void OIFReader::Preprocess()
{
m_type = 0;
m_oif_info.clear();
//separate path and name
int64_t pos = m_path_name.find_last_of(GETSLASH());
if (pos == -1)
return;
wstring path = m_path_name.substr(0, pos+1);
wstring name = m_path_name.substr(pos+1);
//extract time sequence string
int64_t begin = name.find(m_time_id);
size_t end = -1;
size_t id_len = m_time_id.size();
if (begin != -1)
{
wstring t_num;
size_t j;
for (j=begin+id_len; j<name.size(); j++)
{
wchar_t c = name[j];
if (iswdigit(c))
t_num.push_back(c);
else break;
}
if (t_num.size() > 0)
end = j;
else
begin = -1;
}
if (begin == -1)
{
ReadSingleOif();
}
else
{
//search time sequence files
std::vector<std::wstring> list;
int tmp = 0;
FIND_FILES(path,L".oif",list,tmp,name.substr(0,begin+id_len+1));
for(size_t i = 0; i < list.size(); i++) {
size_t start_idx = list.at(i).find(m_time_id) + id_len;
size_t end_idx = list.at(i).find(L".oif");
size_t size = end_idx - start_idx;
std::wstring fileno = list.at(i).substr(start_idx, size);
TimeDataInfo info;
info.filenumber = WSTOI(fileno);
info.filename = list.at(i);
m_oif_info.push_back(info);
}
if (m_oif_info.size() > 0)
{
m_type = 1;
std::sort(m_oif_info.begin(), m_oif_info.end(), OIFReader::oif_sort);
ReadSequenceOif();
}
else
{
m_oif_info.clear();
ReadSingleOif();
}
}
ReadOif();
m_time_num = int(m_oif_info.size());
if (m_type == 0)
m_cur_time = 0;
m_chan_num = m_time_num>0?int(m_oif_info[0].dataset.size()):0;
m_slice_num = m_chan_num>0?int(m_oif_info[0].dataset[0].size()):0;
}
void OIFReader::ReadOifLine(wstring oneline)
{
//process
if (oneline.substr(0, 6) == L"[Axis ")
{
axis_num++;
}
else
{
if (axis_num > -1)
{
size_t pos = oneline.find(L'=');
wstring str1 = oneline.substr(0, oneline.find_last_not_of(L' ', pos));
wstring str2 = oneline.substr(oneline.find_first_not_of(L' ', pos+1));
if (str1 == L"AxisCode")
{
if (cur_axis != axis_num)
{
cur_axis = axis_num;
axis_code.clear();
pix_unit.clear();
max_size.clear();
start_pos.clear();
end_pos.clear();
}
axis_code = str2;
}
else if (str1 == L"PixUnit")
{
if (cur_axis != axis_num)
{
cur_axis = axis_num;
axis_code.clear();
pix_unit.clear();
max_size.clear();
start_pos.clear();
end_pos.clear();
}
pix_unit = str2;
}
else if (str1 == L"MaxSize")
{
if (cur_axis != axis_num)
{
cur_axis = axis_num;
axis_code.clear();
pix_unit.clear();
max_size.clear();
start_pos.clear();
end_pos.clear();
}
max_size = str2;
}
else if (str1 == L"StartPosition")
{
if (cur_axis != axis_num)
{
cur_axis = axis_num;
axis_code.clear();
pix_unit.clear();
max_size.clear();
start_pos.clear();
end_pos.clear();
}
start_pos = str2;
}
else if (str1 == L"EndPosition")
{
if (cur_axis != axis_num)
{
cur_axis = axis_num;
axis_code.clear();
pix_unit.clear();
max_size.clear();
start_pos.clear();
end_pos.clear();
}
end_pos = str2;
}
}
}
if (oneline.substr(0, 9) == L"[Channel ")
{
light_type.clear();
chan_num++;
}
else
{
if (chan_num > -1)
{
size_t pos = oneline.find(L'=');
wstring str1 = oneline.substr(0, oneline.find_last_not_of(L' ', pos));
