:) ilastik 1.3.3, first beta

ilastik
#1

Dearest ilastik users,

this one is for the more adventurous amongst you, our first beta of 1.3.3

New features:

  • Support for n5 volumes (https://github.com/saalfeldlab/n5). We see performance gains here for larger volumes.
  • Support for masks in Pixel Classification (an additional dataset can be supplied that disables computation of probabilities wherever it is 0 -> speeds up computation in cases with a lot of background
  • Atlas Mask overlays for Object classification (an additional dataset can be supplied. Pixel values of this additional mask are included in result tables but not used in classification.)
  • autocontext now takes arbitrary data types (was previously limited to uint8), but mind the memory footprint! We still recommend to use uint8.
  • Lots of internal fixes and an updated dependency stack

Download links for your convenience:

some turbulence should be expected, but in our initial testing it worked quite well, already.

5 Likes
#2

On Windows 7, I get the following error when trying to start ilastik.exe:

image

#3

bummer, we’ve upgrade a lot of dependencies in the process for 1.3.3. Sorry about that. We’ll look into it. I opened a github issue to keep track: https://github.com/ilastik/ilastik/issues/2003

1 Like
#4

Hi,
Glad to see new releases.

Here is an error I got on Linux (mint) in Tracking with learning workflow.:
It poped-up three times and nothing else happened.

I ignored this and launched the tracking itself, it works fine.

ERROR 2019-05-03 09:43:26,542 excepthooks 17782 140070798771968 Unhandled exception in thread: 'Worker #3'
ERROR 2019-05-03 09:43:26,543 excepthooks 17782 140070798771968 Traceback (most recent call last):
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/volumina/volumina/tiling.py", line 782, in _fetch_tile_layer
    img = ims_req.wait()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/volumina/volumina/pixelpipeline/imagesources.py", line 422, in wait
    return self.toImage()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/volumina/volumina/pixelpipeline/imagesources.py", line 428, in toImage
    self._arrayreq.wait()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/volumina/volumina/pixelpipeline/slicesources.py", line 48, in wait
    return self._sp(self._ar.wait())
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/volumina/volumina/pixelpipeline/datasources.py", line 504, in wait
    rawData = self._rawRequest.wait()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/volumina/volumina/pixelpipeline/datasources.py", line 219, in wrapper
    return func(*args, **kwargs)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/volumina/volumina/pixelpipeline/datasources.py", line 243, in wait
    a = self._req.wait()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 531, in wait
    return self._wait(timeout)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 559, in _wait
    self._wait_within_request(current_request)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 688, in _wait_within_request
    raise_with_traceback(exc_value, exc_tb)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/lib/python3.7/site-packages/future/utils/__init__.py", line 421, in raise_with_traceback
    raise exc.with_traceback(traceback)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 350, in _execute
    self._result = self.fn()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/slot.py", line 928, in __call__
    result_op = self.operator.execute(self.slot, (), self.roi, destination)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/operators/opReorderAxes.py", line 171, in execute
    self.Input(*in_roi).writeInto(result_input_view).wait()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 531, in wait
    return self._wait(timeout)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 559, in _wait
    self._wait_within_request(current_request)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 688, in _wait_within_request
    raise_with_traceback(exc_value, exc_tb)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/lib/python3.7/site-packages/future/utils/__init__.py", line 421, in raise_with_traceback
    raise exc.with_traceback(traceback)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 350, in _execute
    self._result = self.fn()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 831, in __call__
    return self.func(*totalargs, **self.kwargs)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/slot.py", line 928, in __call__
    result_op = self.operator.execute(self.slot, (), self.roi, destination)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/operators/opUnblockedArrayCache.py", line 87, in execute
    self._execute_Output(slot, subindex, roi, result)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/operators/opSimpleBlockedArrayCache.py", line 106, in _execute_Output
    pool.wait()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 1363, in wait
    self._clear_finishing_requests()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 1439, in _clear_finishing_requests
    req.block()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 537, in block
    self._wait(timeout)  # No return value. Use wait()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 559, in _wait
    self._wait_within_request(current_request)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 644, in _wait_within_request
    raise_with_traceback(exc_type(exc_value), exc_tb)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/lib/python3.7/site-packages/future/utils/__init__.py", line 421, in raise_with_traceback
    raise exc.with_traceback(traceback)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 350, in _execute
    self._result = self.fn()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/operators/opSimpleBlockedArrayCache.py", line 92, in copy_block
    self._execute_Output_impl(full_block_roi, full_block_data)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/operators/opUnblockedArrayCache.py", line 112, in _execute_Output_impl
    self._fetch_and_store_block(request_roi, out=result)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/operators/opUnblockedArrayCache.py", line 150, in _fetch_and_store_block
    block_data = req.wait()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 531, in wait
    return self._wait(timeout)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 559, in _wait
    self._wait_within_request(current_request)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 688, in _wait_within_request
    raise_with_traceback(exc_value, exc_tb)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/lib/python3.7/site-packages/future/utils/__init__.py", line 421, in raise_with_traceback
    raise exc.with_traceback(traceback)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 350, in _execute
    self._result = self.fn()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 831, in __call__
    return self.func(*totalargs, **self.kwargs)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/slot.py", line 928, in __call__
    result_op = self.operator.execute(self.slot, (), self.roi, destination)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/operators/opCacheFixer.py", line 65, in execute
    self.Input(roi.start, roi.stop).writeInto(result).wait()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 531, in wait
    return self._wait(timeout)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 559, in _wait
    self._wait_within_request(current_request)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 688, in _wait_within_request
    raise_with_traceback(exc_value, exc_tb)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/lib/python3.7/site-packages/future/utils/__init__.py", line 421, in raise_with_traceback
    raise exc.with_traceback(traceback)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 350, in _execute
    self._result = self.fn()
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py", line 831, in __call__
    return self.func(*totalargs, **self.kwargs)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/lazyflow/lazyflow/slot.py", line 928, in __call__
    result_op = self.operator.execute(self.slot, (), self.roi, destination)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/ilastik/ilastik/applets/tracking/structured/opStructuredTracking.py", line 118, in execute
    super(OpStructuredTracking, self).execute(slot, subindex, roi, result)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/ilastik/ilastik/applets/tracking/conservation/opConservationTracking.py", line 167, in execute
    result[t-roi.start[0],...,0] = self._labelLineageIds(result[t-roi.start[0],...,0], t)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/ilastik-meta/ilastik/ilastik/applets/tracking/conservation/opConservationTracking.py", line 588, in _labelLineageIds
    if idx > 0 and hypothesesGraph.hasNode((time,idx)):
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/lib/python3.7/site-packages/hytra/core/hypothesesgraph.py", line 88, in hasNode
    return self._graph.has_node(node)
  File "/home/tongli/Downloads/ilastik-1.3.3b1-Linux/lib/python3.7/site-packages/networkx/classes/graph.py", line 854, in has_node
    return n in self._node
AttributeError: 'DiGraph' object has no attribute '_node'
#5

thx for that one, adding it to the list :slight_smile: and thank you for checking out the new version!!

#6

Is it a clean installation or did you overwrite previous version?
Maybe try this workaround and see if it helps.

#7

I was installing it into its own folder (Program Files\ilastik-1.3.3b1) next to other versions of #ilastik.

Indeed, there were some of those dlls in my C:\Windows\System32, and moving them out of the way solved the issue, thanks!

I wonder what application might have put (and possibly would require) them there, though…

#8

It is probably Intel Math Kernel Library. Can you check if it’s installed and which version is it?