dicom 0.6 → 0.6.1

data/CHANGELOG

@@ -1,3 +1,14 @@
+= 0.6.1
+
+=== 23rd August, 2009
+
+* Fixed a bug (introduced in version 0.6) where the creation of new data elements caused an error.
+* Fixed a bug (introduced in version 0.6) where compressed pixel data were no longer detected correctly.
+* Fixed a bug where writing a DICOM file with no path prefix failed.
+* Fixed a bug where creating a new data element in a DICOM file with tag hierarchies gave an invalid DICOM file.
+* Fixed a bug where retrieving a RMagick image from DICOM files containing two sets of image data failed.
+
+
 = 0.6
 
 === 13th August, 2009

data/DOCUMENTATION

@@ -16,240 +16,240 @@ CLASS DLibrary
 
 PUBLIC CLASS METHODS
 
-	new()
+  new()
 
-		Initialize a new Library (dictionary) object.
-		Useful if you want to make a script that reads hundreds or thousands of DICOM files,
-		because you can save time by loading the library one time at startup instead of
-		having the library being loaded for each DICOM file being read.
-		Example:
-			myLib = DICOM::DLibrary.new
+    Initialize a new Library (dictionary) object.
+    Useful if you want to make a script that reads hundreds or thousands of DICOM files,
+    because you can save time by loading the library one time at startup instead of
+    having the library being loaded for each DICOM file being read.
+    Example:
+      myLib = DICOM::DLibrary.new
 
 
 CLASS DObject
 
 PUBLIC CLASS METHODS
 
-	new(filename, options={})
+  new(filename, options={})
 
-		Initialize a new DICOM object.
-		Example 1: (The simplest way)
-			require 'dicom'
-			obj = DICOM::DObject.new("myFile.dcm")
-		Example 2: (Using a pre-loaded library to speed up reading when reading multiple files)
-			obj = DICOM::DObject.new("myFile.dcm", :verbose => false, :lib => myLib)
-		Example 3: (Open an empty DICOM object)
-			obj = DICOM::DObject.new(nil)
+    Initialize a new DICOM object.
+    Example 1: (The simplest way)
+      require 'dicom'
+      obj = DICOM::DObject.new("myFile.dcm")
+    Example 2: (Using a pre-loaded library to speed up reading when reading multiple files)
+      obj = DICOM::DObject.new("myFile.dcm", :verbose => false, :lib => myLib)
+    Example 3: (Open an empty DICOM object)
+      obj = DICOM::DObject.new(nil)
 
 ACCESSORS (read only)
-	:read_success
-		A boolean that is true if DICOM object was read successfully, and false if not.
-	:write_success
-		A boolean that is true if DICOM object was written successfully, and false if not.
-	:errors
-		An array holding any error messages, warnings or notices that have been logged
-		during your interaction with DObject.
-	:modality
-		A string which holds the description of the modality of the DICOM object that has been read.
-		Example of use:
-			obj = DICOM::DObject.new("myFile.dcm")
-			if obj.read_success
-			  puts obj.modality
-			end
-	The following accessors are the arrays that hold all the information gathered on the DICOM object.
-	As such, their length is equal to the number of tags in a DICOM object.
-	:names
-	:tags
-	:types
-	:lengths
-	:values
-	:raw
-	:levels
+  :read_success
+    A boolean that is true if DICOM object was read successfully, and false if not.
+  :write_success
+    A boolean that is true if DICOM object was written successfully, and false if not.
+  :errors
+    An array holding any error messages, warnings or notices that have been logged
+    during your interaction with DObject.
+  :modality
+    A string which holds the description of the modality of the DICOM object that has been read.
+    Example of use:
+      obj = DICOM::DObject.new("myFile.dcm")
+      if obj.read_success
+        puts obj.modality
+      end
+  The following accessors are the arrays that hold all the information gathered on the DICOM object.
+  As such, their length is equal to the number of tags in a DICOM object.
+  :names
+  :tags
+  :types
+  :lengths
+  :values
+  :raw
+  :levels
 
