fix: The QML cross-component id resolution for root.waferDetected was failing

silently. Exposing a proper waferDetected property on the Python
DeviceController ensures reliable gating, and resetting it on refresh
blocks the actions until the next successful detection.

.gitignore

@@ -40,3 +40,21 @@ dist/
 *.spec
 *.icns
 *.ico
+
+# Runtime scratch data
+tmp/
+
+# Superpowers brainstorming visual companion
+.superpowers/
+.llm-wiki/
+.agents/
+.pi/
+
+# Planning / personal docs (root level)
+CLAUDE.md
+LEARNINGS.md
+MIGRATION.md
+AGENTS.md
+CONVENTIONS.md
+specs/
+graphify-out/

README.md

@@ -14,11 +14,13 @@ The `ISenseCloud` application provides a real-time monitor and analysis dashboar
 - **Custom Safety Limits & Thresholds**: Configurable alarm thresholds and set-points with automatic alerts when temperatures diverge from normal boundaries.
 
 ### App Showcase
+
 ![ISenseCloud UI displaying successful connection on COM6](image-1.png)
 *Figure 1: Main Status Dashboard displaying successful connection, active serial communications, and automated logging terminal.*
 
 > [!NOTE]
 > **Take Screenshots for Visual Placeholders:**
+>
 > - **Wafer Heatmap Tab**: Take a screenshot of the Wafer Map tab showing the radial heatmap interpolation, save it to `docs/design/wafer_heatmap_tab.png` and add it here.
 > - **Temperature Trend Graph**: Take a screenshot of the Graph tab plotting multi-sensor trend lines, save it to `docs/design/temp_trend_tab.png` and add it here.
 
@@ -42,12 +44,15 @@ During the refactoring from the flat-layout prototype (`SettingTab` branch) to t
 From the project root:
 
 ### Option A: Using `uv` (Recommended)
+
 If you have [uv](https://docs.astral.sh/uv/) installed:
+
 ```bash
 uv sync
 ```
 
 ### Option B: Using `pip`
+
 ```bash
 python3 -m venv .venv
 source .venv/bin/activate   # or .venv\Scripts\activate on Windows
@@ -59,19 +64,21 @@ pip install -e .            # install the `pygui` package (src/ layout) in edita
 ## Run
 
 ### Launch PySide6 QML App
+
 ```bash
 make run
 ```
+
 This launches the Qt window and loads the `ISC` QML module from `src/pygui/ISC/Main.qml`.
 
 ## Development
 
-The project uses `uv` for dependency management and tooling, `Ruff` for linting and formatting, `Mypy` for static type checking, and `pytest` for unit tests. 
+The project uses `uv` for dependency management and tooling, `Ruff` for linting and formatting, `Mypy` for static type checking, and `pytest` for unit tests.
 
 A `Makefile` is provided to simplify common development and verification tasks:
 
 | Command | Description |
-|---------|-------------|
+| --------- | ------------- |
 | `make install` | Sync dependencies and set up the local `.venv` using `uv` |
 | `make run` | Launch the ISenseCloud application |
 | `make test` | Run the `pytest` test suite |
@@ -83,6 +90,7 @@ A `Makefile` is provided to simplify common development and verification tasks:
 ### Ruff Configuration
 
 Ruff is configured in `pyproject.toml` to enforce:
+
 - **E/W**: Pycodestyle errors and warnings
 - **F**: Pyflakes linter rules
 - **I**: Import sorting (isort parity)
@@ -174,11 +182,13 @@ Window {
 - If the app does not start, verify the virtual environment is active and dependencies are installed:
 
   *Using `uv`:*
+
   ```bash
   uv sync
   ```
 
   *Using `pip`:*
+
   ```bash
   source .venv/bin/activate   # or .venv\Scripts\activate on Windows
   pip install -r requirements.txt
@@ -186,18 +196,21 @@ Window {
 
 - If no window appears, ensure you are running in a desktop session with GUI access.
 
-- **Windows COM Port Connection Issues:** 
+- **Windows COM Port Connection Issues:**
-  * Standard Windows serial drivers don't support custom baud rates (e.g. `888888`), throwing an expected `OSError(22)` warning before falling back to `115200` baud.
+  - Standard Windows serial drivers don't support custom baud rates (e.g. `888888`), throwing an expected `OSError(22)` warning before falling back to `115200` baud.
 
 ### Step-by-Step Windows Simulator Connection Guide
 
 #### Step 1: Create the Virtual Serial Port Bridge
+
 Open **HHD Virtual Serial Port Tools**. Under the **Local Bridges** panel on the left, click the green **`+`** (Add) button to create a new port pair. Configure it to bridge **`COM5 ↔ COM6`**.
 
 ![HHD Virtual Serial Port Tools showing COM5 ↔ COM6 Local Bridge](image.png)
 
 #### Step 2: Configure and Start the Wafer Simulator
+
 Launch the **Wafer Simulator Control Panel** (`wafer_sim_gui.py`):
+
 1. Set the **Serial Port** to **`COM5`**.
 2. **Uncheck** the `Auto-create Virtual Port (com0com)` checkbox.
 3. Choose your desired **Wafer Type** (e.g., `aepwafer`) and **Family Code** (e.g., `A`).
@@ -206,6 +219,7 @@ Launch the **Wafer Simulator Control Panel** (`wafer_sim_gui.py`):
 ![Wafer Simulator Control Panel configured on COM5 and streaming](image-2.png)
 
 #### Step 3: Run the UI and Connect
+
 Launch the `pygui` client application. On the left navigation rail, click **DETECT WAFER**. The application will scan all active COM ports, automatically detect the virtual wafer simulator on **`COM6`**, and update the status indicator to **Connected** (green).
 
 ![ISenseCloud UI displaying successful connection on COM6](image-1.png)

src/pygui/ISC/HomePage.qml

@@ -17,20 +17,6 @@ Rectangle {
     border.color: Theme.outerFrameBorder
     border.width: Theme.borderStrong
 
-    // ===== Global ToolTip Styling =====
-    ToolTip.toolTip.background: Rectangle {
-        color: Theme.cardBackground
-        border.color: Theme.sideBorder
-        border.width: 1
-        radius: Theme.radiusXs
-    }
-    ToolTip.toolTip.contentItem: Text {
-        text: ToolTip.toolTip.text
-        color: Theme.headingColor
-        font.pixelSize: Theme.fontXs
-        font.family: Theme.uiFontFamily
-    }
-
     // ===== View State =====
     property int selectedTabIndex: 0
     onSelectedTabIndexChanged: {
@@ -420,43 +406,6 @@ Rectangle {
                         }
                     }
 
-                    component PanelCheckBox: CheckBox {
-                        id: toggle
-                        indicator: Rectangle {
-                            implicitWidth: 18
-                            implicitHeight: 18
-                            x: toggle.leftPadding
-                            y: parent.height / 2 - height / 2
-                            radius: Theme.radiusXs
-                            color: toggle.checked ? Theme.primaryAccent : "transparent"
-                            border.width: Theme.borderThin
-                            border.color: toggle.checked ? Theme.primaryAccent : Theme.fieldBorder
-
-                            Behavior on color { ColorAnimation { duration: Theme.durationFast } }
-                            Behavior on border.color { ColorAnimation { duration: Theme.durationFast } }
-
-                            IconImage {
-                                anchors.centerIn: parent
-                                source: "Tabs/icons/check.svg"
-                                width: 12; height: 12
-                                sourceSize.width: 12
-                                sourceSize.height: 12
-                                color: Theme.panelBackground
-                                opacity: toggle.checked ? 1.0 : 0.0
-                                Behavior on opacity { NumberAnimation { duration: Theme.durationFast } }
-                            }
-                        }
-
-                        contentItem: Text {
-                            text: toggle.text
-                            color: Theme.headingColor
-                            font.family: Theme.uiFontFamily
-                            verticalAlignment: Text.AlignVCenter
-                            leftPadding: toggle.indicator.width + toggle.spacing
-                            font.pixelSize: toggle.font.pixelSize || Theme.fontXs
-                        }
-                    }
-
                     ColumnLayout {
                         id: runCompCol
                         anchors.fill: parent
@@ -498,8 +447,10 @@ Rectangle {
                                     color: Theme.bodyColor
                                     anchors.centerIn: parent
                                 }
-                                ToolTip.visible: resetRunBtn.hovered
+                                AppToolTip {
-                                ToolTip.text: "Reset comparison"
+                                    visible: resetRunBtn.hovered
+                                    text: "Reset comparison"
+                                }
                             }
                         }
 
@@ -562,11 +513,13 @@ Rectangle {
                             readonly property bool sameFile: !!dt && fileA !== "" && fileA === dt.compareFileB
                             readonly property string gateError: !!dt ? dt.familyGateError : ""
                             enabled: !!dt && fileA !== "" && dt.compareFileB !== "" && !sameFile && !dt.comparing && !masterMissing && gateError === ""
-                            ToolTip.visible: (sameFile || masterMissing || gateError !== "") && hovered
+                            AppToolTip {
-                            ToolTip.text: masterMissing
+                                visible: (compareRunBtn.sameFile || compareRunBtn.masterMissing || compareRunBtn.gateError !== "") && compareRunBtn.hovered
-                                ? "No master file registered for this wafer type (Settings → Master Files)"
+                                text: compareRunBtn.masterMissing
-                                : gateError !== "" ? gateError
+                                    ? "No master file registered for this wafer type (Settings → Master Files)"
-                                : "Choose two different runs to compare"
+                                    : compareRunBtn.gateError !== "" ? compareRunBtn.gateError
+                                    : "Choose two different runs to compare"
+                            }
                             onClicked: {
                                 dt.comparing = true
                                 dt.clearResults()
@@ -617,100 +570,9 @@ Rectangle {
                     currentIndex: root.selectedTabIndex === 0 ? 0 : 1
 
                     // ── Status tab: Hardware Actions + Log Actions ──────────
-                    ColumnLayout {
+                    StatusActionsPanel {
-                        spacing: Theme.sideRailSpacing
+                        Layout.fillWidth: true
-
+                        Layout.fillHeight: true
-                        Rectangle {
-                            Layout.fillWidth: true
-                            Layout.preferredHeight: hwActionsCol.implicitHeight + 28
-                            radius: Theme.sidePanelRadius
-                            border.color: Theme.sideBorder
-                            border.width: 1
-                            color: Theme.sidePanelBackground
-
-                            ColumnLayout {
-                                id: hwActionsCol
-                                anchors.fill: parent
-                                anchors.margins: 14
-                                spacing: 6
-
-                                Label {
-                                    text: "HARDWARE ACTIONS"
-                                    color: Theme.sideMutedText
-                                    font.family: Theme.uiFontFamily
-                                    font.pixelSize: Theme.fontSm
-                                    font.letterSpacing: 1.5
-                                    font.bold: true
-                                }
-
-                                RailActionButton {
-                                    label: "DETECT WAFER"
-                                    iconSource: "../icons/detect.svg"
-                                    Layout.fillWidth: true
-                                    enabled: !deviceController.operationInProgress
-                                    onClicked: root._doDetect()
-                                }
-
-                                RailActionButton {
-                                    label: "READ MEMORY"
-                                    iconSource: "../icons/read.svg"
-                                    Layout.fillWidth: true
-                                    enabled: root.waferDetected
-                                    onClicked: deviceController.readMemoryAsync()
-                                }
-
-                                RailActionButton {
-                                    label: "ERASE MEMORY"
-                                    iconSource: "../icons/erase.svg"
-                                    Layout.fillWidth: true
-                                    destructive: true
-                                    enabled: root.waferDetected
-                                    onClicked: deviceController.eraseMemory(
-                                        deviceController.selectedPort)
-                                }
-                            }
-                        }
-
-                        Rectangle {
-                            Layout.fillWidth: true
-                            Layout.preferredHeight: logActionsCol.implicitHeight + 28
-                            radius: Theme.sidePanelRadius
-                            border.color: Theme.sideBorder
-                            border.width: 1
-                            color: Theme.sidePanelBackground
-
-                            ColumnLayout {
-                                id: logActionsCol
-                                anchors.fill: parent
-                                anchors.margins: 14
-                                spacing: 6
-
-                                Label {
-                                    text: "LOG ACTIONS"
-                                    color: Theme.sideMutedText
-                                    font.family: Theme.uiFontFamily
-                                    font.pixelSize: Theme.fontSm
-                                    font.letterSpacing: 1.5
-                                    font.bold: true
-                                }
-
-                                RailActionButton {
-                                    label: "REFRESH SESSION"
-                                    iconSource: "../icons/refresh.svg"
-                                    Layout.fillWidth: true
-                                    onClicked: deviceController.clearSession()
-                                }
-
-                                RailActionButton {
-                                    label: "CLEAR LOG"
-                                    iconSource: "../icons/x.svg"
-                                    Layout.fillWidth: true
-                                    onClicked: deviceController.clearActivityLog()
-                                }
-                            }
-                        }
-
-                        Item { Layout.fillHeight: true }
                     }
 
                     // ── Map tab: Source file browser ──────────────
@@ -728,208 +590,14 @@ Rectangle {
                 }
 
                 // ── BOX 3: Hardware Status Footer ──────────────────────────
-                // Not relevant on the Data tab — Run Comparison takes its place above.
+                ConnectionFooter {
-                Rectangle {
                     Layout.fillWidth: true
-                    Layout.preferredHeight: Theme.sideFooterConnection
-                    visible: root.selectedTabIndex !== 1
-                    radius: Theme.sidePanelRadius
-                    border.color: Theme.sideBorder
-                    border.width: 1
-                    color: Theme.sidePanelBackground
-                    clip: true
-
-                    ColumnLayout {
-                        anchors.fill: parent
-                        anchors.margins: 14
-                        spacing: 6
-
-                        // Row 1: Title
-                        Label {
-                            text: "CONNECTION FLOW"
-                            color: Theme.sideMutedText
-                            font.family: Theme.uiFontFamily
-                            font.pixelSize: Theme.fontSm
-                            font.letterSpacing: 1.5
-                            font.bold: true
-                            Layout.fillWidth: true
-                            elide: Text.ElideRight
-                        }
-
-                        // Row 2: Port / descriptive text
-                        Label {
-                            Layout.fillWidth: true
-                            text: {
-                                if (deviceController.connectionStatus === "Connected")
-                                    return deviceController.selectedPort || "Connected"
-                                if (deviceController.selectedPort)
-                                    return deviceController.selectedPort
-                                return "No port selected"
-                            }
-                            color: Theme.bodyColor
-                            font.family: Theme.uiFontFamily
-                            font.pixelSize: Theme.fontSm
-                            elide: Text.ElideRight
-                        }
-
-                        Item { Layout.fillHeight: true }
-
-                        // Row 3: Mode chip left, status badge bottom-right
-                        RowLayout {
-                            spacing: 6
-                            Layout.fillWidth: true
-
-                            Rectangle {
-                                width: modeChipLabel.implicitWidth + 12
-                                height: 18
-                                radius: 4
-                                color: Theme.fieldBackground
-                                border.color: Theme.sideBorder
-                                border.width: 1
-
-                                Label {
-                                    id: modeChipLabel
-                                    anchors.centerIn: parent
-                                    text: streamController.mode
-                                        ? streamController.mode.toUpperCase() : "REVIEW"
-                                    color: Theme.sideMutedText
-                                    font.family: Theme.uiFontFamily
-                                    font.pixelSize: Theme.fontXs
-                                    font.bold: true
-                                    font.letterSpacing: 0.8
-                                }
-                            }
-
-                            Item { Layout.fillWidth: true }
-
-                            Rectangle {
-                                height: 18
-                                width: badgeLabel.implicitWidth + 14
-                                radius: 9
-                                color: {
-                                    var s = deviceController.connectionStatus
-                                    if (s === "Connected") return Theme.statusSuccessColor
-                                    if (s === "Disconnected") return Theme.statusErrorColor
-                                    return Theme.statusWarningColor
-                                }
-
-                                Label {
-                                    id: badgeLabel
-                                    anchors.centerIn: parent
-                                    text: deviceController.connectionStatus || "Disconnected"
-                                    color: Theme.statusBadgeText
-                                    font.pixelSize: Theme.fontXs
-                                    font.bold: true
-                                }
-                            }
-                        }
-                    }
                 }
 
                 // ── BOX 4: Utility Buttons ─────────────────────────────────
-                Rectangle {
+                UtilityFooter {
+                    id: utilFooter
                     Layout.fillWidth: true
-                    Layout.preferredHeight: Theme.sideFooterUtility
-                    radius: Theme.sidePanelRadius
-                    border.color: Theme.sideBorder
-                    border.width: 1
-                    color: Theme.sidePanelBackground
-
-                    RowLayout {
-                        anchors.fill: parent
-                        anchors.margins: 4
-                        spacing: 4
-
-                        Button {
-                            id: settingsBtn
-                            flat: true
-                            Layout.fillWidth: true
-                            Layout.fillHeight: true
-                            icon.source: "Tabs/icons/settings.svg"
-                            onClicked: settingsPopup.open()
-
-                            background: Rectangle {
-                                radius: 8
-                                color: settingsBtn.hovered
-                                    ? Theme.sideActiveBackground : "transparent"
-                            }
-
-                            contentItem: Row {
-                                spacing: 6
-                                anchors.centerIn: parent
-
-                                IconImage {
-                                    anchors.verticalCenter: parent.verticalCenter
-                                    width: 16
-                                    height: 16
-                                    source: "Tabs/icons/settings.svg"
-                                    sourceSize.width: 16
-                                    sourceSize.height: 16
-                                    color: Theme.headingColor
-                                    opacity: 0.75
-                                }
-
-                                Label {
-                                    anchors.verticalCenter: parent.verticalCenter
-                                    text: "SETTINGS"
-                                    color: Theme.headingColor
-                                    font.family: Theme.uiFontFamily
-                                    font.pixelSize: Theme.fontXs
-                                    font.bold: true
-                                    font.letterSpacing: 1.2
-                                    opacity: 0.8
-                                }
-                            }
-                        }
-
-                        Rectangle {
-                            width: 1
-                            height: 24
-                            color: Theme.sideBorder
-                        }
-
-                        Button {
-                            id: aboutBtn
-                            flat: true
-                            Layout.fillWidth: true
-                            Layout.fillHeight: true
-                            icon.source: "Tabs/icons/about.svg"
-                            onClicked: aboutDialog.open()
-
-                            background: Rectangle {
-                                radius: 8
-                                color: aboutBtn.hovered
-                                    ? Theme.sideActiveBackground : "transparent"
-                            }
-
-                            contentItem: Row {
-                                spacing: 6
-                                anchors.centerIn: parent
-
-                                IconImage {
-                                    anchors.verticalCenter: parent.verticalCenter
-                                    width: 16
-                                    height: 16
-                                    source: "Tabs/icons/about.svg"
-                                    sourceSize.width: 16
-                                    sourceSize.height: 16
-                                    color: Theme.headingColor
-                                    opacity: 0.75
-                                }
-
-                                Label {
-                                    anchors.verticalCenter: parent.verticalCenter
-                                    text: "ABOUT"
-                                    color: Theme.headingColor
-                                    font.family: Theme.uiFontFamily
-                                    font.pixelSize: Theme.fontXs
-                                    font.bold: true
-                                    font.letterSpacing: 1.2
-                                    opacity: 0.8
-                                }
-                            }
-                        }
-                    }
                 }
             }
         }

src/pygui/ISC/Tabs/DataTab.qml

@@ -3,6 +3,7 @@ import QtQuick.Controls
 import QtQuick.Controls.impl
 import QtQuick.Layouts
 import ISC
+import ISC.Tabs.components
 import ISC.Wafer
 
 // ===== Data Tab (Compare Content Only) =====
@@ -184,8 +185,8 @@ Item {
                 root.compareWaferShape = result.wafer_shape || "round"
                 root.compareWaferSize = result.wafer_size || 300.0
                 root.errorMessage = ""
-                scrubber.value = Math.floor(root.seriesLen / 2)
+                chartCard.frameIndex = Math.floor(root.seriesLen / 2)
-                scrubber.forceActiveFocus()
+                chartCard.focusScrubber()
                 if (root.frameCountA !== root.frameCountB) {
                     var timeA = root.timeDataA.length > 0 ? root.timeDataA[root.timeDataA.length - 1] : 0
                     var timeB = root.timeDataB.length > 0 ? root.timeDataB[root.timeDataB.length - 1] : 0
@@ -204,250 +205,6 @@ Item {
         }
     }
 
