{
Alignment macros

This is a set of macros for aligning pictures in a stack with manual assistance. First, 
one draws a line between two features on one slice, and defines this as the 
reference line (Refrence [R]). Then, one marks the same reference line on another 
slice and runs the MatchRef [M] macro, which will rotate, scale, and shift the image
in order to match the original reference line.

These macros were originally used for aligning camera lucida drawings of
wholemounted brains to a standard size and orientation; they may prove more
widely useful for rough alignment of images of serial sections.

====== Written by ======
Chi-Bin Chien, Dept. of Biology, UC San Diego
Comments and bug reports to: chien@jeeves.ucsd.edu
(I can't promise any support for these macros, but will do my best to respond.)

Version 1.01, last modified 6/16/94
Requires Image version 1.53
}

{
==== List of Macros ====
Add Slice [+]	adds slice
Delete Slice [-]	deletes slice
Goto [G]		go to desired slice
Double Slice [2]	put an extra copy of this slice in the stack

Reference [R]	pick reference line
StandardRef [R]	use standard reference line
MatchRef [M]	sizes & rotates window so that selected line matches reference			line. Marks magnification and rotation.

Crop [C]		crops the current stack to a new stack, deletes old stack.
Enlarge [E]		copy stack to a bigger stack, extra 50 pixels on each side

Invert [I]		inverts the window, or all slices in the stack
Fill [F]		fills the ROI in the window or all slices

Last modified 1/19/94
}

{ global variables }
var
  xref1,yref1,xref2,yref2:integer;	{ x and y for reference points 1 and 2 }
  refdx,refdy:integer;		{ vector from point 1 to point 2 }
  reflength,refangle:real;		{ distance and angle from point 1 to point 2 }

macro 'Alignment Macros'; begin end;
macro '(-'; begin end;

macro 'Add Slice [+]'; begin AddSlice end;
macro 'Delete Slice [-]'; begin DeleteSlice end;

{ Error and CheckForStack are utility routines. }

{ Error(s) issues the error message S and terminates the macro. }
procedure Error(s:string);
begin
  PutMessage(s); exit;
end;

procedure CheckForStack;
begin
  if nSlices=0 then Error('This window is not a stack');
end;


macro 'Goto [G]';
var s: integer;
begin
  CheckForStack;
  s:=GetNumber('Slice to go to:', 1);
  SelectSlice(s);
end;

macro 'Double Slice [2]';
begin
  CheckForStack;
  SelectAll; Copy;
  AddSlice; Paste;
end;

macro 'Reference [R]';
var tmp:integer;
begin
  GetLine(xref1,yref1,xref2,yref2,tmp);
  if (xref1<0) then Error('Select line between two reference points.');
  if yref1<yref2 then begin
    tmp:=xref1; xref1:=xref2; xref2:=tmp;
    tmp:=yref1; yref1:=yref2; yref2:=tmp;
  end;
  refdx:=xref2-xref1; refdy:=yref2-yref1;
  reflength:=sqrt(refdx*refdx+refdy*refdy);
  if refdy=0 then refangle:=0 else refangle:=90+180*arctan(refdx/refdy)/3.141592654;
  { 0<=refangle<180 }

  ShowMessage(reflength,';',refangle,'¡');
end;

macro 'MatchRef [M]';
var
  x1,y1,x2,y2,lw,w,h,x,y,tmp,x1n,y1n,:integer;
  len,a,mag,rot,r:real;
begin
  GetLine(x1,y1,x2,y2,lw);
  if (x1<0) then begin
    Error('Select line to be matched to reference line.');
  end;
  GetPicSize(w,h);
  if (y1<y2) then begin
    tmp:=x1; x1:=x2; x2:=tmp;
    tmp:=y1; y1:=y2; y2:=tmp;
  end;

  x:=x2-x1; y:=y2-y1;
  len:=sqrt(x*x+y*y);
  if y=0 then a:=0 else a:=90+180*arctan(x/y)/3.141592654;
  ShowMessage(len,';',a,'¡');
  mag:=reflength/len;
  rot:=a-refangle;
  
  SetScaling('Bilinear, Same Window');
  SelectAll; ScaleAndRotate(mag,mag,rot);
  x1:=x1-w/2; y1:=y1-h/2; r:=rot*3.141592654/180;
  x1n:=mag*(x1*cos(r)-y1*sin(r))+w/2;
  y1n:=mag*(x1*sin(r)+y1*cos(r))+h/2;
  SelectAll; Copy; Clear; MoveRoi(xref1-x1n,yref1-y1n); Paste;

  MakeRoi(0,0,75,12); SetForeGroundColor(0); Fill;
  SetForeGroundColor(255); SetFont('Helvetica'); SetFontSize(12);
  MoveTo(0,7); Write(100*mag:5:1,'%, ',rot:4:0,'¡');
  MakeLineRoi(xref1,yref1,xref2,yref2);
end;

macro 'Crop [C]';
var
  l,t,w,h,n,old,new,i:integer;
  wt:string;
begin
  CheckForStack;
  n:=nSlices; old:=PicNumber; wt:=WindowTitle;
  GetRoi(l,t,w,h);
  if (w<=0) then begin		{ default is to shrink by 50 }
    GetPicSize(w,h);
    l:=50; t:=50; w:=w-100; h:=h-100;
  end;
  SetNewSize(w,h);
  MakeNewStack('Cropped ',wt);
  new:=PicNumber;

  for i:=1 to n do begin
    ChoosePic(old); ChooseSlice(1);
    MakeRoi(l,t,w,h); Copy; DeleteSlice;
    ChoosePic(new); ChooseSlice(i); Paste;
    if (i<n) then AddSlice;
  end;
  ChoosePic(old); Dispose;
  SelectPic(new-1);
end;

macro 'Enlarge [E]';
var
  w,h,old,new,i,s,n:integer;
  wt:string;
begin
  old:=PicNumber; wt:=WindowTitle;
  GetPicSize(w,h); SetNewSize(w+100,h+100);
  if (nSlices=0) then begin
    SelectAll; Copy;
    MakeNewWindow('Bigger ',wt); MakeRoi(50,50,w,h); Paste; KillRoi;
    new:=PicNumber-1; ChoosePic(old); Dispose; SelectPic(new);
    exit;
  end;

  s:=SliceNumber; n:=nSlices;
  MakeNewStack('Bigger ',wt); new:=PicNumber;
  for i:=1 to n do begin
    ChoosePic(old); ChooseSlice(1); SelectAll; Copy; if (i<n) then DeleteSlice;
    ChoosePic(new); ChooseSlice(i); MakeRoi(50,50,w,h); Paste; if (i<n) then AddSlice;
  end;
  ChoosePic(old); Dispose; SelectPic(new-1);
end;

macro 'Invert [I]';
var i,s:integer;
begin
  if (nSlices=0) then Invert else begin
    s:=SliceNumber;
    for i:=1 to nSlices do begin
      ChooseSlice(i); Invert;
    end;
    SelectSlice(s);
  end;
end;

macro 'Fill [F]';
var i,s:integer;
begin
  if (nSlices = 0) then Fill else begin
    s:=SliceNumber;
    for i:=1 to nSlices do begin
      ChooseSlice(i); Fill;
    end;
    SelectSlice(s);
  end;
end;