High Resolution Image Segmentation of small features in grey Microstructure (BSE) image

I’m trying to measure the surface fraction of a specific kind of precipitate on a huge back scattered greyscale eletron image. This is an example region of the 30kx20k image:

The background changes per ‘grain’ and the precipitate I want to quantify is sitting at the grain boundary:

they can be described as elongated, at grain boundary (sitting at edges between different background colours/‘Cells’), brighter than the background, limited in size.

Using a normal threshold/denoise combination I always run into the problem that some delta precipitates have the same grey value as the background in other places of the image:

Using edge detection I always have the brighter grain boundaries included in my picture…

Because these parameters are dependet on local differencies in contrast and morphology in parallel I tried the WEKA segmentation plug in. But it easily overloads my RAM (32 GB).

Thanks for any help :slight_smile:

Hi,

i this image looks like should give ZEN Intellesis a try. I has the option for a free trial and you find more information here:

When it comes to memory usage, Intellesis has a built-in tiling client, that hands over the image to be segmented to the actual machine.learning part of the SW. This way it works quite memory effient, but of course on can only tell if it works, when test with the actual sample.

Can I get a hand on the original image somewhere to give it a try?

Sebi (from ZEISS)

At what step are you running out of RAM with Weka? If you are able to train the model, you could chop-up your image into smaller areas/volumes and then classify each separately. If you running out of RAM training the model, then perhaps there are some changes you could make to the training input that might help; it depends on the specifics of what you are doing.

For now I changed to ilastik to try if it runs more RAM efficient.

1 Like

@Sebban,

in order to get best performance with ilastik, i’d recommend resaving your data to hdf5 using the ilastik fiji import/export plugin.
Then of course, if you feel that you can scale the data down without losing your objects, this will also help a lot.

1 Like

I am obviously not sure if I did label correctly, but the image above (example region) gives the following results for me (zoomed in)

Thanks for the tip. So far ilastik seems more efficient indeed. But do you know an easy way to controll the max RAM size it uses?

It seems it only takes half of the available RAM and has some build in limit.

If you don’t specify anything it should be quite greedy. On what platform are you? There is an environment variable to control RAM usage (usually to used to limit it to a lower value): LAZYFLOW_TOTAL_RAM_MB and you give it the value in megabytes of ram it should use.

Just out of curiosity, when do you see ilastik not using all of your resources? During export/batch processing?

During training I’m getting “MemoryError” in my log. Software does not crash though.

hm, could you maybe paste the relevant portion from your log?

*The error seems to appear only when opening a project

eg:

