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http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/404.html ---------------------------------------------------------------------- diff --git a/website/docs/404.html b/website/docs/404.html deleted file mode 100755 index 6904bcd..0000000 --- a/website/docs/404.html +++ /dev/null @@ -1 +0,0 @@ -Sorry this page does not exist =( http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/Gemfile ---------------------------------------------------------------------- diff --git a/website/docs/Gemfile b/website/docs/Gemfile deleted file mode 100755 index 301d29c..0000000 --- a/website/docs/Gemfile +++ /dev/null @@ -1,5 +0,0 @@ -source "https://rubygems.org"; - -gem "jekyll", "~> 3.1" -gem "jekyll-sitemap" -gem "pygments.rb" http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/README.md ---------------------------------------------------------------------- diff --git a/website/docs/README.md b/website/docs/README.md deleted file mode 100755 index 68646fd..0000000 --- a/website/docs/README.md +++ /dev/null @@ -1,16 +0,0 @@ - -### Landing Page - - - -### Tutorials - -Tutorials, Algorithms, MR-Tutorials, and MR-Algorithsm each have an accordion side bar for navigation -(this is the part we need help building) - - -### Old MR Algos - - - - http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/Rakefile ---------------------------------------------------------------------- diff --git a/website/docs/Rakefile b/website/docs/Rakefile deleted file mode 100755 index 183ca1e..0000000 --- a/website/docs/Rakefile +++ /dev/null @@ -1,306 +0,0 @@ -require "rubygems" -require 'rake' -require 'yaml' -require 'time' - -SOURCE = "." -CONFIG = { - 'version' => "0.3.0", - 'themes' => File.join(SOURCE, "_includes", "themes"), - 'layouts' => File.join(SOURCE, "_layouts"), - 'posts' => File.join(SOURCE, "_posts"), - 'post_ext' => "md", - 'theme_package_version' => "0.1.0" -} - -# Path configuration helper -module JB - class Path - SOURCE = "." - Paths = { - :layouts => "_layouts", - :themes => "_includes/themes", - :theme_assets => "assets/themes", - :theme_packages => "_theme_packages", - :posts => "_posts" - } - - def self.base - SOURCE - end - - # build a path relative to configured path settings. - def self.build(path, opts = {}) - opts[:root] ||= SOURCE - path = "#{opts[:root]}/#{Paths[path.to_sym]}/#{opts[:node]}".split("/") - path.compact! - File.__send__ :join, path - end - - end #Path -end #JB - -# Usage: rake post title="A Title" [date="2012-02-09"] [tags=[tag1,tag2]] [category="category"] -desc "Begin a new post in #{CONFIG['posts']}" -task :post do - abort("rake aborted: '#{CONFIG['posts']}' directory not found.") unless FileTest.directory?(CONFIG['posts']) - title = ENV["title"] || "new-post" - tags = ENV["tags"] || "[]" - category = ENV["category"] || "" - category = "\"#{category.gsub(/-/,' ')}\"" if !category.empty? - slug = title.downcase.strip.gsub(' ', '-').gsub(/[^\w-]/, '') - begin - date = (ENV['date'] ? Time.parse(ENV['date']) : Time.now).strftime('%Y-%m-%d') - rescue => e - puts "Error - date format must be YYYY-MM-DD, please check you typed it correctly!" - exit -1 - end - filename = File.join(CONFIG['posts'], "#{date}-#{slug}.#{CONFIG['post_ext']}") - if File.exist?(filename) - abort("rake aborted!") if ask("#{filename} already exists. Do you want to overwrite?", ['y', 'n']) == 'n' - end - - puts "Creating new post: #{filename}" - open(filename, 'w') do |post| - post.puts "---" - post.puts "layout: post" - post.puts "title: \"#{title.gsub(/-/,' ')}\"" - post.puts 'description: ""' - post.puts "category: #{category}" - post.puts "tags: #{tags}" - post.puts "---" - post.puts "{% include JB/setup %}" - end -end # task :post - -# Usage: rake page name="about.html" -# You can also specify a sub-directory path. -# If you don't specify a file extention we create an index.html at the path specified -desc "Create a new page." -task :page do - name = ENV["name"] || "new-page.md" - filename = File.join(SOURCE, "#{name}") - filename = File.join(filename, "index.html") if File.extname(filename) == "" - title = File.basename(filename, File.extname(filename)).gsub(/[\W\_]/, " ").gsub(/\b\w/){$&.upcase} - if File.exist?