rubyfca 0.2.10 → 0.3.0

data/lib/rubyfca.rb

@@ -1,35 +1,39 @@
+# frozen_string_literal: true
+
 ## lib/rubyfca.rb -- Formal Concept Analysis tool in Ruby
 ## Author::    Yoichiro Hasebe (mailto: yohasebe@gmail.com)
-##             Kow Kuroda (mailto: kuroda@nict.go.jp)   
-## Copyright:: Copyright 2010 Yoichiro Hasebe and Kow Kuroda
+##             Kow Kuroda (mailto: kuroda@nict.go.jp)
+## Copyright:: Copyright 2009-2023 Yoichiro Hasebe and Kow Kuroda
 ## License::   GNU GPL version 3
 
-# -*- coding: utf-8 -*-
+require "csv"
+require "optimist"
+require "roo"
 
-require 'csv'
-require 'ruby_graphviz'
+require_relative "./rubyfca/ruby_graphviz"
+require_relative "./rubyfca/version"
 
 private
 
-## Take two arrays each consisting of 0s and 1s and create their logical disjunction 
+## Take two arrays each consisting of 0s and 1s and create their logical disjunction
 def create_and_ary(a, b)
   return false if (s = a.size) != b.size
-  result = (0..(s-1)).to_a.map{|i| a[i].to_i & b[i].to_i}
-  return result
+
+  (0..(s - 1)).to_a.map { |i| a[i].to_i & b[i].to_i }
 end
 
 ## Take two arrays each consisting of 0s and 1s and create their logical conjunction
 def create_or_ary(a, b)
   return false if (s = a.size) != b.size
-  result = (0..(s-1)).to_a.map{|i| a[i].to_i | b[i].to_i}
-  return result
+
+  (0..(s - 1)).to_a.map { |i| a[i].to_i | b[i].to_i }
 end
 
 public
 
 ## Take care of errors
 def showerror(sentence, severity)
-  if severity == 0
+  if severity.zero?
     puts "Warning: #{sentence} The output may not be meaningful."
   elsif severity == 1
     puts "Error: #{sentence} No output generated."
@@ -39,25 +43,27 @@ end
 
