/*-------------------------------------------------------------------
* CTWriteCTF - write a CTF file
*-------------------------------------------------------------------
*/
static int CTWriteCTF(char *path, CTSlice slice)
{
FILE *fp;
unsigned short delta[512];
int i, j, x, left, right, offsetx, offsety;
if ((fp=fopen(path, "w")) == NULL)
return(0);
/* write header */
for (i=0; i<2048; i++)
fputc(255, fp);
if (CTSliceWidth(slice) < 512)
offsetx = (512-CTSliceWidth(slice))/2;
else
offsetx = 512;
if (CTSliceHeight(slice) < 512)
offsety = (512-CTSliceHeight(slice))/2;
else
offsety = 512;
/* write the delta's */
memset(delta, '\0', sizeof(short)*512);
for (x=CTSliceMinX(slice); x<=CTSliceMaxX(slice)&&x-CTSliceMinX(slice)<512; x++)
{
for (left=CTSliceMinY(slice); left<CTSliceYSize(slice)/2; left++)
{
if (CTSliceData(slice, x, left) != 0)
break;
}
for (right=CTSliceMaxY(slice); right>CTSliceYSize(slice)/2; right--)
{
if (CTSliceData(slice, x, right) != 0)
break;
}
if (CTSliceYSize(slice)/2-left > right-CTSliceYSize(slice)/2)
delta[x] = (CTSliceYSize(slice)/2-left);
else
delta[x] = (right-CTSliceYSize(slice)/2);
}
fwrite(delta, 2, 512, fp);
/* write out the slice */
for (i=0; i<offsetx/2; i++)
{
for (i=CTSliceMinX(slice); i<=CTSliceMaxX(slice); i++)
{
for (j=CTSliceYSize(slice)/2-delta[i]; j<CTSliceYSize(slice)/2+delta[i];
j++)
fwrite(&CTSliceShortData(slice, i, j), sizeof(short), 1, fp);
}
}
fclose(fp);
return(1);
}
/*-------------------------------------------------------------------
* CTReadCTF - read a slice from a ctf file
*-------------------------------------------------------------------
*/
static int CTReadCTF(FILE *fp, CTSlice slice, int x1, int y1, int x2, int y2)
{
unsigned short delta[512], row[512];
int i, del, left, right;
long off;
/*
CTSliceXSize(slice) = 512;
CTSliceYSize(slice) = 512;
*/
if (x1==-1)
{
slice->x1=slice->y1=x1=y1=0;
slice->x2=slice->y2=x2=y2=511;
slice->data = (unsigned short *)malloc(sizeof(unsigned short)*(x2-x1+1)*
(y2-y1+1));
memset(slice->data, '\0', sizeof(short)*(x2-x1+1)*(y2-y1+1));
CTSliceWidth(slice) = CTSliceHeight(slice) = 512;
}
/* skip past the 2048 byte header */
fskip(fp, 2048);
/* read the number of data values for each line */
fread(delta, 2, 512, fp);
/* compute offset for rows up to y1 */
for (off=0, i=0; i<x1; i++)
off+=delta[i]*2*2;
#ifdef DEBUG
printf("skipping %ld values\n", off);
#endif
/* skip to the x1'th row of data */
if (off != 0)
fskip(fp, off);
for (; x1<=x2; x1++)
{
/* skip to y1'th column of data in this row */
del=delta[x1];
/* compute how much data is present */
left = (512)/2 - del;
right = (512)/2 + del- 1;
memset(row, '\0', 512*sizeof(short));
fread(&row[left], 2, 2*del, fp);
memcpy(&CTSliceShortData(slice, x1, y1), &row[y1],
sizeof(short)*(y2-y1+1));
}
CTSliceCompMinMaxD(slice);
return(0);
}
/*-------------------------------------------------------------------
* CTWritePGM - write a slice in portable greymap format
*-------------------------------------------------------------------
*/
static int CTWritePGM(char *path, CTSlice slice)
{
FILE *fp;
int i, j;
// int c, width, height, max;
// unsigned char *line;
if ((fp=fopen(path, "w")) == NULL)
return(0);
if (CTSliceMaxD(slice) <= 255)
{
fprintf(fp, "P5\n%d %d\n%d\n", CTSliceXSize(slice), CTSliceYSize(slice),
CTSliceMaxD(slice));
if (CTSliceChars(slice))
{
for (i=CTSliceYSize(slice)-1; i>=0; i--)
{
for (j=0; j<CTSliceXSize(slice); j++)
fputc(CTSliceCharData(slice, j, i), fp);
}
}
