topas-tools 0.0.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 2170b03e20ff05d36be9578bae34c91277c61099
+  data.tar.gz: 36c698ba2ec54a4ceb21a8bd4f858a5baa6f24af
+SHA512:
+  metadata.gz: 02492c79940bf73d62fde03d6b91aa81e57656d8d85c38852392090ba12d35d2f034180997c04d5aa9afa491215470e51a203eeb4f94f654d232a258bb77d40c
+  data.tar.gz: d8be1e2f7db5ce5a8627a809fd472db3d39bf3c699b5b1c0b9bd22721e25d165adb0addc4e3b58f1ff0ea7e0fe0fbd9e5bcfc164915ecd2f6b7382cbb443edb5

data/bin/toparun

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+#!/usr/bin/env ruby
+# -*- coding: utf-8 -*-
+
+require 'optparse'
+require 'topas-tools'
+
+
+options = {points:[100.0, 16.0, 0.0], steps:[4.0, 1.0], smart:false,  system: :wine}
+OptionParser.new do |opts|
+  opts.banner = "Usage: toparun.rb  [-p 100,15,0 -s 1,0.25] filename.inp"
+  opts.on("-p", "--points LIST", Array ,"Array of points, representing intervals with different stepsizes"){|list|
+    options[:points] = list.map(&:to_f)}
+  opts.on("-s", "--steps LIST", Array ,"Well, stepsizes for that intervals"){|list|
+    options[:steps] = list.map(&:to_f)}
+  opts.on("-s", "--[no-]smart", "Gone smart!") do |s|
+    options[:smart] = s
+  end
+  opts.on("--system [SYS]", [:windows, :wine, :dummy],
+              "Select your system (windows, wine, dummy)") do |t|
+        options[:system] = t
+  end
+end.parse!
+
+ARGV[0] || raise("Rrrr! Where is my input file??")
+
+TopasEngine.system = options[:system]
+
+
+runner = TopasEngine.new
+input = TopasInput.new IO.read(ARGV[0], :encoding => "UTF-8"), 
+                       ARGV[0].sub(/\..{2,3}$/, '')
+
+runner.refine input,  options[:points], options[:steps],  (options[:smart] ? QuantileAnalyzer.new : BaseAnalyzer.new)
+

data/bin/toparunGUI

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+#!/usr/bin/env ruby
+# -*- coding: utf-8 -*-
+require 'stringio'
+require 'green_shoes'
+require 'topas-tools'
+
+
+Shoes.app :width => 400, :height => 800  do
+
+  @log = StringIO.new
+  @log.write "Hi, log starts here!\n"
+  
+  def log
+    @log
+  end
+  
+  #base flow
+  flow  :margin=>10 do
+
+    title 'ToparunGUI'    
+
+    #big stack
+    stack do
+      caption 'Your system:'
+      @systemlist = list_box items:['wine','windows','dummy'], choose:'wine' 
+
+      caption 'Your Topas4-2 directory:'
+      
+      #small flow 
+      flow do
+        @topasdir = edit_line
+        button 'Open' do
+          @topasdir.text = ask_open_folder
+        end
+      end
+      #\small flow
+      
+      caption  "Points and steps"
+      para "TODO объяснить, кто все эти люди"
+      flow do
+        para "Points:"
+        @pointline = edit_line
+        @pointline.text = "100,16,0"
+      end
+
+      flow do
+        para "Points:"
+        @stepsline = edit_line
+        @stepsline.text = "4,1"
+      end
+      caption "Your input file"
+      flow do
+        @inpline = edit_line
+        button 'open' do
+          @inpline.text = ask_open_file
+        end
+      end
+
+        button 'Mf button!' do
+          begin
+            points = @pointline.text.split(/[,\s]+/).map(&:to_f)
+            steps  = @stepsline.text.split(/[,\s]+/).map(&:to_f)
+            rescue alert("Блюди формат точек и шагов!!")
+          end
+
+          Thread.new(points, steps, @log ) do  |points, steps|
+            inp = @inpline.text
+            TopasEngine.system = @systemlist.text.to_sym
+            runner = TopasEngine.new File.dirname(inp) 
+            input = TopasInput.new IO.read(inp, :encoding => "UTF-8"),  inp
+            runner.refine input,  points, steps,  BaseAnalyzer.new(@log)
+            @clear = button 'Clear' do
+              @log = StringIO.new
+              @clear.clear
+            end
+          end
+        end
+  
+        para self
+      caption "Log:"
+      stack :width => 300,   :margin => 20 do
+ 
+ 
+         @paralog = para
+        every 1  do |i|
+          a =  @log.string
+          @paralog.text = a  unless @paralog.text == a
+        flush
+        end
+      end
+
+
+    end
+  end
+end
+
+

