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knime-ip / knip-python-extensions

KNIME Image Processing Python Bindings
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Test workflow fails #3

Closed dietzc closed 9 years ago

dietzc commented 9 years ago

Hi all,

I tried to run a test-flow (see https://github.com/knime-ip/knip-python-extensions/blob/master/testflows/Python.zip) which simply produces images with different dimensionalites and copies them in the python node. However, this didn't work a expected. See the following exception

ERROR    PythonKernel                    /home/dietzc/devel/git-repositories/knip-python-extensions/org.knime.knip.python.extensions/py/tifffile.py:156: UserWarning: failed to import the optional _tifffile C extension module.
Loading of some compressed images will be slow.
Tifffile.c can be obtained at http://www.lfd.uci.edu/~gohlke/
  "failed to import the optional _tifffile C extension module.\n"

I'm running it with the latest master. Any idea whats going on?

Cheers and thank you,

Christian

PS: you can simply import the testflow into your KNIME with File -> Import Workflow (Archive File).

abouchar-laurent commented 9 years ago

Hey! Sorry I'm at the retreat in Poland with poor connection. But basically the library tries to use a C code to open certain types of tiff files faster. For simplicity we just omitted the file meaning it should still work fine but be slower on certain types. I have to check if we can just get rid of this warning. I come back tomorrow night, i can have a closer look at it then. Otherwise you can try to comment out the warning and see if it still fails. Cheers, Laurent Le 11 mai 2015 14:08, "Christian Dietz" notifications@github.com a écrit :

Hi all,

I tried to run a test-flow (see https://github.com/knime-ip/knip-python-extensions/blob/master/testflows/Python.zip) which simply produces images with different dimensionalites and copies them in the python node. However, this didn't work a expected. See the following exception

ERROR PythonKernel /home/dietzc/devel/git-repositories/knip-python-extensions/org.knime.knip.python.extensions/py/tifffile.py:156: UserWarning: failed to import the optional _tifffile C extension module. Loading of some compressed images will be slow. Tifffile.c can be obtained at http://www.lfd.uci.edu/~gohlke/ "failed to import the optional _tifffile C extension module.\n"

I'm running it with the latest master. Any idea whats going on?

Cheers and thank you,

Christian

PS: you can simply import the testflow into your KNIME with File -> Import Workflow (Archive File).

— Reply to this email directly or view it on GitHub https://github.com/knime-ip/knip-python-extensions/issues/3.

dietzc commented 9 years ago

Have fun at the retreat. No need to hurry with the fix! Thanks for the help :+1:

paulmueller commented 9 years ago

Fascinating! Python converts a warning to an Error? I uncommented the lines. Could you try again?

dietzc commented 9 years ago

I tried a again. Now I get: ERROR Python Script Execute failed: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all(). Ideas? :-)

paulmueller commented 9 years ago

I can reproduce the error. The execution of the Python node fails at about 15%. I assume one of the input table objects cannot be handled by tifffile. Is it possible to make knime give us the traceback/full error message of the exception? Without it we have to go with trial and error...

patrick-winter-kn commented 9 years ago

The knime.log contains the full output (standard out and error out) of Python.

paulmueller commented 9 years ago

IMHO these are the relevant lines from workspace/.metadata/knime/knime.log, but I don't understand them / can't see any Python traceback.

