09 Apr, 2021

2 commits

26 Mar, 2021

3 commits

24 Mar, 2021

2 commits

23 Mar, 2021

2 commits

22 Mar, 2021

1 commit

19 Mar, 2021

3 commits

18 Mar, 2021

1 commit

17 Mar, 2021

7 commits

16 Mar, 2021

1 commit

12 Mar, 2021

1 commit

09 Mar, 2021

1 commit

  • 50cad05c   FIX: Failed to fetch image coordinates from cross move (#257) ... Browse Code » 
    * FIX: Failed to fetch image coordinates from cross move
- Previous changes to the cross style disrupted the navigation
- Enhanced how image coordinates are communicated through pubsub

* WIP: Fix scroll and cross focal point difference in coordinate

* FIX: Scroll and cross coordinates did not match
- Removed debugging prints
- Commented and removed unnecessary calls and function
- Tested on niftis with 1.0 and 0.488 pixel spacings

* Rename UpdateSlices
    Victor Hugo Souza
     

03 Mar, 2021

1 commit

01 Mar, 2021

1 commit

25 Feb, 2021

2 commits

  • 4d9105d9   Improved mask raycasting color and visibility Browse Code »
    Thiago Franco de Moraes
     
  • ed9f72f9   Tractography-guided navigation (#254) ... Browse Code » 
    * Create Trekker thread

* Tracts style working and save and load project with affine

* ADD: Pipeline for navigation with tract visualiztion and better debug tracker

* FIX: Fixed update cross during navigation and improved tract visualization

* FIX: Seed flip when applying offset and added list to offset user control

* ADD: Brain surface texture mapping with peeling depth

* ENH: Tract computation speed doubled and tracts colors fixed

* ENH: Print removed in tract coloring

* ENH: Improved visualization of tracts

* ENH: Divide tract computation in chuncks

* ADD: Threads using Queue for navigation

* ENH: Navigation working with separate threads and lock

* ENH: Navigation with tracts running in producer-consumer method with locks

* ENH: Refactoring tracts threads

* Update tractography data exchange

* ENH: Improved Trekker GUI and tractography navigation working

* Update optimal Trekker parameters

* ENH: Split the removal and update of tracts

* ENH: Major changes in navigation array management and tracts cleaning
- Replaced all matrix to array, now using python matrix operator
- Refactored flip_x function
- Improved cleaning of tracts

* ENH: Tract visualization enabled in cross function and matrix operations replaced by arrays
- Additional code cleaning and commenting
- Refactoring of tip offset snippet

* ENH: Update trekker parameters after loading files and major refactor in flip_x
- Additional refactor of FRE computation and use of base_creation

* ENH: Improved object load dialog, OnNavigate pipeline and better tracts cleaning

* FIX: Navigation with tractography working
- Improved offset computation for seed
- Improved flip_x. No need to use a function, only multiply Y coordinate by -1

* Refactored compute_seed, affine_to_vtk, and set_message for tracts computation
- Cleaned unecessary comments
- Providing m_img already flip_x while set_message

* FIX: Tract removal with update cross position was disabled

* ENH: Threading of navigation replaced to  LifoQueue, working with dev_tracker but not tested in real tracker

* ENH: Tractography running with new limited Queue and nowait
- Tracts actors are computed all at once, no optimization for computing blocks

* FIX: Update pubsub in tracker
- Navgation with tractography running

* ENH: Multiblock tract computation and fixed tract cleaning
- Tractography navigation working at 0.1-s sleep

* ENH: Documented tractography computation and cleaned code

* DEL: Hided tractography panel and removed brain mesh mask

* ADD: Tractoraphy panel visible and brain mask added

* ENH: Replaced flip_x_m by -1*y coordinate and added initial grid for ACT tracts

* ADD: First version ACT tractography with simulated data
- FIX: Affine transformation not working as a result from weird behaviour from previous saved project

* UPD: First version of anatomic labelling DTI navigation working

* ENH: Added ACT checkbox and empty Queue management
- Added separate ACT tract computation thread
- Improved empty Queue handling in visualization thread

* FIX: Fix navigation callafter order, uncomment file dialogs

* ENH: Improve other files dialog import call

* ADD: Spherical sampling for tractography computation
- Seed marker in debug mode is not alligned with coil

* ADD: Uncertainty visualization in tract computation
- Apply transparency to tracts depending on parameters
- Added comments to ACT thread computation

* ENH: Combined the marker offset to the update tracts

* FIX: Ext trigger working with USB-coaxial cable

* ADD: Save tractography seed. Improved save and load markers.
- Reduced size of the grid for ACT tractography
- Refactored code for saving and loading markers. Requires testing.

* ENH: Fix tractography recompute threshold distance radius

* FIX: Apply missing changes after nav_dti rebase
- Enable ACT dti navigation
- Refactored markers save and load functions
- Cleaned code in viewer_volume.py

* FIX: Missing viewer_volume cross updates

* Load tractography only if has Trekker module

* FIX: Removes object when the tracker is disconnected

Co-authored-by: Thiago Franco de Moraes <totonixsame@gmail.com>
    Victor Hugo Souza
     

22 Feb, 2021

1 commit

18 Feb, 2021

3 commits

01 Feb, 2021

2 commits

29 Jan, 2021

1 commit

27 Jan, 2021

1 commit

26 Jan, 2021

2 commits

  • 19d7313c   Changed auto reload shortcut Browse Code »
    Thiago Franco de Moraes
     
  • 99e6d36b   Mask 3d preview (#252) ... Browse Code » 
    * Added methods to preview mask

* Added a button in viewer volume to activate mask 3d view

* Some cleaning and style modifications

* Showing mask preview and updating after edition

* Created a method to mark mask as modified

* Added update 3D preview in region growing tools

* Added update 3D preview in brain segmentation

* Added update 3D preview in swap and flip mask

* Added update 3D preview in threshold

* Improved rendering of mask

* Better showing mask in volume viewer

* Flip

* Removed the new button in volume viewer

* Increased the size of 3d preview in datanotebook

* Fixed problem with VTK7

* Fixed problem with VTK7

* Avoiding deepcopy

* Using IsoSurface when in VTK > 8 and with GPU support

* Created the class VolumeMask to keep all stuf about mask volume raycasting

* Changing volume mask colour when changing mask colour

* Changing mask axes also change volume mask rendering

* When remove mask removing volume mask visualization

* Changing mask threshold was not updating mask preview

* Added callbacks for when modifying mask

* Added method to remove modified callbacks

* Created menu to mask 3d preview

* Enable mask preview is working

* Rendering volume viewer after activating mask preview

* Loading and removing mask preview via menu

* Autoreload working

* Update working

* Removed mask preview from data notebook and task slice

* Auto reload mask preview shortcut
    Thiago Franco de Moraes
     

15 Jan, 2021

1 commit

08 Jan, 2021

1 commit