select/rank for unset as well as set bits #4
16 changed files with 2316 additions and 594 deletions
2
.envrc
2
.envrc
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@ -1,5 +1,5 @@
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||||||
if ! has nix_direnv_version || ! nix_direnv_version 3.0.4; then
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if ! has nix_direnv_version || ! nix_direnv_version 3.0.4; then
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||||||
source_url "https://raw.githubusercontent.com/nix-community/nix-direnv/3.0.4/direnvrc" "sha256-DzlYZ33mWF/Gs8DDeyjr8mnVmQGx7ASYqA5WlxwvBG4="
|
source_url "https://raw.githubusercontent.com/nix-community/nix-direnv/3.0.4/direnvrc" "sha256-DzlYZ33mWF/Gs8DDeyjr8mnVmQGx7ASYqA5WlxwvBG4="
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||||||
fi
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fi
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watch_file devShell.nix shell.nix flake.nix
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watch_file shell.nix flake.nix
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use flake || use nix
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use flake || use nix
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||||||
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14
Makefile
14
Makefile
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@ -5,14 +5,15 @@ SHARED_LIB = libsparsemap.so
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#CFLAGS = -Wall -Wextra -Wpedantic -Of -std=c11 -Iinclude/ -fPIC
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#CFLAGS = -Wall -Wextra -Wpedantic -Of -std=c11 -Iinclude/ -fPIC
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||||||
#CFLAGS = -Wall -Wextra -Wpedantic -Og -g -std=c11 -Iinclude/ -fPIC
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#CFLAGS = -Wall -Wextra -Wpedantic -Og -g -std=c11 -Iinclude/ -fPIC
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||||||
CFLAGS = -DSPARSEMAP_DIAGNOSTIC -DSPARSEMAP_ASSERT -Wall -Wextra -Wpedantic -Og -g -std=c11 -Iinclude/ -fPIC
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CFLAGS = -DSPARSEMAP_DIAGNOSTIC -DDEBUG -Wall -Wextra -Wpedantic -Og -g -std=c11 -Iinclude/ -fPIC
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||||||
#CFLAGS = -Wall -Wextra -Wpedantic -Og -g -fsanitize=address,leak,object-size,pointer-compare,pointer-subtract,null,return,bounds,pointer-overflow,undefined -fsanitize-address-use-after-scope -std=c11 -Iinclude/ -fPIC
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#CFLAGS = -DSPARSEMAP_DIAGNOSTIC -DDEBUG -Wall -Wextra -Wpedantic -Og -g -fsanitize=address,leak,object-size,pointer-compare,pointer-subtract,null,return,bounds,pointer-overflow,undefined -fsanitize-address-use-after-scope -std=c11 -Iinclude/ -fPIC
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||||||
#CFLAGS = -Wall -Wextra -Wpedantic -Og -g -fsanitize=all -fhardened -std=c11 -Iinclude/ -fPIC
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#CFLAGS = -Wall -Wextra -Wpedantic -Og -g -fsanitize=all -fhardened -std=c11 -Iinclude/ -fPIC
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||||||
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||||||
TEST_FLAGS = -Wall -Wextra -Wpedantic -Og -g -std=c11 -Iinclude/ -Itests/ -fPIC
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TEST_FLAGS = -DDEBUG -Wall -Wextra -Wpedantic -Og -g -std=c11 -Iinclude/ -Itests/ -fPIC
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||||||
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#TEST_FLAGS = -DDEBUG -Wall -Wextra -Wpedantic -Og -g -fsanitize=address,leak,object-size,pointer-compare,pointer-subtract,null,return,bounds,pointer-overflow,undefined -fsanitize-address-use-after-scope -std=c11 -Iinclude/ -fPIC
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||||||
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TESTS = tests/test
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TESTS = tests/test
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TEST_OBJS = tests/test.o tests/munit.o tests/common.o
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TEST_OBJS = tests/test.o tests/munit.o tests/tdigest.o tests/common.o
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EXAMPLES = examples/ex_1 examples/ex_2 examples/ex_3 examples/ex_4
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EXAMPLES = examples/ex_1 examples/ex_2 examples/ex_3 examples/ex_4
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.PHONY: all shared static clean test examples mls
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.PHONY: all shared static clean test examples mls
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@ -39,7 +40,7 @@ check: test
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env ASAN_OPTIONS=detect_leaks=1 LSAN_OPTIONS=verbosity=1:log_threads=1 ./tests/test
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env ASAN_OPTIONS=detect_leaks=1 LSAN_OPTIONS=verbosity=1:log_threads=1 ./tests/test
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tests/test: $(TEST_OBJS) $(STATIC_LIB)
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tests/test: $(TEST_OBJS) $(STATIC_LIB)
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$(CC) $^ -o $@ $(TEST_FLAGS)
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$(CC) $^ -lm -o $@ $(TEST_FLAGS)
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clean:
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clean:
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rm -f $(OBJS)
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rm -f $(OBJS)
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@ -76,4 +77,7 @@ examples/ex_3: examples/common.o examples/ex_3.o $(STATIC_LIB)
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examples/ex_4: examples/common.o examples/ex_4.o $(STATIC_LIB)
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examples/ex_4: examples/common.o examples/ex_4.o $(STATIC_LIB)
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$(CC) $^ -o $@ $(CFLAGS) $(TEST_FLAGS)
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$(CC) $^ -o $@ $(CFLAGS) $(TEST_FLAGS)
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todo:
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rg -i 'todo|gsb|abort'
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# cp src/sparsemap.c /tmp && clang-tidy src/sparsemap.c -fix -fix-errors -checks="readability-braces-around-statements" -- -DDEBUG -DSPARSEMAP_DIAGNOSTIC -DSPARSEMAP_ASSERT -Wall -Wextra -Wpedantic -Og -g -std=c11 -Iinclude/ -fPIC
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# cp src/sparsemap.c /tmp && clang-tidy src/sparsemap.c -fix -fix-errors -checks="readability-braces-around-statements" -- -DDEBUG -DSPARSEMAP_DIAGNOSTIC -DSPARSEMAP_ASSERT -Wall -Wextra -Wpedantic -Og -g -std=c11 -Iinclude/ -fPIC
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@ -60,5 +60,6 @@ to an uncompressed bit vector (sometimes higher due to the bytes required for
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metadata). In such cases, other compression schemes are more efficient (i.e.
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metadata). In such cases, other compression schemes are more efficient (i.e.
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http://lemire.me/blog/archives/2008/08/20/the-mythical-bitmap-index/).
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http://lemire.me/blog/archives/2008/08/20/the-mythical-bitmap-index/).
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This library was originally created for hamsterdb [http://hamsterdb.com] in
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This library was originally created for [hamsterdb](http://hamsterdb.com) in
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C++ and then translated to C99 code by Greg Burd <greg@burd.me>.
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C++ and then translated to C and further improved by Greg Burd <greg@burd.me>
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for use in LMDB and OpenLDAP.
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@ -1,4 +1,7 @@
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#include <assert.h>
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#include <assert.h>
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#include <stdbool.h>
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#include <stddef.h>
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#include <stdint.h>
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#include <stdio.h>
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#include <stdio.h>
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#include "../include/sparsemap.h"
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#include "../include/sparsemap.h"
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@ -14,16 +17,18 @@
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/* !!! Duplicated here for testing purposes. Keep in sync, or suffer. !!! */
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/* !!! Duplicated here for testing purposes. Keep in sync, or suffer. !!! */
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struct sparsemap {
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struct sparsemap {
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uint8_t *m_data;
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size_t m_capacity;
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size_t m_capacity;
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size_t m_data_used;
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size_t m_data_used;
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uint8_t *m_data;
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};
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};
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int
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int
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main()
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main()
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{
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{
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size_t size = 4;
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size_t size = 4;
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setbuf(stderr, 0); // disable buffering
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setvbuf(stdout, NULL, _IONBF, 0); // Disable buffering for stdout
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setvbuf(stderr, NULL, _IONBF, 0); // Disable buffering for stdout
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__diag("Please wait a moment...");
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__diag("Please wait a moment...");
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sparsemap_t mmap, *map = &mmap;
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sparsemap_t mmap, *map = &mmap;
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uint8_t buffer[1024];
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uint8_t buffer[1024];
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@ -135,7 +140,7 @@ main()
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sparsemap_set(map, i, true);
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sparsemap_set(map, i, true);
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}
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}
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for (int i = 0; i < 100000; i++) {
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for (int i = 0; i < 100000; i++) {
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assert(sparsemap_select(map, i) == (unsigned)i);
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assert(sparsemap_select(map, i, true) == (unsigned)i);
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}
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}
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sparsemap_clear(map);
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sparsemap_clear(map);
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@ -145,7 +150,7 @@ main()
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sparsemap_set(map, i, true);
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sparsemap_set(map, i, true);
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}
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}
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for (int i = 1; i < 513; i++) {
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for (int i = 1; i < 513; i++) {
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assert(sparsemap_select(map, i - 1) == (unsigned)i);
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assert(sparsemap_select(map, i - 1, true) == (unsigned)i);
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}
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}
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sparsemap_clear(map);
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sparsemap_clear(map);
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@ -155,7 +160,7 @@ main()
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sparsemap_set(map, i * 10, true);
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sparsemap_set(map, i * 10, true);
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}
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}
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for (size_t i = 0; i < 8; i++) {
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for (size_t i = 0; i < 8; i++) {
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assert(sparsemap_select(map, i) == i * 10);
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assert(sparsemap_select(map, i, true) == (sparsemap_idx_t)i * 10);
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}
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}
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// split and move, aligned to MiniMap capacity
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// split and move, aligned to MiniMap capacity
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@ -1,9 +1,7 @@
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#include <assert.h>
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#include <assert.h>
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#include <stdarg.h>
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#include <stdbool.h>
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#include <stdio.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <stdlib.h>
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#include <time.h>
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#include <unistd.h>
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#include "../include/sparsemap.h"
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#include "../include/sparsemap.h"
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@ -16,29 +14,28 @@
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} while (0)
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} while (0)
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#pragma GCC diagnostic pop
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#pragma GCC diagnostic pop
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#define SEED
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int
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int
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main(void)
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main(void)
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{
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{
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int i = 0;
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int i;
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// disable buffering
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// disable buffering
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setbuf(stderr, 0);
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setvbuf(stdout, NULL, _IONBF, 0); // Disable buffering for stdout
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setvbuf(stderr, NULL, _IONBF, 0); // Disable buffering for stdout
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// start with a 1KiB buffer, 1024 bits
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// start with a 1KiB buffer, 1024 bits
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uint8_t *buf = calloc(1024, sizeof(uint8_t));
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uint8_t *buf = calloc(1024, sizeof(uint8_t));
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// create the sparse bitmap
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// create the sparse bitmap
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sparsemap_t *map = sparsemap(buf, sizeof(uint8_t) * 1024);
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sparsemap_t *map = sparsemap_wrap(buf, sizeof(uint8_t) * 1024);
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// Set every other bit (pathologically worst case) to see what happens
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// Set every other bit (pathologically worst case) to see what happens
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// when the map is full.
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// when the map is full.
