err `n5gest ls <n5_directory.n5>
uint64 labels don't work yet, see the tested/supported table here: https://github.com/catmaid/CATMAID/issues/1801#issuecomment-438747065
And I think the
unique-labels dataset from Paintera is an index of labels, not a label map
Which is why the shapes are incompatible
If you're using H2N5, the only way is to still use float32 labels
Actually the
dev branch of h2n5 already includes the channel packing
So if you can figure that out, then truncate the labels to 32 bits, you could either try to use h2n5 with channel packing, or use the
features/image-block-layer CATMAID branch to access the N5 directly.
Both of those have been tested.
This should installconda update -c hanslovsky painterapaintera-0.8.1. It will also installpaintera-conversion-helper-0.4.0, I made a separate package for that tool for better versioning. I tested very briefly and as far as I can tell, scalar label support works now. Let me know if you encounter any issues.
This is how I created a data set with scalar labels, notice the--winner-takes-all-downsamplingoption:paintera-conversion-helper -r -d /home/hanslovskyp/Downloads/sample_A_padded_20160501.hdf,volumes/raw,raw -d /home/hanslovskyp/Downloads/sample_A_padded_20160501.hdf,volumes/labels/neuron_ids,label -o /data/hanslovskyp/sample_A_padded_20160501-bs=64-winner-takes-all-n5-lookup2.n5 -b 64,64,64 -s 2,2,1 2,2,1 2,2,1 2,2,2 2,2,2 2,2,2 --winner-takes-all-downsampling --label-block-lookup-backend-n5=10000
Those are his instructions for the scalar labels
For my own future reference: the next steps for 64 bit support were updating the
ObjectLabelColorMap shader to shader version 300, making shaders generic/specializable to the datatype of image stacks, and setting the right GL parameters in the image block layer
(I'm on dev branch and start the devserver): After a few seconds, I get an " File "....python3.7/site-packages/asgi_ipc/store.py", line 45, in mutate_value
raise self.deadlock_error
RuntimeError: Semaphore appears to be deadlocked. Kill all channels processes and remove files named like asgi-messages in /dev/shm
"
raise self.deadlock_error
RuntimeError: Semaphore appears to be deadlocked. Kill all channels processes and remove files named like asgi-messages in /dev/shm
"
What could be the problem here?
Nevermind. I removed the locks from /dev/shm and things seem to work again.
Yeah, unfortunately
runserver does start a minimal ASGI server as well that uses shared memory (/dev/shm) for inter-process communication. I typically run in therefore typically as runserver --noasgi and the deadlocks are gone. In production we use Daphne for our WebSockets/ASGI needs.
Can you also briefly check to edit a "data view" in the admin interface on dev? I always get a ""render() got an unexpected keyword argument 'renderer'"" ... "... File \"/.../python3.7/site-packages/django/forms/boundfield.py\", line 93, in as_widget\n renderer=self.form.renderer,\nTypeError: render() got an unexpected keyword argument 'renderer'\n"
Currently, WebSockets are used mainly to refresh widgets that queue async jobs if there are status updates. These are mainly the Neuron Similarity Widget where NBLAST ranking is performed in the back-end and similarity matrices are created. I believe Will also uses WebSockets to do the same thing for updating the status on his GPU back-end jobs. The "Refresh" button in each widget would of course work too, but it's nice if it updates automatically. We also use for the regular message updates (i.e. a cropping job has finished). Currently it is not used for a real feature isn't needed for CATMAID to work. If widgets want to register own WebSockets message handlers they can use the
websocketHandlers option when registering the widget using CATMAID.registerWidget().
And thanks for the pointer to the broken data view edit page, I will fix it.