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Improved the names for the custom chunk manager.
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@LTLA
LTLA committed Jul 10, 2023
1 parent 103ae7b commit 5631c63
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Showing 2 changed files with 184 additions and 148 deletions.
140 changes: 76 additions & 64 deletions include/tatami/chunked/CustomChunkManager.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -78,50 +78,62 @@ class CustomChunkManager {

public:
static constexpr bool sparse_chunk = Chunk_::sparse;
typedef typename Chunk_::value_type Chunkval;
typedef typename Chunk_::index_type Chunkdex;

struct SparseCache {
SparseCache(size_t primary_dim) : cache_indices(primary_dim), cache_values(primary_dim) {}

std::vector<std::vector<Chunkdex> > cache_indices;
std::vector<std::vector<typename Chunk_::value_type> > cache_values;

std::vector<size_t> buffer_indptrs;
std::vector<Chunkdex> buffer_indices;
std::vector<typename Chunk_::value_type> buffer_values;
struct SparseWorkspace {
std::vector<Chunkval> values;
std::vector<Chunkdex> indices;
std::vector<size_t> indptrs;
};

struct SparseSlab {
SparseSlab(size_t primary_dim) : indices(primary_dim), values(primary_dim) {}
std::vector<std::vector<Chunkval> > values;
std::vector<std::vector<Chunkdex> > indices;
void clear() {
for (auto& x : cache_indices) {
for (auto& x : indices) {
x.clear();
}
for (auto& x : cache_values) {
for (auto& x : values) {
x.clear();
}
}
};

struct DenseCache {
DenseCache(size_t length, size_t primary_dim) : cache(length * primary_dim) {}

std::vector<typename Chunk_::value_type> cache;
struct DenseWorkspace {
std::vector<typename Chunk_::value_type> values;
};

std::vector<typename Chunk_::value_type> buffer;
struct DenseSlab {
DenseSlab(size_t length, size_t primary_dim) : values(length * primary_dim) {}
std::vector<Chunkval> values;
};

typedef typename std::conditional<sparse_chunk, SparseCache, DenseCache>::type Cache;
typedef typename std::conditional<sparse_chunk, SparseWorkspace, DenseWorkspace>::type Workspace;

Workspace create_workspace() const {
if constexpr(sparse_chunk) {
return SparseWorkspace();
} else {
return DenseWorkspace();
}
}

typedef typename std::conditional<sparse_chunk, SparseSlab, DenseSlab>::type Slab;

template<bool accrow_, bool exact_>
Cache create_chunk_cache(size_t length) const {
Slab create_slab(size_t length) const {
if constexpr(sparse_chunk) {
return SparseCache(exact_ ? 1 : get_primary_chunkdim<accrow_>());
return SparseSlab(exact_ ? 1 : get_primary_chunkdim<accrow_>());
} else {
return DenseCache(length, exact_ ? 1 : get_primary_chunkdim<accrow_>());
return DenseSlab(length, exact_ ? 1 : get_primary_chunkdim<accrow_>());
}
}

public:
template<bool accrow_, bool exact_>
void extract(size_t primary_chunk_index, size_t primary_chunk_offset, size_t primary_maxdim, size_t start, size_t length, Cache& cache) const {
void extract(size_t primary_chunk_index, size_t primary_chunk_offset, size_t primary_maxdim, size_t start, size_t length, Slab& slab, Workspace& work) const {
if (!length) {
return;

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}
Expand All @@ -144,7 +156,7 @@ class CustomChunkManager {
size_t secondary_start_pos = start_chunk_index * secondary_chunkdim;

if constexpr(sparse_chunk) {
cache.clear();
slab.clear();
}

for (size_t c = start_chunk_index; c < end_chunk_index; ++c) {
Expand All @@ -153,39 +165,39 @@ class CustomChunkManager {
size_t to = (c + 1 == end_chunk_index ? start + length - secondary_start_pos : secondary_chunkdim);

if constexpr(sparse_chunk) {
chunk.inflate(cache.buffer_values, cache.buffer_indices, cache.buffer_indptrs);
chunk.inflate(work.values, work.indices, work.indptrs);
Chunkdex secondary_offset = secondary_start_pos;

