Difference between revisions of "2016 Winter Project Week/Projects/TrackedUltrasoundStandardization"
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Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]] | Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]] | ||
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==Key Investigators== | ==Key Investigators== | ||
+ | [[Image:UltrasoundToolGuidance3dOnly.gif|right]] | ||
* Andras Lasso, Tamas Ungi (PerkLab, Queen's University) | * Andras Lasso, Tamas Ungi (PerkLab, Queen's University) | ||
* Christian Askeland, Ingerid Reinertsen, Ole Vegard Solberg (CustusX, IGT research, SINTEF) | * Christian Askeland, Ingerid Reinertsen, Ole Vegard Solberg (CustusX, IGT research, SINTEF) | ||
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==Project Description== | ==Project Description== | ||
− | + | {| class="wikitable" | |
− | + | ! style="text-align: left; width:27%" | Objective | |
− | + | ! style="text-align: left; width:27%" | Approach and Plan | |
+ | ! style="text-align: left; width:27%" | Progress and Next Steps | ||
+ | |- style="vertical-align:top;" | ||
+ | | | ||
* Establish a common software platform for tracked ultrasound and image-guided interventions by converging existing IGT toolkits: | * Establish a common software platform for tracked ultrasound and image-guided interventions by converging existing IGT toolkits: | ||
** [http://www.slicer.org 3D Slicer], [http://www.slicerigt.org SlicerIGT extension] | ** [http://www.slicer.org 3D Slicer], [http://www.slicerigt.org SlicerIGT extension] | ||
** [http://www.plustoolkit.org Plus toolkit] | ** [http://www.plustoolkit.org Plus toolkit] | ||
** [http://custusx.org/ CustusX] | ** [http://custusx.org/ CustusX] | ||
− | ** [http://www.bic.mni.mcgill.ca/ | + | ** [http://www.bic.mni.mcgill.ca/~sdrouin/Ibis IBIS] |
** [http://www.imaging.robarts.ca/petergrp/Technology Echelon] | ** [http://www.imaging.robarts.ca/petergrp/Technology Echelon] | ||
** [http://mitk.org/wiki/IGT MITK-IGT] | ** [http://mitk.org/wiki/IGT MITK-IGT] | ||
− | + | | | |
− | + | * Pre-Project Week online meetings and emails | |
− | + | ** Notes below | |
− | * | + | ** SINTEF design document [https://github.com/SINTEFMedtek/CustusX/wiki/OpenIGTLink-US-messaging-proposal] |
− | + | * Coordination with the CommonTK effort | |
− | + | * Survey of current implementations and use cases | |
− | + | * Development of long-term development practices to encourage collaboration | |
− | * | + | | |
− | + | * IGSIO [https://github.com/igsio] | |
− | + | * Preparation meeting minutes [[2016_Winter_Project_Week:TrackedUltrasoundStandardization/PreparationMeetings|[0]]] | |
+ | * Live meeting minutes [https://docs.google.com/document/d/1jOHkFQJ5-GPyT3b9XHBJ5rnVkNOQQ2Q6G6evTfnl-CU/edit?usp=sharing] | ||
+ | |} | ||
− | + | == OpenIGTLink Revisions == | |
+ | v3 proposal document [http://openigtlink.org/protocols/v3_proposal.html] | ||
+ | === Tracked ultrasound OpenIGTLink client === | ||
+ | * Move out part of OpenIGTLinkIF | ||
+ | * Only use OpenIGTLink and VTK | ||
− | < | + | ====Commands==== |
+ | =====SetDeviceParameters===== | ||
+ | <b>Message</b> | ||
