Nrrd* LBLReader::Convert(int t, int c, bool get_max)
{
int64_t pos = m_path_name.find_last_of('.');
if (pos == -1)
return 0;
wstring str_name = m_path_name.substr(0, pos);
wostringstream strs;
strs << str_name /*<< "_t" << t << "_c" << c*/ << ".lbl";
str_name = strs.str();
FILE* lbl_file = 0;
if (!WFOPEN(&lbl_file, str_name.c_str(), L"rb"))
return 0;
Nrrd *output = nrrdNew();
NrrdIoState *nio = nrrdIoStateNew();
nrrdIoStateSet(nio, nrrdIoStateSkipData, AIR_TRUE);
if (nrrdRead(output, lbl_file, nio))
{
fclose(lbl_file);
return 0;
}
nio = nrrdIoStateNix(nio);
rewind(lbl_file);
if (output->dim != 3 ||
(output->type != nrrdTypeInt &&
output->type != nrrdTypeUInt))
{
delete []output->data;
nrrdNix(output);
fclose(lbl_file);
return 0;
}
int slice_num = int(output->axis[2].size);
int x_size = int(output->axis[0].size);
int y_size = int(output->axis[1].size);
int data_size = slice_num * x_size * y_size;
output->data = new unsigned int[data_size];
if (nrrdRead(output, lbl_file, NULL))
{
delete []output->data;
nrrdNix(output);
fclose(lbl_file);
return 0;
}
fclose(lbl_file);
return output;
}
Nrrd* LBLReader::Convert(int t, int c, bool get_max)
{
int64_t pos = m_path_name.find_last_of('.');
if (pos == -1)
return 0;
wstring str_name = m_path_name.substr(0, pos);
wostringstream strs;
strs << str_name /*<< "_t" << t << "_c" << c*/ << ".lbl";
str_name = strs.str();
Nrrd *output = nrrdNew();
NrrdIoState *nio = nrrdIoStateNew();
nrrdIoStateSet(nio, nrrdIoStateSkipData, AIR_TRUE);
string str;
str.assign(str_name.length(), 0);
for (int i=0; i<(int)str_name.length(); i++)
str[i] = (char)str_name[i];
if (nrrdLoad(output, str.c_str(), nio))
return 0;
nio = nrrdIoStateNix(nio);
if (output->dim != 3 ||
(output->type != nrrdTypeInt &&
output->type != nrrdTypeUInt))
{
delete []output->data;
nrrdNix(output);
return 0;
}
int slice_num = int(output->axis[2].size);
int x_size = int(output->axis[0].size);
int y_size = int(output->axis[1].size);
int data_size = slice_num * x_size * y_size;
output->data = new unsigned int[data_size];
if (nrrdLoad(output, str.c_str(), NULL))
{
delete []output->data;
nrrdNix(output);
return 0;
}
return output;
}
/* *************************************************************** */
void reg_io_writeNRRDfile(Nrrd *image, const char *filename)
{
// Set the encoding to gziped as it is compiled as part of the NiftyReg project
NrrdIoState *nio=nrrdIoStateNew();
if (nrrdEncodingGzip->available()){
nrrdIoStateEncodingSet(nio, nrrdEncodingGzip);
nrrdIoStateSet(nio, nrrdIoStateZlibLevel, 9);
}
else{
fprintf(stderr, "[NiftyReg ERROR] Can not compress the file: \"%s\"\n", filename);
}
char *err;
if (nrrdSave(filename, image, nio)){
err = biffGetDone(NRRD);
fprintf(stderr, "[NiftyReg ERROR] Can not write the file \"%s\":\n%s\n", filename, err);
free(err);
exit(1);
}
return;
}
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
char me[]="nrrdLoad", *filename, *errPtr, errBuff[AIR_STRLEN_MED];
int filenameLen, sizeI[NRRD_DIM_MAX];
mxClassID mtype;
size_t sizeZ[NRRD_DIM_MAX];
unsigned int axIdx;
Nrrd *nrrd;
NrrdIoState *nio;
airArray *mop;
if (!(1 == nrhs && mxIsChar(prhs[0]))) {
sprintf(errBuff, "%s: requires one string argument (the name of the file)", me);
mexErrMsgTxt(errBuff);
}
mop = airMopNew();
filenameLen = mxGetM(prhs[0])*mxGetN(prhs[0])+1;
filename = mxCalloc(filenameLen, sizeof(mxChar)); /* managed by Matlab */
