Build issue #36

jburel · 2024-10-29T22:31:21Z

Review the installation of ilastik

github-actions · 2024-10-29T22:31:35Z

👈 Launch a binder notebook on branch build_issue

pwalczysko · 2024-10-30T10:48:14Z

notebooks/pixel_classification.ipynb

+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "view(data_viewer)"


data_viewer is not defined in this notebook. I have tried to define it in the previous cell as

" data_viewer = data[:, 0, 0, :, :]\n",

inside the for loop, which stops the error, but still does not draw anything

it was an addition from the previous notebook.
I should have rerun the cell
Let me check

pwalczysko · 2024-10-30T11:03:14Z

I think this line

 "compare(labels[0, 0, 2:, :, :], data[0, 0, 2:, :, :], shadow=False, gradient_opacity=0.2, ui_collapsed=True)"

https://github.com/ome/omero-guide-ilastik/pull/36/files#diff-54c76e03d425145934a460d0cc7ad23c67dbd577e7fb8bf7b42dee58e6c66804L401

should be drawing the comparison of the two images. imho, it draws nothing (it does not fail though).

Also the other 2 drawing cells in the ...zarr notebook behave the same (== do nothing).

pwalczysko

Some drawing problems #36 (comment) and #36 (comment)

But this is minor. lgtm

jburel · 2024-10-30T14:17:00Z

This is a problem with itkwidgets and tornado. I have downgraded tornado but I now have a different problem

jburel · 2024-10-30T22:07:33Z

@pwalczysko I have used matplotlib to view the image.
It is not as nice but that will do for now

pwalczysko · 2024-10-31T20:10:12Z

Now, in the ....zarr notebook, I get ^^^ as draw output - only one plane, not interactive. I believe this was not the intention of the code ?

Edit: After studying the code a bit more, I actually believe this WAS the intention. One has to manually change the number which corresponds to the z index in the cell and then get, e.g. the 100th plane.

pwalczysko · 2024-10-31T20:14:00Z

Edited the comment #36 (comment) - I think it is fine as is, maybe just lets not show the z plane 0 by default, but rather 100 ?

jburel · 2024-10-31T21:34:37Z

The interactive option does not work unfortunately. I will spend a bit more time on it after the workshop

pwalczysko · 2024-11-01T12:17:20Z

I have rebuilt the conda env, and now in the zarr notebook, I am having an error on the Analyze... cell

ERROR 2024-11-01 12:11:11,982 request 62291 13149433856 Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/vigra/arraytypes.py", line 1271, in __getitem__
    res = numpy.ndarray.__getitem__(self, index)
IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 883, in __call__
    return self.func(*totalargs, **self.kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/opPixelFeaturesPresmoothed.py", line 424, in execute
    presmoothed_source[j][i, ...] = self._computeGaussianSmoothing(
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/opPixelFeaturesPresmoothed.py", line 515, in _computeGaussianSmoothing
    result[c_slice] = fastfilters.gaussianSmoothing(vol[c_slice], sigma, window_size=self.WINDOW_SIZE)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/fastfilters/__init__.py", line 32, in func_wrapper
    return res.withAxes(array.axistags)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/vigra/arraytypes.py", line 1130, in withAxes
    res = self[slicing].transposeToNumpyOrder().transpose(permutation)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/vigra/arraytypes.py", line 1277, in __getitem__
    res = numpy.ndarray.__getitem__(self, tmpindex)
IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/opReorderAxes.py", line 171, in execute
    self.Input(*in_roi).writeInto(result_input_view).wait()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 564, in wait
    return self._wait(timeout)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 592, in _wait
    self._wait_within_request(current_request)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 721, in _wait_within_request
    raise RequestError(self.fn) from exc_value
lazyflow.request.request.RequestError: Failed to request data from `OpPixelFeaturesPresmoothed.Output`

