char *readTiff3DFile2Buffer ( char *filename, unsigned char *img, unsigned int img_width, unsigned int img_height, unsigned int first, unsigned int last ) {
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_START(TiffLoadData)
#endif
TIFF *input;
input=TIFFOpen(filename,"r");
if (!input)
{
//throw iim::IOException(strprintf("in IOManager::readTiffMultipage(...): Cannot open the file %s",finName).c_str());
return ((char *) "Cannot open the file.");
}
int b_swap=TIFFIsByteSwapped(input);
char *err_msg = readTiff3DFile2Buffer(input,img,img_width,img_height,first,last,b_swap);
TIFFClose(input);
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_STOP(TiffLoadData, itm::IO, itm::strprintf("loaded block x(%d), y(%d), z(%d-%d) from 3D tiff \"%s\"", img_width, img_height, first, last, filename))
#endif
return err_msg;
}
char *readTiff3DFile2Buffer ( char *filename, unsigned char *img, unsigned int img_width, unsigned int img_height, unsigned int first, unsigned int last,
int downsamplingFactor, int starti, int endi, int startj, int endj ) {
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_START(TiffLoadData)
#endif
TIFF *input;
//disable warning and error handlers to avoid messages on unrecognized tags
TIFFSetWarningHandler(0);
TIFFSetErrorHandler(0);
input=TIFFOpen(filename,"r");
if (!input)
{
//throw iim::IOException(strprintf("in IOManager::readTiffMultipage(...): Cannot open the file %s",finName).c_str());
return ((char *) "Cannot open the file.");
}
int b_swap=TIFFIsByteSwapped(input);
char *err_msg = readTiff3DFile2Buffer(input,img,img_width,img_height,first,last,b_swap,downsamplingFactor,starti,endi,startj,endj);
TIFFClose(input);
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_STOP(TiffLoadData, tf::IO, tf::strprintf("loaded block x(%d), y(%d), z(%d-%d) from 3D tiff \"%s\"", img_width, img_height, first, last, filename))
#endif
return err_msg;
}
char *appendSlice2Tiff3DFile ( char *filename, int slice, unsigned char *img, unsigned int img_width, unsigned int img_height ) {
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_START(TiffAppendData)
#endif
TIFF *output;
uint16 spp, bpp, NPages, pg0;
output=TIFFOpen(filename,"r");
TIFFGetField(output, TIFFTAG_BITSPERSAMPLE, &bpp);
TIFFGetField(output, TIFFTAG_SAMPLESPERPIXEL, &spp);
TIFFGetField(output, TIFFTAG_PAGENUMBER, &pg0, &NPages);
TIFFClose(output);
// since we are
output = (slice==0)? TIFFOpen(filename,"w") : TIFFOpen(filename,"a");
TIFFSetDirectory(output,slice); // WARNING: slice must be the first page after the last, otherwise the file can be corrupted
TIFFSetField(output, TIFFTAG_IMAGEWIDTH, img_width);
TIFFSetField(output, TIFFTAG_IMAGELENGTH, img_height);
TIFFSetField(output, TIFFTAG_BITSPERSAMPLE, bpp);
TIFFSetField(output, TIFFTAG_SAMPLESPERPIXEL, spp);
TIFFSetField(output, TIFFTAG_ROWSPERSTRIP, img_height);
TIFFSetField(output, TIFFTAG_COMPRESSION, COMPRESSION_LZW);
//TIFFSetField(output, TIFFTAG_COMPRESSION, COMPRESSION_NONE);
TIFFSetField(output, TIFFTAG_PLANARCONFIG,PLANARCONFIG_CONTIG);
TIFFSetField(output, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_MINISBLACK);
//TIFFSetField(output, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_RGB);
// We are writing single page of the multipage file
TIFFSetField(output, TIFFTAG_SUBFILETYPE, FILETYPE_PAGE);
TIFFSetField(output, TIFFTAG_PAGENUMBER, (uint16)slice, NPages);
TIFFWriteEncodedStrip(output, 0, img, img_width * img_height * spp * (bpp/8));
//img += img_width * img_height;
