Target Buffer Uint16 support? about cornerstone3d HOT 6 CLOSED

cornerstonejs commented on June 18, 2024

Target Buffer Uint16 support?

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sedghi commented on June 18, 2024 2

Yeah I started this yesterday, there are some parts in wado that need to be changed too

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swederik commented on June 18, 2024 1

So there are a couple options. You need to minimize both RAM and VRAM but their usage is not 1:1 depending on the WebGL internal format. If you have a Uint16 array and pass it through the pipeline now it can be mapped to half float as an internal format but this has less precision that 16 bits (see https://en.m.wikipedia.org/wiki/Half-precision_floating-point_format) so it might not completely accurately represent the image. If the range of the image is within a specific range it will, though (I think something like 0-3000ish, it's in the half float conversion code in vtk). There is another option which is here but it's not merged yet: Kitware/vtk-js#2058 which will allow Int16 to be faithfully represented using the EXT_texture_norm16 extension. That is probably a better option for the Tomo I think Having said that, I think we would use a stack viewport for tomo and not make one massive buffer anyway. Especially because the array buffer length for the whole volume is likely going to exceed the chrome max array buffer length of around 2gb.

…

On Tue., Jun. 28, 2022, 5:53 a.m. Ouwen Huang, ***@***.***> wrote: I noticed that when loading the image we provide a target buffer of either Float32 or Uint8. In cornerstonejs I believe there was support for Uint16 type. Larger medical image volumes (tomo) can be quite large when decompressed (200 slices of 2000x3000 uint16 pixels). This would translate to about 2.4GB if the native Uint16 is used, but would double to 4.8GB using Float32. I was curious if there were any challenges in supporting uint16 with the underlying vtk engine. — Reply to this email directly, view it on GitHub <#141>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAEUMMP3PB4VARFDYWOSHVLVRJZKDANCNFSM52AVMITQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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sedghi commented on June 18, 2024 1

Hey, it is not a priority but on the roadmap

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Ouwen commented on June 18, 2024

Thanks for the above @swederik, just starting to revisit this issue now that Kitware/vtk-js#2058 is merged.

@sedghi, based on our conversation today... I was looking through where changes would need to have a cornerstone3D flag to use 16bit/half float. My understanding based on our conversation is that if the vtk mapper sets the preferSizeOverAccuracy flag to true it will properly use norm 16 or half float depending on the extensions available.

For norm16 and half float to be used, it requires the data provided to VTK to either be UNSIGNED_SHORT or SHORT (uint16/int16), but we currently type cast to Float32 in cornerstonejs

For half float implementation, it seems like the dynamic range is scaled to better fall in between [-2048, 2048] for accuracy purposes. For dicom pixel data, the BitsStored is usually smaller than BitsAllocated. For CT machines it is usually 12 bit stored and 16 bit allocated. Uint16 values beyond the BitsStored is typically burned in data where the dynamic range is less important. When we transition to the UNSIGNED_SHORT or SHORT dtype, it might make sense to clamp the data to BitsStored so the important part of the pixelData can be better preserved.

Here are the immediate code lines which might need to be changed:

https://github.com/cornerstonejs/cornerstone3D-beta/blob/d58c9fbe3f8bfc09aa9ece28f8ae1ca1141c2c7e/packages/core/src/RenderingEngine/vtkClasses/vtkStreamingOpenGLTexture.js#L59-L70

https://github.com/cornerstonejs/cornerstone3D-beta/blob/d58c9fbe3f8bfc09aa9ece28f8ae1ca1141c2c7e/packages/core/src/volumeLoader.ts#L234-L248

https://github.com/cornerstonejs/cornerstone3D-beta/blob/d58c9fbe3f8bfc09aa9ece28f8ae1ca1141c2c7e/packages/core/src/RenderingEngine/StackViewport.ts#L1198-L1223

https://github.com/cornerstonejs/cornerstone3D-beta/blob/d58c9fbe3f8bfc09aa9ece28f8ae1ca1141c2c7e/packages/streaming-image-volume-loader/src/cornerstoneStreamingImageVolumeLoader.ts#L109-L137

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Zelzahn commented on June 18, 2024

Hey @sedghi, what's the current status of this?

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sedghi commented on June 18, 2024

Done in main branch

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Target Buffer Uint16 support? about cornerstone3d HOT 6 CLOSED

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