Updates to make after 8-5-19 demo test #57

Closed tdowrick closed 3 years ago

In GitLab by @RolandGuichard on May 8, 2019, 11:14

Few changes/updates to make after today's demo:

[x] To automate: Make the CT scan visible in the volume module and the name is blank in Slicer4.8 (this is why it doesn’t happen as to does in 4.10). A solution might be to get the node by ID and rename it to SLD-001 as soon as we fetch it from the StealthStation
[x] Make the pivot calibration delay and duration to 10s by default
[x] With Slicer4.8 the scout scan makes the CT invisible when completed
[x] A (or 2?) slider in the 3D viewer to change the opacity go the CT scan and the 3D reconstruction ?
[x] Getting rid of the scout/live scan buttons as we are now using the ones from the PLUS remote
[ ] Install the dependencies of sksurgerybk in Slicer4.8 either manually
[x] Autoselect the connector in the PlusRemote widget (for getting the CT image)

In GitLab by @ThomasDowrick on May 13, 2019, 12:11

marked the task A (or 2?) slider in the 3D viewer to change the opacity go the CT scan and the 3D reconstruction ? as completed

In GitLab by @ThomasDowrick on May 13, 2019, 12:12

I have added the opacity slider in a new branch, and I also added setting the colour maps on the CT/MRI and US views.

In GitLab by @ThomasDowrick on May 13, 2019, 12:14

mentioned in commit 25df910dd9bf5b75f3d4f9986ef1e829e5204309

In GitLab by @RolandGuichard on May 13, 2019, 12:14

OK cool.

In GitLab by @ThomasDowrick on May 13, 2019, 12:31

mentioned in commit e913b051345cf32f2db6f8b985d2ee766f89e9f6

In GitLab by @ThomasDowrick on May 13, 2019, 12:31

marked the task Make the pivot calibration delay and duration to 10s by default as completed

In GitLab by @AnastasisGeorgoulas on May 13, 2019, 13:05

mentioned in commit 366fa3709e5500b0f5c81c33c5d7be5967fac356

In GitLab by @AnastasisGeorgoulas on May 13, 2019, 13:05

I set the calibration time too, oops!

In GitLab by @AnastasisGeorgoulas on May 13, 2019, 14:06

@ThomasDowrick Just to be clear, you added an opacity slider for the slice viewers, correct? I thought we also want to display both volumes at the same time, and control their opacity in the 3D viewer. But maybe I was wrong! (which would be useful, because that may be hard to do...)

In GitLab by @AnastasisGeorgoulas on May 13, 2019, 14:20

In fact, I'm not sure you can show multiple volumes at the same time in 4.8 (I didn't manage to from a quick look and docs say you can't, but maybe they weren't updated). You can in 4.10, although I can't see how to set their opacity.

In GitLab by @ThomasDowrick on May 13, 2019, 14:28

Yes, we did discuss doing this for volumes (although I forgot about it until just now!), but I don't think it is especially important at the moment, as we wont' actually get much/any useful clinical information from the 3D view. I think to show multiple volumes in 4.8 you have to make one of the volumes into a segmentation.

@JonathanShapey Do you have any thoughts as to what is the most useful thing to show in the 3D view?

In GitLab by @AnastasisGeorgoulas on May 13, 2019, 14:48

Here is how to get the opacity slider in 4.8 and 4.10, for future reference. It's in the Volume Rendering module, under multiple layers of widgets...

vrw = slicer.modules.volumerendering.widgetRepresentation()
opacity_widget = slicer.util.findChild(vrw, 'OpacitySliderWidget')
# We need the above step because there are other "Slider"s and "SpinBox"es in the module
slider = slicer.util.findChild(opacity_widget, 'Slider')
# Equivalently, can get the spin box;
# they're both tied to each other and are updated together
spinbox = slicer.util.findChild(opacity_widget, 'SpinBox')

And if we're setting its value from elsewhere:

slider.setValue(whatever)
# same for the spin box

In GitLab by @RolandGuichard on May 14, 2019, 16:55

marked the task To automate: Make the CT scan visible in the volume module and the name is blank in Slicer4.8 (this is why it doesn’t happen as to does in 4.10). A solution might be to get the node by ID and rename it to SLD-001 as soon as we fetch it from the StealthStation as completed

In GitLab by @RolandGuichard on May 14, 2019, 16:56

I've added the CT renaming and enabling of visibility in this branch.

In GitLab by @AnastasisGeorgoulas on May 15, 2019, 09:13

changed the description

In GitLab by @AnastasisGeorgoulas on May 15, 2019, 15:46

mentioned in commit 162a219a38b8cef6c23541908c2755e673d8f339

In GitLab by @AnastasisGeorgoulas on May 16, 2019, 09:41

marked the task Getting rid of the scout/live scan buttons as we are now using the ones from the PLUS remote as completed

In GitLab by @AnastasisGeorgoulas on May 16, 2019, 09:41

marked the task Autoselect the connector in the PlusRemote widget (for getting the CT image) as completed

In GitLab by @AnastasisGeorgoulas on May 16, 2019, 09:46

Our custom reconstruction button has now been renamed to Visualise and is used to set the slice viewers to the right configuration.

Have pushed a change to select the connector node automatically in ageorgou/autoselect-connector.

There was a problem with installing crcmod, one of the dependencies of the scikitsurgery-bk package that we need to automatically start the dependencies. Maybe this will not come up when setting up the new laptop (#59), but otherwise we can look into whether it is needed or how to work around it.

In GitLab by @JonathanShapey on May 16, 2019, 10:26

I think that it would be most useful to show the predefined MR tumour volume in the 3D viewer together with overlaid tractogrpahy and then have the ability bring the reconstructed ultrasound data in and out of view.

Hopefully, with further work this will evolve to just having the reconstructed US tumour volume (rather than the complete US reconstructed view). This would required the software to automatically recognise and segment out the tumour from the US data but at the moment, my understanding from @RemiDelaunay is that this is a way off.

In GitLab by @RemiDelaunay on May 16, 2019, 11:48

Yes I don't think segmenting the tumour on the US image and register it to the MRI in real-time will be possible during this study. I don't think it's crucial to see both volumes on the 3D viewer as long as you can display a 2D overlay on the other views (red/yellow/green). I don't think we would be able to see much by overlaying the two 3D volumes together anyway.

In GitLab by @ThomasDowrick on Jun 19, 2019, 10:38

marked the task With Slicer4.8 the scout scan makes the CT invisible when completed as completed

In GitLab by @ThomasDowrick on Jun 19, 2019, 10:38

Closing as remaining tick box is in a different issue already.

In GitLab by @ThomasDowrick on Jun 19, 2019, 10:38

closed

UCL / SkullBaseNavigation

Updates to make after 8-5-19 demo test #57