 PUBLIC INSTANCE METHODS
 
-	children(element, options={})
-		Returns the positions of all data elements inside the hierarchy of a sequence or an item.
-		This is useful if you later want to get the position(s) of a certain element,
-		restricted to the positions inside the given sequence or item.
-		Element may be an array index, element name or element tag.
-		Example 1: (Return all element positions that is contained in the following sequence)
-			pos = obj.children("3006,0082")
-		Example 2: (Return all element positions that is contained only directly beneath the following sequence)
-			pos = obj.children("3006,0082", :next_only => true)
-
-	get_frames
-		Returns the number of frames present in the image data in the DICOM file.
-
-	get_image_magick
-		Returns an array of RMagick image objects, where the size of the array corresponds
-		with the number of frames in the image data.
-		To call this method the user needs to have loaded the RMagick bindings in advance (require 'RMagick').
-		Example (retrieve object and display first frame):
-		require 'RMagick'
-		data = dicom.get_image_magick()
-		data[0].display
-
-	get_image_narray
-		Returns a 3d NArray object where the array dimensions are related to [frames, columns, rows].
-		To call this method the user needs to have loaded the NArray library in advance (require 'narray').
-		Example (retrieve object and display first frame):
-			require 'narray'
-			require 'nimage'
-			data = obj.get_image_narray()
-			NImage.show data[0,true,true]
-
-	get_image_pos
-		Returns the index(es) of the data element(s) that contain image data.
-
-	get_pos(string, options={})
-		Returns the index(es) of the data element(s) in the DICOM file that match
-		the supplied element tag or name.
-		Example 1: (Find all occurences of the specified tag in the object)
-			pos = obj.get_pos("3006,0080")
-		Example 2: (Find all occurences of the specified tag inside the specified sequence)
-			selection = obj.children("3006,0082")
-			pos = obj.get_pos("3006,0080", :array => selection)
-		Example 3: (Using the :partial argument to find position of all elements containing a specific string)
-			pos = obj.get_pos("0010", :partial => true)
-			pos = obj.get_pos("Name", :partial => true)
-
-	get_raw(element, options={})
-		Returns the raw data of the requested DICOM data element.
-		Element may be an array index, element name or element tag.
-		If you wish to return multiple data values of a tag that occurs several times in the file,
-		use the keyword :array => true .
-		Example: (Returns all data values in a array)
-			contour_data = obj.get_raw("3006,0050", :array => true)
-
-	get_value(element)
-		Returns the value (processed raw data) of the requested DICOM data element.
-		Element may be an array index, element name or element tag.
-		If you wish to return multiple values of a tag that occurs several times in the file,
-		use the keyword :array => true .
-		Example: (Returns all data values in a array)
-			contour_data = obj.get_value("3006,0050", :array => true)
-
-	image_to_file(file)
-		Dumps the pixel data of the DICOM object directly to the specified file.
-		This is useful if you wish to extract this data to process it with another program.
-
-	parents(element)
-		Returns the positions of all parents of this tag in the hierarchy.
-		This is useful if you want to know the position of the items or sequence tags that 'hold' your tag.
-		Element may be an array index, element name or element tag.
-		Example:
-			pos = obj.parents("300C,0006")
-
-	print(pos, options={})
-		Prints the information gathered on one or several/all tag(s) in the DICOM object:
-			(index, [hierarchy level,] label, name, type, length, value)
-		The method can print to both screen or to a text file. If print to file is chosen,
-		the text file will be put in the folder of the original DICOM file with a '.txt' extension.
-		The argument pos may be a number (array position), an array of numbers, or true.
-		Example 1: (Print all tags to file, with both tree visualization and level numbers)
-			obj.print(true, :levels => true, :tree => true, :file => true)
-		Example 2: (Print an array of tags to screen, no level or tree visualization)
-			obj.print([4,5,6])
-
-	print_all
-		Prints information of all tags stored in the DICOM object to the screen.
-
-	print_properties
-		Prints the key structural properties of the DICOM file to the screen.
-
-	remove(element)
-		Removes the specified data element from the DICOM object. You can use this method
-		if you are editing a DICOM object and wants to get rid of one or more elements.
-		Element may be an array index, element name or element tag.
-
-	set_value(value, element, options={})
-		This method can be used both to edit an existing data element, or to create
-		new data elements in your DICOM object.
-		Element may be an array index, element name or element tag.
-		Example 1: (Edit patient name)
-			obj.set_value("Anonymous", "0010,0010", :create => false)
-		Example 2: (Insert binary data for a specific tag)
-			obj.set_value(data, 52, :bin => true, :create => false)
-
-	set_image_magick(object)
-		Inserts a RMagick image object to the pixel data tag of your DICOM object.
-
-	set_image_file(file)
-		Inserts the binary content of a file to the Pixel Data tag in your DICOM object.
-		This can be useful if you have processed some image data using a custom program
-		and just wants to put that data back into a DICOM object.
-
-	write(file)
-		Writes the DICOM object to the specified file.
-		Example:
-			obj.write(myPath + "test_file.dcm")
+  children(element, options={})
+    Returns the positions of all data elements inside the hierarchy of a sequence or an item.
