bash script for running anima metrics across folds of 2d/3d models

testing/run_anima_metrics.sh

@@ -0,0 +1,82 @@
+#!/bin/bash
+# Training nnUNet on just the Zurich dataset
+
+
+path_data_dir=$1
+
+# get the base name of the path_data_dir
+dataset_name=$(basename $path_data_dir)
+
+if [ $dataset_name == "Dataset901_tumMSChunksRegion" ]; then
+    # site="muc_stacked_lesion"
+    site="muc_lesion_chunk-3"
+    training_type="single-channel"
+    # NOTE: we have already separated lesion and sc masks for MetricsReloaded, 
+    # so using the same niftis. `single-channel` arg directly computes anima metrics
+    # without separating the masks
+
+elif [ $dataset_name == "DeepSegLesionInference_tumNeuropoly" ]; then
+    site="tum_deepseg-lesion_stacked"
+    training_type="single-channel"
+
+elif [ $dataset_name == "Dataset902_tumMSStitchedRegion" ]; then
+    site="muc"
+    training_type="region-based"
+
+elif [ $dataset_name == "Dataset903_tumMSChunksStraightRegion" ]; then
+    site="muc_native_stacked"
+    training_type="region-based"
+
+elif [ $dataset_name == "Dataset904_tumMSStitchedStraightRegion" ]; then
+    site="muc_native"
+    training_type="region-based"
+
+elif [ $dataset_name == "Dataset905_tumMSChunksMulti" ]; then
+    site="muc_stacked"
+    training_type="multi-channel"
+
+elif [ $dataset_name == "Dataset906_tumMSStitchedMulti" ]; then
+    site="muc"
+    training_type="multi-channel"
+
+elif [ $dataset_name == "Dataset907_tumMSChunksStraightMulti" ]; then
+    site="muc_native_stacked"
+    training_type="multi-channel"
+
+elif [ $dataset_name == "Dataset908_tumMSStitchedStraightMulti" ]; then
+    site="muc_native"
+    training_type="multi-channel"
+
+else
+    echo "Unknown dataset name: ${dataset_name}"
+    exit 1
+fi
+
+nnunet_trainer=("nnUNetTrainerDiceCELoss_noSmooth")
+
+# configurations=("3d_fullres" "2d")
+configurations=("2d") # "3d_fullres")
+
+# folds=(2 1 0)
+folds=(0) # 1 2)
+
+for configuration in ${configurations[@]}; do
+
+    for fold in ${folds[@]}; do
+
+        echo "-----------------------------------------------------------------------------------------------------"
+        echo "Running ANIMA evaluation on ${site} of ${dataset_name} with ${configuration} model and fold ${fold}"
+        echo "-----------------------------------------------------------------------------------------------------"
+
+        python ~/tum-poly/miccai_amai_lesions_spine/testing/compute_anima_metrics.py \
+            --pred-folder ~/nnunet-v2/nnUNet_results/${dataset_name}/${nnunet_trainer}__nnUNetPlans__${configuration}/fold_${fold}/test_${site} \
+            --gt-folder ${nnUNet_raw}/${dataset_name}/labelsTs_${site} \
+            --training-type ${training_type}
+        # python ~/tum-poly/miccai_amai_lesions_spine/testing/compute_anima_metrics.py \
+        #     --pred-folder ~/nnunet-v2/nnUNet_results/${dataset_name}/test_${site} \
+        #     --gt-folder ${nnUNet_raw}/Dataset910_tumMSChunksPolyNYUAxialRegion/labelsTs_tum_for_deepseg_stacked \
+        #     --training-type ${training_type}
+
+    done
+
+done