EasyXT (EasyXT 0.1.0 API)

java.lang.Object
- ch.epfl.biop.imaris.EasyXT

```
public class EasyXT
extends Object
```
EasyXT static class: Wrap Imaris Extension API in a convenient way

Field Summary

Fields
Modifier and Type Field and Description

static Map<Imaris.tType,Integer> datatype

Fields
Modifier and Type	Field and Description
`static Map<Imaris.tType,Integer>`	`datatype`

Constructor Summary

Constructors
Constructor and Description

EasyXT()

Constructors
Constructor and Description
`EasyXT()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`addChannels(Imaris.IDataSetPrx dataset, ij.ImagePlus imp)` Adds the selected ImagePlus to the provided IDatasetPrx by appending it as new channels
`static void`	`addChannels(Imaris.IDataSetPrx dataset, ij.ImagePlus imp, int xstart, int ystart, int zstart, int tstart)` Adds the selected ImagePlus to the provided IDatasetPrx by appending each channel of the ImagePlus as new channels into the provided IDataSetPrx, at a given starting location in XYCZT
`static void`	`addChannels(ij.ImagePlus imp)` Adds the selected ImagePlus to the current Dataset by appending it as new channels If the dataset is visible in the Imaris Scene, this is a lot slower
`static void`	`addToScene(Imaris.IDataContainerPrx parent, Imaris.IDataItemPrx item)` Adds the provided item as the last child to the provided parent item
`static void`	`addToScene(Imaris.IDataItemPrx item)` Adds the provided Item to the Main Imaris Scene (at the bottom)
`static void`	`appendResults(ij.measure.ResultsTable source, ij.measure.ResultsTable target)` Helps append results to another results table
`static Imaris.IDataContainerPrx`	`createGroup(String groupName)` Creates a "Group" (folder) that can contain other items
`static List<Imaris.IDataItemPrx>`	`getAll(String type)` Get all items of the requested type
`static List<Imaris.ISpotsPrx>`	`getAllSpots()` Get all spots objects in the main scene as a list
`static List<Imaris.ISurfacesPrx>`	`getAllSurfaces()` Get all surfaces objects in the main scene as a list
`static int`	`getBitDepth(Imaris.IDataSetPrx dataset)` Returns bitdepth of a dataset.
`static Color`	`getColorFromInt(int color)` Recover a Color for use to set ImagePlus LUTs
`static Color`	`getColorIntFromIntArray(int[] color)` recover an RGB color for use with ImageJ from a 3 element (R,G,B) array
`static Imaris.IDataSetPrx`	`getCurrentDataset()` Convenience method to return the currently active dataset
`static ij.ImagePlus`	`getImagePlus(Imaris.IDataSetPrx dataset)` Returns an ImagePlus image of a dataset TODO : add a way to select only a subpart of it
`static Imaris.IApplicationPrx`	`getImaris()` Returns instance of Imaris App
`static Imaris.IDataItemPrx`	`getItem(String name)` Return the first item with the selected name.
`static Imaris.IDataItemPrx`	`getItem(String type, int position)` Returns nth item of a given type
`static String`	`getName(Imaris.IDataItemPrx item)` Get the name of the requested item, to avoid using GetName()
`static String`	`getOpenImageName()`
`static Imaris.ISpotsPrx`	`getSpots(int position)` Get the n-th spots object in the scene
`static Imaris.ISpotsPrx`	`getSpots(String name)` Get the first spots object with the given name
`static ij.measure.ResultsTable`	`getStatistics(Imaris.IDataItemPrx item, List<String> names)` returns the selected statistics
`static ij.measure.ResultsTable`	`getStatistics(Imaris.IDataItemPrx item, List<String> names, Integer channel)` returns the selected statistics at the selected channel Careful.
`static ij.measure.ResultsTable`	`getStatistics(Imaris.IDataItemPrx item, List<String> names, List<Integer> channels)` returns the selected statistics at the selected channels Careful.
`static ij.measure.ResultsTable`	`getStatistics(Imaris.IDataItemPrx item, String name)` returns the selected statistic from the selected item
`static ij.measure.ResultsTable`	`getStatistics(Imaris.IDataItemPrx item, String name, Integer channel)` returns only the selected statistic at the selected channel Careful.
`static Imaris.IDataSetPrx`	`getSurfaceDataset(Imaris.ISurfacesPrx surface)`
`static Imaris.IDataSetPrx`	`getSurfaceDataset(Imaris.ISurfacesPrx surface, double downsample, int timepoint)`
`static ij.ImagePlus`	`getSurfaceMask(Imaris.ISurfacesPrx surface)`
`static ij.ImagePlus`	`getSurfaceMask(Imaris.ISurfacesPrx surface, double downsample, int timepoint)`
`static ij.ImagePlus`	`getSurfaceMask(Imaris.ISurfacesPrx surface, int timepoint)`
`static Imaris.ISurfacesPrx`	`getSurfaces(int position)` Get the first surfaces object with the given name
`static Imaris.ISurfacesPrx`	`getSurfaces(String name)` Get the first surfaces object with the given name
`static void`	`openImage(File filepath)` overloaded method , see `openImage(File, String)`
`static void`	`openImage(File filepath, String options)`
`static void`	`removeFromScene(Imaris.IDataItemPrx item)` Removes the provided item from its parent
`static void`	`saveImage(File filepath)` overloaded method , see `saveImage(File, String)`
`static void`	`saveImage(File filepath, String options)` Saves the current imaris scene to an imaris file
`static void`	`setCurrentDataset(Imaris.IDataSetPrx dataset)` Convenience method to set/replace the current dataset within the current Imaris scene with the one provided
`static void`	`setImagePlus(Imaris.IDataSetPrx dataset, ij.ImagePlus imp)` Set data from an ImagePlus image into a dataset TODO : add a way to select only a subpart of it
`static void`	`setSurfaceMask(Imaris.ISurfacesPrx surface, ij.ImagePlus imp)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - datatype
```
public static Map<Imaris.tType,Integer> datatype
```
- Constructor Detail
  - EasyXT
```
public EasyXT()
```
- Method Detail
  - getImaris
```
public static Imaris.IApplicationPrx getImaris()
```
    Returns instance of Imaris App
    
