OMERO Matlab language bindings
==============================
See |DevelopingOmeroClients| and |OmeroModel|, for an introduction to
**Object**.
.. highlight:: matlab
Installing the OMERO.matlab toolbox
-----------------------------------
- Download the latest released version from the
:downloads:`download page <>` . For the latest build, go
:omerojob:`here <lastSuccessfulBuild/>`, and download the OMERO.matlab zip
file.
- Unzip the directory anywhere on your system.
- In Matlab, move to the newly unzipped directory and run ``loadOmero;``.
- The Matlab files are now on your path, and the necessary jars are on
your java classpath. You can change directories and still have access
to OMERO.
Once OMERO.matlab is installed, the typical workflow is:
#. :ref:`connection_init`
#. :ref:`connection_keepalive`
#. :ref:`unsecure_client` (optional)
#. Do some work (load objects, work with them, upload to the server...)
#. :ref:`connection_close`
#. :ref:`unload` (optional)
As a quickstart example, the following lines create a secure connection to a
server, read a series of images and close the connection.
::
client = loadOmero(servername, port);
session = client.createSession(user, password);
client.enableKeepAlive(60);
images = getImages(session, ids);
client.closeSession();
Configuring the OMERO.matlab connection
---------------------------------------
.. _connection_init:
Creating a connection
^^^^^^^^^^^^^^^^^^^^^
As described under |OmeroClients|, there are several ways to configure your
connection to an OMERO server. OMERO.matlab comes with a few conveniences for
making this work.
If you run ``client = loadOmero;`` (i.e. loadOmero with a return value),
then OMERO.matlab 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 OMERO.matlab 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()
.. _connection_keepalive:
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
:source:`omeroKeepAlive.m <components/tools/OmeroM/src/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
.. _unsecure_client:
Creating an unencrypted session
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If you want to speed up the data transfer, you can create and use an
unencrypted session as::
unsecureClient = client.createClient(false);
sessionUnencrypted = unsecureClient.getSession();
.. _connection_close:
Closing your connection
^^^^^^^^^^^^^^^^^^^^^^^
When you are done with OMERO, it is critical that you close your connection to
save resources::
client.closeSession();
clear client1;
clear session1;
If you created an unencrypted session, you will need to close the unsecure
session as well::
client.closeSession();
unsecureClient.closeSession();
.. _unload:
Unloading OMERO
^^^^^^^^^^^^^^^
Then if you would like, you can unload OMERO as well::
unloadOmero();
You may see the following warning when unloading OMERO::
>> unloadOmero()
Warning: Objects of omero/client class exist - not clearing java
> In javaclasspath>doclear at 377
In javaclasspath>local_javapath at 194
In javaclasspath at 105
In javarmpath at 48
In unloadOmero at 75
===============================================================
While unloading OMERO, found java objects left in workspace.
Please remove with 'clear <name>' and then run 'unloadOmero'
again. Printing all objects...
===============================================================
Name Size Bytes Class Attributes
c 1x1 omero.client
Closing session(s) for 1 found client(s): c
This means that there is still an OMERO.matlab object in your workspace. If
not listed, use ``whos`` to find such objects, and ``clear`` to remove them.
After that, run ``unloadOmero()`` again::
>> clear c
>> unloadOmero()
.. warning::
You should also unload OMERO before installing a new version of
OMERO.matlab 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();
Reading data
------------
The ``IContainer`` service provides methods to load the data management
hierarchy in OMERO -- projects, datasets, etc. A list of examples
follows, indicating how to load projects, datasets, screens, etc.
- **Projects**
The projects owned by the user currently logged in can be retrieved using the
:source:`getProjects <components/tools/OmeroM/src/io/getProjects.m>`
function::
projects = getProjects(session)
If the project identifiers are known, they can be specified as::
projects = getProjects(session, ids)
If the projects contains datasets, the datasets will automatically be loaded::
for j = 1 : numel(projects)
datasetsList = projects(j).linkedDatasetList;
for i = 0:datasetsList.size()-1,
d = datasetsList.get(i);
end
end
If the datasets contains images, the images will automatically be loaded::
imageList = projects(1).linkedDatasetList.get(0).linkedImageList;
To avoid loading the whole graph (projects, datasets, images), pass `false` as
a second optional argument. Only datasets will be loaded::
unloadedProjects = getProjects(session, ids, false)
- **Datasets**
The datasets owned by the user currently logged in can be retrieved using the
:source:`getDatasets <components/tools/OmeroM/src/io/getDatasets.m>`
function::
datasets = getDatasets(session)
If the dataset identifiers are known, they can be specified as::
datasets = getDatasets(session, ids)
If the datasets contain images, the images will automatically be loaded::
imageList = datasets(1).linkedImageList;
To avoid loading the images, pass `false` as a second optional argument::
unloadedDatasets = getDatasets(session, ids, false)
- **Images**
All the images owned by the user currently logged in can be retrieved using
the :source:`getImages <components/tools/OmeroM/src/io/getImages.m>`
function::
images = getImages(session)
If the image identifiers are known, they can be specified as::
images = getImages(session, ids)
Alternately, all the images contained in projects or datasets can be returned
by specifying the parent type and identifiers as::
projectImages = getImages(session, 'project', projectIds)
datasetImages = getImages(session, 'dataset', datasetsIds)
The Image-Pixels model implies you need to use the pixels objects to access
valuable data about the image::
pixels = image.getPrimaryPixels();
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.
