void Config::init ()
{
if (Path::is_file (MRTRIX_SYS_CONFIG_FILE)) {
INFO ("reading config file \"" MRTRIX_SYS_CONFIG_FILE "\"...");
try {
KeyValue kv (MRTRIX_SYS_CONFIG_FILE);
while (kv.next()) {
config[kv.key()] = kv.value();
}
}
catch (...) { }
}
std::string path = Path::join (Path::home(), MRTRIX_USER_CONFIG_FILE);
if (Path::is_file (path)) {
INFO ("reading config file \"" + path + "\"...");
try {
KeyValue kv (path);
while (kv.next()) {
config[kv.key()] = kv.value();
}
}
catch (...) { }
}
}
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");
}
}