ctioga2 0.12 → 0.13

checksums.yaml

@@ -1,7 +1,7 @@
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data/Changelog

@@ -1,3 +1,15 @@
+ctioga2 (0.13)
+
+  * Change the stroke width when using draw-marker
+  * Customizable outut PDF resolution
+  * Can now get the standard deviation as error bars using avg-dup-last
+  * Handling of histograms with 'holes' in X values (closes: SF issue #1)
+  * Various improvements in the emacs mode, including contextual help
+  * Automatic generation of dependencies (makefile format)
+  * Many bug fixes
+
+ -- Vincent <vincent.fourmond@9online.fr>  Thu 11 Jun 23:01:19 CEST 2015
+
 ctioga2 (0.12)
 
   * The xyz-map plot type now handles correctly inhomogeneous grids (so long

data/lib/ctioga2/commands/doc/doc.rb

@@ -90,6 +90,40 @@ module CTioga2
             print_commandline_options(*self.documented_commands)
         end
 
+        # Displays help on a given command
+        def display_help_on(cmd, options)
+          if ! cmd.is_a? Command
+            cd = Interpreter::commands[cmd]
+            raise "Unkown command '#{cmd}'" unless cd
+            cmd = cd
+          end
+          puts text_doc(cmd)
+        end
+
+        # Returns a string that represents a plain text documentation
+        def text_doc(cmd, options = {})
+
+          size ||= 80
+
+          str = "Synopsis: "
+          str << cmd.name
+          for arg in cmd.arguments
+            str << " #{arg.type.name}"
+          end
+
+          os = ""
+          for k,v in cmd.optional_arguments
+            os << " /#{k}=#{v.type.name}"
+          end
+          s2 = WordWrapper.wrap(os, size-4) # 4 for the spaces
+          str << "\nOptions: #{s2.join("\n    ")}"
+          shrt = MarkedUpText.new(self, cmd.short_description).to_s
+          mup = MarkedUpText.new(self, cmd.long_description).to_s
+          s2 = WordWrapper.wrap(mup.to_s, size)
+          return "#{cmd.name} -- #{shrt}\n#{str}\n#{s2.join("\n")}"
+        end
+
+
         protected 
 
 

data/lib/ctioga2/commands/doc/help.rb

@@ -140,6 +140,9 @@ module CTioga2
         # Formats one entry of the commands
         def format_one_entry(cmd)
           sh, long, desc = cmd.option_strings
+
+          # Hmmm...
+          # desc = MarkedUpText.new(@doc, desc).to_s
           
           str = "#{leading_spaces}%2s%1s %-#{@options_column_width}s" % 
             [ sh, (sh ? "," : " "), long]

data/lib/ctioga2/commands/doc/html.rb

@@ -144,7 +144,7 @@ module CTioga2
                       ln.gsub!(/<a[^>]+>(.*?)<\/a>/) { || $1 }
                       str += "<pre class='#{s[:cls]}'><a href='#{k}'>#{ln}</a></pre>\n"
                     end
-                    out.puts "<h5 id='#snippets-h5-#{cmd.name}' onclick='toggleExamples(this);'>Examples...</h5>\n<div id='#snippets-#{cmd.name}' class='snippets'>#{str}</div>"
+                    out.puts "<h5 id='snippets-h5-#{cmd.name}' onclick='toggleExamples(this);'>Examples...</h5>\n<div id='snippets-#{cmd.name}' class='snippets'>#{str}</div>"
                   end
                 end
               end

data/lib/ctioga2/commands/doc/man.rb

@@ -48,7 +48,7 @@ module CTioga2
           passed_header = false
           if input.is_a? String
             filename = input
-            input = File::open(input)
+            input = Utils::open(input)
           elsif input.respond_to? :path
             filename = input.path
           else

data/lib/ctioga2/commands/doc/markup.rb

@@ -280,6 +280,12 @@ module CTioga2
           flush_element
         end
 
+        def to_s
+          return @elements.map do |x|
+            x.to_s
+          end.join("")
+        end
+
         protected 
 
         # A few constants to help writing out the paragraph markup

data/lib/ctioga2/commands/general-commands.rb

@@ -42,7 +42,20 @@ module CTioga2
 Prints helps about short and long options available when run from the
 command-line.
 EOH
+
+        # Display help on the command-line
+    HelpOnCommand = 
+      Cmd.new("help-on", nil, 
+              "--help-on", [CmdArg.new('text') ]) do |plotmaker, cmd, options|
+      plotmaker.interpreter.doc.display_help_on(cmd, options)
+      exit 
+    end
     
