vptree 0.1.0

checksums.yaml

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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/

data/.rspec

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+--format documentation
+--color

data/.travis.yml

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+language: ruby
+rvm:
+  - 2.2.1
+before_install: gem install bundler -v 1.10.6

data/CODE_OF_CONDUCT.md

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+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the [Contributor Covenant](http://contributor-covenant.org), version 1.0.0, available at [http://contributor-covenant.org/version/1/0/0/](http://contributor-covenant.org/version/1/0/0/)

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in vptree.gemspec
+gemspec

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2015 generall
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+# Vptree
+
+[![Build Status](https://travis-ci.org/generall/vptree.svg)](https://travis-ci.org/generall/vptree)
+
+Implementation of VP-tree (https://en.wikipedia.org/wiki/Vantage-point_tree) for fast kNN search with any measure function.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'vptree'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install vptree
+
+## Usage
+
+
+Building tree:
+
+```ruby
+data = [[1,2], [2,1] , [2,2]]
+# any measure, satisfies the triangle inequality, is allowed
+# and may be passed as block
+tree = Vptree::VPTree.new(data) # data - array of vectors of objects with special mixin, see https://github.com/generall/Distance-Measures
+```
+Quering tree:
+
+```ruby
+nearest = tree.find_k_nearest([3,3], 1)
+```
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/generall/vptree. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](contributor-covenant.org) code of conduct.
+
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
+

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "vptree"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

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+#!/bin/bash
+set -euo pipefail
+IFS=$'\n\t'
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/lib/vptree/version.rb

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+module Vptree
+  VERSION = "0.1.0"
+end

