalHeight,\n  axisType,\n  allowUnitSelection,\n  onUnitSelected,\n  selectedUnit,\n  ref,\n}: ColumnDataProviderProps<T>) {\n  /** Internal provider for Macrostrat column data.\n   * As a general rule, we want to provide data and column-axis\n   * height calculations through the context, since these need to\n   * be accessed by any component that lays out information on the\n   * column.\n   *\n   * Cross-axis layout and view configuration (e.g., showing and hiding\n   * of different components or labels) should be handled through passing\n   * props to the components themselves.\n   * */\n\n  const value = useMemo(() => {\n    // For now, change ordinal axis types to age axis types\n    return {\n      units,\n      sections,\n      totalHeight,\n      axisType,\n    };\n  }, [units, sections, totalHeight, axisType]);\n\n  return h(\n    MacrostratColumnStateProvider,\n    {\n      units,\n      allowUnitSelection,\n      onUnitSelected,\n      selectedUnit,\n      ref,\n    },\n    [\n      h(ColumnRefManager, { ref }),\n      h(MacrostratColumnDataContext.Provider, { value }, children),\n    ],\n  );\n}\n\nfunction ColumnRefManager({ ref }: { ref?: RefObject<ColumnRef> }) {\n  const selectedUnitElement = scope.useAtomValue(selectedUnitElementAtom);\n  useEffect(() => {\n    if (ref == null) return;\n    ref.current = {\n      scrollSelectedUnitIntoView(opts?: ScrollIntoViewOptions) {\n        selectedUnitElement?.scrollIntoView(\n          opts ?? {\n            behavior: \"smooth\",\n            block: \"center\",\n            inline: \"nearest\",\n          },\n        );\n      },\n    };\n  }, [ref, selectedUnitElement]);\n\n  return null;\n}\n\nexport function UnitSelectionProvider(props: ColumnStateProviderProps<any>) {\n  /* A basic unit selection provider without column data context.\n  Mostly for use with the CorrelationChart component.\n   */\n  return h(MacrostratColumnStateProvider, {\n    ...props,\n    allowUnitSelection: true,\n  });\n}\n\nexport function useMacrostratColumnData() {\n  const ctx = useContext(MacrostratColumnDataContext);\n  if (!ctx) {\n    throw new Error(\n      \"useMacrostratColumnData must be used within a MacrostratColumnDataProvider\",\n    );\n  }\n  return ctx;\n}\n\nexport function useMacrostratUnits() {\n  return scope.useAtomValue(columnUnitsAtom);\n}\n\nexport function useColumnUnitsMap(): Map<number, ExtUnit> | null {\n  try {\n    return scope.useAtomValue(columnUnitsMapAtom) as Map<number, ExtUnit>;\n  } catch {\n    return null;\n  }\n}\n\nexport function useCompositeScale(): CompositeColumnScale {\n  const ctx = useMacrostratColumnData();\n  return useMemo(\n    () => createCompositeScale(ctx.sections, true),\n    [ctx.sections],\n  );\n}\n\nexport function MacrostratColumnProvider(props) {\n  /** A column provider specialized the Macrostrat API. Maps more\n   * generic concepts to Macrostrat-specific ones.\n   */\n\n  const { axisType } = useMacrostratColumnData();\n  const { units, domain, pixelScale, scale, children } = props;\n  return h(\n    ColumnProvider,\n    {\n      axisType,\n      divisions: units,\n      range: domain,\n      pixelsPerMeter: pixelScale,\n      scale,\n    },\n    children,\n  );\n}\n\n/** This is now a legacy provider */\nexport function LithologiesProvider({ children }) {\n  useEffect(() => {\n    console.warn(\n      \"LithologiesProvider is deprecated. 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package/dist/data-provider/store.d.ts

@@ -4,7 +4,7 @@ import { ColumnAxisType } from '@macrostrat/column-components';
 import { ExtUnit, PackageLayoutData } from '../prepare-units';
 import { UnitSelectionCallbacks } from './unit-selection';
 import { BaseUnit } from '@macrostrat/api-types';
-import { AtomMap, StateIsolation } from '@macrostrat/data-components';
+import { AtomMap, StateIsolation } from '@macrostrat/scoped-store';
