public class EasyXT extends Object
| Modifier and Type | Field and Description |
|---|---|
static Map<Imaris.tType,Integer> |
datatype |
| Constructor and Description |
|---|
EasyXT() |
| 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) |
public static Imaris.IApplicationPrx getImaris()
public static Imaris.IDataItemPrx getItem(String name) throws Imaris.Error
name - the name of the item in the Imaris SceneImaris.Error - an Imaris Error Objectpublic static Imaris.IDataItemPrx getItem(String type, int position) throws Imaris.Error
type - its type, as defined by the enum ItemQuery.ItemTypeposition - the 0-based position of the objectImaris.Error - an Imaris Error Objectpublic static Imaris.ISpotsPrx getSpots(String name) throws Imaris.Error
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)Imaris.Error - an Imaris Error Objectpublic static Imaris.ISpotsPrx getSpots(int position)
throws Imaris.Error
position - the 0-based position of the spots. a value of 2 would try to return the 3rd spots objectImaris.Error - an Imaris Error Objectpublic static Imaris.ISurfacesPrx getSurfaces(String name) throws Imaris.Error
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)Imaris.Error - an Imaris Error Objectpublic static Imaris.ISurfacesPrx getSurfaces(int position)
throws Imaris.Error
position - the 0-based position of the surfaces. a value of 2 would try to return the 3rd surfaces objectImaris.Error - an Imaris Error Objectpublic static List<Imaris.IDataItemPrx> getAll(String type) throws Imaris.Error
type - the type, defined by a String. See ItemQuery.ItemTypeImaris.Error - an Imaris Error Objectpublic static List<Imaris.ISpotsPrx> getAllSpots() throws Imaris.Error
Imaris.Error - an Imaris Error Objectpublic static List<Imaris.ISurfacesPrx> getAllSurfaces() throws Imaris.Error
Imaris.Error - an Imaris Error Objectpublic static ij.ImagePlus getImagePlus(Imaris.IDataSetPrx dataset)
throws Imaris.Error
dataset - Imaris.Errorpublic static void setImagePlus(Imaris.IDataSetPrx dataset,
ij.ImagePlus imp)
throws Imaris.Error
dataset - the dataset to insert the imagePlus intoImaris.Error - an Imaris Error Objectpublic static Imaris.IDataSetPrx getCurrentDataset()
throws Imaris.Error
Imaris.Error - an Imaris Error Objectpublic static void setCurrentDataset(Imaris.IDataSetPrx dataset)
throws Imaris.Error
dataset - a IDataSetPrx object containing a reference to all the pixel dataImaris.Error - an Imaris Error Objectpublic static void addChannels(ij.ImagePlus imp)
throws Imaris.Error
imp - the image to add to the current datasetImaris.Error - an Imaris Error objectpublic static void addChannels(Imaris.IDataSetPrx dataset,
ij.ImagePlus imp)
throws Imaris.Error
dataset - imp - the image to add to the current datasetImaris.Error - an Imaris Error objectpublic 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:
imp - the image from which to extract the channels to appenddataset - the receiver datasetxstart - 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)Imaris.Error - an Imaris Error Objectpublic static void addToScene(Imaris.IDataItemPrx item)
throws Imaris.Error
item - the item (Spot, Surface, Folder) to addImaris.Error - an Imaris Error Objectpublic static void addToScene(Imaris.IDataContainerPrx parent,
Imaris.IDataItemPrx item)
throws Imaris.Error
parent - The parent itemitem - the item to add as a childImaris.Error - an Imaris Error Objectpublic static void removeFromScene(Imaris.IDataItemPrx item)
throws Imaris.Error
item - the item in questionImaris.Error - an Imaris Error Objectpublic static Imaris.IDataContainerPrx createGroup(String groupName) throws Imaris.Error
groupName - the name to identify the group withaddToScene(IDataItemPrx)) or to which other items
