Ilastik pixel classification prediction in FIJI

Dear @ilastik_team

I have a question concerning the Ilastik pixel classification integration in FIJI:

My raw files are 8-bit tif stacks (0.25 um isotropic voxels) with two channels. I’m mainly interested in segmenting one of them.

I have two Ilastik projects, both are running the 2-stage Autocontext mode:

Number one uses only my one channel of interest that I saved separately. In FIJI, I can call the project via the Plugin->Ilastik->Run Pixel Classification Prediction and it produces the desired output.

Number two uses both channels for training and it produces better predictions, so I would prefer to use it for my downstream analysis. In FIJI, however, I get the following error when I want to run it:

> (Fiji Is Just) ImageJ 2.0.0-rc-69/1.52p; Java 1.8.0_202 [64-bit]; Mac OS X 10.14.5; 908MB of 4613MB (19%)
> 
>  
> 
> java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Execution of ilastik was not successful.
> 
> at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:309)
> 
> at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163)
> 
> at ij.IJ.runPlugIn(IJ.java)
> 
> at ij.Executer.runCommand(Executer.java:137)
> 
> at ij.Executer.run(Executer.java:63)
> 
> at java.lang.Thread.run(Thread.java:748)
> 
> Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Execution of ilastik was not successful.
> 
> at java.util.concurrent.FutureTask.report(FutureTask.java:122)
> 
> at java.util.concurrent.FutureTask.get(FutureTask.java:192)
> 
> at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:305)
> 
> ... 5 more
> 
> Caused by: java.lang.RuntimeException: Execution of ilastik was not successful.
> 
> at org.ilastik.ilastik4ij.executors.AbstractIlastikExecutor.executeCommandLine(AbstractIlastikExecutor.java:134)
> 
> at org.ilastik.ilastik4ij.executors.AbstractIlastikExecutor.executeIlastik(AbstractIlastikExecutor.java:61)
> 
> at org.ilastik.ilastik4ij.executors.PixelClassification.classifyPixels(PixelClassification.java:24)
> 
> at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.runClassification(IlastikPixelClassificationCommand.java:72)
> 
> at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.run(IlastikPixelClassificationCommand.java:60)
> 
> at org.scijava.command.CommandModule.run(CommandModule.java:199)
> 
> at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
> 
> at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
> 
> at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
> 
> at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
> 
> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> 
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
> 
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
> 
> ... 1 more

Any ideas what is happening? It runs nicely in the Ilastik stand-alone application.

Thanks in advance!
Tobias

Hi @TobiasKletter,

> java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Execution of ilastik was not successful.

based on the exception you’ve provided looks like the ilastik prediction failed. You’ve attached just the java stacktrace, so we won’t be able to tell you what went wrong. Could you also provide us with logs from ilastik? They should be displayed in the Log window of Fiji.

Best,
Adrian

Hi @wolny
thanks for the reply!
Sure, here’s the entire log from FIJI, starting with Part 1 (due to character limit…):

