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Task #5419 (closed)

Opened 8 years ago

Closed 8 years ago

Last modified 8 years ago

Pyramid support for float data

Reported by: wmoore Owned by: cxallan
Priority: major Milestone: OMERO-Beta4.3.1
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2011-07-07 (1)

Description

I understand that this is not planned for 4.3.0 but just got this import BUG importing mrc

omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.RuntimeException):
                        loci.formats.FormatException: Unsupported image type 'float'.
                        	at ome.io.bioformats.BfPyramidPixelBuffer.setTile(BfPyramidPixelBuffer.java:408)
                        	at ome.services.RawPixelsBean.setTile(RawPixelsBean.java:764)
                        	at sun.reflect.GeneratedMethodAccessor1640.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:592)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:150)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)
                        	at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:111)

Change History (17)

comment:1 Changed 8 years ago by mlinkert

  • Sprint set to 2011-06-02 (13)

comment:2 Changed 8 years ago by mlinkert

  • Status changed from new to accepted

comment:3 Changed 8 years ago by mlinkert

  • Owner mlinkert-x deleted
  • Status changed from accepted to new

comment:4 Changed 8 years ago by mlinkert

  • Owner set to mlinkert-x

comment:5 Changed 8 years ago by jburel

  • Sprint changed from 2011-06-02 (13) to 2011-06-16 (14)

Moved from sprint 2011-06-02 (13)

comment:6 Changed 8 years ago by mlinkert

  • Cc cxallan removed
  • Owner changed from mlinkert-x to cxallan

Not a whole lot I can do about this, unfortunately, so re-assigning to Chris. If there's anything specific that I can do to help just let me know.

comment:7 Changed 8 years ago by jburel

  • Milestone changed from OMERO-Beta4.3 to OMERO-Beta4.3.1
  • Sprint changed from 2011-06-16 (14) to 2011-06-30 (1)

Moved from sprint 2011-06-16 (14)

comment:8 Changed 8 years ago by jmoore

Leaving in 4.3.1 for investigation, but this will need the rendering engine work from 4.3.2.

comment:9 Changed 8 years ago by cxallan

  • Remaining Time set to 0.5

comment:10 Changed 8 years ago by cxallan

  • Status changed from new to accepted

comment:11 Changed 8 years ago by cxallan

The state of the JAI ImageIO implementation.

java.lang.IllegalArgumentException: Only byte/short/ushort/int types are supported.
	at com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter.checkSampleModel(J2KImageWriter.java:510)
	at com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter.write(J2KImageWriter.java:232)
	at loci.formats.services.JAIIIOServiceImpl.writeImage(JAIIIOServiceImpl.java:119)
	at loci.formats.utests.JAIIIOServiceTest.testWriteFloatingPointLossy(JAIIIOServiceTest.java:290)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:74)
	at org.testng.internal.Invoker.invokeMethod(Invoker.java:673)
	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:846)
	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1168)
	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
	at org.testng.TestRunner.runWorkers(TestRunner.java:1125)
	at org.testng.TestRunner.privateRun(TestRunner.java:749)
	at org.testng.TestRunner.run(TestRunner.java:600)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:317)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:312)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:274)
	at org.testng.SuiteRunner.run(SuiteRunner.java:223)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:954)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:883)
	at org.testng.TestNG.run(TestNG.java:817)
	at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:110)
	at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:205)
	at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:174)

comment:12 Changed 8 years ago by Chris Allan <callan@…>

  • Remaining Time changed from 0.5 to 0
  • Resolution set to fixed
  • Status changed from accepted to closed

(In [3efadb03246b6a5912d3f5de8b0aef796b5008c1/bioformats.git]) Merge branch 'feature/5419' into develop

This closes #5419 for now. We'll have to pick this up later.

comment:13 Changed 8 years ago by Chris Allan <callan@…>

(In [8b7bba364888a98e940dc93a32e5ba7222af5011/bioformats.git]) Merge branch 'feature/5419' into develop

This closes #5419 for now. We'll have to pick this up later.
(cherry picked from commit 3efadb03246b6a5912d3f5de8b0aef796b5008c1)

comment:14 Changed 8 years ago by Chris Allan <callan@…>

(In [3efadb03246b6a5912d3f5de8b0aef796b5008c1/bioformats.git]) Merge branch 'feature/5419' into develop

This closes #5419 for now. We'll have to pick this up later.

comment:15 Changed 8 years ago by Chris Allan <callan@…>

(In [8b7bba364888a98e940dc93a32e5ba7222af5011/bioformats.git]) Merge branch 'feature/5419' into develop

This closes #5419 for now. We'll have to pick this up later.
(cherry picked from commit 3efadb03246b6a5912d3f5de8b0aef796b5008c1)

comment:16 Changed 8 years ago by Chris Allan <callan@…>

(In [3efadb03246b6a5912d3f5de8b0aef796b5008c1/bioformats.git]) Merge branch 'feature/5419' into develop

This closes #5419 for now. We'll have to pick this up later.

comment:17 Changed 8 years ago by Chris Allan <callan@…>

(In [3efadb03246b6a5912d3f5de8b0aef796b5008c1/bioformats.git]) Merge branch 'feature/5419' into develop

This closes #5419 for now. We'll have to pick this up later.

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