From 341da3ceb13a35a42f9a0a3c603a473f1100bb8b Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Mon, 26 Jan 2026 14:47:19 +0100
Subject: [PATCH 01/12] plot control in Experiment and Analysis

---
 .../Backends/Mock/Plotting.qml                |  42 ++++
 .../Backends/Py/plotting_1d.py                | 189 ++++++++++++++++--
 .../Gui/Globals/BackendWrapper.qml            |  25 +++
 .../Analysis/MainContent/AnalysisView.qml     |  18 ++
 .../Analysis/MainContent/CombinedView.qml     |  18 ++
 .../Sidebar/Advanced/Groups/PlotControl.qml   |  50 +++++
 .../Analysis/Sidebar/Advanced/Layout.qml      |   2 +
 .../Gui/Pages/Experiment/Layout.qml           |   8 +-
 .../Experiment/MainContent/ExperimentView.qml |  18 ++
 .../Sidebar/Advanced/Groups/PlotControl.qml   |  50 +++++
 .../Experiment/Sidebar/Advanced/Layout.qml    |  17 ++
 .../Pages/Sample/MainContent/CombinedView.qml |  12 ++
 .../Pages/Sample/MainContent/SampleView.qml   |  12 ++
 .../Sidebar/Advanced/Groups/PlotControl.qml   |  10 +
 14 files changed, 450 insertions(+), 21 deletions(-)
 create mode 100644 EasyReflectometryApp/Gui/Pages/Analysis/Sidebar/Advanced/Groups/PlotControl.qml
 create mode 100644 EasyReflectometryApp/Gui/Pages/Experiment/Sidebar/Advanced/Groups/PlotControl.qml
 create mode 100644 EasyReflectometryApp/Gui/Pages/Experiment/Sidebar/Advanced/Layout.qml

diff --git a/EasyReflectometryApp/Backends/Mock/Plotting.qml b/EasyReflectometryApp/Backends/Mock/Plotting.qml
index 537eb221..ea36965f 100644
--- a/EasyReflectometryApp/Backends/Mock/Plotting.qml
+++ b/EasyReflectometryApp/Backends/Mock/Plotting.qml
@@ -23,6 +23,20 @@ QtObject {
 
     property int modelCount: 1
 
+    // Plot mode properties
+    property bool plotRQ4: false
+    property string yMainAxisTitle: 'R(q)'
+    property bool xAxisLog: false
+    property string xAxisType: 'linear'
+    property bool sldXDataReversed: false
+    property bool scaleShown: false
+    property bool bkgShown: false
+
+    // Signals for plot mode changes
+    signal plotModeChanged()
+    signal axisTypeChanged()
+    signal sldAxisReversedChanged()
+    signal referenceLineVisibilityChanged()
     signal samplePageDataChanged()
 
     function setQtChartsSerieRef(value1, value2, value3) {
@@ -52,4 +66,32 @@ QtObject {
         return '#0000FF'
     }
 
+    // Plot mode toggle functions
+    function togglePlotRQ4() {
+        plotRQ4 = !plotRQ4
+        yMainAxisTitle = plotRQ4 ? 'R(q)×q⁴' : 'R(q)'
+        plotModeChanged()
+    }
+
+    function toggleXAxisType() {
+        xAxisLog = !xAxisLog
+        xAxisType = xAxisLog ? 'log' : 'linear'
+        axisTypeChanged()
+    }
+
+    function reverseSldXData() {
+        sldXDataReversed = !sldXDataReversed
+        sldAxisReversedChanged()
+    }
+
+    function flipScaleShown() {
+        scaleShown = !scaleShown
+        referenceLineVisibilityChanged()
+    }
+
+    function flipBkgShown() {
+        bkgShown = !bkgShown
+        referenceLineVisibilityChanged()
+    }
+
 }
diff --git a/EasyReflectometryApp/Backends/Py/plotting_1d.py b/EasyReflectometryApp/Backends/Py/plotting_1d.py
index e06fdf6a..72ef0204 100644
--- a/EasyReflectometryApp/Backends/Py/plotting_1d.py
+++ b/EasyReflectometryApp/Backends/Py/plotting_1d.py
@@ -20,6 +20,12 @@ class Plotting1d(QObject):
     experimentDataChanged = Signal()
     samplePageDataChanged = Signal()  # Signal for QML to refresh sample page charts
 
+    # New signals for plot mode properties
+    plotModeChanged = Signal()
+    axisTypeChanged = Signal()
+    sldAxisReversedChanged = Signal()
+    referenceLineVisibilityChanged = Signal()
+
     def __init__(self, project_lib: ProjectLib, parent=None):
         super().__init__(parent)
         self._project_lib = project_lib
@@ -27,6 +33,13 @@ def __init__(self, project_lib: ProjectLib, parent=None):
         self._currentLib1d = 'QtCharts'
         self._sample_data = {}
         self._sld_data = {}
+
+        # Plot mode state
+        self._plot_rq4 = False
+        self._x_axis_log = False
+        self._sld_x_reversed = False
+        self._scale_shown = False
+        self._bkg_shown = False
         self._chartRefs = {
             'QtCharts': {
                 'samplePage': {
@@ -51,6 +64,80 @@ def reset_data(self):
         self._sld_data = {}
         console.debug(IO.formatMsg('sub', 'Sample and SLD data cleared'))
 
+    # R(q)×q⁴ mode
+    @Property(bool, notify=plotModeChanged)
+    def plotRQ4(self) -> bool:
+        """Return whether R(q)×q⁴ mode is enabled."""
+        return self._plot_rq4
+
+    @Slot()
+    def togglePlotRQ4(self) -> None:
+        """Toggle R(q)×q⁴ plotting mode."""
+        self._plot_rq4 = not self._plot_rq4
+        self.plotModeChanged.emit()
+        # Refresh all charts with new mode
+        self.sampleChartRangesChanged.emit()
+        self.experimentChartRangesChanged.emit()
+        self.samplePageDataChanged.emit()
+
+    @Property(str, notify=plotModeChanged)
+    def yMainAxisTitle(self) -> str:
+        """Return Y-axis title based on current plot mode."""
+        return 'R(q)×q⁴' if self._plot_rq4 else 'R(q)'
+
+    # X-axis type (log/linear)
+    @Property(bool, notify=axisTypeChanged)
+    def xAxisLog(self) -> bool:
+        """Return whether X-axis is logarithmic."""
+        return self._x_axis_log
+
+    @Slot()
+    def toggleXAxisType(self) -> None:
+        """Toggle between linear and logarithmic X-axis."""
+        self._x_axis_log = not self._x_axis_log
+        self.axisTypeChanged.emit()
+
+    @Property(str, notify=axisTypeChanged)
+    def xAxisType(self) -> str:
+        """Return X-axis type as string for QML."""
+        return 'log' if self._x_axis_log else 'linear'
+
+    # SLD X-axis reversal
+    @Property(bool, notify=sldAxisReversedChanged)
+    def sldXDataReversed(self) -> bool:
+        """Return whether SLD X-axis is reversed."""
+        return self._sld_x_reversed
+
+    @Slot()
+    def reverseSldXData(self) -> None:
+        """Toggle SLD X-axis reversal."""
+        self._sld_x_reversed = not self._sld_x_reversed
+        self.sldAxisReversedChanged.emit()
+        self.sldChartRangesChanged.emit()
+
+    # Reference line visibility
+    @Property(bool, notify=referenceLineVisibilityChanged)
+    def scaleShown(self) -> bool:
+        """Return whether scale reference line is shown."""
+        return self._scale_shown
+
+    @Slot()
+    def flipScaleShown(self) -> None:
+        """Toggle scale line visibility."""
+        self._scale_shown = not self._scale_shown
+        self.referenceLineVisibilityChanged.emit()
+
+    @Property(bool, notify=referenceLineVisibilityChanged)
+    def bkgShown(self) -> bool:
+        """Return whether background reference line is shown."""
+        return self._bkg_shown
+
+    @Slot()
+    def flipBkgShown(self) -> None:
+        """Toggle background line visibility."""
+        self._bkg_shown = not self._bkg_shown
+        self.referenceLineVisibilityChanged.emit()
+
     @property
     def sample_data(self) -> DataSet1D:
         idx = self._project_lib.current_model_index
@@ -154,8 +241,13 @@ def _get_all_models_sample_range(self):
                     min_x = min(min_x, data.x.min())
                     max_x = max(max_x, data.x.max())
                 if data.y.size > 0:
-                    valid_y = data.y[data.y > 0]
+                    valid_mask = data.y > 0
+                    valid_y = data.y[valid_mask]
+                    valid_x = data.x[valid_mask]
                     if valid_y.size > 0:
+                        # Apply R×q⁴ transformation if enabled
+                        if self._plot_rq4:
+                            valid_y = valid_y * (valid_x**4)
                         min_y = min(min_y, np.log10(valid_y.min()))
                         max_y = max(max_y, np.log10(valid_y.max()))
             except (IndexError, ValueError):
@@ -233,13 +325,25 @@ def experimentMinX(self):
     @Property(float, notify=experimentChartRangesChanged)
     def experimentMaxY(self):
         data = self.experiment_data
-        return np.log10(data.y.max()) if data.y.size > 0 else 1.0
+        if data.y.size == 0:
+            return 1.0
+        y_values = data.y
+        # Apply R×q⁴ transformation if enabled
+        if self._plot_rq4:
+            y_values = y_values * (data.x**4)
+        return np.log10(y_values.max())
 
     @Property(float, notify=experimentChartRangesChanged)
     def experimentMinY(self):
         data = self.experiment_data
         valid_y = data.y[data.y > 0] if data.y.size > 0 else np.array([1e-10])
-        return np.log10(valid_y.min()) if valid_y.size > 0 else -10.0
+        if valid_y.size == 0:
+            return -10.0
+        # Apply R×q⁴ transformation if enabled
+        if self._plot_rq4:
+            valid_x = data.x[data.y > 0] if data.y.size > 0 else np.array([1.0])
+            valid_y = valid_y * (valid_x**4)
+        return np.log10(valid_y.min())
 
     @Property('QVariant', notify=chartRefsChanged)
     def chartRefs(self):
@@ -284,7 +388,13 @@ def getSampleDataPointsForModel(self, model_index: int) -> list:
             data = self._project_lib.sample_data_for_model_at_index(model_index)
             points = []
             for point in data.data_points():
-                points.append({'x': float(point[0]), 'y': float(np.log10(point[1])) if point[1] > 0 else -10.0})
+                x_val = float(point[0])
+                y_val = float(point[1])
+                # Apply R×q⁴ transformation if enabled
+                if self._plot_rq4 and y_val > 0:
+                    y_val = y_val * (x_val**4)
+                y_log = float(np.log10(y_val)) if y_val > 0 else -10.0
+                points.append({'x': x_val, 'y': y_log})
             return points
         except Exception as e:
             console.debug(f'Error getting sample data points for model {model_index}: {e}')
@@ -324,12 +434,25 @@ def getExperimentDataPoints(self, experiment_index: int) -> list:
             points = []
             for point in data.data_points():
                 if point[0] < self._project_lib.q_max and self._project_lib.q_min < point[0]:
+                    q = point[0]
+                    r = point[1]
+                    error_var = point[2]
+                    # Apply R×q⁴ transformation if enabled
+                    if self._plot_rq4:
+                        q4 = q**4
+                        r_val = r * q4
+                        error_upper = (r + np.sqrt(error_var)) * q4
+                        error_lower = max((r - np.sqrt(error_var)) * q4, 1e-10)
+                    else:
+                        r_val = r
+                        error_upper = r + np.sqrt(error_var)
+                        error_lower = max(r - np.sqrt(error_var), 1e-10)
                     points.append(
                         {
-                            'x': float(point[0]),
-                            'y': float(np.log10(point[1])),
-                            'errorUpper': float(np.log10(point[1] + np.sqrt(point[2]))),
-                            'errorLower': float(np.log10(max(point[1] - np.sqrt(point[2]), 1e-10))),  # Avoid log(0)
+                            'x': float(q),
+                            'y': float(np.log10(r_val)),
+                            'errorUpper': float(np.log10(error_upper)),
+                            'errorLower': float(np.log10(error_lower)),
                         }
                     )
             return points
@@ -373,11 +496,18 @@ def getAnalysisDataPoints(self, experiment_index: int) -> list:
             calc_idx = 0
             for point in exp_points:
                 if point[0] < self._project_lib.q_max and self._project_lib.q_min < point[0]:
-                    calc_y_val = calc_y[calc_idx] if calc_idx < len(calc_y) else point[1]
+                    q = point[0]
+                    r_meas = point[1]
+                    calc_y_val = calc_y[calc_idx] if calc_idx < len(calc_y) else r_meas
+                    # Apply R×q⁴ transformation if enabled
+                    if self._plot_rq4:
+                        q4 = q**4
+                        r_meas = r_meas * q4
+                        calc_y_val = calc_y_val * q4
                     points.append(
                         {
-                            'x': float(point[0]),
-                            'measured': float(np.log10(point[1])),
+                            'x': float(q),
+                            'measured': float(np.log10(r_meas)),
                             'calculated': float(np.log10(calc_y_val)),
                         }
                     )
@@ -446,6 +576,7 @@ def qtchartsReplaceCalculatedOnSldChartAndRedraw(self):
                 nr_points = nr_points + 1
             console.debug(IO.formatMsg('sub', 'Sld curve', f'{nr_points} points', 'on analysis page', 'replaced'))
 
+    @Slot()
     def drawMeasuredOnExperimentChart(self):
         if PLOT_BACKEND == 'QtCharts':
             if self.is_multi_experiment_mode:
@@ -463,9 +594,22 @@ def qtchartsReplaceMeasuredOnExperimentChartAndRedraw(self):
         nr_points = 0
         for point in self.experiment_data.data_points():
             if point[0] < self._project_lib.q_max and self._project_lib.q_min < point[0]:
-                series_measured.append(point[0], np.log10(point[1]))
-                series_error_upper.append(point[0], np.log10(point[1] + np.sqrt(point[2])))
-                series_error_lower.append(point[0], np.log10(max(point[1] - np.sqrt(point[2]), 1e-10)))
+                q = point[0]
+                r = point[1]
+                error_var = point[2]
+                # Apply R×q⁴ transformation if enabled
+                if self._plot_rq4:
+                    q4 = q**4
+                    r_val = r * q4
+                    error_upper = (r + np.sqrt(error_var)) * q4
+                    error_lower = max((r - np.sqrt(error_var)) * q4, 1e-10)
+                else:
+                    r_val = r
+                    error_upper = r + np.sqrt(error_var)
+                    error_lower = max(r - np.sqrt(error_var), 1e-10)
+                series_measured.append(q, np.log10(r_val))
+                series_error_upper.append(q, np.log10(error_upper))
+                series_error_lower.append(q, np.log10(error_lower))
                 nr_points = nr_points + 1
 
         console.debug(IO.formatMsg('sub', 'Measured curve', f'{nr_points} points', 'on experiment page', 'replaced'))
@@ -486,6 +630,7 @@ def qtchartsReplaceMultiExperimentChartAndRedraw(self):
         # This method is called to trigger the refresh, actual drawing is handled by QML
         self.experimentDataChanged.emit()
 
+    @Slot()
     def drawCalculatedAndMeasuredOnAnalysisChart(self):
         if PLOT_BACKEND == 'QtCharts':
             if self.is_multi_experiment_mode:
@@ -515,11 +660,21 @@ def qtchartsReplaceCalculatedAndMeasuredOnAnalysisChartAndRedraw(self):
         nr_points = 0
         for point in self.experiment_data.data_points():
             if point[0] < self._project_lib.q_max and self._project_lib.q_min < point[0]:
-                series_measured.append(point[0], np.log10(point[1]))
+                q = point[0]
+                r_meas = point[1]
+                # Apply R×q⁴ transformation if enabled
+                if self._plot_rq4:
+                    r_meas = r_meas * (q**4)
+                series_measured.append(q, np.log10(r_meas))
                 nr_points = nr_points + 1
-        console.debug(IO.formatMsg('sub', 'Measurede curve', f'{nr_points} points', 'on analysis page', 'replaced'))
+        console.debug(IO.formatMsg('sub', 'Measured curve', f'{nr_points} points', 'on analysis page', 'replaced'))
 
         for point in self.sample_data.data_points():
-            series_calculated.append(point[0], np.log10(point[1]))
+            q = point[0]
+            r_calc = point[1]
+            # Apply R×q⁴ transformation if enabled
+            if self._plot_rq4:
+                r_calc = r_calc * (q**4)
+            series_calculated.append(q, np.log10(r_calc))
             nr_points = nr_points + 1
         console.debug(IO.formatMsg('sub', 'Calculated curve', f'{nr_points} points', 'on analysis page', 'replaced'))
diff --git a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
index 15e23f18..ea468040 100644
--- a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
+++ b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
@@ -328,9 +328,29 @@ QtObject {
     readonly property var plottingAnalysisMaxY: activeBackend.plotting.sampleMaxY
     readonly property var calcSerieColor: activeBackend.plotting.calcSerieColor
 
