feat: add interactive folder selection for CSV saves and stabilize cross-platform dependency locking

- Define WaferLayout subclass to wrap sensor lists with shape and size attributes.
- Add resolve_shape_and_size resolver to infer wafer shape/size from filename prefix or sensor count.
- Update Sensor dataclass to support dynamic side alignments and coordinates offsets.
- Expose waferShape and waferSize properties from SessionController for QML data-bindings.

.gitignore

@@ -5,6 +5,9 @@ __pycache__/
 *.pyd
 *.so
 *.a
+*.egg-info/
+.pytest_cache/
+.ruff_cache/
 
 # Virtual environment
 .venv/
@@ -14,10 +17,11 @@ env/
 # IDE
 .vscode/
 .idea/
+.qtcreator/
 *.swp
 *.swo
 *~
-
+docs
 # OS
 .DS_Store
 Thumbs.db
@@ -34,4 +38,6 @@ build/
 dist/
 *.spec
 *.icns
-*.ico
+*.ico
+# Superpowers brainstorming visual companion
+.superpowers/

ISC.qmlproject

@@ -0,0 +1,16 @@
+import type QmlProjectModel 1.0
+
+QmlProject {
+    name: "ISC"
+    version: "1.0"
+    mainFile: "src/pygui/ISC/Main.qml"
+
+    dependencies {
+        module: "QtQuick"
+        minimumVersion: "6.0.0"
+    }
+
+    importPaths: [
+        "src/pygui"
+    ]
+}

ISC/Tabs/qmldir

@@ -1,5 +0,0 @@
-# ===== ISC Tabs Module =====
-module ISC.Tabs
-
-# ===== Tab Components =====
-SettingsTab 1.0 SettingsTab.qml

README.md

@@ -16,34 +16,42 @@ python3 -m venv .venv
 source .venv/bin/activate
 python -m pip install --upgrade pip
 pip install -r requirements.txt
+pip install -e .            # install the `pygui` package (src/ layout) in editable mode
 ```
 
 ## Run
 
 ```bash
 source .venv/bin/activate
-python main.py
+python -m pygui             # or run the `isc` console script
 ```
 
-This launches the Qt window and loads the `ISC` QML module from `ISC/Main.qml`.
+This launches the Qt window and loads the `ISC` QML module from `src/pygui/ISC/Main.qml`.
 
 ## Project Structure
 
-- `main.py`: PySide6 bootstrap; creates the Qt app and loads QML module `ISC/Main`.
-- `ISC/Main.qml`: top-level window definition.
-- `ISC/HomePage.qml`: main UI layout (left action rail, workspace panel, footer tabs).
-- `ISC/Theme.qml`: shared theme constants and dark/light mode tokens.
-- `ISC/qmldir`: QML module registration.
+The application lives under a `src/` layout as the `pygui` package:
+
+- `src/pygui/__main__.py`: PySide6 bootstrap; creates the Qt app and loads QML module `ISC/Main`. Entry point for `python -m pygui`.
+- `src/pygui/backend/`: Qt-facing models and controllers (device, settings, file browser, wafer parsing).
+- `src/pygui/serialcomm/`: serial port, device service, and data-parser layer.
+- `src/pygui/ISC/`: the `ISC` QML module (UI).
+  - `Main.qml`: top-level window definition.
+  - `HomePage.qml`: main UI layout (left action rail, workspace panel, footer tabs).
+  - `Theme.qml`: shared theme constants and dark/light mode tokens.
+  - `qmldir`: QML module registration.
+- `tests/`: pytest suite.
+- `packaging/`: PyInstaller spec (`isc.spec`) and app icons.
 
 ## Window Configuration
 
-Window dimensions and constraints are defined in `ISC/Main.qml`:
+Window dimensions and constraints are defined in `src/pygui/ISC/Main.qml`:
 
 - **Default size**: 1400 × 820 pixels
 - **Minimum size**: 1100 × 700 pixels
 - **Title bar**: "ISenseCloud"
 
-To adjust the window, edit the `Window` block in `ISC/Main.qml`:
+To adjust the window, edit the `Window` block in `src/pygui/ISC/Main.qml`:
 
 ```qml
 Window {
@@ -58,8 +66,8 @@ Window {
 
 ## Customization
 
-- Toggle dark/light mode in `ISC/Theme.qml` via `isDarkMode`.
-- Update sidebar and footer labels in `ISC/HomePage.qml` through `sideActions` and `bottomTabs`.
+- Toggle dark/light mode in `src/pygui/ISC/Theme.qml` via `isDarkMode`.
+- Update sidebar and footer labels in `src/pygui/ISC/HomePage.qml` through `sideActions` and `bottomTabs`.
 
 ## Troubleshooting
 

assets/layouts/aepwafer.yaml

@@ -0,0 +1,44 @@
+# This will be the name of the output files
+name: aepwafer
+wafers: ["A", "E", "P"]
+
+# round or square wafer
+shape: round
+
+# diameter/edge size of the wafer
+size: 300
+
+# large or small markers and labels
+marker_size: large
+font_size: large
+
+# origin settings.  x_origin can be left, right, or center.  y_origin can
+# be top, bottom, or center.  Using right or top implies that the X/Y values
+# for that axis are negative, or else we'll be drawing outside the image.
+x_origin: left
+y_origin: bottom
+
+# sensor X and Y values, in mm relative to the origin
+X: [150, 204, 249, 280, 290, 280, 249, 204, 150, 97, 51, 21, 10, 21, 51, 97,
+    150, 203, 241, 255, 241, 203, 150, 98, 59, 45, 59, 98, 171, 207, 228, 228,
+    207, 171, 130, 94, 73, 73, 94, 130, 150, 186, 200, 186, 150, 115, 100, 115]
+Y: [290, 280, 249, 204, 150, 97, 51, 21, 10, 21, 51, 97, 150, 204, 249, 280,
+    255, 241, 203, 150, 98, 59, 45, 59, 98, 150, 203, 241, 228, 207, 171, 130,
+    94, 73, 73, 94, 130, 171, 207, 228, 200, 186, 150, 115, 100, 115, 150, 186]
+
+# set this to either 0 or 1 for the initial sensor number (usually 1)
+start_sn: 1
+
+# Normally, positive X is to the right, and positive Y is up.
+# These settings can be used to reverse one or both of these.
+reverse_x: false
+reverse_y: false
+
+# these are sensors whose labels need to be repositioned.  Sensor numbers
+# start at start_sn.  Directions are up, down, left, and right, and values
+# are multiples of the marker size.
+label_exceptions: {
+    4: { top: [0, 0] },
+    5: { top: [0, 0] },
+    6: { top: [0, 0] },
+}

assets/layouts/bcdwafer.yaml

@@ -0,0 +1,46 @@
+# This will be the name of the output files
+name: bcdwafer
+wafers: ["B", "C", "D"]
+
+# round or square wafer
+shape: round
+
+# diameter/edge size of the wafer
+size: 300
+
+# large or small markers and labels
+marker_size: large
+font_size: large
+
+# origin settings.  x_origin can be left, right, or center.  y_origin can
+# be top, bottom, or center.  Using right or top implies that the X/Y values
+# for that axis are negative, or else we'll be drawing outside the image.
+x_origin: center
+y_origin: center
+
+# sensor X and Y values, in mm relative to the origin
+X: [0, 72.50, 125.57, 145.00, 125.57, 72.50, 0, -72.50, -125.57, -145.00,
+    -125.57, -72.50, 0, 47.50, 82.27, 95.00, 82.27, 47.50, 0, -47.50, -82.27,
+    -95.00, -82.27, -47.50, 38.97, 22.50, -38.97, -22.50, 0]
+Y: [145.00, 125.57, 72.50, 0, -72.50, -125.57, -145.00, -125.57, -72.50, 0,
+    72.50, 125.57, 95.00, 82.27, 47.50, 0, -47.50, -82.27, -95.00, -82.27,
+    -47.50, 0, 47.50, 82.27, 22.50, -38.97, -22.50, 38.97, 0]
+
+# set this to either 0 or 1 for the initial sensor number (usually 1)
+start_sn: 1
+
+# Normally, positive X is to the right, and positive Y is up.
+# These settings can be used to reverse one or both of these.
+reverse_x: false
+reverse_y: false
+
+# these are sensors whose labels need to be repositioned.  Sensor numbers
+# start at start_sn.  Directions are up, down, left, and right, and values
+# are multiples of the marker size.
+label_exceptions: {
+    2: { left: [1, 0] },
+    3: { left: [1, 0] },
+    4: { left: [1, 0] },
+    5: { left: [1, 0] },
+    6: { left: [1, 0] },
+}

assets/layouts/fwafer.yaml

@@ -0,0 +1,43 @@
+# This will be the name of the output files
+name: fwafer
+wafers: ["F"]
+
+# round or square wafer
+shape: round
+
+# diameter/edge size of the wafer
+size: 200
+
+# large or small markers and labels
+marker_size: large
+font_size: large
+
+# origin settings.  x_origin can be left, right, or center.  y_origin can
+# be top, bottom, or center.  Using right or top implies that the X/Y values
+# for that axis are negative, or else we'll be drawing outside the image.
+x_origin: center
+y_origin: center
+
+# sensor X and Y values, in mm relative to the origin
+X: [0.0, 47.5, 82.3, 95.0, 82.3, 47.5, 0.0, -47.5, -82.3, -95.0, -82.3, -47.5,
+    -55.0, -14.8, 39.7, 55.0, 14.8, -39.7, -14.7, 25.5, 14.7, -25.5]
+Y: [95.0, 82.3, 47.5, 0.0, -47.5, -82.3, -95.0, -82.3, -47.5, 0.0, 47.5, 82.3,
+    13.3, 54.4, 40.0, -13.3, -54.4, -40.0, 25.5, 14.7, -25.5, -14.7]
+
+# set this to either 0 or 1 for the initial sensor number (usually 1)
+start_sn: 1
+
+# Normally, positive X is to the right, and positive Y is up.
+# These settings can be used to reverse one or both of these.
+reverse_x: false
+reverse_y: false
+
+# these are sensors whose labels need to be repositioned.  Sensor numbers
+# start at start_sn.  Directions are up, down, left, and right, and values
+# are multiples of the marker size.
+label_exceptions: {
+    2: { left: [1, 0] },
+    3: { left: [1, 0] },
+    4: { left: [1, 0] },
+    5: { left: [1, 0] },
+}

assets/layouts/xwafer.yaml

@@ -0,0 +1,69 @@
+# This will be the name of the output files
+name: xwafer
+wafers: ["X"]
+
+# round or square wafer
+shape: square
+
+# diameter/edge size of the wafer
+size: 310
+
+# large or small markers and labels
+marker_size: small
+font_size: small
+
+# origin settings.  x_origin can be left, right, or center.  y_origin can
+# be top, bottom, or center.  Using right or top implies that the X/Y values
+# for that axis are negative, or else we'll be drawing outside the image.
+x_origin: left
+y_origin: bottom
+
+# sensor X and Y values, in mm relative to the origin
+X: [ 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00,
+    13.00, 23.00, 46.43, 89.86, 133.29, 176.72, 220.15, 263.58, 287.01, 297.01,
+    307.01, 307.01, 307.01, 307.01, 307.01, 307.01, 307.01, 307.01, 307.01,
+    307.01, 307.01, 307.01, 297.01, 287.01, 263.58, 220.15, 176.72, 133.29,
+    89.86, 46.43, 23.00, 13.00, 46.43, 46.43, 46.43, 46.43, 46.43, 46.43,
+    89.86, 133.29, 176.72, 220.15, 263.58, 263.58, 263.58, 263.58, 263.58,
+    263.58, 220.15, 176.72, 133.29, 89.86, 89.86, 89.86, 89.86, 89.86,
+    133.29, 176.72, 220.15, 220.15, 220.15, 220.15, 176.72, 133.29, 133.29,
+    133.29, 176.72, 176.72]
+Y: [ 3.00, 13.07, 23.07, 46.50, 89.93, 133.36, 176.79, 220.22, 263.65, 287.08,
+    297.08, 307.08, 307.08, 307.08, 307.08, 307.08, 307.08, 307.08, 307.08,
+    307.08, 307.08, 307.08, 307.08, 297.08, 287.08, 263.65, 220.22, 176.79,
+    133.36, 89.93, 46.50, 23.07, 13.07, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00,
+    3.00, 3.00, 3.00, 3.00, 3.00, 46.50, 89.93, 133.36, 176.79, 220.22, 263.65,
+    263.65, 263.65, 263.65, 263.65, 263.65, 220.22, 176.79, 133.36, 89.93,
+    46.50, 46.50, 46.50, 46.50, 46.50, 89.93, 133.36, 176.79, 220.22, 220.22,
+    220.22, 220.22, 176.79, 133.36, 89.93, 89.93, 89.93, 133.36, 176.79,
+    176.79, 133.36 ]
+
+# set this to either 0 or 1 for the initial sensor number (usually 1)
+start_sn: 1
+
+# Normally, positive X is to the right, and positive Y is up.
+# These settings can be used to reverse one or both of these.
+reverse_x: false
+reverse_y: false
+
+# these are sensors whose labels need to be repositioned.  Sensor numbers
+# start at start_sn.  Directions are up, down, left, and right, and values
+# are multiples of the marker size.
+label_exceptions: {
+    21: { left: [0, 0] },
+    22: { left: [0, 0] },
+    23: { left: [0, 0] },
+    24: { left: [0, 0] },
+    25: { left: [0, 0] },
+    26: { left: [0, 0] },
+    27: { left: [0, 0] },
+    28: { left: [0, 0] },
+    29: { left: [0, 0] },
+    30: { left: [0, 0] },
+    31: { left: [0, 0] },
+    32: { left: [0, 0] },
+    33: { left: [0, 0] },
+    34: { left: [0, 0] },
+    35: { left: [0, 0] },
+    36: { left: [0, 0] }
+}

assets/layouts/zwafer.yaml

@@ -0,0 +1,68 @@
+# This will be the name of the output files
+name: zwafer
+wafers: ["Z"]
+
+# round or square wafer
+shape: round
+
+# diameter/size of the wafer
+size: 300
+
+# large or small markers and labels
+marker_size: small
+font_size: small
+
+# origin settings.  x_origin can be left, right, or center.  y_origin can
+# be top, bottom, or center.  Using right or top probably also needs
+# reverse_x/reverse_y to be set as well.
+x_origin: center
+y_origin: center
+
+# sensor X and Y values, in mm relative to the wafer center
+X: [0.00, -1.17, 8.92, 1.17, -8.92, 22.52, 29.35, -22.52, -29.35, 45.05, 73.37,
+     58.71, 9.66, -45.05, -73.37, -58.71, -9.66, 79.85, 89.06, 46.10, -23.86,
+     -79.85, -89.06, -46.10, 23.86, 66.96, 109.06, 87.27, 14.36, -66.96,
+     -109.06, -87.27, -14.36, 121.24, 135.23, 70.00, -36.23, -121.24, -135.23,
+     -70.00, 36.23, 124.71, 139.09, 72.00, -37.27, -124.71, -139.09, -72.00,
+     37.27, 89.49, 127.31, 145.74, 141.99, 116.62, 73.50, 19.19, -38.05, -89.49,
+     -127.31, -145.74, -141.99, -116.62, -73.50, -19.19, 38.05]
+Y: [0.00, -8.92, -1.17, 8.92, 1.17, -29.35, 22.52, 29.35, -22.52, -58.71,
+     -9.66, 45.05, 73.37, 58.71, 9.66, -45.05, -73.37, -46.10, 23.86, 79.85,
+     89.06, 46.10, -23.86, -79.85, -89.06, -87.27, -14.36, 66.96, 109.06, 87.27,
+     14.36, -66.96, -109.06, -70.00, 36.23, 121.24, 135.23, 70.00, -36.23,
+     -121.24, -135.23, -72.00, 37.27, 124.71, 139.09, 72.00, -37.27, -124.71,
+     -139.09, -116.62, -73.50, -19.19, 38.05, 89.49, 127.31, 145.74, 141.99,
+     116.62, 73.50, 19.19, -38.05, -89.49, -127.31, -145.74, -141.99]
+
+# set this to either 0 or 1 for the initial sensor number (usually 1)
+start_sn: 0
+
+# If one or both axes are reversed, this can be used to fix it
+# without having to edit all of the coordinates.
+# These should be false for most normal wafers.
+reverse_x: false
+reverse_y: false
+
+# these are sensors whose labels need to be repositioned.  Sensor numbers
+# start at start_sn.  Directions are up, down, left, and right, and values
+# are multiples of the marker size.
+label_exceptions: {
+    33: { left: [0, 0] },
+    34: { left: [0, 0] },
+    41: { top: [0, 0] },
+    42: { bottom: [0, 0] },
+    45: { top: [1, 0] },
+    46: { bottom: [0.5, 0] },
+    49: { left: [0, 0] },
+    50: { bottom: [-1.75, -0.5] },
+    51: { top: [-1, 0] },
+    52: { top: [-1, 0] },
+    53: { bottom: [0, 0] },
+    54: { left: [0, -0.75] },
+    55: { right: [0, 0.5] },
+    58: { bottom: [-0.75, 0] },
+    60: { top: [0, 0] },
+    62: { right: [0, 1] },
+    63: { right: [0, 0] },
+    64: { left: [0, 0.25] }
+}

assets/layouts/zwafer_rev.yaml

@@ -0,0 +1,71 @@
+# This will be the name of the output files
+name: zwafer_rev
+wafers: []     # the reversed version doesn't represent any real wafer
+
+# round or square wafer
+shape: round
+
+# diameter/size of the wafer
+size: 300
+
+# large or small markers and labels
+marker_size: small
+font_size: small
+
+# origin settings.  x_origin can be left, right, or center.  y_origin can
+# be top, bottom, or center.  Using right or top probably also needs
+# reverse_x/reverse_y to be set as well.
+x_origin: center
+y_origin: center
+
+# sensor X and Y values, in mm relative to the wafer center
+X: [0.00, -1.17, 8.92, 1.17, -8.92, 22.52, 29.35, -22.52, -29.35, 45.05, 73.37,
+     58.71, 9.66, -45.05, -73.37, -58.71, -9.66, 79.85, 89.06, 46.10, -23.86,
+     -79.85, -89.06, -46.10, 23.86, 66.96, 109.06, 87.27, 14.36, -66.96,
+     -109.06, -87.27, -14.36, 121.24, 135.23, 70.00, -36.23, -121.24, -135.23,
+     -70.00, 36.23, 124.71, 139.09, 72.00, -37.27, -124.71, -139.09, -72.00,
+     37.27, 89.49, 127.31, 145.74, 141.99, 116.62, 73.50, 19.19, -38.05, -89.49,
+     -127.31, -145.74, -141.99, -116.62, -73.50, -19.19, 38.05]
+Y: [0.00, -8.92, -1.17, 8.92, 1.17, -29.35, 22.52, 29.35, -22.52, -58.71,
+     -9.66, 45.05, 73.37, 58.71, 9.66, -45.05, -73.37, -46.10, 23.86, 79.85,
+     89.06, 46.10, -23.86, -79.85, -89.06, -87.27, -14.36, 66.96, 109.06, 87.27,
+     14.36, -66.96, -109.06, -70.00, 36.23, 121.24, 135.23, 70.00, -36.23,
+     -121.24, -135.23, -72.00, 37.27, 124.71, 139.09, 72.00, -37.27, -124.71,
+     -139.09, -116.62, -73.50, -19.19, 38.05, 89.49, 127.31, 145.74, 141.99,
+     116.62, 73.50, 19.19, -38.05, -89.49, -127.31, -145.74, -141.99]
+
+# set this to either 0 or 1 for the initial sensor number (usually 1)
+start_sn: 0
+
+# If one or both axes are reversed, this can be used to fix it
+# without having to edit all of the coordinates.
+# These should be false for most normal wafers.
+reverse_x: true
+reverse_y: true
+
+# these are sensors whose labels need to be repositioned.  Sensor numbers
+# start at start_sn.  Directions are up, down, left, and right, and values
+# are multiples of the marker size.
+label_exceptions: {
+    37: { left: [0, 0] },
+    38: { left: [0, 0] },
+    39: { left: [0, 0] },
+    41: { top: [1.5, 0] },
+    42: { bottom: [1, 0] },
+    43: { left: [0, -1] },
+    45: { bottom: [-1, -1] },
+    46: { bottom: [0, -1] },
+    47: { right: [0, 1] },
+    48: { left: [0, 0] },
+    50: { bottom: [-1, 0] },
+    52: { top: [0, 0] },
+    54: { right: [0.5, 1] },
+    56: { left: [0, 0.5] },
+    57: { left: [0, 0] },
+    58: { top: [0.5, 0] },
+    59: { left: [0, 0] },
+    60: { top: [-1, 0] },
+    61: { left: [0, 0] },
+    62: { left: [0, -1] },
+    63: { right: [0, 1] },
+}

backend/__init__.py

@@ -1 +0,0 @@
-# ===== Backend Package Marker =====

pyproject.toml

@@ -1,16 +1,98 @@
+# ===== Build System =====
+[build-system]
+requires = ["setuptools>=61"]
+build-backend = "setuptools.build_meta"
+
 # ===== Project Metadata =====
 [project]
 name = "pygui"
 version = "0.1.0"
+requires-python = ">=3.11"
+dependencies = [
+    "PySide6>=6.6.0",
+    "pyqtgraph>=0.13.0",
+    "numpy>=1.24.0",
+    "pyserial>=3.5",
+    "pandas>=2.0.0",
+    "matplotlib>=3.7.0",
+    "scipy>=1.17.1",
+    "pyyaml>=6.0.3",
+]
 
 [project.optional-dependencies]
 dev = ["pytest"]
 
