@macrostrat/column-views 3.3.5 → 3.4.0

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 \"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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+{"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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package/dist/prepare-units/helpers.d.ts

@@ -1,10 +1,27 @@
 import { BaseUnit, UnitLong } from '@macrostrat/api-types';
 import { ColumnAxisType } from '@macrostrat/column-components';
-import { ExtUnit, SectionInfo } from './types';
+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 {};

package/dist/prepare-units/helpers.js

@@ -1,66 +1,99 @@
 import { group } from "d3-array";
 import { ColumnAxisType } from "@macrostrat/column-components";
-import { getUnitHeightRange, ensureRealFloat, ensureArray, unitsOverlap, createUnitSorter } from "./utils.js";
+import { ensureRealFloat, getUnitHeightRange, ensureArray, createUnitSorter, unitsOverlap } from "./utils.js";
 import { compareAgeRanges, AgeRangeRelationship } from "@macrostrat/stratigraphy-utils";
 const dt = 1e-3;
-function preprocessUnits(section, axisType = 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] = getUnitHeightRange(d, axisType);
-    if (axisType == 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,
+    ColumnAxisType.AGE,
+    tolerance
+  );
+  return sections.map((d) => {
+    return new UnitGroup(d.units);
+  });
+}
+const sortByAge = createUnitSorter(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 (!unitsOverlap(unit, lastUnit, ColumnAxisType.AGE, dt)) {
+        column.push(unit);
+        didAddToExistingColumn = true;
+        break;
       }
     }
-    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 (!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 = ColumnAxisType.AGE) {
+function preprocessUnits(section, axisType = ColumnAxisType.AGE) {
+  let units = section.units;
   let tolerance = 1e-3;
   if (axisType != ColumnAxisType.AGE) {
     tolerance = 0.01;
   }
-  const overlappingUnits = divisions.filter(
-    (d) => d.unit_id != unit.unit_id && 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 = getUnitHeightRange(unit, axisType);
-  const bottomOverlap = overlappingUnits.some((d) => {
-    const d_pos = 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] = getUnitHeightRange(d, axisType);
+  if (axisType == 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 == 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 = ColumnAxisType.AGE) {
   let groups = Array.from(group(units, (d) => d.section_id));
@@ -75,12 +108,12 @@ function groupUnitsIntoSectionsBySectionID(units, axisType = ColumnAxisType.AGE)
   groups1.sort(compareSections);
   return groups1;
 }
-function groupUnitsIntoSectionsByOverlap(units, axisType = ColumnAxisType.AGE) {
+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) !== AgeRangeRelationship.Disjoint
+      (s) => compareAgeRanges(heightRange, s.heightRange, tolerance) !== AgeRangeRelationship.Disjoint
     );
     if (section == null) {
       sectionList.push({
@@ -187,6 +220,7 @@ function preprocessSectionUnit(unit) {
   };
 }
 export {
+  enhanceUnitWithClippingPosition,
   getSectionAgeRange,
   getSectionPosRange,
   groupUnitsIntoSectionsByOverlap,

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

@@ -1 +1 @@
-{"version":3,"file":"helpers.js","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.js","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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package/dist/prepare-units/index.cjs.map

