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NM_ModelTab0.ipf
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NM_ModelTab0.ipf
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#pragma rtGlobals=3 // Use modern global access method and strict wave access.
#pragma hide = 1
//****************************************************************
//****************************************************************
//
// NeuroMatic: data aquisition, analyses and simulation software that runs with the Igor Pro environment
// Copyright (C) 2024 The Silver Lab, UCL
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <https://www.gnu.org/licenses/>.
//
// Contact Jason@ThinkRandom.com
// www.NeuroMatic.ThinkRandom.com
//
//****************************************************************
//****************************************************************
//
// Model Tab Functions
//
// Set and Get functions:
//
// NMModelSet( [ modelSelect, clampSelect, history ] )
// NMModelVarSet( varName, value [ history ] )
// NMModelStrSet( strVarName, strValue [ history ] )
// NMModelVarGet( varName )
// NMModelStrGet( strVarName )
//
// Useful functions:
//
// NMModelRun( [ history ] )
// NMModelEdit( [ history ] )
// NMModelKineticWavesAll( [ plotWaves, history ] )
// NMModelProcedureCode( [ history ] )
//
//****************************************************************
//****************************************************************
StrConstant NMModelDF = "root:Packages:NeuroMatic:Model:"
Static StrConstant GnmdaBlockFxnList = "Boltzmann;GC_Rothman2009;GC_Schwartz2012;"
Static Constant GnmdaBlockVhalf = -12.8
Static Constant GnmdaBlockVslope = 22.4
Static Constant printIntegrateODE = 0 // print IntegrateODE command to history ( 0 ) no ( 1 ) yes
Static StrConstant IonChannelList = "TonicGABA;Leak;Na;NaR;NaP;K;KA;KD;KCa;Kir;Kslow;H;Ca;"
Static StrConstant iClampParList = "iClampAmp;iClampAmpInc;iClampOnset;iClampDuration;"
Static StrConstant vClampParList = "vClampAmp;vClampAmpInc;vClampOnset;vClampDuration;"
//****************************************************************
//****************************************************************
//****************************************************************
Function /S NMTabPrefix_Model()
return "MD_"
End // NMTabPrefix_Model
//****************************************************************
//****************************************************************
//****************************************************************
Function /S NMModelDF() // data folder where tab globals are stored
String pdf = NMModelSubDF()
if ( DataFolderExists( pdf ) )
return pdf
endif
return NMModelDF
End // NMModelDF
//****************************************************************
//****************************************************************
//****************************************************************
Function /S NMModelSubDF()
String currentFolder = CurrentNMFolder( 1 )
String subFolder
if ( strlen( currentFolder ) == 0 )
return ""
endif
subfolder = "Model"
//subfolder = "Model_" + StrVarOrDefault( "ModelSelect" )
return currentFolder + subfolder + ":" // subfolder in current data folder
End // NMModelSubDF
//****************************************************************
//****************************************************************
//****************************************************************
Function ModelTab( enable ) // activate or inactivate the tab
Variable enable
if ( enable )
CheckNMPackage( "Model" , 1 ) // declare globals if necessary
NMModelTabMake( 0 )
endif
End // ModelTab
//****************************************************************
//****************************************************************
//****************************************************************
Function NMModelCheck() // create global variables for tab display
Variable icnt, initModel
String aList, cName
String df = NMModelDF()
if ( exists( df + "ModelSelect" ) == 0 )
initModel = 1
endif
CheckNMvar( NMModelDF + "OverwriteMode", 1 )
CheckNMvar( NMModelDF + "IntegrateODEMethod", 1 )
zCheckStrList( "ModelSelect;CellName;ClampSelect;WavePrefix;" )
