From df26b7f675241cf00632b6f98e10ae28dca81fca Mon Sep 17 00:00:00 2001 From: Wenqi Li Date: Tue, 23 Mar 2021 16:02:22 +0000 Subject: [PATCH 1/2] fixes tutorial issue 152 Signed-off-by: Wenqi Li --- modules/nifti_read_example.ipynb | 35 ++++++++++++++++++-------------- 1 file changed, 20 insertions(+), 15 deletions(-) diff --git a/modules/nifti_read_example.ipynb b/modules/nifti_read_example.ipynb index 588576a0d2..996df73a09 100644 --- a/modules/nifti_read_example.ipynb +++ b/modules/nifti_read_example.ipynb @@ -47,23 +47,23 @@ "name": "stdout", "output_type": "stream", "text": [ - "MONAI version: 0.4.0+35.g6adbcde\n", + "MONAI version: 0.4.0+189.g20209fe0\n", "Numpy version: 1.19.5\n", - "Pytorch version: 1.7.1\n", + "Pytorch version: 1.8.0\n", "MONAI flags: HAS_EXT = False, USE_COMPILED = False\n", - "MONAI rev id: 6adbcdee45c16f18f5b713575af3410437177311\n", + "MONAI rev id: 20209fe07a8237a261336c08c1b3aa1faee117db\n", "\n", "Optional dependencies:\n", - "Pytorch Ignite version: 0.4.2\n", + "Pytorch Ignite version: 0.4.4\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", + "Pillow version: 8.1.2\n", + "Tensorboard version: 2.4.1\n", "gdown version: 3.12.2\n", - "TorchVision version: 0.8.2\n", + "TorchVision version: 0.9.0\n", "ITK version: 5.1.2\n", - "tqdm version: 4.51.0\n", - "lmdb version: 1.0.0\n", + "tqdm version: 4.59.0\n", + "lmdb version: 1.1.1\n", "psutil version: 5.8.0\n", "\n", "For details about installing the optional dependencies, please visit:\n", @@ -94,7 +94,8 @@ "import torch\n", "\n", "from monai.config import print_config\n", - "from monai.data import ArrayDataset, GridPatchDataset, create_test_image_3d\n", + "from monai.data import (\n", + " ArrayDataset, GridPatchDataset, create_test_image_3d, PatchIter)\n", "from monai.transforms import (\n", " AddChannel,\n", " Compose,\n", @@ -130,7 +131,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "/workspace/data/medical\n" + "/var/folders/6f/fdkl7m0x7sz3nj_t7p3ccgz00000gp/T/tmpfu_1o4w0\n" ] } ], @@ -235,7 +236,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "torch.Size([10, 1, 64, 64, 64]) torch.Size([10, 1, 64, 64, 64])\n" + "image shapes: torch.Size([3, 1, 64, 64, 64]) torch.Size([3, 1, 64, 64, 64])\n", + "coordinates shapes: torch.Size([3, 4, 2]) torch.Size([3, 4, 2])\n" ] } ], @@ -246,13 +248,16 @@ "segtrans = Compose([LoadImage(image_only=True), AddChannel(), ToTensor()])\n", "\n", "ds = ArrayDataset(images, imtrans, segs, segtrans)\n", - "ds = GridPatchDataset(ds, (64, 64, 64))\n", + "patch_iter = PatchIter(patch_size=(64, 64, 64), start_pos=(0, 0, 0))\n", + "img_seg_iter = lambda x: (zip(patch_iter(x[0]), patch_iter(x[1])),)\n", + "ds = GridPatchDataset(ds, img_seg_iter, with_coordinates=False)\n", "\n", "loader = torch.utils.data.DataLoader(\n", " ds, batch_size=10, num_workers=2, pin_memory=torch.cuda.is_available()\n", ")\n", "im, seg = first(loader)\n", - "print(im.shape, seg.shape)" + "print(\"image shapes:\", im[0].shape, seg[0].shape)\n", + "print(\"coordinates shapes:\", im[1].shape, seg[1].shape)" ] }, { @@ -291,7 +296,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.5" + "version": "3.7.10" } }, "nbformat": 4, From fc7f2d6761fe6027f50791573e6706db24e6fa1a Mon Sep 17 00:00:00 2001 From: Wenqi Li Date: Tue, 23 Mar 2021 16:13:36 +0000 Subject: [PATCH 2/2] style fixes Signed-off-by: Wenqi Li --- modules/nifti_read_example.ipynb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/modules/nifti_read_example.ipynb b/modules/nifti_read_example.ipynb index 996df73a09..056181905b 100644 --- a/modules/nifti_read_example.ipynb +++ b/modules/nifti_read_example.ipynb @@ -131,7 +131,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "/var/folders/6f/fdkl7m0x7sz3nj_t7p3ccgz00000gp/T/tmpfu_1o4w0\n" + "/var/folders/6f/fdkl7m0x7sz3nj_t7p3ccgz00000gp/T/tmp75rr_5zk\n" ] } ], @@ -249,7 +249,12 @@ "\n", "ds = ArrayDataset(images, imtrans, segs, segtrans)\n", "patch_iter = PatchIter(patch_size=(64, 64, 64), start_pos=(0, 0, 0))\n", - "img_seg_iter = lambda x: (zip(patch_iter(x[0]), patch_iter(x[1])),)\n", + "\n", + "\n", + "def img_seg_iter(x):\n", + " return (zip(patch_iter(x[0]), patch_iter(x[1])),)\n", + "\n", + "\n", "ds = GridPatchDataset(ds, img_seg_iter, with_coordinates=False)\n", "\n", "loader = torch.utils.data.DataLoader(\n",