Last modified 6 weeks ago

Table of Contents

  1. Installing and Configuring
    1. Installing the OmeroMatlab Toolbox
    2. Configuring the OmeroMatlab connection
    3. Using the OmeroMatlab omero.client
    4. Keeping your session alive
    5. Closing & unloading OMERO
  2. Connect to OMERO
  3. Read Data
  4. Raw Data access
  5. Write Data
  6. How to use OMERO tables
  7. ROIs
  8. Delete data
  9. Render Images
  10. Create Image

A Matlab interface to OMERO.blitz

See DevelopingOmeroClients and ObjectModel, for an introduction about Object.

Installing and Configuring

Installing the OmeroMatlab Toolbox

Configuring the OmeroMatlab connection

As described under OmeroClients, there are several ways to configure your connection to an OMERO server. OmeroMatlab comes with a few conveniences for making this work.

If you run client = loadOmero; (i.e. loadOmero with a return value), then OmeroMatlab will try to configure the omero.client object for you. First, it checks the ICE_CONFIG environment variable. If set, it will let the omero.client constructor initialize itself. Otherwise, it looks for the file ice.config in the current directory. The OmeroMatlab toolbox comes with a default ice.config file pointing at localhost, which you can edit for your server.

Alternatively, you can pass the same parameters to loadOmero; that you would pass to omero.client: 

>> omero_client_1 = loadOmero('localhost');
>> omero_client_2 = omero.client('localhost');

Or, if you want a session created directly, the following are equivalent: 

>>> [client1, session1] = loadOmero('localhost');
>>> client2 = loadOmero('localhost');
>>> session2 = client2.createSession()

Using the OmeroMatlab omero.client

Once an active session is available in your workspace, you can acquire services, make queries, and load binary data. In short, anything the OmeroApi can do. Helper functions and demos are available for getting a feel for the API.

TODO: Review the links See the examples under source:ome.git/examples or source:ome.git/components/tools/OmeroM/demo on what you can do with OmeroMatlab.

Keeping your session alive

For executing any long running task, you will need a background thread which keeps your session alive. If you are familiar with Matlab Timers you can use omeroKeepAlive.m directly or modify it to your liking. 

>> [c,s] = loadOmero;
>> t = omeroKeepAlive(c); % Creates a 60-second timer and starts it
>> ...
>> delete(t);             % Disables the keep-alive

Alternatively, you can use the Java-based enableKeepAlive-method, but it is not configurable from within Matlab: 

>> c.enableKeepAlive(60); % Calls session.keepAlive() every 60 seconds
>> c.closeSession();      % Close session to end the keep-alive

Closing & unloading OMERO

When you are done with OMERO, it is critical that you close your connection to save resources. 

>> client1.closeSession();
>> clear client1;
>> clear session1;

Then if you would like, you can unload OMERO as well: 

>> unloadOmero;

Note: you may see the following warning when unloading OMERO: 

>> unloadOmero
Warning: Objects of omero/client class exist - not clearing java
> In javaclasspath>local_javapath at 167
  In javaclasspath at 88
  In javarmpath at 46
  In unloadOmero at 4
Warning: Objects of omero/client class exist - not clearing java
> In unloadOmero at 6

This means that there is still an OmeroMatlab object in your workspace. Use "who" to find such objects, and "clear" to remove them. After that, run clear java: 

>> who

Your variables are:

omero_client

>> clear omero_client
>> clear java

You should also unload OMERO before installing a new version of OmeroMatlab or calling loadOmero again. If you need to create another session without unloading/loading OMERO again, use the omero.client object directly: 

>> [c,s] = loadOmero(arg1,arg2);
>> c = omero.client(arg3,arg4);
>> s = c.createSession();

Code in Action

Follow several code samples showing how to interact with some objects.

Connect to OMERO

  • Connect to server.