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 883, in __call__
    return self.func(*totalargs, **self.kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/classifierOperators.py", line 483, in execute
    probabilities = self._calculate_probabilities(roi)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/classifierOperators.py", line 595, in _calculate_probabilities
    input_data = self.Image[newKey].wait()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 564, in wait
    return self._wait(timeout)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 592, in _wait
    self._wait_within_request(current_request)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 721, in _wait_within_request
    raise RequestError(self.fn) from exc_value
lazyflow.request.request.RequestError: Failed to request data from `OpReorderAxes.Output`

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 883, in __call__
    return self.func(*totalargs, **self.kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/generic.py", line 418, in execute
    self.Input(*input_roi).writeInto(result).wait()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 564, in wait
    return self._wait(timeout)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 592, in _wait
    self._wait_within_request(current_request)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 721, in _wait_within_request
    raise RequestError(self.fn) from exc_value
lazyflow.request.request.RequestError: Failed to request data from `OpVectorwiseClassifierPredict.PMaps`

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 883, in __call__
    return self.func(*totalargs, **self.kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/valueProviders.py", line 130, in execute
    req.wait()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 564, in wait
    return self._wait(timeout)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 592, in _wait
    self._wait_within_request(current_request)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 721, in _wait_within_request
    raise RequestError(self.fn) from exc_value
lazyflow.request.request.RequestError: Failed to request data from `OpSubRegion.Output`

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 883, in __call__
    return self.func(*totalargs, **self.kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/generic.py", line 570, in execute
    matrix = req.wait()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 564, in wait
    return self._wait(timeout)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 592, in _wait
    self._wait_within_request(current_request)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 721, in _wait_within_request
    raise RequestError(self.fn) from exc_value
lazyflow.request.request.RequestError: Failed to request data from `Metadata injector.Output`

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/opReorderAxes.py", line 171, in execute
    self.Input(*in_roi).writeInto(result_input_view).wait()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 564, in wait
    return self._wait(timeout)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 592, in _wait
    self._wait_within_request(current_request)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 721, in _wait_within_request
    raise RequestError(self.fn) from exc_value
lazyflow.request.request.RequestError: Failed to request data from `OpPixelOperator.Output`

ERROR 2024-11-01 12:11:11,983 request 62291 13149433856 Encountered exception while processing roi: (array([  0,   0,   0, 148,   0]), array([  1, 148, 149, 253,   2]))
ERROR 2024-11-01 12:11:12,090 request 62291 13166223360 Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/vigra/arraytypes.py", line 1271, in __getitem__
    res = numpy.ndarray.__getitem__(self, index)
IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 883, in __call__
    return self.func(*totalargs, **self.kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/opPixelFeaturesPresmoothed.py", line 424, in execute
    presmoothed_source[j][i, ...] = self._computeGaussianSmoothing(
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/opPixelFeaturesPresmoothed.py", line 515, in _computeGaussianSmoothing
    result[c_slice] = fastfilters.gaussianSmoothing(vol[c_slice], sigma, window_size=self.WINDOW_SIZE)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/fastfilters/__init__.py", line 32, in func_wrapper
    return res.withAxes(array.axistags)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/vigra/arraytypes.py", line 1130, in withAxes
    res = self[slicing].transposeToNumpyOrder().transpose(permutation)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/vigra/arraytypes.py", line 1277, in __getitem__
    res = numpy.ndarray.__getitem__(self, tmpindex)
IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/opReorderAxes.py", line 171, in execute
    self.Input(*in_roi).writeInto(result_input_view).wait()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 564, in wait
    return self._wait(timeout)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 592, in _wait
    self._wait_within_request(current_request)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 721, in _wait_within_request
    raise RequestError(self.fn) from exc_value
lazyflow.request.request.RequestError: Failed to request data from `OpPixelFeaturesPresmoothed.Output`

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 883, in __call__
    return self.func(*totalargs, **self.kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/classifierOperators.py", line 483, in execute
    probabilities = self._calculate_probabilities(roi)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/classifierOperators.py", line 595, in _calculate_probabilities
    input_data = self.Image[newKey].wait()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 564, in wait
    return self._wait(timeout)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 592, in _wait
    self._wait_within_request(current_request)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 721, in _wait_within_request
    raise RequestError(self.fn) from exc_value
lazyflow.request.request.RequestError: Failed to request data from `OpReorderAxes.Output`

