/*!
* \return Object read from file.
* \ingroup WlzExtFF
* \brief Reads a Woolz object from the given stream using the '.ipl'
* file format.
* \param fP Input file stream.
* \param dstErr Destination error number ptr,
* may be NULL.
*/
WlzObject *WlzEffReadObjIPL(FILE *fP, WlzErrorNum *dstErr)
{
int idxZ, i,
planeSz, pixelSz;
void ***data = NULL;
unsigned char ***ubData = NULL;
short ***shData = NULL;
int ***inData = NULL;
float ***flData = NULL;
unsigned char *planeBuf = NULL,
*planePtr;
WlzIVertex3 origin, size;
WlzObject *obj = NULL;
WlzErrorNum errNum = WLZ_ERR_READ_INCOMPLETE;
WlzEffIPLHeader header;
WlzGreyType gType;
origin.vtX = origin.vtY = origin.vtZ = 0;
if(fP == NULL)
{
errNum = WLZ_ERR_PARAM_NULL;
}
else
{
(void )memset((void *)&header, 0, sizeof(WlzEffIPLHeader));
errNum = WlzEffHeadReadIPL(&header, fP);
size.vtX = header.nWidth;
size.vtY = header.nHeight;
size.vtZ = header.nFrames;
}
if(errNum == WLZ_ERR_NONE)
{
switch( header.dType ){
case WLZEFF_IPL_TYPE_UBYTE:
gType = WLZ_GREY_UBYTE;
pixelSz = sizeof(char);
if((AlcUnchar3Malloc(&ubData, size.vtZ, size.vtY,
size.vtX) != ALC_ER_NONE) || (ubData == NULL))
{
errNum = WLZ_ERR_MEM_ALLOC;
}
data = (void ***) ubData;
break;
case WLZEFF_IPL_TYPE_SHORT:
case WLZEFF_IPL_TYPE_U_16:
case WLZEFF_IPL_TYPE_COL_16:
gType = WLZ_GREY_SHORT;
pixelSz = sizeof(short);
if((AlcShort3Malloc(&shData, size.vtZ, size.vtY,
size.vtX) != ALC_ER_NONE) || (shData == NULL))
{
errNum = WLZ_ERR_MEM_ALLOC;
}
data = (void ***) shData;
break;
case WLZEFF_IPL_TYPE_INT:
case WLZEFF_IPL_TYPE_COL_24:
gType = WLZ_GREY_INT;
pixelSz = sizeof(int);
if((AlcInt3Malloc(&inData, size.vtZ, size.vtY,
size.vtX) != ALC_ER_NONE) || (inData == NULL))
{
errNum = WLZ_ERR_MEM_ALLOC;
}
data = (void ***) inData;
break;
case WLZEFF_IPL_TYPE_FLOAT:
gType = WLZ_GREY_FLOAT;
pixelSz = sizeof(float);
if((AlcFloat3Malloc(&flData, size.vtZ, size.vtY,
size.vtX) != ALC_ER_NONE) || (flData == NULL))
{
errNum = WLZ_ERR_MEM_ALLOC;
}
data = (void ***) flData;
break;
default:
errNum = WLZ_ERR_PARAM_TYPE;
break;
}
}
if(errNum == WLZ_ERR_NONE)
{
planeSz = size.vtX * size.vtY;
idxZ = 0;
while((idxZ < size.vtZ) && (errNum == WLZ_ERR_NONE))
{
/* Read in each slice into the buffer */
planePtr = (unsigned char *) (**(data + idxZ));
switch( header.dType ){
case WLZEFF_IPL_TYPE_UBYTE:
case WLZEFF_IPL_TYPE_SHORT:
case WLZEFF_IPL_TYPE_U_16:
case WLZEFF_IPL_TYPE_COL_16:
case WLZEFF_IPL_TYPE_INT:
case WLZEFF_IPL_TYPE_FLOAT:
if(fread(planePtr, pixelSz, planeSz, fP) != planeSz)
{
errNum = WLZ_ERR_READ_INCOMPLETE;
}
break;
case WLZEFF_IPL_TYPE_COL_24:
for(i=0; (i < planeSz) && (errNum == WLZ_ERR_NONE); i++, planePtr++){
if(fread(planePtr, sizeof(char)*3, 1, fP) != 1)
{
errNum = WLZ_ERR_READ_INCOMPLETE;
}
planePtr[3] = 0;
}
break;
default:
break;
}
++idxZ;
}
}
if(errNum == WLZ_ERR_NONE)
{
obj = WlzFromArray3D((void ***)data, size, origin,
gType, gType,
0.0, 1.0, 0, 1, &errNum);
}
if(errNum == WLZ_ERR_NONE)
{
obj->domain.p->voxel_size[0] = 1.0;
obj->domain.p->voxel_size[1] = 1.0;
obj->domain.p->voxel_size[2] = 1.0;
}
if(planeBuf)
{
AlcFree(planeBuf);
}
if(errNum != WLZ_ERR_NONE)
{
if(obj)
{
WlzFreeObj(obj);
}
else if(data)
{
Alc3Free((void ***)data);
}
}
if(dstErr)
{
*dstErr = errNum;
}
return(obj);
}
/*!
