Revision b9d40510b04e23174dc618b8b31953294ffb3050 authored by richard defazio on 19 July 2021, 13:38:38 UTC, committed by richard defazio on 19 July 2021, 13:38:38 UTC
Merge AGG VBW Regions into master See merge request um-mip/coding-project!2
! macros - v11.ipf
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
#pragma TextEncoding = "MacRoman"
strconstant sc_version = "20210202 AGG VBW"
macro version()
print sc_version
endmacro
macro JPsmartConcPanel ()
buildPanel()
endmacro
macro onlySpont()
onlySpontRegion()
endmacro
macro SpontSenk()
SpontSenkRegions()
endmacro
macro AGG_VBWPanel()
AGG_build_MultCellVBW_panel()
endmacro
// macro cccapRunner()
// //function CCcap( ntraces, [ maxCurrent ] )
// variable ntraces = 5 // for original CC-IV
// variable maxCurrent = -1 // cuts off before zero
// // get list of series for batch mode
// string series_list = "", series_listw = "serieslistw", series_list_selw = "", listboxn = "list_series", pathn = "collector_data"
// string thisseries = ""
// variable seriesn = inf
// // WAVE/Z/T slistw = serieslistw // $series_listw
// if( !waveexists( $series_listw ) )
// print "no series wave for batchmode:", series_listw
// abort
// endif
// variable iseries=0, nseries = numpnts( $series_listw )
// string sweeplist1 //= returnallwavesfromserieslist( "", tracen = 1, slistw = $series_listw, pathn = pathn )
// string sweeplist2 //= returnallwavesfromserieslist( "", tracen = 2, slistw = $series_listw, pathn = pathn )
// //print "here is the series list:", sweeplist
// variable isweeps = 0, nsweeps = itemsinlist( sweeplist1 )
// do
// thisSeries = $series_Listw[ iseries ]
// seriesn = seriesnumberGREP( thisSeries )
// sweeplist1 = returnwavesfromseries( thisseries, tracen = 1 )
// //print thisSeries, sweeplist1
// sweeplist2 = returnwavesfromseries( thisseries, tracen = 2 )
// print cccap( ntraces, maxCurrent = maxCurrent, slist = sweeplist1 )
// iseries += 1
// while( iseries < nseries )
// endmacro
// macro makeitso()
// // make all visible graph use the same axes
// string wl = winlist( "*", ";", "WIN:1,VISIBLE:1")
// print wl
// endmacro
macro dectaumac()
dectau()
endmacro
function dectau()
string wl=tracenamelist("",";",1)
string wn=stringfromlist(0,wl)
variable i=0,n=itemsinlist(wl), xs = xcsr(A), xe = xcsr(B)
make/O/N=(3) W_coef
make/O/N=(n) results
do
wn=removequotes( stringfromlist(i,wl) )
WAVE w = $wn
CurveFit/Q/TBOX=256 exp w(xs, xe) /D
print wn, 1000/w_coef[2]
results[i] = 1000/w_coef[2]
i += 1
while( i < n )
end
//\\//\\//\\//\\//\\//\\//\\//\\
macro Table2QuB()
// convert each wave in table to simple QuB binary :: compton = 1
// get list of waves in top table
string wl = wavelistfromtoptable(), wn = ""
// loop over wave list
variable nw = itemsinlist( wl ), iw=0
do
// export to QuB
wn = stringfromlist( iw, wl )
// print w
print xy2qub( wn, compton=1 )
iw += 1
while( iw < nw )
// clean up
endmacro
//\\//\\//\\//\\//\\//\\//\\//\\
macro graph2QuBX(scale)
variable scale = 1000 // necessary to convert SI units (Patchmaster) to mV, pA, pF in QuB
// convert each wave in table to simple QuB binary :: compton = 1
// get list of waves in top table
string wl = tracenamelist("",";",1), wn = ""
// loop over wave list
variable nw = itemsinlist( wl ), iw=0
do
// export to QuB
wn = removequotes( stringfromlist( iw, wl ) )
// print w
print xy2qub( wn, scale=scale ) //, compton=1 )
iw += 1
while( iw < nw )
// clean up
endmacro
//\\//\\//\\//\\//\\//\\//\\//\\
//\\//\\//\\//\\//\\//\\//\\//\\
macro inSilicoPSP( )
variable peaksign = inf //1 // sets optional parameter to determine sign of peak, +1 for positive, -1 for negative peak
// required parameters
variable m_rin = 0 // disable input resistance measurement, only works for current clamp :: DO NOT SET TO 1 ::
variable use_csr = 0 // :: -1 use x-axis for range, :: 0 use default range -inf, inf sec, :: 1 use cursors A and B for range
// optional parameters in function call
variable trace // set tr = trace if you want to specify which trace, only use if multiple traces
variable baseline // set bsl = baseline if you want to specify when the baseline measurement starts (5 msec dur)
variable xstart = 0.02, xend = inf // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
variable peakwin = 0.02 // set pwin = peakwin, this sets the window to search for the peak if multiple peaks, starts at xstart