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 883, in __call__
    return self.func(*totalargs, **self.kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/generic.py", line 418, in execute
    self.Input(*input_roi).writeInto(result).wait()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 564, in wait
    return self._wait(timeout)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 592, in _wait
    self._wait_within_request(current_request)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 721, in _wait_within_request
    raise RequestError(self.fn) from exc_value
lazyflow.request.request.RequestError: Failed to request data from `OpVectorwiseClassifierPredict.PMaps`

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 883, in __call__
    return self.func(*totalargs, **self.kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/valueProviders.py", line 130, in execute
    req.wait()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 564, in wait
    return self._wait(timeout)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 592, in _wait
    self._wait_within_request(current_request)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 721, in _wait_within_request
    raise RequestError(self.fn) from exc_value
lazyflow.request.request.RequestError: Failed to request data from `OpSubRegion.Output`

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 883, in __call__
    return self.func(*totalargs, **self.kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/generic.py", line 570, in execute
    matrix = req.wait()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 564, in wait
    return self._wait(timeout)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 592, in _wait
    self._wait_within_request(current_request)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 721, in _wait_within_request
    raise RequestError(self.fn) from exc_value
lazyflow.request.request.RequestError: Failed to request data from `Metadata injector.Output`

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 383, in _execute
    self._result = self.fn()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py", line 876, in __call__
    result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py", line 608, in call_execute
    return self.execute(slot, subindex, roi, result, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/opReorderAxes.py", line 171, in execute
    self.Input(*in_roi).writeInto(result_input_view).wait()
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 564, in wait
    return self._wait(timeout)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 592, in _wait
    self._wait_within_request(current_request)
  File "/Users/pwalczysko/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py", line 721, in _wait_within_request
    raise RequestError(self.fn) from exc_value
lazyflow.request.request.RequestError: Failed to request data from `OpPixelOperator.Output`

ERROR 2024-11-01 12:11:12,124 request 62291 13166223360 Encountered exception while processing roi: (array([0, 0, 0, 0, 0]), array([  1, 148, 149, 148,   2]))

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/vigra/arraytypes.py:1271, in VigraArray.__getitem__(self, index)
   1270 try:
-> 1271     res = numpy.ndarray.__getitem__(self, index)
   1272 except:

IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

During handling of the above exception, another exception occurred:

IndexError                                Traceback (most recent call last)
File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:383, in Request._execute(self)
    381 try:
    382     # Do the actual work
--> 383     self._result = self.fn()
    384 except Request.CancellationException:
    385     # Don't propagate cancellations back to the worker thread,
    386     # even if the user didn't catch them.

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:883, in Request._PartialWithAppendedArgs.__call__(self, *args)
    882 totalargs = args + self.args
--> 883 return self.func(*totalargs, **self.kwargs)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py:876, in Slot.RequestExecutionWrapper.__call__(self, destination)
    874 # Execute the workload, which might not ever return
    875 # (if we get cancelled).
--> 876 result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
    878 # copy data from result_op to destination, if
    879 # destination was actually given by the user, and the
    880 # returned result_op is different from destination.
    881 # (but don't copy if result_op is None, this means
    882 # legacy op which wrote into destination anyway)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py:608, in Operator.call_execute(self, slot, subindex, roi, result, **kwargs)
    607     self._incrementOperatorExecutionCount()
--> 608     return self.execute(slot, subindex, roi, result, **kwargs)
    609 finally:

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/opPixelFeaturesPresmoothed.py:424, in OpPixelFeaturesPresmoothed.execute(self, slot, subindex, slot_roi, target)
    423         for i, vsa in enumerate(sourceV.timeIter()):
--> 424             presmoothed_source[j][i, ...] = self._computeGaussianSmoothing(
    425                 vsa, tempSigma, droi, in2d=self.ComputeIn2d.value[j]
    426             )
    428 except RuntimeError as e:

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/opPixelFeaturesPresmoothed.py:515, in OpPixelFeaturesPresmoothed._computeGaussianSmoothing(self, vol, sigma, roi, in2d)
    514     else:
--> 515         result[c_slice] = fastfilters.gaussianSmoothing(vol[c_slice], sigma, window_size=self.WINDOW_SIZE)
    517 roi = roiToSlice(*roi)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/fastfilters/__init__.py:32, in __p_fix_array.<locals>.func_wrapper(array, *args, **kwargs)
     31 		res = vigra.taggedView( res, list(squeezed.axistags) + [vigra.AxisInfo.c] )
---> 32 	return res.withAxes(array.axistags)
     33 else:

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/vigra/arraytypes.py:1130, in VigraArray.withAxes(self, *axistags, **kw)
   1129     permutation = AxisTags(axisinfo).permutationFromNumpyOrder()
-> 1130     res = self[slicing].transposeToNumpyOrder().transpose(permutation)
   1131 else:

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/vigra/arraytypes.py:1277, in VigraArray.__getitem__(self, index)
   1276     tmpindex = [None if isinstance(x, AxisInfo) else x for x in index]
-> 1277     res = numpy.ndarray.__getitem__(self, tmpindex)
   1278 if res is not self and hasattr(res, 'axistags'):

IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

The above exception was the direct cause of the following exception:

RequestError                              Traceback (most recent call last)
File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:383, in Request._execute(self)
    381 try:
    382     # Do the actual work
--> 383     self._result = self.fn()
    384 except Request.CancellationException:
    385     # Don't propagate cancellations back to the worker thread,
    386     # even if the user didn't catch them.

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py:876, in Slot.RequestExecutionWrapper.__call__(self, destination)
    874 # Execute the workload, which might not ever return
    875 # (if we get cancelled).
--> 876 result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
    878 # copy data from result_op to destination, if
    879 # destination was actually given by the user, and the
    880 # returned result_op is different from destination.
    881 # (but don't copy if result_op is None, this means
    882 # legacy op which wrote into destination anyway)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py:608, in Operator.call_execute(self, slot, subindex, roi, result, **kwargs)
    607     self._incrementOperatorExecutionCount()
--> 608     return self.execute(slot, subindex, roi, result, **kwargs)
    609 finally:

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/opReorderAxes.py:171, in OpReorderAxes.execute(self, slot, subindex, out_roi, result)
    170 # Now write into the special result view
--> 171 self.Input(*in_roi).writeInto(result_input_view).wait()
    172 return result

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:564, in Request.wait(self, timeout)
    563 assert not self._cleaned, "Can't wait() for a request that has already been cleaned."
--> 564 return self._wait(timeout)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:592, in Request._wait(self, timeout)
    589     assert (
    590         timeout is None
    591     ), "The timeout parameter may only be used when wait() is called from a foreign thread."
--> 592     self._wait_within_request(current_request)
    594 assert self.finished

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:721, in Request._wait_within_request(self, current_request)
    720 exc_type, exc_value, exc_tb = self.exception_info
--> 721 raise RequestError(self.fn) from exc_value

RequestError: Failed to request data from `OpPixelFeaturesPresmoothed.Output`

The above exception was the direct cause of the following exception:

RequestError                              Traceback (most recent call last)
File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:383, in Request._execute(self)
    381 try:
    382     # Do the actual work
--> 383     self._result = self.fn()
    384 except Request.CancellationException:
    385     # Don't propagate cancellations back to the worker thread,
    386     # even if the user didn't catch them.

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:883, in Request._PartialWithAppendedArgs.__call__(self, *args)
    882 totalargs = args + self.args
--> 883 return self.func(*totalargs, **self.kwargs)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py:876, in Slot.RequestExecutionWrapper.__call__(self, destination)
    874 # Execute the workload, which might not ever return
    875 # (if we get cancelled).
--> 876 result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
    878 # copy data from result_op to destination, if
    879 # destination was actually given by the user, and the
    880 # returned result_op is different from destination.
    881 # (but don't copy if result_op is None, this means
    882 # legacy op which wrote into destination anyway)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py:608, in Operator.call_execute(self, slot, subindex, roi, result, **kwargs)
    607     self._incrementOperatorExecutionCount()
--> 608     return self.execute(slot, subindex, roi, result, **kwargs)
    609 finally:

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/classifierOperators.py:483, in OpBaseClassifierPredict.execute(self, slot, subindex, roi, result)
    481         return result
--> 483 probabilities = self._calculate_probabilities(roi)
    485 # We're expecting a channel for each label class.
    486 # If we didn't provide at least one sample for each label,
    487 #  we may get back fewer channels.

