static bool
archive_file (char file_name[], size_t file_name_size,
int archive_fd, bool *write_error)
{
int file_fd = open (file_name);
if (file_fd >= 0)
{
bool success;
if (inumber (file_fd) != inumber (archive_fd))
{
if (!isdir (file_fd))
success = archive_ordinary_file (file_name, file_fd,
archive_fd, write_error);
else
success = archive_directory (file_name, file_name_size, file_fd,
archive_fd, write_error);
}
else
{
/* Nothing to do: don't try to archive the archive file. */
success = true;
}
close (file_fd);
return success;
}
else
{
printf ("%s: open failed\n", file_name);
return false;
}
}
int main(int argc, char *argv[])
{
const char *dir, *out;
FILE *file;
if (argc < 3) {
printf("Usage: packer [dir] [out]\n");
exit(1);
}
dir = argv[1];
out = argv[2];
file = fopen(out, "wb");
if (!file) {
printf("Error opening '%s', aborting\n", out);
exit(1);
}
archive_directory(file, dir, "");
fclose(file);
return 0;
}
void Test2DSimulations() throw(Exception)
{
double conductivity_scale = 1;
double h = 0.01; // cm
double ode_time_step = 0.005; //ms
double pde_time_step = 0.01; //ms
unsigned num_stims = 1;
TetrahedralMesh<2,2> mesh;
unsigned num_elem_x = (unsigned)(0.5/h); // num elements to make 5mm
unsigned num_elem_y = (unsigned)(0.5/h); // num elements to make 5mm
//unsigned num_elem_z = (unsigned)(0.15/h);// Num elements to make 0.3cm
double pacing_cycle_length = 350;
double stim_mag = -500000;
double stim_dur = 3;
double area = 0.005;
mesh.ConstructRectangularMesh(num_elem_x, num_elem_y);
mesh.Scale(h,h); // Get mesh into units of cm.
std::string archive_dir_base("LongPostprocessing_archives/archive");
std::string archive_dir_current;
// Setup
HeartConfig::Instance()->SetSimulationDuration(pacing_cycle_length); //ms
HeartConfig::Instance()->SetOutputDirectory("LongPostprocessing");
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
// These lines make postprocessing fast or slow.
HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(ode_time_step, pde_time_step, 10); // Leads to 10MB VTK file
//HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(ode_time_step, pde_time_step, 0.01); // Leads to 1GB VTK file
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(1.4*conductivity_scale*1.171, 1.4*conductivity_scale*1.171));
HeartConfig::Instance()->SetSurfaceAreaToVolumeRatio(1400.0); // 1/cm
HeartConfig::Instance()->SetCapacitance(1.0); // uF/cm^2
HeartConfig::Instance()->SetVisualizeWithMeshalyzer();
#ifdef CHASTE_VTK
HeartConfig::Instance()->SetVisualizeWithVtk();
#endif
std::vector<std::pair<double,double> > apds_requested;
apds_requested.push_back(std::pair<double, double>(90,-30)); //repolarisation percentage and threshold
HeartConfig::Instance()->SetApdMaps(apds_requested);
// std::vector<double> excitation_threshold;
// excitation_threshold.push_back(-30.0);
// HeartConfig::Instance()->SetUpstrokeTimeMaps(excitation_threshold);
// HeartConfig::Instance()->SetMaxUpstrokeVelocityMaps(excitation_threshold);
for (unsigned stim_counter=0; stim_counter < num_stims; stim_counter++ )
{
// Load problem
MonodomainProblem<2> *p_monodomain_problem;
if (stim_counter==0)
{
PointStimulusCellFactory<2> cell_factory(stim_mag, stim_dur, pacing_cycle_length, area);
p_monodomain_problem = new MonodomainProblem<2>( &cell_factory );
p_monodomain_problem->SetMesh(&mesh);
p_monodomain_problem->Initialise();
}
else
{
p_monodomain_problem = CardiacSimulationArchiver<MonodomainProblem<2> >::Load(archive_dir_current);
}
HeartConfig::Instance()->SetSimulationDuration((double) (stim_counter+1)*pacing_cycle_length); //ms
// set new directories to work from
std::stringstream stringoutput;
stringoutput << stim_counter;
std::string stim_counter_string = stringoutput.str();
archive_dir_current = archive_dir_base + "_" + stim_counter_string;
OutputFileHandler archive_directory(archive_dir_current, true); // Clean a folder for new results
HeartConfig::Instance()->SetOutputFilenamePrefix("results_" + stim_counter_string);
// Solve problem (this does the postprocessing too when HeartConfig options are set).
p_monodomain_problem->Solve();
HeartEventHandler::Headings();
HeartEventHandler::Report();
// Save problem to archive
CardiacSimulationArchiver<MonodomainProblem<2> >::Save(*p_monodomain_problem, archive_dir_current, false);
std::cout << "Archived to " << archive_dir_current << "\n" << std::flush;
// Copy the postprocessing results into the archive folders so they aren't wiped.
std::vector<std::string> files;
files.push_back("Apd_90_minus_30_Map");
// files.push_back("MaxUpstrokeVelocityMap_-30");
// files.push_back("UpstrokeTimeMap_-30");
for (unsigned i=0; i<files.size(); i++)
{
FileFinder file_to_copy(HeartConfig::Instance()->GetOutputDirectory() + "/output/" + files[i] + ".dat", RelativeTo::ChasteTestOutput);
TS_ASSERT(file_to_copy.IsFile());
archive_directory.CopyFileTo(file_to_copy);
}
}// close for loop
}//close void Test2dSimulations
int archive_directory(FILE *file, const char *path, const char *relative)
{
DIR *dir;
struct dirent *ent;
struct stat st;
char fullpath[256] = "";
char relpath[256] = "";
FILE *ent_file;
int length;
int result = 0;
char *blob;
dir = opendir(path);
if (dir) {
while ((ent = readdir(dir))) {
if (ent->d_name[0] == '.')
continue;
strcpy(fullpath, path);
strcat(fullpath, "/");
strcat(fullpath, ent->d_name);
strcpy(relpath, "");
if (strlen(relative) > 0) {
strcpy(relpath, relative);
strcat(relpath, "/");
}
strcat(relpath, ent->d_name);
printf("%s", relpath);
stat(fullpath, &st);
if (st.st_mode & S_IFREG) {
/* Write this file to the archive */
ent_file = fopen(fullpath, "rb");
fseek(ent_file, 0, SEEK_END);
length = ftell(ent_file);
fseek(ent_file, 0, SEEK_SET);
printf(" (%d bytes)\n", length);
archive_size += length;
if (archive_size > MAX_FILESIZE) {
printf("Archive exceeds maximum size, aborting\n");
result = 1;
goto done;
}
blob = malloc(length);
fread(blob, 1, length, ent_file);
fwrite(relpath, 1, 256, file);
fwrite(&length, 4, 1, file);
fwrite(blob, 1, length, file);
free(blob);
fclose(ent_file);
} else if (st.st_mode & S_IFDIR) {
printf("\n");
/* Recurse into this directory */
if (archive_directory(file, fullpath, relpath) != 0) {
result = 1;
goto done;
}
}
}
done:
closedir(dir);
return result;
} else {
printf("FAILED!\n");
return 1;
}
}
