Class: TasciMerger

Inherits:
Object
  • Object
show all
Defined in:
lib/tasci_merger.rb

Instance Method Summary collapse

Constructor Details

#initialize(subject_code, tasci_directory, output_directory) ⇒ TasciMerger

Returns a new instance of TasciMerger.



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# File 'lib/tasci_merger.rb', line 9

def initialize(subject_code, tasci_directory, output_directory)
  @subject_code = subject_code.chomp
  @tasci_directory = tasci_directory.chomp
  @output_directory = output_directory.chomp
  @master_file_path
end

Instance Method Details

#create_master_list ⇒ Object 



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# File 'lib/tasci_merger.rb', line 21

def create_master_list
  puts "New Version"

  master_file_name = File.join(@output_directory, "tasci_master_#{Time.zone.now.strftime("%Y%m%d")}.csv")
  master_file = CSV.open(master_file_name, "wb")

  master_file << %w(file_name file_labtime file_full_time total_epochs start_labtime end_labtime)
  master_file_contents = []

  puts @tasci_directory
  puts File.exists?(@tasci_directory)

  Dir.foreach(@tasci_directory) do |file|
    next if file == '.' or file == '..' or File.extname(file).upcase != ".TASCI"

    puts file

    tasci_file = File.open(File.join(@tasci_directory, file))
    file_info = {}

    ## HEADER INFO
    # Header Line
    tasci_file.readline

    # File Name
    read_line = tasci_file.readline
    matched_name =  /\W*File name \|\W*(.*\.vpd)/i.match(read_line)
    puts "ERROR: #{read_line}" unless matched_name
    file_info[:source_file_name] = matched_name[1]

    # Record Date
    read_line = tasci_file.readline
    matched_date = /RecordDate\W*\|\W*(..)\/(..)\/(....)\W*\|.*/.match(read_line)
    puts "ERROR: #{read_line}" unless matched_date
    #MY_LOG.info "matched_date: #{matched_date[3]} #{matched_date[1]} #{matched_date[2]}"
    file_info[:record_date] = (matched_date ? Time.zone.local(matched_date[3].to_i, matched_date[2].to_i, matched_date[1].to_i) : nil)

    # Record Time
    read_line = tasci_file.readline
    matched_time = /RecordTime\W*\|\W*(..):(..):(..)\W*\|\W*Patient ID\W*\|\W*.*\W*\|/.match(read_line)
    puts "ERROR: #{read_line}" unless matched_time
    file_info[:record_full_time] = ((matched_time and matched_date) ? Time.zone.local(matched_date[3].to_i, matched_date[2].to_i, matched_date[1].to_i, matched_time[1].to_i, matched_time[2].to_i, matched_time[3].to_i) : nil)
    file_info[:record_labtime] = Labtime.parse(file_info[:record_full_time])

    6.times do
      tasci_file.readline
    end

    # Epochs and duration
    read_line = tasci_file.readline
    matched_line = /\W*# Epochs\W*\|\W*(\d+)\W*\|\W*Duration\(S\)\W*\|\W*(\d+)\|/.match(read_line)
    puts "ERROR: #{read_line}" unless matched_line
    file_info[:epochs] = matched_line[1].to_i - 1
    file_info[:epoch_duration] = matched_line[2].to_i

    5.times do
      tasci_file.readline
    end


    first_labtime = nil
    last_labtime = nil

    until tasci_file.eof?
      line = tasci_file.readline

      matched_line = /(\d+)\|\W*(\d+)\|\W*(\d+)\|\W*(\d+)\|\W*(\d\d):(\d\d):(\d\d)\|\W*(.+)\|\W*(.+)\|/.match(line)
      fields = matched_line.to_a
      fields.delete_at(0)

      raise StandardError, "fields should have 9 fields: #{fields.length} #{fields} #{line}" unless fields.length == 9

      # Calculating labtime is tricky - file may span two days
      calculated_line_time = file_info[:record_full_time] + fields[1].to_i.hours + fields[2].to_i.minutes + fields[3].to_i.seconds
      if calculated_line_time.hour == fields[4].to_i and calculated_line_time.min == fields[5].to_i and calculated_line_time.sec == fields[6].to_i
        line_time = calculated_line_time
        line_labtime = Labtime.parse(line_time)
      elsif file_info[:record_full_time].dst? != calculated_line_time.dst?
        if (calculated_line_time.hour - fields[4].to_i).abs == 1 and calculated_line_time.min == fields[5].to_i and calculated_line_time.sec == fields[6].to_i
          line_time = calculated_line_time
          line_labtime = Labtime.parse(line_time)
        else
          raise StandardError, "Times DO NOT MATCH IN TASCI FILE #{File.basename(tasci_file_path)}!!! #{calculated_line_time.to_s} #{fields[4]} #{fields[5]} #{fields[6]}"
        end
      else
        raise StandardError, "Times DO NOT MATCH IN TASCI FILE #{File.basename(tasci_file_path)}!!! #{calculated_line_time.to_s} #{fields[4]} #{fields[5]} #{fields[6]}"
      end

      first_labtime = line_labtime if first_labtime.nil?
      last_labtime = line_labtime

