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synca_plot.go
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synca_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.
// synca_plot plots kinase SynCa update equations
package main
//go:generate core generate -add-types
import (
"math"
"strconv"
"cogentcore.org/core/core"
"cogentcore.org/core/icons"
"cogentcore.org/core/plot/plotview"
"cogentcore.org/core/tensor/table"
_ "cogentcore.org/core/tensor/tensorview" // include to get gui views
_ "cogentcore.org/core/vgpu/gosl/slboolview" // ditto
"cogentcore.org/core/views"
"github.com/emer/axon/v2/kinase"
)
func main() {
sim := &Sim{}
sim.Config()
sim.Run()
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 {
// Ca time constants
CaDt kinase.CaParams `view:"inline"`
Minit float64
Pinit float64
Dinit float64
// adjustment to dt to account for discrete time updating
MdtAdj float64 `default:"0,0.11"`
// adjustment to dt to account for discrete time updating
PdtAdj float64 `default:"0.0.03"`
// adjustment to dt to account for discrete time updating
DdtAdj float64 `default:"0.0.03"`
// number of time steps
TimeSteps int
// table for plot
Table *table.Table `view:"no-inline"`
// the plot
Plot *plotview.PlotView `view:"-"`
// table for plot
TimeTable *table.Table `view:"no-inline"`
// the plot
TimePlot *plotview.PlotView `view:"-"`
}
// Config configures all the elements using the standard functions
func (ss *Sim) Config() {
ss.CaDt.Defaults()
ss.Minit = 0.7
ss.Pinit = 0.5
ss.Dinit = 0.3
ss.MdtAdj = 0
ss.PdtAdj = 0
ss.DdtAdj = 0
ss.TimeSteps = 1000
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() {
}
// Run runs the equation.
func (ss *Sim) Run() { //types:add
ss.Update()
dt := ss.Table
dt.SetNumRows(200)
mi := ss.Minit
pi := ss.Pinit
di := ss.Dinit
mdt := float64(ss.CaDt.Dt.MDt) * (1.0 + ss.MdtAdj)
pdt := float64(ss.CaDt.Dt.PDt) * (1.0 + ss.PdtAdj)
ddt := float64(ss.CaDt.Dt.DDt) * (1.0 + ss.DdtAdj)
for ti := 0; ti < 200; ti++ {
t := float64(ti)
m := ss.Minit * math.Exp(-t*mdt)
em := math.Exp(t * mdt)
ep := math.Exp(t * pdt)
p := ss.Pinit*math.Exp(-t*pdt) - (pdt*ss.Minit*math.Exp(-t*(mdt+pdt))*(em-ep))/(pdt-mdt)
epd := math.Exp(t * (pdt + ddt))
emd := math.Exp(t * (mdt + ddt))
emp := math.Exp(t * (mdt + pdt))
d := pdt*ddt*ss.Minit*math.Exp(-t*(mdt+pdt+ddt))*(ddt*(emd-epd)+(pdt*(epd-emp))+mdt*(emp-emd))/((mdt-pdt)*(mdt-ddt)*(pdt-ddt)) - ddt*ss.Pinit*math.Exp(-t*(pdt+ddt))*(ep-math.Exp(t*ddt))/(ddt-pdt) + ss.Dinit*math.Exp(-t*ddt)
// test eqs:
caM := float32(ss.Minit)
caP := float32(ss.Pinit)
caD := float32(ss.Dinit)
ss.CaDt.Dt.CaAtT(int32(ti), &caM, &caP, &caD)
m = float64(caM)
p = float64(caP)
d = float64(caD)
caM = float32(ss.Minit)
caP = float32(ss.Pinit)
caD = float32(ss.Dinit)
ss.CaDt.CurCa(float32(ti), 0, &caM, &caP, &caD)
mi4 := float64(caM)
pi4 := float64(caP)
di4 := float64(caD)
dt.SetFloat("t", ti, t)
dt.SetFloat("mi", ti, mi)
dt.SetFloat("pi", ti, pi)
dt.SetFloat("di", ti, di)
dt.SetFloat("mi4", ti, mi4)
dt.SetFloat("pi4", ti, pi4)
dt.SetFloat("di4", ti, di4)
dt.SetFloat("m", ti, m)
dt.SetFloat("p", ti, p)
dt.SetFloat("d", ti, d)
mi += float64(ss.CaDt.Dt.MDt) * (0 - mi)
pi += float64(ss.CaDt.Dt.PDt) * (mi - pi)
di += float64(ss.CaDt.Dt.DDt) * (pi - di)
}
if ss.Plot != nil {
ss.Plot.UpdatePlot()
}
}
func (ss *Sim) ConfigTable(dt *table.Table) {
dt.SetMetaData("name", "SynCa(t)")
