void OIFReader::ReadSingleOif()
{
m_subdir_name = m_path_name + L".files" + GETSLASH();
std::vector<std::wstring> list;
int tmp;
FIND_FILES(m_subdir_name,L".tif",list,tmp);
//read file sequence
for(size_t f = 0; f < list.size(); f++)
ReadTifSequence(list.at(f));
}
void LSMReader::SetBatch(bool batch)
{
if (batch)
{
//read the directory info
FIND_FILES(m_path_name,L".lsm",m_batch_list,m_cur_batch);
m_batch = true;
}
else
m_batch = false;
}
void OIFReader::SetBatch(bool batch)
{
if (batch)
{
//read the directory info
wstring search_path = m_path_name.substr(0, m_path_name.find_last_of(GETSLASH())) + GETSLASH();
FIND_FILES(search_path,L".oif",m_batch_list,m_cur_batch);
m_batch = true;
}
else
m_batch = false;
}
void OIFReader::ReadSequenceOif()
{
for (int i=0; i<(int)m_oif_info.size(); i++)
{
wstring path_name = m_oif_info[i].filename;
m_oif_info[i].subdirname = path_name + L".files" + GETSLASH();
if (path_name == m_path_name)
m_cur_time = i;
m_subdir_name = path_name + L".files" + GETSLASH();
std::vector<std::wstring> list;
FIND_FILES(m_subdir_name,L".tif",list,m_oif_t);
//read file sequence
for(size_t f = 0; f < list.size(); f++)
ReadTifSequence(list.at(f), i);
}
}
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 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();
}