back to resample of nnunet + separete custom no resampling + rewrite …

…scripts
bluemindai · Jun 19, 2024 · 9b8642d · 9b8642d
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diff --git a/README.md b/README.md
@@ -21,6 +21,6 @@ export nnUNet_results="/bluemind/nnunet/trains/nnUNet_results"
 Use [generate_json](scripts/generate_json.ipynb) for this.
 
 4. #### Use scripts for training.
-There are several scripts written by me (Roma) for datgaset  [preprocessing](scripts/preprocess_data.sh), [training](scripts/train.sh), [finetuning](scripts/finetune.sh) and [predicting](scripts/predict.py).
+There are several scripts written by me (Roma) for datgaset  [preprocessing](scripts/preprocess.sh), [training](scripts/train.sh), [finetuning](scripts/finetune.sh).
 
 ### READ NNUUNET [README](readme.md) FOR MORE INFORMATION
diff --git a/configs/mosaic_planner.json b/configs/mosaic_planner.json
@@ -2,23 +2,26 @@
     "3d_fullres_no_resampling": {
         "inherits_from": "3d_fullres",
         "resampling_fn_data": "no_resampling_data_or_seg_to_shape",
+        "resampling_fn_data_kwargs": {},
         "resampling_fn_seg": "no_resampling_data_or_seg_to_shape",
+        "resampling_fn_seg_kwargs": {},
         "resampling_fn_probabilities": "no_resampling_data_or_seg_to_shape",
-        "data_identifier": "3d_fullres_no_resampling"
+        "resampling_fn_probabilities_kwargs": {},
+        "data_identifier": "nnUNetPlans_3d_fullres_NoRsmp"
     },
-    "3d_fullres_mosaic_spacing_highres_NoRsmp": {
+    "3d_fullres_highres_NoRsmp": {
         "inherits_from": "3d_fullres_no_resampling",
         "spacing": [1.0, 1.0, 1.0],
-        "data_identifier": "3d_fullres_mosaic_spacing_highres_NoRsmp"
+        "data_identifier": "nnUNetPlans_3d_fullres_highres_NoRsmp"
     },
-    "3d_fullres_mosaic_spacing_stdres_NoRsmp": {
+    "3d_fullres_stdres_NoRsmp": {
         "inherits_from": "3d_fullres_no_resampling",
         "spacing": [1.5, 1.5, 1.5],
-        "data_identifier": "3d_fullres_mosaic_spacing_stdres_NoRsmp"
+        "data_identifier": "nnUNetPlans_3d_fullres_stdres_NoRsmp"
     },
-    "3d_fullres_mosaic_spacing_lowres_NoRsmp": {
+    "3d_fullres_lowres_NoRsmp": {
         "inherits_from": "3d_fullres_no_resampling",
         "spacing": [3.0, 3.0, 3.0],
-        "data_identifier": "3d_fullres_mosaic_spacing_lowres_NoRsmp"
+        "data_identifier": "nnUNetPlans_3d_fullres_lowres_NoRsmp"
     }
 }
diff --git a/nnunetv2/experiment_planning/experiment_planners/default_experiment_planner.py b/nnunetv2/experiment_planning/experiment_planners/default_experiment_planner.py
@@ -544,19 +544,19 @@ def plan_experiment(self):
 
         plans['configurations']['3d_fullres_no_resampling'] = mosaic_planner['3d_fullres_no_resampling']
 
-        plans['configurations']['3d_fullres_mosaic_spacing_highres_NoRsmp'] = mosaic_planner['3d_fullres_mosaic_spacing_highres_NoRsmp']
+        plans['configurations']['3d_fullres_highres_NoRsmp'] = mosaic_planner['3d_fullres_highres_NoRsmp']
         print('3D fullres Mosaic HighRes spacing No Resampling U-Net configuration:')
-        print(plans['configurations']['3d_fullres_mosaic_spacing_highres_NoRsmp'])
+        print(plans['configurations']['3d_fullres_highres_NoRsmp'])
         print()
 
-        plans['configurations']['3d_fullres_mosaic_spacing_stdres_NoRsmp'] = mosaic_planner['3d_fullres_mosaic_spacing_stdres_NoRsmp']
+        plans['configurations']['3d_fullres_stdres_NoRsmp'] = mosaic_planner['3d_fullres_stdres_NoRsmp']
         print('3D fullres Mosaic StdRes spacing No Resampling U-Net configuration:')
-        print(plans['configurations']['3d_fullres_mosaic_spacing_stdres_NoRsmp'])
+        print(plans['configurations']['3d_fullres_stdres_NoRsmp'])
         print()
 
