No output image displayed

[tischi]

Hi @k-dominik & @wolny,

I am running

run("Run Pixel Classification Prediction", "projectfilename=/Users/tischer/Documents/edoardo-dimprima-3d-nucleus-segmentation/ilastik/nuclei-pixel-classification-iso1.5.ilp inputimage=/Users/tischer/Documents/edoardo-dimprima-3d-nucleus-segmentation/data/ilastik_input/HT6_hoechst_L2822_overview_crop2.h5/data pixelclassificationtype=Probabilities");

[INFO] Running ilastik headless command:
[INFO] [/Applications/ilastik-1.3.3post3-OSX.app/Contents/MacOS/ilastik, --headless, --project=/Users/tischer/Documents/edoardo-dimprima-3d-nucleus-segmentation/ilastik/nuclei-pixel-classification-iso1.5.ilp, --output_format=hdf5, --output_axis_order=tzyxc, --input_axes=tzyxc, --readonly=1, --output_internal_path=exported_data, --input_axes=tzyxc, --export_source=Simple Segmentation, --raw_data=/var/folders/91/6n93mtg108g6161n3sx_x33m0000gn/T/ilastik4j5288792121280052670_in_raw.h5, --output_filename_format=/var/folders/91/6n93mtg108g6161n3sx_x33m0000gn/T/ilastik4j2283209731093810355_out.h5]
[ERROR] /Applications/ilastik-1.3.3post3-OSX.app/Contents/ilastik-release/ilastik-meta/lazyflow/lazyflow/classifiers/__init__.py:20: UserWarning: init: Could not import tiktorch classifier
[ERROR]   warnings.warn("init: Could not import tiktorch classifier")
[INFO] INFO ilastik_main: Starting ilastik from "/Applications/ilastik-1.3.3post3-OSX.app/Contents/ilastik-release".
[INFO] Starting ilastik from "/Applications/ilastik-1.3.3post3-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 2021-08-06 14:15:11,101 opConservationTracking 96261 4350125504 Could not find any ILP solver
[ERROR] WARNING 2021-08-06 14:15:11,114 opStructuredTracking 96261 4350125504 Could not find any ILP solver
[ERROR] WARNING 2021-08-06 14:15:11,120 structuredTrackingWorkflow 96261 4350125504 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/edoardo-dimprima-3d-nucleus-segmentation/ilastik/nuclei-pixel-classification-iso1.5.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.pixelClassification.pixelClassificationWorkflow: Beginning Batch Processing
[INFO] INFO ilastik.applets.batchProcessing.batchProcessingApplet: Exporting to /var/folders/91/6n93mtg108g6161n3sx_x33m0000gn/T/ilastik4j2283209731093810355_out.h5/exported_data
[INFO] INFO lazyflow.operators.ioOperators.ioOperators.OpH5N5WriterBigDataset: Data shape: (1, 68, 33, 31, 1)
[INFO] INFO lazyflow.utility.bigRequestStreamer: Estimated RAM usage per pixel is 192.0B * safety factor (2.0)
[INFO] INFO lazyflow.utility.bigRequestStreamer: determining blockshape assuming available_ram is 3.0GiB, split between 4 threads
[INFO] INFO lazyflow.utility.bigRequestStreamer: Chose blockshape: (1, 68, 33, 31, 2)
[INFO] INFO lazyflow.utility.bigRequestStreamer: Estimated RAM usage per block is 25.5MiB
[INFO] DEBUG lazyflow.operators.classifierOperators: Features took 0.069627 seconds. Prediction took 0.04328 seconds. Subregion: start '[0, 0, 0, 0]' stop '[68, 33, 31, 2]'
[INFO] INFO ilastik.workflows.pixelClassification.pixelClassificationWorkflow: Completed Batch Processing
[INFO] ilastik execution finished successfully!
[INFO] Found dataset 'exported_data' of type 'uint8'
[INFO] Constructing output image of shape (31, 33, 1, 68, 1). Axis order: 'XYCZT'
[INFO] Deleted tmp file: /var/folders/91/6n93mtg108g6161n3sx_x33m0000gn/T/ilastik4j5288792121280052670_in_raw.h5
[INFO] Deleted tmp file: /var/folders/91/6n93mtg108g6161n3sx_x33m0000gn/T/ilastik4j2283209731093810355_out.h5

...which appears OK to me but the output image is not displayed.

Do you know what could be going on?

[k-dominik]

that is weird - the [INFO] Constructing output image of shape (31, 33, 1, 68, 1). Axis order: 'XYCZT' indicates that it is already loading the data. Are you running this in some kind of batch / loop?

[tischi]

Are you running this in some kind of batch / loop?

yes, for-loop in a macro

[tischi]

Nope, sorry, this was the aim... right now just running from the UI.

[tischi]

@k-dominik short zoom to show you?

[k-dominik]

reinstallation of fiji solved the issue.