Class CellGrid

java.lang.Object
net.imglib2.img.cell.CellGrid
public class CellGrid extends Object
Defines AbstractCellImg geometry and translates between image, cell, and grid coordinates.

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    static class 
    CellGrid.CellDimensionsAndSteps
     
    class 
    CellGrid.CellIntervals
     
    private class 
    CellGrid.CellIntervalsRA
     

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    private final int[]
    borderSize
     
    private final int[]
    cellDimensions
     
    private final CellGrid.CellDimensionsAndSteps[]
    cellDimensionsAndSteps
    Pre-computed dimensions[], steps[], and numPixels for each distinct cell type (inner, X border, Y border, XY border, etc).
    private final CellGrid.CellIntervals
    cellIntervals
     
    private final long[]
    dimensions
     
    private final int
    hashcode
     
    private final int
    n
     
    private final long[]
    numCells
     
    private final long[]
    steps
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    CellGrid(long[] dimensions, int[] cellDimensions)
     
    CellGrid(CellGrid grid)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    cellDimension(int d)
    Get the number of pixels in a standard cell in dimension d.
    void
    cellDimensions(int[] dimensions)
    Write the number of pixels in a standard cell in each dimension into the provided dimensions array.
    CellGrid.CellIntervals
    cellIntervals()
     
    boolean
    equals(Object obj)
     
    (package private) void
    getCellAndPixelIndices(long index, long[] indices)
    From a global index (in CellIterationOrder, with flat iteration order of the cells), compute the flattened grid index of the cell containing index, and the flattened pixel index within the cell.
    (package private) int
    getCellCoordinates(long[] position, int[] cellSteps, long[] cellMin, long[] cellMax)
    Compute all cell-related coordinates/sizes required by CellRandomAccess.
    int
    getCellDimension(int d, long cellGridPosition)
    From the position of a cell in the grid, compute the size of the cell in dimension d.
    int[]
    getCellDimensions()
    Get the number of pixels in a standard cell in each dimension as a new int[].
    CellGrid.CellDimensionsAndSteps
    getCellDimensions(long[] cellGridPosition, long[] cellMin)
    From the position of a cell in the grid, compute the image position of the first pixel of the cell (the offset of the cell in image coordinates) and the dimensions of the cell.
    void
    getCellDimensions(long[] cellGridPosition, long[] cellMin, int[] cellDims)
    From the position of a cell in the grid, compute the image position of the first pixel of the cell (the offset of the cell in image coordinates) and the dimensions of the cell.
    CellGrid.CellDimensionsAndSteps
    getCellDimensions(long index, long[] cellMin)
    From the index of a cell in the grid, compute the image position of the first pixel of the cell (the offset of the cell in image coordinates) and the dimensions of the cell.
    void
    getCellDimensions(long index, long[] cellMin, int[] cellDims)
    From the index of a cell in the grid, compute the image position of the first pixel of the cell (the offset of the cell in image coordinates) and the dimensions of the cell.
    long
    getCellGridIndexFlat(long[] cellGridPosition)
    From the position of a cell in the grid, compute the flattened index of the cell in the grid.
    void
    getCellGridPositionFlat(long index, long[] cellGridPosition)
    From the flattened index of a cell in the grid, compute the position of a cell in the grid.
    void
    getCellInterval(long[] cellGridPosition, long[] cellMin, long[] cellMax)
     
