Skip to content

update tutorials/modules for metatensor #771

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 18 commits into from
Jul 13, 2022
Merged

update tutorials/modules for metatensor #771

Show file tree
Hide file tree
Changes from 17 commits
Commits
Show all changes
18 commits
Select commit Hold shift + click to select a range
65b826b
update load image demo
wyli Jul 5, 2022
6c200f8
update 2d_slices_from_3d_training.ipynb
wyli Jul 11, 2022
87ee5c2
image_dataset.ipynb
wyli Jul 11, 2022
7e844a3
fixes fasttraining
wyli Jul 11, 2022
694399f
update tta
wyli Jul 11, 2022
aaf6b6a
nifti read
wyli Jul 11, 2022
11057b2
update tta
wyli Jul 11, 2022
6ddb8ab
fixes typos
wyli Jul 11, 2022
50c2345
fixes interpretability/cats_and_dogs.ipynb
wyli Jul 11, 2022
7cd4d0a
fixes pep8
wyli Jul 11, 2022
fb6f994
pep8
wyli Jul 11, 2022
eaf509d
update 2d_slices_from_3d_sampling.ipynb
wyli Jul 12, 2022
822b719
modules/resample_benchmark.ipynb
wyli Jul 12, 2022
8cf3839
modules/benchmark_global_mutual_information.ipynb
wyli Jul 12, 2022
73ac6b9
update modules/nifti_read_example.ipynb
wyli Jul 12, 2022
2febe80
modules/integrate_3rd_party_transforms.ipynb
wyli Jul 12, 2022
fd2f684
fixes pep8
wyli Jul 12, 2022
36efcc0
update based on comments
wyli Jul 13, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion acceleration/fast_training_tutorial.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -614,7 +614,7 @@
" with torch.no_grad():\n",
" val_loader_iterator = iter(val_loader)\n",
"\n",
" for val_step in range(len(val_loader)):\n",
" for _ in range(len(val_loader)):\n",
" # profiling: val dataload\n",
" with nvtx.annotate(\"dataload\", color=\"red\") if profiling else no_profiling:\n",
" val_data = next(val_loader_iterator)\n",
Expand Down
2 changes: 1 addition & 1 deletion modules/2d_slices_from_3d_sampling.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -519,7 +519,7 @@
" device=torch.device(\"cpu\"),\n",
" padding_mode=\"replicate\",\n",
" )\n",
" val_output = slice_inferer(val_images, model)\n",
" val_output = slice_inferer(val_images, model).cpu()\n",
" dice_metric(y_pred=val_output > 0.5, y=val_data[\"seg\"])\n",
" print(\"Dice: \", dice_metric.get_buffer()[-1][0])\n",
" fig = plt.figure(figsize=(10, 4))\n",
Expand Down
4 changes: 2 additions & 2 deletions modules/2d_slices_from_3d_training.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -501,7 +501,7 @@
" device=torch.device(\"cpu\"),\n",
" padding_mode=\"replicate\",\n",
" )\n",
" val_output = slice_inferer(val_images, model)\n",
" val_output = slice_inferer(val_images, model).to(\"cpu\")\n",
" dice_metric(y_pred=val_output > 0.5, y=val_data[\"seg\"])\n",
" print(\"Dice: \", dice_metric.get_buffer()[-1][0])\n",
" fig = plt.figure(figsize=(10, 4))\n",
Expand Down Expand Up @@ -549,7 +549,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.8.0"
}
},
"nbformat": 4,
Expand Down
155 changes: 86 additions & 69 deletions modules/3d_image_transforms.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

