Worker::Thresholds::Thresholds (Tractography::Properties& properties) :
max_length (std::numeric_limits<float>::infinity()),
min_length (0.0f),
max_weight (std::numeric_limits<float>::infinity()),
min_weight (0.0f),
step_size (get_step_size (properties))
{
if (properties.find ("max_dist") != properties.end()) {
try {
max_length = to<float>(properties["max_dist"]);
} catch (...) { }
}
if (properties.find ("min_dist") != properties.end()) {
try {
min_length = to<float>(properties["min_dist"]);
} catch (...) { }
}
if (std::isfinite (step_size)) {
// User may set these values to a precise value, which may then fail due to floating-point
// calculation of streamline length
// Therefore throw a bit of error margin in here
float error_margin = 0.1;
if (properties.find ("downsample_factor") != properties.end())
error_margin = 0.5 / to<float>(properties["downsample_factor"]);
max_length += error_margin * step_size;
min_length -= error_margin * step_size;
}
if (properties.find ("max_weight") != properties.end())
max_weight = to<float>(properties["max_weight"]);
if (properties.find ("min_weight") != properties.end())
min_weight = to<float>(properties["min_weight"]);
}
size_t determine_upsample_ratio (const Image::Info& info, const Tractography::Properties& properties, const float ratio)
{
if (info.ndim() < 3)
throw Exception ("Cannot perform streamline mapping on image with less than three dimensions");
Properties::const_iterator i = properties.find ("output_step_size");
if (i == properties.end()) {
i = properties.find ("step_size");
if (i == properties.end())
throw Exception ("Cannot perform streamline mapping: no step size information in track file header");
}
const float step_size = to<float> (i->second);
return determine_upsample_ratio (info, step_size, ratio);
}
void run () {
Tractography::Properties properties;
Tractography::Reader<float> file (argument[0], properties);
const size_t num_tracks = properties["count"].empty() ? 0 : to<size_t> (properties["count"]);
float step_size = 0.0;
if (properties.find ("output_step_size") != properties.end())
step_size = to<float> (properties["output_step_size"]);
else
step_size = to<float> (properties["step_size"]);
std::vector<float> voxel_size;
Options opt = get_options("vox");
if (opt.size())
voxel_size = opt[0][0];
if (voxel_size.size() == 1)
voxel_size.assign (3, voxel_size.front());
else if (!voxel_size.empty() && voxel_size.size() != 3)
throw Exception ("voxel size must either be a single isotropic value, or a list of 3 comma-separated voxel dimensions");
if (!voxel_size.empty())
INFO ("creating image with voxel dimensions [ " + str(voxel_size[0]) + " " + str(voxel_size[1]) + " " + str(voxel_size[2]) + " ]");
Image::Header header;
opt = get_options ("template");
if (opt.size()) {
Image::Header template_header (opt[0][0]);
header = template_header;
header.comments().clear();
if (!voxel_size.empty())
oversample_header (header, voxel_size);
}
else {
if (voxel_size.empty())
throw Exception ("please specify either a template image or the desired voxel size");
generate_header (header, argument[0], voxel_size);
}
header.set_ndim (3);
opt = get_options ("contrast");
contrast_t contrast = opt.size() ? contrast_t(int(opt[0][0])) : TDI;
opt = get_options ("stat_vox");
vox_stat_t stat_vox = opt.size() ? vox_stat_t(int(opt[0][0])) : V_SUM;
opt = get_options ("stat_tck");
tck_stat_t stat_tck = opt.size() ? tck_stat_t(int(opt[0][0])) : T_MEAN;
float gaussian_fwhm_tck = 0.0, gaussian_denominator_tck = 0.0;
opt = get_options ("fwhm_tck");
if (opt.size()) {
if (stat_tck != GAUSSIAN) {
INFO ("Overriding per-track statistic to Gaussian as a full-width half-maximum has been provided.");
stat_tck = GAUSSIAN;
}
gaussian_fwhm_tck = opt[0][0];
const float gaussian_theta_tck = gaussian_fwhm_tck / (2.0 * sqrt (2.0 * log (2.0)));
gaussian_denominator_tck = 2.0 * gaussian_theta_tck * gaussian_theta_tck;
} else if (stat_tck == GAUSSIAN) {
