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Merged
wyli merged 4 commits into from
May 19, 2022
Merged

Meta tensor orientation #722

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05022e3
spleen_segmentation_3d
rijobro May 16, 2022
016b864
spleen_segmentation_3d_lightning.ipynb
rijobro May 16, 2022
3455e64
brats_segmentation_3d.ipynb
rijobro May 16, 2022
2eeb89f
fixes
rijobro May 16, 2022
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6 changes: 3 additions & 3 deletions 3d_segmentation/brats_segmentation_3d.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -266,9 +266,9 @@
" # load 4 Nifti images and stack them together\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" EnsureChannelFirstd(keys=\"image\"),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" ConvertToMultiChannelBasedOnBratsClassesd(keys=\"label\"),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.0, 1.0, 1.0),\n",
Expand All @@ -288,9 +288,9 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" EnsureChannelFirstd(keys=\"image\"),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" ConvertToMultiChannelBasedOnBratsClassesd(keys=\"label\"),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.0, 1.0, 1.0),\n",
Expand Down Expand Up @@ -787,9 +787,9 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" EnsureChannelFirstd(keys=[\"image\"]),\n",
" Orientationd(keys=[\"image\"], axcodes=\"RAS\"),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" ConvertToMultiChannelBasedOnBratsClassesd(keys=\"label\"),\n",
" Orientationd(keys=[\"image\"], axcodes=\"RAS\"),\n",
" Spacingd(keys=[\"image\"], pixdim=(1.0, 1.0, 1.0), mode=\"bilinear\"),\n",
" NormalizeIntensityd(keys=\"image\", nonzero=True, channel_wise=True),\n",
" EnsureTyped(keys=[\"image\", \"label\"]),\n",
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8 changes: 4 additions & 4 deletions 3d_segmentation/spleen_segmentation_3d.ipynb
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Expand Up @@ -281,8 +281,8 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" EnsureChannelFirstd(keys=[\"image\", \"label\"]),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" Spacingd(keys=[\"image\", \"label\"], pixdim=(\n",
" 1.5, 1.5, 2.0), mode=(\"bilinear\", \"nearest\")),\n",
" ScaleIntensityRanged(\n",
Expand Down Expand Up @@ -314,8 +314,8 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" EnsureChannelFirstd(keys=[\"image\", \"label\"]),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" Spacingd(keys=[\"image\", \"label\"], pixdim=(\n",
" 1.5, 1.5, 2.0), mode=(\"bilinear\", \"nearest\")),\n",
" ScaleIntensityRanged(\n",
Expand Down Expand Up @@ -696,8 +696,8 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" EnsureChannelFirstd(keys=[\"image\", \"label\"]),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\"], axcodes=\"RAS\"),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" Spacingd(keys=[\"image\"], pixdim=(\n",
" 1.5, 1.5, 2.0), mode=\"bilinear\"),\n",
" ScaleIntensityRanged(\n",
Expand Down Expand Up @@ -791,8 +791,8 @@
" [\n",
" LoadImaged(keys=\"image\"),\n",
" EnsureChannelFirstd(keys=\"image\"),\n",
" FromMetaTensord(keys=\"image\"),\n",
" Orientationd(keys=[\"image\"], axcodes=\"RAS\"),\n",
" FromMetaTensord(keys=\"image\"),\n",
" Spacingd(keys=[\"image\"], pixdim=(\n",
" 1.5, 1.5, 2.0), mode=\"bilinear\"),\n",
" ScaleIntensityRanged(\n",
Expand Down
4 changes: 2 additions & 2 deletions 3d_segmentation/spleen_segmentation_3d_lightning.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -271,8 +271,8 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" AddChanneld(keys=[\"image\", \"label\"]),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.5, 1.5, 2.0),\n",
