Class: SciYAG::Backends::TextBackend

Inherits:
Backend
  • Object
show all
Includes:
Dobjects
Defined in:
lib/SciYAG/Backends/text.rb

Direct Known Subclasses

MultiTextBackend

Constant Summary collapse

UNCOMPRESSORS =

A constant holding a relation extension -> command to decompress (to be fed to sprintf with the filename as argument)

{
  ".gz" => "gunzip -c %s",
  ".bz2" => "bunzip2 -c %s",
  ".lzma" => "unlzma -c %s",
}
InvalidLineRE =

A line is invalid if it is blank or starts neither with a digit nor +, - or .

Maybe to be improved later.

/^\s*$|^\s*[^\d+.\s-]+/

Instance Method Summary collapse

Methods inherited from Backend

#base_line=, #clear_xy_filters, default_state, describe, #get_cached_entry, #has_set?, list_backends, list_descriptions, logger=, #meta_data, #pop_xy_filter, #push_xy_filter, #set_type, #sets_available, #xy_data, #xyz_data

Methods included from MetaBuilder::DescriptionExtend

#base_description, #create_factory, #describe, #description, #factory_class, #factory_description, #factory_description_hash, #factory_description_list, #group, #has_factory?, #inherit_parameters, #param, #param_accessor, #param_reader, #param_writer, #register_class, #set_description

Methods included from MetaBuilder::DescriptionInclude

#description, #get_param, #get_param_raw, #long_name, #option_parser_banner, #option_parser_fill, #option_parser_options, #parameter, #restore_state, #save_state, #set_param, #set_param_raw

Constructor Details

#initialize ⇒ TextBackend

param_accessor :select, ‘select’, “Select lines”, => :string,

"Skips line where the code returns false"



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# File 'lib/SciYAG/Backends/text.rb', line 78

def initialize
  @dummy = nil
  @current = nil   
  # Current is the name of the last file used. Necessary for '' specs.
  @current_data = nil       # The data of the last file used.
  @skip = 0
  @included_modules = [NaN]    # to make sure we give them to
  # Dvector.compute_formula
  @default_column_spec = "1:2"

  @separator = /\s+/

  # We don't split data by default.
  @split = false

  super()

  # Override Backend's cache - for now.
  @cache = {}               # A cache file_name -> data

end

Instance Method Details

#compute_error_bars(values) ⇒ Object

Turns a target => values specification into something usable as error bars, that is :xmin, :xmax and the like hashes. The rules are the following:

  • ?min/?max are passed on directly;

  • ?e(abs) are transformed into ?min = ? - ?eabs, ?max = ? + ?eabs

  • ?eu(p/?ed(own) are transformed respectively into ? +/- ?…

  • ?er(el) become ?min = ?*(1 - ?erel, ?max = ?(1 + ?erel)

  • ?erup/?erdown follow the same pattern…



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# File 'lib/SciYAG/Backends/text.rb', line 281

def compute_error_bars(values)
  target = {}
  for key in values.keys
    case key.to_s
    when /^[xy](min|max)?$/
      target[key] = values[key].dup # Just to make sure.
    when /^(.)e(a(bs?)?)?$/
      target["#{$1}min".to_sym] = values[$1.to_sym] - values[key]
      target["#{$1}max".to_sym] = values[$1.to_sym] + values[key]
    when /^(.)eu(p)?$/
      target["#{$1}max".to_sym] = values[$1.to_sym] + values[key]
    when /^(.)ed(o(wn?)?)?$/
      target["#{$1}min".to_sym] = values[$1.to_sym] - values[key]
    when /^(.)er(el?)?$/
      target["#{$1}min".to_sym] = values[$1.to_sym] * 
        (values[key].neg + 1)
      target["#{$1}max".to_sym] = values[$1.to_sym] * 
        (values[key] + 1)
    when /^(.)erd(o(wn?)?)?$/
      target["#{$1}min".to_sym] = values[$1.to_sym] * 
        (values[key].neg + 1)
    when /^(.)erup?$/
      target["#{$1}max".to_sym] = values[$1.to_sym] * 
        (values[key] + 1)
    else
      warn "Somehow, the target specification #{key} " +
        "didn't make it through"
    end
  end
  return target
end

#expand_sets(spec) ⇒ Object

Expands specifications into few sets. This function will separate the set into a file spec and a col spec. Within the col spec, the 2##6 keyword is used to expand to 2,3,4,5,6. 2## followed by a non-digit expands to 2,…,last column in the file. For now, the expansions stops on the first occurence found, and the second form doesn’t work yet. But soon…



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# File 'lib/SciYAG/Backends/text.rb', line 319

def expand_sets(spec)
  if m = /(\d+)##(\D|$)/.match(spec)
    a = m[1].to_i 
    trail = m[2]
    b = read_file(spec)
    b = (b.length - 1) 
    ret = []
    a.upto(b) do |i|
      ret << m.pre_match + i.to_s + trail + m.post_match
    end
    return ret
  else
    return super
  end
end

#extend(mod) ⇒ Object 



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# File 'lib/SciYAG/Backends/text.rb', line 100

def extend(mod)
  super
  @included_modules << mod
end

#get_data(col_spec) ⇒ Object

Reads the data using the columns specification, provided that the appropriate fle has already been loaded into @current. For now no single sanity check.