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for (i = 0; i < 7744; i++) {
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for (i = 0; i < 7744; i++) {
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if (i % 2)
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if (!i % 2) {
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continue;
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sparsemap_set(map, i, true);
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sparsemap_set(map, i, true);
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assert(sparsemap_is_set(map, i) == true);
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assert(sparsemap_is_set(map, i) == true);
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}
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}
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}
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// On 1024 KiB of buffer with every other bit set the map holds 7744 bits
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// On 1024 KiB of buffer with every other bit set the map holds 7744 bits
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// and then runs out of space. This next _set() call will fail/abort.
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// and then runs out of space. This next _set() call will fail/abort.
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@ -1,9 +1,7 @@
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#include <assert.h>
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#include <assert.h>
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#include <stdarg.h>
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#include <stdbool.h>
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#include <stdio.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <stdlib.h>
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#include <time.h>
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#include <unistd.h>
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#include "../include/sparsemap.h"
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#include "../include/sparsemap.h"
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#include "../tests/common.h"
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#include "../tests/common.h"
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@ -11,7 +9,7 @@
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int
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int
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main(void)
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main(void)
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{
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{
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int i = 0;
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int i;
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int array[1024] = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
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int array[1024] = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
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38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
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38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
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77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,
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77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,
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||||||
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@ -60,7 +58,7 @@ main(void)
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uint8_t *buf = calloc(1024, sizeof(uint8_t));
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uint8_t *buf = calloc(1024, sizeof(uint8_t));
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|
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// create the sparse bitmap
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// create the sparse bitmap
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sparsemap_t *map = sparsemap(buf, sizeof(uint8_t) * 1024);
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sparsemap_t *map = sparsemap_wrap(buf, sizeof(uint8_t) * 1024);
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||||||
|
|
||||||
// set all the bits on in a random order
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// set all the bits on in a random order
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for (i = 0; i < 1024; i++) {
|
for (i = 0; i < 1024; i++) {
|
||||||
|
|
|
@ -24,7 +24,7 @@ main(void)
|
||||||
uint8_t *buf = calloc((size_t)3 * 1024, sizeof(uint8_t));
|
uint8_t *buf = calloc((size_t)3 * 1024, sizeof(uint8_t));
|
||||||
|
|
||||||
// create the sparse bitmap
|
// create the sparse bitmap
|
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sparsemap_t *map = sparsemap(buf, sizeof(uint8_t) * 3 * 1024);
|
sparsemap_t *map = sparsemap_wrap(buf, sizeof(uint8_t) * 3 * 1024);
|
||||||
|
|
||||||
// create an array of ints
|
// create an array of ints
|
||||||
setup_test_array(array, TEST_ARRAY_SIZE, 1024 * 3);
|
setup_test_array(array, TEST_ARRAY_SIZE, 1024 * 3);
|
||||||
|
@ -60,7 +60,7 @@ main(void)
|
||||||
assert(sparsemap_is_set(map, array[i]) == true);
|
assert(sparsemap_is_set(map, array[i]) == true);
|
||||||
}
|
}
|
||||||
has_span(map, array, TEST_ARRAY_SIZE, (int)len);
|
has_span(map, array, TEST_ARRAY_SIZE, (int)len);
|
||||||
size_t l = sparsemap_span(map, 0, len);
|
size_t l = sparsemap_span(map, 0, len, true);
|
||||||
if (l != (size_t)-1) {
|
if (l != (size_t)-1) {
|
||||||
__diag("Found span in map starting at %lu of length %lu\n", l, len);
|
__diag("Found span in map starting at %lu of length %lu\n", l, len);
|
||||||
__diag("is_span(%lu, %lu) == %s\n", l, len, is_span(array, TEST_ARRAY_SIZE, l, len) ? "yes" : "no");
|
__diag("is_span(%lu, %lu) == %s\n", l, len, is_span(array, TEST_ARRAY_SIZE, l, len) ? "yes" : "no");
|
||||||
|
|
48
flake.lock
48
flake.lock
|
@ -1,43 +1,25 @@
|
||||||
{
|
{
|
||||||
"nodes": {
|
"nodes": {
|
||||||
"flake-utils": {
|
|
||||||
"inputs": {
|
|
||||||
"systems": "systems"
|
|
||||||
},
|
|
||||||
"locked": {
|
|
||||||
"lastModified": 1710146030,
|
|
||||||
"narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
|
|
||||||
"owner": "numtide",
|
|
||||||
"repo": "flake-utils",
|
|
||||||
"rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
|
|
||||||
"type": "github"
|
|
||||||
},
|
|
||||||
"original": {
|
|
||||||
"owner": "numtide",
|
|
||||||
"repo": "flake-utils",
|
|
||||||
"type": "github"
|
|
||||||
}
|
|
||||||
},
|
|
||||||
"nixpkgs": {
|
"nixpkgs": {
|
||||||
"locked": {
|
"locked": {
|
||||||
"lastModified": 1712192574,
|
"lastModified": 1701282334,
|
||||||
"narHash": "sha256-LbbVOliJKTF4Zl2b9salumvdMXuQBr2kuKP5+ZwbYq4=",
|
"narHash": "sha256-MxCVrXY6v4QmfTwIysjjaX0XUhqBbxTWWB4HXtDYsdk=",
|
||||||
"owner": "NixOS",
|
"owner": "NixOS",
|
||||||
"repo": "nixpkgs",
|
"repo": "nixpkgs",
|
||||||
"rev": "f480f9d09e4b4cf87ee6151eba068197125714de",
|
"rev": "057f9aecfb71c4437d2b27d3323df7f93c010b7e",
|
||||||
"type": "github"
|
"type": "github"
|
||||||
},
|
},
|
||||||
"original": {
|
"original": {
|
||||||
"owner": "NixOS",
|
"owner": "NixOS",
|
||||||
"ref": "nixpkgs-unstable",
|
"ref": "23.11",
|
||||||
"repo": "nixpkgs",
|
"repo": "nixpkgs",
|
||||||
"type": "github"
|
"type": "github"
|
||||||
}
|
}
|
||||||
},
|
},
|
||||||
"root": {
|
"root": {
|
||||||
"inputs": {
|
"inputs": {
|
||||||
"flake-utils": "flake-utils",
|
"nixpkgs": "nixpkgs",
|
||||||
"nixpkgs": "nixpkgs"
|
"utils": "utils"
|
||||||
}
|
}
|
||||||
},
|
},
|
||||||
"systems": {
|
"systems": {
|
||||||
|
@ -54,6 +36,24 @@
|
||||||
"repo": "default",
|
"repo": "default",
|
||||||
"type": "github"
|
"type": "github"
|
||||||
}
|
}
|
||||||
|
},
|
||||||
|
"utils": {
|
||||||
|
"inputs": {
|
||||||
|
"systems": "systems"
|
||||||
|
},
|
||||||
|
"locked": {
|
||||||
|
"lastModified": 1710146030,
|
||||||
|
"narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
|
||||||
|
"owner": "numtide",
|
||||||
|
"repo": "flake-utils",
|
||||||
|
"rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
|
||||||
|
"type": "github"
|
||||||
|
},
|
||||||
|
"original": {
|
||||||
|
"owner": "numtide",
|
||||||
|
"repo": "flake-utils",
|
||||||
|
"type": "github"
|
||||||
|
}
|
||||||
}
|
}
|
||||||
},
|
},
|
||||||
"root": "root",
|
"root": "root",
|
||||||
|
|
100
flake.nix
100
flake.nix
|
@ -1,59 +1,55 @@
|
||||||
{
|
{
|
||||||
description = "A Concurrent Skip List library for key/value pairs.";
|
description = "A sparse bitmapped index library in C.";
|
||||||
|
|
||||||
inputs = {
|
inputs = {
|
||||||
nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-unstable";
|
# nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-unstable";
|
||||||
flake-utils.url = "github:numtide/flake-utils";
|
nixpkgs.url = "github:NixOS/nixpkgs/23.11";
|
||||||
|
utils.url = "github:numtide/flake-utils";
|
||||||
|
utils.inputs.nixpkgs.follows = "nixpkgs";
|
||||||
};
|
};
|
||||||
|
|
||||||
outputs =
|
outputs = { self, nixpkgs, ... }
|
||||||
{ self
|
@inputs: inputs.utils.lib.eachSystem [
|
||||||
, nixpkgs
|
"x86_64-linux" "i686-linux" "aarch64-linux" "x86_64-darwin"
|
||||||
, flake-utils
|
] (system:
|
||||||
, ...
|
let pkgs = import nixpkgs {
|
||||||
}:
|
inherit system;
|
||||||
flake-utils.lib.eachDefaultSystem (system:
|
overlays = [];
|
||||||
let
|
config.allowUnfree = true;
|
||||||
pkgs = import nixpkgs {
|
|
||||||
inherit system;
|
|
||||||
config = { allowUnfree = true; };
|
|
||||||
};
|
|
||||||
supportedSystems = [ "x86_64-linux" ];
|
|
||||||
forAllSystems = nixpkgs.lib.genAttrs supportedSystems;
|
|
||||||
nixpkgsFor = forAllSystems (system: import nixpkgs {
|
|
||||||
inherit system;
|
|
||||||
overlays = [ self.overlay ];
|
|
||||||
});
|
|
||||||
in {
|
|
||||||
pkgs = import nixpkgs {
|
|
||||||
inherit system;
|
|
||||||
devShell = nixpkgs.legacyPackages.${system} {
|
|
||||||
pkgs.mkShell = {
|
|
||||||
nativeBuildInputs = with pkgs.buildPackages; [
|
|
||||||
act
|
|
||||||
autoconf
|
|
||||||
clang
|
|
||||||
ed
|
|
||||||
gcc
|
|
||||||
gdb
|
|
||||||
gettext
|
|
||||||
graphviz-nox
|
|
||||||
libtool
|
|
||||||
m4
|
|
||||||
perl
|
|
||||||
pkg-config
|
|
||||||
python3
|
|
||||||
ripgrep
|
|
||||||
valgrind
|
|
||||||
];
|
|
||||||
buildInputs = with pkgs; [
|
|
||||||
libbacktrace
|
|
||||||
glibc.out
|
|
||||||
glibc.static
|
|
||||||
];
|
|
||||||
};
|
|
||||||
DOCKER_BUILDKIT = 1;
|
|
||||||
};
|
};
|
||||||
};
|
in {
|
||||||
});
|
devShell = pkgs.mkShell rec {
|
||||||
|
name = "sparsemap";
|
||||||
|
packages = with pkgs; [
|
||||||
|
act
|
||||||
|
autoconf
|
||||||
|
clang
|
||||||
|
ed
|
||||||
|
gcc
|
||||||
|
gdb
|
||||||
|
gettext
|
||||||
|
graphviz-nox
|
||||||
|
libtool
|
||||||
|
m4
|
||||||
|
perl
|
||||||
|
pkg-config
|
||||||
|
python3
|
||||||
|
ripgrep
|
||||||
|
valgrind
|
||||||
|
];
|
||||||
|
|
||||||
|
buildInputs = with pkgs; [
|
||||||
|
libbacktrace
|
||||||
|
glibc.out
|
||||||
|
glibc.static
|
||||||
|
];
|
||||||
|
|
||||||
|
shellHook = let
|
||||||
|
icon = "f121";
|
||||||
|
in ''
|
||||||
|
export PS1="$(echo -e '\u${icon}') {\[$(tput sgr0)\]\[\033[38;5;228m\]\w\[$(tput sgr0)\]\[\033[38;5;15m\]} (${name}) \\$ \[$(tput sgr0)\]"
|
||||||
|
'';
|
||||||
|
};
|
||||||
|
DOCKER_BUILDKIT = 1;
|
||||||
|
});
|
||||||
}
|
}
|
||||||
|
|
|
@ -69,14 +69,14 @@
|
||||||
#ifndef SPARSEMAP_H
|
#ifndef SPARSEMAP_H
|
||||||
#define SPARSEMAP_H
|
#define SPARSEMAP_H
|
||||||
|
|
||||||
#include <sys/types.h>
|
|
||||||
|
|
||||||
#include <assert.h>
|
|
||||||
#include <limits.h>
|
#include <limits.h>
|
||||||
#include <stdbool.h>
|
#include <stdbool.h>
|
||||||
|
#include <stddef.h>
|
||||||
#include <stdint.h>
|
#include <stdint.h>
|
||||||
#include <stdio.h>
|
|
||||||
#include <string.h>
|
#if defined(__cplusplus)
|
||||||
|
extern "C" {
|
||||||
|
#endif
|
||||||
|
|
||||||
/*
|
/*
|
||||||
* The public interface for a sparse bit-mapped index, a "sparse map".