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/classifierOperators.py:595, in OpVectorwiseClassifierPredict._calculate_probabilities(self, roi)
    594 with Timer() as features_timer:
--> 595     input_data = self.Image[newKey].wait()
    597 input_data = numpy.asarray(input_data, numpy.float32)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:564, in Request.wait(self, timeout)
    563 assert not self._cleaned, "Can't wait() for a request that has already been cleaned."
--> 564 return self._wait(timeout)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:592, in Request._wait(self, timeout)
    589     assert (
    590         timeout is None
    591     ), "The timeout parameter may only be used when wait() is called from a foreign thread."
--> 592     self._wait_within_request(current_request)
    594 assert self.finished

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:721, in Request._wait_within_request(self, current_request)
    720 exc_type, exc_value, exc_tb = self.exception_info
--> 721 raise RequestError(self.fn) from exc_value

RequestError: Failed to request data from `OpReorderAxes.Output`

The above exception was the direct cause of the following exception:

RequestError                              Traceback (most recent call last)
File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:383, in Request._execute(self)
    381 try:
    382     # Do the actual work
--> 383     self._result = self.fn()
    384 except Request.CancellationException:
    385     # Don't propagate cancellations back to the worker thread,
    386     # even if the user didn't catch them.

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:883, in Request._PartialWithAppendedArgs.__call__(self, *args)
    882 totalargs = args + self.args
--> 883 return self.func(*totalargs, **self.kwargs)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py:876, in Slot.RequestExecutionWrapper.__call__(self, destination)
    874 # Execute the workload, which might not ever return
    875 # (if we get cancelled).
--> 876 result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
    878 # copy data from result_op to destination, if
    879 # destination was actually given by the user, and the
    880 # returned result_op is different from destination.
    881 # (but don't copy if result_op is None, this means
    882 # legacy op which wrote into destination anyway)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py:608, in Operator.call_execute(self, slot, subindex, roi, result, **kwargs)
    607     self._incrementOperatorExecutionCount()
--> 608     return self.execute(slot, subindex, roi, result, **kwargs)
    609 finally:

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/generic.py:418, in OpSubRegion.execute(self, slot, subindex, output_roi, result)
    417 input_roi = list(map(tuple, input_roi))
--> 418 self.Input(*input_roi).writeInto(result).wait()
    419 return result

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:564, in Request.wait(self, timeout)
    563 assert not self._cleaned, "Can't wait() for a request that has already been cleaned."
--> 564 return self._wait(timeout)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:592, in Request._wait(self, timeout)
    589     assert (
    590         timeout is None
    591     ), "The timeout parameter may only be used when wait() is called from a foreign thread."
--> 592     self._wait_within_request(current_request)
    594 assert self.finished

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:721, in Request._wait_within_request(self, current_request)
    720 exc_type, exc_value, exc_tb = self.exception_info
--> 721 raise RequestError(self.fn) from exc_value

RequestError: Failed to request data from `OpVectorwiseClassifierPredict.PMaps`

The above exception was the direct cause of the following exception:

RequestError                              Traceback (most recent call last)
File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:383, in Request._execute(self)
    381 try:
    382     # Do the actual work
--> 383     self._result = self.fn()
    384 except Request.CancellationException:
    385     # Don't propagate cancellations back to the worker thread,
    386     # even if the user didn't catch them.

