static int load_file(const char* fileName, byte* buf, word32 bufSz)
{
FILE* file;
word32 fileSz;
word32 readSz;
if (fileName == NULL) return 0;
if (WFOPEN(&file, fileName, "rb") != 0)
return 0;
fseek(file, 0, SEEK_END);
fileSz = (word32)ftell(file);
rewind(file);
if (fileSz > bufSz) {
fclose(file);
return 0;
}
readSz = (word32)fread(buf, 1, fileSz, file);
if (readSz < fileSz) {
fclose(file);
return 0;
}
fclose(file);
return fileSz;
}
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;
}
void LSMReader::Preprocess()
{
FILE* pfile = 0;
if (!WFOPEN(&pfile, m_path_name.c_str(), L"rb"))
return;
m_lsm_info.clear();
m_l4gb = false;
int i, j;
unsigned int ioffset = 0;
fread(&ioffset, sizeof(unsigned int), 1, pfile);
if (ioffset!=0x002A4949)
{
fclose(pfile);
return;
}
int cnt_image = 0;
bool full_image = false;
//first offset
if (fread(&ioffset, sizeof(unsigned int), 1, pfile)<1)
{
fclose(pfile);
return;
}
unsigned int prev_offset = 0;
unsigned int offset_high = 0;
//images
while (fseek(pfile, ioffset, SEEK_SET)==0)
{
unsigned short entry_num;
//entry number
if (fread(&entry_num, sizeof(unsigned short), 1, pfile)<1)
{
fclose(pfile);
return;
}
vector<unsigned int> offsets;
vector<unsigned int> offset_highs;
vector<unsigned int> sizes;
for (i=0; i<entry_num; i++)
{
unsigned short tag;
if (fread(&tag, sizeof(unsigned short), 1, pfile)<1)
{
fclose(pfile);
return;
}
unsigned short type;
if (fread(&type, sizeof(unsigned short), 1, pfile)<1)
{
fclose(pfile);
return;
}
unsigned int length;
if (fread(&length, sizeof(unsigned int), 1, pfile)<1)
{
fclose(pfile);
return;
}
unsigned int value;
if (fread(&value, sizeof(unsigned int), 1, pfile)<1)
{
fclose(pfile);
return;
}
//remember current position
long cur_pos = ftell(pfile);
switch (tag)
{
case 0x00FE://254, new subfile type
if (value==0)
{
full_image = true;
cnt_image++;
}
else
full_image = false;
break;
case 0x0100://256, image width
if (full_image && cnt_image == 1)
m_x_size = value;
break;
case 0x0101://257, image length
if (full_image && cnt_image == 1)
m_y_size = value;
break;
case 0x0102://258, bits per sample
break;
case 0x0103://259, compression
if (full_image && cnt_image == 1)
m_compression = value<<16>>16;
break;
case 0x0106://262, photometric interpretation
break;
case 0x0111://273, strip offsets
if (full_image)
{
if (length==1)
{
offsets.push_back(value);
if (value < prev_offset)
{
m_l4gb = true;
offset_high++;
}
prev_offset = value;
offset_highs.push_back(offset_high);
}
else
{
if (fseek(pfile, value, SEEK_SET)==0)
{
unsigned int vtemp;
for (j=0; j<(int)length; j++)
{
if (fread(&vtemp, sizeof(unsigned int), 1, pfile)==1)
{
offsets.push_back(vtemp);
if (vtemp < prev_offset)
{
m_l4gb = true;
offset_high++;
}
prev_offset = vtemp;
offset_highs.push_back(offset_high);
}
}
}
}
}
break;
case 0x0115://277, samples per pixel
if (full_image && cnt_image == 1)
m_chan_num = value<<16>>16;
break;
case 0x0117://279, strip byte counts
if (full_image)
{
if (length==1)
{
sizes.push_back(value);
}
else
{
if (fseek(pfile, value, SEEK_SET)==0)
{
unsigned int vtemp;
for (j=0; j<(int)length; j++)
{
if (fread(&vtemp, sizeof(unsigned int), 1, pfile)==1)
sizes.push_back(vtemp);
}
}
}
}
break;
case 0x011C://284, planar configuration
break;
case 0x013D://317, predictor
if (full_image && cnt_image == 1)
m_predictor = value<<16>>16;
break;
break;
case 0x0140://320, colormap
break;
case 0x866C://34412, zeiss lsm info
if (type == 1)
{
if (fseek(pfile, value, SEEK_SET)!=0)
{
fclose(pfile);
return;
}
unsigned char* pdata = new unsigned char[length];
if (fread(pdata, sizeof(unsigned char), length, pfile)!=length)
{
fclose(pfile);
return;
}
//read lsm info
ReadLsmInfo(pfile, pdata, length);
//delete
delete []pdata;
}
break;
}
//reset position
if (fseek(pfile, cur_pos, SEEK_SET)!=0)
{
fclose(pfile);
return;
}
}
//build lsm info, which contains all offset values and sizes
if (full_image)
{
int time = (cnt_image-1) / m_slice_num;
if (time+1 > (int)m_lsm_info.size())
{
DatasetInfo dinfo;
for (i=0; i<m_chan_num; i++)
{
ChannelInfo cinfo;
dinfo.push_back(cinfo);
}
m_lsm_info.push_back(dinfo);
}
//int slice = (cnt_image-1) % m_slice_num;
for (i=0; i<m_chan_num; i++)
{
SliceInfo sinfo;
sinfo.offset = offsets[i];
sinfo.offset_high = offset_highs[i];
sinfo.size = sizes[i];
//add slice info to lsm info
m_lsm_info[time][i].push_back(sinfo);
}
}
//next image
if (fread(&ioffset, sizeof(unsigned int), 1, pfile)<1)
{
fclose(pfile);
return;
}
if (!ioffset)
break;
}
fclose(pfile);
m_cur_time = 0;
m_data_name = m_path_name.substr(m_path_name.find_last_of(GETSLASH())+1);
}
Nrrd* LSMReader::Convert(int t, int c, bool get_max)
{
Nrrd *data = 0;
FILE* pfile = 0;
if (!WFOPEN(&pfile, m_path_name.c_str(), L"rb"))
return 0;
int i, j;
if (t>=0 && t<m_time_num &&
c>=0 && c<m_chan_num &&
m_slice_num > 0 &&
m_x_size > 0 &&
m_y_size > 0 &&
t<(int)m_lsm_info.size() &&
c<(int)m_lsm_info[t].size())
{
//allocate memory for nrrd
switch (m_datatype)
{
case 1://8-bit
{
unsigned long long mem_size = (unsigned long long)m_x_size*
(unsigned long long)m_y_size*(unsigned long long)m_slice_num;
unsigned char *val = new (std::nothrow) unsigned char[mem_size];
ChannelInfo *cinfo = &m_lsm_info[t][c];
for (i=0; i<(int)cinfo->size(); i++)
{
if (m_l4gb?
