fix inits & add todos to dopa

examples/dopa-sweep.py

@@ -13,17 +13,27 @@
     )
 
 # initial conditions
-y0 = jp.array([0., -2.0, 0.0, 0.0, 0.0, 0.0])
+y0 = jp.array([0.1, -60.0, 0.0, 0.0, 0.0, 0.0])
 
 # run sweep
 end_time = 256.0
 pkeys, ys = sweep_node(y0, params, T=end_time, cores=4)
 
+# for large sweeps, ys may not yet be filled with outputs
+ys.block_until_ready()
+
 # pkeys provides the names for the extra dims of ys result
 print(pkeys, ys.shape)
 
 # now similar for network sweep
 n_nodes = 8
-Ci, Ce, Cd = jp.zeros((3, n_nodes))
+Ci, Ce, Cd = vb.randn(3, n_nodes, n_nodes)
 pkeys, ys = sweep_network(y0, params, Ci, Ce, Cd, T=end_time, cores=4)
+ys.block_until_ready()
 print(pkeys, ys.shape)
+
+# plot some of it
+import matplotlib.pyplot as pl
+
+pl.plot(ys[0,0,:,0], 'k')
+pl.show()

vbjax/app/dopa/sweep.py

@@ -5,6 +5,19 @@
 import vbjax as vb
 
 
+# TODO can't continue simulations b/c init doesn't vmap w/ params
+# TODO need to run long time tavg and bold
+# TODO allow predefined set of params for e.g. random sample
+# TODO regional parameters?
+# TODO abstract over simulation configuration e.g. noise
+# TODO ISPC impl for benchmark comparison
+# TODO use delays if available
+# TODO implement memory limits & test them
+# TODO memmap raw/tavg/bold direct to file
+# TODO automate inner vs outer loop over parameters
+
+
+
 def sweep_node(init, params, T=10.0, dt=0.01, sigma=1e-3, seed=42, cores=4):
     "Run sweep for single dopa node on params matrix"