Phantom registration algorithm

Phantom registration using landmarks

This algorithm computes transformation between a phantom object coordinate system (Phantom) and the coordinate system of tracking marker attached to the object (Reference) by point matching. Point coordinates are defined in the Phantom coordinate system and coordinates of the same points are also acquired in the Reference coordinate system by using a tracked stylus (StylusTip). To detect and select points in the Reference coordinate system the landmark detection algorithm can be used by detecting the stylus tip point when the tracked stylus is swiveling.

Configuration settings

• 
  vtkPlusPhantomLandmarkRegistrationAlgo
  • 
    PhantomCoordinateFrame
    
  • 
    ReferenceCoordinateFrame
    
  • 
    StylusTipCoordinateFrame
    
  • 
    AcquisitionRate
    

    Default = "20"
  • 
    FilterWindowTimeSec
    

    Default = "0.2"
  • 
    DetectionTimeSec
    

    Default = "1.0"
  • 
    StylusShaftMinimumDisplacementThresholdMm
    

    Default = "30"
  • 
    StylusTipMaximumDisplacementThresholdMm
    

    Default = "1.5"
• 
  PhantomDefinition
  • 
    Geometry
    • 
      Landmarks
      

Phantom registration using linear object features

This is an experimental algorithm that can use linear features (points, lines, and surfaces) to register a phantom to an attached tracker marker.

Configuration settings

• 
  vtkPlusPhantomLinearObjectRegistrationAlgo
  • 
    PhantomCoordinateFrame
    
  • 
    ReferenceCoordinateFrame
    
  • 
    StylusTipCoordinateFrame
    
• 
  PhantomDefinition
  • 
    Geometry
    • 
      Planes
      
    • 
      References
      

Example configuration file PlusDeviceSet_fCal_Ultrasonix_L14-5_Ascension3DG_2.0.xml

