fixed bug with summarization script crashing for min and max value ag…

…gregations due to a coo matrix being returned rather than a dense matrix as with sum and count operations

src/MEDS_tabular_automl/generate_summarized_reps.py

@@ -142,10 +142,17 @@ def aggregate_matrix(windows, matrix, agg, num_features, use_tqdm=False):
         max_index = window["max_index"]
         subset_matrix = matrix[min_index : max_index + 1, :]
         agg_matrix = sparse_aggregate(subset_matrix, agg).astype(out_dtype)
-        nozero_ind = np.nonzero(agg_matrix)[0]
-        col.append(nozero_ind)
-        data.append(agg_matrix[nozero_ind])
-        row.append(np.repeat(np.array(i, dtype=np.int32), len(nozero_ind)))
+        if isinstance(agg_matrix, np.ndarray):
+            nozero_ind = np.nonzero(agg_matrix)[0]
+            col.append(nozero_ind)
+            data.append(agg_matrix[nozero_ind])
+            row.append(np.repeat(np.array(i, dtype=np.int32), len(nozero_ind)))
+        elif isinstance(agg_matrix, coo_array):
+            col.append(agg_matrix.col)
+            data.append(agg_matrix.data)
+            row.append(agg_matrix.row)
+        else:
+            raise TypeError(f"Invalid matrix type {type(agg_matrix)}")
     row = np.concatenate(row)
     out_matrix = coo_array(
         (np.concatenate(data), (row, np.concatenate(col))),
@@ -355,16 +362,16 @@ def generate_summary(
     df = pl.scan_parquet(
         Path("/storage/shared/meds_tabular_ml/ebcl_dataset/processed")
         / "final_cohort"
-        / "held_out"
-        / "7.parquet"
+        / "train"
+        / "3.parquet"
     )
-    agg = "code/count"
+    agg = "value/min"
     index_df, sparse_matrix = get_flat_ts_rep(agg, feature_columns, df)
     generate_summary(
         feature_columns=feature_columns,
         index_df=index_df,
         matrix=sparse_matrix,
-        window_size="1d",
+        window_size="30d",
         agg=agg,
         use_tqdm=True,
     )