zCheckVarList( "FirstSimulation;LastSimulation;NumSimulations;SimulationCounter;" )
zCheckVarList( "SimulationTime;TimeStep;NumTimeSteps;" )
zCheckVarList( "Temperature;gQ10;tauQ10;CaInside;CaOutside;V0;" )
zCheckVarList( "Diameter;SurfaceArea;CmDensity;Cm;" )
zCheckVarList( iClampParList )
zCheckVarList( vClampParList )
zCheckStrList( "gGABA_WavePrefix;gAMPA_WavePrefix;gNMDA_WavePrefix;gNMDA_BlockFxnList;" )
zCheckVarList( "gGABA_NumWaves;gAMPA_NumWaves;gNMDA_NumWaves;" )
zCheckVarList( "eGABA;eAMPA;eNMDA;" )
zCheckVarList( "AP_Threshold;AP_Peak;AP_Reset;AP_Refrac;" )
zCheckVarList( "AP_ThreshSlope;W_Tau;W_A;W_B;" )
for ( icnt = 0 ; icnt < ItemsInList( IonChannelList ) ; icnt += 1 )
cName = StringFromList( icnt, IonChannelList )
aList = AddListItem( "g" + cName + "Density", "", ";", inf )
aList = AddListItem( "g" + cName, aList, ";", inf )
aList = AddListItem( "e" + cName, aList, ";", inf )
zCheckVarList( aList )
endfor
if ( initModel )
NMModelSelect( NMModelStrGet( "ModelSelect" ) )
else
NMModelVariablesInit()
endif
End // NMModelCheck
//****************************************************************
//****************************************************************
//****************************************************************
Static Function zCheckVarList( varNameList )
String varNameList
Variable icnt
String varName, df = NMModelDF()
for ( icnt = 0 ; icnt < ItemsInList( varNameList ) ; icnt += 1 )
varName = StringFromList( icnt, varNameList )
CheckNMvar( df + varName, NMModelVarGet( varName ) )
endfor
End // zCheckVarList
//****************************************************************
//****************************************************************
//****************************************************************
Static Function zCheckStrList( strVarNameList )
String strVarNameList
Variable icnt
String strVarName, df = NMModelDF()
for ( icnt = 0 ; icnt < ItemsInList( strVarNameList ) ; icnt += 1 )
strVarName = StringFromList( icnt, strVarNameList )
CheckNMstr( df+strVarName, NMModelStrGet( strVarName ) )
endfor
End // zCheckStrList
//****************************************************************
//****************************************************************
//****************************************************************
Function NMModelConfigs()
NMConfigVar( "Model", "OverwriteMode", 1, "overwrite existing waves, tables and graphs if their is a name conflict", "boolean" )
NMConfigVar( "Model", "IntegrateODEMethod", 0, "see IntegrateODE Method flag, 0, 1, 2, 3", "" )
End // NMModelConfigs
//****************************************************************
//****************************************************************
//****************************************************************
//
// Model Variable / String functions
//
//****************************************************************
//****************************************************************
//****************************************************************
Function NMModelSet( [ modelSelect, clampSelect, history ] )
String modelSelect
String clampSelect
Variable history // print function command to history ( 0 ) no ( 1 ) yes
String vlist = ""
if ( !ParamIsDefault( modelSelect ) )
vlist = NMCmdStrOptional( "modelSelect", modelSelect, vlist )
NMModelSelect( modelSelect )
endif
if ( !ParamIsDefault( clampSelect ) )
vlist = NMCmdStrOptional( "clampSelect", clampSelect, vlist )
NMModelClampSelect( clampSelect )
endif
if ( history )
NMCommandHistory( vlist )
endif
End // NMModelSet
//****************************************************************
//****************************************************************
//****************************************************************
Function NMModelVarGet( varName )
String varName
String sdf = NMModelDF()
String thisfxn = GetRTStackInfo( 1 )
Variable defaultVal = NaN
strswitch( varName )
case "OverwriteMode":
defaultVal = 1
sdf = NMModelDF
break
case "IntegrateODEMethod":
defaultVal = 0
sdf = NMModelDF
break
case "FirstSimulation":
defaultVal = 0
break
case "LastSimulation":
defaultVal = 0
break