+# ===== Console Entry Point =====
+[project.scripts]
+isc = "pygui.__main__:main"
+
+# ===== Package Discovery (src layout) =====
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+# Ship the QML module alongside the Python package.
+pygui = ["ISC/**/*.qml", "ISC/**/qmldir"]
+
 # ===== PySide Build Inputs =====
 [tool.pyside6-project]
-files = ["ISC/HomePage.qml", "ISC/Main.qml", "ISC/Tabs/DataTab.qml", "ISC/Tabs/GraphTab.qml", "ISC/Tabs/SelectFileDialog.qml", "ISC/Tabs/SettingsTab.qml", "ISC/Tabs/StatusTab.qml", "ISC/Tabs/qmldir", "ISC/Theme.qml", "ISC/qmldir", "backend/data_model.py", "backend/device_controller.py", "backend/graph_view.py", "backend/file_browser.py", "backend/local_settings.py", "backend/local_settings_model.py", "main.py", "serialcomm/__init__.py", "serialcomm/data_parser.py", "serialcomm/serial_port.py", "serialcomm/device_service.py"]
+files = [
+    "src/pygui/ISC/HomePage.qml",
+    "src/pygui/ISC/Main.qml",
+    "src/pygui/ISC/Theme.qml",
+    "src/pygui/ISC/qmldir",
+    "src/pygui/ISC/Tabs/DataTab.qml",
+    "src/pygui/ISC/Tabs/SelectFileDialog.qml",
+    "src/pygui/ISC/Tabs/SettingsTab.qml",
+    "src/pygui/ISC/Tabs/StatusTab.qml",
+    "src/pygui/ISC/Tabs/qmldir",
+    "src/pygui/__main__.py",
+    "src/pygui/backend/contour_models.py",
+    "src/pygui/backend/crypto_helper.py",
+    "src/pygui/backend/csv_file_metadata.py",
+    "src/pygui/backend/data_model.py",
+    "src/pygui/backend/data_segment.py",
+    "src/pygui/backend/device_controller.py",
+    "src/pygui/backend/file_browser.py",
+    "src/pygui/backend/frame.py",
+    "src/pygui/backend/graph_view.py",
+    "src/pygui/backend/local_settings.py",
+    "src/pygui/backend/local_settings_model.py",
+    "src/pygui/backend/marching_squares.py",
+    "src/pygui/backend/zwafer_models.py",
+    "src/pygui/backend/zwafer_parser.py",
+    "src/pygui/backend/frame_stats.py",
+    "src/pygui/backend/threshold_classifier.py",
+    "src/pygui/backend/stability_detector.py",
+    "src/pygui/backend/csv_recorder.py",
+    "src/pygui/backend/frame_player.py",
+    "src/pygui/backend/stream_reader.py",
+    "src/pygui/backend/session_model.py",
+    "src/pygui/backend/session_controller.py",
+    "src/pygui/backend/wafer_layouts.py",
+    "src/pygui/backend/rbf_heatmap.py",
+    "src/pygui/backend/wafer_map_item.py",
+    "src/pygui/serialcomm/__init__.py",
+    "src/pygui/serialcomm/data_parser.py",
+    "src/pygui/serialcomm/device_service.py",
+    "src/pygui/serialcomm/serial_port.py",
+    "src/pygui/ISC/Tabs/WaferMapTab.qml",
+    "src/pygui/ISC/Tabs/components/WaferMapView.qml",
+    "src/pygui/ISC/Tabs/components/SourcePanel.qml",
+    "src/pygui/ISC/Tabs/components/ReadoutPanel.qml",
+    "src/pygui/ISC/Tabs/components/TransportBar.qml",
+    "src/pygui/ISC/Tabs/components/ReplaceSensorDialog.qml",
+    "src/pygui/ISC/Tabs/components/qmldir",
+]
 
 [dependency-groups]
 dev = [
     "pytest>=9.0.3",
 ]
+
+[tool.uv]
+environments = [
+    "sys_platform == 'darwin'",
+    "sys_platform == 'win32'",
+    "sys_platform == 'linux'",
+]

requirements.txt

@@ -3,3 +3,7 @@ PySide6>=6.6.0
 pyqtgraph>=0.13.0
 numpy>=1.24.0
 pyserial>=3.5
+pandas>=2.0.0
+matplotlib>=3.7.0
+scipy>=1.10.0
+pyyaml>=6.0

src/pygui/ISC/HomePage.qml

@@ -24,7 +24,42 @@ Rectangle {
     property int selectedTabIndex: 0
     property int selectedSideActionIndex: -1   // nothing active on startup
 
-    // ===== Main Two-Column Layout =====
+    property bool memoryRead: false
+    property bool waferDetected: false
+
+    Connections {
+        target: deviceController
+        function onDetectResult(result){ 
+            //result is a waferInfo dict on success, None on failure
+            root.waferDetected = (result != null && result!= undefined)
+        }
+        function onParsedDataReady(result) {
+            if (result.success && result.csv_path) {
+                // Load the freshly read CSV into the player
+                streamController.loadFile(result.csv_path)
+
+                // Automatically switch to the "Wafer Map Tab"  (index 3)
+                root.selectedTabIndex = 3
+            }
+        }
+    }
+   Connections {
+       target: deviceController
+       function onReadResult(result) {
+           // result has "success" key on success, "error" key on failure
+           root.memoryRead = (result !== null &&
+                              result !== undefined &&
+                              result.success === true)
+
+           if (root.memoryRead) {
+               console.log(`[P1.1] Memory read complete: ${result.bytes} bytes`)
+           } else {
+               console.log(`[P1.1] Read failed: ${result.error || "unknown"}`)
+           }
+       }
+   }
+
+    // ===== Main Two-Column Layout ======
     RowLayout {
         anchors.fill: parent
         spacing: 0
@@ -53,6 +88,16 @@ Rectangle {
                     Button {
                         id: control
                         text: modelData
+                        enabled: {
+                            switch (index) {
+                                case 0: return true              // DETECT WAFER
+                                case 1: return root.waferDetected // READ MEMORY
+                                case 2: return root.memoryRead    // OPEN CSV IN EXCEL
+                                case 3: return root.waferDetected // ERASE MEMORY
+                                case 4: return root.memoryRead    // IMPORT DATA
+                                default: return true              // STORED DATA
+                            }
+                        }
                         property bool isActive: index === root.selectedSideActionIndex
                         Layout.fillWidth: true
                         Layout.preferredHeight: Math.max(Theme.sideButtonMinHeight, sideRail.computedButtonHeight)
@@ -60,9 +105,20 @@ Rectangle {
                         onClicked: {
                             root.selectedSideActionIndex = index
                             root.selectedTabIndex = 0          // always jump to Status tab
-                            if (index === 0) deviceController.detectWafer()
-                            else if (index === 1) deviceController.readMemoryAsync()
-                            else if (index === 2) deviceController.openCsvFile()
+                            if (index === 0) {
+                                root.memoryRead = false
+                                streamController.setMode("review")
+                                streamController.stopStream()
+                                deviceController.detectWafer()
+                            }
+                            else if (index === 1) {
+                                streamController.setMode("review")
+                                streamController.stopStream()
+                                deviceController.readMemoryAsync()
+                            }
+                            else if (index === 2) {
+                                deviceController.openCsvFile()
+                            }
                         }
 
                         background: Rectangle {
@@ -158,11 +214,17 @@ Rectangle {
 
                                 Label {
                                     anchors.centerIn: parent
-                                    visible: parent.tabName !== "Settings" && parent.tabName !== "Status" && parent.tabName !== "Data"
+                                    visible: parent.tabName !== "Settings" && parent.tabName !== "Status" && parent.tabName !== "Data" && parent.tabName !== "Wafer Map"
                                     text: parent.tabName + " content"
                                     color: Theme.bodyColor
                                     font.pixelSize: 20
                                 }
+
+                                Loader{
+                                    anchors.fill: parent
+                                    active: parent.tabName === "Wafer Map"
+                                    source: parent.tabName === "Wafer Map" ? "Tabs/WaferMapTab.qml" : ""
+                                }
                             }
                         }
                     }
@@ -176,6 +238,7 @@ Rectangle {
                     color: Theme.tabBarBackground
                     border.color: Theme.workspaceBorder
                     border.width: Theme.borderThin
+                    radius: Theme.radiusMd
 
                     RowLayout {
                         anchors.fill: parent

src/pygui/ISC/Tabs/SettingsTab.qml

@@ -107,25 +107,29 @@ Item {
             x: toggle.leftPadding
             y: parent.height / 2 - height / 2
             radius: Theme.radiusXs
-            color: toggle.checked ? Theme.primaryAccent : Theme.fieldBackground
+            color: toggle.checked ? Theme.primaryAccent : "transparent"
             border.width: Theme.borderThin
             border.color: toggle.checked ? Theme.primaryAccent : Theme.fieldBorder
 
-            Rectangle {
+            Text {
                 anchors.centerIn: parent
-                width: 9
-                height: 9
-                radius: Theme.radiusXs
+                text: "✓"
+                font.pixelSize: 14
+                font.bold: true
+                color: Theme.panelBackground
                 visible: toggle.checked
-                color: Theme.fieldBackground
+                // Small nudge to center the checkmark perfectly
+                verticalAlignment: Text.AlignVCenter
+                horizontalAlignment: Text.AlignHCenter
             }
         }
 
         contentItem: Text {
             text: toggle.text
-            color: Theme.checkboxText
+            color: Theme.headingColor
             verticalAlignment: Text.AlignVCenter
             leftPadding: toggle.indicator.width + toggle.spacing
+            font.pixelSize: 13
         }
     }
 

src/pygui/ISC/Tabs/StatusTab.qml

@@ -1,6 +1,7 @@
 import QtQuick
 import QtQuick.Layouts
 import QtQuick.Controls
+import QtQuick.Dialogs
 import ISC
 
 // ===== Status Tab =====
@@ -29,6 +30,28 @@ ColumnLayout {
     property string csvPath: ""
     property bool dataParsed: false
 
+    function cleanFolderUrl(url) {
+        return decodeURIComponent(String(url).replace(/^file:\/\//, ""))
+    }
+
+    function currentFamilyCode() {
+        var info = deviceController.lastWaferInfo
+        return info && info.length > 0 ? (info[0] || "") : ""
+    }
+
+    function parseAndSavePendingRead() {
+        deviceController.parseAndSaveData(root.currentFamilyCode(), deviceController.selectedPort || "")
+    }
+
+    FolderDialog {
+        id: saveDirDialog
+        title: "Choose CSV Save Folder"
+        onAccepted: {
+            deviceController.setSaveDataDir(root.cleanFolderUrl(selectedFolder))
+            root.parseAndSavePendingRead()
+        }
+    }
+
     // ===== Empty state — nothing shown until detect fires =====
     Item {
         Layout.fillWidth: true
@@ -47,11 +70,7 @@ ColumnLayout {
         Rectangle {
             Layout.fillWidth: true
             Layout.preferredHeight: 86
-            color: {
-                if (deviceController.connectionStatus === "Connected") return Theme.statusSuccessColor + "22"
-                if (deviceController.connectionStatus === "Disconnected") return Theme.statusErrorColor + "22"
-                return Theme.cardBackground
-            }
+            color: Theme.cardBackground
             border.color: {
                 if (deviceController.connectionStatus === "Connected") return Theme.statusSuccessColor
                 if (deviceController.connectionStatus === "Disconnected") return Theme.statusErrorColor
@@ -187,27 +206,105 @@ ColumnLayout {
         }
 
         // --- Activity Log ---
-        GroupBox {
-            title: "Activity Log"
+        Rectangle {
             Layout.fillWidth: true
             Layout.fillHeight: true
+            color: Theme.cardBackground
+            border.color: Theme.cardBorder
+            radius: Theme.radiusMd
+            clip: true
 
-            ScrollView {
+            ColumnLayout {
                 anchors.fill: parent
-                clip: true
+                spacing: 0
 
-                 TextArea {
-                     id: activityLog
-                     width: parent.width
-                     text: ""
-                     readOnly: true
-                     font.family: "monospace"
-                     font.pixelSize: 12
-                     wrapMode: TextArea.WordWrap
-                     leftPadding: 4
-                     rightPadding: 4
-                     color: Theme.bodyColor
-                 }
+                // Header
+                Rectangle {
+                    Layout.fillWidth: true
+                    Layout.preferredHeight: 40
+                    color: Theme.subtleSectionBackground
+                    
+                    RowLayout {
+                        anchors.fill: parent
+                        anchors.leftMargin: Theme.panelPadding
+                        anchors.rightMargin: Theme.panelPadding
+                        
+                        Label {
+                            text: "ACTIVITY LOG"
+                            color: Theme.bodyColor
+                            font.pixelSize: 10
+                            font.letterSpacing: 1.8
+                            font.weight: Font.Medium
+                            Layout.fillWidth: true
+                            Layout.alignment: Qt.AlignVCenter
+                        }
+                        
+                        Button {
+                            text: "REFRESH SESSION"
+                            font.pixelSize: 10
+                            implicitHeight: 24
+                            hoverEnabled: true
+                            background: Rectangle {
+                                color: parent.hovered ? Theme.buttonNeutralHover : "transparent"
+                                radius: Theme.radiusSm
+                            }
+                            contentItem: Text {
+                                text: parent.text
+                                color: Theme.bodyColor
+                                font: parent.font
+                                horizontalAlignment: Text.AlignHCenter
+                                verticalAlignment: Text.AlignVCenter
+                            }
+                            onClicked: deviceController.clearSession()
+                        }
+                        
+                        Button {
+                            text: "CLEAR LOG"
+                            font.pixelSize: 10
+                            implicitHeight: 24
+                            hoverEnabled: true
+                            background: Rectangle {
+                                color: parent.hovered ? Theme.buttonNeutralHover : "transparent"
+                                radius: Theme.radiusSm
+                            }
+                            contentItem: Text {
+                                text: parent.text
+                                color: Theme.bodyColor
+                                font: parent.font
+                                horizontalAlignment: Text.AlignHCenter
+                                verticalAlignment: Text.AlignVCenter
+                            }
+                            onClicked: deviceController.clearActivityLog()
+                        }
+                    }
+                    
+                    Rectangle {
+                        anchors.bottom: parent.bottom
+                        anchors.left: parent.left
+                        anchors.right: parent.right
+                        height: 1
+                        color: Theme.cardBorder
+                    }
+                }
+
+                ScrollView {
+                    Layout.fillWidth: true
+                    Layout.fillHeight: true
+                    Layout.margins: Theme.panelPadding
+                    clip: true
+
+                     TextArea {
+                         id: activityLog
+                         width: parent.width
+                         text: ""
+                         readOnly: true
+                         font.family: "monospace"
+                         font.pixelSize: 12
+                         wrapMode: TextArea.WordWrap
+                         color: Theme.bodyColor
+                         background: null
+                     }
+                }
             }
 
             Connections {
@@ -271,6 +368,9 @@ ColumnLayout {
             root.dataRows   = 0
             root.dataCols   = 0
             root.csvPath    = ""
+
+            if (result && result.success === true)
+                saveDirDialog.open()
         }
     }
 

src/pygui/ISC/Tabs/WaferMapTab.qml

@@ -0,0 +1,270 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Layouts
+import ISC
+import ISC.Tabs.components
+
+Item {
+    id: root
+    anchors.fill: parent
+
+    // Live elapsed-time counter
+    property int _liveSecs: 0
+    Timer {
+        id: liveTimer
+        interval: 1000
+        repeat: true
+        running: streamController.mode === "live" && streamController.state !== "idle"
+        onTriggered: root._liveSecs++
+        onRunningChanged: if (!running) root._liveSecs = 0
+    }
+    function fmtTime(s) {
+        var m = Math.floor(s / 60)
+        var ss = s % 60
+        return (m < 10 ? "0" : "") + m + ":" + (ss < 10 ? "0" : "") + ss
+    }
+
+    ColumnLayout {
+        anchors.fill: parent
+        anchors.margins: 16
+        spacing: 16
+
+        // ── Toolbar ───────────────────────────────────────────────────────
+        RowLayout {
+            Layout.fillWidth: true
+            spacing: 10
+
+            // Mode toggle
+            TabBar {
+                id: modeBar
+                currentIndex: 1  // Default to "Review"
+                spacing: 2
+                padding: 2
+                background: Rectangle {
+                    color: Theme.subtleSectionBackground
+                    radius: Theme.radiusSm
+                    border.color: Theme.cardBorder
+                    border.width: Theme.borderThin
+                }
+                TabButton {
+                    text: "Live"
+                    enabled: deviceController.connectionStatus === "Connected"
+                    opacity: enabled ? 1.0 : 0.4
+                    implicitWidth: 58; implicitHeight: 28
+                    background: Rectangle {
+                        color: parent.checked ? Theme.tabActiveBackground : "transparent"
+                        radius: Theme.radiusSm - 1
+                    }
+                    contentItem: Text {
+                        text: parent.text
+                        color: parent.checked ? Theme.headingColor : Theme.bodyColor
+                        font.pixelSize: 11
+                        font.weight: parent.checked ? Font.Medium : Font.Normal
+                        horizontalAlignment: Text.AlignHCenter
+                        verticalAlignment: Text.AlignVCenter
+                    }
+                }
+                TabButton {
+                    text: "Review"
+                    implicitWidth: 64; implicitHeight: 28
+                    background: Rectangle {
+                        color: parent.checked ? Theme.tabActiveBackground : "transparent"
+                        radius: Theme.radiusSm - 1
+                    }
+                    contentItem: Text {
+                        text: parent.text
+                        color: parent.checked ? Theme.headingColor : Theme.bodyColor
+                        font.pixelSize: 11
+                        font.weight: parent.checked ? Font.Medium : Font.Normal
+                        horizontalAlignment: Text.AlignHCenter
+                        verticalAlignment: Text.AlignVCenter
+                    }
+                }
+                onCurrentIndexChanged:
+                    if (currentIndex === 0){
+                        // Entering Live mode, only work when wafer detected/connected
+                        streamController.setMode("live")
+                        if (deviceController.connectionStatus === "Connected") {
+                            var fc = ""
+                            if (deviceController.lastWaferInfo && deviceController.lastWaferInfo.length > 0) {
+                                fc = deviceController.lastWaferInfo[0]
+                            }
+                            streamController.startStream(deviceController.selectedPort, fc)
+                        }
+                    } else {
+                        // Entering Review Mode (automatically calls stopStream in backend)
+                        streamController.setMode("review")
+                    }
+            }
+
+            // Live source info: WiFi icon + port · serial
+            RowLayout {
+                visible: streamController.mode === "live"
+                spacing: 5
+                // WiFi icon (Unicode approximation; swap for SVG if available)
+                Label {
+                    id: liveIndicator
+                    text: "◉"
+                    color: (deviceController.connectionStatus === "Connected" && streamController.state !== "idle") 
+                           ? Theme.liveColor : Theme.bodyColor
+                    font.pixelSize: 13
+                    
+                    SequentialAnimation on opacity {
+                        running: deviceController.connectionStatus === "Connected" && streamController.state !== "idle"
+                        loops: Animation.Infinite
+                        NumberAnimation { to: 0.2; duration: 600; easing.type: Easing.InOutQuad }
+                        NumberAnimation { to: 1.0; duration: 600; easing.type: Easing.InOutQuad }
+                        onRunningChanged: {
+                            if (!running) liveIndicator.opacity = 1.0
+                        }
+                    }
+                }
+                Label {
+                    text: "Live stream"
+                    color: Theme.bodyColor
+                    font.pixelSize: 11
+                }
+            }
+
+            Item { Layout.fillWidth: true }
+
+            // SET badge + avg temp
+            Rectangle {
+                visible: streamController.state === "set"
+                height: 22; radius: Theme.radiusSm
+                color: "transparent"
+                border.color: Theme.liveColor
+                border.width: 1
+                implicitWidth: setLabel.implicitWidth + 16
+                Label {
+                    id: setLabel
+                    anchors.centerIn: parent
+                    text: "SET  " + (streamController.stats.avg !== undefined
+                                    ? streamController.stats.avg + " avg" : "")
+                    color: Theme.liveColor
+                    font.pixelSize: 10
+                    font.weight: Font.Medium
+                    font.letterSpacing: 0.8
+                }
+            }
+
+            // Record indicator
+            RowLayout {
+                spacing: 5
+                visible: streamController.recording
+                Rectangle {
+                    width: 7; height: 7; radius: 4
+                    color: Theme.recordColor
+                    SequentialAnimation on opacity {
+                        running: streamController.recording
+                        loops: Animation.Infinite
+                        NumberAnimation { to: 0.2; duration: 600 }
+                        NumberAnimation { to: 1.0; duration: 600 }
+                    }
+                }
+                Label {
+                    text: "REC"
+                    color: Theme.recordColor
+                    font.pixelSize: 10
+                    font.weight: Font.Medium
+                    font.letterSpacing: 1.2
+                }
+            }
+
+            // LIVE timer
+            RowLayout {
+                spacing: 5
+                visible: streamController.mode === "live" && streamController.state !== "idle"
+                Rectangle {
+                    width: 7; height: 7; radius: 4
+                    color: Theme.liveColor
+                }
+                Label {
+                    text: "LIVE  " + root.fmtTime(root._liveSecs)
+                    color: Theme.liveColor
+                    font.pixelSize: 10
+                    font.weight: Font.Medium
+                    font.letterSpacing: 0.8
+                }
+            }
+
+            // IDLE label (review / not connected)
+            Label {
+                visible: streamController.mode === "review" || streamController.state === "idle"
+                text: streamController.state.toUpperCase()
+                color: Theme.bodyColor
+                font.pixelSize: 11
+                font.weight: Font.Medium
+                font.letterSpacing: 1.2
+            }
+        }
+
+        // ── Body: 3 zones ─────────────────────────────────────────────────
+        RowLayout {
+            Layout.fillWidth: true
+            Layout.fillHeight: true
+            spacing: 16
+
+            // Source panel — bordered card
+            Rectangle {
+                Layout.preferredWidth: 220
+                Layout.fillHeight: true
+                color: Theme.cardBackground
+                border.color: Theme.cardBorder
+                border.width: 1
+                radius: Theme.radiusMd
+                clip: true
+
+                SourcePanel {
+                    anchors.fill: parent
+                    anchors.margins: 10
+                }
+            }
+
+            ColumnLayout {
+                Layout.fillWidth: true
+                Layout.fillHeight: true
+                spacing: 8
+
+                WaferMapView {
+                    id: waferView
+                    Layout.fillWidth: true
+                    Layout.fillHeight: true
+                    blend: readoutPanel.heatmapBlend
+                    showLabels: readoutPanel.showLabels
+                }
+
+                // Horizontal separation line with vertical padding
+                Item {
+                    Layout.fillWidth: true
+                    implicitHeight: 32
+                    Rectangle {
+                        anchors.centerIn: parent
+                        width: parent.width
+                        height: 1
+                        color: Theme.cardBorder
+                    }
+                }
+
+                TransportBar { Layout.fillWidth: true }
+            }
+
+            // Readout panel — bordered card
+            Rectangle {
+                Layout.preferredWidth: 220
+                Layout.fillHeight: true
+                color: Theme.cardBackground
+                border.color: Theme.cardBorder
+                border.width: 1
+                radius: Theme.radiusMd
+                clip: true
+
+                ReadoutPanel {
+                    id: readoutPanel
+                    anchors.fill: parent
+                    anchors.margins: 10
+                }
+            }
+        }
+    }
+}