Remember to close the session. 

client = omero.client(server, 4064); 
session = client.createSession(username, password);
%necessary to keep the proxy alive. part of the omero-package
clientAlive = omeroKeepAlive(client); 

% If you want to have the data transfer encrypted then you can 
% use the session variable otherwise use the following 
unsecureClient = client.createClient(false);
sessionUnencrypted = unsecureClient.getSession();

% The id of the user.
userId = session.getAdminService().getEventContext().userId;

% The group the user is currently logged in i.e. his/her default group
groupId = session.getAdminService().getEventContext().groupId;
  • Close connection. IMPORTANT 
client.closeSession();
unsecureClient.closeSession();

Read Data

The IContainer service provides method to load the data management hierarchy in OMERO -- Projects, Datasets, Etc. A list of examples follows, indicating how to load Project, Dataset, Screen, etc.

  • Retrieve the projects owned by the user currently logged in.

If a Project contains Datasets, the Datasets will automatically be loaded. 

proxy = session.getContainerService();
%Set the options
param = omero.sys.ParametersI();
param.leaves();%indicate to load the images
%param.noLeaves(); %no images loaded, this is the default value.
userId = session.getAdminService().getEventContext().userId; %id of the user.
param.exp(omero.rtypes.rlong(userId));
projectsList = proxy.loadContainerHierarchy('omero.model.Project', [], param);
for j = 0:projectsList.size()-1,
    p = projectsList.get(j);
    datasetsList = p.linkedDatasetList;
    for i = 0:datasetsList.size()-1,
        d = datasetsList.get(i);
        % Do something with the dataset 
        dName = d.getName().getValue();
        % If the flag is set to true, you can access the images within the dataset
        % imageList = d.linkedImageList;
        % for k = 0:imageList.size()-1,
           % image = imageList.get(k);
        % end
    end
end
  • Retrieve the Datasets owned by the user currently logged in. 
proxy = session.getContainerService();
param = omero.sys.ParametersI();
param.leaves();%indicate to load the images
userId = session.getAdminService().getEventContext().userId; %id of the user.
param.exp(omero.rtypes.rlong(userId));
datasetsList = proxy.loadContainerHierarchy('omero.model.Dataset', [], param);
  • Retrieve the Images contained in a Dataset. 
proxy = session.getContainerService();
ids = java.util.ArrayList();
ids.add(datasetId); %add the id of the dataset.
param = omero.sys.ParametersI();
param.leaves(); % indicate to load the images.
list = proxy.loadContainerHierarchy('omero.model.Dataset', ids, param);
dataset = list.get(0);
imageList = dataset.linkedImageList; % The images in the dataset.
  • Retrieve an image if the identifier is known. 
ids = java.util.ArrayList();
ids.add(imageId); %add the id of the image.

proxy = session.getContainerService();
list = proxy.getImages('omero.model.Image', ids, omero.sys.ParametersI());
image = list.get(0);
  • Access information about the image for example to draw it.

The model is as follows: Image-Pixels i.e. to access valuable data about the image you need to use the pixels object. We now only support one set of pixels per image (it used to be more!). 

pixelsList = image.copyPixels();
for k = 0:pixelsList.size()-1,
   pixels = pixelsList.get(k);
   sizeZ = pixels.getSizeZ().getValue(); % The number of z-sections.
   sizeT = pixels.getSizeT().getValue(); % The number of timepoints.
   sizeC = pixels.getSizeC().getValue(); % The number of channels.
   sizeX = pixels.getSizeX().getValue(); % The number of pixels along the X-axis.
   sizeY = pixels.getSizeY().getValue(); % The number of pixels along the Y-axis.
end
  • Retrieve Screening data owned by the user currently logged in.