TIFFWriteDirectory(output);
TIFFClose(output);
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_STOP(TiffAppendData, itm::IO, itm::strprintf("appended slice %d x %d to 3D tiff \"%s\"", img_width, img_height, filename))
#endif
return (char *) 0;
}
char *loadTiff3D2Metadata ( char * filename, unsigned int &sz0, unsigned int &sz1, unsigned int &sz2, unsigned int &sz3, int &datatype, int &b_swap, void * &fhandle, int &header_len ) {
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_START(TiffLoadMetadata)
#endif
uint32 XSIZE;
uint32 YSIZE;
uint16 bpp;
uint16 spp;
uint16 Cpage;
uint16 Npages;
TIFF *input;
int check;
input=TIFFOpen(filename,"r");
if (!input)
{
//throw iim::IOException(strprintf("in IOManager::readTiffMultipage(...): Cannot open the file %s",finName).c_str());
return ((char *) "Cannot open the file.");
}
check=TIFFGetField(input, TIFFTAG_IMAGEWIDTH, &XSIZE);
if (!check)
{
TIFFClose(input);
//throw iim::IOException(strprintf("in IOManager::readTiffMultipage(...): Image length of %s undefined\n", finName).c_str());
return ((char *) "Image width of undefined.");
}
check=TIFFGetField(input, TIFFTAG_IMAGELENGTH, &YSIZE);
if (!check)
{
TIFFClose(input);
//throw iim::IOException(strprintf("in IOManager::readTiffMultipage(...): Image length of %s undefined\n", finName).c_str());
return ((char *) "Image length of undefined.");
}
check=TIFFGetField(input, TIFFTAG_BITSPERSAMPLE, &bpp);
if (!check)
{
TIFFClose(input);
//throw iim::IOException(strprintf("in IOManager::readTiffMultipage(...): Undefined bits per sample in %s \n", finName).c_str());
return ((char *) "Undefined bits per sample.");
}
check=TIFFGetField(input, TIFFTAG_SAMPLESPERPIXEL, &spp);
if (!check)
{
TIFFClose(input);
//throw iim::IOException(strprintf("in IOManager::readTiffMultipage(...): Undefined bits per sample in %s \n", finName).c_str());
return ((char *) "Undefined samples per pixel.");
}
// Onofri
check=TIFFGetField(input, TIFFTAG_PAGENUMBER, &Cpage, &Npages);
if (!check || Npages==0) { // the tag has not been read correctly
// Add warning?
Npages = 0;
do {
Npages++;
} while ( TIFFReadDirectory(input) );
}
sz0 = XSIZE;
sz1 = YSIZE;
sz2 = Npages;
sz3 = spp;
datatype = bpp/8;
//b_swap = 0;
b_swap=TIFFIsByteSwapped(input);
fhandle = (void *) input;
header_len = -1;
// the file must non be closed (it is responsibility of the caller)
//TIFFClose(input);
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_STOP(TiffLoadMetadata, itm::IO, itm::strprintf("successfully loaded metadata from file \"%s\"", filename))
#endif
return ((char *) 0);
}
char *initTiff3DFile ( char *filename, unsigned int sz0, unsigned int sz1, unsigned int sz2, unsigned int sz3, int datatype ) {
//int initTiff3DFile ( char *filename, uint32 XSIZE, uint32 YSIZE, uint16 spp, uint16 Npages, int datatype){
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_START(TiffInitData)
#endif
uint32 XSIZE = sz0;
uint32 YSIZE = sz1;
uint16 Npages = sz2;
uint16 spp = sz3;
uint16 bpp=8 * datatype;
unsigned char *fakeData=new unsigned char[XSIZE * YSIZE];
int check;
if ( sz3 == 1 )
spp = sz3;
else if ( sz3 < 4 )
spp = 3;
else
return ((char *) "More than 3 channels in Tiff files.");
char *completeFilename = (char *) 0;
int fname_len = (int) strlen(filename);
char *suffix = strstr(filename,".tif");
while ( suffix && (fname_len - (suffix-filename) > 5) )
suffix = strstr(suffix+4,".tif");
//if ( (suffix != 0) && (fname_len - (suffix-filename) <= 5) ) { // a substring ".tif is already at the end of the filename
