Export is not working in 4.1

[cxallan]

Thanks for the reply, Can you please give any example of a query showing how to retrieve all the images based on the project id, or dataset id ?
I want to download all these images into my system.

You can't export like that currently, as Jean-Marie has already said above. If you want to do that you'll have to write the code to do it in a batch starting with retrieving the images for a Project, for example:

Code: Select all

List<Long> projectIds = new ArrayList();
projectIds.add(1L);
Set images = gateway.getContainerImages(Project.class, projectIds, options);
...


[ryan]

Thanks a lot cxallan for your reply. After getting the images, how i can save them in to my hard disk ?
(In which format do we get them)
By the way, i forgot to ask you, how i can pass the selected project id, or dataset id in the query.

[cxallan]

Thanks a lot cxallan for your reply. After getting the images, how i can save them in to my hard disk ?
(In which format do we get them)
By the way, i forgot to ask you, how i can pass the selected project id, or dataset id in the query.

That does not get the images, it gets the Image objects from the server. You need to look at the following method in OMEROGateway for export as OME-TIFF:

Code: Select all

   synchronized File exportImageAsOMETiff(File f, long imageID)
      throws DSAccessException, DSOutOfServiceException
...


You pass the selected Project or Dataset ID as the node ID.

[ryan]

It seems the present functionality exports only a single image, that is selected, to the "file" that is selected via FileChooser. But how to export all the images of a project? How to pass the selected project/dataset ?
It is not clear. Please throw some light.

[cxallan]

It seems the present functionality exports only a single image, that is selected, to the "file" that is selected via FileChooser. But how to export all the images of a project? How to pass the selected project/dataset ?
It is not clear. Please throw some light.

Correct. You cannot export all the images of a Project without writing your own code to find the Image IDs from a given Project and export each Image. This is what we have been trying to tell you how to do since you started the thread.

[ryan]

I got an error while exporting images. I have connected to an external Omero server. Whatever image i export, i get the error as: "Unable to export as OME-TIFF" in the dialog box. And i have few exceptions as well in java code, like:

org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data.
Cannot access Exporter service.

at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:456)
at org.openmicroscopy.shoola.env.data.OMEROGateway.getExporterService(OMEROGateway.java:1006)
at org.openmicroscopy.shoola.env.data.OMEROGateway.exportImageAsOMETiff(OMEROGateway.java:4873)

Though i get these errors, i see an image exported on my desktop. Why iam getting these errors ?

[cxallan]

Which build of OMERO 4.1? Export in particular has had many changes over the last 10 days or so. Also, can we have the entire exception please?

[ryan]

Iam using Omero Insight 4.1.0 Beta.
This is the complete exception in the eclipse console, after i export an image:

org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data.
Cannot access Exporter service.
at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:456)
at org.openmicroscopy.shoola.env.data.OMEROGateway.getExporterService(OMEROGateway.java:1006)
at org.openmicroscopy.shoola.env.data.OMEROGateway.exportImageAsOMETiff(OMEROGateway.java:4873)
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.exportImageAsOMETiff(OmeroImageServiceImpl.java:713)
at org.openmicroscopy.shoola.env.data.views.calls.ExportLoader$1.doCall(ExportLoader.java:76)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:145)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Unknown Source)
Caused by: Ice.OperationNotExistException
id.name = "30f394f6-3565-4893-9ef8-91d34182ffe6"
id.category = "session-fcf4ee94-d2b6-462f-a323-5c208efaffb3"
facet = ""
operation = "createExporter"
at IceInternal.Outgoing.invoke(Outgoing.java:147)
at omero.api._ServiceFactoryDelM.createExporter(_ServiceFactoryDelM.java:227)
at omero.api.ServiceFactoryPrxHelper.createExporter(ServiceFactoryPrxHelper.java:286)
at omero.api.ServiceFactoryPrxHelper.createExporter(ServiceFactoryPrxHelper.java:258)
at org.openmicroscopy.shoola.env.data.OMEROGateway.getExporterService(OMEROGateway.java:1001)
... 10 more

[cxallan]

Which version of the server? Export is only available using a Beta 4.1 server.

[ryan]

i hope iam using a 4.0 version of server.