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+ "grid_template_columns": null,
+ "grid_template_rows": null,
+ "height": null,
+ "justify_content": null,
+ "justify_items": null,
+ "left": null,
+ "margin": null,
+ "max_height": null,
+ "max_width": null,
+ "min_height": null,
+ "min_width": null,
+ "object_fit": null,
+ "object_position": null,
+ "order": null,
+ "overflow": null,
+ "overflow_x": null,
+ "overflow_y": null,
+ "padding": null,
+ "right": null,
+ "top": null,
+ "visibility": null,
+ "width": null
+ }
+ },
+ "9aa1bc98b74c4a64ac0b815925db5545": {
+ "model_module": "@jupyter-widgets/controls",
+ "model_name": "DescriptionStyleModel",
+ "model_module_version": "1.5.0",
+ "state": {
+ "_model_module": "@jupyter-widgets/controls",
+ "_model_module_version": "1.5.0",
+ "_model_name": "DescriptionStyleModel",
+ "_view_count": null,
+ "_view_module": "@jupyter-widgets/base",
+ "_view_module_version": "1.2.0",
+ "_view_name": "StyleView",
+ "description_width": ""
+ }
+ }
+ }
+ }
+ },
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "view-in-github",
+ "colab_type": "text"
+ },
+ "source": [
+ ""
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "id": "aB8AjX-DOLI1"
+ },
+ "outputs": [],
+ "source": [
+ "!pip install -q datasets nibabel"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "from datasets import load_dataset\n",
+ "\n",
+ "# downloads data from Zenodo through the Hugging Face hub\n",
+ "# - might take several minutes (~5 minutes in CoLab)\n",
+ "# - when finished \"num_rows\" attribute should say '27', which is #CTs in dataset\n",
+ "dataset = load_dataset(\"andreped/LyNoS\")\n",
+ "print(dataset)"
+ ],
+ "metadata": {
+ "colab": {
+ "base_uri": "https://localhost:8080/",
+ "height": 200,
+ "referenced_widgets": [
+ "8704637776df4491aff4cb076ec747b7",
+ "a25def0acbde4f12aa2b4801a055aa9c",
+ "6a071231c92c42af8bf8c916747093d0",
+ "ae4fe03cbe154f8dafeec004bda2ebb3",
+ "d4e9d18824434de18d92844cbe200690",
+ "8d54a2aee61d4a7eaef94cd79b835fb3",
+ "c3fd8e317aa4424bac265e68e20fcdf3",
+ "4084d2e1128244eb834e6b06aada193f",
+ "9674f72f3f7042e380e6bdd7640be8d0",
+ "e604c7ae9fb74a34920d889b125df28f",
+ "e6582c9a929d4b00972856b26d2b302f",
+ "faf30a43a3524dcfb62c023df84cf60f",
+ "5e979c8a86814e76851dcb5e1b374109",
+ "846a6b2c61734d9b8b260e67ed015130",
+ "deff0a759e6b4436a62e5b5f36d6f253",
+ "5c8a04925d3245cca39be5ca0d0a7108",
+ "86eefe0b146b48fbb4a4acb420c8eee2",
+ "f1d2cd7d5e4c47218adb65f51b8bd139",
+ "847ac67c5fe34f03ada4c18eca01010d",
+ "2543dcd0cdea4437bd9b68c8b2075aaa",
+ "d447567cf4294705bb16c4fba36c4ee1",
+ "9aa1bc98b74c4a64ac0b815925db5545"
+ ]
+ },
+ "id": "gmRtqpxoPnTb",
+ "outputId": "28c24cb5-934e-41bd-8bd5-275ce86ba1f4"
+ },
+ "execution_count": 13,
+ "outputs": [
+ {
+ "output_type": "display_data",
+ "data": {
+ "text/plain": [
+ "Downloading builder script: 0%| | 0.00/6.06k [00:00, ?B/s]"
+ ],
+ "application/vnd.jupyter.widget-view+json": {
+ "version_major": 2,
+ "version_minor": 0,
+ "model_id": "8704637776df4491aff4cb076ec747b7"
+ }
+ },
+ "metadata": {}
+ },
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "data is downloaded to: /root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark\n"
+ ]
+ },
+ {
+ "output_type": "display_data",
+ "data": {
+ "text/plain": [
+ "Generating test split: 0 examples [00:00, ? examples/s]"
+ ],
+ "application/vnd.jupyter.widget-view+json": {
+ "version_major": 2,
+ "version_minor": 0,
+ "model_id": "faf30a43a3524dcfb62c023df84cf60f"
+ }
+ },
+ "metadata": {}
+ },
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "DatasetDict({\n",
+ " test: Dataset({\n",
+ " features: ['ct', 'lymphnodes', 'azygos', 'brachiocephalicveins', 'esophagus', 'subclaviancarotidarteries'],\n",
+ " num_rows: 15\n",
+ " })\n",
+ "})\n"
+ ]
+ }
+ ]
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "# get paths of features (ct/airways/lungs) for a single patient\n",
+ "curr = dataset[\"test\"][0]\n",
+ "print(curr)\n",
+ "print(curr[\"ct\"])\n",
+ "print(curr[\"lymphnodes\"])\n",
+ "print(curr[\"azygos\"])\n",
+ "print(curr[\"brachiocephalicveins\"])\n",
+ "print(curr[\"esophagus\"])\n",
+ "print(curr[\"subclaviancarotidarteries\"])"
+ ],
+ "metadata": {
+ "id": "7CaqauK8p7o4",
+ "colab": {
+ "base_uri": "https://localhost:8080/"
+ },
+ "outputId": "5559b932-58f7-46e1-e188-fe0ad1e5d053"
+ },
+ "execution_count": 34,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_SubCarArt.nii.gz'}\n",
