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| − | ==Projects==
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| − | ----
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| − | *[[OsteoPlan]]
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| − | *[[SlicerOnAMIGO]]
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| − | *[[4D Ultrasound]]
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| − | *[[NeuroNav]]
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| − |
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| − |
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| − | *[[Biopsy Module]]
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| − | *[[LineMotion Extension]]
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| − |
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| − | == Progress reports ==
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| − | ----
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| − | ===Brainlab / Slicer integration in AMIGO===
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| − | * BUG: Brainlab system turn off by himself randomly (maybe due to run software on VM)
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| − | * DONE: Update OpenIGTLink version (Laptop)
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| − | ** TODO: Submit modification on trunk (Junichi)
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| − |
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| − | ===Hybrid Probe===
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| − | * Aurora configuration (from IGSTK):
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| − |
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| − | communication->SetBaudRate(SerialCommunication::BaudRate9600); // Baud: 9600
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| − | communication->SetDataBits(SerialCommunication::DataBits8); // DataBits: 8
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| − | communication->SetParity(SerialCommunication::NoParity); // Parity: 0
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| − | communication->SetStopBits(SerialCommunication::StopBits1); // StopBits: 1
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| − | communication->SetHardwareHandshake(SerialCommunication::HandshakeOff); // HandShake: 0
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| − |
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| − | *TODO: Try NDI Toolkit with Brainlab system
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| − |
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| − | ===4D Ultrasound===
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| − | * DONE: Tried to use Timer to be able to run client without freezing slicer when sending data
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| − | ** This solution is not efficient enough, because the system is really slow down
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| − | ** Try thread
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| − | * DONE: Send JB. data to slicer and use volume rendering
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| − | * DONE: Convert Jim Barabas data with matlab (cf. /projects/igtdev/lchauvin/Slicer3-Datasets/complete_data.m)
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| − | * INFO: OpenIGTLink Informations
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| − | ** svsize = size of the full volume (or picture)
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| − | ** spacing = size of the voxels
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| − | ** svsize = size of the sub-volume (a part of the volume)
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| − | ** svoffset = position of the center of the voxel (0,0,0)
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| − | *** TRICK: Offset in nrrd file indicate offset to the corner of the voxel. In OpenIGTLink, it represents the center of the voxel.
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| − | *** To calculate the offset to set on OpenIGTLink, use this equation:
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| − | **** '''OpenIGTLink_Offset = Corner_Offset ± (number_of_voxels * spacing)/2 - spacing/2 '''
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| − | ***** ± sign depends on the orientation of the coordinate system compared to RAS (example for LPS: - for L, - for P, + for S)
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| − | * INFO: Convert gzip to raw using this command
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| − | **'''unu data vol.nrrd | gunzip > vol.raw'''
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| − | * <span style="color:green;">IN PROGRESS:</span> Create GUI for Slicer
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| − | ** DONE: Interface to select nrrd directory
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| − | ** TODO: Create and implement "Parse files" button
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| − | * INFO: Could use vtkZlibDataCompressor to decompress data in nrrd files
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| − | ** Need to know uncompressed data memory space needed before calling uncompress function
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| − | * INFO: Could try to use vtkNRRDReader (in Slicer3/Libs/vtkTeem)
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| − | * INFO: Use this process to send file through OpenIGTLink
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| − | //------------------------------------------------------------
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| − | // size parameters
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| − | int size[] = {130, 256, 256}; // image dimension
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| − | float spacing[] = {-1.3, 1.0, -1.0}; // spacing (mm/pixel)
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| − | int svsize[] = {130, 256, 256}; // sub-volume size
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| − | int svoffset[] = {0,0,0}; // sub-volume offset
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| − | int scalarType = igtl::ImageMessage::TYPE_INT8;// scalar type
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| − | //------------------------------------------------------------
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| − | // Create a new IMAGE type message
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| − | igtl::ImageMessage::Pointer imgMsg = igtl::ImageMessage::New();
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| − | imgMsg->SetDimensions(size);
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| − | imgMsg->SetSpacing(spacing);
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| − | imgMsg->SetScalarType(scalarType);
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| − | imgMsg->SetDeviceName("ImagerClient");
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| − | imgMsg->SetSubVolume(svsize, svoffset);
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| − | imgMsg->AllocateScalars();
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| − |
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| − | Then, add Data to imgMsg using Scalar pointer (GetScalarPointer). But these data should be decompressed before (gzip). Then send Image packet.
