var  {Global variables}
  RoiLeft,RoiTop,RoiWidth,RoiHeight,PlotColor:integer;
  GelWidth,GelHeight,MaxPlotWindowHeight,NeededSize:integer;
  GelWindow,PlotWindow,PlotLeft,PlotTop,PlotWidth,PlotHeight:integer;
  hMargin,vMargin,nLanes,SavePlotTop,PlotWindowSize:integer;
  LeftMargin,TopMargin,RightMargin,BottomMargin:integer;
  FirstBackgroundPlot:boolean;

macro 'Setup to Plot Gel [Z]';
{This macro, along with the Plot Lane macro, is used to generate profile}
{plots of the lanes in a one dimensional electoproretic gel.}
var
  nPixels,mean,mode,min,max:real;
  PlotWinHeight:integer;
begin
  RequiresVersion(1.53);
  PlotHeight:=175;
  PlotWidth:=500;
  MaxPlotWindowHeight:=720;
  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;
  if PlotWidth<RoiWidth then PlotWidth:=RoiWidth;
  if PlotWidth>(2*RoiWidth) then PlotWidth:=2*RoiWidth;
  if RoiHeight>RoiWidth then begin
    PutMessage('Lanes must be horizontal.');
    exit;
  end;
  if nPics<>1 then begin
    PutMessage('The window containing the gel should be the only image window open.');
    exit;
  end;
  nLanes:=GetNumber('Number of lanes?',1);
  GetPicSize(GelWidth,GelHeight);
  MakeRoi(RoiLeft,RoiTop,RoiWidth,GelHeight-RoiTop);
  Measure;
  GetResults(nPixels,mean,mode,min,max);
  hMargin:=5;
  vMargin:=5;
  LeftMargin:=38; {Changed in v1.53}
  TopMargin:=10;
  RightMargin:=20;
  BottomMargin:=20;
  PlotLeft:=hMargin-LeftMargin;
  PlotTop:=vMargin-TopMargin;
  SavePlotTop:=PlotTop;
  PlotWinHeight:=nLanes*PlotHeight+2*vMargin;
  if PlotWinHeight>MaxPlotWindowHeight then begin
    PlotWinHeight:=MaxPlotWindowHeight;
    PlotHeight:=(PlotWinHeight-2*vMargin)/nLanes;
  end;
  PlotWindowSize:=(PlotWidth+2*hMargin)*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;
  SetNewSize(PlotWidth+2*hMargin,PlotWinHeight);
  SetForegroundColor(255);
  SetBackgroundColor(0);
  MakeNewWindow('Plots');
  SetPlotSize(PlotWidth,PlotHeight);
  min:=min-1;
  if min<0 then min:=0;
  max:=max+5;
  if max>255 then max:=255;
  SetPlotScale(cValue(min),cValue(max));
  SetPlotLabels(false);
  GelWindow:=1;
  PlotWindow:=2;
  SelectPic(GelWindow);
  MakeRoi(RoiLeft,RoiTop,RoiWidth,RoiHeight);
  FirstBackgroundPlot:=true;
  PlotColor:=1;
  ResetCounter;
  SetOptions('Area');
  WandAutoMeasure(true);
  AdjustAreas(true);
  LabelParticles(false);
  IncludeInteriorHoles(true);
  SetFontSize(9);
  SetText('Centered');
  SetLineWidth(1);
end;


macro 'Plot Lane [P]';
var
  left,top,width,height:integer;
  GelNotCalibrated:boolean;
begin
  if (GelWidth=0) or (nPics=1) then begin
    PutMessage
      ('Before using the Plot Lane macro you must first use the Setup macro.');
    Exit;
  end;
  GelNotCalibrated:=not Calibrated;
  GetRoi(left,top,width,height);
  MakeRoi(RoiLeft,top,RoiWidth,RoiHeight);
  SetOption;
  ColumnAveragePlot;
  Copy;
  SelectPic(PlotWindow);
  MakeRoi(PlotLeft,PlotTop,PlotWidth+LeftMargin+RightMargin,
          PlotHeight+TopMargin+BottomMargin);
  Paste;
  DoOr;
  if GelNotCalibrated and (PlotTop=SavePlotTop) then begin
    SetText('Left Justified; With Background');
    MoveTo(PlotLeft+LeftMargin+6,PlotTop+TopMargin+1);
    SetFontSize(12);
    Write('Uncalibrated');
    SetFontSize(9);
    SetText('Centered; No Background');
  end;
  PlotTop:=PlotTop+PlotHeight-1;
  SelectPic(GelWindow);
end;


macro 'Plot Background Lane [B]';
{Plot all lanes before plotting backgrounds. Unlike the lane plotting macro,}
{you are allowed to change the height of the selection.}
var
  left,top,width,height:integer;
begin
  if (GelWidth=0) or (nPics=1) then begin
    PutMessage('Use Setup first.');
    Exit;
  end;
  GetRoi(left,top,width,height);
  MakeRoi(RoiLeft,top,RoiWidth,height);
  ColumnAveragePlot;
  Copy;
  SelectPic(PlotWindow);
  if FirstBackgroundPlot then begin
    FirstBackgroundPlot:=false;
    PlotTop:=SavePlotTop;
  end;
  MakeRoi(PlotLeft,PlotTop,PlotWidth+LeftMargin+RightMargin,
          PlotHeight+TopMargin+BottomMargin);
  Paste;
  DoOr;
  PlotTop:=PlotTop+PlotHeight-1;
  SelectPic(GelWindow);
end;


macro 'Plot Overlayed [O]';
var
  left,top,width,height:integer;
begin
  if (GelWidth=0) or (nPics=1) then begin
    PutMessage('Use Setup first.');
    Exit;
  end;
  if PlotColor=1 then SetPalette('256 Color Spectrum');
  GetRoi(left,top,width,height);
  MakeRoi(RoiLeft,top,RoiWidth,height);
  ColumnAveragePlot;
  Copy;
  SelectPic(PlotWindow);
  if PlotColor=1 then SetPalette('256 Color Spectrum');
  SetForegroundColor(PlotColor);
  PlotTop:=PlotTop-PlotHeight+1;
  if PlotTop<SavePlotTop then PlotTop:=SavePlotTop;
  MakeRoi(PlotLeft,PlotTop,PlotWidth+LeftMargin+RightMargin,
          PlotHeight+TopMargin+BottomMargin);
  Paste;
  DoOr;
  PlotTop:=PlotTop+PlotHeight-1;
  SelectPic(GelWindow);
  PlotColor:=(PlotColor+74) mod 254;
end;