Class: ImzML::Spectrum::BinaryData

Inherits:
Object
  • Object
show all
Defined in:
lib/imzml/metadata/run/spectrum.rb

Constant Summary collapse

BINARY_TYPE_8BIT_INTEGER =

Binary data types, always little endian

"IMS:1100000"
BINARY_TYPE_16BIT_INTEGER = 
"IMS:1100001"
BINARY_TYPE_32BIT_INTEGER = 
"MS:1000519"
BINARY_TYPE_64BIT_INTEGER = 
"MS:1000522"
BINARY_TYPE_32BIT_FLOAT = 
"MS:1000521"
BINARY_TYPE_64BIT_FLOAT = 
"MS:1000523"
MZ_ARRAY =

A data array of m/z values

"MS:1000514"
INTENSITY_ARRAY =

A data array of intensity values

"MS:1000515"
EXTERNAL_ARRAY_LENGTH = 
"IMS:1000103"
EXTERNAL_OFFSET = 
"IMS:1000102"
EXTERNAL_ENCODED_LENGHT = 
"IMS:1000104"

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#encoded_length ⇒ Object

Describes the length of the written data



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# File 'lib/imzml/metadata/run/spectrum.rb', line 30

def encoded_length
  @encoded_length
end

#filepath ⇒ Object

Path to the external binary file



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# File 'lib/imzml/metadata/run/spectrum.rb', line 34

def filepath
  @filepath
end

#length ⇒ Object

Describes how many fields an array contains



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# File 'lib/imzml/metadata/run/spectrum.rb', line 22

def length
  @length
end

#offset ⇒ Object

The position where the data of an array of a mass spectrum begins



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# File 'lib/imzml/metadata/run/spectrum.rb', line 26

def offset
  @offset
end

#type ⇒ Object

Binary values type [:int8, :int16, :int32, :int64, :float32, :float64]



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# File 'lib/imzml/metadata/run/spectrum.rb', line 37

def type
  @type
end

Instance Method Details

#data(cached = false) ⇒ Object

Grabs the actual binary data from disk



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# File 'lib/imzml/metadata/run/spectrum.rb', line 40

def data(cached = false)

  # Return the data from the cache
  return @cached_data if cached && !@cached_data.nil?

  # Remove possible data from the cache
  @cached_data = nil

  # Switch binary pattern reading type
  pattern = case type
  when :int8
    "C"
  when :int16
    "S"
  when :int32
    "L"
  when :int64
    "Q"
  when :float32
    "e"
  when :float64
    "E"
  end

  # Read data based on metadata
  data = IO.binread(@filepath, @encoded_length.to_i, @offset.to_i).unpack("#{pattern}*")

  # Save data only if user want's to cache it, saving take some CPU
  if cached
    @cached_data = data
  else
    data
  end
end