EnsureChannelFirst behaves wrong when loading npy files

[danieltudosiu]

Describe the bug
When we are loading .npy files EnsureChannelFirst does not behave as expected because it casts the .npy data to MetaTensor if it is not one and then it picks the channel dimension from the MetaTensor ignoring the passed channel_dim that was passed at construction.

Expected behavior
If a channel_dim is passed then EnsureChannelFirst should move that channel_dim to the first dimension while ignoring the information in the MetaTensor and overwriting the required fields in the MetaTensor.

Environment

Ensuring you use the relevant python executable, please paste the output of:

================================
Printing MONAI config...
================================
MONAI version: 1.0.0
Numpy version: 1.22.1
Pytorch version: 1.11.0+cu113
MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: 170093375ce29267e45681fcec09dfa856e1d7e7
MONAI __file__: /home/danieltudosiu/projects/green-roof-retrofit/venv/lib/python3.8/site-packages/monai/__init__.py

Optional dependencies:
Pytorch Ignite version: 0.4.6
Nibabel version: NOT INSTALLED or UNKNOWN VERSION.
scikit-image version: 0.19.1
Pillow version: 9.0.0
Tensorboard version: 2.8.0
gdown version: NOT INSTALLED or UNKNOWN VERSION.
TorchVision version: 0.12.0+cu113
tqdm version: 4.62.3
lmdb version: NOT INSTALLED or UNKNOWN VERSION.
psutil version: 5.9.0
pandas version: 1.4.0
einops version: NOT INSTALLED or UNKNOWN VERSION.
transformers version: 4.16.2
mlflow version: NOT INSTALLED or UNKNOWN VERSION.
pynrrd version: NOT INSTALLED or UNKNOWN VERSION.

For details about installing the optional dependencies, please visit:
    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies


================================
Printing system config...
================================
System: Linux
Linux version: Ubuntu 18.04.6 LTS
Platform: Linux-5.4.0-120-generic-x86_64-with-glibc2.27
Processor: x86_64
Machine: x86_64
Python version: 3.8.13
Process name: python
Command: ['python', '-c', 'import monai; monai.config.print_debug_info()']
Open files: []
Num physical CPUs: 16
Num logical CPUs: 32
Num usable CPUs: 32
CPU usage (%): [11.4, 13.6, 33.3, 8.1, 12.4, 17.9, 9.1, 64.4, 20.7, 20.2, 14.0, 13.2, 20.5, 15.0, 10.4, 18.6, 12.1, 15.1, 8.5, 11.9, 33.8, 27.4, 8.2, 10.6, 14.7, 27.9, 10.3, 9.5, 42.5, 23.1, 9.8, 10.5]
CPU freq. (MHz): 2
Load avg. in last 1, 5, 15 mins (%): [4.6, 4.3, 4.2]
Disk usage (%): 83.9
Avg. sensor temp. (Celsius): UNKNOWN for given OS
Total physical memory (GB): 62.7
Available memory (GB): 18.5
Used memory (GB): 42.4

================================
Printing GPU config...
================================
Num GPUs: 2
Has CUDA: True
CUDA version: 11.3
cuDNN enabled: True
cuDNN version: 8200
Current device: 0
Library compiled for CUDA architectures: ['sm_37', 'sm_50', 'sm_60', 'sm_70', 'sm_75', 'sm_80', 'sm_86']
GPU 0 Name: TITAN V
GPU 0 Is integrated: False
GPU 0 Is multi GPU board: False
GPU 0 Multi processor count: 80
GPU 0 Total memory (GB): 11.8
GPU 0 CUDA capability (maj.min): 7.0
GPU 1 Name: GeForce GT 1030
GPU 1 Is integrated: False
GPU 1 Is multi GPU board: False
GPU 1 Multi processor count: 3
GPU 1 Total memory (GB): 2.0
GPU 1 CUDA capability (maj.min): 6.1

[wyli]

thanks for reporting, @SachidanandAlle also asked about the same issue and I had some updates but forgot to create a PR..