 export declare const scope: StateIsolation;
 export declare const columnUnitsAtom: import('jotai').PrimitiveAtom<BaseUnit[] | undefined> & {
     init: BaseUnit[] | undefined;

package/dist/data-provider/store.js

@@ -3,7 +3,7 @@ import h from "@macrostrat/hyper";
 import { createCompositeScale } from "../prepare-units/composite-scale.js";
 import { ColumnProvider } from "@macrostrat/column-components";
 import { UnitSelectionCallbackManager, allowUnitSelectionAtom, selectedUnitIDAtom, selectedUnitElementAtom } from "./unit-selection.js";
-import { createScopedStore } from "@macrostrat/data-components";
+import { createScopedStore } from "@macrostrat/scoped-store";
 import { atom } from "jotai";
 const scope = createScopedStore();
 const columnUnitsAtom = atom();

package/dist/data-provider/store.js.map

@@ -1 +1 @@
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+{"version":3,"file":"store.js","sources":["../../src/data-provider/store.ts"],"sourcesContent":["import {\n  createContext,\n  ReactNode,\n  RefObject,\n  useContext,\n  useMemo,\n} from \"react\";\nimport h from \"@macrostrat/hyper\";\nimport {\n  CompositeColumnScale,\n  createCompositeScale,\n} from \"../prepare-units/composite-scale\";\nimport { ColumnAxisType, ColumnProvider } from \"@macrostrat/column-components\";\nimport type { ExtUnit, PackageLayoutData } from \"../prepare-units\";\nimport {\n  allowUnitSelectionAtom,\n  selectedUnitIDAtom,\n  UnitSelectionCallbacks,\n  UnitSelectionCallbackManager,\n  selectedUnitElementAtom,\n} from \"./unit-selection\";\nimport type { BaseUnit } from \"@macrostrat/api-types\";\nimport {\n  type AtomMap,\n  createScopedStore,\n  StateIsolation,\n} from \"@macrostrat/scoped-store\";\nimport { atom } from \"jotai\";\nimport { useEffect } from \"react\";\n\nexport const scope: StateIsolation = createScopedStore();\n\nexport const columnUnitsAtom = atom<BaseUnit[]>();\n\nexport const columnUnitsMapAtom = atom<Map<number, BaseUnit> | null>((get) => {\n  const units = get(columnUnitsAtom);\n  if (!units) return null;\n  const unitMap = new Map<number, BaseUnit>();\n  units.forEach((unit) => {\n    unitMap.set(unit.unit_id, unit);\n  });\n  return unitMap;\n});\n\nexport interface ColumnStateProviderProps<\n  T extends BaseUnit,\n> extends Partial<UnitSelectionCallbacks> {\n  children: ReactNode;\n  units: T[];\n  selectedUnit: number | null;\n  allowUnitSelection?: boolean;\n}\n\nexport function MacrostratColumnStateProvider<T extends BaseUnit>({\n  children,\n  units,\n  allowUnitSelection = false,\n  onUnitSelected,\n  selectedUnit,\n}: ColumnStateProviderProps<T>) {\n  /** Top-level provider for Macrostrat column data.\n   * It is either provided by the Column component itself, or\n   * can be hoisted higher in the tree to provide a common data context\n   */\n\n  /* By default, unit selection is disabled. 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package/dist/prepare-units/helpers.cjs

@@ -7,8 +7,10 @@ const stratigraphyUtils = require("@macrostrat/stratigraphy-utils");
 const dt = 1e-3;
 class UnitGroup {
   units;
-  constructor(units) {
+  axisType;
+  constructor(units, axisType = columnComponents.ColumnAxisType.AGE) {
     this.units = units;
+    this.axisType = axisType;
   }
   get t_age() {
     return Math.min(...this.units.map((d) => d.t_age));
@@ -20,25 +22,28 @@ class UnitGroup {
     return assignColumnsToUnitsWithinOverlappingGroup(this);
   }
 }
-function groupUnitsByMutualOverlap(units, tolerance = dt) {
-  const sections = groupUnitsIntoSectionsByOverlap(
-    units,
-    columnComponents.ColumnAxisType.AGE,
-    tolerance
-  );
+function groupUnitsByMutualOverlap(units, tolerance = dt, axisType = columnComponents.ColumnAxisType.AGE) {
+  const sections = groupUnitsIntoSectionsByOverlap(units, axisType, tolerance);
+  console.log("Grouped sections", sections);
