spatial_stats 0.2.2 → 1.0.4

data/lib/spatial_stats/weights/distant.rb

@@ -15,21 +15,26 @@ module SpatialStats
       #
       # @return [WeightsMatrix]
       def self.distance_band(scope, field, bandwidth)
-        p_key = scope.primary_key
-        keys = scope.pluck(p_key).sort
-
         neighbors = SpatialStats::Queries::Weights
                     .distance_band_neighbors(scope, field, bandwidth)
 
+        # get keys to make sure we have consistent dimensions when
+        # some entries don't have neighbors.
+        # define a new hash that has all the keys from scope
+        keys = SpatialStats::Queries::Variables.query_field(scope, scope.klass.primary_key)
+
         neighbors = neighbors.group_by(&:i_id)
+        missing_neighbors = Hash[(keys - neighbors.keys).map { |key| [key, []] }]
+        neighbors = neighbors.merge(missing_neighbors)
+
         weights = neighbors.transform_values do |value|
           value.map do |neighbor|
-            hash = neighbor.as_json(only: [:j_id]).symbolize_keys
+            hash = { id: neighbor[:j_id] }
             hash[:weight] = 1
             hash
           end
         end
-        SpatialStats::Weights::WeightsMatrix.new(keys, weights)
+        SpatialStats::Weights::WeightsMatrix.new(weights)
       end
 
       ##
@@ -41,21 +46,26 @@ module SpatialStats
       #
       # @return [WeightsMatrix]
       def self.knn(scope, field, k)
-        p_key = scope.primary_key
-        keys = scope.pluck(p_key).sort
-
         neighbors = SpatialStats::Queries::Weights
                     .knn(scope, field, k)
 
+        # get keys to make sure we have consistent dimensions when
+        # some entries don't have neighbors.
+        # define a new hash that has all the keys from scope
+        keys = SpatialStats::Queries::Variables.query_field(scope, scope.klass.primary_key)
+
         neighbors = neighbors.group_by(&:i_id)
+        missing_neighbors = Hash[(keys - neighbors.keys).map { |key| [key, []] }]
+        neighbors = neighbors.merge(missing_neighbors)
+
         weights = neighbors.transform_values do |value|
           value.map do |neighbor|
-            hash = neighbor.as_json(only: [:j_id]).symbolize_keys
+            hash = { id: neighbor[:j_id] }
             hash[:weight] = 1
             hash
           end
         end
-        SpatialStats::Weights::WeightsMatrix.new(keys, weights)
+        SpatialStats::Weights::WeightsMatrix.new(weights)
       end
 
       ##
@@ -68,20 +78,24 @@ module SpatialStats
       #
       # @return [WeightsMatrix]
       def self.idw_band(scope, field, bandwidth, alpha = 1)
-        p_key = scope.primary_key
-        keys = scope.pluck(p_key).sort
-
         neighbors = SpatialStats::Queries::Weights
                     .idw_band(scope, field, bandwidth, alpha)
+
+        # get keys to make sure we have consistent dimensions when
+        # some entries don't have neighbors.
+        # define a new hash that has all the keys from scope
+        keys = SpatialStats::Queries::Variables.query_field(scope, scope.klass.primary_key)
         neighbors = neighbors.group_by { |pair| pair[:i_id] }
+        missing_neighbors = Hash[(keys - neighbors.keys).map { |key| [key, []] }]
+        neighbors = neighbors.merge(missing_neighbors)
 
         # only keep j_id and weight
         weights = neighbors.transform_values do |value|
           value.map do |neighbor|
-            { weight: neighbor[:weight], j_id: neighbor[:j_id] }
+            { weight: neighbor[:weight], id: neighbor[:j_id] }
           end
         end
-        SpatialStats::Weights::WeightsMatrix.new(keys, weights)
+        SpatialStats::Weights::WeightsMatrix.new(weights)
       end
 
