{
Date: Thu, 15 Jul 93 09:05:39 -0400
To: wayne@zippy.nimh.nih.gov
From: mvivino@helix.nih.gov
Subject: gel macro by Boris

I have attached a macro set by somebody named Boris. He stopped by here the
other day to show it to me. His phone number is 301-402-4699.

It has some interesting things about the plotting of a background level.

It also has some things about setting the plotwidth and height which I
think are really needed in the Image gel macro set. Sometimes the plot
height is just not good for the bands to be studied. Of course care must be
made so the area under the curve is properly measured....

Anyway, maybe you will find some of it interesting, maybe not.

Mark Vivino
NIH/DCRT
mvivino@helix.nih.gov
}

{
 Gel Plotting 3.0.
	by Boris, 301-402-4699
}
var  {Global variables}
  Option, hFont:                                                        
integer;
  BoxLeft,        BoxTop,      BoxWidth,   BoxHeight:    integer;
  PicWindow,   PicWidth,   PicHeight:                       integer;
  PlotWidth,     PlotHeight,PlotColor:                       integer;
  ProfWindow,  ProfWidth, ProfHeight, Margin:         integer;
  BackGroundTop,BackGroundHeight,move:                integer;
  NumberArea,  NumberLane, NumberPeacks:              integer;
  SumNumLane, MaxNumLane:                                    integer;
  ScaleMin, ScaleMax, ResWindow,OutputResults:     integer;
  StatusProf, StatusRes:                                           integer;

{
  This marco set parameters.
}
macro 'Setup [S]';
  var  i: integer; 
begin

{Check version of Image}
 RequiresVersion (1.45);

{Check number window}
 if nPics<>1 then begin      
    PutMessage('The image can have only one window open.');
    exit;
  end;

{Set initial size and optins for Plot Profile}
   PlotHeight:= 250;
   PlotWidth := 500;
   BoxLeft := 0;                   
   SetPalette('Grayscale');   { - gray color for window} 
   SetPlotLabel(true);          { - result measure for plot}
   SetLineWidth(1);              { - type of plot line}

{Set options for Analyze}
  ResetCounters;
  MeasureArea(true);
  MeasureDensity(false);
  MeasureStandartDeviation(false);
  MeasureXY(false);
  MeasureMode(false);
  MeasurePerimetr(false);
  MeasureMajorAxis(false);
  MeasureMinorAxis(false);
  MeasureAngle(false);
  MeasureIntegratedDensity(false);
  SetOption ('Area');    
  Redirect(false);
  LabelParticles(false);
  OutlineParticles(false); 
  IgnoreParticlesTouchingEdge(false);
  IncludeInteriorHoles(false);
  WandAutoMeasure(false);
  AdjustAreas(false);
  SetParticleSize(1,999999);
  SetPrecision (0);
  SetScale (0,'pixel');

{ !!!  200 - from Menu Options: if change Options ==> Change Macros,
                 but rUser array not more then 250
}
  for i := 1 to 200 do rUser1[i] := 0;
 
{Set  preferences for text}
  hFont := 18;
  SetFontSize(hFont);      
  SetText('With Background; Bold');  
  SetText('Centered');

{Set initial means for BackGround Lane}
  BackGroundTop := 0;        { - initial size of box for BackGround Lane}
  move := 5;                       { - initial mean for move Background Lane}
 
{ Numbers of Windows}
  PicWindow    :=1;            { - Main picture }
  ProfWindow  :=2;            { - Plot Profile }
  ResWindow    :=3;           { - Results}
  StatusProf    := 0;
  StatusRes     := 0;

{Set initial means for measure area}
 NumberArea := 0;
  NumberLane := 0;         
 NumberPeacks := 0; 
 SumNumLane := 0; 
 MaxNumLane := 0;
 OutputResults := 0;         

 Option := 1;                     { - now All Options are set}

end;

{
    Procedure: c heck the initial options
}
 Procedure InitialOptions;
  begin 
    if Option <> 1 then begin
        PutMessage('Use Setup first.');
        exit;
   end;
 end;

 {
  Procedure: check the Plot Profile 
}
  Procedure CheckProfile;
   begin  
     if nPics < 2 then begin
        PutMessage('Use Plot Profile first.');
        exit;
     end;
   end;

