dicom 0.9.4 → 0.9.5

data/lib/dicom/image_item.rb

@@ -14,6 +14,27 @@ module DICOM
 
     include ImageProcessor
 
+    # Creates an Element with the given arguments and connects it to self.
+    #
+    # @param [String] tag an element tag
+    # @param [String, Integer, Float, Array, NilClass] value an element value
+    # @param [Hash] options any options used for creating the element (see Element.new documentation)
+    #
+    def add_element(tag, value, options={})
+      add(e = Element.new(tag, value, options))
+      e
+    end
+
+    # Creates a Sequence with the given arguments and connects it to self.
+    #
+    # @param [String] tag a sequence tag
+    # @param [Hash] options any options used for creating the sequence (see Sequence.new documentation)
+    #
+    def add_sequence(tag, options={})
+      add(s = Sequence.new(tag, options))
+      s
+    end
+
     # Checks if colored pixel data is present.
     #
     # @return [Boolean] true if the object contains colored pixels, and false if not
@@ -22,7 +43,7 @@ module DICOM
       # "Photometric Interpretation" is contained in the data element "0028,0004":
       begin
         photometric = photometry
-        if photometric.include?("COLOR") or photometric.include?("RGB") or photometric.include?("YBR")
+        if photometric.include?('COLOR') or photometric.include?('RGB') or photometric.include?('YBR')
           return true
         else
           return false
@@ -56,8 +77,8 @@ module DICOM
       raise ArgumentError, "Expected String, got #{bin.class}." unless bin.is_a?(String)
       pixels = false
       # We need to know what kind of bith depth and integer type the pixel data is saved with:
-      bit_depth_element = self["0028,0100"]
-      pixel_representation_element = self["0028,0103"]
+      bit_depth_element = self['0028,0100']
+      pixel_representation_element = self['0028,0103']
       if bit_depth_element and pixel_representation_element
         # Load the binary pixel data to the Stream instance:
         stream.set_string(bin)
@@ -81,8 +102,8 @@ module DICOM
       raise ArgumentError, "Expected Array, got #{pixels.class}." unless pixels.is_a?(Array)
       bin = false
       # We need to know what kind of bith depth and integer type the pixel data is saved with:
-      bit_depth_element = self["0028,0100"]
-      pixel_representation_element = self["0028,0103"]
+      bit_depth_element = self['0028,0100']
+      pixel_representation_element = self['0028,0103']
       if bit_depth_element and pixel_representation_element
         template = template_string(bit_depth_element.value.to_i)
         bin = stream.encode(pixels, template) if template
@@ -187,7 +208,7 @@ module DICOM
     #
     def image_from_file(file)
       raise ArgumentError, "Expected #{String}, got #{file.class}." unless file.is_a?(String)
-      f = File.new(file, "rb")
+      f = File.new(file, 'rb')
       bin = f.read(f.stat.size)
       if bin.length > 0
         # Write the binary data to the Pixel Data Element:
@@ -235,18 +256,18 @@ module DICOM
       parts = file.split('.')
       if parts.length > 1
         base = parts[0..-2].join
-        extension = "." + parts.last
+        extension = '.' + parts.last
       else
         base = file
-        extension = ""
+        extension = ''
       end
       # Get the binary image strings and dump them to the file(s):
       images = image_strings
       images.each_index do |i|
         if images.length == 1
-          f = File.new(file, "wb")
+          f = File.new(file, 'wb')
         else
-          f = File.new("#{base}-#{i}#{extension}", "wb")
+          f = File.new("#{base}-#{i}#{extension}", 'wb')
         end
         f.write(images[i])
         f.close
@@ -265,7 +286,7 @@ module DICOM
     # @param [MagickImage] image the image to be assigned to the pixel data element
     #
     def image=(image)
-      raise ArgumentError, "Expected one of the supported image objects (#{valid_image_objects}), got #{image.class}." unless valid_image_objects.include?(image.class)
+      raise ArgumentError, "Expected one of the supported image classes: #{valid_image_objects} (got #{image.class})" unless valid_image_objects.include?(image.class.to_s)
       # Export to pixels using the proper image processor:
       pixels = export_pixels(image, photometry)
       # Encode and write to the Pixel Data Element:
@@ -277,7 +298,7 @@ module DICOM
     # @return [Integer, NilClass] the number of columns, or nil (if the columns value is undefined)
     #
     def num_cols
-      self["0028,0011"].value rescue nil
+      self['0028,0011'].value rescue nil
     end
 
     # Gives the number of frames in the pixel data.
@@ -286,7 +307,7 @@ module DICOM
     # @return [Integer] the number of rows
     #
     def num_frames
-      (self["0028,0008"].is_a?(Element) == true ? self["0028,0008"].value.to_i : 1)
+      (self['0028,0008'].is_a?(Element) == true ? self['0028,0008'].value.to_i : 1)
     end
 
