3D plots using neurone.plot.flow not properly visualised

[Kanyq]

Hello,

I'm trying to plot the flow field vectors for my 3D warping but the "flow" plot of neurite asks me to convert the 3D array into 2D+2 to plot it. So the actual array (1, 160, 160, 48, 3) has to be compressed to (54, 54, 16, 2) and I end up plotting (1, 54, 16, 2) for each flow plot, which does not give proper visualisation.
I'm squeezing the image in the following way:
flow = pred_warp.squeeze()[::3,::3,::3,::2]

pred_warp.shape = (1, 160, 160, 48, 3)
flow.shape = (54, 54, 16, 2)

Is there a way for me to plot the 3D flow plot or is there a better way to represent this flow vector? Thank you

[adalca]

@Kanyq thanks for the question -- can you check if the dev branch is better for you? @halleewong pushed a modification to the visualization tool that I think might be adressing your problem: 34ae090

[hy-23]

May I ask what the blue and green colors mean? Initially I thought they were supposed to correspond to magnitude, but there seem to be vectors of approximately the same length in both blue and green.

[adalca]

I would guess there's a directionality component, but I honestly forget -- we use plt.quiver under the hood for this one, so take a look at https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.quiver.html