Class: RImageAnalysisTools::CentromereFindingMethod

Inherits:
Method
  • Object
show all
Defined in:
lib/rimageanalysistools/method/centromere_finding_method.rb

Instance Attribute Summary

Attributes inherited from Method

#input_images, #metadata, #output_images, #parameters, #quantification

Instance Method Summary collapse

Instance Method Details

#centromere_finding(im) ⇒ Object 



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# File 'lib/rimageanalysistools/method/centromere_finding_method.rb', line 44

def centromere_finding(im)

  im = ImageFactory.createWritable(im)

  filters = []

  filters << LocalMaximumSeparabilityThresholdingFilter.new
  filters << LabelFilter.new
  filters << RecursiveMaximumSeparabilityFilter.new
  filters << RelabelFilter.new
  filters << SizeAbsoluteFilter.new
  filters << RelabelFilter.new

  filters.each do |f|

    f.setParameters(parameters)
    f.setReferenceImage(input_images.getMarkerImage)
    f.apply(im)

  end
  
  im

end

#go ⇒ Object 



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# File 'lib/rimageanalysistools/method/centromere_finding_method.rb', line 78

def go
  
  mask = ImageFactory.createWritable(input_images.getMarkerImage)

  normalize_input_image(mask)

  bf = BandpassFilter.new
  
  bf.setParameters(parameters)

  band_lower = 3.0
  band_upper = 4.0

  bf.setBand(band_lower, band_upper)

  bf.apply(mask)

  mask = centromere_finding(mask)

  m = IntensityPerPixelMetric.new

  q = m.quantify(mask, input_images)
  
  self.quantification= q

  mask

end

#normalize_input_image(im) ⇒ Object 



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# File 'lib/rimageanalysistools/method/centromere_finding_method.rb', line 69

def normalize_input_image(im)

  rnf = RenormalizationFilter.new
  rnf.setParameters(parameters)
  rnf.apply(im)

end