BrownBiomechanics / SlicerAutoscoperM

This 3D Slicer extension enables users to perform image registration.

https://autoscoperm.slicer.org

MIT License

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Virtual Radiograph Generation Module #53

Closed NicerNewerCar closed 7 months ago

NicerNewerCar commented 11 months ago

Static 3DCT Radiograph generation support

This PR enables the support of virtual radiograph (VRG) generation of static 3DCT volumes
Allows for VRG generation to use either manually placed cameras (markup fiducials) or automatically optimized cameras
Adds CalculateDataIntensityDensity CLI module
- For evaluating each VRG
Adds VirtualRadiographGeneration CLI module
- For rendering a VRG using VTK
Updates the pre-processing tab to use the above CLI modules
- See documentation PR https://github.com/BrownBiomechanics/Autoscoper/pull/202
After this is integrated two follow-up PRs will be opened
- To add a CLI module to perform segmentation
- To add support for Sequential 3DCT and 4DCT

Final ToDo:

[x] Update version of Autoscoper used once the following PRs have been merged over there:
- https://github.com/BrownBiomechanics/Autoscoper/pull/147
- https://github.com/BrownBiomechanics/Autoscoper/pull/202
[x] Better support for getting output from CLI modules (ie not just reading the output) -> See #55
[x] Better event handlers for CLI modules -> See #55

amymmorton commented 10 months ago

Awesome, all tabs tested with PRE PROC LEFT Hop Knee . vrgGenSuces

amymmorton commented 10 months ago

When existing- had issues:

onExit

NicerNewerCar commented 10 months ago

When existing- had issues:

Already fixed see #52

amymmorton commented 9 months ago

after generating a config file- the camera yaml file fails to read in yamlCamerr

NicerNewerCar commented 9 months ago

after generating a config file- the camera yaml file fails to read in

Looks like I forgot to change the yaml file to a json file in the name, sorry about that. Should be good to go now.

amymmorton commented 7 months ago

On launch: dllLoaderr_vrggen

Where did we land with the batch generation of multiple volumes? For a given series of 3d volumes- we'll want to process and create a cfg

vols

NicerNewerCar commented 7 months ago

Where did we land with the batch generation of multiple volumes? For a given series of 3d volumes- we'll want to process and create a cfg

I think it makes the most sense to include the 3d series with the 4DCT PR since Slice represents them with the same data structure.

amymmorton commented 7 months ago

vtk_vrg 0

The auto cam placement seems to have stalled/crashed at 40%: crash40

NicerNewerCar commented 7 months ago

Fixed the stalling, with the auto placement.

jcfr commented 7 months ago

I am addressing the issues

calculateDataIntensityDensity -> CalculateDataIntensityDensity virtualRadiographGeneration -> VirtualRadiographGeneration

jcfr commented 7 months ago

Renamed modules:

calculateDataIntensityDensity -> CalculateDataIntensityDensity
virtualRadiographGeneration -> VirtualRadiographGeneration

Rename VirtualRadiographGeneration parameters:

outputFName -> outputFileName
width -> outputWidth
height -> outputHeight

Update check of CalculateDataIntensityDensity parameters to be consistent with how CalculateDataIntensityDensity are checked.

jcfr commented 7 months ago

Since the CLI are not directly used, I also suggest to move the CLI modules into a called Tracking.Advanced:

How does that sound ?

NicerNewerCar commented 7 months ago

Since the CLI are not directly used, I also suggest to move the CLI modules into a called Tracking.Advanced:

How does that sound ?

Makes sense, I think that's fine.