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knime-ip / knip

KNIME Image Processing Extension
https://www.knime.com/community/image-processing
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Image Calculator: fails with binary data on console in batch mode #424

Open maierl opened 7 years ago

maierl commented 7 years ago

My workflow runs fine in the GUI, but in batch mode the Image Calculator fails. I'll try to extract an example workflow if necessary. Has anyone already seen that behavior?


ERROR    KNIME-Worker-9 Image Calculator         Execute failed: java.lang.RuntimeException: java.lang.ClassCastException: net.imglib2.img.array.ArrayImg cannot be cast to org.knime.knip.base.data.img.ImgPlusCellMetadata
ERROR    KNIME-Worker-8 Image Calculator         Execute failed: java.lang.RuntimeException: java.io.IOException: No externalizer available with id
ERROR    KNIME-Worker-18 Image Calculator        Execute failed: java.lang.RuntimeException: java.io.IOException: No externalizer available with id
ERROR    KNIME-Worker-15 Image Calculator        56:=;/0754=96:9:@=:@OTFG9=FDKRWa][iii|�¡®�¡©�{�§~�¢½¼¨»Á��¤¢Ü±··­¤¬�¡¼³��±¹¶®¼Å»ÁÐȹ־°¸�����ee`~[dgm����y�³¥§ÈÙþIJśƲƸȓʏͮеԿת۩ࡅऌবਬਖ਼ષ௢ച༊ྌླྀ໒༖ཆၑᅑᇯቂቩጒᏏᏰ፜ሳᄩႶႇྸုလཇາ೵ఏହਚঝ঒৖ुࠈܵڠ֗цμ΍˽ɻȭǓǍƯŘŀŁĐÖÑɹ©³�¨�q``
maierl commented 7 years ago

Now I have a shorter workflow now that 100% reproduces that bug. At does behave quite strange, though. If I delete the nodes parallel with the Image Calculator, the error is gone. Are you still interested?

maierl commented 7 years ago

Here's a workflow with a already broken table. https://powerfolder.dkfz.de/dl/fiXKUhttBDXNJPfeYxeGBv7r/img_calc_fail_test.tar.gz

I'm also preparing a workflow that reproduces the process of breaking itself.

maierl commented 7 years ago

There it is. Both workflows just need to be executed to fail. You just need to adjust the image paths for the "splitter test fail" workflow, which fails only in batch mode.

I called it splitter fail because when the batch mode saves the results after execution and I load that, it fails to continue in the GUI. But when I've reset the Splitter, it executed successfully.

https://powerfolder.dkfz.de/dl/fiKRKwY5fSzNzvaH28Te3uzw/splitter_fail_test.tar.gz https://powerfolder.dkfz.de/dl/fiVefEYTMuxTsWJAMmt8f7gV/splitter_fail_test_images.tar.gz

dietzc commented 7 years ago

Puh, this seems to be a tricky one - I'll take a look as soon as possible. Thanks for reporting