case "NumSimulations":
defaultVal = 1
break
case "SimulationCounter":
defaultVal = 0
break
case "SimulationTime":
defaultVal = 50 // ms
break
case "TimeStep":
defaultVal = 0.02 // ms
break
case "NumTimeSteps":
defaultVal = 100 / 0.01
break
case "Temperature":
defaultVal = 37 // C
break
case "gQ10":
defaultVal = 2
break
case "tauQ10":
defaultVal = 3
break
case "CaInside":
defaultVal = 30e-6 // mM
break
case "CaOutside":
defaultVal = 2 // mM
break
case "V0":
defaultVal = -65 // mV
break
case "Diameter":
defaultVal = 20 // um
break
case "SurfaceArea":
defaultVal = NaN
break
case "CmDensity":
defaultVal = 1e-2 // pF / um^2
break
case "Cm":
defaultVal = NaN
break
case "iClampAmp":
defaultVal = 0 // pA
break
case "iClampAmpInc":
defaultVal = 0 // pA
break
case "iClampOnset":
defaultVal = 10 // ms
break
case "iClampDuration":
defaultVal = 100 // ms
break
case "vClampAmp":
defaultVal = 0 // mV
break
case "vClampAmpInc":
defaultVal = 0 // mV
break
case "vClampOnset":
defaultVal = 20 // ms
break
case "vClampDuration":
defaultVal = 100 // ms
break
case "gLeakDensity":
defaultVal = 0
break
case "gLeak":
defaultVal = NaN
break
case "eLeak":
defaultVal = NaN
break
case "gNaDensity":
defaultVal = 0
break
case "gNa":
defaultVal = NaN
break
case "eNa":
defaultVal = NaN
break
case "gNaRDensity":
defaultVal = 0
break
case "gNaR":
defaultVal = NaN
break
case "eNaR":
defaultVal = NaN
break
case "gNaPDensity":
defaultVal = 0
break
case "gNaP":
defaultVal = NaN
break
case "eNaP":
defaultVal = NaN
break
case "gKDensity":
defaultVal = 0
break
case "gK":
defaultVal = NaN
break
case "eK":
defaultVal = NaN
break
case "gKADensity":
defaultVal = 0
break
case "gKA":
defaultVal = NaN
break
case "eKA":
defaultVal = NaN
break
case "gKDDensity":
defaultVal = 0
break
case "gKD":
defaultVal = NaN
break
case "eKD":
defaultVal = NaN
break
case "gKslowDensity":
defaultVal = 0
break
case "gKslow":
defaultVal = NaN
break
case "eKslow":
defaultVal = NaN
break
case "gKCaDensity":
defaultVal = 0
break
case "gKCa":
defaultVal = NaN
break
case "eKCa":
defaultVal = NaN
break
case "gKirDensity":
defaultVal = 0
break
case "gKir":
defaultVal = NaN
break
case "eKir":
defaultVal = NaN
break
case "gHDensity":
defaultVal = 0
break
case "gH":
defaultVal = NaN
break
case "eH":
defaultVal = NaN
break
case "gCaDensity":
defaultVal = 0
break
case "gCa":
defaultVal = NaN
break
case "eCa":
defaultVal = NaN
break
case "gTonicGABADensity":
defaultVal = 0
break
case "gTonicGABA":
defaultVal = NaN
break
case "gGABA_NumWaves":
defaultVal = 0
break
case "eGABA":
case "eTonicGABA":
defaultVal = -75 // mV
break
case "gAMPA_NumWaves":
defaultVal = 0
break
case "eAMPA":
defaultVal = 0
break
case "gNMDA_NumWaves":
defaultVal = 0
break
case "eNMDA":
defaultVal = 0
break
case "AP_Threshold":
defaultVal = -40
break
case "AP_Peak":
defaultVal = -40 + 72
break
case "AP_Reset":
defaultVal = -40 + -21
break
case "AP_Refrac":
defaultVal = 0.9
break
case "AP_ThreshSlope":
defaultVal = 2
break
case "W_Tau":
defaultVal = 300
break
case "W_A":
defaultVal = 2
break
case "W_B":
defaultVal = 60
break
case "gLeak_gRest":
defaultVal = 0.462
break
case "gLeak_gDepo":
defaultVal = 1
break
case "gLeak_vHalf":
defaultVal = -43
break
case "gLeak_vSlope":
defaultVal = 2.2
break
default:
NMDoAlert( thisfxn + " error: no such variable: " + NMQuotes( varName ) )
return NaN
endswitch
if ( !DataFolderExists( sdf ) )
return defaultVal
endif
return NumVarOrDefault( sdf+varName, defaultVal )
End // NMModelVarGet
//****************************************************************
//****************************************************************
//****************************************************************
Function /S NMModelStrGet( strVarName )
String strVarName
String sdf = NMModelDF()
String thisfxn = GetRTStackInfo( 1 )
String defaultStr = ""
strswitch( strVarName )
case "ModelSelect":
defaultStr = "HodgkinHuxley"
break
case "ClampSelect":
defaultStr = "Iclamp"
break
case "CellName":
defaultStr = "Model"
break
case "WavePrefix":
defaultStr = "Sim_"
break
case "gGABA_WavePrefix":
defaultStr = "gGABA_"
break
case "gAMPA_WavePrefix":
defaultStr = "gAMPA_"
