tasci_merger 0.1.0 → 0.2.0

data/lib/tasci_merger.rb

@@ -1,324 +1,333 @@
-require 'csv'
-require 'man_merger'
-require 'labtime'
-
-Time.zone = 'Eastern Time (US & Canada)'
-
-class TasciMerger
-
-  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
-
-  def create_master_list
-    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 == '..'
-
-      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
-      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 "Created master file: #{master_file.path}"
-    @master_file_path = master_file.path
-    master_file_name
-  end
-
-  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)
-
-    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/i.match(fields[7]) # Sleep Onset
-          sleep_period = 1
-        elsif /Lights On/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"
-          line_event = 9
-        elsif fields[8] == "Undefined"
-          line_event = 7
-        elsif fields[8] == "N1"
-          line_event = 1
-        elsif fields[8] == "N2"
-          line_event = 2
-        elsif fields[8] == "N3"
-          line_event = 3
-        elsif 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"
-          simple_line_event = 5
-        elsif fields[8] == "Undefined"
-          simple_line_event = 0
-        elsif fields[8] == "N1"
-          simple_line_event = 1
-        elsif fields[8] == "N2"
-          simple_line_event = 2
-        elsif fields[8] == "N3"
-          simple_line_event = 3
-        elsif 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]
-        merged_file << output_line
-        simple_merged_file << simple_output_line
-
-        #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
-  end
-
-end
-
+require 'csv'
+require_relative 'man_merger'
+require_relative 'labtime'
+
+Time.zone = 'Eastern Time (US & Canada)'
+
+class TasciMerger
+
+  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
+
+  def version
+    '0.0.1'
+  end
+
+
+  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
+
+  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)
+
+    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"
+          line_event = 9
+        elsif fields[8] == "Undefined"
+          line_event = 7
+        elsif fields[8] == "N1"
+          line_event = 1
+        elsif fields[8] == "N2"
+          line_event = 2
+        elsif fields[8] == "N3"
+          line_event = 3
+        elsif 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"
+          simple_line_event = 5
+        elsif fields[8] == "Undefined"
+          simple_line_event = 0
+        elsif fields[8] == "N1"
+          simple_line_event = 1
+        elsif fields[8] == "N2"
+          simple_line_event = 2
+        elsif fields[8] == "N3"
+          simple_line_event = 3
+        elsif 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]
+        merged_file << output_line
+        simple_merged_file << simple_output_line
+
+        #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
+  end
+
+end
+