6 changes: 3 additions & 3 deletions modules/benchmark_global_mutual_information.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -232,8 +232,8 @@
" a2: numpy array of shape HWD\n",
" \"\"\"\n",
" antspyx_result = ants.image_mutual_information(\n",
" ants.from_numpy(a1),\n",
" ants.from_numpy(a2)\n",
" ants.from_numpy(a1.detach().cpu().numpy()),\n",
" ants.from_numpy(a2.detach().cpu().numpy())\n",
" )\n",
" monai_result = GlobalMutualInformationLoss(\n",
" kernel_type=\"b-spline\",\n",
Expand Down Expand Up @@ -471,7 +471,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.8.0"
}
},
"nbformat": 4,
Expand Down
54 changes: 29 additions & 25 deletions modules/image_dataset.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"metadata": {
"execution": {
"iopub.execute_input": "2021-01-14T12:34:04.909819Z",
Expand All @@ -59,26 +59,29 @@
"name": "stdout",
"output_type": "stream",
"text": [
"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",
"MONAI version: 0.9.1rc1+6.gcbe16eb3\n",
"Numpy version: 1.23.0\n",
"Pytorch version: 1.12.0+cu102\n",
"MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False\n",
"MONAI rev id: cbe16eb326830ef31479fd34ae1e44d27fc2d64d\n",
"MONAI __file__: /home/wenqil/Documents/MONAI/monai/__init__.py\n",
"\n",
"Optional dependencies:\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: 2.5.0\n",
"gdown version: 3.13.0\n",
"TorchVision version: 0.10.0a0\n",
"ITK version: 5.1.2\n",
"tqdm version: 4.53.0\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",
"Pytorch Ignite version: 0.4.9\n",
"Nibabel version: 4.0.1\n",
"scikit-image version: 0.19.3\n",
"Pillow version: 9.2.0\n",
"Tensorboard version: 2.9.1\n",
"gdown version: 4.5.1\n",
"TorchVision version: 0.13.0+cu102\n",
"tqdm version: 4.64.0\n",
"lmdb version: 1.3.0\n",
"psutil version: 5.9.1\n",
"pandas version: 1.4.3\n",
"einops version: 0.4.1\n",
"transformers version: 4.20.1\n",
"mlflow version: 1.27.0\n",
"pynrrd version: 0.4.3\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",
Expand Down Expand Up @@ -124,7 +127,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -150,7 +153,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 4,
"metadata": {
"execution": {
"iopub.execute_input": "2021-01-14T12:34:07.530773Z",
Expand All @@ -173,8 +176,9 @@
"source": [
"class TestCompose(Compose):\n",
" def __call__(self, data, meta):\n",
" data = self.transforms[0](data, meta) # ensure channel first\n",
" data, _, meta[\"affine\"] = self.transforms[1](data, meta[\"affine\"]) # spacing\n",
" data = self.transforms[0](data) # ensure channel first\n",
" data = self.transforms[1](data) # spacing\n",
" meta = data.meta\n",
" if len(self.transforms) == 3:\n",
" return self.transforms[2](data), meta # image contrast\n",
" return data, meta\n",
Expand Down Expand Up @@ -213,7 +217,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -227,7 +231,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.10"
"version": "3.8.0"
}
},
"nbformat": 4,
Expand Down
5 changes: 3 additions & 2 deletions modules/integrate_3rd_party_transforms.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -272,6 +272,7 @@
" ScaleIntensityRanged(keys=[\"image\"], a_min=-57,\n",
" a_max=164, b_min=0.0, b_max=1.0, clip=True),\n",
" CropForegroundd(keys=[\"image\", \"label\"], source_key=\"image\"),\n",
" EnsureTyped(keys=[\"image\", \"label\"], data_type=\"numpy\"),\n",
"]"
]
},
Expand Down Expand Up @@ -472,7 +473,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -486,7 +487,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.10"
"version": "3.8.0"
}
},
"nbformat": 4,
Expand Down
4 changes: 2 additions & 2 deletions modules/interpretability/cats_and_dogs.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -200,7 +200,7 @@
" axes = np.asarray(axes) if nims == 1 else axes\n",
" for d, ax in zip(data, axes.ravel()):\n",
" # channel last for matplotlib\n",
" im = np.moveaxis(d[\"image\"], 0, -1)\n",
" im = np.moveaxis(d[\"image\"].detach().cpu().numpy(), 0, -1)\n",
" ax.imshow(im, cmap='gray')\n",
" ax.set_title(Animals(d['label']).name, fontsize=25)\n",
" ax.axis(\"off\")\n",
Expand Down Expand Up @@ -608,7 +608,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.7"
"version": "3.8.0"
}
},
"nbformat": 4,
Expand Down
1,117 changes: 61 additions & 1,056 deletions modules/inverse_transforms_and_test_time_augmentations.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

75 changes: 40 additions & 35 deletions modules/nifti_read_example.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,27 +47,29 @@
"name": "stdout",
"output_type": "stream",
"text": [
"MONAI version: 0.8.1\n",
"Numpy version: 1.21.5\n",
"Pytorch version: 1.10.2\n",
"MONAI flags: HAS_EXT = False, USE_COMPILED = False\n",
"MONAI rev id: 71ff399a3ea07aef667b23653620a290364095b1\n",
"MONAI version: 0.9.1rc2+2.gc0268266.dirty\n",
"Numpy version: 1.23.0\n",
"Pytorch version: 1.12.0+cu102\n",
"MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False\n",
"MONAI rev id: c0268266f688c3bacd9c92ef7458f54b6afdf609\n",
"MONAI __file__: /home/wenqil/Documents/MONAI/monai/__init__.py\n",
"\n",
"Optional dependencies:\n",
"Pytorch Ignite version: 0.4.8\n",
"Nibabel version: 3.2.1\n",
"scikit-image version: 0.19.1\n",
"Pillow version: 9.0.0\n",
"Tensorboard version: 2.8.0\n",
"gdown version: 4.2.0\n",
"TorchVision version: 0.11.3\n",
"tqdm version: 4.62.3\n",
"Pytorch Ignite version: 0.4.9\n",
"Nibabel version: 4.0.1\n",
"scikit-image version: 0.19.3\n",
"Pillow version: 9.2.0\n",
"Tensorboard version: 2.9.1\n",
"gdown version: 4.5.1\n",
"TorchVision version: 0.13.0+cu102\n",
"tqdm version: 4.64.0\n",
"lmdb version: 1.3.0\n",
"psutil version: 5.9.0\n",
"pandas version: 1.1.5\n",
"einops version: 0.4.0\n",
"transformers version: 4.16.1\n",
"mlflow version: 1.23.1\n",
"psutil version: 5.9.1\n",
"pandas version: 1.4.3\n",
"einops version: 0.4.1\n",
"transformers version: 4.20.1\n",
"mlflow version: 1.27.0\n",
"pynrrd version: 0.4.3\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",
Expand Down Expand Up @@ -100,7 +102,6 @@
"from monai.data import (\n",
" ArrayDataset, GridPatchDataset, create_test_image_3d, PatchIter)\n",
"from monai.transforms import (\n",
" AddChannel,\n",
" Compose,\n",
" LoadImage,\n",
" RandSpatialCrop,\n",
Expand All @@ -125,11 +126,19 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"metadata": {
"tags": []
},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/tmp/tmpkzde8m5b\n"
]
}
],
"source": [
"directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
"root_dir = tempfile.mkdtemp() if directory is None else directory\n",
Expand Down Expand Up @@ -177,7 +186,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"torch.Size([5, 1, 64, 64, 64]) torch.Size([5, 1, 64, 64, 64])\n"
"(5, 1, 64, 64, 64) (5, 1, 64, 64, 64)\n"
]
}
],
Expand All @@ -187,27 +196,23 @@
"\n",
"imtrans = Compose(\n",
" [\n",
" LoadImage(image_only=True),\n",
" LoadImage(image_only=True, ensure_channel_first=True),\n",
" ScaleIntensity(),\n",
" AddChannel(),\n",
" RandSpatialCrop((64, 64, 64), random_size=False),\n",
" EnsureType(),\n",
" ]\n",
")\n",
"\n",
"segtrans = Compose(\n",
" [\n",
" LoadImage(image_only=True),\n",
" AddChannel(),\n",
" LoadImage(image_only=True, ensure_channel_first=True),\n",
" RandSpatialCrop((64, 64, 64), random_size=False),\n",
" EnsureType(),\n",
" ]\n",
")\n",
"\n",
"ds = ArrayDataset(images, imtrans, segs, segtrans)\n",
"\n",
"loader = torch.utils.data.DataLoader(\n",
" ds, batch_size=10, num_workers=2, pin_memory=torch.cuda.is_available()\n",
" ds, batch_size=10, num_workers=0, pin_memory=torch.cuda.is_available()\n",
")\n",
"im, seg = first(loader)\n",
"print(im.shape, seg.shape)"
Expand Down Expand Up @@ -236,10 +241,10 @@
}
],
"source": [
"imtrans = Compose([LoadImage(image_only=True),\n",
" ScaleIntensity(), AddChannel(), EnsureType()])\n",
"imtrans = Compose([LoadImage(image_only=True, ensure_channel_first=True),\n",
" ScaleIntensity(), EnsureType()])\n",
"\n",
"segtrans = Compose([LoadImage(image_only=True), AddChannel(), EnsureType()])\n",
"segtrans = Compose([LoadImage(image_only=True, ensure_channel_first=True), EnsureType()])\n",
"\n",
"ds = ArrayDataset(images, imtrans, segs, segtrans)\n",
"patch_iter = PatchIter(patch_size=(64, 64, 64), start_pos=(0, 0, 0))\n",
Expand All @@ -255,7 +260,7 @@
"ds = GridPatchDataset(ds, img_seg_iter, with_coordinates=False)\n",
"\n",
"loader = torch.utils.data.DataLoader(\n",
" ds, batch_size=10, num_workers=0, pin_memory=torch.cuda.is_available()\n",
" ds, batch_size=10, num_workers=2, pin_memory=torch.cuda.is_available()\n",
")\n",
"im, seg = first(loader)\n",
"print(\"image shapes:\", im.shape, seg.shape)"
Expand Down Expand Up @@ -283,7 +288,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -297,7 +302,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.10"
"version": "3.8.0"
}
},
"nbformat": 4,
Expand Down
Loading