@macrostrat/column-views 3.3.4 → 3.4.0

package/dist/index.cjs

@@ -10,7 +10,7 @@ const ageRange = require("./unit-details/age-range.cjs");
 const composite = require("./units/composite.cjs");
 const columns = require("./maps/layers/columns.cjs");
 const base = require("./facets/measurements/base.cjs");
-const panel = require("./unit-details/panel.cjs");
+const identifiers = require("./unit-details/identifiers.cjs");
 const layers = require("./maps/column-navigation/svg/layers.cjs");
 const core = require("./maps/column-correlation/core.cjs");
 const state = require("./maps/column-correlation/state.cjs");
@@ -23,6 +23,7 @@ const provider = require("./facets/fossils/provider.cjs");
 const types = require("./prepare-units/types.cjs");
 const index$4 = require("./maps/inset-map/index.cjs");
 const isotopesColumn = require("./facets/carbon-isotopes/isotopes-column.cjs");
+const panel = require("./unit-details/panel.cjs");
 const store = require("./data-provider/store.cjs");
 const units = require("./maps/layers/units.cjs");
 const dataProvider = require("./facets/carbon-isotopes/data-provider.cjs");
@@ -30,6 +31,7 @@ const utils = require("./prepare-units/utils.cjs");
 const index$5 = require("./facets/fossils/index.cjs");
 const taxonRanges = require("./facets/fossils/taxon-ranges.cjs");
 const sgp = require("./facets/measurements/sgp.cjs");
+const stratNames = require("./unit-details/strat-names.cjs");
 const modalPanel = require("./unit-details/modal-panel.cjs");
 const popover = require("./unit-details/popover.cjs");
 const unitSelection = require("./data-provider/unit-selection.cjs");
@@ -79,13 +81,9 @@ exports.TruncatedList = base.TruncatedList;
 exports.groupNotesByPixelDistance = base.groupNotesByPixelDistance;
 exports.mergeHeightRanges = base.mergeHeightRanges;
 exports.standardizeMeasurementHeight = base.standardizeMeasurementHeight;
-exports.ClickableText = panel.ClickableText;
-exports.Identifier = panel.Identifier;
-exports.LegendPanelHeader = panel.LegendPanelHeader;
-exports.ReferencesField = panel.ReferencesField;
-exports.ThicknessField = panel.ThicknessField;
-exports.UnitDetailsFeature = panel.UnitDetailsFeature;
-exports.UnitDetailsPanel = panel.UnitDetailsPanel;
+exports.ClickableText = identifiers.ClickableText;
+exports.Identifier = identifiers.Identifier;
+exports.UnitIdentifier = identifiers.UnitIdentifier;
 exports.ColumnCenters = layers.ColumnCenters;
 exports.ColumnFeatures = layers.ColumnFeatures;
 exports.ColumnKeyboardNavigation = layers.ColumnKeyboardNavigation;
@@ -113,6 +111,11 @@ exports.HybridScaleType = types.HybridScaleType;
 exports.InsetMap = index$4.InsetMap;
 exports.IsotopesColumn = isotopesColumn.IsotopesColumn;
 exports.IsotopesDataset = isotopesColumn.IsotopesDataset;
+exports.LegendPanelHeader = panel.LegendPanelHeader;
+exports.ReferencesField = panel.ReferencesField;
+exports.ThicknessField = panel.ThicknessField;
+exports.UnitDetailsFeature = panel.UnitDetailsFeature;
+exports.UnitDetailsPanel = panel.UnitDetailsPanel;
 exports.LithologiesProvider = store.LithologiesProvider;
 exports.MacrostratColumnDataProvider = store.MacrostratColumnDataProvider;
 exports.MacrostratColumnProvider = store.MacrostratColumnProvider;
@@ -141,6 +144,7 @@ exports.unitsOverlap = utils.unitsOverlap;
 exports.PBDBFossilsColumn = index$5.PBDBFossilsColumn;
 exports.PBDBOccurrencesMatrix = taxonRanges.PBDBOccurrencesMatrix;
 exports.SGPMeasurementsColumn = sgp.SGPMeasurementsColumn;
+exports.StratNameField = stratNames.StratNameField;
 exports.UnitDetailsPanelWithNavigation = modalPanel.UnitDetailsPanelWithNavigation;
 exports.UnitDetailsPopover = popover.UnitDetailsPopover;
 exports.UnitSelectionPopover = popover.UnitSelectionPopover;
@@ -151,6 +155,7 @@ exports.selectedUnitIDAtom = unitSelection.selectedUnitIDAtom;
 exports.useAtomOverlayPosition = unitSelection.useAtomOverlayPosition;
 exports.useColumnRef = unitSelection.useColumnRef;
 exports.useSelectedUnit = unitSelection.useSelectedUnit;
+exports.useUnitSelection = unitSelection.useUnitSelection;
 exports.useUnitSelectionDispatch = unitSelection.useUnitSelectionDispatch;
 exports.useUnitSelectionTarget = unitSelection.useUnitSelectionTarget;
 exports.flattenLithologies = colors.flattenLithologies;

