dicom 0.6.1 → 0.7

data/lib/{Anonymizer.rb → dicom/Anonymizer.rb}

@@ -1,4 +1,5 @@
-#    Copyright 2008-2009 Christoffer Lervag
+#    Copyright 2008-2010 Christoffer Lervag
+
 module DICOM
 
   # Class for anonymizing DICOM files:
@@ -6,21 +7,25 @@ module DICOM
   # ftp://medical.nema.org/medical/dicom/Supps/sup142_03.pdf
   class Anonymizer
 
-    attr_accessor :blank, :enumeration, :identity_file, :verbose, :write_path
+    attr_accessor :blank, :enumeration, :identity_file, :remove_private, :verbose, :write_path
 
     # Initialize the Anonymizer instance:
     def initialize(opts={})
       # Default verbosity is true: # NB: verbosity is not used currently
       @verbose = opts[:verbose]
       @verbose = true if @verbose == nil
-      # Load library:
-      @lib = DLibrary.new
       # Default value of accessors:
+      # Replace all values with a blank string?
       @blank = false
+      # Enumerate selected replacement values?
       @enumeration = false
+      # All private tags may be removed if desired:
+      @remove_private = false
+      # A separate path may be selected for writing the anonymized files:
       @write_path = nil
       # Array of folders to be processed for anonymization:
       @folders = Array.new
+      # Folders that will be skipped:
       @exceptions = Array.new
       # Data elements which will be anonymized (the array will hold a list of tag strings):
       @tags = Array.new
@@ -36,19 +41,23 @@ module DICOM
       # Write paths will be determined later and put in this array:
       @write_paths = Array.new
       # Set the default data elements to be anonymized:
-      set_defaults()
-    end # of method initialize
+      set_defaults
+    end
 
 
     # Adds a folder who's files will be anonymized:
     def add_folder(path)
-      @folders += [path] if path
+      @folders << path if path
     end
 
 
     # Adds an exception folder that is to be avoided when anonymizing:
     def add_exception(path)
-      @exceptions += [path] if path
+      if path
+        # Remove last character if the path ends with a file separator:
+        path.chop! if path[-1..-1] == File::SEPARATOR
+        @exceptions << path if path
+      end
     end
 
 
@@ -61,9 +70,9 @@ module DICOM
         if tag.is_a?(String)
           if tag.length == 9
             # Add anonymization information for this tag:
-            @tags += [tag]
-            @values += [value]
-            @enum += [enum]
+            @tags << tag
+            @values << value
+            @enum << enum
           else
             puts "Warning: Invalid tag length. Please use the form 'GGGG,EEEE'."
           end
@@ -73,7 +82,7 @@ module DICOM
       else
         puts "Warning: No tag supplied. Nothing to add."
       end
-    end # of method add_tag
+    end
 
 
     # Set enumeration status for a specific tag (toggle true/false)
@@ -88,7 +97,7 @@ module DICOM
       else
         puts "Specified tag not found in anonymization array. No changes made."
       end
-    end # of method change_enum
+    end
 
 
     # Changes the value used in anonymization for a specific tag:
@@ -103,7 +112,7 @@ module DICOM
       else
         puts "Specified tag not found in anonymization array. No changes made."
       end
-    end # of method change_value
+    end
 