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

@@ -0,0 +1,295 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Layouts
+import ISC
+
+ColumnLayout {
+    spacing: 0
+    property var s: streamController.stats
+    property alias showLabels: labelsToggle.checked
+    property alias heatmapBlend: heatmapSlider.value
+
+    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
+
+            Text {
+                anchors.centerIn: parent
+                text: "✓"
+                font.pixelSize: 13
+                font.bold: true
+                color: Theme.panelBackground
+                visible: toggle.checked
+                verticalAlignment: Text.AlignVCenter
+                horizontalAlignment: Text.AlignHCenter
+            }
+        }
+
+        contentItem: Text {
+            text: toggle.text
+            color: Theme.headingColor
+            verticalAlignment: Text.AlignVCenter
+            leftPadding: toggle.indicator.width + toggle.spacing
+            font.pixelSize: toggle.font.pixelSize || 11
+        }
+    }
+
+    // ── READOUT ───────────────────────────────────────────────────────────
+    Label {
+        text: "READOUT"
+        color: Theme.bodyColor
+        font.pixelSize: 10
+        font.letterSpacing: 1.8
+        font.weight: Font.Medium
+        topPadding: 6
+        bottomPadding: 8
+    }
+
+    Rectangle {
+        Layout.fillWidth: true
+        implicitHeight: statsLayout.implicitHeight + 20
+        color: Theme.subtleSectionBackground
+        radius: Theme.radiusSm
+        border.color: Theme.cardBorder
+        border.width: 1
+
+        ColumnLayout {
+            id: statsLayout
+            anchors { fill: parent; margins: 10 }
+            spacing: 8
+
+            // Min Temp Row
+            RowLayout {
+                Layout.fillWidth: true
+                Label { text: "Min Temp"; color: Theme.bodyColor; font.pixelSize: 11 }
+                Item { Layout.fillWidth: true }
+                RowLayout {
+                    spacing: 4
+                    Label {
+                        text: s.min !== undefined ? s.min : "—"
+                        color: Theme.sensorLow
+                        font.pixelSize: 13; font.weight: Font.Bold
+                    }
+                    Label {
+                        text: s.minIndex !== undefined ? "#" + s.minIndex : ""
+                        color: Theme.bodyColor
+                        font.pixelSize: 10
+                    }
+                }
+            }
+
+            // Max Temp Row
+            RowLayout {
+                Layout.fillWidth: true
+                Label { text: "Max Temp"; color: Theme.bodyColor; font.pixelSize: 11 }
+                Item { Layout.fillWidth: true }
+                RowLayout {
+                    spacing: 4
+                    Label {
+                        text: s.max !== undefined ? s.max : "—"
+                        color: Theme.sensorHigh
+                        font.pixelSize: 13; font.weight: Font.Bold
+                    }
+                    Label {
+                        text: s.maxIndex !== undefined ? "#" + s.maxIndex : ""
+                        color: Theme.bodyColor
+                        font.pixelSize: 10
+                    }
+                }
+            }
+
+            Rectangle { Layout.fillWidth: true; height: 1; color: Theme.cardBorder }
+
+            // Differential Row
+            RowLayout {
+                Layout.fillWidth: true
+                Label { text: "Differential"; color: Theme.bodyColor; font.pixelSize: 11 }
+                Item { Layout.fillWidth: true }
+                Label {
+                    text: s.diff !== undefined ? s.diff : "—"
+                    color: Theme.headingColor
+                    font.pixelSize: 13; font.weight: Font.Bold
+                }
+            }
+
+            // Average Row
+            RowLayout {
+                Layout.fillWidth: true
+                Label { text: "Average"; color: Theme.bodyColor; font.pixelSize: 11 }
+                Item { Layout.fillWidth: true }
+                Label {
+                    text: s.avg !== undefined ? s.avg : "—"
+                    color: Theme.headingColor
+                    font.pixelSize: 13; font.weight: Font.Bold
+                }
+            }
+
+            Rectangle { Layout.fillWidth: true; height: 1; color: Theme.cardBorder }
+
+            // Sigma Row
+            RowLayout {
+                Layout.fillWidth: true
+                Label { text: "Sigma (σ)"; color: Theme.bodyColor; font.pixelSize: 11 }
+                Item { Layout.fillWidth: true }
+                Label {
+                    text: s.sigma !== undefined ? s.sigma : "—"
+                    color: Theme.headingColor
+                    font.pixelSize: 13; font.weight: Font.Bold
+                }
+            }
+
+            // 3-Sigma Row
+            RowLayout {
+                Layout.fillWidth: true
+                Label { text: "3σ Value"; color: Theme.bodyColor; font.pixelSize: 11 }
+                Item { Layout.fillWidth: true }
+                Label {
+                    text: s.threeSigma !== undefined ? s.threeSigma : "—"
+                    color: Theme.bodyColor
+                    font.pixelSize: 12; font.weight: Font.Medium
+                }
+            }
+        }
+    }
+
+    Item { height: 12 }
+    Rectangle { Layout.fillWidth: true; height: 1; color: Theme.cardBorder }
+    Item { height: 12 }
+
+    // ── DISPLAY ───────────────────────────────────────────────────────────
+    Label {
+        text: "DISPLAY"
+        color: Theme.bodyColor
+        font.pixelSize: 10
+        font.letterSpacing: 1.8
+        font.weight: Font.Medium
+        topPadding: 6
+        bottomPadding: 8
+    }
+
+    PanelCheckBox {
+        id: labelsToggle
+        text: "Labels"
+        checked: true
+        font.pixelSize: 11
+    }
+
+    PanelCheckBox {
+        id: clusterAverageToggle
+        text: "Average Clusters"
+        checked: streamController.clusterAveragingEnabled
+        font.pixelSize: 11
+        onCheckedChanged: streamController.clusterAveragingEnabled = checked
+    }
+
+    RowLayout {
+        Layout.fillWidth: true
+        spacing: 6
+        Label {
+            text: "Heatmap"
+            color: Theme.bodyColor
+            font.pixelSize: 11
+            Layout.preferredWidth: 52
+        }
+        Slider {
+            id: heatmapSlider
+            from: 0; to: 1; value: 0
+            Layout.fillWidth: true
+            ToolTip.visible: hovered
+            ToolTip.text: Math.round(value * 100) + "%"
+        }
+    }
+
+    Item { height: 12 }
+    Rectangle { Layout.fillWidth: true; height: 1; color: Theme.cardBorder }
+    Item { height: 12 }
+
+    // ── THRESHOLDS ────────────────────────────────────────────────────────
+    Label {
+        text: "THRESHOLDS"
+        color: Theme.bodyColor
+        font.pixelSize: 10
+        font.letterSpacing: 1.8
+        font.weight: Font.Medium
+        topPadding: 6
+        bottomPadding: 8
+    }
+
+    Label {
+        text: "Set Point (°C)"
+        color: Theme.bodyColor
+        font.pixelSize: 11
+        bottomPadding: 3
+    }
+    TextField {
+        id: spField
+        Layout.fillWidth: true
+        text: "149.0"
+        font.pixelSize: 12
+        inputMethodHints: Qt.ImhFormattedNumbersOnly
+        color: Theme.fieldText
+        placeholderTextColor: Theme.fieldPlaceholder
+        selectedTextColor: Theme.fieldBackground
+        selectionColor: Theme.fieldText
+        background: Rectangle {
+            radius: Theme.radiusXs
+            color: Theme.fieldBackground
+            border.width: spField.activeFocus ? Theme.borderStrong : Theme.borderThin
+            border.color: spField.activeFocus ? Theme.fieldBorderFocus : Theme.fieldBorder
+        }
+        onEditingFinished: pushThresholds()
+    }
+
+    Item { height: 10 }
+
+    Label {
+        text: "Margin (±°C)"
+        color: Theme.bodyColor
+        font.pixelSize: 11
+        bottomPadding: 3
+    }
+    TextField {
+        id: mgField
+        Layout.fillWidth: true
+        text: "1.0"
+        font.pixelSize: 12
+        inputMethodHints: Qt.ImhFormattedNumbersOnly
+        color: Theme.fieldText
+        placeholderTextColor: Theme.fieldPlaceholder
+        selectedTextColor: Theme.fieldBackground
+        selectionColor: Theme.fieldText
+        background: Rectangle {
+            radius: Theme.radiusXs
+            color: Theme.fieldBackground
+            border.width: mgField.activeFocus ? Theme.borderStrong : Theme.borderThin
+            border.color: mgField.activeFocus ? Theme.fieldBorderFocus : Theme.fieldBorder
+        }
+        onEditingFinished: pushThresholds()
+    }
+
+    Item { height: 10 }
+
+    PanelCheckBox {
+        id: autoCheck
+        text: "Auto range  (mean ± 1σ)"
+        checked: true
+        font.pixelSize: 11
+        onCheckedChanged: pushThresholds()
+    }
+
+    Item { Layout.fillHeight: true }
+
+    function pushThresholds() {
+        var sp = parseFloat(spField.text) || 149.0
+        var mg = parseFloat(mgField.text) || 1.0
+        streamController.setThresholds(sp, mg, autoCheck.checked)
+    }
+}

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

@@ -0,0 +1,207 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Layouts
+import ISC
+
+Dialog {
+    id: root
+    title: "Sensor Override"
+    modal: true
+    standardButtons: Dialog.NoButton
+    width: 300
+
+    // called by WaferMapView's TapHandler
+    property int sensorIndex: -1
+    property string sensorLabel: ""
+    property real currentValue: 0.0
+    property bool hasOverride: streamController.overriddenSensors.indexOf(sensorIndex) >= 0
+
+    function openFor(index) {
+        sensorIndex = index
+        var dot = streamController.sensorDots[index]
+        if (!dot) return
+        sensorLabel = dot.label !== undefined ? String(dot.label) : String(index + 1)
+        currentValue = dot.value
+        valueField.text = ""
+        offsetField.text = ""
+        open()
+    }
+
+    background: Rectangle {
+        color: Theme.cardBackground
+        radius: Theme.radiusLg
+        border.color: Theme.cardBorder
+        border.width: Theme.borderThin
+    }
+
+    ColumnLayout {
+        anchors.fill: parent
+        spacing: Theme.rightPaneGap
+
+        // ── header ───────────────────────────────────────────────
+        RowLayout {
+            Layout.fillWidth: true
+            Label {
+                text: "Sensor #" + (root.sensorIndex + 1) +
+                      (root.sensorLabel ? "  (" + root.sensorLabel + ")" : "")
+                color: Theme.headingColor
+                font.bold: true
+                font.pixelSize: 13
+                Layout.fillWidth: true
+            }
+            Rectangle {
+                visible: root.hasOverride
+                width: overrideTag.implicitWidth + 12
+                height: overrideTag.implicitHeight + 6
+                radius: 4
+                color: Theme.statusWarningColor
+                opacity: 0.85
+                Label {
+                    id: overrideTag
+                    anchors.centerIn: parent
+                    text: "OVERRIDE"
+                    color: "white"
+                    font.pixelSize: 10
+                    font.bold: true
+                    font.letterSpacing: 1
+                }
+            }
+        }
+
+        Label {
+            text: "Live: " + root.currentValue.toFixed(2)
+            color: Theme.bodyColor
+            font.pixelSize: 12
+        }
+
+        Rectangle { Layout.fillWidth: true; height: 1; color: Theme.cardBorder }
+
+        // ── replace field ─────────────────────────────────────────
+        Label { text: "Replace with value"; color: Theme.bodyColor; font.pixelSize: 11 }
+        TextField {
+            id: valueField
+            Layout.fillWidth: true
+            placeholderText: "100"
+            inputMethodHints: Qt.ImhFormattedNumbersOnly
+            color: Theme.fieldText
+            placeholderTextColor: Theme.fieldPlaceholder
+            selectedTextColor: Theme.fieldBackground
+            selectionColor: Theme.fieldText
+            background: Rectangle {
+                radius: Theme.radiusXs
+                color: Theme.fieldBackground
+                border.width: valueField.activeFocus ? Theme.borderStrong : Theme.borderThin
+                border.color: valueField.activeFocus ? Theme.fieldBorderFocus : Theme.fieldBorder
+            }
+        }
+
+        // ── offset field ──────────────────────────────────────────
+        Label { text: "Or add offset (± delta)"; color: Theme.bodyColor; font.pixelSize: 11 }
+        TextField {
+            id: offsetField
+            Layout.fillWidth: true
+            placeholderText: "e.g. +0.5  or  -0.5  (blank = skip)"
+            inputMethodHints: Qt.ImhFormattedNumbersOnly
+            color: Theme.fieldText
+            placeholderTextColor: Theme.fieldPlaceholder
+            selectedTextColor: Theme.fieldBackground
+            selectionColor: Theme.fieldText
+            background: Rectangle {
+                radius: Theme.radiusXs
+                color: Theme.fieldBackground
+                border.width: offsetField.activeFocus ? Theme.borderStrong : Theme.borderThin
+                border.color: offsetField.activeFocus ? Theme.fieldBorderFocus : Theme.fieldBorder
+            }
+        }
+
+        Rectangle { Layout.fillWidth: true; height: 1; color: Theme.cardBorder }
+
+        // ── buttons ───────────────────────────────────────────────
+        RowLayout {
+            Layout.fillWidth: true
+            spacing: 8
+
+            Button {
+                id: applyBtn
+                text: "Apply"
+                Layout.fillWidth: true
+                hoverEnabled: true
+                enabled: valueField.text !== "" || offsetField.text !== ""
+                opacity: enabled ? 1.0 : 0.4
+                background: Rectangle {
+                    radius: Theme.radiusSm
+                    color: applyBtn.down ? Theme.buttonNeutralPressed : applyBtn.hovered ? Theme.buttonNeutralHover : Theme.buttonNeutralBackground
+                    border.width: Theme.borderThin
+                    border.color: Theme.fieldBorder
+                }
+                contentItem: Text {
+                    text: applyBtn.text
+                    color: Theme.buttonNeutralText
+                    horizontalAlignment: Text.AlignHCenter
+                    verticalAlignment: Text.AlignVCenter
+                    font.bold: true
+                    font.pixelSize: 13
+                }
+                onClicked: {
+                    if (valueField.text !== "") {
+                        var v = parseFloat(valueField.text)
+                        if (!isNaN(v))
+                            streamController.replaceSensor(root.sensorIndex, v)
+                    }
+                    if (offsetField.text !== "") {
+                        var d = parseFloat(offsetField.text)
+                        if (!isNaN(d))
+                            streamController.offsetSensor(root.sensorIndex, d)
+                    }
+                    root.close()
+                }
+            }
+            Button {
+                id: clearBtn
+                text: "Clear"
+                Layout.fillWidth: true
+                hoverEnabled: true
+                enabled: root.hasOverride
+                opacity: enabled ? 1.0 : 0.4
+                background: Rectangle {
+                    radius: Theme.radiusSm
+                    color: clearBtn.down ? Theme.buttonNeutralPressed : clearBtn.hovered ? Theme.buttonNeutralHover : Theme.buttonNeutralBackground
+                    border.width: Theme.borderThin
+                    border.color: Theme.fieldBorder
+                }
+                contentItem: Text {
+                    text: clearBtn.text
+                    color: Theme.buttonNeutralText
+                    horizontalAlignment: Text.AlignHCenter
+                    verticalAlignment: Text.AlignVCenter
+                    font.bold: true
+                    font.pixelSize: 13
+                }
+                onClicked: {
+                    streamController.clearSensorEdit(root.sensorIndex)
+                    root.close()
+                }
+            }
+            Button {
+                id: cancelBtn
+                text: "Cancel"
+                hoverEnabled: true
+                background: Rectangle {
+                    radius: Theme.radiusSm
+                    color: cancelBtn.down ? Theme.buttonNeutralPressed : cancelBtn.hovered ? Theme.buttonNeutralHover : Theme.buttonNeutralBackground
+                    border.width: Theme.borderThin
+                    border.color: Theme.fieldBorder
+                }
+                contentItem: Text {
+                    text: cancelBtn.text
+                    color: Theme.buttonNeutralText
+                    horizontalAlignment: Text.AlignHCenter
+                    verticalAlignment: Text.AlignVCenter
+                    font.bold: true
+                    font.pixelSize: 13
+                }
+                onClicked: root.close()
+            }
+        }
+    }
+}

