//chemesis
//add_output.g
// Create files to save Vm for specified compartments, Gk from specified channels and compartment, and/or calcium objects
//Need to add some string parsing stuff and loops.
function setfilename(fname,prefix,appendval,fheader)
str fname,prefix,fheader
int appendval
if ({exists /output/{fname}})
str filenam = {prefix}@"_"@{fname}@".txt"
setfield /output/{fname} flush 1 leave_open {appendval} append {appendval} \
float_format %0.6g filename {filenam}
call /output/{fname} OUT_OPEN
call /output/{fname} OUT_WRITE {fheader}
else
echo "Could not open file " {fname}
end
reset
end
function fileFLUSH(fname)
str fname
if ({exists /output/{fname}})
call /output/{fname} FLUSH
end
end
function add_outputVm (compString,ascname,cell)
str compString, ascname,cell
create asc_file /output/{ascname}
setfield /output/{ascname} flush 1 leave_open 1 append 1 \
float_format %0.6g
useclock /output/{ascname} 1
str compt
int position=0
str header="/Time "
while ({position} > -1)
position = {findchar {compString} ,}
if ({position}==-1)
compt={compString}
else
compt={substring {compString} 0 {position-1}}
compString={substring {compString} {position+1}}
end
header=header@" "@compt
addmsg {cell}/{compt} /output/{ascname} SAVE Vm
end
return {header}
end
function add_outputGk (compString,ChanString,ascname,cell)
str compString,ChanString, ascname,cell
create asc_file /output/{ascname}
setfield /output/{ascname} flush 1 leave_open 1 append 1 \
float_format %0.6g
useclock /output/{ascname} 1
str compt, chan, chanStrTmp
int chanpos,position=0
str header="/Time "
str NMDAcomp
if ({GABAYesNo})
str gabacompt = "/cell/soma/"
header = {header}@" "@{gabacompt}@"_GABA_Gk"
addmsg {gabacompt}GABA /output/{ascname} SAVE Gk
end
//string parsing for multiple comps
while ({position} > -1)
position = {findchar {compString} ,}
if ({position}==-1)
compt={compString}
else
compt={substring {compString} 0 {position-1}}
compString={substring {compString} {position+1}}
end
if ({spinesYesNo})
NMDAcomp={compt}@"/spine_1/"@{spcomp1}
else
NMDAcomp={compt}
end
if ({exists {cell}/{NMDAcomp}/{subunit}})
header={header}@" "@{NMDAcomp}@"_"@{subunit}@"GHK "@{NMDAcomp}@"_"@{subunit}@"block"
addmsg {cell}/{NMDAcomp}/{subunit}/GHK /output/{ascname} SAVE Gk
addmsg {cell}/{NMDAcomp}/{subunit}/block /output/{ascname} SAVE Gk
end
//string parsing for multiple chans
chanpos=0
chanStrTmp=ChanString
while ({chanpos} > -1)
chanpos = {findchar {chanStrTmp} ,}
if ({chanpos}==-1)
chan={chanStrTmp}
else
chan={substring {chanStrTmp} 0 {chanpos-1}}
chanStrTmp={substring {chanStrTmp} {chanpos+1}}
end
if ({exists {cell}/{compt}/{chan}GHK})
addmsg {cell}/{compt}/{chan}GHK /output/{ascname} SAVE Gk
header={header}@" "@{compt}@"_"@{chan}@"GHK"
elif ({exists {cell}/{compt}/{chan}})
addmsg {cell}/{compt}/{chan} /output/{ascname} SAVE Gk
header={header}@" "@{compt}@"_"@{chan}
else
echo "add_output: channel" {chan} "doesn't exist in compartment" {compt}
end
end
end
return {header}
end
function add_outputIk (compString,ChanString,ascname,cell)
str compString,ChanString, ascname,cell
create asc_file /output/{ascname}
setfield /output/{ascname} flush 1 leave_open 1 append 1 \
float_format %0.6g
useclock /output/{ascname} 1
str compt, chan, chanStrTmp
int chanpos,position=0
str header="/Time "
str NMDAcomp
//string parsing for multiple comps
while ({position} > -1)
position = {findchar {compString} ,}
if ({position}==-1)
compt={compString}
else
