Repository: Project-MONAI/MONAI
File: monai/data/grid_dataset.py (Python)

Code before:
        self._cache_other.append(other_cache)
        return patch_cache

    def __iter__(self):
        if self.cache:
            cache_index = None
            for image in super().__iter__():
                key = self.hash_func(image)
                if key in self._hash_keys:
                    # if existing in cache, try to get the index in cache
                    cache_index = self._hash_keys.index(key)
                if cache_index is None:
                    # no cache for this index, execute all the transforms directly
                    for patch, *others in self.patch_iter(image):
                        out_patch = patch
                        if self.patch_transform is not None:
                            out_patch = apply_transform(self.patch_transform, patch, map_items=False)
                        if (
                            self.with_coordinates and len(others) > 0
                        ):  # patch_iter to yield at least 2 items: patch, coords
                            yield out_patch, others[0]
                        else:
                            yield out_patch

                if self._cache is None:
                    raise RuntimeError("cache buffer is not initialized, please call `set_data()` first.")
                data = self._cache[cache_index]  # type: ignore
                other = self._cache_other[cache_index]  # type: ignore

                # load data from cache and execute from the first random transform
                if not isinstance(self.patch_transform, Compose):
                    raise ValueError("transform must be an instance of monai.transforms.Compose.")

                first_random = self.patch_transform.get_index_of_first(
                    lambda t: isinstance(t, RandomizableTrait) or not isinstance(t, Transform)
                )
                if first_random is not None:
                    data = deepcopy(data) if self.copy_cache is True else data
                    for out_patch, others in zip(data, other):
                        if self.patch_transform is not None:
                            out_patch = self.patch_transform(out_patch, start=first_random)
                        if (
                            self.with_coordinates and len(others) > 0
                        ):  # patch_iter to yield at least 2 items: patch, coords
                            yield out_patch, others
                        else:
                            yield out_patch
        else:
            for image in super().__iter__():
                for patch, *others in self.patch_iter(image):
                    out_patch = patch

Review comment (performance):
```suggestion
                    raise RuntimeError("Cache buffer is not initialized, call `set_data()` before epoch begins.")
```

Does it need to be called before or just after an epoch? It should be stated here when. 

Code after:
        """
        item = self.data[idx]  # type: ignore
        patch_cache, other_cache = [], []
        for patch, *others in self.patch_iter(item):
            if self.first_random is not None:
                patch = self.patch_transform(patch, end=self.first_random, threading=True)  # type: ignore

            if self.as_contiguous:
                patch = convert_to_contiguous(patch, memory_format=torch.contiguous_format)
            if self.with_coordinates and len(others) > 0:  # patch_iter to yield at least 2 items: patch, coords
                other_cache.append(others[0])
            patch_cache.append(patch)
        return patch_cache, other_cache

    def _generate_patches(self, src, **apply_args):
        """
        yield patches optionally post-processed by transform.

        Args:
            src: a iterable of image patches.
            apply_args: other args for `self.patch_transform`.

        """
        for patch, *others in src:
            out_patch = patch
            if self.patch_transform is not None:
                out_patch = self.patch_transform(patch, **apply_args)
            if self.with_coordinates and len(others) > 0:  # patch_iter to yield at least 2 items: patch, coords
                yield out_patch, others[0]
            else:
                yield out_patch

    def __iter__(self):
        if self.cache:
            cache_index = None
            for image in super().__iter__():
                key = self.hash_func(image)
                if key in self._hash_keys:
                    # if existing in cache, try to get the index in cache
                    cache_index = self._hash_keys.index(key)
                if cache_index is None:
                    # no cache for this index, execute all the transforms directly
                    yield from self._generate_patches(self.patch_iter(image))
                else:
                    if self._cache is None:
                        raise RuntimeError(
                            "Cache buffer is not initialized, please call `set_data()` before epoch begins."
                        )
                    data = self._cache[cache_index]  # type: ignore
                    other = self._cache_other[cache_index]  # type: ignore