if (chunk.row_major == accrow_) {
auto refine_start_and_end = [&](size_t& start, size_t& end) -> void {
if (from) {
auto it = cache.buffer_indices.begin();
auto it = work.indices.begin();
start = std::lower_bound(it + start, it + end, static_cast<Chunkdex>(from)) - it;
}
if (to != secondary_chunkdim) {
auto it = cache.buffer_indices.begin();
auto it = work.indices.begin();
end = std::lower_bound(it + start, it + end, static_cast<Chunkdex>(to)) - it;
}
};

if constexpr(exact_) {
auto start = cache.buffer_indptrs[primary_chunk_offset], end = cache.buffer_indptrs[primary_chunk_offset + 1];
auto start = work.indptrs[primary_chunk_offset], end = work.indptrs[primary_chunk_offset + 1];
if (start < end) {
refine_start_and_end(start, end);
cache.cache_values[0].insert(cache.cache_values[0].end(), cache.buffer_values.begin() + start, cache.buffer_values.begin() + end);
slab.values[0].insert(slab.values[0].end(), work.values.begin() + start, work.values.begin() + end);
for (size_t i = start; i < end; ++i) {
cache.cache_indices[0].push_back(cache.buffer_indices[i] + secondary_offset);
slab.indices[0].push_back(work.indices[i] + secondary_offset);
}
}

} else {
for (size_t p = 0; p < primary_end_pos; ++p) {
auto start = cache.buffer_indptrs[p], end = cache.buffer_indptrs[p + 1];
auto start = work.indptrs[p], end = work.indptrs[p + 1];
if (start < end) {
refine_start_and_end(start, end);
cache.cache_values[p].insert(cache.cache_values[p].end(), cache.buffer_values.begin() + start, cache.buffer_values.begin() + end);
slab.values[p].insert(slab.values[p].end(), work.values.begin() + start, work.values.begin() + end);
for (size_t i = start; i < end; ++i) {
cache.cache_indices[p].push_back(cache.buffer_indices[i] + secondary_offset);
slab.indices[p].push_back(work.indices[i] + secondary_offset);
}
}
}
Expand All @@ -195,31 +207,31 @@ class CustomChunkManager {
if constexpr(exact_) {
Chunkdex target = primary_chunk_offset;
for (size_t s = from; s < to; ++s) {
auto start = cache.buffer_indptrs[s], end = cache.buffer_indptrs[s + 1];
auto it = cache.buffer_indices.begin();
auto start = work.indptrs[s], end = work.indptrs[s + 1];
auto it = work.indices.begin();
start = std::lower_bound(it + start, it + end, target) - it;
if (start != end && cache.buffer_indices[start] == target) {
cache.cache_values[0].push_back(cache.buffer_values[start]);
cache.cache_indices[0].push_back(s + secondary_offset);
if (start != end && work.indices[start] == target) {
slab.values[0].push_back(work.values[start]);
slab.indices[0].push_back(s + secondary_offset);
}
}

} else {
for (size_t s = from; s < to; ++s) {
auto start = cache.buffer_indptrs[s], end = cache.buffer_indptrs[s + 1];
auto start = work.indptrs[s], end = work.indptrs[s + 1];
for (size_t i = start; i < end; ++i) {
auto p = cache.buffer_indices[i];
cache.cache_values[p].push_back(cache.buffer_values[i]);
cache.cache_indices[p].push_back(s + secondary_offset);
auto p = work.indices[i];
slab.values[p].push_back(work.values[i]);
slab.indices[p].push_back(s + secondary_offset);
}
}
}
}

} else {
chunk.inflate(cache.buffer);
auto bptr = cache.buffer.data();
auto cptr = cache.cache.data() + dense_cache_offset;
chunk.inflate(work.values);
auto bptr = work.values.data();
auto cptr = slab.values.data() + dense_cache_offset;

if (chunk.row_major == accrow_) {
if constexpr(exact_) {
Expand Down Expand Up @@ -269,7 +281,7 @@ class CustomChunkManager {

public:
template<bool accrow_, bool exact_, typename Index_>
void extract(size_t primary_chunk_index, size_t primary_chunk_offset, size_t primary_maxdim, const std::vector<Index_>& indices, Cache& cache) const {
void extract(size_t primary_chunk_index, size_t primary_chunk_offset, size_t primary_maxdim, const std::vector<Index_>& indices, Slab& slab, Workspace& work) const {
if (indices.empty()) {
return;

