@macrostrat/column-views 3.3.5 → 3.4.1

package/dist/index.js

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

package/dist/index.js.map

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

package/dist/prepare-units/composite-scale.cjs

@@ -207,7 +207,6 @@ function createCompositeScale(sections, interpolateUnconformities = false) {
     for (const scale2 of scales) {
       const range = scale2.range();
       if (pixelHeight > Math.min(...range) && pixelHeight <= Math.max(...range)) {
-        console.log("Inverting scale at pixel height", pixelHeight);
         return scale2.invert(pixelHeight);
       }
     }

package/dist/prepare-units/composite-scale.cjs.map

@@ -1 +1 @@
-{"version":3,"file":"composite-scale.cjs","sources":["../../src/prepare-units/composite-scale.ts"],"sourcesContent":["import { ColumnAxisType } from \"@macrostrat/column-components\";\nimport { ensureArray, getUnitHeightRange } from \"./utils\";\nimport { ScaleContinuousNumeric, scaleLinear } from \"d3-scale\";\nimport { UnitLong } from \"@macrostrat/api-types\";\nimport { buildHybridScale } from \"./dynamic-scales\";\nimport { ExtUnit, HybridScaleType, SectionInfo } from \"./types\";\nimport type {\n  ColumnScaleOptions,\n  CompositeColumnData,\n  CompositeScaleData,\n  PackageLayoutData,\n  PackageScaleInfo,\n  PackageScaleLayoutData,\n  SectionScaleOptions,\n} from \"./types\";\n\n// Composite scale information augmented with units in each package\n\nexport function buildCompositeScaleInfo(\n  inputScales: PackageScaleInfo[],\n  unconformityHeight: number,\n): CompositeScaleData {\n  /** Finalize the heights of sections, including the heights of unconformities\n   * between them.\n   */\n\n  let totalHeight = unconformityHeight / 2;\n  let lastSectionTopHeight = 0;\n\n  const packages2: PackageScaleLayoutData[] = [];\n  for (const group of inputScales) {\n    const { domain, scale } = group;\n    const [b_age, t_age] = domain;\n    const key = `package-${b_age}-${t_age}`;\n\n    packages2.push({\n      ...createPackageScale(group, totalHeight),\n      key,\n      offset: totalHeight,\n      // Unconformity height above this particular section\n      paddingTop: totalHeight - lastSectionTopHeight,\n    });\n\n    const pixelHeight = Math.abs(scale(b_age) - scale(t_age));\n    lastSectionTopHeight = totalHeight + pixelHeight;\n    totalHeight = lastSectionTopHeight + unconformityHeight;\n  }\n  totalHeight += unconformityHeight / 2;\n  return {\n    totalHeight,\n    sections: packages2,\n  };\n}\n\nexport function finalizeSectionHeights<T extends UnitLong>(\n  sections: SectionInfoWithScale<T>[],\n  unconformityHeight: number,\n): CompositeColumnData<T> {\n  /** Finalize the heights of sections, including the heights of unconformities\n   * between them.\n   */\n\n  const sectionScales = sections.map((d) => d.scaleInfo);\n\n  const { totalHeight, sections: packages } = buildCompositeScaleInfo(\n    sectionScales,\n    unconformityHeight,\n  );\n\n  // This could perhaps be simplified.\n  const sections1: PackageLayoutData<T>[] = [];\n  for (const i in sections) {\n    const group = sections[i];\n    const scaleInfo = packages[i];\n    sections1.push({\n      ...group,\n      key: scaleInfo.key,\n      scaleInfo,\n    });\n  }\n  return {\n    totalHeight,\n    sections: sections1,\n  };\n}\n\nexport interface SectionInfoWithScale<\n  T extends UnitLong = ExtUnit,\n> extends SectionInfo<T> {\n  scaleInfo: PackageScaleInfo;\n}\n\nexport function computeSectionHeights<T extends UnitLong>(\n  sections: SectionInfo<T>[],\n  opts: ColumnScaleOptions,\n): SectionInfoWithScale<T>[] {\n  return sections.map((group) => {\n    return addScaleToSection<T>(group, opts);\n  });\n}\n\nfunction addScaleToSection<T extends UnitLong = ExtUnit>(\n  group: SectionInfo<T>,\n  opts: ColumnScaleOptions,\n): SectionInfoWithScale<T> {\n  const { t_age, b_age, t_pos, b_pos, units } = group;\n  let _range = null;\n  // if t_age and b_age are set for a group, use them to define the range...\n  if (opts.axisType == ColumnAxisType.AGE) {\n    _range = [b_age, t_age];\n  } else {\n    _range = [b_pos, t_pos];\n  }\n\n  const scaleInfo = buildSectionScale<T>(units, {\n    ...opts,\n    domain: _range,\n  });\n\n  return {\n    ...group,\n    scaleInfo,\n  };\n}\n\nfunction buildSectionScale<T extends UnitLong>(\n  data: T[],\n  opts: SectionScaleOptions,\n): PackageScaleInfo {\n  const {\n    targetUnitHeight = 20,\n    minPixelScale = 0.2,\n    axisType,\n    minSectionHeight,\n    scale,\n    hybridScale,\n  } = opts;\n  const domain = opts.domain ?? findSectionHeightRange(data, axisType);\n\n  const dAge = Math.abs(domain[0] - domain[1]);\n\n  let _pixelScale = opts.pixelScale;\n  let pixelHeight: number;\n\n  if (hybridScale != null) {\n    /** In an equidistant surfaces scale, we want to determine the heights of surfaces\n     * and then distribute units evenly between them.\n     * This is somewhat like an ordinal scale\n     */\n    if (hybridScale.type === HybridScaleType.EquidistantSurfaces) {\n      _pixelScale ??= targetUnitHeight;\n    }\n\n    return buildHybridScale(hybridScale, data, domain, {\n      pixelOffset: 0,\n      pixelScale: _pixelScale,\n    });\n  }\n\n  if (scale == null) {\n    if (_pixelScale == null) {\n      const avgAgeRange = findAverageUnitHeight(data, axisType);\n      // Get pixel height necessary to render average unit at target height\n      _pixelScale = Math.max(targetUnitHeight / avgAgeRange, minPixelScale);\n\n      // OLD METHOD that cares about overall section height vs. individual unit height\n      // 0.2 pixel per myr is the floor scale\n      //const targetHeight = targetUnitHeight * data.length;\n      // 1 pixel per myr is the floor scale\n      //_pixelScale = Math.max(targetHeight / dAge, minPixelScale);\n    }\n\n    let height = dAge * _pixelScale;\n    // If height is less than minSectionHeight, set it to minSectionHeight\n    const _minSectionHeight = minSectionHeight ?? targetUnitHeight ?? 0;\n    pixelHeight = Math.max(height, _minSectionHeight);\n    _pixelScale = pixelHeight / dAge;\n  } else {\n    // If a scale is provided, use it to compute pixel height\n    pixelHeight = Math.abs(scale(domain[0]) - scale(domain[1]));\n  }\n\n  return createPackageScale(\n    { scale, domain, pixelHeight, pixelScale: _pixelScale },\n    0,\n  );\n}\n\nexport function createPackageScale(\n  def: PackageScaleInfo,\n  offset: number = 0,\n): PackageScaleInfo {\n  /** Build a section scale */\n  // Domain should be oriented from bottom to top, but scale is oriented from top to bottom\n  const { domain, pixelScale, pixelHeight, scale, heightScale } = def;\n\n  if (scale == null && pixelScale == null) {\n    throw new Error(\"Either scale or pixelScale must be provided\");\n  }\n\n  let _scale: ScaleContinuousNumeric<number, number>;\n  if (scale == null) {\n    _scale = scaleLinear()\n      .domain([domain[1], domain[0]])\n      .range([offset, pixelHeight + offset]);\n  } else {\n    const domain0 = scale.domain();\n    const range0 = scale.range();\n    _scale = scale\n      .copy()\n      .domain(domain0)\n      .range(range0.map((d) => d + offset));\n  }\n\n  _scale.clamp();\n\n  let _heightScale = null;\n  if (heightScale != null) {\n    // Adjust height scale as well\n    const range0 = scale.range();\n    _heightScale = heightScale.copy().range(range0.map((d) => d + offset));\n    _heightScale.clamp();\n  }\n\n  return {\n    domain,\n    pixelScale,\n    pixelHeight,\n    scale: _scale,\n    // Internal details for hybrid scales. TODO: improve this\n    heightScale: _heightScale,\n  };\n}\n\nfunction findSectionHeightRange(\n  data: UnitLong[],\n  axisType: ColumnAxisType,\n): [number, number] {\n  if (axisType == null) {\n    throw new Error(\"Axis type is not set\");\n  }\n  if (axisType === ColumnAxisType.AGE) {\n    const t_age = Math.min(...data.map((d) => d.t_age));\n    const b_age = Math.max(...data.map((d) => d.b_age));\n    return [b_age, t_age];\n  } else if (\n    axisType == ColumnAxisType.DEPTH ||\n    axisType == ColumnAxisType.ORDINAL\n  ) {\n    const t_pos = Math.min(...data.map((d) => d.t_pos));\n    const b_pos = Math.max(...data.map((d) => d.b_pos));\n    return [b_pos, t_pos];\n  } else if (axisType == ColumnAxisType.HEIGHT) {\n    const t_pos = Math.max(...data.map((d) => d.t_pos));\n    const b_pos = Math.min(...data.map((d) => d.b_pos));\n    return [b_pos, t_pos];\n  }\n}\n\nfunction findAverageUnitHeight(\n  data: UnitLong[],\n  axisType: ColumnAxisType,\n): number {\n  const unitHeights = data.map((d) => {\n    const [b_pos, t_pos] = getUnitHeightRange(d, axisType);\n    return Math.abs(b_pos - t_pos);\n  });\n  return unitHeights.reduce((a, b) => a + b, 0) / unitHeights.length;\n}\n\nexport interface CompositeColumnScale {\n  (age: number): number | null;\n  copy(): CompositeColumnScale;\n  domain(): [number, number];\n  invert(pixelHeight: number): number | null;\n  clamp(clamp: boolean): void;\n}\n\nexport function createCompositeScale(\n  sections: PackageLayoutData[],\n  interpolateUnconformities: boolean = false,\n): CompositeColumnScale {\n  /** Create a scale that works across multiple packages */\n\n  const scales: ScaleContinuousNumeric<number, number>[] = [];\n\n  let lastScale: ScaleContinuousNumeric<number, number> | null = null;\n  for (const section of sections) {\n    const _scale = section.scaleInfo.scale.copy().clamp(true);\n    scales.push(_scale);\n    if (lastScale != null && interpolateUnconformities) {\n      // Add a new scale that interpolates between lastScale and _scale\n      const lastDomain = lastScale.domain();\n      const lastRange = lastScale.range();\n      const currentDomain = _scale.domain();\n      const currentRange = _scale.range();\n\n      const interpScale = scaleLinear()\n        .domain([lastDomain[lastDomain.length - 1], currentDomain[0]])\n        .range([lastRange[lastRange.length - 1], currentRange[0]])\n        .clamp(true);\n      scales.push(interpScale);\n    }\n    lastScale = _scale;\n  }\n\n  const scale: CompositeColumnScale = (age) => {\n    for (const s of scales) {\n      const domain = s.domain();\n      if (\n        domain[0] < domain[domain.length - 1] &&\n        age >= domain[0] &&\n        age <= domain[domain.length - 1]\n      ) {\n        // Age axes\n        return s(age);\n      } else if (age <= domain[0] && age >= domain[domain.length - 1]) {\n        // Normal axes like height\n        return s(age);\n      }\n    }\n    return null;\n  };\n\n  scale.copy = () => {\n    return createCompositeScale(sections, interpolateUnconformities);\n  };\n\n  scale.domain = () => {\n    /** Return the domain of the scale */\n    const vals = sections.flatMap((d) => d.scaleInfo.domain);\n    if (vals[0] < vals[vals.length - 1]) {\n      // age axes\n      return [Math.min(...vals), Math.max(...vals)];\n    }\n    // Normal axes like height\n    return [Math.max(...vals), Math.min(...vals)];\n  };\n\n  scale.invert = (pixelHeight) => {\n    /** Invert the scale to get the age at a given pixel height */\n    // Iterate through the sections to find the correct one\n    for (const scale of scales) {\n      const range = scale.range();\n      if (\n        pixelHeight > Math.min(...range) &&\n        pixelHeight <= Math.max(...range)\n      ) {\n        console.log(\"Inverting scale at pixel height\", pixelHeight);\n        return scale.invert(pixelHeight);\n      }\n    }\n    return null;\n  };\n\n  scale.clamp = (clamp: boolean) => {\n    /** Clamp all constituent scales */\n    for (const s of scales) {\n      s.clamp(clamp);\n    }\n  };\n\n  return scale;\n}\n\n/** Collapse sections separated by unconformities that are smaller than a given pixel height. */\nexport function collapseUnconformitiesByPixelHeight<T extends UnitLong>(\n  sections: SectionInfoWithScale<T>[],\n  threshold: number,\n  opts: ColumnScaleOptions,\n): SectionInfoWithScale<T>[] {\n  const newSections = [];\n  let currentSection: SectionInfoWithScale<T> | null = null;\n  for (const nextSection of sections) {\n    if (currentSection == null) {\n      currentSection = nextSection;\n      continue;\n    }\n    let heights: [number, number];\n    let pxHeights: [number, number];\n    if (opts.axisType !== ColumnAxisType.AGE) {\n      heights = [nextSection.t_pos, currentSection.b_pos];\n    } else {\n      heights = [nextSection.t_age, currentSection.b_age];\n    }\n\n    const _diff = (vals: number[]) => {\n      return Math.abs(vals[0] - vals[1]);\n    };\n\n    pxHeights = [\n      _diff(heights.map(nextSection.scaleInfo.scale)),\n      _diff(heights.map(currentSection.scaleInfo.scale)),\n    ];\n\n    const pxHeight = Math.min(...pxHeights);\n\n    if (pxHeight < threshold) {\n      let t_pos: number;\n      let b_pos: number;\n      if (\n        opts.axisType == ColumnAxisType.AGE ||\n        opts.axisType == ColumnAxisType.DEPTH\n      ) {\n        t_pos = Math.min(currentSection.t_pos, nextSection.t_pos);\n        b_pos = Math.max(currentSection.b_pos, nextSection.b_pos);\n      } else {\n        t_pos = Math.max(currentSection.t_pos, nextSection.t_pos);\n        b_pos = Math.min(currentSection.b_pos, nextSection.b_pos);\n      }\n\n      // We need to merge the sections\n      const compositeSection0: SectionInfo<T> = {\n        units: [...currentSection.units, ...nextSection.units],\n        section_id: [\n          ...ensureArray(currentSection.section_id),\n          ...ensureArray(nextSection.section_id),\n        ],\n        t_age: Math.min(currentSection.t_age, nextSection.t_age),\n        b_age: Math.max(currentSection.b_age, nextSection.b_age),\n        t_pos,\n        b_pos,\n      };\n\n      currentSection = addScaleToSection(compositeSection0, opts);\n    } else {\n      // We need to keep the section\n      newSections.push(currentSection);\n      currentSection = nextSection;\n    }\n  }\n  if (currentSection != null) {\n    newSections.push(currentSection);\n  }\n\n  return 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TODO: improve this\n    heightScale: _heightScale,\n  };\n}\n\nfunction findSectionHeightRange(\n  data: UnitLong[],\n  axisType: ColumnAxisType,\n): [number, number] {\n  if (axisType == null) {\n    throw new Error(\"Axis type is not set\");\n  }\n  if (axisType === ColumnAxisType.AGE) {\n    const t_age = Math.min(...data.map((d) => d.t_age));\n    const b_age = Math.max(...data.map((d) => d.b_age));\n    return [b_age, t_age];\n  } else if (\n    axisType == ColumnAxisType.DEPTH ||\n    axisType == ColumnAxisType.ORDINAL\n  ) {\n    const t_pos = Math.min(...data.map((d) => d.t_pos));\n    const b_pos = Math.max(...data.map((d) => d.b_pos));\n    return [b_pos, t_pos];\n  } else if (axisType == ColumnAxisType.HEIGHT) {\n    const t_pos = Math.max(...data.map((d) => d.t_pos));\n    const b_pos = Math.min(...data.map((d) => d.b_pos));\n    return [b_pos, t_pos];\n  }\n}\n\nfunction findAverageUnitHeight(\n  data: UnitLong[],\n  axisType: ColumnAxisType,\n): number {\n  const 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package/dist/prepare-units/composite-scale.js