throw Exception ("If using Gaussian per-streamline statistic, need to provide a full-width half-maximum for the Gaussian kernel using the -fwhm option");
}
opt = get_options ("colour");
const bool colour = opt.size();
opt = get_options ("map_zero");
const bool map_zero = opt.size();
if (colour) {
header.set_ndim (4);
header.dim(3) = 3;
//header.set_description (3, "directionally-encoded colour");
Image::Stride::set (header, Image::Stride::contiguous_along_axis (3, header));
}
// Deal with erroneous statistics & provide appropriate messages
switch (contrast) {
case TDI:
if (stat_vox != V_SUM && stat_vox != V_MEAN) {
INFO ("Cannot use voxel statistic other than 'sum' or 'mean' for TDI generation - ignoring");
stat_vox = V_SUM;
}
if (stat_tck != T_MEAN)
INFO ("Cannot use track statistic other than default for TDI generation - ignoring");
stat_tck = T_MEAN;
break;
case PRECISE_TDI:
if (stat_vox != V_SUM) {
INFO ("Cannot use voxel statistic other than 'sum' for precise TDI generation - ignoring");
stat_vox = V_SUM;
}
if (stat_tck != T_MEAN)
INFO ("Cannot use track statistic other than default for precise TDI generation - ignoring");
stat_tck = T_MEAN;
break;
case ENDPOINT:
if (stat_vox != V_SUM && stat_vox != V_MEAN) {
INFO ("Cannot use voxel statistic other than 'sum' or 'mean' for endpoint map generation - ignoring");
stat_vox = V_SUM;
}
if (stat_tck != T_MEAN)
INFO ("Cannot use track statistic other than default for endpoint map generation - ignoring");
stat_tck = T_MEAN;
break;
case LENGTH:
if (stat_tck != T_MEAN)
INFO ("Cannot use track statistic other than default for length-weighted TDI generation - ignoring");
stat_tck = T_MEAN;
break;
case INVLENGTH:
if (stat_tck != T_MEAN)
INFO ("Cannot use track statistic other than default for inverse-length-weighted TDI generation - ignoring");
stat_tck = T_MEAN;
break;
case SCALAR_MAP:
case SCALAR_MAP_COUNT:
break;
case FOD_AMP:
if (stat_tck == ENDS_MIN || stat_tck == ENDS_MEAN || stat_tck == ENDS_MAX || stat_tck == ENDS_PROD)
throw Exception ("Can't use endpoint-based track-wise statistics with FOD_AMP contrast");
break;
case CURVATURE:
break;
default:
throw Exception ("Undefined contrast mechanism");
}
opt = get_options ("datatype");
bool manual_datatype = false;
if (colour) {
header.datatype() = DataType::Float32;
manual_datatype = true;
}
if (opt.size()) {
if (colour) {
INFO ("Can't manually set datatype for directionally-encoded colour processing - overriding to Float32");
} else {
header.datatype() = DataType::parse (opt[0][0]);
manual_datatype = true;
}
}
if (get_options ("tck_weights_in").size() || (manual_datatype && header.datatype().is_integer())) {
if ((manual_datatype && header.datatype().is_integer()))
INFO ("Can't use an integer type if streamline weights are provided; overriding to Float32");
header.datatype() = DataType::Float32;
manual_datatype = true;
}
header.datatype().set_byte_order_native();
for (Tractography::Properties::iterator i = properties.begin(); i != properties.end(); ++i)
header.comments().push_back (i->first + ": " + i->second);
for (std::multimap<std::string,std::string>::const_iterator i = properties.roi.begin(); i != properties.roi.end(); ++i)
header.comments().push_back ("ROI: " + i->first + " " + i->second);
for (std::vector<std::string>::iterator i = properties.comments.begin(); i != properties.comments.end(); ++i)
header.comments().push_back ("comment: " + *i);
size_t upsample_ratio = 1;
opt = get_options ("upsample");
if (opt.size()) {
upsample_ratio = opt[0][0];
INFO ("track upsampling ratio manually set to " + str(upsample_ratio));
}
else if (step_size && std::isfinite (step_size)) {
// If accurately calculating the length through each voxel traversed, need a higher upsampling ratio
// (1/10th of the voxel size was found to give a good quantification of chordal length)
// For all other applications, making the upsampled step size about 1/3rd of a voxel seems sufficient
const float voxel_step_ratio = (contrast == PRECISE_TDI) ? 0.1 : 0.333;
