// dend_shaft_bAP_inhib.hoc
// study inhibition in the dendrite as a function of bAP height
// by reducing the Na and K channels so that the bAP height declines
// in successive pairs (of ctrl and 1xinhib in the dend) simulations.
// This study was an attempt to see if the idea that dendritic shaft
// inhibition as observed experimentally might appear in the model
// if the height of the bAP was reduced at those places (compartments)
// in the dendrite where the inhibition is being observed.

// run first with spines near 100 um from soma, then run again further
// out if bAPs are not fully extinguished by passive spread

// use powers of two: 1, 1/2, 1/4, 1/8, 1/16 Na K conductance densities (gs)
// Let these be part of the folder names
// NaKgs/1/1/ NaKgs/1/2/ NaKgs/1/4/ NaKgs/1/8/ NaKgs/1/16/
// each of which has subfolders, e.g.
// NaKgs/1/16/ctrl/ NaKgs/1/16/dend1xinhib/
// the last subfolder of which is called ctrl_or_inhib below

// In each NaKgs/numerator/denominator/ctrl_or_inhib store:
// bAP_peak_profile.txt, spine0_cai_vec.txt, spine1_cai_vec.txt,
// spine2_cai_vec.txt, dend_cai_vec.txt spine0_v_vec.txt,
// spine1_v_vec.txt, spine2_v_vec.txt, dend_v_vec.txt
//
// and then in the top level NaK_gs/ store
// statistics_table.txt which contains a copy of the below printed
// table (on oc> prompt as simulation runs) that looks like this
//
// Na K g's: 1/(denominator)
// compartment V_peak_ctrl V_peak_inhib Ca_peak Ca_baseline dCa_ctrl dCa_inhib dCa_ratio
// spine0 (A B C D E F)
// spine1 (A B C D E F)
// spine2 (A B C D E F)
// dend (A B C D E F)
//
// Where items in parenthesis represent printed numbers.
// Note param3.hoc had nearly the dCa methods I want to use.
// however they were too oriented towards param3.hoc - so take them to
// create a new file hoc/dend_shaft_bAP_functions.hoc that has the
// modified declaration and functions from param3.hoc for use here.
//
// I need to find out if I can find and store the max cai in each
// compartment similarly to how vmax_ds efficiently finds the max
// voltage in each compartment otherwise I have to do it in hoc (slower).

load_file("hoc/dend_shaft_bAP_functions.hoc")

// store original conductances in vectors
objref gbar_na_vec, gbar_kv_vec
gbar_na_vec = new Vector()
gbar_kv_vec = new Vector()

// Actually only change the dendrites Na K max conductances.  Store default:
dendrite {
  gbar_na_vec.append(gbar_na)
  gbar_kv_vec.append(gbar_kv)
}

for i=0,4 { // loop over the powers of two from 2^0 = 1 to 2^4 = 16
  denominator = 2^i
  // set the Na K densities to orig or successive power of two fractions
  vec_index=0
  dendrite {
    gbar_na = gbar_na_vec.c.div(denominator).x[vec_index]
    gbar_kv = gbar_kv_vec.c.div(denominator).x[vec_index]
    vec_index += 1
  }

  // for each calculate the control (no inhibition) and dendrite inhibited

  bAP_without_with_dendinhib()

}