+    HelpOnCommand.describe("Prints help text about the given command",
+                           <<EOH, GeneralGroup)
+Prints help about the given command
+EOH
+
     # Prints the version of ctioga2 used
     PrintVersion = Cmd.new("version", '-V', "--version", []) do |plotmaker|
       puts "This is ctioga2 version #{CTioga2::Version::version}"

data/lib/ctioga2/commands/interpreter.rb

@@ -224,7 +224,7 @@ module CTioga2
         dir = File::dirname(file)
         base = File::basename(file)
 
-        Dir::chdir(dir) do
+        Utils::chdir(dir) do
           @file_parser.run_command_file(base, self)
         end
       end

data/lib/ctioga2/commands/parsers/file.rb

@@ -44,7 +44,7 @@ module CTioga2
 
         # Runs a command file targeting the given _interpreter_.
         def run_command_file(file, interpreter)
-          f = open(file)
+          f = Utils::open(file)
           parse_io_object(f, interpreter)
         end
 
@@ -208,8 +208,15 @@ module CTioga2
                   end
                 else
                   nxt = all_args.shift
+                  if ! nxt
+                    fatal { "Missing option text for option '#{o}'"}
+                  end
                   if nxt =~ /^\s*=\s*$/
-                    opts[o] = all_args.shift
+                    nxt = all_args.shift
+                    if ! nxt
+                      fatal { "Missing option text for option '#{o}'"}
+                    end
+                    opts[o] = nxt
                   else
                     opts[o] = nxt.gsub(/^\s*=/,'')
                   end

data/lib/ctioga2/commands/parsers/old-file.rb

@@ -52,7 +52,7 @@ module CTioga2
 
         # Runs a command file targeting the given _interpreter_.
         def run_command_file(file, interpreter)
-          f = open(file)
+          f = Utils::open(file)
           parse_io_object(f, interpreter)
         end
 

data/lib/ctioga2/data/backends/backends/gnuplot.rb

@@ -78,7 +78,7 @@ EOD
           date = File::mtime(filename)
           # Get it from the cache !
           debug { "Running gnuplot on file #{filename}" }
-          f = File.open(filename)
+          f = Utils::open(filename)
           # We open a bidirectionnal connection to gnuplot:
           gnuplot = IO.popen("gnuplot", "r+")
           output = ""

data/lib/ctioga2/data/backends/backends/text.rb

@@ -39,15 +39,6 @@ module CTioga2
 
       class TextBackend < Backend
 
-        # A constant holding a relation extension -> command to
-        # decompress (to be fed to sprintf with the filename as argument)
-        UNCOMPRESSORS = {
-          ".gz" => "gunzip -c %s",
-          ".bz2" => "bunzip2 -c %s",
-          ".lzma" => "unlzma -c %s",
-          ".lz" => "unlzma -c %s",
-          ".xz" => "unxz -c %s",
-        }
 
         include Dobjects
 
@@ -171,23 +162,9 @@ EOD
             return $stdin
           elsif file =~ /(.*?)\|\s*$/ # A pipe
             return IO.popen($1)
-          elsif not File.readable?(file)
-            # Try to find a compressed version
-            for ext,method in UNCOMPRESSORS
-              if File.readable? "#{file}#{ext}"
-                info { "Using compressed file #{file}#{ext} in stead of #{file}" }
-                return IO.popen(method % "#{file}#{ext}")
-              end
-            end
-          else 
-            for ext, method in UNCOMPRESSORS
-              if file =~ /#{ext}$/ 
-                info { "Taking file #{file} as a compressed file" }
-                return IO.popen(method % file)
-              end
-            end
+          else
+            return Utils::open(file)
           end
-          return File::open(file)
         end
 