ERROR 2019-02-27 09:15:05,411 excepthooks 9892 5476 Unhandled exception in thread: ‘Worker #7
ERROR 2019-02-27 09:15:05,458 excepthooks 9892 5476 Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\tiling.py”, line 773, in _fetch_tile_layer
img = ims_req.wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\imagesources.py”, line 270, in wait
return self.toImage()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\imagesources.py”, line 276, in toImage
self._arrayreq.wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\slicesources.py”, line 46, in wait
return self._sp(self._ar.wait())
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 473, in wait
rawData = self._rawRequest.wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 228, in wait
a = self._req.wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opReorderAxes.py”, line 160, in execute
self.Input( *in_roi ).writeInto( result_input_view ).wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 793, in call
return self.func( *totalargs, **self.kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1588, in execute
return self.operator.execute(self, totalIndex, roi, result)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\generic.py”, line 153, in execute
self.Input[newKey].writeInto(result).wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 793, in call
return self.func( *totalargs, **self.kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\generic.py”, line 528, in execute
data = self.inputs[“Input”][key[:-1]+(slice(None),)].wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opSlicedBlockedArrayCache.py”, line 178, in execute
op.outputs[“Output”][key].writeInto(result).wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 793, in call
return self.func( *totalargs, **self.kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opUnblockedArrayCache.py”, line 83, in execute
self._execute_Output(slot, subindex, roi, result)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opSimpleBlockedArrayCache.py”, line 100, in _execute_Output
pool.wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 1313, in wait
self._clear_finishing_requests()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 1390, in _clear_finishing_requests
req.block()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 506, in block
self._wait(timeout) # No return value. Use wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 609, in wait_within_request
raise_with_traceback(exc_type(exc_value), exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opSimpleBlockedArrayCache.py”, line 76, in copy_block
self._execute_Output_impl( clipped_block_roi, result[roiToSlice(*output_roi)] )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opUnblockedArrayCache.py”, line 108, in _execute_Output_impl
self._fetch_and_store_block(request_roi, out=result)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opUnblockedArrayCache.py”, line 146, in _fetch_and_store_block
block_data = req.wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 793, in call
return self.func( *totalargs, **self.kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opCacheFixer.py”, line 63, in execute
self.Input(roi.start, roi.stop).writeInto(result).wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 793, in call
return self.func( *totalargs, **self.kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\classifierOperators.py”, line 577, in execute
input_data = self.Image[newKey].wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opSlicedBlockedArrayCache.py”, line 178, in execute
op.outputs[“Output”][key].writeInto(result).wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 793, in call
return self.func( *totalargs, **self.kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opUnblockedArrayCache.py”, line 83, in execute
self._execute_Output(slot, subindex, roi, result)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opSimpleBlockedArrayCache.py”, line 100, in _execute_Output
pool.wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 1313, in wait
self._clear_finishing_requests()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 1390, in _clear_finishing_requests
req.block()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 506, in block
self._wait(timeout) # No return value. Use wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 609, in wait_within_request
raise_with_traceback(exc_type(exc_value), exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opSimpleBlockedArrayCache.py”, line 76, in copy_block
self._execute_Output_impl( clipped_block_roi, result[roiToSlice(*output_roi)] )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opUnblockedArrayCache.py”, line 108, in _execute_Output_impl
self._fetch_and_store_block(request_roi, out=result)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opUnblockedArrayCache.py”, line 146, in _fetch_and_store_block
block_data = req.wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 793, in call
return self.func( *totalargs, **self.kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opCacheFixer.py”, line 63, in execute
self.Input(roi.start, roi.stop).writeInto(result).wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 793, in call
return self.func( *totalargs, **self.kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opReorderAxes.py”, line 160, in execute
self.Input( *in_roi ).writeInto( result_input_view ).wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 793, in call
return self.func( *totalargs, **self.kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opPixelFeaturesPresmoothed.py”, line 355, in execute
source = req.wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opReorderAxes.py”, line 160, in execute
self.Input( *in_roi ).writeInto( result_input_view ).wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 793, in call
return self.func( *totalargs, **self.kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opReorderAxes.py”, line 160, in execute
self.Input( *in_roi ).writeInto( result_input_view ).wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 793, in call
return self.func( *totalargs, **self.kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\valueProviders.py”, line 125, in execute
req.wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 793, in call
return self.func( *totalargs, **self.kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\valueProviders.py”, line 125, in execute
req.wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 500, in wait
return self._wait(timeout)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 651, in wait_within_request
raise_with_traceback(exc_value, exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 793, in call
return self.func( *totalargs, **self.kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 887, in call
result_op = self.operator.execute(self.slot, (), self.roi, destination)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opUnblockedArrayCache.py”, line 83, in execute
self._execute_Output(slot, subindex, roi, result)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opSimpleBlockedArrayCache.py”, line 100, in _execute_Output
pool.wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 1313, in wait
self._clear_finishing_requests()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 1390, in _clear_finishing_requests
req.block()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 506, in block
self._wait(timeout) # No return value. Use wait()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 526, in _wait
self._wait_within_request( current_request )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 609, in wait_within_request
raise_with_traceback(exc_type(exc_value), exc_tb)
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\request\request.py”, line 324, in _execute
self._result = self.fn()
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\operators\opSimpleBlockedArrayCache.py”, line 86, in copy_block
full_block_data = self.Output.stype.allocateDestination( SubRegion(self.Output, *full_block_roi ) )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\stype.py”, line 112, in allocateDestination
storage = numpy.ndarray(shape, dtype=self.slot.meta.dtype)
MemoryError