2015-05-12 15:15:59,424 DEBUG KNIME-Worker-0 Python Script : Configure succeeded. (Python Script)
2015-05-12 15:15:59,424 DEBUG KNIME-Worker-0 NodeContainer : Python 0 has new state: CONFIGURED
2015-05-12 15:15:59,424 DEBUG KNIME-WFM-Parent-Notifier NodeContainer : ROOT  has new state: IDLE
2015-05-12 15:16:00,394 DEBUG main NodeContainerEditPart : Missing Value 0:3 (EXECUTED)
2015-05-12 15:16:00,395 DEBUG main NodeContainerEditPart : Python Script 0:2 (CONFIGURED)
2015-05-12 15:16:01,676 DEBUG main ExecuteAction : Creating execution job for 1 node(s)...
2015-05-12 15:16:01,677 DEBUG main NodeContainer : Setting dirty flag on Python Script 0:2
2015-05-12 15:16:01,678 DEBUG main NodeContainer : Python Script 0:2 has new state: CONFIGURED_MARKEDFOREXEC
2015-05-12 15:16:01,678 DEBUG main NodeContainer : Python Script 0:2 has new state: CONFIGURED_QUEUED
2015-05-12 15:16:01,679 DEBUG main NodeContainer : Python 0 has new state: EXECUTING
2015-05-12 15:16:01,679 DEBUG KNIME-WFM-Parent-Notifier NodeContainer : ROOT  has new state: EXECUTING
2015-05-12 15:16:01,680 DEBUG KNIME-Worker-0 WorkflowManager : Python Script 0:2 doBeforePreExecution
2015-05-12 15:16:01,680 DEBUG KNIME-Worker-0 NodeContainer : Python Script 0:2 has new state: PREEXECUTE
2015-05-12 15:16:01,680 DEBUG KNIME-Worker-0 WorkflowManager : Python Script 0:2 doBeforeExecution
2015-05-12 15:16:01,681 DEBUG KNIME-Worker-0 NodeContainer : Python Script 0:2 has new state: EXECUTING
2015-05-12 15:16:01,681 DEBUG KNIME-Worker-0 WorkflowFileStoreHandlerRepository : Adding handler 604d8bbc-6b2c-49f9-9026-2dbd7ccec112 (Python Script 0:2: <no directory>) - 3 in total
2015-05-12 15:16:01,681 DEBUG KNIME-Worker-0 LocalNodeExecutionJob : Python Script 0:2 Start execute
2015-05-12 15:16:12,913 DEBUG KNIME-Worker-0 Python Script : reset
2015-05-12 15:16:12,913 ERROR KNIME-Worker-0 Python Script : Execute failed: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
2015-05-12 15:16:12,914 DEBUG KNIME-Worker-0 Python Script : Execute failed: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
java.io.IOException: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
    at org.knime.python.kernel.ProtobufConverter.createContainerFromProtobuf(ProtobufConverter.java:454)
    at org.knime.python.kernel.PythonKernel.getDataTable(PythonKernel.java:483)
    at org.knime.python.nodes.script.PythonScriptNodeModel.execute(PythonScriptNodeModel.java:96)
    at org.knime.core.node.NodeModel.execute(NodeModel.java:706)
    at org.knime.core.node.NodeModel.executeModel(NodeModel.java:555)
    at org.knime.core.node.Node.invokeFullyNodeModelExecute(Node.java:1131)
    at org.knime.core.node.Node.execute(Node.java:927)
    at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:559)
    at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:95)
    at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:179)
    at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:110)
    at org.knime.core.util.ThreadUtils$RunnableWithContextImpl.runWithContext(ThreadUtils.java:328)
    at org.knime.core.util.ThreadUtils$RunnableWithContext.run(ThreadUtils.java:204)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:125)
    at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:248)
2015-05-12 15:16:12,916 DEBUG KNIME-Worker-0 WorkflowManager : Python Script 0:2 doBeforePostExecution
2015-05-12 15:16:12,916 DEBUG KNIME-Worker-0 NodeContainer : Python Script 0:2 has new state: POSTEXECUTE
2015-05-12 15:16:12,916 DEBUG KNIME-Worker-0 WorkflowManager : Python Script 0:2 doAfterExecute - failure
dietzc commented 9 years ago

@patrick-winter-knime do you have an idea?

dietzc commented 9 years ago

Hi @paulmueller!

It seems, that the problem was related to how we accessed the images in python. I added a template which demonstrates how to correctly access the images and updated the Python test-workflow.

So the issue should be fixed now.