upsample_ratio = Math::ceil<size_t> (step_size / (minvalue (header.vox(0), header.vox(1), header.vox(2)) * voxel_step_ratio));
INFO ("track upsampling ratio automatically set to " + str(upsample_ratio));
}
else {
if (contrast != PRECISE_TDI)
WARN ("track upsampling off; track step size information in header is absent or malformed");
}
const bool dump = get_options ("dump").size();
if (dump && Path::has_suffix (argument[1], "mih"))
throw Exception ("Option -dump only works when outputting to .mih image format");
std::string msg = str("Generating ") + (colour ? "colour " : "") + "image with ";
switch (contrast) {
case TDI: msg += "density"; break;
case PRECISE_TDI: msg += "density (precise)"; break;
case ENDPOINT: msg += "endpoint density"; break;
case LENGTH: msg += "length"; break;
case INVLENGTH: msg += "inverse length"; break;
case SCALAR_MAP: msg += "scalar map"; break;
case SCALAR_MAP_COUNT: msg += "scalar-map-thresholded tdi"; break;
case FOD_AMP: msg += "FOD amplitude"; break;
case CURVATURE: msg += "curvature"; break;
default: msg += "ERROR"; break;
}
msg += " contrast";
if (contrast == SCALAR_MAP || contrast == SCALAR_MAP_COUNT || contrast == FOD_AMP || contrast == CURVATURE)
msg += ", ";
else
msg += " and ";
switch (stat_vox) {
case V_SUM: msg += "summed"; break;
case V_MIN: msg += "minimum"; break;
case V_MEAN: msg += "mean"; break;
case V_MAX: msg += "maximum"; break;
default: msg += "ERROR"; break;
}
msg += " per-voxel statistic";
if (contrast == SCALAR_MAP || contrast == SCALAR_MAP_COUNT || contrast == FOD_AMP || contrast == CURVATURE) {
msg += " and ";
switch (stat_tck) {
case T_SUM: msg += "summed"; break;
case T_MIN: msg += "minimum"; break;
case T_MEAN: msg += "mean"; break;
case T_MAX: msg += "maximum"; break;
case T_MEDIAN: msg += "median"; break;
case T_MEAN_NONZERO: msg += "mean (nonzero)"; break;
case GAUSSIAN: msg += "gaussian (FWHM " + str (gaussian_fwhm_tck) + "mm)"; break;
case ENDS_MIN: msg += "endpoints (minimum)"; break;
case ENDS_MEAN: msg += "endpoints (mean)"; break;
case ENDS_MAX: msg += "endpoints (maximum)"; break;
case ENDS_PROD: msg += "endpoints (product)"; break;
default: msg += "ERROR"; break;
}
msg += " per-track statistic";
}
INFO (msg);
switch (contrast) {
case TDI: header.comments().push_back ("track density image"); break;
case PRECISE_TDI: header.comments().push_back ("track density image (precise calculation)"); break;
case ENDPOINT: header.comments().push_back ("track endpoint density image"); break;
case LENGTH: header.comments().push_back ("track density image (weighted by track length)"); break;
case INVLENGTH: header.comments().push_back ("track density image (weighted by inverse track length)"); break;
case SCALAR_MAP: header.comments().push_back ("track-weighted image (using scalar image)"); break;
case SCALAR_MAP_COUNT: header.comments().push_back ("track density image (using scalar image thresholding)"); break;
case FOD_AMP: header.comments().push_back ("track-weighted image (using FOD amplitude)"); break;
case CURVATURE: header.comments().push_back ("track-weighted image (using track curvature)"); break;
}
TrackLoader loader (file, num_tracks);
// Use a branching IF instead of a switch statement to permit scope
if (contrast == TDI || contrast == ENDPOINT || contrast == LENGTH || contrast == INVLENGTH || (contrast == CURVATURE && stat_tck != GAUSSIAN)) {
if (!manual_datatype) {
header.datatype() = (contrast == TDI || contrast == ENDPOINT) ? DataType::UInt32 : DataType::Float32;
header.datatype().set_byte_order_native();
}
if (colour) {
TrackMapperTWI <SetVoxelDEC> mapper (header, upsample_ratio, map_zero, step_size, contrast, stat_tck);
MapWriterColour<SetVoxelDEC> writer (header, argument[1], dump, stat_vox);
Thread::run_queue (loader, Tractography::Streamline<float>(), Thread::multi (mapper), SetVoxelDEC(), writer);
} else {
TrackMapperTWI <SetVoxel> mapper (header, upsample_ratio, map_zero, step_size, contrast, stat_tck);