- **Screens**
The screens owned by the user currently logged in can be retrieved using the
:source:`getScreens <components/tools/OmeroM/src/io/getScreens.m>`
function::
screens = getScreens(session)
If the screen identifiers are known, they can be specified as::
screens = getScreens(session, ids)
Note that the wells are not loaded. The plate objects can be accessed using::
for j = 1 : numel(screens),
platesList = screens(j).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
- **Plates**
The plates owned by the user currently logged in can be retrieved using the
:source:`getPlates <components/tools/OmeroM/src/io/getPlates.m>`
function::
plates = getPlates(session)
If the plate identifiers are known, they can be specified as::
plates = getPlates(session, ids)
- **Wells**
Given a plate identifier, the wells can be loaded using 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.
- **Plane**
The plane of an input image at coordinates (z, c, t) can be retrieved using
the :source:`getPlane <components/tools/OmeroM/src/image/getPlane.m>`
function::
plane = getPlane(session, image, z, c, t);
Alternately, the image identifier can be passed to the function::
plane = getPlane(session, imageID, z, c, t);
- **Tile**
The tile of an input image at coordinates (z, c, t) originated at (x, y) and
of dimensions (w, h) can be retrieved using the
:source:`getTile <components/tools/OmeroM/src/image/getTile.m>` function::
tile = getTile(session, image, z, c, t, x, y, w, h);
Alternately, the image identifier can be passed to the function::
tile = getTile(session, imageID, z, c, t, x, y, w, h);
- **Stack**
The tile of an input image at coordinates (c, t) can be retrieved using the
:source:`getStack <components/tools/OmeroM/src/image/getStack.m>` function::
stack = getStack(session, image, c, t);
Alternately, the image identifier can be passed to the function::
stack = getStack(session, imageID, c, t);
- **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();
Thumbnails
----------
- **Single thumbnails**
The cache thumbnail of an input image can be retrieved using the
:source:`getThumbnail <components/tools/OmeroM/src/image/getThumbnail.m>`
function::
thumbnail = getThumbnail(session, image, width, height);
Alternately, the image identifier can be passed to the function::
thumbnail = getThumbnail(session, imageID, width, height);
.. note:: The ``width`` or ``height`` arguments are optional and will be set
to 48 pixels if not specified.
To preserve the aspect ratio of the retrieved thumbnail, use the :source:`getThumbnailByLongestSide <components/tools/OmeroM/src/image/getThumbnailByLongestSide.m>`
function::
thumbnail = getThumbnailByLongestSide(session, image, size);
or alternately using the image identifier::
thumbnail = getThumbnailByLongestSide(session, imageID, size);
- **Thumbnail set**
A set of cached thumbnails can be retrieved from a list of input images using
the :source:`getThumbnailSet <components/tools/OmeroM/src/image/getThumbnailSet.m>`
function::
thumbnailSet = getThumbnailSet(session, images, width, height);
To preserve the aspect ratio of the retrieved thumbnails, use the :source:`getThumbnailByLongestSideSet <components/tools/OmeroM/src/image/getThumbnailByLongestSideSet.m>` function::
thumbnailSet = getThumbnailSetByLongestSide(session, images, size);
Annotations
-----------
- **Reading annotations**
If the identifier of a tag annotation is known, the annotation can be
retrieved from the server using the :source:`getTagAnnotations <components/tools/OmeroM/src/annotations/getTagAnnotations.m>`
function::
tagAnnotations = getTagAnnotations(session, tagIds);
.. seealso::
:source:`getFileAnnotations <components/tools/OmeroM/src/annotations/getFileAnnotations.m>`
Utility function to retrieve file annotations by identifier
:source:`getCommentAnnotations <components/tools/OmeroM/src/annotations/getFileAnnotations.m>`
Utility function to retrieve comment annotations by identifier
:source:`getXmlAnnotations <components/tools/OmeroM/src/annotations/getXmlAnnotations.m>`
Utility function to retrieve xml annotations by identifier
To retrieve the tag annotations linked to a given object, an image for instance, use the :source:`getImageTagAnnotations <components/tools/OmeroM/src/annotations/getImageTagAnnotations.m>`
function::
tagAnnotations = getImageTagAnnotations(session, imageIds);
.. seealso::
:source:`getImageFileAnnotations <components/tools/OmeroM/src/annotations/getImageFileAnnotations.m>`, :source:`getImageCommentAnnotations <components/tools/OmeroM/src/annotations/getImageCommentAnnotations.m>`, :source:`getImageFileAnnotations <components/tools/OmeroM/src/annotations/getImageFileAnnotations.m>`
Utility function to retrieve annotations linked to images
