auto fixes from pre-commit.com hooks (Project-MONAI#1198)

### 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.
- [x] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [x] 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>`

---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/contributing_templates/notebook/example_class.py

@@ -17,15 +17,15 @@
 from PIL import Image
 
 
-class ExampleImageGenerator():
+class ExampleImageGenerator:
     def __init__(self, num_image=40, image_size=(128, 128)):
         self.num_image = num_image
         self.image_size = image_size
 
     def generate(self, tempdir):
         for i in range(self.num_image):
             im, seg = create_test_image_2d(
-                self.image_size[0], self.image_size[1], num_seg_classes=1,random_state=np.random.RandomState(42)
+                self.image_size[0], self.image_size[1], num_seg_classes=1, random_state=np.random.RandomState(42)
             )
             Image.fromarray((im * 255).astype("uint8")).save(os.path.join(tempdir, f"img{i:d}.png"))
             Image.fromarray((seg * 255).astype("uint8")).save(os.path.join(tempdir, f"seg{i:d}.png"))

.pre-commit-config.yaml

@@ -22,30 +22,11 @@ repos:
         args: ['--maxkb=1024']
       - id: detect-private-key
 
-  #- repo: https://github.com/asottile/pyupgrade
-  #  rev: v2.23.2
-  #  hooks:
-  #    - id: pyupgrade
-  #      args: [--py36-plus]
-  #      name: Upgrade code
-
-  #- repo: https://github.com/asottile/yesqa
-  #  rev: v1.2.3
-  #  hooks:
-  #    - id: yesqa
-  #      name: Unused noqa
-
-  #- repo: https://github.com/PyCQA/isort
-  #  rev: 5.9.3
-  #  hooks:
-  #    - id: isort
-  #      name: Format imports
-
-  # - repo: https://github.com/psf/black
-  #   rev: 21.7b0
-  #   hooks:
-  #     - id: black
-  #       name: Format code
+  - repo: https://github.com/psf/black
+    rev: "22.12.0"
+    hooks:
+      - id: black
+      - id: black-jupyter
 