compt={substring {compString} 0 {position-1}}
compString={substring {compString} {position+1}}
end
if ({spinesYesNo})
NMDAcomp={compt}@"/spine_1/"@{spcomp1}
else
NMDAcomp={compt}
end
if ({exists {cell}/{NMDAcomp}/{subunit}})
header={header}@" "@{NMDAcomp}@"_"@{subunit}@"GHK "@{NMDAcomp}@"_"@{subunit}@"block"
addmsg {cell}/{NMDAcomp}/{subunit}/GHK /output/{ascname} SAVE Ik
addmsg {cell}/{NMDAcomp}/{subunit}/block /output/{ascname} SAVE Ik
end
//string parsing for multiple chans
chanpos=0
chanStrTmp=ChanString
while ({chanpos} > -1)
chanpos = {findchar {chanStrTmp} ,}
if ({chanpos}==-1)
chan={chanStrTmp}
else
chan={substring {chanStrTmp} 0 {chanpos-1}}
chanStrTmp={substring {chanStrTmp} {chanpos+1}}
end
if ({exists {cell}/{compt}/{chan}GHK})
addmsg {cell}/{compt}/{chan}GHK /output/{ascname} SAVE Ik
header={header}@" "@{compt}@"_"@{chan}@"GHK"
elif ({exists {cell}/{compt}/{chan}})
addmsg {cell}/{compt}/{chan} /output/{ascname} SAVE Ik
header={header}@" "@{compt}@"_"@{chan}
else
echo "add_output: channel" {chan} "doesn't exist in compartment" {compt}
end
end
end
return {header}
end
function add_outputCal (compString,CaBufStr,ascname,cell)
str compString, CaBufStr, ascname,cell
create asc_file /output/{ascname}
setfield /output/{ascname} flush 1 leave_open 1 append 1 \
float_format %0.6g
useclock /output/{ascname} 1
str compt, CaBuf,bufStrTmp
int bufpos,position=0
str header="/Time "
// string parsing for multiple comps
while ({position} > -1)
position = {findchar {compString} ,}
if ({position}==-1)
compt={compString}
else
compt={substring {compString} 0 {position-1}}
compString={substring {compString} {position+1}}
end
if ({calciumtype}==0)
addmsg {cell}/{compt}/volavg /output/{ascname} SAVE meanValue
header=header@" "@{cell}@"/"@{compt}@"/CaAvg "
if ({calciumdye}>1)
if ({exists {cell}/{compt}/{bnamefluor}Vavg})
addmsg {cell}/{compt}/{bnamefluor}Vavg /output/{ascname} SAVE meanValue
header=header@{cell}@"/"@{compt}@"/"@{bnamefluor}@"_Vavg "
else
echo "No " {cell}/{compt}/{bnamefluor}Vavg
end
elif ({calciumdye}==1)
if ({exists {cell}/{compt}/{bnamefluor}})
addmsg {cell}/{compt}/{bnamefluor} /output/{ascname} SAVE ratio
header=header@{cell}@"/"@{compt}@"/"@{bnamefluor}@"_ratio "
else
echo "No " {cell}/{compt}/{bnamefluor}
end
end
addmsg {cell}/{compt}/Ca_difshell_1 /output/{ascname} SAVE C
header=header@{cell}@"/"@compt@"/Ca1"
end
//string parsing for either multiple Ca_pools for single tau or various buffers
bufpos=0
bufStrTmp=CaBufStr
while ({bufpos} > -1)
bufpos = {findchar {bufStrTmp} ,}
if ({bufpos}==-1)
CaBuf={bufStrTmp}
else
CaBuf={substring {bufStrTmp} 0 {bufpos-1}}
bufStrTmp={substring {bufStrTmp} {bufpos+1}}
end
if ({spinecalcium}==0)
if ({CaBuf} != "X") //may not want to see various buffers
addmsg {cell}/{compt}/Ca_difshell_1{CaBuf} /output/{ascname} SAVE Bbound
header={header}@" "@{cell}@"/"@{compt}@"/Ca1_"@{CaBuf}
else
header={header}@" "
end
elif ({spinecalcium}==1) //single time constant of decay
if ({exists {cell}/{compt}/{CaBuf}}) //may not be nmda pool in dendrites
addmsg {cell}/{compt}/{CaBuf} /output/{ascname} SAVE Ca
header={header}@" "@{cell}@"/"@{compt}@"/"@{CaBuf}
end
else
echo "unrecognized calcium type"
end
end
end
return {header}
end
function write_spine_channel(spinehead,comp_path,ascname,channel)
str spinehead,comp_path,ascname,channel
if ({exists {comp_path}{spcomp1}/{channel}})
addmsg {comp_path}{spcomp1}/{channel}GHK /output/{ascname} SAVE Gk
spinehead={spinehead}@{comp_path}@{spcomp1}@"/"@{channel}@" "
