Open Microscopy Environment

Thanks for replying. I have loaded my omero_client.jar into Netbeans and the ome.formats package is definitely not there. I could be using the wrong version, I suppose.

Where did you get the JAR and which version of OMERO are you attempting to use?

I had to import omero_client.jar and jar_0.jar to get it to find the class.

Our Omero server is version 4.2.2. I get an error about the XML now - Doesn't look like it can be read it. The version of it appears to be 2011-06. I'm looking into this, but any help would be greatly appreciated. I'm wondering if my jar_0.jar is the correct version. I'm quite certain I've got the right version of omero_client.jar and loci_tools.jar, but I just took the jar_0.jar from the only place I could find it (A directory on my computer).

Thanks again.

Code: Select all

2012-01-17 09:57:02,615 0          [      main] WARN        loci.formats.services.OMEXMLService  - Could not transform version  OME-XML.

??? Java exception occurred:
java.lang.AbstractMethodError: ome.formats.OMEROMetadataStoreClient.setImageAcquiredDate(Ljava/lang/String;I)V
   at loci.formats.meta.FilterMetadata.setImageAcquiredDate(FilterMetadata.java:1223)
   at loci.formats.MetadataTools.setDefaultCreationDate(MetadataTools.java:317)
   at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:191)
   at loci.formats.MetadataTools.populatePixels(MetadataTools.java:121)
   at loci.formats.MetadataTools.populatePixels(MetadataTools.java:85)
   at loci.formats.in.BaseTiffReader.initMetadataStore(BaseTiffReader.java:392)
   at loci.formats.in.TiffReader.initMetadataStore(TiffReader.java:210)
   at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:84)
   at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:502)
   at loci.formats.FormatReader.setId(FormatReader.java:1072)
   at loci.formats.ImageReader.setId(ImageReader.java:677)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at loci.formats.ChannelFiller.setId(ChannelFiller.java:249)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:257)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:189)
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:313)

(And I've successfully imported the same OME-TIFF into Omero using the importer app, and the XML is intact)

You now have inconsistencies between the Bio-Formats and OMERO JARs. If you want to use the OMERO.importer infrastructure, you must use the version of Bio-Formats that matches, which in your case would be getting the OmeroImporter.jar from:

http://cvs.openmicroscopy.org.uk/snapsh ... .linux.zip

and then latest 4.2.x version of Bio-Formats with dependencies (loci_tools.jar) from:

http://hudson.openmicroscopy.org.uk/vie ... S-Beta4.2/

Ok, I've done that. And so the OMEWrapper class now asks for an ImportConfig object. Is there anyway I could use the CommandLineImporter.java to do what I want? Is it *just* a case of setting up an ImportConfig and giving it the required paths?

Jake

JakeNewman wrote:Ok, I've done that. And so the OMEWrapper class now asks for an ImportConfig object. Is there anyway I could use the CommandLineImporter.java to do what I want? Is it *just* a case of setting up an ImportConfig and giving it the required paths?

Pretty much. I'll see if I can whip up a quick example that does that here this afternoon.

Thank you so much. I'll keep hacking away for the fun of it.

Well I've knocked up something in Java which does what I want (just about). It uploads a tiff to our Omero server. It doesn't upload the XML, and it isn't putting it into the right dataset. I'll keep playing.

Jake

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import ome.formats.importer.ImportConfig;
import ome.formats.importer.cli.*;
import org.apache.commons.logging.*;
import org.apache.log4j.*;
import org.ini4j.*;
import loci.formats.in.*;

public class JavaApplication2 {
   
    public static void main(String[] args) throws Exception {
        ImportConfig config = new ImportConfig();
        config.email.set("");
        config.sendFiles.set(true);
        config.sendReport.set(false);
        config.contOnError.set(false);
        config.debug.set(false);
        config.hostname.set("omero.institution.ac.uk");
        config.username.set("user");
        config.password.set("pass");
        config.port.set(Integer.parseInt("4064"));
        config.targetId.set(Long.parseLong("908"));
        CommandLineImporter c = null;
        String[] inputImg = new String[1];
        inputImg[0] = "/Users/jacobnewman/Desktop/newIMGwithXML";
        c = new CommandLineImporter(config, inputImg, false);
        int rc = c.start();
        c.cleanup();

When I use the CommandLineImporter, it reports:

Depth: 4 Metadata Level: MINIMUM

and then proceeds to only upload minimal metadata. Is there a way to change the metadata level? I'm using 4.2.2.

And for some reason I'm able to set X,Y,C and T using the .setPixelSizeX,Y,C, and T methods on a omexmlservice object, but not Z. So when I upload my image, it always has the same number of Z channels as the source image. Basically, I'm taking a source Tiff, extracting its metadata, attaching it to a new tiff, and uploading it. I'm getting nowhere with setting the Z size so I was thinking of just writing a simple XML parser to adjust it *manually*.

Any ideas?

Jake