/
newsuperscript.s2s
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newsuperscript.s2s
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'big script for analyzing STG files
'
'heavily insipired by / borrowed from dirk bucher's pylPhConsec.s2s
'
'declare global variables
var UnitsDo%[3]; 'these flag which units are being analyzed
var Thresholds[4][2]; 'holds low and hi cutoffs for spike detection for each channel
var Channels%[4]; 'remembers the channel number for each unit
var fname$, fnumb$, fnum%, nfiles%, fnames$[2000], windname$, exname$; 'variables for interaction with files
var fcount%, ffirst%, counter%; '
var nchans%,chlist%[30]; 'for channel searches
var offsetT; 'time added to start for next file
var PDLPPY%, PDLPPY$[3], memPDLPPY%[3], mode%; 'for looped ananlysis of pyloric units
var PDsubs$:="Don'tSubtract", LPsubs$:="Don'tSubtract", PYsubs$:="Don'tSubtract", jitter[3],delmode%[3];
var BurstChannels%[3], BurstMax[3], BurstNum%[3];
var vh%, cheapvar%, automator%;
var ok%, ok1%, okcursor%, okevents%, oksubs%, okbursts%; 'cursor variables
var outfile%[3], unitcounter%;
'some default value assignments
PDLPPY$[0]:="PD";
PDLPPY$[1]:="LP";
PDLPPY$[2]:="PY";
BurstMax[0]:=0.1;
BurstMax[1]:=0.1;
BurstMax[2]:=0.1;
BurstNum%[0]:=3;
BurstNum%[1]:=3;
BurstNum%[2]:=3;
jitter[0]:=0.1;
jitter[1]:=0.1;
jitter[2]:=0.1;
'procedure to delete events in one channel from another channel
' so performs a subtraction. channel1% and channel2% point to event channels
' and duplicate spikes are subtracted FROM channel1%, if they are within
' time jitter.
proc DeleteEvents (channel1%, channel2%, jitter, delmode%) 'Procedure to delete spikes in event channel2 from event channel1
var DupSpikeTimes[100000], DupCounter%, DupCount%;
var checkchans%[30], checkchancount%, checkchancounter%;
var problemflag%:=0;
'this is to make sure there are no bugs because of non event channels sent to the procedure
checkchancount%:=ChanList(checkchans%[],2);
for checkchancounter%:=0 to checkchancount%-1 step 1 do 'check for event channels
if checkchans%[checkchancounter%]=channel1% or checkchans%[checkchancounter%]=channel2% then 'flag as found event channel
problemflag%:=problemflag%+1;
endif
next
if problemflag%=2 or cheapvar%=1 then 'files have passed error checks, have two event channels
DupCount%:=ChanData(channel2%, DupSpikeTimes[], 0, MaxTime()); 'gets spike times from channel2
for DupCounter%:=0 to DupCount%-1 step 1 do 'stop at each event in channel 2
MemDeleteTime(channel1%, delmode%, DupSpikeTimes[DupCounter%], jitter); 'spike2 function performs deletion
next;
endif
end
offsetT:=0;
' start dialog chooses first file
DlgCreate("Select the first file");
DlgText("Then choose .smr file to start with",0,4);
DlgText("from the files on your computer...",0,5);
DlgReal(1,"First set start time for first file(in s): ",0,1750000);
DlgString(2,"Experiment Name?",16);
DlgButton(0,"Get me out of here");
DlgButton(1, "I'm ready!");
ok%:=DlgShow(offsetT, exname$);
if ok%=0 then 'exit script
halt;
endif
'fills an array with .smr filenames in the directory .