<PlusConfiguration version="2.3">
  <DataCollection StartupDelaySec="1.0" >
    <DeviceSet 
      Name="fCal: Ultrasonix US (L14-5 probe) + Ascension3DG tracker (Probe, Reference, Stylus) - fCal Phantom 2.0"
      Description="Ascension3DG sensors should be plugged in to the Ascension3DG DriveBay mounted on Ultrasonix US in the following order from to leftmost slot (Transducer 1) to the right: 1 Probe, 2 Reference, 3 Stylus." />
    <Device
      Id="TrackerDevice" 
      Type="Ascension3DG" 
      LocalTimeOffsetSec="0.0" 
      FilterAcWideNotch="1"
      ToolReferenceFrame="Tracker" >
      <DataSources>
        <DataSource Type="Tool" Id="Probe" PortName="0"  />
        <DataSource Type="Tool" Id="Reference" PortName="1"  />
        <DataSource Type="Tool" Id="Stylus" PortName="2"  />
      </DataSources>
      <OutputChannels>
        <OutputChannel Id="TrackerStream" >
          <DataSource Id="Probe"/>
          <DataSource Id="Reference"/>
          <DataSource Id="Stylus"/>
        </OutputChannel>
      </OutputChannels>
    </Device>
    <Device
      Id="VideoDevice"
      Type="SonixVideo" 
      AcquisitionRate="30" 
      LocalTimeOffsetSec="-0.2976"
      IP="127.0.0.1"
      AutoClipEnabled="TRUE" >
      <DataSources>
        <DataSource Type="Video" Id="Video" PortName="B" PortUsImageOrientation="UF"  />
      </DataSources>
      <OutputChannels>
        <OutputChannel Id="VideoStream" VideoDataSourceId="Video"/>
      </OutputChannels>
    </Device>
    <Device 
      Id="TrackedVideoDevice" 
      Type="VirtualMixer" >
      <InputChannels>
        <InputChannel Id="TrackerStream" />
        <InputChannel Id="VideoStream" />
      </InputChannels>
      <OutputChannels>
        <OutputChannel Id="TrackedVideoStream"/>
      </OutputChannels>
    </Device>
  </DataCollection>
  <CoordinateDefinitions>
    <Transform From="Image" To="TransducerOriginPixel"
      Matrix="1 0 0 -410
              0 1 0 5
              0 0 1 0
              0 0 0 1"
      Date="2011.12.06 17:57:00" Error="0.0" />    
  </CoordinateDefinitions> 
  <Rendering WorldCoordinateFrame="Reference">
    <DisplayableObject Type="Model" ObjectCoordinateFrame="TransducerOrigin" Id="ProbeModel"
      File="Probe_L14-5_38.stl"
      ModelToObjectTransform="
        -1 0 0 29.7
        0 -1 0 1.5
        0 0 1 -14
        0 0 0 1" />
    <DisplayableObject Type="Model" ObjectCoordinateFrame="Reference" Id="Volume"/>
    <DisplayableObject Type="Model" ObjectCoordinateFrame="StylusTip" Id="StylusModel" File="Stylus_Example.stl" />
    <DisplayableObject Id="PhantomModel" Type="Model" ObjectCoordinateFrame="Phantom"
      Opacity="0.6"
      File="fCal_2.0.stl"
      ModelToObjectTransform="
        1 0 0 -35.0
        0 1 0 -10.0
        0 0 1 -5.0
        0 0 0 1" />
    <DisplayableObject Type="Image" ObjectCoordinateFrame="Image" Id="LiveImage"/>
  </Rendering>
<Segmentation
    ApproximateSpacingMmPerPixel="0.078"
    MorphologicalOpeningCircleRadiusMm="0.27"
    MorphologicalOpeningBarSizeMm="2.0"
    ClipRectangleOrigin="27 27" 
    ClipRectangleSize="766 562" 
    MaxLinePairDistanceErrorPercent="10"
    AngleToleranceDegrees="10"
    MaxAngleDifferenceDegrees="10"
    MinThetaDegrees="-70"
    MaxThetaDegrees="70"
    MaxLineShiftMm="10.0"
    ThresholdImagePercent="10"
    CollinearPointsMaxDistanceFromLineMm="0.6"
    UseOriginalImageIntensityForDotIntensityScore="FALSE"
    NumberOfMaximumFiducialPointCandidates="20"
  />  <PhantomDefinition>
    <Description
      Name="fCAL"
      Type="Multi-N"
      Version="2.0"
      WiringVersion="2.0"
      Institution="Queen's University PerkLab"
    />
    <Geometry>
      <Pattern Type="NWire">
        <Wire Name="7:G1_g1" EndPointFront="30.0 0.0 20.0" EndPointBack="30.0 40.0 20.0" />
        <Wire Name="8:L1_h1" EndPointFront="55.0 0.0 20.0" EndPointBack="35.0 40.0 20.0" />
        <Wire Name="9:M1_m1" EndPointFront="60.0 0.0 20.0" EndPointBack="60.0 40.0 20.0" />
      </Pattern>
      <Pattern Type="NWire">
        <Wire Name="4:G3_g3" EndPointFront="30.0 0.0 10.0" EndPointBack="30.0 40.0 10.0" />
        <Wire Name="5:H3_l3" EndPointFront="35.0 0.0 10.0" EndPointBack="55.0 40.0 10.0" />
        <Wire Name="6:M3_m3" EndPointFront="60.0 0.0 10.0" EndPointBack="60.0 40.0 10.0" />
      </Pattern>
      <Pattern Type="NWire">
        <Wire Name="1:H5_h5" EndPointFront="35.0 0.0 0.0" EndPointBack="35.0 40.0 0.0" />
        <Wire Name="2:L5_i5" EndPointFront="55.0 0.0 0.0" EndPointBack="40.0 40.0 0.0" />
        <Wire Name="3:M5_m5" EndPointFront="60.0 0.0 0.0" EndPointBack="60.0 40.0 0.0" />
      </Pattern>
      <Landmarks>
        <Landmark Name="#1" Position="104.3 5.0 20.0" />
        <Landmark Name="#2" Position="104.3 45.0 20.0" />
        <Landmark Name="#3" Position="104.3 45.0 0.0" />
        <Landmark Name="#4" Position="104.3 -5.0 0.0" />
        
        <Landmark Name="#5" Position="-34.3 45.0 15.0" />
        <Landmark Name="#6" Position="-34.3 -5.0 20.0" />
        <Landmark Name="#7" Position="-34.3 -5.0 0.0" />
        <Landmark Name="#8" Position="-34.3 45.0 0.0" />
      </Landmarks>      
      <Planes>
        <Plane Name="Superior" BasePoint="5.5 3.0 35.0" EndPoint1="135.0 3.0 35.0" EndPoint2="135.0 55.0 35.0" />
        <Plane Name="Inferior" BasePoint="5.5 55.0 0.0" EndPoint1="135.0 55.0 0.0" EndPoint2="135.0 5.5 0.0" />
        <Plane Name="Outside Unmarked" BasePoint="140.0 5.0 30.0" EndPoint1="140.0 50.0 30.0" EndPoint2="140.0 50.0 5.0" />
        <Plane Name="Inside Unmarked" BasePoint="125.0 40.0 30.0" EndPoint1="125.0 20.0 10.0" EndPoint2="125.0 40.0 10.0" />
        <Plane Name="Outside Marked" BasePoint="0.0 40.0 30.0" EndPoint1="0.0 40.0 5.5" EndPoint2="0.0 15.5 5.5" />
        <Plane Name="Outside Posterior" BasePoint="130.0 0.0 30.0" EndPoint1="20.0 0.0 30.0" EndPoint2="20.0 0.0 15.0" />
        <Plane Name="Inside Posterior" BasePoint="110.0 10.0 30.0" EndPoint1="40.0 10.0 30.0" EndPoint2="30.0 10.0 10.0" />
        <Plane Name="Outside Anterior" BasePoint="130.0 60.0 30.0" EndPoint1="20.0 60.0 30.0" EndPoint2="20.0 60.0 5.0" />
      </Planes>      
      <References>
        <Reference Name="#1" Position="104.3 5.0 20.0" />
        <Reference Name="#2" Position="104.3 45.0 20.0" />
        <Reference Name="#3" Position="104.3 45.0 0.0" />
        <Reference Name="#4" Position="104.3 -5.0 0.0" />
        <Reference Name="#5" Position="-34.3 45.0 15.0" />
        <Reference Name="#6" Position="-34.3 -5.0 20.0" />
        <Reference Name="#7" Position="-34.3 -5.0 0.0" />
        <Reference Name="#8" Position="-34.3 45.0 0.0" />
      </References>
    </Geometry>
  </PhantomDefinition>
<VolumeReconstruction OutputSpacing="0.5 0.5 0.5"
    ClipRectangleOrigin="0 0" ClipRectangleSize="820 616"
    Interpolation="LINEAR" Optimization="FULL" CompoundingMode="MEAN" FillHoles="OFF" />
  <fCal
    PhantomModelId="PhantomModel"
    ReconstructedVolumeId="Volume"
    TransducerModelId="ProbeModel"
    StylusModelId="StylusModel"
    ImageDisplayableObjectId="LiveImage"
    NumberOfCalibrationImagesToAcquire="200"
    NumberOfValidationImagesToAcquire="100"
    NumberOfStylusCalibrationPointsToAcquire="200"
    RecordingIntervalMs="100"
    MaxTimeSpentWithProcessingMs="70"
    ImageCoordinateFrame="Image"
    ProbeCoordinateFrame="Probe"
    ReferenceCoordinateFrame="Reference"
    TransducerOriginCoordinateFrame="TransducerOrigin"
    TransducerOriginPixelCoordinateFrame="TransducerOriginPixel"
    TemporalCalibrationDurationSec="10" 
    FixedChannelId="VideoStream" 
    FixedSourceId="Video"
    MovingChannelId="TrackerStream"
    MovingSourceId="ProbeToTracker"
    DefaultSelectedChannelId="TrackedVideoStream" 
    FreeHandStartupDelaySec="5" />

  <vtkPlusPivotCalibrationAlgo
    ObjectMarkerCoordinateFrame="Stylus"
    ReferenceCoordinateFrame="Reference"
    ObjectPivotPointCoordinateFrame="StylusTip" />

  <vtkPlusPhantomLandmarkRegistrationAlgo
    PhantomCoordinateFrame="Phantom"
    ReferenceCoordinateFrame="Reference"
    StylusTipCoordinateFrame="StylusTip" 
    DetectionTimeSec="1.0"
    StylusTipMaximumDisplacementThresholdMm="1.8" />

  <vtkPlusProbeCalibrationAlgo
    ImageCoordinateFrame="Image"
    ProbeCoordinateFrame="Probe"
    PhantomCoordinateFrame="Phantom"
    ReferenceCoordinateFrame="Reference" />

</PlusConfiguration>