 ## Basic structure of the code is the same as Fcastone written in Perl by Uta Priss
 class FormalContext
-
   ## Converte cxt data to three basic structures of objects, attributes, and matrix
-  def initialize(input, mode, label_contraction = false)
-    if input.size == 0
-      showerror("File is empty", 1)
-    end
+  def initialize(input, mode, label_contraction: false)
+    showerror("File is empty", 1) if input.empty?
+    input = input.gsub(" ", " ")
     begin
       case mode
       when /cxt\z/
         read_cxt(input)
       when /csv\z/
         read_csv(input)
+      when /xlsx\z/
+        read_xlsx(input)
       end
-    rescue => e
-      showerror("Input data contains a syntax problem.", 1)
+    rescue StandardError => e
+      pp e.message
+      pp e.backtrace
+      showerror("Input data contains a syntactic problem.", 1)
     end
     @label_contraction = label_contraction
   end
-  
+
   ## process cxt data
   def read_cxt(input)
     lines = input.split
@@ -65,53 +71,65 @@ class FormalContext
     if (lines[0] !~ /B/i || (2 * lines[1].to_i + lines[2].to_i + t1) != lines.size)
       showerror("Wrong cxt format!", 1)
     end
-    @objects    = lines[t1..(lines[1].to_i + t1 - 1)]
-    @attributes = lines[(lines[1].to_i + t1) .. (lines[1].to_i + lines[2].to_i + t1 - 1)]
-    lines      = lines[(lines[1].to_i + lines[2].to_i + t1) .. lines.size]
-    @matrix     = changecrosssymbol("X", "\\.", lines)    
+    @objects = lines[t1..(lines[1].to_i + t1 - 1)]
+    @attributes = lines[(lines[1].to_i + t1)..(lines[1].to_i + lines[2].to_i + t1 - 1)]
+    lines = lines[(lines[1].to_i + lines[2].to_i + t1)..lines.size]
+    @matrix = changecrosssymbol("X", "\\.", lines)
   end
-  
+
   # process csv data using the standard csv library
   def read_csv(input)
     input = remove_blank(input)
     data = CSV.parse(input)
-    @objects = trim_ary(data.transpose.first[1..-1])
-    @attributes = trim_ary(data.first[1..-1])
+    @objects = trim_ary(data.transpose.first[1..])
+    @attributes = trim_ary(data.first[1..])
+    @matrix = []
+    data[1..].each do |line|
+      @matrix << line[1..].collect { |cell| /x/i =~ cell ? 1 : 0 }
+    end
+  end
+
+  # process xlsx data using the roo gem
+  def read_xlsx(file_path)
+    xlsx = Roo::Spreadsheet.open(file_path, extension: :xlsx)
+    @objects = xlsx.sheet(0).column(1)[1..]
+    @attributes = xlsx.sheet(0).row(1)[1..]
     @matrix = []
-    data[1..-1].each do |line|
-      @matrix << line[1..-1].collect { |cell| /x/i =~ cell ? 1 : 0 }
+    (2..xlsx.sheet(0).last_row).each do |row|
+      matrix_row = []
+      (2..xlsx.sheet(0).last_column).each do |col|
+        matrix_row << (xlsx.sheet(0).cell(row, col) =~ /x/i ? 1 : 0)
+      end
+      @matrix << matrix_row
     end
   end
-  
+
   def remove_blank(input)
-    blank_removed = ""
-    input.each do |line|
-      unless /^\s*$/ =~ line
-        blank_removed << line
+    blank_removed = +""
+    input.split("\n").each do |line|
+      line = line.strip
+      unless /\A\s*\z/ =~ line
+        blank_removed << line + "\n"
       end
     end
     blank_removed
   end
-  
+
   def trim_ary(ary)
-    newary = ary.collect do |cell|
-      cell.strip
-    end
-    newary
+    ary.map(&:strip)
   end
-  
+
   ## Apply a formal concept analysis on the matrix
-  def calculate 
+  def calcurate
     @concepts, @extM, @intM = ganter_alg(@matrix)
     @relM, @reltrans, @rank = create_rel(@intM)
     @gammaM, @muM = gammaMu(@extM, @intM, @matrix)
   end
 
-  ## This is an implementation of an algorithm described by Bernhard Ganter 
+  ## This is an implementation of an algorithm described by Bernhard Ganter
   ## in "Two basic algorithms in concept analysis." Technische Hochschule
   ## Darmstadt, FB4-Preprint, 831, 1984.
   def ganter_alg(matrix)
-
     m = matrix
 
     ## all arrays except @idx are arrays of arrays of 0's and 1's
@@ -122,25 +140,25 @@ class FormalContext
     int_B = []
     endkey = []
     temp = []
-    
+
     ## the level in the lattice from the top
-    lvl = 0 
+    lvl = 0
     ## is lower than the index of leftmost attr
-    idx[lvl] = -1     
+    idx[lvl] = -1
     ## number of attr. and objs
-    anzM = m.size   
-    ## only needed for initialization  
+    anzM = m.size
+    ## only needed for initialization
     anzG = m[0].size
     ## initialize extA[0] = [1,...,1]
-    anzG.times do |i|
-      if !ext_A[0]
+    anzG.times do
+      unless ext_A[0]
         ext_A[0] = []
       end
       ext_A[0] << 1
     end
     ## initialize extB[0] = [0,...,0]
-    anzM.times do |i| 
-      if !int_B[0]
+    anzM.times do
+      unless int_B[0]
         int_B[0] = []
       end
       int_B[0] << 0
@@ -148,7 +166,7 @@ class FormalContext
     anzCpt = 0
     extension[0] = ext_A[0]
     intension[0] = int_B[0]
-    anzM.times do |i|
+    anzM.times do
       endkey << 1
     end
 
