gnuplotrb 0.3.1 → 0.3.2

data/lib/gnuplotrb/external_classes/string.rb

@@ -1,6 +1,6 @@
-##
-# Methods to take data for GnuplotRB plots.
-class String
-  # @return [String] data converted to Gnuplot format
-  alias_method :to_gnuplot_points, :clone
-end
+##
+# Methods to take data for GnuplotRB plots.
+class String
+  # @return [String] data converted to Gnuplot format
+  alias_method :to_gnuplot_points, :clone
+end

data/lib/gnuplotrb/fit.rb

@@ -1,204 +1,204 @@
-module GnuplotRB
-  ##
-  # Contains methods relating to Gnuplot's fit function. Covered in
-  # {fit notebook}[http://nbviewer.ipython.org/github/dilcom/gnuplotrb/blob/master/notebooks/fitting_data.ipynb].
-  #
-  # You can also see original gnuplot's fit in
-  # {gnuplot doc}[http://www.gnuplot.info/docs_5.0/gnuplot.pdf] p. 122.
-  module Fit
-    ##
-    # Fit given data with function.
-    #
-    # Fit waits for output from gnuplot Settings.max_fit_delay and throw exception if gets nothing.
-    # One can change this value in order to wait longer (if huge datasets is fitted).
-    #
-    # @param data [#to_gnuplot_points] method accepts the same sources as Dataset.new
-    #   and Dataset object
-    # @param :function [String] function to fit data with
-    # @param :initials [Hash] initial values for coefficients used in fitting
-    # @param :term_options [Hash] terminal options that should be setted to terminal before fit.
-    #   You can see them in Plot's documentation (or even better in gnuplot doc)
-    #   Most useful here are ranges (xrange, yrange etc) and fit option which tunes fit parameters
-    #   (see {gnuplot doc}[http://www.gnuplot.info/docs_5.0/gnuplot.pdf] p. 122)
-    # @param options [Hash] options passed to Gnuplot's fit such as *using*. They are covered in
-    #   {gnuplot doc}[http://www.gnuplot.info/docs_5.0/gnuplot.pdf] (pp. 69-74)
-    #
-    # @return [Hash] hash with four elements:
-    #   - :formula_ds - dataset with best fit curve as data
-    #   - :coefficients - hash of calculated coefficients. So if you gave
-    #     ``{ initials: {a: 1, b: 1, c: 1} }`` it will return hash with keys :a, :b, :c and its values
-    #   - :deltas - Gnuplot calculates possible deltas for coefficients during fitting and
-    #     deltas hash contains this deltas
-    #   - :data - pointer to Datablock with given data
-    # @example
-    #   fit(some_data, function: 'exp(a/x)', initials: {a: 10}, term_option: { xrange: 1..100 })
-    #   fit(some_dataset, using: '1:2:3')
-    def fit(data, function: 'a2*x*x+a1*x+a0', initials: { a2: 1, a1: 1, a0: 1 }, term_options: {}, **options)
-      dataset = data.is_a?(Dataset) ? Dataset.new(data.data) : Dataset.new(data)
-      opts_str = OptionHandling.ruby_class_to_gnuplot(options)
-      output = gnuplot_fit(function, dataset, opts_str, initials, term_options)
-      res = parse_output(initials.keys, function, output)
-      {
-        formula_ds: Dataset.new(res[2], title: 'Fit formula'),
-        coefficients: res[0],
-        deltas: res[1],
-        data: dataset
-      }
-    end
-
-    ##
-    # Shortcut for fit with polynomial. Degree here is max power of *x* in polynomial.
