Uploading from MATLAB

[jmoore]

Would you mind enabling debugging and repeat the failure? Something like:

Code: Select all

loci.common.DebugTools.enableLogging('DEBUG');


Cheers,
~J.

[dballvt]

I get the exact same messages when I add that line (see below). Would there be any information inside any of the variables that are created during this code:

Code: Select all

handler = ErrorHandler(config);
library.addObserver(LoggingImportMonitor());
candidates = ImportCandidates(reader, paths, handler);


[INFO] ImportConfig - OMERO Version: 4.4.4-ice33-b3099
[INFO] ImportConfig - Bioformats version: 4.4.4 revision: 96c615b date: 25 September 2012
[INFO] OMEROMetadataStoreClient - Attempting initial SSL connection to gladden.vbi.vt.edu:4064
[INFO] OMEROMetadataStoreClient - Call context: {omero.group:3}
[INFO] OMEROMetadataStoreClient - Server: 4.4.4
[INFO] OMEROMetadataStoreClient - Client: 4.4.4-ice33-b3099
[INFO] OMEROMetadataStoreClient - Java Version: 1.6.0_35
[INFO] OMEROMetadataStoreClient - OS Name: Mac OS X
[INFO] OMEROMetadataStoreClient - OS Arch: x86_64
[INFO] OMEROMetadataStoreClient - OS Version: 10.8.2
[INFO] ImportCandidates - Depth: 4 Metadata Level: MINIMUM
[INFO] ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 37ms. (38ms total) [0 unknowns]
[INFO] OMEROMetadataStoreClient - Call context: {omero.group:3}
[INFO] OMEROMetadataStoreClient - Call context: {omero.group:3}
[INFO] ImportLibrary - Exiting on error

[jmoore]

Just a heads up: we're looking into what magic it will take to make Matlab print debugging statements for other Java classes. Bear with us.

~J.

[sbesson]

Hi.

Sorry for the delay. Can you try the followig piece of code to set the level of the import library logger:

Code: Select all

log = org.apache.commons.logging.LogFactory.getLog('ome.formats.importer.ImportLibrary');
log.setLevel(0)
success = library.importCandidates(config, candidates);


and let us know if you get a more informative error message?

Cheers,
Sebastien

[dballvt]

OK, now I do get a couple of extra lines (below). I notice the maximum height & width, but the image I'm trying to upload is just a single plane that is 1392 x 1040, and it's a tiff file.

[INFO] ImportConfig - OMERO Version: 4.4.4-ice33-b3099
[INFO] ImportConfig - Bioformats version: 4.4.4 revision: 96c615b date: 25 September 2012
[INFO] OMEROMetadataStoreClient - Attempting initial SSL connection to gladden.vbi.vt.edu:4064
[INFO] OMEROMetadataStoreClient - Call context: {omero.group:3}
[INFO] OMEROMetadataStoreClient - Server: 4.4.4
[INFO] OMEROMetadataStoreClient - Client: 4.4.4-ice33-b3099
[INFO] OMEROMetadataStoreClient - Java Version: 1.6.0_37
[INFO] OMEROMetadataStoreClient - OS Name: Mac OS X
[INFO] OMEROMetadataStoreClient - OS Arch: x86_64
[INFO] OMEROMetadataStoreClient - OS Version: 10.8.2
[DEBUG] ImportLibrary - FS lite enabled readers: [loci.formats.in.TiffDelegateReader, loci.formats.in.APNGReader, loci.formats.in.SVSReader, loci.formats.in.LeicaSCNReader, loci.formats.in.JPEGReader, loci.formats.in.JPEG2000Reader]
[DEBUG] ImportLibrary - Maximum plane width: 3192
[DEBUG] ImportLibrary - Maximum plane height: 3192
[INFO] ImportCandidates - Depth: 4 Metadata Level: MINIMUM
[INFO] ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 36ms. (36ms total) [0 unknowns]
[INFO] OMEROMetadataStoreClient - Call context: {omero.group:3}
[INFO] OMEROMetadataStoreClient - Call context: {omero.group:3}
[INFO] ImportLibrary - Exiting on error

[jmoore]

Unfortunately, it's still not clear what's going wrong. Likely what's happening is an exception is being eaten. I've added a ticket: https://trac.openmicroscopy.org.uk/ome/ticket/9852. We'll have a fix for this shortly, if you'd like to compile your own client jar. Otherwise, the 4.4.5 release will be out soon.

Could you possibly send us the file and the var/log/Blitz-o.log file from the server?

Sorry for the hassle.
Cheers,
~Josh

[dballvt]

I'm not sure what I did differently, but now the image gets imported to the server. However, it doesn't get placed into any dataset. Below is the code I used. I'm trying to add the image to dataset 163, which is part of project 2, which is owned by user 2 (the user that I am logging in), who is part of group 3. The image shows up in the Images tab on the right-hand side of the Insight window, but not under Projects.

