@macrostrat/column-views 2.1.4 → 2.2.1

package/src/prepare-units/dynamic-scales.ts

@@ -0,0 +1,298 @@
+import type { UnitLong } from "@macrostrat/api-types";
+import { scaleLinear } from "d3-scale";
+import { getUnitHeightRange } from "./utils";
+import { ColumnAxisType } from "@macrostrat/column-components";
+import { mergeAgeRanges, MergeMode } from "@macrostrat/stratigraphy-utils";
+import type {
+  ApproxHeightScaleOptions,
+  ExtUnit,
+  HybridScaleDefinition,
+  HybridScaleOptions,
+  PackageScaleInfo,
+} from "./types";
+import { HybridScaleType, HeightMethod } from "./types";
+
+interface BaseSurface {
+  index: number;
+  age: number;
+  units_below: number[];
+  units_above: number[];
+}
+
+export function buildColumnSurfaces<T extends UnitLong>(
+  units: T[],
+  tolerance: number = 0.001,
+): BaseSurface[] {
+  /** Compute age surfaces for a column based on unit tops and bottoms */
+  const surfaces: Omit<BaseSurface, "index">[] = [];
+  for (const unit of units) {
+    // Top surface
+    surfaces.push({
+      age: unit.t_age,
+      units_below: [unit.unit_id],
+      units_above: [],
+    });
+    // Bottom surface
+    surfaces.push({
+      age: unit.b_age,
+      units_above: [unit.unit_id],
+      units_below: [],
+    });
+  }
+
+  // Merge duplicate surfaces (same age)
+  const mergedSurfaces: Omit<BaseSurface, "index">[] = [];
+  for (const surface of surfaces) {
+    const existingSurface = mergedSurfaces.find(
+      (s) => Math.abs(s.age - surface.age) < tolerance,
+    );
+    if (existingSurface) {
+      existingSurface.units_above.push(...surface.units_above);
+      existingSurface.units_below.push(...surface.units_below);
+    } else {
+      mergedSurfaces.push(surface);
+    }
+  }
+
+  // Sort surfaces by age (ascending)
+  mergedSurfaces.sort((a, b) => a.age - b.age);
+
+  return mergedSurfaces.map((s, i) => ({ ...s, index: i }));
+}
+
+interface AgeDomainUnitInfo {
+  t_age: number;
+  b_age: number;
+  units: ExtUnit[];
+}
+
+function getUnitsInAgeDomains(
+  surfaces: BaseSurface[],
+  units: ExtUnit[],
+): AgeDomainUnitInfo[] {
+  // Get unit IDs represented between the same surface, and the proportion of their total height represented
+  const domainUnitInfo: AgeDomainUnitInfo[] = [];
+  for (let i = 0; i < surfaces.length - 1; i++) {
+    const topSurface = surfaces[i];
+    const bottomSurface = surfaces[i + 1];
+    const unitsInDomain = units.filter((unit) => {
+      return (
+        unit.t_age <= topSurface.age + 0.001 &&
+        unit.b_age >= bottomSurface.age - 0.001
+      );
+    });
+    domainUnitInfo.push({
+      t_age: topSurface.age,
+      b_age: bottomSurface.age,
+      units: unitsInDomain,
+    });
+  }
+  return domainUnitInfo;
+}
+
+function proportionOfUnitInDomain(
+  unit: ExtUnit,
+  t_age: number,
+  b_age: number,
+): number {
+  // Compute the proportion of a unit's height that lies within the given age domain
+
+  const rng = getUnitHeightRange(unit, ColumnAxisType.AGE);
+  const rng1: [number, number] = [b_age, t_age];
+  // Compute overlap
+
+  const mergedRange = mergeAgeRanges([rng, rng1], MergeMode.Inner);
+
+  const unitHeight = Math.abs(rng[1] - rng[0]);
+  const mergedHeight = Math.abs(mergedRange[1] - mergedRange[0]);
+
+  return mergedHeight / unitHeight;
+}
+
+export function buildHybridScale<T extends UnitLong>(
+  def: HybridScaleDefinition,
+  units: T[],
+  domain: [number, number],
+  options: HybridScaleOptions = {},
+): PackageScaleInfo {
+  const surfaces = buildColumnSurfaces(units);
+
+  const filteredSurfaces = surfaces.filter(
+    (s) => s.age < Math.max(...domain) && s.age > Math.min(...domain),
+  );
+
+  const s1 = [
+    { index: -1, age: Math.min(...domain), units_above: [], units_below: [] },
+    ...filteredSurfaces,
+    {
+      index: -1,
+      age: Math.max(...domain),
+      units_above: [],
+      units_below: [],
+    },
+  ];
+
+  const { type, ...rest } = def;
+
+  if (type === HybridScaleType.EquidistantSurfaces) {
+    return buildScaleFromSurfacesSimple(s1, options);
+  }
+
+  return buildApproximateHeightScale(s1, units, { ...options, ...rest });
+}
+
+function getApproximateHeight(
+  unit: ExtUnit,
+  method: HeightMethod = HeightMethod.Maximum,
+): number | null {
+  // Get approximate height of a unit based on specified method
+  const heights = [];
+  let minHeight = unit.min_thick;
+  if (method === HeightMethod.Minimum || method === HeightMethod.Average) {