print eventM( m_rin, use_csr, xs = xstart, xe = xend, pwin = peakwin, psign = peaksign )
endmacro
//\\//\\//\\//\\//\\//\\//\\//\\
macro eventAnalysis( peaksign )
variable peaksign = 1 // sets optional parameter to determine sign of peak, +1 for positive, -1 for negative peak
// required parameters
variable m_rin = 0 // disable input resistance measurement, only works for current clamp :: DO NOT SET TO 1 ::
variable use_csr = 0 // :: -1 use x-axis for range, :: 0 use default range -inf, inf sec, :: 1 use cursors A and B for range
// optional parameters in function call
variable trace // set tr = trace if you want to specify which trace, only use if multiple traces
variable baseline // set bsl = baseline if you want to specify when the baseline measurement starts (5 msec dur)
variable xstart = -0.001, xend = inf // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
variable peakwin = 0.01 // set pwin = peakwin, this sets the window to search for the peak if multiple peaks, starts at xstart
print eventM( m_rin, use_csr, xs = xstart, xe = xend, pwin = peakwin, psign = peaksign )
endmacro
//\\//\\//\\//\\//\\//\\//\\//\\
// td version for averaged AMPA PSCs from blast_panel detection
//
macro AMPA_avePSCs( peaksign )
variable peaksign = -1 // sets optional parameter to determine sign of peak, +1 for positive, -1 for negative peak
// required parameters
variable m_rin = 0 // disable input resistance measurement, only works for current clamp :: DO NOT SET TO 1 ::
variable use_csr = 0 // :: -1 use x-axis for range, :: 0 use default range -inf, inf sec, :: 1 use cursors A and B for range
// optional parameters in function call
variable trace // set tr = trace if you want to specify which trace, only use if multiple traces
variable baseline = -0.01 // set bsl = baseline if you want to specify when the baseline is taken
variable xstart = -0.002, xend = inf // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
variable peakwin = 0.01 // set pwin = peakwin, this sets the window to search for the peak if multiple peaks, starts at xstart
print eventM( m_rin, use_csr, bsl = baseline, xs = xstart, xe = xend, pwin = peakwin, psign = peaksign )
endmacro
//
// td version for dcPSP analysis
//
// \\//\\//\\//\\//\\//\\//\\//\\
//\\//\\//\\//\\//\\//\\//\\//\\
macro test_smartPeak()
variable peaksign = -1 // sets optional parameter to determine sign of peak, +1 for positive, -1 for negative peak
// required parameters
variable m_rin = 1 // disable input resistance measurement, only works for current clamp :: DO NOT SET TO 1 unless you are pro ::
variable use_csr = 0 // :: -1 use x-axis for range, :: 0 use default range -inf, inf sec, :: 1 use cursors A and B for range
// optional parameters in function call
variable trace // set tr = trace if you want to specify which trace, only use if multiple traces
variable baseline = 0.25 // set bsl = baseline if you want to specify when the baseline is taken
variable xstart = 0// 0.15
variable xend = 0.1 // 0.35 // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
variable xinc = 0.0
variable peakwin = 0.015 // set pwin = peakwin, this sets the window to search for the peak if multiple peaks, starts at xstart
string nm = "first_", holder=""
string wlist = winlist("*", ";", ""), panelwin = stringfromlist( 0, wlist )
string tablen = "smartPeak"
variable imax = 11
variable nsmooth = 11
string pathn = "collector_data", passwn = "", passTablen="", targetwn = "", expcode = ""
targetwn = removequotes( stringfromlist( 0, tracenamelist( "", ";", 1 ) ) )
expcode = removequotes( datecodefromanything( targetwn ) )
passTablen = "T_" + expcode + "_0"
string wl = tracenamelist( "", ";", 1 ),outwn
//function/S smartPeak( wl, tstart, tend, nsmth, suffix, [do_avg, do_tau, order, posneg ] )
holder = smartpeak( wl, xstart, xend, nsmooth, "spx" )
outwn = stringbykey( "peak", holder )
dowindow/F peaktable0
if(V_Flag == 0 ) // notable
edit/k=1/N=peaktable0 $outwn
else
appendtotable $outwn
endif
holder = smartpeak( wl, xend-0.01, xend, nsmooth, "sps" )
outwn = stringbykey( "peak", holder )
dowindow/F sustable0
if(V_Flag == 0 ) // notable
edit/k=1/N=sustable0 $outwn
else
appendtotable $outwn
endif
dowindow/F $panelwin
passwn = passiveSandwich( setpathn = pathn, passiveTablen = passTablen, targetwn = targetwn ) // acts on top window!