         # A line is invalid if it is blank or starts

data/lib/ctioga2/data/datacolumn.rb

@@ -283,6 +283,40 @@ module CTioga2
           v.replace(v.convolve(kernel,middle)) if v
         end
       end
+
+      # Resize all the columns to the given size. 
+      def resize!(new_size)
+        for v in all_vectors
+          v.resize(new_size) if v
+        end
+      end
+
+      # Averages over the given indices, and puts the result at the
+      # target index.
+      #
+      # Different averaging modes are available.
+      def average_over(istart, iend, itgt, mode = :avg)
+        case mode
+        when :avg
+          # Stupidly average over all the values
+          for v in all_vectors
+            if v
+              av = Utils::average_vector(v, istart, iend)
+              v[itgt] = av[0]
+            end
+          end
+        when :stddev
+          # Ignore errors, and set them from the standard deviation
+          @min_values ||= @values.dup
+          @max_values ||= @values.dup
+
+          av = Utils::average_vector(@values, istart, iend, 2)
+          @values[itgt] = av[0]
+          stddev = (av[1] - av[0]**2)**0.5
+          @min_values[itgt] = av[0] - stddev
+          @max_values[itgt] = av[0] + stddev
+        end
+      end
       
       protected
 

data/lib/ctioga2/data/dataset.rb

@@ -269,18 +269,19 @@ module CTioga2
       # Average all the non-X values of successive data points that
       # have the same X values. It is a naive version that also
       # averages the error columns.
-      def average_duplicates!
+      def average_duplicates!(mode = :avg)
         last_x = nil
         last_x_first_idx = 0
         xv = @x.values
         i = 0
         vectors = all_vectors
+        nb_x = 0
         while i < xv.size
           x = xv[i]
           if ((last_x == x) && (i != (xv.size - 1)))
             # Do nothing
           else
-            if last_x_first_idx < (i - 1)  || 
+            if last_x_first_idx <= (i - 1)  || 
                 ((last_x == x) && (i == (xv.size - 1)))
               if i == (xv.size - 1)
                 e = i
@@ -288,24 +289,21 @@ module CTioga2
                 e = i-1
               end                 # The end of the slice.
 
-              ## \todo In real, to do this properly, one would
-              # have to write a proper function in DataColumn that
-              # does averaging over certain indices possibly more
-              # cleverly than the current way to do.
-              for v in vectors
-                subv = v[last_x_first_idx..e]
-                ave = subv.sum/subv.size
-                v.slice!(last_x_first_idx+1, e - last_x_first_idx)
-                v[last_x_first_idx] = ave
+              # Now, we delegate to the columns the task of averaging.
+              @x.average_over(last_x_first_idx, e, nb_x, :avg)
+              for c in @ys
+                c.average_over(last_x_first_idx, e, nb_x, mode)
               end
-              i -= e - last_x_first_idx
+              nb_x += 1
             end
             last_x = x
             last_x_first_idx = i
           end
           i += 1
         end
-        
+        for c in all_columns
+          c.resize!(nb_x)
+        end
       end
 
       # Applies formulas to values. Formulas are like text-backend

data/lib/ctioga2/data/filters.rb

@@ -123,10 +123,30 @@ Install the {command: cherry-pick-last} command as a dataset hook (see
 false for subsequent datasets will be removed.
 EOH
 
+      AVGDupModeRE = {
+        /naive|avg|average/i => :avg,
+        /stddev/i => :stddev,
+      }
+      
+      AVGDupMode = 
+        CmdType.new('average-mode', 
+                    {:type => :re_list,
+                     :list => AVGDupModeRE}, <<EOD)
+How the {command: avg-dup-last} command :
+
+ * @naive@ or @average@ (the default) treats all columns (values and
+   error bars) the same way, and average everythin
+ * @stddev@ ignores the original errors, and sets the new errors to the 
+   standard deviation of the values
+EOD
+        
+
+
       AverageDupOperation = 
         Cmd.new("avg-dup-last", nil, "--avg-dup-last", 
-                [], {}) do |plotmaker|
-        plotmaker.data_stack.last.average_duplicates!
+                [], {'mode' => CmdArg.new('average-mode')}) do |plotmaker, opts|
+        mode = opts['mode'] || :avg
+        plotmaker.data_stack.last.average_duplicates!(mode)
       end
       
       AverageDupOperation.describe("Average successive elements with identical X values",
@@ -135,9 +155,8 @@ Averages successive points with identical X values. This algorithm is
 naive with respect to the min/max values and averages them just as
 well, whereas one might expect something more clever.
 
