CERN / CERN/TIGRE

Geometry direction

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Python
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Description

Hi

I am trying to understanding the geometric direction assumed in this toolbox. The python implementation is used.

Let's take Demo 03: Simple Image as an example.

This is the first slice of the projection.
![proj1](https://user-images.githubusercontent.com/11166542/77696246-0a23cb80-6f7b-11ea-9901-6d6a32a4cac4.png)

Diagram shows the geometric definition in the Ander Biguri's Thesis (page 76)
![Screenshot_20200326_160426](https://user-images.githubusercontent.com/11166542/77696514-80c0c900-6f7b-11ea-8da6-4525ce9de40b.png)

Slice in the 1st, 2nd, and 3rd dimension of the reconstruction image volume, e.g. imgOSSART[25], imgOSSART[:, 25], and imgOSSART[..., 25] respectively.
![1](https://user-images.githubusercontent.com/11166542/77698132-1bbaa280-6f7e-11ea-8f46-760bb2cdaeb0.png)
![2](https://user-images.githubusercontent.com/11166542/77696893-e2813300-6f7b-11ea-8443-d98c3498a0bd.png)
![3](https://user-images.githubusercontent.com/11166542/77696925-e44af680-6f7b-11ea-935c-e5e5c426a0c2.png)

My confusion comes from here: from the projection image and the diagram of the geometry, the x, y, z direction of the coordinate system seem are parallel with Medial/Lateral, Anterior/Posterior, and Superior/Inferior respectively. In combined with the observation of the slice of the reconstructed volume, the order of the dimension of the volume seems to be organized as [Z, Y, X]. It is a little bit odd for me to have a volume to be organized in this way. In addition, in the function of plotimg, it seems the order is assumed to be [X, Y, Z].

I am not sure if my understanding is correct, so I would like to have your clarification. Thank you!

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