wstring str2 = oneline.substr(oneline.find_first_not_of(L' ', pos+1));
wstring str3 = L"Transmitted Light";
if (str1 == L"LightType") {
light_type = str2;
if (light_type.find(str3) != wstring::npos) {
for (int i = m_excitation_wavelength_list.size() -1; i >=0; i--) {
if (m_excitation_wavelength_list.at(i).chan_num == cur_chan) {
m_excitation_wavelength_list.at(i).wavelength = -1;
break;
}
}
}
}
else if (str1 == L"ExcitationWavelength")
{
if (cur_chan != chan_num)
{
cur_chan = chan_num;
WavelengthInfo info;
info.chan_num = cur_chan;
info.wavelength = WSTOD(str2);
if (light_type == L"Transmitted Light")
info.wavelength = -1;
m_excitation_wavelength_list.push_back(info);
}
}
}
}
//axis
if (!axis_code.empty() &&
!pix_unit.empty() &&
!max_size.empty() &&
!start_pos.empty() &&
!end_pos.empty())
{
//calculate
double spc = 0.0;
double dmax = WSTOD(max_size);
if (dmax > 0.0)
spc= fabs((WSTOD(end_pos)-
WSTOD(start_pos)))/
dmax;
if ((int64_t)pix_unit.find(L"nm")!=-1)
spc /= 1000.0;
if ((int64_t)axis_code.find(L"X")!=-1)
{
m_x_size = WSTOI(max_size);
m_xspc = spc;
}
else if ((int64_t)axis_code.find(L"Y")!=-1)
{
m_y_size = WSTOI(max_size);
m_yspc = spc;
}
else if ((int64_t)axis_code.find(L"Z")!=-1)
m_zspc = spc;
axis_code.clear();
pix_unit.clear();
max_size.clear();
start_pos.clear();
end_pos.clear();
}
}
void OIFReader::ReadTifSequence(wstring file_name, int t)
{
size_t line_size = file_name.size();
if (file_name.substr(line_size-3, 3) == L"tif")
{
//interpret file_name
int64_t pos;
int64_t pos_ = file_name.find_last_of(L'_');
if (pos_!=-1)
{
size_t j;
wstring wstr;
int num_c = -1;
int num_z = -1;
int num_t = -1;
int num_l = -1;
//read channel number 'C'
pos = file_name.find(L'C', pos_+1);
if (pos!=-1)
{
for (j=pos+1; j<file_name.size(); j++)
{
if (iswdigit(file_name[j]))
wstr.push_back(file_name[j]);
else
break;
}
num_c = WSTOI(wstr);
wstr.clear();
}
//read z number 'Z'
pos = file_name.find(L'Z', pos_+1);
if (pos!=-1)
{
for (j=pos+1; j<file_name.size(); j++)
{
if (iswdigit(file_name[j]))
wstr.push_back(file_name[j]);
else
break;
}
num_z = WSTOI(wstr);
wstr.clear();
}
//read time number 'T'
pos = file_name.find(L'T', pos_+1);
if (pos!=-1)
{
for (j=pos+1; j<file_name.size(); j++)
{
if (iswdigit(file_name[j]))
wstr.push_back(file_name[j]);
else
break;
}
num_t = WSTOI(wstr);
wstr.clear();
}
//read lambda number 'L'
pos = file_name.find(L'L', pos_+1);
if (pos!=-1)
{
for (j=pos+1; j<file_name.size(); j++)
{
if (iswdigit(file_name[j]))
wstr.push_back(file_name[j]);
else
break;
}
num_l = WSTOI(wstr);
wstr.clear();
}
//add info to the list
num_c = num_c==-1?0:num_c-1;
num_t = num_t==-1?t:num_t-1;
num_z = num_z==-1?1:num_z;
if (num_z > 0)
{
num_z--;
//allocate
if (m_type == 0)
{
if (int(m_oif_info.size()) < num_t+1)
m_oif_info.resize(num_t+1);
if (int(m_oif_info[num_t].dataset.size()) < num_c+1)
m_oif_info[num_t].dataset.resize(num_c+1);
if (int(m_oif_info[num_t].dataset[num_c].size()) < num_z+1)
m_oif_info[num_t].dataset[num_c].resize(num_z+1);
