Class PixelsWrapper

    • Field Detail

      • MAX_DIST

        public static final int MAX_DIST
        Size of tiles when retrieving pixels
        See Also:
        Constant Field Values
    • Constructor Detail

      • PixelsWrapper

        public PixelsWrapper​(PixelsData pixels)
        Constructor of the PixelsWrapper class
        Parameters:
        pixels - The PixelData to be wrap.
    • Method Detail

      • loadPlanesInfo

        public void loadPlanesInfo​(Browser browser)
                            throws ServiceException,
                                   AccessException,
                                   java.util.concurrent.ExecutionException
        Loads the planes information.
        Specified by:
        loadPlanesInfo in interface Pixels
        Parameters:
        browser - The data browser.
        Throws:
        ServiceException - Cannot connect to OMERO.
        AccessException - Cannot access data.
        java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.
      • getPlanesInfo

        public java.util.List<PlaneInfo> getPlanesInfo()
        Retrieves the planes information (which need to be loaded first).
        Specified by:
        getPlanesInfo in interface Pixels
        Returns:
        See above.
      • getPixelType

        public java.lang.String getPixelType()
        Gets the pixel type.
        Specified by:
        getPixelType in interface Pixels
        Returns:
        the pixel type.
      • getPixelSizeX

        public Length getPixelSizeX()
        Gets the size of a single image pixel on the X axis.
        Specified by:
        getPixelSizeX in interface Pixels
        Returns:
        Size of a pixel on the X axis.
      • getPixelSizeY

        public Length getPixelSizeY()
        Gets the size of a single image pixel on the Y axis.
        Specified by:
        getPixelSizeY in interface Pixels
        Returns:
        Size of a pixel on the Y axis.
      • getPixelSizeZ

        public Length getPixelSizeZ()
        Gets the size of a single image pixel on the Z axis.
        Specified by:
        getPixelSizeZ in interface Pixels
        Returns:
        Size of a pixel on the Z axis.
      • getTimeIncrement

        public Time getTimeIncrement()
        Gets the time increment between time points.
        Specified by:
        getTimeIncrement in interface Pixels
        Returns:
        Time increment between time points.
      • getMeanTimeInterval

        public Time getMeanTimeInterval()
        Computes the mean time interval from the planes deltaTs.

        Planes information needs to be loaded first.

        Specified by:
        getMeanTimeInterval in interface Pixels
        Returns:
        See above.
      • getMeanExposureTime

        public Time getMeanExposureTime​(int channel)
        Computes the mean exposure time for a given channel from the planes exposureTime.

        Planes information needs to be loaded first.

        Specified by:
        getMeanExposureTime in interface Pixels
        Parameters:
        channel - The channel index.
        Returns:
        See above.
      • getPositionX

        public Length getPositionX()
        Retrieves the X stage position.

        Planes information needs to be loaded first.

        Specified by:
        getPositionX in interface Pixels
        Returns:
        See above.
      • getPositionY

        public Length getPositionY()
        Retrieves the Y stage position.

        Planes information needs to be loaded first.

        Specified by:
        getPositionY in interface Pixels
        Returns:
        See above.
      • getPositionZ

        public Length getPositionZ()
        Retrieves the Z stage position.

        Planes information needs to be loaded first.

        Specified by:
        getPositionZ in interface Pixels
        Returns:
        See above.
      • getSizeX

        public int getSizeX()
        Gets the size of the image on the X axis
        Specified by:
        getSizeX in interface Pixels
        Returns:
        Size of the image on the X axis.
      • getSizeY

        public int getSizeY()
        Gets the size of the image on the Y axis
        Specified by:
        getSizeY in interface Pixels
        Returns:
        Size of the image on the Y axis.
      • getSizeZ

        public int getSizeZ()
        Gets the size of the image on the Z axis
        Specified by:
        getSizeZ in interface Pixels
        Returns:
        Size of the image on the Z axis.
      • getSizeC

        public int getSizeC()
        Gets the size of the image on the C axis
        Specified by:
        getSizeC in interface Pixels
        Returns:
        Size of the image on the C axis.
      • getSizeT

        public int getSizeT()
        Gets the size of the image on the T axis
        Specified by:
        getSizeT in interface Pixels
        Returns:
        Size of the image on the T axis.
      • getAllPixels

        public double[][][][][] getAllPixels​(ConnectionHandler client,
                                             int[] xBounds,
                                             int[] yBounds,
                                             int[] cBounds,
                                             int[] zBounds,
                                             int[] tBounds)
                                      throws AccessException,
                                             java.util.concurrent.ExecutionException
        Returns an array containing the value for each voxel corresponding to the bounds
        Specified by:
        getAllPixels in interface Pixels
        Parameters:
        client - The client handling the connection.
        xBounds - Array containing the X bounds from which the pixels should be retrieved.
        yBounds - Array containing the Y bounds from which the pixels should be retrieved.
        cBounds - Array containing the C bounds from which the pixels should be retrieved.
        zBounds - Array containing the Z bounds from which the pixels should be retrieved.
        tBounds - Array containing the T bounds from which the pixels should be retrieved.
        Returns:
        Array containing the value for each voxel of the image.
        Throws:
        AccessException - If an error occurs while retrieving the plane data from the pixels source.
        java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.
      • getRawPixels

        public byte[][][][] getRawPixels​(ConnectionHandler client,
                                         int[] xBounds,
                                         int[] yBounds,
                                         int[] cBounds,
                                         int[] zBounds,
                                         int[] tBounds,
                                         int bpp)
                                  throws java.util.concurrent.ExecutionException,
                                         AccessException
        Returns an array containing the raw values for each voxel for each plane corresponding to the bounds
        Specified by:
        getRawPixels in interface Pixels
        Parameters:
        client - The client handling the connection.
        xBounds - Array containing the X bounds from which the pixels should be retrieved.
        yBounds - Array containing the Y bounds from which the pixels should be retrieved.
        cBounds - Array containing the C bounds from which the pixels should be retrieved.
        zBounds - Array containing the Z bounds from which the pixels should be retrieved.
        tBounds - Array containing the T bounds from which the pixels should be retrieved.
        bpp - Bytes per pixels of the image.
        Returns:
        a table of bytes containing the pixel values
        Throws:
        AccessException - If an error occurs while retrieving the plane data from the pixels source.
        java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.