Ptr< MapWriterBase<SetVoxel> > writer (make_writer<SetVoxel> (header, argument[1], dump, stat_vox));
Thread::run_queue (loader, Tractography::Streamline<float>(), Thread::multi (mapper), SetVoxel(), *writer);
}
} else if (contrast == PRECISE_TDI) {
if (!manual_datatype) {
header.datatype() = DataType::Float32;
header.datatype().set_byte_order_native();
}
if (colour) {
TrackMapperTWI <SetVoxelDir> mapper (header, upsample_ratio, map_zero, step_size, contrast, stat_tck);
MapWriterColour<SetVoxelDir> writer (header, argument[1], dump, stat_vox);
Thread::run_queue (loader, Tractography::Streamline<float>(), Thread::multi (mapper), SetVoxelDir(), writer);
} else {
TrackMapperTWI < SetVoxelDir> mapper (header, upsample_ratio, map_zero, step_size, contrast, stat_tck);
MapWriter <float, SetVoxelDir> writer (header, argument[1], dump, stat_vox);
Thread::run_queue (loader, Tractography::Streamline<float>(), Thread::multi (mapper), SetVoxelDir(), writer);
}
} else if (contrast == CURVATURE && stat_tck == GAUSSIAN) {
if (!manual_datatype) {
header.datatype() = DataType::Float32;
header.datatype().set_byte_order_native();
}
if (colour) {
TrackMapperTWI <SetVoxelDECFactor> mapper (header, upsample_ratio, map_zero, step_size, contrast, stat_tck, gaussian_denominator_tck);
MapWriterColour<SetVoxelDECFactor> writer (header, argument[1], dump, stat_vox);
Thread::run_queue (loader, Tractography::Streamline<float>(), Thread::multi (mapper), SetVoxelDECFactor(), writer);
} else {
TrackMapperTWI <SetVoxelFactor> mapper (header, upsample_ratio, map_zero, step_size, contrast, stat_tck, gaussian_denominator_tck);
Ptr< MapWriterBase<SetVoxelFactor> > writer (make_writer<SetVoxelFactor> (header, argument[1], dump, stat_vox));
Thread::run_queue (loader, Tractography::Streamline<float>(), Thread::multi (mapper), SetVoxelFactor(), *writer);
}
} else if (contrast == SCALAR_MAP || contrast == SCALAR_MAP_COUNT || contrast == FOD_AMP) {
opt = get_options ("image");
if (!opt.size()) {
if (contrast == SCALAR_MAP || contrast == SCALAR_MAP_COUNT)
throw Exception ("If using 'scalar_map' or 'scalar_map_count' contrast, must provide the relevant scalar image using -image option");
else
throw Exception ("If using 'fod_amp' contrast, must provide the relevant spherical harmonic image using -image option");
}
Image::BufferPreload<float> input_image (opt[0][0]);
if ((contrast == SCALAR_MAP || contrast == SCALAR_MAP_COUNT)) {
if (!(input_image.ndim() == 3 || (input_image.ndim() == 4 && input_image.dim(3) == 1)))
throw Exception ("Use of 'scalar_map' contrast option requires a 3-dimensional image; your image is " + str(input_image.ndim()) + "D");
}
if (contrast == FOD_AMP && input_image.ndim() != 4)
throw Exception ("Use of 'fod_amp' contrast option requires a 4-dimensional image; your image is " + str(input_image.ndim()) + "D");
if (!manual_datatype && (input_image.datatype() != DataType::Bit))
header.datatype() = input_image.datatype();
if (colour) {
if (stat_tck == GAUSSIAN) {
TrackMapperTWIImage <SetVoxelDECFactor> mapper (header, upsample_ratio, map_zero, step_size, contrast, stat_tck, gaussian_denominator_tck, input_image);
MapWriterColour <SetVoxelDECFactor> writer (header, argument[1], dump, stat_vox);
Thread::run_queue (loader, Tractography::Streamline<float>(), Thread::multi (mapper), SetVoxelDECFactor(), writer);
} else {
TrackMapperTWIImage <SetVoxelDEC> mapper (header, upsample_ratio, map_zero, step_size, contrast, stat_tck, 0.0, input_image);
MapWriterColour <SetVoxelDEC> writer (header, argument[1], dump, stat_vox);
Thread::run_queue (loader, Tractography::Streamline<float>(), Thread::multi (mapper), SetVoxelDEC(), writer);
}
} else {
if (stat_tck == GAUSSIAN) {
TrackMapperTWIImage <SetVoxelFactor> mapper (header, upsample_ratio, map_zero, step_size, contrast, stat_tck, gaussian_denominator_tck, input_image);
Ptr< MapWriterBase <SetVoxelFactor> > writer (make_writer<SetVoxelFactor> (header, argument[1], dump, stat_vox));