end
return {spinehead}
end
function write_ca_buffers(spinehead,where,label,ascname)
str spinehead,where,label,ascname
int bufpos
str bufStrTmp, CaBuf
bufpos = 0
bufStrTmp = {CaBufs}
while ({bufpos} > -1)
bufpos = {findchar {bufStrTmp} ,}
if ({bufpos} == -1)
CaBuf = {bufStrTmp}
else
CaBuf = {substring {bufStrTmp} 0 {bufpos-1}}
bufStrTmp = {substring {bufStrTmp} {bufpos+1}}
end
if ({spinecalcium})
if ({exists {where}{CaBuf}})
addmsg {where}{CaBuf} /output/{ascname} SAVE Ca
echo addmsg {where}{CaBuf} /output/{ascname} SAVE Ca
spinehead = {spinehead}@" "@{label}@{CaBuf}
end
else
if ({exists {where}{CaBuf}})
addmsg {where}{CaBuf} /output/{ascname} SAVE Bbound
spinehead = {spinehead}@" "@{label}@{CaBuf}
end
end
end
return {spinehead@" "}
end
function write_spine_nmda(comp_path,spinehead,ascname)
str comp_path, spinehead, ascname
if ({spinesYesNo})
str NMDAcomp = {comp_path}@"head"
if ({exists {NMDAcomp}/{subunit}})
spinehead={spinehead}@" "@{NMDAcomp}@"_"@{subunit}@"GHK "@{NMDAcomp}@"_"@{subunit}@"block "
addmsg {NMDAcomp}/{subunit}/GHK /output/{ascname} SAVE Gk
addmsg {NMDAcomp}/{subunit}/block /output/{ascname} SAVE Gk
echo addmsg {NMDAcomp}/{subunit}/GHK /output/{ascname} SAVE Gk
echo addmsg {NMDAcomp}/{subunit}/block /output/{ascname} SAVE Gk
end
end
return spinehead
end
function header_to_file_one_spine(spinehead,head,ascname,prestim)
str spinehead,element,head,ascname,prestim
str CaBuf,bufStrTmp,spcomp,label,name,comp_path
int i,j,slabs, nummsg, bufpos
comp_path = {strsub {head} /head/ /}
echo head {head}
if ({exists {head}})
addmsg {head} /output/{ascname} SAVE Vm
spinehead={spinehead}@{head}@"Vm "
else
echo "No spine " {head}
return
end
if ({exists {head}volavg})
addmsg {head}volavg /output/{ascname} SAVE meanValue
spinehead={spinehead}@{head}@"CaAvg "
else
echo "No volavg on" {head}
end
if (calciumdye==1)
if ({exists {head}{bnamefluor}})
addmsg {head}{bnamefluor} /output/{ascname} SAVE ratio
spinehead={spinehead}@{head}@"Fura2_ratio "
else
echo "No " {head}{bnamefluor}
end
elif ({calciumdye}>1)
if ({exists {head}{bnamefluor}Vavg})
addmsg {head}{bnamefluor}Vavg /output/{ascname} SAVE meanValue
spinehead={spinehead}@{head}@{bnamefluor}@"_Vavg "
else
echo "No " {head}{bnamefluor}Vavg
end
end
if ({plastYesNo})
if ({prestim})
addmsg {head}AMPA /output/{ascname} SAVE synapse[0].weight
spinehead={spinehead}@{head}@"weight "
end
end
if ({spinecalcium}==0)
for (j=1; j<=2; j=j+1)
spcomp={getglobal spcomp{j}} @ "/"
if ({strcmp {spcomp} "head/"} == 0)
slabs = {headSlabs}
label = "head/"
name = "head/"
else
slabs = {neckSlabs}
label = "neck/"
name = ""
end
for (i=1; i<=slabs; i=i+1)
addmsg {comp_path}/{name}Ca_difshell_{i} /output/{ascname} SAVE C
spinehead = {spinehead}@" "@{comp_path}@{label}@"Ca"@{i}
//string parsing for various buffers
if ({CaBufs}!="X")
str where,what
where = {comp_path}@{name}@"Ca_difshell_"@{i}
what = {comp_path}@"_"@{label}@"_Ca"@{i}@"_"
spinehead = {write_ca_buffers {spinehead} {where} {what} {ascname}}
else
spinehead = {spinehead}@" "
end
end
end
//addmsg {cell}/{compt}/fluorescence /output/{ascname} SAVE ratio
elif ({spinecalcium}==1)
spinehead = {write_ca_buffers {spinehead} {head} {comp_path} {ascname}}
end
spinehead = {write_spine_channel {spinehead} {comp_path} {ascname} CaL13_channel}
spinehead = {write_spine_channel {spinehead} {comp_path} {ascname} CaL12_channel}
spinehead = {write_spine_channel {spinehead} {comp_path} {ascname} CaR_channel}
