{Date: Tue, 10 Aug 93 15:52:11 PDT
From: karl%pluto.dnet@loni.ucla.edu
To: "hammer@wana.pbrc.Hawaii.Edu"%GATE.dnet@loni.ucla.edu
Subject: Re: Posting on Image list

To: Anyone interested in my grain counting macros

I am pleased that some people are interested in the grain counting 
macros that I wrote. As I don't do grain counting myself, they have not 
been tested in 'real world' image analysis, and I have had limited 
feedback to help me refine them. I welcome feedback for debugging and 
finding missing essential features, BUT I will be on vacation until Aug. 
28 and so cannot respond immediately.The macros are relatively simple 
and straightforward, so feel free to edit them. There are four macros 
that ASSIST in grain counting, but it is far from automatic.

You must set the Max Measurements to 1000 in the Analyze Options dialog 
box, and can make a maximum of 999 measurements. Use Set Scale to get 
areas and densities in real units. 

GRAINS MUST BE DISTINGUISHABLE BY GRAY SCALE ALONE! Image enhancement 
and editing is to be done beforehand.

Fix LUT - changes black(255) and white(0) pixels to very dark gray(254) 
and very light gray(1), so that all pixels are within the LUT.

Calibrate Area per Grain - initializes a few things, and expects that 
you have selected several 'typical' grains for an average calibration 
with a selection tool. It asks for the number of grains selected, 
calculates and stores the calibration.

Count Grains in Area - expects that you have selected your area of 
interest with a selection tool, and previously calibrated the grains. 
Grays out and numbers your area, and records area, number of grains, and 
density (grains/unit area) in the results table.

Verify Calibration - Works like 'Calibrate Area per Grain' but does not 
change anything. Simply reports previous calibration and verification. 
If the discepency is too large you must re-'Calibrate Area per Grain'. 
THIS RESETS THE RESULTS TABLE SO >>>!!SAVE IT FIRST!!<<<


Have fun, and I hope their useful.
Reply to: (after Aug. 28)
karl@loni.ucla.edu
regardless where this message appears to come from.

--------MACRO FILE FOLLOWS----------------------------------------------}

{Grain Counting Macros        }
{written by Karl Beykirch 1993}

macro 'Fix LUT                              [F5]';
begin
  ChangeValues(255,255,254);
  ChangeValues(0,0,1);
end;

macro 'Calibrate Area per Grain [F6]'
var
  pix,part,i,foo,width:integer;
begin
  RequiresVersion(1.49);
  GetRoi(foo,foo,width,foo);
  if width=0 then begin
    PutMessage('You have not selected an area!!');
    exit;
  end;
  SetOptions('Area, User1, User2');
  SetUser1Label('Grains');
  SetUser2Label('Density');
  SetPrecision(4);
  SetForegroundColor(255);
  SetBackgroundColor(0);
  Copy;
  KillRoi;
  MakeNewWindow('Temp');
  Paste;
  SetDensitySlice(255,255);
  Measure;
  GetResults(pix,foo,foo,foo,foo);
  part:=GetNumber('Enter Number of Grains Selected:',1);
  Dispose;
  ResetCounter;
  rUser2[1000]:=pix/part;
  SetNewSize(275,50);
  MakeNewWindow('Grain Size Calibrated');
  MoveTo(10,25);
  Write('Grain size calibrated as ',rUser2[1000]:5:2,' pixels / grain .');  
  SetNewSize(640,480);
end;

macro 'Count Grains in Area        [F7]'
var
  pixpart:real;
  area,pix,i,foo,left,top,width,height:integer;
begin
  if rUser2[1000]=0 then begin
    PutMessage('Grain size is NOT calibrated!!');
    exit;
  end;
  GetRoi(left,top,width,height);
  if width=0 then begin
    PutMessage('You have not selected an area!!');
    exit;
  end;
  SetBackgroundColor(0);
  Copy;
  i:=rCount;
  SetForegroundColor(128);
  Fill;
  SetForegroundColor(255);
  MoveTo(left+(width/2),top+(height/2));
  Write(i+1);
  KillRoi;
  MakeNewWindow('Temp');
  Paste;
  SetDensitySlice(255,255);
  Measure;
  Dispose;
  rUser1[i+1]:=rArea[i+1]/rUser2[1000];
  SetCounter(i);
  MakeNewWindow('Temp');
  Paste;
  SetThreshold(1);
  Measure;
  GetResults(pix,foo,foo,foo,foo);
  Dispose;
  rUser2[i+1]:=rUser1[i+1]/pix;
end;

macro 'Verify Calibration            [F8]'
var
  verif:real
  pix,part,i,foo,width:integer;
begin
  GetRoi(foo,foo,width,foo);
  if width=0 then begin
    PutMessage('You have not selected an area!!');
    exit;
  end;
  if rUser2[1000]=0 then begin
    PutMessage('Grain size is NOT calibrated!!');
    exit;
  end;
  SetForegroundColor(255);
  SetBackgroundColor(0);
  Copy;
  KillRoi;
  MakeNewWindow('Temp');
  Paste;
  SetDensitySlice(255,255);
  i:=rCount;
  Measure;
  GetResults(pix,foo,foo,foo,foo);
  SetCounter(i);
  part:=GetNumber('Enter Number of Grains Selected:',1);
  Dispose;
  verif:=pix/part;
  SetNewSize(275,50);
  MakeNewWindow('Grain Size Verification');
  MoveTo(10,15);
  Writeln('Grain size calibrated as ',rUser2[1000]:5:2,' pixels / grain.');  
  Writeln('Verification calibrated as ',verif:5:2,' pixels / grain .');  
  SetNewSize(640,480);
end;