     # Gives the number of rows in the pixel data.
@@ -294,7 +315,7 @@ module DICOM
     # @return [Integer, NilClass] the number of rows, or nil (if the rows value is undefined)
     #
     def num_rows
-      self["0028,0010"].value rescue nil
+      self['0028,0010'].value rescue nil
     end
 
     # Creates an NArray containing the pixel data. If the pixel data is an image
@@ -402,22 +423,21 @@ module DICOM
     # @param [Array<Integer>, NArray] values an Array (or NArray) containing integer pixel values
     #
     def pixels=(values)
-      raise ArgumentError, "Expected Array or NArray, got #{values.class}." unless [Array, NArray].include?(values.class)
-      if values.is_a?(NArray)
-        # When NArray, convert to a Ruby Array:
+      raise ArgumentError, "The given argument does not respond to #to_a (got an argument of class #{values.class})" unless values.respond_to?(:to_a)
+      if values.class.ancestors.to_s.include?('NArray')
+        # With an NArray argument, make sure that it gets properly converted to an Array:
         if values.shape.length > 2
-          # We need to take care when reshaping this 3D array so that the pixel values falls properly into place:
+          # For a 3D NArray we need to rearrange to ensure that the pixels get their
+          # proper order when converting to an ordinary Array instance:
           narr = NArray.int(values.shape[1] * values.shape[2], values.shape[0])
           values.shape[0].times do |i|
             narr[true, i] = values[i, true, true].reshape(values.shape[1] * values.shape[2])
           end
-          values = narr.to_a
-        else
-          values = values.to_a
+          values = narr
         end
       end
       # Encode the pixel data:
-      bin = encode_pixels(values.flatten)
+      bin = encode_pixels(values.to_a.flatten)
       # Write the binary data to the Pixel Data Element:
       write_pixels(bin)
     end
@@ -444,7 +464,7 @@ module DICOM
       raise "The 'Bits Allocated' Element is missing from this DICOM instance. Unable to encode/decode pixel data." unless exists?("0028,0100")
       if photometry == PI_PALETTE_COLOR
       # Only one channel is checked and it is assumed that all channels have the same number of bits.
-        return self["0028,1101"].value.split("\\").last.to_i
+        return self['0028,1101'].value.split("\\").last.to_i
       else
         return bit_depth
       end
@@ -458,7 +478,7 @@ module DICOM
     #
     def bit_depth
       raise "The 'Bits Allocated' Element is missing from this DICOM instance. Unable to encode/decode pixel data." unless exists?("0028,0100")
-      return value("0028,0100")
+      return value('0028,0100')
     end
 
     # Performs a run length decoding on the input stream.
@@ -524,7 +544,7 @@ module DICOM
     #
     def photometry
       raise "The 'Photometric Interpretation' Element is missing from this DICOM instance. Unable to encode/decode pixel data." unless exists?("0028,0004")
-      return value("0028,0004").upcase
+      return value('0028,0004').upcase
     end
 
     # Processes the pixel array based on attributes defined in the DICOM object,
@@ -539,16 +559,16 @@ module DICOM
       proper_rgb = false
       photometric = photometry()
       # (With RLE COLOR PALETTE the Planar Configuration is not set)
-      planar = self["0028,0006"].is_a?(Element) ? self["0028,0006"].value : 0
+      planar = self['0028,0006'].is_a?(Element) ? self['0028,0006'].value : 0
       # Step 1: Produce an array with RGB values. At this time, YBR is not supported in ruby-dicom,
       # so this leaves us with a possible conversion from PALETTE COLOR:
-      if photometric.include?("COLOR")
+      if photometric.include?('COLOR')
         # Pseudo colors (rgb values grabbed from a lookup table):
         rgb = Array.new(pixels.length*3)
         # Prepare the lookup data arrays:
-        lookup_binaries = [self["0028,1201"].bin, self["0028,1202"].bin, self["0028,1203"].bin]
+        lookup_binaries = [self['0028,1201'].bin, self['0028,1202'].bin, self['0028,1203'].bin]
         lookup_values = Array.new
-        nr_bits = self["0028,1101"].value.split("\\").last.to_i
+        nr_bits = self['0028,1101'].value.split("\\").last.to_i
         template = template_string(nr_bits)
         lookup_binaries.each do |bin|
           stream.set_string(bin)
@@ -561,7 +581,7 @@ module DICOM
         end
         # As we have now ordered the pixels in RGB order, modify planar configuration to reflect this:
         planar = 0
-      elsif photometric.include?("YBR")
+      elsif photometric.include?('YBR')
         rgb = false
       else
         rgb = pixels
@@ -739,13 +759,13 @@ module DICOM
     #
     def signed_pixels?
       raise "The 'Pixel Representation' data element is missing from this DICOM instance. Unable to process pixel data." unless exists?("0028,0103")
-      case value("0028,0103")
+      case value('0028,0103')
       when 1
         return true
       when 0
         return false
       else
-        raise "Invalid value encountered (#{value("0028,0103")}) in the 'Pixel Representation' data element. Expected 0 or 1."
+        raise "Invalid value encountered (#{value('0028,0103')}) in the 'Pixel Representation' data element. Expected 0 or 1."
       end
     end
 