ok%:=FileOpen("",0);
fname$:=FileName$(3);
fnumb$:=FileName$(4);
fname$:=fname$+fnumb$+".smr";
nfiles%:=FileList(fnames$[], 0);
'... then checks until finds the selected one
ffirst%:=-1;
repeat ffirst%:=ffirst%+1;
until fnames$[ffirst%]=fname$;
FileClose();
'Set up save files
for unitcounter%:=0 to 2 step 1 do
outfile%[unitcounter%]:=FileOpen(exname$ + "_" + PDLPPY$[unitcounter%] + "_bursts.txt",1);
PrintLog(outfile%);
if outfile%[unitcounter%]<0 then
outfile%[unitcounter%]:=FileNew(1);
'Print(PDLPPY$[unitcounter%]+"burstfile,start,end,realstart,realend,period,frequency,dutycycle,spikes/burst,freqinburst,burstintervalparam,burstnumparam");
FileSaveAs(exname$+"_"+PDLPPY$[unitcounter%]+"_bursts.txt",1);
endif
FileClose();
next;
FrontView(App (3));
'big loop for each file
for fcount%:=ffirst% to nfiles%-1 step 1 do
' First get basic information about current file
fname$:=fnames$[fcount%];
ok%:=FileOpen(fname$,0,1);
fnumb$:=FileName$(4);
windname$:=FileName$(3);
if exname$<>"" then windname$:=exname$; endif
fnum%:=val(fnumb$);
XRange(MaxTime()/2,MaxTime()/2+MaxTime()/4); 'range from midpoint to 3/4 of file, Dirk's
Optimise(-1); 'optimize y range for all channelsd
WindowVisible(3); 'show it
'dialog selects which units are to be analyzed
' can be changed from one file to the next, but remembers
' previous settings
repeat ' returns here if "repeat file" selected after burst detection (okbursts%)
if automator%=0 then 'choose units manually
DlgCreate("Choose Units");
DlgText("Set to 1 to analyze",0,5);
DlgInteger(1, "Get PD?",0,1,0,0,"0|1"); 'these define the spinning input boxes
DlgInteger(2, "Get LP?",0,1,0,0,"0|1");
DlgInteger(3, "Get PY?",0,1,0,0,"0|1");
DlgButton(0, "Skip File");
DlgButton(1, "Go!");
DlgButton(2, "Exit Script");
ok%:=DlgShow(UnitsDo%[0], UnitsDo%[1], UnitsDo%[2]); 'these variables take the inputs
if ok%=2 then 'exit script
FrontView (App (3));
halt;
endif
else
ok%:=1;
endif
if ok%=1 then 'analyze file
repeat ' returns here to restart file after spike detection
Fontset("arial",14,2);
XRange(MaxTime()/2,MaxTime()/2+MaxTime()/60);
Optimise(-1);
'for loop here goes through PD, LP, and PY
for PDLPPY%:=0 to 2 step 1 do
if UnitsDo%[PDLPPY%]=1 then 'only do if unit is marked to do
'define string form for channels names, etc
ChanList(chlist%[],2049);
HCursorDelete(-1);
'finds the relevant channel if known, or sets them in first waveform channel by default
if Channels%[PDLPPY%]=0 then
HCursorNew(chlist%[1]);
HCursorNew(chlist%[1]);
else
HCursorNew(Channels%[PDLPPY%]);
HCursorNew(Channels%[PDLPPY%]);
endif
repeat 'for okevents%, repeat point for threshold set retry
'first set cursors appropriately
HCursor(1,Thresholds[PDLPPY%][0]);
HCursor(2,Thresholds[PDLPPY%][1]);
HCursorLabel(4,1,PDLPPY$[PDLPPY%]+" Threshold");
HCursorLabel(4,2,PDLPPY$[PDLPPY%]+" Large Spike Cutoff");
if automator%=0 then
okcursor%:=Interact("Place "+PDLPPY$[PDLPPY%]+" Cursors", 504, 0, " OK ","Stop Script","Skip "+PDLPPY$[PDLPPY%]);
else
okcursor%:=1;
endif
docase
case okcursor%=2 then 'stop script chosen, so we stop the script
FrontView(App(3));
halt
case okcursor%=3 then 'skip unit
Channels%[PDLPPY%]:=0; 'changes reflect settings for next file
Thresholds[PDLPPY%][0]:=0;
Thresholds[PDLPPY%][1]:=0;
UnitsDo%[PDLPPY%]:=0;
okevents%:=1; 'to get out of repeat loop checking for OK on current file
case okcursor%=1 then 'get the spikes
'set the thresholds to cursor values
Channels%[PDLPPY%]:=HCursorChan(1);
Thresholds[PDLPPY%][0]:=HCursor(1);
Thresholds[PDLPPY%][1]:=HCursor(2);
memPDLPPY%[PDLPPY%]:=MemChan(2); 'Creates new event channel to hold PD spikes
'rising or falling?