break
case "gNMDA_WavePrefix":
defaultStr = "gNMDA_"
break
case "gNMDA_BlockFxnList":
defaultStr = "Boltzmann;Vhalf=" + num2str( GnmdaBlockVhalf ) + ";Vslope=" + num2str( GnmdaBlockVslope ) + ";"
break
default:
NMDoAlert( thisfxn + "error: cannot find string variable " + NMQuotes( strVarName ) )
return ""
endswitch
if ( !DataFolderExists( sdf ) )
return defaultStr
endif
return StrVarOrDefault( sdf + strVarName, defaultStr )
End // NMModelStrGet
//****************************************************************
//****************************************************************
//****************************************************************
Function /S NMModelStr2( modelName, strVarName )
String modelName
String strVarName
String tempStr, df = NMModelDF()
String thisfxn = GetRTStackInfo( 1 )
String /G MD_StrVarTemp
String fxn = "NMModelStr_" + modelName
if ( exists( fxn ) != 6 )
NMDoAlert( thisfxn + " error: cannot find function " + NMQuotes( fxn ) )
return ""
endif
Execute "MD_StrVarTemp = " + fxn + "(" + NMQuotes( strVarName ) + ")"
tempStr = MD_StrVarTemp
KillStrings /Z MD_StrVarTemp
return tempStr
End // NMModelStr2
//****************************************************************
//****************************************************************
//****************************************************************
Function /S NMModelList()
String funcList = FunctionList( "NMModelStr_*", ";", "KIND:2" )
funcList = ReplaceString( "NMModelStr_", funcList, "" )
return funcList
End // NMModelList
//****************************************************************
//****************************************************************
//****************************************************************
Function NMModelVariablesInit() // initialize input variables
Variable icnt
String cName
String wPrefix, wList, df = NMModelDF()
String thisfxn = GetRTStackInfo( 1 )
Variable FirstSimulation = NumVarOrDefault( df + "FirstSimulation", 0 )
Variable LastSimulation = NumVarOrDefault( df + "LastSimulation", 0 )
FirstSimulation = min( FirstSimulation, LastSimulation )
LastSimulation = max( FirstSimulation, LastSimulation )
Variable simTime = NMModelSimTime( 0 )
Variable dt = NumVarOrDefault( df + "TimeStep", 0.01 )
Variable npnts = ( simTime / dt ) + 1
Variable numSimulations = LastSimulation - FirstSimulation + 1
if ( ( numtype( numSimulations ) > 0 ) || ( numSimulations < 0 ) )
numSimulations = 0
endif
SetNMvar( df + "NumSimulations", numSimulations )
SetNMvar( df + "NumTimeSteps", npnts )
Variable diameter = NumVarOrDefault( df + "Diameter", 20 ) // um
Variable SA = pi * diameter ^ 2 // um^2
SetNMvar( df + "SurfaceArea", SA )
NMModelVariablesInit2( "Cm", SA )
for ( icnt = 0 ; icnt < ItemsInList( IonChannelList ) ; icnt += 1 )
cName = StringFromList( icnt, IonChannelList )
NMModelVariablesInit2( "g" + cName, SA )
endfor
wPrefix = StrVarOrDefault( df + "gGABA_WavePrefix", "" )
icnt = 0
if ( strlen( wPrefix ) > 0 )
wList = WaveList( wPrefix + "*", ";", "" )
icnt = ItemsInList( wList )
endif
SetNMvar( df + "gGABA_NumWaves", icnt )
wPrefix = StrVarOrDefault( df + "gAMPA_WavePrefix", "" )
icnt = 0
if ( strlen( wPrefix ) > 0 )
wList = WaveList( wPrefix + "*", ";", "" )
icnt = ItemsInList( wList )
endif
SetNMvar( df + "gAMPA_NumWaves", icnt )
wPrefix = StrVarOrDefault( df + "gNMDA_WavePrefix", "" )
icnt = 0
if ( strlen( wPrefix ) > 0 )
wList = WaveList( wPrefix + "*", ";", "" )
icnt = ItemsInList( wList )
endif
SetNMvar( df + "gNMDA_NumWaves", icnt )
return 0
End // NMModelVariablesInit
//****************************************************************
//****************************************************************
//****************************************************************
Static Function NMModelVariablesInit2( varName, SA )
String varName
Variable SA // surface area
String df = NMModelDF()
String thisfxn = GetRTStackInfo( 1 )
String varNameDensity = df + varName + "Density"
if ( exists( varNameDensity ) != 2 )
NMDoAlert( thisfxn + " error: cannot find variable " + NMQuotes( varNameDensity ) )
return -1
endif
Variable density = NumVarOrDefault( varNameDensity, NaN )