else if (CTSliceShorts(slice))
{
for (i=CTSliceYSize(slice)-1; i>=0; i--)
{
for (j=0; j<CTSliceXSize(slice); j++)
fputc(CTSliceShortData(slice, j, i), fp);
}
}
}
else
{
fprintf(fp, "P2\n%d %d\n%d\n", CTSliceXSize(slice), CTSliceYSize(slice),
CTSliceMaxD(slice));
for (i=CTSliceYSize(slice)-1; i>=0; i--)
{
for (j=0; j<CTSliceXSize(slice); j++)
fputc(CTSliceShortData(slice, j, i), fp);
}
}
fclose(fp);
return(1);
}
/*-------------------------------------------------------------------
* CTSliceSetVal - set a value in a CT image
*-------------------------------------------------------------------
*/
void CTSliceSetVal(CTSlice slice, int x, int y, float val)
{
if (CTSliceShorts(slice))
CTSliceShortData(slice, x, y) = (unsigned short) val;
else if (CTSliceChars(slice))
CTSliceCharData(slice, x, y) = (unsigned char) val;
else if (CTSliceFloats(slice))
CTSliceFloatData(slice, x, y) = val;
}
CTVolume
CTVolumeHartley3D(CTVolume vol)
{
CTVolume vol2;
CTSlice slice;
int l,m,n,L,M,N,i,j,k;
#ifdef USE_PTIME
int t1,t2;
#endif
float *d1,*d2,*X,*D,Z,*w,*w1,*w2;
float *Mcas, *Lcos, *Lsin, *Ncos, *Nsin, max, min;
double dL, dM, dN, s, c;
/* Get source volume info. */
L = CTVolXSize(vol);
M = CTVolYSize(vol);
N = CTVolNumSlices(vol);
dL = (double)L;
dM = (double)M;
dN = (double)N;
/* Initialize the new volume. */
vol2 = CTVolumeCreate(CTH3D,CTVolPrefix(vol),".h3d",CTVolXSize(vol),
CTVolYSize(vol),CTVolZSize(vol),CTVolXSep(vol),
CTVolYSep(vol),CTVolZSep(vol),CTVolFirstSlice(vol),
CTVolLastSlice(vol),1.0e10,CT_MSBF,CT_FLOAT);
/* Open the new volume for writing. */
CTVolumeOpen(vol2,CTH3D,CTVolPrefix(vol2),".h3d");
/* Read in the volume data. */
D = (float *)malloc(L*M*N*sizeof(float));
switch (CTVolVoxelBits(vol))
{
/* Read in and convert CT_8BIT values to CT_FLOAT. */
case CT_8BIT:
for (n=0;n<N;n++)
{
slice = CTSliceRead(vol,n+CTVolFirstSlice(vol),-1,-1,-1,-1);
for (l=0;l<L;l++)
{
for (m=0;m<M;m++)
{
D[n+N*(l+L*m)] = (float)CTSliceCharData(slice,l,m);
}
}
CTSliceFree(slice);
}
break;
/* Read in and convert CT_16BIT values to CT_FLOAT. */
case CT_16BIT:
for (n=0;n<N;n++)
{
slice = CTSliceRead(vol,n+CTVolFirstSlice(vol),-1,-1,-1,-1);
for (l=0;l<L;l++)
{
for (m=0;m<M;m++)
{
D[n+N*(l+L*m)] = (float)CTSliceShortData(slice,l,m);
}
}
CTSliceFree(slice);
}
break;
/* Read in CT_FLOAT values. */
case CT_FLOAT:
for (n=0;n<N;n++)
{
slice = CTSliceRead(vol,n+CTVolFirstSlice(vol),-1,-1,-1,-1);
for (l=0;l<L;l++)
{
for (m=0;m<M;m++)
{
D[n+N*(l+L*m)] = CTSliceFloatData(slice,l,m);
}
}
CTSliceFree(slice);
}
break;
}
/* Precompute necessary sin, cos, and cas function values. */
Lcos = (float *)malloc(sizeof(float)*L*L);
Lsin = (float *)malloc(sizeof(float)*L*L);
Ncos = (float *)malloc(sizeof(float)*N*N);
Nsin = (float *)malloc(sizeof(float)*N*N);
Mcas = (float *)malloc(sizeof(float)*M*M);
for (i=0;i<L*L;i++)
{
s = sin(2.0*M_PI*(double)i/dL);
c = cos(2.0*M_PI*(double)i/dL);
Lcos[i] = (float)c;
Lsin[i] = (float)s;
}
for (i=0;i<N*N;i++)
{
s = sin(2.0*M_PI*(double)i/dN);
c = cos(2.0*M_PI*(double)i/dN);
Ncos[i] = (float)c;
Nsin[i] = (float)s;
}
for (i=0;i<M*M;i++)
{
s = sin(2.0*M_PI*(double)i/dM);
c = cos(2.0*M_PI*(double)i/dM);
Mcas[i] = (float)(s+c);
}
/* Algorithm is O(LLMN+LMMN+LMNN). */
X = (float *)malloc(L*M*sizeof(float));
w1 = (float *)malloc(L*M*sizeof(float));
w2 = (float *)malloc(M*sizeof(float));
#ifdef USE_PTIME
t1 = t2 = time(NULL);
#endif
/*
Transfrom the original volume and write the new volume one slice at
a time, in order.
*/
for (k=0;k<N;k++)
{
/* Initialize max and min values for each slice. */
min = 1.0e10;
max = -1.0e10;
/* Compute w1(i,m,n) */
d1 = D;
w = w1;
for (m=0;m<M;m++)
{
for (l=0;l<L;l++)
{
d2 = &D[N*((L-l)%L+L*((M-m)%M))];
*w = 0.0;
for (n=0;n<N;n++)
{
*w += (*d1++)*Ncos[k*n]+(*d2++)*Nsin[k*n];
}
w++;
}
}
/* Compute w2(i,j,n) */
for (i=0;i<L;i++)
{
w = w2;
d1 = w1;
for (m=0;m<M;m++)
{
*w = 0.0;
d2 = &w1[L*((M-m)%M)];
for (l=0;l<L;l++)
{
*w += (*d1++)*Lcos[i*l]+(*d2++)*Lsin[i*l];
}
w++;
}
/* Compute X(i,j,k) */
for (j=0;j<M;j++)
{
Z = 0.0;
w = w2;
for (m=0;m<M;m++)
{
Z += (*w++)*Mcas[j*m];
}
if (Z>max) max = Z;
if (Z<min) min = Z;
X[i+L*j] = Z;
}
}
/* Write the transformed slice. */
slice = CTSliceCreate(L,M,min,max,vol2,k);
for (i=0;i<L;i++)
{
for (j=0;j<M;j++)
{
CTSliceSetVal(slice,i,j,X[i+L*j]);
}
}
CTSliceWrite(NULL,slice);
CTSliceFree(slice);
#ifdef USE_PTIME
printf("Slice %d/%d, ",k+1,N);
ptime((int)((float)(time(NULL)-t1)/(float)(k+1)*(float)(N-k-1)));
printf("\n");
#endif
}
/* Done writing to the new volume. */
CTVolumeClose(vol2);
#ifdef USE_PTIME
t2 = time(NULL);
printf("(3D)Total time: ");
ptime(t2-t1);
printf("\n");
#endif
/* Return the transformed volume. */
return(vol2);
}
/*------------------------------------------------------------------------
* CTSliceCompMinMaxD - compute min and max densities for a slice
*------------------------------------------------------------------------
*/
void CTSliceCompMinMaxD(CTSlice slice)
{
double val;
int i, j;
unsigned long nnonzero;
CTSliceMaxD(slice) = -1e100;
CTSliceMinD(slice) = 1e100;
nnonzero=0;
if (CTSliceShorts(slice))
{
for (i=CTSliceMinX(slice); i<=CTSliceMaxX(slice); i++)
{
for (j=CTSliceMinY(slice); j<=CTSliceMaxY(slice); j++)
{
if ((val=CTSliceShortData(slice, i, j)) > CTVolNoise(slice->vol))
continue;
if (val > CTSliceMaxD(slice))
CTSliceMaxD(slice) = val;
if (val < CTSliceMinD(slice))
CTSliceMinD(slice) = val;
if (val != 0)
nnonzero++;
}
}
}
else if (CTSliceChars(slice))
{
for (i=CTSliceMinX(slice); i<=CTSliceMaxX(slice); i++)
{
for (j=CTSliceMinY(slice); j<=CTSliceMaxY(slice); j++)
{
if ((val=CTSliceCharData(slice, i, j)) > CTVolNoise(slice->vol))
continue;
if (val > CTSliceMaxD(slice))
CTSliceMaxD(slice) = val;
if (val < CTSliceMinD(slice))
CTSliceMinD(slice) = val;
if (val != 0)
nnonzero++;
}
}
}
else if (CTSliceFloats(slice))
{
for (i=CTSliceMinX(slice); i<=CTSliceMaxX(slice); i++)
{
for (j=CTSliceMinY(slice); j<=CTSliceMaxY(slice); j++)
{
if ((val=CTSliceFloatData(slice, i, j)) > CTVolNoise(slice->vol))
continue;
if (val > CTSliceMaxD(slice))
CTSliceMaxD(slice) = val;
if (val < CTSliceMinD(slice))
CTSliceMinD(slice) = val;
if (val != 0)
nnonzero++;
}
}
}
CTSliceRatio(slice) = nnonzero/
(double)(CTSliceWidth(slice)*CTSliceHeight(slice));
}
/*-------------------------------------------------------------------
* CTReadPGM - read a slice from a portable greymap file
*-------------------------------------------------------------------
*/
static int CTReadPGM(FILE *fp, CTSlice slice, int x1, int y1, int x2, int y2)
{
int c, i, j, width, height, max;