   return sections.map((d) => {
-    return new UnitGroup(d.units);
+    return new UnitGroup(d.units, axisType);
   });
 }
 const sortByAge = utils.createUnitSorter(columnComponents.ColumnAxisType.AGE);
 function assignColumnsToUnitsWithinOverlappingGroup(group2) {
-  const sortedUnits = [...group2.units].sort((a, b) => b.b_age - a.b_age);
+  const sortedUnits = [...group2.units].sort(utils.createUnitSorter(group2.axisType));
   const columns = [];
   for (const unit of sortedUnits) {
+    const colHint = unit.layoutHints?.column;
+    if (colHint != null) {
+      columns[colHint] ??= [];
+      columns[colHint].push(unit);
+      continue;
+    }
     let didAddToExistingColumn = false;
     for (const column of columns) {
       const lastUnit = column[column.length - 1];
-      if (!utils.unitsOverlap(unit, lastUnit, columnComponents.ColumnAxisType.AGE, dt)) {
+      if (!utils.unitsOverlap(unit, lastUnit, group2.axisType, dt)) {
         column.push(unit);
         didAddToExistingColumn = true;
         break;
@@ -48,13 +53,15 @@ function assignColumnsToUnitsWithinOverlappingGroup(group2) {
       columns.push([unit]);
     }
   }
+  console.log(columns);
   const units = columns.flatMap(
     (column, columnIndex) => column.map((unit) => {
       return {
         ...unit,
-        overlap: {
+        layout: {
           column: columnIndex,
-          nColumns: columns.length,
+          nColumns: 1,
+          totalColumns: columns.length,
           unitGroup: group2
         }
       };
@@ -68,7 +75,7 @@ function preprocessUnits(section, axisType = columnComponents.ColumnAxisType.AGE
   if (axisType != columnComponents.ColumnAxisType.AGE) {
     tolerance = 0.01;
   }
-  const unitGroups = groupUnitsByMutualOverlap(units, tolerance);
+  const unitGroups = groupUnitsByMutualOverlap(units, tolerance, axisType);
   const divisions = [];
   for (const group2 of unitGroups) {
     divisions.push(...group2.getUnits());
@@ -111,33 +118,48 @@ function groupUnitsIntoSectionsBySectionID(units, axisType = columnComponents.Co
   return groups1;
 }
 function groupUnitsIntoSectionsByOverlap(units, axisType = columnComponents.ColumnAxisType.AGE, tolerance = dt) {
-  const sectionList = [];
-  for (const unit of units) {
-    const heightRange = utils.getUnitHeightRange(unit, axisType);
-    let section = sectionList.find(
-      (s) => stratigraphyUtils.compareAgeRanges(heightRange, s.heightRange, tolerance) !== stratigraphyUtils.AgeRangeRelationship.Disjoint
-    );
-    if (section == null) {
-      sectionList.push({
-        heightRange,
-        units: [unit]
-      });
-    } else {
-      section.units.push(unit);
-      if (axisType == columnComponents.ColumnAxisType.DEPTH || axisType == columnComponents.ColumnAxisType.AGE) {
-        section.heightRange = [
-          Math.max(section.heightRange[0], heightRange[0]),
-          Math.min(section.heightRange[1], heightRange[1])
-        ];
+  const initialSections = units.map((unit) => {
+    return {
+      units: [unit],
+      heightRange: utils.getUnitHeightRange(unit, axisType)
+    };
+  });
+  const isOverlapping = (a, b) => {
+    const res = stratigraphyUtils.compareAgeRanges(a.heightRange, b.heightRange, tolerance);
+    return res !== stratigraphyUtils.AgeRangeRelationship.Disjoint;
+  };
+  const mergeSections = (a, b) => {
+    return {
+      units: [...a.units, ...b.units],
+      heightRange: stratigraphyUtils.mergeAgeRanges(
+        [a.heightRange, b.heightRange],
+        stratigraphyUtils.MergeMode.Outer
+      )
+    };
+  };
+  let finalSectionList = initialSections;
+  while (true) {
+    let merged = false;
+    const nextSections = [];
+    for (const section of finalSectionList) {
+      if (nextSections.length === 0) {
+        nextSections.push(section);
       } else {
-        section.heightRange = [