SetNMvar( df + varName, density * SA )
return 0
End // NMModelVariablesInit2
//****************************************************************
//****************************************************************
//****************************************************************
Function NMModelSelect( modelName [ update ] )
String modelName
Variable update
String fxn, df = NMModelDF()
String thisfxn = GetRTStackInfo( 1 )
if ( ParamIsDefault( update ) )
update = 1
endif
String stateList = NMModelStr2( modelName, "StateList" )
if ( ItemsInList( stateList ) == 0 )
NMDoAlert( thisfxn + " error: cannot find StateList for model " + NMQuotes( modelName ) )
return -1 // no states, something is wrong
endif
SetNMstr( df + "StateList", stateList )
fxn = modelName + "_Init"
if ( exists( fxn ) != 6 )
NMDoAlert( thisfxn + " error: cannot find function " + NMQuotes( fxn ) )
return -1 // no init function, something is wrong
endif
SetNMstr( df + "ModelSelect" , modelName )
NMModelInit()
Execute fxn + "()"
if ( update )
NMModelTabUpdate()
endif
return 0
End // NMModelSelect
//****************************************************************
//****************************************************************
//****************************************************************
Function NMModelInit()
String df = NMModelDF()
SetNMvar( df + "gLeakDensity", 0 )
SetNMvar( df + "gTonicGABADensity", 0 )
End // NMModelInit
//****************************************************************
//****************************************************************
//****************************************************************
Function NMModelSelectNum( modelSelect )
String modelSelect // ( "" ) for current model select
Variable icnt
String itemStr, df = NMModelDF()
String mList = NMModelList()
if ( strlen( modelSelect ) == 0 )
modelSelect = StrVarOrDefault( df + "ModelSelect", "" )
endif
for ( icnt = 0 ; icnt < ItemsInList( mList ) ; icnt += 1 )
itemStr = StringFromList( icnt, mList )
if ( StringMatch( itemStr, modelSelect ) )
return icnt
endif
endfor
return NaN
End // NMModelSelectNum
//****************************************************************
//****************************************************************
//****************************************************************
Function NMModelClampSelectToggle()
Variable clampSelect = NMModelClampSelectNum()
if ( clampSelect == 0 )
return NMModelSet( ClampSelect = "Vclamp", history = 1 )
else
return NMModelSet( ClampSelect = "Iclamp", history = 1 )
endif
End // NMModelClampSelectCall
//****************************************************************
//****************************************************************
//****************************************************************
Function NMModelClampSelect( select [ update ] )
String select // "Iclamp" or "Vclamp"
Variable update
String df = NMModelDF()
if ( ParamIsDefault( update ) )
update = 1
endif
strswitch( select )
case "Voltage Clamp":
case "Vclamp":
SetNMstr( df + "ClampSelect", "Vclamp" )
break
default:
SetNMstr( df + "ClampSelect", "Iclamp" )
endswitch
if ( update )
NMModelTabUpdate()
endif
End // NMModelClampSelect
//****************************************************************
//****************************************************************
//****************************************************************
Function NMModelClampSelectNum()
String df = NMModelDF()
String clampSelect = StrVarOrDefault( df + "ClampSelect", "" )
strswitch( clampSelect )
case "Current":
case "Iclamp":
return 0
case "Voltage":
case "Vclamp":
return 1
endswitch
End // NMModelClampSelectNum
//****************************************************************
//****************************************************************
//****************************************************************
Function NMModelVarSet( varName, value [ history ] )
String varName
Variable value
Variable history // print function command to history ( 0 ) no ( 1 ) yes
String vlist = ""
String df = NMModelDF()
if ( history )
vlist = NMCmdStr( varName, vlist )
vlist = NMCmdNum( value, vlist )
NMCommandHistory( vlist )
endif