Class: Mspire::Imzml::Writer

Inherits:
Object
  • Object
show all
Defined in:
lib/mspire/imzml/writer.rb,
lib/mspire/imzml/writer/commandline.rb

Defined Under Namespace

Modules: Commandline

Constant Summary collapse

DEFAULTS = 
{
  mz_data_type: :float,
  mz_precision: 64,
  intensity_data_type: :float, 
  intensity_precision: 32,
}

Instance Method Summary collapse

Instance Method Details

#create_file_description(source_files, config) ⇒ Object 



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# File 'lib/mspire/imzml/writer.rb', line 216

def create_file_description(source_files, config)
  Mspire::Mzml::FileDescription.new  do |fd|

    fd.file_content = Mspire::Mzml::FileContent.new.describe_many!( [
      'MS:1000579', # MS1 Spectrum
      config[:profile] ? 'MS:1000128' : 'MS:1000127',
      ['IMS:1000080', "{"+config[:uuid_hyphenated]+"}"],
      ['IMS:1000091', config[:ibd_sha1]],
      (config[:data_structure] == :processed) ? 'IMS:1000031' : 'IMS:1000030',
    ] )

    fd.source_files.replace(source_files)
    if [:name, :organization, :address, :email].any? {|key| config[key] }
      contact = Mspire::Mzml::Contact.new
      [ [:name, 'MS:1000586'], 
        [:organization, 'MS:1000590'],
        [:address, 'MS:1000587'],
        [:email, 'MS:1000589']
      ].each do |key, accession|
        contact.describe!(accession, config[key]) if config[key]
      end
      fd.contacts << contact
    end
  end
end

#create_referenceable_params_by_id_hash ⇒ Object 



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# File 'lib/mspire/imzml/writer.rb', line 242

def create_referenceable_params_by_id_hash
  # m/z array and no compression (because we'll ref peaks in different
  # file)
  rparms = {
    :mz_array => [
      ["MS:1000514", "MS:1000040"], # m/z array, units = m/z
      "MS:1000576",                 # no compression
      ["IMS:1000101", true],        # external data
      'MS:1000523'                  # 64-bit float
  ],
    :intensity_array =>  [
      ["MS:1000515", "MS:1000131"], # intensity array, units = number of counts
      "MS:1000576",                 # no compression
      ["IMS:1000101", true],        # external data
      'MS:1000521'                  # 32-bit float
  ],
    :scan1 => [
      # this should probably be ascertained from the mzml file:
      "MS:1000093", # increasing m/z scan
      # "MS:1000095" # linear  # <- this should probably be gathered
      # from mzml (leave outfor now)
      # could include the filter string here in future
  ],
  :spectrum1 => [
    "MS:1000579", # MS1 spectrum
    ["MS:1000511", 1], # ms level - default implementation uses 0 but I disagree...
    "MS:1000127",  # centroid spectrum
    "MS:1000130" # <- positive scan
  ]}.map do |id, list|
    Mspire::Mzml::ReferenceableParamGroup.new(id).describe_many!(list)
  end
  Hash[ rparms.map {|prm_group_obj| [prm_group_obj.id, prm_group_obj]} ]
end

#experiment_hash_to_cvs(hash) ⇒ Object 



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# File 'lib/mspire/imzml/writer.rb', line 154

def experiment_hash_to_cvs(hash)
  cvs = { 
    :matrix_solution_concentration => "MS:1000835",
    :matrix_solution => "MS:1000834",
    :solvent => 'IMS:1001211',
    :solvent_flowrate => 'IMS:1001213',
    :spray_voltage => 'IMS:1001212',
    :target_material => 'IMS:10000202'
  }.map do |key,cv_acc|
    [cv_acc, hash[key]] if hash[key]
  end.compact

  mats = hash[:matrix_application_types]
  if mats
    app_types = mats.map do |typ|
      case typ.to_s
      when 'sprayed' ; 'MS:1000838'
      when 'precoated' ; 'MS:1000839'
      when 'printed' ; 'MS:1000837'
      when 'drieddroplet' ; 'MS:1000836'
      else ; raise "invalid matrix_application_type"
      end
    end
    cvs.push(*app_types)
  end
  cvs
end