-To average over identical X values when they are not successive in the
-dataset, you might want to hand it over to {command: sort-last} first.
-
+To average over all X values when they are not successive in the
+dataset, you should use {command: sort-last} first.
 EOH
 
       AverageDupFilter = 

data/lib/ctioga2/data/stack.rb

@@ -78,8 +78,8 @@ module CTioga2
         end
         
         csv.describe("reads CSV files", 
-                            <<"EOH", "backend-text")
-Now parse the following data files as CSV.
+                     <<"EOH", "backend-text")
+Now parse the following data files as CSV. Equivalent to
 
 # text /separator=/[,;]/
 EOH
@@ -373,6 +373,7 @@ EOH
               }) do |plotmaker,opts|
       ds = plotmaker.data_stack.specified_dataset(opts)
       if opts['save']
+        # Writing
         out = open(opts['save'], 'w')
       else
         out = STDOUT

data/lib/ctioga2/graphics/elements.rb

@@ -69,6 +69,13 @@ EOH
       cmd.describe("Sets the #{x.to_s.upcase} range",
                            <<EOH, PlotCoordinatesGroup)
 Sets the range of the #{x.to_s.upcase} coordinates.
+
+*Important note:* when the axis is in log range (using
+{command: #{x.to_s.upcase}log}), the numbers you give are not the or
+{command: ylog} values, but their @log10@, so that to
+display #{x.to_s.upcase} values from @1e-2@ to @1e3@, use:
+
+# #{x.to_s}yrange -2:3
 EOH
       CoordinateRelatedCommands << cmd
 

data/lib/ctioga2/graphics/elements/histogram.rb

@@ -193,6 +193,25 @@ module CTioga2
           return parent.gp_cache[:histograms]
         end
 
+        # Computes the number of histograms to be displayed in total
+        # -- or, at least, the total number of slots.
+        def compute_hist_number(x_values)
+          case @histogram_style.compute_dx
+          when nil, false
+            return x_values.size
+          when :mindx
+            xv = Dvector.new(x_values.to_a.sort)
+            x1 = xv[0..-2]
+            x2 = xv[1..-1]
+            x2.sub!(x1)
+            x2.abs!
+            subs = (xv.max - xv.min)/(x2.min)
+            return subs.round+1
+          else
+            raise "Invalid compute-dx type: #{@histogram_style.compute_dx}"
+          end
+        end
+
         # Returns the cached metrics of all the histograms,
         # recomputing it in the process.
         def get_cached_metrics(t)
@@ -228,7 +247,9 @@ module CTioga2
             # values (which means in particular that they won't be
             # positioned at the exact X value, but that's already the
             # case anyway).
-            width = (x_values.max - x_values.min)/(x_values.size - 1).to_f
+            number = compute_hist_number(x_values)
+
+            width = (x_values.max - x_values.min)/(number - 1).to_f
             if width.nan? || width == 0.0
               # Only 1 X value, we use a width of 1
               # ?? 

data/lib/ctioga2/graphics/elements/subplot.rb

@@ -131,6 +131,12 @@ module CTioga2
             bounds[k] ||= Types::SimpleRange.new(nil,nil)
             bounds[k].override(b)
           end
+          for k, b in bounds
+            if ! b.valid?
+              error { "Invalid computed range, you probably have only empty datasets" }
+              bounds[k] = Types::SimpleRange.new(0.0,1.0)
+            end
+          end
           return bounds
         end
 
@@ -158,6 +164,7 @@ module CTioga2
         def real_do(t)
           # First thing, we setup the boundaries
           @computed_boundaries = compute_boundaries
+          p @computed_boundaries
 
           real_boundaries = get_boundaries
 
@@ -176,15 +183,16 @@ module CTioga2
               dx = t.convert_figure_to_output_dx(1.0)
               dy = t.convert_figure_to_output_dy(1.0)
               
-              frm = [0.0, dx/@style.frame_real_size, 
-                     -dy/@style.frame_real_size, 0.0]
+              frm = [0.0, dx/(@style.frame_real_size * t.scaling_factor), 
+                     -dy/(@style.frame_real_size * t.scaling_factor), 0.0]
               @computed_boundaries = {
                 :bottom => Types::SimpleRange.new(frm[0], frm[1]),
                 :left => Types::SimpleRange.new(frm[2], frm[3]),
               }                
               t.set_bounds(frm)
             else
-              t.set_bounds(real_boundaries.to_a)
+              bnds = real_boundaries.to_a
+              t.set_bounds(bnds)
             end
 
