User talk:Lchauvin

Projects

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• OsteoPlan
• SlicerOnAMIGO
• 4D Ultrasound
• NeuroNav

• Biopsy Module
• LineMotion Extension

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Hybrid Probe

• Aurora configuration (from IGSTK):

 communication->SetBaudRate(SerialCommunication::BaudRate9600);
 communication->SetDataBits(SerialCommunication::DataBits8);
 communication->SetParity(SerialCommunication::NoParity);
 communication->SetStopBits(SerialCommunication::StopBits1);
 communication->SetHardwareHandshake(SerialCommunication::HandshakeOff);

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
  • File:4DUltrasound-part1.tar.bz2
  • File:4DUltrasound-part2.tar.bz2
  • Backup on Google Docs

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

• • 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, ...

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• 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
    • Study ITK NRRD Reader
    • Getting Started with the NRRD Format
  • 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