spinehead = {write_spine_channel {spinehead} {comp_path} {ascname} CaT_channel}
spinehead = {write_spine_nmda {comp_path} {spinehead} {ascname}}
return {spinehead}
end
function add_output_hook_up(ascname,cell,StimComp,res_spines,PreStim)
str ascname,cell,StimComp, res_spines, PreStim, bufStrTmp, whichSpine,compt
int bufpos=0, position=0
create asc_file /output/{ascname}
setfield /output/{ascname} flush 1 leave_open 1 append 1 float_format %0.6g
useclock /output/{ascname} 1
str spinehead="/Time "
int i,j,k,slabs, nummsg, bufpos
str element,head
if ({strlen {res_spines}}>0)
while ({position} > -1) //loops through selected StimComps
position = {findchar {StimComp} ,}
if ({position}==-1)
compt={StimComp}
else
compt={substring {StimComp} 0 {position-1}}
StimComp={substring {StimComp} {position+1}}
end
bufStrTmp = {res_spines}
bufpos = 0
while ({bufpos} > -1)
bufpos = {findchar {bufStrTmp} ,}
if ({bufpos} == -1)
whichSpine = {bufStrTmp}
else
whichSpine = {substring {bufStrTmp} 0 {bufpos-1}}
bufStrTmp = {substring {bufStrTmp} {bufpos+1}}
end
head = {cell}@"/"@{compt}@"/spine_"@{whichSpine}@"/head/"
spinehead = {header_to_file_one_spine {spinehead} {head} {ascname} {PreStim}}
end
end
end
return {spinehead}
end
function add_outputMultiSpines (ascname,prestim)
str ascname, CaBuf,bufStrTmp,spcomp,label,name
int prestim,nummsg
create asc_file /output/{ascname}
setfield /output/{ascname} flush 1 leave_open 1 append 1 float_format %0.6g
useclock /output/{ascname} 1
str spinehead="/Time "
int i,j,k,slabs, nummsg, bufpos
str element,head
if ({prestim}>0)
nummsg={getmsg {precell}/spikegen -out -count}
str comp_path, previous = ""
//This loop skips the 1st output/vm message - loop from i=0 if that message is eliminated
if ({GABAYesNo})
int begining = 2
else
int begining = 1
end
for (k=begining;k<nummsg-1;k=k+1)
element ={getmsg {precell}/spikegen -out -destination {k}}
echo {element}
head = {getpath {element} -head}
echo {head}
if ({strcmp {head} {previous}} != 0)
spinehead = {header_to_file_one_spine {spinehead} {head} {ascname}}
end
previous = {head}
end
end
return {spinehead}
end
function add_outputOneSpinePerComp(ascname,cell,StimComp)
str ascname, cell, StimComp, compt, head
int position
create asc_file /output/{ascname}
setfield /output/{ascname} flush 1 leave_open 1 append 1 float_format %0.6g
useclock /output/{ascname} 1
str spinehead="/Time "
while ({position} > -1) //loops through selected StimComps
position = {findchar {StimComp} ,}
if ({position}==-1)
compt={StimComp}
else
compt={substring {StimComp} 0 {position-1}}
StimComp={substring {StimComp} {position+1}}
end
head = {cell}@"/"@{compt}@"/spine_1/head/"
if ({exists {head}})
spinehead = {header_to_file_one_spine {spinehead} {head} {ascname}}
else
echo "No spines on " {head}
end
end
return {spinehead}
end
function add_outputPulseGen(ascname,pulsegen)
str ascname, pulsegen
create asc_file /output/{ascname}
setfield /output/{ascname} flush 1 leave_open 1 append 1\
float_format %0.6g
useclock /output/{ascname} 1
str header="/Time "
addmsg {pulsegen} /output/{ascname} SAVE output
header = {header}@"inject"
return header
end
function add_outputSpikeHistory(precell,fname,prefix)
str precell, fname
str filenam = {prefix}@"_"@{fname}@".txt"
echo {filenam}
create spikehistory SynTimes.history
setfield SynTimes.history ident_toggle 1 filename {filenam} initialize 1 leave_open 1 flush 1
addmsg {precell}/spikegen SynTimes.history SPIKESAVE
reset
end
