# SimpleITK - Convert .txt to .h5

**URL:** <https://discourse.itk.org/t/simpleitk-convert-txt-to-h5/7041>\
**Category:** Uncategorized\
**Tags:** simpleitk\
**Created:** [July 10, 2024, 8:20pm UTC](https://discourse.itk.org/t/simpleitk-convert-txt-to-h5/7041 "2024-07-10T20:20:57Z")\
**Posts on this page:** 6\
**Page:** 1

<div class="post-metadata">

**Author:** ![smeisler](https://discourse.itk.org/user_avatar/discourse.itk.org/smeisler/32/4106_2.png) [@smeisler](https://discourse.itk.org/u/smeisler)\
**Post date:** [July 10, 2024, 8:20pm UTC](https://discourse.itk.org/t/simpleitk-convert-txt-to-h5/7041/1 "2024-07-10T20:20:57Z")

</div>

Hello community,

I have a .txt file describing a 6-param rigid body alignment output from AFNI 3dvolreg, converted to ITK style. It has 383 transforms, each one corresponding to a volume to the timeseries it is associated with. The first few and last one are listed below:

```auto
#Insight Transform File V1.0
#Transform 0
Transform: AffineTransform_double_3_3
Parameters: 1 -8.57331e-05 -2.12192e-05 8.57352e-05 1 9.70602e-05 2.12109e-05 -9.7062e-05 1 0.00492098 -0.0215674 0.0185717
FixedParameters: 0 0 0
#Transform 1
Transform: AffineTransform_double_3_3
Parameters: 1 0.000548586 0.000161739 -0.000548728 0.999999 0.000881086 -0.000161255 -0.000881175 1 -6.95764e-05 -0.0130985 -0.0357127
FixedParameters: 0 0 0
#Transform 2
Transform: AffineTransform_double_3_3
Parameters: 1 0.000680698 0.000177318 -0.000680773 1 0.000424417 -0.000177029 -0.000424537 1 -0.0124846 -0.0175981 -0.132785
FixedParameters: 0 0 0
........
#Transform 382
Transform: AffineTransform_double_3_3
Parameters: 0.999996 0.00230603 0.00149425 -0.00229953 0.999988 -0.00433795 -0.00150424 0.0043345 0.999989 0.0429203 0.174521 -0.231928
FixedParameters: 0 0 0

```

My goal is to convert this to an .h5 file for compatibility with some of our registration workflows. What I was trying was something like this:

```auto
import SimpleITK as sitk
txt_xfm_path = "/path/to/xfm.txt" # File described above
h5_out = "/path/to/xfm.h5" # Desired output file
txt_xfm = sitk.ReadTransform(xfm_path)
xfm_obj = sitk.AffineTransform(txt_xfm)
sitk.WriteTransform(xfm_obj, h5_out)

```

While this doesn’t throw an error, I get a warning when loading the txt file:

```auto
WARNING: In /home/conda/feedstock_root/build_artifacts/libsimpleitk_1701713288428/work/Code/Common/src/sitkTransform.cxx, line 674
There is more than one transform in the file! Only using the first transform.

```

Is there a way I can load the file and use all of the embedded transforms?

Thanks,  
Steven

---

<div class="post-metadata">

**Author:** ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Post date:** [July 10, 2024, 9:04pm UTC](https://discourse.itk.org/t/simpleitk-convert-txt-to-h5/7041/2 "2024-07-10T21:04:07Z")

</div>

That should be possible using ITK (instead of SimpleITK). Transform-related code sample [here](https://docs.itk.org/en/latest/learn/python_quick_start.html#itk-and-numpy) should get you started.

---

<div class="post-metadata">

**Author:** ![smeisler](https://discourse.itk.org/user_avatar/discourse.itk.org/smeisler/32/4106_2.png) [@smeisler](https://discourse.itk.org/u/smeisler)\
**Post date:** [July 10, 2024, 9:22pm UTC](https://discourse.itk.org/t/simpleitk-convert-txt-to-h5/7041/3 "2024-07-10T21:22:25Z")

</div>

Great, thanks for pointing me there! Yes, it looked like the following worked:

```auto
import itk
txt_xfm_path = '/path/to/xfm.txt'
h5_out = "/path/to/xfm.h5"
txt_xfm = itk.transformread(txt_xfm_path)
itk.transformwrite(txt_xfm, h5_out)

```

Still yet to see if this works with our pipeline as expected, but at the very least, I could say with more confidence that all transforms are contained in that output H5.

Best,  
Steven

---

<div class="post-metadata">

**Author:** ![cookpa](https://discourse.itk.org/user_avatar/discourse.itk.org/cookpa/32/255_2.png) [@cookpa](https://discourse.itk.org/u/cookpa)\
**Post date:** [July 10, 2024, 10:27pm UTC](https://discourse.itk.org/t/simpleitk-convert-txt-to-h5/7041/4 "2024-07-10T22:27:21Z")

</div>

I have made composite transforms using SimpleITK, using

`composite = sitk.CompositeTransform(list_of_transform_objects) sitk.WriteTransform(composite, outFile)`

As always, the order of transforms (and whether they need to be inverted with a call to GetInverse()) is important!

EDIT: But it seems SimpleITK won’t read multiple transforms from a txt file.

---

<div class="post-metadata">

**Author:** ![blowekamp](https://discourse.itk.org/user_avatar/discourse.itk.org/blowekamp/32/79_2.png) [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Post date:** [July 10, 2024, 11:14pm UTC](https://discourse.itk.org/t/simpleitk-convert-txt-to-h5/7041/5 "2024-07-10T23:14:17Z")

</div>

> [@cookpa](#):
>
> EDIT: But it seems SimpleITK won’t read multiple transforms from a txt file.

I had not seen this use case before.

Please add a feature request to the SimpleITK Github issues: [Issues · SimpleITK/SimpleITK · GitHub](https://github.com/SimpleITK/SimpleITK/issues)

---

<div class="post-metadata">

**Author:** ![cookpa](https://discourse.itk.org/user_avatar/discourse.itk.org/cookpa/32/255_2.png) [@cookpa](https://discourse.itk.org/u/cookpa)\
**Post date:** [July 11, 2024, 1:48pm UTC](https://discourse.itk.org/t/simpleitk-convert-txt-to-h5/7041/6 "2024-07-11T13:48:08Z")

</div>

Thanks @blowekamp , added

> <https://github.com/SimpleITK/SimpleITK/issues/2152>
>
> \*\*Is the feature request related to a problem? Please describe.\*\*
> 
> As reported… on \[discourse\](https://discourse.itk.org/t/simpleitk-convert-txt-to-h5/7041)
> 
> Given a list of affine transforms in a single text file, eg
> 
> \`\`\`
> \#Insight Transform File V1.0
> \#Transform 0
> Transform: AffineTransform\_double\_3\_3
> Parameters: 1 -8.57331e-05 -2.12192e-05 8.57352e-05 1 9.70602e-05 2.12109e-05 -9.7062e-05 1 0.00492098 -0.0215674 0.0185717
> FixedParameters: 0 0 0
> \#Transform 1
> Transform: AffineTransform\_double\_3\_3
> Parameters: 1 0.000548586 0.000161739 -0.000548728 0.999999 0.000881086 -0.000161255 -0.000881175 1 -6.95764e-05 -0.0130985 -0.0357127
> FixedParameters: 0 0 0
> \#Transform 2
> Transform: AffineTransform\_double\_3\_3
> Parameters: 1 0.000680698 0.000177318 -0.000680773 1 0.000424417 -0.000177029 -0.000424537 1 -0.0124846 -0.0175981 -0.132785
> FixedParameters: 0 0 0
> \`\`\`
> 
> ITK can read this into a list of transforms
> 
> \`\`\`
> \>\>\> import itk
> \>\>\> txt\_xfm = itk.transformread('transform\_list.txt')
> \>\>\> txt\_xfm 
> \[\<itk.itkAffineTransformPython.itkAffineTransformD3; proxy of \<Swig Object of type 'itkAffineTransformD3 \*' at 0x7ff198551b10\> \>, \<itk.itkAffineTransformPython.itkAffineTransformD3; proxy of \<Swig Object of type 'itkAffineTransformD3 \*' at 0x7ff1985466f0\> \>, \<itk.itkAffineTransformPython.itkAffineTransformD3; proxy of \<Swig Object of type 'itkAffineTransformD3 \*' at 0x7ff198551a80\> \>\]
> \>\>\> 
> \`\`\`
> 
> However, SimpleITK will only read the first one
> 
> \`\`\`
> \>\>\> import SimpleITK as sitk
> \>\>\> transform = sitk.ReadTransform('transform\_list.txt')
> WARNING: In /Users/runner/work/1/sitk/Code/Common/src/sitkTransform.cxx, line 674
> There is more than one transform in the file! Only using the first transform.
> \`\`\`
> 
> \*\*Describe the proposed solution\*\*
> Return the list of transforms for consistency with ITK Python.
> 
> \*\*Describe any alternatives to consider\*\*
> Return a composite transform.
> 
> \*\*Additional context\*\*