Update Visualization Table on Changes (#197)

* Temporarily shut off plotting during data changes. Closes #192

* Rename yValues when observable is renamed

* Only check datatype for columns, not index. Fixes #180

* Make values redoable

* Aligning default values

Author: PaulJonasJost

src/petab_gui/commands.py

@@ -318,3 +318,46 @@ def _apply(self, src, dst):
         self.model.dataChanged.emit(
             self.model_index, self.model_index, [Qt.DisplayRole]
         )
+
+
+class RenameValueCommand(QUndoCommand):
+    """Command to rename values in specified columns."""
+
+    def __init__(
+        self, model, old_id: str, new_id: str, column_names: str | list[str]
+    ):
+        super().__init__(f"Rename value {old_id} → {new_id}")
+        self.model = model
+        self.old_id = old_id
+        self.new_id = new_id
+        self.column_names = (
+            column_names if isinstance(column_names, list) else [column_names]
+        )
+        self.changes = {}  # {(row_idx, col_name): (old_val, new_val)}
+
+        df = self.model._data_frame
+        for col_name in self.column_names:
+            mask = df[col_name].eq(self.old_id)
+            for row_idx in df.index[mask]:
+                self.changes[(row_idx, col_name)] = (self.old_id, self.new_id)
+
+    def redo(self):
+        self._apply_changes(use_new=True)
+
+    def undo(self):
+        self._apply_changes(use_new=False)
+
+    def _apply_changes(self, use_new: bool):
+        df = self.model._data_frame
+        for (row_idx, col_name), (old_val, new_val) in self.changes.items():
+            df.at[row_idx, col_name] = new_val if use_new else old_val
+
+        if self.changes:
+            rows = [df.index.get_loc(row) for (row, _) in self.changes]
+            cols = [df.columns.get_loc(col) + 1 for (_, col) in self.changes]
+            top_left = self.model.index(min(rows), min(cols))
+            bottom_right = self.model.index(max(rows), max(cols))
+            self.model.dataChanged.emit(
+                top_left, bottom_right, [Qt.DisplayRole, Qt.EditRole]
+            )
+            self.model.something_changed.emit(True)

src/petab_gui/controllers/default_handler.py

@@ -66,7 +66,9 @@ def get_default(
         default_value = column_config.get(DEFAULT_VALUE, "")
 
         if strategy == USE_DEFAULT:
-            if np.issubdtype(self.model.dtypes[column_name], np.floating):
+            if column_name != self.model.index.name and np.issubdtype(
+                self.model.dtypes[column_name], np.floating
+            ):
                 return float(default_value)
             return default_value
         if strategy == NO_DEFAULT:

src/petab_gui/controllers/mother_controller.py

@@ -155,11 +155,11 @@ def __init__(self, view, model: PEtabModel):
         self.actions = self.setup_actions()
         self.view.setup_toolbar(self.actions)
 
+        self.plotter = None
+        self.init_plotter()
         self.setup_connections()
         self.setup_task_bar()
         self.setup_context_menu()
-        self.plotter = None
-        self.init_plotter()
 
     @property
     def window_title(self):
@@ -194,6 +194,13 @@ def setup_connections(self):
                 column_names="observableId",
             )
         )
+        self.observable_controller.observable_2be_renamed.connect(
+            partial(
+                self.visualization_controller.rename_value,
+                column_names="yValues",
+            )
+        )
+        # Maybe TODO: add renaming dataset id?
         # Rename Condition
         self.condition_controller.condition_2be_renamed.connect(
             partial(
@@ -204,6 +211,13 @@ def setup_connections(self):
                 ],
             )
         )
+        # Plotting Disable Temporarily
+        for controller in self.controllers:
+            if controller == self.sbml_controller:
+                continue
+            controller.model.plotting_needs_break.connect(
+                self.plotter.disable_plotting
+            )
         # Add new condition or observable
         self.model.measurement.relevant_id_changed.connect(
             lambda x, y, z: self.observable_controller.maybe_add_observable(

src/petab_gui/controllers/table_controllers.py

@@ -18,6 +18,7 @@
 )
 
 from ..C import COLUMN, INDEX
+from ..commands import RenameValueCommand
 from ..models.pandas_table_model import (
     PandasTableFilterProxy,
     PandasTableModel,
@@ -588,6 +589,25 @@ def save_table(self, file_name):
                 f"Failed to save table: {str(e)}",
             )
 