+    This is useful if you later want to get the position(s) of a certain element,
+    restricted to the positions inside the given sequence or item.
+    Element may be an array index, element name or element tag.
+    Example 1: (Return all element positions that is contained in the following sequence)
+      pos = obj.children("3006,0082")
+    Example 2: (Return all element positions that is contained only directly beneath the following sequence)
+      pos = obj.children("3006,0082", :next_only => true)
+
+  get_frames
+    Returns the number of frames present in the image data in the DICOM file.
+
+  get_image_magick
+    Returns an array of RMagick image objects, where the size of the array corresponds
+    with the number of frames in the image data.
+    To call this method the user needs to have loaded the RMagick bindings in advance (require 'RMagick').
+    Example (retrieve object and display first frame):
+    require 'RMagick'
+    data = dicom.get_image_magick()
+    data[0].display
+
+  get_image_narray
+    Returns a 3d NArray object where the array dimensions are related to [frames, columns, rows].
+    To call this method the user needs to have loaded the NArray library in advance (require 'narray').
+    Example (retrieve object and display first frame):
+      require 'narray'
+      require 'nimage'
+      data = obj.get_image_narray()
+      NImage.show data[0,true,true]
+
+  get_image_pos
+    Returns the index(es) of the data element(s) that contain image data.
+
+  get_pos(string, options={})
+    Returns the index(es) of the data element(s) in the DICOM file that match
+    the supplied element tag or name.
+    Example 1: (Find all occurences of the specified tag in the object)
+      pos = obj.get_pos("3006,0080")
+    Example 2: (Find all occurences of the specified tag inside the specified sequence)
+      selection = obj.children("3006,0082")
+      pos = obj.get_pos("3006,0080", :array => selection)
+    Example 3: (Using the :partial argument to find position of all elements containing a specific string)
+      pos = obj.get_pos("0010", :partial => true)
+      pos = obj.get_pos("Name", :partial => true)
+
+  get_raw(element, options={})
+    Returns the raw data of the requested DICOM data element.
+    Element may be an array index, element name or element tag.
+    If you wish to return multiple data values of a tag that occurs several times in the file,
+    use the keyword :array => true .
+    Example: (Returns all data values in a array)
+      contour_data = obj.get_raw("3006,0050", :array => true)
+
+  get_value(element)
+    Returns the value (processed raw data) of the requested DICOM data element.
+    Element may be an array index, element name or element tag.
+    If you wish to return multiple values of a tag that occurs several times in the file,
+    use the keyword :array => true .
+    Example: (Returns all data values in a array)
+      contour_data = obj.get_value("3006,0050", :array => true)
+
+  image_to_file(file)
+    Dumps the pixel data of the DICOM object directly to the specified file.
+    This is useful if you wish to extract this data to process it with another program.
+
+  parents(element)
+    Returns the positions of all parents of this tag in the hierarchy.
+    This is useful if you want to know the position of the items or sequence tags that 'hold' your tag.
+    Element may be an array index, element name or element tag.
+    Example:
+      pos = obj.parents("300C,0006")
+
+  print(pos, options={})
+    Prints the information gathered on one or several/all tag(s) in the DICOM object:
+      (index, [hierarchy level,] label, name, type, length, value)
+    The method can print to both screen or to a text file. If print to file is chosen,
+    the text file will be put in the folder of the original DICOM file with a '.txt' extension.
+    The argument pos may be a number (array position), an array of numbers, or true.
+    Example 1: (Print all tags to file, with both tree visualization and level numbers)
+      obj.print(true, :levels => true, :tree => true, :file => true)
+    Example 2: (Print an array of tags to screen, no level or tree visualization)
+      obj.print([4,5,6])
+
+  print_all
+    Prints information of all tags stored in the DICOM object to the screen.
+
+  print_properties
+    Prints the key structural properties of the DICOM file to the screen.
+
+  remove(element)
+    Removes the specified data element from the DICOM object. You can use this method
+    if you are editing a DICOM object and wants to get rid of one or more elements.
+    Element may be an array index, element name or element tag.
+
+  set_value(value, element, options={})
+    This method can be used both to edit an existing data element, or to create
+    new data elements in your DICOM object.
+    Element may be an array index, element name or element tag.
+    Example 1: (Edit patient name)
+      obj.set_value("Anonymous", "0010,0010", :create => false)
+    Example 2: (Insert binary data for a specific tag)
+      obj.set_value(data, 52, :bin => true, :create => false)
+
+  set_image_magick(object)
+    Inserts a RMagick image object to the pixel data tag of your DICOM object.
+
+  set_image_file(file)
+    Inserts the binary content of a file to the Pixel Data tag in your DICOM object.
+    This can be useful if you have processed some image data using a custom program
+    and just wants to put that data back into a DICOM object.
+
+  write(file)
+    Writes the DICOM object to the specified file.
+    Example:
+      obj.write(myPath + "test_file.dcm")
 
