rpipe 0.0.3 → 0.1.0

data/VERSION

@@ -1 +1 @@
-0.0.3
+0.1.0

data/bin/rpipe

@@ -5,6 +5,7 @@ begin
   require 'trollop'
   require 'output_catcher'
   require 'pp'
+  require 'etc'
   require 'log4r'
 rescue LoadError
   require 'rubygems'
@@ -24,8 +25,8 @@ EOS
 # Main Function for the CLI runner.
 def run!
   options, driver = setup_options
-  run_with_logging File.basename(driver, File.extname(driver)) do  
-    $Log.info "Begin Pipelining #{driver}"
+  run_with_logging File.basename(driver, File.extname(driver)), options do  
+    $Log.info "Begin Pipelining #{driver} | #{Etc.getlogin} on #{`hostname`}"
     run_pipe(options, driver)
     $Log.info "Finished Pipelining #{driver}"
   end
@@ -61,6 +62,7 @@ def setup_options
   	banner BANNER
   	opt :only, "Perform only a certain step (recon, preproc, stats)", :type => String
   	opt :debug, "Be more wordy than usual for debugging"
+  	opt :log_directory, "Output Directory for processing logs.", :type => String
   end
 
   if opts[:only_given]
@@ -71,7 +73,7 @@ def setup_options
 
   Trollop::die "Driver file not given" if (ARGV.size < 1)
   driver = ARGV.shift
-  Trollop::die :driver, "file does not exist" unless File.exist?(driver)
+  Trollop::die "Driver file #{driver} does not exist.  Check the path to that file and try again" unless File.exist?(driver)
 
   pp opts if opts[:debug]
   
@@ -79,18 +81,28 @@ def setup_options
 end
 
 # Setup Tee IO's for Out and Error and start logs for them.
-def run_with_logging(logfile_stem, &block)
-  out_logfile     = logfile_stem + '.out'
-  error_logfile   = logfile_stem + '.err'
-  command_logfile = logfile_stem + '.log'
+def run_with_logging(logfile_stem, options, &block)
+  if options[:log_directory]
+    log_dir = options[:log_directory]
+  else 
+    # If no explicit directory has been passed as an argument, check to see if
+    # a directory named "logs" exists.  If so, use that, otherwise use the current directory.
+    log_dir = File.directory?('logs') ? 'logs' : '.'
+  end
+  out_logfile     = File.join(log_dir, logfile_stem + '.out')
+  error_logfile   = File.join(log_dir, logfile_stem + '.err')
+  command_logfile = File.join(log_dir, logfile_stem + '.sh')
   
-  teeout = Tee.new(out_logfile, :out)
-  teeerr = Tee.new(error_logfile, :err)
+  teeout = Tee.new(out_logfile, :out, 'a')
+  teeerr = Tee.new(error_logfile, :err, 'a')
   
-  setup_logger(command_logfile, teeout)
+  setup_logger(command_logfile, teeout, teeerr, options)
   
   begin
     yield
+  rescue Exception => e
+    $ErrorLog.error e
+    raise e
   ensure
     # Discard the error log if there were no errors.
     # Size returns nil for an empty file.
@@ -100,15 +112,19 @@ def run_with_logging(logfile_stem, &block)
 end
 
 # Log Commands to a file and Output to stdout
-def setup_logger(command_logfile, tee)
+def setup_logger(command_logfile, teeout, teeerr, options)
   console_pattern = "#{'*' * 10} %m [ %d ]"
   $Log = Log4r::Logger.new('output')
-  $Log.add Log4r::IOOutputter.new(:stdout, tee, :formatter => FlashFormatter.new)
+  $Log.level = Log4r::DEBUG
+  $Log.add Log4r::IOOutputter.new(:stdout, teeout, :formatter => FlashFormatter.new)
 