+    // Plot mode properties
+    readonly property bool plottingPlotRQ4: activeBackend.plotting.plotRQ4
+    readonly property string plottingYAxisTitle: activeBackend.plotting.yMainAxisTitle
+    readonly property bool plottingXAxisLog: activeBackend.plotting.xAxisLog
+    readonly property string plottingXAxisType: activeBackend.plotting.xAxisType
+    readonly property bool plottingSldXReversed: activeBackend.plotting.sldXDataReversed
+
+    // Reference line visibility
+    readonly property bool plottingScaleShown: activeBackend.plotting.scaleShown
+    readonly property bool plottingBkgShown: activeBackend.plotting.bkgShown
+
+    // Plot mode toggle functions
+    function plottingTogglePlotRQ4() { activeBackend.plotting.togglePlotRQ4() }
+    function plottingToggleXAxisType() { activeBackend.plotting.toggleXAxisType() }
+    function plottingReverseSldXData() { activeBackend.plotting.reverseSldXData() }
+    function plottingFlipScaleShown() { activeBackend.plotting.flipScaleShown() }
+    function plottingFlipBkgShown() { activeBackend.plotting.flipBkgShown() }
+
     function plottingSetQtChartsSerieRef(value1, value2, value3) { activeBackend.plotting.setQtChartsSerieRef(value1, value2, value3) }
     function plottingRefreshSample() { activeBackend.plotting.drawCalculatedOnSampleChart() }
     function plottingRefreshSLD() { activeBackend.plotting.drawCalculatedOnSldChart() }
+    function plottingRefreshExperiment() { activeBackend.plotting.drawMeasuredOnExperimentChart() }
+    function plottingRefreshAnalysis() { activeBackend.plotting.drawCalculatedAndMeasuredOnAnalysisChart() }
 
     // Multi-model sample page plotting support
     readonly property int plottingModelCount: activeBackend.plotting.modelCount
@@ -358,12 +378,17 @@ QtObject {
 
     // Signal for sample page data changes - forward from backend
     signal samplePageDataChanged()
+    // Signal for plot mode changes - forward from backend
+    signal plotModeChanged()
 
     // Connect to backend signal (called from Component.onCompleted in QML items)
     function connectSamplePageDataChanged() {
         if (activeBackend && activeBackend.plotting && activeBackend.plotting.samplePageDataChanged) {
             activeBackend.plotting.samplePageDataChanged.connect(samplePageDataChanged)
         }
+        if (activeBackend && activeBackend.plotting && activeBackend.plotting.plotModeChanged) {
+            activeBackend.plotting.plotModeChanged.connect(plotModeChanged)
+        }
     }
 
     Component.onCompleted: {
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
index 0baf81cd..e7c53da5 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
@@ -55,6 +55,24 @@ Rectangle {
                 chartView.updateMultiExperimentSeries()
             }
         }
+
+        // Watch for plot mode changes (R(q)×q⁴ toggle)
+        Connections {
+            target: Globals.BackendWrapper
+            function onPlotModeChanged() {
+                console.debug("AnalysisView: Plot mode changed, refreshing chart")
+                Globals.BackendWrapper.plottingRefreshAnalysis()
+                // Delay resetAxes to allow axis range properties to update first
+                analysisResetAxesTimer.start()
+            }
+        }
+
+        Timer {
+            id: analysisResetAxesTimer
+            interval: 50
+            repeat: false
+            onTriggered: chartView.resetAxes()
+        }
         
         property double xRange: Globals.BackendWrapper.plottingAnalysisMaxX - Globals.BackendWrapper.plottingAnalysisMinX
         axisX.title: "q (Å⁻¹)"
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
index 305fe01c..6bc9357b 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
@@ -69,6 +69,24 @@ Rectangle {
                     }
                 }
 
+                // Watch for plot mode changes (R(q)×q⁴ toggle)
+                Connections {
+                    target: Globals.BackendWrapper
+                    function onPlotModeChanged() {
+                        console.debug("CombinedView Analysis: Plot mode changed, refreshing chart")
+                        Globals.BackendWrapper.plottingRefreshAnalysis()
+                        // Delay resetAxes to allow axis range properties to update first
+                        combinedAnalysisResetAxesTimer.start()
+                    }
+                }
+
+                Timer {
+                    id: combinedAnalysisResetAxesTimer
+                    interval: 50
+                    repeat: false
+                    onTriggered: analysisChartView.resetAxes()
+                }
+
                 // Multi-experiment series management
                 function updateMultiExperimentSeries() {
                     // Always get the latest value from backend
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/Sidebar/Advanced/Groups/PlotControl.qml b/EasyReflectometryApp/Gui/Pages/Analysis/Sidebar/Advanced/Groups/PlotControl.qml
new file mode 100644
index 00000000..0b2e0ce2
--- /dev/null
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/Sidebar/Advanced/Groups/PlotControl.qml
@@ -0,0 +1,50 @@
+// SPDX-FileCopyrightText: 2025 EasyReflectometry contributors <support@easyreflectometry.org>
+// SPDX-License-Identifier: BSD-3-Clause
+// © 2025 Contributors to the EasyReflectometry project <https://github.com/easyscience/EasyReflectometry>
+
+import QtQuick
+import QtQuick.Controls
+
+import EasyApp.Gui.Style as EaStyle
+import EasyApp.Gui.Elements as EaElements
+
+import Gui.Globals as Globals
+
+EaElements.GroupBox {
+    title: qsTr("Plot control")
+    collapsed: true
+
+    Column {
+        spacing: EaStyle.Sizes.fontPixelSize * 0.5
+
+        EaElements.CheckBox {
+            topPadding: 0
+            checked: Globals.BackendWrapper.plottingPlotRQ4
+            text: qsTr("Plot R(q)×q⁴")
+            ToolTip.text: qsTr("Checking this box will plot R(q) multiplied by q⁴")
+            onToggled: {
+                Globals.BackendWrapper.plottingTogglePlotRQ4()
+            }
+        }
+
+        EaElements.CheckBox {
+            topPadding: 0
+            checked: Globals.BackendWrapper.plottingScaleShown
+            text: qsTr("Show scale line")
+            ToolTip.text: qsTr("Checking this box will show the scale reference line on the plot")
+            onToggled: {
+                Globals.BackendWrapper.plottingFlipScaleShown()
+            }
+        }
+
+        EaElements.CheckBox {
+            topPadding: 0
+            checked: Globals.BackendWrapper.plottingBkgShown
+            text: qsTr("Show background line")
+            ToolTip.text: qsTr("Checking this box will show the background reference line on the plot")
+            onToggled: {
+                Globals.BackendWrapper.plottingFlipBkgShown()
+            }
+        }
+    }
+}
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/Sidebar/Advanced/Layout.qml b/EasyReflectometryApp/Gui/Pages/Analysis/Sidebar/Advanced/Layout.qml
index 2571f4d9..deeee520 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/Sidebar/Advanced/Layout.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/Sidebar/Advanced/Layout.qml
@@ -17,4 +17,6 @@ EaComponents.SideBarColumn {
     Groups.Calculator {}
 
     Groups.Minimizer {}
+
+    Groups.PlotControl {}
 }
diff --git a/EasyReflectometryApp/Gui/Pages/Experiment/Layout.qml b/EasyReflectometryApp/Gui/Pages/Experiment/Layout.qml
index f56ede8a..7c6f1c87 100644
--- a/EasyReflectometryApp/Gui/Pages/Experiment/Layout.qml
+++ b/EasyReflectometryApp/Gui/Pages/Experiment/Layout.qml
@@ -22,13 +22,13 @@ EaComponents.ContentPage {
 
     sideBar: EaComponents.SideBar {
         tabs: [
-            EaElements.TabButton { text: qsTr('Basic controls') }
-//            EaElements.TabButton { text: qsTr('Advanced controls') }
+            EaElements.TabButton { text: qsTr('Basic controls') },
+            EaElements.TabButton { text: qsTr('Advanced controls') }
         ]
 
         items: [
-            Loader { source: 'Sidebar/Basic/Layout.qml' }
- //           Loader { source: 'Sidebar/Advanced/Layout.qml' }
+            Loader { source: 'Sidebar/Basic/Layout.qml' },
+            Loader { source: 'Sidebar/Advanced/Layout.qml' }
         ]
 
         continueButton.text: qsTr('Continue') 
diff --git a/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml b/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
index 905dc7c9..03c069c3 100644
--- a/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
@@ -145,6 +145,24 @@ Rectangle {
                 chartView.updateMultiExperimentSeries()
             }
         }
+
+        // Watch for plot mode changes (R(q)×q⁴ toggle)
+        Connections {
+            target: Globals.BackendWrapper
+            function onPlotModeChanged() {
+                console.debug("ExperimentView: Plot mode changed, refreshing chart")
+                Globals.BackendWrapper.plottingRefreshExperiment()
+                // Delay resetAxes to allow axis range properties to update first
+                experimentResetAxesTimer.start()
+            }
+        }
+
+        Timer {
+            id: experimentResetAxesTimer
+            interval: 50
+            repeat: false
+            onTriggered: chartView.resetAxes()
+        }
         
         property double xRange: Globals.BackendWrapper.plottingExperimentMaxX - Globals.BackendWrapper.plottingExperimentMinX
         axisX.title: "q (Å⁻¹)"
diff --git a/EasyReflectometryApp/Gui/Pages/Experiment/Sidebar/Advanced/Groups/PlotControl.qml b/EasyReflectometryApp/Gui/Pages/Experiment/Sidebar/Advanced/Groups/PlotControl.qml
new file mode 100644
index 00000000..0b2e0ce2
--- /dev/null
+++ b/EasyReflectometryApp/Gui/Pages/Experiment/Sidebar/Advanced/Groups/PlotControl.qml
@@ -0,0 +1,50 @@
+// SPDX-FileCopyrightText: 2025 EasyReflectometry contributors <support@easyreflectometry.org>
+// SPDX-License-Identifier: BSD-3-Clause
+// © 2025 Contributors to the EasyReflectometry project <https://github.com/easyscience/EasyReflectometry>
+
+import QtQuick
+import QtQuick.Controls
+
+import EasyApp.Gui.Style as EaStyle
+import EasyApp.Gui.Elements as EaElements
+
+import Gui.Globals as Globals
+
+EaElements.GroupBox {
+    title: qsTr("Plot control")
+    collapsed: true
+
+    Column {
+        spacing: EaStyle.Sizes.fontPixelSize * 0.5
+
+        EaElements.CheckBox {
+            topPadding: 0
+            checked: Globals.BackendWrapper.plottingPlotRQ4
+            text: qsTr("Plot R(q)×q⁴")
+            ToolTip.text: qsTr("Checking this box will plot R(q) multiplied by q⁴")
+            onToggled: {
+                Globals.BackendWrapper.plottingTogglePlotRQ4()
+            }
+        }
+
+        EaElements.CheckBox {
+            topPadding: 0
+            checked: Globals.BackendWrapper.plottingScaleShown
+            text: qsTr("Show scale line")
+            ToolTip.text: qsTr("Checking this box will show the scale reference line on the plot")
+            onToggled: {
+                Globals.BackendWrapper.plottingFlipScaleShown()
+            }
+        }
+
+        EaElements.CheckBox {
+            topPadding: 0
+            checked: Globals.BackendWrapper.plottingBkgShown
+            text: qsTr("Show background line")
+            ToolTip.text: qsTr("Checking this box will show the background reference line on the plot")
+            onToggled: {
+                Globals.BackendWrapper.plottingFlipBkgShown()
+            }
+        }
+    }
+}
diff --git a/EasyReflectometryApp/Gui/Pages/Experiment/Sidebar/Advanced/Layout.qml b/EasyReflectometryApp/Gui/Pages/Experiment/Sidebar/Advanced/Layout.qml
new file mode 100644
index 00000000..600ca675
--- /dev/null
+++ b/EasyReflectometryApp/Gui/Pages/Experiment/Sidebar/Advanced/Layout.qml
@@ -0,0 +1,17 @@
+// SPDX-FileCopyrightText: 2025 EasyReflectometry contributors <support@easyreflectometry.org>
+// SPDX-License-Identifier: BSD-3-Clause
+// © 2025 Contributors to the EasyReflectometry project <https://github.com/easyscience/EasyReflectometry>
+
+import QtQuick
+
+import EasyApp.Gui.Elements as EaElements
+import EasyApp.Gui.Components as EaComponents
+
+import "./Groups" as Groups
+
+
+EaComponents.SideBarColumn {
+
+    Groups.PlotControl {}
+
+}
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml
index fb2f6d4e..e05c715c 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml
@@ -591,6 +591,18 @@ Rectangle {
         function onSamplePageDataChanged() {
             refreshAllCharts()
         }
+        function onPlotModeChanged() {
+            refreshAllCharts()
+            // Delay resetAxes to allow axis range properties to update first
+            sampleCombinedResetAxesTimer.start()
+        }
+    }
+
+    Timer {
+        id: sampleCombinedResetAxesTimer
+        interval: 50
+        repeat: false
+        onTriggered: sampleChartView.resetAxes()
     }
 
     Component.onCompleted: {
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml
index 01645bfa..70bb4fff 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml
@@ -347,6 +347,18 @@ Rectangle {
         function onSamplePageDataChanged() {
             refreshAllCharts()
         }
+        function onPlotModeChanged() {
+            refreshAllCharts()
+            // Delay resetAxes to allow axis range properties to update first
+            sampleResetAxesTimer.start()
+        }
+    }
+
+    Timer {
+        id: sampleResetAxesTimer
+        interval: 50
+        repeat: false
+        onTriggered: chartView.resetAxes()
     }
 
     Component.onCompleted: {
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Advanced/Groups/PlotControl.qml b/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Advanced/Groups/PlotControl.qml
index f7d77177..b448193c 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Advanced/Groups/PlotControl.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Advanced/Groups/PlotControl.qml
@@ -17,6 +17,16 @@ EaElements.GroupBox {
     Column {
         spacing: EaStyle.Sizes.fontPixelSize * 0.5
 
+        EaElements.CheckBox {
+            topPadding: 0
+            checked: Globals.BackendWrapper.plottingPlotRQ4
+            text: qsTr("Plot R(q)×q⁴")
+            ToolTip.text: qsTr("Checking this box will plot R(q) multiplied by q⁴")
+            onToggled: {
+                Globals.BackendWrapper.plottingTogglePlotRQ4()
+            }
+        }
+
         EaElements.CheckBox {
             topPadding: 0
             checked: Globals.Variables.reverseSldZAxis

From 0cedef69856bb2db7a8ffabfb066f29f0c1085e1 Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Mon, 26 Jan 2026 17:04:05 +0100
Subject: [PATCH 02/12] added scale/bg lines to exp and analysis plots

---
 .../Backends/Mock/Plotting.qml                | 19 +++++
 .../Backends/Py/plotting_1d.py                | 69 +++++++++++++++++++
 .../Gui/Globals/BackendWrapper.qml            | 16 +++++
 .../Analysis/MainContent/AnalysisView.qml     | 58 ++++++++++++++++
 .../Analysis/MainContent/CombinedView.qml     | 55 +++++++++++++++
 .../Experiment/MainContent/ExperimentView.qml | 58 ++++++++++++++++
 6 files changed, 275 insertions(+)

diff --git a/EasyReflectometryApp/Backends/Mock/Plotting.qml b/EasyReflectometryApp/Backends/Mock/Plotting.qml
index ea36965f..d973b572 100644
--- a/EasyReflectometryApp/Backends/Mock/Plotting.qml
+++ b/EasyReflectometryApp/Backends/Mock/Plotting.qml
@@ -94,4 +94,23 @@ QtObject {
         referenceLineVisibilityChanged()
     }
 