    long
    getCellMin(int d, long cellGridPosition)
    From the position of a cell in the grid, compute the image position in dimension d of the first pixel of the cell (the offset of the cell in image coordinates).
    void
    getCellPosition(long[] position, long[] cellPos)
    Get the grid position of the cell containing the element at position.
    void
    getCellPosition(long[] position, Positionable cellPos)
    Get the grid position of the cell containing the element at position.
    long[]
    getGridDimensions()
    Get the number of cells in each dimension as a new long[].
    long[]
    getImgDimensions()
    Get the number of pixels in each dimension as a new long[].
    (package private) void
    getIndicesFromGridPosition(long[] cellGridPosition, long[] indices)
    From the grid coordinates of a cell, compute the grid index of the cell, and the global index of the first pixel in the cell.
    (package private) void
    getIndicesFromGridPosition(Localizable cellGridPosition, long[] indices)
    From the grid coordinates of a cell, compute the grid index of the cell, and the global index of the first pixel in the cell.
    long
    gridDimension(int d)
    Get the number of cells in dimension d.
    void
    gridDimensions(long[] dimensions)
    Write the number of cells in each dimension into the provided dimensions array.
    int
    hashCode()
     
    long
    imgDimension(int d)
    Get the number of pixels in dimension d.
    void
    imgDimensions(long[] dimensions)
    Write the number of pixels in each dimension into the provided dimensions array.
    (package private) long
    indexOfFirstPixelInCell(long cellGridIndex)
    Get the global index of the first pixel in the cell with the given cellGridIndex.
    (package private) long
    indexOfFirstPixelInCell(long[] cellGridPosition)
    Get the global index of the first pixel in the cell with the given grid coordinates.
    (package private) long
    indexOfFirstPixelInCell(long cellGridIndex, long[] tmp)
    Get the global index of the first pixel in the cell with the given cellGridIndex.
    (package private) long
    indexOfFirstPixelInCell(Localizable cellGridPosition)
    Get the global index of the first pixel in the cell with the given grid coordinates.
    int
    numDimensions()
     
    String
    toString()
     

    Methods inherited from class Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait

  • Field Details

    • n

      private final int n

    • dimensions

      private final long[] dimensions

    • steps

      private final long[] steps

    • cellDimensions

      private final int[] cellDimensions

    • numCells

      private final long[] numCells

    • borderSize

      private final int[] borderSize

    • hashcode

      private final int hashcode

    • cellDimensionsAndSteps

      private final CellGrid.CellDimensionsAndSteps[] cellDimensionsAndSteps
      Pre-computed dimensions[], steps[], and numPixels for each distinct cell type (inner, X border, Y border, XY border, etc). Indexed by flattened cell type index, where cell type is arranges in a 2^n grid with the inner cell at (0,...,0) etc.

    • cellIntervals

      private final CellGrid.CellIntervals cellIntervals

  • Constructor Details

    • CellGrid

      public CellGrid(long[] dimensions, int[] cellDimensions)
      Parameters:
      dimensions - the dimensions of the image (in pixels, not in cells).
      cellDimensions - the dimensions of a standard cell (in pixels). Cells on the max border of the image may be cut off and have different dimensions.

    • CellGrid

      public CellGrid(CellGrid grid)

  • Method Details

    • numDimensions

      public int numDimensions()

    • getGridDimensions

      public long[] getGridDimensions()
      Get the number of cells in each dimension as a new long[].

    • gridDimensions

      public void gridDimensions(long[] dimensions)
      Write the number of cells in each dimension into the provided dimensions array.

    • gridDimension

      public long gridDimension(int d)
      Get the number of cells in dimension d.

    • getImgDimensions

      public long[] getImgDimensions()
      Get the number of pixels in each dimension as a new long[]. Note, that this is the number of pixels in all cells combined, not the number of cells!

    • imgDimensions

      public void imgDimensions(long[] dimensions)
      Write the number of pixels in each dimension into the provided dimensions array. Note, that this is the number of pixels in all cells combined, not the number of cells!

    • imgDimension

      public long imgDimension(int d)
      Get the number of pixels in dimension d. Note, that this is the number of pixels in all cells combined, not the number of cells!

    • getCellDimensions

      public int[] getCellDimensions()
      Get the number of pixels in a standard cell in each dimension as a new int[]. Cells on the borders of the image may be cut off and have different dimensions.

