Class: RTKIT::StructureSet
Overview
The StructureSet class contains methods that are specific for this modality (RTSTRUCT).
Inheritance
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StructureSet inherits all methods and attributes from the Series class.
Instance Attribute Summary collapse
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#dcm ⇒ Object
readonly
The original DObject instance of the StructureSet.
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#image_series ⇒ Object
readonly
An array of ImageSeries that this Structure Set Series references has ROIs defined for.
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#plans ⇒ Object
readonly
An array of RTPlans associated with this Structure Set Series.
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#rois ⇒ Object
readonly
An array of ROIs belonging to this structure set.
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#sop_uid ⇒ Object
readonly
The SOP Instance UID.
Attributes inherited from Series
#class_uid, #date, #description, #modality, #series_uid, #study, #time
Class Method Summary collapse
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.image_series(dcm, study) ⇒ Object
Identifies the ImageSeries that the StructureSet object belongs to.
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.load(dcm, study) ⇒ Object
Creates a new StructureSet instance by loading the relevant information from the specified DICOM object.
Instance Method Summary collapse
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#==(other) ⇒ Object
(also: #eql?)
Returns true if the argument is an instance with attributes equal to self.
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#add(dcm) ⇒ Object
Registers a DICOM Object to the StructureSet, and processes it to create (and reference) the ROIs contained in the object.
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#add_plan(plan) ⇒ Object
Adds a Plan Series to this StructureSet.
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#add_roi(roi) ⇒ Object
Adds a ROI instance to this StructureSet.
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#create_roi(frame, options = {}) ⇒ Object
Creates a ROI belonging to this StructureSet.
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#hash ⇒ Object
Generates a Fixnum hash value for this instance.
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#initialize(sop_uid, image_series, options = {}) ⇒ StructureSet
constructor
Creates a new StructureSet instance.
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#plan(*args) ⇒ Object
Returns the Plan instance mathcing the specified SOP Instance UID (if an argument is used).
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#remove_roi(instance_or_number) ⇒ Object
Removes the ROI (specified by a ROI Number) from the Structure Set.
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#remove_rois ⇒ Object
Removes all ROIs from the Structure Set.
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#roi(name_or_number) ⇒ Object
Returns a ROI that matches the specified number or name.
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#roi_names ⇒ Object
Returns the ROI Names assigned to the various structures present in the structure set.
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#roi_numbers ⇒ Object
Returns the ROI Numbers assigned to the various structures present in the structure set.
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#rois_in_frame(uid) ⇒ Object
Returns all ROIs defined in this structure set that belongs to the specified Frame of Reference UID.
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#set_colors ⇒ Object
Sets new color values for all ROIs belonging to the StructureSet.
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#set_numbers ⇒ Object
Sets new ROI Numbers to all ROIs belonging to the StructureSet.
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#to_dcm ⇒ Object
Dumps the StructureSet instance to a DObject.
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#to_structure_set ⇒ Object
Returns self.
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#write(path) ⇒ Object
Writes the StructureSet to a DICOM file given by the specified file string.
Methods inherited from Series
Constructor Details
#initialize(sop_uid, image_series, options = {}) ⇒ StructureSet
Creates a new StructureSet instance.
Parameters
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sop_uid
– The SOP Instance UID string. -
image_series
– An Image Series that this StructureSet belongs to. -
options
– A hash of parameters.
Options
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:date
– String. The Series Date (DICOM tag ‘0008,0021’). -
:time
– String. The Series Time (DICOM tag ‘0008,0031’). -
:description
– String. The Series Description (DICOM tag ‘0008,103E’). -
:series_uid
– String. The Series Instance UID (DICOM tag ‘0020,000E’).
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# File 'lib/rtkit/structure_set.rb', line 94 def initialize(sop_uid, image_series, ={}) raise ArgumentError, "Invalid argument 'sop_uid'. Expected String, got #{sop_uid.class}." unless sop_uid.is_a?(String) raise ArgumentError, "Invalid argument 'image_series'. Expected ImageSeries, got #{image_series.class}." unless image_series.is_a?(ImageSeries) # Pass attributes to Series initialization: [:class_uid] = '1.2.840.10008.5.1.4.1.1.481.3' # RT Structure Set Storage # Get a randomized Series UID unless it has been defined in the options hash: series_uid = [:series_uid] || RTKIT.series_uid super(series_uid, 'RTSTRUCT', image_series.study, ) @sop_uid = sop_uid # Default attributes: @image_series = Array.new @rois = Array.new @plans = Array.new @associated_plans = Hash.new # Register ourselves with the ImageSeries: image_series.add_struct(self) @image_series << image_series end |
Instance Attribute Details
#dcm ⇒ Object (readonly)
The original DObject instance of the StructureSet.