   #- repo: https://github.com/executablebooks/mdformat
   #  rev: 0.7.8

2d_classification/mednist_tutorial.ipynb

@@ -237,14 +237,10 @@
     }
    ],
    "source": [
-    "class_names = sorted(x for x in os.listdir(data_dir)\n",
-    "                     if os.path.isdir(os.path.join(data_dir, x)))\n",
+    "class_names = sorted(x for x in os.listdir(data_dir) if os.path.isdir(os.path.join(data_dir, x)))\n",
     "num_class = len(class_names)\n",
     "image_files = [\n",
-    "    [\n",
-    "        os.path.join(data_dir, class_names[i], x)\n",
-    "        for x in os.listdir(os.path.join(data_dir, class_names[i]))\n",
-    "    ]\n",
+    "    [os.path.join(data_dir, class_names[i], x) for x in os.listdir(os.path.join(data_dir, class_names[i]))]\n",
     "    for i in range(num_class)\n",
     "]\n",
     "num_each = [len(image_files[i]) for i in range(num_class)]\n",
@@ -341,9 +337,7 @@
     "test_x = [image_files_list[i] for i in test_indices]\n",
     "test_y = [image_class[i] for i in test_indices]\n",
     "\n",
-    "print(\n",
-    "    f\"Training count: {len(train_x)}, Validation count: \"\n",
-    "    f\"{len(val_x)}, Test count: {len(test_x)}\")"
+    "print(f\"Training count: {len(train_x)}, Validation count: \" f\"{len(val_x)}, Test count: {len(test_x)}\")"
    ]
   },
   {
@@ -370,8 +364,7 @@
     "    ]\n",
     ")\n",
     "\n",
-    "val_transforms = Compose(\n",
-    "    [LoadImage(image_only=True), EnsureChannelFirst(), ScaleIntensity()])\n",
+    "val_transforms = Compose([LoadImage(image_only=True), EnsureChannelFirst(), ScaleIntensity()])\n",
     "\n",
     "y_pred_trans = Compose([Activations(softmax=True)])\n",
     "y_trans = Compose([AsDiscrete(to_onehot=num_class)])"
@@ -397,16 +390,13 @@
     "\n",
     "\n",
     "train_ds = MedNISTDataset(train_x, train_y, train_transforms)\n",
-    "train_loader = DataLoader(\n",
-    "    train_ds, batch_size=300, shuffle=True, num_workers=10)\n",
+    "train_loader = DataLoader(train_ds, batch_size=300, shuffle=True, num_workers=10)\n",
     "\n",
     "val_ds = MedNISTDataset(val_x, val_y, val_transforms)\n",
-    "val_loader = DataLoader(\n",
-    "    val_ds, batch_size=300, num_workers=10)\n",
+    "val_loader = DataLoader(val_ds, batch_size=300, num_workers=10)\n",
     "\n",
     "test_ds = MedNISTDataset(test_x, test_y, val_transforms)\n",
-    "test_loader = DataLoader(\n",
-    "    test_ds, batch_size=300, num_workers=10)"
+    "test_loader = DataLoader(test_ds, batch_size=300, num_workers=10)"
    ]
   },
   {
@@ -430,8 +420,7 @@
    "outputs": [],
    "source": [
     "device = torch.device(\"cuda\" if torch.cuda.is_available() else \"cpu\")\n",
-    "model = DenseNet121(spatial_dims=2, in_channels=1,\n",
-    "                    out_channels=num_class).to(device)\n",
+    "model = DenseNet121(spatial_dims=2, in_channels=1, out_channels=num_class).to(device)\n",
     "loss_function = torch.nn.CrossEntropyLoss()\n",
     "optimizer = torch.optim.Adam(model.parameters(), 1e-5)\n",
     "max_epochs = 4\n",
@@ -477,9 +466,7 @@
     "        loss.backward()\n",
     "        optimizer.step()\n",
     "        epoch_loss += loss.item()\n",
-    "        print(\n",
-    "            f\"{step}/{len(train_ds) // train_loader.batch_size}, \"\n",
-    "            f\"train_loss: {loss.item():.4f}\")\n",
+    "        print(f\"{step}/{len(train_ds) // train_loader.batch_size}, \" f\"train_loss: {loss.item():.4f}\")\n",
     "        epoch_len = len(train_ds) // train_loader.batch_size\n",
     "    epoch_loss /= step\n",
     "    epoch_loss_values.append(epoch_loss)\n",
@@ -509,8 +496,7 @@
     "            if result > best_metric:\n",
     "                best_metric = result\n",
     "                best_metric_epoch = epoch + 1\n",
-    "                torch.save(model.state_dict(), os.path.join(\n",
-    "                    root_dir, \"best_metric_model.pth\"))\n",
+    "                torch.save(model.state_dict(), os.path.join(root_dir, \"best_metric_model.pth\"))\n",
     "                print(\"saved new best metric model\")\n",
     "            print(\n",
     "                f\"current epoch: {epoch + 1} current AUC: {result:.4f}\"\n",
@@ -519,9 +505,7 @@
     "                f\" at epoch: {best_metric_epoch}\"\n",
     "            )\n",
     "\n",
-    "print(\n",
-    "    f\"train completed, best_metric: {best_metric:.4f} \"\n",
-    "    f\"at epoch: {best_metric_epoch}\")"
+    "print(f\"train completed, best_metric: {best_metric:.4f} \" f\"at epoch: {best_metric_epoch}\")"
    ]
   },
   {
@@ -581,8 +565,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model.load_state_dict(torch.load(\n",
-    "    os.path.join(root_dir, \"best_metric_model.pth\")))\n",
+    "model.load_state_dict(torch.load(os.path.join(root_dir, \"best_metric_model.pth\")))\n",
     "model.eval()\n",
     "y_true = []\n",
     "y_pred = []\n",
@@ -626,8 +609,7 @@
     }
    ],
    "source": [
-    "print(classification_report(\n",
-    "    y_true, y_pred, target_names=class_names, digits=4))"
+    "print(classification_report(y_true, y_pred, target_names=class_names, digits=4))"
    ]
   },
   {

