NIH Image Fractal Macro For Computing Surface Fractal Parameters.

{NIH Image Macro to calculate fractal dimension D of Roi}
{0-255 grey scale}

{Paolo B. DePetrillo, October 27, 1999}
{DePetrillo PB, Yang Q, Rackoff J, SanMiguel A, Karimullah K.}
{Surface fractal computation and its application to immunofluorescent}
{histochemical studies of calpain and calpastatin in PC12 cells.}
{J Neurosci Meth 103(2):191-197, 2000.}
var
i:integer
left:integer
top:integer
w:integer
h:integer
numiter:real
index:integer
lefto:integer
topo:integer
hi:integer
wi:integer
wo:integer
ho:integer
size:integer
sindex:integer
pixCount:integer
small:integer
leftb:integer
topb:integer
wb:integer
hb:integer
mean:real
meanxx:real
mcount:real
sindexr:real
dsd:real
n:real
sumx:real
sumy:real
sumy2:real
sumx2:real
sumxy:real
b:real
b1:real
b2:real
b3:real
b4:real
b5:real
b6:real
b7:real
b8:real
b9:real
b10:real
sxx:real
sxy:real
syy:real
coeff:real
a:real
sigmab:real
sigmaa:real
see:real
r2:real
{rUser1 will hold slope values and rUser2 will hold r2 values for the regression}
procedure Fit; {this is a least mean squares fit, with y=ln(stdev*area)

and x=ln(area)}
{used for multiple slope calculation}
begin
b:=0; sumx:=0; sumy:=0; sumx2:=0;sumxy:=0; sumy2:=0;
numiter := rCount;
for index:=2 to numiter do begin
sumx:=sumx+ln(rArea[index]);
sumy:=sumy+ln(rStdDev[index]*rArea[index]);
sumx2:=sumx2+(ln(rArea[index])*ln(rArea[index]));
sumxy:=sumxy+(ln(rArea[index])*ln(rStdDev[index]*rArea[index]));
sumy2:=sumy2+
(ln(rStdDev[index]*rArea[index])*ln(rStdDev[index]*rArea[index]));
end;
numiter:=numiter-1;
sxx:=sumx2-(sumx*sumx/numiter);
sxy:=sumxy-(sumx*sumy/numiter);
syy:=sumy2-(sumy*sumy/numiter);
b:=sxy/sxx;
a:=((sumx2*sumy-sumx*sumxy)/numiter)/sxx;
coeff:=sxy/sqrt(sxx*sxy);
r2:=(sxy*sxy)/(sxx*syy);
see:=sqrt((sumy2 - a*sumy - b*sumxy)/(numiter-2));
sigmab:=see/sqrt(sxx);
sigmaa:=sqrt(sumx2/numiter);
end;
procedure Fits; {this is a least mean squares fit, with y=ln(stdev*area) and
x=ln(area)}
{used for single slope caclulation}
begin
b:=0; sumx:=0; sumy:=0; sumx2:=0;sumxy:=0; sumy2:=0;
numiter := rCount;
for index:=1 to numiter do begin
sumx:=sumx+ln(rArea[index]);
sumy:=sumy+ln(rStdDev[index]*rArea[index]);
sumx2:=sumx2+(ln(rArea[index])*ln(rArea[index]));
sumxy:=sumxy+(ln(rArea[index])*ln(rStdDev[index]*rArea[index]));
sumy2:=sumy2+
(ln(rStdDev[index]*rArea[index])*ln(rStdDev[index]*rArea[index]));
end;
sxx:=sumx2-(sumx*sumx/numiter);
sxy:=sumxy-(sumx*sumy/numiter);
syy:=sumy2-(sumy*sumy/numiter);
b:=sxy/sxx;
a:=((sumx2*sumy-sumx*sumxy)/numiter)/sxx;
coeff:=sxy/sqrt(sxx*sxy);
r2:=(sxy*sxy)/(sxx*syy);
see:=sqrt((sumy2 - a*sumy - b*sumxy)/(numiter-1));
sigmab:=see/sqrt(sxx);
sigmaa:=sqrt(sumx2/numiter);
end;
macro 'MakeRoi'
{get user info and make an Roi}

begin
KillRoi;
hi:=GetNumber('Enter height of Roi',25,0);
wi:=GetNumber('Enter width of Roi',25,0);
MakeRoi(left,top,wi,hi);
end;
macro 'Fractal, multiple slopes'
begin
sindex:=1;
{this resets counter for shrinking rectangle}
ResetCounter;
GetRoi(left,top,w,h);
{but we want to remember the original Roi}
lefto:=left;topo:=top;wo:=w;ho:=h;small:=0;
{this shrinks the Roi and measures}
while (w-2>0) and (h-2>0) do begin
Measure;
small:=small+1;
InsetRoi(1);
end;
leftb:=left;topb:=top;wb:=w;hb:=h;
Fit;
{we have the first estimate of D}
rUser1[sindex]:=b; rUser2[sindex]:=r2;
sindex:=sindex+1;
{let's do it again, this time we shrink from the bottom left to the top right}
KillRoi;
MakeRoi(lefto,topo,wo,ho);
ResetCounter;
i:=1;
while (w-1 >1) and (h-1>1) do begin
Measure;
MakeRoi(left+1,top,w-1,h-1);
end;
Fit;
{we have the second estimate of D}
sindex:=sindex+1;
{let's do it again, this time we shrink the rectangle from the top left to the
bottom right}
KillRoi;
ResetCounter;
i:=1;
Measure;
MakeRoi(left+1,top+1,w-1,h-1);
end;
Fit;
{we have our third estimate of D}
sindex:=sindex+1;
{let's do it again, this time we shrink the rectangle from the top right to the
bottom left}
KillRoi;
ResetCounter;
i:=1;
Measure;
MakeRoi(left,top+1,w-1,h-1);
end;
Fit;
{we have our fourth estimate of D}
sindex:=sindex+1;
{let's do it again, this time we shrink the rectangle from the bottom right to the
top left}
KillRoi;
ResetCounter;
i:=1;
Measure;
MakeRoi(left,top,w-1,h-1);
end;
Fit;
{we have our fifth estimate of D}
sindex:=sindex+1;
{let's do it again, this time we shrink the rectangle from top to bottom}
KillRoi;
ResetCounter;
i:=1;
Measure;
end;
Fit;
{we have our sixth estimate of D}
sindex:=sindex+1;
{let's do it again, this time we shrink the rectangle from bottom to top}
KillRoi;
ResetCounter;
i:=1;
Measure;
i:=i+1;
end;
Fit;
{we have our seventh estimate of D}
sindex:=sindex+1;
{let's do it again, this time we shrink the rectangle left to right}

KillRoi;
ResetCounter;
i:=1;
Measure;
end;
Fit;
{we have our eighth estimate of D}
sindex:=sindex+1;
{let's do it again, this time we shrink the rectangle right to left}

KillRoi;
ResetCounter;
i:=1;
Measure;
MakeRoi(left,top-1,w-1,h-1);
end;
Fit;
{we have our ninth estimate of D}
{and the average is:}

mean:=0;
meanxx:=0;
mcount:=0;
i:=1;
for i:=1 to sindex do begin
if rUser1[i]<.9 then begin
mcount:=mcount+1;
end;
if (rUser1[i]>0.9) or (rUser1[i]=0.9) then begin
mean:=mean+rUser1[i];
meanxx:=meanxx+sqr(rUser1[i]);
end;
end;
sindexr:=sindex;
n:=sindexr-mcount;
dsd:=sqrt((n*meanxx-(mean*mean))/(n*(n-1)));
mean:= mean/(sindexr-mcount);
NewTextWindow('Data Measurements', 500, 600);
SetFont('Monaco');
SetFontSize(12);
for i:=1 to sindex do begin
Writeln(rUser1[i],' ',rUser2[i])
end;
Writeln(mean,' ','±',dsd/sqrt(n),' mean fractal dimension ± sem');
KillRoi;
{this figures out the median pixel value}

KillRoi;
ResetCounter;
pixCount :=0;
Measure;
{rUser1 array is now used for pixel grey values from 0 to 255 and rUser2
array for histogram values}
for i := 0 to 255 do begin
rUser1[i+1] := i;
pixCount := pixCount + Histogram[i];
rUser2[i+1] := pixCount
end;
i:=1;
while (rUser2[i]<wo*ho/2) and (i+1<256) do begin
i:=i+1
end;
Writeln(rMean[1],' mean density',' ',i,' 'rUser2[i],' ',wi,hi);
Writeln(rUser1[i-1],' median pixel density',' ', rUser2[i-1],'
occurred at this pixelcount');
end;
macro 'Fractal, single slope'
begin
sindex:=1;
{this resets counter for shrinking rectangle}
ResetCounter;
{but we want to remember the original Roi}
lefto:=left;topo:=top;wo:=w;ho:=h;small:=0;
{this shrinks the Roi and measures}
while (w-2>0) and (h-2>0) do begin
Measure;
small:=small+1;
InsetRoi(1);
end;
{let's do it again, this time we shrink from the bottom left to the top right}
KillRoi;
i:=1;
Measure;
end;
{let's do it again, this time we shrink the rectangle from the top left to the
bottom right}
KillRoi;
i:=1;
Measure;
end;
{let's do it again, this time we shrink the rectangle from the top right to the
bottom left}
KillRoi;
i:=1;
Measure;
MakeRoi(left,top+1,w-1,h-1);
end;
{let's do it again, this time we shrink the rectangle from the bottom right to the
top left}
KillRoi;
i:=1;
Measure;
MakeRoi(left,top,w-1,h-1);
end;
{let's do it again, this time we shrink the rectangle from top to bottom}
KillRoi;
i:=1;
Measure;
end;
{let's do it again, this time we shrink the rectangle from bottom to top}
KillRoi;
i:=1;
Measure;
i:=i+1;
end;
{let's do it again, this time we shrink the rectangle left to right}

KillRoi;
i:=1;
Measure;
end;
{let's do it again, this time we shrink the rectangle right to left}

KillRoi;
i:=1;
Measure;
MakeRoi(left,top-1,w-1,h-1);
end;
{fit the whole bunch of slopes}
Fits;
NewTextWindow('Data Measurements', 500, 600);

SetFont('Monaco');
SetFontSize(12);
Writeln(b,' ','±',sigmab,' mean fractal dimension ± sem',' r2 is ',r2);
KillRoi;
{this figures out the median pixel value}

KillRoi;
ResetCounter;
pixCount :=0;
Measure;
{rUser1 array is now used for pixel grey values from 0 to 255 and rUser2
array for histogram values}
for i := 0 to 255 do begin
rUser1[i+1] := i;
pixCount := pixCount + Histogram[i];
rUser2[i+1] := pixCount
end;
i:=1;
while (rUser2[i]<wo*ho/2) and (i+1<256) do begin
i:=i+1
end;
Writeln(rMean[1],' mean density',' ',i,' 'rUser2[i],' ',wi,hi);
Writeln(rUser1[i-1],' median pixel density',' ', rUser2[i-1],'
occurred at this pixelcount');
end;

NIH Image Fractal Macro For Computing Surface Fractal Parameters.

Caricato da

Informazioni sul documento

Titolo originale

Copyright

Formati disponibili

Condividi questo documento

Condividi o incorpora il documento

Opzioni di condivisione

Hai trovato utile questo documento?

Questo contenuto è inappropriato?

Copyright:

Formati disponibili

NIH Image Fractal Macro For Computing Surface Fractal Parameters.

Caricato da

Copyright:

Formati disponibili

{NIH Image Macro to calculate fractal dimension D of Roi}

{0-255 grey scale}

procedure Fit; {this is a least mean squares fit, with y=ln(stdev*area)

{get user info and make an Roi}

macro 'Fractal, multiple slopes'

{let's do it again, this time we shrink the rectangle left to right}

{let's do it again, this time we shrink the rectangle right to left}

{and the average is:}

{this figures out the median pixel value}

macro 'Fractal, single slope'

{let's do it again, this time we shrink the rectangle left to right}

{let's do it again, this time we shrink the rectangle right to left}

NewTextWindow('Data Measurements', 500, 600);

{this figures out the median pixel value}

Potrebbero piacerti anche