Class: FSL::FIRST

Inherits:
Object
  • Object
show all
Defined in:
lib/fsl-ruby/first.rb

Constant Summary collapse

@@command_path =

e.g.: run_first_all -i im1 -o output_name

'/usr/local/fsl/bin/run_first_all'
@@options_map = 
{
	method: '-m',
	already_bet: '-b',
	structure: '-s',
	affine: '-a',
	threestage: '-3',
	no_cleanup: '-d',
	verbose: '-v',
	help: '-h'
}

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(input_file, output_file, opt = {}) ⇒ FIRST

Returns a new instance of FIRST.



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# File 'lib/fsl-ruby/first.rb', line 48

def initialize(input_file, output_file, opt = {})
	@input_file = input_file
	@basename = File.basename(input_file, '.nii.gz')
	@output_file = output_file
	@output_dir = File.dirname(output_file)
	@opt = opt
end

Class Method Details

.command_path ⇒ Object 



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# File 'lib/fsl-ruby/first.rb', line 32

def self.command_path
	@@command_path
end

.command_path=(path) ⇒ Object 



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# File 'lib/fsl-ruby/first.rb', line 28

def self.command_path=(path)
	@@command_path = path
end

.options_map ⇒ Object 



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# File 'lib/fsl-ruby/first.rb', line 56

def self.options_map
	@@options_map
end

Instance Method Details

#argument_list ⇒ Object 



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# File 'lib/fsl-ruby/first.rb', line 72

def argument_list
	map_options(@opt).collect {|k,v| v}.join(' ')
end

#command ⇒ Object 



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# File 'lib/fsl-ruby/first.rb', line 76

def command
	command_str = "#{self.class.command_path} #{argument_list} -i #{@input_file} -o #{@output_file}"
	puts "Running FIRST with command: #{command_str}..."
	result = `#{command_str}`
	exit_code = $?
	case exit_code
		when 0
			puts "Done running FIRST."
			return result
		else
			puts "An error ocurred while running FIRST"
	        #   exit_error = Dcm2nii::Runner::UnexpectedExitError.new
	        #   exit_error.exit_code = exit_code
	        #   raise exit_error
	        # end
	end
end

#get_result ⇒ Object 



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# File 'lib/fsl-ruby/first.rb', line 94

def get_result
	first_files = {}
	first_files[:origsegs] = `find #{@output_dir} -name *origsegs.nii*`.chomp
	first_files[:firstseg] = `find #{@output_dir} -name *firstseg.nii*`.chomp
	return first_files
end

#map_options(opt = {}) ⇒ Object 



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# File 'lib/fsl-ruby/first.rb', line 68

def map_options(opt ={})
	opt.inject({}) { |h, (k, v)| h[k] = (self.class.options_map[k] + ' ' + map_vals(v)); h }
end

#map_vals(val) ⇒ Object 



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# File 'lib/fsl-ruby/first.rb', line 60

def map_vals(val)
	if val == true || val == false
		''
	else
		val.to_s
	end
end