@@ -205,7 +205,6 @@ function createCompositeScale(sections, interpolateUnconformities = false) {
     for (const scale2 of scales) {
       const range = scale2.range();
       if (pixelHeight > Math.min(...range) && pixelHeight <= Math.max(...range)) {
-        console.log("Inverting scale at pixel height", pixelHeight);
         return scale2.invert(pixelHeight);
       }
     }

package/dist/prepare-units/composite-scale.js.map

@@ -1 +1 @@
-{"version":3,"file":"composite-scale.js","sources":["../../src/prepare-units/composite-scale.ts"],"sourcesContent":["import { ColumnAxisType } from \"@macrostrat/column-components\";\nimport { ensureArray, getUnitHeightRange } from \"./utils\";\nimport { ScaleContinuousNumeric, scaleLinear } from \"d3-scale\";\nimport { UnitLong } from \"@macrostrat/api-types\";\nimport { buildHybridScale } from \"./dynamic-scales\";\nimport { ExtUnit, HybridScaleType, SectionInfo } from \"./types\";\nimport type {\n  ColumnScaleOptions,\n  CompositeColumnData,\n  CompositeScaleData,\n  PackageLayoutData,\n  PackageScaleInfo,\n  PackageScaleLayoutData,\n  SectionScaleOptions,\n} from \"./types\";\n\n// Composite scale information augmented with units in each package\n\nexport function buildCompositeScaleInfo(\n  inputScales: PackageScaleInfo[],\n  unconformityHeight: number,\n): CompositeScaleData {\n  /** Finalize the heights of sections, including the heights of unconformities\n   * between them.\n   */\n\n  let totalHeight = unconformityHeight / 2;\n  let lastSectionTopHeight = 0;\n\n  const packages2: PackageScaleLayoutData[] = [];\n  for (const group of inputScales) {\n    const { domain, scale } = group;\n    const [b_age, t_age] = domain;\n    const key = `package-${b_age}-${t_age}`;\n\n    packages2.push({\n      ...createPackageScale(group, totalHeight),\n      key,\n      offset: totalHeight,\n      // Unconformity height above this particular section\n      paddingTop: totalHeight - lastSectionTopHeight,\n    });\n\n    const pixelHeight = Math.abs(scale(b_age) - scale(t_age));\n    lastSectionTopHeight = totalHeight + pixelHeight;\n    totalHeight = lastSectionTopHeight + unconformityHeight;\n  }\n  totalHeight += unconformityHeight / 2;\n  return {\n    totalHeight,\n    sections: packages2,\n  };\n}\n\nexport function finalizeSectionHeights<T extends UnitLong>(\n  sections: SectionInfoWithScale<T>[],\n  unconformityHeight: number,\n): CompositeColumnData<T> {\n  /** Finalize the heights of sections, including the heights of unconformities\n   * between them.\n   */\n\n  const sectionScales = sections.map((d) => d.scaleInfo);\n\n  const { totalHeight, sections: packages } = buildCompositeScaleInfo(\n    sectionScales,\n    unconformityHeight,\n  );\n\n  // This could perhaps be simplified.\n  const sections1: PackageLayoutData<T>[] = [];\n  for (const i in sections) {\n    const group = sections[i];\n    const scaleInfo = packages[i];\n    sections1.push({\n      ...group,\n      key: scaleInfo.key,\n      scaleInfo,\n    });\n  }\n  return {\n    totalHeight,\n    sections: sections1,\n  };\n}\n\nexport interface SectionInfoWithScale<\n  T extends UnitLong = ExtUnit,\n> extends SectionInfo<T> {\n  scaleInfo: PackageScaleInfo;\n}\n\nexport function computeSectionHeights<T extends UnitLong>(\n  sections: SectionInfo<T>[],\n  opts: ColumnScaleOptions,\n): SectionInfoWithScale<T>[] {\n  return sections.map((group) => {\n    return addScaleToSection<T>(group, opts);\n  });\n}\n\nfunction addScaleToSection<T extends UnitLong = ExtUnit>(\n  group: SectionInfo<T>,\n  opts: ColumnScaleOptions,\n): SectionInfoWithScale<T> {\n  const { t_age, b_age, t_pos, b_pos, units } = group;\n  let _range = null;\n  // if t_age and b_age are set for a group, use them to define the range...\n  if (opts.axisType == ColumnAxisType.AGE) {\n    _range = [b_age, t_age];\n  } else {\n    _range = [b_pos, t_pos];\n  }\n\n  const scaleInfo = buildSectionScale<T>(units, {\n    ...opts,\n    domain: _range,\n  });\n\n  return {\n    ...group,\n    scaleInfo,\n  };\n}\n\nfunction buildSectionScale<T extends UnitLong>(\n  data: T[],\n  opts: SectionScaleOptions,\n): PackageScaleInfo {\n  const {\n    targetUnitHeight = 20,\n    minPixelScale = 0.2,\n    axisType,\n    minSectionHeight,\n    scale,\n    hybridScale,\n  } = opts;\n  const domain = opts.domain ?? findSectionHeightRange(data, axisType);\n\n  const dAge = Math.abs(domain[0] - domain[1]);\n\n  let _pixelScale = opts.pixelScale;\n  let pixelHeight: number;\n\n  if (hybridScale != null) {\n    /** In an equidistant surfaces scale, we want to determine the heights of surfaces\n     * and then distribute units evenly between them.\n     * This is somewhat like an ordinal scale\n     */\n    if (hybridScale.type === HybridScaleType.EquidistantSurfaces) {\n      _pixelScale ??= targetUnitHeight;\n    }\n\n    return buildHybridScale(hybridScale, data, domain, {\n      pixelOffset: 0,\n      pixelScale: _pixelScale,\n    });\n  }\n\n  if (scale == null) {\n    if (_pixelScale == null) {\n      const avgAgeRange = findAverageUnitHeight(data, axisType);\n      // Get pixel height necessary to render average unit at target height\n      _pixelScale = Math.max(targetUnitHeight / avgAgeRange, minPixelScale);\n\n      // OLD METHOD that cares about overall section height vs. individual unit height\n      // 0.2 pixel per myr is the floor scale\n      //const targetHeight = targetUnitHeight * data.length;\n      // 1 pixel per myr is the floor scale\n      //_pixelScale = Math.max(targetHeight / dAge, minPixelScale);\n    }\n\n    let height = dAge * _pixelScale;\n    // If height is less than minSectionHeight, set it to minSectionHeight\n    const _minSectionHeight = minSectionHeight ?? targetUnitHeight ?? 0;\n    pixelHeight = Math.max(height, _minSectionHeight);\n    _pixelScale = pixelHeight / dAge;\n  } else {\n    // If a scale is provided, use it to compute pixel height\n    pixelHeight = Math.abs(scale(domain[0]) - scale(domain[1]));\n  }\n\n  return createPackageScale(\n    { scale, domain, pixelHeight, pixelScale: _pixelScale },\n    0,\n  );\n}\n\nexport function createPackageScale(\n  def: PackageScaleInfo,\n  offset: number = 0,\n): PackageScaleInfo {\n  /** Build a section scale */\n  // Domain should be oriented from bottom to top, but scale is oriented from top to bottom\n  const { domain, pixelScale, pixelHeight, scale, heightScale } = def;\n\n  if (scale == null && pixelScale == null) {\n    throw new Error(\"Either scale or pixelScale must be provided\");\n  }\n\n  let _scale: ScaleContinuousNumeric<number, number>;\n  if (scale == null) {\n    _scale = scaleLinear()\n      .domain([domain[1], domain[0]])\n      .range([offset, pixelHeight + offset]);\n  } else {\n    const domain0 = scale.domain();\n    const range0 = scale.range();\n    _scale = scale\n      .copy()\n      .domain(domain0)\n      .range(range0.map((d) => d + offset));\n  }\n\n  _scale.clamp();\n\n  let _heightScale = null;\n  if (heightScale != null) {\n    // Adjust height scale as well\n    const range0 = scale.range();\n    _heightScale = heightScale.copy().range(range0.map((d) => d + offset));\n    _heightScale.clamp();\n  }\n\n  return {\n    domain,\n    pixelScale,\n    pixelHeight,\n    scale: _scale,\n    // Internal details for hybrid scales. TODO: improve this\n    heightScale: _heightScale,\n  };\n}\n\nfunction findSectionHeightRange(\n  data: UnitLong[],\n  axisType: ColumnAxisType,\n): [number, number] {\n  if (axisType == null) {\n    throw new Error(\"Axis type is not set\");\n  }\n  if (axisType === ColumnAxisType.AGE) {\n    const t_age = Math.min(...data.map((d) => d.t_age));\n    const b_age = Math.max(...data.map((d) => d.b_age));\n    return [b_age, t_age];\n  } else if (\n    axisType == ColumnAxisType.DEPTH ||\n    axisType == ColumnAxisType.ORDINAL\n  ) {\n    const t_pos = Math.min(...data.map((d) => d.t_pos));\n    const b_pos = Math.max(...data.map((d) => d.b_pos));\n    return [b_pos, t_pos];\n  } else if (axisType == ColumnAxisType.HEIGHT) {\n    const t_pos = Math.max(...data.map((d) => d.t_pos));\n    const b_pos = Math.min(...data.map((d) => d.b_pos));\n    return [b_pos, t_pos];\n  }\n}\n\nfunction findAverageUnitHeight(\n  data: UnitLong[],\n  axisType: ColumnAxisType,\n): number {\n  const unitHeights = data.map((d) => {\n    const [b_pos, t_pos] = getUnitHeightRange(d, axisType);\n    return Math.abs(b_pos - t_pos);\n  });\n  return unitHeights.reduce((a, b) => a + b, 0) / unitHeights.length;\n}\n\nexport interface CompositeColumnScale {\n  (age: number): number | null;\n  copy(): CompositeColumnScale;\n  domain(): [number, number];\n  invert(pixelHeight: number): number | null;\n  clamp(clamp: boolean): void;\n}\n\nexport function createCompositeScale(\n  sections: PackageLayoutData[],\n  interpolateUnconformities: boolean = false,\n): CompositeColumnScale {\n  /** Create a scale that works across multiple packages */\n\n  const scales: ScaleContinuousNumeric<number, number>[] = [];\n\n  let lastScale: ScaleContinuousNumeric<number, number> | null = null;\n  for (const section of sections) {\n    const _scale = section.scaleInfo.scale.copy().clamp(true);\n    scales.push(_scale);\n    if (lastScale != null && interpolateUnconformities) {\n      // Add a new scale that interpolates between lastScale and _scale\n      const lastDomain = lastScale.domain();\n      const lastRange = lastScale.range();\n      const currentDomain = _scale.domain();\n      const currentRange = _scale.range();\n\n      const interpScale = scaleLinear()\n        .domain([lastDomain[lastDomain.length - 1], currentDomain[0]])\n        .range([lastRange[lastRange.length - 1], currentRange[0]])\n        .clamp(true);\n      scales.push(interpScale);\n    }\n    lastScale = _scale;\n  }\n\n  const scale: CompositeColumnScale = (age) => {\n    for (const s of scales) {\n      const domain = s.domain();\n      if (\n        domain[0] < domain[domain.length - 1] &&\n        age >= domain[0] &&\n        age <= domain[domain.length - 1]\n      ) {\n        // Age axes\n        return s(age);\n      } else if (age <= domain[0] && age >= domain[domain.length - 1]) {\n        // Normal axes like height\n        return s(age);\n      }\n    }\n    return null;\n  };\n\n  scale.copy = () => {\n    return createCompositeScale(sections, interpolateUnconformities);\n  };\n\n  scale.domain = () => {\n    /** Return the domain of the scale */\n    const vals = sections.flatMap((d) => d.scaleInfo.domain);\n    if (vals[0] < vals[vals.length - 1]) {\n      // age axes\n      return [Math.min(...vals), Math.max(...vals)];\n    }\n    // Normal axes like height\n    return [Math.max(...vals), Math.min(...vals)];\n  };\n\n  scale.invert = (pixelHeight) => {\n    /** Invert the scale to get the age at a given pixel height */\n    // Iterate through the sections to find the correct one\n    for (const scale of scales) {\n      const range = scale.range();\n      if (\n        pixelHeight > Math.min(...range) &&\n        pixelHeight <= Math.max(...range)\n      ) {\n        console.log(\"Inverting scale at pixel height\", pixelHeight);\n        return scale.invert(pixelHeight);\n      }\n    }\n    return null;\n  };\n\n  scale.clamp = (clamp: boolean) => {\n    /** Clamp all constituent scales */\n    for (const s of scales) {\n      s.clamp(clamp);\n    }\n  };\n\n  return scale;\n}\n\n/** Collapse sections separated by unconformities that are smaller than a given pixel height. */\nexport function collapseUnconformitiesByPixelHeight<T extends UnitLong>(\n  sections: SectionInfoWithScale<T>[],\n  threshold: number,\n  opts: ColumnScaleOptions,\n): SectionInfoWithScale<T>[] {\n  const newSections = [];\n  let currentSection: SectionInfoWithScale<T> | null = null;\n  for (const nextSection of sections) {\n    if (currentSection == null) {\n      currentSection = nextSection;\n      continue;\n    }\n    let heights: [number, number];\n    let pxHeights: [number, number];\n    if (opts.axisType !