|
* The public interface for a sparse bit-mapped index, a "sparse map".
|
||||||
|
@ -88,55 +88,119 @@
|
||||||
*/
|
*/
|
||||||
|
|
||||||
typedef struct sparsemap sparsemap_t;
|
typedef struct sparsemap sparsemap_t;
|
||||||
|
typedef long int sparsemap_idx_t;
|
||||||
|
#define SPARSEMAP_IDX_MAX ((1UL << (sizeof(long) * CHAR_BIT - 1)) - 1)
|
||||||
|
#define SPARSEMAP_IDX_MIN (-(SPARSEMAP_IDX_MAX)-1)
|
||||||
|
#define SPARSEMAP_NOT_FOUND(_x) ((_x) == SPARSEMAP_IDX_MAX || (_x) == SPARSEMAP_IDX_MIN)
|
||||||
typedef uint32_t sm_idx_t;
|
typedef uint32_t sm_idx_t;
|
||||||
typedef uint64_t sm_bitvec_t;
|
typedef uint64_t sm_bitvec_t;
|
||||||
|
|
||||||
/* Allocate on a sparsemap_t on the heap and initialize it. */
|
/**
|
||||||
sparsemap_t *sparsemap(uint8_t *data, size_t size);
|
* Create a new, empty sparsemap_t with a buffer of |size|.
|
||||||
|
* Default when set to 0 is 1024.
|
||||||
|
*/
|
||||||
|
sparsemap_t *sparsemap(size_t size);
|
||||||
|
|
||||||
/* Initialize sparsemap_t with data. */
|
/**
|
||||||
|
* Allocate on a sparsemap_t on the heap to wrap the provided fixed-size
|
||||||
|
* buffer (heap or stack allocated).
|
||||||
|
*/
|
||||||
|
sparsemap_t *sparsemap_wrap(uint8_t *data, size_t size);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Initialize a (possibly stack allocated) sparsemap_t with data (potentially
|
||||||
|
* also on the stack).
|
||||||
|
*/
|
||||||
void sparsemap_init(sparsemap_t *map, uint8_t *data, size_t size);
|
void sparsemap_init(sparsemap_t *map, uint8_t *data, size_t size);
|
||||||
|
|
||||||
/* Clears the whole buffer. */
|
/**
|
||||||
void sparsemap_clear(sparsemap_t *map);
|
* Opens an existing sparsemap contained within the specified buffer.
|
||||||
|
*/
|
||||||
/* Opens an existing sparsemap at the specified buffer. */
|
|
||||||
void sparsemap_open(sparsemap_t *, uint8_t *data, size_t data_size);
|
void sparsemap_open(sparsemap_t *, uint8_t *data, size_t data_size);
|
||||||
|
|
||||||
/* Resizes the data range. */
|
/**
|
||||||
void sparsemap_set_data_size(sparsemap_t *map, size_t data_size);
|
* Resets values and empties the buffer making it ready to accept new data.
|
||||||
|
*/
|
||||||
|
void sparsemap_clear(sparsemap_t *map);
|
||||||
|
|
||||||
/* Calculate remaining capacity, full when 0. */
|
/**
|
||||||
|
* Resizes the data range within the limits of the provided buffer, the map may
|
||||||
|
* move to a new address returned iff the map was created with the sparsemap() API.
|
||||||
|
* Take care to use the new reference (think: realloc()). NOTE: If the returned
|
||||||
|
* value equals NULL then the map was not resized.
|
||||||
|
*/
|
||||||
|
sparsemap_t *sparsemap_set_data_size(sparsemap_t *map, size_t data_size);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Calculate remaining capacity, approaches 0 when full.
|
||||||
|
*/
|
||||||
double sparsemap_capacity_remaining(sparsemap_t *map);
|
double sparsemap_capacity_remaining(sparsemap_t *map);
|
||||||
|
|
||||||
/* Returns the size of the underlying byte array. */
|
/**
|
||||||
|
* Returns the capacity of the underlying byte array.
|
||||||
|
*/
|
||||||
size_t sparsemap_get_capacity(sparsemap_t *map);
|
size_t sparsemap_get_capacity(sparsemap_t *map);
|
||||||
|
|
||||||
/* Returns the value of a bit at index |idx|. */
|
/**
|
||||||
bool sparsemap_is_set(sparsemap_t *map, size_t idx);
|
* Returns the value of a bit at index |idx|, either on/true/1 or off/false/0.
|
||||||
|
* When |idx| is negative it is an error.
|
||||||
|
*/
|
||||||
|
bool sparsemap_is_set(sparsemap_t *map, sparsemap_idx_t idx);
|
||||||
|
|
||||||
/* Sets the bit at index |idx| to true or false, depending on |value|. */
|
/**
|
||||||
void sparsemap_set(sparsemap_t *map, size_t idx, bool value);
|
* Sets the bit at index |idx| to true or false, depending on |value|.
|
||||||
|
* When |idx| is negative is it an error. Returns the |idx| supplied or
|
||||||
|
* SPARSEMAP_IDX_MAX on error with |errno| set to ENOSP when the map is full.
|
||||||
|
*/
|
||||||
|
sparsemap_idx_t sparsemap_set(sparsemap_t *map, sparsemap_idx_t idx, bool value);
|
||||||
|
|
||||||
/* Returns the offset of the very first bit. */
|
/**
|
||||||
sm_idx_t sparsemap_get_start_offset(sparsemap_t *map);
|
* Returns the offset of the very first/last bit in the map.
|
||||||
|
*/
|
||||||
|
sm_idx_t sparsemap_get_starting_offset(sparsemap_t *map);
|
||||||
|
|
||||||
/* Returns the used size in the data buffer. */
|
/**
|
||||||
|
* Returns the used size in the data buffer in bytes.
|
||||||
|
*/
|
||||||
size_t sparsemap_get_size(sparsemap_t *map);
|
size_t sparsemap_get_size(sparsemap_t *map);
|
||||||
|
|
||||||
/* Decompresses the whole bitmap; calls scanner for all bits. */
|
/**
|
||||||
void sparsemap_scan(sparsemap_t *map, void (*scanner)(sm_idx_t[], size_t), size_t skip);
|
* Decompresses the whole bitmap; calls scanner for all bits with a set of
|
||||||
|
* |n| vectors |vec| each a sm_bitmap_t which can be masked and read using
|
||||||
|
* bit operators to read the values for each position in the bitmap index.
|
||||||
|
* Setting |skip| will start the scan after "skip" bits.
|
||||||
|
*/
|
||||||
|
void sparsemap_scan(sparsemap_t *map, void (*scanner)(sm_idx_t vec[], size_t n), size_t skip);
|
||||||
|
|
||||||
/* Appends all chunk maps from |map| starting at |sstart| to |other|, then
|
/**
|
||||||
reduces the chunk map-count appropriately. */
|
* Appends all chunk maps from |map| starting at |offset| to |other|, then
|
||||||
void sparsemap_split(sparsemap_t *map, size_t sstart, sparsemap_t *other);
|
* reduces the chunk map-count appropriately.
|
||||||
|
*/
|
||||||
|
void sparsemap_split(sparsemap_t *map, sparsemap_idx_t offset, sparsemap_t *other);
|
||||||
|
|
||||||
/* Returns the index of the n'th set bit; uses a 0-based index. */
|
/**
|
||||||
size_t sparsemap_select(sparsemap_t *map, size_t n);
|
* Finds the offset of the n'th bit either set (|value| is true) or unset
|
||||||
|
* (|value| is false) from the start (positive |n|), or end (negative |n|),
|
||||||
|
* of the bitmap and returns that (uses a 0-based index). Returns -inf or +inf
|
||||||
|
* if not found (where "inf" is SPARSEMAP_IDX_MAX and "-inf" is SPARSEMAP_IDX_MIN).
|
||||||
|
*/
|
||||||
|
sparsemap_idx_t sparsemap_select(sparsemap_t *map, sparsemap_idx_t n, bool value);
|
||||||
|
|
||||||
/* Counts the set bits in the range [offset, idx]. */
|
/**
|
||||||
size_t sparsemap_rank(sparsemap_t *map, size_t offset, size_t idx);
|
* Counts the set (|value| is true) or unset (|value| is false) bits starting
|
||||||
|
* at |x| bits (0-based) in the range [x, y] (inclusive on either end).
|
||||||
|
*/
|
||||||
|
size_t sparsemap_rank(sparsemap_t *map, size_t x, size_t y, bool value);
|
||||||
|
|
||||||
size_t sparsemap_span(sparsemap_t *map, size_t loc, size_t len);
|
/**
|
||||||
|
* Finds the first span (i.e. a contiguous set of bits), in the bitmap that
|
||||||
|
* are set (|value| is true) or unset (|value| is false) and returns the
|
||||||
|
* starting offset for the span (0-based).