+    const h = unit.min_thick;
+    if (h != null && !isNaN(h) && h > 0) heights.push(h);
+  }
+  if (method === HeightMethod.Average || method === HeightMethod.Maximum) {
+    const h = unit.max_thick;
+    if (h != null && !isNaN(h) && h > 0) heights.push(h);
+  }
+
+  if (heights.length === 0) return null;
+
+  if (method === HeightMethod.Average) {
+    return heights.reduce((sum, h) => sum + h, 0) / heights.length;
+  } else {
+    return heights[0];
+  }
+}
+
+export function buildApproximateHeightScale(
+  surfaces: BaseSurface[],
+  units: UnitLong[],
+  options: HybridScaleOptions & ApproxHeightScaleOptions = {},
+): PackageScaleInfo {
+  /** Build a variable age scale that places age surfaces equally far apart in height space.
+   * It is presumed that gaps are already removed from the unit set provided.
+   * */
+
+  const {
+    pixelScale = 1, // pixels per meter
+    pixelOffset = 0,
+    minHeight = 5,
+    heightMethod = HeightMethod.Maximum,
+    // Default height for when height is unknown
+    defaultHeight = 100,
+  } = options;
+
+  // Get units associated with each surface
+  // Note: we could hoist this if it proved useful for other scale types
+  const domainInfo = getUnitsInAgeDomains(surfaces, units as ExtUnit[]);
+
+  // Compute the height in pixels for each surface
+
+  const surfaceHeights = [];
+  const ageDomain = [];
+  let lastHeight = pixelOffset;
+
+  for (const domain of domainInfo) {
+    if (lastHeight == pixelOffset) {
+      surfaceHeights.push(lastHeight);
+      ageDomain.push(domain.t_age);
+    }
+
+    // Approximate height based on units in this domain
+    const units = domain.units;
+    let unitHeightInfo: { unit: ExtUnit; height: number }[] = [];
+
+    for (const unit of units) {
+      const proportion = proportionOfUnitInDomain(
+        unit,
+        domain.t_age,
+        domain.b_age,
+      );
+      const height = getApproximateHeight(unit, heightMethod);
+      if (height != null) {
+        unitHeightInfo.push({ unit, height: height * proportion });
+      }
+    }
+
+    let thisHeight = 0;
+    if (unitHeightInfo.length === 0) {
+      thisHeight = defaultHeight; // Default height if no units with height info
+    } else {
+      // Normalize weights (take the mean)
+
+      const meanHeight =
+        unitHeightInfo.reduce((sum, d) => sum + d.height, 0) /
+        unitHeightInfo.length;
+
+      if (meanHeight == 0) {
+        thisHeight = defaultHeight; // Arbitrary height for zero-height intervals
+      } else if (meanHeight < minHeight) {
+        thisHeight = minHeight; // Minimum height
+      } else {
+        thisHeight = meanHeight;
+      }
+    }
+
+    lastHeight += thisHeight;
+    surfaceHeights.push(lastHeight);
+    ageDomain.push(domain.b_age);
+  }
+
+  // Build a piecewise linear scale mapping age to pixel height
+  const pixelRange = surfaceHeights.map((h) => h * pixelScale);
+
+  const scale = scaleLinear().domain(ageDomain).range(pixelRange);
+
+  const heightDomain = surfaceHeights.map((h) => lastHeight - h);
+
+  const heightScale = scaleLinear().domain(heightDomain).range(pixelRange);
+
+  const domain: [number, number] = [
+    ageDomain[ageDomain.length - 1],
+    ageDomain[0],
+  ];
+
+  return {
+    scale,
+    pixelScale: null, // pixels per unit
+    domain,
+    pixelHeight: Math.abs(pixelRange[pixelRange.length - 1] - pixelRange[0]),
+    heightScale,
+  };
+}
+
+export function buildScaleFromSurfacesSimple(
+  surfaces: BaseSurface[],
+  options: HybridScaleOptions = {},
+): PackageScaleInfo {
+  /** Build a variable age scale that places age surfaces equally far apart in height space.
+   * It is presumed that gaps are already removed from the unit set provided.
+   * */
+
+  const { pixelScale = 30 } = options;
+
+  const domain: [number, number] = [
+    surfaces[surfaces.length - 1].age,
+    surfaces[0].age,
+  ];
+  // Compute the height in pixels for each surface
+
+  const surfaceHeights = surfaces.map((surface, i) => {
+    return i * pixelScale;
+  });
+
+  // Build a piecewise linear scale mapping age to pixel height
+  const ageDomain = surfaces.map((s) => s.age);
+  const pixelRange = surfaceHeights;
+
+  const scale = scaleLinear().domain(ageDomain).range(pixelRange);
+
+  return {
+    scale,
+    pixelScale: null, // pixels per unit
+    domain,
+    pixelHeight: Math.abs(pixelRange[pixelRange.length - 1] - pixelRange[0]),
+  };
+}