[Tue Jan 21 17:30:35 CET 2020] [INFO] [] Temporary files: {tempFileRawInput=/var/folders/j_/37sjdxtn79g65trlwjj6cxfm0000gn/T/ilastik4j397655704736014426_in_raw.h5, tempFileOutput=/var/folders/j_/37sjdxtn79g65trlwjj6cxfm0000gn/T/ilastik4j5959812526315499710_out.h5}
[Tue Jan 21 17:30:35 CET 2020] [INFO] [] Exporting image of shape (1, 96, 106, 106, 2). Axis order: 'TZYXC'
[Tue Jan 21 17:30:36 CET 2020] [INFO] [] Saving as 'uint8'. Compression level: 1
[Tue Jan 21 17:30:37 CET 2020] [INFO] [] Running ilastik headless command:
[Tue Jan 21 17:30:37 CET 2020] [INFO] [] [/Applications/ilastik-1.3.3post1-OSX.app/Contents/MacOS/ilastik, --headless, --project=/Volumes/TOB_WD1/Ilastik/Ilastik_model_DNA/20191206_DNA_Segmentation_2Ch.ilp, --output_filename_format=/var/folders/j_/37sjdxtn79g65trlwjj6cxfm0000gn/T/ilastik4j5959812526315499710_out.h5, --output_format=hdf5, --output_axis_order=tzyxc, /var/folders/j_/37sjdxtn79g65trlwjj6cxfm0000gn/T/ilastik4j397655704736014426_in_raw.h5]
[Tue Jan 21 17:30:38 CET 2020] [INFO] [] INFO lazyflow.operators.filterOperators: Using fast filters.
[Tue Jan 21 17:30:38 CET 2020] [ERROR] [] WARNING __init__.py(20): UserWarning: init: Could not import tiktorch classifier
[Tue Jan 21 17:30:38 CET 2020] [INFO] [] INFO ilastik_main: Starting ilastik from "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release".
[Tue Jan 21 17:30:38 CET 2020] [INFO] [] Starting ilastik from "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release".
[Tue Jan 21 17:30:38 CET 2020] [INFO] [] INFO ilastik_main: Configuring lazyflow RAM limit to 4.0GiB
[Tue Jan 21 17:30:38 CET 2020] [INFO] [] INFO lazyflow.utility.memory: Available memory set to 4.0GiB
[Tue Jan 21 17:30:40 CET 2020] [ERROR] [] WARNING 2020-01-21 17:30:40,849 opConservationTracking 73040 4356621760 Could not find any ILP solver
[Tue Jan 21 17:30:40 CET 2020] [ERROR] [] WARNING 2020-01-21 17:30:40,873 opStructuredTracking 73040 4356621760 Could not find any ILP solver
[Tue Jan 21 17:30:40 CET 2020] [ERROR] [] WARNING 2020-01-21 17:30:40,881 structuredTrackingWorkflow 73040 4356621760 Could not find any learning solver. Tracking will use flow-based solver (DPCT). Learning for tracking will be disabled!
[Tue Jan 21 17:30:41 CET 2020] [INFO] [] INFO ilastik.shell.projectManager: Opening Project: /Volumes/TOB_WD1/Ilastik/Ilastik_model_DNA/20191206_DNA_Segmentation_2Ch.ilp
[Tue Jan 21 17:30:41 CET 2020] [ERROR] [] WARNING dataset.py(313): H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
[Tue Jan 21 17:30:44 CET 2020] [ERROR] [] WARNING opSimpleBlockedArrayCache.py(43): FutureWarning: Conversion of the second argument of issubdtype from `dtype` to `np.generic` is deprecated. In future, it will be treated as `np.object_ == np.dtype(dtype).type`.
[Tue Jan 21 17:30:44 CET 2020] [ERROR] [] WARNING opSlicedBlockedArrayCache.py(141): FutureWarning: Conversion of the second argument of issubdtype from `dtype` to `np.generic` is deprecated. In future, it will be treated as `np.object_ == np.dtype(dtype).type`.
[Tue Jan 21 17:30:47 CET 2020] [INFO] [] INFO ilastik.workflows.newAutocontext.newAutocontextWorkflow: Beginning Batch Processing
[Tue Jan 21 17:30:47 CET 2020] [ERROR] [] ERROR 2020-01-21 17:30:47,956 log_exception 73040 4356621760 Traceback (most recent call last):
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/shell/projectManager.py", line 461, in _loadProject
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.workflow.onProjectLoaded(self)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/newAutocontext/newAutocontextWorkflow.py", line 479, in onProjectLoaded
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.batchProcessingApplet.run_export_from_parsed_args(self._batch_input_args)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/batchProcessing/batchProcessingApplet.py", line 64, in run_export_from_parsed_args
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     return self.run_export(role_path_dict, parsed_args.input_axes, sequence_axis=parsed_args.stack_along)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/batchProcessing/batchProcessingApplet.py", line 118, in run_export
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     progress_callback=partial(lerpProgressSignal, global_progress_start, global_progress_end),
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/batchProcessing/batchProcessingApplet.py", line 170, in export_dataset
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     batch_lane.DatasetGroup[role_index].setValue(role_info)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 73, in call_in_setup_context
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     return func(self, *args, **kwargs)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1140, in setValue
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self._changed()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1358, in _changed_impl
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self._configureOperator(self)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1371, in _configureOperator
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self.operator._setupOutputs)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/operator.py", line 498, in _setupOutputs
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.setupOutputs()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/dataSelection/opDataSelection.py", line 729, in setupOutputs
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.Image.connect(op5.Output)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 73, in call_in_setup_context
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     return func(self, *args, **kwargs)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 543, in connect
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self._changed()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1358, in _changed_impl
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self._configureOperator(self)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1371, in _configureOperator
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self.operator._setupOutputs)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/operator.py", line 498, in _setupOutputs
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     self.setupOutputs()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/featureSelection/opFeatureSelection.py", line 254, in setupOutputs
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     super().setupOutputs()
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/featureSelection/opFeatureSelection.py", line 178, in setupOutputs
[Tue Jan 21 17:30:47 CET 2020] [ERROR] []     if self.parent.parent.featureSelectionApplet._gui is None:
[Tue Jan 21 17:30:47 CET 2020] [ERROR] [] AttributeError: 'AutocontextTwoStage' object has no attribute 'featureSelectionApplet'
[Tue Jan 21 17:30:47 CET 2020] [ERROR] [] 
[Tue Jan 21 17:30:47 CET 2020] [ERROR] [] ERROR 2020-01-21 17:30:47,956 log_exception 73040 4356621760 Project could not be loaded due to the exception shown above.
[Tue Jan 21 17:30:47 CET 2020] [ERROR] [] Aborting Project Open Action
[Tue Jan 21 17:30:49 CET 2020] [ERROR] [] ERROR 2020-01-21 17:30:49,497 excepthooks 73040 4356621760 Unhandled exception in thread: 'MainThread'
[Tue Jan 21 17:30:49 CET 2020] [ERROR] [] ERROR 2020-01-21 17:30:49,502 excepthooks 73040 4356621760 Traceback (most recent call last):
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/Resources/__boot__.py", line 132, in <module>
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     _run()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/Resources/__boot__.py", line 126, in _run
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     exec(compile(source, script, 'exec'), globals(), globals())
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "ilastik.py", line 134, in <module>
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     main()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "ilastik.py", line 128, in main
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     hShell = ilastik_main.main(parsed_args, workflow_cmdline_args)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik_main.py", line 165, in main
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     f(shell)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik_main.py", line 338, in loadProject
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     shell.openProjectFile(path, parsed_args.readonly)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/shell/headless/headlessShell.py", line 125, in openProjectFile
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.projectManager._loadProject(hdf5File, projectFilePath, readOnly)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/utility/timer.py", line 153, in wrapper
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     return func(*args, **kwargs)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/shell/projectManager.py", line 461, in _loadProject
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.workflow.onProjectLoaded(self)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/newAutocontext/newAutocontextWorkflow.py", line 479, in onProjectLoaded
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.batchProcessingApplet.run_export_from_parsed_args(self._batch_input_args)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/batchProcessing/batchProcessingApplet.py", line 64, in run_export_from_parsed_args
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     return self.run_export(role_path_dict, parsed_args.input_axes, sequence_axis=parsed_args.stack_along)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/batchProcessing/batchProcessingApplet.py", line 118, in run_export
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     progress_callback=partial(lerpProgressSignal, global_progress_start, global_progress_end),
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/batchProcessing/batchProcessingApplet.py", line 170, in export_dataset
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     batch_lane.DatasetGroup[role_index].setValue(role_info)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 73, in call_in_setup_context
1 Like

Part 2:

