MMap::~MMap()
{
if (!first) return;
if (addr) {
DEBUG ("unmapping file \"" + Entry::name + "\"");
#ifdef MRTRIX_WINDOWS
if (!UnmapViewOfFile ( (LPVOID) addr))
#else
if (munmap (addr, msize))
#endif
WARN ("error unmapping file \"" + Entry::name + "\": " + strerror (errno));
close (fd);
}
else {
if (readwrite) {
INFO ("writing back contents of mapped file \"" + Entry::name + "\"...");
File::OFStream out (Entry::name, std::ios::in | std::ios::out | std::ios::binary);
out.seekp (start, out.beg);
out.write ((char*) first, msize);
if (!out.good())
throw Exception ("error writing back contents of file \"" + Entry::name + "\": " + strerror(errno));
}
delete [] first;
}
}
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;
}
std::shared_ptr<Handler::Base> MRtrix_sparse::create (Header& H) const
{
Header::const_iterator name_it = H.find (Image::Sparse::name_key);
if (name_it == H.end())
throw Exception ("Cannot create sparse image " + H.name() + "; no knowledge of underlying data class type");
Header::const_iterator size_it = H.find (Image::Sparse::size_key);
if (size_it == H.end())
throw Exception ("Cannot create sparse image " + H.name() + "; no knowledge of underlying data class size");
H.datatype() = DataType::UInt64;
H.datatype().set_byte_order_native();
File::OFStream out (H.name(), std::ios::out | std::ios::binary);
out << "mrtrix sparse image\n";
write_mrtrix_header (H, out);
bool single_file = Path::has_suffix (H.name(), ".msf");
int64_t image_offset = 0, sparse_offset = 0;
std::string image_path, sparse_path;
if (single_file) {
image_offset = out.tellp() + int64_t(54);
image_offset += ((4 - (image_offset % 4)) % 4);
sparse_offset = image_offset + Image::footprint(H);
out << "file: . " << image_offset << "\nsparse_file: . " << sparse_offset << "\nEND\n";
File::resize (H.name(), sparse_offset);
image_path = H.name();
sparse_path = H.name();
} else {
image_path = Path::basename (H.name().substr (0, H.name().size()-4) + ".dat");
sparse_path = Path::basename (H.name().substr (0, H.name().size()-4) + ".sdat");
out << "file: " << image_path << "\nsparse_file: " << sparse_path << "\nEND\n";
File::create (image_path, Image::footprint(H));
File::create (sparse_path);
}
Handler::Default base_handler (H);
base_handler.files.push_back (File::Entry (image_path, image_offset));
std::shared_ptr<Handler::Base> handler (new Handler::Sparse (base_handler, name_it->second, to<size_t>(size_it->second), File::Entry (sparse_path, sparse_offset)));
return handler;
}
void Default::unload (const Header& header)
{
if (mmaps.empty() && addresses.size()) {
assert (addresses[0].get());
if (writable) {
for (size_t n = 0; n < files.size(); n++) {
File::OFStream out (files[n].name, std::ios::out | std::ios::binary);
out.seekp (files[n].start, out.beg);
out.write ((char*) (addresses[0].get() + n*bytes_per_segment), bytes_per_segment);
if (!out.good())
throw Exception ("error writing back contents of file \"" + files[n].name + "\": " + strerror(errno));
}
}
}
else {
for (size_t n = 0; n < addresses.size(); ++n)
addresses[n].release();
mmaps.clear();
}
}
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();
}
}