dicom 0.4 → 0.5

data/lib/DWrite.rb

@@ -1,31 +1,29 @@
-#    Copyright 2008-2009 Christoffer Lerv�g
+#    Copyright 2008-2009 Christoffer Lervag
 
 # Some notes about this DICOM file writing class:
-# In its current state, this class will always try to write the file such that it is
-# compliant to the official standard (DICOM 3 Part 10), containing header
-# and meta information (group 0002). If this is unwanted behaviour, it is easy
-# to modify the source code here to avoid this.
+# In its current state, this class will always try to write the file such that it is compliant to the
+# official standard (DICOM 3 Part 10), containing header and meta information (group 0002).
+# If this is unwanted behaviour, it is easy to modify the source code here to avoid this.
 #
-# It is important to note, that while the goal is to be fully DICOM compliant, 
-# no guarantees are given that this is actually achieved. You are encouraged
-# to thouroughly test your files for compatibility after creation. 
-#Please contact the author if you discover any issues with file creation.
+# It is important to note, that while the goal is to be fully DICOM compliant, no guarantees are given
+# that this is actually achieved. You are encouraged to thouroughly test your files for compatibility after creation.
+# Please contact the author if you discover any issues with file creation.
 
 module DICOM
   # Class for writing the data from DObject to a valid DICOM file:
   class DWrite
-    attr_writer :labels, :types, :lengths, :raw, :rest_endian, :rest_explicit
+    attr_writer :tags, :types, :lengths, :raw, :rest_endian, :rest_explicit
     attr_reader :success, :msg
-    
+
     # Initialize the DWrite instance.
     def initialize(file_name=nil, opts={})
       # Process option values, setting defaults for the ones that are not specified:
       @lib =  opts[:lib] || DLibrary.new
       @sys_endian = opts[:sys_endian] || false
       @file_name = file_name
-      
-      # Create arrays used for storing tag information:
-      @labels = Array.new
+
+      # Create arrays used for storing data element information:
+      @tags = Array.new
       @types = Array.new
       @lengths = Array.new
       @raw = Array.new
@@ -37,11 +35,11 @@ module DICOM
       # Endianness of the remaining groups after the first group:
       @rest_endian = false
     end # of method initialize
-    
-    
+
+
     # Writes the DICOM information to file.
     def write()
-      if @labels.size > 0
+      if @tags.size > 0
         # Check if we are able to create given file:
         open_file(@file_name)
         # Read the initial header of the file:
@@ -52,11 +50,11 @@ module DICOM
           write_header()
           # Write meta information (if it is not present in the DICOM object):
           write_meta()
-          # Write tags:
-          @labels.each_index do |i|
-            write_tag(i)
+          # Write data elements:
+          @tags.each_index do |i|
+            write_data_element(i)
           end
-          # We are finished writing the tags, and as such, can close the file:
+          # We are finished writing the data elements, and as such, can close the file:
           @file.close()
           # Mark this write session as successful:
           @success = true
@@ -66,15 +64,15 @@ module DICOM
           return
         end # of if @file != nil
       else
-        @msg += ["Error. No tags to write."]
-      end # of if @labels.size > 0
+        @msg += ["Error. No data elements to write."]
+      end # of if @tags.size > 0
     end # of method write
-    
-    
+
+
     # Following methods are private:
     private
-    
-    
+
+
     # Writes the official DICOM header:
     def write_header()
       # Fill in 128 empty bytes:
@@ -82,24 +80,24 @@ module DICOM
       # Write the string "DICM" which is central to DICOM standards compliance:
       @file.write("DICM")
     end # of write_header
-    
-    
+
+
     # Inserts group 0002 if it is missing, to ensure DICOM compliance.
     def write_meta()
       # We will check for the existance of 5 group 0002 elements, and if they are not present, we will insert them:
       pos = Array.new()
       meta = Array.new()
       # File Meta Information Version:
-      pos += [@labels.index("0002,0001")]
+      pos += [@tags.index("0002,0001")]
       meta += [["0002,0001", "OB", 2, ["0100"].pack("H*")]]
