Ilastik - Error when executing Ilastik Headless node.

Hi all,

I would like to use the Ilastik pixel classifier for Image analysis.

Building the prediction model in Ilastik and saving it as project works fine, but I cannot use the headless node in KNIME.

It gives the following error:

ERROR Ilastik Headless (Pixel classification) 0:1        Error when executing Ilastik. Please check the dimensionality of the input images.
ERROR Ilastik Headless (Pixel classification) 0:1        Execute failed: java.lang.IllegalStateException

However, the image I feed into the headless node and the one I used for model prediction is the same. So dimensions should not be a problem for this test case. Any ideas?

Attached the example workflow with the respective files.

Best,

Fritz

 

Hi Fritz,

can you check if your input image e.g. has three channels (because it's a PNG)? You can exclude the channels directly in the Image Reader (Subset Selection).

Best,

Christian

Hi Christian,

it's the "position_95.tif" attached in the Zip file, 16 bit and single channel. Fritz told me using a .ome.tiff didn't help, either.

Best,

Lorenz

Is there any further information available in the knime.log file?

I also ran into some problems using the Ilastik headless node some time ago. My problem was solved using single channel images instead of RGB. I recall that the headless node does not write too much information to the KNIME log since it's the Ilastik process crashing in the background. So the ilastik or system log should provide more information.

 

Cheers

Ole

Hi all,

Thanks for the answers. Image is single channel.

This is what I get in the KNIME log:

2016-07-15 13:57:37,952 : INFO  : KNIME-Worker-15 : KNIPLogService : Image Reader : 2:2 : Reading IFDs
2016-07-15 13:57:37,953 : INFO  : KNIME-Worker-15 : KNIPLogService : Image Reader : 2:2 : Populating metadata
2016-07-15 13:57:37,954 : INFO  : KNIME-Worker-15 : KNIPLogService : Image Reader : 2:2 : Checking comment style
2016-07-15 13:57:37,983 : INFO  : KNIME-Worker-15 : LocalNodeExecutionJob : Image Reader : 2:2 : Image Reader 2:2 End execute (0 secs)
2016-07-15 13:57:37,989 : WARN  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 : Expected positive value for PhysicalSizeX; got 0.0
2016-07-15 13:57:37,990 : WARN  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 : Expected positive value for PhysicalSizeY; got 0.0
2016-07-15 13:57:39,670 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 : INFO ilastik_main: Starting ilastik from "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release".
2016-07-15 13:57:43,944 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 : Starting ilastik from "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release".
2016-07-15 13:57:44,043 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 : ERROR 2016-07-15 13:57:40,378 excepthooks 614 140735198171136 Unhandled exception in thread: 'MainThread'
2016-07-15 13:57:44,045 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 : ERROR 2016-07-15 13:57:40,379 excepthooks 614 140735198171136 Traceback (most recent call last):
2016-07-15 13:57:44,045 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/Resources/__boot__.py", line 102, in <module>
2016-07-15 13:57:44,045 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     _run()
2016-07-15 13:57:44,045 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/Resources/__boot__.py", line 96, in _run
2016-07-15 13:57:44,045 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     exec(compile(source, script, 'exec'), globals(), globals())
2016-07-15 13:57:44,045 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "ilastik.py", line 111, in <module>
2016-07-15 13:57:44,045 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     main()
2016-07-15 13:57:44,045 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "ilastik.py", line 104, in main
2016-07-15 13:57:44,045 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     ilastik_main.main(parsed_args, workflow_cmdline_args)
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik_main.py", line 102, in main
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     f(shell)
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik_main.py", line 317, in loadProject
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     shell.openProjectFile(path, parsed_args.readonly)
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/shell/headless/headlessShell.py", line 84, in openProjectFile
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     import ilastik.workflows
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/__init__.py", line 28, in <module>
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     import pixelClassification
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/pixelClassification/__init__.py", line 21, in <module>
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     from pixelClassificationWorkflow import PixelClassificationWorkflow
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/pixelClassification/pixelClassificationWorkflow.py", line 34, in <module>
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     from ilastik.applets.pixelClassification import PixelClassificationApplet, PixelClassificationDataExportApplet
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/pixelClassification/__init__.py", line 21, in <module>
2016-07-15 13:57:44,046 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     from pixelClassificationApplet import *
2016-07-15 13:57:44,047 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/pixelClassification/pixelClassificationApplet.py", line 22, in <module>
2016-07-15 13:57:44,047 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     from opPixelClassification import OpPixelClassification
2016-07-15 13:57:44,047 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/pixelClassification/opPixelClassification.py", line 46, in <module>
2016-07-15 13:57:44,047 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     from PyQt4.QtCore import pyqtRemoveInputHook, pyqtRestoreInputHook
2016-07-15 13:57:44,047 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/headless_dummy_modules/PyQt4/__init__.py", line 9, in <module>
2016-07-15 13:57:44,047 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     raise Exception("Developer error: When ilastik is running in headless mode, you aren't allowed to import PyQt4.")
2016-07-15 13:57:44,047 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 : Exception: Developer error: When ilastik is running in headless mode, you aren't allowed to import PyQt4.
2016-07-15 13:57:44,047 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 : 
2016-07-15 13:57:44,047 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 : 2016-07-15 13:57:40.443 ilastik[614:16930] ilastik Error
2016-07-15 13:57:44,047 : ERROR : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 : Error when executing Ilastik. Please check the dimensionality of the input images.
2016-07-15 13:57:44,049 : ERROR : KNIME-Worker-17 : Ilastik Headless (Pixel classification) : Ilastik Headless (Pixel classification) : 2:1 : Execute failed: java.lang.IllegalStateException