Code: Select all

java.lang.System.setProperty('java.util.prefs.PreferencesFactory','java.util.prefs.MacOSXPreferencesFactory');
import loci.formats.in.DefaultMetadataOptions;
import loci.formats.in.MetadataLevel;
import loci.common.*;
import ome.formats.OMEROMetadataStoreClient;
import ome.formats.importer.*
import ome.formats.importer.ImportConfig;
import ome.formats.importer.cli.ErrorHandler;
import ome.formats.importer.cli.LoggingImportMonitor;
import omero.model.Dataset;
loadOmero;


loci.common.DebugTools.enableLogging('debug');

config = ImportConfig();
config.email.set('');
config.email.get;
config.sendFiles.set(true);
config.sendReport.set(false);
config.contOnError.set(false);
config.debug.set(true);
config.hostname.set(host);

port = javaObject('java.lang.Integer',4064);
config.port.set(port);
config.username.set(uname);
config.password.set(pword);
config.targetClass.set('omero.model.Dataset');

dataID = javaObject('java.lang.Long',163);

config.targetId.set(dataID);

groupID = javaObject('java.lang.Long',3);
config.group.set(groupID);

projectID = javaObject('java.lang.Long',2);
config.savedProject.set(projectID);

paths = '/Users/dball07/Documents/Projects/Cell-Cycle/FISH/2012.05.09-FISH_Net1-GFP_GFP-Cy3_20/Region01/Cy3/Cy3_t001.tif';

store = config.createStore();

store.logVersionInfo(config.getIniVersionNumber());
reader = OMEROWrapper(config);

library = ImportLibrary(store, reader);
handler = ErrorHandler(config);
library.addObserver(LoggingImportMonitor());
candidates = ImportCandidates(reader, paths, handler);

reader.setMetadataOptions(DefaultMetadataOptions(MetadataLevel.ALL));
log = org.apache.commons.logging.LogFactory.getLog('ome.formats.importer.ImportLibrary');
log.setLevel(0)
success = library.importCandidates(config, candidates);
store.logout();


This is the printout in MATLAB:
[INFO] ImportConfig - OMERO Version: 4.4.4-ice33-b3099
[INFO] ImportConfig - Bioformats version: 4.4.4 revision: 96c615b date: 25 September 2012
[INFO] OMEROMetadataStoreClient - Attempting initial SSL connection to gladden.vbi.vt.edu:4064
[INFO] OMEROMetadataStoreClient - Call context: {omero.group:3}
[INFO] OMEROMetadataStoreClient - Server: 4.4.4
[INFO] OMEROMetadataStoreClient - Client: 4.4.4-ice33-b3099
[INFO] OMEROMetadataStoreClient - Java Version: 1.6.0_37
[INFO] OMEROMetadataStoreClient - OS Name: Mac OS X
[INFO] OMEROMetadataStoreClient - OS Arch: x86_64
[INFO] OMEROMetadataStoreClient - OS Version: 10.8.2
[DEBUG] ImportLibrary - FS lite enabled readers: [loci.formats.in.TiffDelegateReader, loci.formats.in.APNGReader, loci.formats.in.SVSReader, loci.formats.in.LeicaSCNReader, loci.formats.in.JPEGReader, loci.formats.in.JPEG2000Reader]
[DEBUG] ImportLibrary - Maximum plane width: 3192
[DEBUG] ImportLibrary - Maximum plane height: 3192
[INFO] ImportCandidates - Depth: 4 Metadata Level: MINIMUM
[INFO] ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 41ms. (41ms total) [0 unknowns]
[INFO] OMEROMetadataStoreClient - Call context: {omero.group:3}
[INFO] OMEROMetadataStoreClient - Call context: {omero.group:3}
[DEBUG] ImportLibrary - Image Count: 1
[DEBUG] ImportLibrary - Using TIFF/PNG/JPEG reader FS lite handling.
[DEBUG] ImportLibrary - Image does not meet big image size criteria.
[INFO] ImportLibrary - File format: Tagged Image File Format
[INFO] ImportLibrary - Base reader: loci.formats.in.TiffDelegateReader
[INFO] ImportLibrary - Metadata only import? false
[INFO] ImportLibrary - Archiving enabled? false
[INFO] ImportLibrary - Container metadata only import? false
[INFO] ImportLibrary - Reader is not of HCS domain, use metafile: true
[DEBUG] ImportLibrary - Server tile size: [1392, 376]
[DEBUG] ImportLibrary - Plane:0 X:0 Y:0 TileWidth:1392 TileHeight:376 arrayBuf.length:1046784
[DEBUG] ImportLibrary - Plane:0 X:0 Y:376 TileWidth:1392 TileHeight:376 arrayBuf.length:1046784
[DEBUG] ImportLibrary - Plane:0 X:0 Y:752 TileWidth:1392 TileHeight:288 arrayBuf.length:801792
[INFO] LoggingImportMonitor - IMPORT_DONE
Imported pixels:
15955

[jburel]

Hi

We are looking into the problem.
I tried similar code in Java and it works.
We will come back to you with more information in the next few days.

Thanks for your patience.
Jmarie

[sbesson]

Hi,

thanks for reporting this issue. We opened a Pull Request in the source code to fix this bug for OMERO 4.4.x.

If you want to test this fix by yourself, you can download the latest build of OMERO.matlab and use it in your import script. Please be aware this is a development build and may contain other bugs.

Best,
Sebastien