add evaluate

bluemindai · May 28, 2024 · 6192877 · 6192877
1 parent ca04ab1
commit 6192877
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Showing 3 changed files with 90 additions and 29 deletions.
diff --git a/scripts/del_npy.ipynb b/scripts/del_npy.ipynb
@@ -8,7 +8,7 @@
    "source": [
     "import os\n",
     "\n",
-    "dir = \"/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_preprocessed/Dataset101_mosaic_skelet_spine/nnUNetPlans_3d_fullres\"\n",
+    "dir = \"/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_preprocessed/Dataset300_mosaic_cardiovascular/nnUNetPlans_3d_fullres\"\n",
     "files = os.listdir(dir)\n",
     "\n",
     "for file in files:\n",

diff --git a/scripts/evaluate.ipynb b/scripts/evaluate.ipynb
@@ -0,0 +1,63 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from nnunetv2.evaluation.evaluate_predictions import compute_metrics_on_folder, labels_to_list_of_regions\n",
+    "from nnunetv2.imageio.nibabel_reader_writer import NibabelIOWithReorient\n",
+    "import json\n",
+    "\n",
+    "folder_ref = '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset300_mosaic_cardiovascular/labelsTr'\n",
+    "model_folder = '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_results/Dataset300_mosaic_cardiovascular/nnUNetTrainer_1500epochs_NoMirroring__Mosaic_nnUNetPlannerResEncL_stdres_NoRsmp_24G__3d_fullres'\n",
+    "folder_pred = f'{model_folder}/fold_0/validation'\n",
+    "output_file = f'{folder_pred}/summary.json'\n",
+    "dataset_json = f'{model_folder}/dataset.json'\n",
+    "image_reader_writer = NibabelIOWithReorient()\n",
+    "file_ending = '.nii.gz'\n",
+    "ignore_label = None\n",
+    "num_processes = 12\n",
+    "\n",
+    "with open(dataset_json) as f:\n",
+    "    data = json.loads(f.read())\n",
+    "\n",
+    "# regions = labels_to_list_of_regions(list(data['labels'].values())[1:])\n",
+    "\n",
+    "regions = list(data['labels'].values())[1:]\n",
+    "\n",
+    "compute_metrics_on_folder(folder_ref, folder_pred, output_file, image_reader_writer, file_ending, regions, ignore_label,\n",
+    "                            num_processes)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".nnunetv2-venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/scripts/generate_json.ipynb b/scripts/generate_json.ipynb
@@ -11,46 +11,44 @@
     "from nnunetv2.dataset_conversion.generate_dataset_json import generate_dataset_json\n",
     "import os\n",
     "\n",
-    "dataset = \"/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset101_mosaic_skelet_ribs\"\n",
+    "dataset = \"/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset300_mosaic_cardiovascular\"\n",
     "\n",
     "generate_dataset_json(output_folder=dataset,\n",
     "                      channel_names={0: \"CT\"},\n",
     "                      labels={\n",
     "                          'background': 0,\n",
-    "                          \"rib_left_1\": 1,\n",
-    "                          \"rib_left_2\": 2,\n",
-    "                          \"rib_left_3\": 3,\n",
-    "                          \"rib_left_4\": 4,\n",
-    "                          \"rib_left_5\": 5,\n",
-    "                          \"rib_left_6\": 6,\n",
-    "                          \"rib_left_7\": 7,\n",
-    "                          \"rib_left_8\": 8,\n",
-    "                          \"rib_left_9\": 9,\n",
-    "                          \"rib_left_10\": 10,\n",
-    "                          \"rib_left_11\": 11,\n",
-    "                          \"rib_left_12\": 12,\n",
-    "                          \"rib_right_1\": 13,\n",
-    "                          \"rib_right_2\": 14,\n",
-    "                          \"rib_right_3\": 15,\n",
-    "                          \"rib_right_4\": 16,\n",
-    "                          \"rib_right_5\": 17,\n",
-    "                          \"rib_right_6\": 18,\n",
-    "                          \"rib_right_7\": 19,\n",
-    "                          \"rib_right_8\": 20,\n",
-    "                          \"rib_right_9\": 21,\n",
-    "                          \"rib_right_10\": 22,\n",
-    "                          \"rib_right_11\": 23,\n",
-    "                          \"rib_right_12\": 24,\n",
-    "                          \"costal_cartilages\": 25,\n",
-    "                          \"sternum\": 26\n",
+    "                          \"heart_myocardium\": 1,\n",
+    "                          \"heart_atrium_left\": 2,\n",
+    "                          \"heart_ventricle_left\": 3,\n",
+    "                          \"heart_atrium_right\": 4,\n",
+    "                          \"heart_ventricle_right\": 5,\n",
+    "                          \"aorta\": 6,\n",
+    "                          \"pulmonary_vein\": 7,\n",
+    "                          \"pulmonary_artery\": 8,\n",
+    "                          \"brachiocephalic_trunk\": 9,\n",
+    "                          \"subclavian_artery_right\": 10,\n",
+    "                          \"subclavian_artery_left\": 11,\n",
+    "                          \"common_carotid_artery_right\": 12,\n",
+    "                          \"common_carotid_artery_left\": 13,\n",
+    "                          \"brachiocephalic_vein_left\": 14,\n",
+    "                          \"brachiocephalic_vein_right\": 15,\n",
+    "                          \"superior_vena_cava\": 16,\n",
+    "                          \"inferior_vena_cava\": 17,\n",
+    "                          \"portal_vein_and_splenic_vein\": 18,\n",
+    "                          \"iliac_artery_left\": 19,\n",
+    "                          \"iliac_artery_right\": 20,\n",
+    "                          \"iliac_vena_left\": 21,\n",
+    "                          \"iliac_vena_right\": 22,\n",
+    "                          \"liver_vessels\": 23,\n",
+    "                          \"lung_vessels\": 24\n",
     "                        },\n",
     "                        num_training_cases=len(os.listdir(f'{dataset}/imagesTr')), \n",
     "                        file_ending='.nii.gz',\n",
     "                        dataset_name=dataset.split('/')[-1], \n",
     "                        reference='BlueMind AI Inc',\n",
     "                        release='1.0.0',\n",
     "                        overwrite_image_reader_writer='NibabelIOWithReorient',\n",
-    "                        description=\"skelet_ribs\")"
+    "                        description=\"cardiovascular\")"
    ]
   },
   {