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https://github.com/sbrl/Pepperminty-Wiki.git
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Starbeamrainbowlabs
593f16dfb9
....I was gettign increasinly nervous about not committing these to git. Hopefully at some point soon I'll be able to integrate the BkTree into Pepperminty Wiki properly - but I still need to implement word removal first before I can do that. Also, feature-search is getting big. It's refactoring time to be sure, but Im uncertain at this stage precisely _how_ I want to go about that. I've got 2 ideas: 1. Refactor the engine and the storage box into separate "library modules" 2. Refactor them into their own repository/ies or something, and include them as extra data 3. Extend the extra data system to support local files and include them in the main Pepperminty Wiki repository Thought is required. If anyone actually reads this message, do get in touch with your thoughts!
365 lines
12 KiB
PHP
365 lines
12 KiB
PHP
<?php
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/**
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* PHP Library to calculate and compare Nilsimsa digests.
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*
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* The Nilsimsa hash is a locality senstive hash function. Generally similar
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* documents will have similar Nilsimsa digests. The Hamming distance between
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* the digests can be used to approximate the similarity between documents. For
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* further information consult http://en.wikipedia.org/wiki/Nilsimsa_Hash and
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* the references (particularly Damiani et al.)
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*
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* Implementation details:
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* The Nilsimsa class takes in a data parameter which is the string of the
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* document to digest Calling the methods hexdigest() and digest() give the
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* nilsimsa digests in hex or array format. The helper function compare_digests
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* takes in two digests and computes the Nilsimsa score. You can also use
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* compare_files() and compare_strings() to compare files and strings directly.
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*
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* This code is a port of py-nilsimsa located at
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* https://code.google.com/p/py-nilsimsa/
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*/
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/**
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* The MIT License (MIT)
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*
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* Copyright (c) 2015 Bill Eager
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the 'Software'), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in
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* all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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* THE SOFTWARE.
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*/
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class Nilsimsa
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{
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/**
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* Tran53 hash constant
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* @var array
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*/
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const TRAN = [
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0x02,0xd6,0x9e,0x6f,0xf9,0x1d,0x04,0xab,0xd0,0x22,0x16,0x1f,0xd8,0x73,0xa1,0xac,
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0x3b,0x70,0x62,0x96,0x1e,0x6e,0x8f,0x39,0x9d,0x05,0x14,0x4a,0xa6,0xbe,0xae,0x0e,
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0xcf,0xb9,0x9c,0x9a,0xc7,0x68,0x13,0xe1,0x2d,0xa4,0xeb,0x51,0x8d,0x64,0x6b,0x50,
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0x23,0x80,0x03,0x41,0xec,0xbb,0x71,0xcc,0x7a,0x86,0x7f,0x98,0xf2,0x36,0x5e,0xee,
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0x8e,0xce,0x4f,0xb8,0x32,0xb6,0x5f,0x59,0xdc,0x1b,0x31,0x4c,0x7b,0xf0,0x63,0x01,
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0x6c,0xba,0x07,0xe8,0x12,0x77,0x49,0x3c,0xda,0x46,0xfe,0x2f,0x79,0x1c,0x9b,0x30,
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0xe3,0x00,0x06,0x7e,0x2e,0x0f,0x38,0x33,0x21,0xad,0xa5,0x54,0xca,0xa7,0x29,0xfc,
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0x5a,0x47,0x69,0x7d,0xc5,0x95,0xb5,0xf4,0x0b,0x90,0xa3,0x81,0x6d,0x25,0x55,0x35,
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0xf5,0x75,0x74,0x0a,0x26,0xbf,0x19,0x5c,0x1a,0xc6,0xff,0x99,0x5d,0x84,0xaa,0x66,
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0x3e,0xaf,0x78,0xb3,0x20,0x43,0xc1,0xed,0x24,0xea,0xe6,0x3f,0x18,0xf3,0xa0,0x42,
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0x57,0x08,0x53,0x60,0xc3,0xc0,0x83,0x40,0x82,0xd7,0x09,0xbd,0x44,0x2a,0x67,0xa8,
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0x93,0xe0,0xc2,0x56,0x9f,0xd9,0xdd,0x85,0x15,0xb4,0x8a,0x27,0x28,0x92,0x76,0xde,
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0xef,0xf8,0xb2,0xb7,0xc9,0x3d,0x45,0x94,0x4b,0x11,0x0d,0x65,0xd5,0x34,0x8b,0x91,
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0x0c,0xfa,0x87,0xe9,0x7c,0x5b,0xb1,0x4d,0xe5,0xd4,0xcb,0x10,0xa2,0x17,0x89,0xbc,
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0xdb,0xb0,0xe2,0x97,0x88,0x52,0xf7,0x48,0xd3,0x61,0x2c,0x3a,0x2b,0xd1,0x8c,0xfb,
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0xf1,0xcd,0xe4,0x6a,0xe7,0xa9,0xfd,0xc4,0x37,0xc8,0xd2,0xf6,0xdf,0x58,0x72,0x4e,
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];
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/**
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* Stores whether the digest is complete
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*
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* @var boolean
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*/
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private $digestComputed;
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/**
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* Stores the number of characters in the string digested
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*
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* @var int
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*/
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private $numChar;
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/**
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* Stores the accumulator as a 256-bit vector
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*
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* @var array
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*/
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private $acc;
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/**
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* Stores the active window used in {process} for hashing
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*
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* @var array
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*/
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private $window;
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/**
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* @var mixed
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*/
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private $digest;
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/**
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* The target length of the hash.
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* @var int
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*/
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private $length;