-    // ── Reusable pieces ────────────────────────────────────────────
-    component SectionTitle: Label {
-        font.family: Theme.uiFontFamily
-        font.pixelSize: Theme.fontSm
-        font.letterSpacing: 1.5
-        font.bold: true
-        color: Theme.sideMutedText
-    }
-
-    component PanelBox: Rectangle {
-        color: Theme.sidePanelBackground
-        border.color: Theme.sideBorder
-        border.width: 1
-        radius: Theme.sidePanelRadius
-    }
-
-    // Checkbox styled to match MapTab's right-rail ReadoutPanel (square accent
-    // indicator + check icon) instead of the platform-default CheckBox look.
-    component PanelCheckBox: CheckBox {
-        id: toggle
-        indicator: Rectangle {
-            implicitWidth: 18
-            implicitHeight: 18
-            x: toggle.leftPadding
-            y: parent.height / 2 - height / 2
-            radius: Theme.radiusXs
-            color: toggle.checked ? Theme.primaryAccent : "transparent"
-            border.width: Theme.borderThin
-            border.color: toggle.checked ? Theme.primaryAccent : Theme.fieldBorder
-
-            Behavior on color { ColorAnimation { duration: Theme.durationFast } }
-            Behavior on border.color { ColorAnimation { duration: Theme.durationFast } }
-
-            IconImage {
-                anchors.centerIn: parent
-                source: "icons/check.svg"
-                width: 12; height: 12
-                sourceSize.width: 12
-                sourceSize.height: 12
-                color: Theme.panelBackground
-                opacity: toggle.checked ? 1.0 : 0.0
-                Behavior on opacity { NumberAnimation { duration: Theme.durationFast } }
-            }
-        }
-
-        contentItem: Text {
-            text: toggle.text
-            color: Theme.headingColor
-            font.family: Theme.uiFontFamily
-            verticalAlignment: Text.AlignVCenter
-            leftPadding: toggle.indicator.width + toggle.spacing
-            font.pixelSize: toggle.font.pixelSize || Theme.fontXs
-        }
-    }
-
-    // Slider styled to match MapTab's right-rail heatmap slider (circular
-    // accent handle that grows slightly on press).
-    component PanelSlider: Slider {
-        id: panelSlider
-        handle: Rectangle {
-            x: panelSlider.leftPadding + panelSlider.visualPosition * (panelSlider.availableWidth - width)
-            y: panelSlider.topPadding + panelSlider.availableHeight / 2 - height / 2
-            implicitWidth: 18
-            implicitHeight: 18
-            radius: 9
-            color: Theme.primaryAccent
-            scale: panelSlider.pressed ? 1.15 : 1.0
-            Behavior on scale { NumberAnimation { duration: Theme.durationFast; easing.type: Theme.easeStandard } }
-        }
-    }
-
-    // Mini stat box under the alignment scrubber (styled to match DTW ReadoutCard)
-    component ScrubStat: Rectangle {
-        id: scrubStat
-        property string label
-        property string value
-        property color valueColor: Theme.headingColor
-        Layout.fillWidth: true
-        implicitHeight: 52
-        radius: Theme.radiusSm
-        color: Theme.subtleSectionBackground
-        border.color: Theme.cardBorder
-        border.width: 1
-
-        ColumnLayout {
-            anchors.fill: parent
-            anchors.margins: 8
-            spacing: 2
-            Label {
-                text: scrubStat.label.toUpperCase()
-                font.pixelSize: Theme.fontXs
-                font.bold: true
-                font.letterSpacing: 0.2
-                color: Theme.sideMutedText
-            }
-            Label {
-                text: scrubStat.value
-                font.pixelSize: Theme.fontLg
-                font.bold: true
-                font.family: Theme.codeFontFamily
-                color: scrubStat.valueColor
-            }
-        }
-    }
-
-    // Editable stat box for scrubber readout (styled to match DTW ReadoutCard)
-    component EditableScrubStat: Rectangle {
-        id: edStat
-        property string label
-        property real value
-        property string unit
-        property string extraText: ""
-        property bool editable: true
-        signal valueEdited(real newValue)
-
-        Layout.fillWidth: true
-        implicitHeight: edStatRow.implicitHeight + 16
-        radius: Theme.radiusSm
-        color: Theme.subtleSectionBackground
-        border.color: (edStat.editable && inputField.activeFocus) ? Theme.fieldBorderFocus : Theme.cardBorder
-        border.width: (edStat.editable && inputField.activeFocus) ? Theme.borderStrong : Theme.borderThin
-
-        RowLayout {
-            id: edStatRow
-            anchors.fill: parent
-            anchors.margins: 8
-            spacing: 6
-
-            ColumnLayout {
-                Layout.fillWidth: true
-                spacing: 2
-                Label {
-                    text: edStat.label.toUpperCase()
-                    font.pixelSize: Theme.fontXs
-                    font.bold: true
-                    font.letterSpacing: 0.2
-                    color: Theme.sideMutedText
-                }
-                RowLayout {
-                    spacing: 4
-                    TextField {
-                        id: inputField
-                        readOnly: !edStat.editable
-                        hoverEnabled: edStat.editable
-                        font.pixelSize: Theme.fontLg
-                        font.bold: true
-                        font.family: Theme.codeFontFamily
-                        color: edStat.editable ? Theme.headingColor : Theme.sideMutedText
-                        verticalAlignment: TextInput.AlignVCenter
-                        horizontalAlignment: TextInput.AlignHCenter
-                        background: Rectangle {
-                            visible: edStat.editable
-                            color: Theme.fieldBackground
-                            radius: Theme.radiusXs
-                            border.color: inputField.activeFocus ? Theme.fieldBorderFocus : (inputField.hovered ? Theme.fieldBorderFocus : Theme.fieldBorder)
-                            border.width: 1
-                        }
-                        padding: 0
-                        leftPadding: edStat.editable ? 6 : 0
-                        rightPadding: edStat.editable ? 6 : 0
-                        topPadding: edStat.editable ? 5 : 0
-                        bottomPadding: edStat.editable ? 5 : 0
-                        selectByMouse: edStat.editable
-                        inputMethodHints: edStat.label === "Time" ? Qt.ImhFormattedNumbersOnly : Qt.ImhDigitsOnly
-                        Layout.preferredWidth: edStat.editable ? Math.max(36, contentWidth + 12) : contentWidth
-                        Layout.preferredHeight: edStat.editable ? 32 : implicitHeight
-                        
-                        text: edStat.value.toFixed(edStat.label === "Time" ? 1 : 0)
-
-                        onEditingFinished: {
-                            var val = parseFloat(text)
-                            if (!isNaN(val)) {
-                                edStat.valueEdited(val)
-                            }
-                            text = edStat.value.toFixed(edStat.label === "Time" ? 1 : 0)
-                            scrubber.forceActiveFocus()
-                        }
-
-                        Connections {
-                            target: edStat
-                            function onValueChanged() {
-                                if (!inputField.activeFocus) {
-                                    inputField.text = edStat.value.toFixed(edStat.label === "Time" ? 1 : 0)
-                                }
-                            }
-                        }
-                    }
-                    Label {
-                        text: edStat.unit
-                        font.pixelSize: Theme.fontLg
-                        font.bold: true
-                        font.family: Theme.codeFontFamily
-                        color: edStat.editable ? Theme.headingColor : Theme.sideMutedText
-                        Layout.alignment: Qt.AlignVCenter
-                    }
-                }
-            }
-
-            Label {
-                visible: edStat.extraText !== ""
-                text: edStat.extraText
-                font.pixelSize: Theme.fontLg
-                font.bold: true
-                font.family: Theme.codeFontFamily
-                color: Theme.headingColor
-                Layout.alignment: Qt.AlignVCenter
-            }
-        }
-    }
-
-    // Large labeled value card for the DTW readout panel
-    component ReadoutCard: Rectangle {
-        id: readoutCard
-        property string label
-        property string value
-        property color valueColor: Theme.headingColor
-        Layout.fillWidth: true
-        implicitHeight: 52
-        radius: Theme.radiusSm
-        color: Theme.subtleSectionBackground
-        border.color: Theme.cardBorder
-        border.width: 1
-
-        ColumnLayout {
-            anchors.fill: parent
-            anchors.margins: 8
-            spacing: 2
-            Label {
-                text: readoutCard.label
-                font.pixelSize: Theme.fontXs
-                font.bold: true
-                font.letterSpacing: 0.2
-                color: Theme.sideMutedText
-            }
-            Label {
-                text: readoutCard.value
-                font.pixelSize: Theme.fontLg
-                font.bold: true
-                font.family: Theme.codeFontFamily
-                color: readoutCard.valueColor
-            }
-        }
-    }
-
     // ── Main Layout ───────────────────────────────────────────────
     ColumnLayout {
         anchors.fill: parent
@@ -506,533 +263,53 @@ Item {
                 spacing: 12
 
                 // Wafer Map Overlap View card
-                PanelBox {
+                OverlapMapCard {
                     Layout.fillWidth: true
                     Layout.fillHeight: true
                     Layout.minimumHeight: 220
-
+                    sensorLayout: root.compareSensorLayout
-                    ColumnLayout {
+                    diffValues: streamController.getSensorDiffAt(Math.round(chartCard.frameIndex))
-                        anchors.fill: parent
+                    diffBands: root.diffBands
-                        anchors.margins: 12
+                    waferShape: root.compareWaferShape
-                        spacing: 8
+                    waferSize: root.compareWaferSize
-
+                    overlapEnabled: sidePanel.overlapEnabled
-                        RowLayout {
+                    blendAmount: sidePanel.blendAmount
-                            Layout.fillWidth: true
-                            SectionTitle {
-                                text: "WAFER OVERLAP"
-                                Layout.fillWidth: true
-                            }
-                        }
-
-                        Rectangle {
-                            Layout.fillWidth: true
-                            Layout.fillHeight: true
-                            color: Theme.fieldBackground
-                            border.color: Theme.cardBorder
-                            border.width: 1
-                            radius: Theme.radiusSm
-                            clip: true
-
-                            WaferMapItem {
-                                id: overlapMapItem
-                                anchors.fill: parent
-                                visible: root.compareSensorLayout.length > 0 && enableOverlapCheck.checked
-                                sensors: root.compareSensorLayout
-                                values: streamController.getSensorDiffAt(scrubReadout.scrubIdx)
-                                bands: root.diffBands(overlapMapItem.values)
-                                shape: root.compareWaferShape
-                                size: root.compareWaferSize
-                                target: 0
-                                margin: 1.0
-                                blend: blendSlider.value / 100
-                                showLabels: true
-                                ringColor: Theme.waferRingColor
-                                axisColor: Theme.waferAxisColor
-                                lowColor: Theme.sensorLow
-                                inRangeColor: Theme.sensorInRange
-                                highColor: Theme.sensorHigh
-                                textColor: Theme.headingColor
-                            }
-
-                            ColumnLayout {
-                                anchors.centerIn: parent
-                                visible: root.compareSensorLayout.length === 0 || !enableOverlapCheck.checked
-                                spacing: 4
-                                IconImage {
-                                    Layout.alignment: Qt.AlignHCenter
-                                    source: "icons/map.svg"
-                                    width: 24; height: 24
-                                    sourceSize.width: 24
-                                    sourceSize.height: 24
-                                    color: Theme.sideMutedText
-                                }
-                                Label {
-                                    Layout.alignment: Qt.AlignHCenter
-                                    text: !enableOverlapCheck.checked ? "Overlap map disabled"
-                                        : "No sensor map available"
-                                    color: Theme.bodyColor
-                                    font.pixelSize: Theme.fontXs
-                                }
-                            }
-                        }
-                    }
                 }
 
                 // Chart card with alignment scrubber
-                PanelBox {
+                ComparisonChartCard {
+                    id: chartCard
                     Layout.fillWidth: true
-                    Layout.preferredHeight: chartCol.implicitHeight + 24
+                    trendDataA: root.trendDataA
-
+                    trendDataB: root.trendDataB
-                    ColumnLayout {
+                    seriesLen: root.seriesLen
-                        id: chartCol
+                    hasSeries: root.hasSeries
-                        anchors.fill: parent
+                    comparing: root.comparing
-                        anchors.margins: 12
-                        spacing: 8
-
-                        RowLayout {
-                            Layout.fillWidth: true
-                            SectionTitle {
-                                text: "CURVE OVERLAY"
-                                Layout.fillWidth: true
-                            }
-                            Row {
-                                spacing: 16
-                                visible: root.hasSeries
-                                Row {
-                                    spacing: 4
-                                    Rectangle { width: 12; height: 3; radius: 1.5; color: Theme.primaryAccent; anchors.verticalCenter: parent.verticalCenter }
-                                    Label { text: "Run A"; font.pixelSize: Theme.fontXs; color: Theme.bodyColor }
-                                    
-                                }
-                                Row {
-                                    spacing: 4
-                                    Rectangle { width: 12; height: 3; radius: 1.5; color: Theme.themeSkill; anchors.verticalCenter: parent.verticalCenter }
-                                    Label { text: "Run B"; font.pixelSize: Theme.fontXs; color: Theme.bodyColor }
-                                }
-                            }
-                        }
-
-                        Rectangle {
-                            Layout.fillWidth: true
-                            Layout.preferredHeight: 200
-                            color: Theme.fieldBackground
-                            border.color: Theme.cardBorder
-                            border.width: 1
-                            radius: Theme.radiusSm
-                            clip: true
-
-                            Canvas {
-                                id: overlayCanvas
-                                anchors.fill: parent
-                                visible: root.hasSeries
-
-                                readonly property real padLeft: 50
-                                readonly property real padRight: 16
-                                readonly property real padTop: 24
-                                readonly property real padBottom: 36
-
-                                // Nice tick step (1/2/5 × 10^k) — same scheme as TrendChartItem,
-                                // so labels land on round numbers instead of raw data min/max.
-                                function niceStep(rawStep) {
-                                    var mag = Math.pow(10, Math.floor(Math.log10(rawStep)))
-                                    return [1, 2, 5, 10].map(function (s) { return s * mag })
-                                                        .find(function (s) { return s >= rawStep })
-                                }
-
-                                function drawGrid(ctx, minV, maxV, yStep, dataLen) {
-                                    var plotW = width - padLeft - padRight
-                                    var plotH = height - padTop - padBottom
-                                    var range = (maxV - minV) || 1
-
-                                    ctx.strokeStyle = Theme.chartGridLine
-                                    ctx.lineWidth = 1
-                                    ctx.fillStyle = Theme.chartAxisText
-                                    ctx.font = "10px " + Theme.uiFontFamily
-                                    ctx.textAlign = "right"
-
-                                    var ySteps = Math.max(1, Math.round(range / yStep))
-                                    var yDec = Math.max(0, -Math.floor(Math.log10(yStep)))
-                                    for (var yi = 0; yi <= ySteps; yi++) {
-                                        var yFrac = yi / ySteps
-                                        var yPx = padTop + plotH * yFrac
-                                        var yVal = maxV - yFrac * range
-
-                                        ctx.beginPath()
-                                        ctx.moveTo(padLeft, yPx)
-                                        ctx.lineTo(padLeft + plotW, yPx)
-                                        ctx.stroke()
-
-                                        ctx.fillText(yVal.toFixed(yDec), padLeft - 6, yPx + 3)
-                                    }
-
-                                    ctx.textAlign = "center"
-                                    var xMax = dataLen - 1
-                                    if (xMax > 0) {
-                                        var xStep = niceStep(xMax / 5 || 1)
-                                        for (var xIdx = 0; xIdx <= xMax; xIdx += xStep) {
-                                            var xPx = padLeft + (xIdx / xMax) * plotW
-                                            ctx.fillText(xIdx.toString(), xPx, height - 20)
-                                        }
-                                    }
-
-                                    ctx.save()
-                                    ctx.translate(14, padTop + plotH / 2)
-                                    ctx.rotate(-Math.PI / 2)
-                                    ctx.textAlign = "center"
-                                    ctx.font = "12px " + Theme.uiFontFamily
-                                    ctx.fillText("Celcius (°C)", 0, 0)
-                                    ctx.restore()
-
-                                    ctx.textAlign = "center"
-                                    ctx.font = "12px " + Theme.uiFontFamily
-                                    ctx.fillText("Frame", padLeft + plotW / 2, height - 4)
-                                }
-
-                                function drawSeries(ctx, series, minV, range, color, dataLen) {
-                                    // x is mapped against the shared frame domain (dataLen), not the
-                                    // series' own length — otherwise a shorter run's line stretches to
-                                    // fill the whole plot instead of stopping where its data ends.
-                                    if (series.length < 2) return
-                                    var plotW = width - padLeft - padRight
-                                    var plotH = height - padTop - padBottom
-
-                                    ctx.strokeStyle = color
-                                    ctx.lineWidth = 2
-                                    ctx.beginPath()
-                                    for (var i = 0; i < series.length; i++) {
-                                        var x = padLeft + (i / (dataLen - 1)) * plotW
-                                        var y = padTop + plotH - ((series[i] - minV) / range) * plotH
-                                        if (i === 0) ctx.moveTo(x, y)
-                                        else ctx.lineTo(x, y)
-                                    }
-                                    ctx.stroke()
-                                }
-
-                                function drawScrubMarker(ctx) {
-                                    if (root.seriesLen < 2) return
-                                    var plotW = width - padLeft - padRight
-                                    var x = padLeft + (scrubber.value / (root.seriesLen - 1)) * plotW
-                                    ctx.strokeStyle = Theme.primaryAccent
-                                    ctx.lineWidth = 1.5
-                                    ctx.setLineDash([3, 3])
-                                    ctx.beginPath()
-                                    ctx.moveTo(x, padTop)
-                                    ctx.lineTo(x, height - padBottom)
-                                    ctx.stroke()
-                                    ctx.setLineDash([])
-                                }
-
-                                onPaint: {
-                                    var ctx = getContext("2d")
-                                    ctx.reset()
-                                    if (!root.hasSeries) return
-                                    var all = root.trendDataA.concat(root.trendDataB)
-                                    var minV = Math.min.apply(null, all)
-                                    var maxV = Math.max.apply(null, all)
-                                    var padding = (maxV - minV) * 0.05
-                                    minV -= padding
-                                    maxV += padding
-                                    // Snap bounds to nice-step multiples -> stable round-number axis
-                                    var yStep = niceStep((maxV - minV) / 5 || 1)
-                                    minV = Math.floor(minV / yStep) * yStep
-                                    maxV = Math.ceil(maxV / yStep) * yStep
-                                    var range = (maxV - minV) || 1
-
-                                    drawGrid(ctx, minV, maxV, yStep, root.seriesLen)
-                                    drawSeries(ctx, root.trendDataA, minV, range, Theme.primaryAccent, root.seriesLen)
-                                    drawSeries(ctx, root.trendDataB, minV, range, Theme.themeSkill, root.seriesLen)
-                                    drawScrubMarker(ctx)
-                                }
-
-                                Connections {
-                                    target: root
-                                    function onTrendDataAChanged() { overlayCanvas.requestPaint() }
-                                    function onTrendDataBChanged() { overlayCanvas.requestPaint() }
-                                }
-                                Connections {
-                                    target: scrubber
-                                    function onValueChanged() { overlayCanvas.requestPaint() }
-                                }
-                            }
-
-                            // Empty state
-                            ColumnLayout {
-                                anchors.centerIn: parent
-                                visible: !root.hasSeries
-                                spacing: 8
-
-                                IconImage {
-                                    Layout.alignment: Qt.AlignHCenter
-                                    visible: !root.comparing
-                                    source: "icons/bar-chart.svg"
-                                    width: 32; height: 32
-                                    sourceSize.width: 32
-                                    sourceSize.height: 32
-                                    color: Theme.sideMutedText
-                                }
-                                Label {
-                                    Layout.alignment: Qt.AlignHCenter
-                                    text: root.comparing ? "Running DTW comparison…" : "Select two runs and run comparison"
-                                    color: Theme.bodyColor
-                                    font.pixelSize: Theme.fontSm
-                                }
-                                Label {
-                                    Layout.alignment: Qt.AlignHCenter
-                                    visible: !root.comparing
-                                    text: "Click a run box on the right, then select a file from the left panel."
-                                    color: Theme.sideMutedText
-                                    font.pixelSize: Theme.fontXs
-                                }
-                            }
-                        }
-
-                        // ── Alignment Timeline Scrubber ────────────
-                        ColumnLayout {
-                            Layout.fillWidth: true
-                            spacing: 4
-                            visible: root.hasSeries
-
-                            Rectangle {
-                                Layout.fillWidth: true
-                                height: 1
-                                color: Theme.cardBorder
-                            }
-
-                            SectionTitle {
-                                text: "TIMELINE SCRUBBER"
-                                Layout.fillWidth: true
-                                Layout.topMargin: 8
-                            }
-
-                            Slider {
-                                id: scrubber
-                                Layout.fillWidth: true
-                                leftPadding: overlayCanvas.padLeft
-                                rightPadding: overlayCanvas.padRight
-                                from: 0
-                                to: Math.max(1, root.seriesLen - 1)
-                                stepSize: 1
-                                value: 0
-                            }
-
-
-                        }
-                    }
                 }
 }
 
