Fail to generate export file - Ilastik

Hi all,

Some help would be really appreciated, tearing my hair out here! When I run my cell density pipeline and try to export it, it runs for ages and then says “failed to generate export file”. I’ve tried changing to a signed or unsigned 16bit float, and changing the file type. I’ve also tried moving the location it’s supposed to be saved to but this comes up with an error even faster. Any ideas?

Dear all,

I am also struggling with a similar error (as also mentioned here).

Specifically, I’m working on Ubuntu 16.04. with ilastik 1.3.3post2, and running a Cell Density Counting project. My inputs are raw PNG files. Density probability looks fine in the relevant pane.

I can set the images and CSV export files just fine, but when I actually export I get the following error:

Failed to generate export file:
/THEOUTPUTDIRICHOSE/THEFILENAMEICHOSE.h5/exported_data

I have also tried to set the export to a PNG file with conversion to uint8 and the “renormalize” option, but this did not help.
In addition, I have made sure that I have writing permissions in this directory.

If there’s no obvious flaw in the above steps, is there any workaround that I could use to further analyze the cell density, e.g. in FIJI, until the export option is fixed?

Any help would be greatly appreciated!
Best,
Roey

P.S.
Upon running ilastik, I get the following warnings:

Warning: Ignoring your non-empty LD_LIBRARY_PATH
Could not find …MYHOMEDIR/ilastik-1.3.3post2-Linux/python-scripts/ilastik-install. ignoring.
Starting ilastik from “…MYHOMEDIR/ilastik-1.3.3post2-Linux”.
Gtk-Message: 10:20:58.195: Failed to load module “overlay-scrollbar”
Gtk-Message: 10:20:58.215: Failed to load module “atk-bridge”
Gtk-Message: 10:20:58.219: Failed to load module “unity-gtk-module”
Gtk-Message: 10:20:58.241: Failed to load module “canberra-gtk-module”

UPDATE
This is to update that if I restrict the export to a small portion of the image, an output png file is created. While the file appears black when opened in GIMP, I can see gray scale values when I open it in FIJI.

A CSV file is also create, however its input doesn’t seem to be affected by the image cropping I have defined.

Best,
Roey

Hi @Becky_Donaldson, Hi @roeysc,

I think I’d need a few more details in order to reproduce the error. How large are the images you are using? Which features have you selected. How much RAM do you have in your machine?

Also it would be great if one of you can delete the log file (on linux per default in /home/yourusername/ilastik_log.txt, on windows in C:\Users\yourusename\ilastik_log.txt) recreate the error and post the content of the log-file after getting the error here.

Cheers :slight_smile:

Hi @k-dominik,
Thanks for the quick reply!

The image is a 466.5 MB png file.
I have selected 15 Edge features (Laplacian of Gaussian, Gaussian gradient magnitude and Difference of Gaussians for sigmas 0.7 , 1, 1.6, 3.5 and 5).
And the machine I’m using has 31.2 GB RAM

I’m not sure, however, how much RAM is allocated to ilastik. I’ve seen this thread, so I can create the .ilastikrc file if necessary.

Indeed, this seems to be a memory allocation issue, as indicated by the attached log file.