+ | <Command> | ||
+ | <Parameter Name=”Depth” Value=”45” /> | ||
+ | <Parameter Name=”Gain” Value=”35” /> | ||
+ | </Command> | ||
− | + | <b>Response 1</b> | |
+ | <Command> | ||
+ | <Result>SetDeviceParameters: success</Result> | ||
+ | <Parameter Name=”Depth” Value=”45” /> | ||
+ | <Parameter Name=”Gain” Value=”35” /> | ||
+ | ... | ||
+ | </Command> | ||
− | + | <b>Response 2</b> | |
+ | <Command> | ||
+ | <Result>SetDeviceParameters: failure</Result> <!-- see command status error code --> | ||
+ | </Command> | ||
− | + | =====GetDeviceParameters===== | |
− | + | <b>Message</b> | |
− | + | <Command> | |
− | + | <Parameter Name=”Depth” /> | |
− | + | <Parameter Name=”Gain” /> | |
+ | ... | ||
+ | </Command> | ||
− | + | <b>Response</b> | |
+ | <Command> | ||
+ | <Result>GetDeviceParameters: success</Result> | ||
+ | <Parameter Name=”Depth” Value=”45” /> | ||
+ | <Parameter Name=”Gain” Value=”35” /> | ||
+ | ... | ||
+ | </Command> | ||
− | + | =====SubscribeDeviceParameters===== | |
− | + | This will cause the server to send a GetDeviceParameters reply every time any of the subscribed parameters change. | |
− | |||
− | |||
− | + | <b>Message</b> | |
− | + | <Command> | |
− | + | <Parameter Name=”Depth” Subscribe=”TRUE” /> | |
− | + | <Parameter Name=”Gain” Subscribe=”FALSE” /> | |
− | + | ... | |
+ | </Command> | ||
− | + | <b>Response</b> | |
− | + | <Command> | |
− | + | <Result>SubscribeDeviceParameters: success</Result> | |
− | + | <Parameter Name=”Depth” Subscribed="TRUE" /> | |
+ | <Parameter Name=”Gain” Subscribed="FALSE" /> | ||
+ | ... | ||
+ | </Command> | ||
− | + | =====GetCapabilities===== | |
+ | SINTEF will specify and implement. | ||
− | + | <b>Message</b> | |
+ | <Command></Command> | ||
− | + | <b>Response</b> | |
− | + | <Command> | |
− | + | <Result>GetCapabilities: success</Result> | |
− | + | <UltrasoundCapabilities> | |
− | + | <Probes> | |
− | + | <Probe name="L14-5/38"/> | |
− | + | <Probe name="C5-2/42"/> | |
− | + | </Probes> | |
− | + | <ImagingModes> | |
− | + | <ImagingMode Name=”b-mode+angio”>B-Mode,Angio</ImagingMode> | |
− | + | </ImagingModes> | |
− | + | <Streams> | |
− | + | <Stream name="B-Mode"> | |
− | + | <Parameters> | |
− | + | <Parameter name="depth" min="5" max="220" step="5"/> | |
+ | </Parameters> | ||
+ | </Stream> | ||
+ | <Stream name="Angio"> | ||
+ | <Parameters> | ||
+ | <Parameter name="depth" min="5" max="220" step="5"/> | ||
+ | </Parameters> | ||
+ | </Stream> | ||
+ | </Streams> | ||
+ | <Presets> | ||
+ | <Preset name="Vascular small object B+Angio"> | ||
+ | <Probe Name=”L14-5/38” /> | ||
+ | <Parameter Name=”Depth” Value=”50” /> | ||
+ | </Preset> | ||
+ | </Presets> | ||
+ | </UltrasoundCapabilities> | ||
+ | </Command> | ||
+ | ===Tracking=== | ||
+ | Tracked ultrasound communication will use the TDATA message. | ||
− | + | Use 1 bit of the Reserved byte to indicate valid/invalid status | |
− | |||
− | |||
− | |||
− | + | Use metadata attributes for tool status information: | |
− | < | + | ====Attributes==== |
+ | <ToolStatus> | ||
+ | <Tool Id=”Reference” Status=”WARNING” Description=”Marker 1 on tool X is damaged” /> | ||
+ | </ToolStatus> | ||