2d_registration/registration_mednist.ipynb

@@ -230,7 +230,8 @@
     "train_data = MedNISTDataset(root_dir=root_dir, section=\"training\", download=True, transform=None)\n",
     "training_datadict = [\n",
     "    {\"fixed_hand\": item[\"image\"], \"moving_hand\": item[\"image\"]}\n",
-    "    for item in train_data.data if item[\"label\"] == 4  # label 4 is for xray hands\n",
+    "    for item in train_data.data\n",
+    "    if item[\"label\"] == 4  # label 4 is for xray hands\n",
     "]\n",
     "print(\"\\n first training items: \", training_datadict[:3])"
    ]
@@ -247,9 +248,15 @@
     "    [\n",
     "        LoadImageD(keys=[\"fixed_hand\", \"moving_hand\"]),\n",
     "        EnsureChannelFirstD(keys=[\"fixed_hand\", \"moving_hand\"]),\n",
-    "        ScaleIntensityRanged(keys=[\"fixed_hand\", \"moving_hand\"],\n",
-    "                             a_min=0., a_max=255., b_min=0.0, b_max=1.0, clip=True,),\n",
-    "        RandRotateD(keys=[\"moving_hand\"], range_x=np.pi/4, prob=1.0, keep_size=True, mode=\"bicubic\"),\n",
+    "        ScaleIntensityRanged(\n",
+    "            keys=[\"fixed_hand\", \"moving_hand\"],\n",
+    "            a_min=0.0,\n",
+    "            a_max=255.0,\n",
+    "            b_min=0.0,\n",
+    "            b_max=1.0,\n",
+    "            clip=True,\n",
+    "        ),\n",
+    "        RandRotateD(keys=[\"moving_hand\"], range_x=np.pi / 4, prob=1.0, keep_size=True, mode=\"bicubic\"),\n",
     "        RandZoomD(keys=[\"moving_hand\"], min_zoom=0.9, max_zoom=1.1, prob=1.0, mode=\"bicubic\", align_corners=False),\n",
     "    ]\n",
     ")"
@@ -347,8 +354,7 @@
     }
    ],
    "source": [
-    "train_ds = CacheDataset(data=training_datadict[:1000], transform=train_transforms,\n",
-    "                        cache_rate=1.0, num_workers=4)\n",
+    "train_ds = CacheDataset(data=training_datadict[:1000], transform=train_transforms, cache_rate=1.0, num_workers=4)\n",
     "train_loader = DataLoader(train_ds, batch_size=16, shuffle=True, num_workers=2)"
    ]
   },
@@ -370,11 +376,8 @@
    "source": [
     "device = torch.device(\"cuda:0\")\n",
     "model = GlobalNet(\n",
-    "    image_size=(64, 64),\n",
-    "    spatial_dims=2,\n",
-    "    in_channels=2,  # moving and fixed\n",
-    "    num_channel_initial=16,\n",
-    "    depth=3).to(device)\n",
+    "    image_size=(64, 64), spatial_dims=2, in_channels=2, num_channel_initial=16, depth=3  # moving and fixed\n",
+    ").to(device)\n",
     "image_loss = MSELoss()\n",
     "if USE_COMPILED:\n",
     "    warp_layer = Warp(3, \"border\").to(device)\n",
@@ -498,8 +501,7 @@
     }
    ],
    "source": [
-    "val_ds = CacheDataset(data=training_datadict[2000:2500], transform=train_transforms,\n",
-    "                      cache_rate=1.0, num_workers=0)\n",
+    "val_ds = CacheDataset(data=training_datadict[2000:2500], transform=train_transforms, cache_rate=1.0, num_workers=0)\n",
     "val_loader = DataLoader(val_ds, batch_size=16, num_workers=0)\n",
     "for batch_data in val_loader:\n",
     "    moving = batch_data[\"moving_hand\"].to(device)\n",
@@ -543,20 +545,20 @@
     "for b in range(batch_size):\n",
     "    # moving image\n",
     "    plt.subplot(batch_size, 3, b * 3 + 1)\n",
-    "    plt.axis('off')\n",
+    "    plt.axis(\"off\")\n",
     "    plt.title(\"moving image\")\n",
     "    plt.imshow(moving_image[b], cmap=\"gray\")\n",
     "    # fixed image\n",
     "    plt.subplot(batch_size, 3, b * 3 + 2)\n",
-    "    plt.axis('off')\n",
+    "    plt.axis(\"off\")\n",
     "    plt.title(\"fixed image\")\n",
     "    plt.imshow(fixed_image[b], cmap=\"gray\")\n",
     "    # warped moving\n",
     "    plt.subplot(batch_size, 3, b * 3 + 3)\n",
-    "    plt.axis('off')\n",
+    "    plt.axis(\"off\")\n",
     "    plt.title(\"predicted image\")\n",
     "    plt.imshow(pred_image[b], cmap=\"gray\")\n",
-    "plt.axis('off')\n",
+    "plt.axis(\"off\")\n",
     "plt.show()"
    ]
   }