 
 CLASS Anonymizer
 
 PUBLIC CLASS METHODS
 
-	new()
-		Initialize a new Anonymizer instance.
-		Example:
-			a = DICOM::Anonymizer.new
+  new()
+    Initialize a new Anonymizer instance.
+    Example:
+      a = DICOM::Anonymizer.new
 
 ACCESSORS (Read & write)
-	:blank
-		A boolean that you can set if you want to all anonymization tags to be blank
-		instead of having some generic value.
-	:enumeration
-		A boolean that if set will make the script set enumerated values on anonymized tags,
-		such that you are able to separate the DICOM files of unique individuals after anonymization.
-		Example of fictious result:
-			"Joe Sixpack" => "Person1" and "Joe Schmoe" => "Person2"
-	:identity_file
-		If you request enumeration, you can specify an identity file which will enable you to reidentify
-		the anonymized DICOM files at a later stage. The relationship between original names and
-		enumerated values is stored in a text file which you can keep for yourself, while handing out
-		the anonymized DICOM files to a third party.
-
-	:write_path
-		You may set a different path for where the anonymized DICOM files will be stored. If this
-		value is not set, the Anonymizer script will overwrite the old DICOM files.
-		Example:
-			a.write_path = "C:/temp/"
+  :blank
+    A boolean that you can set if you want to all anonymization tags to be blank
+    instead of having some generic value.
+  :enumeration
+    A boolean that if set will make the script set enumerated values on anonymized tags,
+    such that you are able to separate the DICOM files of unique individuals after anonymization.
+    Example of fictious result:
+      "Joe Sixpack" => "Person1" and "Joe Schmoe" => "Person2"
+  :identity_file
+    If you request enumeration, you can specify an identity file which will enable you to reidentify
+    the anonymized DICOM files at a later stage. The relationship between original names and
+    enumerated values is stored in a text file which you can keep for yourself, while handing out
+    the anonymized DICOM files to a third party.
+
+  :write_path
+    You may set a different path for where the anonymized DICOM files will be stored. If this
+    value is not set, the Anonymizer script will overwrite the old DICOM files.
+    Example:
+      a.write_path = "C:/temp/"
 
 PUBLIC INSTANCE METHODS
 
-	add_folder(path)
-		Adds a folder who's files (including all files in subfolders) will be anonymized.
-		Example:
-			a.add_folder("/home/dicom")
+  add_folder(path)
+    Adds a folder who's files (including all files in subfolders) will be anonymized.
+    Example:
+      a.add_folder("/home/dicom")
 
-	add_exception(path)
-		Adds a folder who's files (including all files in its subfolders) will be excluded from anonymization.
+  add_exception(path)
+    Adds a folder who's files (including all files in its subfolders) will be excluded from anonymization.
 
-	add_tag(tag, options={})
-		Adds a tag to the list of tags that will be anonymized. As options you can specify value to be used
-		and whether the tag should be included for enumeration if this feature has been activated.
-		Example:
-			a.add_tag("0010,0010, :value => "MrAnonymous", :enum => true)
+  add_tag(tag, options={})
+    Adds a tag to the list of tags that will be anonymized. As options you can specify value to be used
+    and whether the tag should be included for enumeration if this feature has been activated.
+    Example:
+      a.add_tag("0010,0010, :value => "MrAnonymous", :enum => true)
 
-	change_enum(tag, status)
-		Sets enumeration status for a specific tag. Status = true means the selected tag will get
-		an enumerated value, false means it will not.
+  change_enum(tag, status)
+    Sets enumeration status for a specific tag. Status = true means the selected tag will get
+    an enumerated value, false means it will not.
 
-	execute(verbose)
-		Executes the anonymization process. Run this method when you are finished choosing all your settings.
-		Verbose (=true/false) will apply to the read/update/write process that takes place in DObject, and not
-		the messages of the Anonymization script itself.
+  execute(verbose)
+    Executes the anonymization process. Run this method when you are finished choosing all your settings.
+    Verbose (=true/false) will apply to the read/update/write process that takes place in DObject, and not
+    the messages of the Anonymization script itself.
 
-	print
-		Prints the list of tags that have been selected for anonymization, along with the values
-		that the original tags will be replaced with. If enumeration is selected, this method will also
-		print which tags have been selected for enumeration.
+  print
+    Prints the list of tags that have been selected for anonymization, along with the values
+    that the original tags will be replaced with. If enumeration is selected, this method will also
+    print which tags have been selected for enumeration.
 
-	remove_tag(tag)
-		Removes a tag from the list of tags that will be anonymized.
-		Example:
-			a.remove_tag("0010,0010")
+  remove_tag(tag)
+    Removes a tag from the list of tags that will be anonymized.
+    Example:
+      a.remove_tag("0010,0010")
 