− | + | * Status | |
+ | ** "OK" | ||
+ | ** "WARNING" | ||
+ | ** "ERROR" | ||
+ | * Description: human-readable string | ||
− | + | ===Meta Data=== | |
+ | ====Header V1==== | ||
+ | Bytes | ||
+ | 0 2 14 34 42 50 58 | ||
+ | +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ | ||
+ | | V | TYPE | DEVICE_NAME | TIME_STAMP | BODY_SIZE | CRC64 | | ||
+ | +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ | ||
− | + | ====Header V2==== | |
− | + | <nowiki>#</nowiki>Bytes HEADER_FIELD | |
− | + | +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- | |
− | + | 0 V 2 TYPE 14 DEV_NAME 34 TS 42 BODY_SIZE 50 CRC64 58 EXT_HEADER_SIZE 60 METADATA_SIZE 64 MSG_ID 68 RV 72 CONTENT… | METADATA… | | |
− | + | +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- | |
− | + | * V = VERSION | |
− | + | * DEV_NAME = DEVICE_NAME | |
− | + | * RV = RESERVED | |
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− | * | ||
− | + | =====EXT_HEADER===== | |
− | + | v1 header (58 bytes) + new header (EXT_HEADER_SIZE bytes) | |
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− | + | =====CONTENT (=v1 body)===== | |
− | + | BODY_SIZE - EXT_HEADER_SIZE - METADATA_SIZE | |
− | + | =====METADATA===== | |
+ | <nowiki>#</nowiki>Bytes HEADER_FIELD | ||
+ | +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ | ||
+ | |INDEX_COUNT (uint16) | KEY_SIZE (uint16) | VALUE_ENCODING (uint16) | VALUE_SIZE (uint32) | … | KEY | VALUE | … | | ||
+ | +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ | ||
− | + | =====VALUE_ENCODING===== | |
+ | As specified at http://www.iana.org/assignments/character-sets/character-sets.xhtml | ||
− | + | =====BODY===== | |
+ | Contains extended header data, message content, and metadata. | ||
− | * | + | ==US over OpenIGTLink== |
− | * | + | ===Parameters=== |
− | * | + | <b>Read-write</b> |
− | *** | + | * Depth (mm): (“40”, “45”, “50”, …) |
− | **** | + | * ImagingMode (string): (“bmode”, “bmode+rf”, “bmode+angio”, “rf+angio”, ...) |
− | **** | + | * Probe (string): probe name (“L14-5/38”) |
− | **** | + | * Frequency (MHz) |
− | ** | + | * DynRange (db) |
− | *** | + | * Gain (%) |
− | *** | + | * Power (%) |
+ | * Zoom (%) | ||
+ | * SoundVelocity (m/s) | ||
+ | * TGC (space-separated string, each entry -1.0 to 1.0) | ||
+ | * AcquisitionState (string): “FREEZE” or “RUN” | ||
+ | |||
+ | <b>Read-only</b> | ||
+ | * ClipRectangleOrigin="27 27" | ||
+ | * ClipRectangleSize="766 562" | ||
+ | * FanAnglesDeg=”-30 30” (for 3D: FanAnglesDeg=”-30 30 -15 15”) | ||
+ | * FanOriginPixel=”240 10” | ||
+ | * FanRadiusStartPixel=”30” | ||
+ | * FanRadiusStopPixel=”500” | ||
+ | * Encoding: how to interpret values ("BRIGHTNESS", "RF_REAL", "RF_IQ_LINE", "RF_I_LINE_Q_LINE", "RGB_COLOR") | ||
+ | |||
+ | == Implementation plan == | ||
+ | === Tasks === | ||
+ | * Clean up the vtkMRMLIGTLConnectorNode to be logic, MRML and Slicer free | ||
+ | * Creating a new converter base class which does not depend on MRML | ||
+ | * Implementation of the new Command Message | ||
+ | === Github Fork === | ||
+ | * OpenIGTLinkIF fork [https://github.com/drouin-simon/OpenIGTLinkIF] | ||
+ | * OpenIGTLink fork [https://github.com/lassoan/OpenIGTLink] | ||
