Task #2358 (closed)
Opened 14 years ago
Closed 14 years ago
BUG: Importing lsm
Reported by: | jburel | Owned by: | cxallan |
---|---|---|---|
Priority: | critical | Milestone: | OMERO-Beta4.2 |
Component: | Import | Version: | n.a. |
Keywords: | n.a. | Cc: | cxallan |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | 0.0d |
Sprint: | 2010-05-13 (9) |
Description (last modified by jburel)
Using r6984
Follow the exception when trying to import 2chZT.lsm
2010-05-14 22:24:14,091 57590 [2-thread-1] DEBUG ome.formats.importer.gui.GuiImporter - java.lang.NullPointerException at ome.formats.OMEROMetadataStoreClient.handleAbstractLightSource(OMEROMetadataStoreClient.java:1079) at ome.formats.OMEROMetadataStoreClient.getIObjectContainer(OMEROMetadataStoreClient.java:2322) at ome.formats.OMEROMetadataStoreClient.getSourceObject(OMEROMetadataStoreClient.java:1022) at ome.formats.OMEROMetadataStoreClient.getLaser(OMEROMetadataStoreClient.java:4388) at ome.formats.OMEROMetadataStoreClient.setLaserLaserMedium(OMEROMetadataStoreClient.java:4424) at loci.formats.meta.FilterMetadata.setLaserLaserMedium(FilterMetadata.java:978) at loci.formats.in.ZeissLSMReader.populateMetadataStore(ZeissLSMReader.java:941) at loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:850) at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:400) at loci.formats.FormatReader.setId(FormatReader.java:1011) at loci.formats.ImageReader.setId(ImageReader.java:644) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485) at loci.formats.ChannelFiller.setId(ChannelFiller.java:177) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485) at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:213) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:399) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340) at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215) at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:59) at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269) at java.util.concurrent.FutureTask.run(FutureTask.java:123) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:172) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:651) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:676) at java.lang.Thread.run(Thread.java:613)
Change History (19)
comment:1 Changed 14 years ago by jburel
- Description modified (diff)
comment:2 Changed 14 years ago by cxallan
- Status changed from new to assigned
comment:3 Changed 14 years ago by cxallan
comment:4 Changed 14 years ago by cxallan
- Owner changed from bwzloranger to cxallan
- Status changed from assigned to new
As of bio-formtas:r6301 these files fail with:
2010-05-18 15:50:09,673 1644082 [2-thread-1] DEBUG ome.formats.importer.gui.GuiImporter - Error processing references. at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:150) at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetadataStoreClient.java:1659) at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:251) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:437) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340) at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215) at ome.formats.importer.gui.ImportHandler.access$1(ImportHandler.java:149) at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:637) Caused by: java.lang.RuntimeException: Unable to synchronize reference Dichroic:0:1 --> omero.model.LightPath:0:0 at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:121) ... 15 more
comment:5 Changed 14 years ago by cxallan
- Status changed from new to assigned
comment:6 Changed 14 years ago by cxallan
(In [7038]) Correct LightPath? support. (See #2388, #2358)
comment:7 Changed 14 years ago by cxallan
Back to the ArrayOutOfBoundsException as of r7038. It appears that the channel indexes are being incremented where they don't necessarily need to be.
public void setLightPathDichroicRef(String dichroic, int imageIndex, int channelIndex)
Examples of the containers:
2010-05-18 16:31:09,655 385981 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - omero.model.Channel:0:0 == omero.model.ChannelI@49940c14,Channel:0:0 2010-05-18 16:31:09,657 385983 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - omero.model.Channel:0:1 == omero.model.ChannelI@31818dbc,omero.model.Channel:0:1 2010-05-18 16:31:10,160 386486 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - omero.model.LightPath:0:0 == omero.model.LightPathI@277b8705,omero.model.LightPath:0:0 2010-05-18 16:31:10,160 386486 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - omero.model.LightPath:0:1 == omero.model.LightPathI@5b40c349,omero.model.LightPath:0:1 2010-05-18 16:31:10,160 386486 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - omero.model.LightPath:0:2 == omero.model.LightPathI@6f3d346d,omero.model.LightPath:0:2 2010-05-18 16:31:10,166 386492 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - omero.model.LightPath:0:3 == omero.model.LightPathI@1307e9af,omero.model.LightPath:0:3
comment:8 Changed 14 years ago by cxallan
- Owner changed from cxallan to mlinkert-x
- Status changed from assigned to new
comment:9 Changed 14 years ago by cxallan
(In [7039]) Further LightPath? emission and excitation filter reference fixes. (See #2388, #2358)
comment:10 Changed 14 years ago by mlinkert
Should be fixed in bio-formats:r6337.
comment:11 Changed 14 years ago by cxallan
- Owner changed from mlinkert-x to cxallan
- Status changed from new to assigned
comment:12 Changed 14 years ago by cxallan
- Remaining Time set to 0
- Resolution set to fixed
- Status changed from assigned to closed
comment:13 Changed 14 years ago by cxallan
New exception on different LSM data:
2010-05-19 14:52:09,335 596312 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - INTERNAL_EXCEPTION: /Users/callan/testimages/lsm_martin/01-01.lsm java.lang.IllegalArgumentException: 0 must not be null and positive. at ome.xml.r201004.primitives.PositiveInteger.<init>(PositiveInteger.java:41) at loci.formats.MetadataTools.populatePixels(MetadataTools.java:112) at loci.formats.MetadataTools.populatePixels(MetadataTools.java:91) at loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:643) at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:400) at loci.formats.FormatReader.setId(FormatReader.java:1012) at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:324) at loci.formats.FormatReader.setId(FormatReader.java:1012) at loci.formats.ImageReader.setId(ImageReader.java:644) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485) at loci.formats.ChannelFiller.setId(ChannelFiller.java:177) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485) at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:213) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:399) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340) at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215) at ome.formats.importer.gui.ImportHandler.access$1(ImportHandler.java:149) at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:637)
comment:14 Changed 14 years ago by cxallan
- Resolution fixed deleted
- Status changed from closed to reopened
comment:15 Changed 14 years ago by cxallan
- Owner changed from cxallan to mlinkert-x
- Status changed from reopened to new
comment:16 Changed 14 years ago by mlinkert
Fixed in bio-formats:r6353.
comment:17 Changed 14 years ago by cxallan
- Status changed from new to assigned
comment:18 Changed 14 years ago by cxallan
- Owner changed from mlinkert-x to cxallan
comment:19 Changed 14 years ago by cxallan
- Resolution set to fixed
- Status changed from assigned to closed
As of r7034 fails with: