{
Date: Wed, 5 Jan 1994 20:20:12 -0800 (PST)
From: Glen Macdonald <glenmac@u.washington.edu>
Subject: a rotational align macro
To: Wayne Rasband <wayne%zippy.nimh.nih.gov@hub2.tc.umn.edu>

A macro set is included below to perform simple rotational and x-y
registration of two images.  there has been a lot of sophisticated methods
discussed for doing rotational alignments, but I had a deadline to meet. 
This is very basic, but wholly adequate for counting double labelled
objects immunolabelled in two adjacent semithin sections or counting
objects with a physical disector method. This is the alignment kernel from
a larger macro set for doing double label counts. I think most of the
extraneous variables and commands have been removed.  Anyway, it works. 
Many thanks to Mark Vivino for posting his image translation macro, I used
most of it here. 

 To use: 
1. grab the first image (or open a file);
2. draw a line from left to right between two landmarks;
3. press "4" to mark the image (a copy is created entitled "Register 
To:windowname");
4. get the next image, this is the one that will be rotated and pasted onto 
the "Register to" image;
5. draw a line from left to right between the landmarks, as if you are 
facing the landmarks from the same direction as you were with the first 
image;
6. Press "5", this will create a rotated copy entitled "Image to be 
Registered";
7. If you are happy wth the results Press "7", otherwise delete and remark 
the second image;
8. The rotated image can be dragged in X and Y to complete the alignment.


Glen MacDonald
Hearing Development Laboratories RL-30
University of Washington
Seattle, WA  98195
(206)543-8360
glenmac@u.washington.edu
}

**************************************************************

 {Image rotation macro; Glen MacDonald, for the Child Development and Mental
 Retardation Center, University of Washington, Seattle, WA. November 22, 1993,
 rev. Jan. 3, 1994.  Many thanks to Mark Vivino for posting the x-y image
 registration macros}

var {global variables}
x1,x2,y1,y2,width,height,LineWidth,firstAngle,dx,dy,SecondAngle,deltaAngle,ThisAngle,SinA:real;
x,y,ImageToRegister, RegistrationImage:integer;
 OrigTop,OrigLeft,OrigWidth,OrigHeight,stage:integer;

Procedure GetSinA; 
var
	Hypot:real;
	
begin
	Hypot:=sqrt(sqr(dx)+sqr(dY)); {gives the hypotenuse of the 		angle}
	SinA:=dY/Hypot;
	ThisAngle:=rAngle[rCount]; {grab the angle for this image}
	if ((SinA=0) and (dX<0)) then ThisAngle:=0 else if 
	((SinA<0) or ((SinA=0) and (dX>0))) then
	ThisAngle:=(180-rAngle[rCount]) else
	ThisAngle:=((rAngle[rCount])*(-1));
end;


Procedure FindLineMidPoint;
begin
	GetLine(x1,y1,x2,y2,LineWidth); {get x,y coords. of line ends}
	if LineWidth = 0 then begin
		putMessage('You must draw a line from left to right between two landmarks.');
		exit;
	end;
	measure;
	dx:=x1-x2;
	dy:=y1-y2;
	GetSinA;
end;

macro 'Mark First Image [4]';
var
	regpicname:string;
begin
	SetOptions('Angle');
	regpicname:=WindowTitle;
	SelectAll;
	Duplicate('Register to:' regpicname);
	RestoreRoi;
	  if WindowTitle='Camera' then begin
    PutMessage('The active window cannot be "Camera".');
    exit;
  end;
	RegistrationImage:=pidnumber;
	FindLineMidPoint;
	firstAngle:=ThisAngle;
	PutMessage('Now go to the image to be aligned to this one.');
end;

macro 'Mark and Rotate Second Image [5]';
begin
	FindLineMidPoint;
	secondAngle:=ThisAngle;
	deltaAngle:=(firstAngle-secondAngle);
	SelectAll;
	ScaleandRotate(1,1,deltaangle);
	SetPicName('Image to Register');
	SelectAll;
	GetROI(OrigLeft,OrigTop,OrigWidth,OrigHeight);
	if OrigWidth=0 then begin PutMessage('Use Select All or create an ROI on the image you want registered.');
		exit;
	end;
	ImageToRegister := PidNumber;
	ShowPasteControl;
	Copy;
	SelectPic(RegistrationImage);
	Showmessage('Run the next macro.');
	RestoreRoi;
end;


macro 'Register the Images [6]';
begin
 Showmessage('Move the ROI to the visual registration point.');
 Paste;
 SetOption; 
DoXOr; 
end;