if Thresholds[PDLPPY%][0]<0 then
mode%:=3;
else
mode%:=2;
endif
'gets the events above the low threshold
MemImport(memPDLPPY%[PDLPPY%], Channels%[PDLPPY%], 0, MaxTime(), mode%, 0.001, Thresholds[PDLPPY%][0]);
var LargeMemChan%;
LargeMemChan%:=MemChan(2);
'gets events above the high cutoff threshold
MemImport(LargeMemChan%, Channels%[PDLPPY%], 0, MaxTime(), mode%, 0.001, Thresholds[PDLPPY%][1]);
'subtract the high events from the low events
cheapvar%:=1;
DeleteEvents(memPDLPPY%[PDLPPY%], LargeMemChan%, 0.004,0);
cheapvar%:=0;
'show the events for user check
ChanShow(memPDLPPY%[PDLPPY%]);
ChanTitle$(memPDLPPY%[PDLPPY%], PDLPPY$[PDLPPY%]+"spikes");
DrawMode(memPDLPPY%[PDLPPY%], 2);
ChanOrder(Channels%[PDLPPY%],-1, memPDLPPY%[PDLPPY%]);
'and ask
if automator%=0 then
okevents%:=Interact("Spikes good? (Subtraction is later)", 504, 0, "Good!", "No. Try again.");
if okevents%=2 then
ChanDelete(memPDLPPY%[PDLPPY%]);
endif
else
okevents%:=1;
endif
endcase
until okevents%=1;
endif 'UnitsDo check
next; 'PDLPPY%
' Now Subtractions
if UnitsDo%[0]=1 or UnitsDo%[1]=1 or UnitsDo%[2]=1 then
repeat 'continues until subtractions are done
if automator%=0 then
'define the dialog
DlgCreate("Spike Subtractions");
DlgString(1, "PD Spikes - ",12, "", 0, 0, "Don'tSubtract|SubtractPY|SubtractLP|SubtractBoth");
DlgReal(2, "PD subtraction jitter - ",0,1);
DlgInteger(3, "PD - one spike only? (0 for yes, 1 to clear all within jitter) - ", 0, 1, 0, 0, "0|1");
DlgString(4, "LP Spikes - ",12, "", 0, 0, "Don'tSubtract|SubtractPD|SubtractPY|SubtractBoth");
DlgReal(5, "LP subtraction jitter - ",0,1);
DlgInteger(6, "LP - one spike only? (0 for yes, 1 to clear all within jitter) - ", 0, 1, 0, 0, "0|1");
DlgString(7, "PY Spikes - ",12, "", 0, 0, "Don'tSubtract|SubtractPD|SubtractLP|SubtractBoth");
DlgReal(8,"PY subtraction jitter - ",0,1);
DlgInteger(9, "PY - one spike only? (0 for yes, 1 to clear all within jitter) - ", 0, 1, 0, 0, "0|1");
DlgButton(0,"Done. Ready for Bursts.");
DlgButton(1,"Do Subtractions!");
DlgButton(2,"Start File Over.");
oksubs%:=DlgShow(PDsubs$, jitter[0], delmode%[0], LPsubs$, jitter[1], delmode%[1], PYsubs$, jitter[2], delmode%[2]); 'Get the string inputs
'Note these strings are unchanged from file to file
