var
    vectPid, mrkvPid, maskPid, markPid, newPid, playPid, x16Pid, b16Pid: Integer;
    xlate16uto8Pid, ymin, ymax: integer;
    kmin, kdelta, knum, koverlap: integer;
    kernelPid, smoothPid: integer;
    fore,foredef: integer;
    std16uto8Pid: integer;

procedure Std16To8;
begin
    RequiresUser('pixel16u', 1);
    SaveState;
    SetNewSize(256, 256);
    SetBackgroundColor(0);
    MakeNewWindow('BioVision 16 to 8 conversion table');
    xlate16uto8Pid := pidNumber;
    linLUT16uto8(xlate16uto8Pid, 0, 65535, 0, 255);
    RestoreState;
end;


macro 'Dispose All ** CAREFUL **';
begin
    DisposeAll;
end;

macro '-)';
begin
end;

{Global variable values are lost when macros are reloaded.}
{This is mainly for use during macro development.}
macro 'Create global variable save image';
begin
    setNewSize(32, 32);
    MakeNewWindow('Global Variables');
end;




macro 'Save global variables';
var
    savePid, globalPid: integer;
begin
    savePid := pidNumber;
    SelectWindow('Global Variables');
    globalPid := pidNumber;
    PutPixVec32s(globalPid, 1, vectPid);
    PutPixVec32s(globalPid, 2, mrkvPid);
    PutPixVec32s(globalPid, 3, maskPid);
    PutPixVec32s(globalPid, 4, markPid);
    PutPixVec32s(globalPid, 5, newPid);
    PutPixVec32s(globalPid, 6, playPid);
    PutPixVec32s(globalPid, 7, x16Pid);
    PutPixVec32s(globalPid, 8, xlate16uto8Pid);
    PutPixVec32s(globalPid, 9, ymin);
    PutPixVec32s(globalPid, 10, ymax);
    PutPixVec32s(globalPid, 11, kmin);
    PutPixVec32s(globalPid, 12, kdelta);
    PutPixVec32s(globalPid, 13, knum);
    PutPixVec32s(globalPid, 14, koverlap);
    PutPixVec32s(globalPid, 15, kernelPid);
    PutPixVec32s(globalPid, 16, b16Pid);
    PutPixVec32s(globalPid, 17, smoothPid);
    SelectPic(savePid);
end;

macro 'Restore global variables';
var
    savePid, globalPid: integer;
begin
    savePid := pidNumber;
    SelectWindow('Global Variables');
    globalPid := pidNumber;
    vectPid := GetPixVec32s(globalPid, 1);
    mrkvPid := GetPixVec32s(globalPid, 2);
    maskPid := GetPixVec32s(globalPid, 3);
    markPid := GetPixVec32s(globalPid, 4);
    newPid := GetPixVec32s(globalPid, 5);
    playPid := GetPixVec32s(globalPid, 6);
    x16Pid := GetPixVec32s(globalPid, 7);
    xlate16uto8Pid := GetPixVec32s(globalPid, 8);
    ymin := GetPixVec32s(globalPid, 9);
    ymax := GetPixVec32s(globalPid, 10);
    kmin := GetPixVec32s(globalPid, 11);
    kdelta := GetPixVec32s(globalPid, 12);
    knum := GetPixVec32s(globalPid, 13);
    koverlap := GetPixVec32s(globalPid, 14);
    kernelPid := GetPixVec32s(globalPid, 15);
    b16Pid := GetPixVec32s(globalPid, 16);
    smoothPid := GetPixVec32s(globalPid, 17);
    if pidExists(savePid) then
        SelectPic(savePid);
end;

macro 'Front image is mask image';
begin
    maskPid := pidNumber;
end;

macro 'Front image is mark image';
begin
    markPid := pidNumber;
end;

macro 'Front image is 16 bit cropped stack';
begin
    vectPid := pidNumber;
end;

macro 'Front image is 16 to 8 conversion table';
begin
    xlate16uto8Pid := pidNumber;
end;