 
     # Executes the anonymization process:
@@ -113,7 +122,7 @@ module DICOM
       puts "Initiating anonymization process."
       start_time = Time.now.to_f
       puts "Searching for files..."
-      load_files()
+      load_files
       puts "Done."
       if @files.length > 0
         if @tags.length > 0
@@ -121,7 +130,7 @@ module DICOM
           if @write_path
             # Determine the write paths, as anonymized files will be written to a separate location:
             puts "Processing write paths..."
-            process_write_paths()
+            process_write_paths
             puts "Done"
           else
             # Overwriting old files:
@@ -130,59 +139,71 @@ module DICOM
           end
           # If the user wants enumeration, we need to prepare variables for storing
           # existing information associated with each tag:
-          create_enum_hash() if @enumeration
+          create_enum_hash if @enumeration
           # Start the read/update/write process:
           puts "Initiating read/update/write process (This may take some time)..."
           # Monitor whether every file read/write was successful:
           all_read = true
           all_write = true
+          files_written = 0
+          files_failed_read = 0
           @files.each_index do |i|
             # Read existing file to DICOM object:
-            obj = DICOM::DObject.new(@files[i], :verbose => verbose, :lib => @lib)
+            obj = DICOM::DObject.new(@files[i], :verbose => verbose)
             if obj.read_success
               # Anonymize the desired tags:
               @tags.each_index do |j|
-                if @blank
-                  value = ""
-                elsif @enumeration
-                  # Get old value:
-                  current = obj.get_value(@tags[j])
-                  # Only launch enumeration logic if tag exists:
-                  if current != false
-                    value = get_enumeration_value(current, j)
-                  else
+                positions = obj.get_pos(@tags[j])
+                positions.each do |pos|
+                  if @blank
                     value = ""
+                  elsif @enumeration
+                    old_value = obj.get_value(pos, :silent => true)
+                    # Only launch enumeration logic if tag exists:
+                    if old_value
+                      value = get_enumeration_value(old_value, j)
+                    else
+                      value = ""
+                    end
+                  else
+                    # Value is simply value in array:
+                    value = @values[j]
                   end
-                else
-                  # Value is simply value in array:
-                  value = @values[j]
-                end # of if @blank..else..
-                # Update DICOM object with new value:
-                obj.set_value(value, @tags[j], :create => false)
+                  # Update DICOM object with new value:
+                  obj.set_value(value, pos, :create => false, :silent => true)
+                end
               end
+              # Remove private tags?
+              obj.remove_private if @remove_private
               # Write DICOM file:
               obj.write(@write_paths[i])
-              all_write = false unless obj.write_success
+              if obj.write_success
+                files_written += 1
+              else
+                all_write = false
+              end
             else
               all_read = false
+              files_failed_read += 1
             end
-          end # of @files.each...
+          end
+          # Finished anonymizing files. Print elapsed time and status of anonymization:
           end_time = Time.now.to_f
           puts "Anonymization process completed!"
           if all_read
             puts "All files in specified folder(s) were SUCCESSFULLY read to DICOM objects."
           else
-            puts "Some files were NOT successfully read. If folder(s) contain non-DICOM files, then this is probably the reason."
+            puts "Some files were NOT successfully read (#{files_failed_read} files). If folder(s) contain non-DICOM files, this is probably the reason."
           end
           if all_write
-            puts "All DICOM objects were SUCCESSFULLY written as DICOM files."
+            puts "All DICOM objects were SUCCESSFULLY written as DICOM files (#{files_written} files)."
           else
-            puts "Some DICOM objects were NOT succesfully written to file. You are advised to have a closer look."
+            puts "Some DICOM objects were NOT succesfully written to file. You are advised to have a closer look (#{files_written} files succesfully written)."
           end
           # Has user requested enumeration and specified an identity file in which to store the anonymized values?
           if @enumeration and @identity_file
             puts "Writing identity file."
-            write_identity_file()
+            write_identity_file
             puts "Done"
           end
           elapsed = (end_time-start_time).to_s
@@ -199,7 +220,7 @@ module DICOM
 
     # Prints a list of which tags are currently selected for anonymization along with
     # replacement values that will be used and enumeration status.
-    def print()
+    def print
       # Extract the string lengths which are needed to make the formatting nice:
       names = Array.new
       types = Array.new
@@ -208,9 +229,9 @@ module DICOM
       type_lengths = Array.new
       value_lengths = Array.new
       @tags.each_index do |i|
-        arr = @lib.get_name_vr(@tags[i])
-        names += [arr[0]]
-        types += [arr[1]]
+        arr = LIBRARY.get_name_vr(@tags[i])
+        names << arr[0]
+        types << arr[1]
         tag_lengths[i] = @tags[i].length
         name_lengths[i] = names[i].length
         type_lengths[i] = types[i].length
@@ -243,13 +264,13 @@ module DICOM
           value = @values[i]
         end
         tag = @tags[i]
-        lines += [tag + f1 + names[i] + f2 + types[i] + f3 + value.to_s + f4 + enum.to_s ]
+        lines << tag + f1 + names[i] + f2 + types[i] + f3 + value.to_s + f4 + enum.to_s
       end
       # Print to screen:
       lines.each do |line|
         puts line
       end
-    end # of method print_tags
+    end
 
