std::unique_ptr<ImageIO::Base> MRtrix::create (Header& H) const
{
File::OFStream out (H.name(), std::ios::out | std::ios::binary);
out << "mrtrix image\n";
write_mrtrix_header (H, out);
bool single_file = Path::has_suffix (H.name(), ".mif");
int64_t offset = 0;
out << "file: ";
if (single_file) {
offset = out.tellp() + int64_t(18);
offset += ((4 - (offset % 4)) % 4);
out << ". " << offset << "\nEND\n";
}
else out << Path::basename (H.name().substr (0, H.name().size()-4) + ".dat") << "\n";
out.close();
std::unique_ptr<ImageIO::Base> io_handler (new ImageIO::Default (H));
if (single_file) {
File::resize (H.name(), offset + footprint(H));
io_handler->files.push_back (File::Entry (H.name(), offset));
}
else {
std::string data_file (H.name().substr (0, H.name().size()-4) + ".dat");
File::create (data_file, footprint(H));
io_handler->files.push_back (File::Entry (data_file));
}
return io_handler;
}
void run ()
{
const bool weights_provided = get_options ("tck_weights_in").size();
float step_size = NAN;
size_t count = 0, header_count = 0;
float min_length = std::numeric_limits<float>::infinity();
float max_length = 0.0f;
double sum_lengths = 0.0, sum_weights = 0.0;
std::vector<double> histogram;
std::vector<LW> all_lengths;
all_lengths.reserve (header_count);
{
Tractography::Properties properties;
Tractography::Reader<float> reader (argument[0], properties);
if (properties.find ("count") != properties.end())
header_count = to<size_t> (properties["count"]);
if (properties.find ("output_step_size") != properties.end())
step_size = to<float> (properties["output_step_size"]);
else
step_size = to<float> (properties["step_size"]);
if (!std::isfinite (step_size) || !step_size) {
WARN ("Streamline step size undefined in header");
if (get_options ("histogram").size())
WARN ("Histogram will be henerated using a 1mm interval");
}
std::unique_ptr<File::OFStream> dump;
Options opt = get_options ("dump");
if (opt.size())
dump.reset (new File::OFStream (std::string(opt[0][0]), std::ios_base::out | std::ios_base::trunc));
ProgressBar progress ("Reading track file... ", header_count);
Tractography::Streamline<> tck;
while (reader (tck)) {
++count;
const float length = std::isfinite (step_size) ? tck.calc_length (step_size) : tck.calc_length();
min_length = std::min (min_length, length);
max_length = std::max (max_length, length);
sum_lengths += tck.weight * length;
sum_weights += tck.weight;
all_lengths.push_back (LW (length, tck.weight));
const size_t index = std::isfinite (step_size) ? std::round (length / step_size) : std::round (length);
while (histogram.size() <= index)
histogram.push_back (0.0);
histogram[index] += tck.weight;
if (dump)
(*dump) << length << "\n";
++progress;
}
}
if (histogram.front())
WARN ("read " + str(histogram.front()) + " zero-length tracks");
if (count != header_count)
WARN ("expected " + str(header_count) + " tracks according to header; read " + str(count));
const float mean_length = sum_lengths / sum_weights;
float median_length = 0.0f;
if (weights_provided) {
// Perform a weighted median calculation
std::sort (all_lengths.begin(), all_lengths.end());
size_t median_index = 0;
double sum = sum_weights - all_lengths[0].get_weight();
while (sum > 0.5 * sum_weights) { sum -= all_lengths[++median_index].get_weight(); }
median_length = all_lengths[median_index].get_length();
} else {
median_length = Math::median (all_lengths).get_length();
}
double stdev = 0.0;
for (std::vector<LW>::const_iterator i = all_lengths.begin(); i != all_lengths.end(); ++i)
stdev += i->get_weight() * Math::pow2 (i->get_length() - mean_length);
stdev = std::sqrt (stdev / (((count - 1) / float(count)) * sum_weights));
const size_t width = 12;
std::cout << " " << std::setw(width) << std::right << "mean"
<< " " << std::setw(width) << std::right << "median"
<< " " << std::setw(width) << std::right << "std. dev."
<< " " << std::setw(width) << std::right << "min"
<< " " << std::setw(width) << std::right << "max"
<< " " << std::setw(width) << std::right << "count\n";
std::cout << " " << std::setw(width) << std::right << (mean_length)
<< " " << std::setw(width) << std::right << (median_length)
<< " " << std::setw(width) << std::right << (stdev)
<< " " << std::setw(width) << std::right << (min_length)
<< " " << std::setw(width) << std::right << (max_length)
<< " " << std::setw(width) << std::right << (count) << "\n";
Options opt = get_options ("histogram");
if (opt.size()) {
File::OFStream out (opt[0][0], std::ios_base::out | std::ios_base::trunc);
if (!std::isfinite (step_size))
step_size = 1.0f;
if (weights_provided) {
out << "Length,Sum_weights\n";
for (size_t i = 0; i != histogram.size(); ++i)
out << str(i * step_size) << "," << str(histogram[i]) << "\n";
} else {
out << "Length,Count\n";
for (size_t i = 0; i != histogram.size(); ++i)
out << str(i * step_size) << "," << str<size_t>(histogram[i]) << "\n";
}
out << "\n";
out.close();
}
}