+    // Reference line data accessors (mock implementation)
+    function getBackgroundData() {
+        if (!bkgShown) return []
+        // Return mock horizontal line at background level
+        return [
+            { 'x': 0.01, 'y': -7.0 },
+            { 'x': 0.30, 'y': -7.0 }
+        ]
+    }
+
+    function getScaleData() {
+        if (!scaleShown) return []
+        // Return mock horizontal line at scale level (log10(1.0) = 0)
+        return [
+            { 'x': 0.01, 'y': 0.0 },
+            { 'x': 0.30, 'y': 0.0 }
+        ]
+    }
+
 }
diff --git a/EasyReflectometryApp/Backends/Py/plotting_1d.py b/EasyReflectometryApp/Backends/Py/plotting_1d.py
index 72ef0204..d7b60588 100644
--- a/EasyReflectometryApp/Backends/Py/plotting_1d.py
+++ b/EasyReflectometryApp/Backends/Py/plotting_1d.py
@@ -138,6 +138,75 @@ def flipBkgShown(self) -> None:
         self._bkg_shown = not self._bkg_shown
         self.referenceLineVisibilityChanged.emit()
 
+    @Slot(result='QVariantList')
+    def getBackgroundData(self) -> list:
+        """Return background reference line data for plotting.
+
+        Returns a horizontal line at the model's background value.
+        """
+        if not self._bkg_shown:
+            return []
+        try:
+            model = self._project_lib.models[self._project_lib.current_model_index]
+            exp_data = self._project_lib.experimental_data_for_model_at_index(self._project_lib.current_experiment_index)
+            if exp_data.x is None or len(exp_data.x) == 0:
+                return []
+            x = exp_data.x
+            bkg_value = model.background.value
+            # For log scale plotting, convert background value
+            bkg_log = float(np.log10(bkg_value)) if bkg_value > 0 else -10.0
+            # Apply R×q⁴ transformation if enabled
+            if self._plot_rq4:
+                # For background, we need to transform: bkg * q^4
+                return [
+                    {'x': float(x[0]), 'y': float(np.log10(bkg_value * x[0] ** 4)) if bkg_value * x[0] ** 4 > 0 else -10.0},
+                    {'x': float(x[-1]), 'y': float(np.log10(bkg_value * x[-1] ** 4)) if bkg_value * x[-1] ** 4 > 0 else -10.0},
+                ]
+            else:
+                return [{'x': float(x[0]), 'y': bkg_log}, {'x': float(x[-1]), 'y': bkg_log}]
+        except (IndexError, AttributeError, TypeError) as e:
+            console.debug(f'Error getting background data: {e}')
+            return []
+
+    @Slot(result='QVariantList')
+    def getScaleData(self) -> list:
+        """Return scale reference line data for plotting.
+
+        Returns a horizontal line at the model's scale value.
+        Note: Scale is a multiplicative factor, typically close to 1.0.
+        For reflectometry plots, the scale line at y=scale (log10) shows
+        where R=scale, i.e., where the reflectivity equals the scale factor.
+        """
+        if not self._scale_shown:
+            return []
+        try:
+            model = self._project_lib.models[self._project_lib.current_model_index]
+            exp_data = self._project_lib.experimental_data_for_model_at_index(self._project_lib.current_experiment_index)
+            if exp_data.x is None or len(exp_data.x) == 0:
+                return []
+            x = exp_data.x
+            scale_value = model.scale.value
+            # For log scale plotting, convert scale value
+            scale_log = float(np.log10(scale_value)) if scale_value > 0 else 0.0
+            # Apply R×q⁴ transformation if enabled
+            if self._plot_rq4:
+                # For scale, we need to transform: scale * q^4
+                return [
+                    {
+                        'x': float(x[0]),
+                        'y': float(np.log10(scale_value * x[0] ** 4)) if scale_value * x[0] ** 4 > 0 else -10.0,
+                    },
+                    {
+                        'x': float(x[-1]),
+                        'y': float(np.log10(scale_value * x[-1] ** 4)) if scale_value * x[-1] ** 4 > 0 else -10.0,
+                    },
+                ]
+            else:
+                return [{'x': float(x[0]), 'y': scale_log}, {'x': float(x[-1]), 'y': scale_log}]
+        except (IndexError, AttributeError, TypeError) as e:
+            console.debug(f'Error getting scale data: {e}')
+            return []
+
     @property
     def sample_data(self) -> DataSet1D:
         idx = self._project_lib.current_model_index
diff --git a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
index ea468040..189e6573 100644
--- a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
+++ b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
@@ -346,6 +346,22 @@ QtObject {
     function plottingFlipScaleShown() { activeBackend.plotting.flipScaleShown() }
     function plottingFlipBkgShown() { activeBackend.plotting.flipBkgShown() }
 
+    // Reference line data accessors
+    function plottingGetBackgroundData() {
+        try {
+            return activeBackend.plotting.getBackgroundData()
+        } catch (e) {
+            return []
+        }
+    }
+    function plottingGetScaleData() {
+        try {
+            return activeBackend.plotting.getScaleData()
+        } catch (e) {
+            return []
+        }
+    }
+
     function plottingSetQtChartsSerieRef(value1, value2, value3) { activeBackend.plotting.setQtChartsSerieRef(value1, value2, value3) }
     function plottingRefreshSample() { activeBackend.plotting.drawCalculatedOnSampleChart() }
     function plottingRefreshSLD() { activeBackend.plotting.drawCalculatedOnSldChart() }
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
index e7c53da5..cb11a5ff 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
@@ -31,6 +31,58 @@ Rectangle {
 
         useOpenGL: EaGlobals.Vars.useOpenGL
 
+        // Background reference line series
+        LineSeries {
+            id: backgroundRefLine
+            axisX: chartView.axisX
+            axisY: chartView.axisY
+            useOpenGL: chartView.useOpenGL
+            color: "#888888"
+            width: 1
+            style: Qt.DashLine
+            visible: Globals.BackendWrapper.plottingBkgShown
+        }
+
+        // Scale reference line series
+        LineSeries {
+            id: scaleRefLine
+            axisX: chartView.axisX
+            axisY: chartView.axisY
+            useOpenGL: chartView.useOpenGL
+            color: "#666666"
+            width: 1
+            style: Qt.DotLine
+            visible: Globals.BackendWrapper.plottingScaleShown
+        }
+
+        // Update reference lines when visibility changes
+        Connections {
+            target: Globals.BackendWrapper.activeBackend.plotting
+            function onReferenceLineVisibilityChanged() {
+                chartView.updateReferenceLines()
+            }
+        }
+
+        function updateReferenceLines() {
+            // Update background line
+            backgroundRefLine.clear()
+            if (Globals.BackendWrapper.plottingBkgShown) {
+                var bkgData = Globals.BackendWrapper.plottingGetBackgroundData()
+                for (var i = 0; i < bkgData.length; i++) {
+                    backgroundRefLine.append(bkgData[i].x, bkgData[i].y)
+                }
+            }
+
+            // Update scale line
+            scaleRefLine.clear()
+            if (Globals.BackendWrapper.plottingScaleShown) {
+                var scaleData = Globals.BackendWrapper.plottingGetScaleData()
+                for (var j = 0; j < scaleData.length; j++) {
+                    scaleRefLine.append(scaleData[j].x, scaleData[j].y)
+                }
+            }
+        }
+
         // Multi-experiment support
         property var multiExperimentSeries: []
         property bool isMultiExperimentMode: {
@@ -382,6 +434,9 @@ Rectangle {
 
             // Initialize multi-experiment support
             updateMultiExperimentSeries()
+            
+            // Initialize reference lines
+            updateReferenceLines()
         }
 
         // Update series when chart becomes visible
@@ -389,6 +444,9 @@ Rectangle {
             if (visible && isMultiExperimentMode) {
                 updateMultiExperimentSeries()
             }
+            if (visible) {
+                updateReferenceLines()
+            }
         }
     }
 
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
index 6bc9357b..3c93b205 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
@@ -87,6 +87,58 @@ Rectangle {
                     onTriggered: analysisChartView.resetAxes()
                 }
 
+                // Background reference line series
+                LineSeries {
+                    id: backgroundRefLine
+                    axisX: analysisChartView.axisX
+                    axisY: analysisChartView.axisY
+                    useOpenGL: analysisChartView.useOpenGL
+                    color: "#888888"
+                    width: 1
+                    style: Qt.DashLine
+                    visible: Globals.BackendWrapper.plottingBkgShown
+                }
+
+                // Scale reference line series
+                LineSeries {
+                    id: scaleRefLine
+                    axisX: analysisChartView.axisX
+                    axisY: analysisChartView.axisY
+                    useOpenGL: analysisChartView.useOpenGL
+                    color: "#666666"
+                    width: 1
+                    style: Qt.DotLine
+                    visible: Globals.BackendWrapper.plottingScaleShown
+                }
+
+                // Update reference lines when visibility changes
+                Connections {
+                    target: Globals.BackendWrapper.activeBackend.plotting
+                    function onReferenceLineVisibilityChanged() {
+                        analysisChartView.updateReferenceLines()
+                    }
+                }
+
+                function updateReferenceLines() {
+                    // Update background line
+                    backgroundRefLine.clear()
+                    if (Globals.BackendWrapper.plottingBkgShown) {
+                        var bkgData = Globals.BackendWrapper.plottingGetBackgroundData()
+                        for (var i = 0; i < bkgData.length; i++) {
+                            backgroundRefLine.append(bkgData[i].x, bkgData[i].y)
+                        }
+                    }
+
+                    // Update scale line
+                    scaleRefLine.clear()
+                    if (Globals.BackendWrapper.plottingScaleShown) {
+                        var scaleData = Globals.BackendWrapper.plottingGetScaleData()
+                        for (var j = 0; j < scaleData.length; j++) {
+                            scaleRefLine.append(scaleData[j].x, scaleData[j].y)
+                        }
+                    }
+                }
+
                 // Multi-experiment series management
                 function updateMultiExperimentSeries() {
                     // Always get the latest value from backend
@@ -399,6 +451,9 @@ Rectangle {
 
                     // Initialize multi-experiment support
                     updateMultiExperimentSeries()
+                    
+                    // Initialize reference lines
+                    updateReferenceLines()
                 }
             }
         }
diff --git a/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml b/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
index 03c069c3..dc0dc9a7 100644
--- a/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
@@ -32,6 +32,58 @@ Rectangle {
 
         useOpenGL: EaGlobals.Vars.useOpenGL
 
+        // Background reference line series
+        LineSeries {
+            id: backgroundRefLine
+            axisX: chartView.axisX
+            axisY: chartView.axisY
+            useOpenGL: chartView.useOpenGL
+            color: "#888888"
+            width: 1
+            style: Qt.DashLine
+            visible: Globals.BackendWrapper.plottingBkgShown
+        }
+
+        // Scale reference line series
+        LineSeries {
+            id: scaleRefLine
+            axisX: chartView.axisX
+            axisY: chartView.axisY
+            useOpenGL: chartView.useOpenGL
+            color: "#666666"
+            width: 1
+            style: Qt.DotLine
+            visible: Globals.BackendWrapper.plottingScaleShown
+        }
+
+        // Update reference lines when visibility changes
+        Connections {
+            target: Globals.BackendWrapper.activeBackend.plotting
+            function onReferenceLineVisibilityChanged() {
+                chartView.updateReferenceLines()
+            }
+        }
+
+        function updateReferenceLines() {
+            // Update background line
+            backgroundRefLine.clear()
+            if (Globals.BackendWrapper.plottingBkgShown) {
+                var bkgData = Globals.BackendWrapper.plottingGetBackgroundData()
+                for (var i = 0; i < bkgData.length; i++) {
+                    backgroundRefLine.append(bkgData[i].x, bkgData[i].y)
+                }
+            }
+
+            // Update scale line
+            scaleRefLine.clear()
+            if (Globals.BackendWrapper.plottingScaleShown) {
+                var scaleData = Globals.BackendWrapper.plottingGetScaleData()
+                for (var j = 0; j < scaleData.length; j++) {
+                    scaleRefLine.append(scaleData[j].x, scaleData[j].y)
+                }
+            }
+        }
+
         // Multi-experiment support
         property var multiExperimentSeries: []
         property bool isMultiExperimentMode: {
@@ -509,6 +561,9 @@ Rectangle {
             // Initialize multi-experiment support
             // console.log("ExperimentView initialized - checking multi-experiment mode...")
             updateMultiExperimentSeries()
+
+            // Initialize reference lines
+            updateReferenceLines()
         }
 
         // Update series when chart becomes visible
@@ -516,6 +571,9 @@ Rectangle {
             if (visible && isMultiExperimentMode) {
                 updateMultiExperimentSeries()
             }
+            if (visible) {
+                updateReferenceLines()
+            }
         }
     }
 

From a8c88c6985c4e8e95be491041c823ab8566ad5eb Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Mon, 26 Jan 2026 17:24:00 +0100
Subject: [PATCH 03/12] Y axis label fix

---
 .../Gui/Pages/Analysis/MainContent/AnalysisView.qml             | 2 +-
 .../Gui/Pages/Analysis/MainContent/CombinedView.qml             | 2 +-
 .../Gui/Pages/Experiment/MainContent/ExperimentView.qml         | 2 +-
 .../Gui/Pages/Sample/MainContent/CombinedView.qml               | 2 +-
 .../Gui/Pages/Sample/MainContent/SampleView.qml                 | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
index cb11a5ff..c453d75d 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
@@ -134,7 +134,7 @@ Rectangle {
         axisX.maxAfterReset: Globals.BackendWrapper.plottingAnalysisMaxX + xRange * 0.01
 
         property double yRange: Globals.BackendWrapper.plottingAnalysisMaxY - Globals.BackendWrapper.plottingAnalysisMinY
-        axisY.title: "Log10 R(q)"
+        axisY.title: "Log10 " + Globals.BackendWrapper.plottingYAxisTitle
         axisY.min: Globals.BackendWrapper.plottingAnalysisMinY - yRange * 0.01
         axisY.max: Globals.BackendWrapper.plottingAnalysisMaxY + yRange * 0.01
         axisY.minAfterReset: Globals.BackendWrapper.plottingAnalysisMinY - yRange * 0.01
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
index 3c93b205..44dc438b 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
@@ -253,7 +253,7 @@ Rectangle {
                 axisX.maxAfterReset: Globals.BackendWrapper.plottingAnalysisMaxX + xRange * 0.01
 
                 property double yRange: Globals.BackendWrapper.plottingAnalysisMaxY - Globals.BackendWrapper.plottingAnalysisMinY
-                axisY.title: "Log10 R(q)"
+                axisY.title: "Log10 " + Globals.BackendWrapper.plottingYAxisTitle
                 axisY.min: Globals.BackendWrapper.plottingAnalysisMinY - yRange * 0.01
                 axisY.max: Globals.BackendWrapper.plottingAnalysisMaxY + yRange * 0.01
                 axisY.minAfterReset: Globals.BackendWrapper.plottingAnalysisMinY - yRange * 0.01
diff --git a/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml b/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
index dc0dc9a7..a2a5f9ac 100644
--- a/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
@@ -224,7 +224,7 @@ Rectangle {
         axisX.maxAfterReset: Globals.BackendWrapper.plottingExperimentMaxX + xRange * 0.01
 
         property double yRange: Globals.BackendWrapper.plottingExperimentMaxY - Globals.BackendWrapper.plottingExperimentMinY
-        axisY.title: "Log10 R(q)"
+        axisY.title: "Log10 " + Globals.BackendWrapper.plottingYAxisTitle
         axisY.min: Globals.BackendWrapper.plottingExperimentMinY - yRange * 0.01
         axisY.max: Globals.BackendWrapper.plottingExperimentMaxY + yRange * 0.01
         axisY.minAfterReset: Globals.BackendWrapper.plottingExperimentMinY - yRange * 0.01
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml
index e05c715c..257d6b6f 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml
@@ -101,7 +101,7 @@ Rectangle {
 
                 ValueAxis {
                     id: sampleAxisY
-                    titleText: "Log10 R(q)"
+                    titleText: "Log10 " + Globals.BackendWrapper.plottingYAxisTitle
                     // min/max set imperatively to avoid binding reset during zoom
                     property double minAfterReset: Globals.BackendWrapper.plottingSampleMinY - sampleChartView.yRange * 0.01
                     property double maxAfterReset: Globals.BackendWrapper.plottingSampleMaxY + sampleChartView.yRange * 0.01
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml
index 70bb4fff..8bed9517 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml
@@ -87,7 +87,7 @@ Rectangle {
 
         ValueAxis {
             id: axisY
-            titleText: "Log10 R(q)"
+            titleText: "Log10 " + Globals.BackendWrapper.plottingYAxisTitle
             // min/max set imperatively to avoid binding reset during zoom
             property double minAfterReset: Globals.BackendWrapper.plottingSampleMinY - chartView.yRange * 0.01
             property double maxAfterReset: Globals.BackendWrapper.plottingSampleMaxY + chartView.yRange * 0.01

From b981817d2296999b8e43f03e0dee52001c0eecbc Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Tue, 27 Jan 2026 15:57:58 +0100
Subject: [PATCH 04/12] fixed profile lines.