   File.delete command_logfile if File.exist? command_logfile
   $CommandLog = Log4r::Logger.new('command::output')
-  $CommandLog.add Log4r::FileOutputter.new(:file, :filename => command_logfile, :formatter => Log4r::PatternFormatter.new(:pattern => "%m"))
-  $CommandLog.add Log4r::IOOutputter.new(:stdout, tee, :formatter => FlashFormatter.new)
+  $CommandLog.add Log4r::FileOutputter.new(:file, :filename => command_logfile, :trunc => false, :formatter => Log4r::PatternFormatter.new(:pattern => "%m"))
+  $CommandLog.add Log4r::IOOutputter.new(:stdout, teeout, :formatter => FlashFormatter.new)
+  
+  $ErrorLog = Log4r::Logger.new('error::output')
+  $ErrorLog.add Log4r::IOOutputter.new(:stderr, teeerr, :formatter => Log4r::PatternFormatter.new(:pattern => "%m"))
 end
 
 

data/lib/custom_methods/JohnsonMerit220Visit1Preproc.rb

@@ -25,12 +25,15 @@ module JohnsonMerit220Visit1Preproc
 	
 	def run_preproc_mfile
 	  raise ScriptError, "Can't find any slice-time corrected images in #{@origdir}" if image_files.empty?
+
+	  validate_existence_of @image_files
+
 	  queue = MatlabQueue.new
-	  queue.paths << ['/Applications/spm/spm8/spm8_current',
-	    '/apps/spm/spm8_current',
-      File.join(@libdir, 'custom_methods'), 
-      File.join(@libdir, 'matlab_helpers')
-    ]
+	  queue.paths << [
+	    File.join(@spmdir, 'config'),
+	    File.join(@spmdir, 'matlabbatch'),
+	    File.expand_path(File.join(@libdir, 'custom_methods')), 
+      File.expand_path(File.join(@libdir, 'matlab_helpers')) ]
 
 	  queue << "JohnsonMerit220Visit1Preproc('#{@procdir}/', \
     { #{image_files.collect {|im| "'#{File.basename(im)}'"}.join(' ')} },  \

data/lib/custom_methods/JohnsonMerit220Visit1Stats.rb

@@ -44,10 +44,11 @@ module JohnsonMerit220Visit1Stats
     raise ScriptError, "Can't find any smoothed, warped images in #{@statsdir}" if images.empty?
     
     queue = MatlabQueue.new
-	  queue.paths << ['/Applications/spm/spm8/spm8_current',
-	    '/apps/spm/spm8_current',
-      File.join(@libdir, 'custom_methods'), 
-      File.join(@libdir, 'matlab_helpers')    ]
+	  queue.paths << [
+	    File.join(@spmdir, 'config'),
+	    File.join(@spmdir, 'matlabbatch'),
+	    File.expand_path(File.join(@libdir, 'custom_methods')), 
+      File.expand_path(File.join(@libdir, 'matlab_helpers')) ]
 
 	  queue << "#{@method}('#{@statsdir}/', \
     { #{images.collect {|im| "'#{File.basename(im)}'"}.join(' ')} }, \

data/lib/default_methods/default_stats.rb

@@ -46,6 +46,7 @@ module DefaultStats
 	# Finally runs the stats job and writes output to current working directory.
 	def run_stats_spm_job
 		# TODO
+		# These are mostly being implemented in custom methods.
 	end
 	
 	# Create onsets files using logfile responses for given conditions.

data/lib/default_methods/recon/raw_sequence.rb

@@ -81,7 +81,7 @@ module DefaultRecon
       epirecon_cmd_format = "epirecon_ex -f %s -NAME %s -skip %d -scltype=0"
       epirecon_cmd_options = [@pfile_data, outfile, volumes_to_skip]
       epirecon_cmd = epirecon_cmd_format % epirecon_cmd_options
-      raise ScriptError, "Problem running #{epirecon_cmd}" unless run(epirecon_cmd)
+			raise ScriptError, "Problem running #{epirecon_cmd}" unless run(epirecon_cmd)
     end
     
     alias_method :prepare, :reconstruct_sequence
@@ -99,11 +99,13 @@ module DefaultRecon
     # Create a new unzipped local copy of the ref.dat file and link it into 
     # pwd for reconstruction.
     def setup_refdat(refdat_stem)
-      base_refdat_path = File.join(@rawdir, refdat_stem)
+      $Log.debug "Using refdat file: #{refdat_stem}"
+			base_refdat_path = File.join(@rawdir, refdat_stem)
       refdat_path = File.exist?(base_refdat_path) ? base_refdat_path : base_refdat_path + ".bz2"
       raise IOError, "#{refdat_path} does not exist." unless File.exist?(refdat_path)
       local_refdat_file = Pathname.new(refdat_path).local_copy
-      FileUtils.ln_s(local_refdat_file, Dir.pwd, :force => true)
+			# epirecon expects a reference named _exactly_ ref.dat, so that's what the link should be named.
+      FileUtils.ln_s(local_refdat_file, File.join(Dir.pwd, 'ref.dat'), :force => true)
     end    
    end
-end
+end

data/lib/generators/stats_job_generator.rb

@@ -51,10 +51,14 @@ class StatsJobGenerator < JobGenerator
   
   def logfiles
     return @logfiles if @logfiles
-    logfiles = Dir.glob(File.join(@responses['directory'], @config['subid'] + "*.txt"))
-    raise IOError, "No logfiles found in #{@responses['directory']} matching #{@config['subid']}" if logfiles.empty?
-    logfiles = logfiles.collect! {|file| Logfile.new(file)}.sort
-    @logfiles = logfiles.collect! {|file| File.basename(file.textfile) }
+    if @responses['directory']
+      logfiles = Dir.glob(File.join(@responses['directory'], @config['subid'] + "*.txt"))
+      raise IOError, "No logfiles found in #{@responses['directory']} matching #{@config['subid']}" if logfiles.empty?
+      logfiles = logfiles.collect! {|file| Logfile.new(file)}.sort
+      @logfiles = logfiles.collect! {|file| File.basename(file.textfile) }
+    else
+      puts "Warning: No responses specified."
+    end
   end
   
   def regressorsfiles

data/lib/generators/workflow_generator.rb

@@ -31,7 +31,7 @@ class WorkflowGenerator < JobGenerator
     @spec['subid'] = parse_subid
     @spec['study_procedure'] = @config['study_procedure'] ||= guess_study_procedure_from(@rawdir)
 
-    config_requires 'responses_dir'
+    # config_requires 'responses_dir'
   end
   
   # Create and return a workflow spec to drive processing

data/lib/global_additions.rb

@@ -6,7 +6,7 @@ def run(command)
   
   status = POpen4::popen4(command) do |stdout, stderr|
     puts stdout.read.strip
-    puts stderr.read.strip
+    $Log.error stderr.read.strip
   end
       
   status && status.exitstatus == 0 ? true : false

data/lib/logfile.rb

@@ -76,12 +76,12 @@ class Logfile
   def write_mat(prefix)
     queue = MatlabQueue.new    
     queue.paths << [
-      Pathname.new(File.join(File.dirname(__FILE__), 'matlab_helpers'))
+      Pathname.new(File.join(File.dirname(__FILE__), 'matlab_helpers')).realpath
     ]
     
     raise ScriptError, "Can't find #{@csv_filename}" unless File.exist?(@csv_filename)
 
-    queue << "prepare_onsets_xls( \
+    queue << "prepare_onsets( \
       '#{@csv_filename}', \
       '#{prefix}', \
       { #{@conditions.collect {|c| "'#{c}'"}.join(' ') } } \

data/lib/matlab_helpers/matlab_queue.rb

@@ -15,14 +15,12 @@ class MatlabQueue
   end
   
   def to_s
-    [
-      @paths.flatten.collect {|path| "addpath(genpath('#{path}'))"},
-      @commands
-    ].flatten.join('; ')
+    @commands.flatten.join(', ')
   end
   
   def run!
-    cmd = @ml_command + " -r \"#{ to_s }; exit\" "
+    set_matlabpath
+    cmd = @ml_command + " -r \"#{ escape_error(to_s) }, exit\" "
     @success = run(cmd)
   end
   