Many thanks for your help, again,
Roey

The log file content

INFO 2020-01-08 09:23:55,968 ilastik_main 16956 139938709907200 Starting ilastik from “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux”.
INFO 2020-01-08 09:23:56,857 filterOperators 16956 139938709907200 Using fast filters.
WARNING 2020-01-08 09:23:56,867 warnings 16956 139938709907200 init.py(20): UserWarning: init: Could not import tiktorch classifier
WARNING 2020-01-08 09:23:59,723 opConservationTracking 16956 139938709907200 Could not find any ILP solver
WARNING 2020-01-08 09:23:59,748 opStructuredTracking 16956 139938709907200 Could not find any ILP solver
WARNING 2020-01-08 09:23:59,752 structuredTrackingWorkflow 16956 139938709907200 Could not find any learning solver. Tracking will use flow-based solver (DPCT). Learning for tracking will be disabled!
INFO 2020-01-08 09:24:01,745 projectManager 16956 139938709907200 Opening Project: /ems/elsc-labs/mezer-a/Mezer-Lab/ilastik_projects/cell_density_test.ilp
WARNING 2020-01-08 09:24:01,751 warnings 16956 139938709907200 dataset.py(313): H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
WARNING 2020-01-08 09:24:01,898 warnings 16956 139938709907200 slot.py(1287): UserWarning: Deprecated use slot.operator property instead
INFO 2020-01-08 09:24:02,114 acceleratesupport 16956 139938709907200 No OpenGL_accelerate module loaded: No module named ‘OpenGL_accelerate’
WARNING 2020-01-08 09:24:02,613 warnings 16956 139938709907200 opSimpleBlockedArrayCache.py(43): FutureWarning: Conversion of the second argument of issubdtype from dtype to np.generic is deprecated. In future, it will be treated as np.object_ == np.dtype(dtype).type.
WARNING 2020-01-08 09:24:02,710 warnings 16956 139938709907200 opSlicedBlockedArrayCache.py(141): FutureWarning: Conversion of the second argument of issubdtype from dtype to np.generic is deprecated. In future, it will be treated as np.object_ == np.dtype(dtype).type.
WARNING 2020-01-08 09:24:03,265 warnings 16956 139938709907200 tiling.py(366): UserWarning: FIXME: This is a slow way to look for the items we want.
_TilesCache._layerCache should be a dict-of-dict-of-dict for faster lookup!
WARNING 2020-01-08 09:24:26,996 warnings 16956 139938709907200 valueRangeWidget.py(66): FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
INFO 2020-01-08 09:24:52,701 countingWorkflow 16956 139938255968000 Exporting object counts to CSV: /ems/elsc-labs/mezer-a/Mezer-Lab/ilastik_projects/out/csvtestagain.csv
WARNING 2020-01-08 09:24:52,711 warnings 16956 139938255968000 bigRequestStreamer.py(220): UserWarning: Unknown per-pixel RAM requirement. Making a guess.
INFO 2020-01-08 09:24:52,712 bigRequestStreamer 16956 139938255968000 Estimated RAM usage per pixel is 8.0B * safety factor (2.0)
WARNING 2020-01-08 09:24:52,714 warnings 16956 139938255968000 bigRequestStreamer.py(236): UserWarning: Chose an arbitrary request blockshape
INFO 2020-01-08 09:24:52,714 bigRequestStreamer 16956 139938255968000 Chose blockshape: (8286, 18737, 1)
INFO 2020-01-08 09:24:52,714 bigRequestStreamer 16956 139938255968000 Estimated RAM usage per block is 2.3GiB
ERROR 2020-01-08 09:24:52,797 request 16956 139937752020736 Traceback (most recent call last):
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 869, in call
result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operator.py”, line 591, in call_execute
return self.execute(slot, subindex, roi, result, **kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operators/opReorderAxes.py”, line 171, in execute
self.Input(*in_roi).writeInto(result_input_view).wait()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 541, in wait
return self._wait(timeout)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 569, in _wait
self._wait_within_request(current_request)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 698, in _wait_within_request
raise_with_traceback(exc_value, exc_tb)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/lib/python3.7/site-packages/future/utils/init.py”, line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 841, in call
return self.func(*totalargs, **self.kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 869, in call
result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operator.py”, line 591, in call_execute