unsigned char *line;
char buf[1024];
/* read for the magic number, skipping comments */
while ((c=fgetc(fp)) == '#')
fgets(buf, 1024, fp);
ungetc(c, fp);
if (fscanf(fp, "P%d\n", &c) != 1)
return(-1);
if (c != 2 && c != 5)
{
/* file is not PGM, fail */
return(-1);
}
if (c==2)
{
while ((c=fgetc(fp)) == '#')
fgets(buf, 1024, fp);
ungetc(c, fp);
if (fscanf(fp, "%d%d%d", &width, &height, &max) != 3)
return(-1);
if (x1==-1)
{
slice->x1=slice->y1=x1=y1=0;
slice->x2=x2=width-1;
slice->y2=y2=height-1;
slice->data = (unsigned short *)malloc(sizeof(unsigned short)*
(x2-x1+1)*(y2-y1+1));
memset(slice->data, 0, sizeof(short)*(x2-x1+1)*(y2-y1+1));
CTSliceWidth(slice) = width;
CTSliceHeight(slice) = height;
}
/* eat extra character */
getc(fp);
for (i=height-1; i>=0; i--)
{
for (j=0; j<width; j++)
{
int val;
fscanf(fp, "%d", &val);
CTSliceShortData(slice, j, i) = val;
}
}
CTSliceCompMinMaxD(slice);
return(0);
}
else if (c==5)
{
while ((c=fgetc(fp)) == '#')
fgets(buf, 1024, fp);
ungetc(c, fp);
if (fscanf(fp, "%d%d%d", &width, &height, &max) != 3)
{
printf("failed to read width/height/max\n");
return(-1);
}
if (x1==-1)
{
slice->x1=slice->y1=x1=y1=0;
slice->x2=x2=width-1;
slice->y2=y2=height-1;
slice->cdata = (unsigned char *)malloc(sizeof(unsigned char)*
(x2-x1+1)*(y2-y1+1));
memset(slice->cdata, '\0', sizeof(char)*(x2-x1+1)*(y2-y1+1));
CTSliceWidth(slice) = width;
CTSliceHeight(slice) = height;
}
/* eat extra character */
getc(fp);
line = (unsigned char *)malloc(sizeof(char)*width);
for (i=height-1; i>=0; i--)
{
fread(line, 1, width, fp);
if (y1 <= i && i <= y2)
{
for (j=0; j<width; j++)
{
if (x1 <= j && j <= x2)
CTSliceCharData(slice, j, i) = line[j];
}
}
}
free(line);
CTSliceCompMinMaxD(slice);
return(0);
}
return(1);
}
/*-------------------------------------------------------------------
* CTSliceSetVals - set a block of values in a CT image
*-------------------------------------------------------------------
*/
void CTSliceSetVals(CTSlice slice, int x1, int y1, int x2, int y2,
int val, int z)
{
int x, y;
if (x1 > x2)
{
x = x1;
x1 = x2;
x2 = x;
}
if (y1 > y2)
{
y = y1;
y1 = y2;
y2 = y;
}
x1 = MAX(x1, slice->x1);
y1 = MAX(y1, slice->y1);
x2 = MIN(x2, slice->x2);
y2 = MIN(y2, slice->y2);
if (z)
{
if (x1 <= x2)
{
/* set the first line */
if (CTSliceShorts(slice))
{
for (y=y1; y<=y2; y++)
CTSliceShortData(slice, x1, y) = val;
for (x1++; x1<=x2; x1++)
memcpy(&CTSliceShortData(slice, x1, y1),&CTSliceShortData(slice, x1-1, y1),
sizeof(short)*(y2-y1+1));
}
else
{
for (y=y1; y<=y2; y++)
CTSliceCharData(slice, x1, y) = val;
for (x1++; x1<=x2; x1++)
memcpy(&CTSliceCharData(slice, x1, y1),&CTSliceCharData(slice, x1-1, y1),
sizeof(char)*(y2-y1+1));
}
}
}
else
{
if (CTSliceShorts(slice))
{
for (x=x1; x<=x2; x++)
{
for (y=y1; y<=y2; y++)
if (CTSliceShortData(slice, x, y) > 1000)
CTSliceShortData(slice, x, y) = val;
else
CTSliceShortData(slice, x, y) = 0;
}
}
else
{
for (x=x1; x<=x2; x++)
{
for (y=y1; y<=y2; y++)
if (CTSliceCharData(slice, x, y) > 1000)
CTSliceCharData(slice, x, y) = val;
else
CTSliceCharData(slice, x, y) = 0;
}
}
}
}