@@ -757,22 +777,22 @@ module DICOM
     #
     def template_string(depth)
       template = false
-      pixel_representation = self["0028,0103"].value.to_i
+      pixel_representation = self['0028,0103'].value.to_i
       # Number of bytes used per pixel will determine how to unpack this:
       case depth
       when 8 # (1 byte)
-        template = "BY" # Byte/Character/Fixnum
+        template = 'BY' # Byte/Character/Fixnum
       when 16 # (2 bytes)
         if pixel_representation == 1
-         template = "SS" # Signed short
+         template = 'SS' # Signed short
         else
-          template = "US" # Unsigned short
+          template = 'US' # Unsigned short
         end
       when 32 # (4 bytes)
         if pixel_representation == 1
-          template = "SL" # Signed long
+          template = 'SL' # Signed long
         else
-          template = "UL" # Unsigned long
+          template = 'UL' # Unsigned long
         end
       when 12
         # 12 BIT SIMPLY NOT IMPLEMENTED YET!
@@ -793,10 +813,10 @@ module DICOM
     # @return [Array<Integer, NilClass>] center, width, intercept and slope
     #
     def window_level_values
-      center = (self["0028,1050"].is_a?(Element) == true ? self["0028,1050"].value.to_i : nil)
-      width = (self["0028,1051"].is_a?(Element) == true ? self["0028,1051"].value.to_i : nil)
-      intercept = (self["0028,1052"].is_a?(Element) == true ? self["0028,1052"].value.to_i : 0)
-      slope = (self["0028,1053"].is_a?(Element) == true ? self["0028,1053"].value.to_i : 1)
+      center = (self['0028,1050'].is_a?(Element) == true ? self['0028,1050'].value.to_i : nil)
+      width = (self['0028,1051'].is_a?(Element) == true ? self['0028,1051'].value.to_i : nil)
+      intercept = (self['0028,1052'].is_a?(Element) == true ? self['0028,1052'].value.to_i : 0)
+      slope = (self['0028,1053'].is_a?(Element) == true ? self['0028,1053'].value.to_i : 1)
       return center, width, intercept, slope
     end
 

data/lib/dicom/image_processor.rb

@@ -47,10 +47,10 @@ module DICOM
 
     # Gives an array containing the image objects that are supported by the image processor.
     #
-    # @return [Array] the valid image classes
+    # @return [Array<String>] the valid image classes
     #
     def valid_image_objects
-      return [Magick::Image, MiniMagick::Image]
+      return ['Magick::Image', 'MiniMagick::Image']
     end
 
 

data/lib/dicom/image_processor_mini_magick.rb

@@ -45,7 +45,7 @@ module DICOM
         # @param [String] format the image format to use
         # @return [Magick::Image] a mini_magick image object
         #
-        def import_pixels(blob, columns, rows, depth, photometry, format="png")
+        def import_pixels(blob, columns, rows, depth, photometry, format='png')
           image = MiniMagick::Image.import_pixels(blob, columns, rows, depth, im_map(photometry), format)
         end
 
@@ -56,12 +56,12 @@ module DICOM
         #
         def im_map(photometry)
           raise ArgumentError, "Expected String, got #{photometry.class}." unless photometry.is_a?(String)
-          if photometry.include?("COLOR") or photometry.include?("RGB")
-            return "rgb"
-          elsif photometry.include?("YBR")
-            return "ybr"
+          if photometry.include?('COLOR') or photometry.include?('RGB')
+            return 'rgb'
+          elsif photometry.include?('YBR')
+            return 'ybr'
           else
-            return "gray" # (Assuming monochromeX - greyscale)
+            return 'gray' # (Assuming monochromeX - greyscale)
           end
         end
 

data/lib/dicom/image_processor_r_magick.rb

@@ -63,7 +63,7 @@ module DICOM
         # @param [String] format the image format to use
         # @return [Magick::Image] an RMagick image object
         #
-        def import_pixels(blob, columns, rows, depth, photometry, format="png")
+        def import_pixels(blob, columns, rows, depth, photometry, format='png')
           image = Magick::Image.new(columns,rows).import_pixels(0, 0, columns, rows, rm_map(photometry), blob, rm_data_type(depth))
         end
 