{
  Marco: change size of window.
}
macro 'Window Size [W]';
begin

   InitialOptions;

      {Reset size of window}
  PlotHeight := GetNumber (' New height of window ?',PlotHeight);
  PlotWidth  := GetNumber (' New width of window ?',PlotWidth);
  if PlotHeight*PlotWidth > 155000 then begin
      PutMessage('You want too big window: Height*Width <= 155000. Try again !');
      exit;
  end;

end;

{
  Marco: fix box width.
}
macro 'Input Width [I]';
var
 BL,BW,lw,w1,h1,w,h:  integer;
begin

 InitialOptions;

     {Get size  box }
  GetRoi (BL,w1,BW,h1);
  KillRoi;
  GetPicSize (w,h);

     {Chose and Clear picture before fix new width}
 if BoxWidth <> 0 then begin
    if(nPics = 2) then begin
       SelectPic(ProfWindow);
       Close;
    end;
    SelectPic(PicWindow); 
    RevertToSaved;
 end; 
 BoxLeft   := BL;
 BoxWidth := BW;

      {Draw fixed border} 
  MoveTo(BL-1,0);
  LineTo (BL-1,h);
  MoveTo(BL+BW,0);
  LineTo (BL+BW,h);

     {Draw chosen roi}
  MakeRoi(BL,w1,BW,h1);

end;

{
  Macro: built Profile Plot for choosen box.
}
macro 'Plot profile [P]';
var
   left,width,NumPcx,min,max:integer;
   mean,mode:real;
begin

 InitialOptions;

    {Check width}
if BoxLeft = 0 then begin
     PutMessage('Use Input Width first.')
     exit;
 end;

{Set "right" box}
  GetRoi(left,BoxTop,width,BoxHeight);
  KillRoi;
  MakeRoi(BoxLeft+1,BoxTop,BoxWidth-2,BoxHeight);

  if BoxHeight > BoxWidth then begin
    PutMessage('The height of the box must be less then the width.');
    exit;
  end;

{Fix number of Lane  and number of peacks}
  NumberLane := GetNumber (' Input number of Lane ?',NumberLane+1);  
  if (NumberLane <= 0) or (NumberLane > 199) then begin
       PutMessage ('Wrong number Lane (1 - 199).');
       exit;
  end;

  if SumNumLane = 0 then  begin
       NumberPeacks := GetNumber (' Input number Peacks: ',NumberPeacks);
       if (NumberPeacks <= 0) or (NumberPeacks > 199)  then begin
            PutMessage ('Wrong number Peacks (1 - 199).');
            exit;
       end;
  end; 

  if NumberPeacks*NumberLane > 199 then begin
       PutMessage ('Too much Data (not more then 199).');
       exit;
 end;  

 NumberArea := 0;
 if NumberLane > MaxNumLane then MaxNumLane := NumberLane; 

{Make new window - Profile  Plot}
  if (StatusProf = 0) or (nPics = 1) then begin  
      Margin := 35;                                   { - fix area around
picture}
      ProfHeight := PlotHeight + Margin;
      ProfWidth  := PlotWidth  + Margin;
      SetNewSize(ProfWidth,ProfHeight);
      SetForegroundColor(255);
      SetBackgroundColor(0);

      MakeNewWindow('Profile plot');
      StatusProf := 1;
  end;

{Set size and scale Plot}
  SelectPic(PicWindow);
 
  ResetCounters;
  Measure;
  GetResults(NumPcx,mean,mode,min,max);
 
  min := min - 5;
  if min < 0     then min := 0;
  max := max + 5;
  if max > 255 then max := 255;

  SetPlotSize(PlotWidth,PlotHeight);
  ScaleMin  := cValue(min);
  ScaleMax := cValue(max);
  SetPlotScale(ScaleMin,ScaleMax);
 
{Build Profile Plot and copy it to Clipboard} 
  ColumnAveragePlot; 
  Copy;

{Choose Profile Plot window and put Clipboard to it}
  SelectPic(ProfWindow);
  Paste;

{Set initial means for color of Plot}
   PlotColor := 1;