and the software crashes (no visible progress “not responding”) when saving the project:
WARNING 2019-02-27 11:33:07,313 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:07,421 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:07,504 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:07,505 excepthooks 9892 10780 Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 221, in init
self._req = op.Output[slicing]
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1033, in getitem
return self(pslice=key)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1362, in call
return self.get(roi)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 829, in get
raise Slot.SlotNotReadyError(msg)
lazyflow.slot.Slot.SlotNotReadyError: Can’t get data from slot <class ‘lazyflow.operators.opReorderAxes.OpReorderAxes’>.Output yet. It isn’t ready.First upstream problem slot is: OpReorderAxes/OpReorderAxes.Input : {_ready : False, NOTREADY : None, shape : (24576, 32768, 1), axistags : y x c, original_axistags : y x c, dtype : <class ‘numpy.uint8’>, drange : (0, 255), has_mask : None, _dirty : False, ideal_blockshape : (24576, 32768, 1), dontcache : False, ram_usage_per_requested_pixel : 3.0, ram_per_pixelram_usage_per_requested_pixel : 3, display_mode : ‘default’, channel_names : [‘Raw Data-0’, ‘Raw Data-1’, ‘Raw Data-2’], normalizeDisplay : True, max_blockshape : None, original_shape : (24576, 32768, 3)}

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\tiling.py”, line 649, in _refreshTile
ims_req = ims.request(dataRect, stack_id[1])
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\imagesources.py”, line 527, in request
r = self._channels[0].request(s, along_through)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\slicesources.py”, line 142, in request
return SliceRequest(self._datasource.request(slicing), self.sliceProjection)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 532, in request
rawRequest = self._rawSource.request(slicing)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 321, in request
return LazyflowRequest( self._op5, clipped_slicing, self.priority, objectName=self.objectName() )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 207, in wrapper
raise_with_traceback( IndeterminateRequestError(ex) ).with_traceback(sys.exc_info()[2])
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 221, in init
self._req = op.Output[slicing]
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1033, in getitem
return self(pslice=key)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1362, in call
return self.get(roi)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 829, in get
raise Slot.SlotNotReadyError(msg)
volumina.pixelpipeline.asyncabcs.IndeterminateRequestError: Can’t get data from slot <class ‘lazyflow.operators.opReorderAxes.OpReorderAxes’>.Output yet. It isn’t ready.First upstream problem slot is: OpReorderAxes/OpReorderAxes.Input : {_ready : False, NOTREADY : None, shape : (24576, 32768, 1), axistags : y x c, original_axistags : y x c, dtype : <class ‘numpy.uint8’>, drange : (0, 255), has_mask : None, _dirty : False, ideal_blockshape : (24576, 32768, 1), dontcache : False, ram_usage_per_requested_pixel : 3.0, ram_per_pixelram_usage_per_requested_pixel : 3, display_mode : ‘default’, channel_names : [‘Raw Data-0’, ‘Raw Data-1’, ‘Raw Data-2’], normalizeDisplay : True, max_blockshape : None, original_shape : (24576, 32768, 3)}

WARNING 2019-02-27 11:33:07,506 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:07,588 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:07,670 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:07,671 excepthooks 9892 10780 Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 221, in init
self._req = op.Output[slicing]
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1033, in getitem
return self(pslice=key)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1362, in call
return self.get(roi)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 829, in get
raise Slot.SlotNotReadyError(msg)
lazyflow.slot.Slot.SlotNotReadyError: Can’t get data from slot <class ‘lazyflow.operators.opReorderAxes.OpReorderAxes’>.Output yet. It isn’t ready.First upstream problem slot is: OpReorderAxes/OpReorderAxes.Input : {_ready : False, NOTREADY : None, shape : (24576, 32768, 1), axistags : y x c, original_axistags : y x c, dtype : <class ‘numpy.uint8’>, drange : (0, 255), has_mask : None, _dirty : False, ideal_blockshape : (24576, 32768, 1), dontcache : False, ram_usage_per_requested_pixel : 3.0, ram_per_pixelram_usage_per_requested_pixel : 3, display_mode : ‘default’, channel_names : [‘Raw Data-0’, ‘Raw Data-1’, ‘Raw Data-2’], normalizeDisplay : True, max_blockshape : None, original_shape : (24576, 32768, 3)}