'so next file comes pre populated with values from previous file
else
oksubs%:=1;
endif
'do relevant subtractions, if possible
if oksubs%=1 then
docase
case PDsubs$="SubtractLP" then
DeleteEvents(memPDLPPY%[0],memPDLPPY%[1],jitter[0],delmode%[0]);
case PDsubs$="SubtractPY" then
DeleteEvents(memPDLPPY%[0],memPDLPPY%[2],jitter[0],delmode%[0]);
case PDsubs$="SubtractBoth" then
DeleteEvents(memPDLPPY%[0],memPDLPPY%[1],jitter[0],delmode%[0]);
DeleteEvents(memPDLPPY%[0],memPDLPPY%[2],jitter[0],delmode%[0]);
endcase
docase
case LPsubs$="SubtractPD" then
DeleteEvents(memPDLPPY%[1],memPDLPPY%[0],jitter[1],delmode%[1]);
case LPsubs$="SubtractPY"then
DeleteEvents(memPDLPPY%[1],memPDLPPY%[2],jitter[1],delmode%[1]);
case LPsubs$="SubtractBoth" then
DeleteEvents(memPDLPPY%[1],memPDLPPY%[0],jitter[1],delmode%[1]);
DeleteEvents(memPDLPPY%[1],memPDLPPY%[2],jitter[1],delmode%[1]);
endcase
docase
case PYsubs$="SubtractPD" then
DeleteEvents(memPDLPPY%[2],memPDLPPY%[0],jitter[2],delmode%[2]);
case PYsubs$="SubtractLP" then
DeleteEvents(memPDLPPY%[2],memPDLPPY%[1],jitter[2],delmode%[2]);
case PYsubs$="SubtractBoth" then
DeleteEvents(memPDLPPY%[2],memPDLPPY%[0],jitter[2],delmode%[2]);
DeleteEvents(memPDLPPY%[2],memPDLPPY%[1],jitter[2],delmode%[2]);
endcase
endif 'if oksubs%=1
if automator%=1 then oksubs%:=0; endif
until oksubs%<>1; 'no more subtractions to do
else oksubs%:=0;
endif
if oksubs%=2 then 'start file over, delete channels
if UnitsDo%[0]=1 then ChanDelete(memPDLPPY%[0]); endif
if UnitsDo%[1]=1 then ChanDelete(memPDLPPY%[1]); endif
if UnitsDo%[2]=1 then ChanDelete(memPDLPPY%[2]); endif
endif
until oksubs%<>2; 'repeat file if user wanted
'onward to burst detection
'
'create initial bursts based on default settings:
for counter%:=0 to 2 step 1 do 'check all three units
if UnitsDo%[counter%]=1 then 'if we are doing this unit, do it
BurstChannels%[counter%]:=MemChan(5);
BurstMake(BurstChannels%[counter%], memPDLPPY%[counter%], 0, MaxTime(), BurstMax[counter%], BurstMax[counter%], Burstnum%[counter%]);
ChanShow(BurstChannels%[counter%]);
ChanTitle$(BurstChannels%[counter%],PDLPPY$[counter%]+" Bursts");
ChanOrder(memPDLPPY%[counter%], -1, BurstChannels%[counter%]);
endif
next
repeat 'for okbursts%
HCursorDelete(-1);
var onlyfourcursors%; 'yea... dumb!