if ( suffix ) { // a substring ".tif is already at the very end of the filename
completeFilename = new char[fname_len+1];
strcpy(completeFilename,filename);
}
else {
completeFilename = new char[fname_len+4+1];
strcpy(completeFilename,filename);
strcat(completeFilename,".");
strcat(completeFilename,TIFF3D_SUFFIX);
}
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_STOP(TiffInitData, itm::CPU, itm::strprintf("generated fake data for 3D tiff \"%s\"", completeFilename))
TERAFLY_TIME_RESTART(TiffInitData)
#endif
TIFF *output;
output = TIFFOpen(completeFilename,"w");
if (!output) {
return ((char *) "Cannot open the file.");
}
check = TIFFSetField(output, TIFFTAG_IMAGEWIDTH, XSIZE);
if (!check) {
return ((char *) "Cannot set the image width.");
}
check = TIFFSetField(output, TIFFTAG_IMAGELENGTH, YSIZE);
if (!check) {
return ((char *) "Cannot set the image width.");
}
check = TIFFSetField(output, TIFFTAG_BITSPERSAMPLE, bpp);
if (!check) {
return ((char *) "Cannot set the image width.");
}
check = TIFFSetField(output, TIFFTAG_SAMPLESPERPIXEL, spp);
if (!check) {
return ((char *) "Cannot set the image width.");
}
check = TIFFSetField(output, TIFFTAG_ROWSPERSTRIP, YSIZE); // one page per strip
if (!check) {
return ((char *) "Cannot set the image height.");
}
check = TIFFSetField(output, TIFFTAG_COMPRESSION, COMPRESSION_LZW);
if (!check) {
return ((char *) "Cannot set the compression tag.");
}
check = TIFFSetField(output, TIFFTAG_PLANARCONFIG,PLANARCONFIG_CONTIG);
if (!check) {
return ((char *) "Cannot set the planarconfig tag.");
}
if ( spp == 1 )
check = TIFFSetField(output, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_MINISBLACK);
else // spp == 3
check = TIFFSetField(output, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_RGB);
if (!check) {
return ((char *) "Cannot set the photometric tag.");
}
/* We are writing single page of the multipage file */
check = TIFFSetField(output, TIFFTAG_SUBFILETYPE, FILETYPE_PAGE);
if (!check) {
return ((char *) "Cannot set the subfiletype tag.");
}
check = TIFFSetField(output, TIFFTAG_PAGENUMBER, 0, Npages);
if (!check) {
return ((char *) "Cannot set the page number.");
}
check = (int)TIFFWriteEncodedStrip(output, 0, fakeData, XSIZE * YSIZE);
if (!check) {
return ((char *) "Cannot write encoded strip to file.");
}
delete[] fakeData;
delete []completeFilename;
check = TIFFWriteDirectory(output);
if (!check) {
return ((char *) "Cannot write a new directory.");
}
TIFFClose(output);
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_STOP(TiffInitData, itm::IO, itm::strprintf("written initialized 3D tiff \"%s\"", completeFilename))
#endif
return (char *) 0;
}
char *appendSlice2Tiff3DFile ( char *filename, int slice, unsigned char *img, unsigned int img_width, unsigned int img_height ) {
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_START(TiffAppendData)
#endif
TIFF *output;
uint16 spp, bpp, NPages, pg0;
//disable warning and error handlers to avoid messages on unrecognized tags
TIFFSetWarningHandler(0);
TIFFSetErrorHandler(0);
output=TIFFOpen(filename,"r");
TIFFGetField(output, TIFFTAG_BITSPERSAMPLE, &bpp);
TIFFGetField(output, TIFFTAG_SAMPLESPERPIXEL, &spp);
TIFFGetField(output, TIFFTAG_PAGENUMBER, &pg0, &NPages);
TIFFClose(output);
// since we are
output = (slice==0)? TIFFOpen(filename,"w") : TIFFOpen(filename,"a");
TIFFSetDirectory(output,slice); // WARNING: slice must be the first page after the last, otherwise the file can be corrupted
TIFFSetField(output, TIFFTAG_IMAGEWIDTH, img_width);