---
 .../Backends/Mock/Plotting.qml                | 19 +++++
 .../Backends/Py/plotting_1d.py                | 80 +++++++++++++------
 .../Gui/Globals/BackendWrapper.qml            | 16 ++++
 .../Analysis/MainContent/AnalysisView.qml     |  8 +-
 .../Analysis/MainContent/CombinedView.qml     |  8 +-
 5 files changed, 99 insertions(+), 32 deletions(-)

diff --git a/EasyReflectometryApp/Backends/Mock/Plotting.qml b/EasyReflectometryApp/Backends/Mock/Plotting.qml
index d973b572..ff856611 100644
--- a/EasyReflectometryApp/Backends/Mock/Plotting.qml
+++ b/EasyReflectometryApp/Backends/Mock/Plotting.qml
@@ -113,4 +113,23 @@ QtObject {
         ]
     }
 
+    // Analysis-specific reference line data accessors (use sample/calculated x-range)
+    function getBackgroundDataForAnalysis() {
+        if (!bkgShown) return []
+        // Return mock horizontal line at background level using sample x-range
+        return [
+            { 'x': sampleMinX, 'y': -7.0 },
+            { 'x': sampleMaxX, 'y': -7.0 }
+        ]
+    }
+
+    function getScaleDataForAnalysis() {
+        if (!scaleShown) return []
+        // Return mock horizontal line at scale level using sample x-range
+        return [
+            { 'x': sampleMinX, 'y': 0.0 },
+            { 'x': sampleMaxX, 'y': 0.0 }
+        ]
+    }
+
 }
diff --git a/EasyReflectometryApp/Backends/Py/plotting_1d.py b/EasyReflectometryApp/Backends/Py/plotting_1d.py
index d7b60588..aae4c810 100644
--- a/EasyReflectometryApp/Backends/Py/plotting_1d.py
+++ b/EasyReflectometryApp/Backends/Py/plotting_1d.py
@@ -143,6 +143,7 @@ def getBackgroundData(self) -> list:
         """Return background reference line data for plotting.
 
         Returns a horizontal line at the model's background value.
+        Note: Reference lines are always horizontal, even in R×q⁴ mode.
         """
         if not self._bkg_shown:
             return []
@@ -155,15 +156,8 @@ def getBackgroundData(self) -> list:
             bkg_value = model.background.value
             # For log scale plotting, convert background value
             bkg_log = float(np.log10(bkg_value)) if bkg_value > 0 else -10.0
-            # Apply R×q⁴ transformation if enabled
-            if self._plot_rq4:
-                # For background, we need to transform: bkg * q^4
-                return [
-                    {'x': float(x[0]), 'y': float(np.log10(bkg_value * x[0] ** 4)) if bkg_value * x[0] ** 4 > 0 else -10.0},
-                    {'x': float(x[-1]), 'y': float(np.log10(bkg_value * x[-1] ** 4)) if bkg_value * x[-1] ** 4 > 0 else -10.0},
-                ]
-            else:
-                return [{'x': float(x[0]), 'y': bkg_log}, {'x': float(x[-1]), 'y': bkg_log}]
+            # Reference lines are always horizontal (no R×q⁴ transformation)
+            return [{'x': float(x[0]), 'y': bkg_log}, {'x': float(x[-1]), 'y': bkg_log}]
         except (IndexError, AttributeError, TypeError) as e:
             console.debug(f'Error getting background data: {e}')
             return []
@@ -176,6 +170,7 @@ def getScaleData(self) -> list:
         Note: Scale is a multiplicative factor, typically close to 1.0.
         For reflectometry plots, the scale line at y=scale (log10) shows
         where R=scale, i.e., where the reflectivity equals the scale factor.
+        Reference lines are always horizontal, even in R×q⁴ mode.
         """
         if not self._scale_shown:
             return []
@@ -188,25 +183,62 @@ def getScaleData(self) -> list:
             scale_value = model.scale.value
             # For log scale plotting, convert scale value
             scale_log = float(np.log10(scale_value)) if scale_value > 0 else 0.0
-            # Apply R×q⁴ transformation if enabled
-            if self._plot_rq4:
-                # For scale, we need to transform: scale * q^4
-                return [
-                    {
-                        'x': float(x[0]),
-                        'y': float(np.log10(scale_value * x[0] ** 4)) if scale_value * x[0] ** 4 > 0 else -10.0,
-                    },
-                    {
-                        'x': float(x[-1]),
-                        'y': float(np.log10(scale_value * x[-1] ** 4)) if scale_value * x[-1] ** 4 > 0 else -10.0,
-                    },
-                ]
-            else:
-                return [{'x': float(x[0]), 'y': scale_log}, {'x': float(x[-1]), 'y': scale_log}]
+            # Reference lines are always horizontal (no R×q⁴ transformation)
+            return [{'x': float(x[0]), 'y': scale_log}, {'x': float(x[-1]), 'y': scale_log}]
         except (IndexError, AttributeError, TypeError) as e:
             console.debug(f'Error getting scale data: {e}')
             return []
 
+    @Slot(result='QVariantList')
+    def getBackgroundDataForAnalysis(self) -> list:
+        """Return background reference line data for the Analysis chart.
+
+        Uses the analysis/sample x-range (calculated model data range) instead of
+        experimental data range to ensure the line spans the full chart width.
+        Reference lines are always horizontal, even in R×q⁴ mode.
+        """
+        if not self._bkg_shown:
+            return []
+        try:
+            model = self._project_lib.models[self._project_lib.current_model_index]
+            # Use sample/analysis x-range instead of experimental data
+            x_min, x_max = self._get_all_models_sample_range()[0:2]
+            if x_min == float('inf') or x_max == float('-inf'):
+                return []
+            bkg_value = model.background.value
+            # For log scale plotting, convert background value
+            bkg_log = float(np.log10(bkg_value)) if bkg_value > 0 else -10.0
+            # Reference lines are always horizontal (no R×q⁴ transformation)
+            return [{'x': float(x_min), 'y': bkg_log}, {'x': float(x_max), 'y': bkg_log}]
+        except (IndexError, AttributeError, TypeError) as e:
+            console.debug(f'Error getting background data for analysis: {e}')
+            return []
+
+    @Slot(result='QVariantList')
+    def getScaleDataForAnalysis(self) -> list:
+        """Return scale reference line data for the Analysis chart.
+
+        Uses the analysis/sample x-range (calculated model data range) instead of
+        experimental data range to ensure the line spans the full chart width.
+        Reference lines are always horizontal, even in R×q⁴ mode.
+        """
+        if not self._scale_shown:
+            return []
+        try:
+            model = self._project_lib.models[self._project_lib.current_model_index]
+            # Use sample/analysis x-range instead of experimental data
+            x_min, x_max = self._get_all_models_sample_range()[0:2]
+            if x_min == float('inf') or x_max == float('-inf'):
+                return []
+            scale_value = model.scale.value
+            # For log scale plotting, convert scale value
+            scale_log = float(np.log10(scale_value)) if scale_value > 0 else 0.0
+            # Reference lines are always horizontal (no R×q⁴ transformation)
+            return [{'x': float(x_min), 'y': scale_log}, {'x': float(x_max), 'y': scale_log}]
+        except (IndexError, AttributeError, TypeError) as e:
+            console.debug(f'Error getting scale data for analysis: {e}')
+            return []
+
     @property
     def sample_data(self) -> DataSet1D:
         idx = self._project_lib.current_model_index
diff --git a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
index 189e6573..0da30766 100644
--- a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
+++ b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
@@ -362,6 +362,22 @@ QtObject {
         }
     }
 
+    // Analysis-specific reference line data accessors (use sample/calculated x-range)
+    function plottingGetBackgroundDataForAnalysis() {
+        try {
+            return activeBackend.plotting.getBackgroundDataForAnalysis()
+        } catch (e) {
+            return []
+        }
+    }
+    function plottingGetScaleDataForAnalysis() {
+        try {
+            return activeBackend.plotting.getScaleDataForAnalysis()
+        } catch (e) {
+            return []
+        }
+    }
+
     function plottingSetQtChartsSerieRef(value1, value2, value3) { activeBackend.plotting.setQtChartsSerieRef(value1, value2, value3) }
     function plottingRefreshSample() { activeBackend.plotting.drawCalculatedOnSampleChart() }
     function plottingRefreshSLD() { activeBackend.plotting.drawCalculatedOnSldChart() }
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
index c453d75d..212ff3cf 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
@@ -64,19 +64,19 @@ Rectangle {
         }
 
         function updateReferenceLines() {
-            // Update background line
+            // Update background line (use analysis-specific method for correct x-range)
             backgroundRefLine.clear()
             if (Globals.BackendWrapper.plottingBkgShown) {
-                var bkgData = Globals.BackendWrapper.plottingGetBackgroundData()
+                var bkgData = Globals.BackendWrapper.plottingGetBackgroundDataForAnalysis()
                 for (var i = 0; i < bkgData.length; i++) {
                     backgroundRefLine.append(bkgData[i].x, bkgData[i].y)
                 }
             }
 
-            // Update scale line
+            // Update scale line (use analysis-specific method for correct x-range)
             scaleRefLine.clear()
             if (Globals.BackendWrapper.plottingScaleShown) {
-                var scaleData = Globals.BackendWrapper.plottingGetScaleData()
+                var scaleData = Globals.BackendWrapper.plottingGetScaleDataForAnalysis()
                 for (var j = 0; j < scaleData.length; j++) {
                     scaleRefLine.append(scaleData[j].x, scaleData[j].y)
                 }
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
index 44dc438b..52e5940d 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
@@ -120,19 +120,19 @@ Rectangle {
                 }
 
                 function updateReferenceLines() {
-                    // Update background line
+                    // Update background line (use analysis-specific method for correct x-range)
                     backgroundRefLine.clear()
                     if (Globals.BackendWrapper.plottingBkgShown) {
-                        var bkgData = Globals.BackendWrapper.plottingGetBackgroundData()
+                        var bkgData = Globals.BackendWrapper.plottingGetBackgroundDataForAnalysis()
                         for (var i = 0; i < bkgData.length; i++) {
                             backgroundRefLine.append(bkgData[i].x, bkgData[i].y)
                         }
                     }
 
-                    // Update scale line
+                    // Update scale line (use analysis-specific method for correct x-range)
                     scaleRefLine.clear()
                     if (Globals.BackendWrapper.plottingScaleShown) {
-                        var scaleData = Globals.BackendWrapper.plottingGetScaleData()
+                        var scaleData = Globals.BackendWrapper.plottingGetScaleDataForAnalysis()
                         for (var j = 0; j < scaleData.length; j++) {
                             scaleRefLine.append(scaleData[j].x, scaleData[j].y)
                         }

From abd0201fd371ad906f5d0f134147cd0c6b709841 Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Tue, 27 Jan 2026 21:54:56 +0100
Subject: [PATCH 05/12] code review fixes

---
 .../Backends/Py/plotting_1d.py                | 38 ++++++++++++++-----
 .../Analysis/MainContent/AnalysisView.qml     |  6 ++-
 .../Analysis/MainContent/CombinedView.qml     |  6 ++-
 .../Experiment/MainContent/ExperimentView.qml |  6 ++-
 4 files changed, 40 insertions(+), 16 deletions(-)

diff --git a/EasyReflectometryApp/Backends/Py/plotting_1d.py b/EasyReflectometryApp/Backends/Py/plotting_1d.py
index aae4c810..84d6852b 100644
--- a/EasyReflectometryApp/Backends/Py/plotting_1d.py
+++ b/EasyReflectometryApp/Backends/Py/plotting_1d.py
@@ -148,8 +148,11 @@ def getBackgroundData(self) -> list:
         if not self._bkg_shown:
             return []
         try:
-            model = self._project_lib.models[self._project_lib.current_model_index]
-            exp_data = self._project_lib.experimental_data_for_model_at_index(self._project_lib.current_experiment_index)
+            # Capture indices atomically to prevent race conditions
+            model_idx = self._project_lib.current_model_index
+            exp_idx = self._project_lib.current_experiment_index
+            model = self._project_lib.models[model_idx]
+            exp_data = self._project_lib.experimental_data_for_model_at_index(exp_idx)
             if exp_data.x is None or len(exp_data.x) == 0:
                 return []
             x = exp_data.x
@@ -175,8 +178,11 @@ def getScaleData(self) -> list:
         if not self._scale_shown:
             return []
         try:
-            model = self._project_lib.models[self._project_lib.current_model_index]
-            exp_data = self._project_lib.experimental_data_for_model_at_index(self._project_lib.current_experiment_index)
+            # Capture indices atomically to prevent race conditions
+            model_idx = self._project_lib.current_model_index
+            exp_idx = self._project_lib.current_experiment_index
+            model = self._project_lib.models[model_idx]
+            exp_data = self._project_lib.experimental_data_for_model_at_index(exp_idx)
             if exp_data.x is None or len(exp_data.x) == 0:
                 return []
             x = exp_data.x
@@ -200,7 +206,9 @@ def getBackgroundDataForAnalysis(self) -> list:
         if not self._bkg_shown:
             return []
         try:
-            model = self._project_lib.models[self._project_lib.current_model_index]
+            # Capture index atomically to prevent race conditions
+            model_idx = self._project_lib.current_model_index
+            model = self._project_lib.models[model_idx]
             # Use sample/analysis x-range instead of experimental data
             x_min, x_max = self._get_all_models_sample_range()[0:2]
             if x_min == float('inf') or x_max == float('-inf'):
@@ -225,7 +233,9 @@ def getScaleDataForAnalysis(self) -> list:
         if not self._scale_shown:
             return []
         try:
-            model = self._project_lib.models[self._project_lib.current_model_index]
+            # Capture index atomically to prevent race conditions
+            model_idx = self._project_lib.current_model_index
+            model = self._project_lib.models[model_idx]
             # Use sample/analysis x-range instead of experimental data
             x_min, x_max = self._get_all_models_sample_range()[0:2]
             if x_min == float('inf') or x_max == float('-inf'):
@@ -444,6 +454,10 @@ def experimentMinY(self):
         if self._plot_rq4:
             valid_x = data.x[data.y > 0] if data.y.size > 0 else np.array([1.0])
             valid_y = valid_y * (valid_x**4)
+            # Filter again after transformation to avoid log of zero/negative
+            valid_y = valid_y[valid_y > 0]
+            if valid_y.size == 0:
+                return -10.0
         return np.log10(valid_y.min())
 
     @Property('QVariant', notify=chartRefsChanged)
@@ -539,15 +553,17 @@ def getExperimentDataPoints(self, experiment_index: int) -> list:
                     r = point[1]
                     error_var = point[2]
                     # Apply R×q⁴ transformation if enabled
+                    # Clamp error_lower before transformation to ensure positive values
+                    error_lower_linear = max(r - np.sqrt(error_var), 1e-20)
                     if self._plot_rq4:
                         q4 = q**4
                         r_val = r * q4
                         error_upper = (r + np.sqrt(error_var)) * q4
-                        error_lower = max((r - np.sqrt(error_var)) * q4, 1e-10)
+                        error_lower = error_lower_linear * q4
                     else:
                         r_val = r
                         error_upper = r + np.sqrt(error_var)
-                        error_lower = max(r - np.sqrt(error_var), 1e-10)
+                        error_lower = error_lower_linear
                     points.append(
                         {
                             'x': float(q),
@@ -699,15 +715,17 @@ def qtchartsReplaceMeasuredOnExperimentChartAndRedraw(self):
                 r = point[1]
                 error_var = point[2]
                 # Apply R×q⁴ transformation if enabled
+                # Clamp error_lower before transformation to ensure positive values
+                error_lower_linear = max(r - np.sqrt(error_var), 1e-20)
                 if self._plot_rq4:
                     q4 = q**4
                     r_val = r * q4
                     error_upper = (r + np.sqrt(error_var)) * q4
-                    error_lower = max((r - np.sqrt(error_var)) * q4, 1e-10)
+                    error_lower = error_lower_linear * q4
                 else:
                     r_val = r
                     error_upper = r + np.sqrt(error_var)
-                    error_lower = max(r - np.sqrt(error_var), 1e-10)
+                    error_lower = error_lower_linear
                 series_measured.append(q, np.log10(r_val))
                 series_error_upper.append(q, np.log10(error_upper))
                 series_error_lower.append(q, np.log10(error_lower))
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
index 212ff3cf..9fef7a8f 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
@@ -57,7 +57,8 @@ Rectangle {
 