data/lib/topas-tools.rb

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+require 'topas-tools/TopasEngine.rb'
+require 'topas-tools/TopasInput.rb'
+require 'topas-tools/Analyzers.rb'

data/lib/topas-tools/Analyzers.rb

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+class BaseAnalyzer
+  def initialize output = $stdout
+    @out = output
+    @count = 0
+  end
+  
+  def analyze inp
+    @out.print "Analizing #{inp.name}... \n"
+    @count = @count + 1
+    true
+  end
+  
+  def report 
+    @out.print "Refinement  was finished in #{@count} steps.\n"
+    true
+  end
+end

data/lib/topas-tools/TopasEngine.rb

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+class TopasEngine
+  
+  Systems = [:windows, :wine, :dummy]
+  
+  @@topasdir = "/home/dmitrienka/.wine/drive_c/TOPAS4-2/" #Depends!
+  @@system     = :dummy                                   #[:wine, : :windows, :dummy]
+
+  
+  def self.system=(system)
+    if Systems.any?{|sys| sys = system}
+      @@system = system
+    else
+      raise "Unknown system!"
+    end
+  end
+
+  def self.topasdir=(topasdir)
+    @@topasdir = topasdir
+  end
+
+
+  def initialize dir = Dir.getwd
+    @base_dir = dir
+    Dir.chdir @base_dir
+    @enc = "UTF-8"
+  end
+
+  def tc input
+    infile = "#{input.name}.inp"
+    File.open(infile, mode:'w'){|f| f.write input.text}
+    case @@system
+    when :wine
+      path = `winepath -w #{infile}`.gsub('\\', '\\\\\\').gsub("\n", "")
+      command = "wine tc.exe #{path}"
+      go_n_do command
+    when :windows
+      command = "tc.exe #{File.expand_path(infile)}"
+      go_n_do command
+    when :dummy
+     outfile = "#{input.name}.out"
+      p "Say hello to #{outfile} with k1 = #{input.k1}"
+      File.open(outfile , mode:'w'){|f| f.write input.text}
+    end
+    TopasInput.new IO.read("#{input.name}.out", :encoding => @enc)
+  end
+  
+
+  def  refine input, ps, ss,  analyzer = BaseAnalyzer.new
+    k1s = get_k1s ps, ss
+    name = input.base_name
+    Dir.mkdir(name) unless Dir.exists? name
+    @work_dir = File.expand_path(name)
+    Dir.chdir @work_dir
+    k1s.reduce(input) do |inp, k1|
+      out = tc inp.set_k1(k1)
+      analyzer.analyze(out) ? out : break
+    end
+    Dir.chdir @base_dir
+    analyzer.report
+  end
+
+  private
+  
+  def go_n_do command
+    Dir.chdir @@topasdir
+    system(command)
+    Dir.chdir @work_dir
+  end
+
+  def get_k1s points, stepsizes 
+    stepsizes.inject([]){|result, stepsize| 
+      a = result + points[0].step(points[1] ,-stepsize).to_a
+      points.shift
+      a}.uniq
+  end
+  
+end