    • cellDimensions

      public void cellDimensions(int[] dimensions)
      Write the number of pixels in a standard cell in each dimension into the provided dimensions array. Cells on the max border of the image may be cut off and have different dimensions.

    • cellDimension

      public int cellDimension(int d)
      Get the number of pixels in a standard cell in dimension d. Cells on the max border of the image may be cut off and have different dimensions.

    • getCellDimensions

      public void getCellDimensions(long index, long[] cellMin, int[] cellDims)
      From the index of a cell in the grid, compute the image position of the first pixel of the cell (the offset of the cell in image coordinates) and the dimensions of the cell. The dimensions will be the standard cellDimensions unless the cell is at the border of the image in which case it might be truncated.

      Note, that this method assumes that the cell grid has flat iteration order. It this is not the case, use getCellDimensions(long[], long[], int[]).

      Parameters:
      index - flattened grid coordinates of the cell.
      cellMin - offset of the cell in image coordinates are written here.
      cellDims - dimensions of the cell are written here.

    • getCellDimensions

      public void getCellDimensions(long[] cellGridPosition, long[] cellMin, int[] cellDims)
      From the position of a cell in the grid, compute the image position of the first pixel of the cell (the offset of the cell in image coordinates) and the dimensions of the cell. The dimensions will be the standard cellDimensions unless the cell is at the border of the image in which case it might be truncated.
      Parameters:
      cellGridPosition - grid coordinates of the cell.
      cellMin - offset of the cell in image coordinates are written here.
      cellDims - dimensions of the cell are written here.

    • getCellDimensions

      public CellGrid.CellDimensionsAndSteps getCellDimensions(long index, long[] cellMin)
      From the index of a cell in the grid, compute the image position of the first pixel of the cell (the offset of the cell in image coordinates) and the dimensions of the cell. The dimensions will be the standard cellDimensions unless the cell is at the border of the image in which case it might be truncated.

      Note, that this method assumes that the cell grid has flat iteration order. It this is not the case, use getCellDimensions(long[], long[], int[]).

      Parameters:
      index - flattened grid coordinates of the cell.
      cellMin - offset of the cell in image coordinates are written here.
      Returns:
      the dimensions of the cell and derived strides and number of pixels.

    • getCellDimensions

      public CellGrid.CellDimensionsAndSteps getCellDimensions(long[] cellGridPosition, long[] cellMin)
      From the position of a cell in the grid, compute the image position of the first pixel of the cell (the offset of the cell in image coordinates) and the dimensions of the cell. The dimensions will be the standard cellDimensions unless the cell is at the border of the image in which case it might be truncated.
      Parameters:
      cellGridPosition - grid coordinates of the cell.
      cellMin - offset of the cell in image coordinates are written here.
      Returns:
      the dimensions of the cell and derived strides and number of pixels.

    • getCellInterval

      public void getCellInterval(long[] cellGridPosition, long[] cellMin, long[] cellMax)

    • getCellDimension

      public int getCellDimension(int d, long cellGridPosition)
      From the position of a cell in the grid, compute the size of the cell in dimension d. The size will be the standard cellDimensions unless the cell is at the border of the image in which case it might be truncated.
      Parameters:
      d - dimension index
      cellGridPosition - grid coordinates of the cell in dimension d.
      Returns:
      size of the cell in dimension d.

    • getCellMin

      public long getCellMin(int d, long cellGridPosition)
      From the position of a cell in the grid, compute the image position in dimension d of the first pixel of the cell (the offset of the cell in image coordinates).
      Parameters:
      d - dimension index
      cellGridPosition - grid coordinates of the cell in dimension d.
      Returns:
      offset of the cell in dimension d (in image coordinates).

    • getCellGridPositionFlat

      public void getCellGridPositionFlat(long index, long[] cellGridPosition)
      From the flattened index of a cell in the grid, compute the position of a cell in the grid.
      Parameters:
      index - flattened grid coordinates of the cell.
      cellGridPosition - grid coordinates of the cell are written here.