       # Transfer Syntax UID:
-      pos += [@labels.index("0002,0010")]
+      pos += [@tags.index("0002,0010")]
       meta += [["0002,0010", "UI", 18, ["1.2.840.10008.1.2"].pack("a*")+["00"].pack("H*")]] # Implicit, little endian
       # Implementation Class UID:
-      pos += [@labels.index("0002,0012")]
+      pos += [@tags.index("0002,0012")]
       meta += [["0002,0012", "UI", 26, ["1.2.826.0.1.3680043.8.641"].pack("a*")+["00"].pack("H*")]] # Ruby DICOM UID
       # Implementation Version Name:
-      pos += [@labels.index("0002,0013")]
+      pos += [@tags.index("0002,0013")]
       meta += [["0002,0013", "SH", 10, ["RUBY_DICOM"].pack("a*")]]
       # Insert meta information:
       meta_added = false
@@ -107,14 +105,14 @@ module DICOM
         # Only insert element if it does not already exist (corresponding pos element shows no match):
         if pos[i] == nil
           meta_added = true
-          # Find where to insert this data element
+          # Find where to insert this data element.
           index = -1
-          label = meta[i][0]
+          tag = meta[i][0]
           quit = false
           while quit != true do
-            if label < @labels[index+1]
+            if tag < @tags[index+1]
               quit = true
-            elsif @labels[index+1][0..3] != "0002"
+            elsif @tags[index+1][0..3] != "0002"
               # Abort to avoid needlessly going through the whole array.
               quit = true
             else
@@ -125,13 +123,13 @@ module DICOM
           # Insert data element in the correct array position:
           if index == -1
             # Insert at the beginning of array:
-            @labels = [meta[i][0]] + @labels
+            @tags = [meta[i][0]] + @tags
             @types = [meta[i][1]] + @types
             @lengths = [meta[i][2]] + @lengths
             @raw = [meta[i][3]] + @raw
           else
             # One or more elements comes before this element:
-            @labels = @labels[0..index] + [meta[i][0]] + @labels[(index+1)..(@labels.length-1)]
+            @tags = @tags[0..index] + [meta[i][0]] + @tags[(index+1)..(@tags.length-1)]
             @types = @types[0..index] + [meta[i][1]] + @types[(index+1)..(@types.length-1)]
             @lengths = @lengths[0..index] + [meta[i][2]] + @lengths[(index+1)..(@lengths.length-1)]
             @raw = @raw[0..index] + [meta[i][3]] + @raw[(index+1)..(@raw.length-1)]
@@ -143,86 +141,86 @@ module DICOM
       quit = false
       j = 0
       while quit == false do
-        if @labels[j][0..3] != "0002"
+        if @tags[j][0..3] != "0002"
           quit = true
         else
           # Add to length if group 0002:
-          if @labels[j] != "0002,0000"
+          if @tags[j] != "0002,0000"
             if @types[j] == "OB"
               length += 12 + @lengths[j]
             else
               length += 8 + @lengths[j]
             end
           end
-          j += 1 
-        end # of if @labels[j][0..3]..
+          j += 1
+        end # of if @tags[j][0..3]..
       end # of while
       # Set group length:
-      gl_pos = @labels.index("0002,0000")
+      gl_pos = @tags.index("0002,0000")
       gl_info = ["0002,0000", "UL", 4, [length].pack("I*")]
       # Update group length, but only if there have been some modifications or GL is nonexistant:
       if meta_added == true or gl_pos != nil
         if gl_pos == nil
           # Add group length (to beginning of arrays):
-          @labels = [gl_info[0]] + @labels
+          @tags = [gl_info[0]] + @tags
           @types = [gl_info[1]] + @types
           @lengths = [gl_info[2]] + @lengths
           @raw = [gl_info[3]] + @raw
         else
           # Edit existing group length:
-          @labels[gl_pos] = gl_info[0]
+          @tags[gl_pos] = gl_info[0]
           @types[gl_pos] = gl_info[1]
           @lengths[gl_pos] = gl_info[2]
           @raw[gl_pos] = gl_info[3]
         end
       end
     end # of method write_meta
-    
-    
-    # Writes the tags to file:
-    def write_tag(i)
-      # Step 1: Write label:
-      write_label(i)
+
+
+    # Writes each data element to file:
+    def write_data_element(i)
+      # Step 1: Write tag:
+      write_tag(i)
       # Step 2: Write [type] and value length:
       write_type_length(i)
       # Step 3: Write value:
       write_value(i)
       # If DICOM object contains encapsulated pixel data, we need some special handling for its items:
-      if @labels[i] == "7FE0,0010"
+      if @tags[i] == "7FE0,0010"
         @enc_image = true if @lengths[i].to_i == 0
       end
       # Should have some kind of test that the last data was written succesfully?
-    end # of method write_tag
-    
-    
-    # Writes the label (first part of the data element):
-    def write_label(i)
-      # Label is originally of the form 0002,0010.
+    end # of method write_data_element
+
+
+    # Writes the tag (first part of the data element):
+    def write_tag(i)
+      # Tag is originally of the form "0002,0010".
       # We need to reformat to get rid of the comma:
-      label = @labels[i][0..3] + @labels[i][5..8]
+      tag = @tags[i][0..3] + @tags[i][5..8]
       # Whether DICOM file is big or little endian, the first 0002 group is always little endian encoded.
       # On a big endian system, I believe the order of the numbers need not be changed,
       # but this has not been tested yet.
       if @sys_endian == false
         # System is little endian:
         # Change the order of the numbers so that it becomes correct when packed as hex:
-        label_corr = label[2..3] + label[0..1] + label[6..7] + label[4..5]
+        tag_corr = tag[2..3] + tag[0..1] + tag[6..7] + tag[4..5]
       end
       # When we shift from group 0002 to another group we need to update our endian/explicitness variables:
-      if label[0..3] != "0002" and @switched == false
+      if tag[0..3] != "0002" and @switched == false
         switch_syntax()
       end
-      # Perhaps we need to rearrange the labels if the file encoding is now big endian:
+      # Perhaps we need to rearrange the tag if the file encoding is now big endian:
       if not @endian
         # Need to rearrange the first and second part of each string:
-        label_corr = label
+        tag_corr = tag
       end
       # Write to file:
-      @file.write([label_corr].pack('H*'))
-    end # of method write_label
-    
-    
-    # Writes the type (if to be written) and length value (these two are the middle part of the data element):
+      @file.write([tag_corr].pack('H*'))
+    end # of method write_tag
+
+
+    # Writes the type (VR) (if it is to be written) and length value (these two are the middle part of the data element):
     def write_type_length(i)
       # First some preprocessing:
       # Set length value:
@@ -243,12 +241,12 @@ module DICOM
       # *****EXPLICIT*****:
       if @explicit == true
         # Step 1: Write VR (if it is to be written)
-        unless @labels[i] == "FFFE,E000" or @labels[i] == "FFFE,E00D" or @labels[i] == "FFFE,E0DD"
-          # Write tag type field (2 bytes - since we are not dealing with an item related tag):
+        unless @tags[i] == "FFFE,E000" or @tags[i] == "FFFE,E00D" or @tags[i] == "FFFE,E0DD"
+          # Write data element type (VR) (2 bytes - since we are not dealing with an item related element):
           @file.write([@types[i]].pack('a*'))
         end
         # Step 2: Write length
-        # Three possible structures for value length here, dependent on tag type:
+        # Three possible structures for value length here, dependent on data element type:
         case @types[i]
           when "OB","OW","SQ","UN"
             if @enc_image
@@ -264,11 +262,11 @@ module DICOM
             end
           when "()"
             # 4 bytes:
-            # For labels "FFFE,E000", "FFFE,E00D" and "FFFE,E0DD"
+            # For tags "FFFE,E000", "FFFE,E00D" and "FFFE,E0DD"
             @file.write(length4)
           else
             # 2 bytes:
-            # For all the other tag types, value length is 2 bytes:
+            # For all the other data element types, value length is 2 bytes:
             @file.write(length2)
         end # of case type
       else
@@ -278,15 +276,15 @@ module DICOM
         @file.write(length4)
       end # of if @explicit == true
     end # of method write_type_length
-    
-    
+
+
     # Writes the value (last part of the data element):
     def write_value(i)
       # This is pretty straightforward, just dump the binary data to the file:
       @file.write(@raw[i])
     end # of method write_value
-    
-    
+
+
     # Tests if the file is writable and opens it.
     def open_file(file)
       # Two cases: File already exists or it does not.
@@ -324,7 +322,7 @@ module DICOM
 
