global action headers in log + remove microseconds + log number of red flags after each after (#88)

Author: TeunHuijben

trackedit/DatabaseHandler.py

@@ -190,7 +190,7 @@ def __init__(
         self.toannotate = self.find_all_toannotate()
         self.divisions = self.find_all_divisions()
         self.log(
-            f"Start annotation session - TrackEdit v{__version__} ({datetime.now()})"
+            f"Start annotation session - TrackEdit v{__version__} ({datetime.now().replace(microsecond=0)})"
         )
         self.log(
             f"Parameters: Tmax: {self.Tmax}, working_directory: {self.working_directory}, "
@@ -242,11 +242,14 @@ def initialize_logfile(self, log_filename_new, work_in_existing_db):
 
         return log_file_path
 
-    def log(self, message):
+    def log(self, message, is_header=True):
         """Append a message to the log file."""
         with open(self.log_file, "a") as log:
-            time_stap = f"[{datetime.now()}]"
-            log.write(time_stap + " " + message + "\n")
+            time_stamp = f"[{datetime.now().replace(microsecond=0)}]"
+            if is_header:
+                log.write(message + "\n")
+            else:
+                log.write("\t\t" + time_stamp + " " + message + "\n")
 
     def initialize_config(self):
         # import db filename properly into an Ultrack config, neccesary for chaning values in database
@@ -429,7 +432,7 @@ def get_same_db_filename(self, old_filename):
         log_filename_new = f"{name}_changelog.txt"
         return old_filename, db_filename_new, log_filename_new
 
-    def change_values(self, indices, field, values):
+    def change_values(self, indices, field, values, log_header=None):
         """Change values in the database for one or multiple indices.
 
         Parameters
@@ -441,13 +444,18 @@ def change_values(self, indices, field, values):
         value : int or list
             Value(s) to set. If a single value is provided, it will be applied to all indices.
             If a list is provided, it must match the length of indices.
+        log_header : str, optional
+            Optional header to prepend to log messages.
         """
         # Convert single index to list
         if isinstance(indices, (int, np.integer)):
             indices = [int(indices)]
         else:
             indices = [int(i) for i in indices]
 
+        if log_header is not None:
+            self.log(log_header)
+
         # Handle value input
         if isinstance(values, (list, np.ndarray)):
             if len(values) != len(indices):
@@ -483,7 +491,7 @@ def change_values(self, indices, field, values):
                 else old_vals
             )
             message = f"db: setting {field.name}[id={indices[i]}] = {values[i]} (was {old_val})"
-            self.log(message)
+            self.log(message, is_header=False)
 
     def calc_time_window(self):
         time_chunk_starts = np.arange(
@@ -1146,7 +1154,12 @@ def annotate_track(
             indices = self.df_full[track_mask].index.tolist()
 
         if indices:
-            self.change_values(indices, NodeDB.generic, label)
+            self.change_values(
+                indices,
+                NodeDB.generic,
+                label,
+                log_header="annotate_track:" + str(track_id),
+            )
 
     def clear_nodes_annotations(self, nodes):
         """Clear the annotations for the entire track of a list of nodes. Called when a node is deleted."""

trackedit/motile_overwrites.py

@@ -62,7 +62,12 @@ def db_add_nodes(self):
         )
 
         # Change the selected/annotation status of the nodes
-        DB_handler.change_values(indices=self.nodes, field=NodeDB.selected, values=1)
+        DB_handler.change_values(
+            indices=self.nodes,
+            field=NodeDB.selected,
+            values=1,
+            log_header="AddNodes:" + str(self.nodes),
+        )
         DB_handler.change_values(
             indices=self.nodes, field=NodeDB.generic, values=NodeDB.generic.default.arg
         )
@@ -85,18 +90,25 @@ def db_delete_nodes(self):
             DB_handler.df_full["parent_id"].isin(self.nodes)
         ].index.tolist()
         print("orphaned_children", orphaned_children)
+        log_header = "DeleteNodes:" + str(self.nodes)
         if orphaned_children:
             DB_handler.change_values(
-                indices=orphaned_children, field=NodeDB.parent_id, values=-1
+                indices=orphaned_children,
+                field=NodeDB.parent_id,
+                values=-1,
+                log_header=log_header,
             )
+            log_header = None  # prevent printing twice
             show_warning(
                 "An edge in the next time window is removed, so 'UNDO' will not work."
             )
             # ToDo: potentially only remove orphan edges into the next time window,
             # because normal edges are already properly removed
 
         # Set nodes as unselected
-        DB_handler.change_values(indices=self.nodes, field=NodeDB.selected, values=0)
+        DB_handler.change_values(
+            indices=self.nodes, field=NodeDB.selected, values=0, log_header=log_header
+        )
 
     return db_delete_nodes
 
@@ -120,7 +132,10 @@ def db_add_edges(self):
 
         # Batch the changes into a single call
         DB_handler.change_values(
-            indices=child_nodes, field=NodeDB.parent_id, values=parent_nodes
+            indices=child_nodes,
+            field=NodeDB.parent_id,
+            values=parent_nodes,
+            log_header="AddEdges:" + str(self.edges),
         )
 
     return db_add_edges
@@ -141,7 +156,12 @@ def db_delete_edges(self):
         child_nodes = [e[1] for e in self.edges]
 
         # Batch the changes into a single call
-        DB_handler.change_values(indices=child_nodes, field=NodeDB.parent_id, values=-1)
+        DB_handler.change_values(
+            indices=child_nodes,
+            field=NodeDB.parent_id,
+            values=-1,
+            log_header="DeleteEdges:" + str(self.edges),
+        )
 
     return db_delete_edges
 

trackedit/widgets/navigation/red_flag_box.py

@@ -69,6 +69,10 @@ def update_red_flags(self, *args):
             )
 
         self.update_red_flag_counter_and_info()
+        self.databasehandler.log(
+            f"Number of remaining red flags: {len(self.databasehandler.red_flags)}",
+            is_header=False,
+        )
 
     def _update_button_states(self):
         """Update the enabled state of navigation buttons based on red flag count."""