Visualization cache (#224)

* More efficient dataframe creation from proxy model

* Dataframe caching, should reduce calls to proxy by ~50%

* Function for proxy connections + PEtab constants usage

* Update src/petab_gui/views/utils.py

* fixed problem with updating

Author: PaulJonasJost

src/petab_gui/views/main_view.py

@@ -126,16 +126,16 @@ def __init__(self):
 
         self.tab_widget.currentChanged.connect(self.set_docks_visible)
 
+        # Track if we're in a minimize/restore cycle (must be set before load_ui_settings)
+        self._was_minimized = False
+
         settings_manager.load_ui_settings(self)
 
         # drag drop
         self.setAcceptDrops(True)
 
         self.find_replace_bar = None
 
-        # Track if we're in a minimize/restore cycle
-        self._was_minimized = False
-
     def default_view(self):
         """Reset the view to a fixed 3x2 grid using manual geometry."""
         if hasattr(self, "dock_visibility"):

src/petab_gui/views/simple_plot_view.py

@@ -1,5 +1,6 @@
 from collections import defaultdict
 
+import petab.v1.C as PETAB_C
 import qtawesome as qta
 from matplotlib import pyplot as plt
 from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg as FigureCanvas
@@ -77,6 +78,42 @@ def __init__(self, parent=None):
         self.observable_to_subplot = {}
         self.no_plotting_rn = False
 
+        # DataFrame caching system for performance optimization
+        self._df_cache = {
+            "measurements": None,
+            "simulations": None,
+            "conditions": None,
+            "visualization": None,
+        }
+        self._cache_valid = {
+            "measurements": False,
+            "simulations": False,
+            "conditions": False,
+            "visualization": False,
+        }
+
+    def _invalidate_cache(self, table_name):
+        """Invalidate cache for specific table."""
+        self._cache_valid[table_name] = False
+
+    def _get_cached_df(self, table_name, proxy_model):
+        """Get cached DataFrame or convert if invalid."""
+        if not self._cache_valid[table_name]:
+            self._df_cache[table_name] = proxy_to_dataframe(proxy_model)
+            self._cache_valid[table_name] = True
+        return self._df_cache[table_name]
+
+    def _connect_proxy_signals(self, proxy, cache_key):
+        """Connect proxy signals for cache invalidation and plotting."""
+
+        def on_data_change(*args, **kwargs):
+            self._invalidate_cache(cache_key)
+            self._debounced_plot()
+
+        proxy.dataChanged.connect(on_data_change)
+        proxy.rowsInserted.connect(on_data_change)
+        proxy.rowsRemoved.connect(on_data_change)
+
     def initialize(
         self, meas_proxy, sim_proxy, cond_proxy, vis_proxy, petab_model
     ):
@@ -86,20 +123,19 @@ def initialize(
         self.vis_proxy = vis_proxy
         self.petab_model = petab_model
 
-        # Connect data changes
+        # Clear all cache when reinitializing
+        for key in self._cache_valid:
+            self._cache_valid[key] = False
+
+        # Connect cache invalidation and data changes
         self.options_manager.option_changed.connect(self._debounced_plot)
-        self.meas_proxy.dataChanged.connect(self._debounced_plot)
-        self.meas_proxy.rowsInserted.connect(self._debounced_plot)
-        self.meas_proxy.rowsRemoved.connect(self._debounced_plot)
-        self.cond_proxy.dataChanged.connect(self._debounced_plot)
-        self.cond_proxy.rowsInserted.connect(self._debounced_plot)
-        self.cond_proxy.rowsRemoved.connect(self._debounced_plot)
-        self.sim_proxy.dataChanged.connect(self._debounced_plot)
-        self.sim_proxy.rowsInserted.connect(self._debounced_plot)
-        self.sim_proxy.rowsRemoved.connect(self._debounced_plot)
-        self.vis_proxy.dataChanged.connect(self._debounced_plot)
-        self.vis_proxy.rowsInserted.connect(self._debounced_plot)
-        self.vis_proxy.rowsRemoved.connect(self._debounced_plot)
+
+        # Connect proxy signals for all tables
+        self._connect_proxy_signals(self.meas_proxy, "measurements")
+        self._connect_proxy_signals(self.cond_proxy, "conditions")
+        self._connect_proxy_signals(self.sim_proxy, "simulations")
+        self._connect_proxy_signals(self.vis_proxy, "visualization")
+
         self.visibilityChanged.connect(self._debounced_plot)
 
         self.plot_it()
@@ -113,10 +149,11 @@ def plot_it(self):
             # If the dock is not visible, do not plot
             return
 
-        measurements_df = proxy_to_dataframe(self.meas_proxy)
-        simulations_df = proxy_to_dataframe(self.sim_proxy)
-        conditions_df = proxy_to_dataframe(self.cond_proxy)
-        visualisation_df = proxy_to_dataframe(self.vis_proxy)
+        # Use cached DataFrames for performance
+        measurements_df = self._get_cached_df("measurements", self.meas_proxy)
+        simulations_df = self._get_cached_df("simulations", self.sim_proxy)
+        conditions_df = self._get_cached_df("conditions", self.cond_proxy)
+        visualisation_df = self._get_cached_df("visualization", self.vis_proxy)
         group_by = self.options_manager.get_option()
         # group_by different value in petab.visualize
         if group_by == "condition":
@@ -184,6 +221,9 @@ def _render_on_main_thread(self, payload):
         self._update_tabs(fig)
 
     def _update_tabs(self, fig: plt.Figure):
+        # Save current tab index before clearing
+        current_tab_index = self.tab_widget.currentIndex()
+
         # Clean previous tabs
         self.tab_widget.clear()
         # Clear Highlighter
@@ -295,15 +335,19 @@ def _update_tabs(self, fig: plt.Figure):
         # Plot residuals if necessary
         self.plot_residuals()
 
