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Updates for the most recent Binsparse specification #3

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Merged
merged 5 commits into from
Mar 4, 2025
Merged

Updates for the most recent Binsparse specification #3

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02b85c2
Update `nnz` -> `number_of_stored_values`
BenBrock Mar 4, 2025
d67cfa6
Updates to conform with current version of Binsparse
BenBrock Mar 4, 2025
730d554
Update for Mac OS.
BenBrock Mar 4, 2025
44b02fb
Update for Mac OS.
BenBrock Mar 4, 2025
fbbe4d0
Update for Mac OS.
BenBrock Mar 4, 2025
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7 changes: 3 additions & 4 deletions examples/convert_matrixmarket.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,8 @@
#include <iostream>

int main(int argc, char** argv) {

if (argc < 2) {
std::cout << "usage: ./inspect_binsparse [matrix.bsp.h5]\n";
std::cout << "usage: ./convert_binsparse [matrix.bsp.h5]\n";
return 1;
}

Expand All @@ -18,8 +17,8 @@ int main(int argc, char** argv) {

std::cout << "Inspecting Binsparse v" << metadata["version"] << " file...\n";
std::cout << metadata["format"] << " format matrix of dimension "
<< metadata["shape"] << " with " << metadata["nnz"]
<< " nonzeros\n";
<< metadata["shape"] << " with "
<< metadata["number_of_stored_values"] << " nonzeros\n";

if (metadata["format"] == "COO") {
auto i0 = metadata["data_types"]["indices_0"];
Expand Down
4 changes: 2 additions & 2 deletions examples/inspect_binsparse.cpp
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Expand Up @@ -21,8 +21,8 @@ int main(int argc, char** argv) {

std::cout << "Inspecting Binsparse v" << metadata["version"] << " file...\n";
std::cout << metadata["format"] << " format matrix of dimension "
<< metadata["shape"] << " with " << metadata["nnz"]
<< " nonzeros\n";
<< metadata["shape"] << " with "
<< metadata["number_of_stored_values"] << " nonzeros\n";

if (metadata["format"] == "COO") {
auto i0 = metadata["data_types"]["indices_0"];
Expand Down
87 changes: 68 additions & 19 deletions include/binsparse/binsparse.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@

namespace binsparse {

inline constexpr double version = 0.1;
inline const std::string version = "0.1";

template <typename T>
void write_dense_vector(H5::Group& f, std::span<T> v,
Expand All @@ -25,7 +25,7 @@ void write_dense_vector(H5::Group& f, std::span<T> v,
j["binsparse"]["version"] = version;
j["binsparse"]["format"] = "DVEC";
j["binsparse"]["shape"] = {v.size()};
j["binsparse"]["nnz"] = v.size();
j["binsparse"]["number_of_stored_values"] = v.size();
j["binsparse"]["data_types"]["values"] = type_info<T>::label();

for (auto&& v : user_keys.items()) {
Expand All @@ -51,7 +51,7 @@ auto read_dense_vector(std::string fname, Allocator&& alloc = Allocator{}) {
assert(format == "DVEC");

auto nvalues = binsparse_metadata["shape"][0];
auto nnz = binsparse_metadata["nnz"];
auto nnz = binsparse_metadata["number_of_stored_values"];

assert(nvalues == nnz);

Expand All @@ -76,8 +76,14 @@ void write_dense_matrix(H5::Group& f, dense_matrix<T, I, Order> m,
j["binsparse"]["version"] = version;
j["binsparse"]["format"] = __detail::get_matrix_format_string(m);
j["binsparse"]["shape"] = {m.m, m.n};
j["binsparse"]["nnz"] = m.m * m.n;
j["binsparse"]["data_types"]["values"] = type_info<T>::label();
j["binsparse"]["number_of_stored_values"] = m.m * m.n;

if (!m.is_iso) {
j["binsparse"]["data_types"]["values"] =
std::string("iso[") + type_info<T>::label() + "]";
} else {
j["binsparse"]["data_types"]["values"] = type_info<T>::label();
}

