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skca_plot.go
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skca_plot.go
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// Copyright (c) 2020, The Emergent Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
// ska_plot plots an equation updating over time in a table.Table and PlotView.
package main
//go:generate core generate -add-types
import (
"strconv"
"cogentcore.org/core/core"
"cogentcore.org/core/icons"
"cogentcore.org/core/plot/plotcore"
"cogentcore.org/core/tensor/table"
"cogentcore.org/core/tree"
"github.com/emer/axon/v2/chans"
"github.com/emer/axon/v2/kinase"
)
func main() {
sim := &Sim{}
sim.Config()
sim.CamRun()
b := sim.ConfigGUI()
b.RunMainWindow()
}
// LogPrec is precision for saving float values in logs
const LogPrec = 4
// Sim holds the params, table, etc
type Sim struct {
// SKCa params
SKCa chans.SKCaParams
// time constants for integrating Ca from spiking across M, P and D cascading levels
CaParams kinase.NeurCaParams
// threshold of SK M gating factor above which the neuron cannot spike
NoSpikeThr float32 `default:"0.5"`
// Ca conc increment for M gating func plot
CaStep float32 `default:"0.05"`
// number of time steps
TimeSteps int
// do spiking instead of Ca conc ramp
TimeSpike bool
// spiking frequency
SpikeFreq float32
// table for plot
Table *table.Table `display:"no-inline"`
// the plot
Plot *plotcore.PlotEditor `display:"-"`
// table for plot
TimeTable *table.Table `display:"no-inline"`
// the plot
TimePlot *plotcore.PlotEditor `display:"-"`
}
// Config configures all the elements using the standard functions
func (ss *Sim) Config() {
ss.SKCa.Defaults()
ss.SKCa.Gbar = 1
ss.CaParams.Defaults()
ss.CaStep = .05
ss.TimeSteps = 200 * 3
ss.TimeSpike = true
ss.NoSpikeThr = 0.5
ss.SpikeFreq = 100
ss.Update()
ss.Table = &table.Table{}
ss.ConfigTable(ss.Table)
ss.TimeTable = &table.Table{}
ss.ConfigTimeTable(ss.TimeTable)
}
// Update updates computed values
func (ss *Sim) Update() {
}
// CamRun plots the equation as a function of Ca
func (ss *Sim) CamRun() { //types:add
ss.Update()
dt := ss.Table
nv := int(1.0 / ss.CaStep)
dt.SetNumRows(nv)
for vi := 0; vi < nv; vi++ {
cai := float32(vi) * ss.CaStep
mh := ss.SKCa.MAsympHill(cai)
mg := ss.SKCa.MAsympGW06(cai)
dt.SetFloat("Ca", vi, float64(cai))
dt.SetFloat("Mhill", vi, float64(mh))
dt.SetFloat("Mgw06", vi, float64(mg))
}
if ss.Plot != nil {
ss.Plot.UpdatePlot()
}
}
func (ss *Sim) ConfigTable(dt *table.Table) {
dt.SetMetaData("name", "SKCaPlotTable")
dt.SetMetaData("read-only", "true")
dt.SetMetaData("precision", strconv.Itoa(LogPrec))
dt.AddFloat64Column("Ca")
dt.AddFloat64Column("Mhill")
dt.AddFloat64Column("Mgw06")
dt.SetNumRows(0)
}
func (ss *Sim) ConfigPlot(plt *plotcore.PlotEditor, dt *table.Table) *plotcore.PlotEditor {
plt.Options.Title = "SKCa Ca-G Function Plot"
plt.Options.XAxis = "Ca"
plt.SetTable(dt)
// order of params: on, fixMin, min, fixMax, max
plt.SetColumnOptions("Ca", plotcore.Off, plotcore.FloatMin, 0, plotcore.FloatMax, 0)
plt.SetColumnOptions("Mhill", plotcore.On, plotcore.FixMin, 0, plotcore.FixMax, 1)
plt.SetColumnOptions("Mgw06", plotcore.Off, plotcore.FixMin, 0, plotcore.FloatMax, 1)
return plt
}
/////////////////////////////////////////////////////////////////
// TimeRun runs the equation over time.
