Module: Mspire::Imzml::Writer::Commandline

Defined in:
lib/mspire/imzml/writer/commandline.rb

Class Method Summary collapse

Class Method Details

.parser ⇒ Object

generates the Trollop parser



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# File 'lib/mspire/imzml/writer/commandline.rb', line 17

def self.parser
  return @parser if @parser

  default_config = "config.yaml"
  scan_patterns = %w(flyback meandering random)
  scan_types = %w(horizontal vertical)
  scan_direction = %w(left-right right-left bottom-up top-down none)
  scan_sequence = %w(top-down bottom-up left-right right-left)
  default_dims = '800x600'
  default_pixel_size = '1x1'
  matrix_application_types = %w(sprayed precoated printed drieddroplet)

  @parser = Trollop::Parser.new do
    banner <<-EOS
usage: mspire to_imzml [OPTIONS] <file>.mzML ..."
output: <file>.imzML and <file>.ibd

* imzML docs: 
  http://www.maldi-msi.org/index.php?option=com_content&view=article&id=187&Itemid=67
* explanation of vocabulary (followed here): 
  http://www.maldi-msi.org/index.php?option=com_content&view=article&id=193&Itemid=66
* github repository:
  https://github.com/princelab/mzml_to_imzml
    EOS
    text "\ngeneral:"
    opt :config, "read a config file for default values. Command line options overide those from the config file ", :type => :string
    opt :print_config, "print current options to #{default_config} and exit"
    opt :omit_zeros, "remove zero values"
    opt :combine, "combine all files and set the base name of resulting imzML and ibd files", :type => String
    opt :outfile, "use a specific basename for the resulting file. Acts like --combine for multiple files", :type => String

    text "\nediting:"
    opt :trim_files, "determines the least number of spectra in a file and shortens all spectra to be the same length"

    text "\nimaging:"
    opt :continuous, "assumes m/z values are the same for every scan. The 'processed' storage format is used unless this flag is given."
    opt :scan_pattern, scan_patterns.join('|'), :default => scan_patterns.first
    opt :scan_type, scan_types.join('|'), :default => scan_types.first
    opt :linescan_direction, scan_direction.join('|'), :default => scan_direction.first
    opt :linescan_sequence, scan_sequence.join('|'), :default => scan_sequence.first
    opt :max_dimensions_pixels, "maximum X by Y pixels (e.g. 300x100)", :default => default_dims
    opt :shots_per_position, "number of spectra per position", :default => 1
    opt :pixel_size, "X by Y of a single pixel in microns (μm)", :default => default_pixel_size 
    opt :max_dimensions_microns, "maximum X by Y in microns (e.g. 25x20)", :default => default_dims

    text "\ncontact: "
    opt :name, "name of the person or organization", :type => :string
    opt :address, "address of the person or organization", :type => :string
    opt :url, "url of person or organization", :type => :string
    opt :email, "email of person or organization", :type => :string
    opt :organization, "home institution of contact", :type => :string

    text "\nDESI: "
    opt :solvent, "the solvent used", :type => :string
    opt :solvent_flowrate, "flowrate of the solvent (ml/min)", :type => :float
    opt :spray_voltage, "spray voltage in kV", :type => :float
    opt :target_material, "the material the target is made of", :type => :string

    text "\nMALDI: "
    opt :matrix_application_types, "#{matrix_application_types.join('|')} (comma separated)", :type => :string
    opt :matrix_solution_concentration, "in grams per liter", :type => :float
    opt :matrix_solution, "the chemical solution used as matrix (e.g., DHB)", :type => :string

    # things to add: data types for m/z and intensity
    # filters (cutoff / max # peaks, etc.)
    # ms_level, etc.
  end
end

.run(argv, globalopts = []) ⇒ Object 



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# File 'lib/mspire/imzml/writer/commandline.rb', line 86

def self.run(argv, globalopts=[])
  begin
    opts = parser.parse(argv)
  rescue Trollop::HelpNeeded
    return parser.educate
  end

  opts = Hash[YAML.load_file(opts[:config]).map {|k,v| [k.to_sym, v]}].merge(opts) if opts[:config]

  opts[:combine] ||= opts.delete(:outfile)

  if opts.delete(:print_config)
    puts "writing defaults to: #{default_config}"
    string_opts = Hash[ opts.map {|k,v| [k.to_s, v] } ]
    %w(help).each {|key| string_opts.delete key }
    string_opts.delete_if {|k,v| k =~ /_given$/ }
    File.write(default_config, string_opts.to_yaml) 
    exit
  end

  if argv.size == 0
    return parser.educate
  end

  opts[:data_structure] = (opts.delete(:continuous) ? :continuous : :processed)
  opts[:matrix_application_types] = opts[:matrix_application_types].split(',') if opts[:matrix_application_types]

  # prep args a little
  writer = Mspire::Imzml::Writer.new
  writer.write(argv, opts)

end