[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     return func(self, *args, **kwargs)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1140, in setValue
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self._changed()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1358, in _changed_impl
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self._configureOperator(self)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1371, in _configureOperator
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self.operator._setupOutputs)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/operator.py", line 498, in _setupOutputs
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.setupOutputs()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/dataSelection/opDataSelection.py", line 729, in setupOutputs
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.Image.connect(op5.Output)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 73, in call_in_setup_context
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     return func(self, *args, **kwargs)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 543, in connect
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self._changed()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1351, in _changed_impl
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     c._changed()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1325, in _changed
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self._changed_impl)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1358, in _changed_impl
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self._configureOperator(self)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1371, in _configureOperator
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.maybe_call_within_transaction(self.operator._setupOutputs)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1320, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.graph.maybe_call_within_transaction(fn)
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     fn()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/operator.py", line 498, in _setupOutputs
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     self.setupOutputs()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/featureSelection/opFeatureSelection.py", line 254, in setupOutputs
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     super().setupOutputs()
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []   File "/Applications/ilastik-1.3.3post1-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/featureSelection/opFeatureSelection.py", line 178, in setupOutputs
[Tue Jan 21 17:30:49 CET 2020] [ERROR] []     if self.parent.parent.featureSelectionApplet._gui is None:
[Tue Jan 21 17:30:49 CET 2020] [ERROR] [] AttributeError: 'AutocontextTwoStage' object has no attribute 'featureSelectionApplet'
[Tue Jan 21 17:30:49 CET 2020] [ERROR] [] 
[Tue Jan 21 17:30:49 CET 2020] [ERROR] [] 2020-01-21 17:30:49.581 ilastik[73040:12577603] ilastik Error
[Tue Jan 21 17:30:52 CET 2020] [ERROR] [] ilastik execution crashed
[Tue Jan 21 17:30:52 CET 2020] [INFO] [] Deleted tmp file: /var/folders/j_/37sjdxtn79g65trlwjj6cxfm0000gn/T/ilastik4j397655704736014426_in_raw.h5
[Tue Jan 21 17:30:52 CET 2020] [ERROR] [] Module threw exception
java.lang.RuntimeException: Execution of ilastik was not successful.
	at org.ilastik.ilastik4ij.executors.AbstractIlastikExecutor.executeCommandLine(AbstractIlastikExecutor.java:134)
	at org.ilastik.ilastik4ij.executors.AbstractIlastikExecutor.executeIlastik(AbstractIlastikExecutor.java:61)
	at org.ilastik.ilastik4ij.executors.PixelClassification.classifyPixels(PixelClassification.java:24)
	at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.runClassification(IlastikPixelClassificationCommand.java:72)
	at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.run(IlastikPixelClassificationCommand.java:60)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

gotta love those ilastik stack traces :wink:

Are you trying to predict on a smaller image somehow?

1 Like

No, I’m actually trying to predict an image that’s part of the training set…

Would you mind sharing the project and one of the files with us? (team@ilastik.org)

Could you in any case try the ilastik version 1.3.3post2?

1.3.3post2 is giving me the same, unfortunately!
I will share the project via mail! :slight_smile: Thanks

Hi @TobiasKletter,

thank you very much for kindly providing the data and project file. I was able to reproduce the problem. The issue is that the fiji plugin exports the data into a different axis ordering (our default tzyxc). I’m working on a fix to the plugin in order to make ilastik understand the axes better. Then it should work (hopefully) after updating the plugin. Will keep you up to date.

1 Like

Thanks a lot @k-dominik, looking forward!

just updated the plugin to 1.7.1, could you please update it in your fiji and confirm that it’s working :slight_smile:

1 Like

Hi @k-dominik
it’s working smoothly now! Thanks :pray:

2 Likes

Awesome :slight_smile: Thank you for making us aware of this issue and providing everything for us to fix it!

1 Like

Hi,

I also have an issue in running Ilastik plugin in Fiji with a Autocontext 2-stage project. I would like to export the Simple Segmentation Stage 2. When I try to run a Pixel Classification Prediction from Fiji (Plugin->Ilastik->Run Pixel Classification Prediction - Output Type: segmentation), I get the following error message:

[INFO] Temporary files: {tempFileRawInput=/var/folders/bc/ykpw38zs5mg3mgq9nzmn9cf00000gn/T/ilastik4j3921484104717816810_in_raw.h5, tempFileOutput=/var/folders/bc/ykpw38zs5mg3mgq9nzmn9cf00000gn/T/ilastik4j3117817834747150501_out.h5}
[INFO] Exporting image of shape (1, 1, 241, 68, 1). Axis order: 'TZYXC'
[WARNING] Could not determine the IP address of https://imagej.net. Make sure you are connected to a network.
[INFO] Reading available sites from https://imagej.net/
[ERROR] java.net.UnknownHostException: imagej.net
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
	at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1944)
	at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1939)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1938)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1508)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:263)
	at net.imagej.util.MediaWikiClient.request(MediaWikiClient.java:234)
	at net.imagej.util.MediaWikiClient.query(MediaWikiClient.java:243)
	at net.imagej.util.MediaWikiClient.getPageSource(MediaWikiClient.java:109)
	at net.imagej.updater.util.AvailableSites.getAvailableSites(AvailableSites.java:79)
	at net.imagej.updater.util.AvailableSites.getAvailableSites(AvailableSites.java:69)
	at net.imagej.updater.util.AvailableSites.hasUpdateSiteURLUpdates(AvailableSites.java:271)
	at net.imagej.updater.UpToDate.check(UpToDate.java:114)
	at net.imagej.updater.UpToDate.check(UpToDate.java:86)
	at net.imagej.updater.CheckForUpdates.run(CheckForUpdates.java:63)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.net.UnknownHostException: imagej.net
	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
	at java.net.Socket.connect(Socket.java:589)
	at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:673)
	at sun.security.ssl.BaseSSLSocketImpl.connect(BaseSSLSocketImpl.java:173)
	at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)
	at sun.net.www.protocol.https.HttpsClient.<init>(HttpsClient.java:264)
	at sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:367)
	at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:191)
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1156)
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1050)
	at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1564)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at sun.net.www.protocol.http.HttpURLConnection.getHeaderFields(HttpURLConnection.java:3023)
	at sun.net.www.protocol.https.HttpsURLConnectionImpl.getHeaderFields(HttpsURLConnectionImpl.java:292)
	at net.imagej.util.MediaWikiClient.request(MediaWikiClient.java:223)
	... 17 more
[INFO] Saving as 'uint8'. Compression level: 1
[INFO] Running ilastik headless command:
[INFO] [/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/MacOS/ilastik, --headless, --project=/Users/ella/Desktop/2017-04-19_trops_cy5bovineseeds_cy3_6uM001/ilastik_fiji/kymograph.ilp, --output_filename_format=/var/folders/bc/ykpw38zs5mg3mgq9nzmn9cf00000gn/T/ilastik4j3117817834747150501_out.h5, --output_format=hdf5, --output_axis_order=tzyxc, --export_source=Simple Segmentation, --input_axes=tzyxc, /var/folders/bc/ykpw38zs5mg3mgq9nzmn9cf00000gn/T/ilastik4j3921484104717816810_in_raw.h5]
[INFO] INFO lazyflow.operators.filterOperators: Using fast filters.
[ERROR] WARNING __init__.py(20): UserWarning: init: Could not import tiktorch classifier
[INFO] INFO ilastik_main: Starting ilastik from "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release".
[INFO] Starting ilastik from "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release".
[INFO] INFO ilastik_main: Configuring lazyflow RAM limit to 4.0GiB
[INFO] INFO lazyflow.utility.memory: Available memory set to 4.0GiB
[ERROR] WARNING 2020-02-04 17:44:13,308 opConservationTracking 2243 4444659136 Could not find any ILP solver
[ERROR] WARNING 2020-02-04 17:44:13,325 opStructuredTracking 2243 4444659136 Could not find any ILP solver
[ERROR] WARNING 2020-02-04 17:44:13,335 structuredTrackingWorkflow 2243 4444659136 Could not find any learning solver. Tracking will use flow-based solver (DPCT). Learning for tracking will be disabled!
[INFO] INFO ilastik.shell.projectManager: Opening Project: /Users/ella/Desktop/2017-04-19_trops_cy5bovineseeds_cy3_6uM001/ilastik_fiji/kymograph.ilp
[ERROR] WARNING dataset.py(313): H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
[ERROR] WARNING opSimpleBlockedArrayCache.py(43): FutureWarning: Conversion of the second argument of issubdtype from `dtype` to `np.generic` is deprecated. In future, it will be treated as `np.object_ == np.dtype(dtype).type`.
[ERROR] WARNING opSlicedBlockedArrayCache.py(141): FutureWarning: Conversion of the second argument of issubdtype from `dtype` to `np.generic` is deprecated. In future, it will be treated as `np.object_ == np.dtype(dtype).type`.
[ERROR] ERROR 2020-02-04 17:44:24,896 log_exception 2243 4444659136 Traceback (most recent call last):
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/dataExport/dataExportApplet.py", line 284, in _configure_operator_with_parsed_args
[ERROR]     source_index = source_choices.index(export_source)
[ERROR] ValueError: 'simple segmentation' is not in list
[ERROR] 
[ERROR] During handling of the above exception, another exception occurred:
[ERROR] 
[ERROR] Traceback (most recent call last):
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/shell/projectManager.py", line 467, in _loadProject
[ERROR]     self.workflow.onProjectLoaded(self)
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/newAutocontext/newAutocontextWorkflow.py", line 466, in onProjectLoaded
[ERROR]     self.dataExportApplet.configure_operator_with_parsed_args(self._batch_export_args)
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/dataExport/dataExportApplet.py", line 261, in configure_operator_with_parsed_args
[ERROR]     self._configure_operator_with_parsed_args(parsed_args, opDataExport)
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/dataExport/dataExportApplet.py", line 288, in _configure_operator_with_parsed_args
[ERROR]     "Valid options are: {}".format(parsed_args.export_source, source_choices)
[ERROR] Exception: Invalid option for --export_source: 'Simple Segmentation'
[ERROR] Valid options are: ['probabilities stage 2', 'simple segmentation stage 2', 'uncertainty stage 2', 'features stage 2', 'labels stage 2', 'input stage 2', 'probabilities stage 1', 'simple segmentation stage 1', 'uncertainty stage 1', 'features stage 1', 'labels stage 1', 'input stage 1', 'probabilities all stages']
[ERROR] 
[ERROR] ERROR 2020-02-04 17:44:24,896 log_exception 2243 4444659136 Project could not be loaded due to the exception shown above.
[ERROR] Aborting Project Open Action
[ERROR] ERROR 2020-02-04 17:44:35,914 excepthooks 2243 4444659136 Unhandled exception in thread: 'MainThread'
[ERROR] ERROR 2020-02-04 17:44:35,915 excepthooks 2243 4444659136 Traceback (most recent call last):
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/dataExport/dataExportApplet.py", line 284, in _configure_operator_with_parsed_args
[ERROR]     source_index = source_choices.index(export_source)
[ERROR] ValueError: 'simple segmentation' is not in list
[ERROR] 
[ERROR] During handling of the above exception, another exception occurred:
[ERROR] 
[ERROR] Traceback (most recent call last):
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/Resources/__boot__.py", line 132, in <module>
[ERROR]     _run()
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/Resources/__boot__.py", line 126, in _run
[ERROR]     exec(compile(source, script, 'exec'), globals(), globals())
[ERROR]   File "ilastik.py", line 134, in <module>
[ERROR]     main()
[ERROR]   File "ilastik.py", line 128, in main
[ERROR]     hShell = ilastik_main.main(parsed_args, workflow_cmdline_args)
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik_main.py", line 165, in main
[ERROR]     f(shell)
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik_main.py", line 338, in loadProject
[ERROR]     shell.openProjectFile(path, parsed_args.readonly)
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/shell/headless/headlessShell.py", line 125, in openProjectFile
[ERROR]     self.projectManager._loadProject(hdf5File, projectFilePath, readOnly)
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/utility/timer.py", line 153, in wrapper
[ERROR]     return func(*args, **kwargs)
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/shell/projectManager.py", line 467, in _loadProject
[ERROR]     self.workflow.onProjectLoaded(self)
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/newAutocontext/newAutocontextWorkflow.py", line 466, in onProjectLoaded
[ERROR]     self.dataExportApplet.configure_operator_with_parsed_args(self._batch_export_args)
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/dataExport/dataExportApplet.py", line 261, in configure_operator_with_parsed_args
[ERROR]     self._configure_operator_with_parsed_args(parsed_args, opDataExport)
[ERROR]   File "/Users/ella/Downloads/ilastik-1.3.3post2-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/dataExport/dataExportApplet.py", line 288, in _configure_operator_with_parsed_args
[ERROR]     "Valid options are: {}".format(parsed_args.export_source, source_choices)
[ERROR] Exception: Invalid option for --export_source: 'Simple Segmentation'
[ERROR] Valid options are: ['probabilities stage 2', 'simple segmentation stage 2', 'uncertainty stage 2', 'features stage 2', 'labels stage 2', 'input stage 2', 'probabilities stage 1', 'simple segmentation stage 1', 'uncertainty stage 1', 'features stage 1', 'labels stage 1', 'input stage 1', 'probabilities all stages']
[ERROR] 
[ERROR] 2020-02-04 17:44:35.990 ilastik[2243:138227] ilastik Error
[ERROR] ilastik execution crashed
[INFO] Deleted tmp file: /var/folders/bc/ykpw38zs5mg3mgq9nzmn9cf00000gn/T/ilastik4j3921484104717816810_in_raw.h5
[ERROR] Module threw exception
java.lang.RuntimeException: Execution of ilastik was not successful.
	at org.ilastik.ilastik4ij.executors.AbstractIlastikExecutor.executeCommandLine(AbstractIlastikExecutor.java:134)
	at org.ilastik.ilastik4ij.executors.AbstractIlastikExecutor.executeIlastik(AbstractIlastikExecutor.java:61)
	at org.ilastik.ilastik4ij.executors.PixelClassification.classifyPixels(PixelClassification.java:24)
	at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.runClassification(IlastikPixelClassificationCommand.java:72)
	at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.run(IlastikPixelClassificationCommand.java:60)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

When running this project directly in Ilastik on the same image I do not have any issue.