if (m.structure != general) {
j["binsparse"]["structure"] =
Expand Down Expand Up @@ -118,7 +124,13 @@ auto read_dense_matrix(std::string fname, Allocator&& alloc = Allocator{}) {

auto nrows = binsparse_metadata["shape"][0];
auto ncols = binsparse_metadata["shape"][1];
auto nnz = binsparse_metadata["nnz"];
auto nnz = binsparse_metadata["number_of_stored_values"];

bool is_iso = false;
if (std::string(binsparse_metadata["data_types"]["values"])
.starts_with("iso")) {
is_iso = true;
}

auto values = hdf5_tools::read_dataset<T>(f, "values", alloc);

Expand All @@ -128,7 +140,8 @@ auto read_dense_matrix(std::string fname, Allocator&& alloc = Allocator{}) {
structure = __detail::parse_structure(binsparse_metadata["structure"]);
}

return dense_matrix<T, I, Order>{values.data(), nrows, ncols, structure};
return dense_matrix<T, I, Order>{values.data(), nrows, ncols, structure,
is_iso};
}

// CSR Format
Expand All @@ -149,10 +162,16 @@ void write_csr_matrix(H5::Group& f, csr_matrix<T, I> m,
j["binsparse"]["version"] = version;
j["binsparse"]["format"] = "CSR";
j["binsparse"]["shape"] = {m.m, m.n};
j["binsparse"]["nnz"] = m.nnz;
j["binsparse"]["number_of_stored_values"] = m.nnz;
j["binsparse"]["data_types"]["pointers_to_1"] = type_info<I>::label();
j["binsparse"]["data_types"]["indices_1"] = type_info<I>::label();
j["binsparse"]["data_types"]["values"] = type_info<T>::label();

if (!m.is_iso) {
j["binsparse"]["data_types"]["values"] =
std::string("iso[") + type_info<T>::label() + "]";
} else {
j["binsparse"]["data_types"]["values"] = type_info<T>::label();
}

if (m.structure != general) {
j["binsparse"]["structure"] =
Expand Down Expand Up @@ -189,7 +208,13 @@ csr_matrix<T, I> read_csr_matrix(std::string fname, Allocator&& alloc) {

auto nrows = binsparse_metadata["shape"][0];
auto ncols = binsparse_metadata["shape"][1];
auto nnz = binsparse_metadata["nnz"];
auto nnz = binsparse_metadata["number_of_stored_values"];

bool is_iso = false;
if (std::string(binsparse_metadata["data_types"]["values"])
.starts_with("iso")) {
is_iso = true;
}

typename std::allocator_traits<
std::remove_cvref_t<Allocator>>::template rebind_alloc<I>
Expand All @@ -206,7 +231,7 @@ csr_matrix<T, I> read_csr_matrix(std::string fname, Allocator&& alloc) {
}

return csr_matrix<T, I>{values.data(), colind.data(), row_ptr.data(), nrows,
ncols, nnz, structure};
ncols, nnz, structure, is_iso};
}

template <typename T, typename I>
Expand All @@ -232,10 +257,16 @@ void write_csc_matrix(H5::Group& f, csc_matrix<T, I> m,
j["binsparse"]["version"] = version;
j["binsparse"]["format"] = "CSR";
j["binsparse"]["shape"] = {m.m, m.n};
j["binsparse"]["nnz"] = m.nnz;
j["binsparse"]["number_of_stored_values"] = m.nnz;
j["binsparse"]["data_types"]["pointers_to_1"] = type_info<I>::label();
j["binsparse"]["data_types"]["indices_1"] = type_info<I>::label();
j["binsparse"]["data_types"]["values"] = type_info<T>::label();

if (!m.is_iso) {
j["binsparse"]["data_types"]["values"] =
std::string("iso[") + type_info<T>::label() + "]";
} else {
j["binsparse"]["data_types"]["values"] = type_info<T>::label();
}