    • getCellGridIndexFlat

      public long getCellGridIndexFlat(long[] cellGridPosition)
      From the position of a cell in the grid, compute the flattened index of the cell in the grid.
      Parameters:
      cellGridPosition - grid coordinates of the cell
      Returns:
      flattened grid coordinates of the cell.

    • getCellPosition

      public void getCellPosition(long[] position, long[] cellPos)
      Get the grid position of the cell containing the element at position.
      Parameters:
      position - position of an element in the image.
      cellPos - is set to the grid position of the cell containing the element.

    • getCellPosition

      public void getCellPosition(long[] position, Positionable cellPos)
      Get the grid position of the cell containing the element at position.
      Parameters:
      position - position of an element in the image.
      cellPos - is set to the grid position of the cell containing the element.

    • getCellAndPixelIndices

      void getCellAndPixelIndices(long index, long[] indices)
      From a global index (in CellIterationOrder, with flat iteration order of the cells), compute the flattened grid index of the cell containing index, and the flattened pixel index within the cell.
      Parameters:
      index - pixel index in flat iteration order
      indices - array with 2 elements, which will be set to the flattened cell index (indices[0]), and the flattened pixel index within the cell (indices[1]).

    • getIndicesFromGridPosition

      void getIndicesFromGridPosition(long[] cellGridPosition, long[] indices)
      From the grid coordinates of a cell, compute the grid index of the cell, and the global index of the first pixel in the cell.
      Parameters:
      cellGridPosition - grid coordinates of a cell
      indices - array with 2 elements, which will be set to the grid index of the cell (indices[0]), and the global pixel index of the first pixel in the cell (indices[1]).

    • getIndicesFromGridPosition

      void getIndicesFromGridPosition(Localizable cellGridPosition, long[] indices)
      From the grid coordinates of a cell, compute the grid index of the cell, and the global index of the first pixel in the cell.
      Parameters:
      cellGridPosition - grid coordinates of a cell
      indices - array with 2 elements, which will be set to the grid index of the cell (indices[0]), and the global pixel index of the first pixel in the cell (indices[1]).

    • indexOfFirstPixelInCell

      long indexOfFirstPixelInCell(long cellGridIndex)
      Get the global index of the first pixel in the cell with the given cellGridIndex.
      Parameters:
      cellGridIndex - grid index of a cell
      Returns:
      global index of the first pixel in the cell

    • indexOfFirstPixelInCell

      long indexOfFirstPixelInCell(long cellGridIndex, long[] tmp)
      Get the global index of the first pixel in the cell with the given cellGridIndex.
      Parameters:
      cellGridIndex - grid index of a cell
      tmp - temporary array used to store the gird coordinates of the cell
      Returns:
      global index of the first pixel in the cell

    • indexOfFirstPixelInCell

      long indexOfFirstPixelInCell(long[] cellGridPosition)
      Get the global index of the first pixel in the cell with the given grid coordinates.
      Parameters:
      cellGridPosition - grid coordinates of a cell
      Returns:
      global index of the first pixel in the cell

    • indexOfFirstPixelInCell

      long indexOfFirstPixelInCell(Localizable cellGridPosition)
      Get the global index of the first pixel in the cell with the given grid coordinates.
      Parameters:
      cellGridPosition - grid coordinates of a cell
      Returns:
      global index of the first pixel in the cell

    • getCellCoordinates

      int getCellCoordinates(long[] position, int[] cellSteps, long[] cellMin, long[] cellMax)
      Compute all cell-related coordinates/sizes required by CellRandomAccess.
      Parameters:
      position - current image position
      cellSteps - allocation steps for cell are written here.
      cellMin - offset of the cell in image coordinates are written here.
      cellMax - is set to the max of the cell in image coordinates are written here.
      Returns:
      index within the cell.

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • cellIntervals

      public CellGrid.CellIntervals cellIntervals()