 {Draw Plot Profile picture over other}
   SelectPic(PicWindow);
   SelectPic(ProfWindow);

end;
 
{
 Macro:  draw BackGround Lane
}

macro 'Background Lane [B]';

var
  left,width:integer;
begin

 InitialOptions;
 CheckProfile; 

      {Set "right" box}
 GetRoi(left,BackGroundTop,width,BackGroundHeight);
 KillRoi;
 MakeRoi(BoxLeft,BackGroundTop,BoxWidth,BackGroundHeight);

      {Build plot and draw it above Plot Profile}
  SetPlotLabel(false);
  ColumnAveragePlot;
  Copy;

  SelectPic(ProfWindow);
  Paste;
  DoOr;
  SetPlotLabel(true);

       {Draw Plot Profile picture over other}
  SelectPic(PicWindow);
  SelectPic(ProfWindow);

end;

{
  Macro: move background line 
}
macro 'Move Background Lane [M]';

var
  left,top,width,height:integer;
begin

  InitialOptions;
  CheckProfile;

{Check background line}
  if BackGroundTop = 0 then begin
      PutMessage('Use BackGround Lane first.')
      exit;
  end;

{Get distance for move lane}
 move := GetNumber(' Distance to move:',move);
 if (move < -255) or (move > 255) then begin
    PutMessage(' You can move between -255  and 255 only. Try again ! ');
    exit; 
 end;

{Restore Plot Profile}
  { 1. Restore box } 
  SelectPic(PicWindow);
  KillRoi;
  MakeRoi(BoxLeft,BoxTop,BoxWidth,BoxHeight);

  {2. Build Profile Plot and copy it to Clipboard} 
  Measure;
  ColumnAveragePlot; 
  Copy;

  {3. Choose Profile Plot and put Clipboard to it}
  SelectPic(ProfWindow);
  Paste;

{Set old box for background lane and add constant}
  SelectPic(PicWindow); 
  MakeRoi(BoxLeft, BackGroundTop,BoxWidth,BackGroundHeight);
  AddConstant(move);

{Build plot and draw it above Plot Profile}
  SetPlotLabel(false);
  ColumnAveragePlot;
  Copy;

  SelectPic(ProfWindow);
  Paste;
  DoOr;
  SetPlotLabel(true);

 {Draw Plot Profile picture over other}
  SelectPic(PicWindow);
  AddConstant(-move);
  SelectPic(ProfWindow);

end;

{
  Macro: change colors of Profile Plot.
}
macro 'Plot Overlayed [O]';

begin

 InitialOptions;
 CheckProfile;

{Set old box}
  SelectPic(PicWindow); 
  MakeRoi(BoxLeft, BackGroundTop,BoxWidth,BackGroundHeight);

{Build plot and copy to clipboard}
  SetPlotLabel(false);
  ColumnAveragePlot;
  Copy;
 
{Set Color for Plot Profile}
  SelectPic(ProfWindow);
  if PlotColor=1 then SetPalette('256 Color Spectrum');
  SetForegroundColor(PlotColor);

{Draw plot above Plot Profile}
  Paste;
  DoOr;

  SetPlotLabel(true);

  PlotColor := (PlotColor+74) mod 254;  { - step changing color for Plot
Profile}

end;

{
   Measure for area and save area
}

Macro 'Measure area [A]';
 var
    NumPcx,mean,mode,min,max,i:     integer;

begin

  InitialOptions;
  CheckProfile;

{Measure for fixed area}   
   ResetCounters;
   Measure;

{Calculate and save number results}
   NumberArea := NumberArea + 1;

{Check number results}
 if NumberArea > NumberPeacks then begin
     PutMessage
     ('You try to measure too much Peaks. If it nesasary - delete all and start again.');
     exit;
 end;

   i := (NumberLane - 1)*(NumberPeacks+1) + NumberArea;         
   if NumberArea = 1 then  begin
       SumNumLane := SumNumLane + 1;
       rUser1[i] := NumberLane;  
   end;     

{Get and save Area }
   GetResults(NumPcx,mean,mode,min,max);  
   rUser1[i+1] :=  NumPcx*(ScaleMax-ScaleMin)/100;

end;