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/**
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* Constructor
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*
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* @param string $data The data to process
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*/
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public function __construct($data = null, $length = null)
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{
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if($length !== null) $this->length = $length;
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$this->digestComputed = false;
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$this->numChar = 0;
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$this->acc = array_fill(0, $this->length, 0);
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$this->window = [];
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if ($data) {
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$this->process($data);
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}
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}
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/**
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* Computes the hash of all of the trigrams in the chunk using a window of
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* length 5
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*
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* @param string $chunk The chunk to process
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*/
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public function process($chunk)
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{
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foreach (str_split($chunk) as $char) {
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$this->numChar++;
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$c = ord($char);
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$windowLength = count($this->window);
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if ($windowLength > 1) {
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// seen at least three characters
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$this->acc[$this->tranHash(
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$c, $this->window[0], $this->window[1], 0
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)]
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+= 1;
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}
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if ($windowLength > 2) {
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// seen at least four characters
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$this->acc[$this->tranHash(
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$c, $this->window[0], $this->window[2], 1
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)]
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+= 1;
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$this->acc[$this->tranHash(
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$c, $this->window[1], $this->window[2], 2
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)]
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+= 1;
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}
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if ($windowLength > 3) {
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// have a full window
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$this->acc[$this->tranHash(
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$c, $this->window[0], $this->window[3], 3
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)]
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+= 1;
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$this->acc[$this->tranHash(
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$c, $this->window[1], $this->window[3], 4
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)]
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+= 1;
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$this->acc[$this->tranHash(
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$c, $this->window[2], $this->window[3], 5
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)]
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+= 1;
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// duplicate hashes, used to maintain 8 trigrams per character
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$this->acc[$this->tranHash(
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$this->window[3], $this->window[0], $c, 6
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)]
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+= 1;
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$this->acc[$this->tranHash(
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$this->window[3], $this->window[2], $c, 7
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)]
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+= 1;
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}
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// add current character to the window, remove the previous character
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array_unshift($this->window, $c);
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if ($windowLength >= 4) {
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$this->window = array_slice($this->window, 0, 4);
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}
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}
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}
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/**
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* Implementation of the Tran53 hash algorithm
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*
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* @param int $a Input A
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* @param int $b Input B
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* @param int $c Input C
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* @param int $n Input N
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*
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* @return int
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*/
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public function tranHash($a, $b, $c, $n)
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{
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return ((
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(self::TRAN[($a + $n) & 255] ^ self::TRAN[$b] * ($n + $n + 1)) +
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self::TRAN[($c) ^ self::TRAN[$n]]
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) & ($this->length-1)); // Was 255
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}
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/**
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* Returns the digest as a hex string. Computes it if it isn't computed
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* already.
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*
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* @return string The digest
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*/
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public function hexDigest()
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{
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if ( ! $this->digestComputed) {
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$this->computeDigest();
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}
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$output = null;
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foreach ($this->digest as $i) {
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$output .= sprintf('%02x', $i);
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}
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return $output;
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}
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/**
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* Returns the digest as an array. Computes it if it isn't computed already.