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# File 'lib/rtkit/structure_set.rb', line 12 def dcm @dcm end |
#image_series ⇒ Object (readonly)
An array of ImageSeries that this Structure Set Series references has ROIs defined for.
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# File 'lib/rtkit/structure_set.rb', line 14 def image_series @image_series end |
#plans ⇒ Object (readonly)
An array of RTPlans associated with this Structure Set Series.
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# File 'lib/rtkit/structure_set.rb', line 16 def plans @plans end |
#rois ⇒ Object (readonly)
An array of ROIs belonging to this structure set.
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# File 'lib/rtkit/structure_set.rb', line 18 def rois @rois end |
#sop_uid ⇒ Object (readonly)
The SOP Instance UID.
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# File 'lib/rtkit/structure_set.rb', line 20 def sop_uid @sop_uid end |
Class Method Details
.image_series(dcm, study) ⇒ Object
Identifies the ImageSeries that the StructureSet object belongs to. If the referenced instances (ImageSeries & Frame) does not exist, they are created by this method.
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# File 'lib/rtkit/structure_set.rb', line 53 def self.image_series(dcm, study) raise ArgumentError, "Invalid argument 'dcm'. Expected DObject, got #{dcm.class}." unless dcm.is_a?(DICOM::DObject) raise ArgumentError, "Invalid argument 'study'. Expected Study, got #{study.class}." unless study.is_a?(Study) raise ArgumentError, "Invalid argument 'dcm'. Expected DObject with modality 'RTSTUCT', got #{dcm.value(MODALITY)}." unless dcm.value(MODALITY) == 'RTSTRUCT' # Extract the Referenced Frame UID: begin ref_frame_of_ref = dcm[REF_FRAME_OF_REF_SQ][0].value(FRAME_OF_REF) rescue ref_frame_of_ref = nil end # Extract referenced Image Series UID: begin ref_series_uid = dcm[REF_FRAME_OF_REF_SQ][0][RT_REF_STUDY_SQ][0][RT_REF_SERIES_SQ][0].value(SERIES_UID) rescue ref_series_uid = nil end # Create the Frame if it doesn't exist: f = study.patient.dataset.frame(ref_frame_of_ref) f = Frame.new(ref_frame_of_ref, study.patient) unless f # Create the ImageSeries if it doesnt exist: is = f.series(ref_series_uid) is = ImageSeries.new(ref_series_uid, 'CT', f, study) unless is study.add_series(is) return is end |
.load(dcm, study) ⇒ Object
Creates a new StructureSet instance by loading the relevant information from the specified DICOM object. The SOP Instance UID string value is used to uniquely identify a StructureSet instance.
Parameters
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dcm
– An instance of a DICOM object (DICOM::DObject) with modality ‘RTSTRUCT’. -
study
– The Study instance that this StructureSet belongs to.
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# File 'lib/rtkit/structure_set.rb', line 30 def self.load(dcm, study) raise ArgumentError, "Invalid argument 'dcm'. Expected DObject, got #{dcm.class}." unless dcm.is_a?(DICOM::DObject) raise ArgumentError, "Invalid argument 'study'. Expected Study, got #{study.class}." unless study.is_a?(Study) raise ArgumentError, "Invalid argument 'dcm'. Expected DObject with modality 'RTSTUCT', got #{dcm.value(MODALITY)}." unless dcm.value(MODALITY) == 'RTSTRUCT' # Required attributes: sop_uid = dcm.value(SOP_UID) # Optional attributes: class_uid = dcm.value(SOP_CLASS) date = dcm.value(SERIES_DATE) time = dcm.value(SERIES_TIME) description = dcm.value(SERIES_DESCR) series_uid = dcm.value(SERIES_UID) # Get the corresponding image series: image_series = self.image_series(dcm, study) # Create the StructureSet instance: ss = self.new(sop_uid, image_series, :class_uid => class_uid, :date => date, :time => time, :description => description, :series_uid => series_uid) ss.add(dcm) return ss end |
Instance Method Details
#==(other) ⇒ Object Also known as: eql?