-    #
-    # @param data [#to_gnuplot_points] method accepts the same sources as Dataset.new
-    #   and Dataset object
-    # @param :degree [Integer] degree of polynomial
-    # @param options [Hash] all of this options will be passed to #fit so you
-    #   can set here any options listed in its docs. If you pass here :initials hash, it
-    #   will be merged into default initals hash. Formula by default is
-    #   "xn*x**n + ... + x0*x**0", initials by default "{ an: 1, ..., a0: 1 }"
-    #
-    # @return [Hash] hash with four elements:
-    #   - :formula_ds - dataset with best fit curve as data
-    #   - :coefficients - hash of calculated coefficients. So for degree = 3
-    #     it will return hash with keys :a3, :a2, :a1, :a0 and calculated values
-    #   - :deltas - Gnuplot calculates possible deltas for coefficients during fitting and
-    #     deltas hash contains this deltas
-    #   - :data - pointer to Datablock with given data
-    # @example
-    #   fit_poly(some_data, degree: 5, initials: { a4: 10, a2: -1 }, term_option: { xrange: 1..100 })
-    #   #=> The same as:
-    #   #=> fit(
-    #   #=>   some_data,
-    #   #=>   function: 'a5*x**5 + a4*x**4 + ... + a0*x**0',
-    #   #=>   initals: {a5: 1, a4: 10, a3: 1, a2: -1, a1: 1, a0: 1},
-    #   #=>   term_option: { xrange: 1..100 }
-    #   #=> )
-    def fit_poly(data, degree: 2, **options)
-      sum_count = degree + 1
-      initials = {}
-      sum_count.times { |i| initials["a#{i}".to_sym] = 1 }
-      options[:initials] = initials.merge(options[:initials] || {})
-      function = sum_count.times.map { |i| "a#{i}*x**#{i}" }.join(' + ')
-      fit(data, **options, function: function)
-    end
-
-    ##
-    # @!method fit_exp(data, **options)
-    # @!method fit_log(data, **options)
-    # @!method fit_sin(data, **options)
-    #
-    # Shortcuts for fitting with several math functions (exp, log, sin).
-    #
-    # @param data [#to_gnuplot_points] method accepts the same sources as Dataset.new
-    #   and Dataset object
-    # @param options [Hash] all of this options will be passed to #fit so you
-    #   can set here any options listed in its docs. If you pass here :initials hash, it
-    #   will be merged into default initals hash. Formula by default is
-    #   "yscale * (yoffset + #{function name}((x - xoffset) / xscale))", initials by default
-    #   "{ yoffset: 0.1, xoffset: 0.1, yscale: 1, xscale: 1 }"
-    #
-    # @return [Hash] hash with four elements:
-    #   - :formula_ds - dataset with best fit curve as data
-    #   - :coefficients - hash of calculated coefficients. So for this case
-    #     it will return hash with keys :yoffset, :xoffset, :yscale, :xscale and calculated values
-    #   - :deltas - Gnuplot calculates possible deltas for coefficients during fitting and
-    #     deltas hash contains this deltas
-    #   - :data - pointer to Datablock with given data
-    #
-    # @example
-    #   fit_exp(some_data, initials: { yoffset: -11 }, term_option: { xrange: 1..100 })
-    #   #=> The same as:
-    #   #=> fit(
-    #   #=>   some_data,
-    #   #=>   function: 'yscale * (yoffset + exp((x - xoffset) / xscale))',
-    #   #=>   initals: { yoffset: -11, xoffset: 0.1, yscale: 1, xscale: 1 },
-    #   #=>   term_option: { xrange: 1..100 }
-    #   #=> )
-    #   fit_log(...)
-    #   fit_sin(...)
-    %w(exp log sin).map do |fname|
-      define_method("fit_#{fname}".to_sym) do |data, **options|
-        options[:initials] = {
-          yoffset: 0.1,
-          xoffset: 0.1,
-          yscale: 1,
-          xscale: 1
-        }.merge(options[:initials] || {})
-        function = "yscale * (yoffset + #{fname} ((x - xoffset) / xscale))"
-        fit(data, **options, function: function)
-      end
-    end
-
-    private
-
-    ##
-    # It takes some time to produce output so here we need
-    # to wait for it.
-    #
-    # Max time to wait is stored in Settings.max_fit_delay, so one
-    # can change it in order to wait longer.
-    def wait_for_output(term, variables)
-      # now we should catch 'error' from terminal: it will contain approximation data
-      # but we can get a real error instead of output, so lets wait for limited time
-      start = Time.now
-      output = ''
-      until output_ready?(output, variables)
-        begin
-          term.check_errors(raw: true)
-        rescue GnuplotRB::GnuplotError => e
-          output += e.message
-        end
-        if Time.now - start > Settings.max_fit_delay
-          fail GnuplotError, "Seems like there is an error in gnuplotrb: #{output}"
-        end
-      end
-      output
-    end
-
-    ##
-    # Check if current output contains all the
-    # variables given to fit.
-    def output_ready?(output, variables)
-      output =~ /Final set .*#{variables.join('.*')}/
-    end
-
-    ##
-    # Parse Gnuplot's output to get coefficients and their deltas
-    # from it. Also replaces coefficients in given function with
-    # exact values.