//add
m_oif_info[num_t].dataset[num_c][num_z] = file_name;
}
else
{
//if (num_t == 0)
{
if (int(m_oif_info[num_t].dataset.size()) < num_c+1)
m_oif_info[num_t].dataset.resize(num_c+1);
if (int(m_oif_info[num_t].dataset[num_c].size()) < num_z+1)
m_oif_info[num_t].dataset[num_c].resize(num_z+1);
//add
m_oif_info[num_t].dataset[num_c][num_z] = file_name;
}
}
}
}
}
}
void NRRDReader::Preprocess()
{
m_4d_seq.clear();
//separate path and name
int64_t pos = m_path_name.find_last_of(GETSLASH());
if (pos == -1)
return;
wstring path = m_path_name.substr(0, pos+1);
wstring name = m_path_name.substr(pos+1);
//generate search name for time sequence
int64_t begin = name.find(m_time_id);
size_t end = -1;
size_t id_len = m_time_id.size();
wstring t_num;
if (begin != -1)
{
size_t j;
for (j=begin+id_len; j<name.size(); j++)
{
wchar_t c = name[j];
if (iswdigit(c))
t_num.push_back(c);
else
break;
}
if (t_num.size() > 0)
end = j;
else
begin = -1;
}
//build 4d sequence
if (begin == -1)
{
TimeDataInfo info;
info.filenumber = 0;
info.filename = m_path_name;
m_4d_seq.push_back(info);
m_cur_time = 0;
}
else
{
//search time sequence files
std::vector<std::wstring> list;
int tmp = 0;
FIND_FILES(path,L".nrrd",list,tmp,name.substr(0,begin+id_len+1));
for(size_t i = 0; i < list.size(); i++) {
size_t start_idx = list.at(i).find(m_time_id) + id_len;
size_t end_idx = list.at(i).find(L".nrrd");
size_t size = end_idx - start_idx;
std::wstring fileno = list.at(i).substr(start_idx, size);
TimeDataInfo info;
info.filenumber = WSTOI(fileno);
info.filename = list.at(i);
m_4d_seq.push_back(info);
}
}
if (m_4d_seq.size() > 0)
{
std::sort(m_4d_seq.begin(), m_4d_seq.end(), NRRDReader::nrrd_sort);
for (int t=0; t<(int)m_4d_seq.size(); t++)
{
if (m_4d_seq[t].filename == m_path_name)
{
m_cur_time = t;
break;
}
}
}
else
m_cur_time = 0;
//3D nrrd file
m_chan_num = 1;
//get time number
m_time_num = (int)m_4d_seq.size();
}
void OIBReader::ReadOif(unsigned char *pbyData, size_t size)
{
if (!pbyData || !size)
return;
//reset
m_excitation_wavelength_list.clear();
m_x_size = 0;
m_y_size = 0;
m_xspc = 0.0;
m_yspc = 0.0;
m_zspc = 0.0;
uint16_t* data = (uint16_t*)pbyData;
size_t i = 1;
wstring oneline;
//axis info
wstring axis_code;
wstring pix_unit;
wstring max_size;
wstring start_pos;
wstring end_pos;
//axis count
int axis_num = -1;
int cur_axis = -1;
//channel count
int chan_num = -1;
int cur_chan = -1;
while (i<size/2)
{
if (data[i] != L'\n')
{
oneline.push_back(data[i]);
}
else
{
//process
if (oneline.substr(0, 6) == L"[Axis ")
{
axis_num++;
}
else
{
if (axis_num > -1)
{
size_t pos = oneline.find(L'=');
wstring str1 = oneline.substr(0, oneline.find_last_not_of(L' ', pos));
wstring str2 = oneline.substr(oneline.find_first_not_of(L' ', pos+1));
if (str1 == L"AxisCode")
{
if (cur_axis != axis_num)
{
cur_axis = axis_num;
axis_code.clear();
pix_unit.clear();
max_size.clear();
start_pos.clear();
end_pos.clear();
}
axis_code = str2;
}
else if (str1 == L"PixUnit")
{
