Class: Mspire::Mzml::DataArray

Inherits:
Array
  • Object
show all
Includes:
CV::Paramable
Defined in:
lib/mspire/mzml/data_array.rb

Constant Summary collapse

DEFAULT_DTYPE = 
:float64
DEFAULT_COMPRESSION = 
true
DTYPE_TO_ACC = 
{
  float64: 'MS:1000523',
  float32: 'MS:1000521',
  # float16: 'MS:1000520',  # <- not supported w/o other gems
  int64: 'MS:1000522', # signed
  int32: 'MS:1000519', # signed
}

Instance Attribute Summary collapse

Attributes included from CV::Paramable

#cv_params, #ref_param_groups, #user_params

Class Method Summary collapse

Instance Method Summary collapse

Methods included from CV::Paramable

#accessionable_params, #describe!, #describe_many!, #fetch, #fetch_by_accession, #param?, #param_by_accession, #params, #params?

Methods inherited from Array

#in_groups

Constructor Details

#initialize(*args) ⇒ DataArray

Returns a new instance of DataArray.



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# File 'lib/mspire/mzml/data_array.rb', line 49

def initialize(*args)
  array_initialize(*args)
  params_initialize
end

Instance Attribute Details

#external ⇒ Object

set this if the data is written to an external file (such as the ibd file for imzML files)



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# File 'lib/mspire/mzml/data_array.rb', line 47

def external
  @external
end

Class Method Details

.from_binary(base64, *args) ⇒ Object

returns a new Mspire::Mzml::DataArray object (an array)

args:
  base64, set-like               # where set-like responds to include?
  base64, type=:float64, compression=true

examples:
Mspire::Mzml::Spectrum.unpack_binary('eJxjYACBD/YMEOAAoTgcABe3Abg=', ['MS:1000574', MS:1000523']).
Mspire::Mzml::Spectrum.unpack_binary("ADBA/=", :float32, true)
Mspire::Mzml::Spectrum.unpack_binary("ADBA/=") # uses float64 and compression



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# File 'lib/mspire/mzml/data_array.rb', line 64

def self.from_binary(base64, *args)
  if args.first.respond_to?(:include?)
    accessions = args.first
    compressed =
      if accessions.include?('MS:1000574') then true # zlib compression
      elsif accessions.include?('MS:1000576') then false # no compression
      else raise 'no compression info: check your MS accession numbers'
      end
    precision_unpack = 
      if accessions.include?('MS:1000523') then 'E*'
      elsif accessions.include?('MS:1000521') then 'e*'
      else raise 'unrecognized precision: check your MS accession numbers'
      end
  else
    compressed = args.last || true
    precision_unpack =
      case args.first
      when :float64
        'E*'
      when :float32
        'e*'
      when nil
        'E*'
      else
        raise ArgumentError, "#{args.first} must be one of :float64, :float32 or other acceptable type"
      end
  end
  data = base64.unpack("m*").first
  # some implementations leave data blank if there aren't peaks
  # even if they say it is zlib compressed...
  unzipped = 
    if data.size > 0  
      compressed ? Zlib::Inflate.inflate(data) : data
    else
      data
    end
  self.new( unzipped.unpack(precision_unpack) )
end

.list_xml(arrays, builder) ⇒ Object

takes an array of DataArray objects or other kinds of objects



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# File 'lib/mspire/mzml/data_array.rb', line 163

def self.list_xml(arrays, builder)
  builder.binaryDataArrayList(count: arrays.size) do |bdal_n|
    arrays.zip([:mz, :intensity]) do |data_ar, typ|
      ar = 
        if data_ar.is_a?(Mspire::Mzml::DataArray)
          data_ar
        else
          Mspire::Mzml::DataArray.new(data_ar)
        end
      ar.type = typ unless ar.type
      ar.to_xml(bdal_n)
    end
  end
end

.to_binary(array_ish, *args) ⇒ Object

returns a base64 string that can be used for xml representations of the data

args:
  array-like  set-like               # where set-like responds to include?
  array-like  dtype=:float64, compression=true



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# File 'lib/mspire/mzml/data_array.rb', line 109

def self.to_binary(array_ish, *args)
  if args.first.respond_to?(:include?)
    accessions = args.first
    dtype = 
      if accessions.include?('MS:1000521') 
        :float32
      else
        :float64
      end
    compression = accessions.include?('MS:1000576') ? false : true 
  else
    dtype = args[0] || DEFAULT_DTYPE
    compression = args[1] || DEFAULT_COMPRESSION
  end

  pack_code = 
    case dtype
    when :float64 ; 'E*'
    when :float32 ; 'e*'
    when :int64   ; 'q<*'
    when :int32   ; 'l<*'
    else ; raise "unsupported dtype: #{dtype}"
    end
  # TODO: support faster pack method for NArray's in future
  string = array_ish.to_a.pack(pack_code) 
  string = Zlib::Deflate.deflate(string) if compression
  Base64.strict_encode64(string)
end

Instance Method Details

#array_initialize ⇒ Object 



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# File 'lib/mspire/mzml/data_array.rb', line 8

alias_method :array_initialize, :initialize

#params_initialize ⇒ Object 



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# File 'lib/mspire/mzml/data_array.rb', line 10

alias_method :params_initialize, :initialize

#params_to_xml ⇒ Object 



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# File 'lib/mspire/mzml/data_array.rb', line 11

alias_method :params_to_xml, :to_xml

#to_binary(*args) ⇒ Object

calls the class to_binary method with self and the given args



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# File 'lib/mspire/mzml/data_array.rb', line 139

def to_binary(*args)
  self.class.to_binary(self, *args)
end

#to_xml(builder, dtype = DEFAULT_DTYPE, compression = DEFAULT_COMPRESSION) ⇒ Object 



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# File 'lib/mspire/mzml/data_array.rb', line 143

def to_xml(builder, dtype=DEFAULT_DTYPE, compression=DEFAULT_COMPRESSION)
  encoded_length = 
    if @external
      0
    else
      base64 = self.class.to_binary(self, dtype, compression)
      base64.bytesize
    end

  builder.binaryDataArray(encodedLength: encoded_length) do |bda_n|
    params_to_xml(bda_n)
    unless self.external
      Mspire::CV::Param[ DTYPE_TO_ACC[dtype] ].to_xml(bda_n)
      Mspire::CV::Param[ compression ? 'MS:1000574' : 'MS:1000576' ].to_xml(bda_n)
      bda_n.binary(base64)
    end
  end
end

#type ⇒ Object 



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# File 'lib/mspire/mzml/data_array.rb', line 35

def type
  if params
    if params.any? {|param| param.accession == 'MS:1000514' }
      :mz
    elsif params.any? {|param| param.accession == 'MS:1000515' }
      :intensity
    end
  end
end

#type=(arg) ⇒ Object 



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# File 'lib/mspire/mzml/data_array.rb', line 23

def type=(arg)
  all_accs = %w(MS:1000514 MS:1000515)
  params.delete_if {|param| all_accs.include?(param.accession) } if params
  case arg
  when :mz
    describe! all_accs[0] # , nil, "MS:1000040"
  when :intensity
    describe! all_accs[1] # , nil, "MS:1000131"
  end
  arg
end