@@ -157,13 +175,11 @@ class FormalContext
       (anzM - 1).downto(0) do |i|
         breakkey = false
         if (int_B[lvl][i] != 1)
-          while (i < idx[lvl])
-            lvl -= 1
-          end
+          lvl -= 1 while (i < idx[lvl])
           idx[lvl + 1] = i
           ext_A[lvl + 1] = create_and_ary(ext_A[lvl], m[i])
           0.upto(i - 1) do |j|
-            if(!breakkey && int_B[lvl][j] != 1)
+            if (!breakkey && int_B[lvl][j] != 1)
               temp = create_and_ary(ext_A[lvl + 1], m[j])
               if temp == ext_A[lvl + 1]
                 breakkey = true
@@ -173,7 +189,7 @@ class FormalContext
           unless breakkey
             int_B[lvl + 1] = int_B[lvl].dup
             int_B[lvl + 1][i] = 1
-            (i+1).upto(anzM - 1) do |k|
+            (i + 1).upto(anzM - 1) do |k|
               if int_B[lvl + 1][k] != 1
                 temp = create_and_ary(ext_A[lvl + 1], m[k])
                 if temp == ext_A[lvl + 1]
@@ -187,7 +203,7 @@ class FormalContext
             intension[anzCpt] = int_B[lvl]
             break
           end
-        end      
+        end
       end
     end
 
@@ -207,7 +223,7 @@ class FormalContext
     [c, intension, extension]
   end
 
-  ## Output arrayconsists of the following: 
+  ## Output arrayconsists of the following:
   ## r (subconcept superconcept relation)
   ## rt (trans. closure of r)
   ## s (ranked concepts)
@@ -224,11 +240,11 @@ class FormalContext
         unless r[i]
           r[i] = []
         end
-        r[i][j] = 0;
+        r[i][j] = 0
         unless rt[i]
           rt[i] = []
         end
-        rt[i][j] = 0;
+        rt[i][j] = 0
       end
     end
 
@@ -258,16 +274,15 @@ class FormalContext
         s[rank[i]] = []
       end
       s[rank[i]] << i
-    end  
+    end
     s = s.collect do |i|
-      i ? i : [0]
+      i || [0]
     end
 
     [r, rt, s]
-  end 
+  end
 
   def gammaMu(extent, intent, cxt)
-    
     gamma = []
     mu = []
     invcxt = []
@@ -281,31 +296,31 @@ class FormalContext
     0.upto(intent.size - 1) do |j|
       0.upto(cxt.size - 1) do |i|
         gamma[i] = [] unless gamma[i]
-        if cxt[i] == intent[j]
-          gamma[i][j] = 2
-        elsif (!@label_contraction && create_or_ary(cxt[i], intent[j]) == cxt[i])
-          gamma[i][j] = 1
-        else
-          gamma[i][j] = 0
-        end
+        gamma[i][j] = if cxt[i] == intent[j]
+                        2
+                      elsif (!@label_contraction && create_or_ary(cxt[i], intent[j]) == cxt[i])
+                        1
+                      else
+                        0
+                      end
       end
-      
+
       0.upto(invcxt.size - 1) do |i|
         # next unless invcxt[i]
         mu[i] = [] unless mu[i]
-        if invcxt[i] == extent[j]
-          mu[i][j] = 2
-        elsif (!@label_contraction && create_or_ary(invcxt[i], extent[j]) == invcxt[i])
-          mu[i][j] = 1
-        else
-          mu[i][j] = 0
-        end        
+        mu[i][j] = if invcxt[i] == extent[j]
+                     2
+                   elsif (!@label_contraction && create_or_ary(invcxt[i], extent[j]) == invcxt[i])
+                     1
+                   else
+                     0
+                   end
       end
     end
-    
+
     [gamma, mu]
   end
-  
+
   def changecrosssymbol(char1, char2, lns)
     rel = []
     lns.each do |ln|
@@ -326,36 +341,36 @@ class FormalContext
   ## Generate Graphviz dot data (not creating a file)
   ## For options, see 'rubyfca'
   def generate_dot(opts)
-    index_max_width = @concepts.size.to_s.split(//).size
-     nodesep = opts[:nodesep] ? opts[:nodesep].to_s : "0.4"
-     ranksep = opts[:ranksep] ? opts[:ranksep].to_s : "0.2"
-    clattice = RubyGraphviz.new("clattice", :rankdir => "", :nodesep => nodesep, :ranksep => ranksep)
-
-    if opts[:circle] and opts[:legend]
-      legend   = RubyGraphviz.new("legend", :rankdir => "TB", :lebelloc => "t", :centered => "false")
-      legend.node_default(:shape => "plaintext")
-      legend.edge_default(:color => "gray60") if opts[:coloring]
+    # index_max_width = @concepts.size.to_s.split(//).size
+    nodesep = opts[:nodesep] ? opts[:nodesep].to_s : "0.4"
+    ranksep = opts[:ranksep] ? opts[:ranksep].to_s : "0.2"
+    clattice = RubyGraphviz.new("clattice", rankdir: "", nodesep: nodesep, ranksep: ranksep)
+
+    if opts[:circle] && opts[:legend]
+      legend = RubyGraphviz.new("legend", rankdir: "TB", lebelloc: "t", centered: "false")
+      legend.node_default(shape: "plaintext")
+      legend.edge_default(color: "gray60") if opts[:coloring]
       legends = []
     end
 