{
   Procedure:  draw results 
}
Procedure DrawMeasureResults;
 var
   i, j,n,k:   integer;
 begin

{Check existance results}
 if SumNumLane = 0 then begin
     PutMessage('You do  not have any results. Use Measure Area first.');
     exit;
 end;
{Check number results}
 if NumberArea < NumberPeacks then begin
     PutMessage('You do not have to measure all Peaks. Use Measure Area.');
     exit;
 end;
{Delete Old Results}
  if (StatusRes = 1) and (nPics = 3) then begin   
       SelectPic(ResWindow);
       Dispose;
       StatusRes := 0; 
   end; 
  
{Make new window Results}
   SetNewSize (7*(NumberPeacks + 1)*hFont/2, 20*(SumNumLane + 3));
   SetForegroundColor(255);
   SetBackgroundColor(0);

   MakeNewWindow('Results');
   StatusRes := 1; 

{Output head of Results}
   MoveTo(20,20);
   DrawText(' Lane    ');
   MoveTo (20 + 60*(NumberPeacks+1)/2, 20);
   DrawText(' Peak') 
   for i := 1 to NumberPeacks do   begin     
         MoveTo(20+60*i, 40);
         DrawNumber(i);
   end;   
   
{Output "body" of result}  
    k := 0;
    for i := 1 to  MaxNumLane do   begin 
         n := (i-1)*(NumberPeacks+1) + 1;
         if rUser1[n] > 0 then   begin
             k := k + 1;
             for j := 0 to  NumberPeacks do   begin   
                MoveTo(20+60*j, 40+20*k);
                DrawNumber (rUser1[n+j]);
             end;
         end; 
    end;   

end;

{
  Macro:  draw results 
}
Macro 'Draw Results [V]';
 begin
   DrawMeasureResults;   
 end;

{
   Macro:  delete Lane
}
Macro 'Delete Lane [D]';
  var  n, j:  integer;
begin
{Get and check number}
     n := GetNumber (' Input number of Lane: ',0);
     if (n <= 0) or (n > MaxNumLane) then  begin
         PutMessage ('You do not have such Lane!  Try another number.');
         exit;
     end;  

{Delete lane}  
     NumberLane := n - 1;
     n := (n -1)*(NumberPeacks+1) + 1;
     for j := 0 to  NumberPeacks do  rUser1[n+j] := 0;
     SumNumLane := SumNumLane - 1;
    

     DrawMeasureResults;
end;

{
   Macro:  delete all Lanes
}
Macro 'Delete All Lanes /D';
  var  i:  integer;
begin
  SelectPic(ResWindow);
  Dispose;
  SelectPic(PicWindow);
 
  for i := 1 to MaxNumLane*(NumberPeacks+1) do rUser1[i] := 0;  
  SumNumLane   := 0;
  MaxNumLane    := 0;
  NumberPeacks := 0; 
  StatusRes       := 0;
  NumberLane    := 0;
end;  

{
   Macro:  input zero
}
Macro 'Input Zero [Z]';
  var  i:  integer;
begin

   NumberArea := NumberArea + 1;
   i := (NumberLane - 1)*(NumberPeacks+1) + NumberArea;         
   if NumberArea = 1 then  begin
       SumNumLane := SumNumLane + 1;
       rUser1[i] := NumberLane;  
   end;     
 
   rUser1[i+1] := 0;

end;  

{
  Macro:  save results 
}
Macro 'Save Results [R]';
  var  i, n: integer;
begin

{Check existance results}
    if (SumNumLane = 0) or (StatusRes = 0) then begin
        PutMessage('You do not have or check results. Use Draw Results first.');
        exit;
    end;

{Rewrite results for export}
    n := MaxNumLane*(NumberPeacks+1);

    SelectPic(PicWindow);        {Clear rArea}
    MakeRoi(0,0,3,3);
    ResetCounters;
    Measure;

    rArea[1] := NumberPeacks;    {Save Results}
    for i := 2 to  n + 1  do  begin
       Measure;
       rArea[i] := rUser1[i-1];
    end;

    KillRoi;
 
{ Export results}
   SetExport('Measurements');
   Export('Measurements'); 
 
end;