dowindow/F $tablen
//WAVE/Z pw = $passwn
//if( waveexists( pw ) )
if( waveexists( $passwn ) )
appendtotable/W=$tablen $passwn
endif
equilibrateTable()
endmacro
//\\//\\//\\//\\//\\//\\//\\//\\
// \\//\\//\\//\\//\\//\\//\\//\\
//
// td version for dcPSP analysis
//
// \\//\\//\\//\\//\\//\\//\\//\\
//\\//\\//\\//\\//\\//\\//\\//\\
macro dcPSP()
variable peaksign = 1 // sets optional parameter to determine sign of peak, +1 for positive, -1 for negative peak
// required parameters
variable m_rin = 1 // disable input resistance measurement, only works for current clamp :: DO NOT SET TO 1 unless you are pro ::
variable use_csr = 0 // :: -1 use x-axis for range, :: 0 use default range -inf, inf sec, :: 1 use cursors A and B for range
// optional parameters in function call
variable trace // set tr = trace if you want to specify which trace, only use if multiple traces
variable baseline = 0.25 // set bsl = baseline if you want to specify when the baseline is taken
variable xstart = 0.4
variable xend = 0.5 // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
variable peakwin = 0.01 // set pwin = peakwin, this sets the window to search for the peak if multiple peaks, starts at xstart
print eventM( m_rin, use_csr, bsl = baseline, xs = xstart, xe = xend, pwin = peakwin, psign = peaksign )
endmacro
//\\//\\//\\//\\//\\//\\//\\//\\
// \\//\\//\\//\\//\\//\\//\\//\\
//
// td version for dcPSP analysis
//
// \\//\\//\\//\\//\\//\\//\\//\\
//\\//\\//\\//\\//\\//\\//\\//\\
macro dcPSP_completo()
variable peaksign = 1 // sets optional parameter to determine sign of peak, +1 for positive, -1 for negative peak
// required parameters
variable m_rin = 1 // disable input resistance measurement, only works for current clamp :: DO NOT SET TO 1 unless you are pro ::
variable use_csr = 0 // :: -1 use x-axis for range, :: 0 use default range -inf, inf sec, :: 1 use cursors A and B for range
// optional parameters in function call
variable trace // set tr = trace if you want to specify which trace, only use if multiple traces
variable baseline = 0.25 // set bsl = baseline if you want to specify when the baseline is taken
variable xstart = 0.3
variable xend = 0.4 // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
variable xinc = 0.01
variable peakwin = 0.015 // set pwin = peakwin, this sets the window to search for the peak if multiple peaks, starts at xstart
string nm = "first_", holder=""
string wlist = winlist("*", ";", ""), panelwin = stringfromlist( 0, wlist )
string tablen = "dcPSPcompleto"
variable imax = 11
string pathn = "collector_data", passwn = "", passTablen="", targetwn = "", expcode = ""
targetwn = removequotes( stringfromlist( 0, tracenamelist( "", ";", 1 ) ) )
expcode = removequotes( datecodefromanything( targetwn ) )
passTablen = "T_" + expcode + "_0"
// 1st pulse
holder = eventM( m_rin, use_csr, bsl = baseline, xs = xstart, xe = xend, xinc = xinc, pwin = peakwin, psign = peaksign, name = nm, tablen = tablen, maxsweep = imax )
xstart = 0.4
xend = 0.5 // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
xinc = 0.0
peakwin = 0.015 // set pwin = peakwin, this sets the window to search for the peak if multiple peaks, starts at xstart
// 2nd pulse
dowindow/F $panelwin
nm = "second_"
holder = eventM( m_rin, use_csr, bsl = baseline, xs = xstart, xe = xend, xinc = xinc, pwin = peakwin, psign = peaksign, name = nm, tablen = tablen, maxsweep = imax )
dowindow/F $panelwin
passwn = passiveSandwich( setpathn = pathn, passiveTablen = passTablen, targetwn = targetwn ) // acts on top window!
dowindow/F $tablen
//WAVE/Z pw = $passwn
//if( waveexists( pw ) )
if( waveexists( $passwn ) )
appendtotable/W=$tablen $passwn
endif
equilibrateTable()
endmacro
//\\//\\//\\//\\//\\//\\//\\//\\
// \\//\\//\\//\\//\\//\\//\\//\\
//
// td version for dcPSP analysis
//
// \\//\\//\\//\\//\\//\\//\\//\\
//\\//\\//\\//\\//\\//\\//\\//\\
macro dcPSP_batchMode( increment )
variable increment = 0.01 // default is to increment timing of 1st pulse
// get list of series for batch mode
string series_list = "", series_listw = "serieslistw", series_list_selw = "", listboxn = "list_series", pathn = "collector_data"
// WAVE/Z/T slistw = serieslistw // $series_listw
if( !waveexists( $series_listw ) )
print "no series wave for batchmode:", series_listw
abort
endif
string sweeplist = returnallwavesfromserieslist( "", tracen = 1, slistw = $series_listw, pathn = pathn )
//print "here is the series list:", sweeplist
variable isweeps = 0, nsweeps = itemsinlist( sweeplist )
// string wavel = returnwavesfromseries( serieslistw[0], tracen = 1, pathn = pathn )
string wlist = winlist("*", ";", ""), panelwin = stringfromlist( 0, wlist )
string tablen = "dcPSP_batchMode0"
string passwn = "", passTablen="", targetwn = "", expcode = ""
targetwn = removequotes( stringfromlist( 0, sweeplist ) )
expcode = removequotes( datecodefromanything( targetwn ) )
passTablen = "T_" + expcode + "_0"
string PGFlabel = stringbykey( "LABEL", note( $targetwn ) )
