Update GDSDataset (#6787)

Fixes #6786 .

### Description

- Update rst
- Update the type of dtype to str

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: KumoLiu <[email protected]>

.github/workflows/docker.yml

@@ -89,7 +89,7 @@ jobs:
     steps:
     - name: Import
       run: |
-        export CUDA_VISIBLE_DEVICES=  # cpu-only
+        export OMP_NUM_THREADS=4 MKL_NUM_THREADS=4 CUDA_VISIBLE_DEVICES=  # cpu-only
         python -c 'import monai; monai.config.print_debug_info()'
         cd /opt/monai
         ls -al

docs/source/data.rst

@@ -45,6 +45,13 @@ Generic Interfaces
   :members:
   :special-members: __getitem__
 
+`GDSDataset`
+~~~~~~~~~~~~~~~~~~~
+.. autoclass:: GDSDataset
+  :members:
+  :special-members: __getitem__
+
+
 `CacheNTransDataset`
 ~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: CacheNTransDataset

monai/data/dataset.py

@@ -1521,6 +1521,8 @@ class GDSDataset(PersistentDataset):
     bandwidth while decreasing latency and utilization load on the CPU and GPU.
 
     A tutorial is available: https://github.com/Project-MONAI/tutorials/blob/main/modules/GDS_dataset.ipynb.
+
+    See also: https://github.com/rapidsai/kvikio
     """
 
     def __init__(
@@ -1607,17 +1609,20 @@ def _cachecheck(self, item_transformed):
                     return item
                 elif isinstance(item_transformed, (np.ndarray, torch.Tensor)):
                     _meta = self._load_meta_cache(meta_hash_file_name=f"{hashfile.name}-meta")
-                    _data = kvikio_numpy.fromfile(f"{hashfile}", dtype=_meta.pop("dtype"), like=cp.empty(()))
-                    _data = convert_to_tensor(_data.reshape(_meta.pop("shape")), device=f"cuda:{self.device}")
-                    if bool(_meta):
+                    _data = kvikio_numpy.fromfile(f"{hashfile}", dtype=_meta["dtype"], like=cp.empty(()))
+                    _data = convert_to_tensor(_data.reshape(_meta["shape"]), device=f"cuda:{self.device}")
+                    filtered_keys = list(filter(lambda key: key not in ["dtype", "shape"], _meta.keys()))
+                    if bool(filtered_keys):
                         return (_data, _meta)
                     return _data
                 else:
                     item: list[dict[Any, Any]] = [{} for _ in range(len(item_transformed))]  # type:ignore
                     for i, _item in enumerate(item_transformed):
                         for k in _item:
                             meta_i_k = self._load_meta_cache(meta_hash_file_name=f"{hashfile.name}-{k}-meta-{i}")
-                            item_k = kvikio_numpy.fromfile(f"{hashfile}-{k}-{i}", dtype=np.float32, like=cp.empty(()))
+                            item_k = kvikio_numpy.fromfile(
+                                f"{hashfile}-{k}-{i}", dtype=meta_i_k["dtype"], like=cp.empty(())
+                            )
                             item_k = convert_to_tensor(item[i].reshape(meta_i_k["shape"]), device=f"cuda:{self.device}")
                             item[i].update({k: item_k, f"{k}_meta_dict": meta_i_k})
                     return item
@@ -1653,7 +1658,7 @@ def _create_new_cache(self, data, data_hashfile, meta_hash_file_name):
         if isinstance(_item_transformed_data, torch.Tensor):
             _item_transformed_data = _item_transformed_data.numpy()
         self._meta_cache[meta_hash_file_name]["shape"] = _item_transformed_data.shape
-        self._meta_cache[meta_hash_file_name]["dtype"] = _item_transformed_data.dtype
+        self._meta_cache[meta_hash_file_name]["dtype"] = str(_item_transformed_data.dtype)
         kvikio_numpy.tofile(_item_transformed_data, data_hashfile)
         try:
             # NOTE: Writing to a temporary directory and then using a nearly atomic rename operation

tests/test_gdsdataset.py

@@ -17,6 +17,7 @@
 import unittest
 
 import numpy as np
+import torch
 from parameterized import parameterized
 
 from monai.data import GDSDataset, json_hashing
@@ -48,6 +49,19 @@
 
 TEST_CASE_3 = [None, (128, 128, 128)]
 
+DTYPES = {
+    np.dtype(np.uint8): torch.uint8,
+    np.dtype(np.int8): torch.int8,
+    np.dtype(np.int16): torch.int16,
+    np.dtype(np.int32): torch.int32,
+    np.dtype(np.int64): torch.int64,
+    np.dtype(np.float16): torch.float16,
+    np.dtype(np.float32): torch.float32,
+    np.dtype(np.float64): torch.float64,
+    np.dtype(np.complex64): torch.complex64,
+    np.dtype(np.complex128): torch.complex128,
+}
+
 
 class _InplaceXform(Transform):
     def __call__(self, data):
@@ -93,16 +107,28 @@ def test_metatensor(self):
         shape = (1, 10, 9, 8)
         items = [TEST_NDARRAYS[-1](np.arange(0, np.prod(shape)).reshape(shape))]
         with tempfile.TemporaryDirectory() as tempdir:
-            ds = GDSDataset(
-                data=items,
-                transform=_InplaceXform(),
-                cache_dir=tempdir,
-                device=0,
-                pickle_module="pickle",
-                pickle_protocol=pickle.HIGHEST_PROTOCOL,
-            )
+            ds = GDSDataset(data=items, transform=_InplaceXform(), cache_dir=tempdir, device=0)
             assert_allclose(ds[0], ds[0][0], type_test=False)
 
+    def test_dtype(self):
+        shape = (1, 10, 9, 8)
+        data = np.arange(0, np.prod(shape)).reshape(shape)
+        for _dtype in DTYPES.keys():
+            items = [np.array(data).astype(_dtype)]
+            with tempfile.TemporaryDirectory() as tempdir:
+                ds = GDSDataset(data=items, transform=_InplaceXform(), cache_dir=tempdir, device=0)
+                ds1 = GDSDataset(data=items, transform=_InplaceXform(), cache_dir=tempdir, device=0)
+                self.assertEqual(ds[0].dtype, _dtype)
+                self.assertEqual(ds1[0].dtype, DTYPES[_dtype])
+
+        for _dtype in DTYPES.keys():
+            items = [torch.tensor(data, dtype=DTYPES[_dtype])]
+            with tempfile.TemporaryDirectory() as tempdir:
+                ds = GDSDataset(data=items, transform=_InplaceXform(), cache_dir=tempdir, device=0)
+                ds1 = GDSDataset(data=items, transform=_InplaceXform(), cache_dir=tempdir, device=0)
+                self.assertEqual(ds[0].dtype, DTYPES[_dtype])
+                self.assertEqual(ds1[0].dtype, DTYPES[_dtype])
+
     @parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
     def test_shape(self, transform, expected_shape):
         test_image = nib.Nifti1Image(np.random.randint(0, 2, size=[128, 128, 128]).astype(float), np.eye(4))