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\tiling.py”, line 649, in _refreshTile
ims_req = ims.request(dataRect, stack_id[1])
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\imagesources.py”, line 527, in request
r = self._channels[0].request(s, along_through)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\slicesources.py”, line 142, in request
return SliceRequest(self._datasource.request(slicing), self.sliceProjection)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 532, in request
rawRequest = self._rawSource.request(slicing)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 321, in request
return LazyflowRequest( self._op5, clipped_slicing, self.priority, objectName=self.objectName() )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 207, in wrapper
raise_with_traceback( IndeterminateRequestError(ex) ).with_traceback(sys.exc_info()[2])
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 221, in init
self._req = op.Output[slicing]
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1033, in getitem
return self(pslice=key)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1362, in call
return self.get(roi)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 829, in get
raise Slot.SlotNotReadyError(msg)
volumina.pixelpipeline.asyncabcs.IndeterminateRequestError: Can’t get data from slot <class ‘lazyflow.operators.opReorderAxes.OpReorderAxes’>.Output yet. It isn’t ready.First upstream problem slot is: OpReorderAxes/OpReorderAxes.Input : {_ready : False, NOTREADY : None, shape : (24576, 32768, 1), axistags : y x c, original_axistags : y x c, dtype : <class ‘numpy.uint8’>, drange : (0, 255), has_mask : None, _dirty : False, ideal_blockshape : (24576, 32768, 1), dontcache : False, ram_usage_per_requested_pixel : 3.0, ram_per_pixelram_usage_per_requested_pixel : 3, display_mode : ‘default’, channel_names : [‘Raw Data-0’, ‘Raw Data-1’, ‘Raw Data-2’], normalizeDisplay : True, max_blockshape : None, original_shape : (24576, 32768, 3)}

WARNING 2019-02-27 11:33:07,672 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:07,754 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:07,839 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:07,840 excepthooks 9892 10780 Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 221, in init
self._req = op.Output[slicing]
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1033, in getitem
return self(pslice=key)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1362, in call
return self.get(roi)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 829, in get
raise Slot.SlotNotReadyError(msg)
lazyflow.slot.Slot.SlotNotReadyError: Can’t get data from slot <class ‘lazyflow.operators.opReorderAxes.OpReorderAxes’>.Output yet. It isn’t ready.First upstream problem slot is: OpReorderAxes/OpReorderAxes.Input : {_ready : False, NOTREADY : None, shape : (24576, 32768, 1), axistags : y x c, original_axistags : y x c, dtype : <class ‘numpy.uint8’>, drange : (0, 255), has_mask : None, _dirty : False, ideal_blockshape : (24576, 32768, 1), dontcache : False, ram_usage_per_requested_pixel : 3.0, ram_per_pixelram_usage_per_requested_pixel : 3, display_mode : ‘default’, channel_names : [‘Raw Data-0’, ‘Raw Data-1’, ‘Raw Data-2’], normalizeDisplay : True, max_blockshape : None, original_shape : (24576, 32768, 3)}

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\tiling.py”, line 649, in _refreshTile
ims_req = ims.request(dataRect, stack_id[1])
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\imagesources.py”, line 527, in request
r = self._channels[0].request(s, along_through)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\slicesources.py”, line 142, in request
return SliceRequest(self._datasource.request(slicing), self.sliceProjection)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 532, in request
rawRequest = self._rawSource.request(slicing)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 321, in request
return LazyflowRequest( self._op5, clipped_slicing, self.priority, objectName=self.objectName() )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 207, in wrapper
raise_with_traceback( IndeterminateRequestError(ex) ).with_traceback(sys.exc_info()[2])
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 221, in init
self._req = op.Output[slicing]
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1033, in getitem
return self(pslice=key)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1362, in call
return self.get(roi)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 829, in get
raise Slot.SlotNotReadyError(msg)
volumina.pixelpipeline.asyncabcs.IndeterminateRequestError: Can’t get data from slot <class ‘lazyflow.operators.opReorderAxes.OpReorderAxes’>.Output yet. It isn’t ready.First upstream problem slot is: OpReorderAxes/OpReorderAxes.Input : {_ready : False, NOTREADY : None, shape : (24576, 32768, 1), axistags : y x c, original_axistags : y x c, dtype : <class ‘numpy.uint8’>, drange : (0, 255), has_mask : None, _dirty : False, ideal_blockshape : (24576, 32768, 1), dontcache : False, ram_usage_per_requested_pixel : 3.0, ram_per_pixelram_usage_per_requested_pixel : 3, display_mode : ‘default’, channel_names : [‘Raw Data-0’, ‘Raw Data-1’, ‘Raw Data-2’], normalizeDisplay : True, max_blockshape : None, original_shape : (24576, 32768, 3)}

