Cellprofiler: Resolve Java library exceptions

Created on 15 Aug 2016  路  7Comments  路  Source: CellProfiler/CellProfiler

When running the example pipeline:

INFO:cellprofiler.analysis:Worker 2: Warning:  org.apache.xerces.parsers.SAXParser: Feature 'http://javax.xml.XMLConstants/feature/secure-processing' is not recognized.
INFO:cellprofiler.analysis:Worker 2: Warning:  org.apache.xerces.parsers.SAXParser: Property 'http://javax.xml.XMLConstants/property/accessExternalDTD' is not recognized.
INFO:cellprofiler.analysis:Worker 2: Warning:  org.apache.xerces.parsers.SAXParser: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.
INFO:cellprofiler.analysis:Worker 2: Exception in thread "Thread-2" java.io.EOFException: Attempting to read beyond end of file.
INFO:cellprofiler.analysis:Worker 2:    at loci.common.NIOFileHandle.readFloat(NIOFileHandle.java:350)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.RandomAccessInputStream.readFloat(RandomAccessInputStream.java:501)
INFO:cellprofiler.analysis:Worker 2:    at loci.formats.in.PQBinReader.isThisType(PQBinReader.java:96)
INFO:cellprofiler.analysis:Worker 2: Caused by: java.nio.BufferUnderflowException
INFO:cellprofiler.analysis:Worker 2:    at java.nio.Buffer.nextGetIndex(Buffer.java:506)
INFO:cellprofiler.analysis:Worker 2:    at java.nio.HeapByteBuffer.getFloat(HeapByteBuffer.java:463)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.NIOFileHandle.readFloat(NIOFileHandle.java:348)
INFO:cellprofiler.analysis:Worker 2:    ... 2 more
INFO:cellprofiler.analysis:Worker 2: Caught exception in class loci.formats.in.PQBinReader.isThisType
INFO:cellprofiler.analysis:Worker 2: Exception in thread "Thread-2" java.lang.IllegalArgumentException
INFO:cellprofiler.analysis:Worker 2:    at java.nio.Buffer.position(Buffer.java:244)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:603)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.NIOFileHandle.seek(NIOFileHandle.java:291)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:174)
INFO:cellprofiler.analysis:Worker 2:    at loci.formats.tiff.TiffParser.<init>(TiffParser.java:113)
INFO:cellprofiler.analysis:Worker 2:    at loci.formats.in.FlowSightReader.isThisType(FlowSightReader.java:101)
INFO:cellprofiler.analysis:Worker 2: Caught exception in class loci.formats.in.FlowSightReader.isThisType
INFO:cellprofiler.analysis:Worker 2: Exception in thread "Thread-2" java.io.EOFException: Attempting to read beyond end of file.
INFO:cellprofiler.analysis:Worker 2:    at loci.common.NIOFileHandle.readFloat(NIOFileHandle.java:350)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.RandomAccessInputStream.readFloat(RandomAccessInputStream.java:501)
INFO:cellprofiler.analysis:Worker 2:    at loci.formats.in.PQBinReader.isThisType(PQBinReader.java:96)
INFO:cellprofiler.analysis:Worker 2: Caused by: java.nio.BufferUnderflowException
INFO:cellprofiler.analysis:Worker 2:    at java.nio.Buffer.nextGetIndex(Buffer.java:506)
INFO:cellprofiler.analysis:Worker 2:    at java.nio.HeapByteBuffer.getFloat(HeapByteBuffer.java:463)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.NIOFileHandle.readFloat(NIOFileHandle.java:348)
INFO:cellprofiler.analysis:Worker 2:    ... 2 more
INFO:cellprofiler.analysis:Worker 2: Caught exception in class loci.formats.in.PQBinReader.isThisType
INFO:cellprofiler.analysis:Worker 2: Exception in thread "Thread-2" java.lang.IllegalArgumentException
INFO:cellprofiler.analysis:Worker 2:    at java.nio.Buffer.position(Buffer.java:244)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:603)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.NIOFileHandle.seek(NIOFileHandle.java:291)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:174)
INFO:cellprofiler.analysis:Worker 2:    at loci.formats.tiff.TiffParser.<init>(TiffParser.java:113)
INFO:cellprofiler.analysis:Worker 2:    at loci.formats.in.FlowSightReader.isThisType(FlowSightReader.java:101)
INFO:cellprofiler.analysis:Worker 2: Caught exception in class loci.formats.in.FlowSightReader.isThisType
INFO:cellprofiler.analysis:Worker 2: Exception in thread "Thread-2" java.io.EOFException: Attempting to read beyond end of file.
INFO:cellprofiler.analysis:Worker 2:    at loci.common.NIOFileHandle.readFloat(NIOFileHandle.java:350)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.RandomAccessInputStream.readFloat(RandomAccessInputStream.java:501)
INFO:cellprofiler.analysis:Worker 2:    at loci.formats.in.PQBinReader.isThisType(PQBinReader.java:96)
INFO:cellprofiler.analysis:Worker 2: Caused by: java.nio.BufferUnderflowException
INFO:cellprofiler.analysis:Worker 2:    at java.nio.Buffer.nextGetIndex(Buffer.java:506)
INFO:cellprofiler.analysis:Worker 2:    at java.nio.HeapByteBuffer.getFloat(HeapByteBuffer.java:463)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.NIOFileHandle.readFloat(NIOFileHandle.java:348)
INFO:cellprofiler.analysis:Worker 2:    ... 2 more
INFO:cellprofiler.analysis:Worker 2: Caught exception in class loci.formats.in.PQBinReader.isThisType
INFO:cellprofiler.analysis:Worker 2: Exception in thread "Thread-2" java.lang.IllegalArgumentException
INFO:cellprofiler.analysis:Worker 2:    at java.nio.Buffer.position(Buffer.java:244)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:603)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.NIOFileHandle.seek(NIOFileHandle.java:291)
INFO:cellprofiler.analysis:Worker 2:    at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:174)
INFO:cellprofiler.analysis:Worker 2:    at loci.formats.tiff.TiffParser.<init>(TiffParser.java:113)
INFO:cellprofiler.analysis:Worker 2:    at loci.formats.in.FlowSightReader.isThisType(FlowSightReader.java:101)
INFO:cellprofiler.analysis:Worker 2: Caught exception in class loci.formats.in.FlowSightReader.isThisType
INFO:cellprofiler.analysis:Worker 2: Mon Aug 15 10:03:32 2016: Image # 1, module NamesAndTypes # 3: 1.95 secs
INFO:cellprofiler.analysis:Worker 2: Running module Groups 4
INFO:cellprofiler.analysis:Worker 2: Mon Aug 15 10:03:35 2016: Image # 1, module Groups # 4: 0.00 secs
INFO:cellprofiler.analysis:Worker 2: Running module Crop 5
INFO:cellprofiler.analysis:Worker 2: /Users/mcquin/code/CellProfiler/CellProfiler/cellprofiler/image.py:473: VisibleDeprecationWarning: converting an array with ndim > 0 to an index will result in an error in the future
INFO:cellprofiler.analysis:Worker 2:   return image[i_first:i_end, j_first:j_end].copy()
INFO:cellprofiler.analysis:Worker 2: Mon Aug 15 10:03:35 2016: Image # 1, module Crop # 5: 0.61 secs
INFO:cellprofiler.analysis:Worker 2: Running module Crop 6
INFO:cellprofiler.analysis:Worker 2: Mon Aug 15 10:03:36 2016: Image # 1, module Crop # 6: 0.01 secs
INFO:cellprofiler.analysis:Worker 2: Running module Crop 7
INFO:cellprofiler.analysis:Worker 2: Mon Aug 15 10:03:38 2016: Image # 1, module Crop # 7: 0.01 secs
INFO:cellprofiler.analysis:Worker 2: Running module IdentifyPrimaryObjects 8
INFO:cellprofiler.analysis:Worker 2: Mon Aug 15 10:03:39 2016: Image # 1, module IdentifyPrimaryObjects # 8: 0.10 secs
INFO:cellprofiler.analysis:Worker 2: Running module IdentifySecondaryObjects 9
INFO:cellprofiler.analysis:Worker 2: Mon Aug 15 10:03:40 2016: Image # 1, module IdentifySecondaryObjects # 9: 0.07 secs
INFO:cellprofiler.analysis:Worker 2: Running module IdentifyTertiaryObjects 10
INFO:cellprofiler.analysis:Worker 2: Mon Aug 15 10:03:41 2016: Image # 1, module IdentifyTertiaryObjects # 10: 0.04 secs
INFO:cellprofiler.analysis:Worker 2: Running module MeasureObjectSizeShape 11
INFO:cellprofiler.analysis:Worker 2: Mon Aug 15 10:03:42 2016: Image # 1, module MeasureObjectSizeShape # 11: 0.25 secs
INFO:cellprofiler.analysis:Worker 2: Running module MeasureObjectIntensity 12
INFO:cellprofiler.analysis:Worker 2: Mon Aug 15 10:03:42 2016: Image # 1, module MeasureObjectIntensity # 12: 0.16 secs
INFO:cellprofiler.analysis:Worker 2: Running module MeasureTexture 13
Bug
Source
picture mcquin
👍3

