remove the draft version of the GDSDataset (#1473)

### Description
- After Project-MONAI/MONAI#6778, `GDSDataset`
has been added in core, remove the draft version in the tutorial.
- Update the result based on the new version

### Checks
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Avoid including large-size files in the PR.
- [x] Clean up long text outputs from code cells in the notebook.
- [ ] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [ ] Ensure (1) hyperlinks and markdown anchors are working (2) use
relative paths for tutorial repo files (3) put figure and graphs in the
`./figure` folder
- [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

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

Author: KumoLiu

modules/GDS_dataset.ipynb

@@ -39,10 +39,6 @@
     "        \n",
     "        (Replace X with the major version of the CUDA toolkit, and Y with the minor version.)\n",
     "\n",
-    "- `GDSDataset` inherited from `PersistentDataset`.\n",
-    "\n",
-    "    In this tutorial, we have implemented a `GDSDataset` that inherits from `PersistentDataset`. We have re-implemented the `_cachecheck` method to create and save cache using GDS.\n",
-    "\n",
     "- A simple demo comparing the time taken with and without GDS.\n",
     "\n",
     "   In this tutorial, we are creating a conda environment to install `kvikio`, which provides a Python API for GDS. To install `kvikio` using other methods, refer to https://github.com/rapidsai/kvikio#install.\n",
@@ -79,28 +75,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "import os\n",
     "import time\n",
-    "import cupy\n",
     "import torch\n",
     "import shutil\n",
     "import tempfile\n",
-    "import numpy as np\n",
-    "from typing import Any\n",
-    "from pathlib import Path\n",
-    "from copy import deepcopy\n",
-    "from collections.abc import Callable, Sequence\n",
-    "from kvikio.numpy import fromfile, tofile\n",
     "\n",
     "import monai\n",
     "import monai.transforms as mt\n",
     "from monai.config import print_config\n",
-    "from monai.data.utils import pickle_hashing, SUPPORTED_PICKLE_MOD\n",
-    "from monai.utils import convert_to_tensor, set_determinism, look_up_option\n",
+    "from monai.data.dataset import GDSDataset\n",
+    "from monai.utils import set_determinism\n",
     "\n",
     "print_config()"
    ]
@@ -135,100 +124,6 @@
     "print(root_dir)"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## GDSDataset"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "class GDSDataset(monai.data.PersistentDataset):\n",
-    "    def __init__(\n",
-    "        self,\n",
-    "        data: Sequence,\n",
-    "        transform: Sequence[Callable] | Callable,\n",
-    "        cache_dir: Path | str | None,\n",
-    "        hash_func: Callable[..., bytes] = pickle_hashing,\n",
-    "        hash_transform: Callable[..., bytes] | None = None,\n",
-    "        reset_ops_id: bool = True,\n",
-    "        device: int = None,\n",
-    "        **kwargs: Any,\n",
-    "    ) -> None:\n",
-    "        super().__init__(\n",
-    "            data=data,\n",
-    "            transform=transform,\n",
-    "            cache_dir=cache_dir,\n",
-    "            hash_func=hash_func,\n",
-    "            hash_transform=hash_transform,\n",
-    "            reset_ops_id=reset_ops_id,\n",
-    "            **kwargs,\n",
-    "        )\n",
-    "        self.device = device\n",
-    "\n",
-    "    def _cachecheck(self, item_transformed):\n",
-    "        \"\"\"given the input dictionary ``item_transformed``, return a transformed version of it\"\"\"\n",
-    "        hashfile = None\n",
-    "        # compute a cache id\n",
-    "        if self.cache_dir is not None:\n",
-    "            data_item_md5 = self.hash_func(item_transformed).decode(\"utf-8\")\n",
-    "            data_item_md5 += self.transform_hash\n",
-    "            hashfile = self.cache_dir / f\"{data_item_md5}.pt\"\n",
-    "\n",
-    "        if hashfile is not None and hashfile.is_file():  # cache hit\n",
-    "            with cupy.cuda.Device(self.device):\n",
-    "                item = {}\n",
-    "                for k in item_transformed:\n",
-    "                    meta_k = torch.load(self.cache_dir / f\"{hashfile.name}-{k}-meta\")\n",
-    "                    item[k] = fromfile(f\"{hashfile}-{k}\", dtype=np.float32, like=cupy.empty(()))\n",
-    "                    item[k] = convert_to_tensor(item[k].reshape(meta_k[\"shape\"]), device=f\"cuda:{self.device}\")\n",
-    "                    item[f\"{k}_meta_dict\"] = meta_k\n",
