User talk:Lchauvin

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Projects


Progress reports

Brainlab / Slicer integration in AMIGO

  • BUG: Brainlab system turn off by himself randomly (maybe due to run software on VM)
  • DONE: Update OpenIGTLink version (Laptop)
    • TODO: Submit modification on trunk (Junichi)

Hybrid Probe

  • Aurora configuration (from IGSTK):
 communication->SetBaudRate(SerialCommunication::BaudRate9600);                   // Baud: 9600
 communication->SetDataBits(SerialCommunication::DataBits8);                      // DataBits: 8
 communication->SetParity(SerialCommunication::NoParity);                         // Parity: 0
 communication->SetStopBits(SerialCommunication::StopBits1);                      // StopBits: 1
 communication->SetHardwareHandshake(SerialCommunication::HandshakeOff);          // HandShake: 0
  • TODO: Try NDI Toolkit with Brainlab system

4D Ultrasound

  • DONE: Tried to use Timer to be able to run client without freezing slicer when sending data
    • This solution is not efficient enough, because the system is really slow down
    • Try thread
  • DONE: Send JB. data to slicer and use volume rendering
  • DONE: Convert Jim Barabas data with matlab (cf. /projects/igtdev/lchauvin/Slicer3-Datasets/complete_data.m)
  • INFO: OpenIGTLink Informations
    • svsize = size of the full volume (or picture)
    • spacing = size of the voxels
    • svsize = size of the sub-volume (a part of the volume)
    • svoffset = position of the center of the voxel (0,0,0)
      • TRICK: Offset in nrrd file indicate offset to the corner of the voxel. In OpenIGTLink, it represents the center of the voxel.
      • To calculate the offset to set on OpenIGTLink, use this equation:
        • OpenIGTLink_Offset = Corner_Offset ± (number_of_voxels * spacing)/2 - spacing/2
          • ± sign depends on the orientation of the coordinate system compared to RAS (example for LPS: - for L, - for P, + for S)
  • INFO: Convert gzip to raw using this command
    • unu data vol.nrrd | gunzip > vol.raw
  • IN PROGRESS: Create GUI for Slicer
    • DONE: Interface to select nrrd directory
    • TODO: Create and implement "Parse files" button
  • INFO: Could use vtkZlibDataCompressor to decompress data in nrrd files
    • Need to know uncompressed data memory space needed before calling uncompress function
  • INFO: Could try to use vtkNRRDReader (in Slicer3/Libs/vtkTeem)
  • INFO: Use this process to send file through OpenIGTLink
   //------------------------------------------------------------
   // size parameters
   int   size[]     = {130, 256, 256};       // image dimension
   float spacing[]  = {-1.3, 1.0, -1.0};     // spacing (mm/pixel)
   int   svsize[]   = {130, 256, 256};       // sub-volume size
   int   svoffset[] = {0,0,0};           // sub-volume offset
   int   scalarType = igtl::ImageMessage::TYPE_INT8;// scalar type
   //------------------------------------------------------------
   // Create a new IMAGE type message
   igtl::ImageMessage::Pointer imgMsg = igtl::ImageMessage::New();
   imgMsg->SetDimensions(size);
   imgMsg->SetSpacing(spacing);
   imgMsg->SetScalarType(scalarType);
   imgMsg->SetDeviceName("ImagerClient");
   imgMsg->SetSubVolume(svsize, svoffset);
   imgMsg->AllocateScalars();

Then, add Data to imgMsg using Scalar pointer (GetScalarPointer). But these data should be decompressed before (gzip). Then send Image packet.

  • ISSUE: How to send a set of file (not just one file) with OpenIGTLink
  • INFO: nrrd files are compressed with gzip
    • Need an nrrd reader
      • ITK provide one
      • Teem use unu (command line) to convert nrrd file (not really useful for now)
  • PLANNED: Meeting with Junichi on March, 4th
    • TOPIC: Send Image with OpenIGTLink and use timestamps
    • SUMMARY
      • Junichi explained me how image were send with OpenIGTLink
      • He shew me example ImagerClient
  • DONE: Create and upload dataset