|
||||||
|
*/
|
||||||
|
size_t sparsemap_span(sparsemap_t *map, sparsemap_idx_t idx, size_t len, bool value);
|
||||||
|
|
||||||
|
#if defined(__cplusplus)
|
||||||
|
}
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
|
#endif /* !defined(SPARSEMAP_H) */
|
||||||
|
|
636
src/sparsemap.c
636
src/sparsemap.c
File diff suppressed because it is too large
Load diff
205
tests/common.c
205
tests/common.c
|
@ -1,13 +1,20 @@
|
||||||
#include <sys/types.h>
|
#define _POSIX_C_SOURCE 199309L
|
||||||
|
#define X86_INTRIN
|
||||||
|
|
||||||
#include <assert.h>
|
#include <assert.h>
|
||||||
#include <pthread.h>
|
#include <pthread.h> // If using threads
|
||||||
#include <sparsemap.h>
|
|
||||||
#include <stdbool.h>
|
#include <stdbool.h>
|
||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
#include <stdlib.h>
|
#include <stdlib.h>
|
||||||
|
#include <string.h>
|
||||||
|
#include <time.h>
|
||||||
#include <unistd.h>
|
#include <unistd.h>
|
||||||
|
#ifdef X86_INTRIN
|
||||||
|
#include <errno.h>
|
||||||
|
#include <x86intrin.h>
|
||||||
|
#endif
|
||||||
|
|
||||||
|
#include "../include/sparsemap.h"
|
||||||
#include "common.h"
|
#include "common.h"
|
||||||
|
|
||||||
#pragma GCC diagnostic push
|
#pragma GCC diagnostic push
|
||||||
|
@ -22,84 +29,25 @@
|
||||||
uint64_t
|
uint64_t
|
||||||
tsc(void)
|
tsc(void)
|
||||||
{
|
{
|
||||||
|
#ifdef X86_INTRIN
|
||||||
|
return __rdtsc();
|
||||||
|
#else
|
||||||
uint32_t low, high;
|
uint32_t low, high;
|
||||||
__asm__ volatile("rdtsc" : "=a"(low), "=d"(high));
|
__asm__ volatile("rdtsc" : "=a"(low), "=d"(high));
|
||||||
return ((uint64_t)high << 32) | low;
|
return ((uint64_t)high << 32) | low;
|
||||||
}
|
#endif
|
||||||
|
|
||||||
static uint64_t
|
|
||||||
get_tsc_frequency()
|
|
||||||
{
|
|
||||||
uint32_t high, low;
|
|
||||||
__asm__ volatile("rdtsc" : "=a"(low), "=d"(high));
|
|
||||||
__asm__ volatile("rdtsc");
|
|
||||||
return ((uint64_t)high << 32) | low;
|
|
||||||
}
|
}
|
||||||
|
|
||||||
double
|
double
|
||||||
tsc_ticks_to_ns(uint64_t tsc_ticks)
|
nsts()
|
||||||
{
|
{
|
||||||
static uint64_t tsc_freq = 0;
|
struct timespec ts;
|
||||||
if (tsc_freq == 0) {
|
|
||||||
tsc_freq = get_tsc_frequency();
|
|
||||||
}
|
|
||||||
return (double)tsc_ticks / (double)tsc_freq * 1e9;
|
|
||||||
}
|
|
||||||
|
|
||||||
void
|
if (clock_gettime(CLOCK_REALTIME, &ts) == -1) {
|
||||||
est_sift_up(uint64_t *heap, int child_index)
|
perror("clock_gettime");
|
||||||
{
|
return -1.0; // Return -1.0 on error
|
||||||
while (child_index > 0) {
|
|
||||||
int parent_index = (child_index - 1) / 2;
|
|
||||||
if (heap[parent_index] > heap[child_index]) {
|
|
||||||
// Swap parent and child
|
|
||||||
uint64_t temp = heap[parent_index];
|
|
||||||
heap[parent_index] = heap[child_index];
|
|
||||||
heap[child_index] = temp;
|
|
||||||
child_index = parent_index;
|
|
||||||
} else {
|
|
||||||
break; // Heap property satisfied
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void
|
|
||||||
est_sift_down(uint64_t *heap, int heap_size, int parent_index)
|
|
||||||
{
|
|
||||||
int child_index = 2 * parent_index + 1; // Left child
|
|
||||||
while (child_index < heap_size) {
|
|
||||||
// Right child exists and is smaller than left child
|
|
||||||
if (child_index + 1 < heap_size && heap[child_index + 1] < heap[child_index]) {
|
|
||||||
child_index++;
|
|
||||||
}
|
|
||||||
// If the smallest child is smaller than the parent, swap them
|
|
||||||
if (heap[child_index] < heap[parent_index]) {
|
|
||||||
uint64_t temp = heap[child_index];
|
|
||||||
heap[child_index] = heap[parent_index];
|
|
||||||
heap[parent_index] = temp;
|
|
||||||
parent_index = child_index;
|
|
||||||
child_index = 2 * parent_index + 1;
|
|
||||||
} else {
|
|
||||||
break; // Heap property satisfied
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void
|
|
||||||
est_insert_value(uint64_t *heap, int heap_max_size, int *heap_size, uint64_t value)
|
|
||||||
{
|
|
||||||
if (*heap_size < heap_max_size) { // Heap not full, insert value
|
|
||||||
heap[*heap_size] = value;
|
|
||||||
est_sift_up(heap, *heap_size);
|
|
||||||
(*heap_size)++;
|
|
||||||
} else {
|
|
||||||
// Heap is full, replace root with new value with a certain probability
|
|
||||||
// This is a very naive approach to maintain a sample of the input
|
|
||||||
if (rand() % 2) {
|
|
||||||
heap[0] = value;
|
|
||||||
est_sift_down(heap, heap_max_size, 0);
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
return ts.tv_sec + ts.tv_nsec / 1e9;
|
||||||
}
|
}
|
||||||
|
|
||||||
int __xorshift32_state = 0;
|
int __xorshift32_state = 0;
|
||||||
|
@ -170,7 +118,7 @@ has_sequential_set(int a[], int l, int r)
|
||||||
int
|
int
|
||||||
ensure_sequential_set(int a[], int l, int r)
|
ensure_sequential_set(int a[], int l, int r)
|
||||||
{
|
{
|
||||||
if (!a || l == 0 || r < 1 || r > l) {
|
if (!a || l == 0 || r < 1 || r > l - 1) {
|
||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -199,21 +147,6 @@ ensure_sequential_set(int a[], int l, int r)
|
||||||
return value;
|
return value;
|
||||||
}
|
}
|
||||||
|
|
||||||
int
|
|
||||||
create_sequential_set_in_empty_map(sparsemap_t *map, int s, int r)
|
|
||||||
{
|
|
||||||
int placed_at;
|
|
||||||
if (s >= r + 1) {
|
|
||||||
placed_at = 0;
|
|
||||||
} else {
|
|
||||||
placed_at = random_uint32() % (s - r - 1);
|
|
||||||
}
|
|
||||||
for (int i = placed_at; i < placed_at + r; i++) {
|
|
||||||
sparsemap_set(map, i, true);
|
|
||||||
}
|
|
||||||
return placed_at;
|
|
||||||
}
|
|
||||||
|
|
||||||
void
|
void
|
||||||
print_array(int *array, int l)
|
print_array(int *array, int l)
|
||||||
{
|
{
|
||||||
|
@ -340,6 +273,20 @@ is_unique(int a[], int l, int value)
|
||||||
return 1; // Unique
|
return 1; // Unique
|
||||||
}
|
}
|
||||||
|
|
||||||
|
int
|
||||||
|
whats_set_uint64(uint64_t number, int pos[64])
|
||||||
|
{
|
||||||
|
int length = 0;
|
||||||
|
|
||||||
|
for (int i = 0; i < 64; i++) {
|
||||||
|
if (number & ((uint64_t)1 << i)) {
|
||||||
|
pos[length++] = i;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return length;
|
||||||
|
}
|
||||||
|
|
||||||
void
|
void
|
||||||
setup_test_array(int a[], int l, int max_value)
|
setup_test_array(int a[], int l, int max_value)
|
||||||
{
|
{
|
||||||
|
@ -364,15 +311,6 @@ bitmap_from_uint32(sparsemap_t *map, uint32_t number)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
void
|
|
||||||
bitmap_from_uint64(sparsemap_t *map, uint64_t number)
|
|
||||||
{
|
|
||||||
for (int i = 0; i < 64; i++) {
|
|
||||||
bool bit = number & (1 << i);
|
|
||||||
sparsemap_set(map, i, bit);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
uint32_t
|
uint32_t
|
||||||
rank_uint64(uint64_t number, int n, int p)
|
rank_uint64(uint64_t number, int n, int p)
|
||||||
{
|
{
|
||||||
|
@ -400,22 +338,53 @@ rank_uint64(uint64_t number, int n, int p)
|
||||||
return count;
|
return count;
|
||||||
}
|
}
|
||||||
|
|
||||||
int
|
void
|
||||||
whats_set_uint64(uint64_t number, int pos[64])
|
print_bits(char *name, uint64_t value)
|
||||||
{
|
{
|
||||||
int length = 0;
|
if (name) {
|
||||||
|
printf("%s\t", name);
|
||||||
for (int i = 0; i < 64; i++) {
|
}
|
||||||
if (number & ((uint64_t)1 << i)) {
|
for (int i = 63; i >= 0; i--) {
|
||||||
pos[length++] = i;
|
printf("%ld", (value >> i) & 1);
|
||||||
|
if (i % 8 == 0) {
|
||||||
|
printf(" "); // Add space for better readability
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
printf("\n");
|
||||||
return length;
|
|
||||||
}
|
}
|
||||||
|
|
||||||
void
|
void
|
||||||
whats_set(sparsemap_t *map, int m)
|
sm_bitmap_from_uint64(sparsemap_t *map, uint64_t number)
|
||||||
|
{
|
||||||
|
for (int i = 0; i < 64; i++) {
|
||||||
|
bool bit = number & ((uint64_t)1 << i);
|
||||||
|
sparsemap_set(map, i, bit);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
sparsemap_idx_t
|
||||||
|
sm_add_span(sparsemap_t *map, int map_size, int span_length)
|
||||||
|
{
|
||||||
|
int attempts = map_size / span_length;
|
||||||
|
sparsemap_idx_t placed_at;
|
||||||
|
do {
|
||||||
|
placed_at = random_uint32() % (map_size - span_length - 1);
|
||||||
|
if (sm_occupied(map, placed_at, span_length, true)) {
|
||||||
|
attempts--;
|
||||||
|
} else {
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
} while (attempts);
|
||||||
|
for (int i = placed_at; i < placed_at + span_length; i++) {
|
||||||
|
if (sparsemap_set(map, i, true) != i) {
|
||||||
|
return placed_at; // TODO error?