data/lib/vptree.rb

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+require "vptree/version"
+require 'distance_measures'
+require 'algorithms'
+
+module Vptree
+
+  class FixedLengthQueue < Containers::PriorityQueue
+    def initialize(limit = 4) # 4 for example
+      super()
+      @limit = limit
+    end
+
+    def max_priority
+      @heap.next_key
+    end
+
+    def push(value, priority)
+      if size < @limit
+        super(value, priority)
+      else
+        if priority < @heap.next_key
+          pop
+          super(value, priority)
+        end
+      end
+    end
+
+    def dump()
+      size.times.map{ @heap.pop }
+    end
+  end
+
+  class VPNode
+    attr_accessor :is_block, :distance_measure, :data, :vp_point, :left_node, :right_node, :mu
+
+    def initialize(data, options={}, &block)
+      @data = data
+      @is_block = block != nil
+      @distance_measure = block || options[:distance_measure]  || :euclidean_distance
+      @left_node = nil
+      @right_node = nil
+      @mu = 0
+    end
+
+    def setup(other_node)
+      @is_block = other_node.is_block
+      @distance_measure = other_node.distance_measure
+    end
+
+    def calc_dist(obj1, obj2)
+      begin
+        return  @is_block ? obj1.calc_distance(obj2, &@distance_measure) : obj1.calc_distance(obj2, @distance_measure)
+      rescue
+        return @is_block ? @distance_measure.call(obj1, obj2) : obj1.send(@distance_measure, obj2) # old fasion distance gem, for arrays only
+      end
+    end
+
+    def separate()
+
+      if @data.size <= 2
+        @vp_point = @data.first
+        @right_node = nil
+        if @data.size == 2
+          @mu = calc_dist(@data[0],@data[1])/2
+          @left_node = VPNode.new([@data[1]])
+        end
+      else
+        @vp_point = @data.sample
+        # all sorted nodes
+        next_node_data = @data.sort_by{ |a| calc_dist(a, @vp_point) }[1..-1]
+        len = next_node_data.size
+        r_points = next_node_data[0..(len/2 - 1)];
+        l_points = next_node_data[(len/2)..-1]
+        @mu = (calc_dist(r_points.last, @vp_point) + calc_dist(l_points.first, @vp_point))/2.0
+        @right_node = VPNode.new(r_points)
+        @left_node  = VPNode.new(l_points)
+      end
+      @right_node.setup(self) if @right_node
+      @left_node.setup(self) if @left_node
+
+      @right_node.separate if @right_node
+      @left_node.separate if @left_node
+      @data = nil
+    end
+
+  end
+
+  class VPTree
+
+    attr_accessor :root
+
+    def initialize(data, options={}, &block)
+      @data = data
+      @is_block = block != nil
+      @distance_measure = block || options[:distance_measure]  || :euclidean_distance
+      @root = VPNode.new(data, options, &block)
+    end
+
+    def calc_dist(obj1, obj2)
+      begin
+        return  @is_block ? obj1.calc_distance(obj2, &@distance_measure) : obj1.calc_distance(obj2, @distance_measure)
+      rescue
+        return @is_block ? @distance_measure.call(obj1, obj2) : obj1.send(@distance_measure, obj2) # old fasion distance gem, for arrays only
+      end
+    end
+
+
+    def build_tree()
+      @root.separate
+    end
+
+    def find_k_nearest(obj, k)
+      tau = Float::INFINITY
+      nodes_to_visit = Containers::Queue.new
+      nodes_to_visit.push(@root)
+
+      # fixed size array for nearest neightbors
+      # sorted from closest to farthest neighbor
+      neighbors = FixedLengthQueue.new(k)
+
+      while nodes_to_visit.size() > 0 do
+        node = nodes_to_visit.pop()
+        d = calc_dist(obj, node.vp_point)
+        if d < tau
+          # store node.vp_point as a neighbor if it's closer than any other point
+          # seen so far
+          neighbors.push(node.vp_point, d)
+          # shrink tau
+          tau = neighbors.max_priority
+        end
+        # check for intersection between q-tau and vp-mu regions
+        # and see which branches we absolutely must search
+
+        if d < node.mu
+          # the object is in mu range of Vintage Point
+          nodes_to_visit.push(node.right_node) if node.right_node # d < node.mu + tau # permanent true
+          nodes_to_visit.push(node.left_node) if node.left_node && d >= node.mu - tau # partial overlap
+        else
+          nodes_to_visit.push(node.left_node) if node.left_node # d >= node.mu - tau
+          nodes_to_visit.push(node.right_node) if node.right_node && d < node.mu + tau # partial overlap
+        end
+      end
+
+      return neighbors.dump
+    end
+  end
+end

data/vptree.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'vptree/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "vptree"
+  spec.version       = Vptree::VERSION
+  spec.authors       = ["generall"]
+  spec.email         = ["vasnetsov93@gmail.com"]
+
+  spec.summary       = %q{ VP-tree implemented in ruby }
+  spec.description   = %q{ Implementation of VP-tree https://en.wikipedia.org/wiki/Vantage-point_tree }
+  spec.homepage      = "https://github.com/generall/vptree"
+  spec.license       = "MIT"
+
+  # Prevent pushing this gem to RubyGems.org by setting 'allowed_push_host', or
+  # delete this section to allow pushing this gem to any host.
+  #if spec.respond_to?(:metadata)
+  #  spec.metadata['allowed_push_host'] = "TODO: Set to 'http://mygemserver.com'"
+  #else
+  #  raise "RubyGems 2.0 or newer is required to protect against public gem pushes."
+  #end
+
+  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.10"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec"
+  spec.add_development_dependency "distance_measures", '~> 0'
+  spec.add_development_dependency "algorithms", '~> 0'
+  #spec.add_development_dependency "pry"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: vptree
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- generall
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2015-12-27 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: distance_measures
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: algorithms
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0'
+description: " Implementation of VP-tree https://en.wikipedia.org/wiki/Vantage-point_tree "
+email:
+- vasnetsov93@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/vptree.rb
+- lib/vptree/version.rb
+- vptree.gemspec
+homepage: https://github.com/generall/vptree
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.8
+signing_key: 
+specification_version: 4
+summary: VP-tree implemented in ruby
+test_files: []