Add check for duration of time columns in DynamicTable

CHANGELOG.md

@@ -1,6 +1,7 @@
 # v0.6.6 (Upcoming)
 
 ### New Checks
+* Added checks for the duration of DynamicTables by checking start_time, stop_time, timestamp, duration, and spike_times columns. [#628](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/628)
 * Added `check_file_extension` for NWB file extension best practice recommendations (`.nwb`, `.nwb.h5`, or `.nwb.zarr`) [#625](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/625)
 
 ### Improvements

src/nwbinspector/checks/__init__.py

@@ -73,6 +73,7 @@
     check_ids_unique,
     check_single_row,
     check_table_time_columns_are_not_negative,
+    check_table_time_columns_duration,
     check_table_values_for_dict,
     check_time_interval_time_columns,
     check_time_intervals_stop_after_start,
@@ -142,6 +143,7 @@
     "check_time_intervals_stop_after_start",
     "check_table_values_for_dict",
     "check_table_time_columns_are_not_negative",
+    "check_table_time_columns_duration",
     "check_resolution",
     "check_missing_unit",
     "check_regular_timestamps",

src/nwbinspector/checks/_tables.py

@@ -292,3 +292,90 @@ def check_table_time_columns_are_not_negative(table: DynamicTable) -> Optional[I
                 )
 
     return None
+
+
+@register_check(importance=Importance.BEST_PRACTICE_SUGGESTION, neurodata_type=DynamicTable)
+def check_table_time_columns_duration(
+    table: DynamicTable, duration_threshold: float = 31557600.0
+) -> Optional[InspectorMessage]:
+    """
+    Check if the duration spanned by time columns in a DynamicTable exceeds a threshold.
+
+    This check examines time-related columns (start_time, stop_time, timestamp, spike_times)
+    and calculates the duration as max(time) - min(time). If this exceeds the threshold
+    (default: 1 year = 31,557,600 seconds), a warning is issued.
+
+    Parameters
+    ----------
+    table: DynamicTable
+        The table to check
+    duration_threshold: float, optional
+        Maximum expected duration in seconds. Default is 1 year (365.25 days).
+
+    Returns
+    -------
+    Optional[InspectorMessage]
+        Warning message if duration exceeds threshold, None otherwise
+    """
+    if len(table.id) == 0:
+        return None  # Empty table
+
+    start_times = []
+    end_times = []
+
+    # Check for start_time and stop_time columns (e.g., trials)
+    if "start_time" in table.colnames and len(table["start_time"]) > 0:
+        start_times.append(float(table["start_time"][0]))
+        if "stop_time" in table.colnames and len(table["stop_time"]) > 0:
+            end_times.append(float(table["stop_time"][-1]))
+
+    # Check for timestamp column (possibly with duration)
+    if "timestamp" in table.colnames and len(table["timestamp"]) > 0:
+        timestamp_data = table["timestamp"]
+        start_times.append(float(timestamp_data[0]))
+
+        if "duration" in table.colnames and len(table["duration"]) > 0:
+            duration_data = table["duration"]
+            end_times.append(float(timestamp_data[-1] + duration_data[-1]))
+        else:
+            end_times.append(float(timestamp_data[-1]))
+
+    # Check for spike_times column (Units table)
+    # Assume spike times are ordered within each unit
+    if "spike_times" in table.colnames and len(table["spike_times"]) > 0:
+        idxs = table["spike_times"].data[:]
+
+        # Remove zeros from idxs (units with no spikes)
+        idxs = idxs[idxs != 0]
+
+        if len(idxs) > 0:
+            st_data = table["spike_times"].target
+
+            if len(idxs) > 1:
+                start = float(np.min(np.r_[st_data[0], st_data[idxs[:-1]]]))
+            else:
+                start = float(st_data[0])
+
+            end = float(np.max(st_data[idxs - 1]))
+            start_times.append(start)
+            end_times.append(end)
+
+    # Calculate duration if we found any time data
+    if start_times and end_times:
+        duration = max(end_times) - min(start_times)
+
+        # Check if duration exceeds threshold
+        if duration > duration_threshold:
+            # Convert to years for the message
+            duration_years = duration / 31557600.0
+            threshold_years = duration_threshold / 31557600.0
+            return InspectorMessage(
+                message=(
+                    f"DynamicTable '{table.name}' has a duration of {duration:.2f} seconds "
+                    f"({duration_years:.2f} years), which exceeds the threshold of "
+                    f"{duration_threshold:.2f} seconds ({threshold_years:.2f} years). "
+                    "Please verify that this is correct."
+                )
+            )
+
+    return None