         // Update reference lines when visibility changes
         Connections {
-            target: Globals.BackendWrapper.activeBackend.plotting
+            target: Globals.BackendWrapper.activeBackend?.plotting ?? null
+            enabled: target !== null
             function onReferenceLineVisibilityChanged() {
                 chartView.updateReferenceLines()
             }
@@ -101,7 +102,8 @@ Rectangle {
 
         // Watch for changes in multi-experiment selection
         Connections {
-            target: Globals.BackendWrapper.activeBackend
+            target: Globals.BackendWrapper.activeBackend ?? null
+            enabled: target !== null
             function onMultiExperimentSelectionChanged() {
                 console.log("Analysis: Multi-experiment selection changed - updating series")
                 chartView.updateMultiExperimentSeries()
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
index 52e5940d..6f19845b 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
@@ -63,7 +63,8 @@ Rectangle {
 
                 // Watch for changes in multi-experiment selection
                 Connections {
-                    target: Globals.BackendWrapper.activeBackend
+                    target: Globals.BackendWrapper.activeBackend ?? null
+                    enabled: target !== null
                     function onMultiExperimentSelectionChanged() {
                         analysisChartView.updateMultiExperimentSeries()
                     }
@@ -113,7 +114,8 @@ Rectangle {
 
                 // Update reference lines when visibility changes
                 Connections {
-                    target: Globals.BackendWrapper.activeBackend.plotting
+                    target: Globals.BackendWrapper.activeBackend?.plotting ?? null
+                    enabled: target !== null
                     function onReferenceLineVisibilityChanged() {
                         analysisChartView.updateReferenceLines()
                     }
diff --git a/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml b/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
index a2a5f9ac..04277a8e 100644
--- a/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
@@ -58,7 +58,8 @@ Rectangle {
 
         // Update reference lines when visibility changes
         Connections {
-            target: Globals.BackendWrapper.activeBackend.plotting
+            target: Globals.BackendWrapper.activeBackend?.plotting ?? null
+            enabled: target !== null
             function onReferenceLineVisibilityChanged() {
                 chartView.updateReferenceLines()
             }
@@ -189,7 +190,8 @@ Rectangle {
 
         // Watch for changes in multi-experiment selection
         Connections {
-            target: Globals.BackendWrapper.activeBackend
+            target: Globals.BackendWrapper.activeBackend ?? null
+            enabled: target !== null
             function onMultiExperimentSelectionChanged() {
                 // Update series when selection changes
                 // The function will handle showing/hiding appropriate series

From 2b6c4d6d284c23cdb7181a90bd08d1d1394d108e Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Thu, 5 Feb 2026 19:08:15 +0100
Subject: [PATCH 06/12] proper orso sample conversion into layers

---
 EasyReflectometryApp/Backends/Py/logic/project.py     |  8 ++++++++
 EasyReflectometryApp/Backends/Py/plotting_1d.py       |  1 +
 EasyReflectometryApp/Backends/Py/project.py           |  9 +++++++++
 EasyReflectometryApp/Backends/Py/py_backend.py        |  3 +++
 EasyReflectometryApp/Gui/Globals/BackendWrapper.qml   |  5 +++++
 .../Gui/Pages/Analysis/MainContent/AnalysisView.qml   |  4 ++++
 .../Gui/Pages/Analysis/MainContent/CombinedView.qml   |  4 ++++
 .../Pages/Experiment/MainContent/ExperimentView.qml   |  4 ++++
 .../Gui/Pages/Sample/MainContent/CombinedView.qml     |  9 ++++++++-
 .../Gui/Pages/Sample/MainContent/SampleView.qml       |  4 ++++
 .../Gui/Pages/Sample/MainContent/SldView.qml          | 11 +++++++++++
 .../Sidebar/Basic/Groups/Assemblies/MultiLayer.qml    |  2 ++
 .../Basic/Groups/Assemblies/SurfactantLayer.qml       |  7 ++++++-
 13 files changed, 69 insertions(+), 2 deletions(-)

diff --git a/EasyReflectometryApp/Backends/Py/logic/project.py b/EasyReflectometryApp/Backends/Py/logic/project.py
index adf8976c..2ec5d133 100644
--- a/EasyReflectometryApp/Backends/Py/logic/project.py
+++ b/EasyReflectometryApp/Backends/Py/logic/project.py
@@ -122,6 +122,14 @@ def add_sample_from_orso(self, sample) -> None:
         new_model_index = len(self._project_lib.models) - 1
         self._update_enablement_of_fixed_layers_for_model(new_model_index)
 
+    def is_only_default_model(self) -> bool:
+        """Check if there is only one model and it is the default model."""
+        return len(self._project_lib.models) == 1 and self._project_lib.is_default_model(0)
+
+    def remove_model_at_index(self, index: int) -> None:
+        """Remove the model at the given index."""
+        self._project_lib.remove_model_at_index(index)
+
     def reset(self) -> None:
         self._project_lib.reset()
         self._project_lib.default_model()
diff --git a/EasyReflectometryApp/Backends/Py/plotting_1d.py b/EasyReflectometryApp/Backends/Py/plotting_1d.py
index d7b60588..5e5415aa 100644
--- a/EasyReflectometryApp/Backends/Py/plotting_1d.py
+++ b/EasyReflectometryApp/Backends/Py/plotting_1d.py
@@ -19,6 +19,7 @@ class Plotting1d(QObject):
     experimentChartRangesChanged = Signal()
     experimentDataChanged = Signal()
     samplePageDataChanged = Signal()  # Signal for QML to refresh sample page charts
+    chartAxesResetRequested = Signal()  # Signal to request QML to reset chart axes
 
     # New signals for plot mode properties
     plotModeChanged = Signal()
diff --git a/EasyReflectometryApp/Backends/Py/project.py b/EasyReflectometryApp/Backends/Py/project.py
index 5217c0df..3e4ad0b3 100644
--- a/EasyReflectometryApp/Backends/Py/project.py
+++ b/EasyReflectometryApp/Backends/Py/project.py
@@ -110,7 +110,16 @@ def sampleLoad(self, url: str) -> None:
         orso_data = orso.load_orso(generalizePath(url))
         # Load the sample model
         sample = load_orso_model(orso_data)
+
+        # Check if we should replace the default model or append
+        should_replace_default = self._logic.is_only_default_model()
+
         # Add the sample as a new model in the project
         self._logic.add_sample_from_orso(sample)
+
+        # If we replaced the default model, remove it (it's now at index 0)
+        if should_replace_default:
+            self._logic.remove_model_at_index(0)
+
         # notify listeners
         self.externalProjectLoaded.emit()
diff --git a/EasyReflectometryApp/Backends/Py/py_backend.py b/EasyReflectometryApp/Backends/Py/py_backend.py
index ce924fe8..41a681af 100644
--- a/EasyReflectometryApp/Backends/Py/py_backend.py
+++ b/EasyReflectometryApp/Backends/Py/py_backend.py
@@ -179,6 +179,7 @@ def _relay_project_page_created(self):
     def _relay_project_page_project_changed(self):
         self._sample.materialsTableChanged.emit()
         self._sample.modelsTableChanged.emit()
+        self._sample.modelsIndexChanged.emit()
         self._sample.assembliesTableChanged.emit()
         self._sample._clearCacheAndEmitLayersChanged()
         self._experiment.experimentChanged.emit()
@@ -188,6 +189,8 @@ def _relay_project_page_project_changed(self):
         self._summary.summaryChanged.emit()
         self._plotting_1d.reset_data()
         self._refresh_plots()
+        # Request QML to reset axes to fit new data
+        self._plotting_1d.chartAxesResetRequested.emit()
 
     def _relay_sample_page_sample_changed(self):
         self._plotting_1d.reset_data()
diff --git a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
index 189e6573..d18f078e 100644
--- a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
+++ b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
@@ -396,6 +396,8 @@ QtObject {
     signal samplePageDataChanged()
     // Signal for plot mode changes - forward from backend
     signal plotModeChanged()
+    // Signal to request QML to reset chart axes (e.g., after model load)
+    signal chartAxesResetRequested()
 
     // Connect to backend signal (called from Component.onCompleted in QML items)
     function connectSamplePageDataChanged() {
@@ -405,6 +407,9 @@ QtObject {
         if (activeBackend && activeBackend.plotting && activeBackend.plotting.plotModeChanged) {
             activeBackend.plotting.plotModeChanged.connect(plotModeChanged)
         }
+        if (activeBackend && activeBackend.plotting && activeBackend.plotting.chartAxesResetRequested) {
+            activeBackend.plotting.chartAxesResetRequested.connect(chartAxesResetRequested)
+        }
     }
 
     Component.onCompleted: {
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
index c453d75d..4aa387ee 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
@@ -117,6 +117,10 @@ Rectangle {
                 // Delay resetAxes to allow axis range properties to update first
                 analysisResetAxesTimer.start()
             }
+            function onChartAxesResetRequested() {
+                // Reset axes when model is loaded (e.g., from ORSO file)
+                analysisResetAxesTimer.start()
+            }
         }
 
         Timer {
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
index 44dc438b..03e2ea7f 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
@@ -78,6 +78,10 @@ Rectangle {
                         // Delay resetAxes to allow axis range properties to update first
                         combinedAnalysisResetAxesTimer.start()
                     }
+                    function onChartAxesResetRequested() {
+                        // Reset axes when model is loaded (e.g., from ORSO file)
+                        combinedAnalysisResetAxesTimer.start()
+                    }
                 }
 
                 Timer {
diff --git a/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml b/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
index a2a5f9ac..5cd9d546 100644
--- a/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
@@ -207,6 +207,10 @@ Rectangle {
                 // Delay resetAxes to allow axis range properties to update first
                 experimentResetAxesTimer.start()
             }
+            function onChartAxesResetRequested() {
+                // Reset axes when model is loaded (e.g., from ORSO file)
+                experimentResetAxesTimer.start()
+            }
         }
 
         Timer {
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml
index 257d6b6f..cd435517 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml
@@ -596,13 +596,20 @@ Rectangle {
             // Delay resetAxes to allow axis range properties to update first
             sampleCombinedResetAxesTimer.start()
         }
+        function onChartAxesResetRequested() {
+            // Reset axes when model is loaded (e.g., from ORSO file)
+            sampleCombinedResetAxesTimer.start()
+        }
     }
 
     Timer {
         id: sampleCombinedResetAxesTimer
         interval: 50
         repeat: false
-        onTriggered: sampleChartView.resetAxes()
+        onTriggered: {
+            sampleChartView.resetAxes()
+            sldChartView.resetAxes()
+        }
     }
 
     Component.onCompleted: {
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml
index 8bed9517..88a8c975 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml
@@ -352,6 +352,10 @@ Rectangle {
             // Delay resetAxes to allow axis range properties to update first
             sampleResetAxesTimer.start()
         }
+        function onChartAxesResetRequested() {
+            // Reset axes when model is loaded (e.g., from ORSO file)
+            sampleResetAxesTimer.start()
+        }
     }
 
     Timer {
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SldView.qml b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SldView.qml
index e27d98f5..6656eaf3 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SldView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SldView.qml
@@ -317,6 +317,17 @@ Rectangle {
         function onSamplePageDataChanged() {
             refreshAllCharts()
         }
+        function onChartAxesResetRequested() {
+            // Reset axes when model is loaded (e.g., from ORSO file)
+            sldResetAxesTimer.start()
+        }
+    }
+
+    Timer {
+        id: sldResetAxesTimer
+        interval: 50
+        repeat: false
+        onTriggered: chartView.resetAxes()
     }
 
     Component.onCompleted: {
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/Assemblies/MultiLayer.qml b/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/Assemblies/MultiLayer.qml
index 213ab528..8697204f 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/Assemblies/MultiLayer.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/Assemblies/MultiLayer.qml
@@ -78,6 +78,7 @@ EaElements.GroupColumn {
                 horizontalAlignment: Text.AlignHCenter
                 enabled: Globals.BackendWrapper.sampleLayers[index].thickness_enabled === "True"
                 text: (isNaN(Globals.BackendWrapper.sampleLayers[index].thickness)) ? '--' : Number(Globals.BackendWrapper.sampleLayers[index].thickness).toFixed(2)
+                onActiveFocusChanged: if (activeFocus && Globals.BackendWrapper.sampleCurrentLayerIndex !== index) Globals.BackendWrapper.sampleSetCurrentLayerIndex(index)
                 onEditingFinished: Globals.BackendWrapper.sampleSetCurrentLayerThickness(text)
             }
 
@@ -85,6 +86,7 @@ EaElements.GroupColumn {
                 horizontalAlignment: Text.AlignHCenter
                 enabled: Globals.BackendWrapper.sampleLayers[index].roughness_enabled === "True"
                 text: (isNaN(Globals.BackendWrapper.sampleLayers[index].roughness)) ? '--' : Number(Globals.BackendWrapper.sampleLayers[index].roughness).toFixed(2)
+                onActiveFocusChanged: if (activeFocus && Globals.BackendWrapper.sampleCurrentLayerIndex !== index) Globals.BackendWrapper.sampleSetCurrentLayerIndex(index)
                 onEditingFinished: Globals.BackendWrapper.sampleSetCurrentLayerRoughness(text)
             }
 
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/Assemblies/SurfactantLayer.qml b/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/Assemblies/SurfactantLayer.qml
index dd33ea8d..231e02f1 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/Assemblies/SurfactantLayer.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/Assemblies/SurfactantLayer.qml
@@ -60,6 +60,7 @@ EaElements.GroupColumn {
             EaComponents.TableViewTextInput {
                 horizontalAlignment: Text.AlignHCenter
                 text: Globals.BackendWrapper.sampleLayers[index].formula
+                onActiveFocusChanged: if (activeFocus && Globals.BackendWrapper.sampleCurrentLayerIndex !== index) Globals.BackendWrapper.sampleSetCurrentLayerIndex(index)
                 onEditingFinished: Globals.BackendWrapper.sampleSetCurrentLayerFormula(text)
             }
 
@@ -67,6 +68,7 @@ EaElements.GroupColumn {
                 horizontalAlignment: Text.AlignHCenter
                 enabled: Globals.BackendWrapper.sampleLayers[index].thickness_enabled === "True"
                 text: (isNaN(Globals.BackendWrapper.sampleLayers[index].thickness)) ? '--' : Number(Globals.BackendWrapper.sampleLayers[index].thickness).toFixed(2)
+                onActiveFocusChanged: if (activeFocus && Globals.BackendWrapper.sampleCurrentLayerIndex !== index) Globals.BackendWrapper.sampleSetCurrentLayerIndex(index)
                 onEditingFinished: Globals.BackendWrapper.sampleSetCurrentLayerThickness(text)
             }
 
@@ -74,12 +76,14 @@ EaElements.GroupColumn {
                 horizontalAlignment: Text.AlignHCenter
                 enabled: Globals.BackendWrapper.sampleLayers[index].roughness_enabled === "True"
                 text: (isNaN(Globals.BackendWrapper.sampleLayers[index].roughness)) ? '--' : Number(Globals.BackendWrapper.sampleLayers[index].roughness).toFixed(2)
+                onActiveFocusChanged: if (activeFocus && Globals.BackendWrapper.sampleCurrentLayerIndex !== index) Globals.BackendWrapper.sampleSetCurrentLayerIndex(index)
                 onEditingFinished: Globals.BackendWrapper.sampleSetCurrentLayerRoughness(text)
             }
 
             EaComponents.TableViewTextInput {
                 horizontalAlignment: Text.AlignHCenter
                 text: (isNaN(Globals.BackendWrapper.sampleLayers[index].solvation)) ? '--' : Number(Globals.BackendWrapper.sampleLayers[index].solvation).toFixed(2)
+                onActiveFocusChanged: if (activeFocus && Globals.BackendWrapper.sampleCurrentLayerIndex !== index) Globals.BackendWrapper.sampleSetCurrentLayerIndex(index)
                 onEditingFinished: Globals.BackendWrapper.sampleSetCurrentLayerSolvation(text)
             }
 
@@ -87,6 +91,7 @@ EaElements.GroupColumn {
                 horizontalAlignment: Text.AlignHCenter
                 enabled: Globals.BackendWrapper.sampleLayers[index].apm_enabled === "True"
                 text: (isNaN(Globals.BackendWrapper.sampleLayers[index].apm)) ? '--' : Number(Globals.BackendWrapper.sampleLayers[index].apm).toFixed(2)
+                onActiveFocusChanged: if (activeFocus && Globals.BackendWrapper.sampleCurrentLayerIndex !== index) Globals.BackendWrapper.sampleSetCurrentLayerIndex(index)
                 onEditingFinished: Globals.BackendWrapper.sampleSetCurrentLayerAPM(text)
             }
 