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:883, in Request._PartialWithAppendedArgs.__call__(self, *args)
    882 totalargs = args + self.args
--> 883 return self.func(*totalargs, **self.kwargs)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py:876, in Slot.RequestExecutionWrapper.__call__(self, destination)
    874 # Execute the workload, which might not ever return
    875 # (if we get cancelled).
--> 876 result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
    878 # copy data from result_op to destination, if
    879 # destination was actually given by the user, and the
    880 # returned result_op is different from destination.
    881 # (but don't copy if result_op is None, this means
    882 # legacy op which wrote into destination anyway)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py:608, in Operator.call_execute(self, slot, subindex, roi, result, **kwargs)
    607     self._incrementOperatorExecutionCount()
--> 608     return self.execute(slot, subindex, roi, result, **kwargs)
    609 finally:

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/valueProviders.py:130, in OpMetadataInjector.execute(self, slot, subindex, roi, result)
    129 req.writeInto(result)
--> 130 req.wait()
    131 return result

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:564, in Request.wait(self, timeout)
    563 assert not self._cleaned, "Can't wait() for a request that has already been cleaned."
--> 564 return self._wait(timeout)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:592, in Request._wait(self, timeout)
    589     assert (
    590         timeout is None
    591     ), "The timeout parameter may only be used when wait() is called from a foreign thread."
--> 592     self._wait_within_request(current_request)
    594 assert self.finished

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:721, in Request._wait_within_request(self, current_request)
    720 exc_type, exc_value, exc_tb = self.exception_info
--> 721 raise RequestError(self.fn) from exc_value

RequestError: Failed to request data from `OpSubRegion.Output`

The above exception was the direct cause of the following exception:

RequestError                              Traceback (most recent call last)
File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:383, in Request._execute(self)
    381 try:
    382     # Do the actual work
--> 383     self._result = self.fn()
    384 except Request.CancellationException:
    385     # Don't propagate cancellations back to the worker thread,
    386     # even if the user didn't catch them.

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:883, in Request._PartialWithAppendedArgs.__call__(self, *args)
    882 totalargs = args + self.args
--> 883 return self.func(*totalargs, **self.kwargs)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py:876, in Slot.RequestExecutionWrapper.__call__(self, destination)
    874 # Execute the workload, which might not ever return
    875 # (if we get cancelled).
--> 876 result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
    878 # copy data from result_op to destination, if
    879 # destination was actually given by the user, and the
    880 # returned result_op is different from destination.
    881 # (but don't copy if result_op is None, this means
    882 # legacy op which wrote into destination anyway)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py:608, in Operator.call_execute(self, slot, subindex, roi, result, **kwargs)
    607     self._incrementOperatorExecutionCount()
--> 608     return self.execute(slot, subindex, roi, result, **kwargs)
    609 finally:

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/generic.py:570, in OpPixelOperator.execute(self, slot, subindex, roi, result)
    569     req.writeInto(result)
--> 570 matrix = req.wait()
    571 result[:] = self.function(matrix)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:564, in Request.wait(self, timeout)
    563 assert not self._cleaned, "Can't wait() for a request that has already been cleaned."
--> 564 return self._wait(timeout)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:592, in Request._wait(self, timeout)
    589     assert (
    590         timeout is None
    591     ), "The timeout parameter may only be used when wait() is called from a foreign thread."
--> 592     self._wait_within_request(current_request)
    594 assert self.finished

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:721, in Request._wait_within_request(self, current_request)
    720 exc_type, exc_value, exc_tb = self.exception_info
--> 721 raise RequestError(self.fn) from exc_value

RequestError: Failed to request data from `Metadata injector.Output`

The above exception was the direct cause of the following exception:

RequestError                              Traceback (most recent call last)
File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:383, in Request._execute(self)
    381 try:
    382     # Do the actual work
--> 383     self._result = self.fn()
    384 except Request.CancellationException:
    385     # Don't propagate cancellations back to the worker thread,
    386     # even if the user didn't catch them.