+    def rename_value(
+        self, old_id: str, new_id: str, column_names: str | list[str]
+    ):
+        """Rename the values in the dataframe.
+
+        Triggered by changes in the original observable_df or condition_df id.
+
+        Parameters
+        ----------
+        old_id:
+            The old id, which was changed.
+        new_id:
+            The new id.
+        column_names:
+            The column or list of columns in which the id should be changed.
+        """
+        command = RenameValueCommand(self.model, old_id, new_id, column_names)
+        self.undo_stack.push(command)
+
 
 class MeasurementController(TableController):
     """Controller of the Measurement table."""
@@ -608,45 +628,6 @@ def check_petab_lint(
             observable_df=observable_df,
         )
 
-    def rename_value(
-        self, old_id: str, new_id: str, column_names: str | list[str]
-    ):
-        """Rename the values in the measurement_df.
-
-        Triggered by changes in the original observable_df or condition_df id.
-
-        Parameters
-        ----------
-        old_id:
-            The old id, which was changed.
-        new_id:
-            The new id.
-        """
-        if not isinstance(column_names, list):
-            column_names = [column_names]
-
-        for col_name in column_names:
-            # Find occurrences
-            mask = self.model._data_frame[col_name].eq(old_id)
-            if not mask.any():
-                continue
-
-            self.model._data_frame.loc[mask, col_name] = new_id
-            first_row, last_row = (
-                mask.idxmax(),
-                mask[::-1].idxmax(),
-            )
-            top_left = self.model.index(first_row, 1)
-            bottom_right = self.model.index(
-                last_row, self.model.columnCount() - 1
-            )
-            self.model.dataChanged.emit(
-                top_left, bottom_right, [Qt.DisplayRole, Qt.EditRole]
-            )
-
-            # Emit change signal
-            self.model.something_changed.emit(True)
-
     def copy_noise_parameters(
         self, observable_id: str, condition_id: str | None = None
     ) -> str:

src/petab_gui/models/pandas_table_model.py

@@ -45,6 +45,7 @@ class PandasTableModel(QAbstractTableModel):
     cell_needs_validation = Signal(int, int)  # row, column
     something_changed = Signal(bool)
     inserted_row = Signal(QModelIndex)
+    plotting_needs_break = Signal(bool)
 
     def __init__(
         self,
@@ -310,6 +311,7 @@ def setData(
 
         if is_invalid(value) or value == "":
             value = None
+        self.plotting_needs_break.emit(True)  # Temp disable plotting
         multi_row_change = False
         if check_multi:
             # check whether multiple rows but only one column is selected
@@ -318,13 +320,15 @@ def setData(
             self.undo_stack.beginMacro("Set data")
             success = self._set_data_single(index, value)
             self.undo_stack.endMacro()
+            self.plotting_needs_break.emit(False)
             return success
         # multiple rows but only one column is selected
         all_set = []
         self.undo_stack.beginMacro("Set data")
         for index in selected:
             all_set.append(self._set_data_single(index, value))
         self.undo_stack.endMacro()
+        self.plotting_needs_break.emit(False)
         return all(all_set)
 
     def _set_data_single(self, index, value):

src/petab_gui/settings_manager.py

@@ -286,7 +286,7 @@ def save_current_settings(self):
 
     def default_col_config(self):
         """Return default config for new columns."""
-        return {"strategy": NO_DEFAULT}
+        return settings_manager.get_table_defaults(self.table_name)
 
 
 class SettingsDialog(QDialog):
@@ -332,7 +332,8 @@ def init_general_page(self):
         # Header
         header = QLabel("<b>Profile</b>")
         desc = QLabel(
-            "These information can be automatically used when saving a COMBINE archive."
+            "These information can be automatically used when saving "
+            "a COMBINE archive."
         )
         desc.setWordWrap(True)
 

src/petab_gui/views/simple_plot_view.py

@@ -75,6 +75,7 @@ def __init__(self, parent=None):
         self.update_timer.setSingleShot(True)
         self.update_timer.timeout.connect(self.plot_it)
         self.observable_to_subplot = {}
+        self.no_plotting_rn = False
 
     def initialize(
         self, meas_proxy, sim_proxy, cond_proxy, vis_proxy, petab_model
@@ -104,6 +105,8 @@ def initialize(
         self.plot_it()
 
     def plot_it(self):
+        if self.no_plotting_rn:
+            return
         if not self.meas_proxy or not self.cond_proxy:
             return
         if not self.isVisible():
@@ -336,6 +339,12 @@ def plot_residuals(self):
         # fig_fit.tight_layout()
         create_plot_tab(fig_fit, self, "Goodness of Fit")
 
+    def disable_plotting(self, disable: bool):
+        """Set self.no_plotting_rn to enable/disable plotting."""
+        self.no_plotting_rn = disable
+        if not self.no_plotting_rn:
+            self._debounced_plot()
+
 
 class MeasurementHighlighter:
     def __init__(self):