edfize 0.1.0.beta1

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data/CHANGELOG.md

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+## 0.1.0
+- Initial EDF class to load headers and signals into Ruby objects
+- `edfize` command has the following actions:
+  - `check`: Validates EDFs in the current directory for errors
+  - `test`: Same as `check`
+  - `run`: Prints out the headers of all edfs in the current directory
+  - `help`: Displays information about `edfize` along with all available commands
+  - `version`: Displays the current `edfize` version
+- `edfize test` checks for the following:
+  - Expected Length Check: The expected total size is computed from the (`number
+    of data records` * `total samples across all signals`) + `size of header` and
+    this is compared to the actual file size.

data/LICENSE.txt

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+https://github.com/sleepepi
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data/README.md

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+# Edfize
+
+[![Build Status](https://travis-ci.org/sleepepi/edfize.svg?branch=master)](https://travis-ci.org/sleepepi/edfize)
+[![Dependency Status](https://gemnasium.com/sleepepi/edfize.svg)](https://gemnasium.com/sleepepi/edfize)
+[![Code Climate](https://codeclimate.com/github/sleepepi/edfize.png)](https://codeclimate.com/github/sleepepi/edfize)
+
+Ruby gem used to load, validate, and parse European Data Format files. Used for batch testing EDFs for errors. Ruby 2.0+ compatible.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'edfize'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install edfize
+
+## Usage
+
+### Validate EDFs
+
+Use `edfize check` to check that EDFs stored in the current directory have a valid format.
+
+    cd <edf-directory>
+    edfize check
+
+### Print Signal Header information
+
+Use `edfize run` to print out signal header information for each EDF in the current directory.
+
+    cd <edf-directory>
+    edfize run
+
+### View A List of All Available Commands for Edfize
+
+Use `edfize help` to list available commands and descriptions for Edfize.
+
+    edfize help
+
+### View Current Version of Edfize
+
+Use `edfize version` to check the version of Edfize.
+
+    edfize version
+
+### Upgrade Edfize
+
+Use `gem install edfize` to update Edfize to the latest stable
+
+Use `gem install edfize --pre` to update Edfize to the latest prerelease
+
+## Contributing
+
+1. Fork it ( https://github.com/sleepepi/edfize/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/Rakefile

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+require 'bundler/gem_tasks'
+
+require 'rake/testtask'
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << 'lib'
+  t.libs << 'test'
+  t.pattern = 'test/**/*_test.rb'
+  t.verbose = false
+end
+
+task default: :test

data/bin/edfize

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+#!/usr/bin/env ruby
+
+require File.expand_path('../../lib/edfize', __FILE__)
+
+Edfize.launch(ARGV)

data/edfize.gemspec

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+# Compiling the Gem
+# gem build edfize.gemspec
+# gem install ./edfize-x.x.x.gem --no-ri --no-rdoc --local
+#
+# gem push edfize-x.x.x.gem
+# gem list -r edfize
+# gem install edfize
+
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'edfize/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "edfize"
+  spec.version       = Edfize::VERSION::STRING
+  spec.authors       = ["Remo Mueller"]
+  spec.email         = ["remosm@gmail.com"]
+  spec.summary       = %q{Load, validate, and parse European Data Format files. Used for batch testing EDFs for errors.}
+  spec.description   = %q{Load, validate, and parse European Data Format files. Used for batch testing EDFs for errors. Run `edfize` on command line to view full list of options.}
+  spec.homepage      = "https://github.com/sleepepi/edfize"
+  spec.license       = "CC BY-NC-SA 3.0"
+
+  spec.files         = Dir['{bin,lib}/**/*'] + ['CHANGELOG.md', 'LICENSE.txt', 'Rakefile', 'README.md', 'edfize.gemspec']
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency "colorize", "~> 0.7.2"
+
+  spec.add_development_dependency "bundler", "~> 1.6"
+  spec.add_development_dependency "rake"
+end