Returns true if the argument is an instance with attributes equal to self.
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# File 'lib/rtkit/structure_set.rb', line 115 def ==(other) if other.respond_to?(:to_structure_set) other.send(:state) == state end end |
#add(dcm) ⇒ Object
Registers a DICOM Object to the StructureSet, and processes it to create (and reference) the ROIs contained in the object.
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# File 'lib/rtkit/structure_set.rb', line 126 def add(dcm) raise ArgumentError, "Invalid argument 'dcm'. Expected DObject, got #{dcm.class}." unless dcm.is_a?(DICOM::DObject) @dcm = dcm load_rois end |
#add_plan(plan) ⇒ Object
Adds a Plan Series to this StructureSet. Note: Intended for internal use in the library only.
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# File 'lib/rtkit/structure_set.rb', line 135 def add_plan(plan) raise ArgumentError, "Invalid argument 'plan'. Expected Plan, got #{plan.class}." unless plan.is_a?(Plan) @plans << plan unless @associated_plans[plan.uid] @associated_plans[plan.uid] = plan end |
#add_roi(roi) ⇒ Object
Adds a ROI instance to this StructureSet.
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# File 'lib/rtkit/structure_set.rb', line 143 def add_roi(roi) raise ArgumentError, "Invalid argument 'roi'. Expected ROI, got #{roi.class}." unless roi.is_a?(ROI) @rois << roi unless @rois.include?(roi) end |
#create_roi(frame, options = {}) ⇒ Object
Creates a ROI belonging to this StructureSet. Returns the created ROI.
Notes
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The ROI is created without Slices, and these must be added after the ROI creation.
Parameters
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frame
– The Frame instance which the ROI will belong to. -
options
– A hash of parameters.
Options
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:algorithm
– String. The ROI Generation Algorithm. Defaults to ‘Automatic’. -
:name
– String. The ROI Name. Defaults to ‘RTKIT-VOLUME’. -
:number
– Integer. The ROI Number. Defaults to the first available ROI Number in the StructureSet. -
:interpreter
– String. The ROI Interpreter. Defaults to ‘RTKIT’. -
:type
– String. The ROI Interpreted Type. Defaults to ‘CONTROL’.
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# File 'lib/rtkit/structure_set.rb', line 168 def create_roi(frame, ={}) raise ArgumentError, "Expected Frame, got #{frame.class}." unless frame.is_a?(Frame) # Set values: algorithm = [:algorithm] || 'Automatic' name = [:name] || 'RTKIT-VOLUME' interpreter = [:interpreter] || 'RTKIT' type = [:type] || 'CONTROL' if [:number] raise ArgumentError, "Expected Integer, got #{options[:number].class} for the option :number." unless [:number].is_a?(Integer) raise ArgumentError, "The specified ROI Number (#{options[:roi_number]}) is already used by one of the existing ROIs (#{roi_numbers})." if roi_numbers.include?([:number]) number = [:number] else number = (roi_numbers.max ? roi_numbers.max + 1 : 1) end # Create ROI: roi = ROI.new(name, number, frame, self, :algorithm => algorithm, :name => name, :number => number, :interpreter => interpreter, :type => type) return roi end |
#hash ⇒ Object
Generates a Fixnum hash value for this instance.
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# File 'lib/rtkit/structure_set.rb', line 189 def hash state.hash end |
#plan(*args) ⇒ Object
Returns the Plan instance mathcing the specified SOP Instance UID (if an argument is used). If a specified UID doesn’t match, nil is returned. If no argument is passed, the first Plan instance associated with the StructureSet is returned.
Parameters
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uid
– String. The value of the SOP Instance UID element.
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# File 'lib/rtkit/structure_set.rb', line 201 def plan(*args) raise ArgumentError, "Expected one or none arguments, got #{args.length}." unless [0, 1].include?(args.length) if args.length == 1 raise ArgumentError, "Expected String (or nil), got #{args.first.class}." unless [String, NilClass].include?(args.first.class) return @associated_plans[args.first] else # No argument used, therefore we return the first Plan instance: return @plans.first end end |
#remove_roi(instance_or_number) ⇒ Object
Removes the ROI (specified by a ROI Number) from the Structure Set.
Parameters
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instance_or_number
– The ROI Instance (or ROI Number of the instance) to be removed.