 
     # Removes a tag from the list of tags that will be anonymized:
@@ -262,7 +283,7 @@ module DICOM
       else
         puts "Specified tag not found in anonymization array. No changes made."
       end
-    end # of method remove_tag
+    end
 
 
     # The following methods are private:
@@ -287,11 +308,11 @@ module DICOM
         result = index - 1
       end
       return result
-    end # of method common_path
+    end
 
 
     # Creates a hash that is used for storing information used when enumeration is desired.
-    def create_enum_hash()
+    def create_enum_hash
       @enum.each_index do |i|
         @enum_old_hash[@tags[i]] = Array.new
         @enum_new_hash[@tags[i]] = Array.new
@@ -311,23 +332,23 @@ module DICOM
           # Current value has not been encountered before:
           value = @values[j]+(p_index + 1).to_s
           # Store value in array (and hash):
-          previous_old += [current]
-          previous_new += [value]
+          previous_old << current
+          previous_new << value
           @enum_old_hash[@tags[j]] = previous_old
           @enum_new_hash[@tags[j]] = previous_new
         else
           # Current value has been observed before:
           value = previous_new[previous_old.index(current)]
-        end # of if previous.index...else..
+        end
       else
         value = @values[j]
-      end # of if @enum[j]..else..
+      end
       return value
-    end # of method handle_enumeration
+    end
 
 
     # Discover all the files contained in the specified directory and all its sub-directories:
-    def load_files()
+    def load_files
       # Load find library:
       require 'find'
       # Iterate through the folders (and its subfolders) to extract all files:
@@ -344,50 +365,50 @@ module DICOM
               Find.prune  # Don't look any further into this directory.
             end
           else
-            @files += [path]  # Store the file in our array
+            @files << path  # Store the file in our array
           end
         end
-      end # of for dir...
-    end # of method load_files
+      end
+    end
 
 
     # Analyses the write_path and the 'read' file path to determine if the have some common root.
     # If there are parts of file that exist also in write path, it will not add those parts to write_path.
-    def process_write_paths()
-      # First make sure @write_path ends with a "/":
-      last_character = @write_path[(@write_path.length-1)..(@write_path.length-1)]
-      @write_path = @write_path + "/" unless last_character == "/"
-      # Separate behaviour if we have one, or several files in our array:
+    def process_write_paths
+      # First make sure @write_path ends with a file separator character:
+      last_character = @write_path[-1..-1]
+      @write_path = @write_path + File::SEPARATOR unless last_character == File::SEPARATOR
+      # Differing behaviour if we have one, or several files in our array:
       if @files.length == 1
         # One file.
         # Write path is requested write path + old file name:
-        str_arr = @files[0].split("/")
-        @write_paths += [@write_path + str_arr.last]
+        str_arr = @files[0].split(File::SEPARATOR)
+        @write_paths << @write_path + str_arr.last
       else
         # Several files.
         # Find out how much of the path they have in common, remove that and
         # add the remaining to the @write_path:
-        str_arr = @files[0].split("/")
+        str_arr = @files[0].split(File::SEPARATOR)
         last_match_index = common_path(str_arr, 0)
         if last_match_index >= 0
           # Remove the matching folders from the path that will be added to @write_path:
           @files.each do |file|
-            arr = file.split("/")
-            part_to_write = arr[(last_match_index+1)..(arr.length-1)].join("/")
-            @write_paths += [@write_path + part_to_write]
+            arr = file.split(File::SEPARATOR)
+            part_to_write = arr[(last_match_index+1)..(arr.length-1)].join(File::SEPARATOR)
+            @write_paths << @write_path + part_to_write
           end
         else
           # No common folders. Add all of original path to write path:
           @files.each do |file|
-            @write_paths += [@write_path + file]
+            @write_paths << @write_path + file
           end
         end
-      end # of if @files.length..
-    end # of method process_write_paths
+      end
+    end
 
 
-    # Default tags that will be anonymized, along with some settings for each:
-    def set_defaults()
+    # Default tags that will be anonymized, along with default replacement value and enumeration setting.
+    def set_defaults
       data = [
       ["0008,0012", "20000101", false], # Instance Creation Date
       ["0008,0013", "000000.00", false], # Instance Creation Time
@@ -398,6 +419,7 @@ module DICOM
       ["0008,0080", "Institution", true], # Institution name
       ["0008,0090", "Physician", true], # Referring Physician's name
       ["0008,1010", "Station", true], # Station name
+      ["0008,1070", "Operator", true], # Operator's Name
       ["0010,0010", "Patient", true], # Patient's name
       ["0010,0020", "ID", true], # Patient's ID
       ["0010,0030", "20000101", false], # Patient's Birth Date
@@ -407,12 +429,12 @@ module DICOM
       @tags = data[0]
       @values = data[1]
       @enum = data[2]
-    end # of method set_defaults
+    end
 