Biopsy Module

  • IN PROGRESS: Snap fiducial to model
    • Need a representation to apply vtkPolygonalSurfacePointPlacer
      • Don't have with vtkSourceLine, tried to use vtkLineWidget2. Don't have GetRepresentation() method anymore.
    • Check AbdoNav Module (Measurement tool)
  • DONE: Update line and planes when moving fiducials
    • Slowing down the system (maybe could be improved)
  • INFO: Snapping point seems to come from vtkPolygonalSurfacePointPlacer class (find from vtkMeasurementsRulerWidget (L1348, L1447) -> vtkMeasurementsDistanceWidgetClass)
    • Need to set as input (with AddProp) properties of the model (vtkProp)
  • BUG: When slider is smaller than line's length, both sliders are moved
    • FIXED: Add test to watch witch one reach limit, and update range
  • DONE: Use new planes to reslice
    • ISSUE: Render and reslice are two different things, render is called when reslicing (don't call it again)
      • SOLUTION: Add a checkbox
        • Not rendering twice, but render is not call anymore if not reslicing (need to put mouse on 3D Render to update)
  • DONE: Create 3 planes (instead of one): Perpendicular, In-Plane 0 and In-Plane 90
  • DONE: Posibility to create and use different fiducial list to draw line
  • DONE: Add toggle checkbox to turn on/off plane visibility
  • DONE: Translate plane along the axis
  • DONE: Create plane along the line
    • MODIFIED: Plane is now perpendicular to the line
  • DONE: Use two sliders to extend line
    • Line could be extended and retracted, but the distance between fiducials define minimal distance of the line allowed
  • DONE: Create line between two fiducials

OsteoPlan

    • Use vtkLoopSubdivisionFilter to reduce polygons size before clipping (longer but efficient)
    • To come back to original position with fiducials
      • Look at parent transformation node if existing (GetParentTransformNode() )
      • If yes, get matrix 4x4 (GetMatrixTransformToParent())
      • make a copy, and set the original one to Identity
      • Invert copied matrix
      • Set it under original transform node (SetAndObserveTransformNodeID(transformNodeID) and call InvokeEvent(vtkMRMLScene::SceneEditedEvent) )
      • Move fiducial list under inverted matrix (SetAndObserveTransformNodeID(transformNodeID) and call InvokeEvent(vtkMRMLScene::SceneEditedEvent) )
      • Apply Identity matrix to top node
  • DONE: Place markers on models where the screws will be (Second Milestone Reached)
    • Use Fiducials synchronized with models (vtkCollection)
  • DONE: Be able to separate different regions by clicking on them (First Milestone Reached)
    • Use the same method as on OsteoPlan.tcl
    • Create model from these regions instead of using actors
  • DONE: Fix memory leaks on clipping function in Logic
    • Delete cleanPoly at the end
  • DONE: Study OsteoPlan.tcl obtained from Hua Li (MGH)
    • METHOD USED
      • Clipping model (with vtkPolyBoolean, not existing anymore, but could probably be replaced by vtkImplicitBoolean and vtkClippingPolyData)
      • Use vtkCellPicker to pick a cell of first part of the model
      • Use vtkPolyDataConnectivityFilter with Seeding option (seed used is the cell picked with vtkCellPicker)
      • Create a model with the output of connectivity filter
      • Do the same for the second part of the model
  • MEETING: Send an email to Hua Lee (MGH) to set up a meeting
    • DONE: Meeting on Friday, 4th. 3pm. 25 New Chardon Street, 4th Floor.
    • TOPICS: See a demonstration of OsteoPlan, get source code, ask questions about user interface
    • SUMMARY
      • Possibility to cut a model with a plan on version 2.1
      • Got the source code
      • Explain what we already have on Slicer 3.6
      • User documentation of OsteoPlan on 2.1 received
      • Get models used
  • BUG: Issue with vtk when trying to reinitialize array PointMap
    • A message has been sent to vtk mailing list
      • See bug section (problem coming from TraverseAndMark() )
        • Don't need to use this way now
  • DONE: Fixed issue that didn't allow to show/hide model from polydata
    • FIX: Use this piece of code to create a MRMLModelNode from polydata:
 // Create new polydata 
 vtkPolyData* polyDataModel1 = vtkPolyData::New();
 //
 // Create New vtkMRMLNode
 this->part1 = vtkMRMLModelNode::New();
 //
 // Create New vtkMRMLModelDisplayNode
 vtkMRMLModelDisplayNode* dnode1 = vtkMRMLModelDisplayNode::New();
 //
 // Add them to the scene 
 this->part1->SetScene(this->GetMRMLScene());
 dnode1->SetScene(this->GetMRMLScene());
 //
 this->GetMRMLScene()->AddNode(dnode1);
 this->GetMRMLScene()->AddNode(part1);
 //
 // Use new polydata model to be "ready" to receive data
 part1->SetAndObservePolyData(polyDataModel1);
 part1->SetAndObserveDisplayNodeID(dnode1->GetID());
 //
 // Copy polydata to the new polydata model
 dnode1->SetPolyData(clipper->GetOutput());
 //
 // Clean
 polyDataModel1->Delete();
  • DONE: Enable to resize cutter and keep same position
  • DONE: Study the OsteoPlan.tcl from Slicer2
    • VTK class vtkPolyBoolean does not exist anymore
    • Need to compare this version of OsteoPlan.tcl to OsteoPlan.tcl obtained from Hua Li (MGH).
  • DONE: Clipped part inside the box, and use vtkPolyDataConnectivityFilter to extract largest and second largest region
    • Could be good with SpecifiedRegion if the model was not empty (too many regions else)
      • Is there a way to fill a surface in slicer ?
    • Use Largest region
      • Need a new function on this classs to get "second largest region"
        • Largest region use a sorted array -> Need to find second largest region and return it
          • Second largest region seems not to be the "piece" I needed
  • FAILED: Try to use boudingbox and perform one first positive clipping, and a second negative clipping on the output of the first one.
    • Not possible because of the output of the clipping. Return inside of the box as a model and outside (everything outside, which mean top and bottom part) as another
  • DONE: Installed VTK 5.7, and tried vtkClipClosedSurface
    • Good function, but use infinite plane
  • FAILED: Tried to use kind of boolean operation (vtkExtractPolyDataGeometry, with filters, etc...)
    • Took 15 minutes to perform clipping, with infinite plane, and with model bugs
    • Do not use this way
  • DONE: Clipping with big boundingbox
    • Working, fast, but not really a cutter
    • A cap is missing on the clipped part