       ##
@@ -94,20 +108,24 @@ module SpatialStats
       #
       # @return [WeightsMatrix]
       def self.idw_knn(scope, field, k, alpha = 1)
-        p_key = scope.primary_key
-        keys = scope.pluck(p_key).sort
-
         neighbors = SpatialStats::Queries::Weights
                     .idw_knn(scope, field, k, alpha)
+
+        # get keys to make sure we have consistent dimensions when
+        # some entries don't have neighbors.
+        # define a new hash that has all the keys from scope
+        keys = SpatialStats::Queries::Variables.query_field(scope, scope.klass.primary_key)
         neighbors = neighbors.group_by { |pair| pair[:i_id] }
+        missing_neighbors = Hash[(keys - neighbors.keys).map { |key| [key, []] }]
+        neighbors = neighbors.merge(missing_neighbors)
 
         # only keep j_id and weight
         weights = neighbors.transform_values do |value|
           value.map do |neighbor|
-            { weight: neighbor[:weight], j_id: neighbor[:j_id] }
+            { weight: neighbor[:weight], id: neighbor[:j_id] }
           end
         end
-        SpatialStats::Weights::WeightsMatrix.new(keys, weights)
+        SpatialStats::Weights::WeightsMatrix.new(weights)
       end
     end
   end

data/lib/spatial_stats/weights/weights_matrix.rb

@@ -11,56 +11,113 @@ module SpatialStats
       ##
       # A new instance of WeightsMatrix
       #
-      # @param [Array] keys ordered list of keys used in weights
-      # @param [Hash] weights hash of format +{key: [{j_id: neighbor_key, weight: 1}]}+ that describe the relations between neighbors
+      # @param [Hash] weights hash of format +{key: [{id: neighbor_key, weight: 1}]}+ that describe the relations between neighbors
       #
       # @return [WeightsMatrix]
-      def initialize(keys, weights)
-        @keys = keys
+      def initialize(weights)
         @weights = weights
+        @keys = weights.keys
         @n = keys.size
       end
       attr_accessor :keys, :weights, :n
 
+      ##
+      # Equality operator
+      #
+      # @param [WeightsMatrix] other WeightsMatrix
+      #
+      # @return [TrueClass, FalseClass] equality result
+      def ==(other)
+        weights == other.weights
+      end
+
       ##
       # Compute the n x n Numo::Narray of the weights hash.
       #
       # @example
-      #   hash = {1 => [{j_id: 2, weight: 1}], 2 => [{j_id: 1, weight: 1},
-      #       {j_id: 3, weight: 1}], 3 => [{j_id: 2, weight: 1}]}
+      #   hash = {1 => [{id: 2, weight: 1}], 2 => [{id: 1, weight: 1},
+      #       {id: 3, weight: 1}], 3 => [{id: 2, weight: 1}]}
       #   wm = WeightsMatrix.new(hash.keys, hash)
       #   wm.full
       #   # => Numo::DFloat[[0, 1, 0], [1, 0, 1], [0, 1, 0]]
       #
       # @return [Numo::DFloat]
-      def full
-        # returns a square matrix Wij using @keys as the order of items
-        @full ||= begin
-          rows = []
-          @keys.each do |i|
-            # iterate through each key to get the data for the row
-            row = @keys.map do |j|
-              neighbors = @weights[i]
-              match = neighbors.find { |neighbor| neighbor[:j_id] == j }
-              if match
-                match[:weight]
-              else
-                0
-              end
+      def dense
+        @dense ||= begin
+          mat = Numo::DFloat.zeros(n, n)
+          keys.each_with_index do |key, i|
+            neighbors = weights[key]
+            neighbors.each do |neighbor|
+              j = keys.index(neighbor[:id])
+              weight = neighbor[:weight]
+
+              # assign the weight to row and column
+              mat[i, j] = weight
             end
-            rows << row
           end
 