    Returns:
  - getItem
```
public static Imaris.IDataItemPrx getItem(String name)
                                   throws Imaris.Error
```
    Return the first item with the selected name. Returns null if not found
    
    Parameters:
    
    name - the name of the item in the Imaris Scene
    
    Returns:
    
    the requested item, null if not found
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getItem
```
public static Imaris.IDataItemPrx getItem(String type,
                                          int position)
                                   throws Imaris.Error
```
    Returns nth item of a given type
    
    Parameters:
    
    type - its type, as defined by the enum ItemQuery.ItemType
    
    position - the 0-based position of the object
    
    Returns:
    
    the requested item, null if not found
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getSpots
```
public static Imaris.ISpotsPrx getSpots(String name)
                                 throws Imaris.Error
```
    Get the first spots object with the given name
    
    Parameters:
    
    name - the name of the spots object to get. Returns the first spots object if there are multiple spots with the same name (Don't do that)
    
    Returns:
    
    the requested spots, null if not found
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getSpots
```
public static Imaris.ISpotsPrx getSpots(int position)
                                 throws Imaris.Error
```
    Get the n-th spots object in the scene
    
    Parameters:
    
    position - the 0-based position of the spots. a value of 2 would try to return the 3rd spots object
    
    Returns:
    
    the requested spots, null if not found
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getSurfaces
```
public static Imaris.ISurfacesPrx getSurfaces(String name)
                                       throws Imaris.Error
```
    Get the first surfaces object with the given name
    
    Parameters:
    
    name - the name of the surfaces object to get. Returns the first surfaces object if there are multiple surfaces with the same name (Don't do that)
    
    Returns:
    
    the requested surfaces, null if not found
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getSurfaces
```
public static Imaris.ISurfacesPrx getSurfaces(int position)
                                       throws Imaris.Error
```
    Get the first surfaces object with the given name
    
    Parameters:
    
    position - the 0-based position of the surfaces. a value of 2 would try to return the 3rd surfaces object
    
    Returns:
    
    the requested surfaces, null if not found
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getAll
```
public static List<Imaris.IDataItemPrx> getAll(String type)
                                        throws Imaris.Error
```
    Get all items of the requested type
    