-    "                return item\n",
-    "\n",
-    "        # create new cache\n",
-    "        _item_transformed = self._pre_transform(deepcopy(item_transformed))  # keep the original hashed\n",
-    "        if hashfile is None:\n",
-    "            return _item_transformed\n",
-    "\n",
-    "        for k in _item_transformed:  # {'image': ..., 'label': ...}\n",
-    "            _item_transformed_meta = _item_transformed[k].meta\n",
-    "            _item_transformed_data = _item_transformed[k].array\n",
-    "            _item_transformed_meta[\"shape\"] = _item_transformed_data.shape\n",
-    "            tofile(_item_transformed_data, f\"{hashfile}-{k}\")\n",
-    "            try:\n",
-    "                # NOTE: Writing to a temporary directory and then using a nearly atomic rename operation\n",
-    "                #       to make the cache more robust to manual killing of parent process\n",
-    "                #       which may leave partially written cache files in an incomplete state\n",
-    "                with tempfile.TemporaryDirectory() as tmpdirname:\n",
-    "                    meta_hash_file_name = f\"{hashfile.name}-{k}-meta\"\n",
-    "                    meta_hash_file = self.cache_dir / meta_hash_file_name\n",
-    "                    temp_hash_file = Path(tmpdirname) / meta_hash_file_name\n",
-    "                    torch.save(\n",
-    "                        obj=_item_transformed_meta,\n",
-    "                        f=temp_hash_file,\n",
-    "                        pickle_module=look_up_option(self.pickle_module, SUPPORTED_PICKLE_MOD),\n",
-    "                        pickle_protocol=self.pickle_protocol,\n",
-    "                    )\n",
-    "                    if temp_hash_file.is_file() and not meta_hash_file.is_file():\n",
-    "                        # On Unix, if target exists and is a file, it will be replaced silently if the\n",
-    "                        # user has permission.\n",
-    "                        # for more details: https://docs.python.org/3/library/shutil.html#shutil.move.\n",
-    "                        try:\n",
-    "                            shutil.move(str(temp_hash_file), meta_hash_file)\n",
-    "                        except FileExistsError:\n",
-    "                            pass\n",
-    "            except PermissionError:  # project-monai/monai issue #3613\n",
-    "                pass\n",
-    "        open(hashfile, \"a\").close()  # store cacheid\n",
-    "\n",
-    "        return _item_transformed"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -245,16 +140,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "2023-07-12 09:26:17,878 - INFO - Expected md5 is None, skip md5 check for file samples.zip.\n",
-      "2023-07-12 09:26:17,878 - INFO - File exists: samples.zip, skipped downloading.\n",
-      "2023-07-12 09:26:17,879 - INFO - Writing into directory: /raid/yliu/test_tutorial.\n"
+      "2023-07-27 07:59:12,054 - INFO - Expected md5 is None, skip md5 check for file samples.zip.\n",
+      "2023-07-27 07:59:12,055 - INFO - File exists: samples.zip, skipped downloading.\n",
+      "2023-07-27 07:59:12,056 - INFO - Writing into directory: /raid/yliu/test_tutorial.\n"
      ]
     }
    ],
@@ -283,7 +178,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -299,7 +194,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -332,19 +227,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "epoch0 time 19.746733903884888\n",
-      "epoch1 time 0.9976603984832764\n",
-      "epoch2 time 0.982248067855835\n",
-      "epoch3 time 0.9838874340057373\n",
-      "epoch4 time 0.9793403148651123\n",
-      "total time 23.69102692604065\n"
+      "epoch0 time 20.148560762405396\n",
+      "epoch1 time 0.9835140705108643\n",
+      "epoch2 time 0.9708101749420166\n",
+      "epoch3 time 0.9711742401123047\n",
+      "epoch4 time 0.9711296558380127\n",
+      "total time 24.04619812965393\n"
      ]
     }
    ],
@@ -372,19 +267,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "epoch0 time 21.206729650497437\n",
-      "epoch1 time 1.510526180267334\n",
-      "epoch2 time 1.588256597518921\n",
-      "epoch3 time 1.4431262016296387\n",
-      "epoch4 time 1.4594802856445312\n",
-      "total time 27.20927882194519\n"
+      "epoch0 time 21.170511722564697\n",
+      "epoch1 time 1.482978105545044\n",
+      "epoch2 time 1.5378782749176025\n",
+      "epoch3 time 1.4499244689941406\n",
+      "epoch4 time 1.4379286766052246\n",
+      "total time 27.08065962791443\n"
      ]
     }
    ],