return self.execute(slot, subindex, roi, result, **kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operators/generic.py”, line 592, in execute
matrix = req.wait()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 541, in wait
return self._wait(timeout)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 569, in _wait
self._wait_within_request(current_request)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 698, in _wait_within_request
raise_with_traceback(exc_value, exc_tb)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/lib/python3.7/site-packages/future/utils/init.py”, line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 869, in call
result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operator.py”, line 591, in call_execute
return self.execute(slot, subindex, roi, result, **kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operators/valueProviders.py”, line 130, in execute
req.wait()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 541, in wait
return self._wait(timeout)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 569, in _wait
self._wait_within_request(current_request)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 698, in _wait_within_request
raise_with_traceback(exc_value, exc_tb)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/lib/python3.7/site-packages/future/utils/init.py”, line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 841, in call
return self.func(*totalargs, **self.kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 869, in call
result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operator.py”, line 591, in call_execute
return self.execute(slot, subindex, roi, result, **kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operators/generic.py”, line 443, in execute
self.Input(*input_roi).writeInto(result).wait()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 541, in wait
return self._wait(timeout)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 569, in _wait
self._wait_within_request(current_request)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 698, in _wait_within_request
raise_with_traceback(exc_value, exc_tb)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/lib/python3.7/site-packages/future/utils/init.py”, line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 841, in call
return self.func(*totalargs, **self.kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 869, in call
result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operator.py”, line 591, in call_execute
return self.execute(slot, subindex, roi, result, **kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/ilastik/ilastik/applets/counting/opCounting.py”, line 180, in execute
data = self.inputs[“Input”][key].wait()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 541, in wait
return self._wait(timeout)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 569, in _wait
self._wait_within_request(current_request)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 698, in _wait_within_request
raise_with_traceback(exc_value, exc_tb)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/lib/python3.7/site-packages/future/utils/init.py”, line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 869, in call
result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operator.py”, line 591, in call_execute
return self.execute(slot, subindex, roi, result, **kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/ilastik/ilastik/applets/counting/countingOperators.py”, line 454, in execute
res = self.inputs[“Image”][newKey].wait()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 541, in wait
return self._wait(timeout)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 569, in _wait
self._wait_within_request(current_request)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 698, in _wait_within_request
raise_with_traceback(exc_value, exc_tb)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/lib/python3.7/site-packages/future/utils/init.py”, line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 859, in call
destination = self.slot.stype.allocateDestination(self.roi)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/stype.py”, line 121, in allocateDestination
storage = numpy.ndarray(shape, dtype=self.slot.meta.dtype)
MemoryError