#image_hash_to_cvs(hash) ⇒ Object

converts image related hash values to an array of loose describe! params



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# File 'lib/mspire/imzml/writer.rb', line 105

def image_hash_to_cvs(hash)
  cvs = []
  cvs << case hash[:data_structure].to_sym
  when :processed ; 'IMS:1000031'
  when :continuous ; 'IMS:1000030'
  else ; raise ":data_structure must be :processed or :continuous"
  end 

  cvs << case hash[:scan_pattern].to_sym
  when :meandering ; 'IMS:1000410'
  when :random ; 'IMS:1000412'
  when :flyback ; 'IMS:1000413'
  else ; raise ":scan_pattern must be :meandering, :random or :flyback"
  end

  cvs << case hash[:scan_type].to_sym
  when :horizontal ; 'IMS:1000480'
  when :vertical ; 'IMS:1000481'
  else ; raise ":scan_type must be :horizontal or :vertical"
  end

  cvs << case hash[:linescan_direction].to_s
  when 'left-right' ; 'IMS:1000402'
  when 'right-left' ; 'IMS:1000403'
  when 'bottom-up' ; 'IMS:1000400'
  when 'top-down' ; 'IMS:1000401'
  when 'none' ; 'IMS:1000404'
  else ; raise ":linescan_direction unacceptable"
  end

  cvs << case hash[:linescan_sequence].to_s
  when 'top-down' ; 'IMS:1000493'
  when 'bottom-up' ; 'IMS:1000492'
  when 'left-right' ; 'IMS:1000491'
  when 'right-left' ; 'IMS:1000490'
  else ; raise "linescan_sequence unacceptable"
  end

  max_pix_dims = hash[:max_dimensions_pixels].split(/x/i)
  cvs.push *['IMS:1000042', 'IMS:1000043'].zip(max_pix_dims).to_a

  real_dims = hash[:max_dimensions_microns].split(/x/i)
  cvs.push *['IMS:1000044', 'IMS:1000045'].zip(real_dims).map {|pair| [*pair, "UO:0000017"] }

  pix_dims = hash[:pixel_size].split(/x/i)
  cvs.push *["IMS:1000046", "IMS:1000047"].zip(pix_dims).map {|pair| [*pair, "UO:0000017"] }
  cvs
end

#write(mzml_filenames, config = {}) ⇒ Object

mzml_filenames can each be a partial or relative path by default the file will write to the same directory and basename

contact:
  :name => name of the person or organization
  :address => address of the person or organization
  :url => url of person or organization
  :email => email of person or organization
  :organization => home institution of contact
experiment:
  :solvent => the solvent used
  :solvent_flowrate => flowrate of the solvent (ml/min)
  :spray_voltage => spray voltage in kV
  :target_material => the material the target is made of
editing:
  :trim_files => determines min # spectra in file and lops
                 off the ends of other files.
general:
  :omit_zeros => remove zero values
  :combine => use this outfile base name to combine files
              also works on single files to rename them.
              MUST be present if more than one mzml given.
imaging:
  :data_structure => :processed or :continuous  
  :scan_pattern => meandering random flyback
  :scan_type => horizontal or vertical
  :linescan_direction => scan_direction.join('|')
  :linescan_sequence => scan_sequence.join('|')
  :max_dimensions_pixels => maximum X by Y pixels (e.g. 300x100)
  :shots_per_position => number of spectra per position
  :pixel_size => X by Y of a single pixel in microns (μm)
  :max_dimensions_microns => maximum X by Y in microns (e.g. 25x20)



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# File 'lib/mspire/imzml/writer.rb', line 308

def write(mzml_filenames, config={})

  base = config[:combine] || mzml_filenames.first.chomp(File.extname(mzml_filenames.first))
  config[:imzml_filename] = base + ".imzML"
  config[:ibd_filename] = base + ".ibd"

  uuid_with_hyphens = SecureRandom.uuid
  config[:uuid_hyphenated] = uuid_with_hyphens
  config[:uuid] = uuid_with_hyphens.gsub('-','')

  if config[:trim_files]
    config[:trim_to] = mzml_filenames.map {|fn| Mspire::Mzml.open(fn, &:size) }.min
  end

  sourcefile_id_parallel_to_spectra = []
  sourcefile_ids = []
  all_spectra_iter = Enumerator.new do |yielder|
    mzml_filenames.each_with_index do |mzml_filename,i|
      sourcefile_id = "source_file_#{i}"
      sourcefile_ids << sourcefile_id
      Mspire::Mzml.open(mzml_filename) do |mzml|
        enumerates_spectra = 
          # handle SIM files "MS:1001472", "selected ion monitoring chromatogram"
          if mzml.file_description.file_content.fetch_by_acc('MS:1001472')
            # handle normal mzml files
            mz_ars = []
            its_ars = []
            mzml.each_chromatogram.each do |chromatogram,i| 
              next unless chromatogram.fetch_by_acc('MS:1001472')
              target_mz = chromatogram.precursor.isolation_window.fetch_by_acc('MS:1000827').to_f
              its = chromatogram.intensities
              mz_ars << Array.new(its.size, target_mz)
              its_ars << its
            end
            mz_ars.transpose.zip(its_ars.transpose).map {|mzs, its| Mspire::Spectrum.new([mzs, its]) }
          else
            # normal mzml file with spectra
            mzml
          end
        enumerates_spectra.each_with_index do |spec,i| 
          break if config[:trim_to] && (i >= config[:trim_to])
          sourcefile_id_parallel_to_spectra << sourcefile_id 
          yielder << spec
        end
      end
    end
  end

