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LoadImageD NibabelReader preserve original data type #5505
Description
It's currently seems impossible to load ".nib/.nib.gz" image in the original data type (e.g. label in uint8), it always converts to float.
In LoadImageD transform we have an option dtype , which states that if dtype==None, it should keep the original format, but internally
but internally NibabelReader always reads in dtype (usually float) because of get_fdata(), and does not preserve original format
MONAI/monai/data/image_reader.py
Lines 1008 to 1018 in ef68f16
| def _get_array_data(self, img): | |
| """ | |
| Get the raw array data of the image, converted to Numpy array. | |
| Args: | |
| img: a Nibabel image object loaded from an image file. | |
| """ | |
| _array = np.array(img.get_fdata(dtype=self.dtype)) | |
| img.uncache() | |
| return _array |
I think we should replace
_array = np.array(img.get_fdata(dtype=self.dtype))
with np.asarray(img.dataobj)
_array = np.asarray(img.dataobj) if dtype is None
(see here https://nipy.org/nibabel/images_and_memory.html how to get in original data type) This has an additional benefit that .uncache() won't be necessary
(and ensure that LoadImageD doesn't copy/convert data unnecessarily of dtype==None (original type))