+        # Restore the previously selected tab (if valid)
+        if 0 <= current_tab_index < self.tab_widget.count():
+            self.tab_widget.setCurrentIndex(current_tab_index)
+
     def highlight_from_selection(
         self, selected_rows: list[int], proxy=None, y_axis_col="measurement"
     ):
         proxy = proxy or self.meas_proxy
         if not proxy:
             return
 
-        x_axis_col = "time"
-        observable_col = "observableId"
+        x_axis_col = PETAB_C.TIME
+        observable_col = PETAB_C.OBSERVABLE_ID
 
         def column_index(name):
             for col in range(proxy.columnCount()):
@@ -345,7 +389,8 @@ def plot_residuals(self):
             return
 
         problem = self.petab_model.current_petab_problem
-        simulations_df = proxy_to_dataframe(self.sim_proxy)
+        # Reuse cached DataFrame instead of converting again
+        simulations_df = self._get_cached_df("simulations", self.sim_proxy)
 
         if simulations_df.empty:
             return
@@ -521,8 +566,13 @@ def __init__(self, canvas, parent):
         self.addWidget(self.settings_btn)
 
     def update_checked_state(self, selected_option):
-        for action in self.groupy_by_options.values():
-            action.setChecked(action.text() == f"Groupy by {selected_option}")
+        for grp, action in self.groupy_by_options.items():
+            if grp == "vis_df":
+                action.setChecked(selected_option == "vis_df")
+            else:
+                action.setChecked(
+                    action.text() == f"Group by {selected_option}"
+                )
 
 
 def create_plot_tab(

src/petab_gui/views/utils.py

@@ -1,45 +1,64 @@
 import pandas as pd
+from petab.v1.C import (
+    CONDITION_ID,
+    MEASUREMENT,
+    OBSERVABLE_ID,
+    PARAMETER_ID,
+    SIMULATION,
+    TIME,
+    X_OFFSET,
+    Y_OFFSET,
+)
 from PySide6.QtCore import Qt
 
 
 def proxy_to_dataframe(proxy_model):
+    """Convert Proxy Model to pandas DataFrame."""
     rows = proxy_model.rowCount()
     cols = proxy_model.columnCount()
 
+    if rows <= 1:  # <=1 due to "New row..." in every table
+        return pd.DataFrame()
+
     headers = [proxy_model.headerData(c, Qt.Horizontal) for c in range(cols)]
-    data = []
 
+    data = []
     for r in range(rows - 1):
-        row = {headers[c]: proxy_model.index(r, c).data() for c in range(cols)}
-        for key, value in row.items():
-            if isinstance(value, str) and value == "":
-                row[key] = None
+        row = []
+        for c in range(cols):
+            value = proxy_model.index(r, c).data()
+            # Convert empty strings to None
+            row.append(
+                None if (isinstance(value, str) and value == "") else value
+            )
         data.append(row)
+
     if not data:
         return pd.DataFrame()
-    if proxy_model.source_model.table_type == "condition":
-        data = pd.DataFrame(data).set_index("conditionId")
-    elif proxy_model.source_model.table_type == "observable":
-        data = pd.DataFrame(data).set_index("observableId")
-    elif proxy_model.source_model.table_type == "parameter":
-        data = pd.DataFrame(data).set_index("parameterId")
-    elif proxy_model.source_model.table_type == "measurement":
-        # turn measurement and time to float
-        data = pd.DataFrame(data)
-        data["measurement"] = data["measurement"].astype(float)
-        data["time"] = data["time"].astype(float)
-    elif proxy_model.source_model.table_type == "simulation":
-        # turn simulation and time to float
-        data = pd.DataFrame(data)
-        data["simulation"] = data["simulation"].astype(float)
-        data["time"] = data["time"].astype(float)
-    elif proxy_model.source_model.table_type == "visualization":
-        data = pd.DataFrame(data)
-        if "xOffset" in data.columns:
-            data["xOffset"] = data["xOffset"].astype(float)
-        if "yOffset" in data.columns:
-            data["yOffset"] = data["yOffset"].astype(float)
-    else:
-        data = pd.DataFrame(data)
-
-    return data
+
+    # Create DataFrame in one shot
+    df = pd.DataFrame(data, columns=headers)
+
+    # Apply type-specific transformations
+    table_type = proxy_model.source_model.table_type
+
+    if table_type == "condition":
+        df = df.set_index(CONDITION_ID)
+    elif table_type == "observable":
+        df = df.set_index(OBSERVABLE_ID)
+    elif table_type == "parameter":
+        df = df.set_index(PARAMETER_ID)
+    elif table_type == "measurement":
+        # Use pd.to_numeric with errors='coerce' for robust conversion
+        df[MEASUREMENT] = pd.to_numeric(df[MEASUREMENT], errors="coerce")
+        df[TIME] = pd.to_numeric(df[TIME], errors="coerce")
+    elif table_type == "simulation":
+        df[SIMULATION] = pd.to_numeric(df[SIMULATION], errors="coerce")
+        df[TIME] = pd.to_numeric(df[TIME], errors="coerce")
+    elif table_type == "visualization":
+        if X_OFFSET in df.columns:
+            df[X_OFFSET] = pd.to_numeric(df[X_OFFSET], errors="coerce")
+        if Y_OFFSET in df.columns:
+            df[Y_OFFSET] = pd.to_numeric(df[Y_OFFSET], errors="coerce")
+
+    return df