LineMotion Extension

  • Extension Completed
  • DONE: Use color for different lines
  • DONE: Keep index of fiducial list and actor synchronized when deleting a fiducial list
  • DONE: Display multiple lines
  • DONE: Posibility to create and use different fiducial list to draw line
  • DONE: Add toggle checkbox to turn on/off plane visibility
  • DONE: Translate plane along the axis
  • DONE: Create plane along the line
    • MODIFIED: Plane is now perpendicular to the line
  • DONE: Use two sliders to extend line
    • Line could be extended and retracted, but the distance between fiducials define minimal distance of the line allowed
  • DONE: Create line between two fiducials

Todo, Bug, Ideas, ...

  • 4D Ultrasound
    • TODO: Have a look at unu (from teem library) to convert nrrd files
      • Cf Ultrasound section(unu data)
    • TODO: Have a look at ITK NRRD Reader (cf. Andriy source code (email))
    • TODO: Have a look at vtkNRRDReader
    • TODO: Contact Jim Barabas to get US Data (barabas@mit.edu)
      • DONE: Data are not in nrrd format as expected
      • DONE: Data converted and sent to slicer
  • Biopsy Module
    • TODO: Snap a fiducial (entry point) to the model
      • Ask Nicole Aucoin and the Measurement module
  • Transform Module
    • ISSUE: Report Transform Module Issue (vtkKWMatrix4x4 observing Matrix4x4 and not vtkMRMLLinearTransformNode, if using ApplyTransform, new node is created and pointer is broken, then Transform Module is not updating anymore)
  • LineMotion Extension
    • BUG: Leaks when clicking several times on "Draw line" button
      • FIXED: Move all "New()" method in constructor instead of event of "draw line" button, and add some verification before using this objects
    • TODO: Find a better way to link Fiducial list and Actor list
      • Synchronize 2 vtkCollections seems not possible -> Need to keep index "synchronized" manually
        • Remove actor when fiducial list deleted to keep the index "synchronized"
  • OsteoPlan Module
    • IDEA: Use vtkImplicitModeller with vtkBoxWidget2 and a clipping function (propably vtkClipPolyData)
      • FAILED: vtkImplicitModeller compute distance with geometry. Not what I'm looking for.
    • ISSUE: VTK pointer of the PointMap array seems to be modified after TraverseAndMark function, creating a crash
      • Tried to comment TraverseAndMark in extractLargestRegion. Worked but dirty and ExtractLargestRegion didn't work anymore.
        • Anyway, secondLargestRegion return nothing.
          • Don't need anymore. Shoud be reported to vtk.
    • BUG: Issue with multiple clipping (clipping seems not to work properly, leaks when leaving)
      • TODO: Check if problem solved after deleting cleanPoly
        • Not fixing
      • Seems to use the original model when clipping the second time (but create a model clipped twice)
      • Clipping function is modifying original model ?
    • ISSUE: Not able to load a scene
      • Probably because pointer of Interactor (or Window) change when loading a scene
      • Need to use Import scene instead for now
    • BUG: Problem with clipping function when cutter is too thin
      • TODO: Maybe apply clipping twice
      • Problem because triangles of models are bigger than thickness of the cutter
        • Tried to subdivide this triangles, better but not working completely, and takes time.
    • BUG: Segmentation Fault when clicking in empty region when selecting parts
      • FIXED: Verify a cell is picked before calling Connectivity Filter
  • Tips
    • Command to create an exe file: ./Slicer3/Script/getbuildtest.tcl --no-slicer-update --release --pack -t ""
      • No updates necessary if Slicer already built (all libraries included)
      • Release to optimize
      • Pack to create a package (NSIS needed for windows: NSIS)
      • -t "" to avoid tests
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