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}
Expand All @@ -293,7 +305,7 @@ class CustomChunkManager {
size_t secondary_start_pos = start_chunk_index * secondary_chunkdim;

if constexpr(sparse_chunk) {
cache.clear();
slab.clear();
}

for (size_t c = start_chunk_index; c < primary_num_chunks && iIt != indices.end(); ++c) {
Expand All @@ -308,42 +320,42 @@ class CustomChunkManager {
const auto& chunk = chunks[offset];

if constexpr(sparse_chunk) {
chunk.inflate(cache.buffer_values, cache.buffer_indices, cache.buffer_indptrs);
chunk.inflate(work.values, work.indices, work.indptrs);
Chunkdex secondary_offset = secondary_start_pos;

auto collect_sparse = [&](size_t start, size_t end, size_t pout) -> void {
if (collected.front()) {
auto it = cache.buffer_indices.begin();
auto it = work.indices.begin();
start = std::lower_bound(it + start, it + end, static_cast<Chunkdex>(collected.front())) - it;
}

auto cIt = collected.begin();
for (size_t i = start; i < end; ++i) {
Index_ target = cache.buffer_indices[i];
Index_ target = work.indices[i];
while (cIt != collected.end() && *cIt < target) {
++cIt;
}
if (cIt == collected.end()) {
break;
}
if (*cIt == target) {
cache.cache_values[pout].push_back(cache.buffer_values[i]);
cache.cache_indices[pout].push_back(cache.buffer_indices[i] + secondary_offset);
slab.values[pout].push_back(work.values[i]);
slab.indices[pout].push_back(work.indices[i] + secondary_offset);
++cIt;
}
}
};

if (chunk.row_major == accrow_) {
if constexpr(exact_) {
auto start = cache.buffer_indptrs[primary_chunk_offset], end = cache.buffer_indptrs[primary_chunk_offset + 1];
auto start = work.indptrs[primary_chunk_offset], end = work.indptrs[primary_chunk_offset + 1];
if (start < end) {
collect_sparse(start, end, 0);
}

} else {
for (size_t p = 0; p < primary_end_pos; ++p) {
auto start = cache.buffer_indptrs[p], end = cache.buffer_indptrs[p + 1];
auto start = work.indptrs[p], end = work.indptrs[p + 1];
if (start < end) {
collect_sparse(start, end, p);
}
Expand All @@ -354,31 +366,31 @@ class CustomChunkManager {
if constexpr(exact_) {
Chunkdex target = primary_chunk_offset;
for (auto s : collected) {
auto start = cache.buffer_indptrs[s], end = cache.buffer_indptrs[s + 1];
auto it = cache.buffer_indices.begin();
auto start = work.indptrs[s], end = work.indptrs[s + 1];
auto it = work.indices.begin();
start = std::lower_bound(it + start, it + end, target) - it;
if (start != end && cache.buffer_indices[start] == target) {
cache.cache_values[0].push_back(cache.buffer_values[start]);
cache.cache_indices[0].push_back(s + secondary_offset);
if (start != end && work.indices[start] == target) {
slab.values[0].push_back(work.values[start]);
slab.indices[0].push_back(s + secondary_offset);
}
}

} else {
for (auto s : collected) {
auto start = cache.buffer_indptrs[s], end = cache.buffer_indptrs[s + 1];
auto start = work.indptrs[s], end = work.indptrs[s + 1];
for (size_t i = start; i < end; ++i) {
auto p = cache.buffer_indices[i];
cache.cache_values[p].push_back(cache.buffer_values[i]);
cache.cache_indices[p].push_back(s + secondary_offset);
auto p = work.indices[i];
slab.values[p].push_back(work.values[i]);
slab.indices[p].push_back(s + secondary_offset);
}
}
}
}

} else {
chunk.inflate(cache.buffer);
auto bptr = cache.buffer.data();
auto cptr = cache.cache.data() + dense_cache_offset;
chunk.inflate(work.values);
auto bptr = work.values.data();
auto cptr = slab.values.data() + dense_cache_offset;

if (chunk.row_major == accrow_) {
if constexpr(exact_) {
Expand Down
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