-          Numo::DFloat.cast(rows)
+          mat
         end
       end
 
       ##
-      # Row standardized version of +#full+
+      # Compute the CSR representation of the weights.
       #
-      # @return [Numo::DFloat]
-      def standardized
-        @standardized ||= full.row_standardized
+      # @return [CSRMatrix]
+      def sparse
+        @sparse ||= CSRMatrix.new(weights, n)
+      end
+
+      ##
+      # Compute the cardinalities of each neighbor into an array
+      #
+      # @return [Array]
+      def wc
+        @wc ||= begin
+          row_index = sparse.row_index
+          (0..n - 1).map do |idx|
+            row_index[idx + 1] - row_index[idx]
+          end
+        end
+      end
+
+      ##
+      # Row standardized version of the weights matrix.
+      # Will return a new version of the weights matrix with standardized
+      # weights.
+      #
+      # @return [WeightsMatrix]
+      def standardize
+        new_weights = weights
+
+        new_weights.transform_values do |neighbors|
+          sum = neighbors.reduce(0.0) { |acc, neighbor| acc + neighbor[:weight] }
+
+          neighbors.map do |neighbor|
+            hash = neighbor
+            hash[:weight] /= sum
+          end
+        end
+
+        self.class.new(new_weights)
+      end
+
+      ##
+      # Windowed version of the weights matrix.
+      # If a row already has an entry for itself, it will be skipped.
+      #
+      # @return [WeightsMatrix]
+      def window
+        new_weights = weights
+
+        new_weights.each do |key, neighbors|
+          unless neighbors.find { |neighbor| neighbor[:id] == key }
+            new_neighbors = (neighbors << { id: key, weight: 1 })
+            new_weights[key] = new_neighbors.sort_by { |neighbor| neighbor[:id] }
+          end
+        end
+
+        self.class.new(new_weights)
       end
     end
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: spatial_stats
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 1.0.4
 platform: ruby
 authors:
 - Keith Doggett
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-04-03 00:00:00.000000000 Z
+date: 2020-12-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: numo-narray
@@ -28,14 +28,14 @@ dependencies:
   name: rails
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 6.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 6.0.0
 - !ruby/object:Gem::Dependency
@@ -80,6 +80,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.0'
+- !ruby/object:Gem::Dependency
+  name: rake-compiler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.1.0
 - !ruby/object:Gem::Dependency
   name: ruby-prof
   requirement: !ruby/object:Gem::Requirement
@@ -98,14 +112,14 @@ dependencies:
   name: tzinfo
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.2.6
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.2.6
 description: An ActiveRecord/PostGIS extension that provides statistical methods to
@@ -113,14 +127,18 @@ description: An ActiveRecord/PostGIS extension that provides statistical methods
   weighting in PostGIS and performs statistical computations inside your rails app.
   Supports contiguious and distance-based calculations.
 email:
-- keith.doggett887@gmail.com
+- kfdoggett@gmail.com
 executables: []
-extensions: []
+extensions:
+- ext/spatial_stats/extconf.rb
 extra_rdoc_files: []
 files:
-- MIT-LICENSE
 - README.md
 - Rakefile
+- ext/spatial_stats/csr_matrix.c
+- ext/spatial_stats/csr_matrix.h
+- ext/spatial_stats/extconf.rb
+- ext/spatial_stats/spatial_stats.c
 - lib/spatial_stats.rb
 - lib/spatial_stats/enumerable_ext.rb
 - lib/spatial_stats/global.rb
@@ -139,6 +157,7 @@ files:
 - lib/spatial_stats/queries/variables.rb
 - lib/spatial_stats/queries/weights.rb
 - lib/spatial_stats/railtie.rb
+- lib/spatial_stats/spatial_stats.so
 - lib/spatial_stats/utils.rb
 - lib/spatial_stats/utils/lag.rb
 - lib/spatial_stats/version.rb
@@ -149,9 +168,12 @@ files:
 - lib/tasks/spatial_stats_tasks.rake
 homepage: https://www.github.com/keithdoggett/spatial_stats
 licenses:
-- MIT
+- BSD-3-Clause
 metadata:
+  homepage_uri: https://www.github.com/keithdoggett/spatial_stats
+  source_code_uri: https://www.github.com/keithdoggett/spatial_stats
   documentation_uri: https://keithdoggett.github.io/spatial_stats/
+  changelog_uri: https://www.github.com/keithdoggett/spatial_stats/CHANGELOG.md
 post_install_message: 
 rdoc_options: []
 require_paths:
@@ -167,7 +189,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubygems_version: 3.0.8
 signing_key: 
 specification_version: 4
 summary: An ActiveRecord/PostGIS extension that provides statistical methods to spatial

data/MIT-LICENSE

@@ -1,20 +0,0 @@
-Copyright 2020 Keith Doggett
-
-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.