             # First, gather up all elements by depth

data/lib/ctioga2/graphics/legends/area.rb

@@ -148,10 +148,10 @@ module CTioga2
           w, h = size(t, container)
           case @legend_type
           when :left, :right
-            return [width + t.convert_figure_to_output_dx(w)/10, 
+            return [width + t.convert_figure_to_output_dx(w)/t.scaling_factor, 
                     height]
           when :top, :bottom
-            return [width, height + t.convert_figure_to_output_dy(h)/10]
+            return [width, height + t.convert_figure_to_output_dy(h)/t.scaling_factor]
           when :inside
             return [width, height]
           end

data/lib/ctioga2/graphics/legends/items.rb

@@ -78,9 +78,9 @@ module CTioga2
           info = t.get_text_size(legend_name)
           
           if info.key? 'width'
-            width += t.convert_output_to_figure_dx(10*info['width'])
+            width += t.convert_output_to_figure_dx(t.scaling_factor*info['width'])
 
-            h = t.convert_output_to_figure_dy(10*info['height'])
+            h = t.convert_output_to_figure_dy(t.scaling_factor*info['height'])
             if h > height
               height = h
             end

data/lib/ctioga2/graphics/styles/background.rb

@@ -95,7 +95,7 @@ EOD
         Cmd.new('background', nil, '--background', 
                 [ CmdArg.new('color-or-false') ]) do |plotmaker, color|
         PlotStyle.current_plot_style(plotmaker).
-          background.background_color = color
+          background.style.background_color = color
       end
 
       BackgroundColorCmd.describe("Background color for the plot", 

data/lib/ctioga2/graphics/styles/image.rb

@@ -62,6 +62,7 @@ EOD
           r = Types::Rect.new(tl, br)
           ul, ll, lr = r.make_corners(t, (@auto_rotate == nil ? true : @auto_rotate), @aspect_ratio || :ignore,
                                       info['width']*1.0/info['height'])
+          
 
           dict = info.dup
           dict.merge!('ul' => ul,

data/lib/ctioga2/graphics/styles/plot-types.rb

@@ -137,6 +137,21 @@ How to specify that histograms should be stacked. Can be:
  * next, in which case the following histograms get stacked on a new slot
 EOD
 
+      ComputeDxRE = {
+        /^no(ne)?$/i => false,
+        /^min(dx)?$/i => :mindx,
+      }
+
+      ComputeDx = 
+        CmdType.new('compute-dx',  {:type => :re_list,
+                                    :list => ComputeDxRE}, <<EOD)
+This controls how the histograms treats unevenly spaced X values:
+ * @none@: ignores the problem, and treats the points as if they were all
+   evenly spaced
+ * @min@, @mindx@: considers that all slots have the size of the
+   smallest variation of X values
+EOD
+
 
       # This class defines various informations about the look of
       # histograms.
@@ -151,6 +166,10 @@ EOD
         # Specs for cumulative 
         typed_attribute :cumulative, 'cumulative-histograms'
 
+        # Whether one should assume evenly spaced X points or be more
+        # clever.
+        typed_attribute :compute_dx, 'compute-dx'
+
         def set_from_hash(hash, name = "%s")
           super
 

data/lib/ctioga2/graphics/styles/plot.rb

@@ -82,7 +82,7 @@ module CTioga2
 
         # If not nil, then the boundaries are computed from the real
         # dimensions of the plot frame, using the given number as a
-        # conversion factor from the output dimensions.
+        # conversion factor from postscript points.
         attr_accessor :frame_real_size
 
 
@@ -478,7 +478,7 @@ EOH
         if u =~ /([\d.]+)?\s*(cm|in|bp|pt|mm)/
           nb = $1 ? $1.to_f : 1.0
           un = $2
-          style.frame_real_size = 10 * nb * 
+          style.frame_real_size = nb * 
             Types::Dimension::DimensionConversion.fetch(un)
         else
           raise 'Invalid unit'

data/lib/ctioga2/graphics/styles/styles.rb

@@ -256,7 +256,7 @@ EOD
                    CmdArg.new('file'),
                   ], {}
                   ) do |plotmaker, file|
-        File.open(file) do |f|
+        Utils::open(file) do |f|
           str = f.read
           StyleSheet.style_sheet.update_from_string(str)
         end

data/lib/ctioga2/graphics/styles/texts.rb

@@ -245,8 +245,9 @@ module CTioga2
 
 
       # The style for a string marker. Hmmm, this is somewhat
-      # redundant with TiogaPrimitiveCall::MarkerOptions and I don't
-      # like that.
+      # redundant with MarkerStyle and I don't like that.
+      #
+      # Worse than that, it's not the same options !
       class MarkerStringStyle < BasicStyle
         