package/src/prepare-units/helpers.ts

@@ -2,48 +2,27 @@ import type { BaseUnit, UnitLong } from "@macrostrat/api-types";
 import { group } from "d3-array";
 import { ColumnAxisType } from "@macrostrat/column-components";
 import {
-  unitsOverlap,
-  getUnitHeightRange,
   createUnitSorter,
   ensureArray,
   ensureRealFloat,
-  PossiblyClippedUnit,
+  getUnitHeightRange,
+  unitsOverlap,
 } from "./utils";
-import { compareAgeRanges } from "@macrostrat/stratigraphy-utils";
+import {
+  AgeRangeRelationship,
+  compareAgeRanges,
+} from "@macrostrat/stratigraphy-utils";
+import type { ExtUnit, SectionInfo, StratigraphicPackage } from "./types";
 
 const dt = 0.001;
 
-export interface StratigraphicPackage {
-  /** A collection of stratigraphic information organized in time, corresponding
-   * to single or multiple columns. */
-  t_age: number;
-  b_age: number;
-}
-
-export interface SectionInfo<T extends UnitLong = ExtUnit>
-  extends StratigraphicPackage {
-  /** A time-bounded part of a single stratigraphic column. */
-  section_id: number | number[];
-  units: T[];
-}
-
-export interface ExtUnit extends UnitLong {
-  bottomOverlap: boolean;
-  overlappingUnits: number[];
-  column?: number;
-  /* Positions (ages or heights) where the unit is clipped to its containing section.
-   * This is relevant if we are filtering by age/height/depth range.
-   */
-  t_clip_pos?: number;
-  b_clip_pos?: number;
-}
-
 export function preprocessUnits<T extends UnitLong = UnitLong>(
   section: SectionInfo<T>,
   axisType: ColumnAxisType = ColumnAxisType.AGE,
 ): ExtUnit[] {
   /** Preprocess units to add overlapping units and columns. */
-  const units = section.units;
+  let units = section.units;
+
   let divisions = units.map((...args) => extendDivision(...args, axisType));
   for (let d of divisions) {
     const overlappingUnits = divisions.filter((u) =>
@@ -63,8 +42,8 @@ export function preprocessUnits<T extends UnitLong = UnitLong>(
     }
 
     // If unit overlaps the edges of a section, set the clip positions
+    const [b_pos, t_pos] = getUnitHeightRange(d, axisType);
     if (axisType == ColumnAxisType.AGE) {
-      const [b_pos, t_pos] = getUnitHeightRange(d, axisType);
       if (b_pos > section.b_age) {
         d.b_clip_pos = section.b_age;
       }
@@ -72,14 +51,24 @@ export function preprocessUnits<T extends UnitLong = UnitLong>(
         d.t_clip_pos = section.t_age;
       }
     }
+    if (axisType == 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 (axisType == ColumnAxisType.HEIGHT) {
+    //   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;
+    //   }
+    // }
   }
 
