Open Microscopy Environment

Hi -
I'm retrieving image data from OMERO and it's working ok except for getting the dimension order.

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            s = obj.sessionHolder.session;
            img = getImages(s, obj.imageID);
            pixelsList = img.copyPixels();
            pixels = pixelsList.get(0);
            obj.szXYZCT = getPixelsSize(pixels);
            pixelsId = pixels.getId().getValue();
            store = s.createRawPixelsStore();
            store.setPixelsId(pixelsId, false);
            dord = pixels.getDimensionOrder();


The last line works, but then

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            dordval = dord.getValue();

throws an UnloadedEntityException. I've run across the Unloaded error before, but I'm not sure how to avoid it.

I'm also assuming that if I do retrieve this value, it will be an ordinal number and I will have to use the Enumeration to learn the string value.

Thanks for help!
Gary

Hi Gary,

the Pixels object for each image is not loaded by default. The following code snippet should give you a series of calls allowing to load it and retrieve the dimension order.

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s = obj.sessionHolder.session;
img = getImages(s, obj.imageID);
pixelsId = img.getPrimaryPixels().getId().getValue();  % Retrieve the primary pixels ID
pixels = s.getPixelsService().retrievePixDescription(pixelsId)  % Load the pixels object
dord = pixels.getDimensionOrder();


Best,
Sebastien

Thanks, Sebastien. I'm having a similar problem with image.linkDataset. How do I get the dataset links loaded?
Best, Gary

Hi again Sebastian - more specifically, here is the code I used to create a new image on the server (which works),

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% helper functions
rint = @(x) omero.rtypes.rint(x);
rstring = @(x) omero.rtypes.rstring(x);

p = omero.sys.ParametersI();
p.add('type',rstring('uint8'));
q=['from PixelsType as p where p.value= :type'];

queryService = session.getQueryService;
pixelsType = queryService.findByQuery(q,p);

pixelsService = session.getPixelsService;

iId = pixelsService.createImage(uint32(128),uint32(128),uint32(1),uint32(15), ...
   toJavaList(uint32(1)),pixelsType,java.lang.String('gyModC3.ome.tif [5]'), ... % name
   java.lang.String('seg of z0 c0 t0:14'));  % description

containerService = session.getContainerService;

imgnew = containerService.getImages('Image',toJavaList(java.lang.Long(iId.getValue)),omero.sys.Parameters);
pixelsId = imgnew.get(0).getPrimaryPixels().getId().getValue();

% prepare to write the pixel data
store = session.createRawPixelsStore;
store.setPixelsId(pixelsId, true);

% make some junk data for testing, then write it
plane = uint8(eye(128,128)*10);
store.setPlane(plane(:),0,0,0);
plane(30:50,30:50)=2;
plane(100:110,10:40)=3;
for k=1:14; store.setPlane(plane(:),0,0,k); end
store.close;

and the code to link to a dataset (which doesn't):

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% now link to data set **** USE A LEGAL DATASET NUMBER ***
dset = session.getDatasets(262);

% next line has had problems
imgnew.get(0).linkDataset(dset);

===== error message =====
Java exception occurred:
omero.UnloadedCollectionException: Error updating collection:datasetLinksSeq
Collection is currently null. This can be seen
by testing "datasetLinksSeqLoaded". This implies
that this collection was unloaded. Please refresh this object
in order to update this collection.


   at omero.model.ImageI.throwNullCollectionException(ImageI.java:38)

   at omero.model.ImageI.linkDataset(ImageI.java:931)

   at omero.model.Image.linkDataset(Image.java:316)


Thanks for any advice,
Gary

Hi Gary,

if the goal is lo link an image to a dataset on the server, you may want to adapt this section of the CreateImage.m example to your needs.

Best
Sebastien

Thanks, Sebastien.
I'm making progress, but still run across Unloaded exceptions that I don't know how to avoid.
My current example is retrieving the annotation links for an ROI object. I've done:

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service = session.getRoiService();
roiResult = service.findByImage(image.getId.getValue, []);
rois = roiResult.rois;
roi0 = rois.get(0);
dscr = char(roi.getDescription().getValue());
maskObj = roi.getShape(0);   
z = maskObj.getTheZ.getValue;
c = maskObj.getTheC.getValue;
t = maskObj.getTheT.getValue;

but I don't know how to load the linkedAnnotationList (roi.isAnnotated=1 but roi.isAnnotationLinksLoaded=0).
I've looked for a retrieve method on the roiService, analogous to the pixels example, but cannot find one.

Thanks again - sorry to be a nuisance!
Gary

Hi Gary,

as a general rule, unless otherwise stated, you should assume linked objects will be unloaded when retrieving objects from the database. If loading linked objects is not available via the API methods (see for instance getProjects), you will need the write the appropriate query to fetch and return both the objects and the linked objects.

If you have examples of images/scripts allowing to reproduce your use case, it would be useful for helping you with the adequate query.

Best,
Sebastien

Hi Sebastien - The code (below) that you recommended does run, but if I then try "dord.getValue;", I get an UnloadedEntityException (and dord.isLoaded returns 0).
best,
gary

sbesson wrote:Hi Gary,

the Pixels object for each image is not loaded by default. The following code snippet should give you a series of calls allowing to load it and retrieve the dimension order.

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s = obj.sessionHolder.session;
img = getImages(s, obj.imageID);
pixelsId = img.getPrimaryPixels().getId().getValue();  % Retrieve the primary pixels ID
pixels = s.getPixelsService().retrievePixDescription(pixelsId)  % Load the pixels object
dord = pixels.getDimensionOrder();


Best,
Sebastien

Hi Yuriy,

You are correct. I just checked and `retrievePixDescription()` does not load the dimension order. The following snippet should retrieve the Pixels object with properly loaded DimensionOrder:

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query = ['select p from Pixels as p'...
  ' left outer join fetch p.dimensionOrder as d'...
  ' where p.id = :id'];
parameters = omero.sys.ParametersI();
parameters.addId(pixelsId);
pixels = s.getQueryService.findByQuery(query, parameters);
dimensionOrder = pixels.getDimensionOrder().getValue().getValue();


Let me know if this works,
Sebastien

Hi Sebastien,
I finally got around to testing this, and the code works... but OMERO gives the incorrect value for the dimension order. I have uploaded a file to QA, with dimension orders of image0=XYCTZ, image1=XYTCZ, image2=XYCTZ. These are correctly seen in the XML block of the .ome.tif, and read properly by Bio-Formats import to Fiji. But OMERO reports all three images as XYZCT.
Best,
Gary