data/lib/edfize/edf.rb

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+require 'edfize/signal'
+
+module Edfize
+  class Edf
+    attr_reader :signals, :filename
+
+    HEADER_OFFSET = 256
+
+    def initialize(filename)
+      @filename = filename
+      @signals = []
+      signal_labels
+      transducer_types
+      physical_dimensions
+      physical_minimums
+      physical_maximums
+      digital_minimums
+      digital_maximums
+      prefilterings
+      samples_in_data_records
+      reserved_areas
+    end
+
+    def size
+      File.size(@filename)
+    end
+
+    def size_of_header
+      HEADER_OFFSET + ns * (16 + 80 + 8 + 8 + 8 + 8 + 8 + 80 + 8 + 32)
+    end
+
+    def expected_size_of_header
+      256 + (ns * 256)
+    end
+
+    def total_size
+      IO.binread(@filename).size
+    end
+
+    def expected_data_size
+      result = 0
+      @signals.each do |signal|
+        result += signal.samples_in_data_record.to_i * 2 # NR * Int(16)
+      end
+      result * number_of_data_records.to_i
+    end
+
+    def expected_total_size
+      expected_data_size + size_of_header
+      # (duration_of_a_data_record.to_i * number_of_data_records.to_i * number_of_signals.to_i) * 8
+    end
+
+    def print_header
+      puts @filename
+      puts "#{size} bytes (Total File Size)"
+      puts "'#{header_version}' (0)"
+      puts "'#{header_local_patient_identification}' (local patient identification)"
+      puts "'#{header_local_recording_identification}' (local recording indentification)"
+      puts "'#{header_start_date_of_recording}' (dd.mm.yy start date of recording)"
+      puts "'#{header_start_time_of_recording}' (hh.mm.ss start time of recording)"
+      # puts "--- RESERVED"
+      puts "'#{number_of_data_records}' (number of data records, -1 if unknown)"
+      puts "'#{duration_of_a_data_record}' seconds (duration of a data record)"
+      puts "'#{number_of_signals}' number of signals (ns) in data record"
+      signals.each_with_index do |signal, index|
+        puts "'#{signal.label}' (signal[#{index+1}] label)"
+        puts "'#{signal.physical_dimension}' (signal[#{index+1}] physical_dimension)"
+        puts "'#{signal.transducer_type}' (signal[#{index+1}] transducer_type)"
+        puts "'#{signal.physical_minimum}' (signal[#{index+1}] physical_minimum)"
+        puts "'#{signal.physical_maximum}' (signal[#{index+1}] physical_maximum)"
+        puts "'#{signal.digital_minimum}' (signal[#{index+1}] digital_minimum)"
+        puts "'#{signal.digital_maximum}' (signal[#{index+1}] digital_maximum)"
+        puts "'#{signal.prefiltering}' (signal[#{index+1}] prefiltering)"
+        puts "'#{signal.samples_in_data_record}' (signal[#{index+1}] samples_in_data_record)"
+        puts "'#{signal.reserved_area}' (signal[#{index+1}] reserved_area)"
+      end
+      puts "#{size} bytes (Total File Size)"
+      puts "Size of Header (bytes)          : #{size_of_header}"
+      puts "Size of Data   (bytes)          : #{data_size}"
+      puts "Total Size     (bytes)          : #{total_size}"
+
+      puts "Expected Size of Header (bytes) : #{expected_size_of_header}"
+      puts "Expected Size of Data   (bytes) : #{expected_data_size}"
+      puts "Expected Total Size     (bytes) : #{expected_total_size}"
+    end
+
+    def header_version
+      IO.binread(@filename, 8)
+    end
+
+    # 80 ascii : local patient identification (mind item 3 of the additional EDF+ specs)
+    def header_local_patient_identification
+      IO.binread(@filename, 80, 8)
+    end
+
+    # 80 ascii : local recording identification (mind item 4 of the additional EDF+ specs)
+    def header_local_recording_identification
+      IO.binread(@filename, 80, 88)
+    end
+
+    # 8 ascii : startdate of recording (dd.mm.yy) (mind item 2 of the additional EDF+ specs)
+    def header_start_date_of_recording
+      IO.binread(@filename, 8, 168)
+    end
+
+    # 8 ascii : starttime of recording (hh.mm.ss)
+    def header_start_time_of_recording
+      IO.binread(@filename, 8, 176)
+    end
+
+    # 8 ascii : number of bytes in header record
+    def number_of_bytes_in_header
+      IO.binread(@filename, 8, 184)
+    end
+
+    # 44 ascii : reserved
+    # def reserved
+    #   IO.binread(@filename, 44, 192)
+    # end
+
+    # 8 ascii : number of data records (-1 if unknown, obey item 10 of the additional EDF+ specs)
+    def number_of_data_records
+      IO.binread(@filename, 8, 236)
+    end
+
+    # 8 ascii : duration of a data record, in seconds
+    def duration_of_a_data_record
+      IO.binread(@filename, 8, 244)
+    end
+
+    # 4 ascii : number of signals (ns) in data record
