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;
}
void OIFReader::ReadTiff(char *pbyData, unsigned short *val, int z)
{
if (*((unsigned int*)pbyData) != 0x002A4949)
return;
int compression = 0;
unsigned int offset = 0;
//directory offset
offset = *((unsigned int*)(pbyData+4));
//the directory
//entry number
int entry_num = *((unsigned short*)(pbyData+offset));
//strip info
int strips = 0;
int rows = 0;
vector <unsigned int> strip_offsets;
vector <unsigned int> strip_bytes;
//get strip info
unsigned int s_num1 = 0;
unsigned int s_num2 = 0;
for (int i=0; i<entry_num; i++)
{
//read each entry (12 bytes)
unsigned short tag = *((unsigned short*)(pbyData+offset+2+12*i));
switch (tag)
{
case 0x0103: //259, compression
{
unsigned short value;
value = *((unsigned short*)(pbyData+offset+2+12*i+8));
compression = value<<16>>16;
}
break;
case 0x0111: //strip offsets
{
unsigned short type = *((unsigned short*)(pbyData+offset+2+12*i+2));
//number of values
s_num1 = *((unsigned int*)(pbyData+offset+2+12*i+4));
unsigned int entry_offset = 0;
entry_offset = *((unsigned int*)(pbyData+offset+2+12*i+8));
for (int j=0; j<int(s_num1); j++)
{
if (type == 3)
{
//unsigned short
unsigned short value;
value = *((unsigned short*)(pbyData+entry_offset+2*j));
strip_offsets.push_back((unsigned int)value);
}
else if (type == 4)
{
//unsigned int
unsigned int value;
value = *((unsigned int*)(pbyData+entry_offset+4*j));
strip_offsets.push_back(value);
}
}
}
break;
case 0x0116: //rows per strip
{
unsigned short type = *((unsigned short*)(pbyData+offset+2+12*i+2));
if (type == 3)
{
//unsigned short
unsigned short value;
value = *((unsigned short*)(pbyData+offset+2+12*i+8));
rows = value;
}
else if (type == 4)
{
//unsigned int
unsigned int value;
value = *((unsigned int*)(pbyData+offset+2+12*i+8));
rows = value;
}
}
break;
case 0x0117: //strip byte counts
{
unsigned short type = *((unsigned short*)(pbyData+offset+2+12*i+2));
//number of values
s_num2 = *((unsigned int*)(pbyData+offset+2+12*i+4));
unsigned int entry_offset = 0;
entry_offset = *((unsigned int*)(pbyData+offset+2+12*i+8));
for (int j=0; j<int(s_num2); j++)
{
if (type == 3)
{
//unsigned short
unsigned short value;
value = *((unsigned short*)(pbyData+entry_offset+2*j));
strip_bytes.push_back((unsigned int)value);
}
else if (type == 4)
{
//unsigned int
unsigned int value;
value = *((unsigned int*)(pbyData+entry_offset+4*j));
strip_bytes.push_back(value);
}
}
}
break;
case 0x0119: //max sample value
{
unsigned short value;
value = *((unsigned short*)(pbyData+offset+2+12*i+8));
if ((double)value > m_max_value)
m_max_value = (double)value;
}
break;
}
}
//read strips
if (s_num1 == s_num2 &&
strip_offsets.size() == s_num1 &&
strip_bytes.size() == s_num2)
{
strips = s_num1;
unsigned int val_pos = z*m_x_size*m_y_size;
for (int i=0; i<strips; i++)
{
unsigned int data_pos = strip_offsets[i];
unsigned int data_size = strip_bytes[i];
if (compression == 1)//no copmression
memcpy((void*)(val+val_pos), (void*)(pbyData+data_pos), data_size);
else if (compression == 5)
LZWDecode((tidata_t)(pbyData+data_pos), (tidata_t)(val+val_pos), m_x_size*rows*2);
val_pos += rows*m_x_size;
}
}
}
void
wxPdfParser::GetStreamBytes(wxPdfStream* stream)
{
GetStreamBytesRaw(stream);
// Do not decode the content of resource object streams
if (m_useRawStream) return;
// Check whether the stream buffer is empty
wxMemoryOutputStream* osIn = stream->GetBuffer();
if (osIn->GetLength() == 0) return;
size_t j;
wxArrayPtrVoid filters;
wxPdfObject* filter = ResolveObject(stream->Get(_T("/Filter")));
if (filter != NULL)
{
int type = filter->GetType();
if (type == OBJTYPE_NAME)
{
filters.Add(filter);
}
else if (type == OBJTYPE_ARRAY)
{
wxPdfArray* filterArray = (wxPdfArray*) filter;
size_t size = filterArray->GetSize();
for (j = 0; j < size; j++)
{
filters.Add(filterArray->Get(j));
}
}
// Read decode parameters if available
wxArrayPtrVoid dp;
wxPdfObject* dpo = ResolveObject(stream->Get(_T("/DecodeParms")));
if (dpo == NULL || (dpo->GetType() != OBJTYPE_DICTIONARY && dpo->GetType() != OBJTYPE_ARRAY))
{
dpo = ResolveObject(stream->Get(_T("/DP")));
}
if (dpo != NULL)
{
if (dpo->GetType() == OBJTYPE_DICTIONARY)
{
dp.Add(dpo);
}
else if (dpo->GetType() == OBJTYPE_ARRAY)
{
wxPdfArray* dpArray = (wxPdfArray*) dpo;
size_t size = dpArray->GetSize();
for (j = 0; j < size; j++)
{
dp.Add(dpArray->Get(j));
}
}
}
wxPdfObject* dicParam = NULL;
wxMemoryOutputStream* osOut = NULL;
for (j = 0; j < filters.GetCount(); j++)
{
osIn = stream->GetBuffer();
wxPdfName* name = (wxPdfName*) filters[j];
if (name->GetName() == _T("/FlateDecode") || name->GetName() == _T("/Fl"))
{
osOut = FlateDecode(osIn);
if (j < dp.GetCount())
{
wxMemoryOutputStream* osIn2 = osOut;
dicParam = (wxPdfObject*) dp[j];
osOut = DecodePredictor(osIn2, dicParam);
if (osOut != osIn2)
{
delete osIn2;
}
}
}
else if(name->GetName() == _T("/ASCIIHexDecode") || name->GetName() == _T("/AHx"))
{
osOut = ASCIIHexDecode(osIn);
}
else if(name->GetName() == _T("/ASCII85Decode") || name->GetName() == _T("/A85"))
{
osOut = ASCII85Decode(osIn);
}
else if(name->GetName() == _T("/LZWDecode"))
{
osOut = LZWDecode(osIn);
if (j < dp.GetCount())
{
wxMemoryOutputStream* osIn2 = osOut;
dicParam = (wxPdfObject*) dp[j];
osOut = DecodePredictor(osIn2, dicParam);
if (osOut != osIn2)
{
delete osIn2;
}
}
}
else
{
wxLogError(wxString(_T("wxPdfParser::GetStreamBytes: Filter '")) +
name->GetName() + wxString(_T("' not supported")));
}
if (osOut != NULL)
{
stream->SetBuffer(osOut);
if (osIn != osOut)
{
delete osIn;
}
}
}
}
}