Any clue on what is going on here?
Many thanks in advance!

Ella

Hi @gldjck,

the plugin does not officially support the autocontext (yet). So currently there is no way getting the simple segmentation output, I’m afraid.

We’ll update the plugin soon in order to include this as well.

Cheers
Dominik

Hi @k-dominik,
Thank you, I will do it directly in Ilastik then. Looking forward to the update!
Cheers,
Ella

1 Like

Hi,

I am also having issues running the pixel classification prediction through FIJI.

I’ve trained a number of classifiers on Ilastik-1.3.3, and calling them through FIJI yielded the following exception:

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52t; Java 1.8.0_172 [64-bit]; Windows 7 6.1; 461MB of 32000MB (1%)
 
java.lang.RuntimeException: java.util.concurrent.ExecutionException: ncsa.hdf.hdf5lib.exceptions.HDF5FileNotFoundException: Path does not exit. (C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j1532876893154804882_out.h5)
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:309)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:150)
	at ij.Executer.run(Executer.java:68)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.concurrent.ExecutionException: ncsa.hdf.hdf5lib.exceptions.HDF5FileNotFoundException: Path does not exit. (C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j1532876893154804882_out.h5)
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:305)
	... 5 more
Caused by: ncsa.hdf.hdf5lib.exceptions.HDF5FileNotFoundException: Path does not exit. (C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j1532876893154804882_out.h5)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:194)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:147)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:126)
	at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:86)
	at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:54)
	at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:64)
	at org.ilastik.ilastik4ij.hdf5.Hdf5DataSetReader.read(Hdf5DataSetReader.java:51)
	at org.ilastik.ilastik4ij.executors.AbstractIlastikExecutor.executeIlastik(AbstractIlastikExecutor.java:64)
	at org.ilastik.ilastik4ij.executors.PixelClassification.classifyPixels(PixelClassification.java:24)
	at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.runClassification(IlastikPixelClassificationCommand.java:72)
	at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.run(IlastikPixelClassificationCommand.java:60)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	... 1 more

and these logs:

[Mon Feb 17 18:26:28 EST 2020] [INFO] [] /m1: DATASET
[Mon Feb 17 18:28:29 EST 2020] [INFO] [] Found dataset '/m1' of type 'uint8'
[Mon Feb 17 18:28:29 EST 2020] [INFO] [] Constructing output image of shape (1024, 1024, 4, 35, 1). Axis order: 'XYCZT'
[Mon Feb 17 18:28:54 EST 2020] [INFO] [] Loading HDF5 dataset took: 25188
[Mon Feb 17 18:28:54 EST 2020] [INFO] [] Done loading HDF5 file!
[Mon Feb 17 18:29:40 EST 2020] [INFO] [] Temporary files: {tempFileRawInput=C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j3986985765066972948_in_raw.h5, tempFileOutput=C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j1296070379917363084_out.h5}
[Mon Feb 17 18:29:40 EST 2020] [INFO] [] Exporting image of shape (1, 35, 1024, 1024, 4). Axis order: 'TZYXC'
[Mon Feb 17 18:29:40 EST 2020] [INFO] [] Saving as 'uint8'. Compression level: 1
[Mon Feb 17 18:30:33 EST 2020] [INFO] [] Running ilastik headless command:
[Mon Feb 17 18:30:33 EST 2020] [INFO] [] [C:\Program Files\ilastik-1.3.3\ilastik.exe, --headless, --project=C:\Users\Patrick Dummer\Patrick\Ilastik - Image Tiles for training\Ilastik_Zstack_TargetPlusPost_PixelClassification.ilp, --output_filename_format=C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j1296070379917363084_out.h5, --output_format=hdf5, --output_axis_order=tzyxc, --input_axes=tzyxc, C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j3986985765066972948_in_raw.h5]
[Mon Feb 17 18:30:35 EST 2020] [INFO] [] INFO lazyflow.operators.filterOperators: Using fast filters.
[Mon Feb 17 18:30:35 EST 2020] [ERROR] [] WARNING __init__.py(20): UserWarning: init: Could not import tiktorch classifier
[Mon Feb 17 18:30:35 EST 2020] [INFO] [] INFO ilastik_main: Starting ilastik from "C:\Program Files\ilastik-1.3.3".
[Mon Feb 17 18:30:35 EST 2020] [INFO] [] Starting ilastik from "C:\Program Files\ilastik-1.3.3".
[Mon Feb 17 18:30:35 EST 2020] [INFO] [] INFO ilastik_main: Configuring lazyflow RAM limit to 16.0GiB
[Mon Feb 17 18:30:35 EST 2020] [INFO] [] INFO lazyflow.utility.memory: Available memory set to 16.0GiB
[Mon Feb 17 18:30:39 EST 2020] [ERROR] [] WARNING 2020-02-17 18:30:39,158 opConservationTracking 6636 3508 Could not find any ILP solver
[Mon Feb 17 18:30:39 EST 2020] [ERROR] [] WARNING 2020-02-17 18:30:39,229 opStructuredTracking 6636 3508 Could not find any ILP solver
[Mon Feb 17 18:30:39 EST 2020] [ERROR] [] WARNING 2020-02-17 18:30:39,232 structuredTrackingWorkflow 6636 3508 Could not find any learning solver. Tracking will use flow-based solver (DPCT). Learning for tracking will be disabled!
[Mon Feb 17 18:30:40 EST 2020] [INFO] [] INFO ilastik.shell.projectManager: Opening Project: C:/Users/Patrick Dummer/Patrick/Ilastik - Image Tiles for training/Ilastik_Zstack_TargetPlusPost_PixelClassification.ilp
[Mon Feb 17 18:30:40 EST 2020] [ERROR] [] WARNING dataset.py(313): H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
[Mon Feb 17 18:30:40 EST 2020] [ERROR] [] WARNING opSimpleBlockedArrayCache.py(43): FutureWarning: Conversion of the second argument of issubdtype from `dtype` to `np.generic` is deprecated. In future, it will be treated as `np.object_ == np.dtype(dtype).type`.
[Mon Feb 17 18:30:40 EST 2020] [ERROR] [] WARNING opSlicedBlockedArrayCache.py(141): FutureWarning: Conversion of the second argument of issubdtype from `dtype` to `np.generic` is deprecated. In future, it will be treated as `np.object_ == np.dtype(dtype).type`.
[Mon Feb 17 18:30:42 EST 2020] [INFO] [] INFO ilastik.workflows.pixelClassification.pixelClassificationWorkflow: Beginning Batch Processing
[Mon Feb 17 18:30:43 EST 2020] [ERROR] [] ERROR 2020-02-17 18:30:43,187 log_exception 6636 3508 Traceback (most recent call last):
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik\shell\projectManager.py", line 461, in _loadProject
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     self.workflow.onProjectLoaded(self)
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik\workflows\pixelClassification\pixelClassificationWorkflow.py", line 382, in onProjectLoaded
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     self.batchProcessingApplet.run_export_from_parsed_args(self._batch_input_args)
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik\applets\batchProcessing\batchProcessingApplet.py", line 60, in run_export_from_parsed_args
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     return self.run_export(role_path_dict, parsed_args.input_axes, sequence_axis=parsed_args.stack_along)
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik\applets\batchProcessing\batchProcessingApplet.py", line 114, in run_export
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     progress_callback=partial(lerpProgressSignal, global_progress_start, global_progress_end),
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik\applets\batchProcessing\batchProcessingApplet.py", line 172, in export_dataset
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     logger.info(f"Exporting to {opDataExport.ExportPath.value}")
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\lazyflow\lazyflow\slot.py", line 1067, in value
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     temp = self[:].wait()
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\lazyflow\lazyflow\slot.py", line 1010, in __getitem__
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     raise Slot.SlotNotReadyError(slotInfoMsg)
[Mon Feb 17 18:30:43 EST 2020] [ERROR] [] lazyflow.slot.Slot.SlotNotReadyError: Can't get data from slot <class 'ilastik.utility.opMultiLaneWrapper.OpMultiLaneWrapper'>.ExportPath yet. It isn't ready.First upstream problem slot is: Couldn't find an upstream problem slot.
[Mon Feb 17 18:30:43 EST 2020] [ERROR] [] 
[Mon Feb 17 18:30:43 EST 2020] [ERROR] [] ERROR 2020-02-17 18:30:43,187 log_exception 6636 3508 Project could not be loaded due to the exception shown above.
[Mon Feb 17 18:30:43 EST 2020] [ERROR] [] Aborting Project Open Action
[Mon Feb 17 18:30:43 EST 2020] [ERROR] [] ERROR 2020-02-17 18:30:43,737 excepthooks 6636 3508 Unhandled exception in thread: 'MainThread'
[Mon Feb 17 18:30:43 EST 2020] [ERROR] [] ERROR 2020-02-17 18:30:43,739 excepthooks 6636 3508 Traceback (most recent call last):
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik.py", line 134, in <module>
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     main()
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik.py", line 128, in main
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     hShell = ilastik_main.main(parsed_args, workflow_cmdline_args)
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik_main.py", line 165, in main
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     f(shell)
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik_main.py", line 338, in loadProject
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     shell.openProjectFile(path, parsed_args.readonly)
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik\shell\headless\headlessShell.py", line 125, in openProjectFile
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     self.projectManager._loadProject(hdf5File, projectFilePath, readOnly)
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\lazyflow\lazyflow\utility\timer.py", line 153, in wrapper
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     return func(*args, **kwargs)
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik\shell\projectManager.py", line 461, in _loadProject
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     self.workflow.onProjectLoaded(self)
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik\workflows\pixelClassification\pixelClassificationWorkflow.py", line 382, in onProjectLoaded
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     self.batchProcessingApplet.run_export_from_parsed_args(self._batch_input_args)
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik\applets\batchProcessing\batchProcessingApplet.py", line 60, in run_export_from_parsed_args
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     return self.run_export(role_path_dict, parsed_args.input_axes, sequence_axis=parsed_args.stack_along)
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik\applets\batchProcessing\batchProcessingApplet.py", line 114, in run_export
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     progress_callback=partial(lerpProgressSignal, global_progress_start, global_progress_end),
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\ilastik\ilastik\applets\batchProcessing\batchProcessingApplet.py", line 172, in export_dataset
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     logger.info(f"Exporting to {opDataExport.ExportPath.value}")
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\lazyflow\lazyflow\slot.py", line 1067, in value
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     temp = self[:].wait()
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3\ilastik-meta\lazyflow\lazyflow\slot.py", line 1010, in __getitem__
[Mon Feb 17 18:30:43 EST 2020] [ERROR] []     raise Slot.SlotNotReadyError(slotInfoMsg)
[Mon Feb 17 18:30:43 EST 2020] [ERROR] [] lazyflow.slot.Slot.SlotNotReadyError: Can't get data from slot <class 'ilastik.utility.opMultiLaneWrapper.OpMultiLaneWrapper'>.ExportPath yet. It isn't ready.First upstream problem slot is: Couldn't find an upstream problem slot.
[Mon Feb 17 18:30:43 EST 2020] [ERROR] [] 
[Mon Feb 17 18:30:44 EST 2020] [ERROR] [] ilastik error: 
[Mon Feb 17 18:30:44 EST 2020] [ERROR] [] The operation completed successfully.
[Mon Feb 17 18:30:44 EST 2020] [ERROR] [] 
[Mon Feb 17 18:30:44 EST 2020] [ERROR] [] 
[Mon Feb 17 18:30:44 EST 2020] [INFO] [] ilastik execution finished successfully!
[Mon Feb 17 18:30:44 EST 2020] [INFO] [] Deleted tmp file: C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j3986985765066972948_in_raw.h5
[Mon Feb 17 18:30:44 EST 2020] [ERROR] [] Module threw exception
ncsa.hdf.hdf5lib.exceptions.HDF5FileNotFoundException: Path does not exit. (C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j1296070379917363084_out.h5)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:194)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:147)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:126)
	at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:86)
	at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:54)
	at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:64)
	at org.ilastik.ilastik4ij.hdf5.Hdf5DataSetReader.read(Hdf5DataSetReader.java:51)
	at org.ilastik.ilastik4ij.executors.AbstractIlastikExecutor.executeIlastik(AbstractIlastikExecutor.java:64)
	at org.ilastik.ilastik4ij.executors.PixelClassification.classifyPixels(PixelClassification.java:24)
	at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.runClassification(IlastikPixelClassificationCommand.java:72)
	at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.run(IlastikPixelClassificationCommand.java:60)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

