Added bit-tree pivot representation. It's available from the command line tool and included in self-test.

git-svn-id: https://phat.googlecode.com/svn/branches/bit-tree@19 8e3bb3c2-eed4-f18f-5264-0b6c94e6926d

1 files changed, 180 insertions, 0 deletions

diff --git a/include/phat/representations/bit_tree_pivot_column.h b/include/phat/representations/bit_tree_pivot_column.h
new file mode 100644
index 0000000..53956a4
--- /dev/null
+++ b/include/phat/representations/bit_tree_pivot_column.h
@@ -0,0 +1,180 @@
+/*  Copyright 2013 IST Austria

+    Contributed by: Ulrich Bauer, Michael Kerber, Jan Reininghaus, Hubert Wagner

+

+    This file is part of PHAT.

+

+    PHAT is free software: you can redistribute it and/or modify

+    it under the terms of the GNU Lesser General Public License as published by

+    the Free Software Foundation, either version 3 of the License, or

+    (at your option) any later version.

+

+    PHAT is distributed in the hope that it will be useful,

+    but WITHOUT ANY WARRANTY; without even the implied warranty of

+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

+    GNU Lesser General Public License for more details.

+

+    You should have received a copy of the GNU Lesser General Public License

+    along with PHAT.  If not, see <http://www.gnu.org/licenses/>. */

+

+#pragma once

+

+#include <phat/helpers/misc.h>

+#include <phat/representations/abstract_pivot_column.h>

+

+namespace phat {

+

+	// This is a bitset indexed with a 32-ary tree. Each node in the index

+	// has 32 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; // present_data[i + offset] = ith block of the data-bitset

+		typedef uint64_t block_type;

+		std::vector<block_type> present_data;

+		block_type * const present; // to prevent error checking in MS's vector...

+

+		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'. First (-x)&x isolates the rightmost bit.

+		// This is much faster than calling log2i, and faster than using ScanBitForward/Reverse intrinsic,

+		// which should be one CPU instruction.

+		inline size_t rightmost_pos(const block_type value) const

+		{

+				static const size_t tab64[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};

+				return 64 - 1 - tab64[((value & (-value))*0x07EDD5E59A4E28C2) >> 58];

+		}

+

+		public:

+		bit_tree_column() : present(0)

+		{

+			init(1);

+		}

+

+		bit_tree_column(const bit_tree_column &other) : present(0)

+		{

+			if (this == &other)

+				return;

+			this->offset = other.offset;

+			this->present_data = other.present_data;

+			*const_cast<block_type**>(&present) = &present_data[0];

+		}

+

+		void init(index num_cols)

+		{

+			size_t n = 1;

+			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;

+			present_data.resize(upper_blocks + bottom_blocks_needed, 0);

+

+			*const_cast<block_type**>(&present) = &present_data[0];

+		}

+

+		inline index max_index() const

+		{

+			if (!present[0])

+				return -1;

+

+			const size_t size = present_data.size();

+			size_t n = 0;

+

+			while(true)

+			{

+				const block_type val = present[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 present[0] == 0;

+		}

+

+		inline void add_index(const size_t entry)

+		{

+			static const block_type ONE = 1;

+			static 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)

+			{

+				present[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 || (present[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 !present[0];

+        }

+	};

+

+	typedef abstract_pivot_column<bit_tree_column> bit_tree_pivot_column;

+}