-        plans['configurations']['3d_fullres_mosaic_spacing_lowres_NoRsmp'] = mosaic_planner['3d_fullres_mosaic_spacing_lowres_NoRsmp']
+        plans['configurations']['3d_fullres_lowres_NoRsmp'] = mosaic_planner['3d_fullres_lowres_NoRsmp']
         print('3D fullres Mosaic LowRes spacing No Resampling U-Net configuration:')
-        print(plans['configurations']['3d_fullres_mosaic_spacing_lowres_NoRsmp'])
+        print(plans['configurations']['3d_fullres_lowres_NoRsmp'])
         print()
 
         self.plans = plans

diff --git a/.../experiment_planning/experiment_planners/residual_unets/residual_encoder_unet_planners.py b/.../experiment_planning/experiment_planners/residual_unets/residual_encoder_unet_planners.py
@@ -207,20 +207,12 @@ def _keygen(patch_size, strides):
             'spacing': spacing,
             'normalization_schemes': normalization_schemes,
             'use_mask_for_norm': mask_is_used_for_norm,
-            #### MOSAIC CHAGES ####
-            # 'resampling_fn_data': resampling_data.__name__,
-            # 'resampling_fn_seg': resampling_seg.__name__,
-            # 'resampling_fn_data_kwargs': resampling_data_kwargs,
-            # 'resampling_fn_seg_kwargs': resampling_seg_kwargs,
-            # 'resampling_fn_probabilities': resampling_softmax.__name__,
-            # 'resampling_fn_probabilities_kwargs': resampling_softmax_kwargs,
-            #### MOSAIC CHAGES ####
-            'resampling_fn_data': 'no_resampling_data_or_seg_to_shape',
-            'resampling_fn_seg': 'no_resampling_data_or_seg_to_shape',
-            'resampling_fn_data_kwargs': {},
-            'resampling_fn_seg_kwargs': {},
-            'resampling_fn_probabilities': 'no_resampling_data_or_seg_to_shape',
-            'resampling_fn_probabilities_kwargs': {},
+            'resampling_fn_data': resampling_data.__name__,
+            'resampling_fn_seg': resampling_seg.__name__,
+            'resampling_fn_data_kwargs': resampling_data_kwargs,
+            'resampling_fn_seg_kwargs': resampling_seg_kwargs,
+            'resampling_fn_probabilities': resampling_softmax.__name__,
+            'resampling_fn_probabilities_kwargs': resampling_softmax_kwargs,
             'architecture': architecture_kwargs
         }
         return plan

diff --git a/scripts/preprocess.sh b/scripts/preprocess.sh
@@ -3,34 +3,38 @@
 echo "Mosaic Preprocessor. Be sure you have a dataset.json file in the raw directory!"
 read -p "Enter dataset id: " id
 read -p "Enter resolution (low | std | high): " res
+read -p "Enter configuration (press Enter to set automatically): " config
 read -p "Enter planner (press Enter to set automatically): " planner
 read -p "Enter GPU memory (press Enter to set automatically): " gpu_mem
-read -p "Enter number of processes (1-20, press Enter to use default 4): " np
+read -p "Enter number of processes (1-20, press Enter to use default 8): " np
 
 # Устанавливаем количество процессов по умолчанию, если не указано
-[[ -z "$np" ]] && np=4
+[[ -z "$np" ]] && np=8
 
 declare -a spacing
 
-# Настройка разрешения, планировщика и автоматическое определение памяти
+# Настройка разрешения, планировщика, автоматическое определение памяти и конфигурации флага
 case "$res" in
     low)
         echo -e "\nLow resolution selected. Setting spacing at 3.0 3.0 3.0"
         spacing=(3.0 3.0 3.0)
         [[ -z "$planner" ]] && planner="nnUNetPlannerResEncM"
         [[ -z "$gpu_mem" ]] && gpu_mem=12
+        [[ -z "$config" ]] && config="3d_fullres_lowres_NoRsmp"
         ;;
     std)
         echo -e "\nStandard resolution selected. Setting spacing at 1.5 1.5 1.5"
         spacing=(1.5 1.5 1.5)
         [[ -z "$planner" ]] && planner="nnUNetPlannerResEncL"
         [[ -z "$gpu_mem" ]] && gpu_mem=24
+        [[ -z "$config" ]] && config="3d_fullres_stdres_NoRsmp"
         ;;
     high)
         echo -e "\nHigh resolution selected. Setting spacing at 1.0 1.0 1.0"
         spacing=(1.0 1.0 1.0)
         [[ -z "$planner" ]] && planner="nnUNetPlannerResEncXL"
         [[ -z "$gpu_mem" ]] && gpu_mem=40
+        [[ -z "$config" ]] && config="3d_fullres_highres_NoRsmp"
         ;;
     *)
         echo -e "\nInvalid resolution option."
@@ -39,7 +43,7 @@ case "$res" in
 esac
 
 nnUNetv2_plan_and_preprocess -d "$id" \
-    -c 3d_fullres \
+    -c "$config" \
     -pl "$planner" \
     -overwrite_target_spacing "${spacing[@]}" \
     -gpu_memory_target "$gpu_mem" \

diff --git a/scripts/train.sh b/scripts/train.sh
@@ -2,25 +2,52 @@
 
 echo "Train model from scratch. Be sure that you have already created the dataset.json file!"
 read -p "Enter dataset id: " id
-read -p "Enter train config (Press enter to set default 3d_fullres): " conf
-read -p "Enter plans identifier (Press enter to set  nnUNetPlans): " p
+echo "Select train config:
+0 - 3d_fullres
+1 - 3d_fullres_lowres_NoRsmp
+2 - 3d_fullres_stdres_NoRsmp
+3 - 3d_fullres_highres_NoRsmp"
+read -p "Enter train config number (Press enter to set default 0 - 3d_fullres): " conf_num
+echo "Select trainer:
+0 - nnUNetTrainer
+1 - nnUNetTrainerNoMirroring
+2 - nnUNetTrainer_250epochs_NoMirroring
+3 - nnUNetTrainer_500epochs_NoMirroring
+4 - nnUNetTrainer_750epochs_NoMirroring
+5 - nnUNetTrainer_2000epochs_NoMirroring
+6 - nnUNetTrainer_4000epochs_NoMirroring
+7 - nnUNetTrainer_8000epochs_NoMirroring"
+read -p "Enter trainer number: " trainer_num
 read -p "Enter train fold ([0-4] or all usually): " fold
-read -p "Enter trainer (nnUNetTrainer, nnUNetTrainerNoMirroring, nnUNetTrainer_Xepochs_NoMirroring etc.): " trainer
 
 # Устанавливаем значение по умолчанию для конфигурации и плана, если они не указаны
-[[ -z "$conf" ]] && conf="3d_fullres"
-[[ -z "$p" ]] && p="nnUNetPlans"
+case "$conf_num" in
+    0) conf="3d_fullres" ;;
+    1) conf="3d_fullres_lowres_NoRsmp" ;;
+    2) conf="3d_fullres_stdres_NoRsmp" ;;
+    3) conf="3d_fullres_highres_NoRsmp" ;;
+    *) conf="3d_fullres" ;;
+esac
+
+plans="nnUNetPlans"
+
+case "$trainer_num" in
+    0) trainer="nnUNetTrainer" ;;
+    1) trainer="nnUNetTrainerNoMirroring" ;;
+    2) trainer="nnUNetTrainer_250epochs_NoMirroring" ;;
+    3) trainer="nnUNetTrainer_500epochs_NoMirroring" ;;
+    4) trainer="nnUNetTrainer_750epochs_NoMirroring" ;;
+    5) trainer="nnUNetTrainer_2000epochs_NoMirroring" ;;
+    6) trainer="nnUNetTrainer_4000epochs_NoMirroring" ;;
+    7) trainer="nnUNetTrainer_8000epochs_NoMirroring" ;;
+    *) echo "Error: Invalid trainer number."; exit 1 ;;
+esac
 
 # Проверяем, указаны ли fold и trainer, и выводим ошибку в противном случае
 if [[ -z "$fold" ]]; then
     echo "Error: Train fold is required."
     exit 1
 fi
 
-if [[ -z "$trainer" ]]; then
-    echo "Error: Trainer is required."
-    exit 1
-fi
-
 echo "Launching the training process..."
-nnUNetv2_train "$id" "$conf" "$fold" -p "$p" -tr "$trainer"
+nnUNetv2_train "$id" "$conf" "$fold" -p "$plans" -tr "$trainer"