Class: NIFTI::NWrite

Inherits:
Object
  • Object
show all
Defined in:
lib/nifti/n_write.rb

Overview

The NWrite class handles the encoding of an NObject instance to a valid NIFTI string. The String is then written to file.

Instance Attribute Summary (collapse)

Instance Method Summary (collapse)

Constructor Details

- (NWrite) initialize(obj, file_name, options = {})

Creates an NWrite instance.

Parameters

  • obj ??? A NObject instance which will be used to encode a NIfTI string.

  • file_name ??? A string, either specifying the path of a DICOM file to be loaded, or a binary DICOM string to be parsed.

  • options ??? A hash of parameters.

Options



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# File 'lib/nifti/n_write.rb', line 23

def initialize(obj, file_name, options = {})
  @obj = obj
  @file_name = file_name
  # Array for storing error/warning messages:
  @msg = Array.new
end

Instance Attribute Details

- (Object) msg (readonly)

An array which records any status messages that are generated while encoding/writing the DICOM string.



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# File 'lib/nifti/n_write.rb', line 9

def msg
  @msg
end

- (Object) success (readonly)

A boolean which reports whether the DICOM string was encoded/written successfully (true) or not (false).



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# File 'lib/nifti/n_write.rb', line 11

def success
  @success
end

Instance Method Details

- (Object) init_variables

Creates various variables used when encoding the DICOM string.



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# File 'lib/nifti/n_write.rb', line 136

def init_variables
  # Until a DICOM write has completed successfully the status is 'unsuccessful':
  @success = false
end

- (Object) open_file(file)

Tests if the path/file is writable, creates any folders if necessary, and opens the file for writing.

Parameters

  • file ??? A path/file string.



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# File 'lib/nifti/n_write.rb', line 104

def open_file(file)
  # Check if file already exists:
  if File.exist?(file)
    # Is it writable?
    if File.writable?(file)
      @file = File.new(file, "wb")
    else
      # Existing file is not writable:
      @msg << "Error! The program does not have permission or resources to create the file you specified: (#{file})"
    end
  else
    # File does not exist.
    # Check if this file's path contains a folder that does not exist, and therefore needs to be created:
    folders = file.split(File::SEPARATOR)
    if folders.length > 1
      # Remove last element (which should be the file string):
      folders.pop
      path = folders.join(File::SEPARATOR)
      # Check if this path exists:
      unless File.directory?(path)
        # We need to create (parts of) this path:
        require 'fileutils'
        FileUtils.mkdir_p path
      end
    end
    # The path to this non-existing file is verified, and we can proceed to create the file:
    @file = File.new(file, "wb")
  end
end

- (Object) write

Handles the encoding of NIfTI information to string as well as writing it to file.



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# File 'lib/nifti/n_write.rb', line 31

def write
  # Check if we are able to create given file:
  open_file(@file_name)
  # Go ahead and write if the file was opened successfully:
  if @file
    # Initiate necessary variables:
    init_variables
    @file_endian = false
    # Create a Stream instance to handle the encoding of content to a binary string:
    @stream = Stream.new(nil, @file_endian)
    # Tell the Stream instance which file to write to:
    @stream.set_file(@file)
    
    # Write Header and Image
    write_basic_header
    write_extended_header
    write_image

    # As file has been written successfully, it can be closed.
    @file.close
    # Mark this write session as successful:
    @success = true
  end
  
end

- (Object) write_basic_header

Write Basic Header



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# File 'lib/nifti/n_write.rb', line 58

def write_basic_header
  HEADER_SIGNATURE.each do |header_item|
    begin
      name, length, type = *header_item
      str = @stream.encode(@obj.header[name], type)
      padded_str = @stream.encode_string_to_length(str, length)
      # puts @stream.index, name, str.unpack(@stream.vr_to_str(type))
      # pp padded_str.unpack(@stream.vr_to_str(type))

      @stream.write padded_str
      @stream.skip length
    rescue StandardError => e
      puts name, length, type, e
      raise e
    end
  end
end

- (Object) write_extended_header

Write Extended Header



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# File 'lib/nifti/n_write.rb', line 77

def write_extended_header
  unless @obj.extended_header.empty?
    @stream.write @stream.encode([1,0,0,0], "BY")
    @obj.extended_header.each do |extension|
    @stream.write @stream.encode extension[:esize], "UL"
    @stream.write @stream.encode extension[:ecode], "UL"
    @stream.write @stream.encode_string_to_length(@stream.encode(extension[:data], "STR"), extension[:esize] - 8)
    end
  else
    @stream.write @stream.encode([0,0,0,0], "BY")
  end
  
  
end

- (Object) write_image

Write Image



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# File 'lib/nifti/n_write.rb', line 93

def write_image
  type = NIFTI_DATATYPES[@obj.header['datatype']]
  @stream.write @stream.encode(@obj.image, type)
end