{Gel_Plotting_Macros_Andreas
This macro was modified by Andreas Becker in may 1995.
If you have questions or suggestions email to 
becker@ps1515.chemie.uni-marburg.de

This macro works in the same way as the original macro.
The chances are: 

1.) The windows are named like the original file they have been 
created from:
Original window:      acb000.tif
Temp window:         Temp abc000.tif
Plots window:          Plots abc000.tif
The name of the window appears in the pictures too.
Peaks are numbered in order of measuring.

2.) In the original macro the plotted lanes were compressed to 
a limited window size in the "plots window", it doesn’t matter 
how many lanes you evaluated. Plotting a lot of lanes each 
lane become very small. This causes an overestimation error 
for small peaks, the impossibility of measuring very small peaks  
and an inaccuracy for all the peaks. This happens always if 
you plot several lanes with quiet different pixel values.
This problem is solved by leaving the lane hight equal for any 
numbers of lanes.

It is an disadvantage of my macro that you need more buffer. 
May be you have to change the UnDoBufferSize in the 
preferences.  

}
var  {Global variables}
  RoiLeft,RoiTop,RoiWidth,RoiHeight:integer;
  GelPid,MarkedPid,TempPid,PlotsPid,nLanes,count,ppv:integer;
  SaveRoiLeft,SaveRoiTop,hOffset,vOffset:integer;
  MinY,MaxY,xscale,yscale:real;
  VerticalLanes,Uncalibrated:boolean;

{
Andreas:
Macro modified
}

                    GelTitel, TempTitel, Plotstitle:string;
                    GelPid,MarkedPid,PlotsPid,nLanes,count,ppv:integer;


procedure MarkLane;
var
  left,top,width,height:integer;
  GelNotCalibrated:boolean;
  min,max:real;
begin
  GetRoi(left,top,width,height);
  if width=0 then begin
    PutMessage('Please outline the next lane.');
    exit;
  end;
  if (VerticalLanes and (left=RoiLeft))
      or  (not VerticalLanes and (top=RoiTop)) then begin
     PutMessage('This lane has already been marked.');
     exit;
  end;
  nLanes:=nLanes+1;
  ChoosePic(GelPid);
  if VerticalLanes then begin
     MakeRoi(left+hOffset,RoiTop+vOffset,RoiWidth,RoiHeight);
     RoiLeft:=left;
     rUser1[nLanes]:=left;
  end else begin
     MakeRoi(RoiLeft+hOffset,top+vOffset,RoiWidth,RoiHeight);
     RoiTop:=top;
     rUser1[nLanes]:=top;
  end;
  GetPlotData(count,ppv,min,max);
  if min<MinY then MinY:=min;
  if max>MaxY then MaxY:=max;
  SelectPic(MarkedPid);
  if VerticalLanes
     then MakeRoi(left,RoiTop,RoiWidth,RoiHeight)
     else MakeRoi(RoiLeft,top,RoiWidth,RoiHeight);
  DrawBoundary;
  SetFontSize(9);
  if VerticalLanes then begin
    SetText('Centered, No Background');
    MoveTo(RoiLeft+RoiWidth/2,RoiTop-6);
  end else begin
    SetText('Right Justified, No Background');
    MoveTo(RoiLeft-2,RoiTop+RoiHeight/2);
  end;
  Write(nLanes:1);
  RestoreRoi;
  SelectPic(MarkedPid);
end;


macro 'Mark First Lane [1]';
var
  GelWidth,GelHeight,left,width:integer;
  margin,leftm,rightm,topm,bottomm:integer;
begin
  RequiresVersion(1.54);
  if WindowTitle='Temp' then begin
    PutMessage('To restart, select the first lane in the gel.');
    exit;
  end;
  GetRoi(RoiLeft,RoiTop,RoiWidth,RoiHeight);
  if RoiWidth=0 then begin
    PutMessage('The Setup macro expects the Gel to be displayed and the first lane outlined.');
    exit;
  end;
  VerticalLanes:=RoiHeight>RoiWidth;
  Uncalibrated:=not Calibrated;
  GelPid:=PidNumber;
  SetForegroundColor(255);
  SetBackgroundColor(0);
  MinY:=999999;
  MaxY:=-999999;
  nLanes:=0;
  margin:=20;
  GetPicSize(GelWidth,GelHeight);
  leftm:=RoiLeft;
  if leftm>margin then leftm:=margin;
  rightm:=GelWidth-(RoiWidth+RoiLeft);
  if rightm>margin then rightm:=margin;
  bottomm:=GelHeight-(RoiHeight+RoiTop);
  if bottomm>margin then bottomm:=margin;
  topm:=RoiTop;
  if topm>margin then topm:=margin;
  if VerticalLanes
    then MakeRoi(RoiLeft-leftm,RoiTop-topm,
           GelWidth-RoiLeft+leftm,RoiHeight+topm+bottomm)
    else MakeRoi(RoiLeft-leftm,RoiTop-topm,
           RoiWidth+leftm+rightm,GelHeight-RoiTop+topm);

{
Andreas:
Macro modified
}
              ChoosePic(GelPid);
              TempTitel:=WindowTitle;
              Duplicate('Temp ',TempTitel);
              TempPid:=PidNumber;
              SetText('centered Justified');
                              SetFontSize(8);
              MoveTo(5,5);
               write(TempTitel);   