Expand Down Expand Up @@ -312,8 +312,8 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" AddChanneld(keys=[\"image\", \"label\"]),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.5, 1.5, 2.0),\n",
Expand Down
2 changes: 1 addition & 1 deletion modules/decollate_batch.ipynb
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Expand Up @@ -246,8 +246,8 @@
" [\n",
" LoadImaged(keys=[\"img\", \"seg\"]),\n",
" EnsureChannelFirstd(keys=[\"img\", \"seg\"]),\n",
" FromMetaTensord(keys=[\"img\", \"seg\"]),\n",
" Orientationd(keys=\"img\", axcodes=\"RAS\"),\n",
" FromMetaTensord(keys=[\"img\", \"seg\"]),\n",
" Resized(keys=\"img\", spatial_size=(96, 96, 96), mode=\"trilinear\", align_corners=True),\n",
" ScaleIntensityd(keys=\"img\"),\n",
" EnsureTyped(keys=[\"img\", \"seg\"]),\n",
Expand Down
4 changes: 2 additions & 2 deletions modules/integrate_3rd_party_transforms.ipynb
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Expand Up @@ -267,10 +267,10 @@
"source": [
"monai_transforms = [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" ToNumpyd(keys=[\"image\", \"label\", \"image_meta_dict\", \"label_meta_dict\"]),\n",
" AddChanneld(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
" ToNumpyd(keys=[\"image\", \"label\", \"image_meta_dict\", \"label_meta_dict\"]),\n",
" Spacingd(keys=[\"image\", \"label\"], pixdim=(\n",
" 1.5, 1.5, 2.0), mode=(\"bilinear\", \"nearest\")),\n",
" ScaleIntensityRanged(keys=[\"image\"], a_min=-57,\n",
Expand Down
4 changes: 2 additions & 2 deletions modules/interpretability/cats_and_dogs.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -165,8 +165,8 @@
"divisible_factor = 20\n",
"transforms = Compose([\n",
" LoadImaged(\"image\"),\n",
" FromMetaTensord(\"image\"),\n",
" AsChannelFirstd(\"image\"),\n",
" FromMetaTensord(\"image\"),\n",
" ScaleIntensityd(\"image\"),\n",
" Rotate90d(\"image\", k=3),\n",
" DivisiblePadd(\"image\", k=divisible_factor),\n",
Expand Down Expand Up @@ -202,7 +202,7 @@
" 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\"].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
49 changes: 3 additions & 46 deletions modules/nifti_read_example.ipynb
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Expand Up @@ -89,7 +89,6 @@
"\n",
"import glob\n",
"import os\n",
"import shutil\n",
"import tempfile\n",
"\n",
"import nibabel as nib\n",
Expand All @@ -113,30 +112,6 @@
"print_config()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Setup data directory\n",
"\n",
"You can specify a directory with the `MONAI_DATA_DIRECTORY` environment variable. \n",
"This allows you to save results and reuse downloads. \n",
"If not specified a temporary directory will be used."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
"root_dir = tempfile.mkdtemp() if directory is None else directory\n",
"print(root_dir)"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand All @@ -150,6 +125,7 @@
"metadata": {},
"outputs": [],
"source": [
"root_dir = tempfile.mkdtemp()\n",
"for i in range(5):\n",
" im, seg = create_test_image_3d(128, 128, 128)\n",
"\n",
Expand Down Expand Up @@ -189,9 +165,9 @@
"imtrans = Compose(\n",
" [\n",
" LoadImage(),\n",
" AddChannel(),\n",
" ToNumpy(),\n",
" ScaleIntensity(),\n",
" AddChannel(),\n",
" RandSpatialCrop((64, 64, 64), random_size=False),\n",
" EnsureType(),\n",
" ]\n",
Expand All @@ -200,8 +176,8 @@
"segtrans = Compose(\n",
" [\n",
" LoadImage(),\n",
" ToNumpy(),\n",
" AddChannel(),\n",
" ToNumpy(),\n",
" RandSpatialCrop((64, 64, 64), random_size=False),\n",
" EnsureType(),\n",
" ]\n",
Expand Down Expand Up @@ -263,25 +239,6 @@
"im, seg = first(loader)\n",
"print(\"image shapes:\", im.shape, seg.shape)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Cleanup data directory\n",
"\n",
"Remove directory if a temporary was used."
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"if directory is None:\n",
" shutil.rmtree(root_dir)"
]
}
],
"metadata": {
Expand Down