-          Math.min(section.heightRange[0], heightRange[0]),
-          Math.max(section.heightRange[1], heightRange[1])
-        ];
+        const lastSection = nextSections[nextSections.length - 1];
+        if (isOverlapping(section, lastSection)) {
+          nextSections[nextSections.length - 1] = mergeSections(lastSection, section);
+          merged = true;
+        } else {
+          nextSections.push(section);
+        }
       }
     }
+    finalSectionList = nextSections;
+    if (!merged) {
+      break;
+    }
   }
-  return sectionList.map((section, i) => {
+  return finalSectionList.map((section, i) => {
     const [b_age, t_age] = getSectionAgeRange(section.units);
     const [b_pos, t_pos] = getSectionPosRange(section.units, axisType);
     return {

package/dist/prepare-units/helpers.cjs.map

@@ -1 +1 @@
-{"version":3,"file":"helpers.cjs","sources":["../../src/prepare-units/helpers.ts"],"sourcesContent":["import type { BaseUnit, UnitLong } from \"@macrostrat/api-types\";\nimport { group } from \"d3-array\";\nimport { ColumnAxisType } from \"@macrostrat/column-components\";\nimport {\n  createUnitSorter,\n  ensureArray,\n  ensureRealFloat,\n  getUnitHeightRange,\n  unitsOverlap,\n} from \"./utils\";\nimport {\n  AgeRangeRelationship,\n  compareAgeRanges,\n} from \"@macrostrat/stratigraphy-utils\";\nimport type { ExtUnit, SectionInfo, StratigraphicPackage } from \"./types\";\n\nconst dt = 0.001;\n\nexport type UnitWithDefinedOverlap<T extends BaseUnit> = T & {\n  overlap: UnitOverlapInfo<T>;\n};\n\ntype UnitOverlapInfo<T extends BaseUnit> = {\n  column: number;\n  nColumns: number;\n  unitGroup: UnitGroup<T>;\n};\n\nclass UnitGroup<T extends BaseUnit> implements StratigraphicPackage {\n  units: T[];\n\n  constructor(units: T[]) {\n    this.units = units;\n  }\n\n  get t_age(): number {\n    return Math.min(...this.units.map((d) => d.t_age));\n  }\n\n  get b_age(): number {\n    return Math.max(...this.units.map((d) => d.b_age));\n  }\n\n  getUnits(): UnitWithDefinedOverlap<T>[] {\n    return assignColumnsToUnitsWithinOverlappingGroup(this);\n  }\n}\n\nfunction groupUnitsByMutualOverlap<T extends BaseUnit>(\n  units: T[],\n  tolerance: number = dt,\n): UnitGroup<T>[] {\n  /** Group units within a section that have mutual overlap. */\n  const sections = groupUnitsIntoSectionsByOverlap(\n    units,\n    ColumnAxisType.AGE,\n    tolerance,\n  );\n  return sections.map((d) => {\n    return new UnitGroup(d.units);\n  });\n}\n\nconst sortByAge = createUnitSorter(ColumnAxisType.AGE);\n\nfunction assignColumnsToUnitsWithinOverlappingGroup<T extends BaseUnit>(\n  group: UnitGroup<T>,\n): UnitWithDefinedOverlap<T>[] {\n  /** A relatively naïve function to assign columns to units within a mutually overlapping group.\n   * This gets the number of columns that would be needed to accommodate the units in the group.\n   * It then assigns columns to units in the group based on the number of columns needed, with\n   * lower units further to the left.\n   */\n\n  const sortedUnits = [...group.units].sort((a, b) => b.b_age - a.b_age);\n\n  const columns: T[][] = [];\n\n  for (const unit of sortedUnits) {\n    // Find a column that is not already occupied by an overlapping unit\n    let didAddToExistingColumn = false;\n    for (const column of columns) {\n      const lastUnit = column[column.length - 1];\n      if (!unitsOverlap(unit, lastUnit, ColumnAxisType.AGE, dt)) {\n        column.push(unit);\n        didAddToExistingColumn = true;\n        break;\n      }\n    }\n    if (!didAddToExistingColumn) {\n      columns.push([unit]);\n    }\n  }\n\n  const units: UnitWithDefinedOverlap<T>[] = columns.flatMap(\n    (column, columnIndex) =>\n      column.map((unit) => {\n        return {\n          ...unit,\n          overlap: {\n            column: columnIndex,\n            nColumns: columns.length,\n            