Also this in the console that oppens in KNIME when Ilastik throws the error:

15.07.16 13:55:33,771 launchservicesd[80]: SecTaskLoadEntitlements failed error=22
15.07.16 13:55:33,780 launchservicesd[80]: SecTaskLoadEntitlements failed error=22
15.07.16 13:55:33,782 launchservicesd[80]: SecTaskLoadEntitlements failed error=22
15.07.16 13:55:36,555 ilastik[598]: ilastik Error
15.07.16 13:55:36,715 appleeventsd[52]: SecTaskLoadEntitlements failed error=22
15.07.16 13:55:36,720 WindowServer[164]: SecTaskLoadEntitlements failed error=22
15.07.16 13:55:36,721 tccd[326]: SecTaskLoadEntitlements failed error=22
15.07.16 13:55:38,248 sharedfilelistd[330]: SecTaskLoadEntitlements failed error=22
15.07.16 13:55:38,320 Console[606]: Failed to connect (_consoleX) outlet from (NSApplication) to (ConsoleX): missing setter or instance variable


Hope this helps!

Thanks a lot!

Cheers,

Fritz

Hi Fritz,

thanks! Can you also post the Ilastik log?

Thanks,

Christian

Hi Christian,

Sorry, where to find the Ilastik log file? Doesn't it correspond to the one I posted above, below the KNIME log?

Cheers,

Fritz
 

Hi everyone,

the project file still contains the relative link to the training image. Maybe your edit was not accepted?

Without a change to the ilastik project, it executes infinitely in Knime. The node cannot be reset, either.

Anyhow, from the error message Fritz posted I don't think it's actually related to the dimensionality of the image.

2016-07-15 13:57:44,047 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :   File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/headless_dummy_modules/PyQt4/__init__.py", line 9, in <module>
2016-07-15 13:57:44,047 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 :     raise Exception("Developer error: When ilastik is running in headless mode, you aren't allowed to import PyQt4.")
2016-07-15 13:57:44,047 : INFO  : KNIME-Worker-17 : KNIPLogService : Ilastik Headless (Pixel classification) : 2:1 : Exception: Developer error: When ilastik is running in headless mode, you aren't allowed to import PyQt4.

When I try to reproduce, I get a different error:

ERROR Ilastik Headless (Pixel classification) 0:2        Error when executing Ilastik. Please check the dimensionality of the input images.
DEBUG Ilastik Headless (Pixel classification) 0:2        reset
ERROR Ilastik Headless (Pixel classification) 0:2        Execute failed: Unable to delete file: D:\TEMP\ilastik\e0c877fe-846a-4359-a97f-2d35307187d0\file0_result.tif
DEBUG Ilastik Headless (Pixel classification) 0:2        Execute failed: Unable to delete file: D:\TEMP\ilastik\e0c877fe-846a-4359-a97f-2d35307187d0\file0_result.tif
java.io.IOException: Unable to delete file: D:\TEMP\ilastik\e0c877fe-846a-4359-a97f-2d35307187d0\file0_result.tif
	at org.apache.commons.io.FileUtils.forceDelete(FileUtils.java:2279)

 

In summary, that makes three different problems.

