@macrostrat/column-views 3.12.1 → 3.12.2

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  mergeAgeRanges,\n  MergeMode,\n} from \"@macrostrat/stratigraphy-utils\";\nimport type { ExtUnit, SectionInfo, StratigraphicPackage } from \"./types\";\n\nconst dt = 0.001;\n\nexport type UnitWithLayoutParameters<T extends BaseUnit> = T & {\n  layout: UnitLayoutData<T>;\n};\n\nexport type UnitWithLayoutHints<T extends BaseUnit> = T & {\n  layoutHints?: UnitLayoutHints;\n};\n\ninterface UnitLayoutInfo {\n  column: number;\n  nColumns: number;\n}\n\ntype UnitLayoutHints = Partial<UnitLayoutInfo>;\n\ntype UnitLayoutData<T extends BaseUnit> = UnitLayoutInfo & {\n  totalColumns: number;\n  unitGroup: UnitGroup<T>;\n};\n\nclass UnitGroup<T extends BaseUnit> implements StratigraphicPackage {\n  units: T[];\n  axisType: ColumnAxisType;\n\n  constructor(units: T[], axisType: ColumnAxisType = ColumnAxisType.AGE) {\n    this.units = units;\n    this.axisType = axisType;\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(): UnitWithLayoutParameters<T>[] {\n    return assignColumnsToUnitsWithinOverlappingGroup(this);\n  }\n}\n\nfunction groupUnitsByMutualOverlap<T extends BaseUnit>(\n  units: T[],\n  tolerance: number = dt,\n  axisType: ColumnAxisType = ColumnAxisType.AGE,\n): UnitGroup<T>[] {\n  /** Group units within a section that have mutual overlap. */\n\n  const sections = groupUnitsIntoSectionsByOverlap(units, axisType, tolerance);\n\n  return sections.map((d) => {\n    return new UnitGroup(d.units, axisType);\n  });\n}\n\nconst sortByAge = createUnitSorter(ColumnAxisType.AGE);\n\nfunction assignColumnsToUnitsWithinOverlappingGroup<T extends BaseUnit>(\n  group: UnitGroup<UnitWithLayoutHints<T>>,\n): UnitWithLayoutParameters<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(createUnitSorter(group.axisType));\n\n  const columns: T[][] = [];\n\n  let nColumns = 1;\n\n  for (const unit of sortedUnits) {\n    let startIndex = 0;\n    let endIndex = 0;\n    // Find a column that is not already occupied by an overlapping unit\n    const colHint = unit.layoutHints?.column;\n    if (colHint != null) {\n      columns[colHint] ??= [];\n      columns[colHint].push(unit);\n      continue;\n    }\n    let didAddToExistingColumn = false;\n\n    for (const column of columns) {\n      const lastUnit = column[column.length - 1];\n      if (!unitsOverlap(unit, lastUnit, group.axisType, 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: UnitWithLayoutParameters<T>[] = columns.flatMap(\n    (column, columnIndex) =>\n      column.map((unit) => {\n        return {\n          ...unit,\n          layout: {\n            column: columnIndex,\n            nColumns: 1,\n            totalColumns: 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, axisType);\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\n  const initialSections: WorkingSection[] = units.map((unit) => {\n    return {\n      units: [unit],\n      heightRange: getUnitHeightRange(unit, axisType),\n    };\n  });\n\n  const isOverlapping = (a: WorkingSection, b: WorkingSection) => {\n    const res = compareAgeRanges(a.heightRange, b.heightRange, tolerance);\n    return res !== AgeRangeRelationship.Disjoint;\n  };\n\n  const mergeSections = (a: WorkingSection, b: WorkingSection) => {\n    return {\n      units: [...a.units, ...b.units],\n      heightRange: mergeAgeRanges(\n        [a.heightRange, b.heightRange],\n        MergeMode.Outer,\n      ),\n    };\n  };\n\n  // Merge overlapping sections progressively until no more merges are possible\n  let finalSectionList = initialSections;\n\n  while (true) {\n    let merged = false;\n    const nextSections: WorkingSection[] = [];\n\n    for (const section of finalSectionList) {\n      if (nextSections.length === 0) {\n        nextSections.push(section);\n      } else {\n        const lastSection = nextSections[nextSections.length - 1];\n        if (isOverlapping(section, lastSection)) {\n          // Merge with the last section\n          nextSections[nextSections.length - 1] = mergeSections(\n            lastSection,\n            section,\n          );\n          merged = true;\n        } else {\n          nextSections.push(section);\n        }\n      }\n    }\n\n    finalSectionList = nextSections;\n\n    // Stop when no more merges occurred in this pass\n    if (!merged) {\n      break;\n    }\n  }\n\n  return finalSectionList.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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1];\n      if (!unitsOverlap(unit, lastUnit, group.axisType, 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: UnitWithLayoutParameters<T>[] = columns.flatMap(\n    (column, columnIndex) =>\n      column.map((unit) => {\n        return {\n          ...unit,\n          layout: {\n            column: columnIndex,\n            nColumns: 1,\n            totalColumns: 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, axisType);\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\n  const initialSections: WorkingSection[] = units.map((unit) => {\n    return {\n      units: [unit],\n      heightRange: getUnitHeightRange(unit, axisType),\n    };\n  });\n\n  const isOverlapping = (a: WorkingSection, b: WorkingSection) => {\n    const res = compareAgeRanges(a.heightRange, b.heightRange, tolerance);\n    return res !== AgeRangeRelationship.Disjoint;\n  };\n\n  const mergeSections = (a: WorkingSection, b: WorkingSection) => {\n    return {\n      units: [...a.units, ...b.units],\n      heightRange: mergeAgeRanges(\n        [a.heightRange, b.heightRange],\n        MergeMode.Outer,\n      ),\n    };\n  };\n\n  // Merge overlapping sections progressively until no more merges are possible\n  let finalSectionList = initialSections;\n\n  while (true) {\n    let merged = false;\n    const nextSections: WorkingSection[] = [];\n\n    for (const section of finalSectionList) {\n      if (nextSections.length === 0) {\n        nextSections.push(section);\n      } else {\n        const lastSection = nextSections[nextSections.length - 1];\n        if (isOverlapping(section, lastSection)) {\n          // Merge with the last section\n          nextSections[nextSections.length - 1] = mergeSections(\n            lastSection,\n            section,\n          );\n          merged = true;\n        } else {\n          nextSections.push(section);\n        }\n      }\n    }\n\n    finalSectionList = nextSections;\n\n    // Stop when no more merges occurred in this pass\n    if (!merged) {\n      break;\n    }\n  }\n\n  const s1 = finalSectionList.