// assemble the batch mode wave list
variable peaksign = 1 // sets optional parameter to determine sign of peak, +1 for positive, -1 for negative peak
// required parameters
variable m_rin = 1 // 0 disable input resistance measurement, only works for current clamp :: DO NOT SET TO 1 unless you are pro ::
variable use_csr = 0 // :: -1 use x-axis for range, :: 0 use default range -inf, inf sec, :: 1 use cursors A and B for range
// optional parameters in function call
variable trace // set tr = trace if you want to specify which trace, only use if multiple traces
variable baseline = 0.25 // set bsl = baseline if you want to specify when the baseline is taken
variable xstart = 0.2 // 0.3
variable xend = 0.3 //0.4 // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
variable xinc = increment // 0.01
variable peakwin = 0.015 // set pwin = peakwin, this sets the window to search for the peak if multiple peaks, starts at xstart
string nm = expcode + PGFlabel + "_1", holder=""
tablen = "T_" + expcode + "_dcPSP_BM0"
variable imax = nsweeps
variable ignoreSweep = 11 // ignores sweeps >= to param
variable target_baseline = -75 // mV
variable target_thresh = 2 // mV range
//for( isweep = 0; isweep < nsweeps; ++ isweep )
// 1st pulse
dowindow/F $panelwin
xstart = 0.2 //0.3
xend = 0.3 // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
xinc = 0.01 //0 // 0.01
peakwin = 0.015 // set pwin = peakwin, this sets the window to search for the peak if
if( strlen( pgflabel ) > 6 )
print "BATCH MODE warning pgflabel too long", pgflabel
pgflabel = "a"
endif
nm = expcode + PGFlabel + "_1"
holder = eventM( m_rin, use_csr, bsl = baseline, xs = xstart, xe = xend, xinc = xinc, pwin = peakwin, psign = peaksign, name = nm, tablen = tablen, maxsweep = imax, wlist = sweeplist, ignoreSweep = ignoreSweep, target_baseline = target_baseline, target_threshold = target_thresh )
// 2nd pulse
dowindow/F $panelwin
xstart = 0.4
xend = 0.5 // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
xinc = 0.0
peakwin = 0.015 // set pwin = peakwin, this sets the window to search for the peak if multiple peaks, starts at xstart
nm = expcode + PGFlabel + "_2"
holder = eventM( m_rin, use_csr, bsl = baseline, xs = xstart, xe = xend, xinc = xinc, pwin = peakwin, psign = peaksign, name = nm, tablen = tablen, maxsweep = imax, wlist = sweeplist, target_baseline = target_baseline, target_threshold = target_thresh )
dowindow/F $panelwin
graphResults( expcode, PGFlabel )
// passwn = passiveSandwich( setpathn = pathn, passiveTablen = passTablen, targetwn = targetwn ) // acts on top window!
// dowindow/F $tablen
// if( waveexists( $passwn ) )
// appendtotable/W=$tablen $passwn
// endif
// equilibrateTable()
//endfor
endmacro
// end of dcPSP batchmode
//\\//\\//\\//\\//\\//\\//\\//\\
// \\//\\//\\//\\//\\//\\//\\//\\
//
// td version for dcPSP analysis
//
// \\//\\//\\//\\//\\//\\//\\//\\
//\\//\\//\\//\\//\\//\\//\\//\\
macro dcPSP_beastMode(wlwn)
// provide a text wave listing the series for analysis
string wlwn = "g2"
string series_listw = wlwn
string series_list = "", series_list_selw = "", listboxn = "list_series", pathn = "collector_data"
// WAVE/Z/T slistw = serieslistw // $series_listw
if( !waveexists( $series_listw ) )
print "no series wave for batchmode:", series_listw
abort
endif
string sweeplist = returnallwavesfromserieslist( "", tracen = 1, slistw = $series_listw, pathn = pathn )
//print "here is the series list:", sweeplist
variable isweeps = 0, nsweeps = itemsinlist( sweeplist )
// string wavel = returnwavesfromseries( serieslistw[0], tracen = 1, pathn = pathn )
string wlist = winlist("*", ";", ""), panelwin = stringfromlist( 0, wlist )
string tablen = "dcPSP_batchMode0"
string passwn = "", passTablen="", targetwn = "", expcode = ""
targetwn = removequotes( stringfromlist( 0, sweeplist ) )
expcode = removequotes( datecodefromanything( targetwn ) )
passTablen = "T_" + expcode + "_0"
string PGFlabel = stringbykey( "LABEL", note( $targetwn ) )
// assemble the batch mode wave list
variable peaksign = 1 // sets optional parameter to determine sign of peak, +1 for positive, -1 for negative peak
// required parameters
variable m_rin = 1 // 0 disable input resistance measurement, only works for current clamp :: DO NOT SET TO 1 unless you are pro ::
variable use_csr = 0 // :: -1 use x-axis for range, :: 0 use default range -inf, inf sec, :: 1 use cursors A and B for range
// optional parameters in function call
variable trace // set tr = trace if you want to specify which trace, only use if multiple traces
variable baseline = 0.25 // set bsl = baseline if you want to specify when the baseline is taken
variable xstart = 0.3
variable xend = 0.4 // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
variable xinc = 0.01
variable peakwin = 0.015 // set pwin = peakwin, this sets the window to search for the peak if multiple peaks, starts at xstart
string nm, holder //= expcode + PGFlabel + "_1", holder=""
tablen = "T_" + expcode + "_dcPSP_BM0"
variable imax = nsweeps