+    def number_of_signals
+      IO.binread(@filename, 4, 252)
+    end
+
+    def ns
+      Integer(self.number_of_signals) rescue 0
+    end
+
+    # ns * 16 ascii : ns * label (e.g. EEG Fpz-Cz or Body temp) (mind item 9 of the additional EDF+ specs)
+    def signal_labels
+      offset = HEADER_OFFSET
+      (0..ns-1).to_a.each do |signal_number|
+        @signals[signal_number] ||= Signal.new()
+        @signals[signal_number].label = IO.binread(@filename, 16, offset+(signal_number*16))
+      end
+    end
+
+    # ns * 80 ascii : ns * transducer type (e.g. AgAgCl electrode)
+    def transducer_types
+      offset = HEADER_OFFSET + ns * 16
+      (0..ns-1).to_a.each do |signal_number|
+        @signals[signal_number] ||= Signal.new()
+        @signals[signal_number].transducer_type = IO.binread(@filename, 80, offset+(signal_number*80))
+      end
+    end
+
+    # ns * 8 ascii : ns * physical dimension (e.g. uV or degreeC)
+    def physical_dimensions
+      offset = HEADER_OFFSET + ns * (16 + 80)
+      (0..ns-1).to_a.each do |signal_number|
+        @signals[signal_number] ||= Signal.new()
+        @signals[signal_number].physical_dimension = IO.binread(@filename, 8, offset+(signal_number*8))
+      end
+    end
+
+    # ns * 8 ascii : ns * physical minimum (e.g. -500 or 34)
+    def physical_minimums
+      offset = HEADER_OFFSET + ns * (16 + 80 + 8)
+      (0..ns-1).to_a.each do |signal_number|
+        @signals[signal_number] ||= Signal.new()
+        @signals[signal_number].physical_minimum = IO.binread(@filename, 8, offset+(signal_number*8))
+      end
+    end
+
+    # ns * 8 ascii : ns * physical maximum (e.g. 500 or 40)
+    def physical_maximums
+      offset = HEADER_OFFSET + ns * (16 + 80 + 8 + 8)
+      (0..ns-1).to_a.each do |signal_number|
+        @signals[signal_number] ||= Signal.new()
+        @signals[signal_number].physical_maximum = IO.binread(@filename, 8, offset+(signal_number*8))
+      end
+    end
+
+    # ns * 8 ascii : ns * digital minimum (e.g. -2048)
+    def digital_minimums
+      offset = HEADER_OFFSET + ns * (16 + 80 + 8 + 8 + 8)
+      (0..ns-1).to_a.each do |signal_number|
+        @signals[signal_number] ||= Signal.new()
+        @signals[signal_number].digital_minimum = IO.binread(@filename, 8, offset+(signal_number*8))
+      end
+    end
+
+    # ns * 8 ascii : ns * digital maximum (e.g. 2047)
+    def digital_maximums
+      offset = HEADER_OFFSET + ns * (16 + 80 + 8 + 8 + 8 + 8)
+      (0..ns-1).to_a.each do |signal_number|
+        @signals[signal_number] ||= Signal.new()
+        @signals[signal_number].digital_maximum = IO.binread(@filename, 8, offset+(signal_number*8))
+      end
+    end
+
+    # ns * 80 ascii : ns * prefiltering (e.g. HP:0.1Hz LP:75Hz)
+    def prefilterings
+      offset = HEADER_OFFSET + ns * (16 + 80 + 8 + 8 + 8 + 8 + 8)
+      (0..ns-1).to_a.each do |signal_number|
+        @signals[signal_number] ||= Signal.new()
+        @signals[signal_number].prefiltering = IO.binread(@filename, 80, offset+(signal_number*80))
+      end
+    end
+
+    # ns * 8 ascii : ns * nr of samples in each data record
+    def samples_in_data_records
+      offset = HEADER_OFFSET + ns * (16 + 80 + 8 + 8 + 8 + 8 + 8 + 80)
+      (0..ns-1).to_a.each do |signal_number|
+        @signals[signal_number] ||= Signal.new()
+        @signals[signal_number].samples_in_data_record = IO.binread(@filename, 8, offset+(signal_number*8))
+      end
+    end
+
+    # ns * 32 ascii : ns * reserved
+    def reserved_areas
+      offset = HEADER_OFFSET + ns * (16 + 80 + 8 + 8 + 8 + 8 + 8 + 80 + 8)
+      (0..ns-1).to_a.each do |signal_number|
+        @signals[signal_number] ||= Signal.new()
+        @signals[signal_number].reserved_area = IO.binread(@filename, 32, offset+(signal_number*32))
+      end
+    end
+
+    def get_samples
+      offset = size_of_header
+      current_read_offset = 0
+      (0..ns-1).to_a.each do |signal_number|
+        @signals[signal_number] ||= Signal.new()
+        read_size = @signals[signal_number].samples_in_data_record.to_i * 2 * number_of_data_records.to_i
+        @signals[signal_number].samples = IO.binread(@filename, read_size, size_of_header + current_read_offset).unpack('s*')
+        current_read_offset += read_size
+      end
+    end
+
+    # 2-byte integer
+    # [16Bit]signed short: -32767 to 32767
+    # .unpack('s*')
+    def data_signals
+      data_section = IO.binread(@filename, nil, size_of_header)
+      dataset_section.unpack('s*')
+    end
+
+    def data_size
+      data_section = IO.binread(@filename, nil, size_of_header)
+      data_section.size
+    end
+  end
+end