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  return sortUnits(s1, axisType);\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\nfunction forEachSection(fn, sections, ...args) {\n  return sections.map((section) => {\n    return {\n      ...section,\n      units: fn(section.units, ...args),\n    };\n  });\n}\n\nfunction sortUnits(units: BaseUnit[], axisType: ColumnAxisType) {\n  return units.sort((a, b) => {\n    if (\n      axisType === ColumnAxisType.HEIGHT &&\n      b.t_pos !== undefined &&\n      a.t_pos !== undefined\n    ) {\n      return b.t_pos - 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Here, we merge overlapping\n   * sections into a single section to correctly render gap-bound packages.\n   */\n  const [firstSection, ...rest] = sections;\n  const newSections = [firstSection];\n  for (const section of rest) {\n    const lastSection = newSections[newSections.length - 1];\n    if (\n      lastSection.b_age < section.t_age ||\n      lastSection.t_age > section.b_age\n    ) {\n      // No overlap, add the section as normal\n      newSections.push(section);\n      continue;\n    }\n\n    // Overlap, merge the sections\n    lastSection.section_id = [\n      ...ensureArray(lastSection.section_id),\n      ...ensureArray(section.section_id),\n    ];\n    lastSection.units.push(...section.units);\n    lastSection.b_age = Math.max(lastSection.b_age, section.b_age);\n    lastSection.t_age = Math.min(lastSection.t_age, section.t_age);\n  }\n  return newSections;\n}\n\nexport function preprocessSectionUnit(unit: UnitLong): UnitLong {\n  /** Preprocess a single unit for a 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package/dist/prepare-units/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  UnitWithLayoutHints,\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  padWindowByPixels,\n  resolveWindowScales,\n  trimSectionsToWindow,\n  type CompositeColumnScale,\n} from \"./composite-scale\";\nimport {\n  agesOverlap,\n  MergeSectionsMode,\n  PrepareColumnOptions,\n  PreparedColumnData,\n  unitsOverlap,\n} from \"./utils\";\nimport { type ColumnHeightScaleOptions, SectionInfo } from \"./types\";\n\nexport * from \"./utils\";\nexport * from \"./types\";\nexport * from \"./density\";\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: UnitWithLayoutHints<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    windowPadding = 0,\n  } = options;\n\n  let _totalHeight: number | null = 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  /** Age columns lay every section out at its full extent and clip to the\n   * window at the end (see below), so that a section abutting the window is\n   * sized by its own content rather than by the sliver that survives the clip.\n   * Hybrid and externally-supplied scales build their own mapping and can't be\n   * re-derived that way, so they keep the original clip-then-lay-out path. */\n  const clipBeforeLayout =\n    axisType != ColumnAxisType.AGE || hybridScale != null || scale != null;\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  /** A bound that isn't set doesn't bound anything. 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+{"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  UnitWithLayoutHints,\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  padWindowByPixels,\n  resolveWindowScales,\n  trimSectionsToWindow,\n  type CompositeColumnScale,\n} from \"./composite-scale\";\nimport {\n  agesOverlap,\n  MergeSectionsMode,\n  PrepareColumnOptions,\n  PreparedColumnData,\n  unitsOverlap,\n} from \"./utils\";\nimport { type ColumnHeightScaleOptions, SectionInfo } from \"./types\";\n\nexport * from \"./utils\";\nexport * from \"./types\";\nexport * from \"./density\";\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: UnitWithLayoutHints<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    windowPadding = 0,\n  } = options;\n\n  let _totalHeight: number | null = 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  /** Age columns lay every section out at its full extent and clip to the\n   * window at the end (see below), so that a section abutting the window is\n   * sized by its own content rather than by the sliver that survives the clip.\n   * Hybrid and externally-supplied scales build their own mapping and can't be\n   * re-derived that way, so they keep the original clip-then-lay-out path. */\n  const clipBeforeLayout =\n    axisType != ColumnAxisType.AGE || hybridScale != null || scale != null;\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  /** A bound that isn't set doesn't bound anything. Passing `null` for one is\n   * the ordinary way to say \"no window\", and comparing against it as though\n   * it were an age would throw every unit out. */\n  const window = {\n    t_age: t_age ?? -Infinity,\n    b_age: b_age ?? Infinity,\n    t_pos: t_pos ?? -Infinity,\n    b_pos: b_pos ?? Infinity,\n  };\n  const isWindowed =\n    axisType == ColumnAxisType.AGE\n      ? t_age != null || b_age != null\n      : t_pos != null || b_pos != null;\n\n  if (clipBeforeLayout && isWindowed) {\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, window);\n      } else {\n        return unitsOverlap(d, window as any, axisType);\n      }\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 clipBeforeLayout ? 