WARNING 2019-02-27 11:33:07,840 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:07,922 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:08,006 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:08,007 excepthooks 9892 10780 Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 221, in init
self._req = op.Output[slicing]
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1033, in getitem
return self(pslice=key)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1362, in call
return self.get(roi)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 829, in get
raise Slot.SlotNotReadyError(msg)
lazyflow.slot.Slot.SlotNotReadyError: Can’t get data from slot <class ‘lazyflow.operators.opReorderAxes.OpReorderAxes’>.Output yet. It isn’t ready.First upstream problem slot is: OpReorderAxes/OpReorderAxes.Input : {_ready : False, NOTREADY : None, shape : (24576, 32768, 1), axistags : y x c, original_axistags : y x c, dtype : <class ‘numpy.uint8’>, drange : (0, 255), has_mask : None, _dirty : False, ideal_blockshape : (24576, 32768, 1), dontcache : False, ram_usage_per_requested_pixel : 3.0, ram_per_pixelram_usage_per_requested_pixel : 3, display_mode : ‘default’, channel_names : [‘Raw Data-0’, ‘Raw Data-1’, ‘Raw Data-2’], normalizeDisplay : True, max_blockshape : None, original_shape : (24576, 32768, 3)}

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\tiling.py”, line 649, in _refreshTile
ims_req = ims.request(dataRect, stack_id[1])
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\imagesources.py”, line 527, in request
r = self._channels[0].request(s, along_through)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\slicesources.py”, line 142, in request
return SliceRequest(self._datasource.request(slicing), self.sliceProjection)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 532, in request
rawRequest = self._rawSource.request(slicing)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 321, in request
return LazyflowRequest( self._op5, clipped_slicing, self.priority, objectName=self.objectName() )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 207, in wrapper
raise_with_traceback( IndeterminateRequestError(ex) ).with_traceback(sys.exc_info()[2])
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 221, in init
self._req = op.Output[slicing]
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1033, in getitem
return self(pslice=key)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1362, in call
return self.get(roi)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 829, in get
raise Slot.SlotNotReadyError(msg)
volumina.pixelpipeline.asyncabcs.IndeterminateRequestError: Can’t get data from slot <class ‘lazyflow.operators.opReorderAxes.OpReorderAxes’>.Output yet. It isn’t ready.First upstream problem slot is: OpReorderAxes/OpReorderAxes.Input : {_ready : False, NOTREADY : None, shape : (24576, 32768, 1), axistags : y x c, original_axistags : y x c, dtype : <class ‘numpy.uint8’>, drange : (0, 255), has_mask : None, _dirty : False, ideal_blockshape : (24576, 32768, 1), dontcache : False, ram_usage_per_requested_pixel : 3.0, ram_per_pixelram_usage_per_requested_pixel : 3, display_mode : ‘default’, channel_names : [‘Raw Data-0’, ‘Raw Data-1’, ‘Raw Data-2’], normalizeDisplay : True, max_blockshape : None, original_shape : (24576, 32768, 3)}

WARNING 2019-02-27 11:33:08,008 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:08,090 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:08,172 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:08,173 excepthooks 9892 10780 Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 221, in init
self._req = op.Output[slicing]
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1033, in getitem
return self(pslice=key)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1362, in call
return self.get(roi)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 829, in get
raise Slot.SlotNotReadyError(msg)
lazyflow.slot.Slot.SlotNotReadyError: Can’t get data from slot <class ‘lazyflow.operators.opReorderAxes.OpReorderAxes’>.Output yet. It isn’t ready.First upstream problem slot is: OpReorderAxes/OpReorderAxes.Input : {_ready : False, NOTREADY : None, shape : (24576, 32768, 1), axistags : y x c, original_axistags : y x c, dtype : <class ‘numpy.uint8’>, drange : (0, 255), has_mask : None, _dirty : False, ideal_blockshape : (24576, 32768, 1), dontcache : False, ram_usage_per_requested_pixel : 3.0, ram_per_pixelram_usage_per_requested_pixel : 3, display_mode : ‘default’, channel_names : [‘Raw Data-0’, ‘Raw Data-1’, ‘Raw Data-2’], normalizeDisplay : True, max_blockshape : None, original_shape : (24576, 32768, 3)}

