/** Function for loading TIFF images.
Function for loading TIFF images. Supports RGB (8 bits) and
grayscale (8 and 16 bits) images, 2D and 3D. Alternative version with simpler code.
*/
VglImage* vglLoadTiffAlt(char* inFilename)
{
TIFF* tif;
VglImage* img;
uint16 pageNumber, numberPages, subfileType;
tif = TIFFOpen(inFilename, "r");
if (tif == NULL){
fprintf(stderr, "%s:%s: Error: File %s not found.\n", __FILE__, __FUNCTION__, inFilename);
return NULL;
}
int width = tif_Width(tif);
int height = tif_Height(tif);
int is3d = tif_Is3d(tif);
int layers = tif_Layers(tif);
int depth = tif_BytesPerPixel(tif); // bytes per pixel
int iplDepth = convertDepthTiffToVgl(depth); // depth \in {IPL_DEPTH_8U, ...}
int nChannels = tif_nChannels(tif); // number of channels
if (is3d)
{
img = vglCreate3dImage(cvSize(width,height), iplDepth, nChannels, layers, 0);
}
else
{
img = vglCreateImage(cvSize(width,height), iplDepth, nChannels);
}
char* imageData = img->getImageData();
int widthStep = img->getWidthStep();
char* buffer = (char*) tif_Malloc(tif);
int pixelsPerLine = img->getWidth()*img->getNChannels();
int bytesPerLine = pixelsPerLine*depth;
int i = 0;
int offset = 0;
do
{
/*
for(int i = 0; i < height; i++)
{
printf("i = %d\n", i);
TIFFReadScanline(tif, buffer, i);
memcpy(imageData + offset, buffer, bytesPerLine);
offset += widthStep;
}
*/
TIFFReadRGBAImage(tif, width, height, (uint32*) buffer, 0);
memcpy(imageData + offset, buffer, widthStep*height);
offset += widthStep + height;
}
while(TIFFReadDirectory(tif));
TIFFClose(tif);
vglSetContext(img, VGL_RAM_CONTEXT);
return img;
}
VglImage* vglColorDeconv(VglImage *imagevgl, double *mInitial, int find3rdColor /*=0*/)
{
double *mNormal = (double *) malloc(9*sizeof(double));
double *mInverse = (double *) malloc(9*sizeof(double));
double log255 = log(255.0);
if(find3rdColor != 0)
{
normalizeMatrix3x3(mInitial, mNormal);
invertMatrix3x3(mNormal, mInverse);
} else
{
normalizeMatrix(mInitial, mNormal);
rightInverseMatrix2x3(mNormal, mInverse);
}
convertBGRToRGB(imagevgl);
//vglPrintImageInfo(imagevgl);
// Creation of structure for the new image
VglImage *newimagevgl;
newimagevgl = vglCreate3dImage(cvSize(imagevgl->shape[0], imagevgl->shape[1]), imagevgl->depth, imagevgl->nChannels, imagevgl->shape[2]);
// Composition of the new image
int nPixels = imagevgl->shape[0]*imagevgl->shape[1];
for(int j = 0; j < nPixels; j++)
{
// log transform the RGB data
unsigned char r = ((unsigned char *)imagevgl->ndarray)[j*3];
unsigned char g = ((unsigned char *)imagevgl->ndarray)[j*3+1];
unsigned char b = ((unsigned char *)imagevgl->ndarray)[j*3+2];
double rLog = -((255.0 * log(((double)r+1)/255.0))/log255);
double gLog = -((255.0 * log(((double)g+1)/255.0))/log255);
double bLog = -((255.0 * log(((double)b+1)/255.0))/log255);
for(int i = 0; i < 3; i++)
{
double rScaled = rLog * mInverse[i*3];
double gScaled = gLog * mInverse[i*3+1];
double bScaled = bLog * mInverse[i*3+2];
double output = exp(-((rScaled + gScaled + bScaled) - 255.0) * log255 / 255.0);
if(output > 255)
output = 255;
((unsigned char *)newimagevgl->ndarray)[j*3+i] = (unsigned char)output;
}
}
convertRGBToBGR(newimagevgl);
return newimagevgl;
}
/** Function for loading TIFF images.
Function for loading TIFF images. Supports RGB (8 bits) and
grayscale (8 and 16 bits) images, 2D and 3D.