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

@@ -0,0 +1,295 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Layouts
+import ISC
+import ".."
+
+ColumnLayout {
+    spacing: 6
+
+    // ── Section label & Refresh ───────────────────────────────────────────
+    RowLayout {
+        Layout.fillWidth: true
+        spacing: 4
+
+        Label {
+            text: "SOURCE"
+            color: Theme.bodyColor
+            font.pixelSize: 10
+            font.letterSpacing: 1.8
+            font.weight: Font.Medium
+            topPadding: 6
+            bottomPadding: 8
+            Layout.fillWidth: true
+            Layout.alignment: Qt.AlignVCenter
+        }
+
+        Button {
+            id: editBtn
+            text: "✎"
+            implicitWidth: 26
+            implicitHeight: 26
+            hoverEnabled: true
+            font.pixelSize: 14
+            background: Rectangle {
+                color: editBtn.pressed ? Theme.buttonPressed
+                     : editBtn.hovered ? Theme.buttonNeutralHover
+                     : "transparent"
+                radius: Theme.radiusSm
+            }
+            contentItem: Text {
+                text: parent.text
+                color: Theme.bodyColor
+                font: parent.font
+                horizontalAlignment: Text.AlignHCenter
+                verticalAlignment: Text.AlignVCenter
+            }
+            onClicked: {
+                file_browser.refreshFiles()
+                csvEditorDialog.open()
+            }
+        }
+
+        Button {
+            id: refreshBtn
+            text: "⟳"
+            implicitWidth: 26
+            implicitHeight: 26
+            hoverEnabled: true
+            font.pixelSize: 14
+            background: Rectangle {
+                color: refreshBtn.pressed ? Theme.buttonPressed
+                     : refreshBtn.hovered ? Theme.buttonNeutralHover
+                     : "transparent"
+                radius: Theme.radiusSm
+            }
+            contentItem: Text {
+                text: parent.text
+                color: Theme.bodyColor
+                font: parent.font
+                horizontalAlignment: Text.AlignHCenter
+                verticalAlignment: Text.AlignVCenter
+            }
+            onClicked: file_browser.refreshFiles()
+        }
+    }
+
+    // ── Directory button ──────────────────────────────────────────────────
+    Button {
+        id: dirBtn
+        Layout.fillWidth: true
+        hoverEnabled: true
+        implicitHeight: 32
+        leftPadding: 8
+        rightPadding: 8
+        background: Rectangle {
+            radius: Theme.radiusSm
+            color: dirBtn.pressed ? Theme.buttonNeutralPressed
+                 : dirBtn.hovered ? Theme.buttonNeutralHover
+                 : Theme.buttonNeutralBackground
+            border.width: Theme.borderThin
+            border.color: Theme.fieldBorder
+        }
+        contentItem: RowLayout {
+            spacing: 6
+            Label {
+                text: "▤"
+                color: Theme.bodyColor
+                font.pixelSize: 12
+            }
+            Label {
+                text: file_browser.currentDirectory.split("/").pop() || file_browser.currentDirectory
+                color: Theme.headingColor
+                font.pixelSize: 11
+                elide: Text.ElideMiddle
+                Layout.fillWidth: true
+            }
+        }
+        onClicked: file_browser.chooseDirectory()
+    }
+
+    // ── Filter ────────────────────────────────────────────────────────────
+    TextField {
+        id: filter
+        Layout.fillWidth: true
+        placeholderText: "Filter…"
+        font.pixelSize: 11
+        color: Theme.fieldText
+        placeholderTextColor: Theme.fieldPlaceholder
+        selectedTextColor: Theme.fieldBackground
+        selectionColor: Theme.fieldText
+        background: Rectangle {
+            radius: Theme.radiusXs
+            color: Theme.fieldBackground
+            border.width: filter.activeFocus ? Theme.borderStrong : Theme.borderThin
+            border.color: filter.activeFocus ? Theme.fieldBorderFocus : Theme.fieldBorder
+        }
+    }
+
+    // ── File list ─────────────────────────────────────────────────────────
+    ListView {
+        id: fileList
+        Layout.fillWidth: true
+        Layout.fillHeight: true
+        clip: true
+        spacing: 2
+        highlight: null
+        highlightFollowsCurrentItem: false
+
+        model: file_browser.files
+
+        delegate: ItemDelegate {
+            id: fileItem
+            width: ListView.view.width
+            padding: 8
+            highlighted: false
+            focusPolicy: Qt.NoFocus
+
+            readonly property bool matchesFilter: {
+                if (filter.text === "") return true
+                var q = filter.text.toLowerCase()
+                return (modelData.baseName + modelData.waferType + modelData.date)
+                       .toLowerCase().indexOf(q) >= 0
+            }
+
+            // Active only in review mode; no highlight during live streaming
+            readonly property bool isActive:
+                streamController.mode === "review" &&
+                streamController.loadedFile !== "" &&
+                modelData.fileName === streamController.loadedFile
+
+            visible: matchesFilter
+            height: matchesFilter ? implicitHeight : 0
+
+            onClicked: streamController.loadFile(modelData.fileName)
+
+            background: Rectangle {
+                color: fileItem.isActive
+                    ? Qt.rgba(1, 1, 1, 0.06)
+                    : fileItem.hovered ? Qt.rgba(1, 1, 1, 0.04) : "transparent"
+                radius: Theme.radiusSm
+
+                // Left accent bar — shown only when active
+                Rectangle {
+                    visible: fileItem.isActive
+                    width: 3
+                    radius: 1.5
+                    anchors {
+                        top: parent.top; bottom: parent.bottom; left: parent.left
+                        topMargin: 5; bottomMargin: 5
+                    }
+                    color: {
+                        var t = modelData.waferType
+                        if (t === "A" || t === "E" || t === "P") return "#3B82F6"
+                        if (t === "B" || t === "C" || t === "D") return "#10B981"
+                        if (t === "Z") return "#8B5CF6"
+                        return Theme.headingColor
+                    }
+                }
+            }
+
+            contentItem: RowLayout {
+                spacing: 8
+
+                // Wafer-type avatar (circle)
+                Rectangle {
+                    implicitWidth: 28; implicitHeight: 28
+                    Layout.preferredWidth: 28
+                    Layout.preferredHeight: 28
+                    Layout.alignment: Qt.AlignVCenter
+                    radius: 14
+                    color: {
+                        var t = modelData.waferType
+                        if (t === "A" || t === "E" || t === "P") return "#1D4ED8"
+                        if (t === "B" || t === "C" || t === "D") return "#065F46"
+                        if (t === "Z") return "#7C3AED"
+                        return "#374151"
+                    }
+                    Label {
+                        anchors.centerIn: parent
+                        text: modelData.waferType || "?"
+                        font.pixelSize: 12
+                        font.weight: Font.Bold
+                        color: "#FFFFFF"
+                    }
+                }
+
+                // Typography hierarchy
+                ColumnLayout {
+                    spacing: 1
+                    Layout.fillWidth: true
+
+                    // Primary: wafer type + serial number
+                    Label {
+                        text: modelData.serialNumber ? (modelData.waferType + modelData.serialNumber) : modelData.baseName
+                        color: Theme.headingColor
+                        font.pixelSize: 13
+                        font.weight: Font.Bold
+                        elide: Text.ElideRight
+                        Layout.fillWidth: true
+                    }
+
+                    // Secondary: date · time
+                    RowLayout {
+                        spacing: 3
+                        Layout.fillWidth: true
+                        Label {
+                            text: {
+                                var d = modelData.date || ""
+                                return d.length >= 10 ? d.substring(0, 10) : (d || "—")
+                            }
+                            color: Theme.bodyColor
+                            font.pixelSize: 10
+                        }
+                        Label {
+                            visible: (modelData.timeStr || "") !== ""
+                            text: "·"
+                            color: Theme.bodyColor
+                            font.pixelSize: 10
+                            opacity: 0.45
+                        }
+                        Label {
+                            visible: (modelData.timeStr || "") !== ""
+                            text: modelData.timeStr || ""
+                            color: Theme.bodyColor
+                            font.pixelSize: 10
+                            opacity: 0.65
+                        }
+                    }
+
+                    // Tertiary: edited metadata (chamber · notes) if any
+                    Label {
+                        visible: {
+                            var c = modelData.chamber || ""
+                            var n = modelData.notes || ""
+                            return c !== "" || n !== ""
+                        }
+                        text: {
+                            var parts = []
+                            if (modelData.chamber) parts.push(modelData.chamber)
+                            if (modelData.notes)   parts.push(modelData.notes)
+                            return parts.join("  ·  ")
+                        }
+                        color: Theme.bodyColor
+                        font.pixelSize: 9
+                        opacity: 0.7
+                        elide: Text.ElideRight
+                        Layout.fillWidth: true
+                    }
+                }
+            }
+        }
+    }
+
+    // ── Footer ────────────────────────────────────────────────────────────
+    Label {
+        text: file_browser.files.length + " files · CSV only"
+        color: Theme.bodyColor
+        font.pixelSize: 10
+    }
+
+    SelectFileDialog {
+        id: csvEditorDialog
+        tableModel: file_browser.files
+    }
+}

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

@@ -0,0 +1,103 @@
+import QtQuick
+import QtQuick.Controls
+import QtQuick.Layouts
+import ISC
+
+RowLayout {
+    spacing: 2
+
+    component TBtn: Button {
+        implicitWidth: 44
+        implicitHeight: 32
+        hoverEnabled: true
+        font.pixelSize: 13
+        background: Rectangle {
+            color: parent.pressed ? Theme.transportButtonHover
+                 : parent.hovered ? Theme.transportButtonBg
+                 : Theme.transportBackground
+            radius: Theme.radiusSm
+        }
+        contentItem: Text {
+            text: parent.text
+            color: Theme.headingColor
+            font: parent.font
+            horizontalAlignment: Text.AlignHCenter
+            verticalAlignment: Text.AlignVCenter
+        }
+    }
+
+    // Frame counter badge on the left
+    Rectangle {
+        id: frameCounter
+        implicitWidth: frameCounterText.implicitWidth + 16
+        implicitHeight: 32
+        color: Theme.fieldBackground
+        border.color: Theme.cardBorder
+        border.width: Theme.borderThin
+        radius: Theme.radiusSm
+
+        Text {
+            id: frameCounterText
+            anchors.centerIn: parent
+            text: "Frame " + (streamController.frameIndex + 1) + " / " + streamController.frameTotal
+            color: Theme.headingColor
+            font.pixelSize: 11
+            font.weight: Font.Medium
+        }
+    }
+
+    // Left fill — centers the button cluster
+    Item { Layout.fillWidth: true }
+
+    TBtn { text: "⏮"; onClicked: streamController.step(-1) }
+    TBtn { text: "⏹"; onClicked: streamController.stop() }
+    TBtn { text: "⏸"; onClicked: streamController.pause() }
+    // Play: slightly wider; leftPadding nudge compensates for ▶ optical offset
+    TBtn {
+        text: "▶"
+        implicitWidth: 52
+        contentItem: Text {
+            text: parent.text
+            color: Theme.headingColor
+            font: parent.font
+            horizontalAlignment: Text.AlignHCenter
+            verticalAlignment: Text.AlignVCenter
+            leftPadding: 2
+        }
+        onClicked: streamController.play()
+    }
+    TBtn { text: "⏭"; onClicked: streamController.step(1) }
+
+    // Right fill — balances centering
+    Item { Layout.fillWidth: true }
+
+    // Speed cycle
+    Button {
+        id: speedBtn
+        property var speeds: [1, 2, 5]
+        property int idx: 0
+        implicitWidth: 44
+        implicitHeight: 32
+        hoverEnabled: true
+        text: speeds[idx] + "×"
+        font.pixelSize: 11
+        font.weight: Font.Medium
+        background: Rectangle {
+            color: parent.pressed ? Theme.transportButtonHover
+                 : parent.hovered ? Theme.transportButtonBg
+                 : Theme.transportBackground
+            radius: Theme.radiusSm
+        }
+        contentItem: Text {
+            text: parent.text
+            color: Theme.bodyColor
+            font: parent.font
+            horizontalAlignment: Text.AlignHCenter
+            verticalAlignment: Text.AlignVCenter
+        }
+        onClicked: {
+            idx = (idx + 1) % speeds.length
+            streamController.setSpeed(speeds[idx])
+        }
+    }
+}

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

@@ -0,0 +1,45 @@
+import QtQuick
+import QtQuick.Controls
+import ISC
+import ISC.Wafer  
+
+
+Item {
+    id: root
+    property real blend: 0.0
+    property bool showLabels: true
+
+    WaferMapItem {
+        id: map
+        anchors.fill: parent
+        sensors: streamController.sensorLayout      // [{label,x,y}]
+        values: streamController.sensorValues       // [float]
+        bands: streamController.sensorBands         // ["in_range"|"high"|"low"]
+        shape: streamController.waferShape
+        size: streamController.waferSize
+        target: streamController.target
+        margin: streamController.margin
+        blend: root.blend
+        showLabels: root.showLabels
+        // Bind to Theme so colors update on dark/light mode switch
+        ringColor:    Theme.waferRingColor
+        axisColor:    Theme.waferAxisColor
+        lowColor:     Theme.sensorLow
+        inRangeColor: Theme.sensorInRange
+        highColor:    Theme.sensorHigh
+        textColor:    Theme.headingColor
+
+
+        TapHandler {
+            onTapped: (ev) => {
+                var idx = map.which_marker(ev.position.x, ev.position.y)
+                if (idx >= 0) replaceDialog.openFor(idx)    
+            }
+        }
+    }
+
+    ReplaceSensorDialog { id: replaceDialog}
+
+
+
+}

src/pygui/ISC/Tabs/components/qmldir

@@ -0,0 +1,7 @@
+# ===== ISC Tabs Components Module =====
+module ISC.Tabs.components
+SourcePanel 1.0 SourcePanel.qml
+ReadoutPanel 1.0 ReadoutPanel.qml
+TransportBar 1.0 TransportBar.qml
+WaferMapView 1.0 WaferMapView.qml
+ReplaceSensorDialog 1.0 ReplaceSensorDialog.qml

src/pygui/ISC/Tabs/qmldir

@@ -0,0 +1,8 @@
+# ===== ISC Tabs Module =====
+module ISC.Tabs
+
+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/ISC/Theme.qml

@@ -21,15 +21,18 @@ import QtQuick
 
 QtObject {
     // ── 1. Mode ──────────────────────────────────────────────────────────────
-    property bool isDarkMode: false
+    property bool isDarkMode: true
 
     // ── 2. Tone palette (base values; consume via semantic tokens below) ─────
     readonly property color tone100: isDarkMode ? "#111111" : "#FAFAFA"
-    readonly property color tone200: isDarkMode ? "#1A1A1A" : "#F2F2F2"
-    readonly property color tone300: isDarkMode ? "#242424" : "#E8E8E8"
+    readonly property color tone150: isDarkMode ? "#161616" : "#F6F6F6"
+    readonly property color tone200: isDarkMode ? "#1A1A1A" : "#F0F0F0"
+    readonly property color tone250: isDarkMode ? "#212121" : "#EAEAEA"
+    readonly property color tone300: isDarkMode ? "#282828" : "#E2E2E2"
+    readonly property color tone350: isDarkMode ? "#303030" : "#D6D6D6"
     readonly property color toneText: isDarkMode ? "#F2F2F2" : "#111111"
     readonly property color toneMute: isDarkMode ? "#A8A8A8" : "#8A8A8A"
-    readonly property color toneBorder: isDarkMode ? "#2B2B2B" : "#D8D8D8"
+    readonly property color toneBorder: isDarkMode ? "#2E2E2E" : "#D4D4D4"
 
     // ── 3. Surfaces ──────────────────────────────────────────────────────────
     readonly property color pageBackground: tone100
@@ -41,11 +44,12 @@ QtObject {
 
     // ── 4. Borders ───────────────────────────────────────────────────────────
     readonly property color cardBorder: toneBorder
+    readonly property color cardSurfaceBorder: isDarkMode ? "#3C3C3C" : "#C8C8C8"
     readonly property color responseBorder: toneBorder
     readonly property color workspaceBorder: toneBorder
     readonly property color innerFrameBorder: toneBorder
-    readonly property color outerFrameBorder: isDarkMode ? "#343434" : "#CECECE"
-    readonly property color softBorder: isDarkMode ? "#222222" : "#E2E2E2"
+    readonly property color outerFrameBorder: isDarkMode ? "#383838" : "#CACACA"
+    readonly property color softBorder: isDarkMode ? "#252525" : "#E0E0E0"
 
     // ── 5. Text ──────────────────────────────────────────────────────────────
     readonly property color headingColor: toneText
@@ -77,7 +81,7 @@ QtObject {
     // ── 8. Tabs (footer tab bar) ─────────────────────────────────────────────
     readonly property color tabBarBackground: tone200
     readonly property color tabBackground: "transparent"
-    readonly property color tabActiveBackground: "transparent"
+    readonly property color tabActiveBackground: isDarkMode ? "#333333" : "#FFFFFF"
     readonly property color tabHoverBackground: tone300
     readonly property color tabBorder: "transparent"
     readonly property color tabText: toneMute
@@ -87,17 +91,31 @@ QtObject {
     readonly property color sideRailBackground: tone200
     readonly property color sideActiveBackground: tone300
 
+    // ── 10a. Transport / toolbar surfaces ────────────────────────────────────
+    readonly property color transportBackground:  isDarkMode ? "#0D0D0D" : "#E8E8E8"
+    readonly property color transportButtonBg:    isDarkMode ? "#2A2A2A" : "#D4D4D4"
+    readonly property color transportButtonHover: isDarkMode ? "#3A3A3A" : "#C4C4C4"
+    readonly property color liveColor:   isDarkMode ? "#22C55E" : "#16A34A"
+    readonly property color recordColor: isDarkMode ? "#EF4444" : "#DC2626"
+
     // ── 10. Status ───────────────────────────────────────────────────────────
     readonly property color statusSuccessColor: isDarkMode ? "#63D471" : "#2E9E44"
     readonly property color statusWarningColor: isDarkMode ? "#F5C15C" : "#C88A18"
     readonly property color statusErrorColor: isDarkMode ? "#FF6B6B" : "#D64545"
 
+    // -- 10b. Sensor bands (wafer map dots)
+    readonly property color sensorInRange: statusSuccessColor
+    readonly property color sensorHigh: statusErrorColor
+    readonly property color sensorLow: isDarkMode ? "#5B9DF5" : "#2F6FE0"
+    readonly property color waferRingColor: toneBorder
+    readonly property color waferAxisColor: softBorder
+
     // ── 11. Geometry ─────────────────────────────────────────────────────────
     // Radius
-    readonly property int radiusXs: 4   // fields, tight elements
-    readonly property int radiusSm: 6   // buttons
-    readonly property int radiusMd: 10  // cards, group boxes
-    readonly property int radiusLg: 14  // large panels / dialogs
+    readonly property int radiusXs: 6   // fields, tight elements
+    readonly property int radiusSm: 8   // buttons
+    readonly property int radiusMd: 12  // cards, group boxes
+    readonly property int radiusLg: 18  // large panels / dialogs
     // Border width
     readonly property int borderThin: 1
     readonly property int borderStrong: 2
@@ -114,7 +132,7 @@ QtObject {
     readonly property int tabBarHeight: 34
     readonly property int tabBarPadding: 6
     readonly property int tabSpacing: 2
-    readonly property int tabRadius: 2
+    readonly property int tabRadius: 8
     readonly property int tabFontSize: 12
     readonly property int tabButtonMinWidth: 80
     // Settings page layout

src/pygui/__main__.py

@@ -1,17 +1,25 @@
 import sys
 from pathlib import Path
+import logging
 
 from PySide6.QtQml import QQmlApplicationEngine
 from PySide6.QtQuickControls2 import QQuickStyle
 from PySide6.QtWidgets import QApplication
 
-from backend.device_controller import DeviceController
-from backend.local_settings import LocalSettings
-from backend.local_settings_model import LocalSettingsModel
-from backend.file_browser import FileBrowser
+from pygui.backend.controllers.device_controller import DeviceController
+from pygui.backend.data.local_settings import LocalSettings
+from pygui.backend.data.local_settings_model import LocalSettingsModel
+from pygui.backend.data.file_browser import FileBrowser
+from pygui.backend.controllers.session_controller import SessionController
+# Importing wafer_map_item registers the @QmlElement WaferMapItem (QML: import ISC.Wafer).
+from pygui.backend.visualization.wafer_map_item import WaferMapItem
 
 # ===== Application Entry Point =====
-if __name__ == "__main__":
+def main() -> int:
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s [%(levelname)s] %(name)s: %(message)s"
+    )
     # ===== UI Style Setup =====
     # Use a non-native controls style so our custom QML button backgrounds are supported.
     QQuickStyle.setStyle("Basic")
@@ -34,12 +42,22 @@ if __name__ == "__main__":
     device_controller = DeviceController(raw_settings, data_dir)
     engine.rootContext().setContextProperty("deviceController", device_controller)
 
+    # ===== Session Controller (live/review wafer dashboard) =====
+    stream_controller = SessionController()
+    engine.rootContext().setContextProperty("streamController", stream_controller)
+
     # ===== 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.
     engine.addImportPath(Path(__file__).parent)
     engine.loadFromModule("ISC", "Main")
 
     # ===== Exit Handling =====
     if not engine.rootObjects():
-        sys.exit(-1)
+        return -1
 
-    sys.exit(app.exec())
+    return app.exec()
+
+
+if __name__ == "__main__":
+    sys.exit(main())

src/pygui/assets/layouts/aepwafer.yaml

@@ -0,0 +1,44 @@
+# This will be the name of the output files
+name: aepwafer
+wafers: ["A", "E", "P"]
+
+# round or square wafer
+shape: round
+
+# diameter/edge size of the wafer
+size: 300
+
+# large or small markers and labels
+marker_size: large
+font_size: large
+
+# origin settings.  x_origin can be left, right, or center.  y_origin can
+# be top, bottom, or center.  Using right or top implies that the X/Y values
+# for that axis are negative, or else we'll be drawing outside the image.
+x_origin: left
+y_origin: bottom
+
+# sensor X and Y values, in mm relative to the origin
+X: [150, 204, 249, 280, 290, 280, 249, 204, 150, 97, 51, 21, 10, 21, 51, 97,
+    150, 203, 241, 255, 241, 203, 150, 98, 59, 45, 59, 98, 171, 207, 228, 228,
+    207, 171, 130, 94, 73, 73, 94, 130, 150, 186, 200, 186, 150, 115, 100, 115]
+Y: [290, 280, 249, 204, 150, 97, 51, 21, 10, 21, 51, 97, 150, 204, 249, 280,
+    255, 241, 203, 150, 98, 59, 45, 59, 98, 150, 203, 241, 228, 207, 171, 130,
+    94, 73, 73, 94, 130, 171, 207, 228, 200, 186, 150, 115, 100, 115, 150, 186]
+
+# set this to either 0 or 1 for the initial sensor number (usually 1)
+start_sn: 1
+
+# Normally, positive X is to the right, and positive Y is up.
+# These settings can be used to reverse one or both of these.
+reverse_x: false
+reverse_y: false
+
+# these are sensors whose labels need to be repositioned.  Sensor numbers
+# start at start_sn.  Directions are up, down, left, and right, and values
+# are multiples of the marker size.
+label_exceptions: {
+    4: { top: [0, 0] },
+    5: { top: [0, 0] },
+    6: { top: [0, 0] },
+}

src/pygui/assets/layouts/bcdwafer.yaml

@@ -0,0 +1,46 @@
+# This will be the name of the output files
+name: bcdwafer
+wafers: ["B", "C", "D"]
+
+# round or square wafer
+shape: round
+
+# diameter/edge size of the wafer
+size: 300
+
+# large or small markers and labels
+marker_size: large
+font_size: large
+
+# origin settings.  x_origin can be left, right, or center.  y_origin can
+# be top, bottom, or center.  Using right or top implies that the X/Y values
+# for that axis are negative, or else we'll be drawing outside the image.
+x_origin: center
+y_origin: center
+
+# sensor X and Y values, in mm relative to the origin
+X: [0, 72.50, 125.57, 145.00, 125.57, 72.50, 0, -72.50, -125.57, -145.00,
+    -125.57, -72.50, 0, 47.50, 82.27, 95.00, 82.27, 47.50, 0, -47.50, -82.27,
+    -95.00, -82.27, -47.50, 38.97, 22.50, -38.97, -22.50, 0]
+Y: [145.00, 125.57, 72.50, 0, -72.50, -125.57, -145.00, -125.57, -72.50, 0,
+    72.50, 125.57, 95.00, 82.27, 47.50, 0, -47.50, -82.27, -95.00, -82.27,
+    -47.50, 0, 47.50, 82.27, 22.50, -38.97, -22.50, 38.97, 0]
+
+# set this to either 0 or 1 for the initial sensor number (usually 1)
+start_sn: 1
+
+# Normally, positive X is to the right, and positive Y is up.
+# These settings can be used to reverse one or both of these.
+reverse_x: false
+reverse_y: false
+
+# these are sensors whose labels need to be repositioned.  Sensor numbers
+# start at start_sn.  Directions are up, down, left, and right, and values
+# are multiples of the marker size.
+label_exceptions: {
+    2: { left: [1, 0] },
+    3: { left: [1, 0] },
+    4: { left: [1, 0] },
+    5: { left: [1, 0] },
+    6: { left: [1, 0] },
+}