-  // TODO: we may want to re-enable this simpler processing for sections,
-  // but we want it to be less universally applied.
-  // if (axisType != ColumnAxisType.AGE) {
-  //   return preprocessSectionUnits(divisions, axisType);
-  // }
-  //
   return divisions;
 }
 
@@ -89,8 +78,15 @@ function extendDivision(
   divisions: UnitLong[],
   axisType: ColumnAxisType = ColumnAxisType.AGE,
 ): ExtUnit {
+  // TODO: make this configurable
+  let tolerance = 0.001; // 1 kyr tolerance for age columns
+  if (axisType != ColumnAxisType.AGE) {
+    tolerance = 0.01; // 1cm tolerance for height/depth columns
+  }
+
   const overlappingUnits = divisions.filter(
-    (d) => d.unit_id != unit.unit_id && unitsOverlap(unit, d, axisType),
+    (d) =>
+      d.unit_id != unit.unit_id && unitsOverlap(unit, d, axisType, tolerance),
   );
   const u_pos = getUnitHeightRange(unit, axisType);
   const bottomOverlap = overlappingUnits.some((d) => {
@@ -111,14 +107,10 @@ function extendDivision(
   };
 }
 
-export function groupUnitsIntoSections<T extends UnitLong>(
+export function groupUnitsIntoSectionsBySectionID<T extends UnitLong>(
   units: T[],
   axisType: ColumnAxisType = ColumnAxisType.AGE,
 ): SectionInfo<T>[] {
-  if (axisType != ColumnAxisType.AGE) {
-    return groupUnitsIntoSectionByOverlap(units, axisType);
-  }
-
   /** Group units into sections by section_id.
    * This works for large-scale Macrostrat columns, where units are grouped by section_id.
    * */
@@ -127,13 +119,15 @@ export function groupUnitsIntoSections<T extends UnitLong>(
 
   const groups1 = groups.map(([section_id, sectionUnits]) => {
     const [b_age, t_age] = getSectionAgeRange(sectionUnits);
+    const [b_pos, t_pos] = getSectionPosRange(sectionUnits, axisType);
+
     // sort units by position
     sectionUnits.sort(unitComparator);
-    return { section_id, t_age, b_age, units: sectionUnits };
+    return { section_id, t_age, b_age, b_pos, t_pos, units: sectionUnits };
   });
   // Sort sections by increasing top age, then increasing bottom age.
   // Sections have no relative ordinal position other than age...
-  const compareSections = createUnitSorter(ColumnAxisType.AGE) as (
+  const compareSections = createUnitSorter(axisType) as (
     a: StratigraphicPackage,
     b: StratigraphicPackage,
   ) => number;
@@ -147,7 +141,7 @@ interface WorkingSection {
   heightRange?: [number, number];
 }
 
-function groupUnitsIntoSectionByOverlap<T extends UnitLong>(
+export function groupUnitsIntoSectionsByOverlap<T extends UnitLong>(
   units: T[],
   axisType: ColumnAxisType = ColumnAxisType.AGE,
 ): SectionInfo<T>[] {
@@ -161,8 +155,10 @@ function groupUnitsIntoSectionByOverlap<T extends UnitLong>(
   for (const unit of units) {
     // Check if the unit overlaps with any existing section
     const heightRange = getUnitHeightRange(unit, axisType);
-    let section: WorkingSection | undefined = sectionList.find((s) =>
-      compareAgeRanges(heightRange, s.heightRange),
+    let section: WorkingSection | undefined = sectionList.find(
+      (s) =>
+        compareAgeRanges(heightRange, s.heightRange) !==
+        AgeRangeRelationship.Disjoint,
     );
     if (section == null) {
       // No overlap, create a new section
@@ -174,10 +170,17 @@ function groupUnitsIntoSectionByOverlap<T extends UnitLong>(
       // Overlap, merge the unit into the section
       section.units.push(unit);
       // Update the height range
-      section.heightRange = [
-        Math.max(section.heightRange[0], heightRange[0]),
-        Math.min(section.heightRange[1], heightRange[1]),
-      ];
+      if (axisType == ColumnAxisType.DEPTH || axisType == ColumnAxisType.AGE) {
+        section.heightRange = [
+          Math.max(section.heightRange[0], heightRange[0]),
+          Math.min(section.heightRange[1], heightRange[1]),
+        ];
+      } else {
+        section.heightRange = [
+          Math.min(section.heightRange[0], heightRange[0]),
+          Math.max(section.heightRange[1], heightRange[1]),
+        ];
+      }
     }
   }
   // We should have a section for each unit, now we can convert to SectionInfo
@@ -185,23 +188,58 @@ function groupUnitsIntoSectionByOverlap<T extends UnitLong>(
 