             // --- Right Column: run selection, overlap settings, readout ---
-            ColumnLayout {
+            ComparisonSidePanel {
-                Layout.fillWidth: false
+                id: sidePanel
+                Layout.fillWidth: false                
                 Layout.preferredWidth: 280
                 Layout.minimumWidth: 280
                 Layout.maximumWidth: 280
                 Layout.fillHeight: true
-                spacing: 12
+                warpingDistance: root.warpingDistance
-
+                frameOffset: root.frameOffset
-                // Bento 3: DTW Comparison Readout
+                frameOffsetSeconds: root.frameOffsetSeconds
-                PanelBox {
+                maxSensorDeviation: root.maxSensorDeviation
-                    Layout.fillWidth: true
+                seriesLen: root.seriesLen
-                    Layout.preferredHeight: readoutCol.implicitHeight + 24
+                hasSeries: root.hasSeries
-
+                trendDataA: root.trendDataA
-                    ColumnLayout {
+                trendDataB: root.trendDataB
-                        id: readoutCol
+                timeDataA: root.timeDataA
-                        anchors.fill: parent
+                timeDataB: root.timeDataB
-                        anchors.margins: 12
+                frameForTime: root.frameForTime
-                        spacing: 8
+                frameIndex: chartCard.frameIndex
-
+                onFrameIndexRequested: (idx) => chartCard.frameIndex = idx
-                        SectionTitle { text: "DTW READOUT" }
+                onScrubberFocusRequested: chartCard.focusScrubber()
-
-                        ReadoutCard {
-                            label: "DTW ALIGNMENT DISTANCE"
-                            value: root.warpingDistance >= 0 ? root.warpingDistance.toFixed(2) : "--"
-                            valueColor: root.warpingDistance >= 0
-                                ? (root.warpingDistance < 50 ? Theme.metricGood : root.warpingDistance < 100 ? Theme.metricWarn : Theme.metricBad)
-                                : Theme.sideMutedText
-                        }
-                        ReadoutCard {
-                            label: "TEMPORAL FRAME OFFSET"
-                            value: root.warpingDistance >= 0
-                                ? ((root.frameOffset >= 0 ? "+" : "") + root.frameOffset + " frames / "
-                                   + (root.frameOffsetSeconds >= 0 ? "+" : "") + root.frameOffsetSeconds.toFixed(1) + "s")
-                                : "--"
-                            valueColor: root.warpingDistance >= 0 ? Theme.headingColor : Theme.sideMutedText
-                        }
-                        ReadoutCard {
-                            label: "MAX SENSOR DEVIATION"
-                            value: root.maxSensorDeviation >= 0 ? root.maxSensorDeviation.toFixed(2) + "°C" : "--"
-                            valueColor: root.maxSensorDeviation >= 0
-                                ? (root.maxSensorDeviation < 1.0 ? Theme.metricGood : root.maxSensorDeviation < 3.0 ? Theme.metricWarn : Theme.metricBad)
-                                : Theme.sideMutedText
-                        }
-                    }
-                }
-
-                // Bento 2: Overlap Map Settings
-                PanelBox {
-                    Layout.fillWidth: true
-                    Layout.preferredHeight: overlapCol.implicitHeight + 24
-
-                    ColumnLayout {
-                        id: overlapCol
-                        anchors.fill: parent
-                        anchors.margins: 12
-                        spacing: 8
-
-                        SectionTitle { text: "OVERLAP SETTINGS" }
-
-                        PanelCheckBox {
-                            id: enableOverlapCheck
-                            Layout.fillWidth: true
-                            checked: true
-                            text: "Enable Overlap Map"
-                            font.pixelSize: Theme.fontSm
-                        }
-
-                        ColumnLayout {
-                            Layout.fillWidth: true
-                            spacing: 6
-                            visible: enableOverlapCheck.checked
-
-                            Rectangle {
-                                Layout.fillWidth: true
-                                height: 1
-                                color: Theme.cardBorder
-                            }
-
-                            RowLayout {
-                                Layout.fillWidth: true
-                                spacing: 6
-                                Label {
-                                    text: "Blend"
-                                    font.pixelSize: Theme.fontSm
-                                    color: Theme.bodyColor
-                                    Layout.preferredWidth: 40
-                                }
-                                PanelSlider {
-                                    id: blendSlider
-                                    Layout.fillWidth: true
-                                    from: 0; to: 100; value: 50
-                                    stepSize: 1
-                                }
-                                Label {
-                                    text: Math.round(blendSlider.value) + "%"
-                                    font.pixelSize: Theme.fontSm
-                                    color: Theme.sideMutedText
-                                    Layout.preferredWidth: 30
-                                }
-                            }
-
-                            // Diff color legend
-                            Row {
-                                Layout.fillWidth: true
-                                spacing: 10
-                                Row {
-                                    spacing: 3
-                                    Rectangle { width: 8; height: 8; radius: 4; color: Theme.sensorLow; anchors.verticalCenter: parent.verticalCenter }
-                                    Label { text: "B cooler"; font.pixelSize: Theme.fontSm; color: Theme.sideMutedText }
-                                }
-                                Row {
-                                    spacing: 3
-                                    Rectangle { width: 8; height: 8; radius: 4; color: Theme.sensorInRange; anchors.verticalCenter: parent.verticalCenter }
-                                    Label { text: "Match"; font.pixelSize: Theme.fontSm; color: Theme.sideMutedText }
-                                }
-                                Row {
-                                    spacing: 3
-                                    Rectangle { width: 8; height: 8; radius: 4; color: Theme.sensorHigh; anchors.verticalCenter: parent.verticalCenter }
-                                    Label { text: "B hotter"; font.pixelSize: Theme.fontSm; color: Theme.sideMutedText }
-                                }
-                            }
-                        }
-                    }
-                }
-
-                // Bento: Frame / Time Controls
-                PanelBox {
-                    Layout.fillWidth: true
-                    Layout.preferredHeight: frameTimeCol.implicitHeight + 32
-
-                    ColumnLayout {
-                        id: frameTimeCol
-                        anchors.fill: parent
-                        anchors.margins: 16
-                        spacing: 20
-
-                        SectionTitle { text: "FRAME / TIME" }
-
-                        EditableScrubStat {
-                            label: "Frame"
-                            value: scrubReadout.scrubIdx
-                            unit: "/ " + Math.max(0, root.seriesLen - 1) + (Math.max(0, root.seriesLen - 1) <= 1 ? " frame" : " frames")
-                            editable: root.hasSeries
-                            onValueEdited: (newValue) => {
-                                var maxVal = Math.max(0, root.seriesLen - 1)
-                                var val = Math.max(0, Math.min(newValue, maxVal))
-                                scrubber.value = val
-                            }
-                        }
-
-                        EditableScrubStat {
-                            label: "Time"
-                            value: scrubReadout.scrubTime
-                            unit: "/ " + scrubReadout.maxTime.toFixed(1) + "s"
-                            editable: root.hasSeries
-                            onValueEdited: (newValue) => {
-                                var closestIdx = root.frameForTime(newValue)
-                                scrubber.value = closestIdx
-                            }
-                        }
-                    }
-                }
-
-                // Bento: Scrub Readout
-                PanelBox {
-                    Layout.fillWidth: true
-                    Layout.preferredHeight: scrubReadout.implicitHeight + 24
-
-                    ColumnLayout {
-                        id: scrubReadout
-                        anchors.fill: parent
-                        anchors.margins: 12
-                        spacing: 8
-
-                        readonly property int scrubIdx: Math.round(scrubber.value)
-                        readonly property bool hasA: scrubIdx < root.trendDataA.length
-                        readonly property bool hasB: scrubIdx < root.trendDataB.length
-                        readonly property real tempA: hasA ? root.trendDataA[scrubIdx] : 0
-                        readonly property real tempB: hasB ? root.trendDataB[scrubIdx] : 0
-                        readonly property real scrubTime: {
-                            var t = scrubIdx < root.timeDataA.length ? root.timeDataA[scrubIdx]
-                                  : (scrubIdx < root.timeDataB.length ? root.timeDataB[scrubIdx] : 0)
-                            return t
-                        }
-                        readonly property real maxTime: {
-                            var ta = root.timeDataA.length > 0 ? root.timeDataA[root.timeDataA.length - 1] : 0
-                            var tb = root.timeDataB.length > 0 ? root.timeDataB[root.timeDataB.length - 1] : 0
-                            return Math.max(ta, tb)
-                        }
-
-                        SectionTitle { text: "SCRUBBER READOUT" }
-
-                        ScrubStat {
-                            label: "Temp (Run A)"
-                            value: scrubReadout.hasA ? scrubReadout.tempA.toFixed(1) + "°C" : "none"
-                            valueColor: Theme.primaryAccent
-                        }
-                        ScrubStat {
-                            label: "Temp (Run B)"
-                            value: scrubReadout.hasB ? scrubReadout.tempB.toFixed(1) + "°C" : "none"
-                            valueColor: Theme.themeSkill
-                        }
-                        ScrubStat {
-                            label: "Difference"
-                            value: (scrubReadout.hasA && scrubReadout.hasB)
-                                ? Math.abs(scrubReadout.tempA - scrubReadout.tempB).toFixed(1) + "°C" : "none"
-                        }
-                    }
-                }
-
-                Item { Layout.fillHeight: true }
             }
         }
     }

src/pygui/ISC/Tabs/SettingsTab.qml

@@ -4,6 +4,7 @@ import QtQuick.Controls.impl
 import QtQuick.Layouts
 import QtQuick.Dialogs
 import ISC
+import ISC.Tabs.components
 
 Item {
     id: root

src/pygui/ISC/Tabs/WaferMapTab.qml

@@ -98,9 +98,11 @@ Item {
                     implicitHeight: 34
                     // Disabled controls swallow no events at all, so hover for the
                     // "why is this greyed out" tooltip needs its own MouseArea.
-                    ToolTip.visible: disabledHover.containsMouse && !enabled
+                    AppToolTip {
-                    ToolTip.text: "Connect a wafer to enable Live mode"
+                        visible: disabledHover.containsMouse && !liveTab.enabled
-                    ToolTip.delay: 300
+                        text: "Connect a wafer to enable Live mode"
+                        delay: 300
+                    }
                     MouseArea {
                         id: disabledHover
                         anchors.fill: parent

src/pygui/ISC/Tabs/components/AppToolTip.qml

@@ -0,0 +1,25 @@
+import QtQuick
+import QtQuick.Controls
+import ISC
+
+// Single seam for tooltip chrome — every hover tip in the app instantiates
+// this instead of styling QtQuick.Controls ToolTip.background/contentItem
+// inline at each call site.
+ToolTip {
+    id: root
+    delay: 400
+    font.pixelSize: Theme.fontXs
+    font.family: Theme.uiFontFamily
+
+    contentItem: Text {
+        text: root.text
+        color: Theme.headingColor
+        font: root.font
+    }
+    background: Rectangle {
+        color: Theme.cardBackground
+        border.color: Theme.sideBorder
+        border.width: 1
+        radius: Theme.radiusXs
+    }
+}

src/pygui/ISC/Tabs/components/ComparisonChartCard.qml

@@ -0,0 +1,260 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Controls.impl
+import QtQuick.Layouts
+import ISC
+
+// Curve overlay chart card with the alignment timeline scrubber.
+PanelBox {
+    id: card
+
+    required property var trendDataA
+    required property var trendDataB
+    required property int seriesLen
+    required property bool hasSeries
+    required property bool comparing
+
+    // Scrubber position — the internal Slider is private; consumers
+    // read/write frameIndex and call focusScrubber().
+    property alias frameIndex: scrubber.value
+
+    function focusScrubber() { scrubber.forceActiveFocus() }
+
+    implicitHeight: chartCol.implicitHeight + 24
+
+    ColumnLayout {
+        id: chartCol
+        anchors.fill: parent
+        anchors.margins: 12
+        spacing: 8
+
+        RowLayout {
+            Layout.fillWidth: true
+            SectionTitle {
+                text: "CURVE OVERLAY"
+                Layout.fillWidth: true
+            }
+            Row {
+                spacing: 16
+                visible: card.hasSeries
+                Row {
+                    spacing: 4
+                    Rectangle { width: 12; height: 3; radius: 1.5; color: Theme.primaryAccent; anchors.verticalCenter: parent.verticalCenter }
+                    Label { text: "Run A"; font.pixelSize: Theme.fontXs; color: Theme.bodyColor }
+
+                }
+                Row {
+                    spacing: 4
+                    Rectangle { width: 12; height: 3; radius: 1.5; color: Theme.themeSkill; anchors.verticalCenter: parent.verticalCenter }
+                    Label { text: "Run B"; font.pixelSize: Theme.fontXs; color: Theme.bodyColor }
+                }
+            }
+        }
+
+        Rectangle {
+            Layout.fillWidth: true
+            Layout.preferredHeight: 200
+            color: Theme.fieldBackground
+            border.color: Theme.cardBorder
+            border.width: 1
+            radius: Theme.radiusSm
+            clip: true
+
+            Canvas {
+                id: overlayCanvas
+                anchors.fill: parent
+                visible: card.hasSeries
+
+                readonly property real padLeft: 50
+                readonly property real padRight: 16
+                readonly property real padTop: 24
+                readonly property real padBottom: 36
+
+                // Nice tick step (1/2/5 × 10^k) — same scheme as TrendChartItem,
+                // so labels land on round numbers instead of raw data min/max.
+                function niceStep(rawStep) {
+                    var mag = Math.pow(10, Math.floor(Math.log10(rawStep)))
+                    return [1, 2, 5, 10].map(function (s) { return s * mag })
+                                        .find(function (s) { return s >= rawStep })
+                }
+
+                function drawGrid(ctx, minV, maxV, yStep, dataLen) {
+                    var plotW = width - padLeft - padRight
+                    var plotH = height - padTop - padBottom
+                    var range = (maxV - minV) || 1
+
+                    ctx.strokeStyle = Theme.chartGridLine
+                    ctx.lineWidth = 1
+                    ctx.fillStyle = Theme.chartAxisText
+                    ctx.font = "10px " + Theme.uiFontFamily
+                    ctx.textAlign = "right"
+
+                    var ySteps = Math.max(1, Math.round(range / yStep))
+                    var yDec = Math.max(0, -Math.floor(Math.log10(yStep)))
+                    for (var yi = 0; yi <= ySteps; yi++) {
+                        var yFrac = yi / ySteps
+                        var yPx = padTop + plotH * yFrac
+                        var yVal = maxV - yFrac * range
+
+                        ctx.beginPath()
+                        ctx.moveTo(padLeft, yPx)
+                        ctx.lineTo(padLeft + plotW, yPx)
+                        ctx.stroke()
+
+                        ctx.fillText(yVal.toFixed(yDec), padLeft - 6, yPx + 3)
+                    }
+
+                    ctx.textAlign = "center"
+                    var xMax = dataLen - 1
+                    if (xMax > 0) {
+                        var xStep = niceStep(xMax / 5 || 1)
+                        for (var xIdx = 0; xIdx <= xMax; xIdx += xStep) {
+                            var xPx = padLeft + (xIdx / xMax) * plotW
+                            ctx.fillText(xIdx.toString(), xPx, height - 20)
+                        }
+                    }
+
+                    ctx.save()
+                    ctx.translate(14, padTop + plotH / 2)
+                    ctx.rotate(-Math.PI / 2)
+                    ctx.textAlign = "center"
+                    ctx.font = "12px " + Theme.uiFontFamily
+                    ctx.fillText("Celcius (°C)", 0, 0)
+                    ctx.restore()
+
+                    ctx.textAlign = "center"
+                    ctx.font = "12px " + Theme.uiFontFamily
+                    ctx.fillText("Frame", padLeft + plotW / 2, height - 4)
+                }
+
+                function drawSeries(ctx, series, minV, range, color, dataLen) {
+                    // x is mapped against the shared frame domain (dataLen), not the
+                    // series' own length — otherwise a shorter run's line stretches to
+                    // fill the whole plot instead of stopping where its data ends.
+                    if (series.length < 2) return
+                    var plotW = width - padLeft - padRight
+                    var plotH = height - padTop - padBottom
+
+                    ctx.strokeStyle = color
+                    ctx.lineWidth = 2
+                    ctx.beginPath()
+                    for (var i = 0; i < series.length; i++) {
+                        var x = padLeft + (i / (dataLen - 1)) * plotW
+                        var y = padTop + plotH - ((series[i] - minV) / range) * plotH
+                        if (i === 0) ctx.moveTo(x, y)
+                        else ctx.lineTo(x, y)
+                    }
+                    ctx.stroke()
+                }
+
+                function drawScrubMarker(ctx) {
+                    if (card.seriesLen < 2) return
+                    var plotW = width - padLeft - padRight
+                    var x = padLeft + (scrubber.value / (card.seriesLen - 1)) * plotW
+                    ctx.strokeStyle = Theme.primaryAccent
+                    ctx.lineWidth = 1.5
+                    ctx.setLineDash([3, 3])
+                    ctx.beginPath()
+                    ctx.moveTo(x, padTop)
+                    ctx.lineTo(x, height - padBottom)
+                    ctx.stroke()
+                    ctx.setLineDash([])
+                }
+
+                onPaint: {
+                    var ctx = getContext("2d")
+                    ctx.reset()
+                    if (!card.hasSeries) return
+                    var all = card.trendDataA.concat(card.trendDataB)
+                    var minV = Math.min.apply(null, all)
+                    var maxV = Math.max.apply(null, all)
+                    var padding = (maxV - minV) * 0.05
+                    minV -= padding
+                    maxV += padding
+                    // Snap bounds to nice-step multiples -> stable round-number axis
+                    var yStep = niceStep((maxV - minV) / 5 || 1)
+                    minV = Math.floor(minV / yStep) * yStep
+                    maxV = Math.ceil(maxV / yStep) * yStep
+                    var range = (maxV - minV) || 1
+
+                    drawGrid(ctx, minV, maxV, yStep, card.seriesLen)
+                    drawSeries(ctx, card.trendDataA, minV, range, Theme.primaryAccent, card.seriesLen)
+                    drawSeries(ctx, card.trendDataB, minV, range, Theme.themeSkill, card.seriesLen)
+                    drawScrubMarker(ctx)
+                }
+
+                Connections {
+                    target: card
+                    function onTrendDataAChanged() { overlayCanvas.requestPaint() }
+                    function onTrendDataBChanged() { overlayCanvas.requestPaint() }
+                }
+                Connections {
+                    target: scrubber
+                    function onValueChanged() { overlayCanvas.requestPaint() }
+                }
+            }
+
+            // Empty state
+            ColumnLayout {
+                anchors.centerIn: parent
+                visible: !card.hasSeries
+                spacing: 8
+
+                IconImage {
+                    Layout.alignment: Qt.AlignHCenter
+                    visible: !card.comparing
+                    source: "../icons/bar-chart.svg"
+                    width: 32; height: 32
+                    sourceSize.width: 32
+                    sourceSize.height: 32
+                    color: Theme.sideMutedText
+                }
+                Label {
+                    Layout.alignment: Qt.AlignHCenter
+                    text: card.comparing ? "Running DTW comparison…" : "Select two runs and run comparison"
+                    color: Theme.bodyColor
+                    font.pixelSize: Theme.fontSm
+                }
+                Label {
+                    Layout.alignment: Qt.AlignHCenter
+                    visible: !card.comparing
+                    text: "Click a run box on the right, then select a file from the left panel."
+                    color: Theme.sideMutedText
+                    font.pixelSize: Theme.fontXs
+                }
+            }
+        }
+
+        // ── Alignment Timeline Scrubber ────────────
+        ColumnLayout {
+            Layout.fillWidth: true
+            spacing: 4
+            visible: card.hasSeries
+
+            Rectangle {
+                Layout.fillWidth: true
+                height: 1
+                color: Theme.cardBorder
+            }
+
+            SectionTitle {
+                text: "TIMELINE SCRUBBER"
+                Layout.fillWidth: true
+                Layout.topMargin: 8
+            }
+
+            Slider {
+                id: scrubber
+                Layout.fillWidth: true
+                leftPadding: overlayCanvas.padLeft
+                rightPadding: overlayCanvas.padRight
+                from: 0
+                to: Math.max(1, card.seriesLen - 1)
+                stepSize: 1
+                value: 0
+            }
+
+
+        }
+    }
+}