if (m.structure != general) {
j["binsparse"]["structure"] =
Expand Down Expand Up @@ -272,7 +303,13 @@ csc_matrix<T, I> read_csc_matrix(std::string fname, Allocator&& alloc) {

auto nrows = binsparse_metadata["shape"][0];
auto ncols = binsparse_metadata["shape"][1];
auto nnz = binsparse_metadata["nnz"];
auto nnz = binsparse_metadata["number_of_stored_values"];

bool is_iso = false;
if (std::string(binsparse_metadata["data_types"]["values"])
.starts_with("iso")) {
is_iso = true;
}

typename std::allocator_traits<
std::remove_cvref_t<Allocator>>::template rebind_alloc<I>
Expand All @@ -289,7 +326,7 @@ csc_matrix<T, I> read_csc_matrix(std::string fname, Allocator&& alloc) {
}

return csc_matrix<T, I>{values.data(), rowind.data(), col_ptr.data(), nrows,
ncols, nnz, structure};
ncols, nnz, structure, is_iso};
}

template <typename T, typename I>
Expand All @@ -315,10 +352,16 @@ void write_coo_matrix(H5::Group& f, coo_matrix<T, I> m,
j["binsparse"]["version"] = version;
j["binsparse"]["format"] = "COO";
j["binsparse"]["shape"] = {m.m, m.n};
j["binsparse"]["nnz"] = m.nnz;
j["binsparse"]["number_of_stored_values"] = m.nnz;
j["binsparse"]["data_types"]["indices_0"] = type_info<I>::label();
j["binsparse"]["data_types"]["indices_1"] = type_info<I>::label();
j["binsparse"]["data_types"]["values"] = type_info<T>::label();

if (!m.is_iso) {
j["binsparse"]["data_types"]["values"] =
std::string("iso[") + type_info<T>::label() + "]";
} else {
j["binsparse"]["data_types"]["values"] = type_info<T>::label();
}

if (m.structure != general) {
j["binsparse"]["structure"] =
Expand Down Expand Up @@ -357,7 +400,13 @@ coo_matrix<T, I> read_coo_matrix(std::string fname, Allocator&& alloc) {

auto nrows = binsparse_metadata["shape"][0];
auto ncols = binsparse_metadata["shape"][1];
auto nnz = binsparse_metadata["nnz"];
auto nnz = binsparse_metadata["number_of_stored_values"];

bool is_iso = false;
if (std::string(binsparse_metadata["data_types"]["values"])
.starts_with("iso")) {
is_iso = true;
}

typename std::allocator_traits<
std::remove_cvref_t<Allocator>>::template rebind_alloc<I>
Expand All @@ -374,7 +423,7 @@ coo_matrix<T, I> read_coo_matrix(std::string fname, Allocator&& alloc) {
}

return coo_matrix<T, I>{values.data(), rows.data(), cols.data(), nrows,
ncols, nnz, structure};
ncols, nnz, structure, is_iso};
}

template <typename T, typename I>
Expand Down
4 changes: 4 additions & 0 deletions include/binsparse/containers/matrices.hpp
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Expand Up @@ -34,6 +34,7 @@ struct csr_matrix {

I m, n, nnz;
structure_t structure = general;
bool is_iso = false;
};

template <typename T, typename I>
Expand All @@ -44,6 +45,7 @@ struct csc_matrix {

I m, n, nnz;
structure_t structure = general;
bool is_iso = false;
};

template <typename T, typename I>
Expand All @@ -54,6 +56,7 @@ struct coo_matrix {

I m, n, nnz;
structure_t structure = general;
bool is_iso = false;
};

template <typename T, typename I = std::size_t, typename Order = row_major>
Expand All @@ -64,6 +67,7 @@ struct dense_matrix {
structure_t structure = general;

using order = Order;
bool is_iso = false;
};

} // namespace binsparse