unitGroup: group,\n          },\n        };\n      }),\n  );\n\n  return units.toSorted(sortByAge);\n}\n\nexport function preprocessUnits<T extends UnitLong = UnitLong>(\n  section: SectionInfo<T>,\n  axisType: ColumnAxisType = ColumnAxisType.AGE,\n): ExtUnit[] {\n  /** Preprocess units to add overlapping units and columns. */\n  let units = section.units;\n\n  let tolerance = 0.001; // 1 kyr tolerance for age columns\n  if (axisType != ColumnAxisType.AGE) {\n    tolerance = 0.01; // 1cm tolerance for height/depth columns\n  }\n\n  const unitGroups = groupUnitsByMutualOverlap(units, tolerance);\n\n  const divisions: any[] = [];\n  // Serialize all groups' units to a single array\n  for (const group of unitGroups) {\n    divisions.push(...group.getUnits());\n  }\n\n  return divisions.map((d) =>\n    enhanceUnitWithClippingPosition(section, d, axisType),\n  );\n}\n\nexport function enhanceUnitWithClippingPosition(section, d, axisType) {\n  const [b_pos, t_pos] = getUnitHeightRange(d, axisType);\n  if (axisType == ColumnAxisType.AGE) {\n    if (b_pos > section.b_age) {\n      d.b_clip_pos = section.b_age;\n    }\n    if (t_pos < section.t_age) {\n      d.t_clip_pos = section.t_age;\n    }\n  }\n  if (axisType == ColumnAxisType.DEPTH) {\n    if (b_pos > section.b_pos) {\n      d.b_clip_pos = section.b_pos;\n    }\n    if (t_pos < section.t_pos) {\n      d.t_clip_pos = section.t_pos;\n    }\n  }\n  return d;\n}\n\nexport function groupUnitsIntoSectionsBySectionID<T extends UnitLong>(\n  units: T[],\n  axisType: ColumnAxisType = ColumnAxisType.AGE,\n): SectionInfo<T>[] {\n  /** Group units into sections by section_id.\n   * This works for large-scale Macrostrat columns, where units are grouped by section_id.\n   * */\n  let groups = Array.from(group(units, (d) => d.section_id));\n  const unitComparator = createUnitSorter(axisType);\n\n  const groups1 = groups.map(([section_id, sectionUnits]) => {\n    const [b_age, t_age] = getSectionAgeRange(sectionUnits);\n    const [b_pos, t_pos] = getSectionPosRange(sectionUnits, axisType);\n\n    // sort units by position\n    sectionUnits.sort(unitComparator);\n    return { section_id, t_age, b_age, b_pos, t_pos, units: sectionUnits };\n  });\n  // Sort sections by increasing top age, then increasing bottom age.\n  // Sections have no relative ordinal position other than age...\n  const compareSections = createUnitSorter(axisType) as (\n    a: StratigraphicPackage,\n    b: StratigraphicPackage,\n  ) => number;\n  groups1.sort(compareSections);\n  return groups1;\n}\n\ninterface WorkingSection {\n  units: UnitLong[];\n  // Position or age\n  heightRange?: [number, number];\n}\n\nexport function groupUnitsIntoSectionsByOverlap<T extends BaseUnit>(\n  units: T[],\n  axisType: ColumnAxisType = ColumnAxisType.AGE,\n  tolerance: number = dt,\n): SectionInfo<T>[] {\n  /** Group units into sections by overlap.\n   * This creates \"synthetic\" sections that correspond to packages bound by scale gaps.\n   * This is most useful in the height and depth domains, where gaps (e.g., missing core) are\n   * common.\n   * */\n  // Start with each unit as its own \"section\", and progressively merge...\n  const sectionList: WorkingSection[] = [];\n  for (const unit of units) {\n    // Check if the unit overlaps with any existing section\n    const heightRange = getUnitHeightRange(unit, axisType);\n    let section: WorkingSection | undefined = sectionList.find(\n      (s) =>\n        compareAgeRanges(heightRange, s.heightRange, tolerance) !