src/pygui/ISC/Tabs/components/ComparisonSidePanel.qml

@@ -0,0 +1,239 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Layouts
+import ISC
+
+// Right-column bento stack: DTW readout, overlap settings, frame/time
+// controls, and scrubber readout. Pure view — all comparison state lives
+// on DataTab; scrubber writes go up via frameIndexRequested.
+ColumnLayout {
+    id: panel
+
+    required property real warpingDistance
+    required property int frameOffset
+    required property real frameOffsetSeconds
+    required property real maxSensorDeviation
+    required property int seriesLen
+    required property bool hasSeries
+    required property var trendDataA
+    required property var trendDataB
+    required property var timeDataA
+    required property var timeDataB
+    required property var frameForTime   // function(seconds) -> frame index
+    required property real frameIndex    // bound from ComparisonChartCard.frameIndex
+
+    // Overlap settings outputs (consumed by OverlapMapCard via DataTab)
+    property alias overlapEnabled: enableOverlapCheck.checked
+    property alias blendAmount: blendSlider.value
+
+    signal frameIndexRequested(real idx)
+    signal scrubberFocusRequested()
+
+    spacing: 12
+
+    // Bento 3: DTW Comparison Readout
+    PanelBox {
+        Layout.fillWidth: true
+        Layout.preferredHeight: readoutCol.implicitHeight + 24
+
+        ColumnLayout {
+            id: readoutCol
+            anchors.fill: parent
+            anchors.margins: 12
+            spacing: 8
+
+            SectionTitle { text: "DTW READOUT" }
+
+            ReadoutStat {
+                label: "DTW ALIGNMENT DISTANCE"
+                value: panel.warpingDistance >= 0 ? panel.warpingDistance.toFixed(2) : "--"
+                valueColor: panel.warpingDistance >= 0
+                    ? (panel.warpingDistance < 50 ? Theme.metricGood : panel.warpingDistance < 100 ? Theme.metricWarn : Theme.metricBad)
+                    : Theme.sideMutedText
+            }
+            ReadoutStat {
+                label: "TEMPORAL FRAME OFFSET"
+                value: panel.warpingDistance >= 0
+                    ? ((panel.frameOffset >= 0 ? "+" : "") + panel.frameOffset + " frames / "
+                       + (panel.frameOffsetSeconds >= 0 ? "+" : "") + panel.frameOffsetSeconds.toFixed(1) + "s")
+                    : "--"
+                valueColor: panel.warpingDistance >= 0 ? Theme.headingColor : Theme.sideMutedText
+            }
+            ReadoutStat {
+                label: "MAX SENSOR DEVIATION"
+                value: panel.maxSensorDeviation >= 0 ? panel.maxSensorDeviation.toFixed(2) + "°C" : "--"
+                valueColor: panel.maxSensorDeviation >= 0
+                    ? (panel.maxSensorDeviation < 1.0 ? Theme.metricGood : panel.maxSensorDeviation < 3.0 ? Theme.metricWarn : Theme.metricBad)
+                    : Theme.sideMutedText
+            }
+        }
+    }
+
+    // Bento 2: Overlap Map Settings
+    PanelBox {
+        Layout.fillWidth: true
+        Layout.preferredHeight: overlapCol.implicitHeight + 24
+
+        ColumnLayout {
+            id: overlapCol
+            anchors.fill: parent
+            anchors.margins: 12
+            spacing: 8
+
+            SectionTitle { text: "OVERLAP SETTINGS" }
+
+            PanelCheckBox {
+                id: enableOverlapCheck
+                Layout.fillWidth: true
+                checked: true
+                text: "Enable Overlap Map"
+                font.pixelSize: Theme.fontSm
+            }
+
+            ColumnLayout {
+                Layout.fillWidth: true
+                spacing: 6
+                visible: enableOverlapCheck.checked
+
+                Rectangle {
+                    Layout.fillWidth: true
+                    height: 1
+                    color: Theme.cardBorder
+                }
+
+                RowLayout {
+                    Layout.fillWidth: true
+                    spacing: 6
+                    Label {
+                        text: "Blend"
+                        font.pixelSize: Theme.fontSm
+                        color: Theme.bodyColor
+                        Layout.preferredWidth: 40
+                    }
+                    PanelSlider {
+                        id: blendSlider
+                        Layout.fillWidth: true
+                        from: 0; to: 100; value: 50
+                        stepSize: 1
+                    }
+                    Label {
+                        text: Math.round(blendSlider.value) + "%"
+                        font.pixelSize: Theme.fontSm
+                        color: Theme.sideMutedText
+                        Layout.preferredWidth: 30
+                    }
+                }
+
+                // Diff color legend
+                Row {
+                    Layout.fillWidth: true
+                    spacing: 10
+                    Row {
+                        spacing: 3
+                        Rectangle { width: 8; height: 8; radius: 4; color: Theme.sensorLow; anchors.verticalCenter: parent.verticalCenter }
+                        Label { text: "B cooler"; font.pixelSize: Theme.fontSm; color: Theme.sideMutedText }
+                    }
+                    Row {
+                        spacing: 3
+                        Rectangle { width: 8; height: 8; radius: 4; color: Theme.sensorInRange; anchors.verticalCenter: parent.verticalCenter }
+                        Label { text: "Match"; font.pixelSize: Theme.fontSm; color: Theme.sideMutedText }
+                    }
+                    Row {
+                        spacing: 3
+                        Rectangle { width: 8; height: 8; radius: 4; color: Theme.sensorHigh; anchors.verticalCenter: parent.verticalCenter }
+                        Label { text: "B hotter"; font.pixelSize: Theme.fontSm; color: Theme.sideMutedText }
+                    }
+                }
+            }
+        }
+    }
+
+    // Bento: Frame / Time Controls
+    PanelBox {
+        Layout.fillWidth: true
+        Layout.preferredHeight: frameTimeCol.implicitHeight + 32
+
+        ColumnLayout {
+            id: frameTimeCol
+            anchors.fill: parent
+            anchors.margins: 16
+            spacing: 20
+
+            SectionTitle { text: "FRAME / TIME" }
+
+            EditableScrubStat {
+                label: "Frame"
+                value: scrubReadout.scrubIdx
+                unit: "/ " + Math.max(0, panel.seriesLen - 1) + (Math.max(0, panel.seriesLen - 1) <= 1 ? " frame" : " frames")
+                editable: panel.hasSeries
+                onValueEdited: (newValue) => {
+                    var maxVal = Math.max(0, panel.seriesLen - 1)
+                    var val = Math.max(0, Math.min(newValue, maxVal))
+                    panel.frameIndexRequested(val)
+                }
+                onEditingDone: panel.scrubberFocusRequested()
+            }
+
+            EditableScrubStat {
+                label: "Time"
+                value: scrubReadout.scrubTime
+                unit: "/ " + scrubReadout.maxTime.toFixed(1) + "s"
+                editable: panel.hasSeries
+                onValueEdited: (newValue) => {
+                    var closestIdx = panel.frameForTime(newValue)
+                    panel.frameIndexRequested(closestIdx)
+                }
+                onEditingDone: panel.scrubberFocusRequested()
+            }
+        }
+    }
+
+    // Bento: Scrub Readout
+    PanelBox {
+        Layout.fillWidth: true
+        Layout.preferredHeight: scrubReadout.implicitHeight + 24
+
+        ColumnLayout {
+            id: scrubReadout
+            anchors.fill: parent
+            anchors.margins: 12
+            spacing: 8
+
+            readonly property int scrubIdx: Math.round(panel.frameIndex)
+            readonly property bool hasA: scrubIdx < panel.trendDataA.length
+            readonly property bool hasB: scrubIdx < panel.trendDataB.length
+            readonly property real tempA: hasA ? panel.trendDataA[scrubIdx] : 0
+            readonly property real tempB: hasB ? panel.trendDataB[scrubIdx] : 0
+            readonly property real scrubTime: {
+                var t = scrubIdx < panel.timeDataA.length ? panel.timeDataA[scrubIdx]
+                      : (scrubIdx < panel.timeDataB.length ? panel.timeDataB[scrubIdx] : 0)
+                return t
+            }
+            readonly property real maxTime: {
+                var ta = panel.timeDataA.length > 0 ? panel.timeDataA[panel.timeDataA.length - 1] : 0
+                var tb = panel.timeDataB.length > 0 ? panel.timeDataB[panel.timeDataB.length - 1] : 0
+                return Math.max(ta, tb)
+            }
+
+            SectionTitle { text: "SCRUBBER READOUT" }
+
+            ReadoutStat {
+                label: "Temp (Run A)"
+                value: scrubReadout.hasA ? scrubReadout.tempA.toFixed(1) + "°C" : "none"
+                valueColor: Theme.primaryAccent
+            }
+            ReadoutStat {
+                label: "Temp (Run B)"
+                value: scrubReadout.hasB ? scrubReadout.tempB.toFixed(1) + "°C" : "none"
+                valueColor: Theme.themeSkill
+            }
+            ReadoutStat {
+                label: "Difference"
+                value: (scrubReadout.hasA && scrubReadout.hasB)
+                    ? Math.abs(scrubReadout.tempA - scrubReadout.tempB).toFixed(1) + "°C" : "none"
+            }
+        }
+    }
+
+    Item { Layout.fillHeight: true }
+}

src/pygui/ISC/Tabs/components/ConnectionFooter.qml

@@ -0,0 +1,102 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Layouts
+import ISC
+
+// ── BOX 3: Hardware Status Footer ──────────────────────────
+Rectangle {
+    Layout.fillWidth: true
+    Layout.preferredHeight: Theme.sideFooterConnection
+    visible: root.selectedTabIndex !== 1
+    radius: Theme.sidePanelRadius
+    border.color: Theme.sideBorder
+    border.width: 1
+    color: Theme.sidePanelBackground
+    clip: true
+
+    ColumnLayout {
+        anchors.fill: parent
+        anchors.margins: 14
+        spacing: 6
+
+        // Row 1: Title
+        Label {
+            text: "CONNECTION FLOW"
+            color: Theme.sideMutedText
+            font.family: Theme.uiFontFamily
+            font.pixelSize: Theme.fontSm
+            font.letterSpacing: 1.5
+            font.bold: true
+            Layout.fillWidth: true
+            elide: Text.ElideRight
+        }
+
+        // Row 2: Port / descriptive text
+        Label {
+            Layout.fillWidth: true
+            text: {
+                if (deviceController.connectionStatus === "Connected")
+                    return deviceController.selectedPort || "Connected"
+                if (deviceController.selectedPort)
+                    return deviceController.selectedPort
+                return "No port selected"
+            }
+            color: Theme.bodyColor
+            font.family: Theme.uiFontFamily
+            font.pixelSize: Theme.fontSm
+            elide: Text.ElideRight
+        }
+
+        Item { Layout.fillHeight: true }
+
+        // Row 3: Mode chip left, status badge bottom-right
+        RowLayout {
+            spacing: 6
+            Layout.fillWidth: true
+
+            Rectangle {
+                width: modeChipLabel.implicitWidth + 12
+                height: 18
+                radius: 4
+                color: Theme.fieldBackground
+                border.color: Theme.sideBorder
+                border.width: 1
+
+                Label {
+                    id: modeChipLabel
+                    anchors.centerIn: parent
+                    text: streamController.mode
+                        ? streamController.mode.toUpperCase() : "REVIEW"
+                    color: Theme.sideMutedText
+                    font.family: Theme.uiFontFamily
+                    font.pixelSize: Theme.fontXs
+                    font.bold: true
+                    font.letterSpacing: 0.8
+                }
+            }
+
+            Item { Layout.fillWidth: true }
+
+            Rectangle {
+                height: 18
+                width: badgeLabel.implicitWidth + 14
+                radius: 9
+                color: {
+                    var s = deviceController.connectionStatus
+                    if (s === "Connected") return Theme.statusSuccessColor
+                    if (s === "Disconnected") return Theme.statusErrorColor
+                    return Theme.statusWarningColor
+                }
+
+                Label {
+                    id: badgeLabel
+                    anchors.centerIn: parent
+                    text: deviceController.connectionStatus || "Disconnected"
+                    color: Theme.statusBadgeText
+                    font.pixelSize: Theme.fontXs
+                    font.bold: true
+                }
+            }
+        }
+    }
+}

src/pygui/ISC/Tabs/components/EditableScrubStat.qml

@@ -0,0 +1,113 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Layouts
+import ISC
+
+// Editable stat box for scrubber readout (styled to match DTW ReadoutCard)
+Rectangle {
+    id: edStat
+    property string label
+    property real value
+    property string unit
+    property string extraText: ""
+    property bool editable: true
+    signal valueEdited(real newValue)
+    // Fires when the input field commits (Enter/focus loss), even if the
+    // entered text was invalid — callers use it to hand focus back to the
+    // timeline scrubber, matching the pre-extraction behavior.
+    signal editingDone()
+
+    Layout.fillWidth: true
+    implicitHeight: edStatRow.implicitHeight + 16
+    radius: Theme.radiusSm
+    color: Theme.subtleSectionBackground
+    border.color: (edStat.editable && inputField.activeFocus) ? Theme.fieldBorderFocus : Theme.cardBorder
+    border.width: (edStat.editable && inputField.activeFocus) ? Theme.borderStrong : Theme.borderThin
+
+    RowLayout {
+        id: edStatRow
+        anchors.fill: parent
+        anchors.margins: 8
+        spacing: 6
+
+        ColumnLayout {
+            Layout.fillWidth: true
+            spacing: 2
+            Label {
+                text: edStat.label.toUpperCase()
+                font.pixelSize: Theme.fontXs
+                font.bold: true
+                font.letterSpacing: 0.2
+                color: Theme.sideMutedText
+            }
+            RowLayout {
+                spacing: 4
+                TextField {
+                    id: inputField
+                    readOnly: !edStat.editable
+                    hoverEnabled: edStat.editable
+                    font.pixelSize: Theme.fontLg
+                    font.bold: true
+                    font.family: Theme.codeFontFamily
+                    color: edStat.editable ? Theme.headingColor : Theme.sideMutedText
+                    verticalAlignment: TextInput.AlignVCenter
+                    horizontalAlignment: TextInput.AlignHCenter
+                    background: Rectangle {
+                        visible: edStat.editable
+                        color: Theme.fieldBackground
+                        radius: Theme.radiusXs
+                        border.color: inputField.activeFocus ? Theme.fieldBorderFocus : (inputField.hovered ? Theme.fieldBorderFocus : Theme.fieldBorder)
+                        border.width: 1
+                    }
+                    padding: 0
+                    leftPadding: edStat.editable ? 6 : 0
+                    rightPadding: edStat.editable ? 6 : 0
+                    topPadding: edStat.editable ? 5 : 0
+                    bottomPadding: edStat.editable ? 5 : 0
+                    selectByMouse: edStat.editable
+                    inputMethodHints: edStat.label === "Time" ? Qt.ImhFormattedNumbersOnly : Qt.ImhDigitsOnly
+                    Layout.preferredWidth: edStat.editable ? Math.max(36, contentWidth + 12) : contentWidth
+                    Layout.preferredHeight: edStat.editable ? 32 : implicitHeight
+
+                    text: edStat.value.toFixed(edStat.label === "Time" ? 1 : 0)
+
+                    onEditingFinished: {
+                        var val = parseFloat(text)
+                        if (!isNaN(val)) {
+                            edStat.valueEdited(val)
+                        }
+                        text = edStat.value.toFixed(edStat.label === "Time" ? 1 : 0)
+                        edStat.editingDone()
+                    }
+
+                    Connections {
+                        target: edStat
+                        function onValueChanged() {
+                            if (!inputField.activeFocus) {
+                                inputField.text = edStat.value.toFixed(edStat.label === "Time" ? 1 : 0)
+                            }
+                        }
+                    }
+                }
+                Label {
+                    text: edStat.unit
+                    font.pixelSize: Theme.fontLg
+                    font.bold: true
+                    font.family: Theme.codeFontFamily
+                    color: edStat.editable ? Theme.headingColor : Theme.sideMutedText
+                    Layout.alignment: Qt.AlignVCenter
+                }
+            }
+        }
+
+        Label {
+            visible: edStat.extraText !== ""
+            text: edStat.extraText
+            font.pixelSize: Theme.fontLg
+            font.bold: true
+            font.family: Theme.codeFontFamily
+            color: Theme.headingColor
+            Layout.alignment: Qt.AlignVCenter
+        }
+    }
+}

src/pygui/ISC/Tabs/components/OverlapMapCard.qml

@@ -0,0 +1,86 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Controls.impl
+import QtQuick.Layouts
+import ISC
+import ISC.Wafer
+
+// Wafer overlap map card — renders per-sensor Run A/Run B temperature
+// differences at the current scrub position.
+PanelBox {
+    id: card
+
+    required property var sensorLayout
+    required property var diffValues
+    required property var diffBands      // function(values) -> band thresholds
+    required property string waferShape
+    required property real waferSize
+    required property bool overlapEnabled
+    required property real blendAmount   // 0–100, percent
+
+    ColumnLayout {
+        anchors.fill: parent
+        anchors.margins: 12
+        spacing: 8
+
+        RowLayout {
+            Layout.fillWidth: true
+            SectionTitle {
+                text: "WAFER OVERLAP"
+                Layout.fillWidth: true
+            }
+        }
+
+        Rectangle {
+            Layout.fillWidth: true
+            Layout.fillHeight: true
+            color: Theme.fieldBackground
+            border.color: Theme.cardBorder
+            border.width: 1
+            radius: Theme.radiusSm
+            clip: true
+
+            WaferMapItem {
+                id: overlapMapItem
+                anchors.fill: parent
+                visible: card.sensorLayout.length > 0 && card.overlapEnabled
+                sensors: card.sensorLayout
+                values: card.diffValues
+                bands: card.diffBands(overlapMapItem.values)
+                shape: card.waferShape
+                size: card.waferSize
+                target: 0
+                margin: 1.0
+                blend: card.blendAmount / 100
+                showLabels: true
+                ringColor: Theme.waferRingColor
+                axisColor: Theme.waferAxisColor
+                lowColor: Theme.sensorLow
+                inRangeColor: Theme.sensorInRange
+                highColor: Theme.sensorHigh
+                textColor: Theme.headingColor
+            }
+
+            ColumnLayout {
+                anchors.centerIn: parent
+                visible: card.sensorLayout.length === 0 || !card.overlapEnabled
+                spacing: 4
+                IconImage {
+                    Layout.alignment: Qt.AlignHCenter
+                    source: "../icons/map.svg"
+                    width: 24; height: 24
+                    sourceSize.width: 24
+                    sourceSize.height: 24
+                    color: Theme.sideMutedText
+                }
+                Label {
+                    Layout.alignment: Qt.AlignHCenter
+                    text: !card.overlapEnabled ? "Overlap map disabled"
+                        : "No sensor map available"
+                    color: Theme.bodyColor
+                    font.pixelSize: Theme.fontXs
+                }
+            }
+        }
+    }
+}

src/pygui/ISC/Tabs/components/PanelBox.qml

@@ -0,0 +1,10 @@
+import QtQuick
+import ISC
+
+// Card container for the Data tab bento boxes.
+Rectangle {
+    color: Theme.sidePanelBackground
+    border.color: Theme.sideBorder
+    border.width: 1
+    radius: Theme.sidePanelRadius
+}