 
     # Writes an identity file, which allows reidentification of DICOM files that have been anonymized
     # using the enumeration feature. Values will be saved in a text file, using semi colon delineation.
-    def write_identity_file()
+    def write_identity_file
       # Open file and prepare to write text:
       File.open( @identity_file, 'w' ) do |output|
         # Cycle through each
@@ -428,10 +450,10 @@ module DICOM
             end
             # Print empty line for separation between different tags:
             output.print "\n"
-          end # of if @enum[i]
-        end # of @tags.each...
-      end # of File.open...
-    end # of method write...
+          end
+        end
+      end
+    end
 
 
   end # of class

data/lib/{DClient.rb → dicom/DClient.rb}

@@ -1,4 +1,4 @@
-#    Copyright 2009 Christoffer Lervag
+#    Copyright 2009-2010 Christoffer Lervag
 
 module DICOM
 
@@ -16,7 +16,6 @@ module DICOM
       @port = port
       # Optional parameters (and default values):
       @ae =  options[:ae]  || "RUBY_DICOM"
-      @lib =  options[:lib]  || DLibrary.new
       @host_ae =  options[:host_ae]  || "DEFAULT"
       @max_package_size = options[:max_package_size] || 32768 # 16384
       @timeout = options[:timeout] || 10 # seconds
@@ -139,7 +138,7 @@ module DICOM
     # Send a DICOM file to a service class provider (SCP/PACS).
     def send(file_path)
       # Load the DICOM file from the specified path:
-      obj = DObject.new(file_path, :verbose => false, :lib => @lib)
+      obj = DObject.new(file_path, :verbose => false)
       if obj.read_success
         # Get the SOP Class UID (abstract syntax) from the DICOM obj:
         @abstract_syntax = obj.get_value("0008,0016")
@@ -219,7 +218,7 @@ module DICOM
       @link.build_association_request(@application_context_uid, @abstract_syntax, @transfer_syntax, @user_information)
       @connection = TCPSocket.new(@host_ip, @port)
       @link.transmit(@connection)
-      info = @link.receive_single_transmission(@connection).first
+      info = @link.receive_multiple_transmissions(@connection).first
       # Interpret the results:
       if info[:valid]
         if info[:pdu] == "02"
@@ -309,9 +308,11 @@ module DICOM
           @link.build_data_fragment(@data_elements) # (uses flag = 02)
           @link.transmit(@connection)
           # Listen for incoming file data:
-          @link.handle_incoming_data(@connection, path)
-          # Send confirmation response:
-          @link.handle_response(@connection)
+          success = @link.handle_incoming_data(@connection, path)
+          if success
+            # Send confirmation response:
+            @link.handle_response(@connection)
+          end
         end
         # Close the DICOM link:
         establish_release
@@ -409,7 +410,7 @@ module DICOM
       @command_elements = [
         ["0000,0002", "UI", @abstract_syntax], # Affected SOP Class UID
         ["0000,0100", "US", 16], # Command Field: 16 (C-GET-RQ)
-        ["0000,0600", "AE", destination], # Move destination
+        ["0000,0600", "AE", @ae], # Destination is ourselves
         ["0000,0700", "US", 0], # Priority: 0: medium
         ["0000,0800", "US", 1] # Data Set Type: 1
       ]
@@ -570,12 +571,12 @@ module DICOM
     end
 
 
-    # Set user information [item type code, vr/type, value]
+    # Set user information [item type code, VR, value]
     def set_user_information_array
       @user_information = [
         ["51", "UL", @max_package_size], # Max PDU Length
-        ["52", "STR", "1.2.826.0.1.3680043.8.641"], # Implementation UID
-        ["55", "STR", "RUBY_DICOM"] # Implementation Version
+        ["52", "STR", UID], # Implementation UID
+        ["55", "STR", NAME] # Implementation Version (Name & version)
       ]
     end