if (cur_axis != axis_num)
{
cur_axis = axis_num;
axis_code.clear();
pix_unit.clear();
max_size.clear();
start_pos.clear();
end_pos.clear();
}
pix_unit = str2;
}
else if (str1 == L"MaxSize")
{
if (cur_axis != axis_num)
{
cur_axis = axis_num;
axis_code.clear();
pix_unit.clear();
max_size.clear();
start_pos.clear();
end_pos.clear();
}
max_size = str2;
}
else if (str1 == L"StartPosition")
{
if (cur_axis != axis_num)
{
cur_axis = axis_num;
axis_code.clear();
pix_unit.clear();
max_size.clear();
start_pos.clear();
end_pos.clear();
}
start_pos = str2;
}
else if (str1 == L"EndPosition")
{
if (cur_axis != axis_num)
{
cur_axis = axis_num;
axis_code.clear();
pix_unit.clear();
max_size.clear();
start_pos.clear();
end_pos.clear();
}
end_pos = str2;
}
}
}
if (oneline.substr(0, 9) == L"[Channel ")
{
light_type.clear();
chan_num++;
}
else
{
if (chan_num > -1)
{
size_t pos = oneline.find(L'=');
wstring str1 = oneline.substr(0, oneline.find_last_not_of(L' ', pos));
wstring str2 = oneline.substr(oneline.find_first_not_of(L' ', pos+1));
wstring str3 = L"Transmitted Light";
if (str1 == L"LightType") {
light_type = str2;
if (light_type.find(str3) != wstring::npos) {
for (int i = m_excitation_wavelength_list.size() - 1; i >= 0; i--) {
if (m_excitation_wavelength_list.at(i).chan_num == cur_chan) {
m_excitation_wavelength_list.at(i).wavelength = -1;
break;
}
}
}
}
else if (str1 == L"ExcitationWavelength")
{
if (cur_chan != chan_num)
{
cur_chan = chan_num;
WavelengthInfo info;
info.chan_num = cur_chan;
info.wavelength = WSTOD(str2.c_str());
if (light_type == L"Transmitted Light")
info.wavelength = -1;
m_excitation_wavelength_list.push_back(info);
}
}
}
}
//clear
oneline.clear();
}
//axis
if (!axis_code.empty() &&
!pix_unit.empty() &&
!max_size.empty() &&
!start_pos.empty() &&
!end_pos.empty())
{
//calculate
double spc = 0.0;
double dmax = WSTOD(max_size.c_str());
if (dmax > 0.0)
spc= fabs((WSTOD(end_pos.c_str())-
WSTOD(start_pos.c_str())))/
dmax;
if ((int64_t)pix_unit.find(L"nm")!=-1)
spc /= 1000.0;
if ((int64_t)axis_code.find(L"X")!=-1)
{
m_x_size = WSTOI(max_size.c_str());
m_xspc = spc;
}
else if ((int64_t)axis_code.find(L"Y")!=-1)
{
m_y_size = WSTOI(max_size.c_str());
m_yspc = spc;
}
else if ((int64_t)axis_code.find(L"Z")!=-1)
m_zspc = spc;
axis_code.clear();
pix_unit.clear();
max_size.clear();
start_pos.clear();
end_pos.clear();
}
i++;
}
if (m_xspc>0.0 && m_xspc<100.0 &&
m_yspc>0.0 && m_yspc<100.0)
{
m_valid_spc = true;
if (m_zspc<=0.0 || m_zspc>100.0)
m_zspc = max(m_xspc, m_yspc);
}
else
{
m_valid_spc = false;
m_xspc = 1.0;
m_yspc = 1.0;
m_zspc = 1.0;
}
}
void OIBReader::ReadOibInfo(unsigned char* pbyData, size_t size)
{
if (!pbyData || !size)
return;
uint16_t * data = (uint16_t *)pbyData;
size_t i = 1;
wstring oneline;
while (i<size/2)
{
if (data[i] != L'\n')
{
oneline.push_back(data[i]);
}
else
{
//process
size_t line_size = oneline.size();
if (oneline.substr(line_size-3, 3) == L"oif")
{
if (m_type==0 || (m_type==1&&m_oib_t==m_cur_time))
{