(filename) - abort("rake aborted!") if ask("#{filename} already exists. Do you want to overwrite?", ['y', 'n']) == 'n' - end - - mkdir_p File.dirname(filename) - puts "Creating new page: #{filename}" - open(filename, 'w') do |post| - post.puts "---" - post.puts "layout: page" - post.puts "title: \"#{title}\"" - post.puts 'description: ""' - post.puts "---" - post.puts "{% include JB/setup %}" - end -end # task :page - -desc "Launch preview environment" -task :preview do - system "jekyll serve -w" -end # task :preview - -# Public: Alias - Maintains backwards compatability for theme switching. -task :switch_theme => "theme:switch" - -namespace :theme do - - # Public: Switch from one theme to another for your blog. - # - # name - String, Required. name of the theme you want to switch to. - # The theme must be installed into your JB framework. - # - # Examples - # - # rake theme:switch name="the-program" - # - # Returns Success/failure messages. - desc "Switch between Jekyll-bootstrap themes." - task :switch do - theme_name = ENV["name"].to_s - theme_path = File.join(CONFIG['themes'], theme_name) - settings_file = File.join(theme_path, "settings.yml") - non_layout_files = ["settings.yml"] - - abort("rake aborted: name cannot be blank") if theme_name.empty? - abort("rake aborted: '#{theme_path}' directory not found.") unless FileTest.directory?(theme_path) - abort("rake aborted: '#{CONFIG['layouts']}' directory not found.") unless FileTest.directory?(CONFIG['layouts']) - - Dir.glob("#{theme_path}/*") do |filename| - next if non_layout_files.include?(File.basename(filename).downcase) - puts "Generating '#{theme_name}' layout: #{File.basename(filename)}" - - open(File.join(CONFIG['layouts'], File.basename(filename)), 'w') do |page| - page.puts "---" - page.puts File.read(settings_file) if File.exist?(settings_file) - page.puts "layout: default" unless File.basename(filename, ".html").downcase == "default" - page.puts "---" - page.puts "{% include JB/setup %}" - page.puts "{% include themes/#{theme_name}/#{File.basename(filename)} %}" - end - end - - puts "=> Theme successfully switched!" - puts "=> Reload your web-page to check it out =)" - end # task :switch - - # Public: Install a theme using the theme packager. - # Version 0.1.0 simple 1:1 file matching. - # - # git - String, Optional path to the git repository of the theme to be installed. - # name - String, Optional name of the theme you want to install. - # Passing name requires that the theme package already exist. - # - # Examples - # - # rake theme:install git="https://github.com/jekyllbootstrap/theme-twitter.git"; - # rake theme:install name="cool-theme" - # - # Returns Success/failure messages. - desc "Install theme" - task :install do - if ENV["git"] - manifest = theme_from_git_url(ENV["git"]) - name = manifest["name"] - else - name = ENV["name"].to_s.downcase - end - - packaged_theme_path = JB::Path.build(:theme_packages, :node => name) - - abort("rake aborted! - => ERROR: 'name' cannot be blank") if name.empty? - abort("rake aborted! - => ERROR: '#{packaged_theme_path}' directory not found. - => Installable themes can be added via git. You can find some here: http://github.com/jekyllbootstrap - => To download+install run: `rake theme:install git='[PUBLIC-CLONE-URL]'` - => example : rake theme:install git='[email protected]:jekyllbootstrap/theme-the-program.git' - ") unless FileTest.directory?(packaged_theme_path) - - manifest = verify_manifest(packaged_theme_path) - - # Get relative paths to packaged theme files - # Exclude directories as they'll be recursively created. Exclude meta-data files. - packaged_theme_files = [] - FileUtils.cd(packaged_theme_path) { - Dir.glob("**/*.*") { |f| - next if ( FileTest.directory?(f) || f =~ /^(manifest|readme|packager)/i ) - packaged_theme_files << f - } - } - - # Mirror each file into the framework making sure to prompt if already exists. - packaged_theme_files.each do |filename| - file_install_path = File.join(JB::Path.base, filename) - if File.exist? file_install_path and ask("#{file_install_path} already exists. Do you want to overwrite?", ['y', 'n']) == 'n' - next - else - mkdir_p File.dirname(file_install_path) - cp_r File.join(packaged_theme_path, filename), file_install_path - end - end - - puts "=> #{name} theme has been installed!" - puts "=> ---" - if ask("=> Want to switch themes now?", ['y', 'n']) == 'y' - system("rake switch_theme name='#{name}'") - end - end - - # Public: Package a theme using the theme packager. - # The theme must be structured using valid JB API. - # In other words packaging is essentially the reverse of installing. - # - # name - String, Required name of the theme you want to package. - # - # Examples - # - # rake theme:package name="twitter" - # - # Returns Success/failure messages. - desc "Package theme" - task :package do - name = ENV["name"].to_s.downcase - theme_path = JB::Path.build(:themes, :node => name) - asset_path = JB::Path.build(:theme_assets, :node => name) - - abort("rake aborted: name cannot be blank") if name.empty? - abort("rake aborted: '#{theme_path}' directory not found.") unless FileTest.directory?