Null pointer exception
dkurt opened this issue · 3 comments
dkurt commented
Hi! I'm trying to run a script from https://www.orbit.bio/deep-learning-models/ in command line:
$ groovy -cp "build/libs/orbit-image-analysis-3.64.jar:build/libs/lib/*" src/main/groovy/com/actelion/research/orbit/imageAnalysis/scripts/deepLearning/DeepLearningSegmentation.groovy
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.codehaus.groovy.vmplugin.v7.Java7$1 (file:/home/dkurt/orbit-image-analysis/build/libs/lib/groovy-2.5.7.jar) to constructor java.lang.invoke.MethodHandles$Lookup(java.lang.Class,int)
WARNING: Please consider reporting this to the maintainers of org.codehaus.groovy.vmplugin.v7.Java7$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2021-01-25 20:11:58.168786: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2021-01-25 20:11:58.192078: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 4008000000 Hz
2021-01-25 20:11:58.192452: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7fe029b82c40 executing computations on platform Host. Devices:
2021-01-25 20:11:58.192477: I tensorflow/compiler/xla/service/service.cc:175] StreamExecutor device (0): <undefined>, <undefined>
using Tensorflow 1.14.0
20:11:58.444 INFO c.a.r.o.i.dal.DALConfig:230 - using config file: resources/config.properties
20:11:58.448 INFO c.a.r.o.i.dal.DALConfig:74 - Configured image provider: com.actelion.research.orbit.imageprovider.ImageProviderOmero
20:11:58.448 INFO c.a.r.o.i.dal.DALConfig:75 - Different image providers can be configured in resources/config.properties or resources/config_custom.properties (priority).
20:11:58.466 INFO c.a.r.o.i.ImageProviderOmero:133 - searching for OrbitOmero.properties in current directory (/home/dkurt/orbit-image-analysis)
20:11:58.478 INFO c.a.r.o.i.ImageProviderOmero:143 - searching for OrbitOmero.properties in user home (/home/dkurt)
20:11:58.488 INFO c.a.r.o.i.ImageProviderOmero:176 - Omero host: localhost
20:11:58.490 INFO c.a.r.o.i.ImageProviderOmero:177 - Omero port: 4064
20:11:58.490 INFO c.a.r.o.i.ImageProviderOmero:178 - Omero web port: 443
20:11:58.491 INFO c.a.r.o.i.ImageProviderOmero:179 - Omero use SSL: false
20:11:58.491 INFO c.a.r.o.i.ImageProviderOmero:180 - Omero use WebSockets: false
20:11:58.491 INFO c.a.r.o.i.ImageProviderOmero:181 - Search limit: 1000
20:11:58.491 INFO c.a.r.o.i.ImageProviderOmero:182 - Omero User Scaleout:
20:11:58.503 WARN c.a.r.o.i.dal.DALConfig:85 - Orbit will continue with the fallback local filesystem image provider.
20:11:58.507 INFO c.a.r.o.i.dal.DALConfig:104 - scaleout mode: true
20:11:58.509 INFO c.a.r.o.i.dal.DALConfig:152 - image provider: com.actelion.research.orbit.imageAnalysis.dal.ImageProviderLocal@7c2312fa
20:11:58.510 INFO c.a.r.o.i.dal.DALConfig:153 - scaleOut: com.actelion.research.orbit.imageAnalysis.dal.ScaleoutNoop@4cb0a000
20:11:58.511 INFO c.a.r.o.i.dal.DALConfig:169 - local db file: /home/dkurt/orbit.db
Caught: java.lang.NullPointerException
java.lang.NullPointerException
at com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment.generateSegmentationAnnotations(DLSegment.java:87)
at com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment.generateSegmentationAnnotations(DLSegment.java:78)
at com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment$generateSegmentationAnnotations$0.call(Unknown Source)
at DeepLearningSegmentation.run(DeepLearningSegmentation.groovy:50)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
orbit.db
exists (downloaded from https://doi.org/10.5061/dryad.fqz612jpc). But there is an error at the following line because rdf
is null
:
/cc @mstritt
dkurt commented
With sqlitebrowser
found valid ids:
int[] images = [88]
Going to fix subsequent error:
logs
13:23:27.208 INFO c.a.r.o.i.d.DLSegment:88 - rdfid: 88
java.io.FileNotFoundException: /train/6666718.tiff (No such file or directory)
at java.base/java.io.RandomAccessFile.open0(Native Method)
at java.base/java.io.RandomAccessFile.open(RandomAccessFile.java:345)
at java.base/java.io.RandomAccessFile.<init>(RandomAccessFile.java:259)
at java.base/java.io.RandomAccessFile.<init>(RandomAccessFile.java:214)
at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:130)
at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:151)
at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:165)
at loci.common.Location.getHandle(Location.java:522)
at loci.common.Location.getHandle(Location.java:462)
