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fedorovfedorov
committedAug 27, 2015
Merge pull request #1 from che85/master
ProstateTRUSNav improvements
2 parents 32ce125 + bcf08f8 commit a5fb30b

12 files changed

+1162
-177
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‎CMakeLists.txt

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cmake_minimum_required(VERSION 2.8.9)
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project(ProstateTrusNav)
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project(ProstateTRUSNav)
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#-----------------------------------------------------------------------------
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# Extension meta-information
@@ -18,7 +18,7 @@ include(${Slicer_USE_FILE})
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#-----------------------------------------------------------------------------
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# Extension modules
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add_subdirectory(ProstateTrusNav)
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add_subdirectory(ProstateTRUSNav)
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## NEXT_MODULE
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#-----------------------------------------------------------------------------

‎ProstateTrusNav.png ‎ProstateTRUSNav.png

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‎ProstateTrusNav/CMakeLists.txt ‎ProstateTRUSNav/CMakeLists.txt

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#-----------------------------------------------------------------------------
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set(MODULE_NAME ProstateTrusNav)
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set(MODULE_NAME ProstateTRUSNav)
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#-----------------------------------------------------------------------------
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set(MODULE_PYTHON_SCRIPTS

‎ProstateTRUSNav/Plus_Configs/Realtime/PostCalibration_5_3cm_e.xml

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<PlusConfiguration version="2.3" PlusRevision="Plus-2.1.0.3427">
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<DataCollection StartupDelaySec="1">
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<DeviceSet Name="BK8818E depth 5.3cm w Slicer post calibration" Description="Epiphan frame grabber with Ascension EM trackers. Sensors in order: Red (111), Green (222), Blue (unmarked)."/>
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<Device
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Id="TrackerDevice"
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Type="Ascension3DG"
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AcquisitionRate="10"
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LocalTimeOffsetSec="0.15"
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FilterAcWideNotch="1"
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FilterAcNarrowNotch="0"
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FilterDcAdaptive="0"
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FilterLargeChange="0"
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FilterAlpha="0"
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ToolReferenceFrame="Tracker">
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<DataSources>
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<DataSource Type="Tool" Id="Stylus" BufferSize="500" PortName="0" AveragedItemsForFiltering="20"/>
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<DataSource Type="Tool" Id="Probe" BufferSize="500" PortName="1" AveragedItemsForFiltering="20"/>
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<DataSource Type="Tool" Id="Reference" BufferSize="500" PortName="2" AveragedItemsForFiltering="20"/>
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</DataSources>
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<OutputChannels>
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<OutputChannel Id="TrackerStream">
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<DataSource Id="Probe"/>
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<DataSource Id="Reference"/>
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<DataSource Id="Stylus"/>
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</OutputChannel>
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</OutputChannels>
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</Device>
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<Device
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Id="VideoDevice"
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Type="Epiphan"
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AcquisitionRate="30"
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LocalTimeOffsetSec="0"
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VideoFormat="Y8"
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ClipRectangleOrigin="0 0"
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ClipRectangleSize="0 0">
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<DataSources>
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<DataSource Type="Video" Id="Video" PortUsImageOrientation="MN" BufferSize="100" AveragedItemsForFiltering="20"/>
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</DataSources>
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<OutputChannels>
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<OutputChannel Id="VideoStream" VideoDataSourceId="Video"/>
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</OutputChannels>
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</Device>
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<Device Id="TrackedVideoDevice" Type="VirtualMixer" LocalTimeOffsetSec="0">
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<InputChannels>
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<InputChannel Id="TrackerStream"/>
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<InputChannel Id="VideoStream"/>
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</InputChannels>
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<OutputChannels>
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<OutputChannel Id="TrackedVideoStream"/>
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</OutputChannels>
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</Device>
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<Device
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Id="CaptureDevice"
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AcquisitionRate="8"
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RequestedFrameRate="30"
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Type="VirtualDiscCapture"
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BaseFilename="Record.mha"
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EnableCapturing="FALSE" >
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<InputChannels>
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<InputChannel Id="TrackedVideoStream" />
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</InputChannels>
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</Device>
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<Device
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Id="VolumeReconstructorDevice"
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Type="VirtualVolumeReconstructor">
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<InputChannels>
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<InputChannel Id="TrackedVideoStream" />
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</InputChannels>
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<VolumeReconstruction
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ImageCoordinateFrame="Image" ReferenceCoordinateFrame="Reference"
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Interpolation="NEAREST_NEIGHBOR" Optimization="NONE" Compounding="OFF" FillHoles="OFF" NumberOfThreads="2"
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FanAngles="-45 45" FanOrigin="613 193" FanDepth="600"
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OutputOrigin="-34 -144 -59" OutputExtent="0 150 0 130 0 70" OutputSpacing="0.5 0.5 0.5"
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ClipRectangleOrigin="278 283" ClipRectangleSize="670 600"/>
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</Device>
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</DataCollection>
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<PlusOpenIGTLinkServer MaxNumberOfIgtlMessagesToSend="1" MaxTimeSpentWithProcessingMs="10" ListeningPort="18944" OutputChannelId="TrackedVideoStream">
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<DefaultClientInfo>
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<MessageTypes>
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<Message Type="TRANSFORM"/>
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<Message Type="IMAGE"/>
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</MessageTypes>
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<TransformNames>
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<Transform Name="StylusToReference"/>
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<Transform Name="ImageToReference"/>
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</TransformNames>
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<ImageNames>
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<Image Name="Image" EmbeddedTransformToFrame="Reference"/>
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</ImageNames>
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</DefaultClientInfo>
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</PlusOpenIGTLinkServer>
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<CoordinateDefinitions>
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<Transform From="Image" To="Probe"
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Matrix="
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-0.00625236 -0.0934791 -0.000162447 253.598
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0.00193054 -0.0002919 0.0936677 -0.272276
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-0.0934593 0.00624765 0.00194572 14.6551
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0 0 0 1"
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Error="0.8" Date="20150325"/>
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</CoordinateDefinitions>
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</PlusConfiguration>

‎ProstateTRUSNav/Plus_Configs/Realtime/Processing_5_3cm.xml

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<PlusConfiguration version="2.1">
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<DataCollection StartupDelaySec="1.0" >
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<DeviceSet
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Name="PROCESSING BK8818E depth 5.3cm w Slicer post calibration"
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Description="Epiphan frame grabber with Ascension EM trackers. Sensors in order: Red (111), Green (222), Blue (unmarked)."/>
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<Device
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Id="TrackedVideoDevice"
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Type="OpenIGTLinkVideo"
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MessageType="TRACKEDFRAME"
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ServerAddress="127.0.0.1"
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ServerPort="18000"
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IgtlMessageCrcCheckEnabled="false"
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LocalTimeOffsetSec="0" >
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<DataSources>
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<DataSource Type="Video" Id="Video" PortUsImageOrientation="MN" />
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</DataSources>
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<OutputChannels>
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<OutputChannel Id="TrackedVideoStream" VideoDataSourceId="Video" />
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</OutputChannels>
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</Device>
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<Device
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Id="CaptureDevice"
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AcquisitionRate="8"
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RequestedFrameRate="30"
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Type="VirtualDiscCapture"
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BaseFilename="Record.mha"
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EnableCapturing="FALSE" >
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<InputChannels>
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<InputChannel Id="TrackedVideoStream" />
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</InputChannels>
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</Device>
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<Device
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Id="VolumeReconstructorDevice"
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Type="VirtualVolumeReconstructor">
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<InputChannels>
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<InputChannel Id="TrackedVideoStream" />
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</InputChannels>
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<VolumeReconstruction
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ImageCoordinateFrame="Image" ReferenceCoordinateFrame="Reference"
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Interpolation="NEAREST_NEIGHBOR" Optimization="NONE" Compounding="OFF" FillHoles="OFF" NumberOfThreads="2"
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FanAngles="-45 45" FanOrigin="613 193" FanDepth="600"
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OutputOrigin="-34 -144 -59" OutputExtent="0 150 0 130 0 70" OutputSpacing="0.5 0.5 0.5"
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ClipRectangleOrigin="278 283" ClipRectangleSize="670 600"/>
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</Device>
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<!-- <Device
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Id="VolumeReconstructorDevice"
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Type="VirtualVolumeReconstructor"
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OutputVolDeviceName="RecVol_Reference">
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<InputChannels>
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<InputChannel Id="TrackedVideoStream" />
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</InputChannels>
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<VolumeReconstruction
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ImageCoordinateFrame="Image" ReferenceCoordinateFrame="Reference"
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Interpolation="LINEAR" Optimization="NONE" CompoundingMode="MEAN" FillHoles="OFF" NumberOfThreads="2"
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ClipRectangleOrigin="0 0" ClipRectangleSize="820 616"
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OutputOrigin="-15 -15 30" OutputExtent="0 300 0 300 0 300" OutputSpacing="0.15 0.15 0.15" />
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</Device> -->
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</DataCollection>
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<PlusOpenIGTLinkServer
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MaxNumberOfIgtlMessagesToSend="1"
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MaxTimeSpentWithProcessingMs="10"
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ListeningPort="18944"
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SendValidTransformsOnly="true"
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OutputChannelId="TrackedVideoStream" >
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<DefaultClientInfo>
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<MessageTypes>
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<Message Type="IMAGE" />
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<Message Type="TRANSFORM" />
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</MessageTypes>
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<TransformNames>
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<Transform Name="StylusToReference"/>
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<Transform Name="ImageToReference"/>
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</TransformNames>
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<ImageNames>
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<Image Name="Image" EmbeddedTransformToFrame="Reference" />
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</ImageNames>
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</DefaultClientInfo>
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</PlusOpenIGTLinkServer>
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<CoordinateDefinitions>
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<Transform From="Image" To="Probe"
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Matrix="
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-0.00625236 -0.0934791 -0.000162447 253.598
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0.00193054 -0.0002919 0.0936677 -0.272276
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-0.0934593 0.00624765 0.00194572 14.6551
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0 0 0 1"
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Error="0.8" Date="20150325"/>
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</CoordinateDefinitions>
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</PlusConfiguration>

‎ProstateTRUSNav/Plus_Configs/Realtime/acquisition_5_3cm.xml

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<PlusConfiguration version="2.1">
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<DataCollection StartupDelaySec="1">
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<DeviceSet
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Name="ACQUISITION BK8818E depth 5.3cm w Slicer post calibration"
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Description="Epiphan frame grabber with Ascension EM trackers. Sensors in order: Red (111), Green (222), Blue (unmarked)."/>
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<Device
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Id="TrackerDevice"
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Type="Ascension3DG"
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AcquisitionRate="10"
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LocalTimeOffsetSec="0.15"
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FilterAcWideNotch="1"
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FilterAcNarrowNotch="0"
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FilterDcAdaptive="0"
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FilterLargeChange="0"
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FilterAlpha="0"
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ToolReferenceFrame="Tracker">
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<DataSources>
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<DataSource Type="Tool" Id="Stylus" BufferSize="500" PortName="0" AveragedItemsForFiltering="20"/>
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<DataSource Type="Tool" Id="Probe" BufferSize="500" PortName="1" AveragedItemsForFiltering="20"/>
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<DataSource Type="Tool" Id="Reference" BufferSize="500" PortName="2" AveragedItemsForFiltering="20"/>
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</DataSources>
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<OutputChannels>
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<OutputChannel Id="TrackerStream">
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<DataSource Id="Probe"/>
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<DataSource Id="Reference"/>
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<DataSource Id="Stylus"/>
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</OutputChannel>
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</OutputChannels>
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</Device>
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<Device
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Id="VideoDevice"
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Type="Epiphan"
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AcquisitionRate="30"
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LocalTimeOffsetSec="0"
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VideoFormat="Y8"
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ClipRectangleOrigin="0 0"
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ClipRectangleSize="0 0">
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<DataSources>
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<DataSource Type="Video" Id="Video" PortUsImageOrientation="MN" BufferSize="100" AveragedItemsForFiltering="20"/>
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</DataSources>
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<OutputChannels>
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<OutputChannel Id="VideoStream" VideoDataSourceId="Video"/>
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</OutputChannels>
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</Device>
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<Device Id="TrackedVideoDevice" Type="VirtualMixer" LocalTimeOffsetSec="0">
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<InputChannels>
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<InputChannel Id="TrackerStream"/>
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<InputChannel Id="VideoStream"/>
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</InputChannels>
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<OutputChannels>
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<OutputChannel Id="TrackedVideoStream"/>
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</OutputChannels>
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</Device>
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</DataCollection>
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<PlusOpenIGTLinkServer
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MaxNumberOfIgtlMessagesToSend="1"
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MaxTimeSpentWithProcessingMs="50"
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ListeningPort="18000"
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SendValidTransformsOnly="true"
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OutputChannelId="TrackedVideoStream" >
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<DefaultClientInfo>
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<MessageTypes>
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<Message Type="TRACKEDFRAME" />
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</MessageTypes>
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</DefaultClientInfo>
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</PlusOpenIGTLinkServer>
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</PlusConfiguration>

‎ProstateTRUSNav/ProstateTRUSNav.py

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‎ProstateTrusNav/Testing/CMakeLists.txt ‎ProstateTRUSNav/Testing/CMakeLists.txt

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‎ProstateTrusNav/ProstateTrusNav.py

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‎README.md

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# ProstateTrusNav
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# ProstateTRUSNav
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Fused ultrasound/MRI guided prostate biopsy

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