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return placed_at;
|
||||||
|
}
|
||||||
|
|
||||||
|
void
|
||||||
|
sm_whats_set(sparsemap_t *map, int m)
|
||||||
{
|
{
|
||||||
logf("what's set in the range [0, %d): ", m);
|
logf("what's set in the range [0, %d): ", m);
|
||||||
for (int i = 0; i < m; i++) {
|
for (int i = 0; i < m; i++) {
|
||||||
|
@ -425,3 +394,25 @@ whats_set(sparsemap_t *map, int m)
|
||||||
}
|
}
|
||||||
logf("\n");
|
logf("\n");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
bool
|
||||||
|
sm_is_span(sparsemap_t *map, sparsemap_idx_t m, int len, bool value)
|
||||||
|
{
|
||||||
|
for (sparsemap_idx_t i = m; i < m + len; i++) {
|
||||||
|
if (sparsemap_is_set(map, i) != value) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
|
||||||
|
bool
|
||||||
|
sm_occupied(sparsemap_t *map, sparsemap_idx_t m, int len, bool value)
|
||||||
|
{
|
||||||
|
for (sparsemap_idx_t i = m; i < (sparsemap_idx_t)len; i++) {
|
||||||
|
if (sparsemap_is_set(map, i) == value) {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
|
@ -23,20 +23,9 @@
|
||||||
#define XORSHIFT_SEED_VALUE ((unsigned int)time(NULL) ^ getpid())
|
#define XORSHIFT_SEED_VALUE ((unsigned int)time(NULL) ^ getpid())
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
#define EST_MEDIAN_DECL(decl, size) \
|
|
||||||
uint64_t heap_##decl[size] = { 0 }; \
|
|
||||||
int heap_##decl##_max_size = size; \
|
|
||||||
int heap_##decl##_size = 0;
|
|
||||||
|
|
||||||
#define EST_MEDIAN_ADD(decl, value) est_insert_value(heap_##decl, heap_##decl##_max_size, &heap_##decl##_size, (value));
|
|
||||||
|
|
||||||
#define EST_MEDIAN_GET(decl) heap_##decl[0]
|
|
||||||
|
|
||||||
uint64_t tsc(void);
|
uint64_t tsc(void);
|
||||||
double tsc_ticks_to_ns(uint64_t tsc_ticks);
|
double tsc_ticks_to_ns(uint64_t tsc_ticks);
|
||||||
void est_sift_up(uint64_t *heap, int child_index);
|
double nsts();
|
||||||
void est_sift_down(uint64_t *heap, int heap_size, int parent_index);
|
|
||||||
void est_insert_value(uint64_t *heap, int heap_max_size, int *heap_size, uint64_t value);
|
|
||||||
|
|
||||||
void xorshift32_seed();
|
void xorshift32_seed();
|
||||||
uint32_t xorshift32();
|
uint32_t xorshift32();
|
||||||
|
@ -52,11 +41,16 @@ int is_unique(int a[], int l, int value);
|
||||||
void setup_test_array(int a[], int l, int max_value);
|
void setup_test_array(int a[], int l, int max_value);
|
||||||
void shuffle(int *array, size_t n);
|
void shuffle(int *array, size_t n);
|
||||||
int ensure_sequential_set(int a[], int l, int r);
|
int ensure_sequential_set(int a[], int l, int r);
|
||||||
int create_sequential_set_in_empty_map(sparsemap_t *map, int s, int r);
|
sparsemap_idx_t sm_add_span(sparsemap_t *map, int map_size, int span_length);
|
||||||
|
|
||||||
|
void print_bits(char *name, uint64_t value);
|
||||||
|
|
||||||
void bitmap_from_uint32(sparsemap_t *map, uint32_t number);
|
void bitmap_from_uint32(sparsemap_t *map, uint32_t number);
|
||||||
void bitmap_from_uint64(sparsemap_t *map, uint64_t number);
|
void sm_bitmap_from_uint64(sparsemap_t *map, uint64_t number);
|
||||||
uint32_t rank_uint64(uint64_t number, int n, int p);
|
uint32_t rank_uint64(uint64_t number, int n, int p);
|
||||||
int whats_set_uint64(uint64_t number, int bitPositions[64]);
|
int whats_set_uint64(uint64_t number, int bitPositions[64]);
|
||||||
|
|
||||||
void whats_set(sparsemap_t *map, int m);
|
void sm_whats_set(sparsemap_t *map, int m);
|
||||||
|
|
||||||
|
bool sm_is_span(sparsemap_t *map, sparsemap_idx_t m, int len, bool value);
|
||||||
|
bool sm_occupied(sparsemap_t *map, sparsemap_idx_t m, int len, bool value);
|
||||||
|
|
680
tests/tdigest.c
Normal file
680
tests/tdigest.c
Normal file
|
@ -0,0 +1,680 @@
|
||||||
|
#include <stdlib.h>
|
||||||
|
#include <stdbool.h>
|
||||||
|
#include <string.h>
|
||||||
|
#include <math.h>
|
||||||
|
#include "tdigest.h"
|
||||||
|
#include <errno.h>
|
||||||
|
#include <stdint.h>
|
||||||
|
|
||||||
|
#ifndef TD_MALLOC_INCLUDE
|
||||||
|
#define TD_MALLOC_INCLUDE "td_malloc.h"
|
||||||
|
#endif
|
||||||
|
|
||||||
|
#ifndef TD_ALLOC_H
|
||||||
|
#define TD_ALLOC_H
|
||||||
|
#define __td_malloc malloc
|
||||||
|
#define __td_calloc calloc
|
||||||
|
#define __td_realloc realloc
|
||||||
|
#define __td_free free
|
||||||
|
#endif
|
||||||
|
|
||||||
|
#define __td_max(x, y) (((x) > (y)) ? (x) : (y))
|
||||||
|
#define __td_min(x, y) (((x) < (y)) ? (x) : (y))
|
||||||
|
|
||||||
|
static inline double weighted_average_sorted(double x1, double w1, double x2, double w2) {
|
||||||
|
const double x = (x1 * w1 + x2 * w2) / (w1 + w2);
|
||||||
|
return __td_max(x1, __td_min(x, x2));
|
||||||
|
}
|
||||||
|
|
||||||
|
static inline bool _tdigest_long_long_add_safe(long long a, long long b) {
|
||||||
|
if (b < 0) {
|
||||||
|
return (a >= __LONG_LONG_MAX__ - b);
|
||||||
|
} else {
|
||||||
|
return (a <= __LONG_LONG_MAX__ - b);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
static inline double weighted_average(double x1, double w1, double x2, double w2) {
|
||||||
|
if (x1 <= x2) {
|
||||||
|
return weighted_average_sorted(x1, w1, x2, w2);
|
||||||
|
} else {
|
||||||
|
return weighted_average_sorted(x2, w2, x1, w1);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
static inline void swap(double *arr, int i, int j) {
|
||||||
|
const double temp = arr[i];
|
||||||
|
arr[i] = arr[j];
|
||||||
|
arr[j] = temp;
|
||||||
|
}
|
||||||
|
|
||||||
|
static inline void swap_l(long long *arr, int i, int j) {
|
||||||
|
const long long temp = arr[i];
|
||||||
|
arr[i] = arr[j];
|
||||||
|
arr[j] = temp;
|
||||||
|
}
|
||||||
|
|
||||||
|
static unsigned int partition(double *means, long long *weights, unsigned int start,
|
||||||
|
unsigned int end, unsigned int pivot_idx) {
|
||||||
|
const double pivotMean = means[pivot_idx];
|
||||||
|
swap(means, pivot_idx, end);
|
||||||
|
swap_l(weights, pivot_idx, end);
|
||||||
|
|
||||||
|
int i = start - 1;
|
||||||
|
|
||||||
|
for (unsigned int j = start; j < end; j++) {
|
||||||
|
// If current element is smaller than the pivot
|
||||||
|
if (means[j] < pivotMean) {
|
||||||
|
// increment index of smaller element
|
||||||
|
i++;
|
||||||
|
swap(means, i, j);
|
||||||
|
swap_l(weights, i, j);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
swap(means, i + 1, end);
|
||||||
|
swap_l(weights, i + 1, end);
|
||||||
|
return i + 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Standard quick sort except that sorting rearranges parallel arrays
|
||||||
|
*
|
||||||
|
* @param means Values to sort on
|
||||||
|
* @param weights The auxillary values to sort.
|
||||||
|
* @param start The beginning of the values to sort
|
||||||
|
* @param end The value after the last value to sort
|
||||||
|
*/
|
||||||
|
static void td_qsort(double *means, long long *weights, unsigned int start, unsigned int end) {
|
||||||
|
if (start < end) {
|
||||||
|
// two elements can be directly compared
|
||||||
|
if ((end - start) == 1) {
|
||||||
|
if (means[start] > means[end]) {
|
||||||
|
swap(means, start, end);
|
||||||
|
swap_l(weights, start, end);
|
||||||
|
}
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
// generating a random number as a pivot was very expensive vs the array size
|
||||||
|
// const unsigned int pivot_idx = start + rand()%(end - start + 1);
|
||||||
|
const unsigned int pivot_idx = (end + start) / 2; // central pivot
|
||||||
|
const unsigned int new_pivot_idx = partition(means, weights, start, end, pivot_idx);
|
||||||
|
if (new_pivot_idx > start) {
|
||||||
|
td_qsort(means, weights, start, new_pivot_idx - 1);
|
||||||
|
}
|
||||||
|
td_qsort(means, weights, new_pivot_idx + 1, end);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
static inline size_t cap_from_compression(double compression) {
|
||||||
|
if ((size_t)compression > ((SIZE_MAX / sizeof(double) / 6) - 10)) {
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
return (6 * (size_t)(compression)) + 10;
|
||||||
|
}
|
||||||
|
|
||||||
|
static inline bool should_td_compress(td_histogram_t *h) {
|
||||||
|
return ((h->merged_nodes + h->unmerged_nodes) >= (h->cap - 1));
|
||||||
|
}
|
||||||
|
|
||||||
|
static inline int next_node(td_histogram_t *h) { return h->merged_nodes + h->unmerged_nodes; }
|
||||||
|
|
||||||
|
int td_compress(td_histogram_t *h);
|
||||||
|
|
||||||
|
static inline int _check_overflow(const double v) {
|
||||||
|
// double-precision overflow detected on h->unmerged_weight
|
||||||
|
if (v == INFINITY) {
|
||||||
|
return EDOM;
|
||||||
|
}
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
static inline int _check_td_overflow(const double new_unmerged_weight,
|
||||||
|
const double new_total_weight) {
|
||||||
|
// double-precision overflow detected on h->unmerged_weight
|
||||||
|
if (new_unmerged_weight == INFINITY) {
|
||||||
|
return EDOM;
|
||||||
|
}
|
||||||
|
if (new_total_weight == INFINITY) {
|
||||||
|
return EDOM;
|
||||||
|
}
|
||||||
|
const double denom = 2 * MM_PI * new_total_weight * log(new_total_weight);
|
||||||
|
if (denom == INFINITY) {
|
||||||
|
return EDOM;
|
||||||
|
}
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
int td_centroid_count(td_histogram_t *h) { return next_node(h); }
|
||||||
|
|
||||||
|
void td_reset(td_histogram_t *h) {
|
||||||
|
if (!h) {
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
h->min = __DBL_MAX__;
|
||||||
|
h->max = -h->min;
|
||||||
|
h->merged_nodes = 0;
|
||||||
|
h->merged_weight = 0;
|
||||||
|
h->unmerged_nodes = 0;
|
||||||
|
h->unmerged_weight = 0;
|
||||||
|
h->total_compressions = 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
int td_init(double compression, td_histogram_t **result) {
|
||||||
|
|
||||||
|
const size_t capacity = cap_from_compression(compression);
|
||||||
|
if (capacity < 1) {
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
td_histogram_t *histogram;
|
||||||
|
histogram = (td_histogram_t *)__td_malloc(sizeof(td_histogram_t));
|
||||||
|
if (!histogram) {
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
histogram->cap = capacity;
|
||||||
|
histogram->compression = (double)compression;
|
||||||
|
td_reset(histogram);
|
||||||
|
histogram->nodes_mean = (double *)__td_calloc(capacity, sizeof(double));
|
||||||
|
if (!histogram->nodes_mean) {
|
||||||
|
td_free(histogram);
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
histogram->nodes_weight = (long long *)__td_calloc(capacity, sizeof(long long));
|
||||||
|
if (!histogram->nodes_weight) {
|
||||||
|
td_free(histogram);
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
*result = histogram;
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
td_histogram_t *td_new(double compression) {
|
||||||
|
td_histogram_t *mdigest = NULL;
|
||||||
|
td_init(compression, &mdigest);
|
||||||
|
return mdigest;
|
||||||
|
}
|
||||||
|
|
||||||
|
void td_free(td_histogram_t *histogram) {
|
||||||
|
if (histogram->nodes_mean) {
|
||||||
|
__td_free((void *)(histogram->nodes_mean));
|
||||||
|
}
|
||||||
|
if (histogram->nodes_weight) {
|
||||||
|
__td_free((void *)(histogram->nodes_weight));
|
||||||
|
}
|
||||||
|
__td_free((void *)(histogram));
|
||||||
|
}
|
||||||
|
|
||||||
|
int td_merge(td_histogram_t *into, td_histogram_t *from) {
|
||||||
|
if (td_compress(into) != 0)
|
||||||
|
return EDOM;
|
||||||
|
if (td_compress(from) != 0)
|
||||||
|
return EDOM;
|
||||||
|
const int pos = from->merged_nodes + from->unmerged_nodes;
|
||||||
|
for (int i = 0; i < pos; i++) {
|
||||||
|
const double mean = from->nodes_mean[i];
|
||||||
|
const long long weight = from->nodes_weight[i];
|
||||||
|
if (td_add(into, mean, weight) != 0) {
|
||||||
|
return EDOM;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
long long td_size(td_histogram_t *h) { return h->merged_weight + h->unmerged_weight; }
|
||||||
|
|
||||||
|
double td_cdf(td_histogram_t *h, double val) {
|
||||||
|
td_compress(h);
|
||||||
|
// no data to examine
|
||||||
|
if (h->merged_nodes == 0) {
|
||||||
|
return NAN;
|
||||||
|
}
|
||||||
|
// bellow lower bound
|
||||||
|
if (val < h->min) {
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
