From 90e3ea32fabccf91a915f305eb0f5373154d6f2c Mon Sep 17 00:00:00 2001 From: kndahl Date: Mon, 1 Jul 2024 14:42:29 +0300 Subject: [PATCH] fix --- scripts/del_npy.ipynb | 2 +- scripts/evaluate.ipynb | 64238 +++++++++++++++++++++++++++++++++- scripts/generate_json.ipynb | 9 +- scripts/train.sh | 18 +- 4 files changed, 64247 insertions(+), 20 deletions(-) diff --git a/scripts/del_npy.ipynb b/scripts/del_npy.ipynb index a9373efb9..25a2b901b 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/Dataset102_mosaic_skelet_ribs/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 index 9560249ef..448ceaaa6 100644 --- a/scripts/evaluate.ipynb +++ b/scripts/evaluate.ipynb @@ -2,16 +2,64246 @@ "cells": [ { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "{'metric_per_case': [{'reference_file': '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset300_mosaic_cardiovascular/labelsTr/adrenal_Ki67_Seg_001_native.nii.gz',\n", + " 'prediction_file': '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_results/Dataset300_mosaic_cardiovascular/nnUNetTrainerNoMirroring__Mosaic_nnUNetPlannerResEncL_stdres_NoRsmp_24G__3d_fullres/fold_0/validation/adrenal_Ki67_Seg_001_native.nii.gz',\n", + " 'metrics': {1: {'Dice': 0.8295648370872513,\n", + " 'IoU': 0.7087661609745161,\n", + " 'FP': 17071,\n", + " 'TP': 56904,\n", + " 'FN': 6311,\n", + " 'TN': 41434914,\n", + " 'n_pred': 73975,\n", + " 'n_ref': 63215},\n", + " 2: {'Dice': 0.9180217561960301,\n", + " 'IoU': 0.8484660033167496,\n", + " 'FP': 978,\n", 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280.3333333333333,\n", + " 'TN': 59055158.236363634,\n", + " 'n_pred': 1682.990909090909,\n", + " 'n_ref': 1699.2454545454545},\n", + " 13: {'Dice': 0.8538252881304343,\n", + " 'IoU': 0.7636921420129191,\n", + " 'FP': 267.330303030303,\n", + " 'TP': 2279.9848484848485,\n", + " 'FN': 388.91212121212124,\n", + " 'TN': 59054185.333333336,\n", + " 'n_pred': 2547.3151515151517,\n", + " 'n_ref': 2668.89696969697},\n", + " 14: {'Dice': 0.9051349980772401,\n", + " 'IoU': 0.8423272093484971,\n", + " 'FP': 482.6575757575758,\n", + " 'TP': 6022.739393939394,\n", + " 'FN': 435.0,\n", + " 'TN': 59050181.163636364,\n", + " 'n_pred': 6505.39696969697,\n", + " 'n_ref': 6457.739393939394},\n", + " 15: {'Dice': 0.9015640028820675,\n", + " 'IoU': 0.8359022084851699,\n", + " 'FP': 232.2,\n", + " 'TP': 3226.4636363636364,\n", + " 'FN': 292.5,\n", + " 'TN': 59053370.3969697,\n", + " 'n_pred': 3458.663636363636,\n", + " 'n_ref': 3518.9636363636364},\n", + " 16: {'Dice': 0.8969577846999788,\n", + " 'IoU': 0.8455883404742279,\n", + " 'FP': 596.8727272727273,\n", + " 'TP': 10925.0,\n", + " 'FN': 589.5757575757576,\n", + " 'TN': 59045010.11212121,\n", + " 'n_pred': 11521.872727272726,\n", + " 'n_ref': 11514.575757575758},\n", + " 17: {'Dice': 0.8823686481008686,\n", + " 'IoU': 0.8085150589477921,\n", + " 'FP': 4128.242424242424,\n", + " 'TP': 42822.27575757576,\n", + " 'FN': 3745.5,\n", + " 'TN': 59006425.54242424,\n", + " 'n_pred': 46950.51818181818,\n", + " 'n_ref': 46567.77575757576},\n", + " 18: {'Dice': 0.7419036197263417,\n", + " 'IoU': 0.6183200680766724,\n", + " 'FP': 2268.9636363636364,\n", + " 'TP': 9878.824242424242,\n", + " 'FN': 2467.8424242424244,\n", + " 'TN': 59042505.93030303,\n", + " 'n_pred': 12147.787878787878,\n", + " 'n_ref': 12346.666666666666},\n", + " 19: {'Dice': 0.8400727086472031,\n", + " 'IoU': 0.7608881410145808,\n", + " 'FP': 863.2939393939394,\n", + " 'TP': 7533.969696969697,\n", + " 'FN': 867.1848484848484,\n", + " 'TN': 59047857.11212121,\n", + " 'n_pred': 8397.263636363636,\n", + " 'n_ref': 8401.154545454545},\n", + " 20: {'Dice': 0.8479009631978062,\n", + " 'IoU': 0.7633359098495737,\n", + " 'FP': 890.8545454545455,\n", + " 'TP': 7371.127272727273,\n", + " 'FN': 1016.5969696969697,\n", + " 'TN': 59047842.981818184,\n", + " 'n_pred': 8261.981818181817,\n", + " 'n_ref': 8387.724242424243},\n", + " 21: {'Dice': 0.8522481515403717,\n", + " 'IoU': 0.7823048325268072,\n", + " 'FP': 1239.9939393939394,\n", + " 'TP': 