@@ -91,12 +91,12 @@ module DICOM
         #
         def rm_map(photometry)
           raise ArgumentError, "Expected String, got #{photometry.class}." unless photometry.is_a?(String)
-          if photometry.include?("COLOR") or photometry.include?("RGB")
-            return "RGB"
-          elsif photometry.include?("YBR")
-            return "YBR"
+          if photometry.include?('COLOR') or photometry.include?('RGB')
+            return 'RGB'
+          elsif photometry.include?('YBR')
+            return 'YBR'
           else
-            return "I" # (Assuming monochromeX - greyscale)
+            return 'I' # (Assuming monochromeX - greyscale)
           end
         end
 

data/lib/dicom/link.rb

@@ -1415,7 +1415,7 @@ module DICOM
         # Convert the variable to an empty string.
         data = ""
       end
-      return data
+      data
     end
 
     # Receives the data from an incoming network transmission.
@@ -1423,17 +1423,13 @@ module DICOM
     #
     def receive_transmission_data
       data = false
-      t1 = Time.now.to_f
-      @receive = true
-      thr = Thread.new{ data=@session.recv(@max_receive_size); @receive=false }
-      while @receive
-        if (Time.now.to_f - t1) > @timeout
-          Thread.kill(thr)
-          logger.error("No answer was received within the specified timeout period. Aborting.")
-          stop_receiving
-        end
+      response = IO.select([@session], nil, nil, @timeout)
+      if response.nil?
+        logger.error("No answer was received within the specified timeout period. Aborting.")
+      else
+        data = @session.recv(@max_receive_size)
       end
-      return data
+      data
     end
 
     # Sets some default values related to encoding.

data/lib/dicom/logging.rb

@@ -122,6 +122,7 @@ module DICOM
       end
 
       # The logger object setter.
+      #
       # This method is used to replace the default logger instance with
       # a custom logger of your own.
       #
@@ -152,4 +153,4 @@ module DICOM
   # Include the Logging module so we can use DICOM.logger.
   include Logging
 
-end
+end

data/lib/dicom/variables.rb

@@ -36,6 +36,41 @@ module DICOM
       return uid
     end
 
+    # Loads DICOM data to DObject instances and returns them in an array.
+    # Invalid DICOM sources (files) are ignored.
+    # If no valid DICOM source is given, an empty array is returned.
+    #
+    # @param [String, DObject, Array<String, DObject>] data single or multiple DICOM data (directories, file paths, binary strings, DICOM objects)
+    # @return [Array<DObject>] an array of successfully loaded DICOM objects
+    #
+    def load(data)
+      data = Array[data] unless data.respond_to?(:to_ary)
+      ary = Array.new
+      data.each do |element|
+        if element.is_a?(String)
+          begin
+            if File.directory?(element)
+              files = Dir[File.join(element, '**/*')].reject {|f| File.directory?(f) }
+              dcms = files.collect {|f| DObject.read(f)}
+            elsif File.file?(element)
+              dcms = [DObject.read(element)]
+            else
+              dcms = [DObject.parse(element)]
+            end
+          rescue
+            dcms = [DObject.parse(element)]
+          end
+          ary += dcms.keep_if {|dcm| dcm.read?}
+        else
+          # The element was not a string, and the only remaining valid element type is a DICOM object:
+          raise ArgumentError, "Invalid element (#{element.class}) given. Expected string or DObject." unless element.respond_to?(:to_dcm)
+          element.was_dcm_on_input = true
+          ary << element.to_dcm
+        end
+      end
+      ary
+    end
+
     # Use tags as key. Example: '0010,0010'
     #
     def key_use_tags
@@ -65,6 +100,6 @@ module DICOM
   # The default key representation.
   self.key_representation = :name
   # The default source application entity title.
-  self.source_app_title = 'RUBY_DICOM'
+  self.source_app_title = 'RUBY-DICOM'
 
 end

data/lib/dicom/version.rb

@@ -1,6 +1,6 @@
 module DICOM
 
   # The ruby-dicom version string.
-  VERSION = '0.9.4'
+  VERSION = '0.9.5'
 
 end

data/rakefile.rb

@@ -1,8 +1,10 @@
 # Available commands:
 # Testing the specification:
 #   bundle exec rake spec
-# Building a gem package from source:
+# Building a gem from source with rake:
 #   bundle exec rake package
+# Building a gem from source with rubygems:
+#   bundle exec gem build dicom.gemspec
 # Create html documentation files:
 #   bundle exec rake yard