@@ -108,7 +113,7 @@ EaElements.GroupColumn {
                 }
             }
             mouseArea.onPressed: {
-                if (Globals.BackendWrapper.samplCurrentLayerIndex !== index) {
+                if (Globals.BackendWrapper.sampleCurrentLayerIndex !== index) {
                     Globals.BackendWrapper.sampleSetCurrentLayerIndex(index)
                 }
             }

From 1c112b2b09945d6c801b385ed1da1bc3f5560b75 Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Sun, 8 Feb 2026 12:34:14 +0100
Subject: [PATCH 07/12] added checkbox for loaded orso overwrite. fixed axes
 reset on file load

---
 EasyReflectometryApp/Backends/Mock/Plotting.qml      |  1 +
 EasyReflectometryApp/Backends/Py/logic/project.py    |  5 +++++
 EasyReflectometryApp/Backends/Py/plotting_1d.py      |  1 +
 EasyReflectometryApp/Backends/Py/project.py          | 12 ++++++++----
 EasyReflectometryApp/Backends/Py/py_backend.py       |  1 +
 EasyReflectometryApp/Gui/Globals/BackendWrapper.qml  |  7 ++++++-
 .../Gui/Pages/Sample/MainContent/CombinedView.qml    | 11 +++++++++++
 .../Gui/Pages/Sample/MainContent/SampleView.qml      |  3 +++
 .../Gui/Pages/Sample/MainContent/SldView.qml         | 10 ++++++++++
 .../Pages/Sample/Sidebar/Basic/Groups/LoadSample.qml |  9 ++++++++-
 10 files changed, 54 insertions(+), 6 deletions(-)

diff --git a/EasyReflectometryApp/Backends/Mock/Plotting.qml b/EasyReflectometryApp/Backends/Mock/Plotting.qml
index ff856611..57e49717 100644
--- a/EasyReflectometryApp/Backends/Mock/Plotting.qml
+++ b/EasyReflectometryApp/Backends/Mock/Plotting.qml
@@ -38,6 +38,7 @@ QtObject {
     signal sldAxisReversedChanged()
     signal referenceLineVisibilityChanged()
     signal samplePageDataChanged()
+    signal samplePageResetAxes()
 
     function setQtChartsSerieRef(value1, value2, value3) {
         console.debug(`setQtChartsSerieRef ${value1}, ${value2}, ${value3}`)
diff --git a/EasyReflectometryApp/Backends/Py/logic/project.py b/EasyReflectometryApp/Backends/Py/logic/project.py
index adf8976c..47ee5be7 100644
--- a/EasyReflectometryApp/Backends/Py/logic/project.py
+++ b/EasyReflectometryApp/Backends/Py/logic/project.py
@@ -122,6 +122,11 @@ def add_sample_from_orso(self, sample) -> None:
         new_model_index = len(self._project_lib.models) - 1
         self._update_enablement_of_fixed_layers_for_model(new_model_index)
 
+    def replace_models_from_orso(self, sample) -> None:
+        """Replace all existing models with a single model built from the loaded sample."""
+        self._project_lib.replace_models_from_orso(sample)
+        self._update_enablement_of_fixed_layers_for_model(0)
+
     def reset(self) -> None:
         self._project_lib.reset()
         self._project_lib.default_model()
diff --git a/EasyReflectometryApp/Backends/Py/plotting_1d.py b/EasyReflectometryApp/Backends/Py/plotting_1d.py
index 84d6852b..f376564a 100644
--- a/EasyReflectometryApp/Backends/Py/plotting_1d.py
+++ b/EasyReflectometryApp/Backends/Py/plotting_1d.py
@@ -19,6 +19,7 @@ class Plotting1d(QObject):
     experimentChartRangesChanged = Signal()
     experimentDataChanged = Signal()
     samplePageDataChanged = Signal()  # Signal for QML to refresh sample page charts
+    samplePageResetAxes = Signal()  # Signal for QML to reset chart axes after data load
 
     # New signals for plot mode properties
     plotModeChanged = Signal()
diff --git a/EasyReflectometryApp/Backends/Py/project.py b/EasyReflectometryApp/Backends/Py/project.py
index 5217c0df..be758dd7 100644
--- a/EasyReflectometryApp/Backends/Py/project.py
+++ b/EasyReflectometryApp/Backends/Py/project.py
@@ -104,13 +104,17 @@ def reset(self) -> None:
         self.externalNameChanged.emit()
         self.externalProjectReset.emit()
 
-    @Slot(str)
-    def sampleLoad(self, url: str) -> None:
+    @Slot(str, bool)
+    def sampleLoad(self, url: str, append: bool = True) -> None:
         # Load ORSO file content
         orso_data = orso.load_orso(generalizePath(url))
         # Load the sample model
         sample = load_orso_model(orso_data)
-        # Add the sample as a new model in the project
-        self._logic.add_sample_from_orso(sample)
+        if append:
+            # Add the sample as a new model in the project
+            self._logic.add_sample_from_orso(sample)
+        else:
+            # Replace all existing models with the loaded sample
+            self._logic.replace_models_from_orso(sample)
         # notify listeners
         self.externalProjectLoaded.emit()
diff --git a/EasyReflectometryApp/Backends/Py/py_backend.py b/EasyReflectometryApp/Backends/Py/py_backend.py
index ce924fe8..3a0a616d 100644
--- a/EasyReflectometryApp/Backends/Py/py_backend.py
+++ b/EasyReflectometryApp/Backends/Py/py_backend.py
@@ -188,6 +188,7 @@ def _relay_project_page_project_changed(self):
         self._summary.summaryChanged.emit()
         self._plotting_1d.reset_data()
         self._refresh_plots()
+        self._plotting_1d.samplePageResetAxes.emit()
 
     def _relay_sample_page_sample_changed(self):
         self._plotting_1d.reset_data()
diff --git a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
index 0da30766..2fa06e68 100644
--- a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
+++ b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
@@ -78,7 +78,7 @@ QtObject {
     function projectReset() { activeBackend.project.reset() }
     function projectSave() { activeBackend.project.save() }
     function projectLoad(value) { activeBackend.project.load(value) }
-    function sampleFileLoad(value) { activeBackend.project.sampleLoad(value) }
+    function sampleFileLoad(value, append) { activeBackend.project.sampleLoad(value, append) }
 
 
     ///////////////
@@ -410,6 +410,8 @@ QtObject {
 
     // Signal for sample page data changes - forward from backend
     signal samplePageDataChanged()
+    // Signal for resetting chart axes after data load
+    signal samplePageResetAxes()
     // Signal for plot mode changes - forward from backend
     signal plotModeChanged()
 
@@ -418,6 +420,9 @@ QtObject {
         if (activeBackend && activeBackend.plotting && activeBackend.plotting.samplePageDataChanged) {
             activeBackend.plotting.samplePageDataChanged.connect(samplePageDataChanged)
         }
+        if (activeBackend && activeBackend.plotting && activeBackend.plotting.samplePageResetAxes) {
+            activeBackend.plotting.samplePageResetAxes.connect(samplePageResetAxes)
+        }
         if (activeBackend && activeBackend.plotting && activeBackend.plotting.plotModeChanged) {
             activeBackend.plotting.plotModeChanged.connect(plotModeChanged)
         }
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml
index 257d6b6f..07301a5a 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/CombinedView.qml
@@ -591,6 +591,10 @@ Rectangle {
         function onSamplePageDataChanged() {
             refreshAllCharts()
         }
+        function onSamplePageResetAxes() {
+            sampleCombinedResetAxesTimer.start()
+            sldCombinedResetAxesTimer.start()
+        }
         function onPlotModeChanged() {
             refreshAllCharts()
             // Delay resetAxes to allow axis range properties to update first
@@ -605,6 +609,13 @@ Rectangle {
         onTriggered: sampleChartView.resetAxes()
     }
 
+    Timer {
+        id: sldCombinedResetAxesTimer
+        interval: 50
+        repeat: false
+        onTriggered: sldChartView.resetAxes()
+    }
+
     Component.onCompleted: {
         Qt.callLater(recreateAllSeries)
     }
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml
index 8bed9517..b5cbed77 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SampleView.qml
@@ -347,6 +347,9 @@ Rectangle {
         function onSamplePageDataChanged() {
             refreshAllCharts()
         }
+        function onSamplePageResetAxes() {
+            sampleResetAxesTimer.start()
+        }
         function onPlotModeChanged() {
             refreshAllCharts()
             // Delay resetAxes to allow axis range properties to update first
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SldView.qml b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SldView.qml
index e27d98f5..9c034fb1 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SldView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/MainContent/SldView.qml
@@ -317,6 +317,16 @@ Rectangle {
         function onSamplePageDataChanged() {
             refreshAllCharts()
         }
+        function onSamplePageResetAxes() {
+            sldResetAxesTimer.start()
+        }
+    }
+
+    Timer {
+        id: sldResetAxesTimer
+        interval: 50
+        repeat: false
+        onTriggered: chartView.resetAxes()
     }
 
     Component.onCompleted: {
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/LoadSample.qml b/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/LoadSample.qml
index 14973e97..b7ee6ec0 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/LoadSample.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/LoadSample.qml
@@ -13,6 +13,13 @@ EaElements.GroupBox {
     collapsed: false
 
     EaElements.GroupColumn {
+        EaElements.CheckBox {
+            id: appendCheckBox
+            text: qsTr("Append to existing models")
+            checked: true
+            width: EaStyle.Sizes.sideBarContentWidth
+        }
+
         EaElements.SideBarButton {
             width: EaStyle.Sizes.sideBarContentWidth
             fontIcon: "folder-open"
@@ -24,7 +31,7 @@ EaElements.GroupBox {
             id: fileDialog
             title: qsTr("Select a sample file")
             nameFilters: [ "ORT files (*.ort)", "ORSO files (*.orso)", "All files (*.*)" ]
-            onAccepted: Globals.BackendWrapper.sampleFileLoad(selectedFiles[0])
+            onAccepted: Globals.BackendWrapper.sampleFileLoad(selectedFiles[0], appendCheckBox.checked)
         }
     }
 }
\ No newline at end of file

From 77824a6e7a01c21f8054e351c58e7d04b1616e60 Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Wed, 11 Feb 2026 19:22:45 +0100
Subject: [PATCH 08/12] show ORSO name when available

---
 EasyReflectometryApp/Backends/Py/analysis.py     | 3 ++-
 EasyReflectometryApp/Backends/Py/logic/models.py | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/EasyReflectometryApp/Backends/Py/analysis.py b/EasyReflectometryApp/Backends/Py/analysis.py
index b14d351d..0d3049bb 100644
--- a/EasyReflectometryApp/Backends/Py/analysis.py
+++ b/EasyReflectometryApp/Backends/Py/analysis.py
@@ -292,7 +292,8 @@ def modelNamesForExperiment(self) -> list:
         mapped_models = []
         experiments = self._experiments_logic._project_lib._experiments
         for ind in experiments:
-            mapped_models.append(experiments[ind].model.name)
+            name = experiments[ind].model.user_data.get('original_name', experiments[ind].model.name)
+            mapped_models.append(name)
         return mapped_models
 
     @Property('QVariantList', notify=experimentsChanged)
diff --git a/EasyReflectometryApp/Backends/Py/logic/models.py b/EasyReflectometryApp/Backends/Py/logic/models.py
index cf2777d2..29865707 100644
--- a/EasyReflectometryApp/Backends/Py/logic/models.py
+++ b/EasyReflectometryApp/Backends/Py/logic/models.py
@@ -128,7 +128,7 @@ def _from_models_collection_to_list_of_dicts(models_collection: ModelCollection)
     for model in models_collection:
         models_list.append(
             {
-                'label': model.name,
+                'label': model.user_data.get('original_name', model.name),  # Use original name if available
                 'color': str(model.color),
             }
         )

From fcabcabe8941e891f1259168581b1ffa0f1d927e Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Thu, 12 Feb 2026 13:50:05 +0100
Subject: [PATCH 09/12] model prefix based on its name

---
 EasyReflectometryApp/Backends/Py/logic/parameters.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EasyReflectometryApp/Backends/Py/logic/parameters.py b/EasyReflectometryApp/Backends/Py/logic/parameters.py
index bc36f539..2eef21ad 100644
--- a/EasyReflectometryApp/Backends/Py/logic/parameters.py
+++ b/EasyReflectometryApp/Backends/Py/logic/parameters.py
@@ -226,7 +226,7 @@ def _is_layer_parameter(param: Parameter) -> bool:
     # Process parameters for each model
     for model_idx, model in enumerate(models):
         model_unique_name = model.unique_name
-        model_prefix = f'M{model_idx + 1}'
+        model_prefix = model.user_data.get('original_name', model.name)
 
         for parameter in parameters:
             # Skip parameters not in this model's path

From 8ee83bddf4f519e4bf9821a15e9ad5a7b291ec63 Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Thu, 12 Feb 2026 21:38:32 +0100
Subject: [PATCH 10/12] use orso name when available

---
 EasyReflectometryApp/Backends/Py/logic/models.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/EasyReflectometryApp/Backends/Py/logic/models.py b/EasyReflectometryApp/Backends/Py/logic/models.py
index 29865707..0dee4dea 100644
--- a/EasyReflectometryApp/Backends/Py/logic/models.py
+++ b/EasyReflectometryApp/Backends/Py/logic/models.py
@@ -21,7 +21,10 @@ def index(self, new_value: Union[int, str]) -> None:
 
     @property
     def name_at_current_index(self) -> str:
-        return self._models[self.index].name
+        if self._models[self.index].user_data.get('original_name'):
+            return self._models[self.index].user_data['original_name']
+        else:
+            return self._models[self.index].name
 
     @property
     def scaling_at_current_index(self) -> float:

From 5f2639d7458c45c5055577c3ce011b9b0c69b3e0 Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Fri, 13 Feb 2026 15:14:03 +0100
Subject: [PATCH 11/12] enhance safety of ORSO sample file load

---
 EasyReflectometryApp/Backends/Py/project.py   | 13 +++++++++-
 .../Gui/Globals/BackendWrapper.qml            | 10 ++++++++
 .../Sidebar/Basic/Groups/LoadSample.qml       | 24 +++++++++++++++++++
 3 files changed, 46 insertions(+), 1 deletion(-)

diff --git a/EasyReflectometryApp/Backends/Py/project.py b/EasyReflectometryApp/Backends/Py/project.py
index be758dd7..4fba7149 100644
--- a/EasyReflectometryApp/Backends/Py/project.py
+++ b/EasyReflectometryApp/Backends/Py/project.py
@@ -1,3 +1,5 @@
+import warnings
+
 from EasyApp.Logic.Utils.Utils import generalizePath
 from easyreflectometry import Project as ProjectLib
 from easyreflectometry.orso_utils import load_orso_model
@@ -20,6 +22,7 @@ class Project(QObject):
     externalNameChanged = Signal()
     externalProjectLoaded = Signal()
     externalProjectReset = Signal()
+    sampleLoadWarning = Signal(str)
 
     def __init__(self, project_lib: ProjectLib, parent=None):
         super().__init__(parent)
@@ -109,7 +112,15 @@ def sampleLoad(self, url: str, append: bool = True) -> None:
         # Load ORSO file content
         orso_data = orso.load_orso(generalizePath(url))
         # Load the sample model
-        sample = load_orso_model(orso_data)
+        with warnings.catch_warnings(record=True) as caught_warnings:
+            warnings.simplefilter('always')
+            sample = load_orso_model(orso_data)
+        if sample is None:
+            warning_msg = 'The ORSO file does not contain a valid sample model definition. No sample was loaded.'
+            for w in caught_warnings:
+                warning_msg = str(w.message)
+            self.sampleLoadWarning.emit(warning_msg)
+            return
         if append:
             # Add the sample as a new model in the project
             self._logic.add_sample_from_orso(sample)
diff --git a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
index c0e5d5c7..b8479c89 100644
--- a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
+++ b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
@@ -80,6 +80,16 @@ QtObject {
     function projectLoad(value) { activeBackend.project.load(value) }
     function sampleFileLoad(value, append) { activeBackend.project.sampleLoad(value, append) }
 
+    // Sample load warning signal - forwarded from backend
+    signal sampleLoadWarning(string message)
+
+    property var _sampleLoadWarningConnection: {
+        if (activeBackend && activeBackend.project && activeBackend.project.sampleLoadWarning) {
+            activeBackend.project.sampleLoadWarning.connect(sampleLoadWarning)
+        }
+        return null
+    }
+
 
