Class: ReconJobGenerator

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

Overview

A class for parsing a data directory and creating a default Reconstruction Job Intialize the ReconJobGenerator with the following options in a config hash.

Required Options:

  • rawdir : The directory containing EPI runs

Raises an IOError if the Raw Directory cannot be read, and a DriverConfigError if the Raw Directory is not specified.

Instance Attribute Summary

Attributes inherited from JobGenerator

#previous_step, #spec

Instance Method Summary collapse

Methods inherited from JobGenerator

#config_requires, #spec_validates

Constructor Details

#initialize(config) ⇒ ReconJobGenerator

Returns a new instance of ReconJobGenerator.

Raises:

  • (IOError) 


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# File 'lib/generators/recon_job_generator.rb', line 17

def initialize(config)
  # Add job-specific config defaults to config and initialize teh JobGenerator with them.
  config_defaults = {}
  config_defaults['epi_pattern'] = /fMRI/i
  config_defaults['ignore_patterns'] = [/pcasl/i]
  config_defaults['volumes_to_skip'] = 3
  super config_defaults.merge(config)

  @spec['step'] = 'reconstruct'

  config_requires 'rawdir'
  @rawdir = @config['rawdir']
  raise IOError, "Can't find raw directory #{@rawdir}" unless File.readable?(@rawdir)
end

Instance Method Details

#build ⇒ Object 



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# File 'lib/generators/recon_job_generator.rb', line 32

def build
  scans = Array.new
  
  visit = VisitRawDataDirectory.new(@rawdir)
  # Scan the datasets, ignoring unwanted (very large unused) directories.
  visit.scan(:ignore_patterns => [@config['ignore_patterns']].flatten)
  
  visit.datasets.each do |dataset|
    # Only build hashes for EPI datasets
    next unless dataset.series_description =~ @config['epi_pattern']
    
    scans << build_scan_hash(dataset)
  end
  
  @spec['scans'] = scans
  
  return @spec
end

#build_scan_hash(dataset) ⇒ Object

Returns a hash describing how to reconstruct the dataset.



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# File 'lib/generators/recon_job_generator.rb', line 52

def build_scan_hash(dataset)
  scan = {}
  raw_image_file    = dataset.raw_image_files.first
  # phys = Physionoise.new(@rawdir, File.join(@rawdir, '..', 'cardiac' ))
  
  scan['dir']             = dataset.relative_dataset_path
  scan['type']            = 'func'
  scan['z_slices']        = raw_image_file.num_slices.to_i
  scan['bold_reps']       = raw_image_file.bold_reps.to_i
  scan['volumes_to_skip'] = @config['volumes_to_skip'].to_i
  scan['rep_time']        = raw_image_file.rep_time.to_f.in_seconds
  scan['label']           = dataset.series_description.escape_filename
  # scan['task']            = '?'
  # scan['physio_files']    = "#TODO"
  
  return scan
end