  data_info_pairs = write_binary(config[:ibd_filename], all_spectra_iter, config)
  xy_positions_array = x_y_positions(config)

  unless data_info_pairs.size == xy_positions_array.size
    STDERR.puts "Input Error! The number of calculated scans must equal the number of actual scans!" 
    STDERR.puts "The number of calculated positions: #{xy_positions_array.size}"
    STDERR.puts "The number of actual scans: #{data_info_pairs.size}"
    raise
  end

  config[:ibd_sha1] = Digest::SHA1.hexdigest(IO.read(config[:ibd_filename]))

  source_files = mzml_filenames.zip(sourcefile_ids).map do |mzml_filename, source_file_id|
    sfile = Mspire::Mzml::SourceFile[ mzml_filename ]
    sfile.id = source_file_id
    sfile.describe! 'MS:1000584'
    sfile.describe! 'MS:1000569', Digest::SHA1.hexdigest(IO.read(mzml_filename))
    sfile
  end
  sourcefile_id_to_sourcefile = Hash[ source_files.group_by(&:id).map {|k,v| [k,v.first] } ]

  imzml_obj = Mspire::Mzml.new do |imzml|
    imzml.id = SecureRandom.uuid.gsub('-','')
    imzml.cvs = Mspire::Mzml::CV::DEFAULT_CVS

    imzml.file_description = create_file_description(source_files, config)

    rparms_by_id = create_referenceable_params_by_id_hash

    warn "using positive scan in every case but need to get this from original mzml!"

    imzml.referenceable_param_groups = rparms_by_id.values
    # skip sample list for now
    mspire_software = Mspire::Mzml::Software.new("mspire", Mspire::VERSION).describe!("MS:1000799")
    imzml.software_list << mspire_software

    scan_setting_params = image_hash_to_cvs( config )
    scan_setting_params.push *experiment_hash_to_cvs( config )
    imzml.scan_settings_list = [Mspire::Mzml::ScanSettings.new("scansettings1").describe_many!(scan_setting_params)]

    warn 'todo: need to borrow instrumentConfiguration from original mzml'

    default_instrument_config = Mspire::Mzml::InstrumentConfiguration.new("borrow_from_mzml")
    warn 'todo: need to include default softare from mzml in default_instrument_config'
    #default_instrument_config.software = Software.new( from the mzml file! )
    imzml.instrument_configurations << default_instrument_config

    # this is a generic 'file format conversion' but its the closest we
    # have for mzml to imzml (which is really mzml to mzml)
    data_processing_obj = Mspire::Mzml::DataProcessing.new('mzml_to_imzml')
    data_processing_obj.processing_methods << Mspire::Mzml::ProcessingMethod.new(mspire_software).describe!('MS:1000530')
    imzml.data_processing_list << data_processing_obj

    warn "not implemented 'omit_zeros' yet"
    # low intensity data point removal: "MS:1000594"
    imzml.run = Mspire::Mzml::Run.new("run1", default_instrument_config) do |run|
      spectra = []
      data_info_pairs.zip(xy_positions_array, sourcefile_id_parallel_to_spectra).each_with_index do |(pair, xy, sourcefile_id),i|
        # TODO: we should probably copy the id from the orig mzml (e.g.
        # scan=1)
        spectrum = Mspire::Mzml::Spectrum.new("spectrum#{i}").describe!(rparms_by_id[:spectrum1])
        spectrum.source_file = sourcefile_id_to_sourcefile[sourcefile_id]
        scan_list = Mspire::Mzml::ScanList.new.describe!('MS:1000795')  # no combination
        scan = Mspire::Mzml::Scan.new.describe_many!([rparms_by_id[:scan1], ["IMS:1000050", xy[0]], ["IMS:1000051", xy[1]]])
        scan.instrument_configuration = default_instrument_config
        spectrum.scan_list = (scan_list << scan)
        
        data_arrays = %w(mz intensity).zip(pair).map do |type, data_array_info|
          rparmgroup = rparms_by_id[(type + "_array").to_sym]
          # the type is defined in the refparams
          data_array = Mspire::Mzml::DataArray.new
          data_array.external = true
          data_array.describe_many! [rparmgroup, *%w(IMS:1000103 IMS:1000102 IMS:1000104).zip(data_array_info).map.to_a]
          data_array
        end
        spectrum.data_arrays = data_arrays
        spectra << spectrum
      end
      run.spectrum_list = Mspire::Mzml::SpectrumList.new(data_processing_obj, spectra)
    end # run
  end # imzml
  imzml_obj.to_xml(config[:imzml_filename])
end

#write_binary(filename, spectra_iterator, config) ⇒ Object

returns an array of DataArrayInfo pairs

These must be defined in the config hash with valid values (see write_data_array for what those are):

:mz_data_type
:mz_precision
:intensity_data_type
:intensity_precision

Also recognizes :data_structure (:processed or :continuous). If :continuous, then the first spectrum is used to write the initial m/z and intensity pair, then in every spectrum after that the m/z data (if any) is ignored and only the intensities are written). The return is the same, the data info for each intensity is coupled with the m/z info from the first m/z data.



