Incorrect slicing in drishtiimport

[RendersJens]

The following Python snippet generates a volume and stores it as a (float32) tiff stack:

import tomopy
import dxchange

data = tomopy.shepp3d(128)
data = data[:,:120, :] #make sure the slices will be non-square, otherwise the bug does not show
dxchange.write_tiff_stack(data, "shepp/slice")

When loading this tiff stack into drishtiimport, the slicing in the X and Y direction goes wrong seemingly because the the width and height of the tiffs are swapped (the slices show a varying shift in the Y direction).

[AjayLimaye]

H RendersJen, Can you send me the tiff image stack to figure out the solution. Cheers, Ajay

On Tue, Mar 2, 2021 at 9:32 PM RendersJens notifications@github.com wrote:

The following snippet generates a volume and stores it as a (float32) tiff stack:

import tomopy import dxchange

data = tomopy.shepp3d(128) data = data[:,:120, :] #make sure the slices will be non-square, otherwise the bug does not show dxchange.write_tiff_stack(data, "shepp/slice")

When loading this tiff stack into drishtiimport, the slicing in the X and Y direction goes wrong seemingly because the the width and height of the tiffs are swapped (the slices show a varying shift in the Y direction).

[image: image] https://user-images.githubusercontent.com/43435876/109635533-c81be600-7b4a-11eb-88f0-5dcf14903716.png [image: image] https://user-images.githubusercontent.com/43435876/109635571-d4a03e80-7b4a-11eb-98de-9b6dbd93cad2.png

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Ajay Limaye

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[image: cid:image002.png@01D449EE.B750D8C0]

[RendersJens]

Sure, here it is: shepp.zip This is just and example though, it happens everytime when the tiffs are not square. You can generate more examples by editing the Python snippet above.

Thank you for looking in to it! Jens

[AjayLimaye]

Hi Jens, I am unable to reproduce the bug. What version of Drishti do you have? Cheers, Ajay [image: image.png]

On Wed, Mar 3, 2021 at 9:26 AM RendersJens notifications@github.com wrote:

Sure, here it is: shepp.zip https://github.com/nci/drishti/files/6072182/shepp.zip This is just and example though, it happens everytime when the tiffs are not square. You can generate more exampels by editing the Python snippet above.

Thank you for looking in to it! Jens

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[RendersJens]

I was using v2.6.3 (linux) and v2.6.5 (windows), but I also tested it in the latest release v2.7 (linux) and in all cases the bug is there. I see that you attached an image to your comment but it is not uploaded correctly. so I cannot see it.

Jens

[AjayLimaye]

[image: image.png]

On Wed, Mar 3, 2021 at 11:52 PM RendersJens notifications@github.com wrote:

I was using v2.6.3, but I also tested it in the latest release v2.7 (linux) and in both cases the bug is there. I see that you attached an image to your comment but it is not uploaded correctly. so I cannot see it.

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[AjayLimaye]

This one was tested on Windows PC, do you have access to a Windows machine ?

On Thu, Mar 4, 2021 at 9:04 AM Ajay Limaye limaye.ajay@gmail.com wrote:

[image: image.png]

On Wed, Mar 3, 2021 at 11:52 PM RendersJens notifications@github.com wrote:

I was using v2.6.3, but I also tested it in the latest release v2.7 (linux) and in both cases the bug is there. I see that you attached an image to your comment but it is not uploaded correctly. so I cannot see it.

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[RendersJens]

I do, as I said in the previous comment, I saw the bug on v2.6.5 on windows as well. Perhaps that didn't come trough because I edited it later. The image still doesn't come trough, can you check the thread on the github website instead of commenting via email? I think that is the cause of the issue.

Thanks again! Jens

[AjayLimaye]

[RendersJens]

Alright, I see the image now, thank you. This is the same as what I see, the slices look correct when viewing the Z axis in drishtiimport. But once you select the X or Y axis (then the slices are different from the stored tiffs) the bug appears. This is what I show on my screenshots.

Jens

[AjayLimaye]

Ok, got it - yes need to fix slice display in the importer.

[AjayLimaye]

Fixed it - will be available with the next release. Thanks for detecting the bug

[RendersJens]

Great, thanks for the fix!