src/pygui/assets/layouts/fwafer.yaml

@@ -0,0 +1,43 @@
+# This will be the name of the output files
+name: fwafer
+wafers: ["F"]
+
+# round or square wafer
+shape: round
+
+# diameter/edge size of the wafer
+size: 200
+
+# large or small markers and labels
+marker_size: large
+font_size: large
+
+# origin settings.  x_origin can be left, right, or center.  y_origin can
+# be top, bottom, or center.  Using right or top implies that the X/Y values
+# for that axis are negative, or else we'll be drawing outside the image.
+x_origin: center
+y_origin: center
+
+# sensor X and Y values, in mm relative to the origin
+X: [0.0, 47.5, 82.3, 95.0, 82.3, 47.5, 0.0, -47.5, -82.3, -95.0, -82.3, -47.5,
+    -55.0, -14.8, 39.7, 55.0, 14.8, -39.7, -14.7, 25.5, 14.7, -25.5]
+Y: [95.0, 82.3, 47.5, 0.0, -47.5, -82.3, -95.0, -82.3, -47.5, 0.0, 47.5, 82.3,
+    13.3, 54.4, 40.0, -13.3, -54.4, -40.0, 25.5, 14.7, -25.5, -14.7]
+
+# set this to either 0 or 1 for the initial sensor number (usually 1)
+start_sn: 1
+
+# Normally, positive X is to the right, and positive Y is up.
+# These settings can be used to reverse one or both of these.
+reverse_x: false
+reverse_y: false
+
+# these are sensors whose labels need to be repositioned.  Sensor numbers
+# start at start_sn.  Directions are up, down, left, and right, and values
+# are multiples of the marker size.
+label_exceptions: {
+    2: { left: [1, 0] },
+    3: { left: [1, 0] },
+    4: { left: [1, 0] },
+    5: { left: [1, 0] },
+}

src/pygui/assets/layouts/xwafer.yaml

@@ -0,0 +1,69 @@
+# This will be the name of the output files
+name: xwafer
+wafers: ["X"]
+
+# round or square wafer
+shape: square
+
+# diameter/edge size of the wafer
+size: 310
+
+# large or small markers and labels
+marker_size: small
+font_size: small
+
+# origin settings.  x_origin can be left, right, or center.  y_origin can
+# be top, bottom, or center.  Using right or top implies that the X/Y values
+# for that axis are negative, or else we'll be drawing outside the image.
+x_origin: left
+y_origin: bottom
+
+# sensor X and Y values, in mm relative to the origin
+X: [ 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00,
+    13.00, 23.00, 46.43, 89.86, 133.29, 176.72, 220.15, 263.58, 287.01, 297.01,
+    307.01, 307.01, 307.01, 307.01, 307.01, 307.01, 307.01, 307.01, 307.01,
+    307.01, 307.01, 307.01, 297.01, 287.01, 263.58, 220.15, 176.72, 133.29,
+    89.86, 46.43, 23.00, 13.00, 46.43, 46.43, 46.43, 46.43, 46.43, 46.43,
+    89.86, 133.29, 176.72, 220.15, 263.58, 263.58, 263.58, 263.58, 263.58,
+    263.58, 220.15, 176.72, 133.29, 89.86, 89.86, 89.86, 89.86, 89.86,
+    133.29, 176.72, 220.15, 220.15, 220.15, 220.15, 176.72, 133.29, 133.29,
+    133.29, 176.72, 176.72]
+Y: [ 3.00, 13.07, 23.07, 46.50, 89.93, 133.36, 176.79, 220.22, 263.65, 287.08,
+    297.08, 307.08, 307.08, 307.08, 307.08, 307.08, 307.08, 307.08, 307.08,
+    307.08, 307.08, 307.08, 307.08, 297.08, 287.08, 263.65, 220.22, 176.79,
+    133.36, 89.93, 46.50, 23.07, 13.07, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00,
+    3.00, 3.00, 3.00, 3.00, 3.00, 46.50, 89.93, 133.36, 176.79, 220.22, 263.65,
+    263.65, 263.65, 263.65, 263.65, 263.65, 220.22, 176.79, 133.36, 89.93,
+    46.50, 46.50, 46.50, 46.50, 46.50, 89.93, 133.36, 176.79, 220.22, 220.22,
+    220.22, 220.22, 176.79, 133.36, 89.93, 89.93, 89.93, 133.36, 176.79,
+    176.79, 133.36 ]
+
+# set this to either 0 or 1 for the initial sensor number (usually 1)
+start_sn: 1
+
+# Normally, positive X is to the right, and positive Y is up.
+# These settings can be used to reverse one or both of these.
+reverse_x: false
+reverse_y: false
+
+# these are sensors whose labels need to be repositioned.  Sensor numbers
+# start at start_sn.  Directions are up, down, left, and right, and values
+# are multiples of the marker size.
+label_exceptions: {
+    21: { left: [0, 0] },
+    22: { left: [0, 0] },
+    23: { left: [0, 0] },
+    24: { left: [0, 0] },
+    25: { left: [0, 0] },
+    26: { left: [0, 0] },
+    27: { left: [0, 0] },
+    28: { left: [0, 0] },
+    29: { left: [0, 0] },
+    30: { left: [0, 0] },
+    31: { left: [0, 0] },
+    32: { left: [0, 0] },
+    33: { left: [0, 0] },
+    34: { left: [0, 0] },
+    35: { left: [0, 0] },
+    36: { left: [0, 0] }
+}

src/pygui/assets/layouts/zwafer.yaml

@@ -0,0 +1,68 @@
+# This will be the name of the output files
+name: zwafer
+wafers: ["Z"]
+
+# round or square wafer
+shape: round
+
+# diameter/size of the wafer
+size: 300
+
+# large or small markers and labels
+marker_size: small
+font_size: small
+
+# origin settings.  x_origin can be left, right, or center.  y_origin can
+# be top, bottom, or center.  Using right or top probably also needs
+# reverse_x/reverse_y to be set as well.
+x_origin: center
+y_origin: center
+
+# sensor X and Y values, in mm relative to the wafer center
+X: [0.00, -1.17, 8.92, 1.17, -8.92, 22.52, 29.35, -22.52, -29.35, 45.05, 73.37,
+     58.71, 9.66, -45.05, -73.37, -58.71, -9.66, 79.85, 89.06, 46.10, -23.86,
+     -79.85, -89.06, -46.10, 23.86, 66.96, 109.06, 87.27, 14.36, -66.96,
+     -109.06, -87.27, -14.36, 121.24, 135.23, 70.00, -36.23, -121.24, -135.23,
+     -70.00, 36.23, 124.71, 139.09, 72.00, -37.27, -124.71, -139.09, -72.00,
+     37.27, 89.49, 127.31, 145.74, 141.99, 116.62, 73.50, 19.19, -38.05, -89.49,
+     -127.31, -145.74, -141.99, -116.62, -73.50, -19.19, 38.05]
+Y: [0.00, -8.92, -1.17, 8.92, 1.17, -29.35, 22.52, 29.35, -22.52, -58.71,
+     -9.66, 45.05, 73.37, 58.71, 9.66, -45.05, -73.37, -46.10, 23.86, 79.85,
+     89.06, 46.10, -23.86, -79.85, -89.06, -87.27, -14.36, 66.96, 109.06, 87.27,
+     14.36, -66.96, -109.06, -70.00, 36.23, 121.24, 135.23, 70.00, -36.23,
+     -121.24, -135.23, -72.00, 37.27, 124.71, 139.09, 72.00, -37.27, -124.71,
+     -139.09, -116.62, -73.50, -19.19, 38.05, 89.49, 127.31, 145.74, 141.99,
+     116.62, 73.50, 19.19, -38.05, -89.49, -127.31, -145.74, -141.99]
+
+# set this to either 0 or 1 for the initial sensor number (usually 1)
+start_sn: 0
+
+# If one or both axes are reversed, this can be used to fix it
+# without having to edit all of the coordinates.
+# These should be false for most normal wafers.
+reverse_x: false
+reverse_y: false
+
+# these are sensors whose labels need to be repositioned.  Sensor numbers
+# start at start_sn.  Directions are up, down, left, and right, and values
+# are multiples of the marker size.
+label_exceptions: {
+    33: { left: [0, 0] },
+    34: { left: [0, 0] },
+    41: { top: [0, 0] },
+    42: { bottom: [0, 0] },
+    45: { top: [1, 0] },
+    46: { bottom: [0.5, 0] },
+    49: { left: [0, 0] },
+    50: { bottom: [-1.75, -0.5] },
+    51: { top: [-1, 0] },
+    52: { top: [-1, 0] },
+    53: { bottom: [0, 0] },
+    54: { left: [0, -0.75] },
+    55: { right: [0, 0.5] },
+    58: { bottom: [-0.75, 0] },
+    60: { top: [0, 0] },
+    62: { right: [0, 1] },
+    63: { right: [0, 0] },
+    64: { left: [0, 0.25] }
+}

src/pygui/assets/layouts/zwafer_rev.yaml

@@ -0,0 +1,71 @@
+# This will be the name of the output files
+name: zwafer_rev
+wafers: []     # the reversed version doesn't represent any real wafer
+
+# round or square wafer
+shape: round
+
+# diameter/size of the wafer
+size: 300
+
+# large or small markers and labels
+marker_size: small
+font_size: small
+
+# origin settings.  x_origin can be left, right, or center.  y_origin can
+# be top, bottom, or center.  Using right or top probably also needs
+# reverse_x/reverse_y to be set as well.
+x_origin: center
+y_origin: center
+
+# sensor X and Y values, in mm relative to the wafer center
+X: [0.00, -1.17, 8.92, 1.17, -8.92, 22.52, 29.35, -22.52, -29.35, 45.05, 73.37,
+     58.71, 9.66, -45.05, -73.37, -58.71, -9.66, 79.85, 89.06, 46.10, -23.86,
+     -79.85, -89.06, -46.10, 23.86, 66.96, 109.06, 87.27, 14.36, -66.96,
+     -109.06, -87.27, -14.36, 121.24, 135.23, 70.00, -36.23, -121.24, -135.23,
+     -70.00, 36.23, 124.71, 139.09, 72.00, -37.27, -124.71, -139.09, -72.00,
+     37.27, 89.49, 127.31, 145.74, 141.99, 116.62, 73.50, 19.19, -38.05, -89.49,
+     -127.31, -145.74, -141.99, -116.62, -73.50, -19.19, 38.05]
+Y: [0.00, -8.92, -1.17, 8.92, 1.17, -29.35, 22.52, 29.35, -22.52, -58.71,
+     -9.66, 45.05, 73.37, 58.71, 9.66, -45.05, -73.37, -46.10, 23.86, 79.85,
+     89.06, 46.10, -23.86, -79.85, -89.06, -87.27, -14.36, 66.96, 109.06, 87.27,
+     14.36, -66.96, -109.06, -70.00, 36.23, 121.24, 135.23, 70.00, -36.23,
+     -121.24, -135.23, -72.00, 37.27, 124.71, 139.09, 72.00, -37.27, -124.71,
+     -139.09, -116.62, -73.50, -19.19, 38.05, 89.49, 127.31, 145.74, 141.99,
+     116.62, 73.50, 19.19, -38.05, -89.49, -127.31, -145.74, -141.99]
+
+# set this to either 0 or 1 for the initial sensor number (usually 1)
+start_sn: 0
+
+# If one or both axes are reversed, this can be used to fix it
+# without having to edit all of the coordinates.
+# These should be false for most normal wafers.
+reverse_x: true
+reverse_y: true
+
+# these are sensors whose labels need to be repositioned.  Sensor numbers
+# start at start_sn.  Directions are up, down, left, and right, and values
+# are multiples of the marker size.
+label_exceptions: {
+    37: { left: [0, 0] },
+    38: { left: [0, 0] },
+    39: { left: [0, 0] },
+    41: { top: [1.5, 0] },
+    42: { bottom: [1, 0] },
+    43: { left: [0, -1] },
+    45: { bottom: [-1, -1] },
+    46: { bottom: [0, -1] },
+    47: { right: [0, 1] },
+    48: { left: [0, 0] },
+    50: { bottom: [-1, 0] },
+    52: { top: [0, 0] },
+    54: { right: [0.5, 1] },
+    56: { left: [0, 0.5] },
+    57: { left: [0, 0] },
+    58: { top: [0.5, 0] },
+    59: { left: [0, 0] },
+    60: { top: [-1, 0] },
+    61: { left: [0, 0] },
+    62: { left: [0, -1] },
+    63: { right: [0, 1] },
+}

src/pygui/backend/__init__.py

@@ -0,0 +1,32 @@
+# ===== 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.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.session_model import SessionModel  # noqa: F401
+from pygui.backend.models.data_model import TemperatureTableModel  # noqa: F401
+from pygui.backend.models.sensor_editor import SensorEditor  # noqa: F401
+from pygui.backend.models.threshold_classifier import ThresholdConfig  # noqa: F401
+from pygui.backend.models.stability_detector import StabilityDetector  # noqa: F401
+
+from pygui.backend.data.csv_recorder import CsvRecorder  # noqa: F401
+from pygui.backend.data.csv_file_metadata import CSVFileMetadata  # noqa: F401
+from pygui.backend.data.data_records import read_data_records  # noqa: F401
+from pygui.backend.data.data_segment import DataSegment  # 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.visualization.wafer_map_item import WaferMapItem  # 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.contour_models import ContourLine, ContourSegment  # noqa: F401
+
+from pygui.backend.wafer.zwafer_models import ZWaferData, Sensor, DataRecord  # noqa: F401
+from pygui.backend.wafer.zwafer_parser import ZWaferParser  # noqa: F401
+from pygui.backend.wafer.wafer_layouts import load_layout, available_families  # noqa: F401

src/pygui/backend/cluster_average.py

@@ -0,0 +1,60 @@
+"""Cluster Average utility for wafer sensor values."""
+
+
+from __future__ import annotations
+import math
+from pygui.backend.wafer.zwafer_models import Sensor
+
+
+def average_clusters(values: list[float], clusters: list[list[int]]) -> list[float]:
+    """Return a new list of values where members of each cluster are replaced by their mean.
+
+    NaN values are filtered out before computing the mean.
+    If all values in a cluster are NaN, they remain NaN.
+    """
+    result = list(values)
+    for cluster in clusters:
+        valid_vals = []
+        for idx in cluster:
+            if idx < len(values):
+                val = values[idx]
+                if not math.isnan(val):
+                    valid_vals.append(val)
+        
+        if valid_vals:
+            mean_val = sum(valid_vals) / len(valid_vals)
+            for idx in cluster:
+                if idx < len(result):
+                    result[idx] = mean_val
+    return result
+
+
+def group_sensors_by_radius(sensors: list[Sensor], tolerance: float = 2.0) -> list[list[int]]:
+    """Group sensor indices into clusters if their radial distances are within tolerance."""
+    # Compute radii for all sensors
+    radii = [(i, math.hypot(s.x, s.y)) for i, s in enumerate(sensors)]
+    # Filter out center sensors (r < 1.0)
+    non_center = [item for item in radii if item[1] >= 1.0]
+    if not non_center:
+        return []
+
+    # Sort by radius
+    non_center.sort(key=lambda x: x[1])
+
+    clusters: list[list[int]] = []
+    current_cluster: list[int] = [non_center[0][0]]
+    last_r = non_center[0][1]
+
+    for idx, r in non_center[1:]:
+        if r - last_r <= tolerance:
+            current_cluster.append(idx)
+        else:
+            if len(current_cluster) > 1:
+                clusters.append(current_cluster)
+            current_cluster = [idx]
+            last_r = r
+
+    if len(current_cluster) > 1:
+        clusters.append(current_cluster)
+
+    return clusters

src/pygui/backend/controllers/__init__.py

@@ -0,0 +1,6 @@
+# ===== 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

@@ -1,10 +1,4 @@
-"""QML-exposed controller for wafer device communication.
-
-Bridges DeviceService (serialcomm) to QML via @Slot methods and signals.
-All hardware operations run synchronously on the main thread (matching
-C# Form1.cs per-operation open/close pattern).  For long operations
-(erase ~15s, read up to 120s) the caller should show a loading state.
-"""
+"""QML-exposed controller for wafer device communication."""
 
 from __future__ import annotations
 
@@ -15,17 +9,22 @@ from typing import Any, Optional
 
 from PySide6.QtCore import QObject, Property, Qt, Signal, Slot
 
-from backend.data_model import TemperatureTableModel
-from backend.graph_view import GraphView
-from backend.local_settings import LocalSettings
-from serialcomm.data_parser import (
+from pygui.backend.models.data_model import TemperatureTableModel
+from pygui.backend.visualization.graph_view import GraphView
+from pygui.backend.data.local_settings import LocalSettings
+from pygui.serialcomm.data_parser import (
     convert_to_temperatures,
     parse_binary_data,
     remove_trailing_zeros,
     save_to_csv,
 )
-from serialcomm.device_service import DeviceService
-from serialcomm.serial_port import WaferInfo
+from pygui.serialcomm.device_service import DeviceService
+from pygui.serialcomm.serial_port import WaferInfo
+from pygui.backend.controllers.session_controller import SessionController
+# import pygui.backend.wafer_map_item
+
+stream_controller = SessionController()
+# engine.rootContext().setContextProperty("streamController", stream_controller)
 
 log = logging.getLogger(__name__)
 
@@ -62,9 +61,8 @@ class DeviceController(QObject):
         self._operation_in_progress = False
         self._activity_log: list[str] = getattr(settings, 'activity_log', [])
         self._raw_bytes: Optional[bytes] = None
-        # Default save dir lives next to the settings file (~/Documents/isc_data/csv)
         from pathlib import Path
-        self._save_data_dir: str = getattr(settings, 'save_data_dir', str(Path.home() / "Documents" / "isc_data" / "csv"))
+        self._save_data_dir: str = getattr(settings, 'save_data_dir', "") or str(Path(self._data_dir) / "csv")
         self._last_wafer_info: dict[str, Any] = getattr(settings, 'last_wafer_info', {})
         self._last_csv_path: str = getattr(settings, 'last_csv_path', "")
         self._selected_port: str = getattr(settings, 'selected_port', "")
@@ -88,8 +86,8 @@ class DeviceController(QObject):
             self.statusRestored.emit()
 
         # Marshal worker-thread results onto the Qt main thread.
-        self._detectFinished.connect(self._handle_detect_finished, Qt.QueuedConnection)
-        self._readFinished.connect(self._handle_read_finished, Qt.QueuedConnection)
+        self._detectFinished.connect(self._handle_detect_finished, Qt.ConnectionType.QueuedConnection)
+        self._readFinished.connect(self._handle_read_finished, Qt.ConnectionType.QueuedConnection)
 
     # ---- Properties ----
     @Property(list, notify=portsUpdated)
@@ -204,6 +202,28 @@ class DeviceController(QObject):
             self._activity_log = self._activity_log[-200:]
         self.activityLogUpdated.emit("\n".join(self._activity_log))
 
+    @Slot()
+    def clearActivityLog(self) -> None:
+        """Clear the activity log."""
+        self._activity_log.clear()
+        self.activityLogUpdated.emit("")
+        self._save_status()
+
+    @Slot()
+    def clearSession(self) -> None:
+        """Clear the current session state, allowing a clean detect."""
+        self._connection_status = "Disconnected"
+        self._selected_port = ""
+        self._last_wafer_info = {}
+        self._data_row_count = 0
+        self._data_col_count = 0
+        self._raw_bytes = None
+        self._operation_in_progress = False
+        self.detectResult.emit(None)
+        self.portsUpdated.emit(self.availablePorts)
+        self._append_log("Session refreshed/cleared")
+        self._save_status()
+
     def _set_operation_progress(self, in_progress: bool) -> None:
         """Set operation progress state and notify QML.
 
@@ -283,7 +303,8 @@ class DeviceController(QObject):
         """Read wafer memory in a background thread.
 