macro 'Front image is 8 bit display buffer';
begin
    playPid := pidNumber;
end;

macro 'Front image is 16 bit slice buffer';
begin
    x16Pid := pidNumber;
end;

macro 'Front image is background kernel';
begin
    kernelPid := PidNumber;
    kmin := getPixel(0, 0);
    kdelta := getPixel(0, 1);
    knum := getPixel(0, 2);
    koverlap := getPixel(0, 3);
end;

macro 'Front image is smoothing kernel';
begin
    smoothPid := PidNumber;
end;

procedure checkPids;
    var
        left, top, width, height: integer;
begin
    RequiresUser('Pixel16u', 1);
    if not pidExists(maskPid) then begin
            PutMessage('Please run macro "Front image is mask image"');
            Exit;
        end;
    if not pidExists(vectPid) then begin
            PutMessage('Please run macro "Front image is 16 bit cropped stack"');
            Exit;
        end;
    if not pidExists(xlate16uto8Pid) then begin
            PutMessage('Please run macro "Front image is 16 to 8 conversion table"');
            Exit;
        end;
    if not pidExists(playPid) then begin
            selectPic(maskPid);
            GetPicSize(width, height);
            SetNewSize(width, height);
            MakeNewStack('8 bit stack');
            playPid := pidNumber;
        end;
    if not pidExists(x16Pid) then begin
            selectPic(maskPid);
            GetPicSize(width, height);
            SetNewSize(2 * width, height);
            MakeNewWindow('16 bit data buffer -- trash');
            x16Pid := pidNumber;
        end;
    if not pidExists(b16Pid) then begin
            selectPic(maskPid);
            GetPicSize(width, height);
            SetNewSize(2 * width, height);
            MakeNewWindow('16 bit background -- trash');
            b16Pid := pidNumber;
        end;
    if not pidExists(markPid) then begin
            selectPic(maskPid);
            GetPicSize(width, height);
            SetNewSize(width, height);
            MakeNewWindow('mark');
            markPid := pidNumber;
        end;
end;

macro 'make 16 to 8 conversion table';
var
    i, j, x, y: integer;
    width, height: integer;
    inPid, min, max: integer;
begin
    RequiresUser('pixel16u', 1);
    ymin := GetNumber('minimum 8 bit pixel value', 1);
    ymax := GetNumber('maximum 8 bit pixel value', 254);
    SaveState;
    inPid := pidNumber;
    minMax16u(inPid, min, max);
    min := GetNumber('minimum 16 bit pixel value', min);
    max := GetNumber('maximum 16 bit pixel value', max);
    SetNewSize(256, 256);
    SetBackgroundColor(0);
    MakeNewWindow('16 to 8 conversion table');
    xlate16uto8Pid := pidNumber;
    linLUT16uto8(xlate16uto8Pid, min, max, ymin, ymax);
end;



macro 'convert packed 16 to 8 no offset';
var
    i, n: integer;
begin
    CheckPids;
    selectPic(playPid);
    choosePic(vectPid);
    n := nSlices;
    resetCounter;
    linLUT16uto8(xlate16uto8Pid, 0, 8191, 0, 255);
    for i := 1 to n do begin
                    choosePic(vectPid);
                    chooseSlice(i);
                    choosePic(playPid);
                    if i > nSlices then addSlice;
                    chooseSlice(i);
                    CnvMsk16uTo8(vectPid, xlate16uto8Pid, maskPid, playPid);
                    SelectAll;
                    Measure;
        end;
end;

macro 'convert 16 to 8 no offset';
var
    i, n: integer;
begin
    CheckPids;
    selectPic(playPid);
    choosePic(vectPid);
    n := nSlices;
    resetCounter;
    linLUT16uto8(xlate16uto8Pid, 0, 65535, 0, 255);
    SetOptions('Area,Mean,Std. Dev.');
    for i := 1 to n do begin
                    choosePic(vectPid);
                    chooseSlice(i);
                    choosePic(playPid);
                    if i > nSlices then addSlice;
                    chooseSlice(i);
                    Cnvrt16uTo8(vectPid, xlate16uto8Pid, playPid);
                    SelectAll;
                    Measure;
        end;
end;