-    def parse_output(variables, function, output)
-      plottable_function = " #{function.clone} "
-      coefficients = {}
-      deltas = {}
-      variables.each do |var|
-        value, error = output.scan(%r{#{var} *= ([^ ]+) *\+/\- ([^ ]+)})[0]
-        plottable_function.gsub!(/#{var}([^0-9a-zA-Z])/) { value + Regexp.last_match(1) }
-        coefficients[var] = value.to_f
-        deltas[var] = error.to_f
-      end
-      [coefficients, deltas, plottable_function]
-    end
-
-    ##
-    # Make fit command and send it to gnuplot
-    def gnuplot_fit(function, data, options, initials, term_options)
-      variables = initials.keys
-      term = Terminal.new
-      term.set(term_options)
-      initials.each { |var_name, value| term.stream_puts "#{var_name} = #{value}" }
-      command = "fit #{function} #{data.to_s(term, without_options: true)} " \
-                "#{options} via #{variables.join(',')}"
-      term.stream_puts(command)
-      output = wait_for_output(term, variables)
-      begin
-        term.close
-      rescue GnuplotError
-        # Nothing interesting here.
-        # If we had an error, we never reach this line.
-        # Error here may be only additional information
-        # such as correlation matrix.
-      end
-      output
-    end
-  end
-end
+module GnuplotRB
+  ##
+  # Contains methods relating to Gnuplot's fit function. Covered in
+  # {fit notebook}[http://nbviewer.ipython.org/github/dilcom/gnuplotrb/blob/master/notebooks/fitting_data.ipynb].
+  #
+  # You can also see original gnuplot's fit in
+  # {gnuplot doc}[http://www.gnuplot.info/docs_5.0/gnuplot.pdf] p. 122.
+  module Fit
+    ##
+    # Fit given data with function.
+    #
+    # Fit waits for output from gnuplot Settings.max_fit_delay and throw exception if gets nothing.
+    # One can change this value in order to wait longer (if huge datasets is fitted).
+    #
+    # @param data [#to_gnuplot_points] method accepts the same sources as Dataset.new
+    #   and Dataset object
+    # @param :function [String] function to fit data with
+    # @param :initials [Hash] initial values for coefficients used in fitting
+    # @param :term_options [Hash] terminal options that should be setted to terminal before fit.
+    #   You can see them in Plot's documentation (or even better in gnuplot doc)
+    #   Most useful here are ranges (xrange, yrange etc) and fit option which tunes fit parameters
+    #   (see {gnuplot doc}[http://www.gnuplot.info/docs_5.0/gnuplot.pdf] p. 122)
+    # @param options [Hash] options passed to Gnuplot's fit such as *using*. They are covered in
+    #   {gnuplot doc}[http://www.gnuplot.info/docs_5.0/gnuplot.pdf] (pp. 69-74)
+    #
+    # @return [Hash] hash with four elements:
+    #   - :formula_ds - dataset with best fit curve as data
+    #   - :coefficients - hash of calculated coefficients. So if you gave
+    #     ``{ initials: {a: 1, b: 1, c: 1} }`` it will return hash with keys :a, :b, :c and its values
+    #   - :deltas - Gnuplot calculates possible deltas for coefficients during fitting and
+    #     deltas hash contains this deltas
+    #   - :data - pointer to Datablock with given data
+    # @example
+    #   fit(some_data, function: 'exp(a/x)', initials: {a: 10}, term_option: { xrange: 1..100 })
+    #   fit(some_dataset, using: '1:2:3')
+    def fit(data, function: 'a2*x*x+a1*x+a0', initials: { a2: 1, a1: 1, a0: 1 }, term_options: {}, **options)
+      dataset = data.is_a?(Dataset) ? Dataset.new(data.data) : Dataset.new(data)
+      opts_str = OptionHandling.ruby_class_to_gnuplot(options)
+      output = gnuplot_fit(function, dataset, opts_str, initials, term_options)
+      res = parse_output(initials.keys, function, output)
+      {
+        formula_ds: Dataset.new(res[2], title: 'Fit formula'),
+        coefficients: res[0],
+        deltas: res[1],
+        data: dataset
+      }
+    end
+
+    ##
+    # Shortcut for fit with polynomial. Degree here is max power of *x* in polynomial.
+    #
+    # @param data [#to_gnuplot_points] method accepts the same sources as Dataset.new
+    #   and Dataset object
+    # @param :degree [Integer] degree of polynomial
+    # @param options [Hash] all of this options will be passed to #fit so you
+    #   can set here any options listed in its docs. If you pass here :initials hash, it
+    #   will be merged into default initals hash. Formula by default is
+    #   "xn*x**n + ... + x0*x**0", initials by default "{ an: 1, ..., a0: 1 }"
+    #
+    # @return [Hash] hash with four elements:
+    #   - :formula_ds - dataset with best fit curve as data
+    #   - :coefficients - hash of calculated coefficients. So for degree = 3
+    #     it will return hash with keys :a3, :a2, :a1, :a0 and calculated values
+    #   - :deltas - Gnuplot calculates possible deltas for coefficients during fitting and
+    #     deltas hash contains this deltas
+    #   - :data - pointer to Datablock with given data
+    # @example
+    #   fit_poly(some_data, degree: 5, initials: { a4: 10, a2: -1 }, term_option: { xrange: 1..100 })
+    #   #=> The same as:
+    #   #=> fit(
+    #   #=>   some_data,
+    #   #=>   function: 'a5*x**5 + a4*x**4 + ... + a0*x**0',
+    #   #=>   initals: {a5: 1, a4: 10, a3: 1, a2: -1, a1: 1, a0: 1},
+    #   #=>   term_option: { xrange: 1..100 }
+    #   #=> )
+    def fit_poly(data, degree: 2, **options)
+      sum_count = degree + 1
+      initials = {}
+      sum_count.times { |i| initials["a#{i}".to_sym] = 1 }
+      options[:initials] = initials.merge(options[:initials] || {})
+      function = sum_count.times.map { |i| "a#{i}*x**#{i}" }.join(' + ')
+      fit(data, **options, function: function)
+    end
+
+    ##
+    # @!method fit_exp(data, **options)
+    # @!method fit_log(data, **options)
+    # @!method fit_sin(data, **options)
+    #
+    # Shortcuts for fitting with several math functions (exp, log, sin).
+    #
+    # @param data [#to_gnuplot_points] method accepts the same sources as Dataset.new
+    #   and Dataset object
+    # @param options [Hash] all of this options will be passed to #fit so you
+    #   can set here any options listed in its docs. If you pass here :initials hash, it
+    #   will be merged into default initals hash. Formula by default is
+    #   "yscale * (yoffset + #{function name}((x - xoffset) / xscale))", initials by default
+    #   "{ yoffset: 0.1, xoffset: 0.1, yscale: 1, xscale: 1 }"
+    #
+    # @return [Hash] hash with four elements:
+    #   - :formula_ds - dataset with best fit curve as data
+    #   - :coefficients - hash of calculated coefficients. So for this case
+    #     it will return hash with keys :yoffset, :xoffset, :yscale, :xscale and calculated values
+    #   - :deltas - Gnuplot calculates possible deltas for coefficients during fitting and
+    #     deltas hash contains this deltas
+    #   - :data - pointer to Datablock with given data
+    #
+    # @example
+    #   fit_exp(some_data, initials: { yoffset: -11 }, term_option: { xrange: 1..100 })
+    #   #=> The same as:
+    #   #=> fit(
+    #   #=>   some_data,
+    #   #=>   function: 'yscale * (yoffset + exp((x - xoffset) / xscale))',
+    #   #=>   initals: { yoffset: -11, xoffset: 0.1, yscale: 1, xscale: 1 },
+    #   #=>   term_option: { xrange: 1..100 }
+    #   #=> )
+    #   fit_log(...)
+    #   fit_sin(...)
+    %w(exp log sin).map do |fname|
+      define_method("fit_#{fname}".to_sym) do |data, **options|
+        options[:initials] = {
+          yoffset: 0.1,
+          xoffset: 0.1,
+          yscale: 1,
+          xscale: 1
+        }.merge(options[:initials] || {})
+        function = "yscale * (yoffset + #{fname} ((x - xoffset) / xscale))"
+        fit(data, **options, function: function)
+      end
+    end
+
+    private
+
+    ##
+    # It takes some time to produce output so here we need
+    # to wait for it.
+    #
+    # Max time to wait is stored in Settings.max_fit_delay, so one
+    # can change it in order to wait longer.
+    def wait_for_output(term, variables)
+      # now we should catch 'error' from terminal: it will contain approximation data
+      # but we can get a real error instead of output, so lets wait for limited time
+      start = Time.now
+      output = ''
+      until output_ready?(output, variables)
+        begin
+          term.check_errors(raw: true)
+        rescue GnuplotRB::GnuplotError => e
+          output += e.message
+        end
+        if Time.now - start > Settings.max_fit_delay
+          fail GnuplotError, "Seems like there is an error in gnuplotrb: #{output}"
+        end
+      end
+      output
+    end
+
+    ##
+    # Check if current output contains all the
+    # variables given to fit.
