How to open .TRE file?

Duy_H · December 18, 2019, 5:21am

Dataset at “https://public.kitware.com/Wiki/TubeTK/Data” have “VascularNetwork.tre” file. How can i open this file using Python?

matt.mccormick · December 18, 2019, 1:26pm

Hi @Duy_H,

Welcome to ITK!

To read VascularNetwork.tre,

import itk

file_name = '/tmp/path/to/VascularNetwork.tre'

Dimension = 3
reader = itk.SpatialObjectReader[Dimension].New()
reader.SetFileName(file_name)
reader.Update()

tubes = reader.GetGroup()
print(tubes)

alib022 · March 20, 2020, 7:22pm

@matt.mccormick thanks for this.
I am trying to convert the .tre into Nifi file. Looking at old TubeTK example files. I tried to use SpatialObjectToImageFilter with not much luck. Any idea how to convert the tre into a binary mask?

Thanks
Ali

matt.mccormick · March 20, 2020, 8:40pm

Hi Ali,

@Stephen_Aylward has started notebook that demonstrates this here:

github.com

KitwareMedical/ITKTubeTK/blob/master/examples/ConvertTubesToImage.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Convert Tubes To Images"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This notebook contains a few examples of how to call wrapped methods in itk and ITKTubeTK."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [

This file has been truncated. show original

HTH,
Matt

alib022 · March 20, 2020, 8:44pm

@matt.mccormick Thank you so much for the quick response. I am trying to see if I can do it without TubeTK since it’s a real pain to install it. I will see what I can do with this.

Never-less thank you so much for the quick response.

alib022 · March 21, 2020, 5:54pm

@matt.mccormick I spent a lot of time compiling ITK with Module_TubeTK and I am getting errors.

Targets not yet defined:
ITKBioCell;ITKFEM;itkgdcmopenjp2;ITKIOMesh;ITKReview;IsotropicWavelets

Do you have any suggestions to resolve this? I am following your instructions from this:

Any idea?
Ali

dzenanz · March 21, 2020, 7:29pm

@Stephen_Aylward what are the most up-to-date build instructions for TubeTK?

Stephen_Aylward · March 21, 2020, 7:34pm

Build ITK and turn on the TubeTK option.

Only works with ITK master (head) source code.

s

alib022 · March 22, 2020, 12:37pm

@Stephen_Aylward thanks, but I did that. Compiled ITK, then again for TubeTK, and the following error showed at 95% progress

[ 95%] Generating itkGEAdwImageIOPython.cpp, …/…/…/lib/itkGEAdwImageIOPython.py
swig: …/…/swig/Source/Modules/lang.cxx:1657: virtual int Language::enumDeclaration(Node*): Assertion `Getattr(n, “sym:name”)’ failed.
Aborted (core dumped)
Wrapping/Modules/ITKIOGE/CMakeFiles/ITKIOGEPython.dir/build.make:117: recipe for target ‘Wrapping/Modules/ITKIOGE/itkGEAdwImageIOPython.cpp’ failed
make[2]: *** [Wrapping/Modules/ITKIOGE/itkGEAdwImageIOPython.cpp] Error 134
make[2]: *** Deleting file ‘Wrapping/Modules/ITKIOGE/itkGEAdwImageIOPython.cpp’
CMakeFiles/Makefile2:55091: recipe for target ‘Wrapping/Modules/ITKIOGE/CMakeFiles/ITKIOGEPython.dir/all’ failed
make[1]: *** [Wrapping/Modules/ITKIOGE/CMakeFiles/ITKIOGEPython.dir/all] Error 2
Makefile:162: recipe for target ‘all’ failed
make: *** [all] Error 2

Stephen_Aylward · March 22, 2020, 2:01pm

Hi,

Sorry that you’re having troubles. That seems like a bug in the IOGE module.

