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BETA 3.2
Installing the OMERO gateway for Matlab
Compiling OMERO Gateway
1. OMERO Gateway Dependancies
Creating a connection using OMERO Gateway in Java
The Gateway Methods
Matlab Helper methods
Examples in Matlab using OMEROJava
BETA 4.0
1. Installing the new Gateway
2. Examples using the new gateway and GatewayUtils

A Matlab interface to OMERO.blitz

OMERO Gateway is in a state of flux, please be aware that the code is changing alot.

Omero provides a mechanism to access the OMERO.blitz server from Matlab. The interface provides a java gateway to OMERO.blitz which can be accessed from Matlab.

BETA 3.2

Installing the OMERO gateway for Matlab

To install the OMERO gateway you will need to compile the OMERO gateway in the omero/components/blitz directory (see Compiling OMERO Gateway), or the Blitz-3.0-Beta3.jar from ~/omero/dist/client created when compiling the server. The resulting jar should be copied into the libs (MatlabDir/java/libs) directory of Matlab with all the dependent libs(see Compiling The OMERO Gateway, subsection OMEROJava dependancies). The path to the newly added jars should be added to the class path file (MatlabDir/local/toolbox/classpath.txt).

Compiling OMERO Gateway

The OMERO Gateway will be compiled as part of the OMERO.blitz build and the resulting jar, Blitz-3.0-Beta3.jar will be created in the OMERODir/dist/client directory.

OMERO Gateway Dependancies

The OMERO Gateway consists of 3 files which are located in the /dist/client directory once the OMERO.blitz server has been built. These files are

ice-3.2.0.jar
model-psql-3.0-Beta3.jar

Creating a connection using OMERO Gateway in Java

The OMERO gateway provides methods to access the OMERO.blitz server, many of the methods are helper methods which provide extra functionality so that using the OMERO.blitz server does not require understanding of the data model, or server services.

To create a connection to the server we need to create a client object, and a session and then ask to create a gateway object.

client = omero.client('hostname');
session = client.createSession('username','password');
gateway = session.createGateway();

For further information on the connecting to OMERO see [wiki OmeroJava]

The Gateway Methods

The following are a list of methods provided by OMERO Gateway.

Connection Methods

These methods create and maintain connections to the OMERO.blitz server.

Method Detail

isClosed

public boolean isClosed()

Is the session closed?

Returns:: true if closed.

close

public void close()

Close the session with the server.

createSession

public void createSession(java.lang.String username,
                          java.lang.String password)
                   throws DSOutOfServiceException,
                          DSAccessException

Open a session to the server with username and password.

Parameters:: username - see above.; password - see above.
Throws:: DSOutOfServiceException; DSAccessException

keepAlive

public void keepAlive()
               throws DSOutOfServiceException,
                      DSAccessException

Keep service alive.

Throws:: DSOutOfServiceException; DSAccessException

Data Service Methods

These methods work with the data in the server but not on the images or file directly, for instance, methods in the data service will work with project->dataset->image objects.

Method Detail

getProjects

public java.util.List<Project> getProjects(java.util.List<java.lang.Long> ids,
                                           boolean withLeaves)
                                    throws DSOutOfServiceException,
                                           DSAccessException

Get the projects, and datasets in the OMERO.Blitz server in the user account.

Parameters:: ids - user ids to get the projects from, if null will retrieve all projects from the users account.; withLeaves - get the projects, images and pixels too.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getDatasets

public java.util.List<Dataset> getDatasets(java.util.List<java.lang.Long> ids,
                                           boolean withLeaves)
                                    throws DSOutOfServiceException,
                                           DSAccessException

Get the datasets in the OMERO.Blitz server in the projects ids.

Parameters:: ids - of the datasets to retrieve, if null get all users datasets.; withLeaves - get the images and pixels too.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getPixelsFromImage

public java.util.List<Pixels> getPixelsFromImage(long imageId)
                                          throws DSOutOfServiceException,
                                                 DSAccessException

Get the pixels associated with the image, this is normally one pixels per image, but can be more.