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| − | * ISSUE: How to send a set of file (not just one file) with OpenIGTLink
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| − | * INFO: nrrd files are compressed with gzip
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| − | ** Need an nrrd reader
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| − | *** ITK provide one
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| − | *** Teem use unu (command line) to convert nrrd file (not really useful for now)
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| − | * PLANNED: Meeting with Junichi on March, 4th
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| − | ** TOPIC: Send Image with OpenIGTLink and use timestamps
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| − | **SUMMARY
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| − | ***Junichi explained me how image were send with OpenIGTLink
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| − | ***He shew me example ImagerClient
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| − | * DONE: Create and upload dataset
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| − | ** [[File:4DUltrasound-part1.tar.bz2]]
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| − | ** [[File:4DUltrasound-part2.tar.bz2]]
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| − | ** Backup on Google Docs
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| − |
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| − | ===Biopsy Module===
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| − | * <span style="color:green;">IN PROGRESS:</span> Snap fiducial to model
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| − | ** Need a representation to apply vtkPolygonalSurfacePointPlacer
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| − | *** Don't have with vtkSourceLine, tried to use vtkLineWidget2. Don't have GetRepresentation() method anymore.
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| − | ** Check AbdoNav Module (Measurement tool)
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| − | * DONE: Update line and planes when moving fiducials
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| − | ** Slowing down the system (maybe could be improved)
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| − | * INFO: Snapping point seems to come from vtkPolygonalSurfacePointPlacer class (find from vtkMeasurementsRulerWidget (L1348, L1447) -> vtkMeasurementsDistanceWidgetClass)
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| − | ** Need to set as input (with AddProp) properties of the model (vtkProp)
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| − | * <strike>BUG: When slider is smaller than line's length, both sliders are moved</strike>
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| − | ** FIXED: Add test to watch witch one reach limit, and update range
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| − | * DONE: Use new planes to reslice
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| − | ** ISSUE: Render and reslice are two different things, render is called when reslicing (don't call it again)
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| − | *** SOLUTION: Add a checkbox
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| − | **** Not rendering twice, but render is not call anymore if not reslicing (need to put mouse on 3D Render to update)
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| − | * DONE: Create 3 planes (instead of one): Perpendicular, In-Plane 0 and In-Plane 90
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| − | * DONE: Posibility to create and use different fiducial list to draw line
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| − | * DONE: Add toggle checkbox to turn on/off plane visibility
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| − | * DONE: Translate plane along the axis
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| − | * DONE: Create plane along the line
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| − | ** MODIFIED: Plane is now perpendicular to the line
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| − | * DONE: Use two sliders to extend line
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| − | ** Line could be extended and retracted, but the distance between fiducials define minimal distance of the line allowed
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| − | * DONE: Create line between two fiducials
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| − |
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| − | ===OsteoPlan===
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| − | ** Use vtkLoopSubdivisionFilter to reduce polygons size before clipping (longer but efficient)
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| − | ** To come back to original position with fiducials
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| − | *** Look at parent transformation node if existing (GetParentTransformNode() )
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| − | *** If yes, get matrix 4x4 (GetMatrixTransformToParent())
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| − | *** make a copy, and set the original one to Identity
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| − | *** Invert copied matrix
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| − | *** Set it under original transform node (SetAndObserveTransformNodeID(transformNodeID) and call InvokeEvent(vtkMRMLScene::SceneEditedEvent) )
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| − | *** Move fiducial list under inverted matrix (SetAndObserveTransformNodeID(transformNodeID) and call InvokeEvent(vtkMRMLScene::SceneEditedEvent) )
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| − | *** Apply Identity matrix to top node
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| − | * '''DONE: Place markers on models where the screws will be (Second Milestone Reached)'''
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| − | ** Use Fiducials synchronized with models (vtkCollection)
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| − | * '''DONE: Be able to separate different regions by clicking on them (First Milestone Reached)'''
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| − | ** Use the same method as on OsteoPlan.tcl
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| − | ** Create model from these regions instead of using actors
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| − | * DONE: Fix memory leaks on clipping function in Logic
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| − | ** Delete cleanPoly at the end
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| − | * DONE: Study OsteoPlan.tcl obtained from Hua Li (MGH)
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| − | **METHOD USED
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| − | ***Clipping model (with vtkPolyBoolean, not existing anymore, but could probably be replaced by vtkImplicitBoolean and vtkClippingPolyData)
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| − | ***Use vtkCellPicker to pick a cell of first part of the model
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| − | ***Use vtkPolyDataConnectivityFilter with Seeding option (seed used is the cell picked with vtkCellPicker)
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| − | ***Create a model with the output of connectivity filter
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| − | ***Do the same for the second part of the model
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| − | * MEETING: Send an email to Hua Lee (MGH) to set up a meeting
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| − | ** DONE: Meeting on Friday, 4th. 3pm. 25 New Chardon Street, 4th Floor.