(theme_path) - abort("rake aborted: '#{asset_path}' directory not found.") unless FileTest.directory?(asset_path) - - ## Mirror theme's template directory (_includes) - packaged_theme_path = JB::Path.build(:themes, :root => JB::Path.build(:theme_packages, :node => name)) - mkdir_p packaged_theme_path - cp_r theme_path, packaged_theme_path - - ## Mirror theme's asset directory - packaged_theme_assets_path = JB::Path.build(:theme_assets, :root => JB::Path.build(:theme_packages, :node => name)) - mkdir_p packaged_theme_assets_path - cp_r asset_path, packaged_theme_assets_path - - ## Log packager version - packager = {"packager" => {"version" => CONFIG["theme_package_version"].to_s } } - open(JB::Path.build(:theme_packages, :node => "#{name}/packager.yml"), "w") do |page| - page.puts packager.to_yaml - end - - puts "=> '#{name}' theme is packaged and available at: #{JB::Path.build(:theme_packages, :node => name)}" - end - -end # end namespace :theme - -# Internal: Download and process a theme from a git url. -# Notice we don't know the name of the theme until we look it up in the manifest. -# So we'll have to change the folder name once we get the name. -# -# url - String, Required url to git repository. -# -# Returns theme manifest hash -def theme_from_git_url(url) - tmp_path = JB::Path.build(:theme_packages, :node => "_tmp") - abort("rake aborted: system call to git clone failed") if !system("git clone #{url} #{tmp_path}") - manifest = verify_manifest(tmp_path) - new_path = JB::Path.build(:theme_packages, :node => manifest["name"]) - if File.exist?(new_path) && ask("=> #{new_path} theme package already exists. Override?", ['y', 'n']) == 'n' - remove_dir(tmp_path) - abort("rake aborted: '#{manifest["name"]}' already exists as theme package.") - end - - remove_dir(new_path) if File.exist?(new_path) - mv(tmp_path, new_path) - manifest -end - -# Internal: Process theme package manifest file. -# -# theme_path - String, Required. File path to theme package. -# -# Returns theme manifest hash -def verify_manifest(theme_path) - manifest_path = File.join(theme_path, "manifest.yml") - manifest_file = File.open( manifest_path ) - abort("rake aborted: repo must contain valid manifest.yml") unless File.exist? manifest_file - manifest = YAML.load( manifest_file ) - manifest_file.close - manifest -end - -def ask(message, valid_options) - if valid_options - answer = get_stdin("#{message} #{valid_options.to_s.gsub(/"/, '').gsub(/, /,'/')} ") while !valid_options.include?(answer) - else - answer = get_stdin(message) - end - answer -end - -def get_stdin(message) - print message - STDIN.gets.chomp -end - -#Load custom rake scripts -Dir['_rake/*.rake'].each { |r| load r } http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/_config.yml ---------------------------------------------------------------------- diff --git a/website/docs/_config.yml b/website/docs/_config.yml deleted file mode 100755 index 33da780..0000000 --- a/website/docs/_config.yml +++ /dev/null @@ -1,140 +0,0 @@ -# This is the default format. -# For more see: http://jekyllrb.com/docs/permalinks/ -permalink: /:categories/:year/:month/:day/:title - -exclude: [".rvmrc", ".rbenv-version", "README.md", "Rakefile", "changelog.md", "screenshots"] -highlighter: pygments - -# Themes are encouraged to use these universal variables -# so be sure to set them if your theme uses them. -# -title : Apache Mahout Project -tagline: Distributed Linear Algebra -author : - name : Apache Mahout - email : [email protected] - github : apache - twitter : ApacheMahout - - -# The production_url is only used when full-domain names are needed -# such as sitemap.txt -# Most places will/should use BASE_PATH to make the urls -# -# If you have set a CNAME (pages.github.com) set your custom