Parameters:: imageId -
Returns:: the list of pixels.
Throws:: DSOutOfServiceException; DSAccessException

getImage

public Image getImage(long id)
               throws DSOutOfServiceException,
                      DSAccessException

Get the image with id

Parameters:: id - see above
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getImages

public java.util.List<Image> getImages(OMEROClass parentType,
                                       java.util.List<java.lang.Long> ids)
                                throws DSOutOfServiceException,
                                       DSAccessException

Get the images in the OMERO.Blitz server from the object parentType with id's in list ids.

Parameters:: parentType - see above.; ids - see above.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

findAllByQuery

public java.lang.Object findAllByQuery(java.lang.String myQuery)
                                throws DSOutOfServiceException,
                                       DSAccessException

Run the query passed as a string in the iQuery interface. This method will return list of objects.

Parameters:: myQuery - string containing the query.
Returns:: the result.
Throws:: DSOutOfServiceException; DSAccessException

findByQuery

public java.lang.Object findByQuery(java.lang.String myQuery)
                             throws DSOutOfServiceException,
                                    DSAccessException

Run the query passed as a string in the iQuery interface. The method expects to return only one result from the query, if more than one result is to be returned the method will throw an exception.

Parameters:: myQuery - string containing the query.
Returns:: the result.
Throws:: DSOutOfServiceException; DSAccessException

getPixels

public Pixels getPixels(long pixelsId)
                 throws DSOutOfServiceException,
                        DSAccessException

Get the pixels information for an image, this method will also attach the logical channels, channels, and other metadata in the pixels.

Parameters:: pixelsId - image id relating to the pixels.
Returns:: see above.
Throws:: DSAccessException; DSOutOfServiceException; DSOutOfServiceException; DSAccessException

copyPixels

public long copyPixels(long pixelsID,
                       int x,
                       int y,
                       int t,
                       int z,
                       java.util.List<java.lang.Integer> channelList,
                       java.lang.String methodology)
                throws DSOutOfServiceException,
                       DSAccessException

Copy the pixels to a new pixels, this is only the data object and does not create a pixels object in the RawPixelsStore, To load data into the plane the uploadPlane(long, int, int, int, double[][]) to add data to the pixels.

Parameters:: pixelsID - pixels id to copy.; x - width of plane.; y - height of plane.; t - num timepoints; z - num zsections.; channelList - the list of channels to copy, this is the channel index.; methodology - user supplied text, describing the methods that created the pixels.
Returns:: new id.
Throws:: DSOutOfServiceException; DSAccessException

copyImage

public long copyImage(long imageId,
                      int x,
                      int y,
                      int t,
                      int z,
                      java.util.List<java.lang.Integer> channelList,
                      java.lang.String imageName)
               throws DSOutOfServiceException,
                      DSAccessException

Copy the image and it's attached pixels and metadata to a new Image and return the id of the new image. The method will not copy annotations or attachments.

Parameters:: imageId - image id to copy.; x - width of plane.; y - height of plane.; t - The number of time-points; z - The number of zSections.; channelList - the list of channels to copy, [0-(sizeC-1)].; imageName - The new imageName.
Returns:: new id.
Throws:: DSOutOfServiceException; DSAccessException

updatePixels

public Pixels updatePixels(Pixels object)
                    throws DSOutOfServiceException,
                           DSAccessException

Update the pixels object on the server, updating appropriate tables in the database and returning a new copy of the pixels.

Parameters:: object - see above.
Returns:: the new updated pixels.
Throws:: DSOutOfServiceException; DSAccessException

getPixelTypes

public java.util.List<PixelsType> getPixelTypes()
                                         throws DSOutOfServiceException,
                                                DSAccessException

Get a list of all the possible pixelsTypes in the server.

Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getPixelType


public PixelsType getPixelType(java.lang.String type)
                        throws DSOutOfServiceException,
                               DSAccessException

Get the pixelsType for type of name type.

Parameters:: type - see above.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

attachImageToDataset

public void attachImageToDataset(Dataset dataset,
                                 Image image)
                          throws DSOutOfServiceException,
                                 DSAccessException

Attach an image to a dataset.

Parameters:: dataset - see above.; image - see above.
Throws:: DSOutOfServiceException; DSAccessException

createImage

public long createImage(int sizeX,
                        int sizeY,
                        int sizeZ,
                        int sizeT,
                        java.util.List<java.lang.Integer> channelList,
                        PixelsType pixelsType,
                        java.lang.String name,
                        java.lang.String description)
                 throws DSOutOfServiceException,
                        DSAccessException

Create a new Image of X,Y, and zSections+time-points. The channelList is the emission wavelength of the channel and the pixelsType.

Parameters:: sizeX - width of plane.; sizeY - height of plane.; sizeZ - num zSections.; sizeT - num time-points; channelList - the list of channels to copy.; pixelsType - the type of pixels in the image.; name - the image name.; description - the description of the image.
Returns:: new id.
Throws:: DSOutOfServiceException; DSAccessException

getImageFromDatasetByName

public java.util.List<Image> getImageFromDatasetByName(long datasetId,
                                                       java.lang.String imageName)
                                                throws DSOutOfServiceException,
                                                       DSAccessException

Get the images from the dataset with name, this can use wild cards.

Parameters:: datasetId - see above.; imageName - see above.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getImageByName

public java.util.List<Image> getImageByName(java.lang.String imageName)
                                     throws DSOutOfServiceException,
                                            DSAccessException

Get the list of images with name containing imageName.

Parameters:: imageName - see above.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

saveObject

public void saveObject(IObject obj)
                throws DSOutOfServiceException,
                       DSAccessException

Save the object to the db .

Parameters:: obj - see above.
Throws:: DSOutOfServiceException; DSAccessException

saveAndReturnObject

public IObject saveAndReturnObject(IObject obj)
                            throws DSOutOfServiceException,
                                   DSAccessException

Save and return the Object.

Parameters:: obj - see above.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

saveArray

public void saveArray(java.util.List<IObject> graph)
               throws DSOutOfServiceException,
                      DSAccessException

Save the array.

Parameters:: graph - see above.
Throws:: DSOutOfServiceException; DSAccessException

saveAndReturnArray

public <T extends omero.model.IObject> java.util.List<T> saveAndReturnArray(java.util.List<IObject> graph)
                                                                 throws DSOutOfServiceException,
                                                                        DSAccessException

Save and return the array.

Type Parameters:: T - The Type to return.
Parameters:: graph - the object
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

deleteObject

public void deleteObject(IObject row)
                  throws DSOutOfServiceException,
                         DSAccessException

Delete the object.

Parameters:: row - the object.(commonly a row in db)
Throws:: DSOutOfServiceException; DSAccessException

Image Service Methods

These methods manage the interactions with images on the server, creating, copying, uploading and retrieving.

Method Detail

getPlane

public double[][] getPlane(long pixelsId,
                           int z,
                           int c,
                           int t)
                    throws DSOutOfServiceException,
                           DSAccessException

Get the raw plane for the pixels pixelsId, this returns a 2d array representing the plane, it returns doubles but will not lose data.

Parameters:: pixelsId - id of the pixels to retrieve.; c - the channel of the pixels to retrieve.; t - the time point to retrieve.; z - the z section to retrieve.
Returns:: The raw plane in 2-d array of doubles.
Throws:: DSAccessException; DSOutOfServiceException

getPlane

public double[][][] getPlaneStack(long pixelsId,
                           int c,
                           int t)
                    throws DSOutOfServiceException,
                           DSAccessException

Get the zSection stack containing all the planes for the pixels pixelsId, this returns a 3d array representing the z-Stack of the plane for channel c and timepoint t, it returns doubles but will not lose data.

