ctioga 1.11.1

data/lib/SciYAG/Backends/filters.rb

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+# filters.rb : include file for filters
+# Copyright (C) 2007 Vincent Fourmond
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+
+require 'SciYAG/Backends/filters/filter'
+require 'SciYAG/Backends/filters/smooth'
+require 'SciYAG/Backends/filters/average'
+require 'SciYAG/Backends/filters/sort'
+require 'SciYAG/Backends/filters/trim'
+require 'SciYAG/Backends/filters/cumulate'
+require 'SciYAG/Backends/filters/norm'
+require 'SciYAG/Backends/filters/strip'

data/lib/SciYAG/Backends/filters/average.rb

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+# smooth.rb : A simple averageing filter
+# Copyright (C) 2006 Vincent Fourmond
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+
+module SciYAG
+
+  module Backends
+
+    # A filter that sorts data and then averages the Y values of all the
+    # elements which have the same X value.
+    class AverageDupFilter < Filter
+      include Dobjects
+
+      describe "avgdup", "Average duplicates",
+      "Sorts the points according to the X values and average successive "+
+        "points with identical X values"
+
+      def initialize
+      end
+
+      # There you go: a simple sorting/averaging filter.
+      def apply(f)
+        h = {}
+        for x,y in f
+          if h.key? x
+            h[x] << y
+          else
+            h[x] = [y]
+          end
+        end
+        
+        nx = Dvector.new
+        ny = Dvector.new
+        for x in h.keys.sort
+          nx << x
+          y = 0
+          for a in h[x]
+            y += a
+          end
+          y/= h[x].size
+          ny << y
+        end
+        return Function.new(nx,ny)
+      end
+
+      # We simply replace the old vectors by the new ones.
+      def apply!(f)
+        new_f = apply(f)
+        f.x.replace(new_f.x)
+        f.y.replace(new_f.y)
+      end
+    end
+
+    class StandardDeviationFilter < Filter
+      include Dobjects
+
+      describe "stddev", "Compute standard deviation",
+      "Averages successive elements with the same X value and compute standard deviation"
+
+      def initialize
+      end
+
+      def apply(f)
+        last_x = nil    
+        current_y = []
+        x_values = Dvector.new
+        y_values = []
+        f.x.size.times do |i|
+          xval = f.x[i]
+          if (last_x && xval == last_x)
+            current_y << f.y[i]
+          else
+            if last_x
+              y_values << current_y
+              x_values << last_x
+            end
+            current_y = [f.y[i]]
+            last_x = f.x[i]
+          end
+        end
+        if last_x
+          y_values << current_y
+          x_values << last_x
+        end
+
+        target_y = Dvector.new(x_values.size)
+        ymin = target_y.dup
+        ymax = target_y.dup
+        x_values.size.times do |i|
+          sum = 0.0
+          sq_sum = 0.0
+          for y in y_values[i]
+            sum += y
+            sq_sum += y**2
+          end
+          nb = y_values[i].size
+          target_y[i] = sum/nb
+          stddev = Math::sqrt((sq_sum/nb) - target_y[i]**2)
+          ymin[i] = target_y[i] - stddev
+          ymax[i] = target_y[i] + stddev
+        end
+        
+        errors = f.errors.dup.merge!({:ymin => ymin, :ymax => ymax,
+                                     :x => x_values, :y => target_y})
+
+        return DataSet2D.new(f.creation_context, 
+                             Function.new(x_values, target_y), 
+                             errors, f.meta_data) 
+      end
+
+      # We simply replace the old vectors by the new ones.
+      def apply!(f)
+        new_f = apply(f)
+        f.x.replace(new_f.x)
+        f.y.replace(new_f.y)
+        f.errors = new_f.errors
+      end
+    end
+
+  end
+end

data/lib/SciYAG/Backends/filters/cumulate.rb

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+# cumulate.rb : A simple cumulative filter
+# Copyright (C) 2007 Vincent Fourmond
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+
+module SciYAG
+
+  module Backends
+
+    # Removes a given ratio of points
+    class CumulateFilter < Filter
+      include Dobjects
+
+      describe "cumulate", "Cumulate", "Cumulate the Y values of the points"
+
+      def apply!(f)
+        y = 0
+        f.y.size.times do |i|
+          y += f.y[i]
+          f.y[i] = y
+        end
+      end
+    end
+  end
+end