TIFFSetField(output, TIFFTAG_IMAGELENGTH, img_height);
TIFFSetField(output, TIFFTAG_BITSPERSAMPLE, bpp);
TIFFSetField(output, TIFFTAG_SAMPLESPERPIXEL, spp);
TIFFSetField(output, TIFFTAG_ROWSPERSTRIP, (rowsPerStrip == -1) ? img_height : rowsPerStrip);
TIFFSetField(output, TIFFTAG_ORIENTATION, ORIENTATION_TOPLEFT);
TIFFSetField(output, TIFFTAG_COMPRESSION, COMPRESSION_LZW);
//TIFFSetField(output, TIFFTAG_COMPRESSION, COMPRESSION_NONE);
TIFFSetField(output, TIFFTAG_PLANARCONFIG,PLANARCONFIG_CONTIG);
TIFFSetField(output, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_MINISBLACK);
//TIFFSetField(output, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_RGB);
// We are writing single page of the multipage file
TIFFSetField(output, TIFFTAG_SUBFILETYPE, FILETYPE_PAGE);
TIFFSetField(output, TIFFTAG_PAGENUMBER, (uint16)slice, NPages);
if ( rowsPerStrip == -1 )
TIFFWriteEncodedStrip(output, 0, img, img_width * img_height * spp * (bpp/8));
else {
int check,StripsPerImage,LastStripSize;
uint32 rps = rowsPerStrip;
unsigned char *buf = img;
StripsPerImage = (img_height + rps - 1) / rps;
LastStripSize = img_height % rps;
if (LastStripSize==0)
LastStripSize=rps;
for (int i=0; i < StripsPerImage-1; i++){
//if (comp==1) {
// TIFFReadRawStrip(input, i, buf, spp * rps * img_width * (bpp/8));
// buf = buf + spp * rps * img_width * (bpp/8);
//}
//else{
TIFFWriteEncodedStrip(output, i, buf, spp * rps * img_width * (bpp/8));
buf = buf + spp * rps * img_width * (bpp/8);
//}
}
//if (comp==1) {
// TIFFReadRawStrip(input, StripsPerImage-1, buf, spp * LastStripSize * img_width * (bpp/8));
//}
//else{
TIFFWriteEncodedStrip(output, StripsPerImage-1, buf, spp * LastStripSize * img_width * (bpp/8));
//}
buf = buf + spp * LastStripSize * img_width * (bpp/8);
}
//img += img_width * img_height;
TIFFWriteDirectory(output);
TIFFClose(output);
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_STOP(TiffAppendData, tf::IO, tf::strprintf("appended slice %d x %d to 3D tiff \"%s\"", img_width, img_height, filename))
#endif
return (char *) 0;
}
char *initTiff3DFile ( char *filename, unsigned int sz0, unsigned int sz1, unsigned int sz2, unsigned int sz3, int datatype ) {
//int initTiff3DFile ( char *filename, uint32 XSIZE, uint32 YSIZE, uint16 spp, uint16 Npages, int datatype){
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_START(TiffInitData)
#endif
uint32 XSIZE = sz0;
uint32 YSIZE = sz1;
uint16 Npages = sz2;
uint16 spp = sz3;
uint16 bpp=8 * datatype;
unsigned char *fakeData=new unsigned char[XSIZE * YSIZE * spp * (bpp/8)];
int check;
if ( sz3 == 1 )
spp = sz3;
else if ( sz3 < 4 )
spp = 3;
else
return ((char *) "More than 3 channels in Tiff files.");
char *completeFilename = (char *) 0;
int fname_len = (int) strlen(filename);
char *suffix = strstr(filename,".tif");
while ( suffix && (fname_len - (suffix-filename) > 5) )
suffix = strstr(suffix+4,".tif");
//if ( (suffix != 0) && (fname_len - (suffix-filename) <= 5) ) { // a substring ".tif is already at the end of the filename
if ( suffix ) { // a substring ".tif is already at the very end of the filename
completeFilename = new char[fname_len+1];
strcpy(completeFilename,filename);
}
else {
completeFilename = new char[fname_len+4+1];
strcpy(completeFilename,filename);
strcat(completeFilename,".");
strcat(completeFilename,TIFF3D_SUFFIX);
}
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_STOP(TiffInitData, tf::CPU, tf::strprintf("generated fake data for 3D tiff \"%s\"", completeFilename))