Parameters:: pixelsId - id of the pixels to retrieve.; c - the channel of the pixels to retrieve.; t - the time point to retrieve.
Returns:: The raw plane in 3-d array of doubles.
Throws:: DSAccessException; DSOutOfServiceException

getRenderedImage

public java.awt.image.BufferedImage getRenderedImage(long pixelsId,
                                                     int z,
                                                     int t)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Render the pixels for the zSection z and timePoint t.

Parameters:: pixelsId - pixels id of the plane to render; z - z section to render; t - timepoint to render
Returns:: The image as a buffered image.
Throws:: DSOutOfServiceException; DSAccessException

getRenderedImageMatrix

public int[][][] getRenderedImageMatrix(long pixelsId,
                                        int z,
                                        int t)
                                 throws DSOutOfServiceException,
                                        DSAccessException

Render the pixels for the zSection z and timePoint t.

Parameters:: pixelsId - pixels id of the plane to render; z - z section to render; t - timepoint to render
Returns:: The image as a 3d array where it represents the image as [x][y][channel]
Throws:: DSOutOfServiceException; DSAccessException

renderAsPackedInt

public int[] renderAsPackedInt(long pixelsId,

                               int z,
                               int t)
                        throws DSOutOfServiceException,
                               DSAccessException

Render the pixels for the zSection z and timePoint t.

Parameters:: pixelsId - pixels id of the plane to render; z - z section to render; t - timepoint to render
Returns:: The pixels are returned as 4 bytes representing the r,g,b,a of image.
Throws:: DSOutOfServiceException; DSAccessException

setActive

public void setActive(long pixelsId,
                      int w,
                      boolean active)
               throws DSOutOfServiceException,
                      DSAccessException

Set the active channels to be on or off in the rendering engine for the pixels.

Parameters:: pixelsId - the pixels id.; w - the channel; active - set active?
Throws:: DSOutOfServiceException; DSAccessException

isActive

public boolean isActive(long pixelsId,
                        int w)
                 throws DSOutOfServiceException,
                        DSAccessException

Is the channel active, turned on in the rendering engine.

Parameters:: pixelsId - the pixels id.; w - channel
Returns:: true if the channel active.
Throws:: DSOutOfServiceException; DSAccessException

getDefaultZ

public int getDefaultZ(long pixelsId)
                throws DSOutOfServiceException,
                       DSAccessException

Get the default zSection of the image, this is the zSection the image should open on when an image viewer is loaded.

Parameters:: pixelsId - the pixelsId of the image.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getDefaultT

public int getDefaultT(long pixelsId)
                throws DSOutOfServiceException,
                       DSAccessException

Get the default time-point of the image, this is the time-point the image should open on when an image viewer is loaded.

Parameters:: pixelsId - the pixelsId of the image.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

setDefaultZ

public void setDefaultZ(long pixelsId,
                        int z)
                 throws DSOutOfServiceException,
                        DSAccessException

Set the default zSection of the image, this is the zSection the image should open on when an image viewer is loaded.

Parameters:: pixelsId - the pixelsId of the image.; z - see above.
Throws:: DSOutOfServiceException; DSAccessException

setDefaultT

public void setDefaultT(long pixelsId,
                        int t)
                 throws DSOutOfServiceException,
                        DSAccessException

Set the default timepoint of the image, this is the timepoint the image should open on when an image viewer is loaded.

Parameters:: pixelsId - the pixelsId of the image.; t - see above.
Throws:: DSOutOfServiceException; DSAccessException

setChannelWindow

public void setChannelWindow(long pixelsId,
                             int w,
                             double start,
                             double end)
                      throws DSOutOfServiceException,
                             DSAccessException

Set the channel Minimum, Maximum values, that map from image space to rendered space (3 channel, 8 bit, screen).