src/pygui/ISC/Tabs/components/PanelCheckBox.qml

@@ -0,0 +1,43 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Controls.impl
+import ISC
+
+// Checkbox styled to match MapTab's right-rail ReadoutPanel (square accent
+// indicator + check icon) instead of the platform-default CheckBox look.
+CheckBox {
+    id: toggle
+    indicator: Rectangle {
+        implicitWidth: 18
+        implicitHeight: 18
+        x: toggle.leftPadding
+        y: parent.height / 2 - height / 2
+        radius: Theme.radiusXs
+        color: toggle.checked ? Theme.primaryAccent : "transparent"
+        border.width: Theme.borderThin
+        border.color: toggle.checked ? Theme.primaryAccent : Theme.fieldBorder
+
+        Behavior on color { ColorAnimation { duration: Theme.durationFast } }
+        Behavior on border.color { ColorAnimation { duration: Theme.durationFast } }
+
+        IconImage {
+            anchors.centerIn: parent
+            source: "../icons/check.svg"
+            width: 12; height: 12
+            sourceSize.width: 12
+            sourceSize.height: 12
+            color: Theme.panelBackground
+            opacity: toggle.checked ? 1.0 : 0.0
+            Behavior on opacity { NumberAnimation { duration: Theme.durationFast } }
+        }
+    }
+
+    contentItem: Text {
+        text: toggle.text
+        color: Theme.headingColor
+        font.family: Theme.uiFontFamily
+        verticalAlignment: Text.AlignVCenter
+        leftPadding: toggle.indicator.width + toggle.spacing
+        font.pixelSize: toggle.font.pixelSize || Theme.fontXs
+    }
+}

src/pygui/ISC/Tabs/components/PanelSlider.qml

@@ -0,0 +1,19 @@
+import QtQuick
+import QtQuick.Controls
+import ISC
+
+// Slider styled to match MapTab's right-rail heatmap slider (circular
+// accent handle that grows slightly on press).
+Slider {
+    id: panelSlider
+    handle: Rectangle {
+        x: panelSlider.leftPadding + panelSlider.visualPosition * (panelSlider.availableWidth - width)
+        y: panelSlider.topPadding + panelSlider.availableHeight / 2 - height / 2
+        implicitWidth: 18
+        implicitHeight: 18
+        radius: 9
+        color: Theme.primaryAccent
+        scale: panelSlider.pressed ? 1.15 : 1.0
+        Behavior on scale { NumberAnimation { duration: Theme.durationFast; easing.type: Theme.easeStandard } }
+    }
+}

src/pygui/ISC/Tabs/components/ReadoutPanel.qml

@@ -481,8 +481,11 @@ ColumnLayout {
                     to: 1
                     value: 0
                     Layout.fillWidth: true
-                    ToolTip.visible: hovered
+
-                    ToolTip.text: Math.round(value * 100) + "%"
+                    AppToolTip {
+                        visible: heatmapSlider.hovered
+                        text: Math.round(heatmapSlider.value * 100) + "%"
+                    }
 
                     handle: Rectangle {
                         x: heatmapSlider.leftPadding + heatmapSlider.visualPosition * (heatmapSlider.availableWidth - width)

src/pygui/ISC/Tabs/components/ReadoutStat.qml

@@ -0,0 +1,39 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Layouts
+import ISC
+
+// Small labeled value tile — DTW readout panel, scrubber readout, and any
+// other compact label/value stat display share this one shape.
+Rectangle {
+    id: readoutStat
+    property string label
+    property string value
+    property color valueColor: Theme.headingColor
+    Layout.fillWidth: true
+    implicitHeight: 52
+    radius: Theme.radiusSm
+    color: Theme.subtleSectionBackground
+    border.color: Theme.cardBorder
+    border.width: 1
+
+    ColumnLayout {
+        anchors.fill: parent
+        anchors.margins: 8
+        spacing: 2
+        Label {
+            text: readoutStat.label.toUpperCase()
+            font.pixelSize: Theme.fontXs
+            font.bold: true
+            font.letterSpacing: 0.2
+            color: Theme.sideMutedText
+        }
+        Label {
+            text: readoutStat.value
+            font.pixelSize: Theme.fontLg
+            font.bold: true
+            font.family: Theme.codeFontFamily
+            color: readoutStat.valueColor
+        }
+    }
+}

src/pygui/ISC/Tabs/components/SectionTitle.qml

@@ -0,0 +1,12 @@
+import QtQuick
+import QtQuick.Controls
+import ISC
+
+// Uppercase card heading — shared by the Data tab cards.
+Label {
+    font.family: Theme.uiFontFamily
+    font.pixelSize: Theme.fontSm
+    font.letterSpacing: 1.5
+    font.bold: true
+    color: Theme.sideMutedText
+}

src/pygui/ISC/Tabs/components/SelectFileDialog.qml

@@ -186,7 +186,7 @@ Dialog {
             implicitHeight: 32
             onClicked: root.close()
             contentItem: IconImage {
-                source: "icons/x.svg"
+                source: "../icons/x.svg"
                 width: 14; height: 14
                 sourceSize.width: 14
                 sourceSize.height: 14

src/pygui/ISC/Tabs/components/SourcePanel.qml

@@ -46,24 +46,9 @@ ColumnLayout {
                 csvEditorDialog.open();
             }
 
-            ToolTip {
+            AppToolTip {
-                id: editTooltip
                 visible: editBtn.hovered
                 text: "Edit"
-                delay: 400
-                font.pixelSize: Theme.fontXs
-                font.family: Theme.uiFontFamily
-                contentItem: Text {
-                    text: editTooltip.text
-                    color: Theme.headingColor
-                    font: editTooltip.font
-                }
-                background: Rectangle {
-                    color: Theme.cardBackground
-                    border.color: Theme.sideBorder
-                    border.width: 1
-                    radius: Theme.radiusXs
-                }
             }
         }
 
@@ -84,24 +69,9 @@ ColumnLayout {
             }
             onClicked: file_browser.refreshFiles()
 
-            ToolTip {
+            AppToolTip {
-                id: refreshTooltip
                 visible: refreshBtn.hovered
                 text: "Refresh"
-                delay: 400
-                font.pixelSize: Theme.fontXs
-                font.family: Theme.uiFontFamily
-                contentItem: Text {
-                    text: refreshTooltip.text
-                    color: Theme.headingColor
-                    font: refreshTooltip.font
-                }
-                background: Rectangle {
-                    color: Theme.cardBackground
-                    border.color: Theme.sideBorder
-                    border.width: 1
-                    radius: Theme.radiusXs
-                }
             }
         }
     }

src/pygui/ISC/Tabs/components/StatusActionsPanel.qml

@@ -0,0 +1,104 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Controls.impl
+import QtQuick.Layouts
+import ISC
+import ISC.Tabs.components
+
+// ── Status tab: Hardware Actions + Log Actions ──────────
+ColumnLayout {
+    spacing: Theme.sideRailSpacing
+
+    Rectangle {
+        Layout.fillWidth: true
+        Layout.preferredHeight: hwActionsCol.implicitHeight + 28
+        radius: Theme.sidePanelRadius
+        border.color: Theme.sideBorder
+        border.width: 1
+        color: Theme.sidePanelBackground
+
+        ColumnLayout {
+            id: hwActionsCol
+            anchors.fill: parent
+            anchors.margins: 14
+            spacing: 6
+
+            Label {
+                text: "HARDWARE ACTIONS"
+                color: Theme.sideMutedText
+                font.family: Theme.uiFontFamily
+                font.pixelSize: Theme.fontSm
+                font.letterSpacing: 1.5
+                font.bold: true
+            }
+
+            RailActionButton {
+                label: "DETECT WAFER"
+                iconSource: "../icons/detect.svg"
+                Layout.fillWidth: true
+                enabled: !deviceController.operationInProgress
+                onClicked: root._doDetect()
+            }
+
+            RailActionButton {
+                label: "READ MEMORY"
+                iconSource: "../icons/read.svg"
+                Layout.fillWidth: true
+                enabled: deviceController.waferDetected && !deviceController.operationInProgress
+                onClicked: deviceController.readMemoryAsync()
+            }
+
+            RailActionButton {
+                label: "ERASE MEMORY"
+                iconSource: "../icons/erase.svg"
+                Layout.fillWidth: true
+                destructive: true
+                enabled: deviceController.waferDetected && !deviceController.operationInProgress
+                onClicked: deviceController.eraseMemory(
+                    deviceController.selectedPort)
+            }
+        }
+    }
+
+    Rectangle {
+        Layout.fillWidth: true
+        Layout.preferredHeight: logActionsCol.implicitHeight + 28
+        radius: Theme.sidePanelRadius
+        border.color: Theme.sideBorder
+        border.width: 1
+        color: Theme.sidePanelBackground
+
+        ColumnLayout {
+            id: logActionsCol
+            anchors.fill: parent
+            anchors.margins: 14
+            spacing: 6
+
+            Label {
+                text: "LOG ACTIONS"
+                color: Theme.sideMutedText
+                font.family: Theme.uiFontFamily
+                font.pixelSize: Theme.fontSm
+                font.letterSpacing: 1.5
+                font.bold: true
+            }
+
+            RailActionButton {
+                label: "REFRESH SESSION"
+                iconSource: "../icons/refresh.svg"
+                Layout.fillWidth: true
+                enabled: !deviceController.operationInProgress
+                onClicked: deviceController.clearSession()
+            }
+
+            RailActionButton {
+                label: "CLEAR LOG"
+                iconSource: "../icons/x.svg"
+                Layout.fillWidth: true
+                onClicked: deviceController.clearActivityLog()
+            }
+        }
+    }
+
+    Item { Layout.fillHeight: true }
+}

src/pygui/ISC/Tabs/components/UtilityFooter.qml

@@ -0,0 +1,112 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Controls.impl
+import QtQuick.Layouts
+import ISC
+
+// ── BOX 4: Utility Buttons ─────────────────────────────────
+Rectangle {
+    id: utilFooter
+    Layout.fillWidth: true
+    Layout.preferredHeight: Theme.sideFooterUtility
+    radius: Theme.sidePanelRadius
+    border.color: Theme.sideBorder
+    border.width: 1
+    color: Theme.sidePanelBackground
+
+    RowLayout {
+        anchors.fill: parent
+        anchors.margins: 4
+        spacing: 4
+
+        Button {
+            id: settingsBtn
+            flat: true
+            Layout.fillWidth: true
+            Layout.fillHeight: true
+            icon.source: "../icons/settings.svg"
+            onClicked: utilFooter.parent.settingsPopup.open()
+
+            background: Rectangle {
+                radius: 8
+                color: settingsBtn.hovered
+                    ? Theme.sideActiveBackground : "transparent"
+            }
+
+            contentItem: Row {
+                spacing: 6
+                anchors.centerIn: parent
+
+                IconImage {
+                    anchors.verticalCenter: parent.verticalCenter
+                    width: 16
+                    height: 16
+                    source: "../icons/settings.svg"
+                    sourceSize.width: 16
+                    sourceSize.height: 16
+                    color: Theme.headingColor
+                    opacity: 0.75
+                }
+
+                Label {
+                    anchors.verticalCenter: parent.verticalCenter
+                    text: "SETTINGS"
+                    color: Theme.headingColor
+                    font.family: Theme.uiFontFamily
+                    font.pixelSize: Theme.fontXs
+                    font.bold: true
+                    font.letterSpacing: 1.2
+                    opacity: 0.8
+                }
+            }
+        }
+
+        Rectangle {
+            width: 1
+            height: 24
+            color: Theme.sideBorder
+        }
+
+        Button {
+            id: aboutBtn
+            flat: true
+            Layout.fillWidth: true
+            Layout.fillHeight: true
+            icon.source: "../icons/about.svg"
+            onClicked: utilFooter.parent.aboutDialog.open()
+
+            background: Rectangle {
+                radius: 8
+                color: aboutBtn.hovered
+                    ? Theme.sideActiveBackground : "transparent"
+            }
+
+            contentItem: Row {
+                spacing: 6
+                anchors.centerIn: parent
+
+                IconImage {
+                    anchors.verticalCenter: parent.verticalCenter
+                    width: 16
+                    height: 16
+                    source: "../icons/about.svg"
+                    sourceSize.width: 16
+                    sourceSize.height: 16
+                    color: Theme.headingColor
+                    opacity: 0.75
+                }
+
+                Label {
+                    anchors.verticalCenter: parent.verticalCenter
+                    text: "ABOUT"
+                    color: Theme.headingColor
+                    font.family: Theme.uiFontFamily
+                    font.pixelSize: Theme.fontXs
+                    font.bold: true
+                    font.letterSpacing: 1.2
+                    opacity: 0.8
+                }
+            }
+        }
+    }
+}

src/pygui/ISC/Tabs/components/qmldir

@@ -6,5 +6,19 @@ TransportBar 1.0 TransportBar.qml
 WaferMapView 1.0 WaferMapView.qml
 ReplaceSensorDialog 1.0 ReplaceSensorDialog.qml
 RailActionButton 1.0 RailActionButton.qml
+SelectFileDialog 1.0 SelectFileDialog.qml
 SplitDialog 1.0 SplitDialog.qml
-StreamStatsDialog 1.0 StreamStatsDialog.qml
+StreamStatsDialog 1.0 StreamStatsDialog.qml
+StatusActionsPanel 1.0 StatusActionsPanel.qml
+ConnectionFooter 1.0 ConnectionFooter.qml
+UtilityFooter 1.0 UtilityFooter.qml
+PanelCheckBox 1.0 PanelCheckBox.qml
+ReadoutStat 1.0 ReadoutStat.qml
+AppToolTip 1.0 AppToolTip.qml
+SectionTitle 1.0 SectionTitle.qml
+PanelBox 1.0 PanelBox.qml
+PanelSlider 1.0 PanelSlider.qml
+EditableScrubStat 1.0 EditableScrubStat.qml
+ComparisonChartCard 1.0 ComparisonChartCard.qml
+OverlapMapCard 1.0 OverlapMapCard.qml
+ComparisonSidePanel 1.0 ComparisonSidePanel.qml

src/pygui/ISC/Tabs/qmldir

@@ -5,4 +5,3 @@ WaferMapTab 1.0 WaferMapTab.qml
 DataTab 1.0 DataTab.qml
 SettingsTab 1.0 SettingsTab.qml
 StatusTab 1.0 StatusTab.qml
-SelectFileDialog 1.0 SelectFileDialog.qml

src/pygui/__main__.py

@@ -9,12 +9,22 @@ from PySide6.QtWidgets import QApplication
 
 from pygui.backend.controllers.device_controller import DeviceController
 from pygui.backend.controllers.session_controller import SessionController
+from pygui.backend.data.constants import default_data_dir
 from pygui.backend.data.file_browser import FileBrowser
 from pygui.backend.data.local_settings import LocalSettings
 from pygui.backend.data.local_settings_model import LocalSettingsModel
 from pygui.backend.license.license_model import LicenseModel
 
 # Importing wafer_map_item + trend_chart_item registers @QmlElement types (QML: import ISC.Wafer).
+from pygui.backend.visualization import (
+    graph_quick_item as graph_quick_item,  # noqa: F401
+)
+from pygui.backend.visualization import (
+    trend_chart_item as trend_chart_item,  # noqa: F401
+)
+from pygui.backend.visualization import (
+    wafer_map_item as wafer_map_item,  # noqa: F401
+)
 
 
 # ===== Application Entry Point =====
@@ -32,8 +42,15 @@ def main() -> int:
     app = QApplication(sys.argv)
     engine = QQmlApplicationEngine()
 
-    # ===== Shared Models =====
+    # ===== Shared Settings =====
-    settings_model = LocalSettingsModel()
+    # One LocalSettings instance, one disk read. LocalSettingsModel and
+    # DeviceController both hold this same object, so a save from the
+    # Settings tab is visible to the device layer immediately — no reload,
+    # no second copy to go stale.
+    data_dir = str(default_data_dir())
+    raw_settings = LocalSettings.read_settings(data_dir)
+
+    settings_model = LocalSettingsModel(raw_settings, data_dir)
     select_file_dialog_model = FileBrowser()
     settings_model.loadSettings()
     engine.rootContext().setContextProperty("settingsModel", settings_model)
@@ -54,8 +71,6 @@ def main() -> int:
     #   read/erase time (P2.1); a bound Callable[[str], str] avoids a
     #   LicenseModel import in the controller and keeps it testable with a
     #   lambda. See docs/pending/license-gating-plan.md §1.1.
-    data_dir = str(settings_model._data_dir)
-    raw_settings = LocalSettings.read_settings(data_dir)
     device_controller = DeviceController(raw_settings, data_dir)
     engine.rootContext().setContextProperty("deviceController", device_controller)
 
@@ -64,20 +79,9 @@ def main() -> int:
     engine.rootContext().setContextProperty("licenseModel", license_model)
 
     # ===== Session Controller (live/review wafer dashboard) =====
-    raw_settings_dict = raw_settings.__dict__.copy() if hasattr(raw_settings, '__dict__') else {}
+    stream_controller = SessionController()
-    stream_controller = SessionController(settings=raw_settings_dict)
     engine.rootContext().setContextProperty("streamController", stream_controller)
 
-    # Persist session state back to settings when it changes
-    def _persist_session_settings():
-        session_state = stream_controller.collect_settings()
-        for k, v in session_state.items():
-            if hasattr(raw_settings, k):
-                setattr(raw_settings, k, v)
-        LocalSettings.save_settings(data_dir, raw_settings)
-
-    stream_controller.settingsChanged.connect(_persist_session_settings)
-
     # ===== QML Startup =====
     # The "ISC" QML module lives alongside this file (src/pygui/ISC), so the
     # package directory is the import path the engine searches for qmldir.

src/pygui/backend/__init__.py

@@ -1,26 +0,0 @@
-# ===== Backend Package =====
-# Backward-compatible re-exports so existing callers keep working
-# while imports are migrated to the new sub-package paths.
-
-from pygui.backend.controllers.device_controller import DeviceController  # noqa: F401
-from pygui.backend.controllers.session_controller import SessionController  # noqa: F401
-from pygui.backend.data.csv_file_metadata import CSVFileMetadata  # noqa: F401
-from pygui.backend.data.csv_recorder import CsvRecorder  # noqa: F401
-from pygui.backend.data.data_records import read_data_records  # noqa: F401
-from pygui.backend.data.file_browser import FileBrowser  # noqa: F401
-from pygui.backend.data.local_settings import LocalSettings  # noqa: F401
-from pygui.backend.data.local_settings_model import LocalSettingsModel  # noqa: F401
-from pygui.backend.models.data_model import TemperatureTableModel  # noqa: F401
-from pygui.backend.models.frame import Frame  # noqa: F401
-from pygui.backend.models.frame_player import FramePlayer, frames_from_wafer_data  # noqa: F401
-from pygui.backend.models.frame_stats import Stats, compute_stats  # noqa: F401
-from pygui.backend.models.sensor_editor import SensorEditor  # noqa: F401
-from pygui.backend.models.session_model import SessionModel  # noqa: F401
-from pygui.backend.models.stability_detector import StabilityDetector  # noqa: F401
-from pygui.backend.models.threshold_classifier import ThresholdConfig  # noqa: F401
-from pygui.backend.visualization.graph_view import GraphView  # noqa: F401
-from pygui.backend.visualization.rbf_heatmap import interpolate_field  # noqa: F401
-from pygui.backend.visualization.wafer_map_item import WaferMapItem  # noqa: F401
-from pygui.backend.wafer.wafer_layouts import available_families, load_layout  # noqa: F401
-from pygui.backend.wafer.zwafer_models import DataRecord, Sensor, ZWaferData  # noqa: F401
-from pygui.backend.wafer.zwafer_parser import ZWaferParser  # noqa: F401

src/pygui/backend/controllers/__init__.py

@@ -1,5 +0,0 @@
-# ===== Controllers Sub-package =====
-from pygui.backend.controllers.device_controller import DeviceController
-from pygui.backend.controllers.session_controller import SessionController
-
-__all__ = ["DeviceController", "SessionController"]

src/pygui/backend/controllers/device_controller.py

@@ -13,7 +13,6 @@ from typing import Any, Optional
 
 from PySide6.QtCore import Property, QObject, Qt, Signal, Slot
 
-from pygui.backend.controllers.session_controller import SessionController
 from pygui.backend.data.local_settings import LocalSettings
 from pygui.backend.models.data_model import TemperatureTableModel
 from pygui.backend.utils import slot_error_boundary
@@ -26,11 +25,6 @@ from pygui.serialcomm.data_parser import (
 )
 from pygui.serialcomm.serial_port import WaferInfo
 
-# import pygui.backend.wafer_map_item
-
-stream_controller = SessionController()
-# engine.rootContext().setContextProperty("streamController", stream_controller)
-
 log = logging.getLogger(__name__)
 