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 ?? Infinity);\n    } else if (axisType == ColumnAxisType.DEPTH) {\n      section.t_pos = Math.max(section.t_pos, t_pos ?? -Infinity);\n      section.b_pos = Math.min(section.b_pos, b_pos ?? Infinity);\n    } else if (axisType == ColumnAxisType.HEIGHT) {\n      section.t_pos = Math.max(section.t_pos, t_pos ?? -Infinity);\n      section.b_pos = Math.min(section.b_pos, b_pos ?? Infinity);\n    }\n  }\n\n  /** Merging overlapping sections really only makes sense for age/height/depth\n   * columns. Ordinal columns are numbered by section so merging them\n   * results in collisions.\n   */\n  let sections = sections0;\n  if (\n    mergeSections == MergeSectionsMode.OVERLAPPING &&\n    axisType == ColumnAxisType.AGE\n  ) {\n    sections = mergeOverlappingSections(sections);\n  }\n  // Filter out undefined sections just in case\n  sections = sections.filter((d) => d != null);\n\n  // SCALES\n\n  /** The window we've been asked to render. Unit density is derived from what\n   * it shows (see `findAverageUnitHeight`), so it has to be known before any\n   * section is laid out — but nothing is *clipped* to it until the very end.\n   */\n  const focalWindow: [number, number] | null = clipBeforeLayout\n    ? null\n    : [b_age ?? Infinity, t_age ?? -Infinity];\n\n  const layoutOptions = { ...options, visibleWindow: focalWindow };\n\n  /* Compute pixel scales etc. for sections\n   * We need to do this now to determine which unconformities\n   * are small enough to collapse.\n   */\n  let sectionsWithScales = computeSectionHeights(sections, layoutOptions);\n\n  if (collapseSmallUnconformities && hybridScale == null) {\n    // Collapse small unconformities in pixel height space\n    // TODO: this doesn't seem to work properly for non-age columns?\n    let threshold = unconformityHeight ?? 30;\n    if (typeof collapseSmallUnconformities == \"number\") {\n      threshold = collapseSmallUnconformities;\n    }\n\n    sectionsWithScales = collapseUnconformitiesByPixelHeight(\n      sectionsWithScales,\n      threshold,\n      layoutOptions,\n    );\n  }\n\n  /** Now that every section is laid out at full extent — with its own density\n   * and `minSectionHeight` already settled — apply the rendered window. Padding\n   * is spent here, against real pixel heights, so `windowPadding` px of an\n   * abutting section is exactly that many pixels.\n   */\n  if (focalWindow != null && (t_age != null || b_age != null)) {\n    // Resolve final densities first (a section the window cuts short is\n    // stretched to `minSectionHeight`), then spend the padding budget against\n    // them, so a margin is the pixels asked for rather than those pixels times\n    // whatever stretch its neighbor happened to need.\n    const floor =\n      layoutOptions.minSectionHeight ?? layoutOptions.targetUnitHeight ?? 0;\n    const scales = resolveWindowScales(sectionsWithScales, focalWindow, floor);\n    const natural = (section) =>\n      scales.get(section) ?? section.scaleInfo.pixelScale;\n\n    const scaleFor = natural;\n\n    const window =\n      windowPadding > 0\n        ? padWindowByPixels(\n            sectionsWithScales,\n            focalWindow,\n            windowPadding,\n            scaleFor,\n          )\n        : focalWindow;\n\n    sectionsWithScales = trimSectionsToWindow(\n      sectionsWithScales,\n      window,\n      scaleFor,\n    );\n  }\n\n  /** Prepare section scale information using groups.\n   * Total height is computed from section scales.\n   * */\n  let { totalHeight, sections: sections2 } = finalizeSectionHeights(\n    sectionsWithScales,\n    unconformityHeight,\n  );\n\n  /** For each section, find units that are overlapping.\n   * We do this after merging sections so that we can\n   * handle cases where there are overlapping units across sections\n   * */\n  const sectionsOut = sections2.map((section) => {\n    return {\n      ...section,\n      units: preprocessUnits(section, axisType),\n    };\n  });\n\n  /** Reconstitute the units so that they are sorted by section and properly enhanced.\n   * This is mostly important so that unit keyboard navigation\n   * predictably selects adjacent units.\n   */\n  const units2 = sectionsOut.reduce((acc, group) => {\n    const { units } = group;\n    for (const unit of units) {\n      acc.push(unit);\n    }\n    return acc;\n  }, []);\n\n  return {\n    units: units2,\n    totalHeight: _totalHeight ?? 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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  UnitWithLayoutHints,\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  padWindowByPixels,\n  resolveWindowScales,\n  trimSectionsToWindow,\n  type CompositeColumnScale,\n} from \"./composite-scale\";\nimport {\n  agesOverlap,\n  MergeSectionsMode,\n  PrepareColumnOptions,\n  PreparedColumnData,\n  unitsOverlap,\n} from \"./utils\";\nimport { type ColumnHeightScaleOptions, SectionInfo } from \"./types\";\n\nexport * from \"./utils\";\nexport * from \"./types\";\nexport * from \"./density\";\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: UnitWithLayoutHints<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    windowPadding = 0,\n  } = options;\n\n  let _totalHeight: number | null = 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  /** Age columns lay every section out at its full extent and clip to the\n   * window at the end (see below), so that a section abutting the window is\n   * sized by its own content rather than by the sliver that survives the clip.\n   * Hybrid and externally-supplied scales build their own mapping and can't be\n   * re-derived that way, so they keep the original clip-then-lay-out path. */\n  const clipBeforeLayout =\n    axisType != ColumnAxisType.AGE || hybridScale != null || scale != null;\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  /** A bound that isn't set doesn't bound anything. Passing `null` for one is\n   * the ordinary way to say \"no window\", and comparing against it as though\n   * it were an age would throw every unit out. */\n  const window = {\n    t_age: t_age ?? -Infinity,\n    b_age: b_age ?? Infinity,\n    t_pos: t_pos ?? -Infinity,\n    b_pos: b_pos ?? Infinity,\n  };\n  const isWindowed =\n    axisType == ColumnAxisType.AGE\n      ? t_age != null || b_age != null\n      : t_pos != null || b_pos != null;\n\n  if (clipBeforeLayout && isWindowed) {\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, window);\n      } else {\n        return unitsOverlap(d, window as any, axisType);\n      }\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 clipBeforeLayout ? 