domain here. -# Else if you are pushing to username.github.io, replace with your username. -# Finally if you are pushing to a GitHub project page, include the project name at the end. -# -production_url : http://mahout.apache.org - -gems: ["jekyll-sitemap"] - -# All Jekyll-Bootstrap specific configurations are namespaced into this hash -# -JB : - version : 0.3.0 - - # All links will be namespaced by BASE_PATH if defined. - # Links in your website should always be prefixed with {{BASE_PATH}} - # however this value will be dynamically changed depending on your deployment situation. - # - # CNAME (http://yourcustomdomain.com) - # DO NOT SET BASE_PATH - # (urls will be prefixed with "/" and work relatively) - # - # GitHub Pages (http://username.github.io) - # DO NOT SET BASE_PATH - # (urls will be prefixed with "/" and work relatively) - # - # GitHub Project Pages (http://username.github.io/project-name) - # - # A GitHub Project site exists in the `gh-pages` branch of one of your repositories. - # REQUIRED! 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<div class="collapse" id="classification"> - <ul class="nav sidebar-nav"> - <li> <a href="{{ BASE_PATH }}/algorithms/map-reduce/classification/bayesian.html">Bayesian</a></li> - <li> <a href="{{ BASE_PATH }}/algorithms/map-reduce/classification/class-discovery.html">Class Discovery</a></li> - <li> <a href="{{ BASE_PATH }}/algorithms/map-reduce/classification/classifyingyourdata.html">Classifying Your Data</a></li> - <li> <a href="{{ BASE_PATH }}/algorithms/map-reduce/classification/collocations.html">Collocation</a></li> - <li> <a href="{{ BASE_PATH }}/algorithms/map-reduce/classification/gaussian-discriminative-analysis.html">Gaussian Discriminative Analysis</a></li> - <li> <a href="{{ BASE_PATH }}/algorithms/map-reduce/classification/hidden-markov-models.html">Hidden Markov Models</a></li> - <li> <a href="{{ BASE_PATH }}/algorithms/map-reduce/classification/independent-component-analysis.html">Independent Component Analysis</a></li> - <li> <a href="{{ BASE_PATH }}/algorithms/map-reduce/classification/locally-weighted-linear-regression.html">Locally Weighted Linear Regression</a></li> - 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<li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/classification/wikipedia-classifier-example.html">Wikipedia Classifier Example</a></li> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/classification/parallel-frequent-pattern-mining.html">Parallel Frequent Pattern Mining</a></li> - </ul> - </div> - <a href="#clustering" class="list-group-item list-group-item-success" data-toggle="collapse" data-parent="#MrTutorialMenu"><b>Clustering</b><i class="fa fa-caret-down"></i></a> - <div class="collapse" id="clustering"> - <ul class="nav sidebar-nav"> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/clustering/20newsgroups.html">Twenty Newsgroups Example</a></li> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/clustering/canopy-commandline.html">Canopy Clustering from the Commandline</a></li> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/clustering/clustering-of-synthetic-control-data.html">Clustering of Synthetic Control Data</a></li> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/clustering/clustering-seinfeld-episodes.html">Clustering of Seinfeld Episodes</a></li> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/clustering/clusteringyourdata.html">Clustering Your Data</a></li> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/clustering/fuzzy-k-means-commandline.html">Fuzzy K-Means from the Commandline</a></li> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/clustering/k-means-commandline.html">K-Means from the Commandline</a></li> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/clustering/lda-commandline.html">LDA from the Commandline</a></li> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/clustering/viewing-results.html">Viewing Results</a></li> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/clustering/visualizing-sample-clusters.html">Visualizing Sample Clusters</a></li> - </ul> - </div> - <a href="#misc" class="list-group-item list-group-item-success" data-toggle="collapse" data-parent="#MrTutorialMenu"><b>Miscelaneous</b><i class="fa fa-caret-down"></i></a> - <div class="collapse" id="misc"> - <ul class="nav