data/lib/edfize/signal.rb

@@ -0,0 +1,21 @@
+module Edfize
+  class Signal
+    attr_accessor :label, :transducer_type, :physical_dimension, :physical_minimum, :physical_maximum,
+                  :digital_minimum, :digital_maximum, :prefiltering, :samples_in_data_record, :reserved_area, :samples
+
+    def initialize
+      @label = ''
+      @physical_dimension = ''
+      @transducer_type = ''
+      @physical_minimum = ''
+      @physical_maximum = ''
+      @digital_minimum = ''
+      @digital_maximum = ''
+      @prefiltering = ''
+      @samples_in_data_record = ''
+      @reserved_area = ''
+      @samples = []
+    end
+
+  end
+end

data/lib/edfize/tests/check_length.rb

@@ -0,0 +1,15 @@
+module Edfize
+  module Tests
+    # This test checks that the length calculated from the EDF header matches
+    # the total length of the file
+    def self.test_expected_length(edf)
+      passes = (edf.expected_total_size == edf.total_size)
+      puts "  #{passes ? 'PASS' : 'FAIL'}".colorize( passes ? :green : :red ) + " Expected File Size"
+      unless passes or not verbose
+        puts "    Expected : #{edf.expected_total_size} bytes"
+        puts "    Actual   : #{edf.total_size} bytes"
+      end
+      passes
+    end
+  end
+end

