Spacing Transform only rescales spacing on 2 out of 3 Dimensions

[leopold-franz]

Describe the bug
When running the Spacingd transform to a 3D image (dicom read using LoadImage & ITKReader), only the first two dimensions are rescaled.

To Reproduce
Steps to reproduce the behavior:
from monai.transforms import LoadImaged, Spacingd
batch = {"image": dicom_path}
batch = LoadImaged(
reader="monai.data.ITKReader",
keys=["image"],
image_only=True,
)(batch)
print("Original image: ")
print(batch["image"].shape)
print(batch["image"].meta["spacing"])
print(batch["image"].meta["original_affine"])
print(batch["image"].meta["affine"])
print(batch["image"].meta["spatial_shape"])
print(h5_resolution)
batch = Spacingd(keys=["image"], pixdim=np.array([0.157288, 0.157288, 0.157288]), scale_extent=True, diagonal=True)(batch)
print("Transformed image: ")
print(batch["image"].shape)
print(batch["image"].meta["spacing"])
print(batch["image"].meta["original_affine"])
print(batch["image"].meta["affine"])
print(batch["image"].meta["spatial_shape"])

Expected behavior
A clear and concise description of what you expected to happen.
I expected the image to be rescaled along all 3 dimensions like when running the rescale function from skimage.transform.

Screenshots

Here you can see how the image dimensions change. Im expecting a shape of (329, 141, 299) (when run with the skimage rescale function).

Environment

================================
Printing MONAI config...

MONAI version: 1.3.0
Numpy version: 1.25.1
Pytorch version: 2.0.1
MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: 865972f
MONAI file: /Users//mambaforge/envs/follicle_tracker_311/lib/python3.11/site-packages/monai/init.py

Optional dependencies:
Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.
ITK version: 5.3.0
Nibabel version: NOT INSTALLED or UNKNOWN VERSION.
scikit-image version: 0.21.0
scipy version: 1.11.1
Pillow version: 10.0.0
Tensorboard version: 2.13.0
gdown version: NOT INSTALLED or UNKNOWN VERSION.
TorchVision version: 0.15.2
tqdm version: 4.65.0
lmdb version: NOT INSTALLED or UNKNOWN VERSION.
psutil version: 5.9.5
pandas version: 2.0.3
einops version: 0.6.1
transformers version: NOT INSTALLED or UNKNOWN VERSION.
mlflow version: NOT INSTALLED or UNKNOWN VERSION.
pynrrd version: NOT INSTALLED or UNKNOWN VERSION.
clearml 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: Darwin
Mac version: 14.1
Platform: macOS-14.1-x86_64-i386-64bit
Processor: i386
Machine: x86_64
Python version: 3.11.4
Process name: python3.11
Command: ['python', '-c', 'import monai; monai.config.print_debug_info()']
Open files: []
Num physical CPUs: 4
Num logical CPUs: 8
Num usable CPUs: UNKNOWN for given OS
CPU usage (%): [62.6, 10.3, 53.1, 9.6, 44.0, 10.3, 40.6, 11.0]
CPU freq. (MHz): 2000
Load avg. in last 1, 5, 15 mins (%): [77.6, 48.9, 40.8]
Disk usage (%): 75.9
Avg. sensor temp. (Celsius): UNKNOWN for given OS
Total physical memory (GB): 16.0
Available memory (GB): 5.1
Used memory (GB): 9.7

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Printing GPU config...

Num GPUs: 0
Has CUDA: False
cuDNN enabled: False
NVIDIA_TF32_OVERRIDE: None
TORCH_ALLOW_TF32_CUBLAS_OVERRIDE: None

Additional context

[KumoLiu]

Hi @leopold-franz, seems you missing the channel dim. Could you please try to add ensure_channel_first=True in the LoadImage?
Thanks!