mxGetString(prhs[0], filename, filenameLen);
nrrd = nrrdNew();
airMopAdd(mop, nrrd, (airMopper)nrrdNix, airMopAlways);
nio = nrrdIoStateNew();
airMopAdd(mop, nio, (airMopper)nrrdIoStateNix, airMopAlways);
nrrdIoStateSet(nio, nrrdIoStateSkipData, AIR_TRUE);
/* read header, but no data */
if (nrrdLoad(nrrd, filename, nio)) {
errPtr = biffGetDone(NRRD);
airMopAdd(mop, errPtr, airFree, airMopAlways);
sprintf(errBuff, "%s: trouble reading NRRD header:\n%s", me, errPtr);
airMopError(mop);
mexErrMsgTxt(errBuff);
}
mtype = typeNtoM(nrrd->type);
if (mxUNKNOWN_CLASS == mtype) {
sprintf(errBuff, "%s: sorry, can't handle type %s (%d)", me,
airEnumStr(nrrdType, nrrd->type), nrrd->type);
airMopError(mop);
mexErrMsgTxt(errBuff);
}
/* allocate matlab array based on nrrd struct */
for (axIdx=0; axIdx<nrrd->dim; axIdx++) {
sizeI[axIdx] = nrrd->axis[axIdx].size;
}
plhs[0]=mxCreateNumericArray(nrrd->dim,sizeI,mtype,mxREAL);
/* copy data pointer */
nrrd->data = mxGetPr(plhs[0]);
/* read second time, now loading data */
if (nrrdLoad(nrrd, filename, NULL)) {
errPtr = biffGetDone(NRRD);
airMopAdd(mop, errPtr, airFree, airMopAlways);
sprintf(errBuff, "%s: trouble reading NRRD:\n%s", me, errPtr);
airMopError(mop);
mexErrMsgTxt(errBuff);
}
airMopOkay(mop);
return;
}
int NrrdWriter(HxUniformScalarField3* field, const char* filename, int encoding)
{
// Identify data type
int nrrdType = nrrdTypeUnknown;
switch ( field->primType() )
{
case McPrimType::mc_uint8: nrrdType = nrrdTypeUChar; break;
case McPrimType::mc_int8: nrrdType = nrrdTypeChar; break;
case McPrimType::mc_uint16: nrrdType = nrrdTypeUShort; break;
case McPrimType::mc_int16: nrrdType = nrrdTypeShort; break;
case McPrimType::mc_int32: nrrdType = nrrdTypeInt; break;
case McPrimType::mc_float: nrrdType = nrrdTypeFloat; break;
case McPrimType::mc_double: nrrdType = nrrdTypeDouble; break;
default: break;
}
if(nrrdType == nrrdTypeUnknown)
{
theMsg->printf("ERROR: unsupported output type: %s for nrrd",field->primType().getName());
return 0;
}
void* data = field->lattice.dataPtr();
Nrrd *nrrd = nrrdNew();
NrrdIoState *nios = nrrdIoStateNew();
if ( encoding == nrrdEncodingTypeGzip) {
if (nrrdEncodingGzip->available() )
{
nrrdIoStateEncodingSet( nios, nrrdEncodingGzip );
nrrdIoStateSet( nios, nrrdIoStateZlibLevel, 9 );
}
else theMsg->printf("WARNING: Nrrd library does not support Gzip compression encoding.\n Make sure Teem_ZLIB is on in CMAKE when building Nrrd library.\n");
} else if ( encoding == nrrdEncodingTypeBzip2) {
if (nrrdEncodingBzip2->available() )
{
nrrdIoStateEncodingSet( nios, nrrdEncodingBzip2 );
// nrrdIoStateSet( nios, nrrdIoStateBzip2BlockSize, 9 );
}
else theMsg->printf("WARNING: Nrrd library does not support Bzip2 compression encoding.\n Make sure Teem_BZIP2 is on in CMAKE when building Nrrd library.\n");
} else if ( encoding == nrrdEncodingTypeAscii) {
nrrdIoStateEncodingSet( nios, nrrdEncodingAscii );
} else {
theMsg->printf("ERROR: Unimplemented nrrd encoding type: %d\n",encoding);
return 0;
}
try
{
if ( nrrdWrap_va( nrrd, data, nrrdType, (size_t)3,
(size_t)field->lattice.dimsInt()[0],
(size_t)field->lattice.dimsInt()[1],
(size_t)field->lattice.dimsInt()[2] ) )
{
throw( biffGetDone(NRRD) );
}
nrrdSpaceDimensionSet( nrrd, 3 );
// TODO: Would be nice to set space units. How does Amira store this?
