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Error when running ilastik #25

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tischi opened this issue Dec 7, 2019 · 1 comment
Open

Error when running ilastik #25

tischi opened this issue Dec 7, 2019 · 1 comment

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@tischi
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tischi commented Dec 7, 2019

@wolny @k-dominik
I tried to run ilastik headless (from Java) and got below error. Any ideas regarding what is wrong?
Maybe some version mismatch issue (of ilastik and the pipeline file)?

[INFO] Staging raw input image as temporary file /var/folders/91/6n93mtg108g6161n3sx_x33m0000gn/T/ilastik4j5842688821465518189_in_raw.h5
[INFO] Exporting image of shape (1, 32, 100, 100, 2). Axis order: 'TZYXC'
[INFO] Found 10 JHotDraw adapters.
[INFO] Saving as 'uint8'. Compression level: 1
[INFO] Running ilastik headless command:
[INFO] [/Applications/ilastik-1.3.3-OSX.app/Contents/MacOS/ilastik, --headless, --project=/Users/tischer/Documents/tobias-kletter/20191206_DNA_Segmentation_2Ch.ilp, --output_filename_format=/var/folders/91/6n93mtg108g6161n3sx_x33m0000gn/T/ilastik4j5516621146392757981_out.h5, --output_format=hdf5, --output_axis_order=tzyxc, /var/folders/91/6n93mtg108g6161n3sx_x33m0000gn/T/ilastik4j5842688821465518189_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 "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release".
[INFO] Starting ilastik from "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release".
[INFO] INFO ilastik_main: Resetting lazyflow thread pool with 4 threads.
[INFO] INFO ilastik_main: Configuring lazyflow RAM limit to 9.8GiB
[INFO] INFO lazyflow.utility.memory: Available memory set to 9.8GiB
[ERROR] WARNING 2019-12-07 14:19:05,828 opConservationTracking 97719 4561475008 Could not find any ILP solver
[ERROR] WARNING 2019-12-07 14:19:05,844 opStructuredTracking 97719 4561475008 Could not find any ILP solver
[ERROR] WARNING 2019-12-07 14:19:05,846 structuredTrackingWorkflow 97719 4561475008 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/tischer/Documents/tobias-kletter/20191206_DNA_Segmentation_2Ch.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`.
[INFO] INFO ilastik.workflows.newAutocontext.newAutocontextWorkflow: Beginning Batch Processing
[ERROR] ERROR 2019-12-07 14:19:12,909 log_exception 97719 4561475008 Traceback (most recent call last):
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/shell/projectManager.py", line 461, in _loadProject
[ERROR]     self.workflow.onProjectLoaded(self)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/newAutocontext/newAutocontextWorkflow.py", line 479, in onProjectLoaded
[ERROR]     self.batchProcessingApplet.run_export_from_parsed_args(self._batch_input_args)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/batchProcessing/batchProcessingApplet.py", line 60, in run_export_from_parsed_args
[ERROR]     return self.run_export(role_path_dict, parsed_args.input_axes, sequence_axis=parsed_args.stack_along)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/batchProcessing/batchProcessingApplet.py", line 114, in run_export
[ERROR]     progress_callback=partial(lerpProgressSignal, global_progress_start, global_progress_end),
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/batchProcessing/batchProcessingApplet.py", line 162, in export_dataset
[ERROR]     batch_lane.DatasetGroup[role_index].setValue(role_info)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 125, in call_in_setup_context
[ERROR]     return func(self, *args, **kwargs)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1192, in setValue
[ERROR]     self._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1410, in _changed_impl
[ERROR]     self._configureOperator(self)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1423, in _configureOperator
[ERROR]     self.maybe_call_within_transaction(self.operator._setupOutputs)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/operator.py", line 498, in _setupOutputs
[ERROR]     self.setupOutputs()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/dataSelection/opDataSelection.py", line 720, in setupOutputs
[ERROR]     self.Image.connect(op5.Output)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 125, in call_in_setup_context
[ERROR]     return func(self, *args, **kwargs)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 595, in connect
[ERROR]     self._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1410, in _changed_impl
[ERROR]     self._configureOperator(self)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1423, in _configureOperator
[ERROR]     self.maybe_call_within_transaction(self.operator._setupOutputs)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/operator.py", line 498, in _setupOutputs
[ERROR]     self.setupOutputs()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/featureSelection/opFeatureSelection.py", line 254, in setupOutputs
[ERROR]     super().setupOutputs()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/featureSelection/opFeatureSelection.py", line 178, in setupOutputs
[ERROR]     if self.parent.parent.featureSelectionApplet._gui is None:
[ERROR] AttributeError: 'AutocontextTwoStage' object has no attribute 'featureSelectionApplet'
[ERROR] 