size_t pos = oneline.find(L'=');
m_oif_name = oneline.substr(0, oneline.find_last_not_of(L' ', pos));
m_data_name = oneline.substr(oneline.find_first_not_of(L' ', pos+1));
m_data_name = m_data_name.substr(0, m_data_name.find_last_of(L'.')) + L".oib";
}
}
else if (oneline.substr(0, 7) == L"Storage")
{
size_t pos = oneline.find(L'=');
wstring name = oneline.substr(0, oneline.find_last_not_of(L' ', pos));
if (m_type == 0)
m_substg_name = name;
else
m_oib_info[m_oib_t].substgname = name;
}
else if (oneline.substr(line_size-3, 3) == L"tif")
{
int64_t pos1 = oneline.find(L'=');
int64_t pos2 = oneline.find_last_of(L'/');
pos2 = pos2==-1?oneline.find_last_of(L'\\'):pos2;
if (pos1!=-1 && pos2!=-1)
{
wstring stream_name;
wstring file_name;
stream_name = oneline.substr(0, oneline.find_last_not_of(L' ', pos1));
file_name = oneline.substr(oneline.find_first_not_of(L' ', pos2+1));
//interpret file_name
int64_t pos;
int64_t pos_ = file_name.find_last_of(L'_');
if (pos_!=-1)
{
size_t j;
wstring wstr;
int num_c = -1;
int num_z = -1;
int num_t = -1;
int num_l = -1;
//read channel number 'C'
pos = file_name.find(L'C', pos_+1);
if (pos!=-1)
{
for (j=pos+1; j<file_name.size(); j++)
{
if (iswdigit(file_name[j]))
wstr.push_back(file_name[j]);
else
break;
}
num_c = WSTOI(wstr.c_str());
wstr.clear();
}
//read z number 'Z'
pos = file_name.find(L'Z', pos_+1);
if (pos!=-1)
{
for (j=pos+1; j<file_name.size(); j++)
{
if (iswdigit(file_name[j]))
wstr.push_back(file_name[j]);
else
break;
}
num_z = WSTOI(wstr.c_str());
wstr.clear();
}
//read time number 'T'
pos = file_name.find(L'T', pos_+1);
if (pos!=-1)
{
for (j=pos+1; j<file_name.size(); j++)
{
if (iswdigit(file_name[j]))
wstr.push_back(file_name[j]);
else
break;
}
num_t = WSTOI(wstr.c_str());
wstr.clear();
}
//read lambda number 'L'
pos = file_name.find(L'L', pos_+1);
if (pos!=-1)
{
for (j=pos+1; j<file_name.size(); j++)
{
if (iswdigit(file_name[j]))
wstr.push_back(file_name[j]);
else
break;
}
num_l = WSTOI(wstr.c_str());
wstr.clear();
}
//add info to the list
num_c = num_c==-1?0:num_c-1;
num_t = num_t==-1?0:num_t-1;
num_z = num_z==-1?1:num_z;
if (num_z > 0)
{
num_z--;
//allocate
if (m_type == 0)
{
if (int(m_oib_info.size()) < num_t+1)
m_oib_info.resize(num_t+1);
if (int(m_oib_info[num_t].dataset.size()) < num_c+1)
m_oib_info[num_t].dataset.resize(num_c+1);
if (int(m_oib_info[num_t].dataset[num_c].size()) < num_z+1)
m_oib_info[num_t].dataset[num_c].resize(num_z+1);
//add
m_oib_info[num_t].dataset[num_c][num_z].file_name = file_name;
m_oib_info[num_t].dataset[num_c][num_z].stream_name = stream_name;
}
else
{
if (num_t == 0)
{
if (int(m_oib_info[m_oib_t].dataset.size()) < num_c+1)
m_oib_info[m_oib_t].dataset.resize(num_c+1);
if (int(m_oib_info[m_oib_t].dataset[num_c].size()) < num_z+1)
m_oib_info[m_oib_t].dataset[num_c].resize(num_z+1);
//add
m_oib_info[m_oib_t].dataset[num_c][num_z].file_name = file_name;
m_oib_info[m_oib_t].dataset[num_c][num_z].stream_name = stream_name;
}
}
}
}
}
}
//clear
oneline.clear();
}
i++;
}
}