sidebar-nav"> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/misc/mr---map-reduce.html">MR Map-Reduce</a></li> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/misc/parallel-frequent-pattern-mining.html">Parallel Frequent Pattern Mining</a></li> - <li> <a href="{{ BASE_PATH }}/tutorials/map-reduce/misc/using-mahout-with-python-via-jpype.html">Using Mahout (Map Reduce) with Python via Jpype</a></li> - </ul> - </div> - </div> -</div> http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/_layouts/algorithm.html ---------------------------------------------------------------------- diff --git a/website/docs/_layouts/algorithm.html b/website/docs/_layouts/algorithm.html deleted file mode 100644 index 188081e..0000000 --- a/website/docs/_layouts/algorithm.html +++ /dev/null @@ -1,7 +0,0 @@ ---- -theme : -name : mahout3 -layout: default ---- -{% include JB/setup %} -{% include themes/mahout3/algorithm.html %} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/_layouts/default.html ---------------------------------------------------------------------- diff --git a/website/docs/_layouts/default.html b/website/docs/_layouts/default.html deleted file mode 100755 index ec60279..0000000 --- a/website/docs/_layouts/default.html +++ /dev/null @@ -1,6 +0,0 @@ ---- -theme : - name : mahout3 ---- -{% include JB/setup %} -{% include themes/mahout3/default.html %} http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/_layouts/page.html ---------------------------------------------------------------------- diff --git a/website/docs/_layouts/page.html b/website/docs/_layouts/page.html deleted file mode 100755 index 0e123f9..0000000 --- a/website/docs/_layouts/page.html +++ /dev/null @@ -1,7 +0,0 @@ ---- -theme : - name : mahout3 -layout: default ---- -{% include JB/setup %} -{% include themes/mahout3/page.html %} http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/_layouts/post.html ---------------------------------------------------------------------- diff --git a/website/docs/_layouts/post.html b/website/docs/_layouts/post.html deleted file mode 100755 index 9b8f584..0000000 --- a/website/docs/_layouts/post.html +++ /dev/null @@ -1,7 +0,0 @@ ---- -theme : - name : mahout3 -layout: default ---- -{% include JB/setup %} -{% include themes/mahout3/post.html %} http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/_layouts/tutorial.html ---------------------------------------------------------------------- diff --git a/website/docs/_layouts/tutorial.html b/website/docs/_layouts/tutorial.html deleted file mode 100644 index 8ee9223..0000000 --- a/website/docs/_layouts/tutorial.html +++ /dev/null @@ -1,7 +0,0 @@ ---- -theme : -name : mahout3 -layout: default ---- -{% include JB/setup %} -{% include themes/mahout3/tutorial.html %} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/_plugins/debug.rb ---------------------------------------------------------------------- diff --git a/website/docs/_plugins/debug.rb b/website/docs/_plugins/debug.rb deleted file mode 100755 index e1dde39..0000000 --- a/website/docs/_plugins/debug.rb +++ /dev/null @@ -1,38 +0,0 @@ -# A simple way to inspect liquid template variables. -# Usage: -# Can be used anywhere liquid syntax is parsed (templates, includes, posts/pages) -# {{ site | debug }} -# {{ site.posts | debug }} -# -require 'pp' -module Jekyll - # Need to overwrite the inspect method here because the original - # uses < > to encapsulate the psuedo post/page objects in which case - # the output is taken for HTML tags and hidden from view. - # - class Post - def inspect - "#Jekyll:Post @id=#{self.id.inspect}" - end - end - - class Page - def inspect - "#Jekyll:Page @name=#{self.name.inspect}" - end - end - -end # Jekyll - -module Jekyll - module DebugFilter - - def debug(obj, stdout=false) - puts obj.pretty_inspect if stdout - "<pre>#{obj.class}\n#{obj.pretty_inspect}</pre>" - end - - end # DebugFilter -end # Jekyll - -Liquid::Template.register_filter(Jekyll::DebugFilter) \ No newline at end of file http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/algorithms/clustering/canopy/Canopy.png ---------------------------------------------------------------------- diff --git a/website/docs/algorithms/clustering/canopy/Canopy.png b/website/docs/algorithms/clustering/canopy/Canopy.png deleted file mode 100644 index 934efd7..0000000 Binary files a/website/docs/algorithms/clustering/canopy/Canopy.png and /dev/null