ERROR 2020-01-08 09:24:52,798 request 16956 139937752020736 Encountered exception while processing roi: (array([0, 0, 0]), array([ 8286, 18737, 1]))
ERROR 2020-01-08 09:24:52,827 log_exception 16956 139938255968000 Traceback (most recent call last):
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/utility/roiRequestBatch.py”, line 171, in execute
self._activateNewRequest()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/utility/roiRequestBatch.py”, line 216, in _activateNewRequest
roi = next(self._roiIter)
StopIteration

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/ilastik/ilastik/applets/dataExport/dataExportGui.py”, line 413, in exportSync
opLaneView.run_export()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/ilastik/ilastik/applets/dataExport/opDataExport.py”, line 251, in run_export
self._opFormattedExport.run_export()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operators/ioOperators/opFormattedDataExport.py”, line 257, in run_export
self._opExportSlot.run_export()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operators/ioOperators/opExportSlot.py”, line 257, in run_export
export_func()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operators/ioOperators/opExportSlot.py”, line 342, in _export_2d
opExport.run_export()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operators/ioOperators/opExport2DImage.py”, line 76, in run_export
data = self._opExportToArray.run_export_to_array()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operators/ioOperators/opExportToArray.py”, line 37, in run_export_to_array
streamer.execute()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/utility/bigRequestStreamer.py”, line 290, in execute
self._requestBatch.execute()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/utility/roiRequestBatch.py”, line 206, in execute
raise_with_traceback(exc_type(exc_value), exc_tb)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/lib/python3.7/site-packages/future/utils/init.py”, line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 869, in call
result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operator.py”, line 591, in call_execute
return self.execute(slot, subindex, roi, result, **kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operators/opReorderAxes.py”, line 171, in execute
self.Input(*in_roi).writeInto(result_input_view).wait()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 541, in wait
return self._wait(timeout)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 569, in _wait
self._wait_within_request(current_request)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 698, in _wait_within_request
raise_with_traceback(exc_value, exc_tb)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/lib/python3.7/site-packages/future/utils/init.py”, line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 841, in call
return self.func(*totalargs, **self.kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 869, in call
result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operator.py”, line 591, in call_execute
return self.execute(slot, subindex, roi, result, **kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operators/generic.py”, line 592, in execute
matrix = req.wait()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 541, in wait
return self._wait(timeout)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 569, in _wait
self._wait_within_request(current_request)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 698, in _wait_within_request
raise_with_traceback(exc_value, exc_tb)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/lib/python3.7/site-packages/future/utils/init.py”, line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 869, in call
result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operator.py”, line 591, in call_execute
return self.execute(slot, subindex, roi, result, **kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operators/valueProviders.py”, line 130, in execute
req.wait()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 541, in wait
return self._wait(timeout)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 569, in _wait
self._wait_within_request(current_request)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 698, in _wait_within_request
raise_with_traceback(exc_value, exc_tb)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/lib/python3.7/site-packages/future/utils/init.py”, line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 841, in call
return self.func(*totalargs, **self.kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 869, in call
result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operator.py”, line 591, in call_execute
return self.execute(slot, subindex, roi, result, **kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operators/generic.py”, line 443, in execute
self.Input(*input_roi).writeInto(result).wait()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 541, in wait
return self._wait(timeout)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 569, in _wait
self._wait_within_request(current_request)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 698, in _wait_within_request
raise_with_traceback(exc_value, exc_tb)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/lib/python3.7/site-packages/future/utils/init.py”, line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 841, in call
return self.func(*totalargs, **self.kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 869, in call
result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operator.py”, line 591, in call_execute
return self.execute(slot, subindex, roi, result, **kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/ilastik/ilastik/applets/counting/opCounting.py”, line 180, in execute
data = self.inputs[“Input”][key].wait()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 541, in wait
return self._wait(timeout)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 569, in _wait
self._wait_within_request(current_request)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 698, in _wait_within_request
raise_with_traceback(exc_value, exc_tb)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/lib/python3.7/site-packages/future/utils/init.py”, line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 869, in call
result_op = self.operator.call_execute(self.slot.top_level_slot, self.slot.subindex, self.roi, destination)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/operator.py”, line 591, in call_execute
return self.execute(slot, subindex, roi, result, **kwargs)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/ilastik/ilastik/applets/counting/countingOperators.py”, line 454, in execute
res = self.inputs[“Image”][newKey].wait()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 541, in wait
return self._wait(timeout)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 569, in _wait
self._wait_within_request(current_request)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 698, in _wait_within_request
raise_with_traceback(exc_value, exc_tb)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/lib/python3.7/site-packages/future/utils/init.py”, line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/request/request.py”, line 360, in _execute
self._result = self.fn()
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/slot.py”, line 859, in call
destination = self.slot.stype.allocateDestination(self.roi)
File “/ems/elsc-labs/mezer-a/roey.schurr/ilastik-1.3.3post2-Linux/ilastik-meta/lazyflow/lazyflow/stype.py”, line 121, in allocateDestination
storage = numpy.ndarray(shape, dtype=self.slot.meta.dtype)
MemoryError

ERROR 2020-01-08 09:24:52,828 log_exception 16956 139938255968000 Failed to generate export file:
/ems/elsc-labs/mezer-a/Mezer-Lab/ilastik_projects/outpng/img01_cropped_Probabilities.png

Hey @roeysc,

that MemoryError in the end of the log is what I was suspecting is happening. What is the size of the image in terms of pixels in x- and y-direction?

What sigma value are you using for the “objects” in the image? if it is rather large, downscaling the data might help (since it’s counting, it shouldn’t effect the result too much). You’d have to redo the training though.

Thanks for the input, @k-dominik!
The input image is 8286x18737 pixels in size, with sigma of 2.95 (which I thought wasn’t considered especially large). I’ll give downscaling a try, although I suspect I might lose some information that way, especially for the busier images, where objects are more crowded.

In the mean time, I’ll crop the image to smaller images and run the workflow using the –headless mode.
Thanks again

I agree that a sigma of 2.95 doesn’t sound so large. I would still try downsampling by a factor of 0.5 and trying with a sigma of 1.5 then, and see how the numbers compare.

Otherwise, yes, cutting the image up as you suggest is a good option too.

Thanks, @k-dominik, I will give it a try!