TERAFLY_TIME_RESTART(TiffInitData)
#endif
//disable warning and error handlers to avoid messages on unrecognized tags
TIFFSetWarningHandler(0);
TIFFSetErrorHandler(0);
TIFF *output;
output = TIFFOpen(completeFilename,"w");
if (!output) {
return ((char *) "Cannot open the file.");
}
check = TIFFSetField(output, TIFFTAG_IMAGEWIDTH, XSIZE);
if (!check) {
return ((char *) "Cannot set the image width.");
}
check = TIFFSetField(output, TIFFTAG_IMAGELENGTH, YSIZE);
if (!check) {
return ((char *) "Cannot set the image height.");
}
check = TIFFSetField(output, TIFFTAG_BITSPERSAMPLE, bpp);
if (!check) {
return ((char *) "Cannot set the image bit per sample.");
}
check = TIFFSetField(output, TIFFTAG_SAMPLESPERPIXEL, spp);
if (!check) {
return ((char *) "Cannot set the image sample per pixel.");
}
check = TIFFSetField(output, TIFFTAG_ROWSPERSTRIP, (rowsPerStrip == -1) ? YSIZE : rowsPerStrip);
if (!check) {
return ((char *) "Cannot set the image rows per strip.");
}
check = TIFFSetField(output, TIFFTAG_ORIENTATION, ORIENTATION_TOPLEFT);
if (!check) {
return ((char *) "Cannot set the image orientation.");
}
check = TIFFSetField(output, TIFFTAG_COMPRESSION, COMPRESSION_LZW);
if (!check) {
return ((char *) "Cannot set the compression tag.");
}
check = TIFFSetField(output, TIFFTAG_PLANARCONFIG,PLANARCONFIG_CONTIG);
if (!check) {
return ((char *) "Cannot set the planarconfig tag.");
}
if ( spp == 1 )
check = TIFFSetField(output, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_MINISBLACK);
else // spp == 3
check = TIFFSetField(output, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_RGB);
if (!check) {
return ((char *) "Cannot set the photometric tag.");
}
/* We are writing single page of the multipage file */
check = TIFFSetField(output, TIFFTAG_SUBFILETYPE, FILETYPE_PAGE);
if (!check) {
return ((char *) "Cannot set the subfiletype tag.");
}
check = TIFFSetField(output, TIFFTAG_PAGENUMBER, 0, Npages);
if (!check) {
return ((char *) "Cannot set the page number.");
}
check = (int)TIFFWriteEncodedStrip(output, 0, fakeData, XSIZE * YSIZE);
if (!check) {
return ((char *) "Cannot write encoded strip to file.");
}
if ( rowsPerStrip == -1 )
TIFFWriteEncodedStrip(output, 0, fakeData, XSIZE * YSIZE * spp * (bpp/8));
else {
int check,StripsPerImage,LastStripSize;
uint32 rps = rowsPerStrip;
unsigned char *buf = fakeData;
StripsPerImage = (YSIZE + rps - 1) / rps;
LastStripSize = YSIZE % rps;
if (LastStripSize==0)
LastStripSize=rps;
for (int i=0; i < StripsPerImage-1; i++){
//if (comp==1) {
// TIFFReadRawStrip(input, i, buf, spp * rps * img_width * (bpp/8));
// buf = buf + spp * rps * img_width * (bpp/8);
//}
//else{
TIFFWriteEncodedStrip(output, i, buf, spp * rps * XSIZE * (bpp/8));
buf = buf + spp * rps * XSIZE * (bpp/8);
//}
}
//if (comp==1) {
// TIFFReadRawStrip(input, StripsPerImage-1, buf, spp * LastStripSize * img_width * (bpp/8));
//}
//else{
TIFFWriteEncodedStrip(output, StripsPerImage-1, buf, spp * LastStripSize * XSIZE * (bpp/8));
//}
buf = buf + spp * LastStripSize * XSIZE * (bpp/8);
}
delete[] fakeData;
delete []completeFilename;
check = TIFFWriteDirectory(output);
if (!check) {
return ((char *) "Cannot write a new directory.");
}
TIFFClose(output);
// 2015-01-30. Alessandro. @ADDED performance (time) measurement in all most time-consuming methods.
#ifdef _VAA3D_TERAFLY_PLUGIN_MODE
TERAFLY_TIME_STOP(TiffInitData, tf::IO, tf::strprintf("written initialized 3D tiff \"%s\"", completeFilename))
#endif
return (char *) 0;
}
