.. java:import:: ij ImageStack

.. java:import:: ij ImagePlus

.. java:import:: ij.process FloatProcessor

.. java:import:: ij.io FileSaver

.. java:import:: java.io File

.. java:import:: java.nio ByteBuffer

.. java:import:: ch.epfl.leb.sass.utils.images ImageS

.. java:import:: ch.epfl.leb.sass.utils.images ImageShapeException

DefaultImageS
=============

.. java:package:: ch.epfl.leb.sass.utils.images.internal
   :noindex:

.. java:type:: public class DefaultImageS implements ImageS

   The default implementation of the ImageS interface. The default implementation currently wraps ImageJ1's ImageStack class. See https://imagej.nih.gov/ij/developer/api/ij/ImagePlus.html for more information.

   :author: Kyle M. Douglass

Constructors
------------
DefaultImageS
^^^^^^^^^^^^^

.. java:constructor:: public DefaultImageS(int width, int height)
   :outertype: DefaultImageS

   Creates a new and empty DefaultImageS.

DefaultImageS
^^^^^^^^^^^^^

.. java:constructor:: public DefaultImageS(int[][] pixels)
   :outertype: DefaultImageS

   Creates a new DefaultImageS object from a 2D array of ints. The first index of the input array should correspond to x; the second corresponds to y.

   :param pixels: The 2D array of pixel values.

DefaultImageS
^^^^^^^^^^^^^

.. java:constructor:: public DefaultImageS(float[][] pixels)
   :outertype: DefaultImageS

   Creates a new DefaultImageS object from a 2D array of floats. The first index of the input array should correspond to x; the second corresponds to y.

   :param pixels: The 2D array of pixel values.

Methods
-------
addImage
^^^^^^^^

.. java:method:: @Override public void addImage(short[][] image) throws ImageShapeException
   :outertype: DefaultImageS

   Adds a 2D array of shorts to the dataset.

   :param image: A 2D array of shorts.

addImage
^^^^^^^^

.. java:method:: @Override public void addImage(int[][] image) throws ImageShapeException
   :outertype: DefaultImageS

   Converts a 2D array of ints to 16-bit shorts and adds it to the dataset.

   :param image: A 2D array of ints indexed by xy.
   :throws ch.epfl.leb.sass.utils.images.ImageShapeException:

addImage
^^^^^^^^

.. java:method:: @Override public void addImage(float[][] image) throws ImageShapeException
   :outertype: DefaultImageS

   Converts a 2D array of floats to 16-bit shorts and adds it to the dataset.

   :param image: A 2D array of floats indexed by xy.
   :throws ch.epfl.leb.sass.utils.images.ImageShapeException:

concatenate
^^^^^^^^^^^

.. java:method:: @Override public void concatenate(ImageS dataset) throws ImageShapeException
   :outertype: DefaultImageS

   Appends another ImageS dataset to the end of this one.

   :param dataset: The images to add to the dataset.

getBitDepth
^^^^^^^^^^^

.. java:method:: @Override public int getBitDepth()
   :outertype: DefaultImageS

getHeight
^^^^^^^^^

.. java:method:: @Override public int getHeight()
   :outertype: DefaultImageS

   Returns the height of the images in the dataset.

   :return: The height of the images in the dataset.

getPixelData
^^^^^^^^^^^^

.. java:method:: @Override public short[] getPixelData(int index)
   :outertype: DefaultImageS

   Returns the pixel data at the given index as a 1D array.

   :param index: The index of the corresponding slice.
   :return: The pixel data at the provided index.

getSize
^^^^^^^

.. java:method:: @Override public int getSize()
   :outertype: DefaultImageS

   Returns the number of images in the dataset.

   :return: The number of images in the dataset.

getSlice
^^^^^^^^

.. java:method:: @Override public int getSlice()
   :outertype: DefaultImageS

   Gets the active slice of the dataset (0-indexed). This is the image that will be displayed in the viewer.

   :return: The index of the active slice.

getTitle
^^^^^^^^

.. java:method:: @Override public String getTitle()
   :outertype: DefaultImageS

   Returns the title of the image stack.

   :return: The title of the image stack.

getWidth
^^^^^^^^

.. java:method:: @Override public int getWidth()
   :outertype: DefaultImageS

   Returns the width of the images in the dataset.

   :return: The width of the images in the dataset.

saveAsTiffStack
^^^^^^^^^^^^^^^

.. java:method:: @Override public void saveAsTiffStack(File file) throws IllegalArgumentException
   :outertype: DefaultImageS

   Saves the images to a TIFF file.

serializeToArray
^^^^^^^^^^^^^^^^

.. java:method:: @Override public byte[] serializeToArray()
   :outertype: DefaultImageS

   Serializes the image stack to a TIFF-encoded byte array.

   :return: A TIFF-encoded byte array.

serializeToBuffer
^^^^^^^^^^^^^^^^^

.. java:method:: @Override public ByteBuffer serializeToBuffer()
   :outertype: DefaultImageS

   Returns a buffer containing the dataset in a TIFF-encoded byte array.

   :return: A buffer containing the dataset in a TIFF-encoded byte array.

setSlice
^^^^^^^^

.. java:method:: @Override public void setSlice(int index)
   :outertype: DefaultImageS

   Sets the active slice of the dataset (0-indexed). This is the image that will be displayed in the viewer.

   :param index: The index of the slice to activate.

setTitle
^^^^^^^^

.. java:method:: @Override public void setTitle(String title)
   :outertype: DefaultImageS

   Sets the title of the image stack.

   :param title: The title of the image stack.

updateView
^^^^^^^^^^

.. java:method:: @Override public void updateView()
   :outertype: DefaultImageS

   Updates the dataset viewer to show the currently active slice.

view
^^^^

.. java:method:: @Override public void view()
   :outertype: DefaultImageS

   Displays the images in a ImagePlus window.