macro 'convert packed 16 to 8 with offset';
var
    i, n: integer;
    min,max: integer;
begin
    CheckPids;
    selectPic(playPid);
    choosePic(vectPid);
    n := nSlices;
    resetCounter;
    for i := 1 to n do begin
                    choosePic(vectPid);
                    chooseSlice(i);
                    choosePic(playPid);
                    if i > nSlices then addSlice;
                    chooseSlice(i);
                    min := rMean[i] * 8192/256 - 1000;
                    max := min + 4096;
                    linLUT16uto8(xlate16uto8Pid, min, max, 0, 255);
                    CnvMsk16uTo8(vectPid, xlate16uto8Pid, maskPid, playPid);
        end;
end;
macro 'convert 16 to 8 with offset';
var
    i, n: integer;
    min,max: integer;
begin
    CheckPids;
    selectPic(playPid);
    killroi;
    choosePic(vectPid);
    killroi;
    n := nSlices;
    resetCounter;
    for i := 1 to n do begin
                    choosePic(vectPid);
                    chooseSlice(i);
                    choosePic(playPid);
                    if i > nSlices then addSlice;
                    chooseSlice(i);
                    min := (rMean[i]-2*rStdDev[i]) * 65536/256;
                    max := (rMean[i]+6*rStdDev[i]) * 65536/256;
                    linLUT16uto8(xlate16uto8Pid, min, max, 0, 255);
                    Cnvrt16uTo8(vectPid, xlate16uto8Pid, playPid);
        end;
end;

macro 'stacktoMontage';
var
   i,n, stkPid, montPid: integer;
   width, height, perrow, percol, x, y: integer;
begin
  n := nSlices;
  stkPid := pidNumber;
  GetPicSize(width, height);
  perrow := trunc(sqrt(n));
  percol := trunc((n + perrow)/perrow);
  SetNewSize(width * perrow, height*percol);
  MakeNewWindow('montage');
  montPid := PidNumber;
  x := 0;
  y := 0;
  for i := 1 to n do begin
     if x >= perrow then begin
          x := 0;
          y := y + 1;
     end;
     choosePic(stkPid);
     chooseSlice(i);
      selectAll;
      copy;
      choosePic(montPid);
       makeRoi(x * width, y * height, width, height);
      paste;
      setForegroundColor(255);
      moveto(x * width, y * height+10);
      write(i);
      x := x + 1;
  end;
end;

macro 'out dammed spot';
var
  i,n,x,y: integer;
  stkpid, newpid: integer;
  width, height: integer;
begin
  stkpid := pidNumber;
  n := nSlices;
  getPicSize(width,height);
  setNewSize(width,height);
  makeNewStack('noSpot');
  newPid := pidNumber;
  for i := 1 to n do begin
     choosePic(stkpid);
     selectslice(i);
     selectall;
     copy;
     choosePic(newPid);
     if i > nSlices then addslice;
     selectslice(i);
     paste;
     {makeOvalRoi(18,8,7,7);}
     makeOvalRoi(16,6,9,9);
     copy;
     {makeOvalRoi(25,8,7,7);}
     makeOvalRoi(24,6,9,9);
     paste;
     makeOvalRoi(22,4,11,11);
     reduceNoise;
     Smooth;
  end;
end;

macro 'out dammed 16 bit spot';
var
  i,n,x,y: integer;
  stkpid, newpid: integer;
  width, height: integer;
begin
  stkpid := pidNumber;
  n := nSlices;
  getPicSize(width,height);
  setNewSize(width,height);
  makeNewStack('noSpot 16');
  newPid := pidNumber;
  for i := 1 to n do begin
     choosePic(stkpid);
     selectslice(i);
     selectall;
     copy;
     choosePic(newPid);
     if i > nSlices then addslice;
     selectslice(i);
     paste;
     {makeOvalRoi(18,8,7,7);}
     makeRoi(16*2,6,18,9);
     copy;
     {makeOvalRoi(25,8,7,7);}
     makeRoi(24*2,6,18,9);
     paste;
  end;
end;