// above upper bound
|
||||||
|
if (val > h->max) {
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
if (h->merged_nodes == 1) {
|
||||||
|
// exactly one centroid, should have max==min
|
||||||
|
const double width = h->max - h->min;
|
||||||
|
if (val - h->min <= width) {
|
||||||
|
// min and max are too close together to do any viable interpolation
|
||||||
|
return 0.5;
|
||||||
|
} else {
|
||||||
|
// interpolate if somehow we have weight > 0 and max != min
|
||||||
|
return (val - h->min) / width;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
const int n = h->merged_nodes;
|
||||||
|
// check for the left tail
|
||||||
|
const double left_centroid_mean = h->nodes_mean[0];
|
||||||
|
const double left_centroid_weight = (double)h->nodes_weight[0];
|
||||||
|
const double merged_weight_d = (double)h->merged_weight;
|
||||||
|
if (val < left_centroid_mean) {
|
||||||
|
// note that this is different than h->nodes_mean[0] > min
|
||||||
|
// ... this guarantees we divide by non-zero number and interpolation works
|
||||||
|
const double width = left_centroid_mean - h->min;
|
||||||
|
if (width > 0) {
|
||||||
|
// must be a sample exactly at min
|
||||||
|
if (val == h->min) {
|
||||||
|
return 0.5 / merged_weight_d;
|
||||||
|
} else {
|
||||||
|
return (1 + (val - h->min) / width * (left_centroid_weight / 2 - 1)) /
|
||||||
|
merged_weight_d;
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
// this should be redundant with the check val < h->min
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
// and the right tail
|
||||||
|
const double right_centroid_mean = h->nodes_mean[n - 1];
|
||||||
|
const double right_centroid_weight = (double)h->nodes_weight[n - 1];
|
||||||
|
if (val > right_centroid_mean) {
|
||||||
|
const double width = h->max - right_centroid_mean;
|
||||||
|
if (width > 0) {
|
||||||
|
if (val == h->max) {
|
||||||
|
return 1 - 0.5 / merged_weight_d;
|
||||||
|
} else {
|
||||||
|
// there has to be a single sample exactly at max
|
||||||
|
const double dq = (1 + (h->max - val) / width * (right_centroid_weight / 2 - 1)) /
|
||||||
|
merged_weight_d;
|
||||||
|
return 1 - dq;
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
// we know that there are at least two centroids and mean[0] < x < mean[n-1]
|
||||||
|
// that means that there are either one or more consecutive centroids all at exactly x
|
||||||
|
// or there are consecutive centroids, c0 < x < c1
|
||||||
|
double weightSoFar = 0;
|
||||||
|
for (int it = 0; it < n - 1; it++) {
|
||||||
|
// weightSoFar does not include weight[it] yet
|
||||||
|
if (h->nodes_mean[it] == val) {
|
||||||
|
// we have one or more centroids == x, treat them as one
|
||||||
|
// dw will accumulate the weight of all of the centroids at x
|
||||||
|
double dw = 0;
|
||||||
|
while (it < n && h->nodes_mean[it] == val) {
|
||||||
|
dw += (double)h->nodes_weight[it];
|
||||||
|
it++;
|
||||||
|
}
|
||||||
|
return (weightSoFar + dw / 2) / (double)h->merged_weight;
|
||||||
|
} else if (h->nodes_mean[it] <= val && val < h->nodes_mean[it + 1]) {
|
||||||
|
const double node_weight = (double)h->nodes_weight[it];
|
||||||
|
const double node_weight_next = (double)h->nodes_weight[it + 1];
|
||||||
|
const double node_mean = h->nodes_mean[it];
|
||||||
|
const double node_mean_next = h->nodes_mean[it + 1];
|
||||||
|
// landed between centroids ... check for floating point madness
|
||||||
|
if (node_mean_next - node_mean > 0) {
|
||||||
|
// note how we handle singleton centroids here
|
||||||
|
// the point is that for singleton centroids, we know that their entire
|
||||||
|
// weight is exactly at the centroid and thus shouldn't be involved in
|
||||||
|
// interpolation
|
||||||
|
double leftExcludedW = 0;
|
||||||
|
double rightExcludedW = 0;
|
||||||
|
if (node_weight == 1) {
|
||||||
|
if (node_weight_next == 1) {
|
||||||
|
// two singletons means no interpolation
|
||||||
|
// left singleton is in, right is out
|
||||||
|
return (weightSoFar + 1) / merged_weight_d;
|
||||||
|
} else {
|
||||||
|
leftExcludedW = 0.5;
|
||||||
|
}
|
||||||
|
} else if (node_weight_next == 1) {
|
||||||
|
rightExcludedW = 0.5;
|
||||||
|
}
|
||||||
|
double dw = (node_weight + node_weight_next) / 2;
|
||||||
|
|
||||||
|
// adjust endpoints for any singleton
|
||||||
|
double dwNoSingleton = dw - leftExcludedW - rightExcludedW;
|
||||||
|
|
||||||
|
double base = weightSoFar + node_weight / 2 + leftExcludedW;
|
||||||
|
return (base + dwNoSingleton * (val - node_mean) / (node_mean_next - node_mean)) /
|
||||||
|
merged_weight_d;
|
||||||
|
} else {
|
||||||
|
// this is simply caution against floating point madness
|
||||||
|
// it is conceivable that the centroids will be different
|
||||||
|
// but too near to allow safe interpolation
|
||||||
|
double dw = (node_weight + node_weight_next) / 2;
|
||||||
|
return (weightSoFar + dw) / merged_weight_d;
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
weightSoFar += (double)h->nodes_weight[it];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return 1 - 0.5 / merged_weight_d;
|
||||||
|
}
|
||||||
|
|
||||||
|
static double td_internal_iterate_centroids_to_index(const td_histogram_t *h, const double index,
|
||||||
|
const double left_centroid_weight,
|
||||||
|
const int total_centroids, double *weightSoFar,
|
||||||
|
int *node_pos) {
|
||||||
|
if (left_centroid_weight > 1 && index < left_centroid_weight / 2) {
|
||||||
|
// there is a single sample at min so we interpolate with less weight
|
||||||
|
return h->min + (index - 1) / (left_centroid_weight / 2 - 1) * (h->nodes_mean[0] - h->min);
|
||||||
|
}
|
||||||
|
|
||||||
|
// usually the last centroid will have unit weight so this test will make it moot
|
||||||
|
if (index > h->merged_weight - 1) {
|
||||||
|
return h->max;
|
||||||
|
}
|
||||||
|
|
||||||
|
// if the right-most centroid has more than one sample, we still know
|
||||||
|
// that one sample occurred at max so we can do some interpolation
|
||||||
|
const double right_centroid_weight = (double)h->nodes_weight[total_centroids - 1];
|
||||||
|
const double right_centroid_mean = h->nodes_mean[total_centroids - 1];
|
||||||
|
if (right_centroid_weight > 1 &&
|
||||||
|
(double)h->merged_weight - index <= right_centroid_weight / 2) {
|
||||||
|
return h->max - ((double)h->merged_weight - index - 1) / (right_centroid_weight / 2 - 1) *
|
||||||
|
(h->max - right_centroid_mean);
|
||||||
|
}
|
||||||
|
|
||||||
|
for (; *node_pos < total_centroids - 1; (*node_pos)++) {
|
||||||
|
const int i = *node_pos;
|
||||||
|
const double node_weight = (double)h->nodes_weight[i];
|
||||||
|
const double node_weight_next = (double)h->nodes_weight[i + 1];
|
||||||
|
const double node_mean = h->nodes_mean[i];
|
||||||
|
const double node_mean_next = h->nodes_mean[i + 1];
|
||||||
|
const double dw = (node_weight + node_weight_next) / 2;
|
||||||
|
if (*weightSoFar + dw > index) {
|
||||||
|
// centroids i and i+1 bracket our current point
|
||||||
|
// check for unit weight
|
||||||
|
double leftUnit = 0;
|
||||||
|
if (node_weight == 1) {
|
||||||
|
if (index - *weightSoFar < 0.5) {
|
||||||
|
// within the singleton's sphere
|
||||||
|
return node_mean;
|
||||||
|
} else {
|
||||||
|
leftUnit = 0.5;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
double rightUnit = 0;
|
||||||
|
if (node_weight_next == 1) {
|
||||||
|
if (*weightSoFar + dw - index <= 0.5) {
|
||||||
|
// no interpolation needed near singleton
|
||||||
|
return node_mean_next;
|
||||||
|
}
|
||||||
|
rightUnit = 0.5;
|
||||||
|
}
|
||||||
|
const double z1 = index - *weightSoFar - leftUnit;
|
||||||
|
const double z2 = *weightSoFar + dw - index - rightUnit;
|
||||||
|
return weighted_average(node_mean, z2, node_mean_next, z1);
|
||||||
|
}
|
||||||
|
*weightSoFar += dw;
|
||||||
|
}
|
||||||
|
|
||||||
|
// weightSoFar = totalWeight - weight[total_centroids-1]/2 (very nearly)
|
||||||
|
// so we interpolate out to max value ever seen
|
||||||
|
const double z1 = index - h->merged_weight - right_centroid_weight / 2.0;
|
||||||
|
const double z2 = right_centroid_weight / 2 - z1;
|
||||||
|
return weighted_average(right_centroid_mean, z1, h->max, z2);
|
||||||
|
}
|
||||||
|
|
||||||
|
double td_quantile(td_histogram_t *h, double q) {
|
||||||
|
td_compress(h);
|
||||||
|
// q should be in [0,1]
|
||||||
|
if (q < 0.0 || q > 1.0 || h->merged_nodes == 0) {
|
||||||
|
return NAN;
|
||||||
|
}
|
||||||
|
// with one data point, all quantiles lead to Rome
|
||||||
|
if (h->merged_nodes == 1) {
|
||||||
|
return h->nodes_mean[0];
|
||||||
|
}
|
||||||
|
|
||||||
|
// if values were stored in a sorted array, index would be the offset we are interested in
|
||||||
|
const double index = q * (double)h->merged_weight;
|
||||||
|
|
||||||
|
// beyond the boundaries, we return min or max
|
||||||
|
// usually, the first centroid will have unit weight so this will make it moot
|
||||||
|
if (index < 1) {
|
||||||
|
return h->min;
|
||||||
|
}
|
||||||
|
|
||||||
|
// we know that there are at least two centroids now
|
||||||
|
const int n = h->merged_nodes;
|
||||||
|
|
||||||
|
// if the left centroid has more than one sample, we still know
|
||||||
|
// that one sample occurred at min so we can do some interpolation
|
||||||
|
const double left_centroid_weight = (double)h->nodes_weight[0];
|
||||||
|
|
||||||
|
// in between extremes we interpolate between centroids
|
||||||
|
double weightSoFar = left_centroid_weight / 2;
|
||||||
|
int i = 0;
|
||||||
|
return td_internal_iterate_centroids_to_index(h, index, left_centroid_weight, n, &weightSoFar,
|
||||||
|
&i);
|
||||||
|
}
|
||||||
|
|
||||||
|
int td_quantiles(td_histogram_t *h, const double *quantiles, double *values, size_t length) {
|
||||||
|
td_compress(h);
|
||||||
|
|
||||||
|
if (NULL == quantiles || NULL == values) {
|
||||||
|
return EINVAL;
|
||||||
|
}
|
||||||
|
|
||||||
|
const int n = h->merged_nodes;
|
||||||
|
if (n == 0) {
|
||||||
|
for (size_t i = 0; i < length; i++) {
|
||||||
|
values[i] = NAN;
|
||||||
|
}
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
if (n == 1) {
|
||||||
|
for (size_t i = 0; i < length; i++) {
|
||||||
|
const double requested_quantile = quantiles[i];
|
||||||
|
|
||||||
|
// q should be in [0,1]
|
||||||
|
if (requested_quantile < 0.0 || requested_quantile > 1.0) {
|
||||||
|
values[i] = NAN;
|
||||||
|
} else {
|
||||||
|
// with one data point, all quantiles lead to Rome
|
||||||
|
values[i] = h->nodes_mean[0];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
// we know that there are at least two centroids now
|
||||||
|
// if the left centroid has more than one sample, we still know
|
||||||
|
// that one sample occurred at min so we can do some interpolation
|
||||||
|
const double left_centroid_weight = (double)h->nodes_weight[0];
|
||||||
|
|
||||||
|
// in between extremes we interpolate between centroids
|
||||||
|
double weightSoFar = left_centroid_weight / 2;
|
||||||
|
int node_pos = 0;
|
||||||
|
|
||||||
|
// to avoid allocations we use the values array for intermediate computation
|
||||||
|
// i.e. to store the expected cumulative count at each percentile
|
||||||
|
for (size_t qpos = 0; qpos < length; qpos++) {
|
||||||
|
const double index = quantiles[qpos] * (double)h->merged_weight;
|
||||||
|
values[qpos] = td_internal_iterate_centroids_to_index(h, index, left_centroid_weight, n,
|
||||||
|
&weightSoFar, &node_pos);
|
||||||
|
}
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
static double td_internal_trimmed_mean(const td_histogram_t *h, const double leftmost_weight,
|
||||||
|
const double rightmost_weight) {
|
||||||
|
double count_done = 0;
|
||||||
|
double trimmed_sum = 0;
|
||||||
|
double trimmed_count = 0;
|
||||||
|
for (int i = 0; i < h->merged_nodes; i++) {
|
||||||
|
|
||||||
|
const double n_weight = (double)h->nodes_weight[i];
|
||||||
|
// Assume the whole centroid falls into the range
|
||||||
|
double count_add = n_weight;
|
||||||
|
|
||||||
|
// If we haven't reached the low threshold yet, skip appropriate part of the centroid.
|
||||||
|
count_add -= __td_min(__td_max(0, leftmost_weight - count_done), count_add);
|
||||||
|
|
||||||
|
// If we have reached the upper threshold, ignore the overflowing part of the centroid.
|
||||||
|
|
||||||
|
count_add = __td_min(__td_max(0, rightmost_weight - count_done), count_add);
|
||||||
|
|
||||||
|
// consider the whole centroid processed
|
||||||
|
count_done += n_weight;
|
||||||
|
|
||||||
|
// increment the sum / count
|
||||||
|
trimmed_sum += h->nodes_mean[i] * count_add;
|
||||||
|
trimmed_count += count_add;
|
||||||
|
|
||||||
|
// break once we cross the high threshold
|
||||||
|
if (count_done >= rightmost_weight)
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
|
||||||
|
return trimmed_sum / trimmed_count;
|
||||||
|
}
|
||||||
|
|
||||||
|
double td_trimmed_mean_symmetric(td_histogram_t *h, double proportion_to_cut) {
|
||||||
|
td_compress(h);
|
||||||
|
// proportion_to_cut should be in [0,1]
|
||||||
|
if (h->merged_nodes == 0 || proportion_to_cut < 0.0 || proportion_to_cut > 1.0) {
|
||||||
|
return NAN;
|
||||||
|
}
|
||||||
|
// with one data point, all values lead to Rome
|
||||||
|
if (h->merged_nodes == 1) {
|
||||||
|
return h->nodes_mean[0];
|
||||||
|
}
|
||||||
|
|
||||||
|
/* translate the percentiles to counts */
|
||||||
|
const double leftmost_weight = floor((double)h->merged_weight * proportion_to_cut);
|
||||||
|
const double rightmost_weight = ceil((double)h->merged_weight * (1.0 - proportion_to_cut));
|
||||||
|
|
||||||
|
return td_internal_trimmed_mean(h, leftmost_weight, rightmost_weight);
|
||||||
|
}
|
||||||
|
|
||||||
|
double td_trimmed_mean(td_histogram_t *h, double leftmost_cut, double rightmost_cut) {
|
||||||
|
td_compress(h);
|
||||||
|
// leftmost_cut and rightmost_cut should be in [0,1]
|
||||||
|
if (h->merged_nodes == 0 || leftmost_cut < 0.0 || leftmost_cut > 1.0 || rightmost_cut < 0.0 ||
|
||||||
|
rightmost_cut > 1.0) {
|
||||||
|
return NAN;
|
||||||
|
}
|
||||||
|
// with one data point, all values lead to Rome
|
||||||
|
if (h->merged_nodes == 1) {
|
||||||
|
return h->nodes_mean[0];
|
||||||
|
}
|
||||||
|
|
||||||
|
/* translate the percentiles to counts */
|
||||||
|
const double leftmost_weight = floor((double)h->merged_weight * leftmost_cut);
|
||||||
|
const double rightmost_weight = ceil((double)h->merged_weight * rightmost_cut);
|
||||||
|
|
||||||
|
return td_internal_trimmed_mean(h, leftmost_weight, rightmost_weight);
|
||||||
|
}
|
||||||
|
|
||||||
|
int td_add(td_histogram_t *h, double mean, long long weight) {
|
||||||
|
if (should_td_compress(h)) {
|
||||||
|
const int overflow_res = td_compress(h);
|
||||||
|
if (overflow_res != 0)
|
||||||
|
return overflow_res;
|
||||||
|
}
|
||||||
|
const int pos = next_node(h);
|
||||||
|
if (pos >= h->cap)
|
||||||
|
return EDOM;
|
||||||
|
if (_tdigest_long_long_add_safe(h->unmerged_weight, weight) == false)
|
||||||
|
return EDOM;
|
||||||
|
const long long new_unmerged_weight = h->unmerged_weight + weight;
|
||||||
|
if (_tdigest_long_long_add_safe(new_unmerged_weight, h->merged_weight) == false)
|
||||||
|
return EDOM;
|
||||||
|
const long long new_total_weight = new_unmerged_weight + h->merged_weight;
|
||||||
|
// double-precision overflow detected
|
||||||
|
const int overflow_res =
|
||||||
|
_check_td_overflow((double)new_unmerged_weight, (double)new_total_weight);
|
||||||
|
if (overflow_res != 0)
|
||||||
|
return overflow_res;
|
||||||
|
|
||||||
|
if (mean < h->min) {
|
||||||
|
h->min = mean;
|
||||||
|
}
|
||||||
|
if (mean > h->max) {
|
||||||
|
h->max = mean;
|
||||||
|
}
|
||||||
|
h->nodes_mean[pos] = mean;
|
||||||
|
h->nodes_weight[pos] = weight;
|
||||||
|
h->unmerged_nodes++;
|
||||||
|
h->unmerged_weight = new_unmerged_weight;
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
int td_compress(td_histogram_t *h) {
|
||||||
|
if (h->unmerged_nodes == 0) {
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
int N = h->merged_nodes + h->unmerged_nodes;
|
||||||
|
td_qsort(h->nodes_mean, h->nodes_weight, 0, N - 1);
|
||||||
|
const double total_weight = (double)h->merged_weight + (double)h->unmerged_weight;
|
||||||
|
// double-precision overflow detected
|
||||||
|
const int overflow_res = _check_td_overflow((double)h->unmerged_weight, (double)total_weight);
|
||||||
|
if (overflow_res != 0)
|
||||||
|
return overflow_res;
|
||||||
|
if (total_weight <= 1)
|
||||||
|
return 0;
|
||||||
|
const double denom = 2 * MM_PI * total_weight * log(total_weight);
|
||||||
|
if (_check_overflow(denom) != 0)
|
||||||
|
return EDOM;
|
||||||
|
|
||||||
|
// Compute the normalizer given compression and number of points.
|
||||||
|
const double normalizer = h->compression / denom;
|
||||||
|
if (_check_overflow(normalizer) != 0)
|
||||||
|
return EDOM;
|
||||||
|
int cur = 0;
|
||||||
|
double weight_so_far = 0;
|
||||||
|
|
||||||
|
for (int i = 1; i < N; i++) {
|
||||||
|
const double proposed_weight = (double)h->nodes_weight[cur] + (double)h->nodes_weight[i];
|
||||||
|
const double z = proposed_weight * normalizer;
|
||||||
|
// quantile up to cur
|
||||||
|
const double q0 = weight_so_far / total_weight;
|
||||||
|
// quantile up to cur + i
|
||||||
|
const double q2 = (weight_so_far + proposed_weight) / total_weight;
|
||||||
|
// Convert a quantile to the k-scale
|
||||||
|
const bool should_add = (z <= (q0 * (1 - q0))) && (z <= (q2 * (1 - q2)));
|
||||||
|
// next point will fit
|
||||||
|
// so merge into existing centroid
|
||||||
|
if (should_add) {
|
||||||
|
h->nodes_weight[cur] += h->nodes_weight[i];
|
||||||
|
const double delta = h->nodes_mean[i] - h->nodes_mean[cur];
|
||||||
|
const double weighted_delta = (delta * h->nodes_weight[i]) / h->nodes_weight[cur];
|
||||||
|
h->nodes_mean[cur] += weighted_delta;
|
||||||
|
} else {
|
||||||
|
weight_so_far += h->nodes_weight[cur];
|
||||||
|
cur++;
|
||||||
|
h->nodes_weight[cur] = h->nodes_weight[i];
|
||||||
|
h->nodes_mean[cur] = h->nodes_mean[i];
|
||||||
|
}
|
||||||
|
if (cur != i) {
|
||||||
|
h->nodes_weight[i] = 0;
|
||||||
|
h->nodes_mean[i] = 0.0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
h->merged_nodes = cur + 1;
|
||||||
|
h->merged_weight = total_weight;
|
||||||
|
h->unmerged_nodes = 0;
|
||||||
|
h->unmerged_weight = 0;
|
||||||
|
h->total_compressions++;
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
double td_min(td_histogram_t *h) { return h->min; }
|
||||||
|
|
||||||
|
double td_max(td_histogram_t *h) { return h->max; }
|
||||||
|
|
||||||
|
int td_compression(td_histogram_t *h) { return h->compression; }
|
||||||
|
|
||||||
|
const long long *td_centroids_weight(td_histogram_t *h) { return h->nodes_weight; }
|
||||||
|
|
||||||
|
const double *td_centroids_mean(td_histogram_t *h) { return h->nodes_mean; }
|
||||||
|
|
||||||
|
long long td_centroids_weight_at(td_histogram_t *h, int pos) { return h->nodes_weight[pos]; }
|
||||||
|
|
||||||
|
double td_centroids_mean_at(td_histogram_t *h, int pos) {
|
||||||
|
if (pos < 0 || pos > h->merged_nodes) {
|
||||||
|
return NAN;
|
||||||
|
}
|
||||||
|
return h->nodes_mean[pos];
|
||||||
|
}
|
258
tests/tdigest.h
Normal file
258
tests/tdigest.h
Normal file
|
@ -0,0 +1,258 @@
|
||||||
|
#pragma once
|
||||||
|
#include <stdlib.h>
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Adaptive histogram based on something like streaming k-means crossed with Q-digest.
