K divisible

[oscarramirezs]

Hi

thank you guys for this work;

I'm trying to use the function, K divisible in my input data, so that the spatial sizes are divisible by k. but i'm getting the bellow error => RuntimeError: applying transform <monai.transforms.compose.Compose object at 0x0000019132E24310>
can you someone help me ? please.

train_transforms = Compose(
    [
        LoadImaged(keys=["image", "label"]),
        EnsureChannelFirstd(keys=["image", "label"]),
        Orientationd(keys=["image", "label"], axcodes="RAS"), 
        DivisiblePad(keys=["image", "label"], k=64, mode=('constant'), method= ("symmetric")),              
        EnsureTyped(keys=["image", "label"]),
    ]
)

val_transforms = Compose(
    [
        LoadImaged(keys=["image", "label"]),
        EnsureChannelFirstd(keys=["image", "label"]),
        Orientationd(keys=["image", "label"], axcodes="RAS"),
        EnsureTyped(keys=["image", "label"]),
    ]
)

check_ds = Dataset(data=train_files, transform=train_transforms)
check_loader = DataLoader(check_ds, batch_size=1)
check_data = first(check_loader)
image, label = (check_data["image"][0][0], check_data["label"][0][0])
print(f"image shape: {image.shape}, label shape: {label.shape}")
plt.figure("check", (12, 6))
plt.title("image")
plt.subplot(1, 2, 1)
plt.title("image")
plt.imshow(image[:, :, 100], cmap="gray")
plt.subplot(1, 2, 2)
plt.title("label")
plt.imshow(label[:, :, 100])
plt.show()

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
C:\ProgramData\Anaconda3\lib\site-packages\monai\transforms\transform.py in apply_transform(transform, data, map_items, unpack_items, log_stats)
     88             return [_apply_transform(transform, item, unpack_items) for item in data]
---> 89         return _apply_transform(transform, data, unpack_items)
     90     except Exception as e:

C:\ProgramData\Anaconda3\lib\site-packages\monai\transforms\transform.py in _apply_transform(transform, parameters, unpack_parameters)
     52 
---> 53     return transform(parameters)
     54 

C:\ProgramData\Anaconda3\lib\site-packages\monai\transforms\croppad\array.py in __call__(self, img, mode)
    344         """
--> 345         new_size = compute_divisible_spatial_size(spatial_shape=img.shape[1:], k=self.k)
    346         spatial_pad = SpatialPad(spatial_size=new_size, method=self.method, mode=mode or self.mode, **self.kwargs)

AttributeError: 'dict' object has no attribute 'shape'

The above exception was the direct cause of the following exception:

RuntimeError                              Traceback (most recent call last)
C:\ProgramData\Anaconda3\lib\site-packages\monai\transforms\transform.py in apply_transform(transform, data, map_items, unpack_items, log_stats)
     88             return [_apply_transform(transform, item, unpack_items) for item in data]
---> 89         return _apply_transform(transform, data, unpack_items)
     90     except Exception as e:

C:\ProgramData\Anaconda3\lib\site-packages\monai\transforms\transform.py in _apply_transform(transform, parameters, unpack_parameters)
     52 
---> 53     return transform(parameters)
     54 

C:\ProgramData\Anaconda3\lib\site-packages\monai\transforms\compose.py in __call__(self, input_)
    172         for _transform in self.transforms:
--> 173             input_ = apply_transform(_transform, input_, self.map_items, self.unpack_items, self.log_stats)
    174         return input_

C:\ProgramData\Anaconda3\lib\site-packages\monai\transforms\transform.py in apply_transform(transform, data, map_items, unpack_items, log_stats)
    112                 _log_stats(data=data)
--> 113         raise RuntimeError(f"applying transform {transform}") from e
    114 

RuntimeError: applying transform <monai.transforms.croppad.array.DivisiblePad object at 0x0000019132E1FCD0>

The above exception was the direct cause of the following exception:

RuntimeError                              Traceback (most recent call last)
<ipython-input-42-bd006b4d39ed> in <module>
      1 check_ds = Dataset(data=train_files, transform=train_transforms)
      2 check_loader = DataLoader(check_ds, batch_size=1)
----> 3 check_data = first(check_loader)
      4 #check_data = check_loader[2]
      5 image, label = (check_data["image"][0][0], check_data["label"][0][0])

C:\ProgramData\Anaconda3\lib\site-packages\monai\utils\misc.py in first(iterable, default)
     78     Returns the first item in the given iterable or `default` if empty, meaningful mostly with 'for' expressions.
     79     """
---> 80     for i in iterable:
     81         return i
     82     return default

C:\ProgramData\Anaconda3\lib\site-packages\torch\utils\data\dataloader.py in __next__(self)
    519             if self._sampler_iter is None:
    520                 self._reset()
--> 521             data = self._next_data()
    522             self._num_yielded += 1
    523             if self._dataset_kind == _DatasetKind.Iterable and \

C:\ProgramData\Anaconda3\lib\site-packages\torch\utils\data\dataloader.py in _next_data(self)
    559     def _next_data(self):
    560         index = self._next_index()  # may raise StopIteration
--> 561         data = self._dataset_fetcher.fetch(index)  # may raise StopIteration
    562         if self._pin_memory:
    563             data = _utils.pin_memory.pin_memory(data)

C:\ProgramData\Anaconda3\lib\site-packages\torch\utils\data\_utils\fetch.py in fetch(self, possibly_batched_index)
     47     def fetch(self, possibly_batched_index):
     48         if self.auto_collation:
---> 49             data = [self.dataset[idx] for idx in possibly_batched_index]
     50         else:
     51             data = self.dataset[possibly_batched_index]

C:\ProgramData\Anaconda3\lib\site-packages\torch\utils\data\_utils\fetch.py in <listcomp>(.0)
     47     def fetch(self, possibly_batched_index):
     48         if self.auto_collation:
---> 49             data = [self.dataset[idx] for idx in possibly_batched_index]
     50         else:
     51             data = self.dataset[possibly_batched_index]

C:\ProgramData\Anaconda3\lib\site-packages\monai\data\dataset.py in __getitem__(self, index)
     95             # dataset[[1, 3, 4]]
     96             return Subset(dataset=self, indices=index)
---> 97         return self._transform(index)
     98 
     99 

C:\ProgramData\Anaconda3\lib\site-packages\monai\data\dataset.py in _transform(self, index)
     81         """
     82         data_i = self.data[index]
---> 83         return apply_transform(self.transform, data_i) if self.transform is not None else data_i
     84 
     85     def __getitem__(self, index: Union[int, slice, Sequence[int]]):

C:\ProgramData\Anaconda3\lib\site-packages\monai\transforms\transform.py in apply_transform(transform, data, map_items, unpack_items, log_stats)
    111             else:
    112                 _log_stats(data=data)
--> 113         raise RuntimeError(f"applying transform {transform}") from e
    114 
    115 

RuntimeError: applying transform <monai.transforms.compose.Compose object at 0x0000019132E24310>

[wyli]

I think that's a typo -- DivisiblePad -> DivisiblePadD or DivisiblePadDict

[Nic-Ma]

Hi @yiheng-wang-nv , could you please help fix this small typo in any your PR?

Thanks in advance.

[yiheng-wang-nv]

Hi @Nic-Ma , the typo is from @oscarramirezs side, where a dict based transform DivisiblePadD should be used rather than DivisiblePad.

[oscarramirezs]

Hi all

Thank you,,
yes, It was just a typo problem, now it works fine,

Oscar