Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Improve error reporting #24

Open
stelfrich opened this issue Oct 15, 2019 · 1 comment
Open

Improve error reporting #24

stelfrich opened this issue Oct 15, 2019 · 1 comment

Comments

@stelfrich
Copy link
Member

It seems that under certain circumstances (see https://forum.knime.com/t/ilastik-output-file-does-not-exist-error/13734 for more details), expected output files are not available. In such cases, some indication of what has gone wrong should be provided instead of just throwing an exception like:

Caused by: java.nio.file.InvalidPathException: Ilastik output file does not exist: D:\Users\zeiss\AppData\Local\Temp/ilastik/6efb518d-7f62-4140-8b08-122415b18093/file0_result.tiff
@JennyKSSI
Copy link

Hi, I'm getting the same errors described in this Knime community forum and I don't see any solutions in that thread. I just updated Knime two days ago and I'm running Ilastik 1.4.0. Did anyone figure out a fix?

I'm actually getting a lot of errors when I try to run and I don't know how to address them. My paths to the Ilastik .exe file in Knime>Preferences and to the .ilp file in node configuration are both correct, and I have the .ilp file open when I try to execute the node.

WARN  KNIPLogService                  WARNING 2024-07-31 09:52:44,676 opConservationTracking 25004 25896 Could not find any ILP solver
WARN  KNIPLogService                  WARNING 2024-07-31 09:52:44,841 opStructuredTracking 25004 25896 Could not find any ILP solver
WARN  KNIPLogService                  WARNING 2024-07-31 09:52:44,843 structuredTrackingWorkflow 25004 25896 Could not find any learning solver. Tracking will use flow-based solver (DPCT). Learning for tracking will be disabled!
ERROR KNIPLogService                  ERROR 2024-07-31 09:53:00,572 excepthooks 25004 25896 Unhandled exception in thread: 'MainThread'
ERROR KNIPLogService                  ERROR 2024-07-31 09:53:00,575 excepthooks 25004 25896 Traceback (most recent call last):
ERROR KNIPLogService                    File "C:\Program Files\ilastik-1.4.0\lib\site-packages\ilastik\shell\projectManager.py", line 150, in openProjectFile
ERROR KNIPLogService                      hdf5File = h5py.File(projectFilePath, mode)
ERROR KNIPLogService                    File "C:\Program Files\ilastik-1.4.0\lib\site-packages\h5py\_hl\files.py", line 533, in __init__
ERROR KNIPLogService                      fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
ERROR KNIPLogService                    File "C:\Program Files\ilastik-1.4.0\lib\site-packages\h5py\_hl\files.py", line 226, in make_fid
ERROR KNIPLogService                      fid = h5f.open(name, flags, fapl=fapl)
ERROR KNIPLogService                    File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
ERROR KNIPLogService                    File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
ERROR KNIPLogService                    File "h5py\h5f.pyx", line 106, in h5py.h5f.open
ERROR KNIPLogService                  OSError: [Errno 0] Unable to open file (unable to lock file, errno = 0, error message = 'No error', Win32 GetLastError() = 33)
ERROR KNIPLogService                  
ERROR KNIPLogService                  During handling of the above exception, another exception occurred:
ERROR KNIPLogService                  
ERROR KNIPLogService                  Traceback (most recent call last):
ERROR KNIPLogService                    File "C:\Program Files\ilastik-1.4.0\Scripts\ilastik-script.py", line 9, in <module>
ERROR KNIPLogService                      sys.exit(main())
ERROR KNIPLogService                    File "C:\Program Files\ilastik-1.4.0\lib\site-packages\ilastik_scripts\ilastik_startup.py", line 146, in main
ERROR KNIPLogService                      main()
ERROR KNIPLogService                    File "C:\Program Files\ilastik-1.4.0\lib\site-packages\ilastik\__main__.py", line 30, in main
ERROR KNIPLogService                      hShell = app.main(parsed_args, workflow_cmdline_args)
ERROR KNIPLogService                    File "C:\Program Files\ilastik-1.4.0\lib\site-packages\ilastik\app.py", line 204, in main
ERROR KNIPLogService                      f(shell)