onlyfourcursors%:=0;
for counter%:=0 to 2 step 1 do
if UnitsDo%[counter%]=1 then
if onlyfourcursors%<4 then
onlyfourcursors%:=onlyfourcursors%+1;
HCursorNew(Channels%[counter%],Thresholds[counter%][0]);
HCursorLabel(4,onlyfourcursors%,PDLPPY$[counter%]+" Threshold");
else
HCursorDelete(4);
HCursorNew(Channels%[counter%],Thresholds[counter%][0]);
HCursorLabel(4,4,PDLPPY$[counter%]+" Threshold");
endif
if onlyfourcursors%<4 then
onlyfourcursors%:=onlyfourcursors%+1;
HCursorNew(Channels%[counter%],Thresholds[counter%][1]);
HCursorLabel(4, onlyfourcursors%,PDLPPY$[counter%]+" Large Spike Cutoff");
endif
endif
next
if automator%=1 then
XRange(MaxTime()/3, 2*MaxTime()/3);
endif
okbursts%:=Interact("How do you want to proceed?", 504, 0, "Log Data", "Revise Bursts", "Stop Script", "Restart File","Add/Subtract Time","Skip File");
docase
case okbursts%=5 then
var okaddtime%, timeamount%;
timeamount%:=0;
DlgCreate("Add or Subtract Time");
DlgText("Current Overall Experiment Time, Start of This File = "+Str$(offsetT)+" s .",0,1);
DlgInteger(1,"Insert how many seconds into experiment overall time? (can be negative) ",-500000,500000,0,2);
okaddtime%:=DlgShow(timeamount%);
if okaddtime%=1 then offsetT:=offsetT+timeamount%; endif
case okbursts%=3 then 'stop script
PrintLog(offsetT+MaxTime());
HCursorDelete(-1);
FileClose(0,-1);
FrontView(App(3));
halt
case okbursts%=2 then ' revise bursts
var okburstpams%;
DlgCreate("Burst Parameters");
DlgText("PD burst parameters:",0,1);
DlgReal(1,"Max Spike Interval",0,100,0,2);
DlgInteger(2,"Min Spike Number",2,100,0,3);
DlgText("LP burst parameters:",0,5);
DlgReal(3,"Max Spike Interval",0,100,0,6);
DlgInteger(4,"Min Spike Number",2,100,0,7);
DlgText("PY burst parameters:",0,9);
DlgReal(5,"Max Spike Interval",0,100,0,10);
DlgInteger(6,"Min Spike Number",2,100,0,11);
okburstpams%:=DlgShow(BurstMax[0],BurstNum%[0],BurstMax[1],BurstNum%[1],BurstMax[2],BurstNum%[2]);
if okburstpams%=1 then
for counter%:=0 to 2 step 1 do
if UnitsDo%[counter%]=1 then
MemDeleteTime(BurstChannels%[counter%],3,0,MaxTime());
BurstMake(BurstChannels%[counter%],memPDLPPY%[counter%],0,MaxTime(),BurstMax[counter%],BurstMax[counter%],BurstNum%[counter%]);
endif
next
endif
case okbursts%=1 then 'put it down in log
'putting burst start and end times into separate arrays
var burststart[3][100000],burstend[3][100000];
var nburststart%[3],nburstend%[3];
var recordflag%:=0;
'for pd burstchannel:
for unitcounter%:=0 to 2 step 1 do
if UnitsDo%[unitcounter%]=1 then
recordflag%:=1;
MarkMask(BurstChannels%[unitcounter%],-1,1,-1); 'reset = include all codes+
MarkMask(BurstChannels%[unitcounter%],0,-1,-1); 'set all codes off
MarkMask(BurstChannels%[unitcounter%],0,1,0); 'turn on code 0 = burst start only; 1=end code only
nburststart%[unitcounter%]:=ChanData(BurstChannels%[unitcounter%],burststart[unitcounter%][],0,MaxTime()); 'get levator burst start times
MarkMask(BurstChannels%[unitcounter%],-1,1,-1); 'reset = include all codes
MarkMask(BurstChannels%[unitcounter%],0,-1,-1); 'set all codes off
MarkMask(BurstChannels%[unitcounter%],0,1,1); 'turn on code 0 = burst start only; 1=end code only
nburstend%[unitcounter%]:=ChanData(BurstChannels%[unitcounter%],burstend[unitcounter%][],burststart[unitcounter%][0],MaxTime()); 'get levator burst end times
MarkMask(BurstChannels%[unitcounter%],-1,1,-1); 'reset = include all codes
'now output!