+ | === PLUS === | ||
+ | * Interson probe settings [https://www.assembla.com/spaces/plus/tickets/869-interson-probe-settings-/details] | ||
+ | * Interson class cleanup [https://www.assembla.com/spaces/plus/tickets/897-clean-up-interson-video-source-code/details] | ||
+ | * Get/Set TGC support for US devices [https://www.assembla.com/spaces/plus/tickets/1056-add-tgc-support-to-ultrasonix-interface/details] | ||
+ | * Get transform over OpenIGTLink [https://www.assembla.com/spaces/plus/tickets/1054-add-get_transform-command-to-plus-server-to-support-querying-of-transforms/details] | ||
+ | * Sonix transition to imaging parameters [https://www.assembla.com/spaces/plus/tickets/1058-convert-sonixvideo-source-to-use-new-imaging-parameters-design/details] | ||
+ | |||
+ | === CustusX === | ||
+ | * Example CustusX class [https://github.com/SINTEFMedtek/CustusX/blob/master/source/resource/OpenIGTLinkUtilities/cxIGTLinkConversionImage.h] | ||
+ | |||
+ | ==Presentations== | ||
+ | * [[Media:NAMIC - IGT - Adam Rankin.pptx|Adam Rankin, Robarts Research Institute]] | ||
+ | * [[Media:PerkLabTrackedUs.pdf|Andras Lasso, PerkLab, Queen's University]] | ||
+ | * [[Media:MITKTrackedProbes.pdf|Thomas Kirchner, CAI group, German Cancer Research Center]] |
Latest revision as of 18:40, 8 January 2016
Home < 2016 Winter Project Week < Projects < TrackedUltrasoundStandardizationContents
Key Investigators
- Andras Lasso, Tamas Ungi (PerkLab, Queen's University)
- Christian Askeland, Ingerid Reinertsen, Ole Vegard Solberg (CustusX, IGT research, SINTEF)
- Simon Drouin (Mcgill University, Montreal, Canada)
- Junichi Tokuda (BWH)
- Steve Pieper (Isomics)
- Adam Rankin (VASST Laboratory, Western University, Canada)
- Thomas Kirchner, Janek Gröhl (MITK, DKFZ, Heidelberg, Germany)
Project Description
Objective | Approach and Plan | Progress and Next Steps |
---|---|---|
|
|
OpenIGTLink Revisions
v3 proposal document [4]
Tracked ultrasound OpenIGTLink client
- Move out part of OpenIGTLinkIF
- Only use OpenIGTLink and VTK
Commands
SetDeviceParameters
Message
<Command> <Parameter Name=”Depth” Value=”45” /> <Parameter Name=”Gain” Value=”35” /> </Command>
Response 1
<Command> <Result>SetDeviceParameters: success</Result> <Parameter Name=”Depth” Value=”45” /> <Parameter Name=”Gain” Value=”35” /> ... </Command>
Response 2
<Command> <Result>SetDeviceParameters: failure</Result> </Command>
GetDeviceParameters
Message
<Command> <Parameter Name=”Depth” /> <Parameter Name=”Gain” /> ... </Command>
Response
<Command> <Result>GetDeviceParameters: success</Result> <Parameter Name=”Depth” Value=”45” /> <Parameter Name=”Gain” Value=”35” /> ... </Command>
SubscribeDeviceParameters
This will cause the server to send a GetDeviceParameters reply every time any of the subscribed parameters change.
Message
<Command> <Parameter Name=”Depth” Subscribe=”TRUE” /> <Parameter Name=”Gain” Subscribe=”FALSE” /> ... </Command>
Response
<Command> <Result>SubscribeDeviceParameters: success</Result> <Parameter Name=”Depth” Subscribed="TRUE" /> <Parameter Name=”Gain” Subscribed="FALSE" /> ... </Command>
GetCapabilities
SINTEF will specify and implement.
