From 5b7e830857fb877ef8de3e83cb135008559ed692 Mon Sep 17 00:00:00 2001 From: kndahl Date: Sun, 16 Jun 2024 15:42:02 +0300 Subject: [PATCH] minor sync --- scripts/del_npy.ipynb | 2 +- scripts/evaluate.ipynb | 576 +---------------------------------------- 2 files changed, 6 insertions(+), 572 deletions(-) diff --git a/scripts/del_npy.ipynb b/scripts/del_npy.ipynb index 25a2b901b..80b2d3476 100755 --- 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/Dataset300_mosaic_cardiovascular/nnUNetPlans_3d_fullres\"\n", + "dir = \"/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_preprocessed/Dataset101_mosaic_skelet_spine/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 index 701c272a5..57f7e86a3 100644 --- a/scripts/evaluate.ipynb +++ b/scripts/evaluate.ipynb @@ -2,583 +2,17 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'metric_per_case': [{'reference_file': '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset904_mosaic_kidney_stones/labelsTr/adrenal_Ki67_Seg_013_native.nii.gz',\n", - " 'prediction_file': '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_results/Dataset904_mosaic_kidney_stones/nnUNetTrainerNoMirroring__nnUNetPlans__3d_fullres_mosaic_spacing_stdres_NoRsmp/fold_1/validation/adrenal_Ki67_Seg_013_native.nii.gz',\n", - " 'metrics': {1: {'Dice': 0.0,\n", - " 'IoU': 0.0,\n", - " 'FP': 257,\n", - " 'TP': 0,\n", - " 'FN': 0,\n", - " 'TN': 92736203,\n", - " 'n_pred': 257,\n", - " 'n_ref': 0}}},\n", - " {'reference_file': '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset904_mosaic_kidney_stones/labelsTr/kits23_case_00002.nii.gz',\n", - " 'prediction_file': '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_results/Dataset904_mosaic_kidney_stones/nnUNetTrainerNoMirroring__nnUNetPlans__3d_fullres_mosaic_spacing_stdres_NoRsmp/fold_1/validation/kits23_case_00002.nii.gz',\n", - 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" 'metrics': {1: {'Dice': 0.3368654930781063,\n", - " 'IoU': 0.20254855616072345,\n", - " 'FP': 7730,\n", - " 'TP': 1971,\n", - " 'FN': 30,\n", - " 'TN': 140499453,\n", - " 'n_pred': 9701,\n", - " 'n_ref': 2001}}},\n", - " {'reference_file': '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset904_mosaic_kidney_stones/labelsTr/zhukovki_0115.nii.gz',\n", - " 'prediction_file': '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_results/Dataset904_mosaic_kidney_stones/nnUNetTrainerNoMirroring__nnUNetPlans__3d_fullres_mosaic_spacing_stdres_NoRsmp/fold_1/validation/zhukovki_0115.nii.gz',\n", - " 'metrics': {1: {'Dice': 0.9614583333333333,\n", - " 'IoU': 0.925777331995988,\n", - " 'FP': 74,\n", - " 'TP': 923,\n", - " 'FN': 0,\n", - " 'TN': 186383387,\n", - " 'n_pred': 997,\n", - " 'n_ref': 923}}},\n", - " {'reference_file': '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset904_mosaic_kidney_stones/labelsTr/zhukovki_0130.nii.gz',\n", - " 'prediction_file': '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_results/Dataset904_mosaic_kidney_stones/nnUNetTrainerNoMirroring__nnUNetPlans__3d_fullres_mosaic_spacing_stdres_NoRsmp/fold_1/validation/zhukovki_0130.nii.gz',\n", - " 'metrics': {1: {'Dice': 0.7112676056338029,\n", - " 'IoU': 0.5519125683060109,\n", - " 'FP': 277,\n", - " 'TP': 404,\n", - " 'FN': 51,\n", - " 'TN': 141294884,\n", - " 'n_pred': 681,\n", - " 'n_ref': 455}}}],\n", - " 'mean': {1: {'Dice': 0.5938901764207939,\n", - " 'IoU': 0.5355428836661312,\n", - " 'FP': 561.4629629629629,\n", - " 'TP': 3349.037037037037,\n", - " 'FN': 420.81481481481484,\n", - " 'TN': 115663714.4074074,\n", - " 'n_pred': 3910.5,\n", - " 'n_ref': 3769.8518518518517}},\n", - " 'foreground_mean': {'Dice': 0.5938901764207939,\n", - " 'IoU': 0.5355428836661312,\n", - " 'FP': 561.4629629629629,\n", - " 'TP': 3349.037037037037,\n", - " 'FN': 420.81481481481484,\n", - " 'TN': 115663714.4074074,\n", - " 'n_pred': 3910.5,\n", - " 'n_ref': 3769.8518518518517}}" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], + "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/Dataset400_mosaic_organs/labelsTr'\n", - "model_folder = '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_results/Dataset400_mosaic_organs/nnUNetTrainerNoMirroring__Mosaic_nnUNetPlannerResEncL_stdres_NoRsmp_24G__3d_fullres'\n", - "folder_pred = f'{model_folder}/fold_0/validation'\n", + "folder_ref = '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset904_mosaic_kidney_stones/labelsTr'\n", + "model_folder = '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_results/Dataset904_mosaic_kidney_stones/nnUNetTrainerNoMirroring__nnUNetPlans__3d_fullres_mosaic_spacing_stdres_NoRsmp'\n", + "folder_pred = f'{model_folder}/fold_3/validation'\n", "output_file = f'{folder_pred}/summary.json'\n", "dataset_json = f'{model_folder}/dataset.json'\n", "image_reader_writer = NibabelIOWithReorient()\n",