All 7 comments

Cool - any sort of exception in the logs or the CP terminal displayed to the user, causes many questions by users and developers alike. My vote is to minimize all the false positives

dlogan picture dlogan on 16 Aug 2016

The errors were due to uncaught exceptions in isThisType for two image readers. I've submitted a PR which catches these exceptions and it will be included in the 5.6.1 release. Reference: https://github.com/openmicroscopy/bioformats/pull/2929

mcquin picture mcquin on 21 Aug 2017

should this be closed?

AnneCarpenter picture AnneCarpenter on 2 Sep 2017

I will close it once the changes are released in bioformats and incorporated into python-bioformats and prokaryote.

mcquin picture mcquin on 2 Sep 2017
👍1

@AnneCarpenter @mcquin we just released Bio-Formats 5.7.0 which should include these fixes. Let us know if you the exceptions persist.

sbesson picture sbesson on 4 Sep 2017
🎉1

Thanks, @sbesson!

0x00b1 picture 0x00b1 on 4 Sep 2017

Done!

mcquin picture mcquin on 6 Sep 2017
Was this page helpful?
0 / 5 - 0 ratings

Related issues

katrinleinweber picture katrinleinweber  路  3Comments
burgerga picture burgerga  路  8Comments
dlogan picture dlogan  路  9Comments
dlogan picture dlogan  路  9Comments
imagejan picture imagejan  路  8Comments