var burstcounter%, period, frequency, dutycycle, nspikes%[100000], burstfrequency, dummy[100000], start, finish, params$;
params$:=Str$(BurstMax[unitcounter%])+","+Str$(BurstNum%[unitcounter%]);
var b%;
for b%:=0 to nburststart%[unitcounter%]-1 step 1 do
nspikes%[b%]:=ChanData(memPDLPPY%[unitcounter%],dummy[],burststart[unitcounter%][b%],burstend[unitcounter%][b%]);
next ; 'b%;
outfile%[unitcounter%]:=FileOpen(exname$ + "_" + PDLPPY$[unitcounter%] + "_bursts.txt",1);
for b%:=nburststart%[unitcounter%]-1 to 0 step -1 do
burstfrequency:=(nspikes%[b%]-1)/(burstend[unitcounter%][b%]-burststart[unitcounter%][b%]);
start:=burststart[unitcounter%][b%];
finish:=burstend[unitcounter%][b%];
if b%<nburststart%[unitcounter%]-1 then
period:=burststart[unitcounter%][b%+1]-burststart[unitcounter%][b%];
frequency:=1/period;
dutycycle:=(burstend[unitcounter%][b%]-burststart[unitcounter%][b%])/period;
Print("%s,%f,%f,%f,%f,%f,%f,%f,%d,%f,%s\n",exname$+fnumb$,start,finish,start+offsetT,finish+offsetT,period,frequency,dutycycle,nspikes%[b%],burstfrequency,params$);
else
Print("%s,%f,%f,%f,%f,%s,%d,%f,%s\n",exname$+fnumb$,start,finish,start+offsetT,finish+offsetT,",,",nspikes%[b%],burstfrequency,params$);
endif
next; 'b%
FileSave();
FileClose();
endif
next;
docase
case UnitsDo%[0]=1 and UnitsDo%[1]=1 and UnitsDo%[2]=1 then
ExportChanList();
ExportChanList(0,MaxTime(), memPDLPPY%[0], memPDLPPY%[1], memPDLPPY%[2]);
FileSaveAs("spikes_"+windname$+fnumb$+".smr",0);
case UnitsDo%[0]=1 and UnitsDo%[1]=1 and UnitsDo%[2]=0 then
ExportChanList();
ExportChanList(0,MaxTime(),memPDLPPY%[0], memPDLPPY%[1]);
FileSaveAs("spikes_"+windname$+fnumb$+".smr",0);
case UnitsDo%[0]=1 and UnitsDo%[1]=0 and UnitsDo%[2]=1 then
ExportChanList();
ExportChanList(0,MaxTime(),memPDLPPY%[0],memPDLPPY%[2]);
FileSaveAs("spikes_"+windname$+fnumb$+".smr",0);
case UnitsDo%[0]=0 and UnitsDo%[1]=1 and UnitsDo%[2]=1 then
ExportChanList();
ExportChanList(0,MaxTime(),memPDLPPY%[1],memPDLPPY%[2]);
FileSaveAs("spikes_"+windname$+fnumb$+".smr",0);
case UnitsDo%[0]=1 and UnitsDo%[1]=0 and UnitsDo%[2]=0 then
ExportChanList();
ExportChanList(0,MaxTime(),memPDLPPY%[0]);
FileSaveAs("spikes_"+windname$+fnumb$+".smr",0);
case UnitsDo%[0]=0 and UnitsDo%[1]=1 and UnitsDo%[2]=0 then
ExportChanList();
ExportChanList(0,MaxTime(),memPDLPPY%[1]);
FileSaveAs("spikes_"+windname$+fnumb$+".smr",0);
case UnitsDo%[0]=0 and UnitsDo%[1]=0 and UnitsDo%[2]=1 then
ExportChanList();
ExportChanList(0,MaxTime(),memPDLPPY%[2]);
FileSaveAs("spikes_"+windname$+fnumb$+".smr",0);
endcase
automator%:=1;
case okbursts%=4 then
automator%:=0;
if UnitsDo%[0]=1 then
ChanDelete(memPDLPPY%[0]);
ChanDelete(BurstChannels%[0]);
endif
if UnitsDo%[1]=1 then
ChanDelete(memPDLPPY%[1]);
ChanDelete(BurstChannels%[1]);
endif
if UnitsDo%[2]=1 then
ChanDelete(memPDLPPY%[2]);
ChanDelete(BurstChannels%[2]);
endif
endcase
until okbursts%<>2 and okbursts%<>5; 'move to next file unless changed parameters, then check bursts again
endif 'if ok%=1 master for Go! to original choice after file opens to analyze file
until okbursts%<>4;
offsetT:=offsetT+MaxTime(); 'update experiment overall time
FileClose(0,-1);
next; 'fcount%