Merge pull request #48 from KumarLabJax/task/improve-merged-bout-table-naming

Improve the naming functionality of Merge Behavior Tables code

Author: bergsalex

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "jabs-postprocess"
-version = "0.4.1"
+version = "0.4.2"
 description = "A python library for JABS postprocessing utilities."
 readme = "README.md"
 license = "LicenseRef-PLATFORM-LICENSE-AGREEMENT-FOR-NON-COMMERCIAL-USE"

src/jabs_postprocess/cli/main.py

@@ -539,9 +539,9 @@ def merge_multiple_tables(
         typer.Option(help="File pattern to match behavior tables"),
     ] = "*.csv",
     output_prefix: Annotated[
-        str,
+        Optional[str],
         typer.Option(help="File prefix for merged output tables"),
-    ] = "merged_behavior",
+    ] = None,
     overwrite: Annotated[bool, typer.Option(help="Overwrites output files")] = False,
 ):
     """Merge multiple sets of behavior tables, automatically grouping by behavior.

src/jabs_postprocess/generate_behavior_tables.py

@@ -121,14 +121,14 @@ def process_multiple_behaviors(
 
 def merge_behavior_tables(
     input_tables: List[Path],
-    output_prefix: str = "merged_behavior",
+    output_prefix: str | None = None,
     overwrite: bool = False,
 ) -> Tuple[str, str]:
     """Merge multiple behavior tables for the same behavior.
 
     Args:
             input_tables: List of paths to behavior table files to merge
-            output_prefix: Prefix for output filenames
+            output_prefix: Optional prefix for output filenames
             overwrite: Whether to overwrite existing files
 
     Returns:
@@ -174,13 +174,17 @@ def merge_behavior_tables(
 
         tables.append(table)
 
+    output_file = behavior_name.replace(" ", "_").lower()
+    if output_prefix:
+        output_file = f"{output_prefix}_{output_file}"
+
     # Merge the tables using the existing combine_data method
     if table_type == "bout":
         merged_table = BoutTable.combine_data(tables)
-        output_file = f"{output_prefix}_{behavior_name}_bouts_merged.csv"
+        output_file = f"{output_file}_bouts_merged.csv"
     else:
         merged_table = BinTable.combine_data(tables)
-        output_file = f"{output_prefix}_{behavior_name}_summaries_merged.csv"
+        output_file = f"{output_file}_summaries_merged.csv"
 
     # Write the merged table
     merged_table.to_file(output_file, overwrite)
@@ -193,14 +197,14 @@ def merge_behavior_tables(
 
 def merge_multiple_behavior_tables(
     table_groups: Dict[str, List[Path]],
-    output_prefix: str = "merged_behavior",
+    output_prefix: str | None = None,
     overwrite: bool = False,
 ) -> Dict[str, Tuple[str, str]]:
     """Merge multiple sets of behavior tables grouped by behavior.
 
     Args:
             table_groups: Dictionary mapping behavior names to lists of table file paths
-            output_prefix: Prefix for output filenames
+            output_prefix: Optional prefix for output filenames
             overwrite: Whether to overwrite existing files
 
     Returns:
@@ -238,15 +242,13 @@ def merge_multiple_behavior_tables(
         bout_output = None
         if bout_tables:
             bout_output, _ = merge_behavior_tables(
-                bout_tables, f"{output_prefix}_{behavior_name}_bouts", overwrite
+                bout_tables, output_prefix, overwrite
             )
 
         # Merge bin tables if any exist
         bin_output = None
         if bin_tables:
-            bin_output, _ = merge_behavior_tables(
-                bin_tables, f"{output_prefix}_{behavior_name}_summaries", overwrite
-            )
+            bin_output, _ = merge_behavior_tables(bin_tables, output_prefix, overwrite)
 
         results[behavior_name] = (bout_output, bin_output)
 

tests/cli/test_merge_multiple_tables.py

@@ -74,6 +74,8 @@ def mock_csv_reader(file_path, nrows=None):
             "merge-multiple-tables",
             "--table-folder",
             str(table_folder),
+            "--output-prefix",
+            "merged_behavior",
         ]
 
         if overwrite:

tests/test_generate_behavior_tables.py

@@ -749,7 +749,7 @@ def read_csv_side_effect(path, **kwargs):
 
         # Mock merge_behavior_tables to return expected outputs
         def merge_side_effect(tables, prefix, overwrite):
-            behavior = prefix.split("_")[1]
+            behavior = prefix.split("_")[0]
             return f"merged_{behavior}_output.csv", f"merged_{behavior}_output.csv"
 
         mock_merge.side_effect = merge_side_effect