+    def output_ready?(output, variables)
+      output =~ /Final set .*#{variables.join('.*')}/
+    end
+
+    ##
+    # Parse Gnuplot's output to get coefficients and their deltas
+    # from it. Also replaces coefficients in given function with
+    # exact values.
+    def parse_output(variables, function, output)
+      plottable_function = " #{function.clone} "
+      coefficients = {}
+      deltas = {}
+      variables.each do |var|
+        value, error = output.scan(%r{#{var} *= ([^ ]+) *\+/\- ([^ ]+)})[0]
+        plottable_function.gsub!(/#{var}([^0-9a-zA-Z])/) { value + Regexp.last_match(1) }
+        coefficients[var] = value.to_f
+        deltas[var] = error.to_f
+      end
+      [coefficients, deltas, plottable_function]
+    end
+
+    ##
+    # Make fit command and send it to gnuplot
+    def gnuplot_fit(function, data, options, initials, term_options)
+      variables = initials.keys
+      term = Terminal.new
+      term.set(term_options)
+      initials.each { |var_name, value| term.stream_puts "#{var_name} = #{value}" }
+      command = "fit #{function} #{data.to_s(term, without_options: true)} " \
+                "#{options} via #{variables.join(',')}"
+      term.stream_puts(command)
+      output = wait_for_output(term, variables)
+      begin
+        term.close
+      rescue GnuplotError
+        # Nothing interesting here.
+        # If we had an error, we never reach this line.
+        # Error here may be only additional information
+        # such as correlation matrix.
+      end
+      output
+    end
+  end
+end

data/lib/gnuplotrb/mixins/error_handling.rb

@@ -1,48 +1,48 @@
-module GnuplotRB
-  ##
-  # Just a new error name
-  class GnuplotError < ArgumentError
-  end
-
-  ##
-  # Mixin for classes that need to run subprocess and
-  # handle errors from its stderr.
-  module ErrorHandling
-    ##
-    # Check if there were errors in previous commands.
-    # Throws GnuplotError in case of any errors.
-    def check_errors(raw: false)
-      return if @err_array.empty?
-      command = ''
-      rest = ''
-      @semaphore.synchronize do
-        command = @err_array.first
-        rest = @err_array[1..-1].join('; ')
-        @err_array.clear
-      end
-      message = if raw
-        "#{command};#{rest}}"
-      else
-        "Error in previous command (\"#{command}\"): \"#{rest}\""
-      end
-      fail GnuplotError, message
-    end
-
-    private
-
-    ##
-    # Start new thread that will read stderr given as stream
-    # and add errors into @err_array.
-    def handle_stderr(stream)
-      @err_array = []
-      # synchronize access to @err_array
-      @semaphore = Mutex.new
-      Thread.new do
-        until (line = stream.gets).nil?
-          line.strip!
-          @semaphore.synchronize { @err_array << line if line.size > 3 }
-        end
-      end
-    end
-  end
-end
+module GnuplotRB
+  ##
+  # Just a new error name
+  class GnuplotError < ArgumentError
+  end
+
+  ##
+  # Mixin for classes that need to run subprocess and
+  # handle errors from its stderr.
+  module ErrorHandling
+    ##
+    # Check if there were errors in previous commands.
+    # Throws GnuplotError in case of any errors.
+    def check_errors(raw: false)
+      return if @err_array.empty?
+      command = ''
+      rest = ''
+      @semaphore.synchronize do
+        command = @err_array.first
+        rest = @err_array[1..-1].join('; ')
+        @err_array.clear
+      end
+      message = if raw
+        "#{command};#{rest}}"
+      else
+        "Error in previous command (\"#{command}\"): \"#{rest}\""
+      end
+      fail GnuplotError, message
+    end
+
+    private
+
+    ##
+    # Start new thread that will read stderr given as stream
+    # and add errors into @err_array.
+    def handle_stderr(stream)
+      @err_array = []
+      # synchronize access to @err_array
+      @semaphore = Mutex.new
+      Thread.new do
+        until (line = stream.gets).nil?
+          line.strip!
+          @semaphore.synchronize { @err_array << line if line.size > 3 }
+        end
+      end
+    end
+  end
+end