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1420 fixes integration error (#1423)
Fixes #1420 ### Checks <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [ ] Avoid including large-size files in the PR. - [ ] Clean up long text outputs from code cells in the notebook. - [ ] For security purposes, please check the contents and remove any sensitive info such as user names and private key. - [ ] Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the `./figure` folder - [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>` Signed-off-by: Wenqi Li <wenqil@nvidia.com>
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3d_classification/densenet_training_array.ipynb

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{
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"cells": [
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{
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"attachments": {},
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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],
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"source": [
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"# Get the occlusion sensitivity map\n",
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"occ_sens = monai.visualize.OcclusionSensitivity(nn_module=model, mask_size=12, n_batch=10, stride=12)\n",
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"occ_sens = monai.visualize.OcclusionSensitivity(nn_module=model, mask_size=12, n_batch=10)\n",
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"# Only get a single slice to save time.\n",
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"# For the other dimensions (channel, width, height), use\n",
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"# -1 to use 0 and img.shape[x]-1 for min and max, respectively\n",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.12"
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"version": "3.8.13"
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}
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},
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"nbformat": 4,

modules/interpretability/class_lung_lesion.ipynb

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")\n",
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"print(\"upsampled feature shape\", [1, 1] + list(win_size))\n",
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"\n",
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"occ_sens = monai.visualize.OcclusionSensitivity(nn_module=model_3d, mask_size=12, n_batch=1, stride=28)\n",
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"occ_sens = monai.visualize.OcclusionSensitivity(nn_module=model_3d, mask_size=12, n_batch=1)\n",
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"\n",
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"# For occlusion sensitivity, inference must be run many times. Hence, we can use a\n",
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"# bounding box to limit it to a 2D plane of interest (z=the_slice) where each of\n",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.10"
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"version": "3.8.13"
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}
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},
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"nbformat": 4,

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