ERROR KNIPLogService                    File "C:\Program Files\ilastik-1.4.0\lib\site-packages\ilastik\app.py", line 399, in loadProject
ERROR KNIPLogService                      shell.openProjectFile(path, parsed_args.readonly)
ERROR KNIPLogService                    File "C:\Program Files\ilastik-1.4.0\lib\site-packages\ilastik\shell\headless\headlessShell.py", line 94, in openProjectFile
ERROR KNIPLogService                      hdf5File, workflow_class, readOnly = ProjectManager.openProjectFile(projectFilePath, force_readonly)
ERROR KNIPLogService                    File "C:\Program Files\ilastik-1.4.0\lib\site-packages\ilastik\shell\projectManager.py", line 153, in openProjectFile
ERROR KNIPLogService                      hdf5File = h5py.File(projectFilePath, "r")
ERROR KNIPLogService                    File "C:\Program Files\ilastik-1.4.0\lib\site-packages\h5py\_hl\files.py", line 533, in __init__
ERROR KNIPLogService                      fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
ERROR KNIPLogService                    File "C:\Program Files\ilastik-1.4.0\lib\site-packages\h5py\_hl\files.py", line 226, in make_fid
ERROR KNIPLogService                      fid = h5f.open(name, flags, fapl=fapl)
ERROR KNIPLogService                    File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
ERROR KNIPLogService                    File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
ERROR KNIPLogService                    File "h5py\h5f.pyx", line 106, in h5py.h5f.open
ERROR KNIPLogService                  OSError: [Errno 0] Unable to open file (unable to lock file, errno = 0, error message = 'No error', Win32 GetLastError() = 33)
ERROR KNIPLogService                  
ERROR KNIPLogService                  ilastik error: 
ERROR KNIPLogService                  The operation completed successfully.
ERROR KNIPLogService                  
ERROR KNIPLogService                  
ERROR Ilastik Headless (Pixel classification) 4:3        [ERROR] Error while executing Ilastik.
java.lang.IllegalStateException: Can't read image in Ilastik Headless Node at RowId: 264a.tif : java.nio.file.InvalidPathException: Ilastik output file does not exist: C:\Users\JennyKay\AppData\Local\Temp/ilastik/f94025ff-95a3-4634-a88f-fdbbd9f6eecf/file0_result.tiff
	at org.knime.knip.ilastik.nodes.headless.IlastikHeadlessNodeModel.readResultImages(IlastikHeadlessNodeModel.java:378)
	at org.knime.knip.ilastik.nodes.headless.IlastikHeadlessNodeModel.execute(IlastikHeadlessNodeModel.java:314)
	at org.knime.core.node.NodeModel.execute(NodeModel.java:812)
	at org.knime.core.node.NodeModel.executeModel(NodeModel.java:588)
	at org.knime.core.node.Node.invokeFullyNodeModelExecute(Node.java:1286)
	at org.knime.core.node.Node.execute(Node.java:1049)
	at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:594)
	at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
	at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:198)
	at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:117)
	at org.knime.core.util.ThreadUtils$RunnableWithContextImpl.runWithContext(ThreadUtils.java:367)
	at org.knime.core.util.ThreadUtils$RunnableWithContext.run(ThreadUtils.java:221)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
	at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246)
Caused by: java.nio.file.InvalidPathException: Ilastik output file does not exist: C:\Users\JennyKay\AppData\Local\Temp/ilastik/f94025ff-95a3-4634-a88f-fdbbd9f6eecf/file0_result.tiff
	at org.knime.knip.ilastik.nodes.headless.IlastikHeadlessNodeModel.readImageForRow(IlastikHeadlessNodeModel.java:408)
	at org.knime.knip.ilastik.nodes.headless.IlastikHeadlessNodeModel.readResultImages(IlastikHeadlessNodeModel.java:372)
	... 15 more

ERROR Ilastik Headless (Pixel classification) 4:3        Execute failed: java.lang.IllegalStateException: Can't read image in Ilastik Headless Node at RowId: 264a.tif : java.nio.file.InvalidPathException: Ilastik output file does not exist: C:\Users\JennyKay\AppData\Local\Temp/ilastik/f94025ff-95a3-4634-a88f-fdbbd9f6eecf/file0_result.tiff

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@stelfrich @JennyKSSI