|
||||||
|
* The implementation is a direct descendent of MergingDigest
|
||||||
|
* https://github.com/tdunning/t-digest/
|
||||||
|
*
|
||||||
|
* Copyright (c) 2021 Redis, All rights reserved.
|
||||||
|
* Copyright (c) 2018 Andrew Werner, All rights reserved.
|
||||||
|
*
|
||||||
|
* The special characteristics of this algorithm are:
|
||||||
|
*
|
||||||
|
* - smaller summaries than Q-digest
|
||||||
|
*
|
||||||
|
* - provides part per million accuracy for extreme quantiles and typically <1000 ppm accuracy
|
||||||
|
* for middle quantiles
|
||||||
|
*
|
||||||
|
* - fast
|
||||||
|
*
|
||||||
|
* - simple
|
||||||
|
*
|
||||||
|
* - easy to adapt for use with map-reduce
|
||||||
|
*/
|
||||||
|
|
||||||
|
#define MM_PI 3.14159265358979323846
|
||||||
|
|
||||||
|
struct td_histogram {
|
||||||
|
// compression is a setting used to configure the size of centroids when merged.
|
||||||
|
double compression;
|
||||||
|
|
||||||
|
double min;
|
||||||
|
double max;
|
||||||
|
|
||||||
|
// cap is the total size of nodes
|
||||||
|
int cap;
|
||||||
|
// merged_nodes is the number of merged nodes at the front of nodes.
|
||||||
|
int merged_nodes;
|
||||||
|
// unmerged_nodes is the number of buffered nodes.
|
||||||
|
int unmerged_nodes;
|
||||||
|
|
||||||
|
// we run the merge in reverse every other merge to avoid left-to-right bias in merging
|
||||||
|
long long total_compressions;
|
||||||
|
|
||||||
|
long long merged_weight;
|
||||||
|
long long unmerged_weight;
|
||||||
|
|
||||||
|
double *nodes_mean;
|
||||||
|
long long *nodes_weight;
|
||||||
|
};
|
||||||
|
|
||||||
|
typedef struct td_histogram td_histogram_t;
|
||||||
|
|
||||||
|
#ifdef __cplusplus
|
||||||
|
extern "C" {
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Allocate the memory, initialise the t-digest, and return the histogram as output parameter.
|
||||||
|
* @param compression The compression parameter.
|
||||||
|
* 100 is a common value for normal uses.
|
||||||
|
* 1000 is extremely large.
|
||||||
|
* The number of centroids retained will be a smallish (usually less than 10) multiple of this
|
||||||
|
* number.
|
||||||
|
* @return the histogram on success, NULL if allocation failed.
|
||||||
|
*/
|
||||||
|
td_histogram_t *td_new(double compression);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Allocate the memory and initialise the t-digest.
|
||||||
|
*
|
||||||
|
* @param compression The compression parameter.
|
||||||
|
* 100 is a common value for normal uses.
|
||||||
|
* 1000 is extremely large.
|
||||||
|
* The number of centroids retained will be a smallish (usually less than 10) multiple of this
|
||||||
|
* number.
|
||||||
|
* @param result Output parameter to capture allocated histogram.
|
||||||
|
* @return 0 on success, 1 if allocation failed.
|
||||||
|
*/
|
||||||
|
int td_init(double compression, td_histogram_t **result);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Frees the memory associated with the t-digest.
|
||||||
|
*
|
||||||
|
* @param h The histogram you want to free.
|
||||||
|
*/
|
||||||
|
void td_free(td_histogram_t *h);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Reset a histogram to zero - empty out a histogram and re-initialise it
|
||||||
|
*
|
||||||
|
* If you want to re-use an existing histogram, but reset everything back to zero, this
|
||||||
|
* is the routine to use.
|
||||||
|
*
|
||||||
|
* @param h The histogram you want to reset to empty.
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
void td_reset(td_histogram_t *h);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Adds a sample to a histogram.
|
||||||
|
*
|
||||||
|
* @param val The value to add.
|
||||||
|
* @param weight The weight of this point.
|
||||||
|
* @return 0 on success, EDOM if overflow was detected as a consequence of adding the provided
|
||||||
|
* weight.
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
int td_add(td_histogram_t *h, double val, long long weight);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Re-examines a t-digest to determine whether some centroids are redundant. If your data are
|
||||||
|
* perversely ordered, this may be a good idea. Even if not, this may save 20% or so in space.
|
||||||
|
*
|
||||||
|
* The cost is roughly the same as adding as many data points as there are centroids. This
|
||||||
|
* is typically < 10 * compression, but could be as high as 100 * compression.
|
||||||
|
* This is a destructive operation that is not thread-safe.
|
||||||
|
*
|
||||||
|
* @param h The histogram you want to compress.
|
||||||
|
* @return 0 on success, EDOM if overflow was detected as a consequence of adding the provided
|
||||||
|
* weight. If overflow is detected the histogram is not changed.
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
int td_compress(td_histogram_t *h);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Merges all of the values from 'from' to 'this' histogram.
|
||||||
|
*
|
||||||
|
* @param h "This" pointer
|
||||||
|
* @param from Histogram to copy values from.
|
||||||
|
* * @return 0 on success, EDOM if overflow was detected as a consequence of merging the the
|
||||||
|
* provided histogram. If overflow is detected the original histogram is not detected.
|
||||||
|
*/
|
||||||
|
int td_merge(td_histogram_t *h, td_histogram_t *from);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Returns the fraction of all points added which are ≤ x.
|
||||||
|
*
|
||||||
|
* @param x The cutoff for the cdf.
|
||||||
|
* @return The fraction of all data which is less or equal to x.
|
||||||
|
*/
|
||||||
|
double td_cdf(td_histogram_t *h, double x);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Returns an estimate of the cutoff such that a specified fraction of the data
|
||||||
|
* added to this TDigest would be less than or equal to the cutoff.
|
||||||
|
*
|
||||||
|
* @param q The desired fraction
|
||||||
|
* @return The value x such that cdf(x) == q;
|
||||||
|
*/
|
||||||
|
double td_quantile(td_histogram_t *h, double q);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Returns an estimate of the cutoff such that a specified fraction of the data
|
||||||
|
* added to this TDigest would be less than or equal to the cutoffs.
|
||||||
|
*
|
||||||
|
* @param quantiles The ordered percentiles array to get the values for.
|
||||||
|
* @param values Destination array containing the values at the given quantiles.
|
||||||
|
* The values array should be allocated by the caller.
|
||||||
|
* @return 0 on success, ENOMEM if the provided destination array is null.
|
||||||
|
*/
|
||||||
|
int td_quantiles(td_histogram_t *h, const double *quantiles, double *values, size_t length);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Returns the trimmed mean ignoring values outside given cutoff upper and lower limits.
|
||||||
|
*
|
||||||
|
* @param leftmost_cut Fraction to cut off of the left tail of the distribution.
|
||||||
|
* @param rightmost_cut Fraction to cut off of the right tail of the distribution.
|
||||||
|
* @return The trimmed mean ignoring values outside given cutoff upper and lower limits;
|
||||||
|
*/
|
||||||
|
double td_trimmed_mean(td_histogram_t *h, double leftmost_cut, double rightmost_cut);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Returns the trimmed mean ignoring values outside given a symmetric cutoff limits.
|
||||||
|
*
|
||||||
|
* @param proportion_to_cut Fraction to cut off of the left and right tails of the distribution.
|
||||||
|
* @return The trimmed mean ignoring values outside given cutoff upper and lower limits;
|
||||||
|
*/
|
||||||
|
double td_trimmed_mean_symmetric(td_histogram_t *h, double proportion_to_cut);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Returns the current compression factor.
|
||||||
|
*
|
||||||
|
* @return The compression factor originally used to set up the TDigest.
|
||||||
|
*/
|
||||||
|
int td_compression(td_histogram_t *h);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Returns the number of points that have been added to this TDigest.
|
||||||
|
*
|
||||||
|
* @return The sum of the weights on all centroids.
|
||||||
|
*/
|
||||||
|
long long td_size(td_histogram_t *h);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Returns the number of centroids being used by this TDigest.
|
||||||
|
*
|
||||||
|
* @return The number of centroids being used.
|
||||||
|
*/
|
||||||
|
int td_centroid_count(td_histogram_t *h);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Get minimum value from the histogram. Will return __DBL_MAX__ if the histogram
|
||||||
|
* is empty.
|
||||||
|
*
|
||||||
|
* @param h "This" pointer
|
||||||
|
*/
|
||||||
|
double td_min(td_histogram_t *h);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Get maximum value from the histogram. Will return - __DBL_MAX__ if the histogram
|
||||||
|
* is empty.
|
||||||
|
*
|
||||||
|
* @param h "This" pointer
|
||||||
|
*/
|
||||||
|
double td_max(td_histogram_t *h);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Get the full centroids weight array for 'this' histogram.
|
||||||
|
*
|
||||||
|
* @param h "This" pointer
|
||||||
|
*
|
||||||
|
* @return The full centroids weight array.
|
||||||
|
*/
|
||||||
|
const long long *td_centroids_weight(td_histogram_t *h);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Get the full centroids mean array for 'this' histogram.
|
||||||
|
*
|
||||||
|
* @param h "This" pointer
|
||||||
|
*
|
||||||
|
* @return The full centroids mean array.
|
||||||
|
*/
|
||||||
|
const double *td_centroids_mean(td_histogram_t *h);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Get the centroid weight for 'this' histogram and 'pos'.
|
||||||
|
*
|
||||||
|
* @param h "This" pointer
|
||||||
|
* @param pos centroid position.
|
||||||
|
*
|
||||||
|
* @return The centroid weight.
|
||||||
|
*/
|
||||||
|
long long td_centroids_weight_at(td_histogram_t *h, int pos);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Get the centroid mean for 'this' histogram and 'pos'.
|
||||||
|
*
|
||||||
|
* @param h "This" pointer
|
||||||
|
* @param pos centroid position.
|
||||||
|
*
|
||||||
|
* @return The centroid mean.
|
||||||
|
*/
|
||||||
|
double td_centroids_mean_at(td_histogram_t *h, int pos);
|
||||||
|
|
||||||
|
#ifdef __cplusplus
|
||||||
|
}
|
||||||
|
#endif
|
760
tests/test.c
760
tests/test.c
File diff suppressed because it is too large
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Reference in a new issue