 
 CLASS DClient
@@ -289,7 +289,7 @@ ACCESSORS (Read only)
 PUBLIC INSTANCE METHODS
 
   get_image(path, options={})
-    Retrieve a DICOM image file from a server (C-GET-RQ) (this method is probably not working yet).
+    Retrieve a DICOM image file from a server (C-GET-RQ) (this method is untested (might not work)).
     Accepted options:
       "0008,0018" (SOP Instance UID)
       "0008,0052" (Query/Retrieve Level)
@@ -307,7 +307,7 @@ PUBLIC INSTANCE METHODS
       "0020,000E" (Series Instance UID)
       "0020,0013" (Instance Number)
     Example:
-      find_images("0010,0020" => patient_id, "0020,000D" => study_uid, "0020,000E" => series_uid)
+      result = node.find_images("0010,0020" => patient_id, "0020,000D" => study_uid, "0020,000E" => series_uid)
 
   find_patients(options={})
     Query a server for patients that matches your specified criteria.
@@ -318,7 +318,7 @@ PUBLIC INSTANCE METHODS
       "0010,0030" (Patient's Birth Date)
       "0010,0040" (Patient's Sex)
     Example:
-      find_patients("0010,0010" => "James*")
+      result = node.find_patients("0010,0010" => "James*")
 
   find_series(options={})
     Query a server for series that matches your specified criteria.
@@ -330,7 +330,7 @@ PUBLIC INSTANCE METHODS
       "0020,000E" (Series Instance UID)
       "0020,0011" (Series Number)
     Example:
-      find_series("0010,0020" => patient_id, "0020,000D" => study_uid)
+      result = node.find_series("0010,0020" => patient_id, "0020,000D" => study_uid)
 
   find_studies(options={})
     Query a server for studies that matches your specified criteria.
@@ -349,7 +349,7 @@ PUBLIC INSTANCE METHODS
       "0020,000D" (Study Instance UID)
       "0020,0010" (Study ID)
     Example:
-      find_studies("0008,0020" => study_date, "0010,000D" => patient_id)
+      result = node.find_studies("0008,0020" => study_date, "0010,000D" => patient_id)
 
   move_image(destination, options={})
     Move an image to a dicom node other than yourself.
@@ -359,7 +359,7 @@ PUBLIC INSTANCE METHODS
       "0020,000D" (Study Instance UID)
       "0020,000E" (Series Instance UID)
     Example:
-      move_image("MYDICOM", "0008,0018" => sop_uid, "0020,000D" => study_uid, "0020,000E" => series_uid)
+      node.move_image("MYDICOM", "0008,0018" => sop_uid, "0020,000D" => study_uid, "0020,000E" => series_uid)
 
   move_study(destination, options={})
     Move an entire study to a dicom node other than yourself.
@@ -368,12 +368,12 @@ PUBLIC INSTANCE METHODS
       "0010,0020" (Patient ID)
       "0020,000D" (Study Instance UID)
     Example:
-      move_study("MYDICOM", "0010,0020" => patient_id, "0020,000D" => study_uid)
+      node.move_study("MYDICOM", "0010,0020" => patient_id, "0020,000D" => study_uid)
 
   send(file_path)
     Send a DICOM file to a service class provider (SCP/PACS).
     Example:
-      send("myFile.dcm")
+      node.send("myFile.dcm")
 
   test
     Tests a connection with your DICOM server by trying a simple association.
@@ -386,7 +386,7 @@ PUBLIC CLASS METHODS
   new(port, options={})
     Initialize a new DServer instance.
     Example:
-      node = DICOM::DServer.new(104)
+      server = DICOM::DServer.new(104)
 
 ACCESSORS (Read & write)
   :host_ae
@@ -420,4 +420,4 @@ PUBLIC INSTANCE METHODS
     Completely clears the list of syntaxes that the server instance will accept.
 
   start_scp(path)
-    Launch the simple storage server (Storage Content Provider - SCP)
+    Launch the simple storage server (Storage Content Provider - SCP).

data/lib/DClient.rb

@@ -42,20 +42,6 @@ module DICOM
     end
 
 
-    # Retrieve a dicom file from a service class provider (SCP/PACS).
-    # Example:  get_image("c:/dicom/", "0008,0018" => sop_uid, "0020,000D" => study_uid, "0020,000E" => series_uid)
-    def get_image(path, options={})
-      # Study Root Query/Retrieve Information Model - GET:
-      @abstract_syntax = "1.2.840.10008.5.1.4.1.2.2.3"
-      # Transfer the current options to the data_elements hash:
-      set_command_fragment_get
-      # Prepare data elements for this operation:
-      set_data_fragment_get_image
-      set_data_options(options)
-      perform_get(path)
-    end
-
-
     # Query a service class provider for images that match the specified criteria.
     # Example:   find_images("0010,0020" => "123456789", "0020,000D" => "1.2.840.1145.342", "0020,000E" => "1.3.6.1.4.1.2452.6.687844") # (Patient ID, Study Instance UID & Series Instance UID)
     def find_images(options={})
@@ -65,6 +51,7 @@ module DICOM
       set_data_fragment_find_images
       set_data_options(options)
       perform_find
+      return @data_results
     end
 
 
@@ -77,6 +64,7 @@ module DICOM
       set_data_fragment_find_patients
       set_data_options(options)
       perform_find
+      return @data_results
     end
 