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| − | ** TOPICS: See a demonstration of OsteoPlan, get source code, ask questions about user interface
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| − | ** SUMMARY
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| − | ***Possibility to cut a model with a plan on version 2.1
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| − | ***Got the source code
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| − | ***Explain what we already have on Slicer 3.6
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| − | ***User documentation of OsteoPlan on 2.1 received
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| − | ***Get models used
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| − | * <strike>BUG: Issue with vtk when trying to reinitialize array PointMap</strike>
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| − | ** A message has been sent to vtk mailing list
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| − | *** See bug section (problem coming from TraverseAndMark() )
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| − | **** Don't need to use this way now
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| − | * DONE: Fixed issue that didn't allow to show/hide model from polydata
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| − | ** FIX: Use this piece of code to create a MRMLModelNode from polydata:
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| − |
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| − | // Create new polydata
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| − | vtkPolyData* polyDataModel1 = vtkPolyData::New();
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| − | //
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| − | // Create New vtkMRMLNode
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| − | this->part1 = vtkMRMLModelNode::New();
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| − | //
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| − | // Create New vtkMRMLModelDisplayNode
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| − | vtkMRMLModelDisplayNode* dnode1 = vtkMRMLModelDisplayNode::New();
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| − | //
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| − | // Add them to the scene
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| − | this->part1->SetScene(this->GetMRMLScene());
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| − | dnode1->SetScene(this->GetMRMLScene());
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| − | //
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| − | this->GetMRMLScene()->AddNode(dnode1);
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| − | this->GetMRMLScene()->AddNode(part1);
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| − | //
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| − | // Use new polydata model to be "ready" to receive data
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| − | part1->SetAndObservePolyData(polyDataModel1);
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| − | part1->SetAndObserveDisplayNodeID(dnode1->GetID());
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| − | //
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| − | // Copy polydata to the new polydata model
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| − | dnode1->SetPolyData(clipper->GetOutput());
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| − | //
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| − | // Clean
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| − | polyDataModel1->Delete();
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| − |
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| − | * DONE: Enable to resize cutter and keep same position
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| − | * DONE: Study the OsteoPlan.tcl from Slicer2
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| − | **VTK class vtkPolyBoolean does not exist anymore
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| − | **Need to compare this version of OsteoPlan.tcl to OsteoPlan.tcl obtained from Hua Li (MGH).
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| − | * DONE: Clipped part inside the box, and use vtkPolyDataConnectivityFilter to extract largest and second largest region
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| − | ** Could be good with SpecifiedRegion if the model was not empty (too many regions else)
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| − | *** Is there a way to fill a surface in slicer ?
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| − | ** Use Largest region
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| − | *** Need a new function on this classs to get "second largest region"
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| − | **** Largest region use a sorted array -> Need to find second largest region and return it
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| − | ***** Second largest region seems not to be the "piece" I needed
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| − | * FAILED: Try to use boudingbox and perform one first positive clipping, and a second negative clipping on the output of the first one.
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| − | ** 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
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| − | * DONE: Installed VTK 5.7, and tried vtkClipClosedSurface
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| − | ** Good function, but use infinite plane
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| − | * FAILED: Tried to use kind of boolean operation (vtkExtractPolyDataGeometry, with filters, etc...)
