Parse XML Annotation Files and retrieve time asleep and number of obstructive apnea events.

annotation_testing.rb

# frozen_string_literal: true

# gem install xml-simple colorize --no-document

# ruby annotation_testing.rb

require 'rubygems'
require 'colorize'
require 'json'
require 'xmlsimple'

# Take the XML files in this folder `/annotation-testing` and answer two
# questions:
#   1) How many epochs/minutes was the subject asleep?
#   2) How many obstructive apnea events were marked on the recording?
# Asleep is defined as SleepStage = 1,2,3,4,5

def extract(hash, key, convert: nil)
  value = hash[key] ? hash[key][0] : nil
  convert && value ? value.send(convert) : value
end

Dir.glob('**/*.xml', File::FNM_CASEFOLD).each do |xml_path|
  xml = XmlSimple.xml_in(xml_path)

  epoch_length = xml['EpochLength'][0].to_i
  sleep_stages = xml['SleepStages'][0]['SleepStage']
  # awake_stages = sleep_stages.select { |stage| %w(0).include?(stage) }
  asleep_stages = sleep_stages.select { |stage| %w(1 2 3 4 5).include?(stage) }
  scored_events = xml['ScoredEvents'][0]['ScoredEvent'].collect do |hash|
    {
      name: extract(hash, 'Name'),
      lowest_spo2: extract(hash, 'LowestSpO2', convert: :to_f),
      desaturation: extract(hash, 'Desaturation', convert: :to_f),
      start: extract(hash, 'Start', convert: :to_f),
      duration: extract(hash, 'Duration', convert: :to_f),
      input: extract(hash, 'Input')
    }
  end
  obstructive_apnea_events = scored_events.select do |event|
    event[:name] == 'Obstructive Apnea'
  end

  message = \
    "\n#{xml_path}\n"\
    "The subject was asleep for #{asleep_stages.count} of total "\
    "#{sleep_stages.count} sleep stages.\nThis comes to "\
    "#{(asleep_stages.count * epoch_length / 60.0).to_s.colorize(:green)} "\
    "minutes of #{sleep_stages.count * epoch_length / 60.0} minutes total.\n"\
    "#{obstructive_apnea_events.count.to_s.colorize(:green)} obstructive apnea"\
    " were scored.\n\n"

  puts message
end