After reading over the above posts, I updated Ilastik to the Ilastik-1.3.3post2 version. Unfortunately, this didn’t fix the problem and led to some additional issues (mentioned below). When I try to call the pixel classification prediction in FIJI using Ilastik-1.3.3post2 I get the following exception (I believe its the same as the above, but not quite sure):

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52t; Java 1.8.0_172 [64-bit]; Windows 7 6.1; 369MB of 32000MB (1%)
 
java.lang.RuntimeException: java.util.concurrent.ExecutionException: ncsa.hdf.hdf5lib.exceptions.HDF5FileNotFoundException: Path does not exit. (C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j5751635177140637917_out.h5)
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:309)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:150)
	at ij.Executer.run(Executer.java:68)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.concurrent.ExecutionException: ncsa.hdf.hdf5lib.exceptions.HDF5FileNotFoundException: Path does not exit. (C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j5751635177140637917_out.h5)
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:305)
	... 5 more
Caused by: ncsa.hdf.hdf5lib.exceptions.HDF5FileNotFoundException: Path does not exit. (C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j5751635177140637917_out.h5)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:194)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:147)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:126)
	at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:86)
	at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:54)
	at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:64)
	at org.ilastik.ilastik4ij.hdf5.Hdf5DataSetReader.read(Hdf5DataSetReader.java:51)
	at org.ilastik.ilastik4ij.executors.AbstractIlastikExecutor.executeIlastik(AbstractIlastikExecutor.java:64)
	at org.ilastik.ilastik4ij.executors.PixelClassification.classifyPixels(PixelClassification.java:24)
	at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.runClassification(IlastikPixelClassificationCommand.java:72)
	at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.run(IlastikPixelClassificationCommand.java:60)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	... 1 more

and logs (again, looks similar to above for Ilastik-1.3.3, but I haven’t gone through it with a fine-tooth comb::