package/dist/index.cjs.map

@@ -1 +1 @@
-{"version":3,"file":"index.cjs","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;"}
+{"version":3,"file":"index.cjs","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;"}

package/dist/index.js

@@ -8,7 +8,7 @@ import { AgeField, AgeLabel, AgeRange, Duration, IntervalProportions, getAge, ge
 import { AnnotatedUnitsColumn, ColumnNotesProvider, CompositeUnitComponent, CompositeUnitsColumn, LabelTrackerProvider, SectionLabelsColumn, TrackedLabeledUnit } from "./units/composite.js";
 import { BaseColumnsLayer, SelectedColumnOverlay, buildColumnsStyle } from "./maps/layers/columns.js";
 import { BaseMeasurementsColumn, TruncatedList, groupNotesByPixelDistance, mergeHeightRanges, standardizeMeasurementHeight } from "./facets/measurements/base.js";
-import { ClickableText, Identifier, LegendPanelHeader, ReferencesField, ThicknessField, UnitDetailsFeature, UnitDetailsPanel } from "./unit-details/panel.js";
+import { ClickableText, Identifier, UnitIdentifier } from "./unit-details/identifiers.js";
 import { ColumnCenters, ColumnFeatures, ColumnKeyboardNavigation, Columns, CurrentColumn, MeasurementsLayer } from "./maps/column-navigation/svg/layers.js";
 import { ColumnCorrelationMap } from "./maps/column-correlation/core.js";
 import { ColumnCorrelationProvider, useCorrelationMapStore } from "./maps/column-correlation/state.js";
@@ -21,6 +21,7 @@ import { FossilDataType, useFossilData } from "./facets/fossils/provider.js";
 import { HeightMethod, HybridScaleType } from "./prepare-units/types.js";
 import { InsetMap } from "./maps/inset-map/index.js";
 import { IsotopesColumn, IsotopesDataset } from "./facets/carbon-isotopes/isotopes-column.js";
+import { LegendPanelHeader, ReferencesField, ThicknessField, UnitDetailsFeature, UnitDetailsPanel } from "./unit-details/panel.js";
 import { LithologiesProvider, MacrostratColumnDataProvider, MacrostratColumnProvider, MacrostratColumnStateProvider, UnitSelectionProvider, columnUnitsAtom, columnUnitsMapAtom, scope, useColumnUnitsMap, useCompositeScale, useMacrostratColumnData, useMacrostratUnits } from "./data-provider/store.js";
 import { MacrostratUnitsOverlay, buildUnitsStyle } from "./maps/layers/units.js";
 import { MeasurementDataContext, MeasurementDataProvider, useMeasurementData } from "./facets/carbon-isotopes/data-provider.js";
@@ -28,9 +29,10 @@ import { MergeSectionsMode, agesOverlap, createUnitSorter, ensureArray, ensureRe
 import { PBDBFossilsColumn } from "./facets/fossils/index.js";
 import { PBDBOccurrencesMatrix } from "./facets/fossils/taxon-ranges.js";
 import { SGPMeasurementsColumn } from "./facets/measurements/sgp.js";
+import { StratNameField } from "./unit-details/strat-names.js";
 import { UnitDetailsPanelWithNavigation } from "./unit-details/modal-panel.js";
 import { UnitDetailsPopover, UnitSelectionPopover } from "./unit-details/popover.js";
-import { UnitKeyboardNavigation, UnitSelectionCallbackManager, allowUnitSelectionAtom, selectedUnitIDAtom, useAtomOverlayPosition, useColumnRef, useSelectedUnit, useUnitSelectionDispatch, useUnitSelectionTarget } from "./data-provider/unit-selection.js";
+import { UnitKeyboardNavigation, UnitSelectionCallbackManager, allowUnitSelectionAtom, selectedUnitIDAtom, useAtomOverlayPosition, useColumnRef, useSelectedUnit, useUnitSelection, useUnitSelectionDispatch, useUnitSelectionTarget } from "./data-provider/unit-selection.js";
 import { flattenLithologies, getMixedColorForData, getMixedUnitColor } from "./units/colors.js";
 import { parseLineFromString, stringifyLine } from "./correlation-chart/hash-string.js";
 import { preprocessUnits } from "./prepare-units/helpers.js";
@@ -102,6 +104,7 @@ export {
   SectionLabelsColumn,
   SelectedColumnOverlay,
   SimpleUnitsColumn,
+  StratNameField,
   ThicknessField,
   TrackedLabeledUnit,
   TruncatedList,
@@ -110,6 +113,7 @@ export {
   UnitDetailsPanel,
   UnitDetailsPanelWithNavigation,
   UnitDetailsPopover,
+  UnitIdentifier,
   UnitKeyboardNavigation,
   UnitSelectionCallbackManager,
   UnitSelectionPopover,
@@ -156,6 +160,7 @@ export {
   useSelectedUnit,
   useUnitColor,
   useUnitColorByEnvironment,
+  useUnitSelection,
   useUnitSelectionDispatch,
   useUnitSelectionTarget
 };