at loci.common.Location.getHandle(Location.java:443)
at loci.common.Location.getHandle(Location.java:426)
at loci.common.RandomAccessInputStream.<init>(RandomAccessInputStream.java:125)
at loci.formats.tiff.TiffParser.<init>(TiffParser.java:105)
at com.actelion.research.orbit.imageAnalysis.dal.localImage.OrbitImageTiff$1.initialValue(OrbitImageTiff.java:117)
at com.actelion.research.orbit.imageAnalysis.dal.localImage.OrbitImageTiff$1.initialValue(OrbitImageTiff.java:113)
at java.base/java.lang.ThreadLocal.setInitialValue(ThreadLocal.java:195)
at java.base/java.lang.ThreadLocal.get(ThreadLocal.java:172)
at com.actelion.research.orbit.imageAnalysis.dal.localImage.OrbitImageTiff.<init>(OrbitImageTiff.java:124)
at com.actelion.research.orbit.imageAnalysis.dal.ImageProviderLocal.createOrbitImage(ImageProviderLocal.java:283)
at com.actelion.research.orbit.imageAnalysis.utils.TiledImagePainter.loadImage(TiledImagePainter.java:182)
at com.actelion.research.orbit.imageAnalysis.utils.TiledImagePainter.loadImage(TiledImagePainter.java:176)
at com.actelion.research.orbit.imageAnalysis.utils.TiledImagePainter.loadImage(TiledImagePainter.java:171)
at com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.loadImage(RecognitionFrame.java:555)
at com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.loadImage(RecognitionFrame.java:534)
at com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.<init>(RecognitionFrame.java:165)
at com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.<init>(RecognitionFrame.java:152)
at com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment.generateSegmentationAnnotations(DLSegment.java:99)
at com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment.generateSegmentationAnnotations(DLSegment.java:78)
at com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment$generateSegmentationAnnotations$0.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:115)
at DeepLearningSegmentation.run(DeepLearningSegmentation.groovy:50)
at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:260)
at groovy.lang.GroovyShell.run(GroovyShell.java:370)
at groovy.lang.GroovyShell.run(GroovyShell.java:359)
at groovy.ui.GroovyMain.processOnce(GroovyMain.java:592)
at groovy.ui.GroovyMain.run(GroovyMain.java:336)
at groovy.ui.GroovyMain.access$1400(GroovyMain.java:69)
at groovy.ui.GroovyMain$GroovyCommand.process(GroovyMain.java:295)
at groovy.ui.GroovyMain.processArgs(GroovyMain.java:134)
at groovy.ui.GroovyMain.main(GroovyMain.java:116)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:116)
at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:138)
13:23:27.269 ERROR c.a.r.o.i.c.RecognitionFrame:559 - Error loading image. Probably the Orbit image server down or not accessible.
Error Details:
com.actelion.research.orbit.exceptions.OrbitImageServletException: Tiffparser error, cannot open tiff file /train/6666718.tiff
at com.actelion.research.orbit.imageAnalysis.dal.localImage.OrbitImageTiff.<init>(OrbitImageTiff.java:124)
at com.actelion.research.orbit.imageAnalysis.dal.ImageProviderLocal.createOrbitImage(ImageProviderLocal.java:283)
Caught: com.actelion.research.orbit.exceptions.OrbitImageServletException: Tiffparser error, cannot open tiff file /train/6666718.tiff
com.actelion.research.orbit.exceptions.OrbitImageServletException: Tiffparser error, cannot open tiff file /train/6666718.tiff
at com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.loadImage(RecognitionFrame.java:561)
at com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.loadImage(RecognitionFrame.java:534)
at com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.<init>(RecognitionFrame.java:165)
at com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.<init>(RecognitionFrame.java:152)
at com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment.generateSegmentationAnnotations(DLSegment.java:99)
at com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment.generateSegmentationAnnotations(DLSegment.java:78)
at com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment$generateSegmentationAnnotations$0.call(Unknown Source)
at DeepLearningSegmentation.run(DeepLearningSegmentation.groovy:50)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
mstritt commented
Hi Dimitry,
you have to set the correct image id.
Either you use the function
(ImageProviderLocal)DAlConfig.getImageProvider().registerFile(...)
or you first open the image in the GUI and get the image ID from the tab
"File" (right side)....