         # The angle of the text
@@ -272,6 +273,8 @@ module CTioga2
         typed_attribute :stroke_color, 'color-or-false'
         typed_attribute :fill_color, 'color-or-false'
 
+        typed_attribute :stroke_width, 'float'
+
 
         # A number between 1 to 14 -- a PDF font
         typed_attribute :font, "pdf-font"

data/lib/ctioga2/graphics/subplot-commands.rb

@@ -117,7 +117,7 @@ EOH
       Cmd.new("root-plot",nil,"--root-plot", 
               [
               ], Elements::TiogaElement::StyleBaseOptions) do |plotmaker, opts|
-      Log::debug { "Starting a subplot with specs #{box.inspect}" }
+      Log::debug { "Explicitly starting the root plot, options #{opts.inspect}" }
       opts['id'] ||= 'root'
       plotmaker.root_object.
         enter_subobject(Elements::Subplot.new(nil,plotmaker.root_object, opts))

data/lib/ctioga2/graphics/types/boundaries.rb

@@ -44,6 +44,13 @@ module CTioga2
           end
         end
 
+        # Checks if the range is valid, that is both elements are
+        # finite numbers
+        def valid?
+          return (Utils::finite_number?(@first) and
+                  Utils::finite_number?(@last))
+        end
+
         # Minimum value
         def min
           @first < @last ? @first : @last

data/lib/ctioga2/graphics/types/dimensions.rb

@@ -134,7 +134,7 @@ module CTioga2
           
           case @type
           when :bp
-            return t.send("convert_output_to_figure_d#{orientation}", @value) * 10
+            return t.send("convert_output_to_figure_d#{orientation}", @value) * t.scaling_factor
           when :dy
             return t.send("default_text_height_d#{orientation}") * @value
           when :frame
@@ -158,7 +158,7 @@ module CTioga2
         def to_bp(t, orientation = nil)
           orientation ||= @orientation
           return t.send("convert_figure_to_output_d#{orientation}", 
-                        to_figure(t, orientation)) / 10.0
+                        to_figure(t, orientation)) / t.scaling_factor
         end
 
         # Converts the Dimension to the *frame* coordinates of the

data/lib/ctioga2/graphics/types/grid.rb

@@ -131,6 +131,11 @@ module CTioga2
               @hscales, @vscales = nup.split(/\s*x\s*/).map { |x| 
                 x.split(/\s*,\s*/).map { |y| y.to_f }
               }
+              if @hscales.size == 1
+                @hscales = [1] * @hscales[0].to_i
+              elsif @vscales.size == 1
+                @vscales = [1] * @vscales[0].to_i
+              end
               @nup = [@hscales.size, @vscales.size]
             else
               @nup = nup.split(/\s*x\s*/).map { |s| s.to_i }

data/lib/ctioga2/graphics/types/point.rb

@@ -128,8 +128,8 @@ module CTioga2
           xl, yt = @tl.to_figure_xy(t)
           xr, yb = @br.to_figure_xy(t)
 
-          return [t.convert_figure_to_output_dx(xr - xl) * 10,
-                  t.convert_figure_to_output_dy(yb - yt) * 10]
+          return [t.convert_figure_to_output_dx(xr - xl) * t.scaling_factor,
+                  t.convert_figure_to_output_dy(yb - yt) * t.scaling_factor]
         end
 
         # Returns an array of [ul, ll, lr] coordinates. If an aspect

data/lib/ctioga2/plotmaker.rb

@@ -226,6 +226,12 @@ module CTioga2
     # errors. Useful on windows, where the windows closes before one
     # has a chance to see anything.
     attr_accessor :pause_on_errors
+
+    # If not empty, a Makefile file where the dependencies are written out
+    attr_accessor :makefile_dependencies
+
+    # The resolution of the PDF file
+    attr_accessor :pdf_resolution
     
 
     # The first instance of PlotMaker created
@@ -368,7 +374,7 @@ module CTioga2
       end
 
       # We always cd into the target directory for creading the
-      Dir.chdir(path.dirname) do
+      Utils::chdir(path.dirname) do
         fn = path.basename.to_s
 
         efn = fn.gsub(/[.\s]/) do |x|
@@ -405,6 +411,14 @@ module CTioga2
 
       file = path.to_s + ".pdf"
 