FSEEK64(pfile, ((uint64_t((*cinfo)[i].offset_high))<<32)+(*cinfo)[i].offset, SEEK_SET)==0:
fseek(pfile, (*cinfo)[i].offset, SEEK_SET)==0)
{
unsigned int val_pos = m_x_size*m_y_size*i;
if (m_compression==1)
fread(val+val_pos, sizeof(unsigned char), (*cinfo)[i].size, pfile);
else if (m_compression==5)
{
unsigned char* tif = new (std::nothrow) unsigned char[(*cinfo)[i].size];
fread(tif, sizeof(unsigned char), (*cinfo)[i].size, pfile);
LZWDecode(tif, val+val_pos, (*cinfo)[i].size);
for (j=0; j<m_y_size; j++)
DecodeAcc8(val+val_pos+j*m_x_size, m_x_size,1);
delete []tif;
}
}
}
//create nrrd
data = nrrdNew();
nrrdWrap(data, val, nrrdTypeUChar, 3, (size_t)m_x_size, (size_t)m_y_size, (size_t)m_slice_num);
nrrdAxisInfoSet(data, nrrdAxisInfoSpacing, m_xspc, m_yspc, m_zspc);
nrrdAxisInfoSet(data, nrrdAxisInfoMax, m_xspc*m_x_size, m_yspc*m_y_size, m_zspc*m_slice_num);
nrrdAxisInfoSet(data, nrrdAxisInfoMin, 0.0, 0.0, 0.0);
nrrdAxisInfoSet(data, nrrdAxisInfoSize, (size_t)m_x_size, (size_t)m_y_size, (size_t)m_slice_num);
}
break;
case 2://16-bit
case 3:
{
unsigned long long mem_size = (unsigned long long)m_x_size*
(unsigned long long)m_y_size*(unsigned long long)m_slice_num;
unsigned short *val = new (std::nothrow) unsigned short[mem_size];
ChannelInfo *cinfo = &m_lsm_info[t][c];
for (i=0; i<(int)cinfo->size(); i++)
{
if (m_l4gb?
FSEEK64(pfile, ((uint64_t((*cinfo)[i].offset_high))<<32)+(*cinfo)[i].offset, SEEK_SET)==0:
fseek(pfile, (*cinfo)[i].offset, SEEK_SET)==0)
{
unsigned int val_pos = m_x_size*m_y_size*i;
if (m_compression==1)
fread(val+val_pos, sizeof(unsigned char), (*cinfo)[i].size, pfile);
else if (m_compression==5)
{
unsigned char* tif = new (std::nothrow) unsigned char[(*cinfo)[i].size];
fread(tif, sizeof(unsigned char), (*cinfo)[i].size, pfile);
LZWDecode(tif, (tidata_t)(val+val_pos), (*cinfo)[i].size);
for (j=0; j<m_y_size; j++)
DecodeAcc16((tidata_t)(val+val_pos+j*m_x_size), m_x_size,1);
delete []tif;
}
}
}
//create nrrd
data = nrrdNew();
nrrdWrap(data, val, nrrdTypeUShort, 3, (size_t)m_x_size, (size_t)m_y_size, (size_t)m_slice_num);
nrrdAxisInfoSet(data, nrrdAxisInfoSpacing, m_xspc, m_yspc, m_zspc);
nrrdAxisInfoSet(data, nrrdAxisInfoMax, m_xspc*m_x_size, m_yspc*m_y_size, m_zspc*m_slice_num);
nrrdAxisInfoSet(data, nrrdAxisInfoMin, 0.0, 0.0, 0.0);
nrrdAxisInfoSet(data, nrrdAxisInfoSize, (size_t)m_x_size, (size_t)m_y_size, (size_t)m_slice_num);
}
break;
}
}
fclose(pfile);
return data;
}
