Difference between revisions of "User talk:Lchauvin"
From NAMIC Wiki
Line 172: | Line 172: | ||
** TODO: Have a look at unu (from teem library) to convert nrrd files | ** TODO: Have a look at unu (from teem library) to convert nrrd files | ||
** TODO: Have a look at ITK NRRD Reader | ** TODO: Have a look at ITK NRRD Reader | ||
+ | ** TODO: Have a look at vtkNRRDReader | ||
***Study ITK NRRD Reader | ***Study ITK NRRD Reader | ||
***[http://www.vtk.org/Wiki/Getting_Started_with_the_NRRD_Format Getting Started with the NRRD Format] | ***[http://www.vtk.org/Wiki/Getting_Started_with_the_NRRD_Format Getting Started with the NRRD Format] | ||
+ | ** TODO: Contact Jim Barabas to get US Data (barabas@mit.edu) | ||
* <u>Biopsy Module</u> | * <u>Biopsy Module</u> |
Revision as of 14:23, 17 March 2011
Home < User talk:LchauvinContents
Projects
Progress reports
4D Ultrasound
- 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)
- Need an nrrd reader
- 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.
- Need a representation to apply vtkPolygonalSurfacePointPlacer
- 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)
- SOLUTION: Add a checkbox
- ISSUE: Render and reslice are two different things, render is called when reslicing (don't call it again)
- 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
- 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
- METHOD USED
- 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
- See bug section (problem coming from TraverseAndMark() )
- A message has been sent to vtk mailing list
- 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
- Largest region use a sorted array -> Need to find second largest region and return it
- Need a new function on this classs to get "second largest region"
- Could be good with SpecifiedRegion if the model was not empty (too many regions else)
- 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
- TODO: Have a look at ITK NRRD Reader
- 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)
- Biopsy Module
- TODO: Snap a fiducial (entry point) to the model
- Ask Nicole Aucoin and the Measurement module
- TODO: Snap a fiducial (entry point) to the model
- 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"
- Synchronize 2 vtkCollections seems not possible -> Need to keep index "synchronized" manually
- OsteoPlan Module
- STEP1: Use cutter to clip model
- Deadline: February, 27th
- STEP2: Use widget to move clipped parts of the model
- Deadline: February, 27th
- STEP3: Overlap different parts (snap them ?)
- Deadline: March, 13th
- STEP4: Put marks on parts
- Dealine: March, 20th
- STEP5: Back to original model with marks on it (use original model ? Inverse transformation matrix ?)
- Deadline: March, 27th
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.
- Anyway, secondLargestRegion return nothing.
- Tried to comment TraverseAndMark in extractLargestRegion. Worked but dirty and ExtractLargestRegion didn't work anymore.
- 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 ?
- TODO: Check if problem solved after deleting cleanPoly
- 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
BUG: Segmentation Fault when clicking in empty region when selecting parts- FIXED: Verify a cell is picked before calling Connectivity Filter
- STEP1: Use cutter to clip model