13651.357575757576,\n", + " 'FN': 1223.5424242424242,\n", + " 'TN': 59041006.666666664,\n", + " 'n_pred': 14891.351515151515,\n", + " 'n_ref': 14874.9},\n", + " 22: {'Dice': 0.8436015394026848,\n", + " 'IoU': 0.7707062312211415,\n", + " 'FP': 1128.360606060606,\n", + " 'TP': 11295.051515151516,\n", + " 'FN': 1093.6848484848485,\n", + " 'TN': 59043604.46363636,\n", + " 'n_pred': 12423.41212121212,\n", + " 'n_ref': 12388.736363636364},\n", + " 23: {'Dice': 0.46391434677402615,\n", + " 'IoU': 0.3628503045173878,\n", + " 'FP': 2025.1151515151514,\n", + " 'TP': 7609.727272727273,\n", + " 'FN': 6913.148484848485,\n", + " 'TN': 59040573.56969697,\n", + " 'n_pred': 9634.842424242424,\n", + " 'n_ref': 14522.875757575757},\n", + " 24: {'Dice': 0.7121320289123777,\n", + " 'IoU': 0.5658583641347404,\n", + " 'FP': 23224.051515151514,\n", + " 'TP': 101834.39393939394,\n", + " 'FN': 46650.2303030303,\n", + " 'TN': 58885412.88484848,\n", + " 'n_pred': 125058.44545454545,\n", + " 'n_ref': 148484.62424242424}},\n", + " 'foreground_mean': {'Dice': 0.8542500325491073,\n", + " 'IoU': 0.780367450028388,\n", + " 'FP': 2808.6731060606057,\n", + " 'TP': 31878.676388888893,\n", + " 'FN': 3940.342550505051,\n", + " 'TN': 59018493.86856061,\n", + " 'n_pred': 34687.3494949495,\n", + " 'n_ref': 35819.018939393936}}" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], "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/Dataset102_mosaic_skelet_ribs/labelsTr'\n", - "model_folder = '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_results/Dataset102_mosaic_skelet_ribs/nnUNetTrainerNoMirroring__Mosaic_nnUNetPlannerResEncL_stdres_NoRsmp_24G__3d_fullres'\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/nnUNetTrainerNoMirroring__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", diff --git a/scripts/generate_json.ipynb b/scripts/generate_json.ipynb index 314bffd1b..cd0eeef46 100755 --- a/scripts/generate_json.ipynb +++ b/scripts/generate_json.ipynb @@ -11,15 +11,14 @@ "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/Dataset903_mosaic_head_pathology\"\n", + "dataset = \"/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset301_mosaic_renal_vessels\"\n", "\n", "generate_dataset_json(output_folder=dataset,\n", " channel_names={0: \"CT\"},\n", " labels={\n", " 'background': 0,\n", - " \"brain\": 1,\n", - " \"ischemic_stroke\": 2,\n", - " \"intracerebral_hemorrhage\": 3\n", + " \"renal_artery\": 1,\n", + " \"renal_vein\": 2\n", " },\n", " num_training_cases=len(os.listdir(f'{dataset}/imagesTr')), \n", " file_ending='.nii.gz',\n", @@ -27,7 +26,7 @@ " reference='BlueMind AI Inc',\n", " release='1.0.0',\n", " overwrite_image_reader_writer='NibabelIOWithReorient',\n", - " description=\"head_pathology\")" + " description=\"renal_vessels\")" ] }, { diff --git a/scripts/train.sh b/scripts/train.sh index 5cb253f77..6505e1167 100755 --- a/scripts/train.sh +++ b/scripts/train.sh @@ -43,20 +43,18 @@ esac # Adding custom plans options echo "Select plan: 0 - nnUNetPlans -1 - nnUNetPlans_3d_fullres_NoRsmp -2 - nnUNetPlans_3d_fullres_highres_NoRsmp -3 - nnUNetPlans_3d_fullres_stdres_NoRsmp -4 - nnUNetPlans_3d_fullres_lowres_NoRsmp -5 - Custom plan" +1 - nnUNetPlans_3d_fullres_highres_NoRsmp +2 - nnUNetPlans_3d_fullres_stdres_NoRsmp +3 - nnUNetPlans_3d_fullres_lowres_NoRsmp +4 - Custom plan" read -p "Enter plan number (Press enter to set default 0 - nnUNetPlans): " plan_num case "$plan_num" in 0) plans="nnUNetPlans" ;; - 1) plans="nnUNetPlans_3d_fullres_NoRsmp" ;; - 2) plans="nnUNetPlans_3d_fullres_highres_NoRsmp" ;; - 3) plans="nnUNetPlans_3d_fullres_stdres_NoRsmp" ;; - 4) plans="nnUNetPlans_3d_fullres_lowres_NoRsmp" ;; - 5) read -p "Enter custom plan name: " custom_plan + 1) plans="Mosaic_nnUNetPlannerResEncXL_stdres_NoRsmp_40G" ;; + 2) plans="Mosaic_nnUNetPlannerResEncL_stdres_NoRsmp_24G" ;; + 3) plans="Mosaic_nnUNetPlannerResEncM_stdres_NoRsmp_12G" ;; + 4) read -p "Enter custom plan name: " custom_plan if [[ -z "$custom_plan" ]]; then echo "Error: Custom plan name is required." exit 1