 
@@ -44,6 +38,7 @@ class DeviceController(QObject):
     portsUpdated = Signal(list)
     connectionStatusChanged = Signal()
     operationInProgressChanged = Signal()
+    waferDetectedChanged = Signal()
     selectedPortChanged = Signal()
     detectResult = Signal(object)  # WaferInfo dict or None
     readResult = Signal(dict)  # {"success": bool, "bytes": int} or {"error": str}
@@ -83,6 +78,7 @@ class DeviceController(QObject):
         #   → denied = safe default. Called by P2.1.
         #   See docs/pending/license-gating-plan.md §1.2.
         self._last_wafer_info: dict[str, Any] = {}
+        self._wafer_detected: bool = False
         self._last_csv_path: str = ""
         self._selected_port: str = ""
         self._data_row_count: int = 0
@@ -218,6 +214,17 @@ class DeviceController(QObject):
             info.get("cycleCount", 0),
         ]
 
+    @Property(bool, notify=waferDetectedChanged)
+    def waferDetected(self) -> bool:
+        """Whether a wafer is currently detected and ready for read/erase."""
+        return self._wafer_detected
+
+    def _set_wafer_detected(self, detected: bool) -> None:
+        if self._wafer_detected != detected:
+            self._wafer_detected = detected
+            self.waferDetectedChanged.emit()
+
+
     @Property(object, notify=detectResult)
     def dataModel(self) -> TemperatureTableModel:
         """QAbstractTableModel for the parsed temperature data table."""
@@ -282,6 +289,7 @@ class DeviceController(QObject):
         self._set_connection_status("Disconnected")
         self._selected_port = ""
         self._last_wafer_info = {}
+        self._set_wafer_detected(False)
         self._data_row_count = 0
         self._data_col_count = 0
         self._raw_bytes = None
@@ -372,6 +380,7 @@ class DeviceController(QObject):
                 wafer_dict = self._wafer_info_to_dict(info)
                 self._selected_port = port or ""
                 self._last_wafer_info = wafer_dict
+                self._set_wafer_detected(True)
                 self._set_connection_status("Connected")
                 self.detectResult.emit(wafer_dict)
                 self.selectedPortChanged.emit()
@@ -381,6 +390,7 @@ class DeviceController(QObject):
                 self._set_connection_status("Disconnected")
                 self._append_log("No wafer detected on any port")
                 self._last_wafer_info = {}
+                self._set_wafer_detected(False)
                 self.detectResult.emit(None)
                 self.selectedPortChanged.emit()
         finally:

src/pygui/backend/controllers/session_controller.py

@@ -14,7 +14,7 @@ from pygui.backend.models.frame import Frame
 from pygui.backend.models.frame_player import FramePlayer, frames_from_wafer_data
 from pygui.backend.models.replay_stats import ReplayStatsTracker
 from pygui.backend.models.sensor_editor import SensorEditor
-from pygui.backend.models.session_model import SessionModel
+from pygui.backend.models.session_model import SessionModel, SessionUpdate
 from pygui.backend.models.threshold_classifier import ThresholdConfig
 from pygui.backend.utils import slot_error_boundary
 from pygui.backend.wafer.zwafer_models import Sensor
@@ -37,7 +37,6 @@ class SessionController(QObject):
     loadedFileChanged = Signal()
     loadFileError = Signal(str)
     clusterAveragingEnabledChanged = Signal()
-    settingsChanged = Signal()  # emitted when session state changes that should be persisted
     liveStatsChanged = Signal()  # emitted when receivedCount or errorCount change
     # trend: per-frame avg for live graph
     trendData = Signal(str)  # JSON array of floats
@@ -50,8 +49,7 @@ class SessionController(QObject):
     _liveFrame = Signal(object)    # Frame
     _liveError = Signal()          # worker-thread error ping
 
-    def __init__(self, parent: QObject | None = None,
+    def __init__(self, parent: QObject | None = None) -> None:
-                 settings: dict | None = None) -> None:
         super().__init__(parent)
         self._mode = MODE_REVIEW
         self._model = SessionModel()
@@ -59,7 +57,7 @@ class SessionController(QObject):
         self._reader: Optional[StreamReader] = None
         self._recorder = CsvRecorder()
         self._sensors: list[Sensor] = []
-        self._last = None              # last SessionUpdate
+        self._last: Optional[SessionUpdate] = None
         self._elapsed = 0.0
         self._trend_buffer: list[float] = [] # rolling window
         self._trend_timestamps: list[float] = []  # monotonic timestamps
@@ -96,21 +94,6 @@ class SessionController(QObject):
         self._compare_recs_b: list = []
         self._compare_alignment_map: dict[int, int] = {}
 
-        # Restore persisted state if available
-        self._load_settings(settings or {})
-
-    # ---- persisted settings ----
-
-    def _load_settings(self, settings: dict) -> None:
-        """Restore session state from persisted settings dict."""
-        # Do NOT auto-restore the last session file — always start fresh.
-
-    def collect_settings(self) -> dict:
-        """Return a dict of session state to persist."""
-        return {
-            "session_last_file": self._loaded_file,
-        }
-
     # ---- properties QML binds to ----
     @Property(str, notify=modeChanged)
     def mode(self) -> str: return self._mode
@@ -150,7 +133,7 @@ class SessionController(QObject):
                         "value": round(v, 2), "band": band, "index": i})
         return out
 
-    @Property("QVariantList", notify=sensorsChanged)
+    @Property("QVariantList", notify=sensorsChanged)  # type: ignore[arg-type]
     def sensorLayout(self) -> list:
         """[{label, x, y, side, offset_x, offset_y}] for WaferMapItem.sensors."""
         return [
@@ -175,14 +158,14 @@ class SessionController(QObject):
         """Wafer size in mm."""
         return getattr(self._sensors, "size", 300.0)
 
-    @Property("QVariantList", notify=frameUpdated)
+    @Property("QVariantList", notify=frameUpdated)  # type: ignore[arg-type]
     def sensorValues(self) -> list:
         """[float] in sensor order."""
         if not self._last:
             return []
         return [round(v, 3) for v in self._last.values]
 
-    @Property("QVariantList", notify=frameUpdated)
+    @Property("QVariantList", notify=frameUpdated)  # type: ignore[arg-type]
     def sensorBands(self) -> list:
         """['in_range'|'high'|'low'] in sensor order."""
         if not self._last:
@@ -212,7 +195,7 @@ class SessionController(QObject):
     @Property(str, notify=loadedFileChanged)
     def loadedFile(self) -> str: return self._loaded_file
 
-    @Property("QVariantList", notify=frameUpdated)
+    @Property("QVariantList", notify=frameUpdated)  # type: ignore[arg-type]
     def overriddenSensors(self) -> list[int]:
         """Indices of sensors that currently have a replacement or offset."""
         return self._sensor_editor.active_indices()
@@ -221,7 +204,7 @@ class SessionController(QObject):
     def clusterAveragingEnabled(self) -> bool:
         return self._cluster_averaging_enabled
 
-    @clusterAveragingEnabled.setter
+    @clusterAveragingEnabled.setter  # type: ignore[no-redef]
     def clusterAveragingEnabled(self, value: bool) -> None:
         if self._cluster_averaging_enabled == value:
             return
@@ -319,7 +302,6 @@ class SessionController(QObject):
         for frame in self._player._frames:
             self._stats_tracker.track(frame.seq, frame.values)
         self.trendData.emit(json.dumps(self._stats_tracker.get_trend()))
-        self.settingsChanged.emit()
 
     @Slot()
     @slot_error_boundary
@@ -331,7 +313,6 @@ class SessionController(QObject):
         self._loaded_file = ""
         self.loadedFileChanged.emit()
         self.sensorsChanged.emit()
-        self.settingsChanged.emit()
 
     # ---- comparison: DTW between two CSV files ----
     @Slot(str, str)
@@ -475,7 +456,7 @@ class SessionController(QObject):
         """Return the per-sensor temp diff (Run B - Run A) at the given scrub frame index of Run A, using DTW alignment."""
         if not self._compare_recs_a or not self._compare_recs_b:
             return []
-        
+
         idx_a = min(max(0, scrub_idx), len(self._compare_recs_a) - 1)
         if idx_a not in self._compare_alignment_map:
             # DTW path only covers indices up to the shorter run's length —
@@ -485,7 +466,7 @@ class SessionController(QObject):
 
         values_a = self._compare_recs_a[idx_a].values
         values_b = self._compare_recs_b[idx_b].values
-        
+
         n = min(len(values_a), len(values_b))
         return [round(values_b[i] - values_a[i], 3) for i in range(n)]
 

src/pygui/backend/crypto/__init__.py

@@ -1,2 +0,0 @@
-# ===== Crypto Sub-package =====
-from pygui.backend.crypto.crypto_helper import *  # noqa: F403

src/pygui/backend/data/__init__.py

@@ -1,14 +0,0 @@
-# ===== Data Sub-package =====
-from pygui.backend.data.csv_file_metadata import CSVFileMetadata
-from pygui.backend.data.csv_recorder import CsvRecorder
-from pygui.backend.data.data_records import is_official_csv, read_data_records, read_official_csv
-from pygui.backend.data.file_browser import FileBrowser
-from pygui.backend.data.local_settings import LocalSettings
-from pygui.backend.data.local_settings_model import LocalSettingsModel
-
-__all__ = [
-    "CsvRecorder", "CSVFileMetadata",
-    "read_data_records", "is_official_csv", "read_official_csv",
-    "FileBrowser",
-    "LocalSettings", "LocalSettingsModel",
-]

src/pygui/backend/data/constants.py

@@ -1,3 +1,14 @@
 # ===== Backend Data Constants =====
 
+from pathlib import Path
+
+from PySide6.QtCore import QStandardPaths
+
 DEFAULT_DATA_DIR_NAME = "isc_data"
+
+
+def default_data_dir() -> Path:
+    """Documents-folder isc_data directory used as the default app data location."""
+    documents_dir = QStandardPaths.writableLocation(QStandardPaths.StandardLocation.DocumentsLocation)
+    base_dir = Path(documents_dir) if documents_dir else (Path.home() / "Documents")
+    return base_dir / DEFAULT_DATA_DIR_NAME

src/pygui/backend/data/csv_file_metadata.py

@@ -19,8 +19,8 @@ class CSVFileMetadata:
         """Return the first character of the wafer string, or empty if none"""
         return self.wafer[0] if self.wafer else ""
 
-    def get_date(self) -> datetime:
+    def get_date(self) -> datetime | None:
-        """Parsifes the date string. Returns current time if parsing fails"""
+        """Parsifes the date string. Returns None if parsing fails"""
         date_format = "%Y-%m-%d %H:%M:%S"
         try:
             return datetime.strptime(self.date, date_format)

src/pygui/backend/data/csv_recorder.py

@@ -1,4 +1,5 @@
 """Append live frames"""
+
 from __future__ import annotations
 
 from datetime import datetime
@@ -12,17 +13,15 @@ from pygui.backend.wafer.zwafer_models import Sensor
 class CsvRecorder:
     def __init__(self) -> None:
         self._file_handle: Optional[TextIO] = None
-        self._oath: Optional[str] = None
+        self._path: Optional[str] = None
-
 
     @property
     def is_recording(self) -> bool:
-            return self._file_handle is not None
+        return self._file_handle is not None
 
-
+    def start(self, path: str, sensors: list[Sensor], serial: str = "") -> None:
-    def start(self, path: str, sensors:list[Sensor], serial: str = "") -> None:
         Path(path).parent.mkdir(parents=True, exist_ok=True)
-        file_handle = open(path, "w", encoding="utf-8", newline ="")
+        file_handle = open(path, "w", encoding="utf-8", newline="")
         file_handle.write(f"Wafer ID={serial}\n")
         file_handle.write(f"Acquisition Date={datetime.now():%m/%d/%Y}\n")
         file_handle.write("Label," + ",".join(s.label for s in sensors) + "\n")
@@ -32,7 +31,7 @@ class CsvRecorder:
         file_handle.flush()
         self._file_handle, self._path = file_handle, path
 
-    def write(self, frame: Frame) ->  None:
+    def write(self, frame: Frame) -> None:
         if self._file_handle is None:
             return
         row = [f"{frame.time:.3f}"] + [f"{v:.3f}" for v in frame.values]
@@ -65,21 +64,11 @@ class CsvRecorder:
         Returns:
             True on success (at least one frame written).
         """
-        from pygui.backend.data.data_records import is_official_csv
+        from pygui.backend.data.data_records import is_data_row, is_official_csv
 
         if start_frame < 0 or end_frame < start_frame:
             return False
 
-        def _is_data_row(stripped: str) -> bool:
-            cols = [c.strip() for c in stripped.split(",") if c.strip()]
-            if not cols:
-                return False
-            try:
-                [float(c) for c in cols]
-            except ValueError:
-                return False
-            return True
-
         with open(source_path, "r", encoding="utf-8") as f:
             lines = f.readlines()
 
@@ -99,7 +88,7 @@ class CsvRecorder:
                 # official format: row 0 is the sensor-name header
                 out.append(line)
                 continue
-            if not stripped or not _is_data_row(stripped):
+            if not stripped or not is_data_row(stripped):
                 continue
             frame_idx += 1
             if start_frame <= frame_idx <= end_frame:
@@ -112,4 +101,3 @@ class CsvRecorder:
         with open(file_path, "w", encoding="utf-8", newline="") as f:
             f.writelines(out)
         return True
-

src/pygui/backend/data/data_records.py

@@ -1,4 +1,5 @@
 """Read the data section of a Z-wafer CSV into DataRecords, or the official headerless CSV."""
+
 from __future__ import annotations
 
 from pathlib import Path
@@ -6,6 +7,20 @@ from pathlib import Path
 from pygui.backend.wafer.zwafer_models import DataRecord, Sensor
 
 
+def is_data_row(line: str) -> bool:
+    """True if *line* is a single CSV row of numeric values (no headers/metadata)."""
+    cols = [c.strip() for c in line.split(",") if c.strip() != ""]
+    return bool(cols) and all(_is_float(c) for c in cols)
+
+
+def _is_float(s: str) -> bool:
+    try:
+        float(s)
+    except ValueError:
+        return False
+    return True
+
+
 def read_data_records(file_path: str) -> list[DataRecord]:
     records: list[DataRecord] = []
     in_data = False
@@ -18,13 +33,10 @@ def read_data_records(file_path: str) -> list[DataRecord]:
                 if line.split(",")[0].lower() == "data":
                     in_data = True
                 continue
+            if not is_data_row(line):
+                continue
             cols = [c.strip() for c in line.split(",") if c.strip() != ""]
-            try:
+            nums = [float(c) for c in cols]
-                nums = [float(c) for c in cols]
-            except ValueError:
-                continue
-            if not nums:
-                continue
             records.append(DataRecord(time=nums[0], values=nums[1:]))
         return records
 

src/pygui/backend/data/file_browser.py

@@ -5,10 +5,10 @@ import re
 from datetime import datetime
 from pathlib import Path
 
-from PySide6.QtCore import Property, QObject, QStandardPaths, Signal, Slot
+from PySide6.QtCore import Property, QObject, Signal, Slot
 from PySide6.QtWidgets import QFileDialog, QMessageBox
 
-from pygui.backend.data.constants import DEFAULT_DATA_DIR_NAME
+from pygui.backend.data.constants import default_data_dir
 from pygui.backend.data.csv_file_metadata import CSVFileMetadata
 from pygui.backend.wafer.zwafer_parser import ZWaferParser
 
@@ -28,7 +28,7 @@ class FileBrowser(QObject):
         self._refresh_files(show_empty_message=False)
 
     # ===== Exposed Properties =====
-    @Property("QVariantList", notify=filesChanged)
+    @Property("QVariantList", notify=filesChanged)  # type: ignore[arg-type]
     def files(self) -> list[dict[str, object]]:
         return [dict(row) for row in self._files]
 
@@ -42,7 +42,7 @@ class FileBrowser(QObject):
         selected_dir = QFileDialog.getExistingDirectory(
             None,
             "Select CSV Folder",
-            self.currentDirectory,
+            str(self._current_directory),
         )
         if not selected_dir:
             return
@@ -235,11 +235,7 @@ class FileBrowser(QObject):
 
     # ===== Internal Helpers =====
     def _resolve_default_directory(self) -> Path:
-        documents_dir = QStandardPaths.writableLocation(
+        return default_data_dir()
-            QStandardPaths.DocumentsLocation
-        )
-        base_dir = Path(documents_dir) if documents_dir else (Path.home() / "Documents")
-        return base_dir / DEFAULT_DATA_DIR_NAME
 
     def _set_current_directory(self, directory: Path) -> None:
         normalized = Path(directory)

src/pygui/backend/data/local_settings.py

@@ -13,8 +13,8 @@ class LocalSettings:
         # Configuration settings
         self.chamber_id = ""
         self.reverse_z_wafer = False
-        self.master = {}  # Dict[str, str]
+        self.master: dict[str, str] = {}
-        self.wafer_data_size = {}  # Dict[str, int]
+        self.wafer_data_size: dict[str, int] = {}
         self.debug = False
         self.wafer_read_retries = 8
         # Timeout in msec for reading from the wafer (default 2 min)
@@ -32,9 +32,6 @@ class LocalSettings:
         self.data_col_count = 0
         self.last_csv_path = ""
 
-        # Session persistence
-        self.session_last_file = ""
-
     # ===== File Path Helpers =====
     @classmethod
     def _settings_path(cls, directory: str) -> Path:

src/pygui/backend/data/local_settings_model.py

@@ -2,17 +2,26 @@ from __future__ import annotations
 
 from copy import deepcopy
 from pathlib import Path
-from typing import Any
+from typing import Any, Callable
 
-from PySide6.QtCore import Property, QDateTime, QObject, QStandardPaths, Signal, Slot
+from PySide6.QtCore import Property, QDateTime, QObject, Signal, Slot
 
-from pygui.backend.data.constants import DEFAULT_DATA_DIR_NAME
 from pygui.backend.data.local_settings import LocalSettings
 
 MASTER_FAMILIES = ("A", "B", "C", "D", "E", "F", "P", "X", "Z")
 
 
 class LocalSettingsModel(QObject):
+    # Draft attrs are seeded via setattr() in __init__ from _new_defaults();
+    # declared here so mypy knows their types.
+    _chamber_id: str
+    _reverse_z_wafer: bool
+    _debug_mode: bool
+    _wafer_read_timeout: int
+    _wafer_detect_timeout: int
+    _wafer_retries: int
+    _masters: dict[str, str]
+
     chamberIdChanged = Signal()
     reverseZWaferChanged = Signal()
     debugModeChanged = Signal()
@@ -26,18 +35,35 @@ class LocalSettingsModel(QObject):
     saveStatusChanged = Signal()
     lastSavedAtChanged = Signal()
 
-    def __init__(self, parent: QObject | None = None) -> None:
+    # Draft attr (this class) <-> LocalSettings attr (the shared, persisted
+    # instance also held by DeviceController) <-> coercer applied on both
+    # load and revert/reset. One table drives load/save/revert/reset instead
+    # of four hand-written field-by-field copies.
+    _FIELD_MAP: tuple[tuple[str, str, Callable[[Any], Any]], ...] = (
+        ("_chamber_id", "chamber_id", str),
+        ("_reverse_z_wafer", "reverse_z_wafer", bool),
+        ("_debug_mode", "debug", bool),
+        ("_wafer_read_timeout", "wafer_read_timeout", int),
+        ("_wafer_detect_timeout", "wafer_detect_timeout", int),
+        ("_wafer_retries", "wafer_read_retries", int),
+    )
+
+    def __init__(
+        self,
+        settings: LocalSettings,
+        data_dir: Path | str,
+        parent: QObject | None = None,
+    ) -> None:
         super().__init__(parent)
-        self._data_dir = self._resolve_data_dir()
+        # Shared with DeviceController — saving here must mutate this same
+        # instance, not a throwaway copy, or the device layer keeps using
+        # stale config until restart.
+        self._settings = settings
+        self._data_dir = Path(data_dir)
         self._defaults = self._new_defaults()
 
-        self._chamber_id = self._defaults["chamberId"]
+        for draft_attr, default_value in self._defaults.items():
-        self._reverse_z_wafer = self._defaults["reverseZWafer"]
+            setattr(self, draft_attr, deepcopy(default_value))
-        self._debug_mode = self._defaults["debugMode"]
-        self._wafer_read_timeout = self._defaults["waferReadTimeout"]
-        self._wafer_detect_timeout = self._defaults["waferDetectTimeout"]
-        self._wafer_retries = self._defaults["waferRetries"]
-        self._masters = deepcopy(self._defaults["masters"])
 
         self._is_dirty = False
         self._is_valid = True
@@ -47,34 +73,21 @@ class LocalSettingsModel(QObject):
         self._saved_snapshot = self._snapshot()
         self._recompute_derived()
 