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 ?? Infinity);\n    } else if (axisType == ColumnAxisType.DEPTH) {\n      section.t_pos = Math.max(section.t_pos, t_pos ?? -Infinity);\n      section.b_pos = Math.min(section.b_pos, b_pos ?? Infinity);\n    } else if (axisType == ColumnAxisType.HEIGHT) {\n      section.t_pos = Math.max(section.t_pos, t_pos ?? -Infinity);\n      section.b_pos = Math.min(section.b_pos, b_pos ?? Infinity);\n    }\n  }\n\n  /** Merging overlapping sections really only makes sense for age/height/depth\n   * columns. Ordinal columns are numbered by section so merging them\n   * results in collisions.\n   */\n  let sections = sections0;\n  if (\n    mergeSections == MergeSectionsMode.OVERLAPPING &&\n    axisType == ColumnAxisType.AGE\n  ) {\n    sections = mergeOverlappingSections(sections);\n  }\n  // Filter out undefined sections just in case\n  sections = sections.filter((d) => d != null);\n\n  // SCALES\n\n  /** The window we've been asked to render. Unit density is derived from what\n   * it shows (see `findAverageUnitHeight`), so it has to be known before any\n   * section is laid out — but nothing is *clipped* to it until the very end.\n   */\n  const focalWindow: [number, number] | null = clipBeforeLayout\n    ? null\n    : [b_age ?? Infinity, t_age ?? -Infinity];\n\n  const layoutOptions = { ...options, visibleWindow: focalWindow };\n\n  /* Compute pixel scales etc. for sections\n   * We need to do this now to determine which unconformities\n   * are small enough to collapse.\n   */\n  let sectionsWithScales = computeSectionHeights(sections, layoutOptions);\n\n  if (collapseSmallUnconformities && hybridScale == null) {\n    // Collapse small unconformities in pixel height space\n    // TODO: this doesn't seem to work properly for non-age columns?\n    let threshold = unconformityHeight ?? 30;\n    if (typeof collapseSmallUnconformities == \"number\") {\n      threshold = collapseSmallUnconformities;\n    }\n\n    sectionsWithScales = collapseUnconformitiesByPixelHeight(\n      sectionsWithScales,\n      threshold,\n      layoutOptions,\n    );\n  }\n\n  /** Now that every section is laid out at full extent — with its own density\n   * and `minSectionHeight` already settled — apply the rendered window. Padding\n   * is spent here, against real pixel heights, so `windowPadding` px of an\n   * abutting section is exactly that many pixels.\n   */\n  if (focalWindow != null && (t_age != null || b_age != null)) {\n    // Resolve final densities first (a section the window cuts short is\n    // stretched to `minSectionHeight`), then spend the padding budget against\n    // them, so a margin is the pixels asked for rather than those pixels times\n    // whatever stretch its neighbor happened to need.\n    const floor =\n      layoutOptions.minSectionHeight ?? layoutOptions.targetUnitHeight ?? 0;\n    const scales = resolveWindowScales(sectionsWithScales, focalWindow, floor);\n    const natural = (section) =>\n      scales.get(section) ?? section.scaleInfo.pixelScale;\n\n\n    const scaleFor = natural;\n\n    const window =\n      windowPadding > 0\n        ? padWindowByPixels(\n            sectionsWithScales,\n            focalWindow,\n            windowPadding,\n            scaleFor,\n          )\n        : focalWindow;\n\n    sectionsWithScales = trimSectionsToWindow(\n      sectionsWithScales,\n      window,\n      scaleFor,\n    );\n  }\n\n  /** Prepare section scale information using groups.\n   * Total height is computed from section scales.\n   * */\n  let { totalHeight, sections: sections2 } = finalizeSectionHeights(\n    sectionsWithScales,\n    unconformityHeight,\n  );\n\n  /** For each section, find units that are overlapping.\n   * We do this after merging sections so that we can\n   * handle cases where there are overlapping units across sections\n   * */\n  const sectionsOut = sections2.map((section) => {\n    return {\n      ...section,\n      units: preprocessUnits(section, axisType),\n    };\n  });\n\n  /** Reconstitute the units so that they are sorted by section and properly enhanced.\n   * This is mostly important so that unit keyboard navigation\n   * predictably selects adjacent units.\n   */\n  const units2 = sectionsOut.reduce((acc, group) => {\n    const { units } = group;\n    for (const unit of units) {\n      acc.push(unit);\n    }\n    return acc;\n  }, []);\n\n  return {\n    units: units2,\n    totalHeight: _totalHeight ?? 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+{"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  UnitWithLayoutHints,\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  padWindowByPixels,\n  resolveWindowScales,\n  trimSectionsToWindow,\n  type CompositeColumnScale,\n} from \"./composite-scale\";\nimport {\n  agesOverlap,\n  MergeSectionsMode,\n  PrepareColumnOptions,\n  PreparedColumnData,\n  unitsOverlap,\n} from \"./utils\";\nimport { type ColumnHeightScaleOptions, SectionInfo } from \"./types\";\n\nexport * from \"./utils\";\nexport * from \"./types\";\nexport * from \"./density\";\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: UnitWithLayoutHints<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    windowPadding = 0,\n  } = options;\n\n  let _totalHeight: number | null = 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  /** Age columns lay every section out at its full extent and clip to the\n   * window at the end (see below), so that a section abutting the window is\n   * sized by its own content rather than by the sliver that survives the clip.