   return sectionList.map((section, i) => {
     const [b_age, t_age] = getSectionAgeRange(section.units);
+    const [b_pos, t_pos] = getSectionPosRange(section.units, axisType);
     return {
       // Negative section IDs are used to indicate that these are synthetic sections
       section_id: -i,
-      t_age: t_age,
-      b_age: b_age,
+      t_age,
+      b_age,
+      t_pos,
+      b_pos,
       units: section.units as T[],
     };
   });
 }
 
+export function getSectionPosRange(
+  units: BaseUnit[],
+  axisType: ColumnAxisType,
+): [number, number] {
+  /** Get the overall position range of a set of units. */
+  const t_positions = units.map((d) => {
+    switch (axisType) {
+      case ColumnAxisType.AGE:
+        return d.t_age;
+      case ColumnAxisType.DEPTH:
+      case ColumnAxisType.HEIGHT:
+      case ColumnAxisType.ORDINAL:
+        return d.t_pos;
+      default:
+        throw new Error(`Unknown axis type: ${axisType}`);
+    }
+  });
+  const b_positions = units.map((d) => {
+    switch (axisType) {
+      case ColumnAxisType.AGE:
+        return d.b_age;
+      case ColumnAxisType.DEPTH:
+      case ColumnAxisType.HEIGHT:
+      case ColumnAxisType.ORDINAL:
+        return d.b_pos;
+      default:
+        throw new Error(`Unknown axis type: ${axisType}`);
+    }
+  });
+  if (axisType == ColumnAxisType.AGE || axisType == ColumnAxisType.DEPTH) {
+    return [Math.max(...b_positions), Math.min(...t_positions)];
+  } else {
+    return [Math.min(...b_positions), Math.max(...t_positions)];
+  }
+}
+
 export function getSectionAgeRange(units: BaseUnit[]): [number, number] {
   /** Get the overall age range of a set of units. */
-  const t_ages = units.map((d) => d.t_age);
-  const b_ages = units.map((d) => d.b_age);
-  const t_age = Math.min(...t_ages);
-  const b_age = Math.max(...b_ages);
-  return [b_age, t_age];
+  return getSectionPosRange(units, ColumnAxisType.AGE);
 }
 
 export function mergeOverlappingSections<T extends UnitLong>(
@@ -235,38 +273,14 @@ export function mergeOverlappingSections<T extends UnitLong>(
   return newSections;
 }
 
-function preprocessSectionUnits(
-  units: UnitLong[],
-  axisType: ColumnAxisType = ColumnAxisType.DEPTH,
-): ExtUnit[] {
-  /** Preprocess units for a "section" column type, which is guaranteed to be simpler. */
-  // We have to assume the units are ordered...
-  let thickness = 0;
-  return units.map((unit, i) => {
-    let u1 = preprocessSectionUnit(unit, i, units, thickness, axisType);
-    thickness += Math.abs(u1.t_pos - u1.b_pos);
-    return u1;
-  });
-}
-
-function preprocessSectionUnit(
-  unit: UnitLong,
-  i: number,
-  units: UnitLong[],
-  accumulatedThickness: number = 0,
-  axisType: ColumnAxisType = ColumnAxisType.DEPTH,
-): ExtUnit {
+export function preprocessSectionUnit(unit: UnitLong): UnitLong {
   /** Preprocess a single unit for a "section" column type.
-   * No provision for overlapping units.
+   * This mostly handles vagaries of eODP-style columns.
    * */
 
   let b_pos = unit.b_pos;
   let t_pos = unit.t_pos;
 
-  if (b_pos == t_pos && axisType == ColumnAxisType.ORDINAL) {
-    t_pos = t_pos - 1;
-  }
-
   let unit_name = unit.unit_name;
 
   // eODP columns sometimes have overlapping core sections, which are encoded in the name field
@@ -285,7 +299,5 @@ function preprocessSectionUnit(
     b_pos: ensureRealFloat(b_pos),
     t_pos: ensureRealFloat(t_pos),
     unit_name,
-    bottomOverlap: false,
-    overlappingUnits: [],
   };
 }