differ http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/algorithms/clustering/canopy/Canopy10.png ---------------------------------------------------------------------- diff --git a/website/docs/algorithms/clustering/canopy/Canopy10.png b/website/docs/algorithms/clustering/canopy/Canopy10.png deleted file mode 100644 index 4bb291c..0000000 Binary files a/website/docs/algorithms/clustering/canopy/Canopy10.png and /dev/null differ http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/algorithms/clustering/canopy/SampleData.png ---------------------------------------------------------------------- diff --git a/website/docs/algorithms/clustering/canopy/SampleData.png b/website/docs/algorithms/clustering/canopy/SampleData.png deleted file mode 100644 index 48c4690..0000000 Binary files a/website/docs/algorithms/clustering/canopy/SampleData.png and /dev/null differ http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/algorithms/clustering/canopy/index.md ---------------------------------------------------------------------- diff --git a/website/docs/algorithms/clustering/canopy/index.md b/website/docs/algorithms/clustering/canopy/index.md deleted file mode 100644 index 923c63a..0000000 --- a/website/docs/algorithms/clustering/canopy/index.md +++ /dev/null @@ -1,128 +0,0 @@ ---- -layout: algorithm -title: Canopy Clustering -theme: - name: retro-mahout ---- - -### About - -[Canopy Clustering](http://www.kamalnigam.com/papers/canopy-kdd00.pdf) - is a very simple, fast and surprisingly accurate method for grouping -objects into clusters. All objects are represented as a point in a -multidimensional feature space. The algorithm uses a fast approximate -distance metric and two distance thresholds T1 > T2 for processing. The -basic algorithm is to begin with a set of points and remove one at random. -Create a Canopy containing this point and iterate through the remainder of -the point set. At each point, if its distance from the first point is < T1, -then add the point to the cluster. If, in addition, the distance is < T2, -then remove the point from the set. This way points that are very close to -the original will avoid all further processing. The algorithm loops until -the initial set is empty, accumulating a set of Canopies, each containing -one or more points. A given point may occur in more than one Canopy. - -Canopy Clustering is often used as an initial step in more rigorous -clustering techniques, such as [K-Means Clustering](k-means-clustering.html) -. By starting with an initial clustering the number of more expensive -distance measurements can be significantly reduced by ignoring points -outside of the initial canopies. - -#### Strategy for parallelization - -Looking at the sample Hadoop implementation in [http://code.google.com/p/canopy-clustering/](http://code.google.com/p/canopy-clustering/) - the processing is done in 3 steps: -1. The data is massaged into suitable input format -1. Each mapper performs canopy clustering on the points in its input set and -outputs its canopies' centers -1. The reducer clusters the canopy centers to produce the final canopy -centers - -The points are then clustered into these final canopies when the `model.cluster(inputDRM)` is called. - -Some ideas can be found in [Cluster computing and MapReduce](https://www.youtube.com/watch?v=yjPBkvYh-ss&list=PLEFAB97242917704A) - lecture video series \[by Google(r)\]; Canopy Clustering is discussed in [lecture #4](https://www.youtube.com/watch?v=1ZDybXl212Q) -. Finally here is the [Wikipedia page](http://en.wikipedia.org/wiki/Canopy_clustering_algorithm) -. - -#### Illustrations - -The following images illustrate Canopy clustering applied to a set of -randomly-generated 2-d data points. The points are generated using a normal -distribution centered at a mean location and with a constant standard -deviation. See the README file in the [/examples/src/main/java/org/apache/mahout/clustering/display/README.txt](https://github.com/apache/mahout/blob/master/examples/src/main/java/org/apache/mahout/clustering/display/README.txt) - for details on running similar examples. - -The points are generated as follows: - -* 500 samples m=\[1.0, 1.0\](1.0,-1.0\.html) - sd=3.0 -* 300 samples m=\[1.0, 0.0\](1.0,-0.0\.html) - sd=0.5 -* 300 samples m=\[0.0, 2.0\](0.0,-2.0\.html) - sd=0.1 - -In the first image, the points are plotted and