Hi,

Lorenz was right, I forgot to incldue the image in the ilastik project file. However, this now changed, I still get the same errors in KNIME as described above.

I also found the ilastic log file, it gives the following:

INFO 2016-07-19 15:28:21,098 ilastik_main 1146 140735211339776 Starting ilastik from "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release".
ERROR 2016-07-19 15:28:22,640 excepthooks 1146 140735211339776 Unhandled exception in thread: 'MainThread'
ERROR 2016-07-19 15:28:22,644 excepthooks 1146 140735211339776 Traceback (most recent call last):
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/Resources/__boot__.py", line 102, in <module>
    _run()
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/Resources/__boot__.py", line 96, in _run
    exec(compile(source, script, 'exec'), globals(), globals())
  File "ilastik.py", line 111, in <module>
    main()
  File "ilastik.py", line 104, in main
    ilastik_main.main(parsed_args, workflow_cmdline_args)
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik_main.py", line 102, in main
    f(shell)
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik_main.py", line 317, in loadProject
    shell.openProjectFile(path, parsed_args.readonly)
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/shell/headless/headlessShell.py", line 84, in openProjectFile
    import ilastik.workflows
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/__init__.py", line 28, in <module>
    import pixelClassification
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/pixelClassification/__init__.py", line 21, in <module>
    from pixelClassificationWorkflow import PixelClassificationWorkflow
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/pixelClassification/pixelClassificationWorkflow.py", line 34, in <module>
    from ilastik.applets.pixelClassification import PixelClassificationApplet, PixelClassificationDataExportApplet
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/pixelClassification/__init__.py", line 21, in <module>
    from pixelClassificationApplet import *
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/pixelClassification/pixelClassificationApplet.py", line 22, in <module>
    from opPixelClassification import OpPixelClassification
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/pixelClassification/opPixelClassification.py", line 46, in <module>
    from PyQt4.QtCore import pyqtRemoveInputHook, pyqtRestoreInputHook
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/headless_dummy_modules/PyQt4/__init__.py", line 9, in <module>
    raise Exception("Developer error: When ilastik is running in headless mode, you aren't allowed to import PyQt4.")
Exception: Developer error: When ilastik is running in headless mode, you aren't allowed to import PyQt4.

INFO 2016-07-19 15:28:38,137 ilastik_main 1154 140735211339776 Starting ilastik from "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release".
ERROR 2016-07-19 15:28:39,055 excepthooks 1154 140735211339776 Unhandled exception in thread: 'MainThread'
ERROR 2016-07-19 15:28:39,057 excepthooks 1154 140735211339776 Traceback (most recent call last):
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/Resources/__boot__.py", line 102, in <module>
    _run()
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/Resources/__boot__.py", line 96, in _run
    exec(compile(source, script, 'exec'), globals(), globals())
  File "ilastik.py", line 111, in <module>
    main()
  File "ilastik.py", line 104, in main
    ilastik_main.main(parsed_args, workflow_cmdline_args)
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik_main.py", line 102, in main
    f(shell)
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik_main.py", line 317, in loadProject
    shell.openProjectFile(path, parsed_args.readonly)
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/shell/headless/headlessShell.py", line 84, in openProjectFile
    import ilastik.workflows
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/__init__.py", line 28, in <module>
    import pixelClassification
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/pixelClassification/__init__.py", line 21, in <module>
    from pixelClassificationWorkflow import PixelClassificationWorkflow
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/pixelClassification/pixelClassificationWorkflow.py", line 34, in <module>
    from ilastik.applets.pixelClassification import PixelClassificationApplet, PixelClassificationDataExportApplet
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/pixelClassification/__init__.py", line 21, in <module>
    from pixelClassificationApplet import *
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/pixelClassification/pixelClassificationApplet.py", line 22, in <module>
    from opPixelClassification import OpPixelClassification
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/pixelClassification/opPixelClassification.py", line 46, in <module>
    from PyQt4.QtCore import pyqtRemoveInputHook, pyqtRestoreInputHook
  File "/Applications/ilastik-1.2.0rc6-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/headless_dummy_modules/PyQt4/__init__.py", line 9, in <module>
    raise Exception("Developer error: When ilastik is running in headless mode, you aren't allowed to import PyQt4.")
Exception: Developer error: When ilastik is running in headless mode, you aren't allowed to import PyQt4.