2d_segmentation/torch/unet_evaluation_dict.py

@@ -23,7 +23,15 @@
 from monai.inferers import sliding_window_inference
 from monai.metrics import DiceMetric
 from monai.networks.nets import UNet
-from monai.transforms import Activations, EnsureChannelFirstd, AsDiscrete, Compose, LoadImaged, SaveImage, ScaleIntensityd
+from monai.transforms import (
+    Activations,
+    EnsureChannelFirstd,
+    AsDiscrete,
+    Compose,
+    LoadImaged,
+    SaveImage,
+    ScaleIntensityd,
+)
 
 
 def main(tempdir):

3d_classification/densenet_training_array.ipynb

@@ -38,7 +38,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!python -c \"import monai\" || pip install -q \"monai-weekly[nibabel, tqdm]\"\n"
+    "!python -c \"import monai\" || pip install -q \"monai-weekly[nibabel, tqdm]\""
    ]
   },
   {
@@ -463,7 +463,7 @@
     "# For the other dimensions (channel, width, height), use\n",
     "# -1 to use 0 and img.shape[x]-1 for min and max, respectively\n",
     "depth_slice = img.shape[2] // 2\n",
-    "occ_sens_b_box = [depth_slice-1, depth_slice, -1, -1, -1, -1]\n",
+    "occ_sens_b_box = [depth_slice - 1, depth_slice, -1, -1, -1, -1]\n",
     "\n",
     "occ_result, _ = occ_sens(x=img, b_box=occ_sens_b_box)\n",
     "occ_result = occ_result[0, label.argmax().item()][None]\n",

3d_classification/ignite/densenet_training_dict.py

@@ -125,7 +125,17 @@ def prepare_batch(batch, device=None, non_blocking=False):
     post_pred = Compose([Activations(softmax=True)])
     # Ignite evaluator expects batch=(img, label) and returns output=(y_pred, y) at every iteration,
     # user can add output_transform to return other values
-    evaluator = create_supervised_evaluator(net, val_metrics, device, True, prepare_batch=prepare_batch, output_transform=lambda x, y, y_pred: ([post_pred(i) for i in decollate_batch(y_pred)], [post_label(i) for i in decollate_batch(y, detach=False)]))
+    evaluator = create_supervised_evaluator(
+        net,
+        val_metrics,
+        device,
+        True,
+        prepare_batch=prepare_batch,
+        output_transform=lambda x, y, y_pred: (
+            [post_pred(i) for i in decollate_batch(y_pred)],
+            [post_label(i) for i in decollate_batch(y, detach=False)],
+        ),
+    )
 
     # add stats event handler to print validation stats via evaluator
     val_stats_handler = StatsHandler(