the 3-sigma boundaries of -their generator are superimposed. - - - -In the second image, the resulting canopies are shown superimposed upon the -sample data. Each canopy is represented by two circles, with radius T1 and -radius T2. - - - -The third image uses the same values of T1 and T2 but only superimposes -canopies covering more than 10% of the population. This is a bit better -representation of the data but it still has lots of room for improvement. -The advantage of Canopy clustering is that it is single-pass and fast -enough to iterate runs using different T1, T2 parameters and display -thresholds. - - - -### Parameters - -<div class="table-striped"> - <table class="table"> - <tr> - <th>Parameter</th> - <th>Description</th> - <th>Default Value</th> - </tr> - <tr> - <td><code>'distanceMeasure</code></td> - <td>The metric used for calculating distance, see <a href="../distance-metrics.html">Distance Metrics</a></td> - <td><code>'Cosine</code></td> - </tr> - <tr> - <td><code>'t1</code></td> - <td>The "loose" distance in the mapping phase</code></td> - <td>0.5</td> - </tr> - <tr> - <td><code>'t2</code></td> - <td>The "tight" distance in the mapping phase</code></td> - <td>0.1</td> - </tr> - <tr> - <td><code>'t3</code></td> - <td>The "loose" distance in the reducing phase</code></td> - <td><code>'t1</code></td> - </tr> - <tr> - <td><code>'t4</code></td> - <td>The "tight" distance in the reducing phase</code></td> - <td><code>'t2</code></td> - </tr> - </table> -</div> - -### Example - - val drmA = drmParallelize(dense((1.0, 1.2, 1.3, 1.4), (1.1, 1.5, 2.5, 1.0), (6.0, 5.2, -5.2, 5.3), (7.0,6.0, 5.0, 5.0), (10.0, 1.0, 20.0, -10.0))) - - import org.apache.mahout.math.algorithms.clustering.CanopyClustering - - val model = new CanopyClustering().fit(drmA, 't1 -> 6.5, 't2 -> 5.5, 'distanceMeasure -> 'Chebyshev) - model.cluster(drmA).collect http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/algorithms/clustering/distance-metrics.md ---------------------------------------------------------------------- diff --git a/website/docs/algorithms/clustering/distance-metrics.md b/website/docs/algorithms/clustering/distance-metrics.md deleted file mode 100644 index 5b25a93..0000000 --- a/website/docs/algorithms/clustering/distance-metrics.md +++ /dev/null @@ -1,82 +0,0 @@ ---- -layout: algorithm -title: Distance Metrics -theme: - name: retro-mahout ---- - -### Distance Metrics Supported By Mahout - -<div class="table-striped"> - <table class="table"> - <tr> - <th>Name</th> - <th>Object</th> - <th>Symbol</th> - </tr> - <tr> - <td><a href="https://en.wikipedia.org/wiki/Chebyshev_distance";>Chebyshev Distance</a></td> - <td><code>org.apache.mahout.math.algorithms.common.distance.Chebyshev</code></td> - <td><code>'Chebyshev</code></td> - </tr> - <tr> - <td><a href="https://en.wikipedia.org/wiki/Cosine_similarity";>Cosine Similarity</a></td> - <td><code>org.apache.mahout.math.algorithms.common.distance.Cosine</code></td> - <td><code>'Cosine</code></td> - </tr> - </table> -</div> - - -<!-- -A beginner JIRA to port the rest of these -[Euclidean](https://en.wikipedia.org/wiki/Euclidean_distance) - -[Mahalanobis](https://en.wikipedia.org/wiki/Mahalanobis_distance) - -[Manhattan](https://en.wiktionary.org/wiki/Manhattan_distance) - -[Minkowski](https://en.wikipedia.org/wiki/Minkowski_distance) - -[Squared Euclidian](https://en.wikipedia.org/wiki/Euclidean_distance#Squared_Euclidean_distance) - -[Tanimoto](https://en.wikipedia.org/wiki/Jaccard_index#Tanimoto_similarity_and_distance) - -Weighted Euclidean - -Weighted Manhattan--> - -### Using Distance Metrics - -In Mahout one can access the distant metrics directly to measure the distance between two arbitrary vectors, or -can specify which distance metric to use as part of an algorithm. In the latter case the distance metric is called -by `Symbol`, we never pass Distance metrics directly to an algorithm. This design choice, in part has to do with -serialization of object and keeping the engine bindings as simple as possible. Behind the scenes, the only thing -that is serialized and sent to the workers is a number which specifies what distant metric to use- this is much more -abstract and easier to maintain on the back end than making sure each function can be serialized by any arbitrary engine. -We feel from the user perspective, it may seem quirky but causes no decrease in