      #MY_LOG.info fields
      #puts fields
    end

    master_file_contents << [file, file_info[:record_labtime].to_short_s, file_info[:record_full_time], file_info[:epochs], first_labtime.to_decimal, last_labtime.to_decimal]
  end

  master_file_contents.sort! {|x, y| x[4] <=> y[4] }
  master_file_contents.each { |row| master_file << row }

  puts "1. Created master file: #{master_file.path}"
  @master_file_path = master_file.path
  master_file_name
  master_file.close 
end

#merge_files ⇒ Object

Raises:

  • (StandardError) 


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# File 'lib/tasci_merger.rb', line 128

def merge_files
  raise StandardError, "No master file path set! You must run create_master_list before running this function." unless @master_file_path

  merged_file = CSV.open(File.join(@output_directory, "#{@subject_code}_merged_#{Time.zone.now.strftime("%Y%m%d")}.csv"), "wb")
  merged_file << %w(SUBJECT_CODE FILE_NAME_SLEEP_WAKE_EPISODE LABTIME SLEEP_STAGE LIGHTS_OFF_ON_FLAG SEM_FLAG)

  simple_merged_file = CSV.open(File.join(@output_directory, "#{@subject_code}_merged_simple_#{Time.zone.now.strftime("%Y%m%d")}.csv"), "wb")
  simple_merged_file << %w(SLEEP_STAGE LABTIME)

  sem_merged_file = CSV.open(File.join(@output_directory, "#{@subject_code}_merged_sem_#{Time.zone.now.strftime("%Y%m%d")}.csv"), "wb")
  simple_merged_file << %w(SUBJECT_CODE LABTIME)

  simple_sem_file = CSV.open(File.join(@output_directory, "#{@subject_code}_merged_simple_sem_#{Time.zone.now.strftime("%Y%m%d")}.csv"), "wb")
  simple_sem_file << %w(SLEEP_STAGE LABTIME SEM_FLAG)

  previous_first_labtime = nil
  previous_last_labtime = nil

  CSV.foreach(@master_file_path, headers: true) do |row|
    puts row
    tasci_file_path = File.join(@tasci_directory, row[0])

    tasci_file = File.open(tasci_file_path)
    file_info = {}

    ## HEADER INFO
    # Header Line
    tasci_file.readline

    # File Name
    read_line = tasci_file.readline
    matched_name =  /\W*File name \|\W*(.*\.vpd)/i.match(read_line)
    puts "ERROR: #{read_line}" unless matched_name
    file_info[:source_file_name] = matched_name[1]

    # Record Date
    read_line = tasci_file.readline
    matched_date = /RecordDate\W*\|\W*(..)\/(..)\/(....)\W*\|.*/.match(read_line)
    puts "ERROR: #{read_line}" unless matched_date
    #MY_LOG.info "matched_date: #{matched_date[3]} #{matched_date[1]} #{matched_date[2]}"
    file_info[:record_date] = (matched_date ? Time.zone.local(matched_date[3].to_i, matched_date[2].to_i, matched_date[1].to_i) : nil)

    # Record Time
    read_line = tasci_file.readline
    matched_time = /RecordTime\W*\|\W*(..):(..):(..)\W*\|\W*Patient ID\W*\|\W*.*_.*_(\w*)\W*\|/.match(read_line)
    puts "ERROR: #{read_line}" unless matched_time
    file_info[:record_full_time] = ((matched_time and matched_date) ? Time.zone.local(matched_date[3].to_i, matched_date[2].to_i, matched_date[1].to_i, matched_time[1].to_i, matched_time[2].to_i, matched_time[3].to_i) : nil)
    file_info[:record_labtime] = Labtime.parse(file_info[:record_full_time])
    file_info[:sleep_wake_episode] = matched_time[4]

    6.times do
      tasci_file.readline
    end

    # Epochs and duration
    read_line = tasci_file.readline
    matched_line = /\W*# Epochs\W*\|\W*(\d+)\W*\|\W*Duration\(S\)\W*\|\W*(\d+)\|/.match(read_line)
    puts "ERROR: #{read_line}" unless matched_line
    file_info[:epochs] = matched_line[1].to_i
    file_info[:epoch_duration] = matched_line[2].to_i

    5.times do
      tasci_file.readline
    end

    first_labtime = nil
    last_labtime = nil

    until tasci_file.eof?
      line = tasci_file.readline

      matched_line = /(\d+)\|\W*(\d+)\|\W*(\d+)\|\W*(\d+)\|\W*(\d\d):(\d\d):(\d\d)\|\W*(.+)\|\W*(.+)\|/.match(line)
      fields = matched_line.to_a
      fields.delete_at(0)

      raise StandardError, "fields should have 9 fields: #{fields.length} #{fields} #{line}" unless fields.length == 9

