Refactoring v1 (#235)

* Strong refactoring, trying to disentangle imports from models views and controllers

* defractured mother controller slightly

* temporary fronzen. Issues with pandas > 3.0.0

* Added #238 back into code (lost due to merge conflict)

* Forgot to commit settings folder

Author: PaulJonasJost

src/petab_gui/controllers/file_io_controller.py

@@ -0,0 +1,342 @@
+"""Plot Coordinator for PEtab GUI.
+
+This module contains the PlotCoordinator class, which handles all plotting
+and selection synchronization operations, including:
+- Initializing and updating plot visualizations
+- Synchronizing selections between tables and plots
+- Handling plot point click interactions
+- Managing plot update debouncing
+"""
+
+from PySide6.QtCore import Qt, QTimer
+
+from ..utils import get_selected
+
+
+class PlotCoordinator:
+    """Coordinator for plotting and selection synchronization.
+
+    Manages the bidirectional synchronization between table selections and plot
+    highlights, handles plot interactions, and coordinates plot updates across
+    multiple data views.
+
+    Attributes
+    ----------
+    main : MainController
+        Reference to the main controller for access to models, views, and other controllers.
+    model : PEtabModel
+        The PEtab model being visualized.
+    view : MainWindow
+        The main application window.
+    logger : LoggerController
+        The logger for user feedback.
+    plotter : PlotDock
+        The plot widget for data visualization.
+    """
+
+    def __init__(self, main_controller):
+        """Initialize the PlotCoordinator.
+
+        Parameters
+        ----------
+        main_controller : MainController
+            The main controller instance.
+        """
+        self.main = main_controller
+        self.model = main_controller.model
+        self.view = main_controller.view
+        self.logger = main_controller.logger
+
+        # Plot widget reference (set by init_plotter)
+        self.plotter = None
+
+        # Selection synchronization flags to prevent redundant updates
+        self._updating_from_plot = False
+        self._updating_from_table = False
+
+        # Plot update timer for debouncing
+        self._plot_update_timer = QTimer()
+        self._plot_update_timer.setSingleShot(True)
+        self._plot_update_timer.setInterval(0)
+        self._plot_update_timer.timeout.connect(self.init_plotter)
+
+    def init_plotter(self):
+        """(Re-)initialize the plotter.
+
+        Sets up the plot widget with the current data models and configures
+        the click callback for interactive plot point selection.
+        """
+        self.view.plot_dock.initialize(
+            self.main.measurement_controller.proxy_model,
+            self.main.simulation_table_controller.proxy_model,
+            self.main.condition_controller.proxy_model,
+            self.main.visualization_controller.proxy_model,
+            self.model,
+        )
+        self.plotter = self.view.plot_dock
+        self.plotter.highlighter.click_callback = self._on_plot_point_clicked
+
+    def handle_selection_changed(self):
+        """Update the plot when selection in the measurement table changes.
+
+        This is a convenience method that delegates to update_plot().
+        """
+        self.update_plot()
+
+    def handle_data_changed(self, top_left, bottom_right, roles):
+        """Update the plot when the data in the measurement table changes.
+
+        Parameters
+        ----------
+        top_left : QModelIndex
+            Top-left index of the changed region.
+        bottom_right : QModelIndex
+            Bottom-right index of the changed region.
+        roles : list[int]
+            List of Qt item data roles that changed.
+        """
+        if not roles or Qt.DisplayRole in roles:
+            self.update_plot()
+
+    def update_plot(self):
+        """Update the plot with the selected measurement data.
+
+        Extracts the selected data points from the measurement table and
+        updates the plot visualization with this data. The plot shows all
+        data for the selected observables with the selected points highlighted.
+        """
+        selection_model = (
+            self.view.measurement_dock.table_view.selectionModel()
+        )
+        indexes = selection_model.selectedIndexes()
+        if not indexes:
+            return
+
+        selected_points = {}
+        for index in indexes:
+            if index.row() == self.model.measurement.get_df().shape[0]:
+                continue
+            row = index.row()
+            observable_id = self.model.measurement._data_frame.iloc[row][
+                "observableId"
+            ]
+            if observable_id not in selected_points:
+                selected_points[observable_id] = []
+            selected_points[observable_id].append(
+                {
+                    "x": self.model.measurement._data_frame.iloc[row]["time"],
+                    "y": self.model.measurement._data_frame.iloc[row][
+                        "measurement"
+                    ],
+                }
+            )
+        if selected_points == {}:
+            return
+
+        measurement_data = self.model.measurement._data_frame
+        plot_data = {"all_data": [], "selected_points": selected_points}
+        for observable_id in selected_points:
+            observable_data = measurement_data[
+                measurement_data["observableId"] == observable_id
+            ]
+            plot_data["all_data"].append(
+                {
+                    "observable_id": observable_id,
+                    "x": observable_data["time"].tolist(),
+                    "y": observable_data["measurement"].tolist(),
+                }
+            )
+
+        self.view.plot_dock.update_visualization(plot_data)
+
+    def _schedule_plot_update(self):
+        """Start the plot schedule timer.
+
+        Debounces plot updates by using a timer to avoid excessive redraws
+        when data changes rapidly.
+        """
+        self._plot_update_timer.start()
+
+    def _floats_match(self, a, b, epsilon=1e-9):
+        """Check if two floats match within epsilon tolerance.
+
+        Parameters
+        ----------
+        a : float
+            First value to compare.
+        b : float
+            Second value to compare.
+        epsilon : float, optional
+            Tolerance for comparison (default: 1e-9).
+
+        Returns
+        -------
+        bool
+            True if |a - b| < epsilon, False otherwise.
+        """
+        return abs(a - b) < epsilon
+
+    def _on_plot_point_clicked(self, x, y, label, data_type):
+        """Handle plot point clicks and select corresponding table row.
+
+        Uses epsilon tolerance for floating-point comparison to avoid
+        precision issues. Synchronizes the table selection with the clicked
+        plot point.
+
+        Parameters
+        ----------
+        x : float
+            X-coordinate of the clicked point (time).
+        y : float
+            Y-coordinate of the clicked point (measurement or simulation value).
+        label : str
+            Label of the clicked point (observable ID).
+        data_type : str
+            Type of data: "measurement" or "simulation".
+        """
+        # Check for None label
+        if label is None:
+            self.logger.log_message(
+                "Cannot select table row: plot point has no label.",
+                color="orange",
+            )
+            return
+
+        # Extract observable ID from label
+        proxy = self.main.measurement_controller.proxy_model
+        view = self.main.measurement_controller.view.table_view
+        if data_type == "simulation":
+            proxy = self.main.simulation_table_controller.proxy_model
+            view = self.main.simulation_table_controller.view.table_view
+        obs = label
+
+        x_axis_col = "time"
+        y_axis_col = data_type
+        observable_col = "observableId"
+
+        # Get column indices with error handling
+        def column_index(name):
+            for col in range(proxy.columnCount()):
+                if proxy.headerData(col, Qt.Horizontal) == name:
+                    return col
+            raise ValueError(f"Column '{name}' not found.")
+
+        try:
+            x_col = column_index(x_axis_col)
+            y_col = column_index(y_axis_col)
+            obs_col = column_index(observable_col)
+        except ValueError as e:
+            self.logger.log_message(
+                f"Table selection failed: {e}",
+                color="red",
+            )
+            return
+
+        # Search for matching row using epsilon tolerance for floats
+        matched = False
+        for row in range(proxy.rowCount()):
+            row_obs = proxy.index(row, obs_col).data()
+            row_x = proxy.index(row, x_col).data()
+            row_y = proxy.index(row, y_col).data()
+            try:
+                row_x, row_y = float(row_x), float(row_y)
+            except ValueError:
+                continue
+
+            # Use epsilon tolerance for float comparison
+            if (
+                row_obs == obs
+                and self._floats_match(row_x, x)
+                and self._floats_match(row_y, y)
+            ):
+                # Manually update highlight BEFORE selecting row
+                # This ensures the circle appears even though we skip the signal handler
+                if data_type == "measurement":
+                    self.plotter.highlight_from_selection([row])
+                else:
+                    self.plotter.highlight_from_selection(
+                        [row],
+                        proxy=self.main.simulation_table_controller.proxy_model,
+                        y_axis_col="simulation",
+                    )
+
+                # Set flag to prevent redundant highlight update from signal
+                self._updating_from_plot = True
+                try:
+                    view.selectRow(row)
+                    matched = True
+                finally:
+                    self._updating_from_plot = False
+                break
+
+        # Provide feedback if no match found
+        if not matched:
+            self.logger.log_message(
+                f"No matching row found for plot point (obs={obs}, x={x:.4g}, y={y:.4g})",
+                color="orange",
+            )
+
+    def _handle_table_selection_changed(
+        self, table_view, proxy=None, y_axis_col="measurement"
+    ):
+        """Common handler for table selection changes.
+
+        Skips update if selection was triggered by plot click to prevent
+        redundant highlight updates. Updates the plot highlights based on
+        the current table selection.
+
+        Parameters
+        ----------
+        table_view : QTableView
+            The table view with selection to highlight.
+        proxy : QSortFilterProxyModel, optional
+            Optional proxy model for simulation data.
+        y_axis_col : str, optional
+            Column name for y-axis data (default: "measurement").
+        """
+        # Skip if selection was triggered by plot point click
+        if self._updating_from_plot:
+            return
+
+        # Set flag to prevent infinite loop if highlight triggers selection
+        self._updating_from_table = True
+        try:
+            selected_rows = get_selected(table_view)
+            if proxy:
+                self.plotter.highlight_from_selection(
+                    selected_rows, proxy=proxy, y_axis_col=y_axis_col
+                )
+            else:
+                self.plotter.highlight_from_selection(selected_rows)
+        finally:
+            self._updating_from_table = False
+
+    def _on_table_selection_changed(self, selected, deselected):
+        """Highlight the cells selected in measurement table.
+
+        Parameters
+        ----------
+        selected : QItemSelection
+            The newly selected items.
+        deselected : QItemSelection
+            The newly deselected items.
+        """
+        self._handle_table_selection_changed(
+            self.main.measurement_controller.view.table_view
+        )
+
+    def _on_simulation_selection_changed(self, selected, deselected):
+        """Highlight the cells selected in simulation table.
+
+        Parameters
+        ----------
+        selected : QItemSelection
+            The newly selected items.
+        deselected : QItemSelection
+            The newly deselected items.
+        """
+        self._handle_table_selection_changed(
+            self.main.simulation_table_controller.view.table_view,
+            proxy=self.main.simulation_table_controller.proxy_model,
+            y_axis_col="simulation",
+        )

src/petab_gui/controllers/mother_controller.py

@@ -9,7 +9,7 @@
 
 from ..C import DEFAULT_ANTIMONY_TEXT
 from ..models.sbml_model import SbmlViewerModel
-from ..utils import sbmlToAntimony
+from ..models.sbml_utils import sbml_to_antimony
 from ..views.sbml_view import SbmlViewer
 
 
@@ -67,7 +67,7 @@ def reset_to_original_model(self):
         self.model.sbml_text = libsbml.writeSBMLToString(
             self.model._sbml_model_original.sbml_model.getSBMLDocument()
         )
-        self.model.antimony_text = sbmlToAntimony(self.model.sbml_text)
+        self.model.antimony_text = sbml_to_antimony(self.model.sbml_text)
         self.view.sbml_text_edit.setPlainText(self.model.sbml_text)
         self.view.antimony_text_edit.setPlainText(self.model.antimony_text)