\n   * Hybrid and externally-supplied scales build their own mapping and can't be\n   * re-derived that way, so they keep the original clip-then-lay-out path. */\n  const clipBeforeLayout =\n    axisType != ColumnAxisType.AGE || hybridScale != null || scale != null;\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  /** A bound that isn't set doesn't bound anything. Passing `null` for one is\n   * the ordinary way to say \"no window\", and comparing against it as though\n   * it were an age would throw every unit out. */\n  const window = {\n    t_age: t_age ?? -Infinity,\n    b_age: b_age ?? Infinity,\n    t_pos: t_pos ?? -Infinity,\n    b_pos: b_pos ?? Infinity,\n  };\n  const isWindowed =\n    axisType == ColumnAxisType.AGE\n      ? t_age != null || b_age != null\n      : t_pos != null || b_pos != null;\n\n  if (clipBeforeLayout && isWindowed) {\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, window);\n      } else {\n        return unitsOverlap(d, window as any, axisType);\n      }\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 clipBeforeLayout ? 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 ?? Infinity);\n    } else if (axisType == ColumnAxisType.DEPTH) {\n      section.t_pos = Math.max(section.t_pos, t_pos ?? -Infinity);\n      section.b_pos = Math.min(section.b_pos, b_pos ?? Infinity);\n    } else if (axisType == ColumnAxisType.HEIGHT) {\n      section.t_pos = Math.max(section.t_pos, t_pos ?? -Infinity);\n      section.b_pos = Math.min(section.b_pos, b_pos ?? Infinity);\n    }\n  }\n\n  /** Merging overlapping sections really only makes sense for age/height/depth\n   * columns. Ordinal columns are numbered by section so merging them\n   * results in collisions.\n   */\n  let sections = sections0;\n  if (\n    mergeSections == MergeSectionsMode.OVERLAPPING &&\n    axisType == ColumnAxisType.AGE\n  ) {\n    sections = mergeOverlappingSections(sections);\n  }\n  // Filter out undefined sections just in case\n  sections = sections.filter((d) => d != null);\n\n  // SCALES\n\n  /** The window we've been asked to render. Unit density is derived from what\n   * it shows (see `findAverageUnitHeight`), so it has to be known before any\n   * section is laid out — but nothing is *clipped* to it until the very end.\n   */\n  const focalWindow: [number, number] | null = clipBeforeLayout\n    ? null\n    : [b_age ?? Infinity, t_age ?? -Infinity];\n\n  const layoutOptions = { ...options, visibleWindow: focalWindow };\n\n  /* Compute pixel scales etc. for sections\n   * We need to do this now to determine which unconformities\n   * are small enough to collapse.\n   */\n  let sectionsWithScales = computeSectionHeights(sections, layoutOptions);\n\n  if (collapseSmallUnconformities && hybridScale == null) {\n    // Collapse small unconformities in pixel height space\n    // TODO: this doesn't seem to work properly for non-age columns?\n    let threshold = unconformityHeight ?? 30;\n    if (typeof collapseSmallUnconformities == \"number\") {\n      threshold = collapseSmallUnconformities;\n    }\n\n    sectionsWithScales = collapseUnconformitiesByPixelHeight(\n      sectionsWithScales,\n      threshold,\n      layoutOptions,\n    );\n  }\n\n  /** Now that every section is laid out at full extent — with its own density\n   * and `minSectionHeight` already settled — apply the rendered window. Padding\n   * is spent here, against real pixel heights, so `windowPadding` px of an\n   * abutting section is exactly that many pixels.\n   */\n  if (focalWindow != null && (t_age != null || b_age != null)) {\n    // Resolve final densities first (a section the window cuts short is\n    // stretched to `minSectionHeight`), then spend the padding budget against\n    // them, so a margin is the pixels asked for rather than those pixels times\n    // whatever stretch its neighbor happened to need.\n    const floor =\n      layoutOptions.minSectionHeight ?? layoutOptions.targetUnitHeight ?? 0;\n    const scales = resolveWindowScales(sectionsWithScales, focalWindow, floor);\n    const natural = (section) =>\n      scales.get(section) ?? section.scaleInfo.pixelScale;\n\n    const scaleFor = natural;\n\n    const window =\n      windowPadding > 0\n        ? padWindowByPixels(\n            sectionsWithScales,\n            focalWindow,\n            windowPadding,\n            scaleFor,\n          )\n        : focalWindow;\n\n    sectionsWithScales = trimSectionsToWindow(\n      sectionsWithScales,\n      window,\n      scaleFor,\n    );\n  }\n\n  /** Prepare section scale information using groups.\n   * Total height is computed from section scales.\n   * */\n  let { totalHeight, sections: sections2 } = finalizeSectionHeights(\n    sectionsWithScales,\n    unconformityHeight,\n  );\n\n  /** For each section, find units that are overlapping.\n   * We do this after merging sections so that we can\n   * handle cases where there are overlapping units across sections\n   * */\n  const sectionsOut = sections2.map((section) => {\n    return {\n      ...section,\n      units: preprocessUnits(section, axisType),\n    };\n  });\n\n  /** Reconstitute the units so that they are sorted by section and properly enhanced.\n   * This is mostly important so that unit keyboard navigation\n   * predictably selects adjacent units.\n   */\n  const units2 = sectionsOut.reduce((acc, group) => {\n    const { units } = group;\n    for (const unit of units) {\n      acc.push(unit);\n    }\n    return acc;\n  }, []);\n\n  return {\n    units: units2,\n    totalHeight: _totalHeight ?? 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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@macrostrat/column-views",
-  "version": "3.12.1",
+  "version": "3.12.2",
   "description": "Data views for Macrostrat stratigraphic columns",
   "repository": {
     "type": "git",
@@ -50,7 +50,7 @@
     "@macrostrat/color-utils": "^1.2.2",
     "@macrostrat/column-components": "^2.2.0",
     "@macrostrat/data-components": "^1.7.0",
-    "@macrostrat/data-provider": "^1.4.0",
+    "@macrostrat/data-provider": "^1.4.1",
     "@macrostrat/hyper": "^3.1.1",
     "@macrostrat/map-views": "^1.1.1",
     "@macrostrat/scoped-store": "^1.1.0",

