LoadImage Transform returns transposed image in MONAI 0.7.0

[aarpon]

Describe the bug
The monai.transforms.LoadImage Transformer (independent of the reader used) erroneously returns a transpose of the image in MONAI 0.7.0, whereas it returned the correct image in previous versions.

To Reproduce
It is most obvious when the image is not square. I saw it when using images with shape (700, 1100).

With MONAI == 0.6.0:

from monai.transforms import LoadImage
loadImage = LoadImage()
out = loadImage("filename")   // shape = (700, 1100)

With MONAI == 0.7.0:

from monai.transforms import LoadImage
loadImage = LoadImage()
out = loadImage("filename")   // shape = (1100, 700)

Changing the reader does not change the behavior.

Expected behavior
The behavior of LoadImage in 0.7.0 should be the same as in previous versions and consistent both with other readers and with the Numpy logic of shape = (rows, columns).

Environment

MONAI 0.6.0:

MONAI version: 0.6.0
Numpy version: 1.21.2
Pytorch version: 1.9.1+cu102
MONAI flags: HAS_EXT = False, USE_COMPILED = False
MONAI rev id: 0ad9e73639e30f4f1af5a1f4a45da9cb09930179

Optional dependencies:
Pytorch Ignite version: 0.4.5
Nibabel version: 3.2.1
scikit-image version: 0.18.3
Pillow version: 8.4.0
Tensorboard version: 2.7.0
gdown version: 4.2.0
TorchVision version: 0.10.1+cu102
ITK version: 5.1.2
tqdm version: 4.62.3
lmdb version: 1.2.1
psutil version: 5.8.0
pandas version: 1.3.4
einops version: 0.3.2

MONAI 0.7.0:

================================
Printing MONAI config...
================================
MONAI version: 0.7.0
Numpy version: 1.21.2
Pytorch version: 1.9.1+cu102
MONAI flags: HAS_EXT = False, USE_COMPILED = False
MONAI rev id: bfa054b9c3064628a21f4c35bbe3132964e91f43

Optional dependencies:
Pytorch Ignite version: 0.4.5
Nibabel version: 3.2.1
scikit-image version: 0.18.3
Pillow version: 8.4.0
Tensorboard version: 2.7.0
gdown version: 4.2.0
TorchVision version: 0.10.1+cu102
tqdm version: 4.62.3
lmdb version: 1.2.1
psutil version: 5.8.0
pandas version: 1.3.4
einops version: 0.3.2
transformers version: 4.11.3

[rijobro]

Just had a very brief look so adding more information -- our unit tests only use cubic images of (128,128,128), so we wouldn't notice this sort of problem. Certainly something that needs to be rectified.

[Nic-Ma]

Hi @rijobro @aarpon ,

To be consistent with other libraries, we added logic to switch the axis in MONAI v0.7:
https://github.com/Project-MONAI/MONAI/blob/dev/monai/data/image_reader.py#L641
We have received 2 feedback related to it, maybe I need to add some doc-string to make it clear.

Thanks.

[Nic-Ma]

Enhanced the doc-string of axis order in PR: #3247.

Thanks.

[aarpon]

Thanks! I'll be happy to test and report.