Thread::run_queue (loader, Tractography::Streamline<float>(), Thread::multi (mapper), SetVoxelFactor(), *writer);
} else {
TrackMapperTWIImage <SetVoxel> mapper (header, upsample_ratio, map_zero, step_size, contrast, stat_tck, 0.0, input_image);
Ptr< MapWriterBase <SetVoxel> > writer (make_writer<SetVoxel> (header, argument[1], dump, stat_vox));
Thread::run_queue (loader, Tractography::Streamline<float>(), Thread::multi (mapper), SetVoxel(), *writer);
}
}
} else {
throw Exception ("Undefined contrast mechanism for output image");
}
}
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;
auto 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);
Streamline<> tck;
while (reader (tck)) {
++count;
const float length = std::isfinite (step_size) ? tck.calc_length (step_size) : tck.calc_length();
if (std::isfinite (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";
auto 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";
}
}
void run ()
{
const std::string path = argument[0];
Tractography::Properties properties;
Tractography::Reader<float> reader (path, properties);
size_t init_count = 0;
if (properties.find ("count") == properties.end()) {
INFO ("\"count\" field not set in file " + path);
} else {
init_count = to<size_t>(properties["count"]);
INFO ("Value of \"count\" in file " + path + " is " + str(init_count));
}
// Read the actual number of streamlines in the file
Tractography::Streamline<float> tck;
size_t count = 0;
{
ProgressBar progress ("evaluating actual streamline data count...");
while (reader (tck)) {
++count;
++progress;
}
}
reader.close();
INFO ("Actual number of streamlines read is " + str(count));
// Find the appropriate file offset in the header
KeyValue kv (argument[0], "mrtrix tracks");
std::string data_file;
int64_t count_offset = 0;
int64_t current_offset = 0;
while (kv.next()) {
std::string key = lowercase (kv.key());
if (key == "count")
count_offset = current_offset;
current_offset = kv.tellg();
}
kv.close();
if (!count_offset)
throw Exception ("could not find location of \"count\" field in file \"" + path + "\"");
DEBUG ("File offset for \"count\" field is " + str(count_offset));
// Overwrite this data
// Used C-style file access here as ofstream would either wipe the file contents, or
// append the data instead of inserting it
FILE* fp;
fp = fopen (path.c_str(), "r+");
if (!fp)
throw Exception ("could not open tracks file \"" + path + "\" for repair");
if (fseek (fp, count_offset, SEEK_SET)) {
fclose (fp);
throw Exception ("unable to seek to the appropriate position in the file");
}
const std::string string = "count: " + str(count) + "\ntotal_count: " + str(count) + "\nEND\n";
const int rvalue = fputs (string.c_str(), fp);
fclose (fp);
if (rvalue == EOF) {
WARN ("\"count\" field may not have been properly updated");
} else {
INFO ("\"count\" field updated successfully");
}
}
void run ()
{
const size_t num_inputs = argument.size() - 1;
const std::string output_path = argument[num_inputs];
// Make sure configuration is sensible
if (get_options("tck_weights_in").size() && num_inputs > 1)
throw Exception ("Cannot use per-streamline weighting with multiple input files");
// Get the consensus streamline properties from among the multiple input files
Tractography::Properties properties;
size_t count = 0;
vector<std::string> input_file_list;
for (size_t file_index = 0; file_index != num_inputs; ++file_index) {
input_file_list.push_back (argument[file_index]);
Properties p;
Reader<float> reader (argument[file_index], p);
for (vector<std::string>::const_iterator i = p.comments.begin(); i != p.comments.end(); ++i) {
bool present = false;
for (vector<std::string>::const_iterator j = properties.comments.begin(); !present && j != properties.comments.end(); ++j)
present = (*i == *j);
if (!present)
properties.comments.push_back (*i);
}
// ROI paths are ignored - otherwise tckedit will try to find the ROIs used
// during streamlines generation!