+ "/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_data.nii.gz\n",
+ "/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_LymphNodes.nii.gz\n",
+ "/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_Azygos.nii.gz\n",
+ "/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_BrachiocephalicVeins.nii.gz\n",
+ "/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_Esophagus.nii.gz\n",
+ "/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_SubCarArt.nii.gz\n"
+ ]
+ }
+ ]
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "# list all available patients and corresponding features (ct/airways/lungs)\n",
+ "for d in dataset[\"test\"]:\n",
+ " print(d)"
+ ],
+ "metadata": {
+ "id": "Ib8QbkOxdaPi",
+ "colab": {
+ "base_uri": "https://localhost:8080/"
+ },
+ "outputId": "256af015-8268-4bec-dae3-aa922e114f60"
+ },
+ "execution_count": 16,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat2/pat2_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat6/pat6_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat6/pat6_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat6/pat6_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat6/pat6_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat6/pat6_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat6/pat6_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat1/pat1_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat1/pat1_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat1/pat1_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat1/pat1_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat1/pat1_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat1/pat1_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat3/pat3_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat3/pat3_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat3/pat3_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat3/pat3_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat3/pat3_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat3/pat3_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat4/pat4_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat4/pat4_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat4/pat4_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat4/pat4_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat4/pat4_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat4/pat4_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat7/pat7_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat7/pat7_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat7/pat7_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat7/pat7_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat7/pat7_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat7/pat7_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat12/pat12_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat12/pat12_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat12/pat12_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat12/pat12_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat12/pat12_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat12/pat12_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat11/pat11_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat11/pat11_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat11/pat11_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat11/pat11_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat11/pat11_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat11/pat11_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat13/pat13_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat13/pat13_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat13/pat13_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat13/pat13_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat13/pat13_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat13/pat13_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat9/pat9_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat9/pat9_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat9/pat9_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat9/pat9_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat9/pat9_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat9/pat9_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat15/pat15_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat15/pat15_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat15/pat15_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat15/pat15_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat15/pat15_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat15/pat15_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat5/pat5_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat5/pat5_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat5/pat5_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat5/pat5_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat5/pat5_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat5/pat5_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat10/pat10_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat10/pat10_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat10/pat10_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat10/pat10_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat10/pat10_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat10/pat10_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat8/pat8_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat8/pat8_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat8/pat8_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat8/pat8_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat8/pat8_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat8/pat8_labels_SubCarArt.nii.gz'}\n",
+ "{'ct': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat14/pat14_data.nii.gz', 'lymphnodes': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat14/pat14_labels_LymphNodes.nii.gz', 'azygos': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat14/pat14_labels_Azygos.nii.gz', 'brachiocephalicveins': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat14/pat14_labels_BrachiocephalicVeins.nii.gz', 'esophagus': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat14/pat14_labels_Esophagus.nii.gz', 'subclaviancarotidarteries': '/root/.cache/huggingface/datasets/downloads/extracted/25432ffc15a3650a47da3d9223aeead84213a3aa1e5b23bbe6b40eec124e7c2c/Benchmark/Pat14/pat14_labels_SubCarArt.nii.gz'}\n"
+ ]
+ }
+ ]
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "import nibabel as nib\n",
+ "import matplotlib.pyplot as plt\n",
+ "\n",
+ "from nibabel.processing import resample_to_output\n",
+ "\n",
+ "# load CT, airways, and lungs to numpy arrays for one patient\n",
+ "patient_1 = dataset[\"test\"][0]\n",
+ "slice_nr = 205\n",
+ "\n",
+ "ct_image = nib.load(patient_1[\"ct\"])\n",
+ "ct_image = resample_to_output(ct_image, order=1)\n",
+ "ct_data = ct_image.get_fdata().astype(\"int32\")\n",
+ "\n",
+ "print(\"CT:\", ct_data.shape, ct_data.dtype)\n",
+ "\n",
+ "airways_image = nib.load(patient_1[\"lymphnodes\"])\n",
+ "airways_image = resample_to_output(airways_image, order=0)\n",
+ "airways_data = airways_image.get_fdata().astype(\"uint8\")\n",
+ "\n",
+ "print(\"Lymph Nodes:\", airways_data.shape, airways_data.dtype)\n",
+ "\n",
+ "azygos_image = nib.load(patient_1[\"azygos\"])\n",
+ "azygos_image = resample_to_output(azygos_image, order=0)\n",
+ "azygos_data = azygos_image.get_fdata().astype(\"uint8\")\n",
+ "\n",
+ "print(\"Azygos:\", azygos_data.shape, azygos_data.dtype)\n",
+ "\n",
+ "# HU-clip CT for better contrast\n",
+ "ct_data[ct_data < -1024] = -1024\n",
+ "ct_data[ct_data > 400] = 400\n",
+ "\n",
+ "# plot corresponding CT, Airways, and Lungs for a single 2D slide side-by-side\n",
+ "fig, ax = plt.subplots(1, 3, figsize=(20, 12))\n",
+ "ax[0].imshow(ct_data[..., slice_nr], cmap=\"gray\")\n",
+ "ax[1].imshow(airways_data[..., slice_nr], cmap=\"jet\", interpolation=\"none\")\n",
+ "ax[2].imshow(azygos_data[..., slice_nr], cmap=\"jet\", interpolation=\"none\")\n",
+ "\n",
+ "for i, title in enumerate([\"CT\", \"Lymph Nodes\", \"Azygos\"]):\n",
+ " ax[i].set_title(title)\n",
+ "plt.show()"
+ ],
+ "metadata": {
+ "id": "At1iznVwf6Zg",
+ "colab": {
+ "base_uri": "https://localhost:8080/",
+ "height": 512
+ },
+ "outputId": "b040b156-64b1-4a94-fde7-b0995b33acaf"
+ },
+ "execution_count": 33,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "CT: (353, 353, 358) int32\n",
+ "Lymph Nodes: (353, 353, 358) uint8\n",
+ "Azygos: (353, 353, 358) uint8\n"
+ ]
+ },
+ {
+ "output_type": "display_data",
+ "data": {
+ "text/plain": [
+ "