==\n        AgeRangeRelationship.Disjoint,\n    );\n    if (section == null) {\n      // No overlap, create a new section\n      sectionList.push({\n        heightRange,\n        units: [unit],\n      });\n    } else {\n      // Overlap, merge the unit into the section\n      section.units.push(unit);\n      // Update the height range\n      if (axisType == ColumnAxisType.DEPTH || axisType == ColumnAxisType.AGE) {\n        section.heightRange = [\n          Math.max(section.heightRange[0], heightRange[0]),\n          Math.min(section.heightRange[1], heightRange[1]),\n        ];\n      } else {\n        section.heightRange = [\n          Math.min(section.heightRange[0], heightRange[0]),\n          Math.max(section.heightRange[1], heightRange[1]),\n        ];\n      }\n    }\n  }\n  // We should have a section for each unit, now we can convert to SectionInfo\n  // Ages have to be really actually ages, not heights\n\n  return sectionList.map((section, i) => {\n    const [b_age, t_age] = getSectionAgeRange(section.units);\n    const [b_pos, t_pos] = getSectionPosRange(section.units, axisType);\n    return {\n      // Negative section IDs are used to indicate that these are synthetic sections\n      section_id: -i,\n      t_age,\n      b_age,\n      t_pos,\n      b_pos,\n      units: section.units as T[],\n    };\n  });\n}\n\nexport function getSectionPosRange(\n  units: BaseUnit[],\n  axisType: ColumnAxisType,\n): [number, number] {\n  /** Get the overall position range of a set of units. */\n  const t_positions = units.map((d) => {\n    switch (axisType) {\n      case ColumnAxisType.AGE:\n        return d.t_age;\n      case ColumnAxisType.DEPTH:\n      case ColumnAxisType.HEIGHT:\n      case ColumnAxisType.ORDINAL:\n        return d.t_pos;\n      default:\n        throw new Error(`Unknown axis type: ${axisType}`);\n    }\n  });\n  const b_positions = units.map((d) => {\n    switch (axisType) {\n      case ColumnAxisType.AGE:\n        return d.b_age;\n      case ColumnAxisType.DEPTH:\n      case ColumnAxisType.HEIGHT:\n      case ColumnAxisType.ORDINAL:\n        return d.b_pos;\n      default:\n        throw new Error(`Unknown axis type: ${axisType}`);\n    }\n  });\n  if (axisType == ColumnAxisType.AGE || axisType == ColumnAxisType.DEPTH) {\n    return [Math.max(...b_positions), Math.min(...t_positions)];\n  } else {\n    return [Math.min(...b_positions), Math.max(...t_positions)];\n  }\n}\n\nexport function getSectionAgeRange(units: BaseUnit[]): [number, number] {\n  /** Get the overall age range of a set of units. */\n  return getSectionPosRange(units, ColumnAxisType.AGE);\n}\n\nexport function mergeOverlappingSections<T extends UnitLong>(\n  sections: SectionInfo<T>[],\n): SectionInfo<T>[] {\n  /** Columns can have sections that overlap in time. Here, we merge overlapping\n   * sections into a single section to correctly render gap-bound packages.\n   */\n  const [firstSection, ...rest] = sections;\n  const newSections = [firstSection];\n  for (const section of rest) {\n    const lastSection = newSections[newSections.length - 1];\n    if (\n      lastSection.b_age < section.t_age ||\n      lastSection.t_age > section.b_age\n    ) {\n      // No overlap, add the section as normal\n      newSections.push(section);\n      continue;\n    }\n\n    // Overlap, merge the sections\n    lastSection.section_id = [\n      ...ensureArray(lastSection.section_id),\n      ...ensureArray(section.section_id),\n    ];\n    lastSection.units.push(...section.units);\n    lastSection.b_age = Math.max(lastSection.b_age, section.b_age);\n    lastSection.t_age = Math.min(lastSection.t_age, section.t_age);\n  }\n  return newSections;\n}\n\nexport function preprocessSectionUnit(unit: UnitLong): UnitLong {\n  /** Preprocess a single unit for a 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Here, we merge overlapping\n   * sections into a single section to correctly render gap-bound packages.