macro 'scaletoMontage';
var
   i,n, start, stkPid, montPid: integer;
   width, height, perrow, percol, x, y: integer;
   del1pid, del2pid: integer;
   scalex,scaley: real;
begin
  n := nSlices;
  stkPid := pidNumber;
  GetPicSize(width, height);
  perrow := 5;
  percol := 6;
  perrow := 3;
  percol := 4;
  SetNewSize(640,480);
  scalex := 640 / (perrow*width);
  scaley := 480 / (percol * height);
  if scalex > scaley then scalex := scaley else scaley := scalex;
  MakeNewWindow('montage');
  montPid := PidNumber;
  x := 0;
  y := 0;
  start := getnumber('start slice',1);
  for i := start to start+perrow*percol-1 do begin
     if x >= perrow then begin
          x := 0;
          y := y + 1;
     end;
     choosePic(stkPid);
     chooseSlice(i*7);
     killRoi;
     Duplicate('deleteme');
     del1pid := pidNumber;
     Smooth;
     Smooth;
     ScaleAndRotate(scalex,scaley,0);
     del2pid := pidNumber;
     SelectAll;
     Copy;
      choosePic(montPid);
       makeRoi(x * width * scalex, y * height * scaley, width*scalex, height*scaley);
      paste;
     choosePic(del1pid);
     Dispose;
     choosePic(del2pid);
     Dispose;
      x := x + 1;
  end;
end;

macro 'scaletoMontage 512x480';
var
   i,n, start, stkPid, montPid: integer;
   width, height, perrow, percol, x, y: integer;
   del1pid, del2pid: integer;
   scalex,scaley: real;
begin
  n := nSlices;
  stkPid := pidNumber;
  GetPicSize(width, height);
  perrow := 5;
  percol := 6;
  perrow := 3;
  percol := 4;
  SetNewSize(512,480);
  scalex := 512 / (perrow*width);
  scaley := 480 / (percol * height);
  if scalex > scaley then scalex := scaley else scaley := scalex;
  MakeNewWindow('montage');
  montPid := PidNumber;
  x := 0;
  y := 0;
  start := getnumber('start slice',1);
  for i := start to start+perrow*percol-1 do begin
     if x >= perrow then begin
          x := 0;
          y := y + 1;
     end;
     choosePic(stkPid);
     chooseSlice(i*7);
     killRoi;
     Duplicate('deleteme');
     del1pid := pidNumber;
     Smooth;
     Smooth;
     ScaleAndRotate(scalex,scaley,0);
     del2pid := pidNumber;
     SelectAll;
     Copy;
      choosePic(montPid);
       makeRoi(x * width * scalex, y * height * scaley, width*scalex, height*scaley);
      paste;
     choosePic(del1pid);
     Dispose;
     choosePic(del2pid);
     Dispose;
      x := x + 1;
  end;
end;