[Mon Feb 17 18:57:09 EST 2020] [INFO] [] Temporary files: {tempFileRawInput=C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j6037178567456391309_in_raw.h5, tempFileOutput=C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j1532876893154804882_out.h5}
[Mon Feb 17 18:57:09 EST 2020] [INFO] [] Exporting image of shape (1, 35, 1024, 1024, 4). Axis order: 'TZYXC'
[Mon Feb 17 18:57:09 EST 2020] [INFO] [] Saving as 'uint8'. Compression level: 1
[Mon Feb 17 18:58:14 EST 2020] [INFO] [] Running ilastik headless command:
[Mon Feb 17 18:58:14 EST 2020] [INFO] [] [C:\Program Files\ilastik-1.3.3post2\ilastik.exe, --headless, --project=C:\Users\Patrick Dummer\Patrick\Ilastik - Image Tiles for training\Ilastik_Zstack_TargetPlusPost_PixelClassification.ilp, --output_filename_format=C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j1532876893154804882_out.h5, --output_format=hdf5, --output_axis_order=tzyxc, --input_axes=tzyxc, C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j6037178567456391309_in_raw.h5]
[Mon Feb 17 18:58:16 EST 2020] [INFO] [] INFO lazyflow.operators.filterOperators: Using fast filters.
[Mon Feb 17 18:58:16 EST 2020] [ERROR] [] WARNING __init__.py(20): UserWarning: init: Could not import tiktorch classifier
[Mon Feb 17 18:58:17 EST 2020] [INFO] [] INFO ilastik_main: Starting ilastik from "C:\Program Files\ilastik-1.3.3post2".
[Mon Feb 17 18:58:17 EST 2020] [INFO] [] Starting ilastik from "C:\Program Files\ilastik-1.3.3post2".
[Mon Feb 17 18:58:17 EST 2020] [INFO] [] INFO ilastik_main: Configuring lazyflow RAM limit to 16.0GiB
[Mon Feb 17 18:58:17 EST 2020] [INFO] [] INFO lazyflow.utility.memory: Available memory set to 16.0GiB
[Mon Feb 17 18:58:20 EST 2020] [ERROR] [] WARNING 2020-02-17 18:58:20,051 opConservationTracking 5264 5640 Could not find any ILP solver
[Mon Feb 17 18:58:20 EST 2020] [ERROR] [] WARNING 2020-02-17 18:58:20,093 opStructuredTracking 5264 5640 Could not find any ILP solver
[Mon Feb 17 18:58:20 EST 2020] [ERROR] [] WARNING 2020-02-17 18:58:20,097 structuredTrackingWorkflow 5264 5640 Could not find any learning solver. Tracking will use flow-based solver (DPCT). Learning for tracking will be disabled!
[Mon Feb 17 18:58:21 EST 2020] [INFO] [] INFO ilastik.shell.projectManager: Opening Project: C:/Users/Patrick Dummer/Patrick/Ilastik - Image Tiles for training/Ilastik_Zstack_TargetPlusPost_PixelClassification.ilp
[Mon Feb 17 18:58:21 EST 2020] [ERROR] [] WARNING dataset.py(313): H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
[Mon Feb 17 18:58:22 EST 2020] [ERROR] [] WARNING opSimpleBlockedArrayCache.py(43): FutureWarning: Conversion of the second argument of issubdtype from `dtype` to `np.generic` is deprecated. In future, it will be treated as `np.object_ == np.dtype(dtype).type`.
[Mon Feb 17 18:58:22 EST 2020] [ERROR] [] WARNING opSlicedBlockedArrayCache.py(141): FutureWarning: Conversion of the second argument of issubdtype from `dtype` to `np.generic` is deprecated. In future, it will be treated as `np.object_ == np.dtype(dtype).type`.
[Mon Feb 17 18:58:23 EST 2020] [ERROR] [] ERROR 2020-02-17 18:58:23,653 log_exception 5264 5640 Traceback (most recent call last):
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik\shell\projectManager.py", line 460, in _loadProject
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     serializer.deserializeFromHdf5(self.currentProjectFile, projectFilePath, self._headless)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik\applets\base\appletSerializer.py", line 1151, in deserializeFromHdf5
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     ss.deserialize(topGroup)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik\applets\pixelClassification\pixelClassificationSerializer.py", line 100, in deserialize
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     super().deserialize(group)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik\applets\base\appletSerializer.py", line 264, in deserialize
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     self._deserialize(group[self.name], self.inslot)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\lazyflow\lazyflow\utility\timer.py", line 153, in wrapper
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     return func(*args, **kwargs)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik\applets\base\appletSerializer.py", line 620, in _deserialize
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     blockArray, slicing, self.inslot[index], Project(mygroup.file)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik\applets\pixelClassification\pixelClassificationSerializer.py", line 82, in reshape_datablock_and_slicing_for_input
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     fixed_block = Array5D(block, saved_data_axiskeys).raw(current_axiskeys)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\lib\site-packages\ndstructs\array5D.py", line 84, in __init__
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     assert len(arr.shape) == len(axiskeys)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] [] AssertionError
[Mon Feb 17 18:58:23 EST 2020] [ERROR] [] 
[Mon Feb 17 18:58:23 EST 2020] [ERROR] [] ERROR 2020-02-17 18:58:23,654 log_exception 5264 5640 Project could not be loaded due to the exception shown above.
[Mon Feb 17 18:58:23 EST 2020] [ERROR] [] Aborting Project Open Action
[Mon Feb 17 18:58:23 EST 2020] [ERROR] [] ERROR 2020-02-17 18:58:23,654 excepthooks 5264 5640 Unhandled exception in thread: 'MainThread'
[Mon Feb 17 18:58:23 EST 2020] [ERROR] [] ERROR 2020-02-17 18:58:23,655 excepthooks 5264 5640 Traceback (most recent call last):
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik.py", line 134, in <module>
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     main()
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik.py", line 128, in main
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     hShell = ilastik_main.main(parsed_args, workflow_cmdline_args)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik_main.py", line 165, in main
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     f(shell)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik_main.py", line 338, in loadProject
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     shell.openProjectFile(path, parsed_args.readonly)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik\shell\headless\headlessShell.py", line 125, in openProjectFile
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     self.projectManager._loadProject(hdf5File, projectFilePath, readOnly)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\lazyflow\lazyflow\utility\timer.py", line 153, in wrapper
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     return func(*args, **kwargs)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik\shell\projectManager.py", line 460, in _loadProject
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     serializer.deserializeFromHdf5(self.currentProjectFile, projectFilePath, self._headless)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik\applets\base\appletSerializer.py", line 1151, in deserializeFromHdf5
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     ss.deserialize(topGroup)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik\applets\pixelClassification\pixelClassificationSerializer.py", line 100, in deserialize
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     super().deserialize(group)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik\applets\base\appletSerializer.py", line 264, in deserialize
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     self._deserialize(group[self.name], self.inslot)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\lazyflow\lazyflow\utility\timer.py", line 153, in wrapper
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     return func(*args, **kwargs)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik\applets\base\appletSerializer.py", line 620, in _deserialize
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     blockArray, slicing, self.inslot[index], Project(mygroup.file)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\ilastik-meta\ilastik\ilastik\applets\pixelClassification\pixelClassificationSerializer.py", line 82, in reshape_datablock_and_slicing_for_input
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     fixed_block = Array5D(block, saved_data_axiskeys).raw(current_axiskeys)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []   File "C:\Program Files\ilastik-1.3.3post2\lib\site-packages\ndstructs\array5D.py", line 84, in __init__
[Mon Feb 17 18:58:23 EST 2020] [ERROR] []     assert len(arr.shape) == len(axiskeys)
[Mon Feb 17 18:58:23 EST 2020] [ERROR] [] AssertionError
[Mon Feb 17 18:58:23 EST 2020] [ERROR] [] 
[Mon Feb 17 18:58:24 EST 2020] [ERROR] [] ilastik error: 
[Mon Feb 17 18:58:24 EST 2020] [ERROR] [] The operation completed successfully.
[Mon Feb 17 18:58:24 EST 2020] [ERROR] [] 
[Mon Feb 17 18:58:24 EST 2020] [ERROR] [] 
[Mon Feb 17 18:58:24 EST 2020] [INFO] [] ilastik execution finished successfully!
[Mon Feb 17 18:58:24 EST 2020] [INFO] [] Deleted tmp file: C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j6037178567456391309_in_raw.h5
[Mon Feb 17 18:58:24 EST 2020] [ERROR] [] Module threw exception
ncsa.hdf.hdf5lib.exceptions.HDF5FileNotFoundException: Path does not exit. (C:\Users\PATRIC~1\AppData\Local\Temp\ilastik4j1532876893154804882_out.h5)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:194)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:147)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:126)
	at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:86)
	at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:54)
	at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:64)
	at org.ilastik.ilastik4ij.hdf5.Hdf5DataSetReader.read(Hdf5DataSetReader.java:51)
	at org.ilastik.ilastik4ij.executors.AbstractIlastikExecutor.executeIlastik(AbstractIlastikExecutor.java:64)
	at org.ilastik.ilastik4ij.executors.PixelClassification.classifyPixels(PixelClassification.java:24)
	at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.runClassification(IlastikPixelClassificationCommand.java:72)
	at org.ilastik.ilastik4ij.ui.IlastikPixelClassificationCommand.run(IlastikPixelClassificationCommand.java:60)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

In addition, with I’m unable to open my prior projects through the standalone version of Ilastik-1.3.3.post2 (I get a “Failed to Load” “Could not load project file.” popup window if I try to open from the “Open Recent Project” area inside the software, and when I try to open the file through windows, Ilastik opens to the project “Open Recent Project” screen, but the project itself doesn’t open). I can still open the files using Ilastik-1.3.3. I still have both installed (not sure if this is the root of this latter problem) but I’m worried about backwards compatibility so I don’t want to delete Ilastik-1.3.3 for fear of having to retrain my classifiers in Ilastik-1.3.3post2.

Both ImageJ/FIJI and the Ilastik plugin are up-to-date. The files I’m using are the same ones I used to train the classifier in the Ilastik standalone program. (I converted them to hdf5 using the Ilastik>export plugin before training and they worked just fine for the standalone program. Starting as .tif leads to the same issue.) I don’t know how to parse any of the logs or exceptions, so I’m stumped. Any help is appreciated. Thanks ahead of time!

Best,
Patrick