open h5 files as image in KNIME

KNIME Extensions
1

Hi,

Is it possible to import ilastik generated probability maps (exported as .h5) files into KNIME? 

The KNIME image reader can not open such files whereas the KNIME file reader reads something but I didn't manage to somehow convert this into an image again (which I suppose should be possible somehow). 

If I export the probabilty maps in ilastik as multipage tif processing takes much longer plus KNIME doesn't read these files correctly either (it just opens the first slice of a z-stack but I guess this is a problem of ilastik). 

Using the ilastik integration doesn't really work for me that's why I try it this way.

 

Christian

2

Hi Christian,

we have something experimental on this front. I will take a look and see if I can get it to run. If not, I will file an issue for the Ilastik integration.

Can you quickly ellaborate why the Ilastik extension is not working for you? Maybe we can fix it?

Best,

Christian

3

Hi Christian

Thanks for your effort. When I use ilastik headless node in KNIME at the same image stack that I used for the training in ilastik (the image is saved to the ilastik project file, image is a three dimensional z-stack) the node executes forever and can't be cancelled similarly as reported recently here: https://tech.knime.org/forum/knime-image-processing/ilastik-error-when-executing-ilastik-headless-node

However it seems that I get a different type of error message. The ilastik log looks like this:

INFO 2016-11-18 10:42:52,269 ilastik_main 4648 964 Starting ilastik from "C:\Program Files\ilastik-1.2.0rc7".
INFO 2016-11-18 10:42:52,834 opThresholdTwoLevels 4648 964 Using 'vigra' labeling implemetation
WARNING 2016-11-18 10:42:52,898 opConservationTracking 4648 964 opConservationTracking.py(6): RuntimeWarning: to-Python converter for class std::vector<unsigned __int64,class std::allocator<unsigned __int64> > already registered; second conversion method ignored.
WARNING 2016-11-18 10:42:52,898 opConservationTracking 4648 964 opConservationTracking.py(6): RuntimeWarning: to-Python converter for class std::vector<double,class std::allocator<double> > already registered; second conversion method ignored.
INFO 2016-11-18 10:42:53,045 projectManager 4648 964 Opening Project: G:/Christian/2016/ilastik_templ/nuclei2.ilp
WARNING 2016-11-18 10:42:53,417 dataset 4648 964 dataset.py(70): DeprecationWarning: numpy boolean negative, the `-` operator, is deprecated, use the `~` operator or the logical_not function instead.
INFO 2016-11-18 10:42:53,568 pixelClassificationWorkflow 4648 964 Beginning Batch Processing
INFO 2016-11-18 10:42:53,924 batchProcessingApplet 4648 964 Exporting to C:/Users/jlabimaging/AppData/Local/Temp/ilastik/47bf6896-4534-4227-92a7-fd4ffe17332a/file0_result.tif
ERROR 2016-11-18 10:42:54,033 log_exception 4648 964 Traceback (most recent call last):
  File "C:\Program Files\ilastik-1.2.0rc7\ilastik-meta\ilastik\ilastik\shell\projectManager.py", line 443, in _loadProject
    self.workflow.onProjectLoaded( self )
  File "C:\Program Files\ilastik-1.2.0rc7\ilastik-meta\ilastik\ilastik\workflows\pixelClassification\pixelClassificationWorkflow.py", line 337, in onProjectLoaded
    self.batchProcessingApplet.run_export_from_parsed_args(self._batch_input_args)
  File "C:\Program Files\ilastik-1.2.0rc7\ilastik-meta\ilastik\ilastik\applets\batchProcessing\batchProcessingApplet.py", line 59, in run_export_from_parsed_args
    return self.run_export(role_path_dict, parsed_args.input_axes)
  File "C:\Program Files\ilastik-1.2.0rc7\ilastik-meta\ilastik\ilastik\applets\batchProcessing\batchProcessingApplet.py", line 120, in run_export
    export_to_array=export_to_array )
  File "C:\Program Files\ilastik-1.2.0rc7\ilastik-meta\ilastik\ilastik\applets\batchProcessing\batchProcessingApplet.py", line 232, in _run_export_with_empty_batch_lane
    opDataExportBatchlaneView.run_export()
  File "C:\Program Files\ilastik-1.2.0rc7\ilastik-meta\ilastik\ilastik\applets\dataExport\opDataExport.py", line 265, in run_export
    self._opFormattedExport.run_export()
  File "C:\Program Files\ilastik-1.2.0rc7\ilastik-meta\lazyflow\lazyflow\operators\ioOperators\opFormattedDataExport.py", line 233, in run_export
    self._opExportSlot.run_export()
  File "C:\Program Files\ilastik-1.2.0rc7\ilastik-meta\lazyflow\lazyflow\operators\ioOperators\opExportSlot.py", line 231, in run_export
    export_func()
  File "C:\Program Files\ilastik-1.2.0rc7\ilastik-meta\lazyflow\lazyflow\operators\ioOperators\opExportSlot.py", line 310, in _export_2d
    opExport.run_export()
  File "C:\Program Files\ilastik-1.2.0rc7\ilastik-meta\lazyflow\lazyflow\operators\ioOperators\opExport2DImage.py", line 67, in run_export
    assert len(nonzero_dims) <= 2, "Image must have no more than 2 non-singleton dimensions."
AssertionError: Image must have no more than 2 non-singleton dimensions.

ERROR 2016-11-18 10:42:54,033 log_exception 4648 964 Project could not be loaded due to the exception shown above.
Aborting Project Open Action
ERROR 2016-11-18 10:42:54,211 excepthooks 4648 964 Unhandled exception in thread: 'MainThread'

 

One more question:
Does it matter at all what file output format was choosen in the ilastik project file (Do I need to choose multipage tiff or would hd5 also be fine)?


Cheers
Christian

4

-

5

Hi Christian,

I just saw that the code changes to avoid the unresponsive Ilastik node is still on the nightly only. Could you try that?

Best,

Lorenz

6

Hi Lorenz,

Thanks for the tip. Using the nightly build made the difference. It works now!

Thanks again!

Christian

7

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