To learn about the model go to ScreenPlateWell. Note that the wells are not loaded. 

proxy = session.getContainerService();
userId = session.getAdminService().getEventContext().userId; %id of the user.
param = omero.sys.ParametersI;
param.exp(omero.rtypes.rlong(userId)); %load data for a given user.

screenList = proxy.loadContainerHierarchy('omero.model.Screen', [], param);
for j = 0:screenList.size()-1,
screen = screenList.get(j);
platesList = screen.linkedPlateList;
for i = 0:platesList.size()-1,
    plate = platesList.get(i);
    plateAcquisitionList = plate.copyPlateAcquisitions();
    for k = 0:plateAcquisitionList.size()-1,
      pa = plateAcquisitionList.get(i);
    end
end

Given a plate ID, load the wells. You will have to use the findAllByQuery method. 

wellList = session.getQueryService().findAllByQuery(
['select well from Well as well '...
'left outer join fetch well.plate as pt '...
'left outer join fetch well.wellSamples as ws '...
'left outer join fetch ws.plateAcquisition as pa '...
'left outer join fetch ws.image as img '...
'left outer join fetch img.pixels as pix '...
'left outer join fetch pix.pixelsType as pt '...
'where well.plate.id = ', num2str(plateId)], []);
for j = 0:wellList.size()-1,
    well = wellList.get(j);
    wellsSampleList = well.copyWellSamples();
    well.getId().getValue()
    for i = 0:wellsSampleList.size()-1,
        ws = wellsSampleList.get(i);
        ws.getId().getValue()
        pa = ws.getPlateAcquisition();
    end
end

Raw Data access

You can retrieve data, plane by plane or retrieve a stack.

  • Retrieve a given plane.

This is useful when you need the pixels intensity. 

% To retrieve the pixels, see above.
sizeZ = pixels.getSizeZ().getValue();
sizeT = pixels.getSizeT().getValue();
sizeC = pixels.getSizeC().getValue();
pixelsId = pixels.getId().getValue();
store = session.createRawPixelsStore(); 
store.setPixelsId(pixelsId, false);
for z = 0:sizeZ-1,
   for t = 0:sizeT-1,
      for c = 0:sizeC-1,
          plane = store.getPlane(z, c, t);
          tPlane = toMatrix(plane, pixels);
          % do something with the plane
      end
   end
end
% close the store
store.close();
  • Retrieve a given tile. 
% To retrieve the pixels, see above.
sizeZ = pixels.getSizeZ().getValue();
sizeT = pixels.getSizeT().getValue();
sizeC = pixels.getSizeC().getValue();
pixelsId = pixels.getId().getValue();
store = session.createRawPixelsStore(); 
store.setPixelsId(pixelsId, false);
x = 0;
y = 0;
width = pixels.getSizeX().getValue()/2;
height = pixels.getSizeY().getValue()/2;
for z = 0:sizeZ-1,
   for t = 0:sizeT-1,
      for c = 0:sizeC-1,
          tile = store.getTile(z, c, t, x, y, width, height);
          % tPlane = toMatrix(tile, pixels);
          % do something with the tile
      end
   end
end
% close the store
store.close();
  • Retrieve a given stack.

This is useful when you need the pixels intensity. 

%Create the store to load the stack. No access via the gateway
store = session.createRawPixelsStore(); 
store.setPixelsId(pixelsId, false); %Indicate the pixels set you are working on
for t = 0:sizeT-1,
    for c = 0:sizeC-1,
        stack = store.getStack(c, t);
        % do something with the stack
      end
   end
end
store.close();
  • Retrieve a given hypercube.

This is useful when you need the pixels intensity. 

%Create the store to load the stack. No access via the gateway
store = session.createRawPixelsStore(); 
store.setPixelsId(pixelsId, false); %Indicate the pixels set you are working on

% offset values in each dimension XYZCT
offset = java.util.ArrayList;
offset.add(java.lang.Integer(0));
offset.add(java.lang.Integer(0));
offset.add(java.lang.Integer(0));
offset.add(java.lang.Integer(0));
offset.add(java.lang.Integer(0));

size = java.util.ArrayList;
size.add(java.lang.Integer(sizeX));
size.add(java.lang.Integer(sizeY));
size.add(java.lang.Integer(sizeZ));
size.add(java.lang.Integer(sizeC));
size.add(java.lang.Integer(sizeT));