* \return New Woolz object read from file.
* \ingroup WlzExtFF
* \brief Reads a Woolz object from the given file using the
* previously parsed Amira lattice file header.
* \param fP Input file pointer.
* \param head Amira lattice file header.
* \param dstErr Destination pointer for error number,
* may be NULL.
*/
static WlzObject *WlzEffAmReadArray3DToObj(FILE *fP, WlzEffAmHead *head,
WlzErrorNum *dstErr)
{
WlzIVertex3 org;
WlzDVertex3 voxSz;
WlzGreyType gType;
WlzObject *obj = NULL;
void ***data = NULL;
WlzErrorNum errNum = WLZ_ERR_NONE;
if((head->dim != WLZEFF_AM_DIM_3) ||
(head->fmt != WLZEFF_AM_FMT_BINARY) ||
(head->latSize.vtX < 1) ||
(head->latSize.vtY < 1) ||
(head->latSize.vtZ < 1) ||
((voxSz.vtX = head->bBox.xMax - head->bBox.xMin) < DBL_EPSILON) ||
((voxSz.vtY = head->bBox.yMax - head->bBox.yMin) < DBL_EPSILON) ||
((voxSz.vtZ = head->bBox.zMax - head->bBox.zMin) < DBL_EPSILON))
{
errNum = WLZ_ERR_READ_INCOMPLETE;
}
if(errNum == WLZ_ERR_NONE)
{
switch(head->latComp)
{
case WLZEFF_AM_LATCOMP_NONE: /* FALLTHROUGH */
case WLZEFF_AM_LATCOMP_HXBYTERLE:
break;
default:
errNum = WLZ_ERR_UNIMPLEMENTED;
break;
}
}
if(errNum == WLZ_ERR_NONE)
{
errNum = WlzEffAmSeekLabel(fP, head->latLabel);
}
if(errNum == WLZ_ERR_NONE)
{
switch(head->latDatType)
{
case WLZEFF_AM_DATTYPE_BYTE:
gType = WLZ_GREY_UBYTE;
if(AlcChar3Malloc((char ****)&data,
head->latSize.vtZ, head->latSize.vtY,
head->latSize.vtX) != ALC_ER_NONE)
{
errNum = WLZ_ERR_MEM_ALLOC;
}
break;
case WLZEFF_AM_DATTYPE_SHORT:
gType = WLZ_GREY_SHORT;
if(AlcShort3Malloc((short ****)&data,
head->latSize.vtZ, head->latSize.vtY,
head->latSize.vtX) != ALC_ER_NONE)
{
errNum = WLZ_ERR_MEM_ALLOC;
}
break;
default:
errNum = WLZ_ERR_GREY_TYPE;
break;
}
}
if(errNum == WLZ_ERR_NONE)
{
errNum = WlzEffAmReadArray3D(fP, data, head, gType);
}
if(errNum == WLZ_ERR_NONE)
{
/* Compute voxel size and origin.
* The Amira bounding box is for voxel centres and NOT
* voxel boundaries. */
if(head->latSize.vtX > 1)
{
voxSz.vtX /= (double )(head->latSize.vtX - 1);
}
if(head->latSize.vtY > 1)
{
voxSz.vtY /= (double )(head->latSize.vtY - 1);
}
if(head->latSize.vtZ > 1)
{
voxSz.vtZ /= (double )(head->latSize.vtZ - 1);
}
org.vtX = head->bBox.xMin / voxSz.vtX;
org.vtY = head->bBox.yMin / voxSz.vtY;
org.vtZ = head->bBox.zMin / voxSz.vtZ;
obj = WlzFromArray3D(data, head->latSize, org,
gType, gType, 0.0, 1.0, 0, 1, &errNum);
}
if(errNum == WLZ_ERR_NONE)
{
obj->domain.p->voxel_size[0] = voxSz.vtX;
obj->domain.p->voxel_size[1] = voxSz.vtY;
obj->domain.p->voxel_size[2] = voxSz.vtZ;
}
if(data)
{
if(obj)
{
**data = NULL;
}
Alc3Free(data);
}
if(errNum != WLZ_ERR_NONE)
{
if(obj)
{
(void )WlzFreeObj(obj);
obj = NULL;
}
}
if(dstErr)
{
*dstErr = errNum;
}
return(obj);
}
/*!
* \return Object read from file.
* \ingroup WlzExtFF
* \brief Reads a 3D Woolz object from the given file(s) using the given
* (2D) file format.
* \param gvnFileName Given file name.
* \param fFmt Given file format (must be a 2D file
* format).
* \param dstErr Destination error number ptr, may be
* NULL.