      # Calculating labtime is tricky - file may span two days
      calculated_line_time = file_info[:record_full_time] + fields[1].to_i.hours + fields[2].to_i.minutes + fields[3].to_i.seconds
      if calculated_line_time.hour == fields[4].to_i and calculated_line_time.min == fields[5].to_i and calculated_line_time.sec == fields[6].to_i
        line_time = calculated_line_time
        line_labtime = Labtime.parse(line_time)
      elsif file_info[:record_full_time].dst? != calculated_line_time.dst?
        if (calculated_line_time.hour - fields[4].to_i).abs == 1 and calculated_line_time.min == fields[5].to_i and calculated_line_time.sec == fields[6].to_i
          line_time = calculated_line_time
          line_labtime = Labtime.parse(line_time)
        else
          raise StandardError, "Times DO NOT MATCH IN TASCI FILE #{File.basename(tasci_file_path)}!!! #{calculated_line_time.to_s} #{fields[4]} #{fields[5]} #{fields[6]}"
        end
      else
        raise StandardError, "Times DO NOT MATCH IN TASCI FILE #{File.basename(tasci_file_path)}!!! #{calculated_line_time.to_s} #{fields[4]} #{fields[5]} #{fields[6]}"
      end

      # Sleep Period Coding:
      # 1      Sleep Onset (Lights Off)
      # 2      Sleep Offset (Lights On)
      if /Lights Off|LOff|LightsOn/i.match(fields[7]) # Sleep Onset
        sleep_period = 1
      elsif /Lights On|LOn|LightsOn/i.match(fields[7]) # Sleep Offset
        sleep_period = 2
      else
        sleep_period = nil
      end

      # Sleep Stage Coding:
      # 1      stage 1
      # 2      stage 2
      # 3      stage 3
      # 4      stage 4
      # 6      MT
      # 7      Undef
      # 5      REM
      # 9      Wake
      line_event = nil
      if fields[8] == "Wake" || fields[8] == 'Awake'
        line_event = 9
      elsif fields[8] == "Undefined"
        line_event = 7
      elsif fields[8] == "N1" ||  fields[8] == '1'
        line_event = 1
      elsif fields[8] == "N2" ||  fields[8] == '2'
        line_event = 2
      elsif fields[8] == "N3" ||  fields[8] == '3'
        line_event = 3
      elsif fields[8] == "N4" || fields[8] == '4'
        line_event = 4
      elsif fields[8] == "REM"
        line_event = 5
      elsif fields[8] == "MVT"
        line_event = 6
      else
        raise StandardError, "Cannot map the following event: #{fields[8]}"
      end

      # SEM Event Coding:
      # 1      Slow Eye Movement
      # 0      No Slow Eye Movement
      sem_event = (fields[7] =~ /SEM/ ? 1 : 0)




      # Alternate Coding:
      # 0 - UNDEF
      # 1 - N1
      # 2 - N2
      # 3 - N3
      # 4 - 4
      # 5 - Wake
      # 6 - REM
      # 7 - MT
      # 8 - Sleep Onset (LIGHTS OFF)
      # 9 - Lights On

      ### SLEEP STAGE, LABTIME
      simple_line_event = nil
      if fields[8] == "Wake" || fields[8] == 'Awake'
        simple_line_event = 5
      elsif fields[8] == "Undefined"
        simple_line_event = 0
      elsif fields[8] == "N1" || fields[8] == '1'
        simple_line_event = 1
      elsif fields[8] == "N2" || fields[8] == '2'
        simple_line_event = 2
      elsif fields[8] == "N3" || fields[8] == '3'
        simple_line_event = 3
      elsif fields[8] == "N4" || fields[8] == '4'
        simple_line_event = 4
      elsif fields[8] == "REM"
        simple_line_event = 6
      elsif fields[8] == "MVT"
        simple_line_event = 7
      else
        raise StandardError, "Cannot map the following event: #{fields[8]}"
      end

      if sleep_period == 1
        simple_line_event = 8
      elsif sleep_period == 2
        simple_line_event = 9
      end
      
      first_labtime = line_labtime if first_labtime.nil?
      last_labtime = line_labtime

      output_line = [@subject_code.upcase, file_info[:sleep_wake_episode], line_labtime.to_decimal, line_event, sleep_period, sem_event]
      simple_output_line = [simple_line_event, line_labtime.to_decimal]
      sem_output_line = [@subject_code.upcase, line_labtime.to_decimal] if sem_event == 1
      # 4th flie added        
      simple_sem = [simple_line_event, line_labtime.to_decimal, sem_event ]        

      merged_file << output_line
      simple_merged_file << simple_output_line
      sem_merged_file << sem_output_line if sem_event == 1
      simple_sem_file << simple_sem
      #MY_LOG.info fields
    end


    unless previous_first_labtime.nil? or previous_last_labtime.nil?
      puts "Start time is before previous end labtime: #{previous_last_labtime.to_short_s} #{first_labtime.to_short_s}" if first_labtime < previous_last_labtime
    end


    previous_first_labtime = first_labtime
    previous_last_labtime = last_labtime
  end
  merged_file.close
  simple_merged_file.close
  sem_merged_file.close
  simple_sem_file.close
end

#version ⇒ Object 



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# File 'lib/tasci_merger.rb', line 16

def version
  '0.0.1'
end