Class: WorkflowGenerator

Inherits:
JobGenerator show all
Defined in:
lib/generators/workflow_generator.rb

Overview

A class for parsing a data directory and creating default Driver Configurations Intialize a WorkflowGenerator with a Raw Directory containing Scans and with the following optional keys in a config hash:

Directory Options:

- processing_dir : A directory common to  orig, proc and stats directories, if they are not explicitly specified..
- origdir : A directory where dicoms will be converted to niftis and basic preprocessing occurs.
- procdir : A directory for detailed preprocessing (normalization and smoothing)
- statsdir : A directory where stats will be saved.  (This should be a final directory.)

Instance Attribute Summary collapse

Attributes inherited from JobGenerator

#previous_step

Instance Method Summary collapse

Methods inherited from JobGenerator

#config_requires, #spec_validates

Constructor Details

#initialize(rawdir, config = Hash.new) ⇒ WorkflowGenerator

Returns a new instance of WorkflowGenerator.



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# File 'lib/generators/workflow_generator.rb', line 23

def initialize(rawdir, config = Hash.new)
  config_defaults = {}
  config_defaults['conditions'] = ['new_correct', 'new_incorrect', 'old_correct', 'old_incorrect']
  config_defaults['processing_dir'] = Dir.mktmpdir
  super config_defaults.merge(config)
  
  @rawdir = rawdir
  @spec['rawdir'] = @rawdir
  @spec['subid'] = parse_subid
  @spec['study_procedure'] = @config['study_procedure'] ||= guess_study_procedure_from(@rawdir)

  # config_requires 'responses_dir'
end

Instance Attribute Details

#config ⇒ Object (readonly)

Returns the value of attribute config.



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# File 'lib/generators/workflow_generator.rb', line 21

def config
  @config
end

#spec ⇒ Object (readonly)

Returns the value of attribute spec.



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# File 'lib/generators/workflow_generator.rb', line 21

def spec
  @spec
end

Instance Method Details

#build ⇒ Object

Create and return a workflow spec to drive processing



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# File 'lib/generators/workflow_generator.rb', line 38

def build    
  configure_directories
  
  @spec['collision'] = 'destroy'
  
  
  jobs = []
  
  # Recon
  recon_options = {'rawdir' => @rawdir, 'epi_pattern' => /(Rest|Task)/i, }
  config_step_method(recon_options, 'recon') if @config['custom_methods']
  jobs << ReconJobGenerator.new(recon_options).build
  
  # Preproc
  preproc_options = {'scans' => jobs.first['scans']}
  config_step_method(preproc_options, 'preproc') if @config['custom_methods']
  jobs << PreprocJobGenerator.new(preproc_options).build
  
  # Stats
  stats_options = {
    'scans' => jobs.first['scans'],
    'conditions' => @config['conditions'],
    'responses_dir' => @config['responses_dir'],
    'subid' => @spec['subid']
  }
  config_step_method(stats_options, 'stats') if @config['custom_methods']
  jobs << StatsJobGenerator.new(stats_options).build
  
  @spec['jobs'] = jobs
  
  return @spec
end

#config_step_method(options, step) ⇒ Object

Configure Custom Methods from the Workflow Driver

Custom methods may be simply set to true for a given job or listed explicitly. If true, they will set the method to the a camelcased version of the study_procedure and step, i.e. JohnsonMerit220Visit1Stats If listed explicitly, it will set the step to the value listed.



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# File 'lib/generators/workflow_generator.rb', line 126

def config_step_method(options, step)
  if @config['custom_methods'][step].class == String
    options['method'] = @config['custom_methods'][step]
  elsif @config['custom_methods'][step] == true
    options['method'] = [@config['study_procedure'], step.capitalize].join("_").dot_camelize
  end
end

#configure_directories ⇒ Object

Handle Directory Configuration and Defaults for orig, proc and stats dirs.



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# File 'lib/generators/workflow_generator.rb', line 82

def configure_directories
  processing_dir = @config['processing_dir']
  if @config['directory_formats']
    @spec['origdir']  = @config['origdir']  || parse_directory_format(@config['directory_formats']['origdir'])  || File.join(processing_dir, @spec['subid'] + '_orig')
    @spec['procdir']  = @config['procdir']  || parse_directory_format(@config['directory_formats']['procdir'])  || File.join(processing_dir, @spec['subid'] + '_proc')
    @spec['statsdir'] = @config['statsdir'] || parse_directory_format(@config['directory_formats']['statsdir']) || File.join(processing_dir, @spec['subid'] + '_stats')
  else
    @spec['origdir']  = @config['origdir']  || File.join(processing_dir, @spec['subid'] + '_orig')
    @spec['procdir']  = @config['procdir']  || File.join(processing_dir, @spec['subid'] + '_proc')
    @spec['statsdir'] = @config['statsdir'] || File.join(processing_dir, @spec['subid'] + '_stats')
  end
end

#guess_study_procedure_from(dir) ⇒ Object

Guess a StudyProcedure from the data’s raw directory. A properly formed study procdure should be: <PI>.<Study>.<Description or Visit> Raises a ScriptError if it couldn’t guess a reasonable procedure.

Raises:

  • (ScriptError) 


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# File 'lib/generators/workflow_generator.rb', line 111

def guess_study_procedure_from(dir)
  dirs = dir.split("/")
  while dirs.empty? == false do
    current_dir = dirs.pop
    return current_dir if current_dir =~ /\w*\.\w*\.\w*/
  end
  raise ScriptError, "Could not guess study procedure from #{dir}"
end

#parse_directory_format(fmt) ⇒ Object

Replace a directory format string with respective values from the spec. For example, replace the string “/Data/<study_procedure>/<subid>/stats” from a workflow_driver[‘statsdir’] with “/Data/johnson.merit220.visit1/mrt00000/stats”



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# File 'lib/generators/workflow_generator.rb', line 99

def parse_directory_format(fmt)
  dir = fmt.dup
  dir.scan(/<\w*>/).each do |replacement|
    key = replacement.to_s.gsub(/(<|>)/, '')
    dir.sub!(/<\w*>/, @spec[key])
  end
  return dir
end

#parse_subid ⇒ Object

Guesses a Subject Id from @rawdir Takes the split basename of rawdir itself if rawdir includes subdir, or the basename of its parent.



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# File 'lib/generators/workflow_generator.rb', line 74

def parse_subid
  subject_path = File.basename(@rawdir) == 'dicoms' ? 
    Pathname.new(File.join(@rawdir, '..')).realpath : Pathname.new(@rawdir).realpath
  
  subject_path.basename.to_s.split('_').first
end