current clamp + MembraneReport

[latimerb]

updated current clamp module to accept gids (small bug in previous commit) and updated MembraneReport class to accept gids so that the user can record the membrane potential of a handful of cells instead of all of them

[pgleeson]

@kaeldai I believe some of these change are required to get the Sonata examples working again with BMTK.

@latimerb have you tested these changes with all of the examples here, as well as the Sonata example networks, e.g. https://github.com/AllenInstitute/sonata/tree/master/examples/5_cells_iclamp?

[latimerb]

@pgleeson I tested with the Jupyter notebook tutorials but not with the Sonata examples. I'm not familiar with Sonata but I will give it a try and let you know if it works.

[latimerb]

@pgleeson @kaeldai OK, I tested it with the Sonata examples and made a small tweak. Now users can specify the node_set to be stimulated, as they do in the Sonata examples. Alternatively, users may specify specific gids to be stimulated.

In order to plot the output of the 5_cells_iclamp Sonata example, this change needs to be made:
AllenInstitute/sonata#116

The example runs without the change, it is only for visualizing the output. I also double-checked the BMTK examples, they also work with this change.

[pgleeson]

Thanks @latimerb. I think a similar update is required in https://github.com/AllenInstitute/bmtk/blob/develop/bmtk/simulator/pointnet/pointsimulator.py#L145, as the example at https://github.com/AllenInstitute/bmtk/tree/develop/docs/examples/point_iclamp is broken.

This should fix the issues with the other Sonata simulation test examples e.g. https://github.com/AllenInstitute/sonata/tree/master/examples/sim_tests/intfire/ten_cells_iclamp_nest

There are also some changes here: AllenInstitute/sonata@b94c27b for Sonata examples. I'll open a PR with these @kaeldai when they all work locally.

Note this script can be used to test most of the sonata examples: https://github.com/AllenInstitute/sonata/blob/master/examples/test.sh