package/src/column.ts

@@ -169,6 +169,22 @@ export function Column(props: ColumnProps) {
     _axisType = ColumnAxisType.AGE;
   }
 
+  let _sectionOptions = sectionOptions;
+  if (_sectionOptions == undefined) {
+    // Build our own section options function based on targetUnitHeight
+    _sectionOptions = (ctx) => {
+      /** Scale targetUnitHeight by the number of units, so that a section with just a few units
+       * is drawn taller than a section with many units.
+       */
+      const n = ctx.units.length;
+      const expansionFactor = 8 / Math.min(Math.max(n, 1), 8);
+
+      return {
+        targetUnitHeight: targetUnitHeight * expansionFactor,
+      };
+    };
+  }
+
   const { sections, units, totalHeight } = usePreparedColumnUnits(rawUnits, {
     axisType: _axisType,
     t_age,
@@ -177,7 +193,7 @@ export function Column(props: ColumnProps) {
     b_pos,
     mergeSections,
     targetUnitHeight,
-    sectionOptions,
+    sectionOptions: _sectionOptions,
     unconformityHeight,
     pixelScale,
     pixelsPerMyr,

package/src/prepare-units/composite-scale.ts

@@ -4,7 +4,6 @@ import { ScaleContinuousNumeric, scaleLinear } from "d3-scale";
 import { UnitLong } from "@macrostrat/api-types";
 import { buildHybridScale } from "./dynamic-scales";
 import { sectionDensity } from "./density";
-import { ExtUnit, HybridScaleType, SectionInfo } from "./types";
 import type {
   ColumnScaleOptions,
   CompositeColumnData,
@@ -14,6 +13,8 @@ import type {
   PackageScaleLayoutData,
   SectionScaleOptions,
 } from "./types";
+import { ExtUnit, HybridScaleType, SectionInfo } from "./types";
+import { mergeAgeRanges, MergeMode } from "@macrostrat/stratigraphy-utils";
 
