245 Update tutorials with new API (part 2) (Project-MONAI#253)

* update with new api Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix pep8 lr Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix format error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update with decollate Signed-off-by: Yiheng Wang <vennw@nvidia.com> * replace to use 0.6.0 Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update inverse example Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update transfer mmar Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update with new api for jupyter_utils.ipynb Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix pep8 Signed-off-by: Yiheng Wang <vennw@nvidia.com>
juampatronics · Jul 12, 2021 · 70ac974 · 70ac974
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diff --git a/modules/3d_image_transforms.ipynb b/modules/3d_image_transforms.ipynb
@@ -73,24 +73,26 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "MONAI version: 0.4.0+35.g6adbcde\n",
-      "Numpy version: 1.19.5\n",
-      "Pytorch version: 1.7.1\n",
-      "MONAI flags: HAS_EXT = False, USE_COMPILED = False\n",
-      "MONAI rev id: 6adbcdee45c16f18f5b713575af3410437177311\n",
+      "MONAI version: 0.6.0rc1+23.gc6793fd0\n",
+      "Numpy version: 1.20.3\n",
+      "Pytorch version: 1.9.0a0+c3d40fd\n",
+      "MONAI flags: HAS_EXT = True, USE_COMPILED = False\n",
+      "MONAI rev id: c6793fd0f316a448778d0047664aaf8c1895fe1c\n",
       "\n",
       "Optional dependencies:\n",
-      "Pytorch Ignite version: 0.4.2\n",
+      "Pytorch Ignite version: 0.4.5\n",
       "Nibabel version: 3.2.1\n",
-      "scikit-image version: 0.18.1\n",
-      "Pillow version: 7.0.0\n",
-      "Tensorboard version: 2.4.0\n",
-      "gdown version: 3.12.2\n",
-      "TorchVision version: 0.8.2\n",
+      "scikit-image version: 0.15.0\n",
+      "Pillow version: 8.2.0\n",
+      "Tensorboard version: 2.5.0\n",
+      "gdown version: 3.13.0\n",
+      "TorchVision version: 0.10.0a0\n",
       "ITK version: 5.1.2\n",
-      "tqdm version: 4.51.0\n",
-      "lmdb version: 1.0.0\n",
+      "tqdm version: 4.53.0\n",
+      "lmdb version: 1.2.1\n",
       "psutil version: 5.8.0\n",
+      "pandas version: 1.1.4\n",
+      "einops version: 0.3.0\n",
       "\n",
       "For details about installing the optional dependencies, please visit:\n",
       "    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies\n",
@@ -800,7 +802,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.10"
   }
  },
  "nbformat": 4,

diff --git a/modules/TorchIO_MONAI_PyTorch_Lightning.ipynb b/modules/TorchIO_MONAI_PyTorch_Lightning.ipynb
@@ -61,7 +61,7 @@
    "source": [
     "%%bash\n",
     "pip install -q torchio==0.18.39\n",
-    "pip install -q \"monai[gdown]\"==0.5.2\n",
+    "pip install -q \"monai[gdown]\"==0.6.0\n",
     "pip install -q pytorch-lightning==1.2.10\n",
     "pip install -q pandas==1.1.5 seaborn==0.11.1"
    ]
@@ -500,8 +500,10 @@
     "        logits = model.net(inputs.to(model.device))\n",
     "        labels = logits.argmax(dim=1)\n",
     "        labels_one_hot = torch.nn.functional.one_hot(labels).permute(0, 4, 1, 2, 3)\n",
-    "        dices, _ = get_dice(labels_one_hot.to(model.device), targets.to(model.device))\n",
-    "        all_dices.append(dices.cpu())\n",
+    "        get_dice(labels_one_hot.to(model.device), targets.to(model.device))\n",
+    "    metric = get_dice.aggregate()\n",
+    "    get_dice.reset()\n",
+    "    all_dices.append(metric)\n",
     "all_dices = torch.cat(all_dices)"
    ]
   },
@@ -867,7 +869,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.10"
+   "version": "3.8.10"
   }
  },
  "nbformat": 4,

diff --git a/modules/autoencoder_mednist.ipynb b/modules/autoencoder_mednist.ipynb
@@ -51,24 +51,26 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "MONAI version: 0.4.0+42.g58bc231.dirty\n",
-      "Numpy version: 1.19.5\n",
-      "Pytorch version: 1.7.1\n",
-      "MONAI flags: HAS_EXT = False, USE_COMPILED = False\n",
-      "MONAI rev id: 58bc231cb8a3eff6864cf857b2b4dc263d6738cc\n",
+      "MONAI version: 0.6.0rc1+23.gc6793fd0\n",
+      "Numpy version: 1.20.3\n",
+      "Pytorch version: 1.9.0a0+c3d40fd\n",
+      "MONAI flags: HAS_EXT = True, USE_COMPILED = False\n",
+      "MONAI rev id: c6793fd0f316a448778d0047664aaf8c1895fe1c\n",
       "\n",
       "Optional dependencies:\n",
-      "Pytorch Ignite version: 0.4.2\n",
+      "Pytorch Ignite version: 0.4.5\n",
       "Nibabel version: 3.2.1\n",
-      "scikit-image version: 0.18.1\n",
-      "Pillow version: 8.1.0\n",
-      "Tensorboard version: 2.4.0\n",
-      "gdown version: 3.12.2\n",
-      "TorchVision version: 0.8.2\n",
+      "scikit-image version: 0.15.0\n",
+      "Pillow version: 8.2.0\n",
+      "Tensorboard version: 2.5.0\n",
+      "gdown version: 3.13.0\n",
+      "TorchVision version: 0.10.0a0\n",
       "ITK version: 5.1.2\n",
-      "tqdm version: 4.51.0\n",
-      "lmdb version: 1.0.0\n",
+      "tqdm version: 4.53.0\n",
+      "lmdb version: 1.2.1\n",
       "psutil version: 5.8.0\n",
+      "pandas version: 1.1.4\n",
+      "einops version: 0.3.0\n",
       "\n",
       "For details about installing the optional dependencies, please visit:\n",
       "    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies\n",
@@ -522,7 +524,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.10"
   }
  },
  "nbformat": 4,

diff --git a/modules/csv_datasets.ipynb b/modules/csv_datasets.ipynb
@@ -37,7 +37,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 61,
+   "execution_count": 1,
    "metadata": {
     "tags": []
    },
@@ -46,25 +46,26 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "MONAI version: 0.4.0+507.g919c88e9\n",
-      "Numpy version: 1.21.0\n",
-      "Pytorch version: 1.9.0+cu102\n",
-      "MONAI flags: HAS_EXT = False, USE_COMPILED = False\n",
-      "MONAI rev id: 919c88e9f636b5f63d3fa8a3527789df15526c12\n",
+      "MONAI version: 0.6.0rc1+23.gc6793fd0\n",
+      "Numpy version: 1.20.3\n",
+      "Pytorch version: 1.9.0a0+c3d40fd\n",
+      "MONAI flags: HAS_EXT = True, USE_COMPILED = False\n",
+      "MONAI rev id: c6793fd0f316a448778d0047664aaf8c1895fe1c\n",
       "\n",
       "Optional dependencies:\n",
-      "Pytorch Ignite version: 0.4.4\n",
+      "Pytorch Ignite version: 0.4.5\n",
       "Nibabel version: 3.2.1\n",
       "scikit-image version: 0.15.0\n",
       "Pillow version: 8.2.0\n",
-      "Tensorboard version: 1.15.0+nv\n",
+      "Tensorboard version: 2.5.0\n",
       "gdown version: 3.13.0\n",
-      "TorchVision version: 0.9.0a0\n",
+      "TorchVision version: 0.10.0a0\n",
       "ITK version: 5.1.2\n",
       "tqdm version: 4.53.0\n",
-      "lmdb version: 1.1.1\n",
+      "lmdb version: 1.2.1\n",
       "psutil version: 5.8.0\n",
       "pandas version: 1.1.4\n",
+      "einops version: 0.3.0\n",
       "\n",
       "For details about installing the optional dependencies, please visit:\n",
       "    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies\n",
@@ -599,7 +600,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.10"
   }
  },
  "nbformat": 4,