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;"}
+{"version":3,"file":"index.js","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;"}

package/dist/maps/column-correlation/state.d.ts

@@ -1,6 +1,6 @@
 import { LineString, Point } from 'geojson';
 import { StoreApi } from 'zustand';
-import { ColumnGeoJSONRecord } from '../../../../api-types/src/index.ts';
+import { ColumnGeoJSONRecord } from '@macrostrat/api-types';
 import { ReactNode } from 'react';
 export interface CorrelationMapInput {
     columns: ColumnGeoJSONRecord[];

package/dist/maps/column-navigation/mapbox/state.d.ts

@@ -1,5 +1,5 @@
 import { StoreApi } from 'zustand';
-import { ColumnGeoJSONRecordWithID } from '../../../../../api-types/src/index.ts';
+import { ColumnGeoJSONRecordWithID } from '@macrostrat/api-types';
 import { ReactNode } from 'react';
 export interface NavigationStore {
     columns: ColumnGeoJSONRecordWithID[];

package/dist/maps/column-navigation/svg/data-fetcher.d.ts

@@ -3,4 +3,4 @@ export declare function useColumnFeatures({ status_code, project_id, format, }:
     status_code?: string;
     project_id?: number;
     format?: "geojson" | "topojson" | "geojson_bare";
-}): import('../../../../../api-types/src/index.ts').ColumnGeoJSONRecord[] | null;
+}): import('@macrostrat/api-types').ColumnGeoJSONRecord[] | null;

package/dist/maps/column-navigation/svg/layers.d.ts

@@ -3,7 +3,7 @@ import { Polygon } from 'geojson';
 export declare function MeasurementsLayer(props: any): import('react').FunctionComponentElement<{
     [k: string]: any;
     geometry?: object;
-    features?: import('../../../../../svg-map-components/src/index.ts').IFeature[];
+    features?: import('@macrostrat/svg-map-components').IFeature[];
     useCanvas?: boolean;
 } & {
     children?: import('react').ReactNode | undefined;
@@ -15,7 +15,7 @@ type ColumnFeature = ExtendedFeature<Polygon, ColumnProps>;
 declare function ColumnFeatures(props: any): import('react').FunctionComponentElement<{
     [k: string]: any;
     geometry?: object;
-    features?: import('../../../../../svg-map-components/src/index.ts').IFeature[];
+    features?: import('@macrostrat/svg-map-components').IFeature[];
     useCanvas?: boolean;
 } & {
     children?: import('react').ReactNode | undefined;
@@ -46,7 +46,7 @@ declare const ColumnCenters: (props: ColumnNavProps) => import('react').Function
 declare const CurrentColumn: (props: any) => import('react').FunctionComponentElement<{
     [k: string]: any;
     geometry?: object;
-    features?: import('../../../../../svg-map-components/src/index.ts').IFeature[];
+    features?: import('@macrostrat/svg-map-components').IFeature[];
     useCanvas?: boolean;
 } & {
     children?: import('react').ReactNode | undefined;