     if opts[:circle]
-      clattice.node_default(:shape => "circle", :style => "filled") 
-      clattice.edge_default(:dir => "none", :minlen => "2")
-      clattice.edge_default(:color => "gray60") if opts[:coloring]
+      clattice.node_default(shape: "circle", style: "filled")
+      clattice.edge_default(dir: "none", minlen: "2")
+      clattice.edge_default(color: "gray60") if opts[:coloring]
     else
-      clattice.node_default(:shape => "record", :margin => "0.2,0.055") 
-      clattice.edge_default(:dir => "none")
-      clattice.edge_default(:color => "gray60") if opts[:coloring]
+      clattice.node_default(shape: "record", margin: "0.2,0.055")
+      clattice.edge_default(dir: "none")
+      clattice.edge_default(color: "gray60") if opts[:coloring]
     end
-    
+
     0.upto(@concepts.size - 1) do |i|
       objfull = []
-      attrfull = []  
+      attrfull = []
       0.upto(@gammaM.size - 1) do |j|
         if @gammaM[j][i] == 2
-	        # pointing finger does not appear correctly in eps... 
+          # pointing finger does not appear correctly in eps...
           # obj = opts[:full] ? @objects[j] + " " + [0x261C].pack("U") : @objects[j]
-          obj = opts[:full] ? @objects[j] + "*" : @objects[j]
+          obj = opts[:full] ? @objects[j].to_s + "*" : @objects[j].to_s
           objfull << obj
         elsif @gammaM[j][i] == 1
           objfull << @objects[j]
@@ -363,9 +378,9 @@ class FormalContext
       end
       0.upto(@muM.size - 1) do |k|
         if @muM[k][i] == 2
-	        # pointing finger does not appear correctly in eps... 
+          # pointing finger does not appear correctly in eps...
           # att = opts[:full] ? @attributes[k] + " " + [0x261C].pack("U") : @attributes[k]
-          att = opts[:full] ? @attributes[k] + "*" : @attributes[k]
+          att = opts[:full] ? @attributes[k].to_s + "*" : @attributes[k].to_s
           attrfull << att
         elsif @muM[k][i] == 1
           attrfull << @attributes[k]
@@ -374,21 +389,21 @@ class FormalContext
 
       concept_id = i + 1
 
-      attr_str = attrfull.join('<br />')
+      attr_str = attrfull.join("<br />")
       attr_str = attr_str == "" ? "     " : attr_str
-      
-      if opts[:coloring] == 0 or /\A\s+\z/ =~ attr_str
+
+      if opts[:coloring].zero? || /\A\s+\z/ =~ attr_str
         attr_color = "white"
       elsif opts[:coloring] == 1
         attr_color = "lightblue"
       elsif opts[:coloring] == 2
         attr_color = "gray87"
       end
-      
-      obj_str = objfull.join('<br />')
+
+      obj_str = objfull.join("<br />")
       obj_str = obj_str == "" ? "     " : obj_str
 