         Uses the family code and port from the last detect.
-        Emits readResult on completion, then auto-chains to parseAndSaveData.
+        Emits readResult on completion; QML prompts for the save directory
+        before calling parseAndSaveData.
         """
         if self._operation_in_progress:
             self._append_log("Already busy — ignoring read request")
@@ -330,9 +351,7 @@ class DeviceController(QObject):
             self._raw_bytes = data
             self.readResult.emit({"success": True, "bytes": len(data)})
             self._set_operation_progress(False)
-            # Auto-chain: read → parse → save (matches C# behavior).
-            # Parse runs on main thread — it's CPU-bound but bounded (~1s).
-            self.parseAndSaveData(family_code, port)
+            self._append_log("Memory read complete - choose save directory to save CSV")
             self._save_status()
             return
         self._connection_status = "Disconnected"
@@ -419,12 +438,10 @@ class DeviceController(QObject):
             return
 
         if not self._save_data_dir:
-            self._append_log("No save data directory set")
-            self.parsedDataReady.emit({
-                "success": False,
-                "error": "No save data directory set",
-            })
-            return
+            from pathlib import Path
+            self._save_data_dir = str(Path(self._data_dir) / "csv")
+            self._append_log(f"Auto-set save directory to: {self._save_data_dir}")
+            self._save_status()
 
         fc = family_code or (
             self._last_wafer_info.get("familyCode", "")
@@ -471,6 +488,7 @@ class DeviceController(QObject):
             return
 
         self._append_log(f"Saved CSV: {csv_path}")
+        self._last_csv_path = csv_path
 
         # Load data into the QAbstractTableModel
         self._data_model.load_data(temp_data, cols)
@@ -504,7 +522,7 @@ class DeviceController(QObject):
         self._settings.last_csv_path = self._last_csv_path
 
         # Save to disk
-        LocalSettings.save_settings(LocalSettings._settings_path(self._data_dir), self._settings)
+        LocalSettings.save_settings(self._data_dir, self._settings)
 
     # ---- Helpers ----
 

src/pygui/backend/controllers/session_controller.py

@@ -0,0 +1,460 @@
+"""QML-facing controller for the live/review wafer dashboard."""
+from __future__ import annotations
+import logging
+import time
+from typing import Any, Optional
+
+from PySide6.QtCore import QObject, Property, QTimer, Qt, Signal, Slot
+
+from pygui.backend.data.csv_recorder import CsvRecorder
+from pygui.backend.models.frame import Frame
+from pygui.backend.models.frame_player import FramePlayer, frames_from_wafer_data
+from pygui.backend.models.session_model import SessionModel
+from pygui.backend.models.threshold_classifier import ThresholdConfig
+from pygui.backend.wafer.zwafer_models import Sensor
+from pygui.backend.wafer.zwafer_parser import ZWaferParser
+from pygui.serialcomm.stream_reader import StreamReader
+from pygui.backend.models.sensor_editor import SensorEditor
+from pygui.backend.cluster_average import average_clusters, group_sensors_by_radius
+log = logging.getLogger(__name__)
+
+MODE_LIVE = "live"
+MODE_REVIEW = "review"
+
+
+class SessionController(QObject):
+    # public signals
+    frameUpdated = Signal()        
+    modeChanged = Signal()
+    stateChanged = Signal()
+    recordingChanged = Signal()
+    sensorsChanged = Signal()
+    loadedFileChanged = Signal()
+    clusterAveragingEnabledChanged = Signal()
+    # private: marshal a worker-thread frame onto the main thread
+    _liveFrame = Signal(object)    # Frame
+
+    def __init__(self, parent: QObject | None = None) -> None:
+        super().__init__(parent)
+        self._mode = MODE_REVIEW
+        self._model = SessionModel()
+        self._player = FramePlayer()
+        self._reader: Optional[StreamReader] = None
+        self._recorder = CsvRecorder()
+        self._sensors: list[Sensor] = []
+        self._last = None              # last SessionUpdate
+        self._elapsed = 0.0
+
+        self._play_timer = QTimer(self)
+        self._play_timer.timeout.connect(self._advance)
+        self._speed = 1.0
+
+        # Q1: coalesce live repaints to ~20 Hz; data is still processed every frame.
+        self._repaint_timer = QTimer(self)
+        self._repaint_timer.setInterval(50)            # ~20 Hz
+        self._repaint_timer.timeout.connect(self._flush_repaint)
+        self._dirty = False
+
+        self._liveFrame.connect(self._on_live_frame, Qt.ConnectionType.QueuedConnection)
+        
+        self._sensor_editor = SensorEditor()
+        self._last_raw_frame: Frame | None = None
+        self._loaded_file: str = ""
+        self._cluster_averaging_enabled = False
+        self._active_clusters: list[list[int]] = []
+
+    # ---- properties QML binds to ----
+    @Property(str, notify=modeChanged)
+    def mode(self) -> str: return self._mode
+
+    @Property(int, notify=frameUpdated)
+    def frameIndex(self) -> int: return self._player.index
+
+    @Property(int, notify=frameUpdated)
+    def frameTotal(self) -> int: return self._player.total
+
+    @Property(str, notify=stateChanged)
+    def state(self) -> str: 
+        if self._last:
+            return self._last.state
+        # IF we dont have data yet, but the reader is running -> Streaming
+        if self._mode == MODE_LIVE and self._reader is not None:
+            return "streaming"
+        
+        return "idle"
+
+    @Property(bool, notify=recordingChanged)
+    def recording(self) -> bool: return self._recorder.is_recording
+
+    @Property(list, notify=frameUpdated)
+    def sensorDots(self) -> list[dict]:
+        """Per-sensor render data for the radial map."""
+        if not self._last:
+            return []
+        out = []
+        for i, s in enumerate(self._sensors):
+            v = self._last.values[i] if i < len(self._last.values) else 0.0
+            band = self._last.bands[i] if i < len(self._last.bands) else "in_range"
+            out.append({"label": s.label, "x": s.x, "y": s.y,
+                        "value": round(v, 2), "band": band, "index": i})
+        return out
+
+    @Property("QVariantList", notify=sensorsChanged)
+    def sensorLayout(self) -> list:
+        """[{label, x, y, side, offset_x, offset_y}] for WaferMapItem.sensors."""
+        return [
+            {
+                "label": s.label,
+                "x": s.x,
+                "y": s.y,
+                "side": getattr(s, "side", "right"),
+                "offset_x": getattr(s, "offset_x", 0.0),
+                "offset_y": getattr(s, "offset_y", 0.0),
+            }
+            for s in self._sensors
+        ]
+
+    @Property(str, notify=sensorsChanged)
+    def waferShape(self) -> str:
+        """Wafer shape: 'round' or 'square'."""
+        return getattr(self._sensors, "shape", "round")
+
+    @Property(float, notify=sensorsChanged)
+    def waferSize(self) -> float:
+        """Wafer size in mm."""
+        return getattr(self._sensors, "size", 300.0)
+
+    @Property("QVariantList", notify=frameUpdated)
+    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)
+    def sensorBands(self) -> list:
+        """['in_range'|'high'|'low'] in sensor order."""
+        if not self._last:
+            return []
+        return list(self._last.bands)
+
+    @Property(float, notify=frameUpdated)
+    def target(self) -> float:
+        """Resolved band center (frame mean in auto mode, else set_point)."""
+        return self._last.target if self._last else 149.0
+
+    @Property(float, notify=frameUpdated)
+    def margin(self) -> float:
+        """Resolved band half-width (frame 1σ in auto mode, else margin)."""
+        return self._last.margin if self._last else 1.0
+
+    @Property(dict, notify=frameUpdated)
+    def stats(self) -> dict:
+        if not self._last:
+            return {}
+        s = self._last.stats
+        return {"min": round(s.min, 2), "minIndex": s.min_index + 1,
+                "max": round(s.max, 2), "maxIndex": s.max_index + 1,
+                "diff": round(s.diff, 2), "avg": round(s.avg, 2),
+                "sigma": round(s.sigma, 2), "threeSigma": round(s.three_sigma, 2)}
+
+    @Property(str, notify=loadedFileChanged)
+    def loadedFile(self) -> str: return self._loaded_file
+
+    @Property("QVariantList", notify=frameUpdated)
+    def overriddenSensors(self) -> list[int]:
+        """Indices of sensors that currently have a replacement or offset."""
+        return self._sensor_editor.active_indices()
+
+    @Property(bool, notify=clusterAveragingEnabledChanged)
+    def clusterAveragingEnabled(self) -> bool:
+        return self._cluster_averaging_enabled
+
+    @clusterAveragingEnabled.setter
+    def clusterAveragingEnabled(self, value: bool) -> None:
+        if self._cluster_averaging_enabled == value:
+            return
+        self._cluster_averaging_enabled = value
+        self.clusterAveragingEnabledChanged.emit()
+        self._reprocess_current()
+
+    # ---- mode + thresholds ----
+    @Slot(str)
+    def setMode(self, mode: str) -> None:
+        if mode == self._mode:
+            return
+        self.stopStream()
+        self._play_timer.stop()
+        self._mode = mode
+        self.modeChanged.emit()
+
+    @Slot(float, float, bool)
+    def setThresholds(self, set_point: float, margin: float, auto: bool) -> None:
+        self._model.set_thresholds(ThresholdConfig(set_point, margin, auto))
+        if self._last:                     # re-band current frame in place
+            self._reprocess_current()
+
+    # ---- review: file load + playback ----
+    @Slot(str)
+    def loadFile(self, file_path: str) -> None:
+        from pathlib import Path
+        from pygui.backend.data.data_records import is_official_csv, read_data_records, read_official_csv
+        from pygui.backend.wafer.wafer_layouts import WaferLayout, resolve_shape_and_size
+
+        frames = []
+
+        if is_official_csv(file_path):
+            sensors, records = read_official_csv(file_path)
+            frames = frames_from_wafer_data(None, records)
+        else:
+            try:
+                data, _ = ZWaferParser().parse(file_path)
+            except (ValueError, KeyError) as exc:
+                log.warning("Could not parse %s: %s", file_path, exc)
+                return
+            if data is None or not data.sensors:
+                log.warning("Could not parse %s", file_path)
+                return
+            records = read_data_records(file_path)
+            sensors = data.sensors
+            frames = frames_from_wafer_data(data, records)
+
+        if not sensors or not frames:
+            log.warning("No sensors or data in %s", file_path)
+            return
+
+        wafer_id = ""
+        if not is_official_csv(file_path):
+            wafer_id = data.serial if (data and data.serial) else ""
+        else:
+            stem = Path(file_path).stem
+            wafer_id = stem.split("-")[0] if "-" in stem else stem
+
+        shape, size = resolve_shape_and_size(sensors, wafer_id)
+        self._sensors = WaferLayout(sensors, shape=shape, size=size)
+        self._active_clusters = getattr(self._sensors, 'clusters', [])
+        if not self._active_clusters:
+            self._active_clusters = group_sensors_by_radius(self._sensors)
+        self._player.load(frames)
+        self._model.reset()
+        self._loaded_file = file_path
+        self.loadedFileChanged.emit()
+        self.sensorsChanged.emit()
+        self._emit_current()
+
+    @Slot()
+    def play(self) -> None:
+        self._play_timer.start(self._next_interval_ms())
+
+    @Slot()
+    def pause(self) -> None: self._play_timer.stop()
+
+    @Slot()
+    def stop(self) -> None:
+        self._play_timer.stop()
+        self._player.seek(0)
+        self._emit_current()
+
+    @Slot(int)
+    def step(self, delta: int) -> None:
+        self._play_timer.stop()
+        self._player.step(delta)
+        self._emit_current()
+
+    @Slot(int)
+    def seek(self, i: int) -> None:
+        self._player.seek(i)
+        self._emit_current()
+
+    @Slot(float)
+    def setSpeed(self, x: float) -> None:
+        self._speed = max(0.1, x)
+        if self._play_timer.isActive():
+            self._play_timer.start(self._next_interval_ms())
+
+    def _next_interval_ms(self) -> int:
+        """Timer interval in ms for the next frame, scaled by playback speed. Falls back to 500ms."""
+        ms = self._player.next_frame_ms()
+        if ms <= 0:
+            ms = 500.0
+        return max(1, int(ms / self._speed))
+
+    def _advance(self) -> None:
+        if self._player.at_end:
+            self._play_timer.stop()
+            return
+        self._player.step(1)
+        self._emit_current()
+        self._play_timer.start(self._next_interval_ms())
+
+    def _apply_pipeline(self, raw_values: list[float]) -> list[float]:
+        """Apply override first, then optional cluster averaging."""
+        edited = self._sensor_editor.apply(raw_values)
+        if getattr(self, "_cluster_averaging_enabled", False):
+            return average_clusters(edited, getattr(self, "_active_clusters", []))
+        return edited
+
+    def _emit_current(self) -> None:
+        frame = self._player.current()
+        if frame is None:
+            return
+        self._last_raw_frame = frame
+        edited = Frame(seq=frame.seq, time=frame.time,
+                    values=self._apply_pipeline(frame.values))
+        self._last = self._model.process(edited)
+        self.frameUpdated.emit()
+        self.stateChanged.emit()
+
+    def _reprocess_current(self) -> None:
+        """Re-run the model on the last raw frame"""
+        frame = self._last_raw_frame
+        if frame is None:
+            return
+        edited = Frame(seq=frame.seq, time=frame.time,
+                    values=self._apply_pipeline(frame.values))
+        self._last = self._model.process(edited)
+        self.frameUpdated.emit()
+        self.stateChanged.emit()
+
+    # ---- live: stream start/stop ----
+    @Slot(str, str)
+    def startStream(self, port: str, family_code: str = "") -> None:
+        from pygui.serialcomm.serial_port import SerialPort  # transport open
+        import serial as pyserial
+        from pygui.backend.wafer.wafer_layouts import load_layout_for_wafer_id
+        import time
+
+        if family_code:
+            try:
+                self._sensors = load_layout_for_wafer_id(family_code)
+                self.sensorsChanged.emit()
+            except Exception as e:
+                log.warning("Could not load layout for %s: %s", family_code, e)
+
+        self._active_clusters = getattr(self._sensors, 'clusters', [])
+        if not self._active_clusters:
+            self._active_clusters = group_sensors_by_radius(self._sensors)
+
+        # The new binary protocol sends payload of (sensorCount * 2) bytes
+        # Each sensor is a big-endian 16-bit value (Sign-Magnitude).
+        expected_sensors = 80 if (family_code or "") == "X" else 244
+
+        def parse_binary_frame(payload: bytes, seq: int) -> Frame:
+            values = []
+            num_sensors = min(expected_sensors, len(payload) // 2)
+            for i in range(num_sensors):
+                high_byte = payload[i * 2]
+                low_byte = payload[i * 2 + 1]
+                val16 = (high_byte << 8) | low_byte
+                
+                is_negative = (val16 & 0x8000) != 0
+                integer_part = (val16 >> 7) & 0xFF
+                fractional_bits = val16 & 0x7F
+                fractional_part = fractional_bits / 128.0
+                result = integer_part + fractional_part
+                if is_negative:
+                    result = -result
+                values.append(result)
+            
+            return Frame(seq=seq, time=time.monotonic(), values=values)
+
+        # Clear out any old data from the prev sessions
+        self._model.reset()
+        self._last = None
+        self._last_raw_frame = None
+
+        transport = SerialPort.open_port(port, timeout=1)
+        # Send 'D2' command padded to 512 bytes to start the stream
+        cmd = b"D2" + SerialPort.COMMAND_PAD.encode()
+        transport.write(cmd)
+
+        def on_error(exc: Exception):
+            log.error("Live stream error: %s", exc)
+
+        self._reader = StreamReader(
+            transport, parse_binary_frame,
+            on_frame=lambda f: self._liveFrame.emit(f),
+            on_error=on_error,
+            family_code=family_code or "A")
+        self._reader.start()
+        self._repaint_timer.start()
+        
+        self.setMode("live")
+        self.stateChanged.emit()
+
+    @Slot()
+    def stopStream(self) -> None:
+        self._repaint_timer.stop()
+        if self._reader:
+            transport = self._reader._transport
+            self._reader.stop()
+            self._reader = None
+            
+            # Send 'D2S' command padded to 512 bytes to stop the stream
+            if transport and transport.is_open:
+                try:
+                    cmd = b"D2S" + (b"F" * 509)
+                    transport.write(cmd)
+                    transport.flush()
+                except Exception as exc:
+                    log.error("Error sending stop command: %s", exc)
+                
+        self.stateChanged.emit()
+        self.stopRecording()
+
+    @Slot(object)
+    def _on_live_frame(self, frame: Frame) -> None:
+        # Main thread (queued). Record raw, process edited; mark dirty for repaint.
+        self._last_raw_frame = frame
+        edited = Frame(seq=frame.seq, time=frame.time,
+                    values=self._apply_pipeline(frame.values))
+        self._last = self._model.process(edited)
+        if self._recorder.is_recording:
+            self._recorder.write(frame)   # always record raw values, never edited
+        self._dirty = True
+
+    def _flush_repaint(self) -> None:
+        if not self._dirty:
+            return
+        self._dirty = False
+        self.frameUpdated.emit()
+        self.stateChanged.emit()
+
+    # ---- recording ----
+    @Slot(str, str)
+    def startRecording(self, path: str, serial: str = "") -> None:
+        self._recorder.start(path, self._sensors, serial)
+        self.recordingChanged.emit()
+
+    @Slot()
+    def stopRecording(self) -> None:
+        if self._recorder.is_recording:
+            self._recorder.stop()
+            self.recordingChanged.emit()
+
+    @Slot(int, float)
+    def replaceSensor(self, index: int, value: float) -> None:
+        """Override sensor `index` to display `value` every frame."""
+        self._sensor_editor.set_replacement(index, value)
+        self._reprocess_current()
+
+    @Slot(int, float)
+    def offsetSensor(self, index: int, delta: float) -> None:
+        """Shift sensor `index` by `delta` every frame."""
+        self._sensor_editor.set_offset(index, delta)
+        self._reprocess_current()
+
+    @Slot(int)
+    def clearSensorEdit(self, index: int) -> None:
+        """Remove all overrides for sensor `index`."""
+        self._sensor_editor.clear(index)
+        self._reprocess_current()
+
+    @Slot()
+    def clearSensorEdits(self) -> None:
+        """Remove all sensor overrides."""
+        self._sensor_editor.clear()
+        self._reprocess_current()
+            
+    
+    

src/pygui/backend/crypto/__init__.py

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

src/pygui/backend/data/__init__.py

@@ -0,0 +1,16 @@
+# ===== Data Sub-package =====
+from pygui.backend.data.csv_recorder import CsvRecorder
+from pygui.backend.data.csv_file_metadata import CSVFileMetadata
+from pygui.backend.data.data_records import read_data_records, is_official_csv, read_official_csv
+from pygui.backend.data.data_segment import DataSegment
+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",
+    "DataSegment",
+    "FileBrowser",
+    "LocalSettings", "LocalSettingsModel",
+]

src/pygui/backend/data/constants.py

@@ -0,0 +1,3 @@
+# ===== Backend Data Constants =====
+
+DEFAULT_DATA_DIR_NAME = "isc_data"

src/pygui/backend/data/csv_file_metadata.py

@@ -25,8 +25,8 @@ class CSVFileMetadata:
         try:
             return datetime.strptime(self.date, date_format)
         except (ValueError, TypeError):
-            # If format is wrong or date is None, return current time
-            return datetime.now()
+            # If format is wrong or date is None, return None
+            return None
 
     # ===== Formatting =====
     @staticmethod
@@ -48,4 +48,5 @@ class CSVFileMetadata:
 
     def string_date_format(self) -> str:
         """Helper to ensure the date is always a string for JSON."""
-        return self.format_date(self.get_date())
+        dt = self.get_date()
+        return self.format_date(dt) if dt else self.date

src/pygui/backend/data/csv_recorder.py

@@ -0,0 +1,46 @@
+"""Append live frames"""
+from __future__ import annotations
+from datetime import datetime
+from pathlib import Path
+from typing import Optional, TextIO
+
+
+from pygui.backend.models.frame import Frame
+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
+        
+        
+    @property
+    def is_recording(self) -> bool:
+            return self._file_handle is not 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.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")
+        file_handle.write("X (mm)," + ",".join(str(s.x) for s in sensors) + "\n")
+        file_handle.write("Y (mm)," + ",".join(str(s.y) for s in sensors) + "\n")
+        file_handle.write("data\n")
+        file_handle.flush()
+        self._file_handle, self._path = file_handle, path
+        
+    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]
+        self._file_handle.write(",".join(row) + "\n")
+        self._file_handle.flush()
+        
+    def stop(self) -> Optional[str]:
+        if self._file_handle is None:
+            return None
+        self._file_handle.close()
+        path, self._file_handle, self._path = self._path, None, None
+        return path

src/pygui/backend/data/data_records.py

@@ -0,0 +1,66 @@
+"""Read the data section of a Z-wafer CSV into DataRecords, or the official headerless CSV."""
+from __future__ import annotations
+from pathlib import Path
+
+from pygui.backend.wafer.zwafer_models import DataRecord, Sensor
+
+def read_data_records(file_path: str) -> list[DataRecord]:
+    records: list[DataRecord] = []
+    in_data = False
+    with Path(file_path).open("r", encoding="utf-8") as file_handle:
+        for line in file_handle:
+            line = line.rstrip().rstrip(",").strip()
+            if not line:
+                continue
+            if not in_data:
+                if line.split(",")[0].lower() == "data":
+                    in_data = True
+                continue
+            cols = [c.strip() for c in line.split(",") if c.strip() != ""]
+            try:
+                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
+
+
+def is_official_csv(file_path: str) -> bool:
+    """Return True if the file uses the headerless official format (sensor-name header row, no 'data' sentinel)."""
+    with Path(file_path).open("r", encoding="utf-8") as f:
+        first = f.readline().rstrip().rstrip(",")
+    if not first:
+        return False
+    parts = [p.strip() for p in first.split(",") if p.strip()]
+    # Official format: first cell looks like "SensorN" (starts with letter, not key=value)
+    return bool(parts) and parts[0].lower().startswith("sensor") and "=" not in parts[0]
+
+
+def read_official_csv(file_path: str) -> tuple[list[Sensor], list[DataRecord]]:
+    """Parse the headerless official CSV: row 0 = sensor names, rows 1+ = values (no timestamp)."""
+    from pygui.backend.wafer.wafer_layouts import load_layout_for_wafer_id
+
+    stem = Path(file_path).stem
+    wafer_id = stem.split("-")[0] if "-" in stem else stem
+    try:
+        sensors = load_layout_for_wafer_id(wafer_id)
+    except KeyError:
+        return [], []
+
+    records: list[DataRecord] = []
+    with Path(file_path).open("r", encoding="utf-8") as f:
+        f.readline()  # skip sensor-name header
+        for i, line in enumerate(f):
+            line = line.rstrip().rstrip(",")
+            if not line:
+                continue
+            cols = [c.strip() for c in line.split(",") if c.strip()]
+            try:
+                values = [float(c) for c in cols]
+            except ValueError:
+                continue
+            if values:
+                records.append(DataRecord(time=float(i) * 0.5, values=values))
+    return sensors, records

src/pygui/backend/data/file_browser.py

@@ -8,8 +8,9 @@ from pathlib import Path
 from PySide6.QtCore import QObject, Property, QStandardPaths, Signal, Slot
 from PySide6.QtWidgets import QFileDialog, QMessageBox
 
-from backend.csv_file_metadata import CSVFileMetadata
-from backend.zwafer_parser import ZWaferParser
+from pygui.backend.data.csv_file_metadata import CSVFileMetadata
+from pygui.backend.wafer.zwafer_parser import ZWaferParser
+from pygui.backend.data.constants import DEFAULT_DATA_DIR_NAME
 