+      if @makefile_dependencies
+        File.open(@makefile_dependencies, "w") do |f|
+          deps = Utils::used_files.values
+          # TODO: handle spaces
+          f.puts "#{file}: #{deps.join(" ")}"
+        end
+      end
+
       # Feed it
       @postprocess.process_file(file, last)
       return file
@@ -451,7 +465,7 @@ module CTioga2
 
     # Creates a new FigureMaker object and returns it
     def create_figure_maker
-      t = Tioga::FigureMaker.new
+      t = Tioga::FigureMaker.new(@pdf_resolution || 100)
       t.tex_preamble += @latex_preamble
       t.autocleanup = @cleanup
 
@@ -624,6 +638,25 @@ EOD
                              <<EOH, OutputSetupGroup)
 Sets the size of the output PDF file, in real units. Takes arguments in the 
 form of 12cm x 3in (spaces can be omitted).
+EOH
+
+    ResolutionCommand = 
+      Cmd.new("resolution", false,"--resolution", 
+              [ CmdArg.new('float') ],
+              ) do |plotmaker, size, options|
+      plotmaker.pdf_resolution = size
+    end
+
+    ResolutionCommand.describe('Sets the output resolution', 
+                               <<EOH, OutputSetupGroup)
+By default, ctioga2 has a resolution of 1/100th of a postscript
+point. This is clearly enough for most tasks, but you can increase it
+should you need, or decrease it to generate possibly a little more
+jaggy but less large PDF files.
+
+The number given is the number of output points per postscript point.
+
+Better change that at the beginning of the plot.
 EOH
 
     CleanupCommand = 
@@ -816,6 +849,17 @@ want any information to leak.
 Please note that this will not log the values of the CTIOGA2_PRE and
 CTIOGA2_POST variables, so you might still get a different output if
 you make heavy use of those.
+EOH
+
+    DepsCommand = 
+      Cmd.new("dependencies",nil,"--dependencies", 
+              [CmdArg.new('file') ]) do |plotmaker,val|
+      plotmaker.makefile_dependencies = val
+    end
+    
+    DepsCommand.describe('Save dependencies', 
+                         <<EOH, OutputSetupGroup)
+Saves the dependencies as a Makefike into the given file name.
 EOH
 
   end

data/lib/ctioga2/ruby.rb

@@ -36,7 +36,7 @@ module CTioga2
     end
 
     def self.run_file(file)
-      File.open(file) do |f|
+      Utils::open(file) do |f|
         run_code(f.read)
       end
     end

data/lib/ctioga2/utils.rb

@@ -59,6 +59,11 @@ module CTioga2
       end
     end
 
+    # Returns true if the argument is a finite number
+    def self.finite_number?(flt)
+      return (flt.is_a?(Numeric) and flt.to_f.finite?)
+    end
+
     # Converts a number to a float while trying to stay as lenient as
     # possible
     def self.txt_to_float(txt)
@@ -160,6 +165,24 @@ module CTioga2
       end
     end
 
+    # Returns the nth first modes
+    def self.average_vector(vect, istart, iend, n = 1)
+      rv = [0] * n
+      nb = 0
+      istart.upto(iend) do |i|
+        v = 1
+        y = vect[i]
+        n.times do |j|
+          v *= y
+          rv[j] += v
+        end
+        nb += 1
+      end
+
+      return rv.map do |v|
+        v/nb
+      end
+    end
 