*/
VglImage* vglLoadTiff(char* inFilename)
{
TIFF* tif;
VglImage* img;
uint16 pageNumber, numberPages, subfileType;
tif = TIFFOpen(inFilename, "r");
if (tif == NULL){
fprintf(stderr, "%s:%s: Error: File %s not found.\n", __FILE__, __FUNCTION__, inFilename);
return NULL;
}
int width = tif_Width(tif);
int height = tif_Height(tif);
int is3d = tif_Is3d(tif);
int layers = tif_Layers(tif);
int depth = tif_BytesPerPixel(tif); // bytes per pixel
int iplDepth = convertDepthTiffToVgl(depth); // depth \in {IPL_DEPTH_8U, ...}
int nChannels = tif_nChannels(tif); // number of channels
if (is3d)
{
img = vglCreate3dImage(cvSize(width,height), iplDepth, nChannels, layers, 0);
}
else
{
img = vglCreateImage(cvSize(width,height), iplDepth, nChannels);
}
char* imageData = img->getImageData();
int pixelsPerFrame = img->getWidth()*img->getHeight()*img->nChannels;
int bytesPerFrame = pixelsPerFrame*depth;
int j = 0;
do{
char* buffer = (char*)tif_ReadData(tif);
memcpy(imageData+j, buffer, bytesPerFrame);
j += bytesPerFrame;
}while(TIFFReadDirectory(tif));
TIFFClose(tif);
vglSetContext(img, VGL_RAM_CONTEXT);
return img;
}
/** Function to save three RGB images, one for each deconvolved color
*/
void vglSaveColorDeconv(VglImage *imagevgl, double *mInitial, char *outFilename, int find3rdColor /*=0*/)
{
double *mNormal = (double *) malloc(9*sizeof(double));
if(find3rdColor != 0)
normalizeMatrix3x3(mInitial, mNormal);
else
normalizeMatrix(mInitial, mNormal);
convertBGRToRGB(imagevgl);
VglImage *newimagevgl[3];
for(int i = 0; i < 3; i++)
newimagevgl[i] = vglCreate3dImage(cvSize(imagevgl->shape[0], imagevgl->shape[1]), imagevgl->depth, imagevgl->nChannels, imagevgl->shape[2]);
int nPixels = imagevgl->shape[0]*imagevgl->shape[1];
for(int j = 0; j < nPixels; j++)
for(int i = 0; i < 3; i++)
{
unsigned char gray = ((unsigned char *)imagevgl->ndarray)[j*3+i];
double rLut = 255.0 - ((255.0 - ((double)gray)) * mNormal[i]);
double gLut = 255.0 - ((255.0 - ((double)gray)) * mNormal[i+3*1]);
double bLut = 255.0 - ((255.0 - ((double)gray)) * mNormal[i+3*2]);
((unsigned char *)newimagevgl[i]->ndarray)[j*3] = ((unsigned char)rLut);
((unsigned char *)newimagevgl[i]->ndarray)[j*3+1] = ((unsigned char)gLut);
((unsigned char *)newimagevgl[i]->ndarray)[j*3+2] = ((unsigned char)bLut);
}
int lStart = 0;
int lEnd = 0;
for(int i = 0; i < 3; i++)
{
convertRGBToBGR(newimagevgl[i]);
char outname[1024];
sprintf(outname, outFilename, i);
vglSave3dImage(newimagevgl[i], outname, lStart, lEnd);
}
}
int vglSave4dTiff(char* filename, VglImage* image, int lStart, int lEnd)
{
vglCheckContext(image, VGL_RAM_CONTEXT);
if ( (image->nChannels != 1) && (image->nChannels != 3) )
{
fprintf(stderr, "%s: %s: Error: image has %d channels but only 1 or 3 channels supported. Use vglImage4to3Channels function before saving\n", __FILE__, __FUNCTION__, image->nChannels);
return 1;
}
char* temp_filename = (char*)malloc(strlen(filename)+256);
int c = 0;
for(int i = lStart; i <= lEnd; i++)
{
VglImage* temp_image = vglCreate3dImage(cvSize(image->getWidth(), image->getHeight()), image->depth, image->nChannels, image->getLength());
temp_image->ndarray = (char*)malloc(temp_image->getTotalSizeInBytes());
memcpy((char*)temp_image->ndarray,((char*)image->ndarray)+c,temp_image->getTotalSizeInBytes());
sprintf(temp_filename, filename, i);
vglSaveTiff(temp_filename, temp_image);
c += temp_image->getTotalSizeInBytes();
vglReleaseImage(&temp_image);
}
return 0;
}
