diff options
| author | hub.wag@gmail.com <hub.wag@gmail.com@8e3bb3c2-eed4-f18f-5264-0b6c94e6926d> | 2013-04-12 00:04:08 +0000 |
|---|---|---|
| committer | hub.wag@gmail.com <hub.wag@gmail.com@8e3bb3c2-eed4-f18f-5264-0b6c94e6926d> | 2013-04-12 00:04:08 +0000 |
| commit | b66953101a196371faf55effb37fd2928832e8e5 (patch) | |
| tree | 46e7427c8e06699618fb8e52bfcfd739c5d3998f /include/phat/representations | |
| parent | 0c0078181f915b9224de69fd52842a77c40ea96c (diff) | |
Updated the README and cleaned the phat.cpp command line options. Now the options match the names in the readme. Small changes to the bit_tree_pivot_column.h.
git-svn-id: https://phat.googlecode.com/svn/trunk@30 8e3bb3c2-eed4-f18f-5264-0b6c94e6926d
Diffstat (limited to 'include/phat/representations')
| -rw-r--r-- | include/phat/representations/bit_tree_pivot_column.h | 282 |
1 files changed, 143 insertions, 139 deletions
diff --git a/include/phat/representations/bit_tree_pivot_column.h b/include/phat/representations/bit_tree_pivot_column.h index 6bf6c3d..b33e786 100644 --- a/include/phat/representations/bit_tree_pivot_column.h +++ b/include/phat/representations/bit_tree_pivot_column.h @@ -1,5 +1,5 @@ /* Copyright 2013 IST Austria
- Contributed by: Hubert Wagner
+ Contributed by: Ulrich Bauer, Michael Kerber, Jan Reininghaus, Hubert Wagner
This file is part of PHAT.
@@ -23,143 +23,147 @@ namespace phat {
- // This is a bitset indexed with a 64-ary tree. Each node in the index
- // has 64 bits; i-th bit says that the i-th subtree is non-empty.
- // Supports practically O(1), inplace, zero-allocation: insert, remove, max_element
- // and clear in O(number of ones in the bitset).
- // 'add_index' is still the real bottleneck in practice.
- class bit_tree_column
- {
- size_t offset; // data[i + offset] = ith block of the data-bitset
- typedef uint64_t block_type;
- std::vector< block_type > data;
- size_t debrujin_magic_table[64];
-
- enum { block_size_in_bits = 64 };
- enum { block_shift = 6 };
-
- // Some magic: http://graphics.stanford.edu/~seander/bithacks.html
- // Gets the position of the rightmost bit of 'x'. 0 means the most significant bit.
- // (-x)&x isolates the rightmost bit.
- // The whole method is much faster than calling log2i, and very comparable to using ScanBitForward/Reverse intrinsic,
- // which should be one CPU instruction, but is not portable.
- size_t rightmost_pos(const block_type value) const
- {
- return 64 - 1 - debrujin_magic_table[((value & ((uint64_t)0 - value))*0x07EDD5E59A4E28C2) >> 58];
+ // This is a bitset indexed with a 64-ary tree. Each node in the index
+ // has 64 bits; i-th bit says that the i-th subtree is non-empty.
+ // Supports practically O(1), inplace, zero-allocation: insert, remove, max_element
+ // and clear in O(number of ones in the bitset).
+ // 'add_index' is still the real bottleneck in practice.
+ class bit_tree_column
+ {
+ size_t offset; // data[i + offset] = ith block of the data-bitset
+ typedef uint64_t block_type;
+ std::vector< block_type > data;
+
+ // this static is not a problem with OMP, it's initialized just after program starts
+ static const size_t debrujin_magic_table[64];
+
+ enum { block_size_in_bits = 64 };
+ enum { block_shift = 6 };
+
+ // Some magic: http://graphics.stanford.edu/~seander/bithacks.html
+ // Gets the position of the rightmost bit of 'x'. 0 means the most significant bit.
+ // (-x)&x isolates the rightmost bit.
+ // The whole method is much faster than calling log2i, and very comparable to using ScanBitForward/Reverse intrinsic,
+ // which should be one CPU instruction, but is not portable.
+ inline size_t rightmost_pos(const block_type value) const
+ {
+ return 64 - 1 - debrujin_magic_table[((value & (-value))*0x07EDD5E59A4E28C2) >> 58];
+ }
+
+ public:
+
+ void init(index num_cols)
+ {
+ int64_t n = 1; // in case of overflow
+ size_t bottom_blocks_needed = (num_cols+block_size_in_bits-1)/block_size_in_bits;
+ size_t upper_blocks = 1;
+
+ // How many blocks/nodes of index needed to index the whole bitset?
+ while(n * block_size_in_bits < bottom_blocks_needed)
+ {
+ n *= block_size_in_bits;
+ upper_blocks += n;
+ }
+
+ offset = upper_blocks;
+ data.resize(upper_blocks + bottom_blocks_needed, 0);
+ }
+
+ inline index max_index() const
+ {
+ if (!data[0])
+ return -1;
+
+ const size_t size = data.size();
+ size_t n = 0;
+
+ while(true)
+ {
+ const block_type val = data[n];
+ const size_t index = rightmost_pos(val);
+ const size_t newn = (n << block_shift) + index + 1;
+
+ if (newn >= size)
+ {
+ const size_t bottom_index = n - offset;
+ return (bottom_index << block_shift) + index;
+ }
+
+ n = newn;
+ }
+
+ return -1;
+ }
+
+ inline bool empty() const
+ {
+ return data[0] == 0;
+ }
+
+ inline void add_index(const size_t entry)
+ {
+ const block_type ONE = 1;
+ const block_type block_modulo_mask = ((ONE << block_shift) - 1);
+ size_t index_in_level = entry >> block_shift;
+ size_t address = index_in_level + offset;
+ size_t index_in_block = entry & block_modulo_mask;
+
+ block_type mask = (ONE << (block_size_in_bits - index_in_block - 1));
+
+ while(true)
+ {
+ data[address]^=mask;
+
+ // First we check if we reached the root.