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# File 'lib/mspire/imzml/writer.rb', line 72

def write_binary(filename, spectra_iterator, config)
  config = DEFAULTS.merge(config)
  raise ":data_structure must be :continuous or :processed" unless [:processed, :continuous].include?(config[:data_structure])
  (mz_dtype, mz_prec, int_dtype, int_prec) = config.values_at(:mz_data_type, :mz_precision, :intensity_data_type, :intensity_precision)
  mz_prec_in_bytes = mz_prec / 8
  int_prec_in_bytes = int_prec / 8
  File.open(filename, 'wb') do |out|
    out.print [config[:uuid]].pack("H*")

    if config[:data_structure] == :continuous
      # write the first m/z and get its info
      mzs = spectra_iterator.peek.mzs
      mz_info = Mspire::Imzml::DataArrayInfo.new mzs.size, out.pos, mzs.size * mz_prec_in_bytes
      write_data_array(out, mzs, mz_dtype, mz_prec)
    end
    spectra_iterator.map do |spec|

      if config[:data_structure] == :processed
        mzs = spec.mzs
        mz_info = Mspire::Imzml::DataArrayInfo.new mzs.size, out.pos, mzs.size * mz_prec_in_bytes
        write_data_array(out, spec.mzs, mz_dtype, mz_prec)
      end

      ints = spec.intensities
      int_info = Mspire::Imzml::DataArrayInfo.new ints.size, out.pos, ints.size * int_prec_in_bytes
      write_data_array(out, spec.intensities, int_dtype, int_prec)
      [mz_info, int_info]
    end
  end
end

#write_data_array(fh, values, dtype = :float, precision = 32) ⇒ Object

Integer values (dtype=:int) may be stored with precision = 8, 16, 32, 64 . Floating point values may be stored as 32 or 64 bit precision. The byte order is always little endian (intel style).

NOTE: the documentation is not clear whether they want signed or unsigned integers! Right now this outputs signed integers (my educated guess as to what is required)



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# File 'lib/mspire/imzml/writer.rb', line 34

def write_data_array(fh, values, dtype=:float, precision=32)
  pack_code = 
    case dtype
    when :float
      precision == 64 ? 'E*' : 'e*'
    when :int
      # using signed!!!! (should these be unsigned??? NOT DOCUMENTED in
      # imzml resources anywhere!)
      case precision
      when 8  ; 'c<*'
      when 16 ; 's<*'
      when 32 ; 'l<*'
      when 64 ; 'q<*'
      else
        raise 'precision must be 8, 16, 32, or 64 for dtype==:int'
      end
    else
      raise 'dtype must be :int or :float!'
    end
  fh.print values.pack(pack_code)
end

#x_y_positions(config) ⇒ Object

returns an array with x, y pairs in the correct order accounts for scan_pattern, scan_type, linescan_direction, linescan_sequence and shots_per_position



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# File 'lib/mspire/imzml/writer.rb', line 185

def x_y_positions(config)
  (scan_pattern, scan_type, scan_direction, scan_sequence, shots_per_pos) = config.values_at(:scan_pattern, :scan_type, :linescan_direction, :linescan_sequence, :shots_per_position).map(&:to_s)
  shots_per_pos = shots_per_pos.to_i
  #puts "EXAMIN ARGS: "
  #p [ scan_pattern, scan_type, scan_direction, scan_sequence, shots_per_pos, shots_per_pos]

  # the true dimensions we need to work off come from the pixel dimensions.
  (slen, plen) = config[:max_dimensions_pixels].split(/x/i).map(&:to_i)

  flip = (scan_type == 'vertical')
  plen, slen = slen, plen if flip

  pindices = (1..plen).to_a  # mindices if linescan_direction is 'horizontal'
  sindices = (1..slen).to_a  # nindices if linescan_direction is 'horizontal'

  if flip
    sindices.reverse! if scan_direction == 'bottom-top' || scan_direction == 'right-left'
    pindices.reverse! if scan_sequence == 'right-left' || scan_sequence == 'bottom-top'
  end

  indices = pindices.map do |a|
    row = sindices.map do |b|
      flip ? [a,b] : [b,a]
    end
    sindices.reverse! if scan_pattern == 'meandering'
    row
  end.flatten(1)

  indices.map {|pair| shots_per_pos.times.map { pair } }.flatten(1)
end