 
@@ -89,6 +77,7 @@ module DICOM
       set_data_fragment_find_series
       set_data_options(options)
       perform_find
+      return @data_results
     end
 
 
@@ -101,6 +90,21 @@ module DICOM
       set_data_fragment_find_studies
       set_data_options(options)
       perform_find
+      return @data_results
+    end
+
+
+    # Retrieve a dicom file from a service class provider (SCP/PACS).
+    # Example:  get_image("c:/dicom/", "0008,0018" => sop_uid, "0020,000D" => study_uid, "0020,000E" => series_uid)
+    def get_image(path, options={})
+      # Study Root Query/Retrieve Information Model - GET:
+      @abstract_syntax = "1.2.840.10008.5.1.4.1.2.2.3"
+      # Transfer the current options to the data_elements hash:
+      set_command_fragment_get
+      # Prepare data elements for this operation:
+      set_data_fragment_get_image
+      set_data_options(options)
+      perform_get(path)
     end
 
 

data/lib/DLibrary.rb

@@ -26,6 +26,36 @@ module DICOM
     end
 
 
+    # Checks whether a given string is a valid transfer syntax or not.
+    def check_ts_validity(uid)
+      result = false
+      value = @uid[uid.rstrip]
+      if value != nil
+        if value[1] == "Transfer Syntax"
+          # Proved valid:
+          result = true
+        end
+      end
+      return result
+    end
+
+
+    # Checks if the supplied transfer syntax indicates the presence of pixel compression or not.
+    def get_compression(uid)
+      result = false
+      if uid
+        value = @uid[uid.rstrip]
+        if value != nil
+          if value[1] == "Transfer Syntax" and not value[0].include?("Endian")
+            # It seems we have compression:
+            result = true
+          end
+        end
+      end
+      return result
+    end
+
+
     # Returns data element name and value representation from the dictionary if the data element
     # is recognized, else it returns "Unknown Name" and "UN".
     def get_name_vr(tag)
@@ -91,20 +121,6 @@ module DICOM
     end
 
 
-    # Checks whether a given string is a valid transfer syntax or not.
-    def check_ts_validity(uid)
-      result = false
-      value = @uid[uid.rstrip]
-      if value != nil
-        if value[1] == "Transfer Syntax"
-          # Proved valid:
-          result = true
-        end
-      end
-      return result
-    end
-
-
     # Returns the name/description corresponding to a given UID.
     def get_uid(uid)
       value = @uid[uid.rstrip]
@@ -118,22 +134,6 @@ module DICOM
     end
 
 
-    # Checks if the supplied transfer syntax indicates the presence of pixel compression or not.
-    def get_compression(uid)
-      result = false
-      if uid
-        value = @uid[uid.rstrip]
-        if value != nil
-          if value[1] == "Transfer Syntax" and not value[0].include?("Endian")
-            # It seems we have compression:
-            res = true
-          end
-        end
-      end
-      return result
-    end
-
-
     # Checks the Transfer Syntax UID and return the encoding settings associated with this value.
     def process_transfer_syntax(value)
       valid = check_ts_validity(value)
@@ -160,8 +160,8 @@ module DICOM
           # For everything else, assume compressed pixel data, with Explicit VR, Little Endian:
           explicit = true
           endian = false
-        end
-        return [valid, explicit, endian]
+      end
+      return [valid, explicit, endian]
     end
 
 

data/lib/DObject.rb

@@ -24,11 +24,11 @@
 # -Support for color image data to get_image_narray and get_image_magick.
 # -Complete support for Big endian (basic support is already featured).
 # -Complete support for multiple frame image data to NArray and RMagick objects (partial support already featured).
-# -Reading of image data in files that contain two different and unrelated images (this problem has been observed with some MR images).
+# -Make the image handling more intelligent with respect to interpreting data elements that hold information on the image and its properties.
 
 module DICOM
 
-  # Class for handling the DICOM contents:
+  # Class for interacting with the DICOM object.
   class DObject
 
     attr_reader :read_success, :write_success, :modality, :errors, :segments,
@@ -172,9 +172,9 @@ module DICOM
         add_msg("Error: Method read_image_magick does not have enough data available to build an image object.")
         return false
       end
-      if @compression != true
+      unless @compression
         # Non-compressed, just return the array contained on the particular element:
-        image_data=get_pixels(pos)
+        image_data = get_pixels(pos)
         image = Magick::Image.new(columns,rows)
         image.import_pixels(0, 0, columns, rows, "I", image_data)
         return image
@@ -192,7 +192,7 @@ module DICOM
 
 
     # Returns a 3d NArray object where the array dimensions are related to [frames, columns, rows].
-		# To call this method the user needs to have performed " require 'narray' " in advance.
+    # To call this method the user needs to have performed " require 'narray' " in advance.
     def get_image_narray
       # Does pixel data exist at all in the DICOM object?
       if @compression == nil
@@ -256,48 +256,46 @@ module DICOM
     end # of get_image_narray
 