% indicate the step in each direction, step = 1, will return values at index 0, 1, 2.
% step = 2, values at index 0, 2, 4 etc.
step = java.util.ArrayList;
step.add(java.lang.Integer(1));
step.add(java.lang.Integer(1));
step.add(java.lang.Integer(1));
step.add(java.lang.Integer(1));
step.add(java.lang.Integer(1));
% Retrieve the data
store.getHypercube(offset, size, step);
% close the store
store.close();

Write Data

  • Create a Dataset and link it to an existing Project. 
dataset = omero.model.DatasetI;
dataset.setName(omero.rtypes.rstring(char('name dataset')));
dataset.setDescription(omero.rtypes.rstring(char('description dataset')));

%link Dataset and Project

link = omero.model.ProjectDatasetLinkI;
link.setChild(dataset);
link.setParent(omero.model.ProjectI(projectId, false));

session.getUpdateService().saveAndReturnObject(link);
  • Create a tag (tag annotation) and link it to an existing project. 
tag = omero.model.TagAnnotationI;
tag.setTextValue(omero.rtypes.rstring(char('name tag')));
tag.setDescription(omero.rtypes.rstring(char('description tag')));

%link tag and project
link = omero.model.ProjectAnnotationLinkI;
link.setChild(tag);
link.setParent(omero.model.ProjectI(projectId, false));

session.getUpdateService().saveAndReturnObject(link);
  • Create a file annotation and link to an image.

To attach a file to an object e.g. an image, few objects need to be created:

  1. an OriginalFile
  2. a FileAnnotation
  3. a link between the Image and the FileAnnotation. 
% To retrieve the image see above.
iUpdate = session.getUpdateService(); % service used to write object

% create the original file object.
%read local file
file = java.io.File(fileToUpload);
name = file.getName();
absolutePath = file.getAbsolutePath();
path = absolutePath.substring(0, absolutePath.length()-name.length());

originalFile = omero.model.OriginalFileI;
originalFile.setName(omero.rtypes.rstring(name));
originalFile.setPath(omero.rtypes.rstring(path));
originalFile.setSize(omero.rtypes.rlong(file.length()));
originalFile.setSha1(omero.rtypes.rstring(generatedSha1));
originalFile.setMimetype(omero.rtypes.rstring(fileMimeType));

% now we save the originalFile object
originalFile = iUpdate.saveAndReturnObject(originalFile);

% Initialize the service to load the raw data
rawFileStore = session.createRawFileStore();
rawFileStore.setFileId(originalFile.getId().getValue());

%  open file and read it

%code for small file.
fid = fopen(fileToUpload);
byteArray = fread(fid,[1, file.length()], 'uint8');
rawFileStore.write(byteArray, 0, file.length());
fclose(fid);


originalFile = rawFileStore.save();
% Important to close the service
rawFileStore.close();
% now we have an original File in DB and raw data uploaded.
% We now need to link the Original file to the image using the File annotation object. That's the way to do it.
fa = omero.model.FileAnnotationI;
fa.setFile(originalFile);
fa.setDescription(omero.rtypes.rstring(description)); % The description set above e.g. PointsModel
fa.setNs(omero.rtypes.rstring(NAME_SPACE_TO_SET)) % The name space you have set to identify the file annotation.

% save the file annotation.
fa = iUpdate.saveAndReturnObject(fa);

% now link the image and the annotation
link = omero.model.ImageAnnotationLinkI;
link.setChild(fa);
link.setParent(image);
% save the link back to the server.
iUpdate.saveAndReturnObject(link);

% To attach to a Dataset use omero.model.DatasetAnnotationLinkI;
  • Load all the annotations with a given namespace linked to images 
userId = session.getAdminService().getEventContext().userId;
nsToInclude = java.util.ArrayList;
nsToInclude.add(NAME_SPACE_TO_SET);
nsToExclude = java.util.ArrayList;
options = omero.sys.ParametersI;
options.exp(omero.rtypes.rlong(userId)); %load the annotation for a given user.
metadataService = session.getMetadataService();
% retrieve the annotations linked to images, for datasets use: 'omero.model.Dataset'
annotations = metadataService.loadSpecifiedAnnotations('omero.model.FileAnnotation', nsToInclude, nsToExclude, options);
for j = 0:annotations.size()-1,
    annotations.get(j).getId().getValue();
end
  • Read the attachment.

