08 Sep, 2021
1 commit
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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
7 commits
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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.
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* modify arrow properties, replace orientation disk with torus * Remove ball actor * Change coil angle arrow projection constant to 5 degrees * Add removing arrow and disk used for coil projection when removing the peel * Modify Add_Torus function to be able to modify the color, Modify colors for arrow and torus, Modify size of coil projected arrow * Modify torus color * Modify arrow color * Undo changes done in commit 5fc6fd12b56e42a22571246c025256c30600deaf
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Change originally courtesy of vhosouza.
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Change originally courtesy of vhosouza.
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Change originally courtesy of vhosouza.
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Change originally courtesy of vhosouza.
18 Aug, 2021
6 commits
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- Removed unused functions and code Co-authored-by: Victor Hugo Souza <victor.souza@aalto.fi>
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- The Panel layout differs depending on if the pedal is in use or not, therefore the pedal needs to be initialized before the panel is created.
17 Aug, 2021
4 commits
16 Aug, 2021
1 commit
12 Aug, 2021
1 commit
09 Aug, 2021
1 commit
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* add add_object_orientation_disk and add_addobjectArrow functions, add orientation disk and projection arrow actors * add getCenter and getNormal functions, create locator and add self.peel_centers and self.peel_normals variables, add to calculate normals and centers when calling getPeelActor (new peel) * add GetPeelCenters and Initlocator_viewer and corresponding publisher call * add in OnLinkBrain and TractographyPanel class (OnSelectPeelingDepth) call to get peel centers and normals and initiator) * remove print on GetPeelCenters and Initlocator_viewer * add objectArrowlocation to calculate coil norms and directions * Add UpdateObjectArrowOrientation and Getcellintersection - getcellintersection function calculates the intersection between the coil normal and the peel center -calculates the angle between the coil normal and the normal of the center of the intersected cell -shows the coil projected with arrow and disk -Color of the disk and arrow change according to the value of the angle between the normal of the coil and the peel center mesh intersected. -updateobjectarroworientation is used to show and update the position of the projected arrow and disk * add comments, removed not used code on class def, modify currentPeel as local variable * modify getPeelActor removing input currentPeel * add affine_vtk matrix as input to getPeelActor, add change position of curent peel * add case when not intersection found in getcellintersection function * add remove arrow and disk actor only when intersecting with the peel * add comments to getcellintersection function, remove TODO * add comment to getcellintersection * add transformpeelposition function * add setvisibility to arrow and disk actor on OnNavigationStatus * add tangent lines for debuggint at getcellintersection function * add coil_dir from coordinates from tracker to objectArrowlocation * modify visibility of disk and coil projection arrow, to be shown when coil is not shown * comment tangent lines for debuggin on getcellintersection * modify names of functions to invesalius naming convention * correct mispelling error when calling GetCellIntersection * add angle threshold for projectio arrow in constansts * add angle threshold for arrow projection in constants * change size of disk and arrow in coil projection * add normal lines for debugging arrow projection * Modify function names to invensalius convention * add condition for track if peel is loaded or not * fix removing arrow and disk projection when distance is larger than set value, removing normal lines for debugging * clean comments * add self.peel_loaded to vis_components * Modify UpdatePeelVisualization to pass peel_loaded from navigation class * change color disk and arrow