[ERROR] ERROR 2019-12-07 14:19:12,909 log_exception 97719 4561475008 Project could not be loaded due to the exception shown above.
[ERROR] Aborting Project Open Action
[ERROR] ERROR 2019-12-07 14:19:14,297 excepthooks 97719 4561475008 Unhandled exception in thread: 'MainThread'
[ERROR] ERROR 2019-12-07 14:19:14,303 excepthooks 97719 4561475008 Traceback (most recent call last):
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/Resources/__boot__.py", line 132, in <module>
[ERROR]     _run()
[ERROR]   File "/Applications/ilastik-1.3.3-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 "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik_main.py", line 165, in main
[ERROR]     f(shell)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik_main.py", line 338, in loadProject
[ERROR]     shell.openProjectFile(path, parsed_args.readonly)
[ERROR]   File "/Applications/ilastik-1.3.3-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 "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/utility/timer.py", line 153, in wrapper
[ERROR]     return func(*args, **kwargs)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/shell/projectManager.py", line 461, in _loadProject
[ERROR]     self.workflow.onProjectLoaded(self)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/workflows/newAutocontext/newAutocontextWorkflow.py", line 479, in onProjectLoaded
[ERROR]     self.batchProcessingApplet.run_export_from_parsed_args(self._batch_input_args)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/batchProcessing/batchProcessingApplet.py", line 60, in run_export_from_parsed_args
[ERROR]     return self.run_export(role_path_dict, parsed_args.input_axes, sequence_axis=parsed_args.stack_along)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/batchProcessing/batchProcessingApplet.py", line 114, in run_export
[ERROR]     progress_callback=partial(lerpProgressSignal, global_progress_start, global_progress_end),
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/batchProcessing/batchProcessingApplet.py", line 162, in export_dataset
[ERROR]     batch_lane.DatasetGroup[role_index].setValue(role_info)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 125, in call_in_setup_context
[ERROR]     return func(self, *args, **kwargs)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1192, in setValue
[ERROR]     self._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1410, in _changed_impl
[ERROR]     self._configureOperator(self)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1423, in _configureOperator
[ERROR]     self.maybe_call_within_transaction(self.operator._setupOutputs)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/operator.py", line 498, in _setupOutputs
[ERROR]     self.setupOutputs()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/dataSelection/opDataSelection.py", line 720, in setupOutputs
[ERROR]     self.Image.connect(op5.Output)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 125, in call_in_setup_context
[ERROR]     return func(self, *args, **kwargs)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 595, in connect
[ERROR]     self._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1403, in _changed_impl
[ERROR]     c._changed()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1377, in _changed
[ERROR]     self.maybe_call_within_transaction(self._changed_impl)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1410, in _changed_impl
[ERROR]     self._configureOperator(self)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1423, in _configureOperator
[ERROR]     self.maybe_call_within_transaction(self.operator._setupOutputs)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/slot.py", line 1372, in maybe_call_within_transaction
[ERROR]     self.graph.maybe_call_within_transaction(fn)
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/graph.py", line 143, in maybe_call_within_transaction
[ERROR]     fn()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/operator.py", line 498, in _setupOutputs
[ERROR]     self.setupOutputs()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/featureSelection/opFeatureSelection.py", line 254, in setupOutputs
[ERROR]     super().setupOutputs()
[ERROR]   File "/Applications/ilastik-1.3.3-OSX.app/Contents/ilastik-release/ilastik-meta/ilastik/ilastik/applets/featureSelection/opFeatureSelection.py", line 178, in setupOutputs
[ERROR]     if self.parent.parent.featureSelectionApplet._gui is None:
[ERROR] AttributeError: 'AutocontextTwoStage' object has no attribute 'featureSelectionApplet'
[ERROR] 
[ERROR] 2019-12-07 14:19:14.376 ilastik[97719:3731295] ilastik Error
[ERROR] ilastik crashed
@k-dominik
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this looks like a genuine bug...

The problem (set aside the code there) is that you are trying to predict with an image in the autocontext workflow, that is most likely "flatter" than the training image, meaning it has less z-slices, so it cannot accommodate filters with larger sigmas. Where the code fails, it would usually try to resolve it. This code, however, was written with the assumption of a single feature selection applet (like in pixel classification).

To kind of get it working, you could select larger sigma filters to operate in 2D only.

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@tischi @k-dominik