package/dist/maps/inset-map/index.d.ts

@@ -1,4 +1,4 @@
-import { MapViewProps } from '../../../../map-interface/src/index.ts';
+import { MapViewProps } from '@macrostrat/map-interface';
 import { ReactNode, CSSProperties } from 'react';
 export interface InsetMapProps extends Omit<MapViewProps, "style"> {
     controls?: ReactNode;

package/dist/maps/layers/columns.d.ts

@@ -1,6 +1,6 @@
 import { default as GeoJSON, FeatureCollection } from 'geojson';
 import { GeoJSONFeature } from 'mapbox-gl';
-import { StyleFragment } from '../../../../mapbox-react/src/index.ts';
+import { StyleFragment } from '@macrostrat/mapbox-react';
 export interface ColumnsStyleOptions {
     color?: string | any[];
     selectedColor?: string | any[];

package/dist/maps/layers/units.d.ts

@@ -1,4 +1,4 @@
-import { StyleFragment } from '../../../../map-styles/src/index.ts';
+import { StyleFragment } from '@macrostrat/map-styles';
 export interface UnitsOverlayProps {
     time: number;
     ageSpan?: number;

package/dist/prepare-units/composite-scale.d.ts

@@ -1,4 +1,4 @@
-import { UnitLong } from '../../../api-types/src/index.ts';
+import { UnitLong } from '@macrostrat/api-types';
 import { ExtUnit, SectionInfo, ColumnScaleOptions, CompositeColumnData, CompositeScaleData, PackageLayoutData, PackageScaleInfo } from './types';
 export declare function buildCompositeScaleInfo(inputScales: PackageScaleInfo[], unconformityHeight: number): CompositeScaleData;
 export declare function finalizeSectionHeights<T extends UnitLong>(sections: SectionInfoWithScale<T>[], unconformityHeight: number): CompositeColumnData<T>;

package/dist/prepare-units/dynamic-scales.d.ts

@@ -1,4 +1,4 @@
-import { UnitLong } from '../../../api-types/src/index.ts';
+import { UnitLong } from '@macrostrat/api-types';
 import { ApproxHeightScaleOptions, HybridScaleDefinition, HybridScaleOptions, PackageScaleInfo } from './types';
 interface BaseSurface {
     index: number;

