3D positions of cells being displayed incorrectly

[pgleeson]

This NeuroML file contains 2 cells, a basket cell on the left (at the origin) and a pyramidal cell on the right (at <location x="400.0" y="-200.0" z="0.0"/>). The soma of the pyramidal cell should be below the basket cell as shown in this export of the cell from NML (use: pynml -png TwoCell.net.nml, see here):

However when this is imported into NetPyNE (e.g. by creating a workspace from https://v2.opensourcebrain.org/repositories/14 and importing the NML file above) the soma is above the basket cell (left below):

The correct position seems to be in netpyne's memory, as the right panel shows its own 3D view, with the yellow dot on the right for the pyramidal cell at the right locaion.

Also a json file exported from the neuroml version has the right location: https://github.com/OpenSourceBrain/NetPyNEShowcase/blob/master/NetPyNE/TwoCells/LEMS_TwoCell_netpyne_data.json#L29

Is it possibly the issue is to do with the "ynorm": -2.0 linked above, as the y position looks like it is wrongly multiplied by -2?

[pgleeson]

This seems to be the source of the error...

NetPyNE-UI/netpyne_ui/netpyne_model_interpreter.py

Lines 100 to 102 in eb3b3a3

	x=float(cell['tags']['x'] * netpyne_model.net.params.cellsVisualizationSpacingMultiplier[0]),
	y=-float(cell['tags']['y'] * netpyne_model.net.params.cellsVisualizationSpacingMultiplier[1]),
	z=float(cell['tags']['z'] * netpyne_model.net.params.cellsVisualizationSpacingMultiplier[2])

The y value is being multiplied by -1, but not x or z... I can't think of any reason why you would explicitly state in the cellList that you want x=10, y=20, z=30 and then use (10,-20,30)... If the y axis should be pointing down for positive y, then why are all the cells displayed correctly with increasing y values on segments pointing up???

[pgleeson]

Seems to have fixed it with OpenSourceBrain@f279c51...