data/lib/edfize/tests.rb

@@ -0,0 +1,21 @@
+require 'edfize/tests/check_length'
+
+module Edfize
+  module Tests
+    def self.verbose
+      true
+    end
+
+    def self.run(edf)
+      puts "\n#{edf.filename}"
+
+      failure_count = 0
+      test_count = 0
+
+      test_expected_length(edf) ? nil : failure_count += 1
+      test_count += 1
+
+      [test_count, failure_count]
+    end
+  end
+end

data/lib/edfize/version.rb

@@ -0,0 +1,10 @@
+module Edfize
+  module VERSION #:nodoc:
+    MAJOR = 0
+    MINOR = 1
+    TINY = 0
+    BUILD = "beta1"
+
+    STRING = [MAJOR, MINOR, TINY, BUILD].compact.join('.')
+  end
+end

data/lib/edfize.rb

@@ -0,0 +1,70 @@
+require 'edfize/edf'
+require 'edfize/tests'
+require 'edfize/version'
+
+require 'colorize'
+
+module Edfize
+  def self.launch(argv)
+    case argv.first.to_s.scan(/\w/).first
+    when 'v'
+      version
+    when 'c', 't'
+      check
+    when 'r'
+      print_headers
+    else
+      help
+    end
+  end
+
+  def self.print_headers
+    puts "----------------"
+    edfs_in_current_directory.each do |edf_file_name|
+      edf = Edfize::Edf.new(edf_file_name)
+      edf.print_header
+      puts "----------------"
+    end
+  end
+
+  def self.version
+    puts "Edfize #{Edfize::VERSION::STRING}"
+  end
+
+  def self.check
+    test_start_time = Time.now
+    edf_count = edfs_in_current_directory.count
+    test_count = 0
+    failure_count = 0
+    puts "Started\n"
+    edfs_in_current_directory.each do |edf_file_name|
+      edf = Edfize::Edf.new(edf_file_name)
+      tests_run, failures = Edfize::Tests.run(edf)
+      test_count += tests_run
+      failure_count += failures
+    end
+    puts "\nFinished in #{Time.now - test_start_time}s"
+    puts "#{edf_count} EDF#{'s' unless edf_count == 1}, #{test_count} test#{'s' unless test_count == 1}, " + "#{failure_count} failure#{'s' unless failure_count == 1}".colorize( failure_count == 0 ? :green : :red )
+  end
+
+  def self.help
+    help_message = <<-EOT
+Usage: edfize COMMAND [ARGS]
+
+The most common edfize commands are:
+  [c]heck           Check EDFs in current directory for errors
+  [t]est            Same as [c]heck
+  [h]elp            Show edfize command-line documentation
+  [v]ersion         Returns the version of Edfize
+
+Commands can be referenced by the first letter:
+  Ex: `edfize t`, for test
+
+EOT
+    puts help_message
+  end
+
+  def self.edfs_in_current_directory
+    Dir.glob('*.edf')
+  end
+end

metadata

@@ -0,0 +1,101 @@
+--- !ruby/object:Gem::Specification
+name: edfize
+version: !ruby/object:Gem::Version
+  version: 0.1.0.beta1
+platform: ruby
+authors:
+- Remo Mueller
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-04-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: colorize
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.7.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.7.2
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Load, validate, and parse European Data Format files. Used for batch
+  testing EDFs for errors. Run `edfize` on command line to view full list of options.
+email:
+- remosm@gmail.com
+executables:
+- edfize
+extensions: []
+extra_rdoc_files: []
+files:
+- CHANGELOG.md
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/edfize
+- edfize.gemspec
+- lib/edfize.rb
+- lib/edfize/edf.rb
+- lib/edfize/signal.rb
+- lib/edfize/tests.rb
+- lib/edfize/tests/check_length.rb
+- lib/edfize/version.rb
+homepage: https://github.com/sleepepi/edfize
+licenses:
+- CC BY-NC-SA 3.0
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">"
+    - !ruby/object:Gem::Version
+      version: 1.3.1
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Load, validate, and parse European Data Format files. Used for batch testing
+  EDFs for errors.
+test_files: []