     ///////////////
     // Sample page
diff --git a/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/LoadSample.qml b/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/LoadSample.qml
index b7ee6ec0..ec9cba86 100644
--- a/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/LoadSample.qml
+++ b/EasyReflectometryApp/Gui/Pages/Sample/Sidebar/Basic/Groups/LoadSample.qml
@@ -34,4 +34,28 @@ EaElements.GroupBox {
             onAccepted: Globals.BackendWrapper.sampleFileLoad(selectedFiles[0], appendCheckBox.checked)
         }
     }
+
+    // Warning dialog for sample load issues
+    EaElements.Dialog {
+        id: sampleLoadWarningDialog
+        title: qsTr("Sample Load Warning")
+        standardButtons: Dialog.Ok
+        closePolicy: Popup.CloseOnEscape | Popup.CloseOnPressOutside
+
+        property string warningMessage: ""
+
+        EaElements.Label {
+            text: sampleLoadWarningDialog.warningMessage
+            wrapMode: Text.WordWrap
+            width: Math.min(implicitWidth, EaStyle.Sizes.sideBarContentWidth * 1.5)
+        }
+    }
+
+    Connections {
+        target: Globals.BackendWrapper
+        function onSampleLoadWarning(message) {
+            sampleLoadWarningDialog.warningMessage = message
+            sampleLoadWarningDialog.open()
+        }
+    }
 }
\ No newline at end of file

From 471f5e1dff7d829f0b1ce49761599227071ecff6 Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Sat, 14 Feb 2026 16:28:07 +0100
Subject: [PATCH 12/12] changes after CR

---
 EasyReflectometryApp/Backends/Py/analysis.py  |   3 +-
 .../Backends/Py/logic/helpers.py              |  11 +
 .../Backends/Py/logic/models.py               |   9 +-
 .../Backends/Py/logic/parameters.py           |   4 +-
 .../Backends/Py/plotting_1d.py                | 209 ++++++------------
 .../Backends/Py/py_backend.py                 |   6 +-
 .../Gui/Globals/BackendWrapper.qml            |  19 ++
 .../Analysis/MainContent/AnalysisView.qml     |  18 +-
 .../Analysis/MainContent/CombinedView.qml     |  18 +-
 .../Sidebar/Advanced/Groups/PlotControl.qml   |  38 +---
 .../Experiment/MainContent/ExperimentView.qml |  18 +-
 .../Sidebar/Advanced/Groups/PlotControl.qml   |  38 +---
 EasyReflectometryApp/Gui/qmldir               |   1 +
 pyproject.toml                                |   2 +-
 14 files changed, 120 insertions(+), 274 deletions(-)

diff --git a/EasyReflectometryApp/Backends/Py/analysis.py b/EasyReflectometryApp/Backends/Py/analysis.py
index 0d3049bb..3f9dacad 100644
--- a/EasyReflectometryApp/Backends/Py/analysis.py
+++ b/EasyReflectometryApp/Backends/Py/analysis.py
@@ -13,6 +13,7 @@
 from .logic.fitting import Fitting as FittingLogic
 from .logic.minimizers import Minimizers as MinimizersLogic
 from .logic.parameters import Parameters as ParametersLogic
+from .logic.helpers import get_original_name
 from .workers import FitterWorker
 
 
@@ -292,7 +293,7 @@ def modelNamesForExperiment(self) -> list:
         mapped_models = []
         experiments = self._experiments_logic._project_lib._experiments
         for ind in experiments:
-            name = experiments[ind].model.user_data.get('original_name', experiments[ind].model.name)
+            name = get_original_name(experiments[ind].model)
             mapped_models.append(name)
         return mapped_models
 
diff --git a/EasyReflectometryApp/Backends/Py/logic/helpers.py b/EasyReflectometryApp/Backends/Py/logic/helpers.py
index bb1a90d0..70465a5b 100644
--- a/EasyReflectometryApp/Backends/Py/logic/helpers.py
+++ b/EasyReflectometryApp/Backends/Py/logic/helpers.py
@@ -16,3 +16,14 @@ def formatMsg(type, *args):
         msg = ' ▌ '.join(msgs)
         msg = f'{mark} {msg}'
         return msg
+
+
+def get_original_name(obj) -> str:
+    """Get original name from user_data, with defensive fallback to obj.name.
+
+    Safely handles cases where user_data is None or not a dict.
+    """
+    user_data = getattr(obj, 'user_data', None)
+    if isinstance(user_data, dict):
+        return user_data.get('original_name', obj.name)
+    return obj.name
diff --git a/EasyReflectometryApp/Backends/Py/logic/models.py b/EasyReflectometryApp/Backends/Py/logic/models.py
index 0dee4dea..37bc1e81 100644
--- a/EasyReflectometryApp/Backends/Py/logic/models.py
+++ b/EasyReflectometryApp/Backends/Py/logic/models.py
@@ -5,6 +5,8 @@
 from easyreflectometry.model import ModelCollection
 from easyreflectometry.model.resolution_functions import PercentageFwhm
 
+from .helpers import get_original_name
+
 
 class Models:
     def __init__(self, project_lib: ProjectLib):
@@ -21,10 +23,7 @@ def index(self, new_value: Union[int, str]) -> None:
 
     @property
     def name_at_current_index(self) -> str:
-        if self._models[self.index].user_data.get('original_name'):
-            return self._models[self.index].user_data['original_name']
-        else:
-            return self._models[self.index].name
+        return get_original_name(self._models[self.index])
 
     @property
     def scaling_at_current_index(self) -> float:
@@ -131,7 +130,7 @@ def _from_models_collection_to_list_of_dicts(models_collection: ModelCollection)
     for model in models_collection:
         models_list.append(
             {
-                'label': model.user_data.get('original_name', model.name),  # Use original name if available
+                'label': get_original_name(model),
                 'color': str(model.color),
             }
         )
diff --git a/EasyReflectometryApp/Backends/Py/logic/parameters.py b/EasyReflectometryApp/Backends/Py/logic/parameters.py
index 2eef21ad..5fb05a53 100644
--- a/EasyReflectometryApp/Backends/Py/logic/parameters.py
+++ b/EasyReflectometryApp/Backends/Py/logic/parameters.py
@@ -9,6 +9,8 @@
 from easyscience import global_object
 from easyscience.variable import Parameter
 
+from .helpers import get_original_name
+
 RESERVED_ALIAS_NAMES = {'np', 'numpy', 'math', 'pi', 'e'}
 
 
@@ -226,7 +228,7 @@ def _is_layer_parameter(param: Parameter) -> bool:
     # Process parameters for each model
     for model_idx, model in enumerate(models):
         model_unique_name = model.unique_name
-        model_prefix = model.user_data.get('original_name', model.name)
+        model_prefix = get_original_name(model)
 
         for parameter in parameters:
             # Skip parameters not in this model's path
diff --git a/EasyReflectometryApp/Backends/Py/plotting_1d.py b/EasyReflectometryApp/Backends/Py/plotting_1d.py
index f376564a..46de877f 100644
--- a/EasyReflectometryApp/Backends/Py/plotting_1d.py
+++ b/EasyReflectometryApp/Backends/Py/plotting_1d.py
@@ -65,6 +65,15 @@ def reset_data(self):
         self._sld_data = {}
         console.debug(IO.formatMsg('sub', 'Sample and SLD data cleared'))
 
+    def _apply_rq4(self, x, y):
+        """Apply R(q)×q⁴ transformation if enabled.
+
+        Works with both numpy arrays and scalar values.
+        """
+        if self._plot_rq4:
+            return y * (x**4)
+        return y
+
     # R(q)×q⁴ mode
     @Property(bool, notify=plotModeChanged)
     def plotRQ4(self) -> bool:
@@ -139,116 +148,62 @@ def flipBkgShown(self) -> None:
         self._bkg_shown = not self._bkg_shown
         self.referenceLineVisibilityChanged.emit()
 
-    @Slot(result='QVariantList')
-    def getBackgroundData(self) -> list:
-        """Return background reference line data for plotting.
+    def _get_reference_line_data(self, param_attr: str, default_log: float, use_analysis_range: bool) -> list:
+        """Build a horizontal reference line for the given model parameter.
 
-        Returns a horizontal line at the model's background value.
-        Note: Reference lines are always horizontal, even in R×q⁴ mode.
+        :param param_attr: Model attribute name ('background' or 'scale')
+        :param default_log: Default log10 value if parameter <= 0
+        :param use_analysis_range: If True, use sample/analysis x-range; if False, use experimental data x-range
         """
-        if not self._bkg_shown:
-            return []
         try:
-            # Capture indices atomically to prevent race conditions
             model_idx = self._project_lib.current_model_index
-            exp_idx = self._project_lib.current_experiment_index
             model = self._project_lib.models[model_idx]
-            exp_data = self._project_lib.experimental_data_for_model_at_index(exp_idx)
-            if exp_data.x is None or len(exp_data.x) == 0:
-                return []
-            x = exp_data.x
-            bkg_value = model.background.value
-            # For log scale plotting, convert background value
-            bkg_log = float(np.log10(bkg_value)) if bkg_value > 0 else -10.0
-            # Reference lines are always horizontal (no R×q⁴ transformation)
-            return [{'x': float(x[0]), 'y': bkg_log}, {'x': float(x[-1]), 'y': bkg_log}]
+
+            if use_analysis_range:
+                x_min, x_max = self._get_all_models_sample_range()[0:2]
+                if x_min == float('inf') or x_max == float('-inf'):
+                    return []
+            else:
+                exp_idx = self._project_lib.current_experiment_index
+                exp_data = self._project_lib.experimental_data_for_model_at_index(exp_idx)
+                if exp_data.x is None or len(exp_data.x) == 0:
+                    return []
+                x_min, x_max = float(exp_data.x[0]), float(exp_data.x[-1])
+
+            param_value = getattr(model, param_attr).value
+            y_log = float(np.log10(param_value)) if param_value > 0 else default_log
+            return [{'x': float(x_min), 'y': y_log}, {'x': float(x_max), 'y': y_log}]
         except (IndexError, AttributeError, TypeError) as e:
-            console.debug(f'Error getting background data: {e}')
+            console.debug(f'Error getting {param_attr} reference line data: {e}')
             return []
 
     @Slot(result='QVariantList')
-    def getScaleData(self) -> list:
-        """Return scale reference line data for plotting.
+    def getBackgroundData(self) -> list:
+        """Return background reference line data for the Experiment chart."""
+        if not self._bkg_shown:
+            return []
+        return self._get_reference_line_data('background', -10.0, use_analysis_range=False)
 
-        Returns a horizontal line at the model's scale value.
-        Note: Scale is a multiplicative factor, typically close to 1.0.
-        For reflectometry plots, the scale line at y=scale (log10) shows
-        where R=scale, i.e., where the reflectivity equals the scale factor.
-        Reference lines are always horizontal, even in R×q⁴ mode.
-        """
+    @Slot(result='QVariantList')
+    def getScaleData(self) -> list:
+        """Return scale reference line data for the Experiment chart."""
         if not self._scale_shown:
             return []
-        try:
-            # Capture indices atomically to prevent race conditions
-            model_idx = self._project_lib.current_model_index
-            exp_idx = self._project_lib.current_experiment_index
-            model = self._project_lib.models[model_idx]
-            exp_data = self._project_lib.experimental_data_for_model_at_index(exp_idx)
-            if exp_data.x is None or len(exp_data.x) == 0:
-                return []
-            x = exp_data.x
-            scale_value = model.scale.value
-            # For log scale plotting, convert scale value
-            scale_log = float(np.log10(scale_value)) if scale_value > 0 else 0.0
-            # Reference lines are always horizontal (no R×q⁴ transformation)
-            return [{'x': float(x[0]), 'y': scale_log}, {'x': float(x[-1]), 'y': scale_log}]
-        except (IndexError, AttributeError, TypeError) as e:
-            console.debug(f'Error getting scale data: {e}')
-            return []
+        return self._get_reference_line_data('scale', 0.0, use_analysis_range=False)
 
     @Slot(result='QVariantList')
     def getBackgroundDataForAnalysis(self) -> list:
-        """Return background reference line data for the Analysis chart.
-
-        Uses the analysis/sample x-range (calculated model data range) instead of
-        experimental data range to ensure the line spans the full chart width.
-        Reference lines are always horizontal, even in R×q⁴ mode.
-        """
+        """Return background reference line data for the Analysis chart (sample x-range)."""
         if not self._bkg_shown:
             return []
-        try:
-            # Capture index atomically to prevent race conditions
-            model_idx = self._project_lib.current_model_index
-            model = self._project_lib.models[model_idx]
-            # Use sample/analysis x-range instead of experimental data
-            x_min, x_max = self._get_all_models_sample_range()[0:2]
-            if x_min == float('inf') or x_max == float('-inf'):
-                return []
-            bkg_value = model.background.value
-            # For log scale plotting, convert background value
-            bkg_log = float(np.log10(bkg_value)) if bkg_value > 0 else -10.0
-            # Reference lines are always horizontal (no R×q⁴ transformation)
-            return [{'x': float(x_min), 'y': bkg_log}, {'x': float(x_max), 'y': bkg_log}]
-        except (IndexError, AttributeError, TypeError) as e:
-            console.debug(f'Error getting background data for analysis: {e}')
-            return []
+        return self._get_reference_line_data('background', -10.0, use_analysis_range=True)
 
     @Slot(result='QVariantList')
     def getScaleDataForAnalysis(self) -> list:
-        """Return scale reference line data for the Analysis chart.
-
-        Uses the analysis/sample x-range (calculated model data range) instead of
-        experimental data range to ensure the line spans the full chart width.
-        Reference lines are always horizontal, even in R×q⁴ mode.
-        """
+        """Return scale reference line data for the Analysis chart (sample x-range)."""
         if not self._scale_shown:
             return []
-        try:
-            # Capture index atomically to prevent race conditions
-            model_idx = self._project_lib.current_model_index
-            model = self._project_lib.models[model_idx]
-            # Use sample/analysis x-range instead of experimental data
-            x_min, x_max = self._get_all_models_sample_range()[0:2]
-            if x_min == float('inf') or x_max == float('-inf'):
-                return []
-            scale_value = model.scale.value
-            # For log scale plotting, convert scale value
-            scale_log = float(np.log10(scale_value)) if scale_value > 0 else 0.0
-            # Reference lines are always horizontal (no R×q⁴ transformation)
-            return [{'x': float(x_min), 'y': scale_log}, {'x': float(x_max), 'y': scale_log}]
-        except (IndexError, AttributeError, TypeError) as e:
-            console.debug(f'Error getting scale data for analysis: {e}')
-            return []
+        return self._get_reference_line_data('scale', 0.0, use_analysis_range=True)
 
     @property
     def sample_data(self) -> DataSet1D:
@@ -355,11 +310,8 @@ def _get_all_models_sample_range(self):
                 if data.y.size > 0:
                     valid_mask = data.y > 0
                     valid_y = data.y[valid_mask]
-                    valid_x = data.x[valid_mask]
                     if valid_y.size > 0:
-                        # Apply R×q⁴ transformation if enabled
-                        if self._plot_rq4:
-                            valid_y = valid_y * (valid_x**4)
+                        valid_y = self._apply_rq4(data.x[valid_mask], valid_y)
                         min_y = min(min_y, np.log10(valid_y.min()))
                         max_y = max(max_y, np.log10(valid_y.max()))
             except (IndexError, ValueError):
@@ -439,10 +391,7 @@ def experimentMaxY(self):
         data = self.experiment_data
         if data.y.size == 0:
             return 1.0
-        y_values = data.y
-        # Apply R×q⁴ transformation if enabled
-        if self._plot_rq4:
-            y_values = y_values * (data.x**4)
+        y_values = self._apply_rq4(data.x, data.y)
         return np.log10(y_values.max())
 
     @Property(float, notify=experimentChartRangesChanged)
@@ -451,14 +400,12 @@ def experimentMinY(self):
         valid_y = data.y[data.y > 0] if data.y.size > 0 else np.array([1e-10])
         if valid_y.size == 0:
             return -10.0
-        # Apply R×q⁴ transformation if enabled
-        if self._plot_rq4:
-            valid_x = data.x[data.y > 0] if data.y.size > 0 else np.array([1.0])
-            valid_y = valid_y * (valid_x**4)
-            # Filter again after transformation to avoid log of zero/negative
-            valid_y = valid_y[valid_y > 0]
-            if valid_y.size == 0:
-                return -10.0
+        valid_x = data.x[data.y > 0] if data.y.size > 0 else np.array([1.0])
+        valid_y = self._apply_rq4(valid_x, valid_y)
+        # Filter again after transformation to avoid log of zero/negative
+        valid_y = valid_y[valid_y > 0]
+        if valid_y.size == 0:
+            return -10.0
         return np.log10(valid_y.min())
 