-      if opts[:coloring] == 0 or /\A\s+\z/ =~ obj_str
+      if opts[:coloring].zero? || /\A\s+\z/ =~ obj_str
         obj_color = "white"
       elsif opts[:coloring] == 1
         obj_color = "pink"
@@ -396,37 +411,36 @@ class FormalContext
         obj_color = "gray92"
       end
 
-      label = "<<table border=\"0\" cellborder=\"1\" cellspacing=\"0\">" + 
-      "<tr><td balign=\"left\" align=\"left\" bgcolor=\"#{attr_color}\">#{attr_str}</td></tr>" +
-      "<tr><td balign=\"left\" align=\"left\"  bgcolor=\"#{obj_color}\">#{obj_str}</td></tr>" +
-      "</table>>"
+      label = "<<table border=\"0\" cellborder=\"1\" cellspacing=\"0\">" \
+        "<tr><td balign=\"left\" align=\"left\" bgcolor=\"#{attr_color}\">#{attr_str}</td></tr>" \
+        "<tr><td balign=\"left\" align=\"left\"  bgcolor=\"#{obj_color}\">#{obj_str}</td></tr>" \
+        "</table>>"
 
-      if opts[:circle] and opts[:legend]
+      if opts[:circle] && opts[:legend]
 
-        leg = "<<table border=\"0\" cellborder=\"1\" cellspacing=\"0\">" + 
-        "<tr><td rowspan=\"2\">#{concept_id}</td><td balign=\"left\" align=\"left\" bgcolor=\"#{attr_color}\">#{attr_str}</td></tr>" + 
-        "<tr><td balign=\"left\" align=\"left\" bgcolor=\"#{obj_color}\">#{obj_str}</td></tr>" +
-        "</table>>"
+        leg = "<<table border=\"0\" cellborder=\"1\" cellspacing=\"0\">" \
+          "<tr><td rowspan=\"2\">#{concept_id}</td><td balign=\"left\" align=\"left\" bgcolor=\"#{attr_color}\">#{attr_str}</td></tr>" \
+          "<tr><td balign=\"left\" align=\"left\" bgcolor=\"#{obj_color}\">#{obj_str}</td></tr>" \
+          "</table>>"
 
-        if !attrfull.empty? or !objfull.empty?
-          legend.node("cl#{concept_id}k", :label => concept_id, :style => "invis")
-          legend.node("cl#{concept_id}v", :label => leg, :fillcolor => "white")
-          legend.rank("cl#{concept_id}k", "cl#{concept_id}v", :style => "invis", :length => "0.0")
+        if !attrfull.empty? || !objfull.empty?
+          legend.node("cl#{concept_id}k", label: concept_id, style: "invis")
+          legend.node("cl#{concept_id}v", label: leg, fillcolor: "white")
+          legend.rank("cl#{concept_id}k", "cl#{concept_id}v", style: "invis", length: "0.0")
           if legends[-1]
-            legend.edge("cl#{legends[-1]}k", "cl#{concept_id}k", :style => "invis", :length => "0.0")
+            legend.edge("cl#{legends[-1]}k", "cl#{concept_id}k", style: "invis", length: "0.0")
           end
           legends << concept_id
         end
       end
-      
+
       if opts[:circle]
-        clattice.node("c#{i}", :width => "0.5", :fontsize => "14.0", :label => concept_id)
+        clattice.node("c#{i}", width: "0.5", fontsize: "14.0", label: concept_id)
       else
-        clattice.node("c#{i}", :label => label, :shape => "plaintext", 
-                               :height => "0.0", :width => "0.0", :margin => "0.0")
+        clattice.node("c#{i}", label: label, shape: "plaintext", height: "0.0", width: "0.0", margin: "0.0")
       end
     end
-    
+
     0.upto(@relM.size - 1) do |i|
       0.upto(@relM.size - 1) do |j|
         if @relM[i][j] == 1
@@ -434,11 +448,11 @@ class FormalContext
         end
       end
     end
-    
-    clattice.subgraph(legend) if opts[:circle] and opts[:legend]
+
+    clattice.subgraph(legend) if opts[:circle] && opts[:legend]
     clattice.to_dot
   end
-  
+
   ## Generate an actual graphic file (Graphviz dot needs to be installed properly)
   def generate_img(outfile, image_type, opts)
     dot = generate_dot(opts)
@@ -446,15 +460,14 @@ class FormalContext
     if isthere_dot !~ /dot.*version/i
       showerror("Graphviz's dot program cannot be found.", 1)
     else
-      if opts[:straight]
-        cmd = "dot | neato -n -T#{image_type} -o#{outfile} 2>rubyfca.log"
-      else
-        cmd = "dot -T#{image_type} -o#{outfile} 2>rubyfca.log"
-      end
-      IO.popen(cmd, 'r+') do |io|
+      cmd = if opts[:straight]
+              "dot | neato -n -T#{image_type} -o#{outfile} 2>rubyfca.log"
+            else
+              "dot -T#{image_type} -o#{outfile} 2>rubyfca.log"
+            end
+      IO.popen(cmd, "r+") do |io|
         io.puts dot
       end
     end
-  end  
+  end
 end
-