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\tiling.py”, line 649, in _refreshTile
ims_req = ims.request(dataRect, stack_id[1])
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\imagesources.py”, line 527, in request
r = self._channels[0].request(s, along_through)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\slicesources.py”, line 142, in request
return SliceRequest(self._datasource.request(slicing), self.sliceProjection)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 532, in request
rawRequest = self._rawSource.request(slicing)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 321, in request
return LazyflowRequest( self._op5, clipped_slicing, self.priority, objectName=self.objectName() )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 207, in wrapper
raise_with_traceback( IndeterminateRequestError(ex) ).with_traceback(sys.exc_info()[2])
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 221, in init
self._req = op.Output[slicing]
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1033, in getitem
return self(pslice=key)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1362, in call
return self.get(roi)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 829, in get
raise Slot.SlotNotReadyError(msg)
volumina.pixelpipeline.asyncabcs.IndeterminateRequestError: Can’t get data from slot <class ‘lazyflow.operators.opReorderAxes.OpReorderAxes’>.Output yet. It isn’t ready.First upstream problem slot is: OpReorderAxes/OpReorderAxes.Input : {_ready : False, NOTREADY : None, shape : (24576, 32768, 1), axistags : y x c, original_axistags : y x c, dtype : <class ‘numpy.uint8’>, drange : (0, 255), has_mask : None, _dirty : False, ideal_blockshape : (24576, 32768, 1), dontcache : False, ram_usage_per_requested_pixel : 3.0, ram_per_pixelram_usage_per_requested_pixel : 3, display_mode : ‘default’, channel_names : [‘Raw Data-0’, ‘Raw Data-1’, ‘Raw Data-2’], normalizeDisplay : True, max_blockshape : None, original_shape : (24576, 32768, 3)}

WARNING 2019-02-27 11:33:08,174 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:08,257 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:08,345 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:08,346 excepthooks 9892 10780 Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 221, in init
self._req = op.Output[slicing]
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1033, in getitem
return self(pslice=key)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1362, in call
return self.get(roi)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 829, in get
raise Slot.SlotNotReadyError(msg)
lazyflow.slot.Slot.SlotNotReadyError: Can’t get data from slot <class ‘lazyflow.operators.opReorderAxes.OpReorderAxes’>.Output yet. It isn’t ready.First upstream problem slot is: OpReorderAxes/OpReorderAxes.Input : {_ready : False, NOTREADY : None, shape : (24576, 32768, 1), axistags : y x c, original_axistags : y x c, dtype : <class ‘numpy.uint8’>, drange : (0, 255), has_mask : None, _dirty : False, ideal_blockshape : (24576, 32768, 1), dontcache : False, ram_usage_per_requested_pixel : 3.0, ram_per_pixelram_usage_per_requested_pixel : 3, display_mode : ‘default’, channel_names : [‘Raw Data-0’, ‘Raw Data-1’, ‘Raw Data-2’], normalizeDisplay : True, max_blockshape : None, original_shape : (24576, 32768, 3)}