data/lib/topas-tools/TopasInput.rb

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+class TopasInput
+  def initialize text, base_name = nil
+    @text = text.dup
+    @k1 = get_k1
+    @base_name  = get_base_name base_name
+    @name = get_name
+    @restrains = get_restrains
+  end
+
+  attr_reader :k1, :name, :base_name, :restrains, :text
+ 
+ 
+  def set_k1!(num)
+    @k1 = num.to_f
+    @text = @text.sub(/(penalties_weighting_K1\s+)[\d.]+/ , "\\1#{@k1}").
+          sub(/[\d.]*(\.cif)/ , "#{@k1}\\1")
+    @name = get_name
+    self
+  end
+
+  def set_k1(num)
+    dup.set_k1!(num)
+  end
+  
+  def restrain_names
+    @restrains.map{|r| r[:name]}
+  end
+
+  def set_restrain!(name, new)
+    if r = @restrains.select{|r| r[:name] == name}[0]
+      r[:restrain] = new
+      @text = write_restrains
+      self
+    else
+      raise  "No restrain with the name #{name}"
+    end
+  end
+
+  def set_restrain(name, new)
+    dup.set_restrain!(name, new)
+  end
+
+  private
+  
+
+
+  def get_k1
+    @text.scan(/penalties_weighting_K1\s+([\d.]+)/)[0][0].to_f
+  end
+
+  def get_base_name bn
+    if   bn
+      base_name = File.basename(bn, File.extname(bn))
+      @text = @text.sub(/phase_name\s+".+"/, %Q[phase_name "#{bn}"])
+      base_name
+    else
+      base_name = @text.match(/phase_name\s+"(.+)"/)[1]
+      base_name
+    end
+  end
+
+
+
+
+  def get_name
+      "#{@base_name}_#{@k1}"
+  end
+
+
+  def get_restrains
+    restrains_pattern = /(Distance_Restrain(?:_Breakable|_Morse)?)\(\s*(\w+\s+\w+)\s*,\s*([\d.]+)\s*,\s*([\d.]+)[`_\d.]*\s*,\s*([\d.]+\s*,\s*[\d.]+)\s*\)/
+    if @text =~ restrains_pattern
+      @text.scan(restrains_pattern).reduce([]){|memo, (type ,name, restrain, value, rest)|
+        memo << {name:name, type:type, restrain:restrain.to_f, value:value.to_f, rest:rest}
+        memo}
+    else
+      nil
+    end
+  end
+
+  def write_restrains
+    @restrains.reduce(@text) { |memo, r|
+      pattern = /#{r[:type]}\s*\(\s*#{r[:name]}\s*,\s*[\d.]+\s*,\s*[\d.]+[`_\d.]*\s*,\s*[\d.]+\s*,\s*[\d.]+\s*\)/ 
+      memo.sub(pattern, "#{r[:type]}(#{r[:name]}, #{r[:restrain]}, #{r[:value]}, #{r[:rest]})")        
+    }
+  end
+
+end
+
+
+def dumbdiff as, bs
+  as = as.split /\n/
+  bs = bs.split /\n/
+  as.zip(bs).reject{ |a, b| a == b}
+end

metadata

@@ -0,0 +1,71 @@
+--- !ruby/object:Gem::Specification
+name: topas-tools
+version: !ruby/object:Gem::Version
+  version: 0.0.0
+platform: ruby
+authors:
+- Artem Dmitrienko
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-08-19 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: green_shoes
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.1.374
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.1.374
+description: Gem for repetitive Rietveld refinements with Topas4-2
+email: dmitrienka@gmail.com
+executables:
+- toparunGUI
+- toparun
+extensions: []
+extra_rdoc_files: []
+files:
+- bin/toparun
+- bin/toparunGUI
+- lib/topas-tools.rb
+- lib/topas-tools/Analyzers.rb
+- lib/topas-tools/TopasEngine.rb
+- lib/topas-tools/TopasInput.rb
+homepage: 
+licenses:
+- GPL2
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Rrrrr!
+test_files: []