diff --git a/modules/image_dataset.ipynb b/modules/image_dataset.ipynb
@@ -44,7 +44,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "metadata": {
     "execution": {
      "iopub.execute_input": "2021-01-14T12:34:04.909819Z",
@@ -59,25 +59,26 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "MONAI version: 0.5.3+144.geec33b6d\n",
-      "Numpy version: 1.21.0\n",
-      "Pytorch version: 1.9.0\n",
-      "MONAI flags: HAS_EXT = False, USE_COMPILED = False\n",
-      "MONAI rev id: eec33b6ddb987dc6be24ec0ace41bb55cc38a661\n",
+      "MONAI version: 0.6.0rc1+23.gc6793fd0\n",
+      "Numpy version: 1.20.3\n",
+      "Pytorch version: 1.9.0a0+c3d40fd\n",
+      "MONAI flags: HAS_EXT = True, USE_COMPILED = False\n",
+      "MONAI rev id: c6793fd0f316a448778d0047664aaf8c1895fe1c\n",
       "\n",
       "Optional dependencies:\n",
-      "Pytorch Ignite version: 0.4.4\n",
+      "Pytorch Ignite version: 0.4.5\n",
       "Nibabel version: 3.2.1\n",
-      "scikit-image version: 0.18.1\n",
+      "scikit-image version: 0.15.0\n",
       "Pillow version: 8.2.0\n",
       "Tensorboard version: 2.5.0\n",
       "gdown version: 3.13.0\n",
-      "TorchVision version: 0.10.0\n",
+      "TorchVision version: 0.10.0a0\n",
       "ITK version: 5.1.2\n",
-      "tqdm version: 4.61.1\n",
+      "tqdm version: 4.53.0\n",
       "lmdb version: 1.2.1\n",
       "psutil version: 5.8.0\n",
-      "pandas version: 1.2.5\n",
+      "pandas version: 1.1.4\n",
+      "einops version: 0.3.0\n",
       "\n",
       "For details about installing the optional dependencies, please visit:\n",
       "    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies\n",
@@ -123,7 +124,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -149,7 +150,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {
     "execution": {
      "iopub.execute_input": "2021-01-14T12:34:07.530773Z",
@@ -226,7 +227,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.10"
+   "version": "3.8.10"
   }
  },
  "nbformat": 4,

diff --git a/modules/integrate_3rd_party_transforms.ipynb b/modules/integrate_3rd_party_transforms.ipynb
@@ -102,24 +102,26 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "MONAI version: 0.4.0+35.g6adbcde\n",
-      "Numpy version: 1.19.5\n",
-      "Pytorch version: 1.7.1\n",
-      "MONAI flags: HAS_EXT = False, USE_COMPILED = False\n",
-      "MONAI rev id: 6adbcdee45c16f18f5b713575af3410437177311\n",
+      "MONAI version: 0.6.0rc1+23.gc6793fd0\n",
+      "Numpy version: 1.20.3\n",
+      "Pytorch version: 1.9.0a0+c3d40fd\n",
+      "MONAI flags: HAS_EXT = True, USE_COMPILED = False\n",
+      "MONAI rev id: c6793fd0f316a448778d0047664aaf8c1895fe1c\n",
       "\n",
       "Optional dependencies:\n",
-      "Pytorch Ignite version: 0.4.2\n",
+      "Pytorch Ignite version: 0.4.5\n",
       "Nibabel version: 3.2.1\n",
-      "scikit-image version: 0.18.1\n",
+      "scikit-image version: 0.15.0\n",
       "Pillow version: 7.0.0\n",
-      "Tensorboard version: 2.4.0\n",
-      "gdown version: 3.12.2\n",
-      "TorchVision version: 0.8.2\n",
+      "Tensorboard version: 2.5.0\n",
+      "gdown version: 3.13.0\n",
+      "TorchVision version: 0.10.0a0\n",
       "ITK version: 5.1.2\n",
-      "tqdm version: 4.51.0\n",
-      "lmdb version: 1.0.0\n",
+      "tqdm version: 4.53.0\n",
+      "lmdb version: 1.2.1\n",
       "psutil version: 5.8.0\n",
+      "pandas version: 1.1.4\n",
+      "einops version: 0.3.0\n",
       "\n",
       "For details about installing the optional dependencies, please visit:\n",
       "    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies\n",
@@ -484,7 +486,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.10"
   }
  },
  "nbformat": 4,