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\tiling.py”, line 649, in _refreshTile
ims_req = ims.request(dataRect, stack_id[1])
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\imagesources.py”, line 527, in request
r = self._channels[0].request(s, along_through)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\slicesources.py”, line 142, in request
return SliceRequest(self._datasource.request(slicing), self.sliceProjection)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 532, in request
rawRequest = self._rawSource.request(slicing)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 321, in request
return LazyflowRequest( self._op5, clipped_slicing, self.priority, objectName=self.objectName() )
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 207, in wrapper
raise_with_traceback( IndeterminateRequestError(ex) ).with_traceback(sys.exc_info()[2])
File "C:\Program Files\ilastik-1.3.2\lib\site-packages\future\utils_init
.py", line 421, in raise_with_traceback
raise exc.with_traceback(traceback)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 221, in init
self._req = op.Output[slicing]
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1033, in getitem
return self(pslice=key)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 1362, in call
return self.get(roi)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\lazyflow\lazyflow\slot.py”, line 829, in get
raise Slot.SlotNotReadyError(msg)
volumina.pixelpipeline.asyncabcs.IndeterminateRequestError: Can’t get data from slot <class ‘lazyflow.operators.opReorderAxes.OpReorderAxes’>.Output yet. It isn’t ready.First upstream problem slot is: OpReorderAxes/OpReorderAxes.Input : {_ready : False, NOTREADY : None, shape : (24576, 32768, 1), axistags : y x c, original_axistags : y x c, dtype : <class ‘numpy.uint8’>, drange : (0, 255), has_mask : None, _dirty : False, ideal_blockshape : (24576, 32768, 1), dontcache : False, ram_usage_per_requested_pixel : 3.0, ram_per_pixelram_usage_per_requested_pixel : 3, display_mode : ‘default’, channel_names : [‘Raw Data-0’, ‘Raw Data-1’, ‘Raw Data-2’], normalizeDisplay : True, max_blockshape : None, original_shape : (24576, 32768, 3)}

WARNING 2019-02-27 11:33:08,860 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:08,959 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:09,034 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:12,419 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:12,496 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:12,599 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:12,675 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:12,777 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:12,840 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:12,942 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:13,004 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:13,121 excepthooks 9892 10780 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:15,561 excepthooks 9892 5476 Caught unhandled IndeterminateRequestError from volumina.
WARNING 2019-02-27 11:33:15,563 excepthooks 9892 5476 Traceback (most recent call last):
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 204, in wrapper
return func(*args, **kwargs)
File “C:\Program Files\ilastik-1.3.2\ilastik-meta\volumina\volumina\pixelpipeline\datasources.py”, line 228, in wait

[…] forum character limit reached :wink:

I’m still working with a combination of a croppef .jpeg and the “raw” .tiff high resolution file. which makes it a messy project file I guess
I will try a hdf5 conversion with the fiji plug in next.

Forget JPEG. Just crop the tif file to experiment with segmentation approaches.

I’d say hdf5 will improve that, thanks for the detailed tracebacks!

2 Likes

Okay so the ‘.tif’ is too large to be opened in fiji. It just stops without error message immediately. But as I can open the .tif in ilastik im going to save the raw as hdf5 and open it in a new project.

*hdf5 files work without error. But since there is a lot of background variation in my pictures, I need quite some re-training. If I zoom out the process switches to “no response” even though the CPU and RAM are not reaching their limits:
usage

that is really unfortunate. I guess the only advice I can give in this situation is to switch off live update while zooming out and looking for a different interesting place in your data and zooming in again, before you enable live update again.

Off-topic but is there a way to get a legend for the probabilty/uncertainty map for error statistics?
At which threshold of probabilty ilastik classifies as “segmentation”?

Or even an overview to track uncertainty/probability values with retraining steps (over time) to see if actual “progress” in terms of redurcing error is reached?

-so far google isn’t pointing to the correct documentation pages on https://www.ilastik.org/ to find this myself
-I’m only using pixel classification till now. would Boundary-based segmentation help to reduce segmentation error due to different background per “grain” help if the features im interested in sit on the boundary of my grains?

Hey Sebban, probabilities sum up to 1.0 over the respective number of classes, so each pixel is associated with a probability vector with as many entries as you have classes. With 4 classes this could be (0.1, 0.2, 0.1, 0.6). The simple segmentation will pick up the class with the highest probability (in this case the last one with 0.6).

The second part regarding how to get an idea if the classifier is improving is a bit hidden in our faq (point 8):

  1. How can I know if the classifier is doing well?

Interactive labeling and visual inspection are the most convenient way. If you want a quantitative measure, Random Forest internally computes the so called Out-of-bag error. It is printed to the ilastik log file, but not (yet) displayed in the ilastik window. The corresponding lines in the log should look something like this: “INFO 2017-02-24 10:41:12,555 parallelVigraRfLazyflowClassifier 12179 140573765494528 Training complete. Average OOB: 0.225149500876”. The OOB here is the out-of-bag error.

Furthermore, you might want to look at the uncertainty layer.

1 Like

In Intellesis you can get a probability map as an optional output which allows you to judge how well the classified is doing.

Sebi