@@ -30,8 +28,22 @@ class MatlabQueue
     @commands.send(m, *args, &block)
   end
   
+  # Add paths that should be available for Matlab scripts.
   def add_to_path(*args)
     args.each { |arg| @paths << arg }
   end
   
+  private 
+  
+  # Ensure all the paths from #MatlabQueue @paths instance var are present. 
+  def set_matlabpath
+    mlpath = ENV['MATLABPATH'].split(":")
+    @paths.flatten.collect { |path| mlpath << path }
+    $Log.debug ENV['MATLABPATH'] = mlpath.uniq.join(":")
+  end
+  
+  def escape_error(command)
+    "try; #{command}; catch exception; display(getReport(exception)); pause(1); end"
+  end
+  
 end

data/lib/matlab_helpers/{prepare_onsets_xls.m → prepare_onsets.m}

@@ -1,9 +1,16 @@
-function [] = prepare_onsets_xls(csvfile, matfileprefix, conditions)
+function [] = prepare_onsets(csvfile, matfileprefix, conditions)
 %IMPORTFILE(FILETOREAD1)
 %  Imports data from the specified file
 %  FILETOREAD1:  file to read
 
-import_csv(csvfile);
+try
+	import_csv(csvfile);
+catch exception
+	% Since this is running in a script, catch errors and force Matlab to exit
+	% instead of hanging.  (Not exactly elegant, but it works.)
+	['Error Importing CSV' exception.identifier]
+	exit
+end
 
 for i = 1:length(conditions)
 	condition = conditions{i};

data/lib/rpipe.rb

@@ -23,7 +23,7 @@ class JobStep
 	
 	COLLISION_POLICY = :panic # options -- :panic, :destroy, :overwrite
 	
-	attr_accessor :subid, :rawdir, :origdir, :procdir, :statsdir, :spmdir, :collision_policy, :libdir
+	attr_accessor :subid, :rawdir, :origdir, :procdir, :statsdir, :spmdir, :collision_policy, :libdir, :step
 	
 	# Intialize with two configuration option hashes - workflow_spec and job_spec
 	def initialize(workflow_spec, job_spec)
@@ -33,10 +33,11 @@ class JobStep
 		@origdir      = job_spec['origdir']     || workflow_spec['origdir']
 		@procdir      = job_spec['procdir']     || workflow_spec['procdir']
 		@statsdir     = job_spec['statsdir']    || workflow_spec['statsdir']
-		@spmdir       = job_spec['spmdir']      || workflow_spec['spmdir']
+		@spmdir       = job_spec['spmdir']      || workflow_spec['spmdir'] || default_spmdir
 		@scans        = job_spec['scans']       || workflow_spec['scans']
 		@scan_labels  = job_spec['scan_labels'] || workflow_spec['scan_labels'] 
 		@collision_policy = (job_spec['collision'] || workflow_spec['collision'] || COLLISION_POLICY).to_sym
+		@step   = job_spec['step']
 		@method = job_spec['method']
 		include_custom_methods(@method)
 		@libdir = File.dirname(Pathname.new(__FILE__).realpath)
@@ -49,8 +50,24 @@ class JobStep
 		if module_name.nil? or ['default','wadrc'].include?(module_name)
 			# do nothing, use default implementation
 		else
-			require module_name
-			extend self.class.const_get(module_name.dot_camelize)
+      # Search the load path and require a file named after the custom method.
+      # Include methods contained in the custom method module.  
+		  # Ensure it's named properly according to file convention or it won't be correctly included.
+			begin 
+  			require module_name
+		    extend self.class.const_get(module_name.dot_camelize)
+			rescue LoadError => e
+			  puts "Unable to find the specified method #{module_name}"
+			  puts "Please either use a standard preprocessing step or put a method in app/methods/#{module_name}.rb"
+			  puts "Looking in: #{$LOAD_PATH.join(":")}"
+			  raise e
+	    rescue NameError => e
+	      $Log.error "Unable to include a module #{module_name.dot_camelize} (for custom #{@step} step)."
+	      puts "Please check app/methods/#{module_name}.rb and ensure that you declared a module named _exactly_ #{module_name.dot_camelize}."
+	      puts
+	      raise e
+      end
+
 		end
 	end
 	