Are you trying to compile the executables in TubeTK? I’ve got a branch in my private repo to fix some bugs in the apps since the merge, but it does seem like your bug is unrelated. In general, if you don’t need the applications, you should compile ITK with the TubeTK module enabled from the start - there is no need to recompile. The C++ and python interfaces should then work fine.

s

alib022 · March 22, 2020, 2:12pm

Hi Stephen,

Thanks for following up. To be honest, I just need to convert a series of TRE files into NIFTI mask. I dont even need TubeTK. Do you have any code which uses ITK only to convert TRE files into NIFTI mask?

Thanks

alib022 · March 22, 2020, 2:16pm

And also, I am getting the above error when I am compiling ITK with TubeTK enabled from start. Based on your suggestion, I thought I have to compile ITK first to build these targets, then recompile. But, again, I dont really need TubeTK, I am only interested to convert a series of TRE file into NIFTI mask.

Stephen_Aylward · March 22, 2020, 2:33pm

There is a Jupyter Notebook that converts TRE to an image using only ITK (no TubeTK):

https://github.com/KitwareMedical/ITKTubeTK/blob/master/examples/ITKSpatialObjects-SimpleExample.ipynb

It only generates an image of the centerlines of the tubes, but perhaps that is enough? You could also build upon it to have it generate the radius without too much additional work.

That is surprising that your ITK isn’t compiling! Are you using ITK head/master? Does it compile without TubeTK enabled?

Thanks,

Stephen

alib022 · March 22, 2020, 3:40pm

Thanks much @Stephen_Aylward

I am trying that example, so far I am getting error:
module ‘itk’ has no attribute ‘CastSpatialObjectFilter’

Regarding the compile, I did try to compile on a fresh server with TubeTK enabled, but it requires those targets which are not available unless I compile the ITK first. Then I can configure the cmake to compile TubeTK and that’s what I did and finally got another error that I mentioned earlier.

Stephen_Aylward · March 22, 2020, 3:48pm

Hi,

It seems like you are not compiling ITK master/head, otherwise it would find CastSpatialObjectFilter. If you are using an older version of ITK, then TubeTK is very likely not going to work. Sorry.

Stephen

alib022 · March 22, 2020, 3:51pm

Stephen,

I am almost certain, but I will double check. Thanks
Ali

alib022 · March 22, 2020, 7:05pm

@Stephen_Aylward First of all, thanks for all the help.
So I managed to convert to nifti, but I am trying to make sense of the centerline position compare to image coordinate. Seems like each object has it’s own coordinate system which is not absolute, is that correct? If so, how compute the world coordinate system for each object? Is there any conversion matrix in each object?

Btw, I am not using cast, I am using the following code:
…
baseSO = sobj[iterChikdID]
baseSOTyped = itkExtras.down_cast(baseSO)

for iterObjectID in range(0,baseSOTyped.GetNumberOfPoints()):
    
    
    position = baseSOTyped.GetPoint(iterObjectID).GetPositionInObjectSpace()
    indx = mra.TransformPhysicalPointToIndex(position)
    mra.SetPixel(indx, 100000)

…

Stephen_Aylward · March 22, 2020, 7:20pm

Hi

Congratulations on the progress!

Is it correct that you are loading a tre file from one patient and displaying it within the mra from that same patient? Is this one of the mra from the database at kitware.com?

Each patient has a unique coordinate space, so vessels from one patient won’t align with vessels or scans from another patient.

In theory you should be calling GetPositionInWorldSpace() instead of GetPositionInObjectSpace(), but that only matters if you have created a hierarchy of objects. I’d have to see the tre file to determine if that is what is happening.

Hope this helps. Sorry for bevity, typing on a phone while in a forest

S

alib022 · March 22, 2020, 7:27pm

@Stephen_Aylward, it wouldnt happened without your help

I am using the same subject data (Normal002_MRA and it’s tre file). I tried the WorldSpace and getting the following error:
The SpatialObject must be set prior to calling.

I have to figure out how to that. But is there anyway to find the conversion matrix of each object?

I really appreciate your response while in a forest!

Stephen_Aylward · March 22, 2020, 10:11pm

Hi

I again suspect that you are seeing an old bug.

When did you clone and update itk last?

S