== ColumnAxisType.AGE) {\n      heights = [nextSection.t_pos, currentSection.b_pos];\n    } else {\n      heights = [nextSection.t_age, currentSection.b_age];\n    }\n\n    const _diff = (vals: number[]) => {\n      return Math.abs(vals[0] - vals[1]);\n    };\n\n    pxHeights = [\n      _diff(heights.map(nextSection.scaleInfo.scale)),\n      _diff(heights.map(currentSection.scaleInfo.scale)),\n    ];\n\n    const pxHeight = Math.min(...pxHeights);\n\n    if (pxHeight < threshold) {\n      let t_pos: number;\n      let b_pos: number;\n      if (\n        opts.axisType == ColumnAxisType.AGE ||\n        opts.axisType == ColumnAxisType.DEPTH\n      ) {\n        t_pos = Math.min(currentSection.t_pos, nextSection.t_pos);\n        b_pos = Math.max(currentSection.b_pos, nextSection.b_pos);\n      } else {\n        t_pos = Math.max(currentSection.t_pos, nextSection.t_pos);\n        b_pos = Math.min(currentSection.b_pos, nextSection.b_pos);\n      }\n\n      // We need to merge the sections\n      const compositeSection0: SectionInfo<T> = {\n        units: [...currentSection.units, ...nextSection.units],\n        section_id: [\n          ...ensureArray(currentSection.section_id),\n          ...ensureArray(nextSection.section_id),\n        ],\n        t_age: 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TODO: improve this\n    heightScale: _heightScale,\n  };\n}\n\nfunction findSectionHeightRange(\n  data: UnitLong[],\n  axisType: ColumnAxisType,\n): [number, number] {\n  if (axisType == null) {\n    throw new Error(\"Axis type is not set\");\n  }\n  if (axisType === ColumnAxisType.AGE) {\n    const t_age = Math.min(...data.map((d) => d.t_age));\n    const b_age = Math.max(...data.map((d) => d.b_age));\n    return [b_age, t_age];\n  } else if (\n    axisType == ColumnAxisType.DEPTH ||\n    axisType == ColumnAxisType.ORDINAL\n  ) {\n    const t_pos = Math.min(...data.map((d) => d.t_pos));\n    const b_pos = Math.max(...data.map((d) => d.b_pos));\n    return [b_pos, t_pos];\n  } else if (axisType == ColumnAxisType.HEIGHT) {\n    const t_pos = Math.max(...data.map((d) => d.t_pos));\n    const b_pos = Math.min(...data.map((d) => d.b_pos));\n    return [b_pos, t_pos];\n  }\n}\n\nfunction findAverageUnitHeight(\n  data: UnitLong[],\n  axisType: ColumnAxisType,\n): number {\n  const 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interpolates between lastScale and _scale\n      const lastDomain = lastScale.domain();\n      const lastRange = lastScale.range();\n      const currentDomain = _scale.domain();\n      const currentRange = _scale.range();\n\n      const interpScale = scaleLinear()\n        .domain([lastDomain[lastDomain.length - 1], currentDomain[0]])\n        .range([lastRange[lastRange.length - 1], currentRange[0]])\n        .clamp(true);\n      scales.push(interpScale);\n    }\n    lastScale = _scale;\n  }\n\n  const scale: CompositeColumnScale = (age) => {\n    for (const s of scales) {\n      const domain = s.domain();\n      if (\n        domain[0] < domain[domain.length - 1] &&\n        age >= domain[0] &&\n        age <= domain[domain.length - 1]\n      ) {\n        // Age axes\n        return s(age);\n      } else if (age <= domain[0] && age >= domain[domain.length - 1]) {\n        // Normal axes like height\n        return s(age);\n      }\n    }\n    return null;\n  };\n\n  scale.copy = () => {\n    return createCompositeScale(sections, interpolateUnconformities);\n  };\n\n  scale.domain = () => {\n    /** Return the domain of the scale */\n    const vals = sections.flatMap((d) => d.scaleInfo.domain);\n    if (vals[0] < vals[vals.length - 1]) {\n      // age axes\n      return [Math.min(...vals), Math.max(...vals)];\n    }\n    // Normal axes like height\n    return [Math.max(...vals), Math.min(...vals)];\n  };\n\n  scale.invert = (pixelHeight) => {\n    /** Invert the scale to get the age at a given pixel height */\n    // Iterate through the sections to find the correct one\n    for (const scale of scales) {\n      const range = scale.range();\n      if (\n        pixelHeight > Math.min(...range) &&\n        pixelHeight <= Math.max(...range)\n      ) {\n        //console.log(\"Inverting scale at pixel height\", pixelHeight);\n        return scale.invert(pixelHeight);\n      }\n    }\n    return null;\n  };\n\n  scale.clamp = (clamp: boolean) => {\n    /** Clamp all constituent scales */\n    for (const s of scales) {\n      s.clamp(clamp);\n    }\n  };\n\n  return scale;\n}\n\n/** Collapse sections separated by unconformities that are smaller than a given pixel height. */\nexport function collapseUnconformitiesByPixelHeight<T extends UnitLong>(\n  sections: SectionInfoWithScale<T>[],\n  threshold: number,\n  opts: ColumnScaleOptions,\n): SectionInfoWithScale<T>[] {\n  const newSections = [];\n  let currentSection: SectionInfoWithScale<T> | null = null;\n  for (const nextSection of sections) {\n    if (currentSection == null) {\n      currentSection = nextSection;\n      continue;\n    }\n    let heights: [number, number];\n    let pxHeights: [number, number];\n    if (opts.axisType !== ColumnAxisType.AGE) {\n      heights = [nextSection.t_pos, currentSection.b_pos];\n    } else {\n      heights = [nextSection.t_age, currentSection.b_age];\n    }\n\n    const _diff = (vals: number[]) => {\n      return Math.abs(vals[0] - vals[1]);\n    };\n\n    pxHeights = [\n      _diff(heights.map(nextSection.scaleInfo.scale)),\n      _diff(heights.map(currentSection.scaleInfo.scale)),\n    ];\n\n    const pxHeight = Math.min(...pxHeights);\n\n    if (pxHeight < threshold) {\n      let t_pos: number;\n      let b_pos: number;\n      if (\n        opts.axisType == ColumnAxisType.AGE ||\n        opts.axisType == ColumnAxisType.DEPTH\n      ) {\n        t_pos = Math.min(currentSection.t_pos, nextSection.t_pos);\n        b_pos = Math.max(currentSection.b_pos, nextSection.b_pos);\n      } else {\n        t_pos = Math.max(currentSection.t_pos, nextSection.t_pos);\n        b_pos = Math.min(currentSection.b_pos, nextSection.b_pos);\n      }\n\n      // We need to merge the sections\n      const compositeSection0: SectionInfo<T> = {\n        units: [...currentSection.units, ...nextSection.units],\n        section_id: [\n          ...ensureArray(currentSection.section_id),\n          ...ensureArray(nextSection.section_id),\n        ],\n        t_age: Math.min(currentSection.t_age, nextSection.t_age),\n        b_age: Math.max(currentSection.b_age, nextSection.b_age),\n        t_pos,\n        b_pos,\n      };\n\n      currentSection = addScaleToSection(compositeSection0, opts);\n    } else {\n      // We need to keep the section\n      newSections.push(currentSection);\n      currentSection = nextSection;\n    }\n  }\n  if (currentSection != null) {\n    newSections.push(currentSection);\n  }\n\n  return 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package/dist/prepare-units/helpers.cjs

