[Question] Visualize the augmented data.

[ArpanGyawali]

I am working on LVO detection. I used the base_more augmentation with some modification. I only wanted rotation on z-axis and only horizontal flip on axial view. So i changed the miror axis to [0]. But i am not sure i did the right thing.
So, i wanted to know if there is a way to visualize the augmented data? Or if i need to create my own script?
Even if i am right or wrong in the case of mirroring, it would be great if i would be able to visualize those dataset.
Thanks.

[mibaumgartner]

Dear @ArpanGyawali ,

there is no build in way of visualising the augmented data, so you need to write your own script.

Best,
Michael

[ArpanGyawali]

Thanks @mibaumgartner
Can you give some insights to in?
Where can i start from?
Where the data is loaded before training and after augmentation?

[ArpanGyawali]

hi @mibaumgartner @partha-ghosh
Also in addition, do you have some say regarding the mirror axis stated in above question.

[partha-ghosh]

Hi @ArpanGyawali,
You can run the code in single threaded mode with multiprocessing: False in the config file. If you debug through the code you will find the data is being loaded in here:

nnDetection/nndet/io/datamodule/bg_loader.py

Line 185 in b0504dc

def generate_train_batch(self) -> Dict[str, Any]:

and the transforms are being applied in batchgenerators: https://github.com/MIC-DKFZ/batchgenerators/blob/f53025bd05fe9642133ac539a0df3559d82415b4/batchgenerators/dataloading/single_threaded_augmenter.py#L38

The documentation on MirrorTransform from batchgenerators says: 'Randomly mirrors data along specified axes. Mirroring is evenly distributed. Probability of mirroring along each axis is 0.5'

Best,
Partha

[mibaumgartner]

Dear @ArpanGyawali ,

please note that nnDetection transposes the data during its preprocessing -> the anisotropic axes (usually denoted by z) is moved to the first position (i.e. index 0). The definition of left/right depends on you data since the other axis do not change their ordering. Setting the mirror axis to [0] results in mirroring which is only performed along the z direction.

Having a visual look is definitely recommended when manipulating augmentation settings :)

Best,
Michael

[ArpanGyawali]

@mibaumgartner @partha-ghosh
Thanks, i will try to do something for visualizing the augmented images.
If i run into some issue then, i shall ask for help.