Parameters:: pixelsId - the pixelsId of the image the mapping applied to.; w - channel of the pixels.; start - The minimum value to map from.; end - The maximum value to map to.
Throws:: DSOutOfServiceException; DSAccessException

getChannelWindowStart

public double getChannelWindowStart(long pixelsId,
                                    int w)
                             throws DSOutOfServiceException,
                                    DSAccessException

Get the channel Minimum value, that maps from image space to rendered space.

Parameters:: pixelsId - the pixelsId of the image the mapping applied to.; w - channel of the pixels.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getChannelWindowEnd

public double getChannelWindowEnd(long pixelsId,
                                  int w)
                           throws DSOutOfServiceException,
                                  DSAccessException

Get the channel Maximum value, that maps from image space to rendered space.

Parameters:: pixelsId - the pixelsId of the image the mapping applied to.; w - channel of the pixels.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

setRenderingDefId

public void setRenderingDefId(long pixelsId,
                              long renderingDefId)
                       throws DSOutOfServiceException,
                              DSAccessException

Set the rendering definition of the rendering engine from the default to the one supplied. This allows for more than one rendering definition- mapping per pixels.

Parameters:: pixelsId - for pixelsId; renderingDefId - see above.
Throws:: DSOutOfServiceException; DSAccessException

getThumbnail

public byte[] getThumbnail(long pixelsId,
                           omero.RInt sizeX,
                           omero.RInt sizeY)
                    throws DSOutOfServiceException,
                           DSAccessException

Get the thumbnail of the image.

Parameters:: pixelsId - for pixelsId; sizeX - size of thumbnail.; sizeY - size of thumbnail.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getThumbnailSet

public java.util.Map<java.lang.Long,byte[]> getThumbnailSet(omero.RInt sizeX,
                                                            omero.RInt sizeY,
                                                            java.util.List<java.lang.Long> pixelsIds)
                                                     throws DSOutOfServiceException,
                                                            DSAccessException

Get a set of thumbnails, of size X, Y from the list of pixelId's supplied in the list.

Parameters:: sizeX - size of thumbnail.; sizeY - size of thumbnail.; pixelsIds - list of ids.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getThumbnailBylongestSideSet

public java.util.Map<java.lang.Long,byte[]> getThumbnailBylongestSideSet(omero.RInt size,
                                                                         java.util.List<java.lang.Long> pixelsIds)
                                                                  throws DSOutOfServiceException,
                                                                         DSAccessException

Get a set of thumbnails from the pixelsId's in the list, maintaining aspect ratio.

Parameters:: size - size of thumbnail.; pixelsIds - list of ids.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getThumbnailBylongestSide

public byte[] getThumbnailBylongestSide(long pixelsId,
                                        omero.RInt size)
                                 throws DSOutOfServiceException,
                                        DSAccessException

Get the thumbnail of the image, maintain aspect ratio.

Parameters:: pixelsId - for pixelsId; size - size of thumbnail.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

uploadPlane

public void uploadPlane(long pixelsId,
                        int z,
                        int c,
                        int t,
                        double[][] data)
                 throws DSOutOfServiceException,
                        DSAccessException

Upload the plane to the server, on pixels id with channel and the time, + z section. the data is the client 2d data values. This will be converted to the raw server bytes.

Parameters:: pixelsId - pixels id to upload to .; z - z section.; c - channel.; t - time point.; data - plane data.
Throws:: DSOutOfServiceException; DSAccessException

getPlaneFromImage

public double[][] getPlaneFromImage(long imageId,
                                    int z,
                                    int c,
                                    int t)
                             throws DSOutOfServiceException,
                                    DSAccessException

Get the plane from the image with imageId.

Parameters:: imageId - see above.; z - zSection of the plane.; c - channel of the plane.; t - timepoint of the plane.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

File Service Methods

These methods deal with the interaction with attached files and scripts.

Method Detail

getScripts

public java.util.Map<java.lang.Long,java.lang.String> getScripts()
                                                          throws DSOutOfServiceException,
                                                                 DSAccessException

Get the scripts from the iScript Service.

Returns:: All the available scripts in a map by id and name.
Throws:: DSOutOfServiceException; DSAccessException

getScriptID

public long getScriptID(java.lang.String name)
                 throws DSOutOfServiceException,
                        DSAccessException

Get the id of the script with name

Parameters:: name - name of the script.
Returns:: the id of the script.
Throws:: DSOutOfServiceException; DSAccessException

uploadScript

public long uploadScript(java.lang.String script)
                  throws DSOutOfServiceException,
                         DSAccessException

Upload the script to the server.

Parameters:: script - script to upload
Returns:: id of the new script.
Throws:: DSOutOfServiceException; DSAccessException

getScript

public java.lang.String getScript(long id)
                           throws DSOutOfServiceException,
                                  DSAccessException

Get the script with id, this returns the actual script as a string.

Parameters:: id - id of the script to retrieve.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getParams

public java.util.Map<java.lang.String,RType> getParams(long id)
                                                throws DSOutOfServiceException,
                                                       DSAccessException

Get the parameters the script takes, this is a map of the parameter name and type.

Parameters:: id - id of the script.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

runScript

public java.util.Map<java.lang.String,RType> runScript(long id,
                                                       java.util.Map<java.lang.String,RType> map)
                                                throws DSOutOfServiceException,
                                                       DSAccessException

Run the script and get the results returned as a name , value map.

Parameters:: id - id of the script to run.; map - the map of parameters, values for inputs.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

deleteScript

public void deleteScript(long id)
                  throws DSOutOfServiceException,
                         DSAccessException

Delete the script with id from the server.

Parameters:: id - id of the script to delete.
Throws:: DSOutOfServiceException; DSAccessException

Helper Methods

These methods provide mechanisms to interact with different omero.model datastructures without making calls to the server.

Method Detail

getImagesFromDataset

public java.util.List<Image> getImagesFromDataset(Dataset dataset)
                                           throws DSOutOfServiceException,
                                                  DSAccessException

getProjects(List, boolean)findAllByQuery(String)findByQuery(String)

Parameters:: dataset - see above.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getDatasetsFromProject

public java.util.List<Dataset> getDatasetsFromProject(Project project)
                                               throws DSOutOfServiceException,
                                                      DSAccessException

This is a helper method and makes no calls to the server. It gets a list of all the dataset in a project if the project has already had the datasets attached, via getLeaves in getProjects(List, boolean) or fetched via HQL in findAllByQuery(String), findByQuery(String)

Parameters:: project - see above.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getPixelsFromDataset

public java.util.List<Pixels> getPixelsFromDataset(Dataset dataset)
                                            throws DSOutOfServiceException,
                                                   DSAccessException

This is a helper method and makes no calls to the server. It gets a list of all the pixels in a dataset if the dataset has already had the pixels attached, via getLeaves in getProjects(List, boolean) getDatasets(List, boolean) or fetched via HQL in findAllByQuery(String), findByQuery(String)

Parameters:: dataset - see above.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getPixelsFromProject

public java.util.List<Pixels> getPixelsFromProject(Project project)
                                            throws DSOutOfServiceException,
                                                   DSAccessException

This is a helper method and makes no calls to the server. It gets a list of all the pixels in a project if the project has already had the pixels attached, via getLeaves in getProjects(List, boolean) or fetched via HQL in findAllByQuery(String), findByQuery(String)

Parameters:: project - see above.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

getPixelsImageMap

public java.util.Map<java.lang.Long,Pixels> getPixelsImageMap(java.util.List<Image> images)

This is a helper methods, which makes no calls to the server. It get all the pixels attached to a list of images. It requires that the pixels are already attached via getProjects(List, boolean) getDatasets(List, boolean) or fetched via HQL in findAllByQuery(String), findByQuery(String) Get the pixels from the images in the list.

Parameters:: images - see above.
Returns:: map of the pixels-->imageId.

getPixelsFromImageList

public java.util.List<Pixels> getPixelsFromImageList(java.util.List<Image> images)

Parameters:: images - see above.
Returns:: list of the pixels.

Matlab Helper methods

Sometimes the data conversion from one type to another that allows methods to be used in Matlab requires to be done by Matlab functions. This section describes these methods and their uses.

Method Detail

getImagesFromDataset

uint8[][][] javaImageToMatlab(BufferedImage javaImage)

getRenderedImage(long, int, int)

Parameters:: dataset - see above.
Returns:: see above.
Throws:: DSOutOfServiceException; DSAccessException

Examples in Matlab using OMEROJava

The following sections contain examples of Matlab code using the OMEROJava Matlab wrappers.

Retrieve all current user Projects, and get Images in datasets

function [images] = findAllImages()
client = omero.client('hostname');
session = client.createSession('username','password');
gateway = session.createGateway();
% Get the current user projects and populate the datasets.
projects = gateway.getProjects([], true)

datasetList = java.util.ArrayList;

for projectCnt = 0:projects.size()-1,
    projectDatasetList = gateway.getDatasetsFromProject(projects.get(projectCnt));
    for j = 0:projectDatasetList.size()-1,
    	datasetList.add(projectDatasetList.get(j));
    end
end
images = java.util.ArrayList;
for i = 0:datasetList.size()-1,
    imageList = gateway.getImagesFromDataset(datasetList.get(i));
    for j = 0:imageList.size()-1,
        images.add(imageList.get(j));
    end
end

Simple Image Viewer

function drawImage(pixelsId)
client = omero.client('hostname');
session = client.createSession('username','password');
gateway = session.createGateway();
pixels = gateway.getPixels(pixelsId);
channel = 0;
figure(1);
for z=1:pixels.sizeZ.val,
    for t=1:pixels.sizeT.val,
        plane = gateway.getPlane(pixelsId, z-1, channel, t-1);
        figure(1);
        imagesc(plane);
        drawnow;
    end
end

Perform Projection on z-Stack

function performProjection(pixelsId, zSection)

client = omero.client('hostname');
session = client.createSession('username','password');
gateway = session.createGateway();
pixels = gateway.getPixels(pixelsId);
stack = gateway.getPlaneStack(pixelsId, zSection);
projectedImage = ProjectionOnStack(stack,'mean');

function [resultImage] = ProjectionOnStack(imageStack,type)

[zSections, X, Y] = size(imageStack);

if(strcmp(type,'mean') || strcmp(type, 'sum'))
    resultImage = squeeze(sum(imageStack));
    if(strcmp(type,'mean'))
        resultImage = resultImage./zSections;
    end
end
if(strcmp(type,'max'))
    resultImage = squeeze(max(imageStack,[],1));
end

BETA 4.0

Installing the new Gateway

The new gateway is installed just like the old gateway except that the jars required are located in OMERO_DIR/dist/lib/client and are:

omero_client.jar
ice.jar
model-psql.jar
blitz.jar

There have been a number of changes between Beta 3.2 and Beta 4, mostly these are the movement of methods which were strictly local transformations of the data from methods in the gateway to methods in a new package in OMEROJava called GatewayUtils.

These methods are:

Plane2D getPlane2D(PixelsI pixels, byte[] databuffer)

This method takes a pixels object and the byte buffer from getPlane and 
returns a Plane2D object which will convert the bytes to the any type.

Plane2D will be described later.

List<Projects> getDatasetsFromProject(Project)
This method is the same as getDatasetsFromProject in the Gateway, except that
the calls are all preformed locally on the client. 

List<Pixels> getPixelsFromProject(Project)
This method is the same as getPixelsFromProject in the Gateway, except that
the calls are all preformed locally on the client. 

List<Pixels> getPixelsFromImageList(List<Image>)
This method is the same as getPixelsFromImageList in the Gateway, except that
the calls are all preformed locally on the client. 

Map<Long, Image> getPixelsImageMap(List<Image>)
This method is the same as getPixelsImageMap in the Gateway, except that
the calls are all preformed locally on the client. 

List<Pixels> getPixelsFromDataset(Dataset)
This method is the same as getPixelsFromDataset in the Gateway, except that
the calls are all preformed locally on the client. 

List<Image> getImagesFromDataset(Dataset)
This method is the same as getImagesFromDataset in the Gateway, except that
the calls are all preformed locally on the client. 

List<Image> getImagesFromProject(Project)
This method is the same as getImagesFromProject in the Gateway, except that
the calls are all preformed locally on the client.

and a new methods

BufferedImage toBufferedImage(PixelsI, int[] databuffer)

This method converts the dataBuffer from getRenderedPlane in the gateway to 
a bufferedImage.

The other class which is new to the gateway is the Plane2D object which will convert byte data of the type in Pixels to the any appropriate 2D array.

The methods in Plane2D are:

double[][] getPixelsArrayAsDouble(boolean)
float[][]getPixelsArrayAsLong(boolean)
int[][]getPixelsArrayAsInt(boolean)
short[][]getPixelsArrayAsShort(boolean)
byte[][]getPixelsArrayAsByte(boolean)


Where the boolean will transpose the matrix from row data to column data.

Examples using the new gateway and GatewayUtils

The differences between the Gateway object in Beta3.2 and Beta4.0 are very small. The gateway is instantiated the same way:

client = omero.client('hostname');
session = client.createSession('username','password');
gateway = session.createGateway();

We retrieve data the same way

pixels = gateway.getPixels(56);

The only difference is using the GatewayUtils to transform the image data

rawPlane = gateway.getPlane(56, 0, 0 , 0);
plane2D = omerojava.util.GatewayUtils.getPlane2D(pixels, rawPlane);
plane = plane2D.getPixelsAsDouble(1);
imagesc(plane);

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Context Navigation

Table of Contents

A Matlab interface to OMERO.blitz

OMERO Gateway is in a state of flux, please be aware that the code is changing alot.

BETA 3.2

Installing the OMERO gateway for Matlab

Compiling OMERO Gateway

OMERO Gateway Dependancies

Creating a connection using OMERO Gateway in Java

The Gateway Methods

Connection Methods

isClosed

close

createSession

keepAlive

Data Service Methods

getProjects

getDatasets

getPixelsFromImage

getImage

getImages

findAllByQuery

findByQuery

getPixels

copyPixels

copyImage

updatePixels

getPixelTypes

getPixelType

attachImageToDataset

createImage

getImageFromDatasetByName

getImageByName

saveObject

saveAndReturnObject

saveArray

saveAndReturnArray

deleteObject

Image Service Methods

getPlane

getPlane

getRenderedImage

getRenderedImageMatrix

renderAsPackedInt

setActive

isActive

getDefaultZ

getDefaultT

setDefaultZ

setDefaultT

setChannelWindow

getChannelWindowStart

getChannelWindowEnd

setRenderingDefId

getThumbnail

getThumbnailSet

getThumbnailBylongestSideSet

getThumbnailBylongestSide

uploadPlane

getPlaneFromImage

File Service Methods

getScripts

getScriptID

uploadScript

getScript

getParams

runScript

deleteScript

Helper Methods

getImagesFromDataset

getDatasetsFromProject

getPixelsFromDataset

getPixelsFromProject

getPixelsImageMap

getPixelsFromImageList

Matlab Helper methods

getImagesFromDataset

Examples in Matlab using OMEROJava

Retrieve all current user Projects, and get Images in datasets

Simple Image Viewer