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# File 'lib/SciYAG/Backends/text.rb', line 234

def get_data(col_spec)
  # First, we must split the column specification into what
  # I would call target specifications. A target is in the form
  # of stuff=spec, where stuff can be basically anything. x=, y=,
  # yea= are implied for the first specifications. 

  defaults = [:x,:y,:yea]
  specifications = {}       # A hash value spec => column spec
  col_spec.split(/:/).each do |spec|
    d = defaults.shift
    if spec =~ /^\s*(\w+)\s*=(.*)/
      spec = $2
      d = $1.to_sym
    end
    specifications[d] = spec
  end
  
  debug "spec #{col_spec} becomes #{specifications.inspect}"

  values = {}
  if col_spec =~ /\$/       # There is a formula in the specification
    for key,spec in specifications
      formula = spec.gsub(/\$(\d+)/, 'column[\1]')
      debug "Using formula '#{formula}' for #{key}"
      values[key] = Dvector.
        compute_formula(formula, 
                        @current_data,
                        @included_modules)
    end
  else
    for key,spec in specifications
      values[key] = @current_data[spec.to_i].dup
    end
  end
  errors = compute_error_bars(values)
  # Now, we're left with a hash...
  return [values[:x],values[:y], errors]
end

#get_io_object(file) ⇒ Object

Returns a IO object suitable to acquire data from it for the given file, which can be one of the following:

  • a real file name

  • a compressed file name

  • a pipe command.



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# File 'lib/SciYAG/Backends/text.rb', line 110

def get_io_object(file)
  if file == "-"
    return $stdin
  elsif file =~ /(.*?)\|\s*$/ # A pipe
    return IO.popen($1)
  elsif not File.readable?(file)
    # Try to find a compressed version
    for ext,method in UNCOMPRESSORS
      if File.readable? "#{file}#{ext}"
        info "Using compressed file #{name}#{ext} in stead of #{name}"
        return IO.popen(method % "#{file}#{ext}")
      end
    end
  else 
    for ext, method in UNCOMPRESSORS
      if file =~ /#{ext}$/ 
        info "Taking file #{file} as a compressed file"
        return IO.popen(method % file)
      end
    end
    return File::open(file)
  end
  error "Could not open #{file}"
  return nil
end

#get_io_set(file) ⇒ Object

Returns an IO object corresponding to the given file.



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# File 'lib/SciYAG/Backends/text.rb', line 175

def get_io_set(file)
  if not @split
    return get_io_object(file)
  else
    file =~ /(.*?)(?:#(\d+))?$/; # ; to make ruby-mode indent correctly.
    filename = $1
    if $2
      set = $2.to_i
    else
      set = 1
    end
    debug "Trying to get set #{set} from file '#{filename}'"
    str = get_set_string(get_io_object(filename), set)
    return StringIO.new(str)
  end
end

#get_set_string(io, set) ⇒ Object

Returns a string corresponding to the given set of the given io object.

Sets are 1-based.



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# File 'lib/SciYAG/Backends/text.rb', line 146

def get_set_string(io, set)
  cur_set = 1
  last_line_is_invalid = true
  str = ""
  line_number = 0
  while line = io.gets
    line_number += 1
    if line =~ InvalidLineRE
      debug "Found invalid line at #{line_number}"
      if ! last_line_is_invalid
        # We begin a new set.
        cur_set += 1
        debug "Found set #{cur_set} at line #{line_number}"
        if(cur_set > set)
          return str
        end
      end
      last_line_is_invalid = true
    else
      last_line_is_invalid = false
      if cur_set == set
        str += line
      end
    end
  end
  return str
end

#query_xy_data(set) ⇒ Object

This is called by the architecture to get the data. It splits the set name into filename@cols, reads the file if necessary and calls get_data



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# File 'lib/SciYAG/Backends/text.rb', line 215

def query_xy_data(set)
  if set =~ /(.*)@(.*)/
    col_spec = $2
    file = $1
  else
    col_spec = @default_column_spec
    file = set
  end
  if file.length > 0
    @current_data = read_file(file)
    @current = file
  end
  x,y,err = get_data(col_spec)
  return [Function.new(x,y),err]
end

#read_file(file) ⇒ Object

Reads data from a file. If needed, extract the file from the columns specification.



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# File 'lib/SciYAG/Backends/text.rb', line 194

def read_file(file)
  if file =~ /(.*)@.*/
    file = $1
  end
  name = file               # As file will be modified.
  if ! @cache.key?(file)    # Read the file if it is not cached.
    fancy_read_options = {'index_col' => true,
      'skip_first' => @skip,
      'sep' => @separator
    }
    io_set = get_io_set(file)
    debug "Fancy read '#{file}', options #{fancy_read_options.inspect}"
    @cache[name] = Dvector.fancy_read(io_set, nil, fancy_read_options)
  end
  return @cache[name]
end