 
 # ===== File Browser Model =====
@@ -120,24 +121,49 @@ class FileBrowser(QObject):
         for csv_path in sorted(self._current_directory.glob("*.csv")):
             try:
                 metadata = self._load_metadata(csv_path)
+                wafer_type = metadata.get_wafer_type().upper() or (csv_path.stem[0].upper() if csv_path.stem else "")
+                date_str = metadata.string_date_format()
+                serial = metadata.wafer[1:] if len(metadata.wafer) > 1 else ""
+                if not serial:
+                    stem = csv_path.stem
+                    serial = stem[1:] if len(stem) > 1 else ""
+                if "-" in serial:
+                    serial = serial.split("-")[0]
+                if "_" in serial:
+                    serial = serial.split("_")[0]
+                time_str = date_str[11:] if len(date_str) > 10 else ""
                 self._files.append(
                     {
                         "selected": selected_state.get(str(csv_path), False),
+                        "baseName": csv_path.stem,
                         "wafer": metadata.wafer,
-                        "date": metadata.string_date_format(),
+                        "waferType": wafer_type,
+                        "serialNumber": serial,
+                        "date": date_str,
+                        "timeStr": time_str,
                         "chamber": metadata.chamber,
                         "notes": metadata.notes,
                         "masterType": master_state.get(str(csv_path), "") or metadata.master_type,
                         "fileName": str(csv_path),
-                        "highlight": metadata.get_wafer_type() in {"A", "B", "C"},
+                        "highlight": wafer_type in {"A", "B", "C"},
                     }
                 )
             except Exception:
+                stem = csv_path.stem
+                serial_fallback = stem[1:] if len(stem) > 1 else ""
+                if "-" in serial_fallback:
+                    serial_fallback = serial_fallback.split("-")[0]
+                if "_" in serial_fallback:
+                    serial_fallback = serial_fallback.split("_")[0]
                 self._files.append(
                     {
                         "selected": selected_state.get(str(csv_path), False),
-                        "wafer": csv_path.stem,
+                        "baseName": stem,
+                        "wafer": stem,
+                        "waferType": stem[0].upper() if stem else "",
+                        "serialNumber": serial_fallback,
                         "date": "",
+                        "timeStr": "",
                         "chamber": "",
                         "notes": "Unable to parse metadata",
                         "masterType": master_state.get(str(csv_path), ""),
@@ -168,25 +194,19 @@ class FileBrowser(QObject):
                 # Fall back to CSV/header parsing if sidecar is malformed.
                 pass
 
+        meta = self._metadata_from_filename(csv_path)
         parser_data, _ = self._parser.parse(str(csv_path))
         if parser_data is not None:
-            wafer = parser_data.serial or ""
-            date_text = ""
+            if parser_data.serial:
+                meta.wafer = parser_data.serial
             if parser_data.date != datetime.min:
-                date_text = CSVFileMetadata.format_date(parser_data.date)
-            return CSVFileMetadata(
-                wafer=wafer,
-                date=date_text,
-                chamber="",
-                notes="",
-                filename=str(csv_path),
-            )
+                meta.date = CSVFileMetadata.format_date(parser_data.date)
 
-        return self._metadata_from_filename(csv_path)
+        return meta
 
     def _metadata_from_filename(self, csv_path: Path) -> CSVFileMetadata:
         match = re.match(
-            r"^(?P<wafer>[^-]+)-(?P<date>\d{8})(?:_(?P<run>\d+))?$",
+            r"^(?P<wafer>[^-]+)-(?P<date>\d{8})(?:_(?P<time>\d{6}))?$",
             csv_path.stem,
         )
         if not match:
@@ -194,7 +214,9 @@ class FileBrowser(QObject):
 
         date_text = ""
         try:
-            parsed = datetime.strptime(match.group("date"), "%Y%m%d")
+            date_part = match.group("date")
+            time_part = match.group("time") or "000000"
+            parsed = datetime.strptime(date_part + time_part, "%Y%m%d%H%M%S")
             date_text = CSVFileMetadata.format_date(parsed)
         except ValueError:
             date_text = ""
@@ -211,7 +233,7 @@ class FileBrowser(QObject):
             QStandardPaths.DocumentsLocation
         )
         base_dir = Path(documents_dir) if documents_dir else (Path.home() / "Documents")
-        return base_dir / "isc_data"
+        return base_dir / DEFAULT_DATA_DIR_NAME
 
     def _set_current_directory(self, directory: Path) -> None:
         normalized = Path(directory)
@@ -236,7 +258,7 @@ class FileBrowser(QObject):
     def showInfo(self, message: str) -> None:
         self._show_info(message)
 
-    @Slot(str, result="QVariantMap")
+    @Slot(str, result=dict)
     def parseCsvMetadata(self, file_path: str) -> dict:
         from pathlib import Path as _Path
 

src/pygui/backend/data/local_settings_model.py

@@ -6,7 +6,8 @@ from typing import Any
 
 from PySide6.QtCore import QObject, Property, QDateTime, QStandardPaths, Signal, Slot
 
-from backend.local_settings import LocalSettings
+from pygui.backend.data.local_settings import LocalSettings
+from pygui.backend.data.constants import DEFAULT_DATA_DIR_NAME
 
 
 MASTER_FAMILIES = ("A", "B", "C", "D", "E", "F", "P", "X", "Z")
@@ -52,7 +53,7 @@ class LocalSettingsModel(QObject):
             QStandardPaths.DocumentsLocation
         )
         base_dir = Path(documents_dir) if documents_dir else (Path.home() / "Documents")
-        return base_dir / "isc_data"
+        return base_dir / DEFAULT_DATA_DIR_NAME
 
     def _new_defaults(self) -> dict[str, Any]:
         return {
@@ -221,7 +222,7 @@ class LocalSettingsModel(QObject):
         self.waferRetriesChanged.emit()
         self._recompute_derived()
 
-    @Property("QVariantMap", notify=mastersChanged)
+    @Property(dict, notify=mastersChanged)
     def masters(self) -> dict[str, str]:
         return dict(self._masters)
 

src/pygui/backend/models/__init__.py

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

src/pygui/backend/models/frame.py

@@ -0,0 +1,11 @@
+from __future__ import annotations
+from dataclasses import dataclass
+
+
+@dataclass(frozen=True)
+class Frame:
+    """One sample across all sensors ata a point in time"""
+
+    seq: int            # monotonically increasing
+    time: float             # seconds (relative or epoch)
+    values: list[float]  # one per sensor, in sensor-layout order

src/pygui/backend/models/frame_player.py

@@ -0,0 +1,51 @@
+from __future__ import annotations 
+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]:
+    """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)]
+
+class FramePlayer:
+    def __init__(self) -> None:
+        self._frames: list[Frame] =[]
+        self._i =0
+        
+    def load(self, frames: list[Frame]) -> "FramePlayer":
+        self._frames = frames
+        self._i = 0
+        return self
+    
+    @property
+    def total(self) -> int:
+        return len(self._frames)
+    
+    @property
+    def index(self) -> int:
+        return self._i 
+    
+    @property
+    def at_end(self) -> bool:
+        return self._i >= len(self._frames) -1
+    
+    def current(self) -> Frame | None:
+        if not self._frames:
+            return None
+        return self._frames[self._i]
+    
+    def _clamp(self, i:int):
+        return max(0, min(i, len(self._frames) - 1)) if self._frames else 0
+    
+    def step(self, delta: int) -> "FramePlayer":
+        self._i = self._clamp(self._i + delta)
+        return self
+    
+    def seek(self, i: int) -> "FramePlayer":
+        self._i = self._clamp(i)
+        return self
+
+    def next_frame_ms(self) -> float:
+        """Wall-clock ms until the next frame based on recorded timestamps; 0 if at end."""
+        if self._i + 1 >= len(self._frames):
+            return 0.0
+        return (self._frames[self._i + 1].time - self._frames[self._i].time) * 1000.0

src/pygui/backend/models/frame_stats.py

@@ -0,0 +1,37 @@
+"""Per-frame descriptive statistics"""
+
+from __future__ import annotations
+import math
+from dataclasses import dataclass
+
+
+@dataclass(frozen=True)
+class Stats:
+    min: float; min_index: int
+    max: float; max_index: int
+    diff: float; avg: float
+    sigma: float; three_sigma: float
+
+
+def compute_stats(values: list[float]) -> Stats:
+    clean = [(i, v) for i, v in enumerate(values) if not math.isnan(v)]
+    if not clean:
+        return Stats(0.0, -1, 0.0, -1, 0.0, 0.0, 0.0, 0.0)
+
+    min_index, min_v = min(clean, key=lambda iv: iv[1])
+    max_index, max_v = max(clean, key=lambda iv: iv[1])
+    nums = [v for _, v in clean]
+    avg = sum(nums) / len(nums)
+    variance = sum((v - avg) ** 2 for v in nums) / len(nums)
+    sigma = math.sqrt(variance)
+
+    return Stats(
+        min=min_v,
+        min_index=min_index,
+        max=max_v,
+        max_index=max_index,
+        diff=max_v - min_v,
+        avg=avg,
+        sigma=sigma,
+        three_sigma=3 * sigma,
+    )

src/pygui/backend/models/sensor_editor.py

@@ -0,0 +1,48 @@
+"""Per-session sensor value overrides (replacement and/or offset)."""
+
+from __future__ import annotations
+
+
+class SensorEditor:
+    def __init__(self) -> None:
+        self._replacements: dict[int, float] = {}
+        self._offsets: dict[int, float] = {}
+        
+        
+    def set_replacement(self, index: int, value: float) -> None:
+        """Force sensor `index` to read `value` for every frame this session."""
+        self._replacements[index] = value
+    
+    def set_offset(self, index: int, value: float) -> None:
+        """Shift sensor `index` by `delta` (applied after any replacement)."""
+        self._offsets[index] = value
+        
+    def clear(self, index: int | None = None) -> None:
+        """Remove overrides. Pass an index to clear one sensor; omit to clear all."""
+        if index is None:
+            self._replacements.clear()
+            self._offsets.clear()
+        else:
+            self._replacements.pop(index, None)
+            self._offsets.pop(index, None)
+    def has_overrides(self) -> bool:
+        return bool(self._replacements or self._offsets)
+    
+    def active_indices(self) -> list[int]:
+        """Return sorted sensor indices that have any override."""
+        return sorted(set(self._replacements) | set(self._offsets))
+    
+    
+    def apply(self, values: list[float]) -> list[float]:
+        """Return a new list wit all overrides applied (original unchanged)"""
+        if not self.has_overrides():
+            return list(values)            
+        result = list(values)
+        for i in range(len(result)):
+            v = result[i]
+            if i in self._replacements:
+                v = self._replacements[i]
+            if i in self._offsets:
+                v += self._offsets[i]
+            result[i] = v
+        return result

src/pygui/backend/models/session_model.py

@@ -0,0 +1,39 @@
+from __future__ import annotations
+from dataclasses import dataclass
+
+from pygui.backend.models.frame import Frame
+from pygui.backend.models.frame_stats import Stats, compute_stats
+from pygui.backend.models.stability_detector import StabilityDetector
+from pygui.backend.models.threshold_classifier import ThresholdConfig, classify, resolve_bounds
+
+@dataclass(frozen=True)
+class SessionUpdate:
+    seq: int
+    values: list[float]
+    bands: list[str]
+    stats: Stats
+    state: str
+    target: float
+    margin: float
+    
+class SessionModel:
+    def __init__(self, thresholds: ThresholdConfig | None = None) -> None:
+        self._config = thresholds or ThresholdConfig()
+        self._stability = StabilityDetector()
+        
+    def set_thresholds(self, config: ThresholdConfig) -> None:
+        self._config = config
+        
+    def reset(self) -> None:
+        self._stability.reset()
+        
+    def process(self, frame: Frame) -> SessionUpdate:
+        stats = compute_stats(frame.values)
+        target, margin = resolve_bounds(frame.values, self._config)
+        bands = [classify(v, target, margin)for v in frame.values]
+        # State always track the user's process set_point, even in auto-color mode.
+        state = self._stability.update(stats.avg, frame.time, self._config.set_point)
+        return SessionUpdate(
+            seq=frame.seq, values=frame.values, bands=bands, 
+            stats=stats, state=state, target=target, margin=margin,
+        )

src/pygui/backend/models/stability_detector.py

@@ -0,0 +1,34 @@
+"""Detect process state (Idle, Ramp, Set) from the running average temp"""
+from __future__ import annotations
+from typing import Optional
+
+STATE_IDLE = "idle"
+STATE_RAMP = "ramp"
+STATE_SET = "set"
+
+
+class StabilityDetector: 
+    def __init__(self, idle_below: float = 50.0, tolerance: float = 1.0, 
+                 settle_seconds: float = 10.0) -> None:
+        self._idle_below = idle_below
+        self._tolerance = tolerance
+        self._settle_seconds = settle_seconds
+        self._near_since: Optional[float] = None    # When avg entered the +- tolerance band
+        
+        
+    def reset(self) -> None:
+        self._near_since = None
+        
+    def update(self, avg: float, time: float, set_point: float) ->str:
+        if avg < self._idle_below:
+            self._near_since = None
+            return STATE_IDLE
+        if abs(avg - set_point) <= self._tolerance:
+            if self._near_since is None:
+                self._near_since = time 
+            if time - self._near_since >= self._settle_seconds:
+                return STATE_SET
+            return STATE_RAMP
+        self._near_since = None
+        return STATE_RAMP
+        

src/pygui/backend/models/threshold_classifier.py

@@ -0,0 +1,42 @@
+"""Classify sensor values into three bands around (target, margin)
+
+Auto mode derives target=mean, margin=1
+"""
+
+from __future__ import annotations
+import math
+from dataclasses import dataclass
+
+BAND_IN = "in_range"
+BAND_HIGH = "high" 
+BAND_LOW = "low"
+
+
+@dataclass(frozen=True)
+class ThresholdConfig:
+    set_point: float = 149.0   # process target: used as band TARGET when auto=False
+    margin: float = 1.0        # used as band MARGIN when auto=False
+    auto: bool = True         # auto=True: target=frame mean, margin=frame 1σ
+
+def resolve_bounds(values: list[float], cfg: ThresholdConfig) -> tuple[float, float]:
+    if not cfg.auto:
+        return cfg.set_point, cfg.margin
+    clean = [v for v in values if not math.isnan(v)]
+    if not clean:
+        return cfg.set_point, cfg.margin
+    mean = sum(clean) / len(clean)
+    variance = sum((v - mean) ** 2 for v in clean) / len(clean)
+    return mean, math.sqrt(variance)
+
+def classify(value: float, target: float, margin: float) -> str:
+    if math.isnan(value):
+        return BAND_IN
+    if value > target + margin:
+        return BAND_HIGH
+    if value < target - margin:
+        return BAND_LOW
+    return BAND_IN
+
+def classify_all(values: list[float], cfg: ThresholdConfig) -> list[str]:
+    target, margin = resolve_bounds(values, cfg)
+    return [classify(v, target, margin)for v in values ]

src/pygui/backend/visualization/__init__.py

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

src/pygui/backend/visualization/marching_squares.py

@@ -2,7 +2,7 @@ from typing import List, Tuple, Optional
 
 import numpy as np
 
-from backend.contour_models import ContourLine, ContourSegment
+from pygui.backend.visualization.contour_models import ContourLine, ContourSegment
 
 
 # ===== Contour Generation =====

src/pygui/backend/visualization/rbf_heatmap.py

@@ -0,0 +1,61 @@
+"""RBF (thin-plate spline) heatmap field.
+
+Uses CuPy for GPU acceleration when available, falls back to NumPy + SciPy.
+"""
+from __future__ import annotations
+
+import numpy as np
+from scipy.interpolate import RBFInterpolator
+
+try:
+    import cupy as _cupy  # type: ignore
+    BACKEND = "cupy"
+except Exception:
+    _cupy = None
+    BACKEND = "numpy"
+
+_KERNEL = "thin_plate_spline"
+_SMOOTHING = 0.0
+
+
+def interpolate_field(
+    xs: np.ndarray,
+    ys: np.ndarray,
+    vs: np.ndarray,
+    *,
+    width: int,
+    height: int,
+    extent: tuple[float, float, float, float],  # (xmin, xmax, ymin, ymax) in mm
+    round_clip: bool = False,
+) -> np.ndarray:
+    """Return a (height, width) float64 array of interpolated values.
+
+    Args:
+        xs, ys:      sensor positions in mm (1-D arrays, length N)
+        vs:          sensor values (length N)
+        width/height: output grid dimensions in pixels
+        extent:      (xmin, xmax, ymin, ymax) in the same mm space as xs/ys
+        round_clip:  if True, pixels outside the inscribed ellipse become NaN
+    """
+    coords = np.column_stack([xs, ys])
+    rbf = RBFInterpolator(coords, vs, kernel=_KERNEL, smoothing=_SMOOTHING)
+
+    xmin, xmax, ymin, ymax = extent
+    gx = np.linspace(xmin, xmax, width)
+    gy = np.linspace(ymin, ymax, height)
+    grid_x, grid_y = np.meshgrid(gx, gy)
+    flat = np.column_stack([grid_x.ravel(), grid_y.ravel()])
+
+    # RBFInterpolator always runs on CPU; CuPy only accelerates other ops if added later
+    field = rbf(flat).reshape(height, width)
+
+    if round_clip:
+        cx = (xmin + xmax) / 2
+        cy = (ymin + ymax) / 2
+        rx = (xmax - xmin) / 2
+        ry = (ymax - ymin) / 2
+        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)
+