*/
static WlzObject *WlzEffReadObjStack3D(const char *gvnFileName,
WlzEffFormat fFmt,
WlzErrorNum *dstErr)
{
int tI0,
planeIdx,
planeOff;
char *tCP0,
*recTok,
*fNameStr = NULL,
*fPathStr = NULL,
*fBodyStr = NULL,
*fExtStr = NULL,
*fCtrStr = NULL;
FILE *fP = NULL,
*fP2D = NULL;
WlzIVertex2 imgSz2D;
WlzErrorNum errNum = WLZ_ERR_NONE;
WlzObject *obj = NULL;
unsigned char ***data = NULL;
char fRecord[WLZEFF_STACK_CTR_RECORDMAX];
WlzEffStackCtrHeader header;
errNum = WlzEffStackFileNameParse(gvnFileName, fFmt, &fPathStr, &fBodyStr,
&fExtStr, &fCtrStr);
if(errNum == WLZ_ERR_NONE)
{
tI0 = strlen(fPathStr) + strlen(fBodyStr) + strlen(fExtStr) + 16;
if((fNameStr = AlcMalloc(tI0 * sizeof(char))) == NULL)
{
errNum = WLZ_ERR_MEM_ALLOC;
}
else
{
sprintf(fNameStr, "%s%s.%s", fPathStr, fBodyStr, fCtrStr);
if((fP = fopen(fNameStr, "r")) == NULL)
{
errNum = WLZ_ERR_READ_EOF;
}
else
{
#ifdef _WIN32
if (fP != NULL){
if(_setmode(_fileno(fP), 0x8000) == -1)
{
errNum = WLZ_ERR_READ_EOF;
}
}
#endif
errNum = WlzEffHeadParseStackCtr(&header, fP);
}
}
}
if(errNum == WLZ_ERR_NONE)
{
imgSz2D.vtX = header.volSize.vtX;
imgSz2D.vtY = header.volSize.vtY;
if((AlcUnchar3Malloc(&data, header.volSize.vtZ, header.volSize.vtY,
header.volSize.vtX) != ALC_ER_NONE) ||
(data == NULL))
{
errNum = WLZ_ERR_MEM_ALLOC;
}
}
if(errNum == WLZ_ERR_NONE)
{
planeOff = 0;
planeIdx = header.volOrigin.vtZ;
while((planeOff < header.volSize.vtZ) && (errNum == WLZ_ERR_NONE))
{
if(fgets(fRecord, WLZEFF_STACK_CTR_RECORDMAX, fP) == NULL)
{
errNum = WLZ_ERR_READ_INCOMPLETE;
}
else
{
fRecord[WLZEFF_STACK_CTR_RECORDMAX - 1] = '\0';
if((tCP0 = strrchr(fRecord, '\n')) != NULL)
{
*tCP0 = '\0';
}
if(((recTok = strtok(fRecord, " \t")) == NULL) ||
(sscanf(recTok, "%d", &tI0) != 1) ||
(tI0 != planeIdx) ||
((recTok = strtok(NULL, " \t\n")) == NULL))
{
errNum = WLZ_ERR_READ_INCOMPLETE;
}
else
{
sprintf(fNameStr, "%s%s", fPathStr, recTok);
if((fP2D = fopen(fNameStr, "r")) == NULL)
{
errNum = WLZ_ERR_READ_EOF;
}
else
{
#ifdef _WIN32
if (fP2D != NULL){
if(_setmode(_fileno(fP2D), 0x8000) == -1)
{
errNum = WLZ_ERR_READ_EOF;
}
}
#endif
errNum = WlzEffReadObjStackData2D(fP2D, fFmt, &imgSz2D,
(data + planeOff));
fclose(fP2D);
}
}
}
++planeOff;
++planeIdx;
}
}
if(errNum == WLZ_ERR_NONE)
{
obj = WlzFromArray3D((void ***)data, header.volSize, header.volOrigin,
WLZ_GREY_UBYTE, WLZ_GREY_UBYTE,
0.0, 1.0, 0, 1, &errNum);
}
if(errNum == WLZ_ERR_NONE)
{
obj->domain.p->voxel_size[0] = header.voxSize.vtX;
obj->domain.p->voxel_size[1] = header.voxSize.vtY;
obj->domain.p->voxel_size[2] = header.voxSize.vtZ;
}
if(data)
{
if(obj)
{
/* **data used in object */
AlcFree(*data);
AlcFree(data);
}
else
{
if(data)
{
Alc3Free((void ***)data);
}
}
}
if(dstErr)
{
*dstErr = errNum;
}
if(fNameStr)
{
AlcFree(fNameStr);
}
if(fPathStr)
{
AlcFree(fPathStr);
}
if(fBodyStr)
{
AlcFree(fBodyStr);
}
if(fExtStr)
{
AlcFree(fExtStr);
}
if(fCtrStr)
{
AlcFree(fCtrStr);
}
if(dstErr)
{
*dstErr = errNum;
}
return(obj);
}
