Class: ImzML::Spectrum

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

Defined Under Namespace

Classes: BinaryData

Constant Summary collapse

POSITION_X = 
"IMS:1000050"
POSITION_Y = 
"IMS:1000051"

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#intensity_binary ⇒ Object

Info about intensity binary data

Represented by class BinaryData



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# File 'lib/imzml/metadata/run/spectrum.rb', line 92

def intensity_binary
  @intensity_binary
end

#mz_binary ⇒ Object

Info about mz binary data

Represented by class BinaryData



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# File 'lib/imzml/metadata/run/spectrum.rb', line 87

def mz_binary
  @mz_binary
end

#position ⇒ Object

Attributes to describe the position of a spectrum in the image.

represented as Point with position x, y



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# File 'lib/imzml/metadata/run/spectrum.rb', line 80

def position
  @position
end

Instance Method Details

#intensity(at, interval) ⇒ Object 



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# File 'lib/imzml/metadata/run/spectrum.rb', line 94

def intensity(at, interval)
  
  # read whole the binary data
  mz_array = mz_binary.data
  intensity_array = intensity_binary.data
  
  default_from, default_to = mz_array.first, mz_array.first
  
  # find designated intensity
  if !at
    from = default_from
    to = default_to
  else
    from = at - interval
    from = default_from if from < 0
    to = at + interval
    to = default_to if to > mz_array.last
  end
  
  # find values in mz array
  low_value = mz_array.binary_search(from, false)
  low_index = mz_array.index(low_value)
  high_value = mz_array.binary_search(to)
  high_index = mz_array.index(high_value)
  
  # sum all values in subarray
  intensity_array[low_index..high_index].inject{|sum, x| sum + x}
  
end