usability. If a user wishes to use a -custom distance metric- simply add it to [math-scala/src/main/org/apache/mahout/math/common/DistanceMetrics.scala](https://github.com/apache/mahout/blob/master/math-scala/src/main/scala/org/apache/mahout/math/algorithms/common/DistanceMetrics.scala) -and recompile. - -### Examples - -**Meausring the distance between two vectors** - - import org.apache.mahout.math.algorithms.common.distance._ - - val v1 = dvec(1.0, 1.5, -1.2, 3.5) - val v2 = dvec(0.1, -1.4, 10.5, 3.2) - - Cosine.distance(v1, v2) - -**Using distance in clustering** - - import org.apache.mahout.math.algorithms.clustering.CanopyClustering - - val drmA = drmParallelize(dense((1.0, 1.2, 1.3, 1.4), - (1.1, 1.5, 2.5, 1.0), - (6.0, 5.2, -5.2, 5.3), - (7.0,6.0, 5.0, 5.0), - (10.0, 1.0, 20.0, -10.0))) - - val model = new CanopyClustering().fit(drmA, 'distanceMeasure -> 'Cosine) \ No newline at end of file http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/algorithms/clustering/index.md ---------------------------------------------------------------------- diff --git a/website/docs/algorithms/clustering/index.md b/website/docs/algorithms/clustering/index.md deleted file mode 100644 index 50030c2..0000000 --- a/website/docs/algorithms/clustering/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -layout: algorithm -title: Clustering Algorithms -theme: - name: retro-mahout ---- http://git-wip-us.apache.org/repos/asf/mahout/blob/978d4467/website/docs/algorithms/linear-algebra/d-qr.md ---------------------------------------------------------------------- diff --git a/website/docs/algorithms/linear-algebra/d-qr.md b/website/docs/algorithms/linear-algebra/d-qr.md deleted file mode 100644 index 8e9cecc..0000000 --- a/website/docs/algorithms/linear-algebra/d-qr.md +++ /dev/null @@ -1,56 +0,0 @@ ---- -layout: algorithm -title: Distributed Cholesky QR -theme: - name: retro-mahout ---- - -## Intro - -Mahout has a distributed implementation of QR decomposition for tall thin matrices[1]. - -## Algorithm - -For the classic QR decomposition of the form `\(\mathbf{A}=\mathbf{QR},\mathbf{A}\in\mathbb{R}^{m\times n}\)` a distributed version is fairly easily achieved if `\(\mathbf{A}\)` is tall and thin such that `\(\mathbf{A}^{\top}\mathbf{A}\)` fits in memory, i.e. *m* is large but *n* < ~5000 Under such circumstances, only `\(\mathbf{A}\)` and `\(\mathbf{Q}\)` are distributed matrices and `\(\mathbf{A^{\top}A}\)` and `\(\mathbf{R}\)` are in-core products. We just compute the in-core version of the Cholesky decomposition in the form of `\(\mathbf{LL}^{\top}= \mathbf{A}^{\top}\mathbf{A}\)`. After that we take `\(\mathbf{R}= \mathbf{L}^{\top}\)` and `\(\mathbf{Q}=\mathbf{A}\left(\mathbf{L}^{\top}\right)^{-1}\)`. The latter is easily achieved by multiplying each vertical block of `\(\mathbf{A}\)` by `\(\left(\mathbf{L}^{\top}\right)^{-1}\)`. (There is no actual matrix inversion happening). - - - -## Implementation - -Mahout `dqrThin(...)` is implemented in the mahout `math-scala` algebraic optimizer which translates Mahout's R-like linear algebra operators into a physical plan for both Spark and H2O distributed engines. - - def dqrThin[K: ClassTag](A: DrmLike[K], checkRankDeficiency: Boolean = true): (DrmLike[K], Matrix) = { - if (drmA.ncol > 5000) - log.warn("A is too fat. A'A must fit in memory and easily broadcasted.") - implicit val ctx = drmA.context - val AtA = (drmA.t %*% drmA).checkpoint() - val inCoreAtA = AtA.collect - val ch = chol(inCoreAtA) - val inCoreR = (ch.getL cloned) t - if (checkRankDeficiency && !ch.isPositiveDefinite) - throw new IllegalArgumentException("R is rank-deficient.") - val bcastAtA = sc.broadcast(inCoreAtA) - val Q = A.mapBlock() { - case (keys, block) => keys -> chol(bcastAtA).solveRight(block) - } - Q -> inCoreR - } - - -## Usage - -The scala `dqrThin(...)` method can easily be called in any Spark or H2O application built with the `math-scala` library and the corresponding `Spark` or `H2O` engine module as follows: - - import org.apache.mahout.math._ - import decompositions._ - import drm._ - - val(drmQ, inCoreR) = dqrThin(drma) - - -## References - -[1]: [Mahout Scala and Mahout Spark Bindings for Linear Algebra Subroutines](http://mahout.apache.org/users/sparkbindings/ScalaSparkBindings.pdf) - -[2]: [Mahout Spark and Scala Bindings](http://mahout.apache.org/users/sparkbindings/home.html) -