    Parameters:
    
    type - the type, defined by a String. See ItemQuery.ItemType
    
    Returns:
    
    a list containins the objects
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getAllSpots
```
public static List<Imaris.ISpotsPrx> getAllSpots()
                                          throws Imaris.Error
```
    Get all spots objects in the main scene as a list
    
    Returns:
    
    the spots as a list
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getAllSurfaces
```
public static List<Imaris.ISurfacesPrx> getAllSurfaces()
                                                throws Imaris.Error
```
    Get all surfaces objects in the main scene as a list
    
    Returns:
    
    the surfaces as a list
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getImagePlus
```
public static ij.ImagePlus getImagePlus(Imaris.IDataSetPrx dataset)
                                 throws Imaris.Error
```
    Returns an ImagePlus image of a dataset TODO : add a way to select only a subpart of it
    
    Parameters:
    
    dataset -
    
    Returns:
    
    Throws:
    
    Imaris.Error
  - setImagePlus
```
public static void setImagePlus(Imaris.IDataSetPrx dataset,
                                ij.ImagePlus imp)
                         throws Imaris.Error
```
    Set data from an ImagePlus image into a dataset TODO : add a way to select only a subpart of it
    
    Parameters:
    
    dataset - the dataset to insert the imagePlus into
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getCurrentDataset
```
public static Imaris.IDataSetPrx getCurrentDataset()
                                            throws Imaris.Error
```
    Convenience method to return the currently active dataset
    
    Returns:
    
    a IDatasetPrx object containing a reference to all the pixel data
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - setCurrentDataset
```
public static void setCurrentDataset(Imaris.IDataSetPrx dataset)
                              throws Imaris.Error
```
    Convenience method to set/replace the current dataset within the current Imaris scene with the one provided
    
    Parameters:
    
    dataset - a IDataSetPrx object containing a reference to all the pixel data
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - addChannels
```
public static void addChannels(ij.ImagePlus imp)
                        throws Imaris.Error
```
    Adds the selected ImagePlus to the current Dataset by appending it as new channels If the dataset is visible in the Imaris Scene, this is a lot slower
    
    Parameters:
    
    imp - the image to add to the current dataset
    
    Throws:
    
    Imaris.Error - an Imaris Error object
  - addChannels
```
public static void addChannels(Imaris.IDataSetPrx dataset,
                               ij.ImagePlus imp)
                        throws Imaris.Error
```
    Adds the selected ImagePlus to the provided IDatasetPrx by appending it as new channels
    
    Parameters:
    
    dataset -
    
    imp - the image to add to the current dataset
    
    Throws:
    
    Imaris.Error - an Imaris Error object
  - addChannels
```
public static void addChannels(Imaris.IDataSetPrx dataset,
                               ij.ImagePlus imp,
                               int xstart,
                               int ystart,
                               int zstart,
                               int tstart)
                        throws Imaris.Error
```
    Adds the selected ImagePlus to the provided IDatasetPrx by appending each channel of the ImagePlus as new channels into the provided IDataSetPrx, at a given starting location in XYCZT
    
    Sanity checks performed:
    - Ensure ImagePlus dimensions are not larger than the provided dataset dimensions (including provided starting locations). Throws an Error if larger than the dataset.
    - Ensure consistent bit-depth between ImagePlus and IDataSetPrx. throws Error if otherwise
    - Ensure consistent voxel size (ignore framerate) between ImagePlus and Dataset. Issues warning if otherwise
    The user can define the start location XYZT in pixel coordinates
    Parameters:
    
    imp - the image from which to extract the channels to append
    
    dataset - the receiver dataset
    
    xstart - start X position, in pixels (from top-left in ImageJ, will translate to bottom-left in Imaris)
    
    ystart - start Y position, in pixels (from top-left in ImageJ, will translate to bottom-left in Imaris)
    
    zstart - start Z position, in pixels (Z=0 is the top slice in Image, will translate to bottom slice in Imaris)
    
    tstart - start T position, in pixels (from top-left in ImageJ, will translate to bottom-left in Imaris)
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - addToScene
```
public static void addToScene(Imaris.IDataItemPrx item)
                       throws Imaris.Error
```
    Adds the provided Item to the Main Imaris Scene (at the bottom)
    