\n   */\n  const [firstSection, ...rest] = sections;\n  const newSections = [firstSection];\n  for (const section of rest) {\n    const lastSection = newSections[newSections.length - 1];\n    if (\n      lastSection.b_age < section.t_age ||\n      lastSection.t_age > section.b_age\n    ) {\n      // No overlap, add the section as normal\n      newSections.push(section);\n      continue;\n    }\n\n    // Overlap, merge the sections\n    lastSection.section_id = [\n      ...ensureArray(lastSection.section_id),\n      ...ensureArray(section.section_id),\n    ];\n    lastSection.units.push(...section.units);\n    lastSection.b_age = Math.max(lastSection.b_age, section.b_age);\n    lastSection.t_age = Math.min(lastSection.t_age, section.t_age);\n  }\n  return newSections;\n}\n\nexport function preprocessSectionUnit(unit: UnitLong): UnitLong {\n  /** Preprocess a single unit for a 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package/dist/prepare-units/helpers.d.ts

@@ -1,20 +1,28 @@
 import { BaseUnit, UnitLong } from '@macrostrat/api-types';
 import { ColumnAxisType } from '@macrostrat/column-components';
 import { ExtUnit, SectionInfo, StratigraphicPackage } from './types';
-export type UnitWithDefinedOverlap<T extends BaseUnit> = T & {
-    overlap: UnitOverlapInfo<T>;
+export type UnitWithLayoutParameters<T extends BaseUnit> = T & {
+    layout: UnitLayoutData<T>;
 };
-type UnitOverlapInfo<T extends BaseUnit> = {
+export type UnitWithLayoutHints<T extends BaseUnit> = T & {
+    layoutHints?: UnitLayoutHints;
+};
+interface UnitLayoutInfo {
     column: number;
     nColumns: number;
+}
+type UnitLayoutHints = Partial<UnitLayoutInfo>;
+type UnitLayoutData<T extends BaseUnit> = UnitLayoutInfo & {
+    totalColumns: number;
     unitGroup: UnitGroup<T>;
 };
 declare class UnitGroup<T extends BaseUnit> implements StratigraphicPackage {
     units: T[];
-    constructor(units: T[]);
+    axisType: ColumnAxisType;
+    constructor(units: T[], axisType?: ColumnAxisType);
     get t_age(): number;
     get b_age(): number;
-    getUnits(): UnitWithDefinedOverlap<T>[];
+    getUnits(): UnitWithLayoutParameters<T>[];
 }
 export declare function preprocessUnits<T extends UnitLong = UnitLong>(section: SectionInfo<T>, axisType?: ColumnAxisType): ExtUnit[];
 export declare function enhanceUnitWithClippingPosition(section: any, d: any, axisType: any): any;

package/dist/prepare-units/helpers.js

@@ -1,12 +1,14 @@
 import { group } from "d3-array";
 import { ColumnAxisType } from "@macrostrat/column-components";
 import { ensureRealFloat, getUnitHeightRange, ensureArray, createUnitSorter, unitsOverlap } from "./utils.js";
-import { compareAgeRanges, AgeRangeRelationship } from "@macrostrat/stratigraphy-utils";
+import { compareAgeRanges, AgeRangeRelationship, mergeAgeRanges, MergeMode } from "@macrostrat/stratigraphy-utils";
 const dt = 1e-3;
 class UnitGroup {
   units;
-  constructor(units) {
+  axisType;
+  constructor(units, axisType = ColumnAxisType.AGE) {
     this.units = units;
+    this.axisType = axisType;
   }
   get t_age() {
     return Math.min(...this.units.map((d) => d.t_age));
@@ -18,25 +20,28 @@ class UnitGroup {
     return assignColumnsToUnitsWithinOverlappingGroup(this);
   }
 }
-function groupUnitsByMutualOverlap(units, tolerance = dt) {
-  const sections = groupUnitsIntoSectionsByOverlap(
-    units,
-    ColumnAxisType.AGE,
-    tolerance
-  );
+function groupUnitsByMutualOverlap(units, tolerance = dt, axisType = ColumnAxisType.AGE) {
+  const sections = groupUnitsIntoSectionsByOverlap(units, axisType, tolerance);
+  console.log("Grouped sections", sections);
   return sections.map((d) => {
-    return new UnitGroup(d.units);
+    return new UnitGroup(d.units, axisType);
   });
 }
 const sortByAge = createUnitSorter(ColumnAxisType.AGE);
 function assignColumnsToUnitsWithinOverlappingGroup(group2) {
-  const sortedUnits = [...group2.units].sort((a, b) => b.b_age - a.b_age);
+  const sortedUnits = [...group2.units].sort(createUnitSorter(group2.axisType));
   const columns = [];
   for (const unit of sortedUnits) {
+    const colHint = unit.layoutHints?.column;