variable ignoreSweep = 11 // ignores sweeps >= to param
variable target_baseline = -75 // mV
variable target_thresh = 2 // mV range
// 1st pulse
xstart = 0.3
xend = 0.4 // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
xinc = 0.01
peakwin = 0.015 // set pwin = peakwin, this sets the window to search for the peak if
//nm = expcode + PGFlabel + "_1"
nm = wlwn + "_1"
holder = eventM( m_rin, use_csr, bsl = baseline, xs = xstart, xe = xend, xinc = xinc, pwin = peakwin, psign = peaksign, name = nm, tablen = tablen, maxsweep = imax, wlist = sweeplist, ignoreSweep = ignoreSweep, target_baseline = target_baseline, target_threshold = target_thresh )
// 2nd pulse
xstart = 0.4
xend = 0.5 // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
xinc = 0.0
peakwin = 0.015 // set pwin = peakwin, this sets the window to search for the peak if multiple peaks, starts at xstart
//nm = expcode + PGFlabel + "_2"
nm = wlwn + "_2"
holder = eventM( m_rin, use_csr, bsl = baseline, xs = xstart, xe = xend, xinc = xinc, pwin = peakwin, psign = peaksign, name=nm, tablen = tablen, maxsweep = imax, wlist = sweeplist, target_baseline = target_baseline, target_threshold = target_thresh )
// process and display
//graphResults( expcode, PGFlabel )
pgflabel = "" // totally faking it here
graphResults( wlwn, PGFlabel )
endmacro
// end of dcPSP beastmode
//\\//\\//\\//\\//\\//\\//\\//\\
// \\//\\//\\//\\//\\//\\//\\//\\
//
// td version for dcPSP analysis
//
// \\//\\//\\//\\//\\//\\//\\//\\
//\\//\\//\\//\\//\\//\\//\\//\\
macro dcPSP_1stpulse()
variable peaksign = 1 // sets optional parameter to determine sign of peak, +1 for positive, -1 for negative peak
// required parameters
variable m_rin = 1 // disable input resistance measurement, only works for current clamp :: DO NOT SET TO 1 unless you are pro ::
variable use_csr = 0 // :: -1 use x-axis for range, :: 0 use default range -inf, inf sec, :: 1 use cursors A and B for range
// optional parameters in function call
variable trace // set tr = trace if you want to specify which trace, only use if multiple traces
variable baseline = 0.25 // set bsl = baseline if you want to specify when the baseline is taken
variable xstart = 0.3
variable xend = 0.4 // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
variable xinc = 0.01
variable peakwin = 0.01 // set pwin = peakwin, this sets the window to search for the peak if multiple peaks, starts at xstart
string nm = ""
print eventM( m_rin, use_csr, bsl = baseline, xs = xstart, xe = xend, xinc = xinc, pwin = peakwin, psign = peaksign, name = nm, tablen = "Test" )
endmacro
//\\//\\//\\//\\//\\//\\//\\//\\
// \\//\\//\\//\\//\\//\\//\\//\\
//
// td version for dcPSP analysis
//
// \\//\\//\\//\\//\\//\\//\\//\\
//\\//\\//\\//\\//\\//\\//\\//\\
macro dcPSP_2ndPulse()
variable peaksign = 1 // sets optional parameter to determine sign of peak, +1 for positive, -1 for negative peak
// required parameters
variable m_rin = 1 // disable input resistance measurement, only works for current clamp :: DO NOT SET TO 1 unless you are pro ::
variable use_csr = 0 // :: -1 use x-axis for range, :: 0 use default range -inf, inf sec, :: 1 use cursors A and B for range
// optional parameters in function call
variable trace // set tr = trace if you want to specify which trace, only use if multiple traces
variable baseline = 0.25 // set bsl = baseline if you want to specify when the baseline is taken
variable xstart = 0.4
variable xend = 0.5 // set xs = xstart, xe = xend to specify a manual range for peak detection and analysis
variable xinc = 0.0
variable peakwin = 0.01 // set pwin = peakwin, this sets the window to search for the peak if multiple peaks, starts at xstart
print eventM( m_rin, use_csr, bsl = baseline, xs = xstart, xe = xend, xinc = xinc, pwin = peakwin, psign = peaksign )
endmacro
macro buildMKP()
variable ntabs = 5
buildmasterkinpanel( ntabs )
offsetpanelmac()
endmacro
macro passSandwich()
string pathn = "collector_data"
print passiveSandwich( setpathn = pathn )
endmacro
function/S textwave2stringlist( twn [, dc, sep ] )
string twn
variable dc // set to 1 to cut text to just datecode
string sep // set this to use something other than ;
WAVE/T tw = $twn
string separator = ";"
if(!paramisdefault( sep ))
separator = sep
endif
variable i, n = numpnts( tw )
string str_list = "", sadd = ""
for( i=0; i<n; i+=1 )
if( paramisdefault( dc ) )
sadd = tw[ i ]
else
if( dc == 1 )
sadd = datecodefromanything( tw[ i ] )
endif
endif
str_list += sadd + separator //";"
endfor
return str_list
end
macro kv2prismOLD( twn ) // access to SIRI etc
string twn // text wave name, date codes for data to process
string dcl = "" //= "20200422c;20200422f;20200423c;20200423e;20200423f;"
//dcl = "20200415b;20200415c;20200415d;20200416f;20200416i;"
//dcl = returntablist() // returns comma separated
// need semicolon separated
string dcls = "" // replacestring( ",", dcl, ";" )
dcls = textwave2stringlist( twn, dc = 1, sep = "," ) // old prism routine uses commas!!!