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

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

@@ -1 +1 @@
-{"version":3,"file":"helpers.cjs","sources":["../../src/prepare-units/helpers.ts"],"sourcesContent":["import type { BaseUnit, UnitLong } from \"@macrostrat/api-types\";\nimport { group } from \"d3-array\";\nimport { ColumnAxisType } from \"@macrostrat/column-components\";\nimport {\n  createUnitSorter,\n  ensureArray,\n  ensureRealFloat,\n  getUnitHeightRange,\n  unitsOverlap,\n} from \"./utils\";\nimport {\n  AgeRangeRelationship,\n  compareAgeRanges,\n} from \"@macrostrat/stratigraphy-utils\";\nimport type { ExtUnit, SectionInfo, StratigraphicPackage } from \"./types\";\n\nconst dt = 0.001;\n\nexport function preprocessUnits<T extends UnitLong = UnitLong>(\n  section: SectionInfo<T>,\n  axisType: ColumnAxisType = ColumnAxisType.AGE,\n): ExtUnit[] {\n  /** Preprocess units to add overlapping units and columns. */\n  let units = section.units;\n\n  let divisions = units.map((...args) => extendDivision(...args, axisType));\n  for (let d of divisions) {\n    const overlappingUnits = divisions.filter((u) =>\n      d.overlappingUnits.includes(u.unit_id),\n    );\n\n    // Overlapping columns\n    const columns = overlappingUnits.map((d) => d.column);\n\n    if (columns.includes(d.column)) {\n      let col = 0;\n      // Go through columns to find a better index\n      while (columns.includes(col)) {\n        col++;\n      }\n      d.column ??= col;\n    }\n\n    // If unit overlaps the edges of a section, set the clip positions\n    const [b_pos, t_pos] = getUnitHeightRange(d, axisType);\n    if (axisType == ColumnAxisType.AGE) {\n      if (b_pos > section.b_age) {\n        d.b_clip_pos = section.b_age;\n      }\n      if (t_pos < section.t_age) {\n        d.t_clip_pos = section.t_age;\n      }\n    }\n    if (axisType == ColumnAxisType.DEPTH) {\n      if (b_pos > section.b_pos) {\n        d.b_clip_pos = section.b_pos;\n      }\n      if (t_pos < section.t_pos) {\n        d.t_clip_pos = section.t_pos;\n      }\n    }\n    // if (axisType == ColumnAxisType.HEIGHT) {\n    //   if (b_pos < section.b_pos) {\n    //     d.b_clip_pos = section.b_pos;\n    //   }\n    //   if (t_pos > section.t_pos) {\n    //     d.t_clip_pos = section.t_pos;\n    //   }\n    // }\n  }\n\n  return divisions;\n}\n\nfunction extendDivision(\n  unit: UnitLong,\n  i: number,\n  divisions: UnitLong[],\n  axisType: ColumnAxisType = ColumnAxisType.AGE,\n): ExtUnit {\n  // TODO: make this configurable\n  let tolerance = 0.001; // 1 kyr tolerance for age columns\n  if (axisType != ColumnAxisType.AGE) {\n    tolerance = 0.01; // 1cm tolerance for height/depth columns\n  }\n\n  const overlappingUnits = divisions.filter(\n    (d) =>\n      d.unit_id != unit.unit_id && unitsOverlap(unit, d, axisType, tolerance),\n  );\n  const u_pos = getUnitHeightRange(unit, axisType);\n  const bottomOverlap = overlappingUnits.some((d) => {\n    const d_pos = getUnitHeightRange(d, axisType);\n    // Check if the unit is below the current unit\n    return d_pos[0] < u_pos[0] + dt;\n  });\n  let column = 0;\n  if (overlappingUnits.length == 1) {\n    column = 1;\n  }\n\n  return {\n    ...unit,\n    bottomOverlap,\n    column: unit.column ?? column,\n    overlappingUnits: overlappingUnits.map((d) => d.unit_id),\n  };\n}\n\nexport function groupUnitsIntoSectionsBySectionID<T extends UnitLong>(\n  units: T[],\n  axisType: ColumnAxisType = ColumnAxisType.AGE,\n): SectionInfo<T>[] {\n  /** Group units into sections by section_id.\n   * This works for large-scale Macrostrat columns, where units are grouped by section_id.\n   * */\n  let groups = Array.from(group(units, (d) => d.section_id));\n  const unitComparator = createUnitSorter(axisType);\n\n  const groups1 = groups.map(([section_id, sectionUnits]) => {\n    const [b_age, t_age] = getSectionAgeRange(sectionUnits);\n    const [b_pos, t_pos] = getSectionPosRange(sectionUnits, axisType);\n\n    // sort units by position\n    sectionUnits.sort(unitComparator);\n    return { section_id, t_age, b_age, b_pos, t_pos, units: sectionUnits };\n  });\n  // Sort sections by increasing top age, then increasing bottom age.\n  // Sections have no relative ordinal position other than age...\n  const compareSections = createUnitSorter(axisType) as (\n    a: StratigraphicPackage,\n    b: StratigraphicPackage,\n  ) => number;\n  groups1.sort(compareSections);\n  return groups1;\n}\n\ninterface WorkingSection {\n  units: UnitLong[];\n  // Position or age\n  heightRange?: [number, number];\n}\n\nexport function groupUnitsIntoSectionsByOverlap<T extends UnitLong>(\n  units: T[],\n  axisType: ColumnAxisType = ColumnAxisType.AGE,\n): SectionInfo<T>[] {\n  /** Group units into sections by overlap.\n   * This creates \"synthetic\" sections that correspond to packages bound by scale gaps.\n   * This is most useful in the height and depth domains, where gaps (e.g., missing core) are\n   * common.\n   * */\n  // Start with each unit as its own \"section\", and progressively merge...\n  const sectionList: WorkingSection[] = [];\n  for (const unit of units) {\n    // Check if the unit overlaps with any existing section\n    const heightRange = getUnitHeightRange(unit, axisType);\n    let section: WorkingSection | undefined = sectionList.find(\n      (s) =>\n        compareAgeRanges(heightRange, s.heightRange) !==\n        AgeRangeRelationship.Disjoint,\n    );\n    if (section == null) {\n      // No overlap, create a new section\n      sectionList.push({\n        heightRange,\n        units: [unit],\n      });\n    } else {\n      // Overlap, merge the unit into the section\n      section.units.push(unit);\n      // Update the height range\n      if (axisType == ColumnAxisType.DEPTH || axisType == ColumnAxisType.AGE) {\n        section.heightRange = [\n          Math.max(section.heightRange[0], heightRange[0]),\n          Math.min(section.heightRange[1], heightRange[1]),\n        ];\n      } else {\n        section.heightRange = [\n          Math.min(section.heightRange[0], heightRange[0]),\n          Math.max(section.heightRange[1], heightRange[1]),\n        ];\n      }\n    }\n  }\n  // We should have a section for each unit, now we can convert to SectionInfo\n  // Ages have to be really actually ages, not heights\n\n  return sectionList.map((section, i) => {\n    const [b_age, t_age] = getSectionAgeRange(section.units);\n    const [b_pos, t_pos] = getSectionPosRange(section.units, axisType);\n    return {\n      // Negative