    Parameters:
    
    item - the item (Spot, Surface, Folder) to add
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - addToScene
```
public static void addToScene(Imaris.IDataContainerPrx parent,
                              Imaris.IDataItemPrx item)
                       throws Imaris.Error
```
    Adds the provided item as the last child to the provided parent item
    
    Parameters:
    
    parent - The parent item
    
    item - the item to add as a child
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - removeFromScene
```
public static void removeFromScene(Imaris.IDataItemPrx item)
                            throws Imaris.Error
```
    Removes the provided item from its parent
    
    Parameters:
    
    item - the item in question
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - createGroup
```
public static Imaris.IDataContainerPrx createGroup(String groupName)
                                            throws Imaris.Error
```
    Creates a "Group" (folder) that can contain other items
    
    Parameters:
    
    groupName - the name to identify the group with
    
    Returns:
    
    an item that can be added to a scene (addToScene(IDataItemPrx)) or to which other items can be added as children addToScene(IDataContainerPrx, IDataItemPrx) IDataContainerPrx extends IDataItemPrx
    
    Throws:
    
    Imaris.Error
  - getSurfaceDataset
```
public static Imaris.IDataSetPrx getSurfaceDataset(Imaris.ISurfacesPrx surface)
                                            throws Imaris.Error
```
    Throws:
    
    Imaris.Error
  - getSurfaceMask
```
public static ij.ImagePlus getSurfaceMask(Imaris.ISurfacesPrx surface)
                                   throws Imaris.Error
```
    Throws:
    
    Imaris.Error
  - setSurfaceMask
```
public static void setSurfaceMask(Imaris.ISurfacesPrx surface,
                                  ij.ImagePlus imp)
                           throws Imaris.Error
```
    Throws:
    
    Imaris.Error
  - getSurfaceMask
```
public static ij.ImagePlus getSurfaceMask(Imaris.ISurfacesPrx surface,
                                          int timepoint)
                                   throws Imaris.Error
```
    Throws:
    
    Imaris.Error
  - getSurfaceMask
```
public static ij.ImagePlus getSurfaceMask(Imaris.ISurfacesPrx surface,
                                          double downsample,
                                          int timepoint)
                                   throws Imaris.Error
```
    Throws:
    
    Imaris.Error
  - getSurfaceDataset
```
public static Imaris.IDataSetPrx getSurfaceDataset(Imaris.ISurfacesPrx surface,
                                                   double downsample,
                                                   int timepoint)
                                            throws Imaris.Error
```
    Throws:
    
    Imaris.Error
  - openImage
```
public static void openImage(File filepath,
                             String options)
                      throws Imaris.Error
```
    Throws:
    
    Imaris.Error
  - openImage
```
public static void openImage(File filepath)
                      throws Imaris.Error
```
    overloaded method , see openImage(File, String)
    
    Parameters:
    
    filepath - to an *.ims file
    
    Throws:
    
    Imaris.Error
  - saveImage
```
public static void saveImage(File filepath,
                             String options)
                      throws Imaris.Error
```
    Saves the current imaris scene to an imaris file
    
    Parameters:
    
    filepath - path to save ims file
    
    options - option string cf : xtinterface/structImaris_1_1IApplication.html/FileSave eg writer="BMPSeries". List of formats available: Imaris5, Imaris3, Imaris2,SeriesAdjustable, TiffSeriesRGBA, ICS, OlympusCellR, OmeXml, BMPSeries, MovieFromSlices.
    
    Throws:
    
    Imaris.Error
  - saveImage
```
public static void saveImage(File filepath)
                      throws Imaris.Error
```
    overloaded method , see saveImage(File, String)
    
    Parameters:
    
    filepath - path to save ims file
    
    Throws:
    
    Imaris.Error
  - getStatistics
```
public static ij.measure.ResultsTable getStatistics(Imaris.IDataItemPrx item,
                                                    String name)
                                             throws Imaris.Error
```
    returns the selected statistic from the selected item
    
    Parameters:
    
    item - the item to query
    
    name - the name of the statistic, as in the IJ GUI minus the "Ch=1 Img=1", ... text
    
    Returns:
    
    a ResultsTable to be used and displayed by ImageJ
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getStatistics
```
public static ij.measure.ResultsTable getStatistics(Imaris.IDataItemPrx item,
                                                    String name,
                                                    Integer channel)
                                             throws Imaris.Error
```
    returns only the selected statistic at the selected channel Careful. Imaris results are one-based for channels
    