size_t this_count = 0, this_total_count = 0;
for (Properties::const_iterator i = p.begin(); i != p.end(); ++i) {
if (i->first == "count") {
this_count = to<float>(i->second);
} else if (i->first == "total_count") {
this_total_count += to<float>(i->second);
} else {
Properties::iterator existing = properties.find (i->first);
if (existing == properties.end())
properties.insert (*i);
else if (i->second != existing->second)
existing->second = "variable";
}
}
count += this_count;
}
DEBUG ("estimated number of input tracks: " + str(count));
load_rois (properties);
// Some properties from tracking may be overwritten by this editing process
// Due to the potential use of masking, we have no choice but to clear the
// properties class of any fields that would otherwise propagate through
// and be applied as part of this editing
erase_if_present (properties, "min_dist");
erase_if_present (properties, "max_dist");
erase_if_present (properties, "min_weight");
erase_if_present (properties, "max_weight");
Editing::load_properties (properties);
// Parameters that the worker threads need to be aware of, but do not appear in Properties
const bool inverse = get_options ("inverse").size();
const bool ends_only = get_options ("ends_only").size();
// Parameters that the output thread needs to be aware of
const size_t number = get_option_value ("number", size_t(0));
const size_t skip = get_option_value ("skip", size_t(0));
Loader loader (input_file_list);
Worker worker (properties, inverse, ends_only);
// This needs to be run AFTER creation of the Worker class
// (worker needs to be able to set max & min number of points based on step size in input file,
// receiver needs "output_step_size" field to have been updated before file creation)
Receiver receiver (output_path, properties, number, skip);
Thread::run_queue (
loader,
Thread::batch (Streamline<>()),
Thread::multi (worker),
Thread::batch (Streamline<>()),
receiver);
}
void erase_if_present (Tractography::Properties& p, const std::string s)
{
auto i = p.find (s);
if (i != p.end())
p.erase (i);
}
void load_properties (Tractography::Properties& properties)
{
// ROIOption
Options opt = get_options ("include");
for (size_t i = 0; i < opt.size(); ++i)
properties.include.add (ROI (opt[i][0]));
opt = get_options ("exclude");
for (size_t i = 0; i < opt.size(); ++i)
properties.exclude.add (ROI (opt[i][0]));
opt = get_options ("mask");
for (size_t i = 0; i < opt.size(); ++i)
properties.mask.add (ROI (opt[i][0]));
// LengthOption
opt = get_options ("maxlength");
if (opt.size()) {
if (properties.find ("max_dist") == properties.end()) {
properties["max_dist"] = str(opt[0][0]);
} else {
try {
const float maxlength = std::min (float(opt[0][0]), to<float>(properties["max_dist"]));
properties["max_dist"] = str(maxlength);
} catch (...) {
properties["max_dist"] = str(opt[0][0]);
}
}
}
opt = get_options ("minlength");
if (opt.size()) {
if (properties.find ("min_dist") == properties.end()) {
properties["min_dist"] = str(opt[0][0]);
} else {
try {
const float minlength = std::max (float(opt[0][0]), to<float>(properties["min_dist"]));
properties["min_dist"] = str(minlength);
} catch (...) {
properties["min_dist"] = str(opt[0][0]);
}
}
}
// ResampleOption
// The relevant entry in Properties is updated at a later stage
// TruncateOption
// These have no influence on Properties
// WeightsOption
// Only the thresholds have an influence on Properties
opt = get_options ("maxweight");
if (opt.size())
properties["max_weight"] = std::string(opt[0][0]);
opt = get_options ("minweight");
if (opt.size())
properties["min_weight"] = std::string(opt[0][0]);
}
value_type AFDConnectivity::get (const std::string& path)
{
Tractography::Properties properties;
Tractography::Reader<value_type> reader (path, properties);
const size_t track_count = (properties.find ("count") == properties.end() ? 0 : to<size_t>(properties["count"]));
DWI::Tractography::Mapping::TrackLoader loader (reader, track_count, "summing apparent fibre density within track");
