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Vtk to Itk converter is created and never deleted here:

and there

Load a scene with LandmarkRegistration and US acquisition. Delete LandmarkRegistration. In US acquisition, you may see a white rectangle instead of a slice, or slices may change color. If you now exit ibis, it may crash.

All the group boxes get squashed when not in full screen mode.
Need to check if it happens for other setting widgets displayed in the left side dock.

When a sceneObject's transform is modified programmatically (e.g. from a plugin) and its tranform panel is visible, the displayed transform is not updated.

In order to configure paths of external execuables that may be needed by plugins or main app.

Create a scene with an image IMG registered using LandmarkRegistrationObject, with an acquisition and a reconstructed volume RV.
Add a parent transform object to IMG (tree LandmarkRegistrationObject ->Transform -> I MG)
Use Rigid registration plugin with IMG as movable object and Transform as transform object. Instead of IMG the planes will move and the position of IMG relative to RV will not change.

ERROR: In /home/anka/ibis_work/deb/ibisExternalDependencies/vtk-6.3.0/src/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx, line 710
vtkCompositeDataPipeline (0x5203600): Input port 0 of algorithm vtkTubeFilter(0x5202580) has 0 connections but is not optional.

Open some files, click on SaveScene, ibis won't ask where to save but will show progress.

When you activate plugin, close it and try to load scene there is a crash, as some objects could not be removed from the scene.

Use target_include_directories(() to replace IBISLIB_INCLUDE_DIR

This is difficult to reproduce, sometimes they show, sometimes not. Sometimes you hide and then show acquisition and they appear if selected. Sometimes you never see them.

Sometimes it is enough to hide and show the acquisition.
Happens in ibis 2.5 and in development version.

Write an import plugin for cases of the BITE database. The plugin should be able to automatically download the data from the server and load it. It should cache the data locally in case it is needed again.

If Stereotactic Frame plugin is activated before loading image, closing plugin leaves frame in 3D.

Note from Jai
1.Whenever I try to record a US acquisition, IBIS crashes. The US image shows up fine, but as soon as I click 'record' in the double-view acquisition plugin, the whole program shuts down.
2.In the US probe settings, the drop-down menu for selecting the probe depth shows up as black. If I click it, it won't allow me to select anything. I'm wondering if this is related at all to the first point.

Explanation - the depth settings for us probe were missing in thew configuration file.
We have to provide a mechanism to create a valid configuration file and make sure there is no crash if the file is incorrect.

There is a line across view windows and you have to manually resize the main window to get rid of it.
The main window position is not properly saved and every time you start ibis, the main window is higher on the screen (if you don't work in full screen mode).

Selecting grayscale in video settings results in distorted images saved in acquisition sequence.

Acquire US from the double view window.
Close the window.
Delete the aquisition
Re-open the double view window -> Ibis crashes.

Axis should be visible when:

1. marked visible in ibis settings, saved in /home//.config/MNI-BIC-IPL/ibis.conf
2. marked as visible in loaded scene.

new scene should get visibility from ibis settings.

When loading a scene that contains a Landmark Registration transform and the transform is ON, the button says ON but the transform is not applied. We have to activate/deactivate for it to work.

When you apply scaling, images in 2D views are distorted.

Color and visibility settings are not saved.

Czaused by using non-existing plane in function TripleCutPlaneObject::IsInPlane()

Not yest found what happens, just not there when needed for Import in Landmark Registration

Closed interface for plugins. Plugins should talk to Ibis only through an interface class (IbisPluginsInterface) instead of directly accessing Application and SceneManager. It should still be possible to Get, add and remove SceneObjects. It should also be possible to access Views.

Move all the functionality from ImageObject and USAcquisition object to separate classes.

When there is no image added, using mouse wheel causes crash.

Local transform should be a vtkTransform and not a vtkLinearTransform

Ibis config directory in Ibis API is not valid at the time where the HW module is initialized so the HW module fails to find the 3D models.

This may be related to #210
When you load scenes one after another without quitting ibis, transformations go wrong.
From ibis_data load Miguet_USAcquisition and then NonLinear_MR_to_MR.

Two volumes with embeded rotations are sometimes transformed differently when their common parent is transformed. This could be caused by the fact that origin and step of image objects are stored in the vtkImageData while the rotation read from a file is stored in the object's transform, which leads to an incorrect order in the transforms.

The solution that should be considered is to store the origin and step with the rotation in the transform of the volume and always have origin = (0,0,0) and step = (1,1,1).

Also, when you remove the last tool from the list.

You may work in the scene with cursor on, close ibis, reopen and the cursor may be there or may be not.
Same for axes.

Selecting USAcquisitionObject from the list will make slices opaque even if settings dialog shows different. Clicking in 3D window will reset the opacity to one from settings.

Modify GPUVolumeReconstruction to programmatically set reconstruction params and execute the algorithm.

Load a scene with LandmarkRegistration. Move LandmarkRegistration children to World. Make LandmarkRegistration visible. Delete it. The source points will remain in 3D view.

That causes abort in SceneManager::Clear() on exit.

Load or make a scene with US acquisition. Reconstruct volume from slices (Plugins menu, US Volume Reconstruction with GPU). In all 4 views the cameras will be reset and images will be zoomed to fit view windows.

Which causes exception in ITK

error:
QAbstractItemModel::endRemoveRows: Invalid index ( 6 , 0 ) in model ObjectTreeModel(0x3a4cb10)

Load a scene with LandmarkRegistration. Make LandmarkRegistration visible. Try to move one of the source points in 3D view. You will pick a new point instead of moving an old one. Behaves correctly in 2D. It also behaves as designed when you load a scene without registration and you create a new LandmarkRegistration.

Load or create a scene with LandmarkRegistration, one ImageObject with surface as its child and US acquisition. Delete ImageObject. In US acquisition, you may see a white rectangle instead of a slice, or slices may change color. If you now exit ibis, it may crash.

It accumulates a very long list that includes deleted objects and non-listable objects (individual points) that cannot be parents.
Should probably use guiutility to fill the combo box

A white block is created instead of US volume

Develop an interface that would allow user to do the reconstruction without using GUI.

It is sometimes useful to have white or clear background for the 3D view, but not for the 2D views. It should be possible to set different background colors for 3D and 2D in the WorldObject settings widget.

When you select a point on the list in LandmarkRegistrationObject propertirs the cursor and planes do not move into selected position.

2D cameras sometimes loose alignment with plane and axes (see screenshot attached).
There may be different ways to reproduce the bug, but one consistent way is to manually modify the transform of the reference object and then press the Identity button in the transform tab of the ImageObject settings widget.
Views rely on the previous transform (as saved by the view) of the reference object to adjust the transform of the camera. One of the possible explanations for this bug is that this previous transform may not always be up to date and thus causes a readjustment of the camera transform that is incorrect.
Solving the bug might involve rethinking the mechanism to update the camera transform.

When you have more than 1 acquisition and reconstruct volumes in one ibis session, the second and next volumes are not properly reconstructed.
You have to reconstruct one volume, save scene, close ibis, start ibis and reconstruct next volume. The order of reconstruction is not important. If you have 2 acquisitions a1 and a2, you reconstruct first a1, you cannot reconstruct a2. You reconstruct first a2, you caannot reconstruct a1.

Move tracker sync code from vtkTrackedVideoBuffer to hardware module or Tracker class. Tools get assigned a video source and not the other way around.