data/rubyfca.gemspec

@@ -1,60 +1,25 @@
-# Generated by jeweler
-# DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
-# -*- encoding: utf-8 -*-
+# frozen_string_literal: true
 
-Gem::Specification.new do |s|
-  s.name = %q{rubyfca}
-  s.version = "0.2.10"
+require File.expand_path("lib/rubyfca/version", __dir__)
 
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Yoichiro Hasebe"]
-  s.date = %q{2010-01-17}
-  s.default_executable = %q{rubyfca}
-  s.description = %q{Command line Formal Concept Ananlysis (FCA) tool written in Ruby}
-  s.email = %q{yohasebe@gmail.com}
-  s.executables = ["rubyfca"]
-  s.extra_rdoc_files = [
-    "LICENSE",
-     "README.rdoc"
-  ]
-  s.files = [
-    ".document",
-     ".gitignore",
-     "LICENSE",
-     "README.rdoc",
-     "Rakefile",
-     "VERSION",
-     "bin/rubyfca",
-     "lib/ruby_graphviz.rb",
-     "lib/rubyfca.rb",
-     "lib/trollop.rb",
-     "rubyfca.gemspec",
-     "test/rubyfca_test.rb",
-     "test/test_data.cxt",
-     "test/test_helper.rb"
-  ]
-  s.homepage = %q{http://github.com/yohasebe/rubyfca}
-  s.rdoc_options = ["--charset=UTF-8"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.3.5}
-  s.summary = %q{Command line Formal Concept Ananlysis (FCA) tool written in Ruby}
-  s.test_files = [
-    "test/rubyfca_test.rb",
-     "test/test_helper.rb"
-  ]
+Gem::Specification.new do |gem|
+  gem.name          = "rubyfca"
+  gem.version       = RubyFCA::VERSION
+  gem.authors       = ["Yoichiro Hasebe", "Kow Kuroda"]
+  gem.email         = ["yohasebe@gmail.com"]
+  gem.summary       = "Command line FCA tool written in Ruby"
+  gem.description   = "Command line Formal Concept Analysis (FCA) tool written in Ruby"
+  gem.homepage      = "http://github.com/yohasebe/rubyfca"
 
-  if s.respond_to? :specification_version then
-    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
-    s.specification_version = 3
+  gem.required_ruby_version = ">= 2.6.10"
+  gem.licenses      = ["GPL-3.0"]
+  gem.files         = `git ls-files`.split("\n")
+  gem.executables   = `git ls-files -- bin/*`.split("\n").map { |f| File.basename(f) }
+  gem.require_paths = ["lib"]
 
-    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
-      s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
-    else
-      s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
-    end
-  else
-    s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
-  end
-end
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
 
+  gem.add_dependency "optimist"
+  gem.add_dependency "roo"
+  gem.add_development_dependency "minitest"
+end