// If WBFT is provided, this is the sum of (volume/length) across streamlines
// Otherwise, it's a sum of lengths of all streamlines (for later scaling by mean streamline length)
double sum_contributions = 0.0;
size_t count = 0;
Tractography::Streamline<value_type> tck;
while (loader (tck)) {
++count;
SetDixel dixels;
mapper (tck, dixels);
double this_length = 0.0, this_volume = 0.0;
for (SetDixel::const_iterator i = dixels.begin(); i != dixels.end(); ++i) {
this_length += i->get_length();
// If wbft has not been provided (i.e. FODs have not been pre-segmented), need to
// check to see if any data have been provided for this voxel; and if not yet,
// run the segmenter
if (!have_wbft) {
VoxelAccessor v (accessor());
assign_pos_of (*i, 0, 3).to (v);
if (!v.value()) {
assign_pos_of (*i, 0, 3).to (v_fod);
DWI::FMLS::SH_coefs fod_data;
DWI::FMLS::FOD_lobes fod_lobes;
fod_data.vox[0] = v_fod.index (0); fod_data.vox[1] = v_fod.index (1); fod_data.vox[2] = v_fod.index (2);
fod_data.resize (v_fod.size (3));
for (auto i = Loop(3) (v_fod); i; ++i)
fod_data[v_fod.index (3)] = v_fod.value();
(*fmls) (fod_data, fod_lobes);
(*this) (fod_lobes);
}
}
const size_t fixel_index = dixel2fixel (*i);
Fixel& fixel = fixels[fixel_index];
fixel.add_to_selection (i->get_length());
if (have_wbft)
this_volume += fixel.get_selected_volume (i->get_length());
}
if (have_wbft)
sum_contributions += (this_volume / this_length);
else
sum_contributions += this_length;
}
if (!have_wbft) {
// Streamlines define a fixel mask; go through and get all the fibre volumes
double sum_volumes = 0.0;
if (all_fixels) {
// All fixels contribute to the result
for (std::vector<Fixel>::const_iterator i = fixels.begin(); i != fixels.end(); ++i) {
if (i->is_selected())
sum_volumes += i->get_FOD();
}
} else {
// Only allow one fixel per voxel to contribute to the result
VoxelAccessor v (accessor());
for (auto l = Loop(v) (v); l; ++l) {
if (v.value()) {
value_type voxel_afd = 0.0, max_td = 0.0;
for (Fixel_map<Fixel>::Iterator i = begin (v); i; ++i) {
if (i().get_selected_length() > max_td) {
max_td = i().get_selected_length();
voxel_afd = i().get_FOD();
}
}
sum_volumes += voxel_afd;
}
}
}
// sum_contributions currently stores sum of streamline lengths;
// turn into a mean length, then combine with volume to get a connectivity value
const double mean_length = sum_contributions / double(count);
sum_contributions = sum_volumes / mean_length;
}
return sum_contributions;
}
Worker::Thresholds::Thresholds (Tractography::Properties& properties) :
max_num_points (std::numeric_limits<size_t>::max()),
min_num_points (0),
max_weight (std::numeric_limits<float>::infinity()),
min_weight (0.0)
{
std::string step_size_string;
if (properties.find ("output_step_size") == properties.end())
step_size_string = ((properties.find ("step_size") == properties.end()) ? "0.0" : properties["step_size"]);
else
step_size_string = properties["output_step_size"];
float maxlength = 0.0, minlength = 0.0;
if (properties.find ("max_dist") != properties.end()) {
try {
maxlength = to<float>(properties["max_dist"]);
} catch (...) { }
}
if (properties.find ("min_dist") != properties.end()) {
try {
minlength = to<float>(properties["min_dist"]);
} catch (...) { }
}
if (step_size_string == "variable" && (maxlength || minlength))
throw Exception ("Cannot apply length threshold; step size is inconsistent between input track files");
const float step_size = to<float>(step_size_string);
if ((!step_size || !std::isfinite (step_size)) && (maxlength || minlength))
throw Exception ("Cannot apply length threshold; step size information is incomplete");
if (maxlength)
max_num_points = Math::round (maxlength / step_size) + 1;
if (minlength)
min_num_points = std::max (2, round (minlength/step_size) + 1);
if (properties.find ("max_weight") != properties.end())
max_weight = to<float>(properties["max_weight"]);
if (properties.find ("min_weight") != properties.end())
min_weight = to<float>(properties["min_weight"]);
}