(the id will stay - based on md5)
Regards,
Manuel
… With sqlitebrowser found valid ids:
int[] images = [88]
Going to fix subsequent error: logs
13:23:27.208 INFO c.a.r.o.i.d.DLSegment:88 - rdfid: 88
java.io.FileNotFoundException: /train/6666718.tiff (No such file or
directory)
at java.base/java.io.RandomAccessFile.open0(Native Method)
at
java.base/java.io.RandomAccessFile.open(RandomAccessFile.java:345)
at
java.base/java.io.RandomAccessFile.<init>(RandomAccessFile.java:259)
at
java.base/java.io.RandomAccessFile.<init>(RandomAccessFile.java:214)
at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:130)
at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:151)
at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:165)
at loci.common.Location.getHandle(Location.java:522)
at loci.common.Location.getHandle(Location.java:462)
at loci.common.Location.getHandle(Location.java:443)
at loci.common.Location.getHandle(Location.java:426)
at
loci.common.RandomAccessInputStream.<init>(RandomAccessInputStream.java:125)
at loci.formats.tiff.TiffParser.<init>(TiffParser.java:105)
at
com.actelion.research.orbit.imageAnalysis.dal.localImage.OrbitImageTiff$1.initialValue(OrbitImageTiff.java:117)
at
com.actelion.research.orbit.imageAnalysis.dal.localImage.OrbitImageTiff$1.initialValue(OrbitImageTiff.java:113)
at
java.base/java.lang.ThreadLocal.setInitialValue(ThreadLocal.java:195)
at java.base/java.lang.ThreadLocal.get(ThreadLocal.java:172)
at
com.actelion.research.orbit.imageAnalysis.dal.localImage.OrbitImageTiff.<init>(OrbitImageTiff.java:124)
at
com.actelion.research.orbit.imageAnalysis.dal.ImageProviderLocal.createOrbitImage(ImageProviderLocal.java:283)
at
com.actelion.research.orbit.imageAnalysis.utils.TiledImagePainter.loadImage(TiledImagePainter.java:182)
at
com.actelion.research.orbit.imageAnalysis.utils.TiledImagePainter.loadImage(TiledImagePainter.java:176)
at
com.actelion.research.orbit.imageAnalysis.utils.TiledImagePainter.loadImage(TiledImagePainter.java:171)
at
com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.loadImage(RecognitionFrame.java:555)
at
com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.loadImage(RecognitionFrame.java:534)
at
com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.<init>(RecognitionFrame.java:165)
at
com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.<init>(RecognitionFrame.java:152)
at
com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment.generateSegmentationAnnotations(DLSegment.java:99)
at
com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment.generateSegmentationAnnotations(DLSegment.java:78)
at
com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment$generateSegmentationAnnotations$0.call(Unknown
Source)
at
org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at
org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:115)
at
DeepLearningSegmentation.run(DeepLearningSegmentation.groovy:50)
at
groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:260)
at groovy.lang.GroovyShell.run(GroovyShell.java:370)
at groovy.lang.GroovyShell.run(GroovyShell.java:359)
at groovy.ui.GroovyMain.processOnce(GroovyMain.java:592)
at groovy.ui.GroovyMain.run(GroovyMain.java:336)
at groovy.ui.GroovyMain.access$1400(GroovyMain.java:69)
at
groovy.ui.GroovyMain$GroovyCommand.process(GroovyMain.java:295)
at groovy.ui.GroovyMain.processArgs(GroovyMain.java:134)
at groovy.ui.GroovyMain.main(GroovyMain.java:116)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at
org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:116)
at
org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:138)
13:23:27.269 ERROR c.a.r.o.i.c.RecognitionFrame:559 - Error loading
image. Probably the Orbit image server down or not accessible.
Error Details:
com.actelion.research.orbit.exceptions.OrbitImageServletException:
Tiffparser error, cannot open tiff file /train/6666718.tiff
at
com.actelion.research.orbit.imageAnalysis.dal.localImage.OrbitImageTiff.<init>(OrbitImageTiff.java:124)
at
com.actelion.research.orbit.imageAnalysis.dal.ImageProviderLocal.createOrbitImage(ImageProviderLocal.java:283)
Caught:
com.actelion.research.orbit.exceptions.OrbitImageServletException:
Tiffparser error, cannot open tiff file /train/6666718.tiff
com.actelion.research.orbit.exceptions.OrbitImageServletException:
Tiffparser error, cannot open tiff file /train/6666718.tiff
at
com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.loadImage(RecognitionFrame.java:561)
at
com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.loadImage(RecognitionFrame.java:534)
at
com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.<init>(RecognitionFrame.java:165)
at
com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame.<init>(RecognitionFrame.java:152)
at
com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment.generateSegmentationAnnotations(DLSegment.java:99)
at
com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment.generateSegmentationAnnotations(DLSegment.java:78)
at
com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment$generateSegmentationAnnotations$0.call(Unknown
Source)
at
DeepLearningSegmentation.run(DeepLearningSegmentation.groovy:50)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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