+ // Also, if anyone else was in this block, we don't need to update the path up.
+ if (!address || (data[address] & ~mask))
+ return;
+
+ index_in_block = index_in_level & block_modulo_mask;
+ index_in_level >>= block_shift;
+ --address;
+ address >>= block_shift;
+ mask = (ONE << (block_size_in_bits - index_in_block - 1));
+ }
+ }
+
+ void get_column_and_clear(column &out)
+ {
+ out.clear();
+ while(true)
+ {
+ index mx = this->max_index();
+ if (mx == -1)
+ break;
+ out.push_back(mx);
+ add_index(mx);
+ }
+
+ std::reverse(out.begin(), out.end());
+ }
+
+ void add_column(const column &col)
+ {
+ for (size_t i = 0; i < col.size(); ++i)
+ {
+ add_index(col[i]);
+ }
+ }
+
+ inline bool empty() {
+ return !data[0];
}
-
- public:
-
- void init(index num_cols)
- {
- const size_t debrujin_for_64_bit[64] = {
- 63, 0, 58, 1, 59, 47, 53, 2,
- 60, 39, 48, 27, 54, 33, 42, 3,
- 61, 51, 37, 40, 49, 18, 28, 20,
- 55, 30, 34, 11, 43, 14, 22, 4,
- 62, 57, 46, 52, 38, 26, 32, 41,
- 50, 36, 17, 19, 29, 10, 13, 21,
- 56, 45, 25, 31, 35, 16, 9, 12,
- 44, 24, 15, 8, 23, 7, 6, 5};
-
- std::copy(debrujin_for_64_bit, debrujin_for_64_bit+64, debrujin_magic_table);
-
- uint64_t n = 1; // in case of overflow
- size_t bottom_blocks_needed = (num_cols+block_size_in_bits-1)/block_size_in_bits;
- size_t upper_blocks = 1;
-
- // How many blocks/nodes of index needed to index the whole bitset?
- while(n * block_size_in_bits < bottom_blocks_needed)
- {
- n *= block_size_in_bits;
- upper_blocks += n;
- }
-
- offset = upper_blocks;
- data.resize(upper_blocks + bottom_blocks_needed, 0);
- }
-
- index max_index() const
- {
- if (!data[0])
- return -1;
-
- const size_t size = data.size();
- size_t n = 0;
-
- while(true)
- {
- const block_type val = data[n];
- const size_t index = rightmost_pos(val);
- const size_t newn = (n << block_shift) + index + 1;
-
- if (newn >= size)
- {
- const size_t bottom_index = n - offset;
- return (bottom_index << block_shift) + index;
- }
-
- n = newn;
- }
-
- return -1;
- }
-
- bool empty() const
- {
- return data[0] == 0;
- }
-
- void add_index(const size_t entry)
- {
- const block_type ONE = 1;
- const block_type block_modulo_mask = ((ONE << block_shift) - 1);
- size_t index_in_level = entry >> block_shift;
- size_t address = index_in_level + offset;
- size_t index_in_block = entry & block_modulo_mask;
-
- block_type mask = (ONE << (block_size_in_bits - index_in_block - 1));
-
- while(true)
- {
- data[address]^=mask;
-
- // First we check if we reached the root.
- // Also, if anyone else was in this block, we don't need to update the path up.
- if (!address || (data[address] & ~mask))
- return;
-
- index_in_block = index_in_level & block_modulo_mask;
- index_in_level >>= block_shift;
- --address;
- address >>= block_shift;
- mask = (ONE << (block_size_in_bits - index_in_block - 1));
- }
- }
-
- void get_column_and_clear(column &out)
- {
- out.clear();
- while(true)
- {
- index mx = this->max_index();
- if (mx == -1)
- break;
- out.push_back(mx);
- add_index(mx);
- }
-
- std::reverse(out.begin(), out.end());
- }
-
- void add_column(const column &col)
- {
- for (size_t i = 0; i < col.size(); ++i)
- {
- add_index(col[i]);
- }
- }
- };
-
- typedef abstract_pivot_column<bit_tree_column> bit_tree_pivot_column;
+ };
+
+ const size_t bit_tree_column::debrujin_magic_table[64] = {
+ 63, 0, 58, 1, 59, 47, 53, 2,
+ 60, 39, 48, 27, 54, 33, 42, 3,
+ 61, 51, 37, 40, 49, 18, 28, 20,
+ 55, 30, 34, 11, 43, 14, 22, 4,
+ 62, 57, 46, 52, 38, 26, 32, 41,
+ 50, 36, 17, 19, 29, 10, 13, 21,
+ 56, 45, 25, 31, 35, 16, 9, 12,
+ 44, 24, 15, 8, 23, 7, 6, 5};
+
+ typedef abstract_pivot_column<bit_tree_column> bit_tree_pivot_column;
}
|