// if ( writeVolume->MetaKeyExists(CMTK_META_SPACE_UNITS_STRING) )
// {
// nrrd->spaceUnits[0] = strdup( writeVolume->m_MetaInformation[CMTK_META_SPACE_UNITS_STRING].c_str() );
// nrrd->spaceUnits[1] = strdup( writeVolume->m_MetaInformation[CMTK_META_SPACE_UNITS_STRING].c_str() );
// nrrd->spaceUnits[2] = strdup( writeVolume->m_MetaInformation[CMTK_META_SPACE_UNITS_STRING].c_str() );
// }
int kind[NRRD_DIM_MAX] = { nrrdKindDomain, nrrdKindDomain, nrrdKindDomain };
nrrdAxisInfoSet_nva( nrrd, nrrdAxisInfoKind, kind );
// TODO: Would be nice to write some kind of space if this exists
// Fetch bounding box information and voxel size
float* bbox = field->bbox();
McVec3f voxelSize = field->getVoxelSize();
// Just deal with space directions orthogonal to data axes
// TODO: Fetch transformation and use that
double spaceDir[NRRD_DIM_MAX][NRRD_SPACE_DIM_MAX];
for ( int i = 0; i < 3; ++i )
{
for ( int j = 0; j < 3; ++j )
{
if (i == j) spaceDir[i][j] = (double) voxelSize[i];
else spaceDir[i][j] = 0.0; // Can't assume that memory is zeroed
}
}
nrrdAxisInfoSet_nva( nrrd, nrrdAxisInfoSpaceDirection, spaceDir );
double origin[NRRD_DIM_MAX] = { bbox[0], bbox[2], bbox[4] };
if ( nrrdSpaceOriginSet( nrrd, origin ) )
{
throw( biffGetDone(NRRD) );
}
nrrdAxisInfoSet_va( nrrd, nrrdAxisInfoLabel, "x", "y", "z" );
if ( nrrdSave( filename, nrrd, nios ) )
{
throw( biffGetDone(NRRD) );
}
}
catch ( char* err )
{
theMsg->printf("ERROR: hxNrrdIO library returned error '%s'\n", err);
free( err );
return 0;
}
nrrdIoStateNix( nios );
nrrdNix(nrrd);
return 1;
}
Nrrd* NRRDReader::Convert(int t, int c, bool get_max)
{
if (t<0 || t>=m_time_num)
return 0;
int i;
m_data_name = m_4d_seq[t].filename.substr(m_4d_seq[t].filename.find_last_of(GETSLASH())+1);
Nrrd *output = nrrdNew();
NrrdIoState *nio = nrrdIoStateNew();
nrrdIoStateSet(nio, nrrdIoStateSkipData, AIR_TRUE);
string str;
str.assign(m_4d_seq[t].filename.length(), 0);
for (i=0; i<(int)m_4d_seq[t].filename.length(); i++)
str[i] = (char)m_4d_seq[t].filename[i];
if (nrrdLoad(output, str.c_str(), nio))
return 0;
nio = nrrdIoStateNix(nio);
if (output->dim != 3)
{
delete []output->data;
nrrdNix(output);
return 0;
}
m_slice_num = int(output->axis[2].size);
m_x_size = int(output->axis[0].size);
m_y_size = int(output->axis[1].size);
m_xspc = output->axis[0].spacing;
m_yspc = output->axis[1].spacing;
m_zspc = output->axis[2].spacing;
if (m_xspc>0.0 && m_xspc<100.0 &&
m_yspc>0.0 && m_yspc<100.0 &&
m_zspc>0.0 && m_zspc<100.0)
m_valid_spc = true;
else
{
m_valid_spc = false;
m_xspc = 1.0;
m_yspc = 1.0;
m_zspc = 1.0;
}
int data_size = m_slice_num * m_x_size * m_y_size;
if (output->type == nrrdTypeUShort || output->type == nrrdTypeShort)
data_size *= 2;
output->data = new unsigned char[data_size];
if (nrrdLoad(output, str.c_str(), NULL))
{
delete []output->data;
nrrdNix(output);
return 0;
}
// turn signed into unsigned
if (output->type == nrrdTypeChar) {
for (i=0; i<m_slice_num*m_x_size*m_y_size; i++) {
char val = ((char*)output->data)[i];
unsigned char n = val + 128;
((unsigned char*)output->data)[i] = n;
}
output->type = nrrdTypeUChar;
}
m_max_value = 0.0;
// turn signed into unsigned
unsigned short min_value = 32768, n;
if (output->type == nrrdTypeShort || output->type == nrrdTypeUShort) {
for (i=0; i<m_slice_num*m_x_size*m_y_size; i++) {
if (output->type == nrrdTypeShort) {
short val = ((short*)output->data)[i];
n = val + 32768;
((unsigned short*)output->data)[i] = n;
min_value = (n < min_value)?n:min_value;
} else {
n = ((unsigned short*)output->data)[i];
}
if (get_max)
m_max_value = (n > m_max_value)?n:m_max_value;
}
output->type = nrrdTypeUShort;
}
//find max value
if (output->type == nrrdTypeUChar)
{
//8 bit
m_max_value = 255.0;
m_scalar_scale = 1.0;
}
else if (output->type == nrrdTypeUShort)
{
m_max_value -= min_value;
//16 bit
for (i=0; i<m_slice_num*m_x_size*m_y_size; i++) {
((unsigned short*)output->data)[i] =
((unsigned short*)output->data)[i] - min_value;
}
if (m_max_value > 0.0)
m_scalar_scale = 65535.0 / m_max_value;
else
m_scalar_scale = 1.0;
}
else
{
delete []output->data;
nrrdNix(output);
return 0;
}
m_cur_time = t;
return output;
}
