{Darin Nelson, Duke University Dept. of Neurobiology (dnelson@neuro.duke.edu)}
{July, 1994}
{this file contains chiefly macros for use with stacks. Some are based on the macros in the file Stacks that comes with NIH Image.  Modify 'em as you see fit, of course. }

{here are a couple of utility macros}

procedure CheckForStack;
{lifted from the Stacks macro file}
begin
  if nPics=0 then begin
    PutMessage('This macro requires a stack.');
    exit;
  end;
  if nSlices=0 then begin
    PutMessage('This window is not a stack.');
    exit;
  end;
end;

procedure CheckForSelection;
{also lifted from the Stacks macro file}
var 
  x1,y1,x2,y2,LineWidth:integer;
begin
  GetRoi(RoiLeft,RoiTop,RoiWidth,RoiHeight);
  GetLine(x1,y1,x2,y2,LineWidth);
  if (RoiWidth=0) or (x1>=0) then begin
    PutMessage('Please make a rectangular selection.');
    exit;
  end;
end;

macro 'Rename Window [R]'
var
   newname : string;
begin
   SetPicName(GetString('Change window name to:',WindowTitle));
end;

macro 'Change Values';
{a stacks version of the macro included with NIH Image}
var
  i,v1,v2,v3:integer;
begin
  CheckForStack;
  v1:=GetNumber('Change pixels ranging from this value:',1);
  v3:=GetNumber('up to this value:',10);
  v2:=GetNumber('into this value:',0);
  for i:= 1 to nSlices do begin
    ChooseSlice(i);
    ChangeValues(v1,v3,v2);
  end;
end;



macro '(-' begin end;

{here are some macros for doing various mathematical manipulations on stacks}
macro 'Multiply Adjacent Frames';
var
  i:integer;
begin
  ScaleMath(true);
  CheckForStack;
  for i:= 1 to (nSlices-1) do begin
    ChooseSlice(i+1);
	   SelectAll;
    Copy;
				ChooseSlice(i);
    Paste;
    Multiply;
  end;
end;
macro 'Subtract Adjacent Frames ';
var
  i:integer;
begin
  ScaleMath(false);
  CheckForStack;
  for i:= 1 to (nSlices-1) do begin
    ChooseSlice(i+1);
	   SelectAll;
    Copy;
				ChooseSlice(i);
    Paste;
    Subtract;
  end;
end;

macro 'Subtract Two Stacks scaled & offset';
{Creates the frame by frame difference of two stacks, offset so that a real difference of 0 becomes equal to 128 in the result. The differences are scaled by 0.5.  All this scaling is necessary to allow the possible range of results (-255 to 255) to fit into the range 0-255. }
var
  i,w1,w2,w3,h1,h2,h3,d1,d2,d3:integer;
begin
  SaveState;
  if nPics<>2 then begin
    PutMessage('This macro operates on exactly two stacks.');
    exit;
  end;
  ChoosePic(1);
  GetPicSize(w1,h1);
  d1:=nSlices;
  ChoosePic(2);
  GetPicSize(w2,h2);
  d2:=nSlices;
  if d1>=d2
    then d3:=d1
    else d3:=d2;
  if (w1<>w2) or (h1<>h2) or (d1<>d2) or (d1=0)  then begin
    PutMessage('This macro requires two stacks that are the same size.');
    exit;
  end;
  ScaleMath(false);
  for i:=1 to d1 do begin
    ChoosePic(1);
    ChooseSlice(i);
    SelectAll;
    MultiplyByConstant(0.5);
    AddConstant(128);
    ChoosePic(2);
    ChooseSlice(i);
    SelectAll;
    MultiplyByConstant(0.5);
    SelectAll;
    Copy;
    ChoosePic(1);
    ChooseSlice(i);
    Paste;
    Subtract;
   end;
  ChoosePic(2);
  Dispose;
  RestoreState;
end;

macro 'Subtract Two Stacks';
{Creates the frame by frame difference of two stacks.  No scaling is performed}
var
  i,w1,w2,w3,h1,h2,h3,d1,d2,d3:integer;
begin
  SaveState;
  if nPics<>2 then begin
    PutMessage('This macro operates on exactly two stacks.');
    exit;
  end;
  ChoosePic(1);
  GetPicSize(w1,h1);
  d1:=nSlices;
  ChoosePic(2);
  GetPicSize(w2,h2);
  d2:=nSlices;
  if d1>=d2
    then d3:=d1
    else d3:=d2;
  if (w1<>w2) or (h1<>h2) or (d1<>d2) or (d1=0)  then begin
    PutMessage('This macro requires two stacks that are the same size.');
    exit;
  end;
  ScaleMath(false);
  for i:=1 to d1 do begin
    ChoosePic(2);
    ChooseSlice(i);
    SelectAll;
    Copy;
    ChoosePic(1);
    ChooseSlice(i);
    Paste;
    Subtract;
  end;
  ChoosePic(2);
  Dispose;
  RestoreState;
end;

