Module: DefaultStats

Included in:
Stats
Defined in:
lib/default_methods/default_stats.rb

Instance Method Summary collapse

Instance Method Details

#create_onsets_files(responses, conditions) ⇒ Object

Create onsets files using logfile responses for given conditions.

Responses is a hash containing a directory and filenames of the .txt button-press response logfiles formatted by Presentation’s SDF.

responses = { ‘directory’ => ‘/path/to/files’, ‘logfiles’ => [‘subid_taskB.txt’, ‘subid_taskA.txt’]}

Conditions is an array of vector labels to extract from the .txt file Each label may be either an individual condition or a hash of multiple conditions, with the combined label as the key and the separate labels as values.

conditions = [:new, :old, => [:new_misses, :old_misses] ]



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# File 'lib/default_methods/default_stats.rb', line 65

def create_onsets_files(responses, conditions)
 onsets_csv_files = []
 onsets_mat_files = []
 wd = Dir.pwd
 matching_directories = Dir.glob(responses['directory'])

 case 
 when matching_directories.length == 0
   raise(IOError, "Response directory #{responses['directory']} doesn't exist or isn't mounted.")
 when matching_directories.length > 1
   raise IOError, "Only one response directory currently accepted (matched directories: #{matching_directories.join(', ')})"
  end
 
 Dir.chdir matching_directories.first  do
   responses['logfiles'].each do |logfile|
	    # Either Strip off the prefix directly without changing the name...
      #   prefix = File.basename(logfile, '.txt')
      # Or create a new name based on standard logfile naming scheme:
      # mrt00000_abc_021110_faces3_recognitionA.txt
      prefix = File.basename(logfile, '.txt').split("_").values_at(0,3,4).join("_")
	    log = Logfile.new(logfile, *conditions)
	    
      # puts log.to_csv
	    onsets_csv_files << log.write_csv(prefix + '.csv')
	    onsets_mat_files << log.write_mat(prefix)
    end
    
    [onsets_csv_files, onsets_mat_files].flatten.each do |response_file|
     FileUtils.move response_file, wd
    end
  end
  
  return onsets_mat_files
end

#customize_template_job ⇒ Object

Copies the template job to the current working directory, then customizes it by performing a set of recursive string replacements specified in the template_spec.



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# File 'lib/default_methods/default_stats.rb', line 42

def customize_template_job
	# TODO
end

#link_files_from_proc_directory(images_wildcard = File.join(@procdir, "swq*.nii"), motion_regressors_wildcard = File.join(@procdir, "md_rp*.txt")) ⇒ Object

Links all the files necessary from the “proc” directory. Links written to current working directory.

Raises:

  • (IOError) 


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# File 'lib/default_methods/default_stats.rb', line 20

def link_files_from_proc_directory(images_wildcard = File.join(@procdir, "swq*.nii"), motion_regressors_wildcard = File.join(@procdir, "md_rp*.txt"))
	puts Dir.glob(images_wildcard), @statsdir
	raise IOError, "No images to link with #{images_wildcard}" if Dir.glob(images_wildcard).empty?
	system("ln -s #{images_wildcard} #{@statsdir}")

	raise IOError, "No motion_regressors to link with #{motion_regressors_wildcard}" if Dir.glob(motion_regressors_wildcard).empty?
	system("ln -s #{motion_regressors_wildcard} #{@statsdir}")
end

#link_onsets_files ⇒ Object

Links to a preconfigured onsets file, a matlab file that contains three cell arrays: names, onsets, durations. This file is used by SPM to configure the conditions of the function task and the onset times to use in the model. Link is written to current working directory.



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# File 'lib/default_methods/default_stats.rb', line 32

def link_onsets_files
	@onsetsfiles.each do |ofile|
		# Check if File Path is Absolute.  If not link from procdir/onsets
		opath = Pathname.new(ofile).absolute? ? ofile : File.join(@procdir, 'onsets', ofile)
		system("ln -s #{File.expand_path(opath)} #{Dir.pwd}")
	end
end

#run_first_level_stats ⇒ Object Also known as: perform

runs the complete set of tasks using data in a subject’s “proc” directory and a preconfigured template spm job.



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# File 'lib/default_methods/default_stats.rb', line 4

def run_first_level_stats
	flash "Highway to the dangerzone..."
	setup_directory(@statsdir, "STATS")
	
	Dir.chdir(@statsdir) do
		link_files_from_proc_directory
		link_onsets_files
		customize_template_job
		run_stats_spm_job
	end
	
end

#run_stats_spm_job ⇒ Object

Finally runs the stats job and writes output to current working directory.



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# File 'lib/default_methods/default_stats.rb', line 47

def run_stats_spm_job
	# TODO
	# These are mostly being implemented in custom methods.
end