Unit test for image_arithm - Githubissues

OpenGATE / GateTools

Python tools and functions for Gate

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Unit test for image_arithm #3

Closed tbaudier closed 5 years ago

tbaudier commented 5 years ago

Hi @djboersma

I debug your unit test for image arithm: https://github.com/OpenGATE/GateTools/blob/34fc70a4f4dbe247516e12e3ff04631d67770c65/gatetools/image_arithm.py#L161

First https://github.com/OpenGATE/GateTools/blob/34fc70a4f4dbe247516e12e3ff04631d67770c65/gatetools/image_arithm.py#L112 you need to add the Update line like this:

         op_instance.SetInput(i,img)
    op_instance.Update()
    return _image_output(op_instance.GetOutput(),output_file)

With itk, all filters need to be updated to create the output. This is why the unit test failed, the output did not exist and it created a segfault.

Next, I suggest you some modifications:

np.arrange(stop) function create an array from 0 to stop -1. So I suggest you to remove 1 to all your tests: https://github.com/OpenGATE/GateTools/blob/34fc70a4f4dbe247516e12e3ff04631d67770c65/gatetools/image_arithm.py#L167 https://github.com/OpenGATE/GateTools/blob/34fc70a4f4dbe247516e12e3ff04631d67770c65/gatetools/image_arithm.py#L169 https://github.com/OpenGATE/GateTools/blob/34fc70a4f4dbe247516e12e3ff04631d67770c65/gatetools/image_arithm.py#L174 https://github.com/OpenGATE/GateTools/blob/34fc70a4f4dbe247516e12e3ff04631d67770c65/gatetools/image_arithm.py#L180 https://github.com/OpenGATE/GateTools/blob/34fc70a4f4dbe247516e12e3ff04631d67770c65/gatetools/image_arithm.py#L185
https://github.com/OpenGATE/GateTools/blob/34fc70a4f4dbe247516e12e3ff04631d67770c65/gatetools/image_arithm.py#L167 I'm not sure the syntax .GetPixel((1,1)) is correct. You may consider to use:
```
index = imgCf.GetLargestPossibleRegion().GetSize() -1
self.assertTrue( imgCf.GetPixel(index) == 4.*5. -1.)
```
Adapt the sum filter to the input data adding
```
valtype=itk.US
```
into https://github.com/OpenGATE/GateTools/blob/34fc70a4f4dbe247516e12e3ff04631d67770c65/gatetools/image_arithm.py#L172 https://github.com/OpenGATE/GateTools/blob/34fc70a4f4dbe247516e12e3ff04631d67770c65/gatetools/image_arithm.py#L183
Remove sitk dependency https://github.com/OpenGATE/GateTools/blob/34fc70a4f4dbe247516e12e3ff04631d67770c65/gatetools/image_arithm.py#L103

Thomas

djboersma commented 5 years ago

I think that this is all fixed now. Thanks! :+1: