From a516408c4ee12c62e6ba53a2bf6967cff84b0472 Mon Sep 17 00:00:00 2001 From: Furen Xiao Date: Thu, 8 Oct 2026 06:13:13 +0800 Subject: [PATCH] Add iterative pseudo-labeling scripts for MONAI and nnU-Net - Implemented 09_run_iterative.py for MONAI to orchestrate iterative pseudo-labeling rounds, including training, predicting, and evaluation. - Created 01_prepare_dataset.py, 02_plan_preprocess.py, 06_pseudo_label.py, 07_train.py, 08_eval.py, and 09_run_iterative.py for nnU-Net to manage dataset preparation, planning, training, evaluation, and iterative pseudo-labeling. - Enhanced error handling and logging throughout the scripts for better traceability. - Added functionality to handle negative pseudo-labels and TTA options during inference. - Included visualization of Dice scores across rounds for both MONAI and nnU-Net. --- scripts_monai/{01_monai_build_rows.py => 01_build_rows.py} | 0 scripts_monai/{03_monai_pseudo_label.py => 06_pseudo_label.py} | 0 scripts_monai/{02_monai_train.py => 07_train.py} | 0 scripts_monai/{04_monai_eval_test.py => 08_eval.py} | 0 scripts_monai/{05_monai_run_iterative.py => 09_run_iterative.py} | 0 scripts_nnu/{01_nnu_prepare_dataset.py => 01_prepare_dataset.py} | 0 scripts_nnu/{02_nnu_plan_preprocess.py => 02_plan_preprocess.py} | 0 scripts_nnu/{04_nnu_pseudo_label.py => 06_pseudo_label.py} | 0 scripts_nnu/{03_nnu_train.py => 07_train.py} | 0 scripts_nnu/{05_nnu_eval_test.py => 08_eval.py} | 0 scripts_nnu/{06_nnu_run_iterative.py => 09_run_iterative.py} | 0 11 files changed, 0 insertions(+), 0 deletions(-) rename scripts_monai/{01_monai_build_rows.py => 01_build_rows.py} (100%) rename scripts_monai/{03_monai_pseudo_label.py => 06_pseudo_label.py} (100%) rename scripts_monai/{02_monai_train.py => 07_train.py} (100%) rename scripts_monai/{04_monai_eval_test.py => 08_eval.py} (100%) rename scripts_monai/{05_monai_run_iterative.py => 09_run_iterative.py} (100%) rename scripts_nnu/{01_nnu_prepare_dataset.py => 01_prepare_dataset.py} (100%) rename scripts_nnu/{02_nnu_plan_preprocess.py => 02_plan_preprocess.py} (100%) rename scripts_nnu/{04_nnu_pseudo_label.py => 06_pseudo_label.py} (100%) rename scripts_nnu/{03_nnu_train.py => 07_train.py} (100%) rename scripts_nnu/{05_nnu_eval_test.py => 08_eval.py} (100%) rename scripts_nnu/{06_nnu_run_iterative.py => 09_run_iterative.py} (100%) diff --git a/scripts_monai/01_monai_build_rows.py b/scripts_monai/01_build_rows.py similarity index 100% rename from scripts_monai/01_monai_build_rows.py rename to scripts_monai/01_build_rows.py diff --git a/scripts_monai/03_monai_pseudo_label.py b/scripts_monai/06_pseudo_label.py similarity index 100% rename from scripts_monai/03_monai_pseudo_label.py rename to scripts_monai/06_pseudo_label.py diff --git a/scripts_monai/02_monai_train.py b/scripts_monai/07_train.py similarity index 100% rename from scripts_monai/02_monai_train.py rename to scripts_monai/07_train.py diff --git a/scripts_monai/04_monai_eval_test.py b/scripts_monai/08_eval.py similarity index 100% rename from scripts_monai/04_monai_eval_test.py rename to scripts_monai/08_eval.py diff --git a/scripts_monai/05_monai_run_iterative.py b/scripts_monai/09_run_iterative.py similarity index 100% rename from scripts_monai/05_monai_run_iterative.py rename to scripts_monai/09_run_iterative.py diff --git a/scripts_nnu/01_nnu_prepare_dataset.py b/scripts_nnu/01_prepare_dataset.py similarity index 100% rename from scripts_nnu/01_nnu_prepare_dataset.py rename to scripts_nnu/01_prepare_dataset.py diff --git a/scripts_nnu/02_nnu_plan_preprocess.py b/scripts_nnu/02_plan_preprocess.py similarity index 100% rename from scripts_nnu/02_nnu_plan_preprocess.py rename to scripts_nnu/02_plan_preprocess.py diff --git a/scripts_nnu/04_nnu_pseudo_label.py b/scripts_nnu/06_pseudo_label.py similarity index 100% rename from scripts_nnu/04_nnu_pseudo_label.py rename to scripts_nnu/06_pseudo_label.py diff --git a/scripts_nnu/03_nnu_train.py b/scripts_nnu/07_train.py similarity index 100% rename from scripts_nnu/03_nnu_train.py rename to scripts_nnu/07_train.py diff --git a/scripts_nnu/05_nnu_eval_test.py b/scripts_nnu/08_eval.py similarity index 100% rename from scripts_nnu/05_nnu_eval_test.py rename to scripts_nnu/08_eval.py diff --git a/scripts_nnu/06_nnu_run_iterative.py b/scripts_nnu/09_run_iterative.py similarity index 100% rename from scripts_nnu/06_nnu_run_iterative.py rename to scripts_nnu/09_run_iterative.py