print "dc list: ", dcls
string dcls_plus = textwave2stringlist( twn )
print "dc list plus: ", dcls_plus
prism( dc_list = dcls, tablename_prefix = twn )
// get the peak
//print modernkvprism( dcls, forcesecond = 1 ) //, forcesecond = 1) //, residual = 1 )
// get the residual
//print modernkvprism( dcls, residual = 1, forcesecond = 1 )
//passiveSummaryCollector( twn )
endmacro
macro kv2prismSLOW( twn )
string twn // text wave name, date codes for data to process
string dcl = "" //= "20200422c;20200422f;20200423c;20200423e;20200423f;"
//dcl = "20200415b;20200415c;20200415d;20200416f;20200416i;"
//dcl = returntablist() // returns comma separated
// need semicolon separated
string dcls = "" // replacestring( ",", dcl, ";" )
dcls = textwave2stringlist( twn, dc = 1 )
print "dc list: ", dcls
string dcls_plus = textwave2stringlist( twn )
print "dc list plus: ", dcls_plus
// get the peak
print modernkvprism( dcls, forcesecond = 1 ) //, forcesecond = 1) //, residual = 1 )
// get the residual
print modernkvprism( dcls, residual = 1, forcesecond = 1 )
passiveSummaryCollector( twn )
endmacro
macro kv2prismFAST( twn )
string twn // text wave name, date codes for data to process
string dcl = "" //= "20200422c;20200422f;20200423c;20200423e;20200423f;"
//dcl = "20200415b;20200415c;20200415d;20200416f;20200416i;"
//dcl = returntablist() // returns comma separated
// need semicolon separated
string dcls = "" // replacestring( ",", dcl, ";" )
dcls = textwave2stringlist( twn, dc = 1 )
print "dc list: ", dcls
string dcls_plus = textwave2stringlist( twn )
print "dc list plus: ", dcls_plus
// dcl = returntablist() // returns comma separated
// need semicolon separated
// string dcls = replacestring( ",", dcl, ";" )
print "kv2prism fast: ", dcls
print modernkvprism( dcls ) //, residual = 1 ) //, forcesecond = 1, residual = 1 )
passiveSummaryCollector( twn )
endmacro
macro ap( )
variable offset = 2.0 // 0.1 //in seconds delay to the stimulus pulse
variable trace = -1, smoothing = 1, threshold = 1
variable preStepBaseDur = 0.01 // 50 msec from offset
threshold = getparam( "Derivative cutoff", "Enter derivative cutoff (V/s, 1 for GnRH):", 2 )
offset = getparam( "Delay to step", "Enter delay to step (s):", 0.1 )
print appropV2_2( trace, smoothing, threshold, disp=2, delay=offset, preStepBase = preStepBaseDur )
print threshold
end
macro ap2qub( )
variable offset = 0.01 // delay to the stimulus pulse
variable trace = -1, smoothing = 1, threshold = 1
variable duration = 0.02 // sec, this is the time before the alignment and the time after alignment
// so total duration is 2x duration
variable resampleRate = 50e3 // resample to 50kHz
// custom for current 20191115 GnRH AP protocol
//threshold = getparam( "Derivative cutoff", "Enter derivative cutoff (V/s, 1 for GnRH):", threshold )
//offset = getparam( "Delay to step", "Enter delay to step (s):", offset )
print appropV2_2( trace, smoothing, threshold, disp=2, delay=offset, ap2qub=duration, resample_rate=ResampleRate )
print threshold
end
macro ap2sweeplist( threshold, offset, series_listwn )
variable threshold = 1 // set this to 1 for GnRH neurons
variable offset = 2.0 // 0.01 // delay to the stimulus pulse, this is used to offset the timing of the event
string series_listwn = "ap_names" // serieslistw" // 20200605 "seriesNames"
variable preStepBaseDur = 0.01 // 50 msec from offset
variable selectTrace = 1 // trace number, actual number of trace to be analyzed, usually 1 or 2
string pathn = "collector_data" // this is the default path, must run collector first!
if( !waveexists( $series_listwn ) )
print "no series wave for ap2 batchmode:", series_listwn
abort
endif
//WAVE/T sl = $series_listw
//string sn = $series_listwn[0]
string sweeplist //= returnwavesfromseries( seriesn=sn, tracen = selectTrace, pathn = pathn )
variable trace = -1, smoothing = 10
variable iseries, nseries = numpnts( $series_listwn ), seriesnum
string temp_wn, wn, datecode
variable sweepnum = 7
iseries = 0
do
temp_wn = $series_listwn[ iseries ]
print "processing series", temp_wn
seriesnum = seriesnumber( temp_wn )
datecode = datecodefromanything( temp_wn )
wn = datecode + "g1s" + num2str( seriesnum ) + "sw" + num2str( sweepnum ) + "t1"
sweeplist = returnwavesfromseries( wn, tracen = selectTrace, pathn = pathn )
print "wave list", sweeplist
// appropV2_2( trace, smoothing, threshold, disp=2, delay=offset, slist = sweeplist )
print appropV2_2( trace, smoothing, threshold, disp=0, delay=offset, preStepBase = preStepBaseDur, slist = sweeplist )
iseries += 1
while( iseries < nseries )
runAPprocessor( series_listwn )
end
macro run_run_sAHP_Xi( slistwn )
string slistwn // name of wave containing series names
variable bstart = 1.9 // baseline start
variable bend = 2.0 // baseline end
variable xstart = 2.5 // time to start looking for minimum
variable xend = 5.0 // end time, set to INF for end of wave
variable binsize = 0.1 // in seconds, between xstart and xend bins
run_sAHPprocessor( slistwn, bstart, bend, xstart, xend, binsize )
endmacro
macro run_run_sAHP_TD( slistwn )
string slistwn // name of wave containing series names
variable bstart = 0.0 // baseline start
variable bend = 0.01 // baseline end
variable xstart = 0.5 // time to start looking for minimum
variable xend = 1.0 // end time, set to INF for end of wave
variable binsize = 0.1 // in seconds, between xstart and xend bins
run_sAHPprocessor( slistwn, bstart, bend, xstart, xend, binsize )
endmacro
function run_sAHPprocessor( slistwn, bstart, bend, xstart, xend, binsize )
string slistwn //= "ap_names"
variable bstart //= 1.9 // baseline start
variable bend //= 2.0 // baseline end
variable xstart //= 2.5 // time to start looking for minimum
variable xend //= 5.0 // end time, set to INF for end of wave
variable binsize //= 0.1 // in seconds, between xstart and xend bins
WAVE/T/Z sl = $slistwn
string pathn = "collector_data" // this is the default path, must run collector first!
variable i, nw = numpnts( sl )
variable j, nparams, nout //= 5 // zero based
string wn, wl, out_wl // wave list to process
string temp_wn, tablen
string paramlist = "sAHPsumBase" + ";" +"sAHPsumMinAbs" + ";" + "sAHPsumMinRel" + ";" + "sAHPsumMinRel2" + ";" + "sAHPsumMint" + ";" + "sAHPsumMaxR2" + ";" + "sAHPsumMaxT"
nparams = itemsinlist( paramlist )
for( j = 0; j < nparams; j += 1 )
tablen = slistwn + "_" + stringfromlist( j, paramlist )
edit/K=1/N=$tablen
endfor
for( i = 0; i < nw; i += 1 )
wn = sl[ i ]
wl = returnwavesfromseries( wn, tracen = 1, pathn = pathn )
// get wave list from top graph
//wl = tracenamelist( "", ";", 1 )
//print wl
out_wl = sAHPprocessor( wl, bstart, bend, xstart, xend, binsize )
nout = itemsinlist(out_wl)
if( nout != nparams )
print "run_sAHPprocessor: param mismatch"
endif
for( j = 0; j < nparams; j += 1 )
temp_wn = stringfromlist( j, out_wl )
WAVE/Z tw = $temp_wn
tablen = slistwn + "_" + stringfromlist( j, paramlist )
appendtotable/W=$tablen tw
endfor
endfor
endmacro
macro runAPprocessor( slistwn )
string slistwn = "ap_names"
APprocessorSL( slistwn )
passiveSummaryCollector( slistwn )
endmacro
function APprocessorSL( series_listwn ) // ( threshold, offset, series_listwn )
string series_listwn //= "ap0" // serieslistw" // 20200605 "seriesNames"
variable threshold = 1 // set this to 1 for GnRH neurons
variable offset = 0.01 // delay to the stimulus pulse, this is used to offset the timing of the event
variable HertzConversionFactor = 0.5 // secs, duration of current pulse
variable selectTrace = 1 // trace number, actual number of trace to be analyzed, usually 1 or 2
string pathn = "collector_data" // this is the default path, must run collector first!
if( !waveexists( $series_listwn ) )
print "no series wave for ap2 batchmode:", series_listwn
abort
endif
string sweeplist //= returnwavesfromseries( seriesn=sn, tracen = selectTrace, pathn = pathn )
variable iseries, nseries = numpnts( $series_listwn )
variable ipar, npar = 12 // number of parameters in all data
variable isweep, nsweeps = 15 // number sweeps in AP protocol
string sn, wavelet, alldataname, tracedataname, abstime, reltime, tabstime, treltime
//string firstSpikeSummary //= "fss_"
//string excitability //= "exc_"
WAVE/T/Z series_listw = $series_listwn
iseries = 0
do
sn = series_listw[ iseries ]
print "processing series", sn
sweeplist = returnwavesfromseries( sn, tracen = selectTrace, pathn = pathn )
//print "wave list", sweeplist
