19 Mar, 2021
1 commit
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Bumps [pillow](https://github.com/python-pillow/Pillow) from 8.1.0 to 8.1.1. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/master/CHANGES.rst) - [Commits](https://github.com/python-pillow/Pillow/compare/8.1.0...8.1.1) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
16 Mar, 2021
1 commit
12 Mar, 2021
1 commit
09 Mar, 2021
1 commit
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* 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
03 Mar, 2021
1 commit
01 Mar, 2021
1 commit
25 Feb, 2021
2 commits
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* 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>
22 Feb, 2021
1 commit
18 Feb, 2021
3 commits
01 Feb, 2021
1 commit
27 Jan, 2021
1 commit
26 Jan, 2021
2 commits
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* 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
15 Jan, 2021
1 commit
30 Dec, 2020
1 commit
29 Dec, 2020
2 commits
06 Sep, 2020
1 commit
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* Added Zoom interactor styles * Added Zoom by region interactor style * Added WWWL interactor style 3D * Added Panning style * Added Spin style * Added Linear measure style * Added Angular measure style and cleanups in linear and angular styels * Added insert seed style * Remove old event methods from volume viewer * Showing WW&WL text in Viewer Volume * Remove old SetInteractorStyle from volume viewer * Removed VOLUME_STYLES from constants
01 Sep, 2020
1 commit
31 Aug, 2020
1 commit
20 Aug, 2020
2 commits
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* ADD: Initial support for real time tracts visualization during navigation * ENH: Improved affine transformations for importing external polydata in world coordinates * ENH: Tracts visualization with cross move started * Create Trekker thread * Tracts style working and save and load project with affine * Tract computing incorporated to navigation pipeline * Add offset to coil normal to get coordinate inside brain * ADD: Pipeline for navigation with tract visualiztion and better debug tracker * ENH: Refactor the cross update feature * 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 * Improved sleep for navigation with tractography * 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 * ADD: Thread computing with class and pipeline * 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 * ADD: Dialog to adjust Trekker parameters * ENH: Dialog to load Trekker JSON configuration file * ENH: Replaced Trekker default list by dictionary with values[C * ENH: Remove tract code comments and refactor navigation pipeline * ENH: Replaced dialog warnings for message box in navigation tab * 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 * ADD: Control of brain mask opacity * FIX: Remove brain surface when closing project * 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 * FIX: Navigation was not running if tracts were not found - created thread in new format for trigger - removed comments of unused pipelines and threading - removed commented old FRE base creation * FIX: Generalize new navigation to objects even without tracts - Navigation with object working seamless with and without tracts - Navigation in other modes (single ref, no object) not working - Added one extra queue to generalize the pipeline in navigation * FIX: Static object navigation working and refactor navigation pipeline - Object corregistration split in functions - Cleaned comments on reference computation * FIX: Tractography navigation working with and without coil - Applied the new threading to the non-object navigations - Improved visualization of the offset marker for tractography - Cleaned commented code * ENH: Clean solved TODOs and commented unused navigation code * FIX: Fixed open and save dialogs for navigation purposes * FIX: Reading affine from old projects and replaced affine function form transformation * UPD: Removed surface back culling prints * DEL: Hided tractography panel and removed brain mesh mask
08 Aug, 2020
1 commit
07 Aug, 2020
2 commits
27 Jul, 2020
1 commit
03 Jul, 2020
1 commit
02 Jul, 2020
4 commits
01 Jul, 2020
4 commits
29 Jun, 2020
1 commit
15 Jun, 2020
1 commit
