transform saveimage didn't work

[lg2578]

my code :

from monai.transforms import (
    Compose,
    LoadImaged,
    SaveImaged,
    Resized,
    EnsureChannelFirstd,
    LoadImage,
    SaveImage,
    Resize,
    EnsureChannelFirst,
    
)
root='E:\projects\datas\Task10_Colon\Task10_Colon'
T=Compose(
    LoadImaged(keys=['image','label']),
    EnsureChannelFirstd(keys=['image','label']),
    Resized(keys=['image','label'],spatial_size=(256,256,-1)),
    SaveImaged(keys=['image','label'],
               output_dir='e:\Colon',
               data_root_dir=root,
               ),
)
import os
root_train=os.path.join(root,'imagesTr','*.nii.gz')
root_label=os.path.join(root,'labelsTr','*.nii.gz')
import glob
files_train=sorted(glob.glob(root_train))
files_label=sorted(glob.glob(root_label))
files=[{'image':imagename,'label':labelname} 
       for imagename,labelname in zip(files_train,files_label)]


loadimage=LoadImage()
resize=Resize(spatial_size=(128,128,-1))
ensureCF=EnsureChannelFirst()
nii,meta=loadimage(files[1]['image'])
nii=ensureCF(nii,meta)
nii=resize(nii)
saveimg=SaveImage(output_dir='e:\Colon',
               data_root_dir=root,
               separate_folder=False,
               output_postfix='',
               output_ext='.nii')
nii=saveimg(nii,meta)
print(nii.shape)

outputs:
torch.Size([1, 128, 128, 98])
2023-02-27 15:00:11,398 INFO image_writer.py:194 - writing: e:\Colon\imagesTr\colon_005.nii
torch.Size([1, 128, 128, 98])
problems:
1.the saved image's size is still 512,512,98,not 128,128,98
2.T function do nothing,do not ouput files into e:\colon,and have no tips at all.

[KumoLiu]

Hi @lg2578, SaveImage resample image based on the spatial_shape (and original_affine) from metadata by default. Could you please try to set resample=False?

MONAI/monai/transforms/io/array.py

Lines 320 to 321 in f519699

	resample: whether to resample image (if needed) before saving the data array,
	based on the `spatial_shape` (and `original_affine`) from metadata.

MONAI/monai/transforms/io/array.py

Line 376 in f519699

resample: bool = True,

Hope it can help you, thanks!

[lg2578]

resample=False works in saveimage, but the T compose still can't works

T=Compose(
    LoadImaged(keys=['image','label']),
    EnsureChannelFirstd(keys=['image','label']),
    Resized(keys=['image','label'],spatial_size=(256,256,-1)),
    SaveImaged(keys=['image','label'],
               output_dir='/kaggle/working',
               data_root_dir=root,
               separate_folder=False,
               output_postfix='',
               output_ext='.nii',
               resample=False,
               ),
)
import os
root_train=os.path.join(root,'imagesTr','*.nii')
root_label=os.path.join(root,'labelsTr','*.nii')
import glob
files_train=sorted(glob.glob(root_train))
files_label=sorted(glob.glob(root_label))

files=[{'image':imagename,'label':labelname} 
       for imagename,labelname in zip(files_train,files_label)]

a=T(files[27])

a get size 512,512,98 , not 256,256,98, and nothing saved

[wyli]

compose takes a sequence of transforms as input... Compose([LoadImage...])

[lg2578]

code like the following works:

post_pred = Compose([EnsureType(), AsDiscrete(argmax=True, to_onehot=2)])

post_label = Compose([EnsureType(), AsDiscrete(to_onehot=2)])
...
 val_outputs = [post_pred(i) for i in decollate_batch(val_outputs)]
 val_labels = [post_label(i) for i in decollate_batch(val_labels)]

why my Compose function T, can't works?

[wyli]

compose([...]) Vs compose(...)