Message
<Command></Command>
Response
<Command> <Result>GetCapabilities: success</Result> <UltrasoundCapabilities> <Probes> <Probe name="L14-5/38"/> <Probe name="C5-2/42"/> </Probes> <ImagingModes> <ImagingMode Name=”b-mode+angio”>B-Mode,Angio</ImagingMode> </ImagingModes> <Streams> <Stream name="B-Mode"> <Parameters> <Parameter name="depth" min="5" max="220" step="5"/> </Parameters> </Stream> <Stream name="Angio"> <Parameters> <Parameter name="depth" min="5" max="220" step="5"/> </Parameters> </Stream> </Streams> <Presets> <Preset name="Vascular small object B+Angio"> <Probe Name=”L14-5/38” /> <Parameter Name=”Depth” Value=”50” /> </Preset> </Presets> </UltrasoundCapabilities> </Command>
Tracking
Tracked ultrasound communication will use the TDATA message.
Use 1 bit of the Reserved byte to indicate valid/invalid status
Use metadata attributes for tool status information:
Attributes
<ToolStatus> <Tool Id=”Reference” Status=”WARNING” Description=”Marker 1 on tool X is damaged” /> </ToolStatus>
- Status
- "OK"
- "WARNING"
- "ERROR"
- Description: human-readable string
Meta Data
Header V1
Bytes 0 2 14 34 42 50 58 +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ | V | TYPE | DEVICE_NAME | TIME_STAMP | BODY_SIZE | CRC64 | +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
Header V2
#Bytes HEADER_FIELD
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- 0 V 2 TYPE 14 DEV_NAME 34 TS 42 BODY_SIZE 50 CRC64 58 EXT_HEADER_SIZE 60 METADATA_SIZE 64 MSG_ID 68 RV 72 CONTENT… | METADATA… | +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
- V = VERSION
- DEV_NAME = DEVICE_NAME
- RV = RESERVED
EXT_HEADER
v1 header (58 bytes) + new header (EXT_HEADER_SIZE bytes)
CONTENT (=v1 body)
BODY_SIZE - EXT_HEADER_SIZE - METADATA_SIZE
METADATA
#Bytes HEADER_FIELD
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ |INDEX_COUNT (uint16) | KEY_SIZE (uint16) | VALUE_ENCODING (uint16) | VALUE_SIZE (uint32) | … | KEY | VALUE | … | +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
VALUE_ENCODING
As specified at http://www.iana.org/assignments/character-sets/character-sets.xhtml
BODY
Contains extended header data, message content, and metadata.
US over OpenIGTLink
Parameters
Read-write
- Depth (mm): (“40”, “45”, “50”, …)
- ImagingMode (string): (“bmode”, “bmode+rf”, “bmode+angio”, “rf+angio”, ...)
- Probe (string): probe name (“L14-5/38”)
- Frequency (MHz)
- DynRange (db)
- Gain (%)
- Power (%)
- Zoom (%)
- SoundVelocity (m/s)
- TGC (space-separated string, each entry -1.0 to 1.0)
- AcquisitionState (string): “FREEZE” or “RUN”
Read-only
- ClipRectangleOrigin="27 27"
- ClipRectangleSize="766 562"
- FanAnglesDeg=”-30 30” (for 3D: FanAnglesDeg=”-30 30 -15 15”)
- FanOriginPixel=”240 10”
- FanRadiusStartPixel=”30”
- FanRadiusStopPixel=”500”
- Encoding: how to interpret values ("BRIGHTNESS", "RF_REAL", "RF_IQ_LINE", "RF_I_LINE_Q_LINE", "RGB_COLOR")
Implementation plan
Tasks
- Clean up the vtkMRMLIGTLConnectorNode to be logic, MRML and Slicer free
- Creating a new converter base class which does not depend on MRML
- Implementation of the new Command Message
Github Fork
PLUS
- Interson probe settings [7]
- Interson class cleanup [8]
- Get/Set TGC support for US devices [9]
- Get transform over OpenIGTLink [10]
- Sonix transition to imaging parameters [11]
CustusX
- Example CustusX class [12]