    Parameters:
    
    item - the item to query
    
    name - the name of the statistic, as in the IJ GUI minus the "Ch=1 Img=1", ... text
    
    channel - the channel for which we want the statistic
    
    Returns:
    
    a ResultsTable to be used and displayed by ImageJ
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getStatistics
```
public static ij.measure.ResultsTable getStatistics(Imaris.IDataItemPrx item,
                                                    List<String> names)
                                             throws Imaris.Error
```
    returns the selected statistics
    
    Parameters:
    
    item - the item to query
    
    names - the names of the statistic, as in the IJ GUI minus the "Ch=1 Img=1", ... text
    
    Returns:
    
    a ResultsTable to be used and displayed by ImageJ
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getStatistics
```
public static ij.measure.ResultsTable getStatistics(Imaris.IDataItemPrx item,
                                                    List<String> names,
                                                    Integer channel)
                                             throws Imaris.Error
```
    returns the selected statistics at the selected channel Careful. Imaris results are one-based for channels
    
    Parameters:
    
    item - the item to query
    
    names - the names of the statistic, as in the IJ GUI minus the "Ch=1 Img=1", ... text
    
    channel - the channel for which we want the statistic
    
    Returns:
    
    a ResultsTable to be used and displayed by ImageJ
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getStatistics
```
public static ij.measure.ResultsTable getStatistics(Imaris.IDataItemPrx item,
                                                    List<String> names,
                                                    List<Integer> channels)
                                             throws Imaris.Error
```
    returns the selected statistics at the selected channels Careful. Imaris results are one-based for channels
    
    Parameters:
    
    item - the item to query
    
    names - the names of the statistic, as in the IJ GUI minus the "Ch=1 Img=1", ... text
    
    channels - the channels for which we want the statistic
    
    Returns:
    
    a ResultsTable to be used and displayed by ImageJ
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - appendResults
```
public static void appendResults(ij.measure.ResultsTable source,
                                 ij.measure.ResultsTable target)
```
    Helps append results to another results table
    
    Parameters:
    
    source - the results table to get the data from
    
    target - the results table to insert the data into.
  - getColorFromInt
```
public static Color getColorFromInt(int color)
```
    Recover a Color for use to set ImagePlus LUTs
    
    Parameters:
    
    color - the Imaris Color descriptor
    
    Returns:
    
    the Java Color
  - getColorIntFromIntArray
```
public static Color getColorIntFromIntArray(int[] color)
```
    recover an RGB color for use with ImageJ from a 3 element (R,G,B) array
    
    Parameters:
    
    color - the Java Color
    
    Returns:
  - getBitDepth
```
public static int getBitDepth(Imaris.IDataSetPrx dataset)
                       throws Imaris.Error
```
    Returns bitdepth of a dataset. See datatype
    
    Parameters:
    
    dataset -
    
    Returns:
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getName
```
public static String getName(Imaris.IDataItemPrx item)
                      throws Imaris.Error
```
    Get the name of the requested item, to avoid using GetName()
    
    Parameters:
    
    item - the item whose name we need
    
    Returns:
    
    the name of the item
    
    Throws:
    
    Imaris.Error - an Imaris Error Object
  - getOpenImageName
```
public static String getOpenImageName()
                               throws Imaris.Error
```
    Throws:
    
    Imaris.Error

Class EasyXT

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

datatype

Constructor Detail

EasyXT

Method Detail

getImaris

getItem

getItem

getSpots

getSpots

getSurfaces

getSurfaces

getAll

getAllSpots

getAllSurfaces

getImagePlus

setImagePlus

getCurrentDataset

setCurrentDataset

addChannels

addChannels

addChannels

addToScene

addToScene

removeFromScene

createGroup

getSurfaceDataset

getSurfaceMask

setSurfaceMask

getSurfaceMask

getSurfaceMask

getSurfaceDataset

openImage

openImage

saveImage

saveImage

getStatistics

getStatistics

getStatistics

getStatistics

getStatistics

appendResults

getColorFromInt

getColorIntFromIntArray

getBitDepth

getName

getOpenImageName