First load the annotation, cf. above. 

% Let's call fa the file annotation
originalFile = fa.getFile();
store = session.createRawFileStore();
store.setFileId(originalFile.getId().getValue());

% read data
    
fid = fopen('mydataBack.txt', 'w');
fwrite(fid, rawFileStore.read(0, originalFile.getSize().getValue()), 'uint8');
fclose(fid);

store.close();

How to use OMERO tables

  • Create a table. In the following example, we create a table with 2 columns. 
name = char(java.util.UUID.randomUUID());
columns = javaArray('omero.grid.Column', 2)
columns(1) = omero.grid.LongColumn('Uid', 'testLong', []);
valuesString = javaArray('java.lang.String', 1);
columns(2) = omero.grid.StringColumn('MyStringColumn', '', 64, valuesString);

%create a new table.
table = session.sharedResources().newTable(1, name);

%initialize the table
table.initialize(columns);
%add data to the table.
data = javaArray('omero.grid.Column', 2);
data(1) = omero.grid.LongColumn('Uid', 'test Long', [2]);
valuesString = javaArray('java.lang.String', 1);
valuesString(1) = java.lang.String('add');
data(2) = omero.grid.StringColumn('MyStringColumn', '', 64, valuesString);
table.addData(data);
file = table.getOriginalFile(); % if you need to interact with the table
  • Read the contents of the table. 
of = omero.model.OriginalFileI(file.getId(), false); 
tablePrx = session.sharedResources().openTable(of);

%read headers
headers = tablePrx.getHeaders();
for i=1:size(headers, 1),
    headers(i).name; % name of the header
    %do something
end

% Depending on size of table, you may only want to read some blocks.
cols = [0:size(headers, 1)-1]; % The number of columns we wish to read.
rows = [0:tablePrx.getNumberOfRows()-1]; % The number of rows we wish to read.
data = tablePrx.slice(cols, rows); % read the data.
c = data.columns;
for i=1:size(c),
    column = c(i);
    %do something
end
tablePrx.close(); % Important to close when done.

ROIs

To learn about the model see http://www.openmicroscopy.org/site/support/file-formats/working-with-ome-xml/roi . Note that annotation can be linked to ROI.

  • Create ROI.

In this example, we create an ROI with a rectangular shape and attach it to an image. 

% First create a rectangular shape.
rect = omero.model.RectI;
rect.setX(omero.rtypes.rdouble(0));
rect.setY(omero.rtypes.rdouble(0));
rect.setWidth(omero.rtypes.rdouble(10));
rect.setHeight(omero.rtypes.rdouble(20));
% indicate on which plane to attach the shape
rect.setTheZ(omero.rtypes.rint(0));
rect.setTheT(omero.rtypes.rint(0));

% First create an ellipse shape.
ellipse = omero.model.EllipseI;
ellipse.setCx(omero.rtypes.rdouble(0));
ellipse.setCy(omero.rtypes.rdouble(0));
ellipse.setRx(omero.rtypes.rdouble(10));
ellipse.setRy(omero.rtypes.rdouble(20));
% indicate on which plane to attach the shape
ellipse.setTheZ(omero.rtypes.rint(0));
ellipse.setTheT(omero.rtypes.rint(0));

% Create the roi.
roi = omero.model.RoiI;
% Attach the shapes to the roi, several shapes can be added.
roi.addShape(rect);
roi.addShape(ellipse);

