updated tabularization script to fix bugs

mmcdermott · Sep 9, 2024 · 9294920 · 9294920
1 parent b289033
commit 9294920
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/MIMICIV_TUTORIAL/tabularize_meds.sh b/MIMICIV_TUTORIAL/tabularize_meds.sh
@@ -24,23 +24,23 @@ MEDS_transform-reshard_to_split \
   'stages=["reshard_to_split"]' \
   stage="reshard_to_split" \
   stage_configs.reshard_to_split.n_subjects_per_shard=2500 \
-  "hydra.sweeper.polling_time=5"
+  "polling_time=5"
 
 # describe codes
 echo "Describing codes"
 meds-tab-describe \
-    "input_dir=$MIMICIV_MEDS_RESHARD_DIR" "output_dir=$OUTPUT_TABULARIZATION_DIR"
+    "input_dir=${MIMICIV_MEDS_RESHARD_DIR}/data" "output_dir=$OUTPUT_TABULARIZATION_DIR"
 
 echo "Tabularizing static data"
 echo meds-tab-tabularize-static \
-    "input_dir=$MIMICIV_MEDS_RESHARD_DIR" "output_dir=$OUTPUT_TABULARIZATION_DIR" \
+    "input_dir=${MIMICIV_MEDS_RESHARD_DIR}/data" "output_dir=$OUTPUT_TABULARIZATION_DIR" \
     do_overwrite=False "$@"
 
 meds-tab-tabularize-time-series \
     --multirun \
     worker="range(0,$N_PARALLEL_WORKERS)" \
     hydra/launcher=joblib \
-    "input_dir=$MIMICIV_MEDS_RESHARD_DIR" "output_dir=$OUTPUT_TABULARIZATION_DIR" \
+    "input_dir=${MIMICIV_MEDS_RESHARD_DIR}/data" "output_dir=$OUTPUT_TABULARIZATION_DIR" \
     do_overwrite=False "$@"
 
 
@@ -51,13 +51,13 @@ do
     --multirun \
     worker="range(0,$N_PARALLEL_WORKERS)" \
     hydra/launcher=joblib \
-    "input_dir=$MIMICIV_MEDS_DIR" "output_dir=$OUTPUT_TABULARIZATION_DIR" \
+    "input_dir=${MIMICIV_MEDS_RESHARD_DIR}/data" "output_dir=$OUTPUT_TABULARIZATION_DIR" \
     "input_label_dir=${TASKS_DIR}" "task_name=${TASK}" do_overwrite=False "$@"
 
   echo "Running xgboost"
   meds-tab-xgboost \
       --multirun \
       worker="range(0,$N_PARALLEL_WORKERS)" \
-      "input_dir=$MIMICIV_MEDS_DIR" "output_dir=$OUTPUT_TABULARIZATION_DIR" \
+      "input_dir=${MIMICIV_MEDS_RESHARD_DIR}/data" "output_dir=$OUTPUT_TABULARIZATION_DIR" \
       "output_model_dir=${OUTPUT_MODEL_DIR}/${TASK}/" "task_name=$TASK" do_overwrite=False "$@"
 done