 // Composite scale information augmented with units in each package
 
@@ -144,7 +145,13 @@ function buildSectionScale<T extends UnitLong>(
   } = opts;
   const domain = opts.domain ?? findSectionHeightRange(data, axisType);
 
-  const dAge = Math.abs(domain[0] - domain[1]);
+  const dAge = dx(domain);
+  let visibleExtent = dAge; // full section is visible
+  if (visibleWindow != null) {
+    visibleExtent = dx(
+      mergeAgeRanges([domain, visibleWindow], MergeMode.Inner),
+    );
+  }
 
   let _pixelScale: any = opts.pixelScale;
   let pixelHeight: number;
@@ -177,6 +184,7 @@ function buildSectionScale<T extends UnitLong>(
      * is what it's for, and never a sliver the window happens to cut. */
     _pixelScale = sectionDensity(opts)({
       extent: dAge,
+      visibleExtent,
       unitExtents: visibleUnitExtents(data, axisType, visibleWindow),
       units: data,
       sectionID,
@@ -194,6 +202,10 @@ function buildSectionScale<T extends UnitLong>(
   );
 }
 
+function dx(range: [number, number]) {
+  return Math.abs(range[0] - range[1]);
+}
+
 /**
  * The density each section will actually render at once the window is applied.
  *
@@ -275,9 +287,12 @@ function spendOutward<T extends UnitLong>(
   // Sections ordered outward from the edge, keeping only what lies beyond it.
   const beyond = sections
     .filter(
-      (s) => direction * (s.b_age - edge) > 0 || direction * (s.t_age - edge) > 0,
+      (s) =>
+        direction * (s.b_age - edge) > 0 || direction * (s.t_age - edge) > 0,
     )
-    .sort((a, b) => direction * (nearEdge(a, direction) - nearEdge(b, direction)));
+    .sort(
+      (a, b) => direction * (nearEdge(a, direction) - nearEdge(b, direction)),
+    );
 
   let bound = edge;
   let budget = padding;
@@ -290,7 +305,8 @@ function spendOutward<T extends UnitLong>(
       direction > 0
         ? Math.max(section.t_age, bound)
         : Math.min(section.b_age, bound);
-    const available = direction > 0 ? section.b_age - from : from - section.t_age;
+    const available =
+      direction > 0 ? section.b_age - from : from - section.t_age;
     if (available <= 0) continue;
 
     const cost = available * pixelScale;
@@ -451,10 +467,7 @@ function visibleUnitExtents(
         const [b_pos, t_pos] = getUnitHeightRange(d, axisType);
         if (!clip) return Math.abs(b_pos - t_pos);
         const [b_win, t_win] = visibleWindow;
-        return Math.max(
-          0,
-          Math.min(b_pos, b_win) - Math.max(t_pos, t_win),
-        );
+        return Math.max(0, Math.min(b_pos, b_win) - Math.max(t_pos, t_win));
       })
       .filter((d) => d > 0);
 

package/src/prepare-units/density.ts

@@ -12,6 +12,8 @@ import type { UnitLong } from "@macrostrat/api-types";
 export interface SectionDensityContext {
   /** The section's extent, in axis units */
   extent: number;
+  /** The section's shown extent, in axis units */
+  visibleExtent: number;
   /** Extents of the units the render window actually shows, each clipped to
    * it. Measuring what's on screen is what makes a unit-height rule mean the
    * same thing at every zoom depth. */
@@ -28,23 +30,14 @@ export type SectionDensity = (ctx: SectionDensityContext) => number;
 
 export type SectionDensityLike = number | SectionDensity;
 
-/** Room for a typical unit on screen: `px` tall, whatever its duration.
- *
- * "Typical" is the median of the visible extents, which is the only summary
- * that survives both tails. Unit durations are spread over orders of
- * magnitude: the arithmetic mean sits above any unit you would point at, so a
- * couple of long ones squeeze everything else below the target — and the
- * geometric mean fails the other way, since a single hair-thin unit (a
- * Holocene sliver beside a Pliocene terrace, say) drags the log-average down
- * and stretches the whole section to give that sliver its 20 pixels.
- */
-export function unitHeight(px: number): SectionDensity {
-  return (ctx) => px / typicalExtent(ctx.unitExtents);
+enum UnitHeightMode {
+  MEDIAN = "median",
+  MEAN = "mean",
 }
 
 /** Room for the section: `px` tall, whatever its extent. */
 export function sectionHeight(px: number): SectionDensity {
-  return (ctx) => px / ctx.extent;
+  return (ctx) => px / ctx.visibleExtent;
 }
 
 /** A density stated outright, in pixels per axis unit. */
@@ -75,15 +68,6 @@ export function resolveDensity(
   return rule(ctx);
 }
 