section IDs are used to indicate that these are synthetic sections\n      section_id: -i,\n      t_age,\n      b_age,\n      t_pos,\n      b_pos,\n      units: section.units as T[],\n    };\n  });\n}\n\nexport function getSectionPosRange(\n  units: BaseUnit[],\n  axisType: ColumnAxisType,\n): [number, number] {\n  /** Get the overall position range of a set of units. */\n  const t_positions = units.map((d) => {\n    switch (axisType) {\n      case ColumnAxisType.AGE:\n        return d.t_age;\n      case ColumnAxisType.DEPTH:\n      case ColumnAxisType.HEIGHT:\n      case ColumnAxisType.ORDINAL:\n        return d.t_pos;\n      default:\n        throw new Error(`Unknown axis type: ${axisType}`);\n    }\n  });\n  const b_positions = units.map((d) => {\n    switch (axisType) {\n      case ColumnAxisType.AGE:\n        return d.b_age;\n      case ColumnAxisType.DEPTH:\n      case ColumnAxisType.HEIGHT:\n      case ColumnAxisType.ORDINAL:\n        return d.b_pos;\n      default:\n        throw new Error(`Unknown axis type: ${axisType}`);\n    }\n  });\n  if (axisType == ColumnAxisType.AGE || axisType == ColumnAxisType.DEPTH) {\n    return [Math.max(...b_positions), Math.min(...t_positions)];\n  } else {\n    return [Math.min(...b_positions), Math.max(...t_positions)];\n  }\n}\n\nexport function getSectionAgeRange(units: BaseUnit[]): [number, number] {\n  /** Get the overall age range of a set of units. */\n  return getSectionPosRange(units, ColumnAxisType.AGE);\n}\n\nexport function mergeOverlappingSections<T extends UnitLong>(\n  sections: SectionInfo<T>[],\n): SectionInfo<T>[] {\n  /** Columns can have sections that overlap in time. Here, we merge overlapping\n   * sections into a single section to correctly render gap-bound packages.\n   */\n  const [firstSection, ...rest] = sections;\n  const newSections = [firstSection];\n  for (const section of rest) {\n    const lastSection = newSections[newSections.length - 1];\n    if (\n      lastSection.b_age < section.t_age ||\n      lastSection.t_age > section.b_age\n    ) {\n      // No overlap, add the section as normal\n      newSections.push(section);\n      continue;\n    }\n\n    // Overlap, merge the sections\n    lastSection.section_id = [\n      ...ensureArray(lastSection.section_id),\n      ...ensureArray(section.section_id),\n    ];\n    lastSection.units.push(...section.units);\n    lastSection.b_age = Math.max(lastSection.b_age, section.b_age);\n    lastSection.t_age = Math.min(lastSection.t_age, section.t_age);\n  }\n  return newSections;\n}\n\nexport function preprocessSectionUnit(unit: UnitLong): UnitLong {\n  /** Preprocess a single unit for a 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+{"version":3,"file":"helpers.cjs","sources":["../../src/prepare-units/helpers.ts"],"sourcesContent":["import type { BaseUnit, UnitLong } from \"@macrostrat/api-types\";\nimport { group } from \"d3-array\";\nimport { ColumnAxisType } from \"@macrostrat/column-components\";\nimport {\n  createUnitSorter,\n  ensureArray,\n  ensureRealFloat,\n  getUnitHeightRange,\n  unitsOverlap,\n} from \"./utils\";\nimport {\n  AgeRangeRelationship,\n  compareAgeRanges,\n} from \"@macrostrat/stratigraphy-utils\";\nimport type { ExtUnit, SectionInfo, StratigraphicPackage } from \"./types\";\n\nconst dt = 0.001;\n\nexport type UnitWithDefinedOverlap<T extends BaseUnit> = T & {\n  overlap: UnitOverlapInfo<T>;\n};\n\ntype UnitOverlapInfo<T extends BaseUnit> = {\n  column: number;\n  nColumns: number;\n  unitGroup: UnitGroup<T>;\n};\n\nclass UnitGroup<T extends BaseUnit> implements StratigraphicPackage {\n  units: T[];\n\n  constructor(units: T[]) {\n    this.units = units;\n  }\n\n  get t_age(): number {\n    return Math.min(...this.units.map((d) => d.t_age));\n  }\n\n  get b_age(): number {\n    return Math.max(...this.units.map((d) => d.b_age));\n  }\n\n  getUnits(): UnitWithDefinedOverlap<T>[] {\n    return assignColumnsToUnitsWithinOverlappingGroup(this);\n  }\n}\n\nfunction groupUnitsByMutualOverlap<T extends BaseUnit>(\n  units: T[],\n  tolerance: number = dt,\n): UnitGroup<T>[] {\n  /** Group units within a section that have mutual overlap. */\n  const sections = groupUnitsIntoSectionsByOverlap(\n    units,\n    ColumnAxisType.AGE,\n    tolerance,\n  );\n  return sections.map((d) => {\n    return new UnitGroup(d.units);\n  });\n}\n\nconst sortByAge = createUnitSorter(ColumnAxisType.AGE);\n\nfunction assignColumnsToUnitsWithinOverlappingGroup<T extends BaseUnit>(\n  group: UnitGroup<T>,\n): UnitWithDefinedOverlap<T>[] {\n  /** A relatively naïve function to assign columns to units within a mutually overlapping group.\n   * This gets the number of columns that would be needed to accommodate the units in the group.\n   * It then assigns columns to units in the group based on the number of columns needed, with\n   * lower units further to the left.\n   */\n\n  const sortedUnits = [...group.units].sort((a, b) => b.b_age - a.b_age);\n\n  const columns: T[][] = [];\n\n  for (const unit of sortedUnits) {\n    // Find a column that is not already occupied by an overlapping unit\n    let didAddToExistingColumn = false;\n    for (const column of columns) {\n      const lastUnit = column[column.length - 1];\n      if (!unitsOverlap(unit, lastUnit, ColumnAxisType.AGE, dt)) {\n        column.push(unit);\n        didAddToExistingColumn = true;\n        break;\n      }\n    }\n    if (!didAddToExistingColumn) {\n      columns.push([unit]);\n    }\n  }\n\n  const units: UnitWithDefinedOverlap<T>[] = columns.flatMap(\n    (column, columnIndex) =>\n      column.map((unit) => {\n        return {\n          ...unit,\n          overlap: {\n            column: columnIndex,\n            nColumns: columns.length,\n            unitGroup: group,\n          },\n        };\n      }),\n  );\n\n  return units.toSorted(sortByAge);\n}\n\nexport function preprocessUnits<T extends UnitLong = UnitLong>(\n  section: SectionInfo<T>,\n  axisType: ColumnAxisType = ColumnAxisType.AGE,\n): ExtUnit[] {\n  /** Preprocess units to add overlapping units and columns. */\n  let units = section.units;\n\n  let tolerance = 0.001; // 1 kyr tolerance for age columns\n  if (axisType != ColumnAxisType.AGE) {\n    tolerance = 0.01; // 1cm tolerance for height/depth columns\n  }\n\n  const unitGroups = groupUnitsByMutualOverlap(units, tolerance);\n\n  const divisions: any[] = [];\n  // Serialize all groups' units to a single array\n  for (const group of unitGroups) {\n    divisions.push(...group.getUnits());\n  }\n\n  return divisions.map((d) =>\n    enhanceUnitWithClippingPosition(section, d, axisType),\n  );\n}\n\nexport function enhanceUnitWithClippingPosition(section, d, axisType) {\n  const [b_pos, t_pos] = getUnitHeightRange(d, axisType);\n  if (axisType == ColumnAxisType.AGE) {\n    if (b_pos > section.b_age) {\n      d.b_clip_pos = section.b_age;\n    }\n    if (t_pos < section.t_age) {\n      d.t_clip_pos = section.t_age;\n    }\n  }\n  if (axisType == ColumnAxisType.DEPTH) {\n    if (b_pos > section.b_pos) {\n      d.b_clip_pos = section.b_pos;\n    }\n    if (t_pos < section.t_pos) {\n      d.t_clip_pos = section.t_pos;\n    }\n  }\n  return d;\n}\n\nexport function groupUnitsIntoSectionsBySectionID<T extends UnitLong>(\n  units: T[],\n  axisType: ColumnAxisType = ColumnAxisType.AGE,\n): SectionInfo<T>[] {\n  /** Group units into sections by section_id.