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| − | ** Took 15 minutes to perform clipping, with infinite plane, and with model bugs
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| − | ** Do not use this way
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| − | * DONE: Clipping with big boundingbox
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| − | ** Working, fast, but not really a cutter
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| − | ** A cap is missing on the clipped part
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| − |
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| − | ===LineMotion Extension===
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| − | * '''Extension Completed'''
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| − | * DONE: Use color for different lines
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| − | * DONE: Keep index of fiducial list and actor synchronized when deleting a fiducial list
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| − | * DONE: Display multiple lines
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| − | * DONE: Posibility to create and use different fiducial list to draw line
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| − | * DONE: Add toggle checkbox to turn on/off plane visibility
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| − | * DONE: Translate plane along the axis
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| − | * DONE: Create plane along the line
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| − | ** MODIFIED: Plane is now perpendicular to the line
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| − | * DONE: Use two sliders to extend line
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| − | ** Line could be extended and retracted, but the distance between fiducials define minimal distance of the line allowed
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| − | * DONE: Create line between two fiducials
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| − |
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| − | ==Todo, Bug, Ideas, ...==
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| − | ----
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| − | * <u>4D Ultrasound</u>
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| − | ** <strike>TODO: Have a look at unu (from teem library) to convert nrrd files</strike>
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| − | *** Cf Ultrasound section(unu data)
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| − | ** TODO: Have a look at ITK NRRD Reader (cf. Andriy source code (email))
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| − | ** <strike>TODO: Have a look at vtkNRRDReader</strike>
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| − | ***Study ITK NRRD Reader
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| − | ***[http://www.vtk.org/Wiki/Getting_Started_with_the_NRRD_Format Getting Started with the NRRD Format]
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| − | ** <strike>TODO: Contact Jim Barabas to get US Data (barabas@mit.edu)</strike>
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| − | *** DONE: Data are not in nrrd format as expected
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| − | *** DONE: Data converted and sent to slicer
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| − |
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| − | * <u>Biopsy Module</u>
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| − | ** TODO: Snap a fiducial (entry point) to the model
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| − | *** Ask Nicole Aucoin and the Measurement module
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| − |
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| − | * <u>Transform Module</u>
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| − | **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)
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| − |
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| − | * <u>LineMotion Extension</u>
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| − | **<strike>BUG: Leaks when clicking several times on "Draw line" button</strike>
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| − | ***FIXED: Move all "New()" method in constructor instead of event of "draw line" button, and add some verification before using this objects
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| − | **<strike>TODO: Find a better way to link Fiducial list and Actor list</strike>
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| − | ***Synchronize 2 vtkCollections seems not possible -> Need to keep index "synchronized" manually
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| − | ****Remove actor when fiducial list deleted to keep the index "synchronized"
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| − |
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| − | * <u>OsteoPlan Module</u>
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| − | **<strike>IDEA: Use vtkImplicitModeller with vtkBoxWidget2 and a clipping function (propably vtkClipPolyData)</strike>
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| − | ***FAILED: vtkImplicitModeller compute distance with geometry. Not what I'm looking for.
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| − | ** <strike>ISSUE: VTK pointer of the PointMap array seems to be modified after TraverseAndMark function, creating a crash</strike>
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| − | *** Tried to comment TraverseAndMark in extractLargestRegion. Worked but dirty and ExtractLargestRegion didn't work anymore.
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| − | ****Anyway, secondLargestRegion return nothing.
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| − | ***** Don't need anymore. Shoud be reported to vtk.
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| − | ** BUG: Issue with multiple clipping (clipping seems not to work properly, leaks when leaving)
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| − | *** TODO: Check if problem solved after deleting cleanPoly
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| − | **** Not fixing
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| − | *** Seems to use the original model when clipping the second time (but create a model clipped twice)
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| − | *** Clipping function is modifying original model ?
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| − | ** ISSUE: Not able to load a scene
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| − | *** Probably because pointer of Interactor (or Window) change when loading a scene
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| − | *** Need to use Import scene instead for now
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| − | ** BUG: Problem with clipping function when cutter is too thin
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| − | *** TODO: Maybe apply clipping twice
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| − | *** Problem because triangles of models are bigger than thickness of the cutter
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| − | **** Tried to subdivide this triangles, better but not working completely, and takes time.
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| − | ** <strike>BUG: Segmentation Fault when clicking in empty region when selecting parts</strike>
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| − | *** FIXED: Verify a cell is picked before calling Connectivity Filter
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| − |
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| − | * <u>Tips</u>
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| − | ** Command to create an exe file: ./Slicer3/Script/getbuildtest.tcl --no-slicer-update --release --pack -t ""
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| − | *** No updates necessary if Slicer already built (all libraries included)
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| − | *** Release to optimize
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| − | *** Pack to create a package (NSIS needed for windows: [http://nsis.sourceforge.net NSIS])
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| − | *** -t "" to avoid tests
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