-function typicalExtent(extents: number[]): number {
-  const sorted = extents.filter((d) => d > 0).sort((a, b) => a - b);
-  if (sorted.length === 0) return NaN;
-  const mid = (sorted.length - 1) / 2;
-  const lower = Math.floor(mid);
-  const upper = Math.ceil(mid);
-  return (sorted[lower] + sorted[upper]) / 2;
-}
-
 /** Mirrors the default in `sectionDensity` */
 export const DEFAULT_TARGET_UNIT_HEIGHT = 20;
 /** Small sections often have a unit or two, and no room for axis labels */
@@ -131,8 +115,7 @@ export interface SectionSizeOptions {
  * holds. What it returns overrides the column-wide options for that section;
  * anything it leaves out keeps the column's value. */
 export type SectionOptionsLike =
-  | SectionSizeOptions
-  | ((ctx: SectionDensityContext) => SectionSizeOptions);
+  SectionSizeOptions | ((ctx: SectionDensityContext) => SectionSizeOptions);
 
 export interface SectionDensityOptions extends SectionSizeOptions {
   /** Sizing decided per section */
@@ -164,7 +147,7 @@ function densityRule(opts: SectionSizeOptions): SectionDensity {
   } = opts;
 
   const derived = atLeast(
-    unitHeight(targetUnitHeight),
+    unitHeight(targetUnitHeight, UnitHeightMode.MEAN),
     fixedDensity(minPixelScale),
     sectionHeight(minSectionHeight ?? targetUnitHeight ?? 0),
   );
@@ -182,6 +165,34 @@ function densityRule(opts: SectionSizeOptions): SectionDensity {
   };
 }
 
+/** Room for a typical unit on screen: `px` tall, whatever its duration.
+ *
+ * "Typical" is the median of the visible extents, which is the only summary
+ * that survives both tails. Unit durations are spread over orders of
+ * magnitude: the arithmetic mean sits above any unit you would point at, so a
+ * couple of long ones squeeze everything else below the target — and the
+ * geometric mean fails the other way, since a single hair-thin unit (a
+ * Holocene sliver beside a Pliocene terrace, say) drags the log-average down
+ * and stretches the whole section to give that sliver its 20 pixels.
+ */
+export function unitHeight(px: number, mode: UnitHeightMode): SectionDensity {
+  return (ctx) => px / typicalExtent(ctx.unitExtents, mode);
+}
+
+function typicalExtent(extents: number[], mode: UnitHeightMode): number {
+  /** The typical extent for a unit, the median of its extents. */
+  const filtered = extents.filter((d) => d > 0);
+  if (filtered.length === 0) return NaN;
+  if (mode === UnitHeightMode.MEAN) {
+    return filtered.reduce((sum, val) => sum + val, 0) / filtered.length;
+  }
+  const sorted = filtered.sort((a, b) => a - b);
+  const mid = (sorted.length - 1) / 2;
+  const lower = Math.floor(mid);
+  const upper = Math.ceil(mid);
+  return (sorted[lower] + sorted[upper]) / 2;
+}
+
 /** The density this axis was given, if any. The axis-specific spellings win
  * over the generic one, which is what lets both be held while the axis
  * changes. */

package/src/prepare-units/helpers.ts

@@ -282,7 +282,7 @@ export function groupUnitsIntoSectionsByOverlap<T extends BaseUnit>(
     }
   }
 
-  return finalSectionList.map((section, i) => {
+  const s1 = finalSectionList.map((section, i) => {
     const [b_age, t_age] = getSectionAgeRange(section.units);
     const [b_pos, t_pos] = getSectionPosRange(section.units, axisType);
     return {
@@ -295,6 +295,8 @@ export function groupUnitsIntoSectionsByOverlap<T extends BaseUnit>(
       units: section.units as T[],
     };
   });
+
+  return sortUnits(s1, axisType);
 }
 
 export function getSectionPosRange(
@@ -338,6 +340,38 @@ export function getSectionAgeRange(units: BaseUnit[]): [number, number] {
   return getSectionPosRange(units, ColumnAxisType.AGE);
 }
 
+function forEachSection(fn, sections, ...args) {
+  return sections.map((section) => {
+    return {
+      ...section,
+      units: fn(section.units, ...args),
+    };
+  });
+}
+
+function sortUnits(units: BaseUnit[], axisType: ColumnAxisType) {
+  return units.sort((a, b) => {
+    if (
+      axisType === ColumnAxisType.HEIGHT &&
+      b.t_pos !== undefined &&
+      a.t_pos !== undefined
+    ) {
+      return b.t_pos - a.t_pos;
+    }
+    if (
+      axisType === ColumnAxisType.DEPTH &&
+      b.t_pos !== undefined &&
+      a.t_pos !== undefined
+    ) {
+      return a.t_pos - b.t_pos;
+    }
+    if (axisType === ColumnAxisType.AGE) {
+      return a.t_age - b.t_age;
+    }
+    return 0;
+  });
+}
+
 export function mergeOverlappingSections<T extends UnitLong>(
   sections: SectionInfo<T>[],
 ): SectionInfo<T>[] {

package/src/prepare-units/index.ts

@@ -228,7 +228,6 @@ export function prepareColumnUnits(
     const natural = (section) =>
       scales.get(section) ?? section.scaleInfo.pixelScale;
 
-
     const scaleFor = natural;
 
     const window =