macro 'scaletoMontage 512x480 selected';
var
   i,n, start, stkPid, montPid: integer;
   width, height, perRow, perCol, x, y: integer;
   del1pid, del2pid: integer;
   scalex,scaley: real;
begin
  rUser1[1] := 1;
  rUser1[2] := 3;
  rUser1[3] := 8;
  rUser1[4] := 46;
  rUser1[5] := 48;
  rUser1[6] := 59;
  rUser1[7] := 68;
  rUser1[8] := 70;
  rUser1[9] := 71;
  rUser1[10] := 80;
  rUser1[11] := 82;
  rUser1[12] := 87;
  n := nSlices;
  stkPid := pidNumber;
  GetPicSize(width, height);
  perRow := 3;
  perCol := 4;
  SetNewSize(512,480);
  scalex := 512 / (perrow*width);
  scaley := 480 / (percol * height);
  if scalex > scaley then scalex := scaley else scaley := scalex;
  MakeNewWindow('montage');
  montPid := PidNumber;
  x := 0;
  y := 0;
  for i := 1 to perRow * perCol do begin
     if x >= perRow then begin
          x := 0;
          y := y + 1;
     end;
     choosePic(stkPid);
     chooseSlice(rUser1[i]);
     killRoi;
     Duplicate('deleteme');
     del1pid := pidNumber;
     SetScaling('Bilinear,New Window');
     ScaleAndRotate(scalex,scaley,0);
     del2pid := pidNumber;
     SelectAll;
     Copy;
      choosePic(montPid);
       makeRoi(x * width * scalex, y * height * scaley, width*scalex, height*scaley);
      paste;
     choosePic(del1pid);
     Dispose;
     choosePic(del2pid);
     Dispose;
      x := x + 1;
  end;
end;

macro 'selected Montage 512x480';
var
   i,n, start, stkPid, montPid: integer;
   width, height, perRow, perCol, x, y: integer;
   del1pid, del2pid: integer;
   scalex,scaley: real;
begin
  rUser1[1] := 1;
  rUser1[2] := 3;
  rUser1[3] := 8;
  rUser1[4] := 46;
  rUser1[5] := 48;
  rUser1[6] := 59;
  rUser1[7] := 68;
  rUser1[8] := 70;
  rUser1[9] := 71;
  rUser1[10] := 80;
  rUser1[11] := 82;
  rUser1[12] := 87;
  n := nSlices;
  stkPid := pidNumber;
  GetPicSize(width, height);
  perRow := 3;
  perCol := 4;
  SetNewSize(512,480);
  scalex := 512 / (perrow*width);
  scaley := 480 / (percol * height);
  if scalex > scaley then scalex := scaley else scaley := scalex;
  MakeNewWindow('montage');
  montPid := PidNumber;
  x := 0;
  y := 0;
  for i := 1 to perRow * perCol do begin
     if x >= perRow then begin
          x := 0;
          y := y + 1;
     end;
     choosePic(stkPid);
     chooseSlice(rUser1[i]);
     killRoi;
     SelectAll;
     Copy;
      choosePic(montPid);
       makeRoi(x * width * scalex + 5, y * height * scaley + 5, width, height);
      paste;
      x := x + 1;
  end;
end;

macro 'selected Montage 512x480 2x3';
var
   i,n, start, stkPid, montPid: integer;
   width, height, perRow, perCol, x, y: integer;
   del1pid, del2pid: integer;
   scalex,scaley: real;
begin
  rUser1[1] := 3;
  rUser1[2] := 8;
  rUser1[3] := 48;
  rUser1[4] := 59;
  rUser1[5] := 66;
  rUser1[6] := 80;
  n := nSlices;
  stkPid := pidNumber;
  GetPicSize(width, height);
  width  := width - 4;
  perRow := 2;
  perCol := 3;
  SetNewSize(512,480);
  scalex := 512 / (perrow*width);
  scaley := 480 / (percol * height);
  if scalex > scaley then scalex := scaley else scaley := scalex;
  MakeNewWindow('montage');
  montPid := PidNumber;
  x := 0;
  y := 0;
  for i := 1 to perRow * perCol do begin
     if x >= perRow then begin
          x := 0;
          y := y + 1;
     end;
     choosePic(stkPid);
     chooseSlice(rUser1[i]);
     killRoi;
     MakeRoi(0,0,width,height);
     Duplicate('deleteme');
     del1pid := pidNumber;
     SetScaling('Bilinear,New Window');
     ScaleAndRotate(scalex,scaley,0);
     del2pid := pidNumber;
     SelectAll;
     Copy;
      choosePic(montPid);
       makeRoi(x * width * scalex, y * height * scaley, width*scalex, height*scaley);
      paste;
     choosePic(del1pid);
     Dispose;
     choosePic(del2pid);
     Dispose;
      x := x + 1;
  end;
end;