round()was that it would often lead to orthoviews with tracing data where you wouldn't see the same node in one view that is selected in another. I am happy to consider alternatives though, as long as they don't break the user expectation of visible tracing data in orthoviews. Wouldn't it maybe work to
floor(( (x - x_translation) / res_x) + epsilon)in each dimension? I agree though that rounding stack coordinates would be more consistent. Maybe the current goal that an active node is visible in all orthoviews at the same time isn't reasonable in the first place. I remember though users were confused when this wasn't the case (before 4c52ce7) and they traced in one view, pressed
ato center and continued in another view and not seeing a new edge linked to the centered node in the orthoviews.
paintera-conversion-helperwith winner-takes-all downsampling to create the appropriate datasets.
This should install
conda update -c hanslovsky paintera
paintera-0.8.1. It will also install
paintera-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.
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
paintera --version [JavaFX Application Thread] INFO org.janelia.saalfeldlab.paintera.PainteraCommandLineArgs - Paintera version: 0.8.1
StackLayerhas a method
http://bocklab.hhmi.org/h2n5/tile/volumes/raw/%SCALE_DATASET%/0_2/256_26/%AXIS_0%/%AXIS_2%/%AXIS_1%. And we started
h2n5just in its most simple form:
http://localhost:8088/group/dataset/etc/%SCALE_DATASET%/[slicing dimensions]/[tile size]/%AXIS_0%/%AXIS_1%/%AXIS_2%/, permuting the
AXISsubstitution parameter order as necessary for xyz, xzy, etc.
h2n5to show the image data using this URL:
http://127.0.0.1:8088/tile/raw/data/%SCALE_DATASET%/0_1/256_256/%AXIS_0%/%AXIS_1%/%AXIS_2%, but struggle to get the labels shown. With http://127.0.0.1:8088/tile/labels/unique-labels/%SCALE_DATASET%/0_1/256_256/%AXIS_0%/%AXIS_1%/%AXIS_2%`. We seem to get binary data back and the browser complains with code 501 (Data type does not have an image renderer implemented), which sounds promising. We tried to use the Randomised Label Color Map, but this doesn't seem to change anything.
unique-labelsdataset from Paintera is an index of labels, not a label map
devbranch of h2n5 already includes the channel packing
features/image-block-layerCATMAID branch to access the N5 directly.