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# File 'lib/rtkit/structure_set.rb', line 218 def remove_roi(instance_or_number) raise ArgumentError, "Invalid argument 'instance_or_number'. Expected a ROI Instance or an Integer (ROI Number). Got #{instance_or_number.class}." unless [ROI, Integer].include?(instance_or_number.class) roi_instance = instance_or_number if instance_or_number.is_a?(Integer) roi_instance = roi(instance_or_number) end index = @rois.index(roi_instance) if index @rois.delete_at(index) roi_instance.remove_references end end |
#remove_rois ⇒ Object
Removes all ROIs from the Structure Set.
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# File 'lib/rtkit/structure_set.rb', line 233 def remove_rois @rois.each do |roi| roi.remove_references end @rois = Array.new end |
#roi(name_or_number) ⇒ Object
Returns a ROI that matches the specified number or name. Returns nil if no match is found.
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# File 'lib/rtkit/structure_set.rb', line 243 def roi(name_or_number) raise ArgumentError, "Invalid argument 'name_or_number'. Expected String or Integer, got #{name_or_number.class}." unless [String, Integer, Fixnum].include?(name_or_number.class) if name_or_number.is_a?(String) @rois.each do |r| return r if r.name == name_or_number end else @rois.each do |r| return r if r.number == name_or_number end end return nil end |
#roi_names ⇒ Object
Returns the ROI Names assigned to the various structures present in the structure set. The names are returned in an array.
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# File 'lib/rtkit/structure_set.rb', line 260 def roi_names names = Array.new @rois.each do |roi| names << roi.name end return names end |
#roi_numbers ⇒ Object
Returns the ROI Numbers assigned to the various structures present in the structure set. The numbers are returned in an array.
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# File 'lib/rtkit/structure_set.rb', line 271 def roi_numbers numbers = Array.new @rois.each do |roi| numbers << roi.number end return numbers end |
#rois_in_frame(uid) ⇒ Object
Returns all ROIs defined in this structure set that belongs to the specified Frame of Reference UID. Returns an empty array if no matching ROIs are found.
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# File 'lib/rtkit/structure_set.rb', line 282 def rois_in_frame(uid) raise ArgumentError, "Expected String, got #{uid.class}." unless uid.is_a?(String) frame_rois = Array.new @rois.each do |roi| frame_rois << roi if roi.frame.uid == uid end return frame_rois end |
#set_colors ⇒ Object
Sets new color values for all ROIs belonging to the StructureSet. Color values will be selected in a way which attempts to make the ROI colors maximally different. The method uses a predefined list containing 54 colors, which means for the rare case of more than 24 ROIs, some will not be assigned a color. Obviously, the more ROIs to assign colors to, the more similar the color values will be.
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# File 'lib/rtkit/structure_set.rb', line 297 def set_colors if @rois.length > 0 # Determine colors: initialize_colors # Set colors: @rois.each_index do |i| @rois[i].color = @colors[i] if i < 24 end end end |
#set_numbers ⇒ Object
Sets new ROI Numbers to all ROIs belonging to the StructureSet. Numbers increase sequentially, starting at 1 for the first ROI.
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# File 'lib/rtkit/structure_set.rb', line 311 def set_numbers @rois.each_with_index do |roi, i| roi.number = i + 1 end end |
#to_dcm ⇒ Object
Dumps the StructureSet instance to a DObject. This overwrites the dcm instance attribute. Returns the DObject instance.
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# File 'lib/rtkit/structure_set.rb', line 321 def to_dcm # Use the original DICOM object as a starting point (keeping all non-sequence elements): #@dcm[REF_FRAME_OF_REF_SQ].delete_children @dcm[STRUCTURE_SET_ROI_SQ].delete_children @dcm[ROI_CONTOUR_SQ].delete_children @dcm[RT_ROI_OBS_SQ].delete_children # Create DICOM @rois.each do |roi| @dcm[STRUCTURE_SET_ROI_SQ].add_item(roi.ss_item) @dcm[ROI_CONTOUR_SQ].add_item(roi.contour_item) @dcm[RT_ROI_OBS_SQ].add_item(roi.obs_item) end return @dcm end |
#to_structure_set ⇒ Object
Returns self.
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# File 'lib/rtkit/structure_set.rb', line 338 def to_structure_set self end |
#write(path) ⇒ Object
Writes the StructureSet to a DICOM file given by the specified file string.
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# File 'lib/rtkit/structure_set.rb', line 344 def write(path) to_dcm @dcm.write(path) end |