Hope this helps!

Hi Friedrich,

this seems to be something on Ilastik side. can you try to run the example project provided on the example server with your ilastik installation and see if the same error occurs?

Best,

Christian

Hi Christian,

I tried the project of the example server and I got the same kind of error message in the ilastik log. ("...you aren't allowed to import PyQt4'). Since Lorenz did not get this error, could it be that this is related to the fact that I am running KNIME on a Mac?

Best,

Friedrich

 

Hi Friedrich,

I'm actually pretty sure that it has nothing to do with KNIME. Can you run Ilastik headless in general (i.e. from the command-line)?

Best,

Christian

 

Hi Christian,

that still leaves the Unable to delete file error.

Best,

Lorenz

Hi Lorenz,

so just to clarify: Unable to delete file error occurs on your linux machine with his project file or with the example project file?

Best,

Christian

 

Hi all,

it seems you were right, Christian, this apparently was an issue in ilastik that should be fixed in the next release.

See https://github.com/ilastik/ilastik/issues/1299

 

Jan

 

The unable to delete error occurs for me with Friedrich's ilastik file on my Windows 10 machine, but not on my Linux machine. Trying to delete the result.tif tells me it can't be deleted because it is still open in knime.exe.

the ilastik.log says

INFO 2016-07-21 14:35:57,990 ilastik_main 10836 10920 Starting ilastik from "C:\Program Files\ilastik-1.2.0rc6".
INFO 2016-07-21 14:36:01,242 opThresholdTwoLevels 10836 10920 Using 'vigra' labeling implemetation
WARNING 2016-07-21 14:36:01,552 __init__ 10836 10920 Failed to import automatic tracking workflow (conservation tracking). For this workflow, see the installationinstructions on our website ilastik.org; check dependencies: No module named pgmlinkNoIlpSolver
WARNING 2016-07-21 14:36:01,601 __init__ 10836 10920 Failed to import structured learning tracking workflow. For this workflow, see the installationinstructions on our website ilastik.org; check dependencies: DLL load failed: The specified module could not be found.
INFO 2016-07-21 14:36:01,841 projectManager 10836 10920 Opening Project: C:/Users/Lorenz/Desktop/ilastik_workflow/ilastik_test.ilp
WARNING 2016-07-21 14:36:02,272 dataset 10836 10920 dataset.py(70): DeprecationWarning: numpy boolean negative, the `-` operator, is deprecated, use the `~` operator or the logical_not function instead.
INFO 2016-07-21 14:36:02,351 pixelClassificationWorkflow 10836 10920 Beginning Batch Processing
INFO 2016-07-21 14:36:02,641 batchProcessingApplet 10836 10920 Exporting to D:/TEMP/ilastik/25967394-3881-4734-b27c-b7e6be017934/file0_result.tif
INFO 2016-07-21 14:36:02,641 bigRequestStreamer 10836 10920 Estimated RAM usage per pixel is 224.0B * safety factor (2.0)
INFO 2016-07-21 14:36:02,641 bigRequestStreamer 10836 10920 determining blockshape assuming available_ram is 47.2GiB, split between 16 threads
INFO 2016-07-21 14:36:02,641 bigRequestStreamer 10836 10920 Chose blockshape: (100, 130, 2)
INFO 2016-07-21 14:36:02,641 bigRequestStreamer 10836 10920 Estimated RAM usage per block is 5.6MiB
DEBUG 2016-07-21 14:36:02,691 classifierOperators 10836 11088 Features took 0.03 seconds, Prediction took 0.01 seconds for roi: [0, 0, 0] : [100, 130, 2]
INFO 2016-07-21 14:36:02,842 pixelClassificationWorkflow 10836 10920 Completed Batch Processing

 

the result.tif is deleteable as long as it is not read by knime.

maybe this is related to: https://github.com/knime-ip/knip/issues/345. We will have a look.

the problem occurs for me only on windows and only with the append / replace column setting.

https://github.com/knime-ip/knip-ilastik/pull/8 fixes that. I'm not sure though if this is the very right spot to close the reader.