@@ -1 +1 @@
-{"version":3,"file":"index.cjs","sources":["../../src/prepare-units/index.ts"],"sourcesContent":["import {\n  getSectionAgeRange,\n  getSectionPosRange,\n  groupUnitsIntoSectionsByOverlap,\n  groupUnitsIntoSectionsBySectionID,\n  mergeOverlappingSections,\n  preprocessSectionUnit,\n  preprocessUnits,\n} from \"./helpers\";\nimport { ColumnAxisType } from \"@macrostrat/column-components\";\nimport { useMemo } from \"react\";\nimport { UnitLong } from \"@macrostrat/api-types\";\nimport {\n  collapseUnconformitiesByPixelHeight,\n  computeSectionHeights,\n  finalizeSectionHeights,\n  type CompositeColumnScale,\n} from \"./composite-scale\";\nimport {\n  agesOverlap,\n  MergeSectionsMode,\n  PrepareColumnOptions,\n  PreparedColumnData,\n  unitsOverlap,\n} from \"./utils\";\nimport { SectionInfo } from \"./types\";\n\nexport * from \"./utils\";\nexport * from \"./types\";\nexport { preprocessUnits };\nexport type { CompositeColumnScale };\n\nexport function usePreparedColumnUnits(\n  data: UnitLong[],\n  options: PrepareColumnOptions,\n): PreparedColumnData {\n  /** This function wraps and memoizes all preparation steps for converting\n   * an array of units from the /units route to a form ready for usage.\n   */\n  return useMemo(() => {\n    return prepareColumnUnits(data, options);\n  }, [data, ...Object.values(options)]);\n}\n\nexport function prepareColumnUnits(\n  units: UnitLong[],\n  options: PrepareColumnOptions,\n): PreparedColumnData {\n  /** Prepare units for rendering into Macrostrat columns */\n\n  let { t_age, b_age, t_pos, b_pos } = options;\n\n  const {\n    mergeSections = MergeSectionsMode.OVERLAPPING,\n    axisType,\n    unconformityHeight,\n    collapseSmallUnconformities = false,\n    hybridScale,\n    scale,\n  } = options;\n\n  let _totalHeight = null;\n\n  if (scale != null) {\n    // Set t_age and b_age based on scale domain if not already set\n    const domain = scale.domain();\n    if (axisType == ColumnAxisType.AGE) {\n      if (t_age == null) t_age = Math.min(...domain);\n      if (b_age == null) b_age = Math.max(...domain);\n      _totalHeight = Math.abs(scale(b_age) - scale(t_age));\n    } else {\n      if (t_pos == null) t_pos = Math.min(...domain);\n      if (b_pos == null) b_pos = Math.max(...domain);\n      _totalHeight = Math.abs(scale(b_pos) - scale(t_pos));\n    }\n  }\n\n  // Start by ensuring that ages and positions are numbers\n  // also set up some values for eODP-style columns\n  let units1 = units.map(preprocessSectionUnit);\n\n  /** Prototype filtering to age range */\n  units1 = units1.filter((d) => {\n    // Filter units by t_age and b_age, inclusive\n    if (axisType == ColumnAxisType.AGE) {\n      return agesOverlap(d, { t_age, b_age });\n    } else {\n      return unitsOverlap(d, { t_pos, b_pos } as any, axisType);\n    }\n  });\n\n  let mergeMode = mergeSections;\n  // if (axisType != ColumnAxisType.AGE) {\n  //   // For non-age columns, we always merge sections.\n  //   // This is because the \"groupUnitsIntoSections\" function is not well-defined\n  //   // for non-age columns.\n  //   mergeMode = MergeSectionsMode.ALL;\n  // }\n\n  let sections0: SectionInfo<UnitLong>[];\n  if (mergeMode == MergeSectionsMode.ALL) {\n    // For the \"merge sections\" mode, we need to create a single section\n    const [b_unit_pos, t_unit_pos] = getSectionPosRange(units1, axisType);\n    const [b_unit_age, t_unit_age] = getSectionAgeRange(units1);\n    sections0 = [\n      {\n        section_id: 0,\n        /**\n         * If ages limits are directly specified, use them to define the section bounds.\n         * */\n        t_pos: t_unit_pos,\n        b_pos: b_unit_pos,\n        t_age: t_unit_age,\n        b_age: b_unit_age,\n        units: units1,\n      },\n    ];\n  } else if (axisType == ColumnAxisType.AGE) {\n    sections0 = groupUnitsIntoSectionsBySectionID(units1, axisType);\n  } else {\n    sections0 = groupUnitsIntoSectionsByOverlap(units1, axisType);\n  }\n\n  // Limit sections to the range specified by t_age/b_age or t_pos/b_pos global options\n  for (let section of sections0) {\n    if (axisType == ColumnAxisType.AGE) {\n      section.t_age = Math.max(section.t_age, t_age ?? -Infinity);\n      section.b_age = Math.min(section.b_age, b_age ?? 