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*
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* @return array The digest
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*/
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public function digest()
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{
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if ( ! $this->digestComputed) {
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$this->computeDigest();
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}
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return $this->digest;
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}
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/**
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* Using a threshold (mean of the accumulator), computes the nilsimsa
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* digest after completion. Sets complete flag to true and stores result in
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* $this->digest
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*/
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public function computeDigest()
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{
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$numTrigrams = 0;
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if ($this->numChar == 3) {
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// 3 chars -> 1 trigram
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$numTrigrams = 1;
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}
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else if ($this->numChar == 4) {
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// 4 chars -> 4 trigrams
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$numTrigrams = 4;
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}
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else if ($this->numChar > 4) {
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// > 4 chars -> 8 for each CHAR
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$numTrigrams = 8 * $this->numChar - 28;
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}
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// threshhold is the mean of the acc buckets
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$threshold = $numTrigrams / $this->length;
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$digest = array_fill(0, $this->length/8, 0);
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for ($i = 0; $i < ($this->length-2); $i++) {
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if ($this->acc[$i] > $threshold) {
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// equivalent to i/8, 2**(i mod 7)
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$digest[$i >> 3] += 1 << ($i & 7);
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}
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}
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// set flag to true
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$this->digestComputed = true;
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// store result in digest, reversed
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$this->digest = array_reverse($digest);
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}
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static function hash($data, $length = 256) {
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$hasher = new self($data, $length);
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return $hasher->hexDigest();
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}
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}
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function lines_count($handle) {
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fseek($handle, 0);
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$count = 0;
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while(fgets($handle) !== false) $count++;
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return $count;
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}
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$mode = $argv[1] ?? "help";
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switch($mode) {
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case "typos":
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$handle = fopen("typos.csv", "r");
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$line_count = lines_count($handle);
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echo("$line_count lines total\n");
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$sizes = [ 256, 128, 64, 32, 16, 8 ];
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foreach($sizes as $size) {
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fseek($handle, 0);fgets($handle); // Skipt he first line since it's the header
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$count = 0; $count_same = 0; $skipped = 0;
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$same = []; $not_same = [];
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while(($line = fgets($handle)) !== false) {
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$parts = explode(",", trim($line), 2);
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if(strlen($parts[1]) < 3) {
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$skipped++;
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continue;
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}
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$hash_a = Nilsimsa::hash($parts[0], $size);
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$hash_b = Nilsimsa::hash($parts[1], $size);
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$count++;
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if($hash_a == $hash_b) {
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$count_same++;
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$same[] = $parts;
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}
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else $not_same[] = $parts;
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echo("$count_same / $count ($skipped skipped)\r");
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}
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file_put_contents("$size-same.csv", implode("\n", array_map(function ($el) {
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return implode(",", $el);
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}, $same)));
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file_put_contents("$size-not-same.csv", implode("\n", array_map(function ($el) {
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return implode(",", $el);
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}, $not_same)));
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echo(str_pad($size, 10)."→ $count_same / $count (".round(($count_same/$count)*100, 2)."%), $skipped skipped\n");
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}
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break;
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case "helloworld":
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foreach([ 256, 128, 64, 32, 16, 8 ] as $size) {
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echo(str_pad($size, 10).Nilsimsa::hash("hello, world!", $size));
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// echo(str_pad($size, 10).Nilsimsa::hash("pinnapple", $size));
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echo("\n");
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}
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break;
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case "help":
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default:
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echo("Mode $mode not recognised. Available modes:\n");
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echo(" helloworld Show different hash sizes\n");
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echo(" typos Compare typos in typos.csv and calculate statistics\n");
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break;
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}
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/*
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* TODO: Explore BK-Trees. SymSpell might be orders of magnitudes faster, but that's compared to a regular BK-Tree - and it's *much* more complicated.
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* If we instead use Nilsimsa + the hamming distance comparison funnction (which we removed & will need to reinstate), is it faster than doing lots of `levenshtein()` calls?
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* Experimentation is needed.
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* See also gmp_hamdist() (which requires the gmp PHP extension).
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*/
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