func (ss *Sim) TimeRun() { //types:add
ss.Update()
dt := ss.TimeTable
caIn := float32(1)
caR := float32(0)
m := float32(0)
spike := float32(0)
msdt := float32(0.001)
caM := float32(0)
caP := float32(0)
caD := float32(0)
isi := int(1000 / ss.SpikeFreq)
trial := 0
dt.SetNumRows(ss.TimeSteps)
for ti := 0; ti < ss.TimeSteps; ti++ {
trial = ti / 200
t := float32(ti) * msdt
m = ss.SKCa.MFromCa(caR, m)
ss.SKCa.CaInRFromSpike(spike, caD, &caIn, &caR)
dt.SetFloat("Time", ti, float64(t))
dt.SetFloat("Spike", ti, float64(spike))
dt.SetFloat("CaM", ti, float64(caM))
dt.SetFloat("CaP", ti, float64(caP))
dt.SetFloat("CaD", ti, float64(caD))
dt.SetFloat("CaIn", ti, float64(caIn))
dt.SetFloat("CaR", ti, float64(caR))
dt.SetFloat("M", ti, float64(m))
if m < ss.NoSpikeThr && trial%2 == 0 && ti%isi == 0 { // spike on even trials
spike = 1
} else {
spike = 0
}
// todo: update
// ss.CaParams.FromSpike(spike, &caM, &caP, &caD)
}
if ss.TimePlot != nil {
ss.TimePlot.UpdatePlot()
}
}
func (ss *Sim) ConfigTimeTable(dt *table.Table) {
dt.SetMetaData("name", "CagCcplotTable")
dt.SetMetaData("read-only", "true")
dt.SetMetaData("precision", strconv.Itoa(LogPrec))
dt.AddFloat64Column("Time")
dt.AddFloat64Column("Spike")
dt.AddFloat64Column("CaM")
dt.AddFloat64Column("CaP")
dt.AddFloat64Column("CaD")
dt.AddFloat64Column("CaIn")
dt.AddFloat64Column("CaR")
dt.AddFloat64Column("M")
dt.SetNumRows(0)
}
func (ss *Sim) ConfigTimePlot(plt *plotcore.PlotEditor, dt *table.Table) *plotcore.PlotEditor {
plt.Options.Title = "Time Function Plot"
plt.Options.XAxis = "Time"
plt.SetTable(dt)
// order of params: on, fixMin, min, fixMax, max
plt.SetColumnOptions("Time", plotcore.Off, plotcore.FloatMin, 0, plotcore.FloatMax, 0)
plt.SetColumnOptions("Spike", plotcore.On, plotcore.FixMin, 0, plotcore.FixMax, 1)
plt.SetColumnOptions("CaM", plotcore.Off, plotcore.FixMin, 0, plotcore.FixMax, 1)
plt.SetColumnOptions("CaP", plotcore.On, plotcore.FixMin, 0, plotcore.FixMax, 1)
plt.SetColumnOptions("CaD", plotcore.Off, plotcore.FixMin, 0, plotcore.FixMax, 1)
plt.SetColumnOptions("CaIn", plotcore.On, plotcore.FixMin, 0, plotcore.FixMax, 1)
plt.SetColumnOptions("CaR", plotcore.On, plotcore.FixMin, 0, plotcore.FixMax, 1)
plt.SetColumnOptions("M", plotcore.On, plotcore.FixMin, 0, plotcore.FixMax, 1)
return plt
}
// ConfigGUI configures the Cogent Core GUI interface for this simulation.
func (ss *Sim) ConfigGUI() *core.Body {
b := core.NewBody("Skca Plot")
split := core.NewSplits(b)
core.NewForm(split).SetStruct(ss)
tv := core.NewTabs(split)
cgp, _ := tv.NewTab("Ca-G Plot")
ss.Plot = plotcore.NewSubPlot(cgp)
ss.ConfigPlot(ss.Plot, ss.Table)
ttp, _ := tv.NewTab("TimePlot")
ss.TimePlot = plotcore.NewSubPlot(ttp)
ss.ConfigTimePlot(ss.TimePlot, ss.TimeTable)
split.SetSplits(.3, .7)
b.AddTopBar(func(bar *core.Frame) {
core.NewToolbar(bar).Maker(func(p *tree.Plan) {
tree.Add(p, func(w *core.FuncButton) {
w.SetFunc(ss.CamRun).SetIcon(icons.PlayArrow)
})
tree.Add(p, func(w *core.FuncButton) {
w.SetFunc(ss.TimeRun).SetIcon(icons.PlayArrow)
})
})
})
return b
}