@@ -78,7 +95,7 @@ class JobStep
       error = "
       Warning: Misconfiguration detected.
       You are missing the following required variables from your spec file:
-      #{missing_vars.collect { |var| "  - #{var} \n" } }
+      #{missing_vars.collect { |var| "\t  - #{var} \n" } }
       "
       
       puts error
@@ -99,6 +116,19 @@ class JobStep
     end
   end
   
+  def validate_existence_of(*args)
+    missing_files = []
+    args.flatten.collect { |file| missing_files << file unless File.exist?(file) }
+    raise ScriptError, "Missing files: #{missing_files.join(", ")}" unless missing_files.empty?
+  end
+  
+  def default_spmdir
+    spmdirs = %w{/Applications/spm/spm8/spm8_current /apps/spm/spm8_current}
+    spmdirs.each do |dir|
+      return dir if File.directory? dir
+    end
+    raise IOError, "Couldn't find default SPM directory in #{spmdirs.join("; ")}."
+  end
 
   	
 end
@@ -182,7 +212,8 @@ class Stats < JobStep
 		@bold_reps = stats_spec['bold_reps']
 		@conditions = stats_spec['conditions'] || workflow_spec['conditions']
 		
-		job_requires 'bold_reps', 'conditions', 'procdir'
+		job_requires 'bold_reps', 'procdir', 'statsdir'
+		job_requires 'conditions' if @responses
 	end
 	
 end
@@ -221,6 +252,7 @@ class RPipe
 		# the configuration.  
 		@workflow_spec = driver.kind_of?(Hash) ? driver : read_driver_file(driver)
 		
+    # lib/default_logger.rb
     setup_logger
     
     jobs = @workflow_spec['jobs']
@@ -229,18 +261,29 @@ class RPipe
 			@preproc_jobs << Preprocessing.new(@workflow_spec, job_params)  if job_params['step'] == 'preprocess'
 			@stats_jobs   << Stats.new(@workflow_spec, job_params)          if job_params['step'] == 'stats'
 		end
-		
-		def jobs
-		  [@recon_jobs, @preproc_jobs, @stats_jobs].flatten
-	  end
-	  
 	end
+		
+	def jobs
+	  [@recon_jobs, @preproc_jobs, @stats_jobs].flatten
+  end
 	
 	# Reads a YAML driver file, parses it with ERB and returns the Configuration Hash.
 	# Raises an error if the file is not found in the file system.
 	def read_driver_file(driver_file)
+	  @matlab_paths = []
+		# Add Application Config files to the path if they are present.
+		application_directory = File.expand_path(File.join(File.dirname(driver_file), '..'))
+		%w( matlab methods jobs ).each do |directory|
+		  code_dir = File.join(application_directory, directory)
+	    if File.directory?(code_dir)
+	      $LOAD_PATH.unshift(code_dir) 
+	      p = ENV['MATLABPATH'].split(":") << code_dir
+	      ENV['MATLABPATH'] = p.join(":")
+      end
+    end
+		
 		raise(IOError, "Driver file not found: #{driver_file}") unless File.exist?(driver_file)
-		YAML.load(ERB.new(File.read(driver_file)).result) 
+		YAML.load(ERB.new(File.read(driver_file)).result)
   end
   