tests/unit_tests/test_tables.py

@@ -16,6 +16,7 @@
     check_ids_unique,
     check_single_row,
     check_table_time_columns_are_not_negative,
+    check_table_time_columns_duration,
     check_table_values_for_dict,
     check_time_interval_time_columns,
     check_time_intervals_stop_after_start,
@@ -498,3 +499,82 @@ def test_table_time_columns_are_not_negative_multidimensional_pass():
     test_table.add_row(test_time=[0.0, 1.0, 2.0, 3.0])
 
     assert check_table_time_columns_are_not_negative(test_table) is None
+
+
+def test_check_table_time_columns_duration_pass_short():
+    """Test that short duration tables pass the check."""
+    table = TimeIntervals(name="trials", description="test trials")
+    table.add_row(start_time=0.0, stop_time=10.0)
+    table.add_row(start_time=15.0, stop_time=25.0)
+    table.add_row(start_time=30.0, stop_time=100.0)
+
+    assert check_table_time_columns_duration(table) is None
+
+
+def test_check_table_time_columns_duration_fail_exceeds_threshold():
+    """Test that tables with duration exceeding 1 year fail."""
+    one_year = 31557600.0
+    table = TimeIntervals(name="trials", description="test trials")
+    table.add_row(start_time=0.0, stop_time=100.0)
+    table.add_row(start_time=one_year + 1000, stop_time=one_year + 2000)
+
+    result = check_table_time_columns_duration(table)
+    assert result is not None
+    assert "trials" in result.message
+    assert "exceeds the threshold" in result.message
+    assert result.importance == Importance.BEST_PRACTICE_SUGGESTION
+
+
+def test_check_table_time_columns_duration_pass_empty():
+    """Test that empty tables pass."""
+    table = TimeIntervals(name="trials", description="test trials")
+    assert check_table_time_columns_duration(table) is None
+
+
+def test_check_table_time_columns_duration_pass_custom_threshold():
+    """Test that custom threshold works correctly."""
+    table = TimeIntervals(name="trials", description="test trials")
+    table.add_row(start_time=0.0, stop_time=100.0)
+    table.add_row(start_time=150.0, stop_time=200.0)
+
+    # Should fail with 100 second threshold
+    result = check_table_time_columns_duration(table, duration_threshold=100.0)
+    assert result is not None
+
+    # Should pass with 300 second threshold
+    result = check_table_time_columns_duration(table, duration_threshold=300.0)
+    assert result is None
+
+
+def test_check_table_time_columns_duration_with_timestamp():
+    """Test with timestamp column."""
+    table = DynamicTable(name="events", description="test events")
+    table.add_column(name="timestamp", description="event timestamps")
+    table.add_row(timestamp=0.0)
+    table.add_row(timestamp=100.0)
+
+    assert check_table_time_columns_duration(table) is None
+
+
+def test_check_table_time_columns_duration_with_timestamp_and_duration():
+    """Test with timestamp and duration columns."""
+    one_year = 31557600.0
+    table = DynamicTable(name="events", description="test events")
+    table.add_column(name="timestamp", description="event timestamps")
+    table.add_column(name="duration", description="event durations")
+    table.add_row(timestamp=0.0, duration=10.0)
+    table.add_row(timestamp=one_year, duration=1000.0)
+
+    result = check_table_time_columns_duration(table)
+    assert result is not None
+    assert "exceeds the threshold" in result.message
+
+
+def test_check_table_time_columns_duration_no_time_columns():
+    """Test that tables without time columns pass."""
+    table = DynamicTable(name="test_table", description="test")
+    table.add_column(name="value", description="some data")
+    table.add_row(value=123)
+    table.add_row(value=456)
+
+    assert check_table_time_columns_duration(table) is None