can be added as children addToScene(IDataContainerPrx, IDataItemPrx)
IDataContainerPrx extends IDataItemPrxImaris.Errorpublic static Imaris.IDataSetPrx getSurfaceDataset(Imaris.ISurfacesPrx surface)
throws Imaris.Error
Imaris.Errorpublic static ij.ImagePlus getSurfaceMask(Imaris.ISurfacesPrx surface)
throws Imaris.Error
Imaris.Errorpublic static void setSurfaceMask(Imaris.ISurfacesPrx surface,
ij.ImagePlus imp)
throws Imaris.Error
Imaris.Errorpublic static ij.ImagePlus getSurfaceMask(Imaris.ISurfacesPrx surface,
int timepoint)
throws Imaris.Error
Imaris.Errorpublic static ij.ImagePlus getSurfaceMask(Imaris.ISurfacesPrx surface,
double downsample,
int timepoint)
throws Imaris.Error
Imaris.Errorpublic static Imaris.IDataSetPrx getSurfaceDataset(Imaris.ISurfacesPrx surface,
double downsample,
int timepoint)
throws Imaris.Error
Imaris.Errorpublic static void openImage(File filepath, String options) throws Imaris.Error
Imaris.Errorpublic static void openImage(File filepath) throws Imaris.Error
openImage(File, String)filepath - to an *.ims fileImaris.Errorpublic static void saveImage(File filepath, String options) throws Imaris.Error
filepath - path to save ims fileoptions - 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.Imaris.Errorpublic static void saveImage(File filepath) throws Imaris.Error
saveImage(File, String)filepath - path to save ims fileImaris.Errorpublic static ij.measure.ResultsTable getStatistics(Imaris.IDataItemPrx item,
String name)
throws Imaris.Error
item - the item to queryname - the name of the statistic, as in the IJ GUI minus the "Ch=1 Img=1", ... textImaris.Error - an Imaris Error Objectpublic static ij.measure.ResultsTable getStatistics(Imaris.IDataItemPrx item,
String name,
Integer channel)
throws Imaris.Error
item - the item to queryname - the name of the statistic, as in the IJ GUI minus the "Ch=1 Img=1", ... textchannel - the channel for which we want the statisticImaris.Error - an Imaris Error Objectpublic static ij.measure.ResultsTable getStatistics(Imaris.IDataItemPrx item,
List<String> names)
throws Imaris.Error
item - the item to querynames - the names of the statistic, as in the IJ GUI minus the "Ch=1 Img=1", ... textImaris.Error - an Imaris Error Objectpublic static ij.measure.ResultsTable getStatistics(Imaris.IDataItemPrx item,
List<String> names,
Integer channel)
throws Imaris.Error
item - the item to querynames - the names of the statistic, as in the IJ GUI minus the "Ch=1 Img=1", ... textchannel - the channel for which we want the statisticImaris.Error - an Imaris Error Objectpublic static ij.measure.ResultsTable getStatistics(Imaris.IDataItemPrx item,
List<String> names,
List<Integer> channels)
throws Imaris.Error
item - the item to querynames - the names of the statistic, as in the IJ GUI minus the "Ch=1 Img=1", ... textchannels - the channels for which we want the statisticImaris.Error - an Imaris Error Objectpublic static void appendResults(ij.measure.ResultsTable source,
ij.measure.ResultsTable target)
source - the results table to get the data fromtarget - the results table to insert the data into.public static Color getColorFromInt(int color)
color - the Imaris Color descriptorpublic static Color getColorIntFromIntArray(int[] color)
color - the Java Colorpublic static int getBitDepth(Imaris.IDataSetPrx dataset)
throws Imaris.Error
datatypedataset - Imaris.Error - an Imaris Error Objectpublic static String getName(Imaris.IDataItemPrx item) throws Imaris.Error
item - the item whose name we needImaris.Error - an Imaris Error Objectpublic static String getOpenImageName() throws Imaris.Error
Imaris.ErrorCopyright © 2011–2020 SciJava. All rights reserved.