\n   * This works for large-scale Macrostrat columns, where units are grouped by section_id.\n   * */\n  let groups = Array.from(group(units, (d) => d.section_id));\n  const unitComparator = createUnitSorter(axisType);\n\n  const groups1 = groups.map(([section_id, sectionUnits]) => {\n    const [b_age, t_age] = getSectionAgeRange(sectionUnits);\n    const [b_pos, t_pos] = getSectionPosRange(sectionUnits, axisType);\n\n    // sort units by position\n    sectionUnits.sort(unitComparator);\n    return { section_id, t_age, b_age, b_pos, t_pos, units: sectionUnits };\n  });\n  // Sort sections by increasing top age, then increasing bottom age.\n  // Sections have no relative ordinal position other than age...\n  const compareSections = createUnitSorter(axisType) as (\n    a: StratigraphicPackage,\n    b: StratigraphicPackage,\n  ) => number;\n  groups1.sort(compareSections);\n  return groups1;\n}\n\ninterface WorkingSection {\n  units: UnitLong[];\n  // Position or age\n  heightRange?: [number, number];\n}\n\nexport function groupUnitsIntoSectionsByOverlap<T extends BaseUnit>(\n  units: T[],\n  axisType: ColumnAxisType = ColumnAxisType.AGE,\n  tolerance: number = dt,\n): SectionInfo<T>[] {\n  /** Group units into sections by overlap.\n   * This creates \"synthetic\" sections that correspond to packages bound by scale gaps.\n   * This is most useful in the height and depth domains, where gaps (e.g., missing core) are\n   * common.\n   * */\n  // Start with each unit as its own \"section\", and progressively merge...\n  const sectionList: WorkingSection[] = [];\n  for (const unit of units) {\n    // Check if the unit overlaps with any existing section\n    const heightRange = getUnitHeightRange(unit, axisType);\n    let section: WorkingSection | undefined = sectionList.find(\n      (s) =>\n        compareAgeRanges(heightRange, s.heightRange, tolerance) !==\n        AgeRangeRelationship.Disjoint,\n    );\n    if (section == null) {\n      // No overlap, create a new section\n      sectionList.push({\n        heightRange,\n        units: [unit],\n      });\n    } else {\n      // Overlap, merge the unit into the section\n      section.units.push(unit);\n      // Update the height range\n      if (axisType == ColumnAxisType.DEPTH || axisType == ColumnAxisType.AGE) {\n        section.heightRange = [\n          Math.max(section.heightRange[0], heightRange[0]),\n          Math.min(section.heightRange[1], heightRange[1]),\n        ];\n      } else {\n        section.heightRange = [\n          Math.min(section.heightRange[0], heightRange[0]),\n          Math.max(section.heightRange[1], heightRange[1]),\n        ];\n      }\n    }\n  }\n  // We should have a section for each unit, now we can convert to SectionInfo\n  // Ages have to be really actually ages, not heights\n\n  return sectionList.map((section, i) => {\n    const [b_age, t_age] = getSectionAgeRange(section.units);\n    const [b_pos, t_pos] = getSectionPosRange(section.units, axisType);\n    return {\n      // Negative section IDs are used to indicate that these are synthetic sections\n      section_id: -i,\n      t_age,\n      b_age,\n      t_pos,\n      b_pos,\n      units: section.units as T[],\n    };\n  });\n}\n\nexport function getSectionPosRange(\n  units: BaseUnit[],\n  axisType: 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Math.max(...t_positions)];\n  }\n}\n\nexport function getSectionAgeRange(units: BaseUnit[]): [number, number] {\n  /** Get the overall age range of a set of units. */\n  return getSectionPosRange(units, ColumnAxisType.AGE);\n}\n\nexport function mergeOverlappingSections<T extends UnitLong>(\n  sections: SectionInfo<T>[],\n): SectionInfo<T>[] {\n  /** Columns can have sections that overlap in time. Here, we merge overlapping\n   * sections into a single section to correctly render gap-bound packages.\n   */\n  const [firstSection, ...rest] = sections;\n  const newSections = [firstSection];\n  for (const section of rest) {\n    const lastSection = newSections[newSections.length - 1];\n    if (\n      lastSection.b_age < section.t_age ||\n      lastSection.t_age > section.b_age\n    ) {\n      // No overlap, add the section as normal\n      newSections.push(section);\n      continue;\n    }\n\n    // Overlap, merge the sections\n    lastSection.section_id = [\n      ...ensureArray(lastSection.section_id),\n      ...ensureArray(section.section_id),\n    ];\n    lastSection.units.push(...section.units);\n    lastSection.b_age = Math.max(lastSection.b_age, section.b_age);\n    lastSection.t_age = Math.min(lastSection.t_age, section.t_age);\n  }\n  return newSections;\n}\n\nexport function preprocessSectionUnit(unit: UnitLong): UnitLong {\n  /** Preprocess a single unit for a \"section\" column type.\n   * This mostly handles vagaries of eODP-style columns.\n   * */\n\n  let b_pos = unit.b_pos;\n  let t_pos = unit.t_pos;\n\n  let unit_name = unit.unit_name;\n\n  // eODP columns sometimes have overlapping core sections, which are encoded in the name field\n  // Match eODP section names\n  const match = unit.unit_name.match(/^(\\d+(\\.\\d+)?)-(\\d+(\\.\\d+)?): (.+)/);\n\n  if (match) {\n    // These values should already be set if we've used the show_positions flag\n    t_pos ??= ensureRealFloat(match[1]);\n    b_pos ??= ensureRealFloat(match[3]);\n    unit_name = match[5];\n  }\n\n  return {\n    ...unit,\n    b_pos: ensureRealFloat(b_pos),\n    t_pos: ensureRealFloat(t_pos),\n    unit_name,\n  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package/dist/prepare-units/helpers.d.ts

@@ -1,10 +1,27 @@
 import { BaseUnit, UnitLong } from '@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 {};