Transformation Information from XML File

[SDLAndrews]

Hello, I had a question regarding the information in the .xml file. I saw issue #8 , but I am still not sure how to extract transformation data from these files. I performed an affine registration on an image stack, and now I want to write an external script that will apply the transformations to a centerline. I have an example .xml file here:

`

<iict_transform invertible="true" class="mpicbg.trakem2.transform.TranslationModel2D" data="-1.0 -6.0" />

`

I am assuming that this data file would include values such as dx, dy, dz, dtheta that I could apply to the centerline. Is there some documentation on the format of this xml file so I can get this information?

[bogovicj]

Hi @SDLAndrews ,

I am assuming that this data file would include values such as dx, dy, dz, dtheta that I could apply to the centerline.

I'm not quite sure what you mean here (what are the dx,dy,dz exactly?), but maybe the explanation below will have the answer for you.

Is there some documentation on the format of this xml file so I can get this information?

There are three transformations there:

• a CoordinateTransformList that contains:
  • an AffineModel2D
  • and a TranslationModel2D

The code I linked to above shows you how the transformations are applied to points.

This code shows how to parse the xml for:

• the list
• the affine
• the translation

I imagine the list and translation will be easy for you to understand (of course, please post back if not). The affine is stored as a "flattened" 2x3 matrix in homogenous coordinate ( with the elements ordered like this m00, m10, m01, m11, m02, m12
e.g. the matrix for your example would be:

  [ 0.9977  -0.0009   0.9995 ]
  [ 0.0027  1.00701   3.4699 ]

[SDLAndrews]

From this, I am able to get a better understanding. To clarify, for the matrix you have listed here, would each term represent the following operations (for [row, column]): [1,1] = Scale along X [2,2] = Scale along Y [1,2] = Shear along X [2,1] = Shear along Y [1,3] = Translation along X [2,3] = Translation along Y

[bogovicj]

@SDLAndrews ,

You have the right idea, yes. It is not generally as simple as what you wrote though. For example, if you scale and rotate and skew, then there is no one number that tells you what the scale of X is.