Package loci.formats.in.LeicaMicrosystemsMetadata

Class MetadataTempBuffer

java.lang.Object
loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
public class MetadataTempBuffer extends Object
This class is used to temporarily store metadata information extracted from Leica XML before it is written to the reader's MetadataStore
Author:
Melissa Linkert melissa at glencoesoftware.com, Constanze Wendlandt constanze.wendlandt at leica-microsystems.com

  • Field Details

    • channelColors

      public List<ArrayList<ome.xml.model.primitives.Color>> channelColors

    • channelPrios

      public int[][] channelPrios

    • physicalSizeXs

      public List<Double> physicalSizeXs

    • physicalSizeYs

      public List<Double> physicalSizeYs

    • fieldPosX

      public List<ome.units.quantity.Length> fieldPosX

    • fieldPosY

      public List<ome.units.quantity.Length> fieldPosY

    • descriptions

      public String[] descriptions

    • microscopeModels

      public String[] microscopeModels

    • serialNumber

      public String[] serialNumber

    • pinholes

      public Double[] pinholes

    • zooms

      public Double[] zooms

    • zSteps

      public Double[] zSteps

    • tSteps

      public Double[] tSteps

    • lensNA

      public Double[] lensNA

    • flipX

      public boolean[] flipX

    • flipY

      public boolean[] flipY

    • swapXY

      public boolean[] swapXY

    • expTimes

      public Double[][] expTimes

    • gains

      public Double[][] gains

    • detectorOffsets

      public Double[][] detectorOffsets

    • channelNames

      public String[][] channelNames

    • detectorModels

      public ArrayList<ArrayList<String>> detectorModels

    • exWaves

      public Double[][] exWaves

    • activeDetector

      public ArrayList<ArrayList<Boolean>> activeDetector

    • detectorIndexes

      public ArrayList<HashMap<Integer,String>> detectorIndexes

    • immersions

      public String[] immersions

    • corrections

      public String[] corrections

    • objectiveModels

      public String[] objectiveModels

    • magnification

      public Double[] magnification

    • posX

      public ome.units.quantity.Length[] posX

    • posY

      public ome.units.quantity.Length[] posY

    • posZ

      public ome.units.quantity.Length[] posZ

    • refractiveIndex

      public Double[] refractiveIndex

    • cutIns

      public ArrayList<ArrayList<ome.units.quantity.Length>> cutIns

    • cutOuts

      public ArrayList<ArrayList<ome.units.quantity.Length>> cutOuts

    • filterModels

      public ArrayList<ArrayList<String>> filterModels

    • timestamps

      public Double[][] timestamps

    • laserIntensity

      public ArrayList<ArrayList<Double>> laserIntensity

    • laserWavelength

      public ArrayList<ArrayList<Double>> laserWavelength

    • laserActive

      public ArrayList<ArrayList<Boolean>> laserActive

    • laserFrap

      public ArrayList<ArrayList<Boolean>> laserFrap

    • imageROIs

      public ROI[][] imageROIs

    • alternateCenter

      public boolean alternateCenter

    • imageNames

      public String[] imageNames

    • acquiredDate

      public double[] acquiredDate

    • tileCount

      public int[] tileCount

    • tileBytesInc

      public long[] tileBytesInc

    • inverseRgb

      public boolean[] inverseRgb

    • dimensions

      private ArrayList<ArrayList<Dimension>> dimensions

    • channels

      public ArrayList<ArrayList<Channel>> channels

  • Constructor Details

    • MetadataTempBuffer

      public MetadataTempBuffer(int len)
      Constructs a MetadataTempBuffer for a given number of images.
      Parameters:
      len - Number of images (one per XLIF)

  • Method Details

    • getDimension

      public Dimension getDimension(int imageIndex, Dimension.DimensionKey key)

    • addDimension

      public void addDimension(int imageIndex, Dimension dimension)
      Inserts dimension to buffer and optionally adapts other dimension-dependent values
      Parameters:
      imageIndex -
      dimension -

    • getDimensionOrder

      public String getDimensionOrder(int imageIndex)
      Returns the dimension order as a string
      Parameters:
      imageIndex -
      Returns:
      dimension order string, as it is expected in CoreMetadata.dimensionOrder

    • sortDimensions

      private void sortDimensions(int coreIndex)
      Sorts list of existing dimensions by increasing bytesInc, beginning with X and Y, ending with stage position
      Parameters:
      coreIndex -

    • getDimensions

      public ArrayList<Dimension> getDimensions(int imageIndex)

    • addMissingDimensions

      public void addMissingDimensions(int imageIndex)
      Adds Z, T and S dimension if they haven't been added already
      Parameters:
      imageIndex -

    • addChannelDimension

      public void addChannelDimension(int coreIndex)
      Adds channel dimension
      Parameters:
      coreIndex -

    • getChannelDimensionBytesInc

      private long getChannelDimensionBytesInc(int coreIndex)

    • ArrayListOfArrayLists

      private <T> ArrayList<ArrayList<T>> ArrayListOfArrayLists(int rows, Class<T> type)

    • ArrayListOfHashMaps

      private <T, S> ArrayList<HashMap<T,S>> ArrayListOfHashMaps(int rows, Class<T> key, Class<S> value)