-    def _resolve_data_dir(self) -> Path:
-        documents_dir = QStandardPaths.writableLocation(
-            QStandardPaths.DocumentsLocation
-        )
-        base_dir = Path(documents_dir) if documents_dir else (Path.home() / "Documents")
-        return base_dir / DEFAULT_DATA_DIR_NAME
-
     def _new_defaults(self) -> dict[str, Any]:
         return {
-            "chamberId": "2",
+            "_chamber_id": "2",
-            "reverseZWafer": False,
+            "_reverse_z_wafer": False,
-            "debugMode": False,
+            "_debug_mode": False,
-            "waferReadTimeout": 120000,
+            "_wafer_read_timeout": 120000,
-            "waferDetectTimeout": 5000,
+            "_wafer_detect_timeout": 5000,
-            "waferRetries": 8,
+            "_wafer_retries": 8,
-            "masters": {family: "" for family in MASTER_FAMILIES},
+            "_masters": {family: "" for family in MASTER_FAMILIES},
         }
 
     def _snapshot(self) -> dict[str, Any]:
-        return {
+        snap = {attr: getattr(self, attr) for attr, _, _ in self._FIELD_MAP}
-            "chamberId": self._chamber_id,
+        snap["_masters"] = deepcopy(self._masters)
-            "reverseZWafer": self._reverse_z_wafer,
+        return snap
-            "debugMode": self._debug_mode,
-            "waferReadTimeout": self._wafer_read_timeout,
-            "waferDetectTimeout": self._wafer_detect_timeout,
-            "waferRetries": self._wafer_retries,
-            "masters": deepcopy(self._masters),
-        }
 
     def _set_is_dirty(self, value: bool) -> None:
         if self._is_dirty != value:
@@ -137,22 +150,19 @@ class LocalSettingsModel(QObject):
         self.waferRetriesChanged.emit()
         self.mastersChanged.emit()
 
-    def _to_local_settings(self) -> LocalSettings:
+    def _normalized_masters(self, source: dict[str, str]) -> dict[str, str]:
-        settings = LocalSettings()
+        masters = {family: "" for family in MASTER_FAMILIES}
-        settings.chamber_id = self._chamber_id
+        for family, value in source.items():
-        settings.reverse_z_wafer = self._reverse_z_wafer
+            normalized = str(family).strip().upper()
-        settings.debug = self._debug_mode
+            if normalized in masters:
-        settings.wafer_read_timeout = self._wafer_read_timeout
+                masters[normalized] = str(value).strip()
-        settings.wafer_detect_timeout = self._wafer_detect_timeout
+        return masters
-        settings.wafer_read_retries = self._wafer_retries
-        settings.master = deepcopy(self._masters)
-        return settings
 
     @Property(str, notify=chamberIdChanged)
     def chamberId(self) -> str:
         return self._chamber_id
 
-    @chamberId.setter
+    @chamberId.setter  # type: ignore[no-redef]
     def chamberId(self, value: str) -> None:
         next_value = str(value).strip()
         if self._chamber_id == next_value:
@@ -165,7 +175,7 @@ class LocalSettingsModel(QObject):
     def reverseZWafer(self) -> bool:
         return self._reverse_z_wafer
 
-    @reverseZWafer.setter
+    @reverseZWafer.setter  # type: ignore[no-redef]
     def reverseZWafer(self, value: bool) -> None:
         if self._reverse_z_wafer == value:
             return
@@ -177,7 +187,7 @@ class LocalSettingsModel(QObject):
     def debugMode(self) -> bool:
         return self._debug_mode
 
-    @debugMode.setter
+    @debugMode.setter  # type: ignore[no-redef]
     def debugMode(self, value: bool) -> None:
         if self._debug_mode == value:
             return
@@ -189,7 +199,7 @@ class LocalSettingsModel(QObject):
     def waferReadTimeout(self) -> int:
         return self._wafer_read_timeout
 
-    @waferReadTimeout.setter
+    @waferReadTimeout.setter  # type: ignore[no-redef]
     def waferReadTimeout(self, value: int) -> None:
         if self._wafer_read_timeout == value:
             return
@@ -201,7 +211,7 @@ class LocalSettingsModel(QObject):
     def waferDetectTimeout(self) -> int:
         return self._wafer_detect_timeout
 
-    @waferDetectTimeout.setter
+    @waferDetectTimeout.setter  # type: ignore[no-redef]
     def waferDetectTimeout(self, value: int) -> None:
         if self._wafer_detect_timeout == value:
             return
@@ -213,7 +223,7 @@ class LocalSettingsModel(QObject):
     def waferRetries(self) -> int:
         return self._wafer_retries
 
-    @waferRetries.setter
+    @waferRetries.setter  # type: ignore[no-redef]
     def waferRetries(self, value: int) -> None:
         if self._wafer_retries == value:
             return
@@ -251,22 +261,11 @@ class LocalSettingsModel(QObject):
 
     @Slot()
     def loadSettings(self) -> None:
-        loaded = LocalSettings.read_settings(str(self._data_dir))
+        """Seed draft fields from the shared LocalSettings instance."""
-        self._chamber_id = str(loaded.chamber_id).strip() or str(
+        for draft_attr, settings_attr, coerce in self._FIELD_MAP:
-            self._defaults["chamberId"]
+            setattr(self, draft_attr, coerce(getattr(self._settings, settings_attr)))
-        )
+        self._chamber_id = self._chamber_id.strip() or str(self._defaults["_chamber_id"])
-        self._reverse_z_wafer = bool(loaded.reverse_z_wafer)
+        self._masters = self._normalized_masters(self._settings.master)
-        self._debug_mode = bool(loaded.debug)
-        self._wafer_read_timeout = int(loaded.wafer_read_timeout)
-        self._wafer_detect_timeout = int(loaded.wafer_detect_timeout)
-        self._wafer_retries = int(loaded.wafer_read_retries)
-
-        masters = {family: "" for family in MASTER_FAMILIES}
-        for family, value in loaded.master.items():
-            normalized = str(family).strip().upper()
-            if normalized in masters:
-                masters[normalized] = str(value).strip()
-        self._masters = masters
 
         self._saved_snapshot = self._snapshot()
         self._emit_all_changed()
@@ -275,13 +274,18 @@ class LocalSettingsModel(QObject):
 
     @Slot()
     def saveSettings(self) -> None:
+        """Write draft fields onto the shared LocalSettings instance and persist it."""
         self._recompute_derived()
         if not self._is_valid:
             self._set_save_status("error: invalid settings")
             return
 
         try:
-            LocalSettings.save_settings(str(self._data_dir), self._to_local_settings())
+            for draft_attr, settings_attr, _coerce in self._FIELD_MAP:
+                setattr(self._settings, settings_attr, getattr(self, draft_attr))
+            self._settings.master = deepcopy(self._masters)
+            LocalSettings.save_settings(str(self._data_dir), self._settings)
+
             self._saved_snapshot = self._snapshot()
             self._recompute_derived()
             self._set_save_status("Saved")
@@ -293,13 +297,9 @@ class LocalSettingsModel(QObject):
     @Slot()
     def revertChanges(self) -> None:
         snap = self._saved_snapshot
-        self._chamber_id = str(snap["chamberId"])
+        for draft_attr, _settings_attr, coerce in self._FIELD_MAP:
-        self._reverse_z_wafer = bool(snap["reverseZWafer"])
+            setattr(self, draft_attr, coerce(snap[draft_attr]))
-        self._debug_mode = bool(snap["debugMode"])
+        self._masters = deepcopy(snap["_masters"])
-        self._wafer_read_timeout = int(snap["waferReadTimeout"])
-        self._wafer_detect_timeout = int(snap["waferDetectTimeout"])
-        self._wafer_retries = int(snap["waferRetries"])
-        self._masters = deepcopy(snap["masters"])
 
         self._emit_all_changed()
         self._recompute_derived()
@@ -307,13 +307,9 @@ class LocalSettingsModel(QObject):
 
     @Slot()
     def resetDefaults(self) -> None:
-        self._chamber_id = str(self._defaults["chamberId"])
+        for draft_attr, _settings_attr, coerce in self._FIELD_MAP:
-        self._reverse_z_wafer = bool(self._defaults["reverseZWafer"])
+            setattr(self, draft_attr, coerce(self._defaults[draft_attr]))
-        self._debug_mode = bool(self._defaults["debugMode"])
+        self._masters = deepcopy(self._defaults["_masters"])
-        self._wafer_read_timeout = int(self._defaults["waferReadTimeout"])
-        self._wafer_detect_timeout = int(self._defaults["waferDetectTimeout"])
-        self._wafer_retries = int(self._defaults["waferRetries"])
-        self._masters = deepcopy(self._defaults["masters"])
 
         self._emit_all_changed()
         self._recompute_derived()

src/pygui/backend/license/__init__.py

@@ -1,15 +0,0 @@
-from pygui.backend.license.license_manager import (
-    LICENSE_FILENAME_RE,
-    License,
-    parse_license_blob,
-    read_license_files,
-)
-from pygui.backend.license.license_model import LicenseModel
-
-__all__ = [
-    "LICENSE_FILENAME_RE",
-    "License",
-    "LicenseModel",
-    "parse_license_blob",
-    "read_license_files",
-]

src/pygui/backend/license/license_model.py

@@ -50,7 +50,7 @@ class LicenseModel(QObject):
         self.refresh()
 
     # ── Grid rows ─────────────────────────────────────────────────────
-    @Property("QVariantList", notify=licensesChanged)
+    @Property("QVariantList", notify=licensesChanged)  # type: ignore[arg-type]
     def licenses(self) -> list:
         """Rows for the About grid: serial, mfg date, level, license date."""
         return [

src/pygui/backend/models/__init__.py

@@ -1,19 +0,0 @@
-# ===== Models Sub-package =====
-from pygui.backend.models.data_model import TemperatureTableModel
-from pygui.backend.models.frame import Frame
-from pygui.backend.models.frame_player import FramePlayer, frames_from_wafer_data
-from pygui.backend.models.frame_stats import Stats, compute_stats
-from pygui.backend.models.sensor_editor import SensorEditor
-from pygui.backend.models.session_model import SessionModel, SessionUpdate
-from pygui.backend.models.stability_detector import StabilityDetector
-from pygui.backend.models.threshold_classifier import ThresholdConfig, classify, resolve_bounds
-
-__all__ = [
-    "Frame", "FramePlayer", "frames_from_wafer_data",
-    "Stats", "compute_stats",
-    "SessionModel", "SessionUpdate",
-    "TemperatureTableModel",
-    "SensorEditor",
-    "ThresholdConfig", "classify", "resolve_bounds",
-    "StabilityDetector",
-]

src/pygui/backend/models/data_model.py

@@ -55,7 +55,7 @@ class TemperatureTableModel(QAbstractTableModel):
         # Column 0 = row index, columns 1..N = sensor values
         return self._col_count + 1
 
-    def data(self, index: Any, role: int = ...) -> Any:
+    def data(self, index: Any, role: int = ...) -> Any:  # type: ignore[assignment]
         if not index.isValid():
             return None
 
@@ -73,7 +73,7 @@ class TemperatureTableModel(QAbstractTableModel):
         return None
 
     def headerData(
-        self, section: int, orientation: int, role: int = ...
+        self, section: int, orientation: Qt.Orientation, role: int = ...  # type: ignore[assignment]
     ) -> Any:
         if role != Qt.ItemDataRole.DisplayRole:
             return None

src/pygui/backend/models/frame_player.py

@@ -4,7 +4,7 @@ from pygui.backend.models.frame import Frame
 from pygui.backend.wafer.zwafer_models import ZWaferData
 
 
-def frames_from_wafer_data(data: ZWaferData, records) -> list[Frame]:
+def frames_from_wafer_data(data: ZWaferData | None, records) -> list[Frame]:
     """Build Frames from parsed DataRecords (records = list[DataRecord].)"""
     return [Frame(seq=i, time=r.time, values=list(r.values)) for i, r in enumerate(records)]
 

src/pygui/backend/visualization/__init__.py

@@ -1,11 +0,0 @@
-# ===== Visualization Sub-package =====
-from pygui.backend.visualization.graph_quick_item import GraphQuickItem
-from pygui.backend.visualization.graph_view import GraphView
-from pygui.backend.visualization.rbf_heatmap import interpolate_field
-from pygui.backend.visualization.trend_chart_item import TrendChartItem
-from pygui.backend.visualization.wafer_map_item import WaferMapItem
-
-__all__ = [
-    "GraphQuickItem", "GraphView", "TrendChartItem", "WaferMapItem",
-    "interpolate_field",
-]

src/pygui/backend/visualization/chart_geometry.py

@@ -0,0 +1,33 @@
+"""Pure coordinate-mapping math shared by the QQuickPaintedItem chart items
+(GraphQuickItem, TrendChartItem). No QPainter or Qt-widget dependency, so
+it's testable without a GUI — unlike the paint() methods that call it.
+"""
+from __future__ import annotations
+
+
+def value_to_pixel(
+    value: float,
+    value_min: float,
+    value_max: float,
+    pixel_start: float,
+    pixel_span: float,
+) -> float:
+    """Map a value onto a pixel range, inverted so larger values sit at
+    smaller pixel coordinates (screen y grows downward).
+
+    Also used for evenly-spaced tick indices: pass the tick index as
+    `value` and `(tick_count - 1)` as `value_max` with `value_min=0`.
+    """
+    value_range = value_max - value_min
+    if value_range < 1e-9:
+        return pixel_start + pixel_span / 2
+    fraction = 1.0 - (value - value_min) / value_range
+    return pixel_start + fraction * pixel_span
+
+
+def index_to_pixel(index: float, count: int, pixel_start: float, pixel_span: float) -> float:
+    """Map a 0-based sample index onto a pixel range, left to right."""
+    if count <= 1:
+        return pixel_start + pixel_span / 2
+    fraction = index / (count - 1)
+    return pixel_start + fraction * pixel_span

src/pygui/backend/visualization/graph_quick_item.py

@@ -26,6 +26,8 @@ from PySide6.QtGui import QColor, QFont, QFontMetrics, QPainter, QPen
 from PySide6.QtQml import QmlElement
 from PySide6.QtQuick import QQuickPaintedItem
 
+from pygui.backend.visualization.chart_geometry import index_to_pixel, value_to_pixel
+
 QML_IMPORT_NAME = "ISC.Wafer"
 QML_IMPORT_MAJOR_VERSION = 1
 
@@ -78,7 +80,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def seriesData(self) -> list:
         return self._series_data
 
-    @seriesData.setter
+    @seriesData.setter  # type: ignore[no-redef]
     def seriesData(self, val: list) -> None:
         self._series_data = [list(s) for s in (val or [])]
         self._auto_range()
@@ -89,7 +91,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def sensorNames(self) -> list:
         return self._sensor_names
 
-    @sensorNames.setter
+    @sensorNames.setter  # type: ignore[no-redef]
     def sensorNames(self, val: list) -> None:
         self._sensor_names = list(val or [])
         self.sensorNamesChanged.emit()
@@ -99,7 +101,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def title(self) -> str:
         return self._title
 
-    @title.setter
+    @title.setter  # type: ignore[no-redef]
     def title(self, val: str) -> None:
         self._title = str(val or "")
         self.titleChanged.emit()
@@ -109,7 +111,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def xLabel(self) -> str:
         return self._x_label
 
-    @xLabel.setter
+    @xLabel.setter  # type: ignore[no-redef]
     def xLabel(self, val: str) -> None:
         self._x_label = str(val or "")
         self.xLabelChanged.emit()
@@ -119,7 +121,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def yLabel(self) -> str:
         return self._y_label
 
-    @yLabel.setter
+    @yLabel.setter  # type: ignore[no-redef]
     def yLabel(self, val: str) -> None:
         self._y_label = str(val or "")
         self.yLabelChanged.emit()
@@ -129,7 +131,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def showLegend(self) -> bool:
         return self._show_legend
 
-    @showLegend.setter
+    @showLegend.setter  # type: ignore[no-redef]
     def showLegend(self, val: bool) -> None:
         self._show_legend = bool(val)
         self.colorsChanged.emit()
@@ -141,7 +143,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def backgroundColor(self) -> QColor:
         return self._bg_color
 
-    @backgroundColor.setter
+    @backgroundColor.setter  # type: ignore[no-redef]
     def backgroundColor(self, c: QColor) -> None:
         self._bg_color = c
         self.update()
@@ -150,7 +152,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def gridColor(self) -> QColor:
         return self._grid_color
 
-    @gridColor.setter
+    @gridColor.setter  # type: ignore[no-redef]
     def gridColor(self, c: QColor) -> None:
         self._grid_color = c
         self.update()
@@ -159,7 +161,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def axisColor(self) -> QColor:
         return self._axis_color
 
-    @axisColor.setter
+    @axisColor.setter  # type: ignore[no-redef]
     def axisColor(self, c: QColor) -> None:
         self._axis_color = c
         self.update()
@@ -168,7 +170,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def textColor(self) -> QColor:
         return self._text_color
 
-    @textColor.setter
+    @textColor.setter  # type: ignore[no-redef]
     def textColor(self, c: QColor) -> None:
         self._text_color = c
         self.update()
@@ -178,7 +180,7 @@ class GraphQuickItem(QQuickPaintedItem):
         """Return hex strings of the current series color palette."""
         return [c.name() for c in self._series_colors]
 
-    @seriesColors.setter
+    @seriesColors.setter  # type: ignore[no-redef]
     def seriesColors(self, hex_list: list) -> None:
         colors = []
         for h in (hex_list or []):
@@ -275,8 +277,7 @@ class GraphQuickItem(QQuickPaintedItem):
 
         for i in range(n_y_ticks):
             y_val = self._min_y + i * y_step
-            y_frac = 1.0 - (i / (n_y_ticks - 1)) if n_y_ticks > 1 else 0.5
+            y_px = value_to_pixel(i, 0, n_y_ticks - 1, plot_top, plot_h)
-            y_px = plot_top + y_frac * plot_h
 
             # Grid line
             painter.setPen(grid_pen)
@@ -325,8 +326,7 @@ class GraphQuickItem(QQuickPaintedItem):
             x_tick_step = (num_points - 1) / max(1, n_x_ticks - 1)
             for i in range(n_x_ticks):
                 idx = int(round(i * x_tick_step))
-                x_frac = idx / (num_points - 1)
+                x_px = index_to_pixel(idx, num_points, plot_left, plot_w)
-                x_px = plot_left + x_frac * plot_w
                 painter.setPen(axis_pen)
                 painter.drawText(
                     int(x_px - 12), int(plot_top + plot_h + 14),
@@ -358,10 +358,8 @@ class GraphQuickItem(QQuickPaintedItem):
                     v = float(val)
                 except (ValueError, TypeError):
                     continue
-                x_frac = i / (max_len - 1) if max_len > 1 else 0.5
+                x_px = index_to_pixel(i, max_len, plot_left, plot_w)
-                y_frac = 1.0 - ((v - self._min_y) / y_range) if y_range > 0 else 0.5
+                y_px = value_to_pixel(v, self._min_y, self._max_y, plot_top, plot_h)
-                x_px = plot_left + x_frac * plot_w
-                y_px = plot_top + y_frac * plot_h
                 pts.append((x_px, y_px))
 
             if len(pts) < 2:

src/pygui/backend/visualization/graph_view.py

@@ -23,6 +23,9 @@ class GraphView(QObject):
     each sensor as a separate line series.
     """
 
+    # Set lazily in updateTrend (guarded by hasattr); declared for mypy.
+    _trend_line: Any
+
     # ---- signals ----
     dataReady = Signal(object)  # {"success": bool, "sensory_names": list, "series": list}
 
@@ -227,7 +230,7 @@ class GraphView(QObject):
             index_a, index_b = path[i]
             if index_a < len(a) and index_b < len(b):
                 line = pg.InfiniteLine(pos=index_a, angle=90, pen=pg.mkPen("#666666", width=1,
-                style=Qt.DashLine))
+                style=Qt.PenStyle.DashLine))
                 self._plot_widget.addItem(line)
 
             self._plot_widget.setTitle("DTW Comparison")

src/pygui/backend/visualization/rbf_heatmap.py

@@ -73,7 +73,8 @@ def interpolate_field(
         dist = ((grid_x - cx) / rx) ** 2 + ((grid_y - cy) / ry) ** 2
         field = np.where(dist <= 1.0, field, np.nan)
 