macro 'Subtract First Frame from Stack';
{Subtracts the first frame of a stack from the rest of the stack  Useful for removing constant background from a series of stacked images. }
var
  i,w1,w2,w3,h1,h2,h3,d1,d2,d3:integer;
begin
  SaveState;
  if nSlices<2 then begin
    PutMessage('This macro requires a stack with at least 2  slices.');
    exit;
  end;
    SelectSlice(1);
    SelectAll;
    Copy;
  ScaleMath(false);
  for i:=2 to nSlices do begin
   SelectSlice(i);
    Paste;
    SetOption;
    Subtract;
  end;
  RestoreState;
end;

macro 'Interpolate Frames';
{interpolates new frames between each frame of a stack by simple averaging}
var
  i,w1,w2,w3,h1,h2,h3,d1,d2,d3:integer;
begin
  SaveState;
   d1 := nSlices;
  ScaleMath(false);
  for i:=1 to d1 do begin
		   ChooseSlice (i*2 - 1);
     SelectAll;
     Copy;
	    AddSlice;
     ChooseSlice (i*2);
     Paste;
     SelectAll;
     MultiplyByConstant(0.5);
     SelectAll;
     Copy;
      if (i > 1) then begin
         ChooseSlice(i*2-2);
         Paste;
         Add;
     end;
  end;
  RestoreState;
end;

macro '(-' begin end;




 procedure INITTEXT
begin
     SetFont ('Helvetica');
      SetFontSize(12);
      SetText ('Bold Left Justified');
      SetForeGroundColor(255);
      SetBackgroundColor(0);
end;
      

procedure MAPNUMSEARCH
{ before calling this routine, select the window to
  be checked.  The routine will search for a number between _01 and _15 in the
 WindowTitle and set mapNum to the number that is found, if any (otherwise it's zero).
}

var 
k, l , : integer;
subStr : string;

begin
  mapNum := 0;
  for k := 1 to 15 do begin
     if (k < 10) then subStr := concat('_0',k:1);
     if (k > 9) then subStr := concat('_',k:2);
     l := pos(subStr,WindowTitle);
     if (l > 0) then mapNum := k;
  end;
end;

macro 'Merge Multiple Stacks';
{
Combines all open stacks into one big stack.   Stacks must be named according to the convention sss_mm.  sss is a number denoting the row, and mm is a number denoting the column. Because of the obnoxious way I originally wrote this macro, mm cannot be greater than about 15.   Sorting by sss is from least to greatest (top to bottom); sorting by mm is absolute.}
}
var
  i,j:integer;
  numPics, maxW, maxH, maxD, curW, curH, curD :integer;
  sliceNum, mapNum, maxSliceNum, minSliceNum, maxMapNum: integer;
  mergedPID : integer;
begin
  SaveState;

{do some varaible initializing}
  numPics :=nPics;
   maxW := 0;
   maxH := 0;
   maxD := 0;
   maxSliceNum := 0;
   minSliceNum := 999;
   maxMapNum := 0;
   TileWindows;

{ find out how big a combined stack we have to make }
   for i := 1 to numPics do begin 
           ChoosePic(i);
           GetPicSize(curW,curH);
           curD := nSlices;
           if curD = 0 then begin
                PutMessage('One of your windows is not a stack.');
                exit;
           end;
           if (curW > maxW) then maxW := curW;
           if (curH > maxH) then maxH := curH;
           if (curD > maxD) then maxD := curD;
          SliceNum := StringToNum(WindowTitle);
          MAPNUMSEARCH;
           if (sliceNum > maxSliceNum) then maxSliceNum := sliceNum;
           if (sliceNum < minSliceNum) then minSliceNum := sliceNum;
           if (mapNum > maxMapNum) then maxMapNum := mapNum;
   end;
  ShowMessage ('width: ',50+(maxW+2)*maxMapNum,'  height:',30 +(maxH+2) * (maxSliceNum-minSliceNum+1));
  SetNewSize(50+ (maxW+2)* maxMapNum, 30 +(maxH+2) * (maxSliceNum-minSliceNum+1) );
  MakeNewStack('Slices',minSliceNum:3,'-'maxSliceNum:3);
  mergedPID := PidNumber;
  INITTEXT;
  MoveWindow(100,300);
  for i:=1 to maxD do begin           {a loop for every image slice}
  for j:=1 to numPics do begin      {a loop for every stack to be merged}
     ChoosePic(j);

                { get some positioning information }
   SliceNum := StringToNum(WindowTitle);
    MAPNUMSEARCH;
    GetPicSize(curW,curH);
               { copy the data and remove the evidence (saves on memory)}
   ChooseSlice(1);
   SelectAll;
   Copy;
   DeleteSlice;
                { choose the merge stack and paste into the proper spot }
    ChoosePic(mergedPID);
    MakeRoi(50+(mapNum-1)*(maxW+2),30+(sliceNum-minSliceNum)*(maxH+2),curW,curH);
    Paste;
                { add the proper labels }
     MoveTo(20,60+(sliceNum-minSliceNum)*(maxH+2));
     DrawNumber(sliceNum);
     MoveTo(65+(mapNum-1)*(maxW+2),10);
     DrawNumber(mapNum);
  end;
               { and finally, add the next slice in our merged stack }
    if i<maxD then AddSlice;
  end;
  for i := 1 to numPics do begin
     ChoosePic(1);
     Dispose;
     end;
 RestoreState;

end;