     # Groups the given strings by prefixes
 
@@ -176,6 +199,76 @@ module CTioga2
       return sets_by_prefix
     end
 
+    # An instrumentized version of Dir::chdir 
+    def self.chdir(dir, &blk)
+      @current_dirs ||= []
+      @current_dirs << Pathname.new(dir)
+      Dir::chdir(dir, &blk)
+      @current_dirs.pop
+    end
+
+    # A constant holding a relation extension -> command to decompress
+    # (to be fed to sprintf with the filename as argument)
+    UNCOMPRESSORS = {
+      ".gz" => "gunzip -c %s",
+      ".bz2" => "bunzip2 -c %s",
+      ".lzma" => "unlzma -c %s",
+      ".lz" => "unlzma -c %s",
+      ".xz" => "unxz -c %s",
+    }
+
+    # This opens a file for reading, keeping track of the opened files
+    # and possibly transparently decompressing files when
+    # applicable. Returns the file object, or runs the given block
+    # with it, closing the file at the end.
+    def self.open(file)
+      if not File.readable?(file)
+        # Try to find a compressed version
+        for ext,method in UNCOMPRESSORS
+          if File.readable? "#{file}#{ext}"
+            info { "Using compressed file #{file}#{ext} in stead of #{file}" }
+            ff = "#{file}#{ext}"
+            handle = IO.popen(method % ff)
+            break
+          end
+        end
+      else
+        for ext, method in UNCOMPRESSORS
+          if file =~ /#{ext}$/
+            info { "Taking file #{file} as a compressed file" }
+            ff = file
+            handle = IO.popen(method % file)
+            break
+          end
+        end
+      end
+      if ! handle
+        ff = file
+        handle = File::open(file)
+      end
+
+      # Unwrap directory 
+      @used_files ||= {}
+
+      @current_dirs ||= []
+      rf = (@current_dirs + [file]).inject :+
+      rff = (@current_dirs + [ff]).inject :+
+      # The files referenced
+      @used_files[rf] = rff
+      if block_given?
+        yield handle
+        handle.close
+      else
+        return handle
+      end
+    end
+
+
+    # Returns the list of files that were read by ctioga2
+    def self.used_files()
+      return @used_files || {}
+    end
+
 
 
     NaturalSubdivisions = [1.0, 2.0, 5.0, 10.0]
@@ -470,8 +563,7 @@ module CTioga2
     # Watched text names
     attr_accessor :watched_names
 
-    # A left, bottom, right, up bounding box (in output coordinates
-    # divided by 10)
+    # A left, bottom, right, up bounding box (postscript points)
     attr_accessor :bb
 
     def initialize
@@ -497,11 +589,11 @@ module CTioga2
         return margins
       end
       left, top, right, bottom = *margins.to_frame_coordinates(t)
-      
-      xl = 0.1 * t.convert_page_to_output_x(t.convert_frame_to_page_x(left))
-      xr = 0.1 * t.convert_page_to_output_x(t.convert_frame_to_page_x(right))
-      yt = 0.1 * t.convert_page_to_output_y(t.convert_frame_to_page_y(top))
-      yb = 0.1 * t.convert_page_to_output_y(t.convert_frame_to_page_y(bottom))
+      scl = 1/t.scaling_factor
+      xl = scl * t.convert_page_to_output_x(t.convert_frame_to_page_x(left))
+      xr = scl * t.convert_page_to_output_x(t.convert_frame_to_page_x(right))
+      yt = scl * t.convert_page_to_output_y(t.convert_frame_to_page_y(top))
+      yb = scl * t.convert_page_to_output_y(t.convert_frame_to_page_y(bottom))
 
       vals = [ xl - @bb[0], @bb[2] - xr, @bb[3] - yt, yb - @bb[1]].map do |x|
         x += padding
@@ -605,6 +697,7 @@ class Hash
 end
 
 
+
 class String
   # Splits a string into substrings at the given regexp, but only if
   # the splitting occurs at top-level with respect to parentheses.

data/lib/ctioga2/version.rb

@@ -2,7 +2,7 @@
 module CTioga2
 
   module Version
-GIT_VERSION = '0.12'
-GIT_DATE = 'Mon 23 Mar 21:27:39 CET 2015'
+GIT_VERSION = '0.13'
+GIT_DATE = 'Thu 11 Jun 23:03:37 CEST 2015'
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ctioga2
 version: !ruby/object:Gem::Version
-  version: '0.12'
+  version: '0.13'
 platform: ruby
 authors:
 - Vincent Fourmond <vincent.fourmond@9online.fr>
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-03-23 00:00:00.000000000 Z
+date: 2015-06-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: tioga
@@ -16,20 +16,20 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '1.18'
+        version: '1.19'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '1.18'
+        version: '1.19'
 description: |
   ctioga2 is a command-driven plotting program that produces
   high quality PDF files. It can be used both from the command-line
   and using command files (at the same time).
 
-  It is based on Tioga (http://tioga.rubyforge.org).
+  It is based on Tioga (http://tioga.sourceforge.net).
 email: vincent.fourmond@9online.fr
 executables:
 - ctioga2