% Link the roi and the image
roi.setImage(omero.model.ImageI(imageId, false));
% save
iUpdate = session.getUpdateService(); 
roi = iUpdate.saveAndReturnObject(roi);
% Check that the shape has been added.
numShapes = roi.sizeOfShapes;
for ns = 1:numShapes
   shape = roi.getShape(ns-1);
end
  • Retrieve ROIs linked to an Image. 
service = session.getRoiService();
roiResult = service.findByImage(imageId, []);
rois = roiResult.rois;
n = rois.size;
shapeType = '';
for thisROI  = 1:n
    roi = rois.get(thisROI-1);
    numShapes = roi.sizeOfShapes; % an ROI can have multiple shapes.
    for ns = 1:numShapes
        shape = roi.getShape(ns-1); % the shape
        if (isa(shape, 'omero.model.Rect'))
           %handle rectangle
           rectangle = shape;
           rectangle.getX().getValue()
        elseif (isa(shape, 'omero.model.Ellipse'))
           ellipse = shape;
           ellipse.getCx().getValue()
        elseif (isa(shape, 'omero.model.Point'))
           point = shape;
           point.getX().getValue();
        elseif (isa(shape, 'omero.model.Line'))
           line = shape;
           line.getX1().getValue();
        end
    end
end
  • Remove a shape from ROI. 
// Retrieve the roi linked to an image
service = session.getRoiService();
roiResult = service.findByImage(imageId, []);
n = rois.size;
for thisROI  = 1:n
    roi = rois.get(thisROI-1);
    numShapes = roi.sizeOfShapes; % an ROI can have multiple shapes.
    for ns = 1:numShapes
        shape = roi.getShape(ns-1); % the shape
        % remove the shape
        roi.removeShape(shape);
    end
    %Update the roi.
    roi = iUpdate.saveAndReturnObject(roi);
end

Delete data

It is possible to delete Projects, Datasets, Images, ROIs etc and objects linked to them depending on the specified options (see Delete).

  • Delete Image.

In the following example, we create an Image and delete it. 

% First create the image.
image = omero.model.ImageI;
image.setName(omero.rtypes.rstring('image name'))
image.setAcquisitionDate(omero.rtypes.rtime(2000000));
image = service.saveAndReturnObject(image);
imageId = image.getId().getValue();

% Create the command to delete the Image using a delete callback.
% You can delete more than one image at a time.
list = javaArray('omero.api.delete.DeleteCommand', 1);
% Indicate the type of object e.g. /Image, /Project etc., the identifier
% and the annotations to keep (nothing in the following example)
list(1) = omero.api.delete.DeleteCommand('/Image', imageId, []);
%Delete the image.
prx = session.getDeleteService().queueDelete(list);

Render Images

  • Initialize the rendering engine and render an Image. 
% See load section to find out how to load pixels.
% Create rendering engine.
pixelsId = pixels.getId().getValue(); % see Load data section
re = session.createRenderingEngine();
re.lookupPixels(pixelsId);
% Check if default required.
if (~re.lookupRenderingDef(pixelsId)) 
    re.resetDefaults();
    re.lookupRenderingDef(pixelsId);
end
% start the rendering engine
re.load();

% render a Plane as compressed. Possible to render it uncompressed.
pDef = omero.romio.PlaneDef;
pDef.z = re.getDefaultZ();
pDef.t = re.getDefaultT();
pDef.slice = omero.romio.XY.value;

% Number of channels.
sizeC = pixels.getSizeC().getValue()-1;
if (sizeC == 0)
    re.setActive(0, 1);
else 
    for k = 0:sizeC,
        re.setActive(k, 0);
        values = re.renderCompressed(pDef);
        stream = java.io.ByteArrayInputStream(values);
        image = javax.imageio.ImageIO.read(stream);
        stream.close();
        figure(k+1);
        imshow(JavaImageToMatlab(image));
        %make all the channels active.
        for i = 0:sizeC,
           re.setActive(i, 1);
        end
    end
end

% All channels active and save the image as a JPEG.
figure(pixels.getSizeC().getValue()+2);
values = re.renderCompressed(pDef);
stream = java.io.ByteArrayInputStream(values);
image = javax.imageio.ImageIO.read(stream);
stream.close();
imshow(JavaImageToMatlab(image));
%file = [imagename '.jpg'];
%fid = fopen(file, 'wb');
%fwrite(fid, values, 'int8');
%fclose(fid);
%delete(file);