package/dist/prepare-units/helpers.cjs

@@ -5,64 +5,97 @@ const columnComponents = require("@macrostrat/column-components");
 const utils = require("./utils.cjs");
 const stratigraphyUtils = require("@macrostrat/stratigraphy-utils");
 const dt = 1e-3;
-function preprocessUnits(section, axisType = columnComponents.ColumnAxisType.AGE) {
-  let units = section.units;
-  let divisions = units.map((...args) => extendDivision(...args, axisType));
-  for (let d of divisions) {
-    const overlappingUnits = divisions.filter(
-      (u) => d.overlappingUnits.includes(u.unit_id)
-    );
-    const columns = overlappingUnits.map((d2) => d2.column);
-    if (columns.includes(d.column)) {
-      let col = 0;
-      while (columns.includes(col)) {
-        col++;
-      }
-      d.column ??= col;
-    }
-    const [b_pos, t_pos] = utils.getUnitHeightRange(d, axisType);
-    if (axisType == columnComponents.ColumnAxisType.AGE) {
-      if (b_pos > section.b_age) {
-        d.b_clip_pos = section.b_age;
-      }
-      if (t_pos < section.t_age) {
-        d.t_clip_pos = section.t_age;
+class UnitGroup {
+  units;
+  constructor(units) {
+    this.units = units;
+  }
+  get t_age() {
+    return Math.min(...this.units.map((d) => d.t_age));
+  }
+  get b_age() {
+    return Math.max(...this.units.map((d) => d.b_age));
+  }
+  getUnits() {
+    return assignColumnsToUnitsWithinOverlappingGroup(this);
+  }
+}
+function groupUnitsByMutualOverlap(units, tolerance = dt) {
+  const sections = groupUnitsIntoSectionsByOverlap(
+    units,
+    columnComponents.ColumnAxisType.AGE,
+    tolerance
+  );
+  return sections.map((d) => {
+    return new UnitGroup(d.units);
+  });
+}
+const sortByAge = utils.createUnitSorter(columnComponents.ColumnAxisType.AGE);
+function assignColumnsToUnitsWithinOverlappingGroup(group2) {
+  const sortedUnits = [...group2.units].sort((a, b) => b.b_age - a.b_age);
+  const columns = [];
+  for (const unit of sortedUnits) {
+    let didAddToExistingColumn = false;
+    for (const column of columns) {
+      const lastUnit = column[column.length - 1];
+      if (!utils.unitsOverlap(unit, lastUnit, columnComponents.ColumnAxisType.AGE, dt)) {
+        column.push(unit);
+        didAddToExistingColumn = true;
+        break;
       }
     }
-    if (axisType == columnComponents.ColumnAxisType.DEPTH) {
-      if (b_pos > section.b_pos) {
-        d.b_clip_pos = section.b_pos;
-      }
-      if (t_pos < section.t_pos) {
-        d.t_clip_pos = section.t_pos;
-      }
+    if (!didAddToExistingColumn) {
+      columns.push([unit]);
     }
   }
-  return divisions;
+  const units = columns.flatMap(
+    (column, columnIndex) => column.map((unit) => {
+      return {
+        ...unit,
+        overlap: {
+          column: columnIndex,
+          nColumns: columns.length,
+          unitGroup: group2
+        }
+      };
+    })
+  );
+  return units.toSorted(sortByAge);
 }
-function extendDivision(unit, i, divisions, axisType = columnComponents.ColumnAxisType.AGE) {
+function preprocessUnits(section, axisType = columnComponents.ColumnAxisType.AGE) {
+  let units = section.units;
   let tolerance = 1e-3;
   if (axisType != columnComponents.ColumnAxisType.AGE) {
     tolerance = 0.01;
   }
-  const overlappingUnits = divisions.filter(
-    (d) => d.unit_id != unit.unit_id && utils.unitsOverlap(unit, d, axisType, tolerance)
+  const unitGroups = groupUnitsByMutualOverlap(units, tolerance);
+  const divisions = [];
+  for (const group2 of unitGroups) {
+    divisions.push(...group2.getUnits());
+  }
+  return divisions.map(
+    (d) => enhanceUnitWithClippingPosition(section, d, axisType)
   );
-  const u_pos = utils.getUnitHeightRange(unit, axisType);
-  const bottomOverlap = overlappingUnits.some((d) => {
-    const d_pos = utils.getUnitHeightRange(d, axisType);
-    return d_pos[0] < u_pos[0] + dt;
-  });
-  let column = 0;
-  if (overlappingUnits.length == 1) {
-    column = 1;
+}
+function enhanceUnitWithClippingPosition(section, d, axisType) {
+  const [b_pos, t_pos] = utils.getUnitHeightRange(d, axisType);
+  if (axisType == columnComponents.ColumnAxisType.AGE) {
+    if (b_pos > section.b_age) {
+      d.b_clip_pos = section.b_age;
+    }
+    if (t_pos < section.t_age) {
+      d.t_clip_pos = section.t_age;
+    }
   }
-  return {
-    ...unit,
-    bottomOverlap,
-    column: unit.column ?? column,
-    overlappingUnits: overlappingUnits.map((d) => d.unit_id)
-  };
+  if (axisType == columnComponents.ColumnAxisType.DEPTH) {
+    if (b_pos > section.b_pos) {
+      d.b_clip_pos = section.b_pos;
+    }
+    if (t_pos < section.t_pos) {
+      d.t_clip_pos = section.t_pos;
+    }
+  }
+  return d;
 }
 function groupUnitsIntoSectionsBySectionID(units, axisType = columnComponents.ColumnAxisType.AGE) {
   let groups = Array.from(d3Array.group(units, (d) => d.section_id));
@@ -77,12 +110,12 @@ function groupUnitsIntoSectionsBySectionID(units, axisType = columnComponents.Co
   groups1.sort(compareSections);
   return groups1;
 }
-function groupUnitsIntoSectionsByOverlap(units, axisType = columnComponents.ColumnAxisType.AGE) {
+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) !== stratigraphyUtils.AgeRangeRelationship.Disjoint
+      (s) => stratigraphyUtils.compareAgeRanges(heightRange, s.heightRange, tolerance) !== stratigraphyUtils.AgeRangeRelationship.Disjoint
     );
     if (section == null) {
       sectionList.push({
@@ -188,6 +221,7 @@ function preprocessSectionUnit(unit) {
     unit_name
   };
 }
+exports.enhanceUnitWithClippingPosition = enhanceUnitWithClippingPosition;
 exports.getSectionAgeRange = getSectionAgeRange;
 exports.getSectionPosRange = getSectionPosRange;
 exports.groupUnitsIntoSectionsByOverlap = groupUnitsIntoSectionsByOverlap;

