int main(int argc, char* argv[])
{
namespace js = anu_am::json;
char* scalarPath = argv[1];
char* fieldPath = argv[2];
if (argc < 3)
{
std::cerr << "Usage:" << argv[0] << " SCALARS FIELD [OUTPUT]"
<< std::endl;
return 1;
}
// Read the data for this process.
NCFileInfo const info = readFileInfo(fieldPath);
Variable const var = findVolumeVariable(info);
std::vector<size_t> dims = readDimensions(info);
CubicalComplex complex(dims.at(0), dims.at(1), dims.at(2));
Vertices vertices(dims.at(0), dims.at(1), dims.at(2));
assert(dims == readDimensions(scalarPath));
Scalars::DataPtr scalarData = readVolumeData<Value>(scalarPath);
Scalars scalars(complex, scalarData);
Field::DataPtr fieldData = readVolumeData<FieldItem>(fieldPath);
Field field = Field(dims.at(0), dims.at(1), dims.at(2), fieldData);
// Process the data.
std::map<Cell, Boundary> chains = chainComplex(complex, field);
std::vector<Cell> const sources =
criticalCellsSorted(complex, scalars, field);
size_t const n = sources.size();
SimpleComplex const simple = simpleChainComplex(
complex, scalars, chains, sources);
std::vector<Pairing<Cell> > const pairs = persistencePairing(simple);
// Generate metadata
std::string const parentID = guessDatasetID(fieldPath, info.attributes());
std::string const thisID = derivedID(parentID, "persistence", "PP");
std::string const outfile =
argc > 3 ? argv[3] : (stripTimestamp(thisID) + ".txt");
js::Array const predecessors = js::Array
(parentID)
(guessDatasetID(scalarPath, readFileInfo(scalarPath).attributes()));
js::Object const description = js::Object
("id" , thisID)
("process" , "Critical Cell Persistence Pairs")
("sourcefile" , __FILE__)
("revision" , js::Object("id", GIT_REVISION)("date", GIT_TIMESTAMP))
("parent" , parentID)
("predecessors", predecessors)
("parameters" , js::Object());
// Write data
std::stringstream tmp;
tmp << "# Persistence pairs for " << scalarPath
<< std::endl
<< "# format: <birth> <death> <dimension> <creator xyz> <destructor xyz>"
<< std::endl;
for (size_t i = 0; i < pairs.size(); ++i)
{
size_t const j = pairs.at(i).partner;
if (j > i)
{
Cell const v = sources.at(i);
Cell const w = j >= n ? sources.at(i) : sources.at(j);
tmp << std::fixed << std::setprecision(6);
tmp << std::setw(12) << cellValue(v, scalars, vertices) << " "
<< std::setw(12);
if (w == v)
tmp << "inf";
else
tmp << cellValue(w, scalars, vertices);
tmp << " "
<< complex.cellDimension(v) << " "
<< complex.cellPosition(v) << " ";
if (w == v)
tmp << " - - - ";
else
tmp << complex.cellPosition(w);
tmp << std::endl;
}
}
std::ofstream ofs(outfile.c_str());
ofs << tmp.str();
// Write metadata
ofs << "#" << std::endl
<< "# Metadata:" << std::endl;
Attributes const attr = inheritableAttributes(info.attributes());
for (size_t i = 0; i < attr.size(); ++i)
{
std::string const key = attr.keyAt(i);
ofs << "#" << std::endl
<< "#+ " << key << std::endl;
if (key == "dataset_id")
ofs << "#= " << thisID << std::endl;
else if (key == "zdim_total")
ofs << "#= " << dims.at(2) << std::endl;
else if (key == "number_of_files")
ofs << "#= 1" << std::endl;
else if (key == "zdim_range")
ofs << "#= 0, " << dims.at(2)-1 << std::endl;
else
printWithPrefix(ofs, attr(key).valuesAsString(), "#= ");
}
ofs << "#" << std::endl
<< "#+ " << "history_"+thisID << std::endl;
ofs << js::toString(description, 2, "#= ") << std::endl;
}
int main(int argc, char* argv[])
{
char* infile = argv[1];
if (argc < 2)
{
std::cerr << "Usage:" << argv[0] << " INPUT" << std::endl;
return 1;
}
FileBuffer data(infile);
NCFile<FileBuffer> file(data);
std::vector<Dimension> const dims = file.dimensions();
std::vector<Variable> const vars = file.variables();
Attributes const attrs = file.attributes();
size_t i;
std::cout << "netcdf " << stripname(infile) << " {" << std::endl;
std::cout << "dimensions:" << std::endl;
for (i = 0; i < dims.size(); ++i)
{
Dimension d = dims.at(i);
std::cout << "\t" << d.name << " = " << d.size
<< " ;" << std::endl;
}
std::cout << std::endl;
std::cout << "variables:" << std::endl;
for (i = 0; i < vars.size(); ++i)
{
Variable v = vars.at(i);
std::cout << "\t" << tname(v.type()) << " " << v.name()
<< "(" << toString(v.dimensionNames())
<< ") ;" << std::endl;
Attributes const attrs = v.attributes();
for (size_t j = 0; j < attrs.size(); ++j)
{
Attribute a = attrs.at(j);
std::cout << "\t\t" << v.name() << ":" << attrs.keyAt(j) << " = "
<< formatString(a.valuesAsString())
<< " ;" << std::endl;
}
}
std::cout << std::endl;
std::cout << "// global attributes:" << std::endl;
for (i = 0; i < attrs.size(); ++i)
{
Attribute a = attrs.at(i);
std::cout << "\t\t:" << attrs.keyAt(i) << " = "
<< formatString(a.valuesAsString())
<< " ;" << std::endl;
}
std::cout << std::endl;
std::cout << "data:" << std::endl;
for (i = 0; i < vars.size(); ++i)
{
Variable v = vars.at(i);
std::cout << std::endl << " " << v.name() << " =" << std::endl;
std::cout << " " << file.valueAsString(v, 0, 0, 0)
<< ", " << file.valueAsString(v, 1, 0, 0)
<< ", " << file.valueAsString(v, 2, 0, 0)
<< ", " << file.valueAsString(v, 3, 0, 0)
<< ", " << file.valueAsString(v, 4, 0, 0)
<< ", ... ;"
<< std::endl;
}
std::cout << "}" << std::endl;
}