%Close the rendering engine.
re.close();
  • Retrieves thumbnails 
store = session.createThumbnailStore();
map = store.getThumbnailByLongestSideSet(omero.rtypes.rint(96), java.util.Arrays.asList(java.lang.Long(pixelsId)));
%Display the thumbnail;
collection = map.values();
i = collection.iterator();
while (i.hasNext())
   figure(100);
   stream = java.io.ByteArrayInputStream(i.next());
   image = javax.imageio.ImageIO.read(stream);
   stream.close();
   imshow(JavaImageToMatlab(image));
end

Create Image

The following example shows how to create an Image from an Image already in OMERO. Similar approach can be applied when uploading an image. 

% See above how to load the pixels


sizeZ = pixels.getSizeZ().getValue() % The number of z-sections.
sizeT = pixels.getSizeT().getValue(); % The number of timepoints.
sizeC = pixels.getSizeC().getValue(); % The number of channels.
sizeX = pixels.getSizeX().getValue();
sizeY = pixels.getSizeY().getValue();

% Initialize the raw pixels store

pixelsId = pixels.getId().getValue()
store = session.createRawPixelsStore();
store.setPixelsId(pixelsId, false);

map = java.util.HashMap;
for z = 0:sizeZ-1,
  for t = 0:sizeT-1,
    planeC1 = store.getPlane(z, 0, t);
    map.put(linearize(z, t, sizeZ), planeC1); % linearize does sizeZ*t+z
  end
end

% Close to free space.
store.close();

% Retrieve the pixels type of the source image

proxy = session.getPixelsService();
l = proxy.getAllEnumerations('omero.model.PixelsType');
original = pixels.getPixelsType().getValue().getValue();
for j = 0:l.size()-1,
    type = l.get(j);
    if (type.getValue().getValue() == original)
        break;
    end
end

% Create the new image
description = char(['Source Image ID: ' int2str(image.getId().getValue())]);
name = char(['newImageFrom' int2str(image.getId().getValue())]);
idNew = proxy.createImage(sizeX, sizeY, sizeZ, sizeT, java.util.Arrays.asList(java.lang.Integer(0)), type, name, description);
    
    
%Load the new image.
list = iContainer.getImages('omero.model.Image', java.util.Arrays.asList(java.lang.Long(idNew.getValue())), omero.sys.ParametersI()); 
if (list.size == 0)
   exception = MException('OMERO:CreateImage', 'Image Id not valid');
   throw(exception);
end

imageNew = list.get(0);

%load the dataset hosting the source image and link it to the new image.
param = omero.sys.ParametersI();
param.noLeaves(); % indicate to load the images.
% load the dataset
results = session.getContainerService().loadContainerHierarchy('omero.model.Dataset', java.util.Arrays.asList(datasetId), param);
if (results.size == 0)
   exception = MException('OMERO:CreateImage', 'Dataset Id not valid');
   throw(exception);
end
dataset = results.get(0);
link = omero.model.DatasetImageLinkI;
link.setChild(omero.model.ImageI(imageNew.getId().getValue(), false));
link.setParent(omero.model.DatasetI(dataset.getId().getValue(), false));

session.getUpdateService().saveAndReturnObject(link);


%Copy the data.
pixelsNewList = imageNew.copyPixels();
pixelsNew = pixelsNewList.get(0);
pixelsNewId = pixelsNew.getId().getValue()
store = session.createRawPixelsStore();
store.setPixelsId(pixelsNewId, false);
    
for z = 0:sizeZ-1,
   for t = 0:sizeT-1,
      index = linearize(z, t, sizeZ);
      store.setPlane(map.get(index), z, 0, t); % copy the raw data
   end
end

%save the data
store.save();

%close
store.close();

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© 2000-2012 University of Dundee & Open Microscopy Environment. All Rights Reserved. …
OME source code is available under the GNU General public license or through commercial license from Glencoe Software

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