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/slot.py:876, in Slot.RequestExecutionWrapper.__call__(self, destination)
    874 # Execute the workload, which might not ever return
    875 # (if we get cancelled).
--> 876 result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
    878 # copy data from result_op to destination, if
    879 # destination was actually given by the user, and the
    880 # returned result_op is different from destination.
    881 # (but don't copy if result_op is None, this means
    882 # legacy op which wrote into destination anyway)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operator.py:608, in Operator.call_execute(self, slot, subindex, roi, result, **kwargs)
    607     self._incrementOperatorExecutionCount()
--> 608     return self.execute(slot, subindex, roi, result, **kwargs)
    609 finally:

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/opReorderAxes.py:171, in OpReorderAxes.execute(self, slot, subindex, out_roi, result)
    170 # Now write into the special result view
--> 171 self.Input(*in_roi).writeInto(result_input_view).wait()
    172 return result

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:564, in Request.wait(self, timeout)
    563 assert not self._cleaned, "Can't wait() for a request that has already been cleaned."
--> 564 return self._wait(timeout)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:592, in Request._wait(self, timeout)
    589     assert (
    590         timeout is None
    591     ), "The timeout parameter may only be used when wait() is called from a foreign thread."
--> 592     self._wait_within_request(current_request)
    594 assert self.finished

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/request/request.py:721, in Request._wait_within_request(self, current_request)
    720 exc_type, exc_value, exc_tb = self.exception_info
--> 721 raise RequestError(self.fn) from exc_value

RequestError: Failed to request data from `OpPixelOperator.Output`

The above exception was the direct cause of the following exception:

RoiRequestBatchException                  Traceback (most recent call last)
Cell In[10], line 15
     13 print('running ilastik using %s' % model_file)
     14 role_data_dict = [ {"Raw Data": PreloadedArrayDatasetInfo(preloaded_array=input_data, axistags=vigra.defaultAxistags("tzyxc"))}]
---> 15 predictions = shell.workflow.batchProcessingApplet.run_export(role_data_dict, export_to_array=True)
     16 for data in predictions:
     17     # Re-organise array from tzyxc to tczyx order
     18     data = data.swapaxes(4, 3).swapaxes(3, 2).swapaxes(2, 1)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/ilastik/applets/batchProcessing/batchProcessingApplet.py:155, in BatchProcessingApplet.run_export(self, lane_configs, export_to_array, export_function)
    152     global_progress_start = batch_index / len(lane_configs)
    153     global_progress_end = (batch_index + 1) / len(lane_configs)
--> 155     result = self.export_dataset(
    156         lane_config,
    157         export_function=export_function,
    158         progress_callback=partial(lerpProgressSignal, global_progress_start, global_progress_end),
    159     )
    160     results.append(result)
    161 self.dataExportApplet.post_process_entire_export()

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/ilastik/applets/batchProcessing/batchProcessingApplet.py:198, in BatchProcessingApplet.export_dataset(self, lane_config, export_function, progress_callback)
    196 opDataExport = self.dataExportApplet.topLevelOperator.getLane(self.dataSelectionApplet.num_lanes - 1)
    197 opDataExport.progressSignal.subscribe(progress_callback or self.progressSignal)
--> 198 result = export_function(opDataExport)
    199 # Call customization hook
    200 self.dataExportApplet.post_process_lane_export(self.dataSelectionApplet.num_lanes - 1)

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/ilastik/applets/batchProcessing/batchProcessingApplet.py:173, in BatchProcessingApplet.do_export_to_array(self, opDataExport)
    171 def do_export_to_array(self, opDataExport):
    172     logger.info("Exporting to in-memory array.")
--> 173     return opDataExport.run_export_to_array()

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/ilastik/applets/dataExport/opDataExport.py:254, in OpDataExport.run_export_to_array(self)
    251 def run_export_to_array(self):
    252     # This function can be used to export the results to an in-memory array, instead of to disk
    253     # (Typically used from pure-python clients in batch mode.)
--> 254     return self._opFormattedExport.run_export_to_array()

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/ioOperators/opFormattedDataExport.py:279, in OpFormattedDataExport.run_export_to_array(self)
    278 def run_export_to_array(self):
--> 279     return self._opExportSlot.run_export_to_array()