data/lib/SciYAG/Backends/filters/filter.rb

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+# filter.rb : The base class for filters
+# Copyright (C) 2006 Vincent Fourmond
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+
+
+module SciYAG
+
+  module Backends
+
+    #  The base class for filters. Just an interface, in the java meaning of
+    #  the term. A filter just provides a function to apply itself.
+    class Filter
+      # Import the main description functions into the appropriate
+      # namespaces
+      extend  Descriptions::DescriptionExtend
+      include Descriptions::DescriptionInclude
+
+
+      def initialize
+      end
+
+      # Creates a description object with the given texts and associates
+      # it with the class. To be used in Filter subclasses, simply this way:
+      #
+      #  describe "biniou", "Biniou filter", "A filter to take out Binious"
+      #
+      # Please remember also that if you don't set a description for
+      # your Filter, it will most likely be of no use to anyone...
+
+      def Filter.describe(name, longname, desc)
+        d = FilterDescription.new(self,name, longname, desc)
+        set_description(d)
+        register_description(d)
+      end
+
+      # Gets a Function (or assimilate ?) and applies the filter on them.
+      # The functions  *should not modify any data in ary*.
+      # By default, the mechanism is to make a copy of the data and apply
+      # apply! on it.
+      def apply(a)
+        f = Dobjects::Function.new(a.x.dup, a.y.dup)
+        apply!(f)
+        return f
+      end
+
+      # This version modifies directly the Function inside the +f+. 
+      def apply!(func)
+        return func
+      end
+    end
+
+    # Specializes Descriptions for filters
+    class FilterDescription < Descriptions::Description
+      
+    end
+  end
+end

data/lib/SciYAG/Backends/filters/norm.rb

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+# norm.rb : normalizing data to 1
+# Copyright (C) 2006 Vincent Fourmond
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+
+module SciYAG
+
+  module Backends
+
+    # A filter that sorts data according to their X values.
+    class NormalizeFilter < Filter
+      include Dobjects
+
+      describe "norm", "Normalize", 
+      "Normalize so that maximum absolute value is 1 " +
+        "(keeping the original sign)"
+
+      def initialize
+      end
+
+      def apply!(f)
+        y_abs_max = Dvector[f.y.min.abs, f.y.max.abs].max
+        f.y.div!(y_abs_max)
+      end
+    end
+  end
+end

data/lib/SciYAG/Backends/filters/smooth.rb

@@ -0,0 +1,63 @@
+# smooth.rb : A simple averageing filter
+# Copyright (C) 2006 Vincent Fourmond
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+
+module SciYAG
+
+  module Backends
+
+    # A simple gaussian filter. You'd better give it an odd number.
+    class SmoothFilter < Filter
+      include Dobjects
+
+      describe "smooth", "Smooth", "Simple gaussian-like convolution filter"
+
+      init_param 'nb', "Number", Integer, 
+      "The number of points over which to average"
+
+      def initialize(nb) 
+        nb = nb.to_i
+        if nb < 2
+          warn "Invalid parameter nb #{nb}, using 5"
+          nb = 5
+        end
+        # initializes to binomial coefficients
+        @kernel = Dvector.new(nb) { |i|
+          SmoothFilter.cnk(nb,i)
+        }
+        @mid = nb - nb/2 - 1
+      end
+
+
+      # Binomial coefficients.
+      def SmoothFilter.cnk(n,k)
+        res = 1.0
+        n.downto(n - k) { |i| res *= i}
+        k.downto(1) {|i| res = res/i }
+        return res
+      end
+
+      # There you go: a simple averageing filter.
+      def apply(f)
+        return Function.new(f.x, f.y.convolve(@kernel, @mid))
+      end
+
+      def apply!(f)
+        f.y.replace(f.y.convolve(@kernel, @mid))
+      end
+    end
+  end
+end

data/lib/SciYAG/Backends/filters/sort.rb

@@ -0,0 +1,43 @@
+# sort.rb : A simple sorting filter
+# Copyright (C) 2006 Vincent Fourmond
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+
+module SciYAG
+
+  module Backends
+
+    # A filter that sorts data according to their X values.
+    class XsortFilter < Filter
+      include Dobjects
+
+      describe "sort", "Sort", "Sorts the points according to the X values"
+
+      def initialize
+      end
+
+      # There you go: a simple averageing filter.
+      def apply(f)
+        a = Function.new(f.x.dup, f.y.dup)
+        a.sort
+        return a
+      end
+
+      def apply!(f)
+        f.sort!
+      end
+    end
+  end
+end

data/lib/SciYAG/Backends/filters/strip.rb

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+# strip.rb : remove all NaN before processing any further
+# Copyright (C) 2006 Vincent Fourmond
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+
+module SciYAG
+
+  module Backends
+
+    # A filter that sorts data according to their X values.
+    class StripNanFilter < Filter
+      include Dobjects
+
+      describe "strip", "Strip", 
+      "Removes all NaN from the input"
+
+      def apply!(f)
+        f.strip_nan
+      end
+    end
+  end
+end