About ValueError: Unsupported output type: <class 'itk.itkPyBufferPython.NDArrayITKBase'> that occurs when transforms compose #2885
Description
Problem Description
Hi,I am a novice to MONAI, and An error occurred when I set up pre-processing transforms,
my image format is dicom.
My development platform is windows10, but my test on ubuntu20.04 is no problem.
I don't know how to solve it, hope to get your help, thank you
The following is information about the code and error
MONAI version: 0.7.dev2135
Numpy version: 1.21.1
Pytorch version: 1.7.1+cu101
MONAI flags: HAS_EXT = False, USE_COMPILED = False
MONAI rev id: fc69e1d96c6250c6479ea7575b9e6f73e70b8baf
Optional dependencies:
Pytorch Ignite version: 0.4.5
Nibabel version: 3.2.1
scikit-image version: 0.18.3
Pillow version: 8.0.1
Tensorboard version: 2.6.0
gdown version: 3.13.0
TorchVision version: 0.8.2+cu101
tqdm version: 4.62.2
lmdb version: 1.2.1
psutil version: 5.8.0
pandas version: 1.3.2
einops version: 0.3.2
For details about installing the optional dependencies, please visit:
https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
transform = Compose([
LoadImaged(keys="image"),
SqueezeDimd(keys="image", dim=-1),
AddChanneld(keys="image"),
ScaleIntensityd("image"),
CropForegroundd(keys="image", source_key="image"),
EnsureTyped(keys="image"),
])
test_data = {"image": newdcmDir}
print(f"filename:{newdcmDir}")
result = transform(test_data)
#print(f"image data shape:{result['image'].shape}")
#print(f"meta data:{result['image_meta_dict']}")=== Transform input info -- ScaleIntensityd ===
=== Transform input info -- ScaleIntensityd ===
=== Transform input info -- ScaleIntensityd ===
=== Transform input info -- ScaleIntensityd ===
=== Transform input info -- ScaleIntensityd ===
=== Transform input info -- ScaleIntensityd ===
=== Transform input info -- ScaleIntensityd ===
=== Transform input info -- ScaleIntensityd ===
=== Transform input info -- ScaleIntensityd ===
=== Transform input info -- ScaleIntensityd ===
image statistics:
Type: <class 'itk.itkPyBufferPython.NDArrayITKBase'>
Shape: (1, 1024, 1024)
Value range: (0.0, 4091.0)
show more (open the raw output data in a text editor) ...
[ 0., 0., 1., 0.],
[ 0., 0., 0., 1.]]), 'affine': array([[-1., 0., 0., 0.],
[ 0., -1., 0., 0.],
[ 0., 0., 1., 0.],
[ 0., 0., 0., 1.]]), 'spatial_shape': array([1024, 1024, 1]), 'original_channel_dim': 'no_channel', 'filename_or_obj': 'C:/Users/Bxd/remote/data_circle/data/imagesTest/1.IMA'}
RuntimeError: applying transform <monai.transforms.intensity.dictionary.ScaleIntensityd object at 0x00000285C81DD910>
ValueError Traceback (most recent call last)
~\AppData\Local\Programs\Python\Python39\lib\site-packages\monai\transforms\transform.py in apply_transform(transform, data, map_items, unpack_items)
91 return [_apply_transform(transform, item, unpack_items) for item in data]
---> 92 return _apply_transform(transform, data, unpack_items)
93 except Exception as e:
~\AppData\Local\Programs\Python\Python39\lib\site-packages\monai\transforms\transform.py in _apply_transform(transform, parameters, unpack_parameters)
59
---> 60 return transform(parameters)
61
~\AppData\Local\Programs\Python\Python39\lib\site-packages\monai\transforms\intensity\dictionary.py in call(self, data)
505 for key in self.key_iterator(d):
--> 506 d[key] = self.scaler(d[key])
507 return d
~\AppData\Local\Programs\Python\Python39\lib\site-packages\monai\transforms\intensity\array.py in call(self, img)
402 if self.minv is not None and self.maxv is not None:
--> 403 return rescale_array(img, self.minv, self.maxv, img.dtype)
404 if self.factor is not None:
~\AppData\Local\Programs\Python\Python39\lib\site-packages\monai\transforms\utils.py in rescale_array(arr, minv, maxv, dtype)
143 if dtype is not None:
--> 144 arr, *_ = convert_data_type(arr, dtype=dtype)
145
~\AppData\Local\Programs\Python\Python39\lib\site-packages\monai\utils\type_conversion.py in convert_data_type(data, output_type, device, dtype)
186 else:
--> 187 raise ValueError(f"Unsupported output type: {output_type}")
188 return data, orig_type, orig_device
ValueError: Unsupported output type: <class 'itk.itkPyBufferPython.NDArrayITKBase'>
The above exception was the direct cause of the following exception:
RuntimeError Traceback (most recent call last)
in
10 test_data = {"image": newdcmDir}
11 print(f"filename:{newdcmDir}")
---> 12 result = transform(test_data)
13 #print(f"image data shape:{result['image'].shape}")
14 #print(f"meta data:{result['image_meta_dict']}")
~\AppData\Local\Programs\Python\Python39\lib\site-packages\monai\transforms\compose.py in call(self, input_)
158 def call(self, input_):
159 for transform in self.transforms:
--> 160 input = apply_transform(transform, input, self.map_items, self.unpack_items)
161 return input_
162
~\AppData\Local\Programs\Python\Python39\lib\site-packages\monai\transforms\transform.py in apply_transform(transform, data, map_items, unpack_items)
114 else:
115 _log_stats(data=data)
--> 116 raise RuntimeError(f"applying transform {transform}") from e
117
118
RuntimeError: applying transform <monai.transforms.intensity.dictionary.ScaleIntensityd object at 0x00000285C81DD910>