sigfil 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/.travis.yml

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+sudo: false
+language: ruby
+rvm:
+  - 2.3.1
+before_install: gem install bundler -v 1.13.2

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in sigfil.gemspec
+gemspec
+
+gem "nmatrix", ">=0.2"
+gem "ffi", ">=1"
+gem "flann", ">=1"
+gem "daru", ">=0.1"
+

data/README.md

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+# Sigfil
+
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'sigfil'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install sigfil
+
+## Usage
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run
+`rake test` 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/tanahiro/sigfil.
+
+## License
+MIT License

data/Rakefile

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+require "bundler/gem_tasks"
+require "rake/testtask"
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.test_files = FileList['test/**/*_test.rb']
+end
+
+task :default => :test

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "sigfil"
+
+# 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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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/lib/sigfil/statistical_outlier_removal.rb

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+require "nmatrix"
+require "flann"
+require "algorithms"
+
+module SigFil
+  class StatisticalOutlierRemoval
+    include Math
+
+    attr_accessor :mean_k, :std_mul, :dataset, :searcher
+
+    SEARCHER = [:kdtree, :flann]
+
+    ##
+    # +mean_k+: Number of points to use mean distance estimation
+    # +std_mul+: Standard deviation multipliera threshold
+    def initialize dataset, mean_k = 2, std_mul = 0.0, searcher = :kdtree
+      @dataset  = dataset
+      @mean_k   = mean_k
+      @std_mul  = std_mul
+      unless SEARCHER.include?(searcher)
+        raise ArgumentError, "Unknown searcher type: #{searcher}"
+      else
+        @searcher = searcher
+      end
+    end
+
+    def apply_filter scale_factors = nil
+      if @searcher == :flann
+        Flann.set_distance_type!(:l2)
+      end
+
+      if scale_factors
+        unless scale_factors.size == @dataset.cols
+          raise ArgumentError, "scale_factors.size != dataset.cols"
+        else
+          dataset = @dataset.clone
+          scale_factors.each_with_index do |s, i|
+            dataset[0..-1, i] *= s
+          end
+        end
+      else
+        dataset = @dataset
+      end
+
+      case @searcher
+      when :flann
+        searcher = Flann::Index.new(@dataset) do |params|
+          params[:algorithm]    = :kdtree
+          params[:trees]        = 4
+          params[:centers_init] = :gonzales
+        end
+        searcher.build!
+      when :kdtree
+        dataset_h = dataset.to_a.each_with_index.map {|pt, i| [i, pt]}.to_h
+        searcher  = Containers::KDTree.new(dataset_h)
+      end
+
+      distances = Array.new(dataset.rows, 0.0)
+      dataset.each_row(:clone).with_index do |row, iii|
+        case @searcher
+        when :flann
+          _, dis= searcher.nearest_neighbors(row, @mean_k + 1)
+          distances[iii] = NMatrix[*dis[1..-1]].mean[0]
+        when :kdtree
+          dis = searcher.find_nearest(row.to_a, @mean_k + 1).map do
+            |r| sqrt(r[0])
+          end
+        end
+
+        distances[iii] = NMatrix[*dis[1..-1]].mean[0]
+      end
+
+      nm_d   = NMatrix[*distances]
+      d_mean = nm_d.mean[0]
+      d_std  = nm_d.std[0]
+      d_th   = d_mean + @std_mul*d_std
+
+      filtered = []
+      distances.each_with_index do |d, i|
+        if d <= d_th
+          filtered << @dataset.row(i).to_a
+        end
+      end
+
+      return NMatrix[*filtered]
+    end
+  end
+end
+

data/lib/sigfil/version.rb

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+module SigFil
+  VERSION = "0.1.0"
+end

data/lib/sigfil/voxel_grid.rb

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+require "nmatrix"
+require "daru"
+
+module SigFil
+  class VoxelGrid
+    attr_accessor :dataset
+    attr_reader :leaf_size
+
+    def initialize dataset, leaf_size
+      @dataset   = dataset
+      @leaf_size = leaf_size
+      get_inverse_leaf_size
+      
+    end
+
+    def apply_filter
+      min, max = get_min_max
+
+      bb_min, bb_max = get_bb(min, max)
+
+      #div_b = bb_max.zip(bb_min).map {|x| x[0] - x[1] + 1}
+
+      index = []
+      @dataset.each_row do |pt|
+        id = (pt*@inverse_leaf_size - bb_min).floor
+        index << id.to_a
+      end
+
+      grid_idx = {}
+      df = Daru::DataFrame.rows(index)
+      #df.sort!(df.vectors)
+      df.each_row_with_index do |row, id|
+        grid_idx[row.to_a] ||= []
+        grid_idx[row.to_a] << id
+      end
+
+      voxel_ary = []
+      grid_idx.each do |g_id, d_id|
+        ary = d_id.map {|i| @dataset.row(i).to_a}
+        nm = NMatrix[*ary]
+        voxel_ary << nm.mean(0).to_a
+      end
+
+      return NMatrix[*voxel_ary]
+    end
+
+    def get_min_max
+      min = @dataset.min(0)
+      max = @dataset.max(0)
+
+      return min, max
+    end
+
+    ##
+    # Get bounding box
+    def get_bb min, max
+      bb_min = (min*@inverse_leaf_size).floor
+      bb_max = (max*@inverse_leaf_size).floor
+
+      return bb_min, bb_max
+    end
+
+    def leaf_size= leaf_size
+      @leaf_size = leaf_size
+    end
+
+    def get_inverse_leaf_size
+      @inverse_leaf_size = NMatrix[@leaf_size.map {|x| 1.0/x}]
+    end
+  end
+end
+

data/lib/sigfil.rb

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+require "#{__dir__}/sigfil/version"
+
+module SigFil
+  # Your code goes here...
+end

data/sigfil.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'sigfil/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "sigfil"
+  spec.version       = SigFil::VERSION
+  spec.authors       = ["Hiroyuki Tanaka"]
+  spec.email         = ["hryktnk@ge.com"]
+
+  spec.summary       = %q{Filters for signal processing}
+  spec.description   = %q{Filters for signal processing.}
+
+  spec.homepage      = "https://github.com/tanahiro/sigfil"
+  spec.license       = "MIT"
+
+  if spec.respond_to?(:metadata)
+    spec.metadata['allowed_push_host'] = "https://rubygems.org"
+  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 do |f|
+    f.match(%r{^(test|spec|features)/})
+  end
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.13"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "minitest", "~> 5.0"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: sigfil
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Hiroyuki Tanaka
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2016-10-12 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.13'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.13'
+- !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: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+description: Filters for signal processing.
+email:
+- hryktnk@ge.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".travis.yml"
+- Gemfile
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/sigfil.rb
+- lib/sigfil/statistical_outlier_removal.rb
+- lib/sigfil/version.rb
+- lib/sigfil/voxel_grid.rb
+- sigfil.gemspec
+homepage: https://github.com/tanahiro/sigfil
+licenses:
+- MIT
+metadata:
+  allowed_push_host: https://rubygems.org
+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: 2.6.7
+signing_key: 
+specification_version: 4
+summary: Filters for signal processing
+test_files: []