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fixes tutorial issue 152 #155

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Merged
wyli merged 2 commits into from
Mar 23, 2021
Merged

fixes tutorial issue 152 #155

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df26b7f
fixes tutorial issue 152
wyli Mar 23, 2021
fc7f2d6
style fixes
wyli Mar 23, 2021
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40 changes: 25 additions & 15 deletions modules/nifti_read_example.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -130,7 +131,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"/workspace/data/medical\n"
"/var/folders/6f/fdkl7m0x7sz3nj_t7p3ccgz00000gp/T/tmp75rr_5zk\n"
]
}
],
Expand Down Expand Up @@ -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"
]
}
],
Expand All @@ -246,13 +248,21 @@
"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",
"\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",
" 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)"
]
},
{
Expand Down Expand Up @@ -291,7 +301,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.5"
"version": "3.7.10"
}
},
"nbformat": 4,
Expand Down