  MarkedPid:=PidNumber;
  SaveRoiLeft:=RoiLeft;
  SaveRoiTop:=RoiTop;
  hOffset:=RoiLeft-leftm;
  vOffset:=RoiTop-topm;
  RoiLeft:=leftm;
  RoiTop:=topm;
  SelectPic(GelPid);
  KillRoi;
  SelectPic(MarkedPid);
  MakeRoi(RoiLeft,RoiTop,RoiWidth,RoiHeight);
  if VerticalLanes
    then RoiLeft:=-1
    else RoiTop:=-1;
  SetPlotScale(0,0);
  MarkLane;
end;

macro 'Mark Next Lane [2]';
var
  left,top,width,height:integer;
  GelNotCalibrated:boolean;
  min,max:real;
begin
  if nLanes=0 then begin
    PutMessage('Please use the "Mark First Lane" macro first.');
    Exit;
  end;
  MarkLane;
end;

macro 'Plot Lanes [3]';
var
  left,top,width,height:integer;
  GelNotCalibrated:boolean;
  i,LaneLength:integer;
  xmin,xmax,ymin,ymax,min,max:real;

{
Andreas:
Macro modified

  MaxPlotWindowHeight:integer;
}

  NeededSize:integer;
  PlotTop,PlotBottom,PlotWidth,PlotHeight:integer;
  hMargin,vMargin,SavePlotTop,PlotWindowSize:integer;
  PlotWinHeight,PlotWinWidth,PlotsPid:integer;
begin
  if nLanes=0 then begin
    PutMessage('Please use the Setup and Mark macros first.');
    Exit;
  end;
  if VerticalLanes
    then LaneLength:=RoiHeight
    else LaneLength:=RoiWidth;
  PlotWidth:=LaneLength;
  if PlotWidth<500 then PlotWidth:=500;
  if PlotWidth>(2*LaneLength) then PlotWidth:=2*LaneLength;
  PlotHeight:=PlotWidth/2;
  if PlotHeight<200 then PlotHeight:=200;
  if PlotHeight>400 then PlotHeight:=400;

{
Andreas:
Macro modified
  
    MaxPlotWindowHeight:=800;
  
}
    
  hMargin:=5;
  vMargin:=25;
  PlotWinHeight:=nLanes*PlotHeight+2*vMargin;

{
Andreas:
Macro modified

 
           if PlotWinHeight>MaxPlotWindowHeight then begin
                PlotWinHeight:=MaxPlotWindowHeight;
                PlotHeight:=(PlotWinHeight-2*vMargin)/nLanes;
            end;
}

  PlotWinWidth:=PlotWidth+2*hMargin;
  PlotWindowSize:=PlotWinWidth*PlotWinHeight;
  if PlotWindowSize>UndoBufferSize then begin
    NeededSize:=(PlotWindowSize+0.05*PlotWindowSize) div 1024;
    PutMessage('Use Preferences(Options Menu) to increase the Undo buffer size to at least ',NeededSize:1,'K.');
    KillRoi;
    exit;
  end;
  SetForegroundColor(255);
  SetBackgroundColor(0);
  SetNewSize(PlotWinWidth,PlotWinHeight);
    
{
Andreas:
Macro modified
}

              ChoosePic(GelPid);
              GelTitel:=WindowTitle;
              MakeNewWindow('Plots ',Geltitel);
              PlotsPid:=PidNumber;
  

 
               SetText('centered Justified');
                            SetFontSize(9);
               MoveTo(PlotWinWidth/2,vmargin-20);
               ChoosePic(GelPid);
               GelTitel:=WindowTitle;
               ChoosePic(Plotspid);
               write(GelTitel);   

if UnCalibrated then begin
                SetText('centerd Justified');
                            SetFontSize(9);
                MoveTo( PlotWinWidth/2,vmargin-10);
               Write('  Uncalibr.');
 end else begin 
                SetText('centered Justified');
                            SetFontSize(9);
                MoveTo(PlotWinWidth/2,vmargin-10);
               Write('  Uncalibr. OD');
 end;


  xmin:=0;
  xmax:=count-1;
  ymin:=MinY;
  ymax:=MaxY;
  xscale:=PlotWidth/(xmax-xmin);
  yscale:=PlotHeight/(ymax-ymin);
  PlotTop:=vMargin;
  SavePlotTop:=PlotTop;
  RoiLeft:=SaveRoiLeft;
  RoiTop:=SaveRoiTop;
  SetLineWidth(1);
  for i:=1 to nLanes do begin
     PlotBottom:=PlotTop+(ymax-ymin)*yscale;
     ChoosePic(GelPid);
     if VerticalLanes
        then MakeRoi(rUser1[i]+hOffset,RoiTop,RoiWidth,RoiHeight)
        else MakeRoi(RoiLeft,rUser1[i]+vOffset,RoiWidth,RoiHeight);
     GetPlotData(count,ppv,min,max);
     SelectPic(PlotsPid);
     MoveTo(hMargin,PlotBottom);
     LineTo(PlotWinWidth-hMargin,PlotBottom);
     MoveTo(hMargin,PlotBottom-(PlotData[0]-ymin)*yscale);
     for i:=1 to count-1 do
        LineTo(hMargin+i*xscale,PlotBottom-(PlotData[i]-ymin)*yscale);
     PlotTop:=PlotTop+PlotHeight;
  end;
  nLanes:=0;
  ResetCounter;
  SetOptions('Area');
  WandAutoMeasure(true);
  AdjustAreas(true);

{
Andreas:
Macro modified
}


                   LabelParticles(true);


  IncludeInteriorHoles(true);
  SetFontSize(9);
  SetText('Centered');
  if Uncalibrated
    then SetScale(0,'pixels')
    else SetScale(sqrt(xscale*yscale/ppv),'unit');
end;