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package/dist/prepare-units/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sources":["../../src/prepare-units/index.ts"],"sourcesContent":["import {\n  getSectionAgeRange,\n  getSectionPosRange,\n  groupUnitsIntoSectionsByOverlap,\n  groupUnitsIntoSectionsBySectionID,\n  mergeOverlappingSections,\n  preprocessSectionUnit,\n  preprocessUnits,\n} from \"./helpers\";\nimport { ColumnAxisType } from \"@macrostrat/column-components\";\nimport { useMemo } from \"react\";\nimport { UnitLong } from \"@macrostrat/api-types\";\nimport {\n  collapseUnconformitiesByPixelHeight,\n  computeSectionHeights,\n  finalizeSectionHeights,\n  type CompositeColumnScale,\n} from \"./composite-scale\";\nimport {\n  agesOverlap,\n  MergeSectionsMode,\n  PrepareColumnOptions,\n  PreparedColumnData,\n  unitsOverlap,\n} from \"./utils\";\nimport { SectionInfo } from \"./types\";\n\nexport * from \"./utils\";\nexport * from \"./types\";\nexport { preprocessUnits };\nexport type { CompositeColumnScale };\n\nexport function usePreparedColumnUnits(\n  data: UnitLong[],\n  options: PrepareColumnOptions,\n): PreparedColumnData {\n  /** This function wraps and memoizes all preparation steps for converting\n   * an array of units from the /units route to a form ready for usage.\n   */\n  return useMemo(() => {\n    return prepareColumnUnits(data, options);\n  }, [data, ...Object.values(options)]);\n}\n\nexport function prepareColumnUnits(\n  units: UnitLong[],\n  options: PrepareColumnOptions,\n): PreparedColumnData {\n  /** Prepare units for rendering into Macrostrat columns */\n\n  let { t_age, b_age, t_pos, b_pos } = options;\n\n  const {\n    mergeSections = MergeSectionsMode.OVERLAPPING,\n    axisType,\n    unconformityHeight,\n    collapseSmallUnconformities = false,\n    hybridScale,\n    scale,\n  } = options;\n\n  let _totalHeight = null;\n\n  if (scale != null) {\n    // Set t_age and b_age based on scale domain if not already set\n    const domain = scale.domain();\n    if (axisType == ColumnAxisType.AGE) {\n      if (t_age == null) t_age = Math.min(...domain);\n      if (b_age == null) b_age = Math.max(...domain);\n      _totalHeight = Math.abs(scale(b_age) - scale(t_age));\n    } else {\n      if (t_pos == null) t_pos = Math.min(...domain);\n      if (b_pos == null) b_pos = Math.max(...domain);\n      _totalHeight = Math.abs(scale(b_pos) - scale(t_pos));\n    }\n  }\n\n  // Start by ensuring that ages and positions are numbers\n  // also set up some values for eODP-style columns\n  let units1 = units.map(preprocessSectionUnit);\n\n  /** Prototype filtering to age range */\n  units1 = units1.filter((d) => {\n    // Filter units by t_age and b_age, inclusive\n    if (axisType == ColumnAxisType.AGE) {\n      return agesOverlap(d, { t_age, b_age });\n    } else {\n      return unitsOverlap(d, { t_pos, b_pos } as any, axisType);\n    }\n  });\n\n  let mergeMode = mergeSections;\n  // if (axisType != ColumnAxisType.AGE) {\n  //   // For non-age columns, we always merge sections.\n  //   // This is because the \"groupUnitsIntoSections\" function is not well-defined\n  //   // for non-age columns.\n  //   mergeMode = MergeSectionsMode.ALL;\n  // }\n\n  let sections0: SectionInfo<UnitLong>[];\n  if (mergeMode == MergeSectionsMode.ALL) {\n    // For the \"merge sections\" mode, we need to create a single section\n    const [b_unit_pos, t_unit_pos] = getSectionPosRange(units1, axisType);\n    const [b_unit_age, t_unit_age] = getSectionAgeRange(units1);\n    sections0 = [\n      {\n        section_id: 0,\n        /**\n         * If ages limits are directly specified, use them to define the section bounds.\n         * */\n        t_pos: t_unit_pos,\n        b_pos: b_unit_pos,\n        t_age: t_unit_age,\n        b_age: b_unit_age,\n        units: units1,\n      },\n    ];\n  } else if (axisType == ColumnAxisType.AGE) {\n    sections0 = groupUnitsIntoSectionsBySectionID(units1, axisType);\n  } else {\n    sections0 = groupUnitsIntoSectionsByOverlap(units1, axisType);\n  }\n\n  // Limit sections to the range specified by t_age/b_age or t_pos/b_pos global options\n  for (let section of sections0) {\n    if (axisType == ColumnAxisType.AGE) {\n      section.t_age = Math.max(section.t_age, t_age ?? -Infinity);\n      section.b_age = Math.min(section.b_age, b_age ?? 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