:source:`getDatasetTagAnnotations <components/tools/OmeroM/src/annotations/getDatasetTagAnnotations.m>`, :source:`getDatasetFileAnnotations <components/tools/OmeroM/src/annotations/getDatasetFileAnnotations.m>`, :source:`getDatasetCommentAnnotations <components/tools/OmeroM/src/annotations/getDatasetCommentAnnotations.m>`, :source:`getDatasetFileAnnotations <components/tools/OmeroM/src/annotations/getDatasetFileAnnotations.m>`
Utility function to retrieve annotations linked to datasets
:source:`getProjectTagAnnotations <components/tools/OmeroM/src/annotations/getProjectTagAnnotations.m>`, :source:`getProjectFileAnnotations <components/tools/OmeroM/src/annotations/getProjectFileAnnotations.m>`, :source:`getProjectCommentAnnotations <components/tools/OmeroM/src/annotations/getProjectCommentAnnotations.m>`, :source:`getProjectFileAnnotations <components/tools/OmeroM/src/annotations/getProjectFileAnnotations.m>`
Utility function to retrieve annotations linked to projects
:source:`getScreenTagAnnotations <components/tools/OmeroM/src/annotations/getScreenTagAnnotations.m>`, :source:`getScreenFileAnnotations <components/tools/OmeroM/src/annotations/getScreenFileAnnotations.m>`, :source:`getScreenCommentAnnotations <components/tools/OmeroM/src/annotations/getScreenCommentAnnotations.m>`, :source:`getScreenFileAnnotations <components/tools/OmeroM/src/annotations/getScreenFileAnnotations.m>`
Utility function to retrieve annotations linked to screens
:source:`getPlateTagAnnotations <components/tools/OmeroM/src/annotations/getPlateTagAnnotations.m>`, :source:`getPlateFileAnnotations <components/tools/OmeroM/src/annotations/getPlateFileAnnotations.m>`, :source:`getPlateCommentAnnotations <components/tools/OmeroM/src/annotations/getPlateCommentAnnotations.m>`, :source:`getPlateFileAnnotations <components/tools/OmeroM/src/annotations/getPlateFileAnnotations.m>`
Utility function to retrieve annotations linked to plates
- **Reading file annotations**
The content of a file annotation can be downloaded locally on disk using the :source:`getFileAnnotationContent <components/tools/OmeroM/src/annotations/getFileAnnotationContent.m>`
function::
getFileAnnotationContent(session, fileAnnotation, target_file);
Alternately, if only the file annotation identifier is known::
getFileAnnotationContent(session, faid, target_file);
Writing 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:
#. an ``OriginalFile``
#. a ``FileAnnotation``
#. 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 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, you have an original File in the database and raw data uploaded.
% You 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;
How to use OMERO tables
-----------------------
- **Create a table**. In the following example, a table is created 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 you wish to read.
rows = [0:tablePrx.getNumberOfRows()-1]; % The number of rows you 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 :model_doc:`developers/roi.html`. Note that
annotation can be linked to ROI.
- **Creating ROI**
This example creates an ROI with a rectangular shape and attach it to an
image::
% First create a rectangular shape.
rectangle = createRectangle(0, 0, 10, 20);
% indicate on which plane to attach the shape
setShapeCoordinates(rectangle, 0, 0, 0);
% First create an ellipse shape.
ellipse = createEllipse(0, 0, 10, 20);
% indicate on which plane to attach the shape
setShapeCoordinates(ellipse, 0, 0, 0);
% Create the roi.
roi = omero.model.RoiI;
% Attach the shapes to the roi, several shapes can be added.
roi.addShape(rectangle);
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
.. seealso::
:sourcedir:`ROI utility functions <components/tools/OmeroM/src/roi>`
OMERO.matlab functions for creating and managing Shape and ROI
objects.
- **Retrieving 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
- **Removing 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
Deleting data
-------------
It is possible to delete projects, datasets, images, ROIs etc. and
objects linked to them depending on the specified options (see
:doc:`/developers/Modules/Delete`). For example, images of known identifiers
can be deleted from the server using the
:source:`deleteImages <components/tools/OmeroM/src/delete/deleteImages.m>`
function::
deleteImages(session, imageIds);
.. seealso::
:source:`deleteProjects <components/tools/OmeroM/src/delete/deleteProjects.m>`, :source:`deleteDatasets <components/tools/OmeroM/src/delete/deleteDatasets.m>`, :source:`deleteScreens <components/tools/OmeroM/src/delete/deleteScreens.m>`, :source:`deletePlates <components/tools/OmeroM/src/delete/deletePlates.m>`
Utility functions to delete objects
Rendering 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();
Creating Image
--------------
The following example shows how to create an image from an image already
in OMERO. A 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();