     @Property('QVariant', notify=chartRefsChanged)
@@ -506,9 +453,8 @@ def getSampleDataPointsForModel(self, model_index: int) -> list:
             for point in data.data_points():
                 x_val = float(point[0])
                 y_val = float(point[1])
-                # Apply R×q⁴ transformation if enabled
-                if self._plot_rq4 and y_val > 0:
-                    y_val = y_val * (x_val**4)
+                if y_val > 0:
+                    y_val = self._apply_rq4(x_val, y_val)
                 y_log = float(np.log10(y_val)) if y_val > 0 else -10.0
                 points.append({'x': x_val, 'y': y_log})
             return points
@@ -553,18 +499,10 @@ def getExperimentDataPoints(self, experiment_index: int) -> list:
                     q = point[0]
                     r = point[1]
                     error_var = point[2]
-                    # Apply R×q⁴ transformation if enabled
-                    # Clamp error_lower before transformation to ensure positive values
-                    error_lower_linear = max(r - np.sqrt(error_var), 1e-20)
-                    if self._plot_rq4:
-                        q4 = q**4
-                        r_val = r * q4
-                        error_upper = (r + np.sqrt(error_var)) * q4
-                        error_lower = error_lower_linear * q4
-                    else:
-                        r_val = r
-                        error_upper = r + np.sqrt(error_var)
-                        error_lower = error_lower_linear
+                    error_lower_linear = max(r - np.sqrt(error_var), 1e-10)
+                    r_val = self._apply_rq4(q, r)
+                    error_upper = self._apply_rq4(q, r + np.sqrt(error_var))
+                    error_lower = self._apply_rq4(q, error_lower_linear)
                     points.append(
                         {
                             'x': float(q),
@@ -617,11 +555,8 @@ def getAnalysisDataPoints(self, experiment_index: int) -> list:
                     q = point[0]
                     r_meas = point[1]
                     calc_y_val = calc_y[calc_idx] if calc_idx < len(calc_y) else r_meas
-                    # Apply R×q⁴ transformation if enabled
-                    if self._plot_rq4:
-                        q4 = q**4
-                        r_meas = r_meas * q4
-                        calc_y_val = calc_y_val * q4
+                    r_meas = self._apply_rq4(q, r_meas)
+                    calc_y_val = self._apply_rq4(q, calc_y_val)
                     points.append(
                         {
                             'x': float(q),
@@ -715,18 +650,10 @@ def qtchartsReplaceMeasuredOnExperimentChartAndRedraw(self):
                 q = point[0]
                 r = point[1]
                 error_var = point[2]
-                # Apply R×q⁴ transformation if enabled
-                # Clamp error_lower before transformation to ensure positive values
-                error_lower_linear = max(r - np.sqrt(error_var), 1e-20)
-                if self._plot_rq4:
-                    q4 = q**4
-                    r_val = r * q4
-                    error_upper = (r + np.sqrt(error_var)) * q4
-                    error_lower = error_lower_linear * q4
-                else:
-                    r_val = r
-                    error_upper = r + np.sqrt(error_var)
-                    error_lower = error_lower_linear
+                error_lower_linear = max(r - np.sqrt(error_var), 1e-10)
+                r_val = self._apply_rq4(q, r)
+                error_upper = self._apply_rq4(q, r + np.sqrt(error_var))
+                error_lower = self._apply_rq4(q, error_lower_linear)
                 series_measured.append(q, np.log10(r_val))
                 series_error_upper.append(q, np.log10(error_upper))
                 series_error_lower.append(q, np.log10(error_lower))
@@ -781,20 +708,14 @@ def qtchartsReplaceCalculatedAndMeasuredOnAnalysisChartAndRedraw(self):
         for point in self.experiment_data.data_points():
             if point[0] < self._project_lib.q_max and self._project_lib.q_min < point[0]:
                 q = point[0]
-                r_meas = point[1]
-                # Apply R×q⁴ transformation if enabled
-                if self._plot_rq4:
-                    r_meas = r_meas * (q**4)
+                r_meas = self._apply_rq4(q, point[1])
                 series_measured.append(q, np.log10(r_meas))
                 nr_points = nr_points + 1
         console.debug(IO.formatMsg('sub', 'Measured curve', f'{nr_points} points', 'on analysis page', 'replaced'))
 
         for point in self.sample_data.data_points():
             q = point[0]
-            r_calc = point[1]
-            # Apply R×q⁴ transformation if enabled
-            if self._plot_rq4:
-                r_calc = r_calc * (q**4)
+            r_calc = self._apply_rq4(q, point[1])
             series_calculated.append(q, np.log10(r_calc))
             nr_points = nr_points + 1
         console.debug(IO.formatMsg('sub', 'Calculated curve', f'{nr_points} points', 'on analysis page', 'replaced'))
diff --git a/EasyReflectometryApp/Backends/Py/py_backend.py b/EasyReflectometryApp/Backends/Py/py_backend.py
index efd5da50..9d3d1e0a 100644
--- a/EasyReflectometryApp/Backends/Py/py_backend.py
+++ b/EasyReflectometryApp/Backends/Py/py_backend.py
@@ -177,11 +177,15 @@ def _relay_project_page_created(self):
         self._summary.summaryChanged.emit()
 
     def _relay_project_page_project_changed(self):
+        # Clear layers cache first so that subsequent signal handlers
+        # (e.g. ComboBox onModelChanged / onCurrentAssemblyNameChanged in
+        # MultiLayer.qml) read up-to-date layer data.
+        self._sample._clearCacheAndEmitLayersChanged()
         self._sample.materialsTableChanged.emit()
         self._sample.modelsTableChanged.emit()
         self._sample.modelsIndexChanged.emit()
         self._sample.assembliesTableChanged.emit()
-        self._sample._clearCacheAndEmitLayersChanged()
+        self._sample.assembliesIndexChanged.emit()
         self._experiment.experimentChanged.emit()
         self._analysis.experimentsChanged.emit()
         self._analysis._clearCacheAndEmitParametersChanged()
diff --git a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
index c0e5d5c7..5d038f6c 100644
--- a/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
+++ b/EasyReflectometryApp/Gui/Globals/BackendWrapper.qml
@@ -378,6 +378,25 @@ QtObject {
         }
     }
 
+    // Helper to update background/scale reference line series on any chart view.
+    // useAnalysisRange: true for Analysis charts (sample x-range), false for Experiment charts.
+    function updateRefLines(bkgSeries, scaleSeries, useAnalysisRange) {
+        bkgSeries.clear()
+        if (plottingBkgShown) {
+            var bkgData = useAnalysisRange ? plottingGetBackgroundDataForAnalysis() : plottingGetBackgroundData()
+            for (var i = 0; i < bkgData.length; i++) {
+                bkgSeries.append(bkgData[i].x, bkgData[i].y)
+            }
+        }
+        scaleSeries.clear()
+        if (plottingScaleShown) {
+            var scaleData = useAnalysisRange ? plottingGetScaleDataForAnalysis() : plottingGetScaleData()
+            for (var j = 0; j < scaleData.length; j++) {
+                scaleSeries.append(scaleData[j].x, scaleData[j].y)
+            }
+        }
+    }
+
     function plottingSetQtChartsSerieRef(value1, value2, value3) { activeBackend.plotting.setQtChartsSerieRef(value1, value2, value3) }
     function plottingRefreshSample() { activeBackend.plotting.drawCalculatedOnSampleChart() }
     function plottingRefreshSLD() { activeBackend.plotting.drawCalculatedOnSldChart() }
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
index 13a686dd..66130a66 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/AnalysisView.qml
@@ -65,23 +65,7 @@ Rectangle {
         }
 
         function updateReferenceLines() {
-            // Update background line (use analysis-specific method for correct x-range)
-            backgroundRefLine.clear()
-            if (Globals.BackendWrapper.plottingBkgShown) {
-                var bkgData = Globals.BackendWrapper.plottingGetBackgroundDataForAnalysis()
-                for (var i = 0; i < bkgData.length; i++) {
-                    backgroundRefLine.append(bkgData[i].x, bkgData[i].y)
-                }
-            }
-
-            // Update scale line (use analysis-specific method for correct x-range)
-            scaleRefLine.clear()
-            if (Globals.BackendWrapper.plottingScaleShown) {
-                var scaleData = Globals.BackendWrapper.plottingGetScaleDataForAnalysis()
-                for (var j = 0; j < scaleData.length; j++) {
-                    scaleRefLine.append(scaleData[j].x, scaleData[j].y)
-                }
-            }
+            Globals.BackendWrapper.updateRefLines(backgroundRefLine, scaleRefLine, true)
         }
 
         // Multi-experiment support
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
index 580d8368..0ad16c6b 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/MainContent/CombinedView.qml
@@ -126,23 +126,7 @@ Rectangle {
                 }
 
                 function updateReferenceLines() {
-                    // Update background line (use analysis-specific method for correct x-range)
-                    backgroundRefLine.clear()
-                    if (Globals.BackendWrapper.plottingBkgShown) {
-                        var bkgData = Globals.BackendWrapper.plottingGetBackgroundDataForAnalysis()
-                        for (var i = 0; i < bkgData.length; i++) {
-                            backgroundRefLine.append(bkgData[i].x, bkgData[i].y)
-                        }
-                    }
-
-                    // Update scale line (use analysis-specific method for correct x-range)
-                    scaleRefLine.clear()
-                    if (Globals.BackendWrapper.plottingScaleShown) {
-                        var scaleData = Globals.BackendWrapper.plottingGetScaleDataForAnalysis()
-                        for (var j = 0; j < scaleData.length; j++) {
-                            scaleRefLine.append(scaleData[j].x, scaleData[j].y)
-                        }
-                    }
+                    Globals.BackendWrapper.updateRefLines(backgroundRefLine, scaleRefLine, true)
                 }
 
                 // Multi-experiment series management
diff --git a/EasyReflectometryApp/Gui/Pages/Analysis/Sidebar/Advanced/Groups/PlotControl.qml b/EasyReflectometryApp/Gui/Pages/Analysis/Sidebar/Advanced/Groups/PlotControl.qml
index 0b2e0ce2..34de6956 100644
--- a/EasyReflectometryApp/Gui/Pages/Analysis/Sidebar/Advanced/Groups/PlotControl.qml
+++ b/EasyReflectometryApp/Gui/Pages/Analysis/Sidebar/Advanced/Groups/PlotControl.qml
@@ -3,48 +3,16 @@
 // © 2025 Contributors to the EasyReflectometry project <https://github.com/easyscience/EasyReflectometry>
 
 import QtQuick
-import QtQuick.Controls
 
 import EasyApp.Gui.Style as EaStyle
 import EasyApp.Gui.Elements as EaElements
 
-import Gui.Globals as Globals
+import Gui as Gui
 
 EaElements.GroupBox {
     title: qsTr("Plot control")
     collapsed: true
 
-    Column {
-        spacing: EaStyle.Sizes.fontPixelSize * 0.5
-
-        EaElements.CheckBox {
-            topPadding: 0
-            checked: Globals.BackendWrapper.plottingPlotRQ4
-            text: qsTr("Plot R(q)×q⁴")
-            ToolTip.text: qsTr("Checking this box will plot R(q) multiplied by q⁴")
-            onToggled: {
-                Globals.BackendWrapper.plottingTogglePlotRQ4()
-            }
-        }
-
-        EaElements.CheckBox {
-            topPadding: 0
-            checked: Globals.BackendWrapper.plottingScaleShown
-            text: qsTr("Show scale line")
-            ToolTip.text: qsTr("Checking this box will show the scale reference line on the plot")
-            onToggled: {
-                Globals.BackendWrapper.plottingFlipScaleShown()
-            }
-        }
-
-        EaElements.CheckBox {
-            topPadding: 0
-            checked: Globals.BackendWrapper.plottingBkgShown
-            text: qsTr("Show background line")
-            ToolTip.text: qsTr("Checking this box will show the background reference line on the plot")
-            onToggled: {
-                Globals.BackendWrapper.plottingFlipBkgShown()
-            }
-        }
-    }
+    Gui.PlotControlRefLines {}
 }
+
diff --git a/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml b/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
index 3bd40092..18513ac7 100644
--- a/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
+++ b/EasyReflectometryApp/Gui/Pages/Experiment/MainContent/ExperimentView.qml
@@ -66,23 +66,7 @@ Rectangle {
         }
 
         function updateReferenceLines() {
-            // Update background line
-            backgroundRefLine.clear()
-            if (Globals.BackendWrapper.plottingBkgShown) {
-                var bkgData = Globals.BackendWrapper.plottingGetBackgroundData()
-                for (var i = 0; i < bkgData.length; i++) {
-                    backgroundRefLine.append(bkgData[i].x, bkgData[i].y)
-                }
-            }
-
-            // Update scale line
-            scaleRefLine.clear()
-            if (Globals.BackendWrapper.plottingScaleShown) {
-                var scaleData = Globals.BackendWrapper.plottingGetScaleData()
-                for (var j = 0; j < scaleData.length; j++) {
-                    scaleRefLine.append(scaleData[j].x, scaleData[j].y)
-                }
-            }
+            Globals.BackendWrapper.updateRefLines(backgroundRefLine, scaleRefLine, false)
         }
 
         // Multi-experiment support
diff --git a/EasyReflectometryApp/Gui/Pages/Experiment/Sidebar/Advanced/Groups/PlotControl.qml b/EasyReflectometryApp/Gui/Pages/Experiment/Sidebar/Advanced/Groups/PlotControl.qml
index 0b2e0ce2..34de6956 100644
--- a/EasyReflectometryApp/Gui/Pages/Experiment/Sidebar/Advanced/Groups/PlotControl.qml
+++ b/EasyReflectometryApp/Gui/Pages/Experiment/Sidebar/Advanced/Groups/PlotControl.qml
@@ -3,48 +3,16 @@
 // © 2025 Contributors to the EasyReflectometry project <https://github.com/easyscience/EasyReflectometry>
 
 import QtQuick
-import QtQuick.Controls
 
 import EasyApp.Gui.Style as EaStyle
 import EasyApp.Gui.Elements as EaElements
 
-import Gui.Globals as Globals
+import Gui as Gui
 
 EaElements.GroupBox {
     title: qsTr("Plot control")
     collapsed: true
 
-    Column {
-        spacing: EaStyle.Sizes.fontPixelSize * 0.5
-
-        EaElements.CheckBox {
-            topPadding: 0
-            checked: Globals.BackendWrapper.plottingPlotRQ4
-            text: qsTr("Plot R(q)×q⁴")
-            ToolTip.text: qsTr("Checking this box will plot R(q) multiplied by q⁴")
-            onToggled: {
-                Globals.BackendWrapper.plottingTogglePlotRQ4()
-            }
-        }
-
-        EaElements.CheckBox {
-            topPadding: 0
-            checked: Globals.BackendWrapper.plottingScaleShown
-            text: qsTr("Show scale line")
-            ToolTip.text: qsTr("Checking this box will show the scale reference line on the plot")
-            onToggled: {
-                Globals.BackendWrapper.plottingFlipScaleShown()
-            }
-        }
-
-        EaElements.CheckBox {
-            topPadding: 0
-            checked: Globals.BackendWrapper.plottingBkgShown
-            text: qsTr("Show background line")
-            ToolTip.text: qsTr("Checking this box will show the background reference line on the plot")
-            onToggled: {
-                Globals.BackendWrapper.plottingFlipBkgShown()
-            }
-        }
-    }
+    Gui.PlotControlRefLines {}
 }
+
diff --git a/EasyReflectometryApp/Gui/qmldir b/EasyReflectometryApp/Gui/qmldir
index d3151d58..9145745f 100644
--- a/EasyReflectometryApp/Gui/qmldir
+++ b/EasyReflectometryApp/Gui/qmldir
@@ -1,4 +1,5 @@
 module Gui
 
 ApplicationWindow ApplicationWindow.qml
+PlotControlRefLines PlotControlRefLines.qml
 StatusBar StatusBar.qml
diff --git a/pyproject.toml b/pyproject.toml
index 58c688b2..22977614 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,7 +32,7 @@ classifiers = [
 requires-python = '>=3.11'
 dependencies = [
   'EasyApp @ git+https://github.com/EasyScience/EasyApp.git@develop',
-  'easyreflectometry @ git+https://github.com/EasyScience/EasyReflectometryLib.git@append_sample',
+  'easyreflectometry @ git+https://github.com/EasyScience/EasyReflectometryLib.git@develop',
   'asteval',
   'PySide6',
   'toml',