 
-    # Returns an array of RMagick image objects, where the size of the array corresponds with the number of frames in the image data.
-		# To call this method the user needs to have performed " require 'RMagick' " in advance.
+    # Returns an array of RMagick image objects, where the size of the array corresponds to the number of frames in the image data.
+    # To call this method the user needs to have loaded the ImageMagick library in advance (require 'RMagick').
     def get_image_magick
       # Does pixel data exist at all in the DICOM object?
       if @compression == nil
-        add_msg("It seems pixel data is not present in this DICOM object: returning false.")
+        add_msg("It seems pixel data is not present in this DICOM object: Returning false.")
         return false
       end
       # No support yet for color pixel data:
       if @color
-        add_msg("Warning: Unpacking color pixel data is not supported yet for this method: aborting.")
+        add_msg("Warning: Unpacking color pixel data is not supported yet for this method: Aborting.")
         return false
       end
       # Gather information about the dimensions of the image data:
-      rows = get_value("0028,0010")
-      columns = get_value("0028,0011")
+      rows = get_value("0028,0010", :array => true)
+      columns = get_value("0028,0011", :array => true)
+      rows = [rows] unless rows.is_a?(Array)
+      columns = [columns] unless columns.is_a?(Array)
       frames = get_frames
       image_pos = get_image_pos
       # Array that will hold the RMagick image objects, one image object for each frame:
       image_arr = Array.new(frames)
+      # A hack for the special case (some MR files), where two images are stored (one is a smaller thumbnail image):
+      if image_pos.length > 1 and columns.length > 1
+        image_pos = [image_pos.last]
+        columns = [columns[0]]
+        rows = [rows[0]]
+      end
       # Handling of image data will depend on whether we have one or more frames,
       if image_pos.size == 1
-        # All of the image data is located in one element:
-        #image_data = get_image_data(image_pos[0])
-        #(0..frames-1).each do |i|
-         # image = Magick::Image.new(columns,rows)
-         # image.import_pixels(0, 0, columns, rows, "I", image_data)
-         # image_arr[i] = image
-        #end
+        # All of the image data is located in one data element:
         if frames > 1
           add_msg("Unfortunately, this method only supports reading the first image frame as of now.")
         end
-        image = read_image_magick(image_pos[0], columns, rows)
+        image = read_image_magick(image_pos[0], columns[0], rows[0])
         image_arr[0] = image
-        #image_arr[i] = image
       else
         # Image data is encapsulated in items:
         (0..frames-1).each do |i|
-          #image_data=get_image_data(image_pos[i])
-          #image = Magick::Image.new(columns,rows)
-          #image.import_pixels(0, 0, columns, rows, "I", image_data)
-          image = read_image_magick(image_pos[i], columns, rows)
+          image = read_image_magick(image_pos[i], columns[0], rows[0])
           image_arr[i] = image
         end
       end
@@ -307,11 +305,9 @@ module DICOM
 
     # Returns the number of frames present in the image data in the DICOM file.
     def get_frames
-      frames = get_value("0028,0008")
-      if frames == false
-        # If the DICOM object does not specify the number of frames explicitly, assume 1 image frame.
-        frames = 1
-      end
+      frames = get_value("0028,0008", :silent => true)
+      # If the DICOM object does not specify the number of frames explicitly, assume 1 image frame:
+      frames = 1 unless frames
       return frames.to_i
     end
 
@@ -320,10 +316,11 @@ module DICOM
     def get_pixels(pos)
       pixels = false
       # We need to know what kind of bith depth the pixel data is saved with:
-      bit_depth = get_value("0028,0100")
-      if bit_depth != false
+      bit_depth = get_value("0028,0100", :array => true)
+      unless bit_depth == false
         # Load the binary pixel data to the Stream instance:
         @stream.set_string(get_raw(pos))
+        bit_depth = bit_depth.first if bit_depth.is_a?(Array)
         # Number of bytes used per pixel will determine how to unpack this:
         case bit_depth
           when 8
@@ -774,7 +771,8 @@ module DICOM
         compression = "No"
       end
       # Bits per pixel (allocated):
-      bits = get_value("0028,0100").to_s
+      bits = get_value("0028,0100", :array => true)
+      bits = bits[0].to_s if bits
       # Print the file properties:
       puts "Key properties of DICOM object:"
       puts "-------------------------------"
@@ -890,7 +888,7 @@ module DICOM
             add_msg("Warning: Method set_value could not create data element, either because data element name was not recognized in the library, or data element tag is invalid (Expected format of tags is 'GGGG,EEEE').")
           else
             # As we wish to create a new data element, we need to find out where to insert it in the element arrays:
-            # We will do this by finding the last array position of the last element that will (alphabetically/numerically) stay in front of this element.
+            # We will do this by finding the array position of the last element that will (alphabetically/numerically) stay in front of this element.
             if @tags.size > 0
               # Search the array:
               index = -1
@@ -898,7 +896,7 @@ module DICOM
               while quit != true do
                 if index+1 >= @tags.length # We have reached end of array.
                   quit = true
-                elsif tag < @tags[index+1] # We are past the correct position.
+                elsif tag < @tags[index+1] and @levels[index+1] == 0 # We are past the correct position (only match against top level tags).
                   quit = true
                 else # Increase index in anticipation of a 'hit'.
                   index += 1
@@ -1005,19 +1003,21 @@ module DICOM
     end # of create_element
 