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/ioOperators/opExportSlot.py:249, in OpExportSlot.run_export_to_array(self)
    247     opExport.progressSignal.subscribe(self.progressSignal)
    248     opExport.Input.connect(self.Input)
--> 249     return opExport.run_export_to_array()
    250 finally:
    251     opExport.cleanUp()

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/operators/ioOperators/opExportToArray.py:37, in OpExportToArray.run_export_to_array(self)
     34 streamer.progressSignal.subscribe(self.progressSignal)
     36 # Perform export
---> 37 streamer.execute()
     38 return final_result

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/utility/bigRequestStreamer.py:291, in BigRequestStreamer.execute(self)
    280 def execute(self):
    281     """
    282     Request the data for the entire roi by breaking it up into many smaller requests,
    283     and wait for all of them to complete.
   (...)
    289     :py:obj:`resultSignal`.
    290     """
--> 291     self._requestBatch.execute()

File ~/opt/anaconda3/envs/omero-guide-ilastik/lib/python3.9/site-packages/lazyflow/utility/roiRequestBatch.py:185, in RoiRequestBatch.execute(self)
    183 if self._failure_excinfo:
    184     exc_type, exc_value, exc_tb = self._failure_excinfo
--> 185     raise RoiRequestBatchException() from exc_value
    187 # Launch new requests until we have the correct number of active requests
    188 while not self._failure_excinfo and self._activated_count - self._completed_count < self._batchSize:

RoiRequestBatchException:

jburel · 2024-11-01T12:59:55Z

I rebuilt the environment following the instructions in the README
Ran both notebooks without issue

pwalczysko · 2024-11-01T13:29:23Z

I have rebuilt again (without the

CONDA_SUBDIR=osx-64

prefix.

This time, the notebooks finished without crash. But, I still have the error (inconsequential, but present inside the NON-zarr notebook)

The error is not consequential, because the ilastik project is being loaded from somewhere else (or at least not being selected in the widget cell) and the notebook passes

pwalczysko

The error #36 (comment) is not consequential.

jburel added 16 commits October 18, 2024 09:56

Cap Python and OMERO.py versions

6762f7a

Remove link to binderhub

3446ff1

Remove job adding binder badge

9e2526d

Update installation instuctions

2796d7a

Build environment on GHA

744c027

remove repo2docker job

c000c35

Remove macos for now

2bb02a8

Ignore checkpoint

730c541

review dependencies

1a737cc

Remove ipykernel installation

b185eb3

Add macos-12 support

acccff3

Fix omero-py version

bbb56c0

Add macos-14

d759fd1

Remove notebook no longer valid

13ed038

Review notebook

1bfa903

update link to build

956878e

jburel requested a review from pwalczysko October 29, 2024 22:31

Update rtd instatllation

4bd674a

This was referenced Oct 30, 2024

build failure #34

Closed

Issue with new fix #35

Closed

jburel added 2 commits October 30, 2024 06:28

Remove tornado

7afcd8f

Pin Python version

af38d6f

pwalczysko reviewed Oct 30, 2024

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pwalczysko requested changes Oct 30, 2024

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jburel added 4 commits October 30, 2024 14:11

Install older version of tornado to avoid error

cec328a

Remove viewing of the results

7b9072a

Add new ilastik workflow

7e3c478

Update link to ilastik model

6d9b66a

jburel added 3 commits October 30, 2024 20:50

Use matplotlib to display image

1eaaff8

Remove itkwidgets and tornado

8c1bd9f

Remove usage of itkwidgets

fd4ad8f

jburel added 3 commits October 31, 2024 21:41

Display the middle section

833738f

Only use matplotlib to display the image

37c2fba

Ensure widgets is imported

0a9b695

pwalczysko approved these changes Nov 1, 2024

View reviewed changes

jburel merged commit 3cd38b0 into ome:master Nov 1, 2024
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Build issue #36

Build issue #36

jburel commented Oct 29, 2024

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pwalczysko Oct 30, 2024

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Build issue #36

Build issue #36

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jburel commented Oct 29, 2024

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