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Merged
wyli merged 2 commits into from
May 4, 2022
Merged

densenet training download data #685

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872f71d
densenet training download data
rijobro May 4, 2022
26bf676
Merge branch 'master' into densenet_training_download_data
wyli May 4, 2022
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91 changes: 59 additions & 32 deletions 3d_classification/densenet_training_array.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -131,40 +131,17 @@
}
],
"source": [
"# set this in your environment or previous cell to wherever IXI is downloaded and extracted\n",
"# Set data directory\n",
"directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
"\n",
"if directory is None:\n",
" resource = \"http://biomedic.doc.ic.ac.uk/brain-development/downloads/IXI/IXI-T1.tar\"\n",
" md5 = \"34901a0593b41dd19c1a1f746eac2d58\"\n",
"\n",
" root_dir = tempfile.mkdtemp()\n",
"\n",
" dataset_dir = os.path.join(root_dir, \"ixi\")\n",
" tarfile_name = f\"{dataset_dir}.tar\"\n",
"\n",
" download_and_extract(resource, tarfile_name, dataset_dir, md5)\n",
"else:\n",
" root_dir = directory\n",
"\n",
"root_dir = tempfile.mkdtemp() if directory is None else directory\n",
"print(root_dir)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<class 'torch.Tensor'> torch.Size([3, 1, 96, 96, 96]) tensor([[1., 0.],\n",
" [1., 0.],\n",
" [1., 0.]]) torch.Size([3, 2])\n"
]
}
],
"outputs": [],
"source": [
"# IXI dataset as a demo, downloadable from https://brain-development.org/ixi-dataset/\n",
"images = [\n",
Expand Down Expand Up @@ -195,8 +172,58 @@
"\n",
"# Represent labels in one-hot format for binary classifier training,\n",
"# BCEWithLogitsLoss requires target to have same shape as input\n",
"labels = torch.nn.functional.one_hot(torch.as_tensor(labels)).float()\n",
"labels = torch.nn.functional.one_hot(torch.as_tensor(labels)).float()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"ixi.tar: 100%|██████████| 4.51G/4.51G [08:19<00:00, 9.70MB/s] \n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"2022-05-04 12:23:06,530 - INFO - Downloaded: /mnt/data/rbrown/Documents/Data/MONAI/ixi.tar\n",
"2022-05-04 12:23:13,734 - INFO - Verified 'ixi.tar', md5: 34901a0593b41dd19c1a1f746eac2d58.\n",
"2022-05-04 12:23:13,735 - INFO - Writing into directory: /mnt/data/rbrown/Documents/Data/MONAI/ixi.\n"
]
}
],
"source": [
"if not os.path.isfile(images[0]):\n",
" resource = \"http://biomedic.doc.ic.ac.uk/brain-development/downloads/IXI/IXI-T1.tar\"\n",
" md5 = \"34901a0593b41dd19c1a1f746eac2d58\"\n",
"\n",
" dataset_dir = os.path.join(root_dir, \"ixi\")\n",
" tarfile_name = f\"{dataset_dir}.tar\"\n",
"\n",
" download_and_extract(resource, tarfile_name, dataset_dir, md5)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<class 'torch.Tensor'> torch.Size([3, 1, 96, 96, 96]) tensor([[1., 0.],\n",
" [1., 0.],\n",
" [1., 0.]]) torch.Size([3, 2])\n"
]
}
],
"source": [
"# Define transforms\n",
"train_transforms = Compose([ScaleIntensity(), AddChannel(), Resize((96, 96, 96)), RandRotate90(), EnsureType()])\n",
"\n",
Expand All @@ -220,7 +247,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 7,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -367,7 +394,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -395,7 +422,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -405,7 +432,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 10,
"metadata": {
"scrolled": true,
"tags": []
Expand Down Expand Up @@ -462,7 +489,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
Expand Down