23 Sep, 2021
3 commits
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* CLP: Move ICP class to its own file (icp.py) * CLP: Remove unused imports from task_navigator.py
22 Sep, 2021
2 commits
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* Updated gitignore to ignore VSCode project setting files * minor fix
21 Sep, 2021
3 commits
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* Add OBJECT_FIDUCIALS dict to constants.py, replacing BTNS_OBJ and TIPS_OBJ, and facilitating cleaning up the code. * Pass PedalConnection object to ObjectCalibrationDialog so that the pedal can be used for object calibration. * Copy and slightly adapt the code that was used to set tracker fiducials using pedal (in OnTrackerFiducials in NeuronavigationPanel class) to do the same for object fiducials. Mark code duplication with TODO comment for later clean-up. * Rename a function (OnGetObjectFiducials -> OnObjectFiducialButton), and rename a few variables (e.g., btn_id -> fiducial_index).
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Namely, do not attempt to add or remove pedal callbacks if the PedalConnection object is not available (e.g., due to missing Python MIDI libraries).
20 Sep, 2021
1 commit
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* CLP: Move Navigation class to its own file (navigation.py) * Also move the classes that Navigation class exclusively uses (namely, QueueCustom and UpdateNavigationScene) to the same file. * Review comment: Change neuronavigation subdirectory to navigation
16 Sep, 2021
3 commits
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* Due to a previous clean-up, r_s0_raw was not computed anymore in object_registration function. However, it is needed as one of the return values of the function, therefore add it back.
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* current_coord is not actually used by Navigator class, in which it resided previously. Instead, it is used by NeuroNavigationPanel when an image fiducial is unselected (the button for selecting the image fiducial is pressed twice). Previously, unselecting an image fiducial caused a crash due to not having current_coord variable in NeuroNavigationPanel. This patch moves it there to fix the bug.
15 Sep, 2021
3 commits
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- The angles returned by translations.decompose_matrix use the axe order 'sxyz'. It is also the default for translations.euler_from_matrix, although that function allows changing the order. Therefore, change to using euler_from_matrix, and instead of defaulting to the axe order 'sxyz', be explicit about it to make it easier to notice any bugs.
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- Add also its inverse function, which will be used in a later patch.
10 Sep, 2021
1 commit
09 Sep, 2021
1 commit
08 Sep, 2021
3 commits
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Bumps [pillow](https://github.com/python-pillow/Pillow) from 8.2.0 to 8.3.2. - [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/8.2.0...8.3.2) --- updated-dependencies: - dependency-name: pillow dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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- This patch does not change the logic of what is done with the tracker samples in OnGetObjectFiducials function. However, maybe the logic indeed should be changed at some point; add a few comments to the code for the future reader of the code to perhaps grasp more easily what is done there.
07 Sep, 2021
2 commits
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- Rather than a property of the tracker object, it should be passed to the tracker object from outside, since it depends on the context. For example, during the navigation, we might want to use a reference mode that is different from what we use during the object calibration. Therefore, move the reference mode that is used during navigation into Navigation class.
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* MOD: Allow setting tracker fiducials by pedal * Review comments: Improve style in boolean check * Review comments: Remove hardcoded size from fiducial buttons
06 Sep, 2021
2 commits
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MOD: Change logic for when to use coil without handle to mark the target
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ADD 5ch coil model to objects folder
03 Sep, 2021
3 commits
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- Previously, coil without handle was used to mark the target only if object calibration had not been done yet. After object calibration was done, the variable polydata stored the coil mesh that was selected by the user when doing the calibration, and hence that coil mesh (typically containing the handle) was used to mark the target. - Change the logic to follow these rules: * When the default coil is selected in object calibration, use the default coil with a handle to mark the coil location, and default coil without a handle to mark the target. * When object calibration is not yet done, use default coil without a handle to mark the target. * When a custom coil is selected in object calibration, use the custom coil to mark both the coil location and the target, regardless of if the mesh contains handle or not. This is done because otherwise the user would need to select two custom meshes, one that is used to mark the coil location and another for the target.
02 Sep, 2021
1 commit
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* WIP * MODIFY red ball visibility when peel is loaded, read ball disappears when projection hits the peel * MODIFY visibility of x_actor, y_actor, z_actor to not be visible. object_orientation_torus_actor and obj_projection_arrow_actor are not visible when loading the obj_actor(coil) * Add commented line for setting visibility when obj_actor is loaded
01 Sep, 2021
1 commit
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* fixed the code for save markers dialog (bug appearing on Linux), minor cleanup * Legacy marker code (mks files) isolated * Added support for marker file versions Strings in marker files are now quoted
29 Aug, 2021
1 commit
26 Aug, 2021
2 commits
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- Also, move code around a bit so that when a pulse is triggered into the serial port, publishing the corresponding event is done inside SerialPortConnection class.
25 Aug, 2021
3 commits
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- The correct way to ask if serial port is enabled is to use SerialPortEnabled function in Navigation class. - While at it, remove the unused Enabled function from SerialPortConnection class.
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- Do more specific error handling in SerialPortConnection class, distinguishing between the error caused by the queue becoming full from the error caused by reading from or writing into the serial port. - Also, add a comment explaining why additional sleeping is needed inside the thread in SerialPortConnection class.
24 Aug, 2021
1 commit
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* CLP: Clean up naming in task_navigator.py Namely, be more specific about the type of trigger input (in this case, the serial port), as nowadays the MIDI input can be used for triggering, as well. * CLP: Remove unused variable 'trigger' from Navigation class * CLP: More clean-up related to serial port communication - Change invesalius.data.trigger to invesalius.data.serial_port_connection - Rename the class TriggerNew to SerialPortConnection - Remove the old, unused Trigger class - Rename a couple of variables in SerialPortConnection class - Replace the incorrect docstring for SerialPortConnection class with a brief but more accurate docstring. * CLP: More clean-up in SerialPortConnection - Remove commented out code - Remove some blank lines from function definitions - Do not import sleep from time library, but instead use time.sleep * MOD: Allow selecting COM port when enabling serial port communication
23 Aug, 2021
1 commit
20 Aug, 2021
2 commits
19 Aug, 2021
1 commit
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- New mkss file format with better structure - Create, save, load markers updated The changes mostly courtesy of vhosouza; I rebased them on top of the current main branch and did a few further changes.