   private

data/rpipe.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{rpipe}
-  s.version = "0.0.3"
+  s.version = "0.1.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher Kosmatka", "Erik Kastman"]
-  s.date = %q{2010-07-16}
+  s.date = %q{2010-09-21}
   s.description = %q{Neuroimaging preprocessing the Ruby way}
   s.email = %q{kjkosmatka@gmail.com}
   s.executables = ["rpipe", "swallow_batch_run.rb", "create_driver.rb"]
@@ -59,7 +59,7 @@ Gem::Specification.new do |s|
      "lib/matlab_helpers/CreateFunctionalVolumeStruct.m",
      "lib/matlab_helpers/import_csv.m",
      "lib/matlab_helpers/matlab_queue.rb",
-     "lib/matlab_helpers/prepare_onsets_xls.m",
+     "lib/matlab_helpers/prepare_onsets.m",
      "lib/rpipe.rb",
      "rpipe.gemspec",
      "spec/generators/preproc_job_generator_spec.rb",
@@ -126,7 +126,7 @@ Gem::Specification.new do |s|
   s.homepage = %q{http://github.com/brainmap/rpipe}
   s.rdoc_options = ["--charset=UTF-8"]
   s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.3.7}
+  s.rubygems_version = %q{1.3.6}
   s.summary = %q{Neuroimaging preprocessing the Ruby way}
   s.test_files = [
     "spec/generators/preproc_job_generator_spec.rb",
@@ -153,7 +153,7 @@ Gem::Specification.new do |s|
     current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
     s.specification_version = 3
 
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
       s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
       s.add_runtime_dependency(%q<metamri>, [">= 0"])
       s.add_runtime_dependency(%q<log4r>, [">= 0"])

data/vendor/output_catcher.rb

@@ -77,7 +77,7 @@ class Tee < IO
   
   def initialize(filename, post = :out, mode_string = 'w')
     super(FILE_DESC[post], mode_string)
-    @file = File.open(filename, 'w')
+    @file = File.open(filename, mode_string)
     eval("$std#{post} = self")
   end
   

metadata

@@ -1,13 +1,12 @@
 --- !ruby/object:Gem::Specification 
 name: rpipe
 version: !ruby/object:Gem::Version 
-  hash: 25
   prerelease: false
   segments: 
   - 0
+  - 1
   - 0
-  - 3
-  version: 0.0.3
+  version: 0.1.0
 platform: ruby
 authors: 
 - Kristopher Kosmatka
@@ -16,18 +15,16 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-07-16 00:00:00 -05:00
+date: 2010-09-21 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: thoughtbot-shoulda
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 3
         segments: 
         - 0
         version: "0"
@@ -37,11 +34,9 @@ dependencies:
   name: metamri
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 3
         segments: 
         - 0
         version: "0"
@@ -51,11 +46,9 @@ dependencies:
   name: log4r
   prerelease: false
   requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 3
         segments: 
         - 0
         version: "0"
@@ -65,11 +58,9 @@ dependencies:
   name: POpen4
   prerelease: false
   requirement: &id004 !ruby/object:Gem::Requirement 
-    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 3
         segments: 
         - 0
         version: "0"
@@ -79,11 +70,9 @@ dependencies:
   name: ruport
   prerelease: false
   requirement: &id005 !ruby/object:Gem::Requirement 
-    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 3
         segments: 
         - 0
         version: "0"
@@ -142,7 +131,7 @@ files:
 - lib/matlab_helpers/CreateFunctionalVolumeStruct.m
 - lib/matlab_helpers/import_csv.m
 - lib/matlab_helpers/matlab_queue.rb
-- lib/matlab_helpers/prepare_onsets_xls.m
+- lib/matlab_helpers/prepare_onsets.m
 - lib/rpipe.rb
 - rpipe.gemspec
 - spec/generators/preproc_job_generator_spec.rb
@@ -215,27 +204,23 @@ rdoc_options:
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
-  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 3
       segments: 
       - 0
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
-  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 3
       segments: 
       - 0
       version: "0"
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.7
+rubygems_version: 1.3.6
 signing_key: 
 specification_version: 3
 summary: Neuroimaging preprocessing the Ruby way