     # Changes encoding variables as the file writing proceeds past the initial 0002 group of the DICOM file.
     def switch_syntax()
-      # The information from the Transfer syntax tag (if present), needs to be processed:
+      # The information from the Transfer syntax element (if present), needs to be processed:
       process_transfer_syntax()
       # We only plan to run this method once:
       @switched = true
@@ -340,11 +338,11 @@ module DICOM
     end
 
 
-    # Checks the Transfer Syntax UID tag and updates class variables to prepare for correct writing of DICOM file.
+    # Checks the Transfer Syntax UID element and updates class variables to prepare for correct writing of DICOM file.
     def process_transfer_syntax()
-      ts_pos = @labels.index("0002,0010")
+      ts_pos = @tags.index("0002,0010")
       if ts_pos != nil
-        ts_value = @raw[ts_pos].unpack('a*').to_s.rstrip
+        ts_value = @raw[ts_pos].unpack('a*').join.rstrip
         valid = @lib.check_ts_validity(ts_value)
         if not valid
           @msg+=["Warning: Invalid/unknown transfer syntax! Will still write the file, but you should give this a closer look."]
@@ -375,8 +373,8 @@ module DICOM
         end # of case ts_value
       end # of if ts_pos != nil
     end # of method process_syntax
-  
-  
+
+
     # Sets the pack format strings that will be used for numbers depending on endianness of file/system.
     def set_pack_strings
       if @endian
@@ -401,14 +399,14 @@ module DICOM
         @fd = "G*"
       end
     end
-    
-    
+
+
     # Initializes the variables used when executing this program.
     def init_variables()
       # Variables that are accesible from outside:
       # Until a DICOM write has completed successfully the status is 'unsuccessful':
       @success = false
-      
+
       # Variables used internally:
       # Default explicitness of start of DICOM file:
       @explicit = true
@@ -424,9 +422,9 @@ module DICOM
       end
       # Set which format strings to use when unpacking numbers:
       set_pack_strings
-      # Items contained under the pixel data tag needs some special attention to write correctly:
+      # Items contained under the Pixel Data element needs some special attention to write correctly:
       @enc_image = false
     end # of method init_variables
-  
+
   end # of class
 end # of module

data/lib/Dictionary.rb

@@ -1,4 +1,6 @@
-#    Copyright 2008-2009 Christoffer Lerv�g
+# coding: ISO-8859-1
+
+#    Copyright 2008-2009 Christoffer Lervag
 
 module DICOM
   # This class holds all the dictionary data.
@@ -6,7 +8,7 @@ module DICOM
   class Dictionary
 
     # Loads the image type library (Photometric Interpretation).
-    # (Tag label: 0028,0004)
+    # (Data element tag: 0028,0004)
     def load_image_types()
       return [
       ["MONOCHROME1", "grey level image description (high values=dark, low values=bright)"],
@@ -58,7 +60,7 @@ module DICOM
     def load_uid()
       return [
       ["1.2.840.10008.1.1", "Verification SOP Class", "SOP Class"],
-      # Start: Transfer syntax (Tag label: 0002,0010)
+      # Start: Transfer syntax (Data element tag: 0002,0010)
       ["1.2.840.10008.1.2", "Implicit VR Little Endian: Default Transfer Syntax for DICOM", "Transfer Syntax"],
       ["1.2.840.10008.1.2.1", "Explicit VR Little Endian", "Transfer Syntax"],
       ["1.2.840.10008.1.2.1.99", "Deflated Explicit VR Little Endian", "Transfer Syntax"],
@@ -360,8 +362,8 @@ module DICOM
     end
 
 
-    # Tag data
-    def load_tags()
+    # Data element dictionary:
+    def load_data_elements()
       return [
       # E.1 Registry of DICOM command elements
       # Group 0000
@@ -2872,16 +2874,16 @@ module DICOM
       ["60xx,1500", ["LO"], "Overlay Label"],
       ["60xx,3000", ["OB","OW"], "Overlay Data"],
       ["60xx,4000", ["LT"], "Overlay Comments"],  # RET
-      # Pixel data and structural tags:
+      # Pixel data and structural data elements:
       ["7FE0,0010", ["OW","OB"], "Pixel Data"],
       ["FFFA,FFFA", ["SQ"], "Digital Signatures Sequence"],
       ["FFFC,FFFC", ["OB"], "Data Set Trailing Padding"],
-      ["FFFE,E000", ["()"], "Item"], # VR does not exist for this tag
-      ["FFFE,E00D", ["()"], "Item Delimitation Item"], # VR does not exist for this tag
-      ["FFFE,E0DD", ["()"], "Sequence Delimitation Item"] # VR does not exist for this tag
+      ["FFFE,E000", ["()"], "Item"], # VR does not exist for this element
+      ["FFFE,E00D", ["()"], "Item Delimitation Item"], # VR does not exist for this element
+      ["FFFE,E0DD", ["()"], "Sequence Delimitation Item"] # VR does not exist for this element
       ].transpose
-    end # End of method load_tags()
-    
-    
+    end # End of method load_data_elements()
+
+
   end # End of class
 end # End of module

data/lib/dicom.rb

@@ -4,5 +4,6 @@ require 'DLibrary'
 require 'DObject'
 require 'DRead'
 require 'DWrite'
+require 'ruby_extensions'
 # Extended library:
 require 'Anonymizer'