-    return field.astype(np.float64)
+    result: np.ndarray = field.astype(np.float64)
+    return result
 
 
 def refine_field(field: np.ndarray, factor: int = REFINE_FACTOR) -> np.ndarray:
@@ -84,7 +85,8 @@ def refine_field(field: np.ndarray, factor: int = REFINE_FACTOR) -> np.ndarray:
     resampling across a NaN/zero-filled hole rings at the boundary, and any
     mask derived from the coarse grid keeps its staircase when upscaled.
     """
-    return _ndi_zoom(field, factor, order=3)
+    refined: np.ndarray = _ndi_zoom(field, factor, order=3)
+    return refined
 
 
 def ellipse_alpha(height: int, width: int, feather_px: float = 1.2) -> np.ndarray:

src/pygui/backend/visualization/trend_chart_item.py

@@ -20,6 +20,8 @@ from PySide6.QtGui import QColor, QFont, QPainter, QPen, QPolygon
 from PySide6.QtQml import QmlElement
 from PySide6.QtQuick import QQuickPaintedItem
 
+from pygui.backend.visualization.chart_geometry import index_to_pixel, value_to_pixel
+
 log = logging.getLogger(__name__)
 
 QML_IMPORT_NAME = "ISC.Wafer"
@@ -60,7 +62,7 @@ class TrendChartItem(QQuickPaintedItem):
     def data(self) -> list[float]:
         return self._data
 
-    @data.setter
+    @data.setter  # type: ignore[no-redef]
     def data(self, val) -> None:
         coerced = self._coerce_floats(val)
         if coerced == self._data:
@@ -82,7 +84,7 @@ class TrendChartItem(QQuickPaintedItem):
     def lineColor(self) -> QColor:
         return self._line_color
 
-    @lineColor.setter
+    @lineColor.setter  # type: ignore[no-redef]
     def lineColor(self, c: QColor) -> None:
         if c == self._line_color:
             return
@@ -94,7 +96,7 @@ class TrendChartItem(QQuickPaintedItem):
     def gridColor(self) -> QColor:
         return self._grid_color
 
-    @gridColor.setter
+    @gridColor.setter  # type: ignore[no-redef]
     def gridColor(self, c: QColor) -> None:
         if c == self._grid_color:
             return
@@ -106,7 +108,7 @@ class TrendChartItem(QQuickPaintedItem):
     def textColor(self) -> QColor:
         return self._text_color
 
-    @textColor.setter
+    @textColor.setter  # type: ignore[no-redef]
     def textColor(self, c: QColor) -> None:
         if c == self._text_color:
             return
@@ -118,7 +120,7 @@ class TrendChartItem(QQuickPaintedItem):
     def padding(self) -> int:
         return self._padding
 
-    @padding.setter
+    @padding.setter  # type: ignore[no-redef]
     def padding(self, val: int) -> None:
         v = max(0, int(val))
         if v == self._padding:
@@ -201,15 +203,10 @@ class TrendChartItem(QQuickPaintedItem):
         return math.floor(lo / step) * step, math.ceil(hi / step) * step
 
     def _x_to_px(self, i: int, n: int, plot_rect: QRectF) -> float:
-        if n <= 1:
+        return index_to_pixel(i, n, plot_rect.left(), plot_rect.width())
-            return plot_rect.left()
-        return plot_rect.left() + (i / (n - 1)) * plot_rect.width()
 
     def _y_to_px(self, v: float, y_min: float, y_max: float, plot_rect: QRectF) -> float:
-        if y_max - y_min < 1e-9:
+        return value_to_pixel(v, y_min, y_max, plot_rect.top(), plot_rect.height())
-            return plot_rect.center().y()
-        t = (v - y_min) / (y_max - y_min)
-        return plot_rect.bottom() - t * plot_rect.height()
 
     def _draw_grid(self, painter: QPainter, plot_rect: QRectF) -> None:
         pen = QPen(self._grid_color)

src/pygui/backend/visualization/wafer_map_item.py

@@ -107,7 +107,7 @@ class WaferMapItem(QQuickPaintedItem):
     def sensors(self) -> list:
         return [{"label": s.label, "x": s.x, "y": s.y} for s in self._sensors]
 
-    @sensors.setter
+    @sensors.setter  # type: ignore[no-redef]
     def sensors(self, val: list) -> None:
         self._sensors = [
             Sensor(
@@ -127,7 +127,7 @@ class WaferMapItem(QQuickPaintedItem):
     def values(self) -> list:
         return self._values
 
-    @values.setter
+    @values.setter  # type: ignore[no-redef]
     def values(self, val: list) -> None:
         self._values = list(val or [])
         self._rebuild_heatmap()
@@ -138,7 +138,7 @@ class WaferMapItem(QQuickPaintedItem):
     def bands(self) -> list:
         return self._bands
 
-    @bands.setter
+    @bands.setter  # type: ignore[no-redef]
     def bands(self, val: list) -> None:
         self._bands = list(val or [])
         self.bandsChanged.emit()
@@ -148,7 +148,7 @@ class WaferMapItem(QQuickPaintedItem):
     def target(self) -> float:
         return self._target
 
-    @target.setter
+    @target.setter  # type: ignore[no-redef]
     def target(self, val: float) -> None:
         self._target = float(val)
         self._rebuild_heatmap()
@@ -159,7 +159,7 @@ class WaferMapItem(QQuickPaintedItem):
     def margin(self) -> float:
         return self._margin
 
-    @margin.setter
+    @margin.setter  # type: ignore[no-redef]
     def margin(self, val: float) -> None:
         self._margin = float(val)
         self._rebuild_heatmap()
@@ -170,7 +170,7 @@ class WaferMapItem(QQuickPaintedItem):
     def blend(self) -> float:
         return self._blend
 
-    @blend.setter
+    @blend.setter  # type: ignore[no-redef]
     def blend(self, val: float) -> None:
         self._blend = max(0.0, min(1.0, float(val)))
         if self._blend > 0 and self._heatmap is None:
@@ -182,7 +182,7 @@ class WaferMapItem(QQuickPaintedItem):
     def showLabels(self) -> bool:
         return self._show_labels
 
-    @showLabels.setter
+    @showLabels.setter  # type: ignore[no-redef]
     def showLabels(self, val: bool) -> None:
         self._show_labels = bool(val)
         self.showLabelsChanged.emit()
@@ -192,7 +192,7 @@ class WaferMapItem(QQuickPaintedItem):
     def shape(self) -> str:
         return self._shape
 
-    @shape.setter
+    @shape.setter  # type: ignore[no-redef]
     def shape(self, val: str) -> None:
         self._shape = str(val).lower()
         self._rebuild()
@@ -202,7 +202,7 @@ class WaferMapItem(QQuickPaintedItem):
     def size(self) -> float:
         return self._size
 
-    @size.setter
+    @size.setter  # type: ignore[no-redef]
     def size(self, val: float) -> None:
         self._size = float(val)
         self._rebuild()
@@ -212,7 +212,7 @@ class WaferMapItem(QQuickPaintedItem):
     def thicknessData(self) -> list:
         return self._thickness_data
 
-    @thicknessData.setter
+    @thicknessData.setter  # type: ignore[no-redef]
     def thicknessData(self, val:list) -> None:
         self._thickness_data = list(val or [])
         self._rebuild_thickness()
@@ -223,7 +223,7 @@ class WaferMapItem(QQuickPaintedItem):
     def showThickness(self) -> bool:
         return self._show_thickness
 
-    @showThickness.setter
+    @showThickness.setter  # type: ignore[no-redef]
     def showThickness(self, val: bool) -> None:
         self._show_thickness = bool(val)
         self.showThicknessChanged.emit()
@@ -233,7 +233,7 @@ class WaferMapItem(QQuickPaintedItem):
     def hoveredIndex(self) -> int:
         return self._hovered_index
 
-    @hoveredIndex.setter
+    @hoveredIndex.setter  # type: ignore[no-redef]
     def hoveredIndex(self, val: int) -> None:
         val = int(val)
         if val == self._hovered_index:
@@ -246,7 +246,7 @@ class WaferMapItem(QQuickPaintedItem):
     def hoverScale(self) -> float:
         return self._hover_scale
 
-    @hoverScale.setter
+    @hoverScale.setter  # type: ignore[no-redef]
     def hoverScale(self, val: float) -> None:
         self._hover_scale = float(val)
         self.hoverScaleChanged.emit()
@@ -255,32 +255,32 @@ class WaferMapItem(QQuickPaintedItem):
     # Colour properties — QML can bind these to Theme tokens
     @Property(QColor, notify=colorsChanged)
     def ringColor(self) -> QColor: return self._ring_color
-    @ringColor.setter
+    @ringColor.setter  # type: ignore[no-redef]
     def ringColor(self, c: QColor) -> None: self._ring_color = c; self.update()
 
     @Property(QColor, notify=colorsChanged)
     def axisColor(self) -> QColor: return self._axis_color
-    @axisColor.setter
+    @axisColor.setter  # type: ignore[no-redef]
     def axisColor(self, c: QColor) -> None: self._axis_color = c; self.update()
 
     @Property(QColor, notify=colorsChanged)
     def lowColor(self) -> QColor: return self._low_color
-    @lowColor.setter
+    @lowColor.setter  # type: ignore[no-redef]
     def lowColor(self, c: QColor) -> None: self._low_color = c; self.update()
 
     @Property(QColor, notify=colorsChanged)
     def inRangeColor(self) -> QColor: return self._in_range_color
-    @inRangeColor.setter
+    @inRangeColor.setter  # type: ignore[no-redef]
     def inRangeColor(self, c: QColor) -> None: self._in_range_color = c; self.update()
 
     @Property(QColor, notify=colorsChanged)
     def highColor(self) -> QColor: return self._high_color
-    @highColor.setter
+    @highColor.setter  # type: ignore[no-redef]
     def highColor(self, c: QColor) -> None: self._high_color = c; self.update()
 
     @Property(QColor, notify=colorsChanged)
     def textColor(self) -> QColor: return self._text_color
-    @textColor.setter
+    @textColor.setter  # type: ignore[no-redef]
     def textColor(self, c: QColor) -> None: self._text_color = c; self.update()
 
     # ── slots ─────────────────────────────────────────────────────────────
@@ -314,7 +314,7 @@ class WaferMapItem(QQuickPaintedItem):
             return False
         try:
             result = self.grabToImage()
-            img = result.image()
+            img = result.image()  # type: ignore[attr-defined]
             img.save(file_path, "PNG")
             return True
         except Exception as e:
@@ -702,11 +702,11 @@ class WaferMapItem(QQuickPaintedItem):
                 painter.setPen(QPen(self._text_color))
                 y1 = ly + id_ascent
                 if side in ("top", "bottom"):
-                    painter.drawText(lx + (text_w - id_w) // 2, y1, id_text)
+                    painter.drawText(lx + (text_w - id_w) // 2, y1, id_text)  # type: ignore[arg-type]
                 elif side == "left":
-                    painter.drawText(lx + (text_w - id_w), y1, id_text)
+                    painter.drawText(lx + (text_w - id_w), y1, id_text)  # type: ignore[arg-type]
                 else:
-                    painter.drawText(lx, y1, id_text)
+                    painter.drawText(lx, y1, id_text)  # type: ignore[arg-type]
 
                 # Draw Temperature (second line)
                 if has_temp:
@@ -714,8 +714,8 @@ class WaferMapItem(QQuickPaintedItem):
                     painter.setPen(QPen(color))
                     y2 = ly + id_line_h + temp_ascent
                     if side in ("top", "bottom"):
-                        painter.drawText(lx + (text_w - temp_w) // 2, y2, temp_text)
+                        painter.drawText(lx + (text_w - temp_w) // 2, y2, temp_text)  # type: ignore[arg-type]
                     elif side == "left":
-                        painter.drawText(lx + (text_w - temp_w), y2, temp_text)
+                        painter.drawText(lx + (text_w - temp_w), y2, temp_text)  # type: ignore[arg-type]
                     else:
-                        painter.drawText(lx, y2, temp_text)
+                        painter.drawText(lx, y2, temp_text)  # type: ignore[arg-type]

src/pygui/backend/wafer/__init__.py

@@ -1,12 +0,0 @@
-# ===== Wafer Sub-package =====
-from pygui.backend.wafer.family_spec import sensor_count_for
-from pygui.backend.wafer.wafer_layouts import available_families, load_layout
-from pygui.backend.wafer.zwafer_models import DataRecord, Sensor, ZWaferData
-from pygui.backend.wafer.zwafer_parser import ZWaferParser
-
-__all__ = [
-    "ZWaferData", "Sensor", "DataRecord",
-    "ZWaferParser",
-    "load_layout", "available_families",
-    "sensor_count_for",
-]

src/pygui/backend/wafer/wafer_layouts.py

@@ -66,7 +66,8 @@ def _family_name(raw_name: str) -> str:
 
 def _load_yaml(path: Path) -> dict:
     with path.open(encoding="utf-8") as f:
-        return yaml.safe_load(f)
+        loaded: dict = yaml.safe_load(f)
+        return loaded
 
 
 # TODO P6.3: expose this list to a new LayoutSelector.qml (4-button chooser)

src/pygui/backend/wafer/zwafer_parser.py

@@ -115,7 +115,7 @@ class ZWaferParser:
         y_coords: Optional[list],
     ) -> None:
         """Build sensor list from layout arrays."""
-        if not all([labels, x_coords, y_coords]):
+        if not (labels and x_coords and y_coords):
             raise ValueError("Sensor layout section is incomplete or missing.")
 
         if len(labels) != len(x_coords) or len(labels) != len(y_coords):

src/pygui/serialcomm/data_parser.py

@@ -10,6 +10,7 @@ Mirrors the C# Form1.cs binary parsing pipeline:
 
 import logging
 import os
+from datetime import datetime
 from typing import Optional
 
 from pygui.backend.wafer.family_spec import sensor_count_for
@@ -266,7 +267,6 @@ def save_to_csv(
     try:
         os.makedirs(output_dir, exist_ok=True)
         # Build filename: P00001-20260505_133045.csv
-        from datetime import datetime
 
         timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
         filename = f"{serial_number}-{timestamp}.csv"

src/pygui/serialcomm/stream_reader.py

@@ -45,7 +45,7 @@ class StreamReader:
         Reads up to 256 bytes in one shot. If nothing is immediately
         available, yields briefly to avoid a busy spin.
         """
-        chunk = self._transport.read(max(min_bytes, 256))
+        chunk: bytes = self._transport.read(max(min_bytes, 256))
         if not chunk:
             time.sleep(0.005)
         return chunk
@@ -106,7 +106,7 @@ class StreamReader:
             except Exception:
                 pass
 
-    def _run_binary(self, initial_bytes: bytes) -> None:
+    def _run_binary(self, initial_bytes: bytes | bytearray) -> None:
         log.info("StreamReader: starting binary stream parsing")
         buf = bytearray(initial_bytes)
         resync_attempts = 0
@@ -149,7 +149,7 @@ class StreamReader:
                 payload = buf[7:7 + payload_len]
 
                 try:
-                    frame = self._parse(payload, seq)
+                    frame = self._parse(payload, seq)  # type: ignore[arg-type]
                     self._on_frame(frame)
                 except Exception as exc:
                     self.error_count += 1
@@ -238,7 +238,7 @@ class StreamReader:
             for hex_val in valid_hex_words:
                 try:
                     swapped = hex_val[2:4] + hex_val[0:2]
-                    t = _convert_hex_to_temp(swapped, self._family_code)
+                    t = _convert_hex_to_temp(swapped, self._family_code)  # type: ignore[arg-type]
                     values.append(t)
                 except Exception:
                     values.append(0.0)
@@ -262,7 +262,7 @@ class StreamReader:
                 line = line_bytes.decode('utf-8', errors='ignore').strip()
                 if line:
                     try:
-                        frame = self._parse(line, seq)
+                        frame = self._parse(line, seq)  # type: ignore[arg-type]
                         if frame:
                             self._on_frame(frame)
                             seq += 1

tests/test_chart_geometry.py

@@ -0,0 +1,28 @@
+import pytest
+
+from pygui.backend.visualization.chart_geometry import index_to_pixel, value_to_pixel
+
+
+def test_value_to_pixel_min_maps_to_bottom():
+    assert value_to_pixel(0.0, 0.0, 100.0, pixel_start=10.0, pixel_span=200.0) == pytest.approx(210.0)
+
+
+def test_value_to_pixel_max_maps_to_top():
+    assert value_to_pixel(100.0, 0.0, 100.0, pixel_start=10.0, pixel_span=200.0) == pytest.approx(10.0)
+
+
+def test_value_to_pixel_midpoint():
+    assert value_to_pixel(50.0, 0.0, 100.0, pixel_start=0.0, pixel_span=200.0) == pytest.approx(100.0)
+
+
+def test_value_to_pixel_degenerate_range_centers():
+    assert value_to_pixel(5.0, 5.0, 5.0, pixel_start=0.0, pixel_span=200.0) == pytest.approx(100.0)
+
+
+def test_index_to_pixel_first_and_last():
+    assert index_to_pixel(0, 5, pixel_start=0.0, pixel_span=100.0) == pytest.approx(0.0)
+    assert index_to_pixel(4, 5, pixel_start=0.0, pixel_span=100.0) == pytest.approx(100.0)
+
+
+def test_index_to_pixel_single_point_centers():
+    assert index_to_pixel(0, 1, pixel_start=0.0, pixel_span=100.0) == pytest.approx(50.0)

tests/test_local_settings_model.py

@@ -0,0 +1,61 @@
+import pytest
+
+from pygui.backend.data.local_settings import LocalSettings
+from pygui.backend.data.local_settings_model import LocalSettingsModel
+
+
+@pytest.fixture
+def shared_settings():
+    return LocalSettings()
+
+
+@pytest.fixture
+def model(qapp, tmp_path, shared_settings):
+    return LocalSettingsModel(shared_settings, tmp_path)
+
+
+def test_save_mutates_the_shared_instance_in_place(model, shared_settings):
+    # This is the bug candidate 1 fixes: DeviceController holds the same
+    # LocalSettings object, so a save here must be visible to it without
+    # a reload — no throwaway copy, no stale read until restart.
+    model.chamberId = "7"
+    model.waferReadTimeout = 45000
+    model.saveSettings()
+
+    assert shared_settings.chamber_id == "7"
+    assert shared_settings.wafer_read_timeout == 45000
+
+
+def test_save_persists_to_disk_and_reload_round_trips(tmp_path, qapp, shared_settings):
+    model = LocalSettingsModel(shared_settings, tmp_path)
+    model.chamberId = "9"
+    model.waferRetries = 3
+    model.saveSettings()
+
+    reloaded_settings = LocalSettings.read_settings(str(tmp_path))
+    other_model = LocalSettingsModel(reloaded_settings, tmp_path)
+    other_model.loadSettings()
+
+    assert other_model.chamberId == "9"
+    assert other_model.waferRetries == 3
+
+
+def test_revert_restores_last_saved_values(model):
+    model.chamberId = "2"
+    model.saveSettings()
+
+    model.chamberId = "unsaved-edit"
+    assert model.isDirty is True
+
+    model.revertChanges()
+    assert model.chamberId == "2"
+    assert model.isDirty is False
+
+
+def test_invalid_chamber_id_blocks_save(model, shared_settings):
+    shared_settings.chamber_id = "before"
+    model.chamberId = ""
+    model.saveSettings()
+
+    assert model.saveStatus.startswith("error:")
+    assert shared_settings.chamber_id == "before"  # unsaved, shared instance untouched

tests/test_session_controller.py

@@ -1,7 +1,10 @@
+from unittest.mock import MagicMock
+
 import pytest
-from unittest.mock import MagicMock, patch
+
 from pygui.backend.controllers.session_controller import SessionController
 
+
 @pytest.fixture
 def controller():
     return SessionController()
@@ -9,7 +12,7 @@ def controller():
 def test_initial_default(controller):
     assert controller.mode == "review"
     assert controller.state == "idle"
-    assert controller.recording == False
+    assert not controller.recording
 
 def test_playback_flow(controller):
     controller.loadFile("tests/fixtures/sample_stream.csv")
@@ -119,10 +122,10 @@ Item {
 def test_recording_toggle(controller, tmp_path):
     csv_path = str(tmp_path / "rec" / "live_test.csv")
     controller.startRecording(csv_path, "SN123")
-    assert controller.recording == True
+    assert controller.recording
 
     controller.stopRecording()
-    assert controller.recording == False
+    assert not controller.recording
 
     # Header written with wafer serial
     content = open(csv_path).read()

tmp/settings.json

@@ -1,2 +0,0 @@
-{
-    "_mock_return_value":