//appropV2_2( trace, smoothing, threshold, disp=2, delay=offset, slist = sweeplist )
wavelet = removequotes( stringfromlist( 0, sweeplist ))
print wavelet
alldataname = wavelet + "_alldata"
tracedataname = wavelet + "_tracedata"
abstime = wavelet + "_abstime"
reltime = wavelet + "_reltime"
tabstime = wavelet + "_tabstime"
treltime = wavelet + "_treltime"
if( iseries == 0 )
// make the tables to store the summaries
string wn = "firstspike_" + series_listwn
duplicate/O $alldataname, $wn
WAVE/Z firstspikesummary = $wn
firstspikesummary = nan
redimension /N=(nseries, npar) firstSpikeSummary
wn = "excite_" + series_listwn
make/O/N=(nsweeps, nseries) $wn
WAVE/Z excitability = $wn
excitability = nan
wn = "snames_" + series_listwn
make/T/O/N=(nseries) $wn
WAVE/Z/T seriesNames = $wn
seriesnames = ""
wn = "stimes_" + series_listwn
make/D/O/N=(nseries) $wn
WAVE/Z seriesTimes = $wn
seriestimes = nan
endif
seriesNames[ iseries ] = wavelet
WAVE/Z alldatawave = $alldataname
WAVE/Z tracedatawave = $tracedataname
WAVE/Z timedatawave = $abstime
seriestimes[ iseries ] = timedatawave[0]
// scaling factors
make/O/N=(npar) scaling
scaling[0] = 1 // sweep
scaling[1] = 1 // spike number
scaling[2] = 1 // interval
scaling[3] = 1000 // latency
scaling[4] = 1000 // amp
scaling[5] = 1000 // width
scaling[6] = 1000 // ahp amp
scaling[7] = 1000 // ahp loc
scaling[8] = 1000 // ahp min
scaling[9] = 1 // rate of rise
scaling[10] = 1000 // threshold
scaling[11] = 1000 // baseline
for( ipar=0; ipar<npar; ipar+=1 )
firstspikesummary[ iseries ][ ipar ] = scaling[ ipar ] * alldatawave[ 0 ][ ipar ] // first spike row
endfor
variable isw = 0, nsw = dimsize( tracedatawave, 0 ) // number of sweeps in current series
isw = nsw-1
for( isweep=(nsweeps-1); isweep>=0; isweep -=1 )
excitability[ isweep ][ iseries ] = tracedatawave[ isw ][ 1 ] / HertzConversionFactor // column containing excitability
isw -= 1
if( isw <0 )
break
endif
endfor
iseries += 1
while( iseries < nseries )
edit/k=1 seriesnames, seriestimes, firstSpikeSummary
ModifyTable format(seriestimes)=8
modifytable title[1]="names"
modifytable title[2]="dateTime"
modifytable title[3]="sweep"
modifytable title[4]="spike"
modifytable title[5]="interval"
modifytable title[6]="ap latency"
modifytable title[7]="ap amp"
modifytable title[8]="ap width"
modifytable title[9]="ahp amp"
modifytable title[10]="ahp loc"
modifytable title[11]="ahp min"
modifytable title[12]="ap rate rise"
modifytable title[13]="ap threshold"
modifytable title[14]="baseline"
edit/k=1 excitability
end
macro makeBlastPanel()
makeBPfunc()
end
macro refreshBlastPanel()
refreshdetect()
end
macro refreshInt()
refreshintervals()
end
macro refreshT50R( )
variable thissign = -1
variable disp = 1
refreshrisetimes( thissign, disp = 1 ) //, disp = 1 )
endmacro
macro scalewaves( str, scalef )
string str = "*1sw*" // string to identify waves to scale
variable scalef = 1000 // scaleing factor
//WaveList(matchStr, separatorStr, optionsStr )
string wn="", wl = wavelist( str, ";", "" )
variable i=0, nw = 0
nw = itemsinlist( wl )
do
wn = removequotes( stringfromlist( i, wl ) )
$wn *= scalef
i+=1
while( i < nw )
endmacro
////////////////////////////////////////////////////////////////////////////////
// uses wavestats to report max(or min) based on sign
// for each trace in active window
////////////////////////////////////////////////////////////////////////////////
macro getMeanCsr()
variable thesign=1
string wavelist=tracenamelist("",";",1)
string wavelet=removequotes(stringfromlist(0,wavelist))
variable nwaves=itemsinlist(wavelist)
variable iwave
variable prepoint=xcsr(A)
variable postpoint=xcsr(B)
variable reg2start=xcsr(c),reg2end=xcsr(d)
variable mean1=0,mean2=0
print "wavename \t mean1 \t mean2"
iwave=0
do
prepoint=xcsr(a)
postpoint=xcsr(b)
wavelet=removequotes(stringfromlist(iwave, wavelist))
wavestats /Q/Z/R=((prepoint), (postpoint)) $wavelet
mean1=V_avg
prepoint=reg2start
postpoint=reg2end
wavestats /Q/Z/R=((prepoint), (postpoint)) $wavelet
mean2=v_avg
print wavelet,mean1,mean2
iwave+=1
while (iwave<nwaves)
end
macro csr()
showinfo /cp=1
end
macro getMaxCsr(thesign)
variable thesign=1
string wavelist=tracenamelist("",";",1)
string wavelet=removequotes(stringfromlist(0,wavelist))
variable nwaves=itemsinlist(wavelist)
variable iwave
variable prepoint=xcsr(A)
variable postpoint=xcsr(B)
variable peak = 0,peak_time=0
print "wavename \t peak \t peak time \t average"
iwave=0
do
wavelet=removequotes(stringfromlist(iwave, wavelist))
wavestats /Q/Z/R=((prepoint), (postpoint)) $wavelet
peak=0
peak_time=0
if(thesign>0)
peak = V_max
peak_time=V_maxloc
else
peak = V_min
peak_time=V_minloc
endif
print wavelet,"\t",peak,"\t",peak_time,"\t",V_avg
iwave+=1
while (iwave<nwaves)
end
macro buildocvmmac()
buildocvmwin()
endmacro
macro nsna()
buildpsnsnapanel()
end
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