dt.SetMetaData("read-only", "true")
dt.SetMetaData("precision", strconv.Itoa(LogPrec))
dt.AddFloat64Column("t")
dt.AddFloat64Column("mi")
dt.AddFloat64Column("pi")
dt.AddFloat64Column("di")
dt.AddFloat64Column("mi4")
dt.AddFloat64Column("pi4")
dt.AddFloat64Column("di4")
dt.AddFloat64Column("m")
dt.AddFloat64Column("p")
dt.AddFloat64Column("d")
dt.SetNumRows(0)
}
func (ss *Sim) ConfigPlot(plt *plotview.PlotView, dt *table.Table) *plotview.PlotView {
plt.Params.Title = "SynCa Exp Decay Plot"
plt.Params.XAxisColumn = "t"
plt.SetTable(dt)
// order of params: on, fixMin, min, fixMax, max
plt.SetColParams("t", plotview.Off, plotview.FloatMin, 0, plotview.FloatMax, 0)
plt.SetColParams("mi", plotview.On, plotview.FixMin, 0, plotview.FloatMax, 0)
plt.SetColParams("pi", plotview.On, plotview.FixMin, 0, plotview.FloatMax, 0)
plt.SetColParams("di", plotview.On, plotview.FixMin, 0, plotview.FloatMax, 0)
plt.SetColParams("mi4", plotview.On, plotview.FixMin, 0, plotview.FloatMax, 0)
plt.SetColParams("pi4", plotview.On, plotview.FixMin, 0, plotview.FloatMax, 0)
plt.SetColParams("di4", plotview.On, plotview.FixMin, 0, plotview.FloatMax, 0)
plt.SetColParams("m", plotview.On, plotview.FixMin, 0, plotview.FloatMax, 0)
plt.SetColParams("p", plotview.On, plotview.FixMin, 0, plotview.FloatMax, 0)
plt.SetColParams("d", plotview.On, plotview.FixMin, 0, plotview.FloatMax, 0)
return plt
}
/////////////////////////////////////////////////////////////////
// TimeRun runs the equation over time.
func (ss *Sim) TimeRun() { //types:add
ss.Update()
/*
dt := ss.TimeTable
v := ss.TimeV
g := 0.0
synca := 0.0
dt.SetNumRows(ss.TimeSteps)
for ti := 0; ti < ss.TimeSteps; ti++ {
t := float64(ti) * .001
gin := ss.TimeGin
if ti < 10 || ti > ss.TimeSteps/2 {
gin = 0
}
synca += gin*(1-synca) - (synca / ss.Tau)
g = synca / (1 + math.Exp(-ss.SYNCav*v)/ss.SYNCad)
dt.SetFloat("Time", ti, t)
dt.SetFloat("Gsynca", ti, g)
dt.SetFloat("SYNCa", ti, synca)
}
ss.TimePlot.Update()
*/
}
func (ss *Sim) ConfigTimeTable(dt *table.Table) {
dt.SetMetaData("name", "SyNcaplotTable")
dt.SetMetaData("read-only", "true")
dt.SetMetaData("precision", strconv.Itoa(LogPrec))
dt.AddFloat64Column("Time")
dt.AddFloat64Column("Gsynca")
dt.AddFloat64Column("SYNCa")
dt.SetNumRows(0)
}
func (ss *Sim) ConfigTimePlot(plt *plotview.PlotView, dt *table.Table) *plotview.PlotView {
plt.Params.Title = "Time Function Plot"
plt.Params.XAxisColumn = "Time"
plt.SetTable(dt)
// order of params: on, fixMin, min, fixMax, max
plt.SetColParams("Time", plotview.Off, plotview.FloatMin, 0, plotview.FloatMax, 0)
plt.SetColParams("Gsynca", plotview.On, plotview.FixMin, 0, plotview.FloatMax, 0)
plt.SetColParams("SYNCa", plotview.On, plotview.FixMin, 0, plotview.FloatMax, 0)
return plt
}
// ConfigGUI configures the Cogent Core GUI interface for this simulation.
func (ss *Sim) ConfigGUI() *core.Body {
b := core.NewBody("Synca Plot")
split := core.NewSplits(b, "split")
sv := views.NewStructView(split, "sv")
sv.SetStruct(ss)
tv := core.NewTabs(split, "tv")
ss.Plot = plotview.NewSubPlot(tv.NewTab("T Exp Plot"))
ss.ConfigPlot(ss.Plot, ss.Table)
ss.TimePlot = plotview.NewSubPlot(tv.NewTab("TimePlot"))
ss.ConfigTimePlot(ss.TimePlot, ss.TimeTable)
split.SetSplits(.3, .7)
b.AddAppBar(func(tb *core.Toolbar) {
views.NewFuncButton(tb, ss.Run).SetIcon(icons.PlayArrow)
views.NewFuncButton(tb, ss.TimeRun).SetIcon(icons.PlayArrow)
})
return b
}