+    if (colHint != null) {
+      columns[colHint] ??= [];
+      columns[colHint].push(unit);
+      continue;
+    }
     let didAddToExistingColumn = false;
     for (const column of columns) {
       const lastUnit = column[column.length - 1];
-      if (!unitsOverlap(unit, lastUnit, ColumnAxisType.AGE, dt)) {
+      if (!unitsOverlap(unit, lastUnit, group2.axisType, dt)) {
         column.push(unit);
         didAddToExistingColumn = true;
         break;
@@ -46,13 +51,15 @@ function assignColumnsToUnitsWithinOverlappingGroup(group2) {
       columns.push([unit]);
     }
   }
+  console.log(columns);
   const units = columns.flatMap(
     (column, columnIndex) => column.map((unit) => {
       return {
         ...unit,
-        overlap: {
+        layout: {
           column: columnIndex,
-          nColumns: columns.length,
+          nColumns: 1,
+          totalColumns: columns.length,
           unitGroup: group2
         }
       };
@@ -66,7 +73,7 @@ function preprocessUnits(section, axisType = ColumnAxisType.AGE) {
   if (axisType != ColumnAxisType.AGE) {
     tolerance = 0.01;
   }
-  const unitGroups = groupUnitsByMutualOverlap(units, tolerance);
+  const unitGroups = groupUnitsByMutualOverlap(units, tolerance, axisType);
   const divisions = [];
   for (const group2 of unitGroups) {
     divisions.push(...group2.getUnits());
@@ -109,33 +116,48 @@ function groupUnitsIntoSectionsBySectionID(units, axisType = ColumnAxisType.AGE)
   return groups1;
 }
 function groupUnitsIntoSectionsByOverlap(units, axisType = ColumnAxisType.AGE, tolerance = dt) {
-  const sectionList = [];
-  for (const unit of units) {
-    const heightRange = getUnitHeightRange(unit, axisType);
-    let section = sectionList.find(
-      (s) => compareAgeRanges(heightRange, s.heightRange, tolerance) !== AgeRangeRelationship.Disjoint
-    );
-    if (section == null) {
-      sectionList.push({
-        heightRange,
-        units: [unit]
-      });
-    } else {
-      section.units.push(unit);
-      if (axisType == ColumnAxisType.DEPTH || axisType == ColumnAxisType.AGE) {
-        section.heightRange = [
-          Math.max(section.heightRange[0], heightRange[0]),
-          Math.min(section.heightRange[1], heightRange[1])
-        ];
+  const initialSections = units.map((unit) => {
+    return {
+      units: [unit],
+      heightRange: getUnitHeightRange(unit, axisType)
+    };
+  });
+  const isOverlapping = (a, b) => {
+    const res = compareAgeRanges(a.heightRange, b.heightRange, tolerance);
+    return res !== AgeRangeRelationship.Disjoint;
+  };
+  const mergeSections = (a, b) => {
+    return {
+      units: [...a.units, ...b.units],
+      heightRange: mergeAgeRanges(
+        [a.heightRange, b.heightRange],
+        MergeMode.Outer
+      )
+    };
+  };
+  let finalSectionList = initialSections;
+  while (true) {
+    let merged = false;
+    const nextSections = [];
+    for (const section of finalSectionList) {
+      if (nextSections.length === 0) {
+        nextSections.push(section);
       } else {
-        section.heightRange = [
-          Math.min(section.heightRange[0], heightRange[0]),
-          Math.max(section.heightRange[1], heightRange[1])
-        ];
+        const lastSection = nextSections[nextSections.length - 1];
+        if (isOverlapping(section, lastSection)) {
+          nextSections[nextSections.length - 1] = mergeSections(lastSection, section);
+          merged = true;
+        } else {
+          nextSections.push(section);
+        }
       }
     }
+    finalSectionList = nextSections;
+    if (!merged) {
+      break;
+    }
   }
-  return sectionList.map((section, i) => {
+  return finalSectionList.map((section, i) => {
     const [b_age, t_age] = getSectionAgeRange(section.units);
     const [b_pos, t_pos] = getSectionPosRange(section.units, axisType);
     return {