 
-    # Encodes a value to binary (used for inserting values to a DICOM object).
+    # Encodes a value to binary (used for inserting values into a DICOM object).
     def encode(value, vr)
-      # Our value needs to be inside an array to be encoded:
-      value = [value] if not value.is_a?(Array)
       # VR will decide how to encode this value:
       case vr
         when "AT" # (Data element tag: Assume it has the format "GGGG,EEEE"
-          bin = @stream.encode_tag(value)
+          if value.is_a_tag?
+            bin = @stream.encode_tag(value)
+          else
+            add_msg("Invalid tag format (#{value}). Expected format: 'GGGG,EEEE'")
+          end
         # We have a number of VRs that are encoded as string:
         when 'AE','AS','CS','DA','DS','DT','IS','LO','LT','PN','SH','ST','TM','UI','UT'
           # In case we are dealing with a number string element, the supplied value might be a number
           # instead of a string, and as such, we convert to string just to make sure this will work nicely:
-          value[0] = value[0].to_s
+          value = value.to_s
           bin = @stream.encode_value(value, "STR")
         # Image related value representations:
         when "OW"
@@ -1049,6 +1049,7 @@ module DICOM
       return bin
     end # of encode
 
+
     # Modifies existing data element:
     def modify_element(value, pos, options={})
       bin_only = options[:bin]

data/lib/DWrite.rb

@@ -10,7 +10,8 @@
 # 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 for writing the data from a DObject to a valid DICOM file.
   class DWrite
 
     attr_writer :tags, :types, :lengths, :raw, :rest_endian, :rest_explicit
@@ -309,7 +310,8 @@ module DICOM
     end
 
 
-    # Tests if the file is writable and opens it.
+    # Tests if the file/path is writable, creates any folders
+    # if necessary, and opens the file for writing.
     def open_file(file)
       # Two cases: File already exists or it does not.
       # Check if file exists:
@@ -323,22 +325,20 @@ module DICOM
         end
       else
         # File does not exist.
-        # Check if this file's path contains a directory that does not exist and so need to be created:
-        arr = file.split('/')
-        if arr != nil
+        # 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):
-          arr.pop
-          if arr != nil
-            path = arr.join('/')
-            # Check if this path exists:
-            if not File.directory?(path)
-              # Need to create this path:
-              require 'fileutils'
-              FileUtils.mkdir_p path
-            end
+          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 should now be prepared, and we will thus create the file:
+        # The path to this non-existing file should now be prepared, and we proceed to creating the file:
         @file = File.new(file, "wb")
       end
     end

data/lib/Stream.rb

@@ -96,14 +96,16 @@ module DICOM
 
     # Encodes content (string, number, array of numbers) and returns the binary string.
     def encode(value, type)
-      bin = [value].pack(vr_to_str(type))
+      value = [value] unless value.is_a?(Array)
+      return value.pack(vr_to_str(type))
     end
 
 
     # Encodes content (string, number, array of numbers) to a binary string and pastes it to
     # the beginning of the @string variable of this instance.
     def encode_first(value, type)
-      bin = [value].pack(vr_to_str(type))
+      value = [value] unless value.is_a?(Array)
+      bin = value.pack(vr_to_str(type))
       @string = bin + @string
     end
 
@@ -111,7 +113,8 @@ module DICOM
     # Encodes content (string, number, array of numbers) to a binary string and pastes it to
     # the end of the @string variable of this instance.
     def encode_last(value, type)
-      bin = [value].pack(vr_to_str(type))
+      value = [value] unless value.is_a?(Array)
+      bin = value.pack(vr_to_str(type))
       @string = @string + bin
     end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: dicom
 version: !ruby/object:Gem::Version 
-  version: "0.6"
+  version: 0.6.1
 platform: ruby
 authors: 
 - Christoffer Lervag
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-08-13 00:00:00 +02:00
+date: 2009-08-23 00:00:00 +02:00
 default_executable: 
 dependencies: []
 
@@ -65,6 +65,6 @@ rubyforge_project: dicom
 rubygems_version: 1.3.3
 signing_key: 
 specification_version: 3
-summary: Library for handling DICOM files and network communication.
+summary: Library for handling DICOM files and DICOM network communication.
 test_files: []