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 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 divisions = units.map((...args) => extendDivision(...args, axisType));\n  for (let d of divisions) {\n    const overlappingUnits = divisions.filter((u) =>\n      d.overlappingUnits.includes(u.unit_id),\n    );\n\n    // Overlapping columns\n    const columns = overlappingUnits.map((d) => d.column);\n\n    if (columns.includes(d.column)) {\n      let col = 0;\n      // Go through columns to find a better index\n      while (columns.includes(col)) {\n        col++;\n      }\n      d.column ??= col;\n    }\n\n    // If unit overlaps the edges of a section, set the clip positions\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    // if (axisType == ColumnAxisType.HEIGHT) {\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  }\n\n  return divisions;\n}\n\nfunction extendDivision(\n  unit: UnitLong,\n  i: number,\n  divisions: UnitLong[],\n  axisType: ColumnAxisType = ColumnAxisType.AGE,\n): ExtUnit {\n  // TODO: make this configurable\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 overlappingUnits = divisions.filter(\n    (d) =>\n      d.unit_id != unit.unit_id && unitsOverlap(unit, d, axisType, tolerance),\n  );\n  const u_pos = getUnitHeightRange(unit, axisType);\n  const bottomOverlap = overlappingUnits.some((d) => {\n    const d_pos = getUnitHeightRange(d, axisType);\n    // Check if the unit is below the current unit\n    return d_pos[0] < u_pos[0] + dt;\n  });\n  let column = 0;\n  if (overlappingUnits.length == 1) {\n    column = 1;\n  }\n\n  return {\n    ...unit,\n    bottomOverlap,\n    column: unit.column ?? column,\n    overlappingUnits: overlappingUnits.map((d) => d.unit_id),\n  };\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 UnitLong>(\n  units: T[],\n  axisType: ColumnAxisType = ColumnAxisType.AGE,\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) !==\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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+{"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 \"section\" column type.\n   * This mostly handles vagaries of eODP-style columns.\n   * */\n\n  let b_pos = unit.b_pos;\n  let t_pos = unit.t_pos;\n\n  let unit_name = unit.unit_name;\n\n  // eODP columns sometimes have overlapping core sections, which are encoded in the name field\n  // Match eODP section names\n  const match = unit.unit_name.match(/^(\\d+(\\.\\d+)?)-(\\d+(\\.\\d+)?): (.+)/);\n\n  if (match) {\n    // These values should already be set if we've used the show_positions flag\n    t_pos ??= ensureRealFloat(match[1]);\n    b_pos ??= ensureRealFloat(match[3]);\n    unit_name = match[5];\n  }\n\n  return {\n    ...unit,\n    b_pos: ensureRealFloat(b_pos),\n    t_pos: ensureRealFloat(t_pos),\n    unit_name,\n  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package/dist/prepare-units/helpers.d.ts

@@ -1,10 +1,27 @@
-import { BaseUnit, UnitLong } from '../../../api-types/src/index.ts';
-import { ColumnAxisType } from '../../../column-components/src/index.ts';
-import { ExtUnit, SectionInfo } from './types';
+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>;
+};
+type UnitOverlapInfo<T extends BaseUnit> = {
+    column: number;
+    nColumns: number;
+    unitGroup: UnitGroup<T>;
+};
+declare class UnitGroup<T extends BaseUnit> implements StratigraphicPackage {
+    units: T[];
+    constructor(units: T[]);
+    get t_age(): number;
+    get b_age(): number;
+    getUnits(): UnitWithDefinedOverlap<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;
 export declare function groupUnitsIntoSectionsBySectionID<T extends UnitLong>(units: T[], axisType?: ColumnAxisType): SectionInfo<T>[];
-export declare function groupUnitsIntoSectionsByOverlap<T extends UnitLong>(units: T[], axisType?: ColumnAxisType): SectionInfo<T>[];
+export declare function groupUnitsIntoSectionsByOverlap<T extends BaseUnit>(units: T[], axisType?: ColumnAxisType, tolerance?: number): SectionInfo<T>[];
 export declare function getSectionPosRange(units: BaseUnit[], axisType: ColumnAxisType): [number, number];
 export declare function getSectionAgeRange(units: BaseUnit[]): [number, number];
 export declare function mergeOverlappingSections<T extends UnitLong>(sections: SectionInfo<T>[]): SectionInfo<T>[];
 export declare function preprocessSectionUnit(unit: UnitLong): UnitLong;
+export {};