src/pygui/backend/visualization/wafer_map_item.py

@@ -0,0 +1,511 @@
+"""QQuickPaintedItem wafer map — ported from the replay app's ReplayWidget.
+
+Draws:
+  • Radial ring template (concentric guides + crosshair axes + top notch)
+  • RBF heatmap layer (blended under markers via `blend` 0→1)
+  • Sensor marker circles colored by band (low/in_range/high)
+  • Numbered labels (toggle via `showLabels`)
+
+All sensor coordinates are center-origin mm (from wafer_layouts or a loaded CSV).
+"""
+from __future__ import annotations
+
+import math
+
+import numpy as np
+from PySide6.QtCore import Property, QPoint, Signal, Slot, Qt
+from PySide6.QtGui import (
+    QBrush, QColor, QFont, QImage, QPainter, QPen, QPolygon,
+)
+from PySide6.QtQml import QmlElement
+from PySide6.QtQuick import QQuickPaintedItem
+
+from pygui.backend.visualization.rbf_heatmap import interpolate_field
+from pygui.backend.wafer.zwafer_models import Sensor
+
+QML_IMPORT_NAME = "ISC.Wafer"
+QML_IMPORT_MAJOR_VERSION = 1
+
+
+@QmlElement
+class WaferMapItem(QQuickPaintedItem):
+    """Painted wafer map; driven by SessionController via QML property bindings."""
+
+    sensorsChanged  = Signal()
+    valuesChanged   = Signal()
+    bandsChanged    = Signal()
+    targetChanged   = Signal()
+    marginChanged   = Signal()
+    blendChanged    = Signal()
+    showLabelsChanged = Signal()
+    colorsChanged   = Signal()
+    shapeChanged    = Signal()
+    sizeChanged     = Signal()
+
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self._sensors:  list[Sensor] = []
+        self._values:   list[float]  = []
+        self._bands:    list[str]    = []
+        self._target:   float = 149.0
+        self._margin:   float = 1.0
+        self._blend:    float = 0.0
+        self._show_labels: bool = True
+        self._shape: str = "round"
+        self._size: float = 300.0
+
+        # Dark-theme color defaults (match Theme.qml tokens)
+        self._ring_color     = QColor("#2A3441")   # waferRingColor  (toneBorder)
+        self._axis_color     = QColor("#3A4D5C")   # waferAxisColor  (softBorder)
+        self._low_color      = QColor("#5B9DF5")   # sensorLow
+        self._in_range_color = QColor("#22C55E")   # sensorInRange
+        self._high_color     = QColor("#EF4444")   # sensorHigh
+        self._text_color     = QColor("#CBD5E1")   # bodyColor
+
+        # Internal draw state
+        self._markers: dict[int, tuple[int, int]] = {}  # sensor index → (px, py)
+        self._marker_r: int = 4
+        self._heatmap:  QImage | None = None
+
+        self.widthChanged.connect(self._on_resize)
+        self.heightChanged.connect(self._on_resize)
+
+    # ── Qt properties ────────────────────────────────────────────────────
+
+    @Property("QVariantList", notify=sensorsChanged)
+    def sensors(self) -> list:
+        return [{"label": s.label, "x": s.x, "y": s.y} for s in self._sensors]
+
+    @sensors.setter
+    def sensors(self, val: list) -> None:
+        self._sensors = [
+            Sensor(
+                label=d["label"],
+                x=float(d["x"]),
+                y=float(d["y"]),
+                side=d.get("side", "right"),
+                offset_x=float(d.get("offset_x", 0.0)),
+                offset_y=float(d.get("offset_y", 0.0))
+            )
+            for d in (val or [])
+        ]
+        self._rebuild()
+        self.sensorsChanged.emit()
+
+    @Property("QVariantList", notify=valuesChanged)
+    def values(self) -> list:
+        return self._values
+
+    @values.setter
+    def values(self, val: list) -> None:
+        self._values = list(val or [])
+        self._rebuild_heatmap()
+        self.valuesChanged.emit()
+        self.update()
+
+    @Property("QVariantList", notify=bandsChanged)
+    def bands(self) -> list:
+        return self._bands
+
+    @bands.setter
+    def bands(self, val: list) -> None:
+        self._bands = list(val or [])
+        self.bandsChanged.emit()
+        self.update()
+
+    @Property(float, notify=targetChanged)
+    def target(self) -> float:
+        return self._target
+
+    @target.setter
+    def target(self, val: float) -> None:
+        self._target = float(val)
+        self._rebuild_heatmap()
+        self.targetChanged.emit()
+        self.update()
+
+    @Property(float, notify=marginChanged)
+    def margin(self) -> float:
+        return self._margin
+
+    @margin.setter
+    def margin(self, val: float) -> None:
+        self._margin = float(val)
+        self._rebuild_heatmap()
+        self.marginChanged.emit()
+        self.update()
+
+    @Property(float, notify=blendChanged)
+    def blend(self) -> float:
+        return self._blend
+
+    @blend.setter
+    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:
+            self._rebuild_heatmap()
+        self.blendChanged.emit()
+        self.update()
+
+    @Property(bool, notify=showLabelsChanged)
+    def showLabels(self) -> bool:
+        return self._show_labels
+
+    @showLabels.setter
+    def showLabels(self, val: bool) -> None:
+        self._show_labels = bool(val)
+        self.showLabelsChanged.emit()
+        self.update()
+
+    @Property(str, notify=shapeChanged)
+    def shape(self) -> str:
+        return self._shape
+
+    @shape.setter
+    def shape(self, val: str) -> None:
+        self._shape = str(val).lower()
+        self._rebuild()
+        self.shapeChanged.emit()
+
+    @Property(float, notify=sizeChanged)
+    def size(self) -> float:
+        return self._size
+
+    @size.setter
+    def size(self, val: float) -> None:
+        self._size = float(val)
+        self._rebuild()
+        self.sizeChanged.emit()
+
+    # Colour properties — QML can bind these to Theme tokens
+    @Property(QColor, notify=colorsChanged)
+    def ringColor(self) -> QColor: return self._ring_color
+    @ringColor.setter
+    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
+    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
+    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
+    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
+    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
+    def textColor(self, c: QColor) -> None: self._text_color = c; self.update()
+
+    # ── slots ─────────────────────────────────────────────────────────────
+
+    @Slot(float, float, result=int)
+    def which_marker(self, x: float, y: float) -> int:
+        """Return the sensor index nearest to (x, y) within marker radius, else -1."""
+        r = max(self._marker_r, 6)
+        for idx, (mx, my) in self._markers.items():
+            if abs(mx - x) <= r and abs(my - y) <= r:
+                return idx
+        return -1
+
+    # ── internal ─────────────────────────────────────────────────────────
+
+    def _on_resize(self) -> None:
+        self._rebuild()
+
+    def _rebuild(self) -> None:
+        self._compute_markers()
+        self._rebuild_heatmap()
+        self.update()
+
+    def _draw_size(self) -> int:
+        return max(1, int(min(self.width(), self.height())))
+
+    def _center(self) -> tuple[int, int]:
+        return int(self.width() / 2), int(self.height() / 2)
+
+    def _wafer_radius_mm(self) -> float:
+        """Radius of the wafer bounding circle in mm (5% padding beyond outermost sensor)."""
+        if not self._sensors:
+            return 150.0
+        r = max(math.hypot(s.x, s.y) for s in self._sensors)
+        return r * 1.05
+
+    def _sensor_ring_radii_mm(self) -> list[float]:
+        """Distinct radial distances of sensor groups, sorted ascending, plus the outer boundary."""
+        if not self._sensors:
+            r = self._wafer_radius_mm()
+            return [r * f for f in (0.25, 0.50, 0.75, 1.0)]
+        # Cluster radii that are within 2 mm of each other into one ring; skip center point.
+        radii = sorted(r for r in {math.hypot(s.x, s.y) for s in self._sensors} if r > 1.0)
+        groups: list[float] = []
+        for r in radii:
+            if not groups or r - groups[-1] > 2.0:
+                groups.append(r)
+            else:
+                groups[-1] = (groups[-1] + r) / 2  # merge close values
+        # Always include the outer boundary ring so the wafer circle is drawn.
+        outer = self._wafer_radius_mm()
+        if not groups or outer - groups[-1] > 2.0:
+            groups.append(outer)
+        return groups
+
+    def _scale(self, ds: int, r_mm: float) -> float:
+        """Pixels per mm. The wafer radius maps to ds//2 - 24 px."""
+        return (ds / 2 - 24) / r_mm
+
+    def _to_px(self, x_mm: float, y_mm: float, cx: int, cy: int, scale: float) -> tuple[int, int]:
+        """Center-origin mm → pixel (top-left origin). Y is flipped."""
+        return cx + int(x_mm * scale), cy - int(y_mm * scale)
+
+    def _compute_markers(self) -> None:
+        ds = self._draw_size()
+        r_mm = self._wafer_radius_mm()
+        sc = self._scale(ds, r_mm)
+        cx, cy = self._center()
+        self._marker_r = max(3, ds // 70)
+        self._markers = {i: self._to_px(s.x, s.y, cx, cy, sc)
+                         for i, s in enumerate(self._sensors)}
+
+    def _rebuild_heatmap(self) -> None:
+        if not self._sensors or not self._values or self._blend == 0.0:
+            self._heatmap = None
+            return
+        ds = self._draw_size()
+        r_mm = self._wafer_radius_mm()
+        xs = np.array([s.x for s in self._sensors])
+        ys = np.array([s.y for s in self._sensors])
+        vs = np.array(self._values[:len(self._sensors)], dtype=float)
+        if len(vs) < len(self._sensors):
+            self._heatmap = None
+            return
+        try:
+            field = interpolate_field(
+                xs, ys, vs,
+                width=ds, height=ds,
+                extent=(-r_mm, r_mm, -r_mm, r_mm),
+                round_clip=(self._shape == "round"),
+            )
+        except Exception:
+            self._heatmap = None
+            return
+        self._heatmap = self._field_to_qimage(field, ds)
+
+    def _field_to_qimage(self, field: np.ndarray, ds: int) -> QImage:
+        """Apply a band-aware tri-color gradient → RGBA QImage."""
+        lo_b = self._target - self._margin
+        hi_b = self._target + self._margin
+        span = hi_b - lo_b or 1.0
+        # t: 0 = lo_b, 1 = hi_b (clipped)
+        t = np.clip((field - lo_b) / span, 0.0, 1.0)
+
+        def c(q: QColor) -> np.ndarray:
+            return np.array([q.redF(), q.greenF(), q.blueF()], dtype=np.float32)
+
+        lo_c = c(self._low_color)
+        mid_c = c(self._in_range_color)
+        hi_c = c(self._high_color)
+
+        t2 = t * 2  # 0→2 across full range
+
+        lower = t <= 0.5
+        t_lo = np.clip(t2,       0.0, 1.0)[:, :, np.newaxis]  # 0→1 in lower half
+        t_hi = np.clip(t2 - 1.0, 0.0, 1.0)[:, :, np.newaxis]  # 0→1 in upper half
+
+        rgb = np.where(
+            lower[:, :, np.newaxis],
+            lo_c * (1 - t_lo) + mid_c * t_lo,
+            mid_c * (1 - t_hi) + hi_c * t_hi,
+        )
+        # Outside the wafer circle `field` is NaN → NaN propagates into rgb. Alpha
+        # masks those pixels anyway, but zero them so the uint8 cast is well-defined.
+        rgb = np.nan_to_num(rgb, nan=0.0)
+        rgba = np.zeros((ds, ds, 4), dtype=np.uint8)
+        rgba[:, :, :3] = (rgb * 255).astype(np.uint8)
+        rgba[:, :, 3]  = np.where(np.isfinite(field), 210, 0).astype(np.uint8)
+
+        return QImage(rgba.tobytes(), ds, ds, QImage.Format.Format_RGBA8888).copy()
+
+    # ── paint ─────────────────────────────────────────────────────────────
+
+    def paint(self, painter: QPainter) -> None:
+        ds   = self._draw_size()
+        r_px = int(ds / 2 - 4)
+        cx, cy = self._center()
+
+        painter.setRenderHint(QPainter.RenderHint.Antialiasing)
+
+        self._paint_template(painter, cx, cy, r_px)
+
+        if self._heatmap and self._blend > 0.0:
+            painter.setOpacity(self._blend)
+            painter.drawImage(cx - self._heatmap.width() // 2,
+                              cy - self._heatmap.height() // 2, self._heatmap)
+            painter.setOpacity(1.0)
+
+        self._paint_markers(painter)
+
+    def _paint_template(self, painter: QPainter, cx: int, cy: int, r_px: int) -> None:
+        ds = self._draw_size()
+        r_mm = self._wafer_radius_mm()
+        sc = self._scale(ds, r_mm)
+
+        if self._shape == "square":
+            # Draw square boundary (thick pen)
+            border_pen = QPen(self._ring_color, 2, Qt.PenStyle.SolidLine)
+            painter.setPen(border_pen)
+            half_size_px = int(self._size / 2 * sc)
+            painter.drawRect(cx - half_size_px, cy - half_size_px, 2 * half_size_px, 2 * half_size_px)
+
+            # Crosshair axes
+            axis_pen = QPen(self._axis_color, 1, Qt.PenStyle.DashLine)
+            painter.setPen(axis_pen)
+            painter.drawLine(cx, cy - half_size_px, cx, cy + half_size_px)
+            painter.drawLine(cx - half_size_px, cy, cx + half_size_px, cy)
+
+            # Draw concentric square guide lines at the distinct radii of sensor rings
+            grid_pen = QPen(self._ring_color, 1, Qt.PenStyle.SolidLine)
+            painter.setPen(grid_pen)
+            for ring_r_mm in self._sensor_ring_radii_mm()[:-1]:  # exclude the outermost border
+                rr = max(1, int(ring_r_mm * sc))
+                painter.drawRect(cx - rr, cy - rr, 2 * rr, 2 * rr)
+        else:
+            # Concentric rings
+            ring_pen = QPen(self._ring_color, 1, Qt.PenStyle.SolidLine)
+            painter.setPen(ring_pen)
+            for ring_r_mm in self._sensor_ring_radii_mm():
+                rr = max(1, int(ring_r_mm * sc))
+                painter.drawEllipse(cx - rr, cy - rr, 2 * rr, 2 * rr)
+
+            # Crosshair axes
+            axis_pen = QPen(self._axis_color, 1, Qt.PenStyle.DashLine)
+            painter.setPen(axis_pen)
+            painter.drawLine(cx, cy - r_px, cx, cy + r_px)
+            painter.drawLine(cx - r_px, cy, cx + r_px, cy)
+
+            # Top notch triangle (wafer orientation marker)
+            nw = max(6, ds // 25)
+            nh = max(4, ds // 35)
+            notch = QPolygon([
+                QPoint(cx,           cy - r_px),
+                QPoint(cx - nw // 2, cy - r_px + nh),
+                QPoint(cx + nw // 2, cy - r_px + nh),
+            ])
+            painter.setPen(Qt.PenStyle.NoPen)
+            painter.setBrush(QBrush(self._axis_color))
+            painter.drawPolygon(notch)
+
+    def _paint_markers(self, painter: QPainter) -> None:
+        r = self._marker_r
+
+        # Scale font size based on the number of sensors to prevent overlap on dense wafers
+        num_sensors = len(self._sensors)
+        font_scale = 1.0
+        if num_sensors > 60:
+            font_scale = 0.7  # reduce font size by 30% for dense wafers
+        elif num_sensors > 40:
+            font_scale = 0.85
+
+        id_font = QFont()
+        id_font.setPointSize(max(4, int(r * font_scale)))
+        id_font.setBold(True)
+
+        temp_font = QFont()
+        temp_font.setPointSize(max(3, int((r - 1) * font_scale)))
+
+        band_color = {
+            "in_range": self._in_range_color,
+            "high":     self._high_color,
+            "low":      self._low_color,
+        }
+
+        for i, s in enumerate(self._sensors):
+            if i not in self._markers:
+                continue
+            px, py = self._markers[i]
+            color = band_color.get(
+                self._bands[i] if i < len(self._bands) else "in_range",
+                self._in_range_color,
+            )
+            # Filled circle with thin dark outline for contrast over heatmap
+            painter.setPen(QPen(QColor(0, 0, 0, 100), 1))
+            painter.setBrush(QBrush(color))
+            painter.drawEllipse(px - r, py - r, 2 * r, 2 * r)
+
+            if self._show_labels:
+                has_temp = i < len(self._values)
+
+                # Fetch text alignment side and offsets
+                side = getattr(s, "side", "right").lower()
+                ox = getattr(s, "offset_x", 0.0) * r
+                oy = getattr(s, "offset_y", 0.0) * r
+
+                # Pre-compute metrics using current scaled fonts
+                painter.setFont(id_font)
+                id_fm = painter.fontMetrics()
+                id_line_h = id_fm.height()
+                id_ascent = id_fm.ascent()
+
+                painter.setFont(temp_font)
+                temp_fm = painter.fontMetrics()
+                temp_line_h = temp_fm.height()
+                temp_ascent = temp_fm.ascent()
+
+                id_text = s.label
+                temp_text = f"{self._values[i]:.2f}" if has_temp else ""
+
+                id_w = id_fm.horizontalAdvance(id_text)
+                temp_w = temp_fm.horizontalAdvance(temp_text) if has_temp else 0
+                text_w = max(id_w, temp_w)
+
+                # Height of the 1 or 2-line text block
+                text_h = (id_line_h + temp_line_h) if has_temp else id_line_h
+
+                # Calculate box top-left (lx, ly) relative to dot center (px, py)
+                gap = 3
+                if side == "left":
+                    lx = px - r - gap - text_w - ox
+                    ly = py - text_h // 2 + oy
+                elif side == "top":
+                    lx = px - text_w // 2 + ox
+                    ly = py - r - gap - text_h - oy
+                elif side == "bottom":
+                    lx = px - text_w // 2 + ox
+                    ly = py + r + gap + oy
+                else: # "right" or default
+                    lx = px + r + gap + ox
+                    ly = py - text_h // 2 + oy
+
+                # Draw Sensor ID (first line)
+                painter.setFont(id_font)
+                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)
+                elif side == "left":
+                    painter.drawText(lx + (text_w - id_w), y1, id_text)
+                else:
+                    painter.drawText(lx, y1, id_text)
+
+                # Draw Temperature (second line)
+                if has_temp:
+                    painter.setFont(temp_font)
+                    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)
+                    elif side == "left":
+                        painter.drawText(lx + (text_w - temp_w), y2, temp_text)
+                    else:
+                        painter.drawText(lx, y2, temp_text)

src/pygui/backend/wafer/__init__.py

@@ -0,0 +1,10 @@
+# ===== Wafer Sub-package =====
+from pygui.backend.wafer.zwafer_models import ZWaferData, Sensor, DataRecord
+from pygui.backend.wafer.zwafer_parser import ZWaferParser
+from pygui.backend.wafer.wafer_layouts import load_layout, available_families
+
+__all__ = [
+    "ZWaferData", "Sensor", "DataRecord",
+    "ZWaferParser",
+    "load_layout", "available_families",
+]

src/pygui/backend/wafer/wafer_layouts.py

@@ -0,0 +1,163 @@
+"""Load wafer sensor layouts from bundled YAML files.
+
+YAML schema mirrors the replay app's wafer_desc.py format:
+  X/Y      — sensor positions in mm relative to x_origin/y_origin
+  size     — wafer diameter/edge in mm
+  shape    — "round" or "square"
+  start_sn — first sensor number (usually 1)
+  x_origin — "left" | "right" | "center"
+  y_origin — "bottom" | "top" | "center"
+
+Returned Sensor coords are center-origin mm (negative values toward the edge).
+"""
+from __future__ import annotations
+
+from pathlib import Path
+
+import yaml
+
+from pygui.backend.wafer.zwafer_models import Sensor
+
+_LAYOUTS_DIR = Path(__file__).parent.parent.parent / "assets" / "layouts"
+
+
+class WaferLayout(list):
+    """Subclass of list that carries wafer shape and size metadata."""
+    def __init__(self, sensors: list[Sensor], shape: str = "round", size: float = 300.0):
+        super().__init__(sensors)
+        self.shape = shape
+        self.size = size
+
+
+def resolve_shape_and_size(sensors: list[Sensor], wafer_id: str = "") -> tuple[str, float]:
+    """Helper to determine the shape and size of a sensor layout.
+
+    Tries matching by wafer_id prefix, falling back to the number of sensors.
+    """
+    if wafer_id:
+        prefix = wafer_id[0].upper()
+        for path in _LAYOUTS_DIR.glob("*.yaml"):
+            try:
+                data = _load_yaml(path)
+                if prefix in data.get("wafers", []):
+                    return data.get("shape", "round"), float(data.get("size", 300.0))
+            except Exception:
+                continue
+
+    # Fallback to sensor count mapping
+    n = len(sensors)
+    if n == 80:
+        return "square", 310.0
+    elif n == 65:
+        return "round", 300.0
+    elif n == 48:
+        return "round", 300.0
+    elif n == 29:
+        return "round", 200.0
+    elif n == 22:
+        return "round", 200.0
+
+    return "round", 300.0
+
+
+def _family_name(raw_name: str) -> str:
+    return raw_name.replace("wafer", "").strip("_")
+
+
+def _load_yaml(path: Path) -> dict:
+    with path.open(encoding="utf-8") as f:
+        return yaml.safe_load(f)
+
+
+def available_families() -> list[str]:
+    return [_family_name(_load_yaml(p)["name"]) for p in _LAYOUTS_DIR.glob("*.yaml")]
+
+
+def load_layout(family: str) -> WaferLayout:
+    for path in _LAYOUTS_DIR.glob("*.yaml"):
+        data = _load_yaml(path)
+        if _family_name(data["name"]) == family:
+            return _to_sensors(data)
+    raise KeyError(f"Unknown wafer family: {family!r}")
+
+
+def load_layout_for_wafer_id(wafer_id: str) -> WaferLayout:
+    """Match 'B00108' → bcdwafer by looking up the first char in each YAML's 'wafers' list."""
+    prefix = wafer_id[0].upper() if wafer_id else ""
+    for path in _LAYOUTS_DIR.glob("*.yaml"):
+        data = _load_yaml(path)
+        if prefix in data.get("wafers", []):
+            return _to_sensors(data)
+    raise KeyError(f"No layout found for wafer ID prefix {prefix!r}")
+
+
+def _to_sensors(data: dict) -> WaferLayout:
+    xs: list[float] = data["X"]
+    ys: list[float] = data["Y"]
+    size: float = float(data["size"])
+    shape: str = data.get("shape", "round")
+    start_sn: int = data.get("start_sn", 1)
+    reverse_x: bool = data.get("reverse_x", False)
+    reverse_y: bool = data.get("reverse_y", False)
+    x_orig: str = data.get("x_origin", "left")
+    y_orig: str = data.get("y_origin", "bottom")
+    label_exceptions = data.get("label_exceptions", {}) or {}
+
+    x_shift = {"left": size / 2, "right": -(size / 2), "center": 0.0}.get(x_orig, 0.0)
+    y_shift = {"bottom": size / 2, "top": -(size / 2), "center": 0.0}.get(y_orig, 0.0)
+
+    sensors: list[Sensor] = []
+    for i, (x_mm, y_mm) in enumerate(zip(xs, ys)):
+        if reverse_x:
+            x_mm = -x_mm
+        if reverse_y:
+            y_mm = -y_mm
+
+        x_coord = x_mm - x_shift
+        y_coord = y_mm - y_shift
+
+        # Determine label position defaults based on quadrants
+        sn = start_sn + i
+        side = "right"
+        offset_x = 0.0
+        offset_y = 0.0
+
+        # Check explicit label exception from layout config
+        if sn in label_exceptions:
+            exc = label_exceptions[sn]
+            if exc:
+                side_key = list(exc.keys())[0]
+                val = exc[side_key]
+                side = side_key
+                if isinstance(val, list) and len(val) >= 2:
+                    offset_x = float(val[0])
+                    offset_y = float(val[1])
+        else:
+            # Smart default quadrant positioning to keep labels pointing inward
+            if x_coord > 30.0 and y_coord > 30.0:
+                side = "left"
+                offset_y = -0.5
+            elif x_coord < -30.0 and y_coord > 30.0:
+                side = "right"
+                offset_y = -0.5
+            elif x_coord < -30.0 and y_coord < -30.0:
+                side = "right"
+                offset_y = 0.5
+            elif x_coord > 30.0 and y_coord < -30.0:
+                side = "left"
+                offset_y = 0.5
+            elif x_coord > 15.0:
+                side = "left"
+            elif x_coord < -15.0:
+                side = "right"
+
+        sensors.append(Sensor(
+            label=str(sn),
+            x=x_coord,
+            y=y_coord,
+            side=side,
+            offset_x=offset_x,
+            offset_y=offset_y,
+        ))
+    return WaferLayout(sensors, shape=shape, size=size)
+

src/pygui/backend/wafer/zwafer_models.py

@@ -9,6 +9,9 @@ class Sensor:
     label: str
     x: float
     y: float
+    side: str = "right"
+    offset_x: float = 0.0
+    offset_y: float = 0.0
 
 
 # ===== Data Row =====

src/pygui/backend/wafer/zwafer_parser.py

@@ -2,7 +2,7 @@ from pathlib import Path
 from typing import Tuple, Optional
 from datetime import datetime, timedelta
 
-from backend.zwafer_models import ZWaferData, Sensor
+from pygui.backend.wafer.zwafer_models import ZWaferData, Sensor
 
 
 # ===== Z-Wafer CSV Parser =====
@@ -32,7 +32,14 @@ class ZWaferParser:
 
     # ===== Header Parsing =====
     def _process_header(self, file_obj) -> ZWaferData:
-        """Parse header and sensor layout from open file object."""
+        """Parse header and sensor layout from open file object.
+        
+        Handles two CSV row orderings:
+          1. Label/X/Y rows BEFORE 'data' (fixture test format)
+          2. 'data' row BEFORE Label/X/Y (some real CSV files)
+        The C# parser handles both by collecting sensor layout rows
+        regardless of whether 'data' has been seen.
+        """
         wafer_data = ZWaferData()
         labels: Optional[list] = None
         x_coords: Optional[list] = None
@@ -47,26 +54,25 @@ class ZWaferParser:
             parts = [p.strip() for p in line.split(",")]
             first_part = parts[0].lower()
 
+            # Collect sensor layout rows (Label, X (mm), Y (mm))
+            # regardless of whether 'data' has been seen.
+            # This matches the C# parser behavior.
+            if first_part == "label":
+                labels = parts[1:]
+            elif first_part == "x (mm)":
+                x_coords = parts[1:]
+            elif first_part == "y (mm)":
+                y_coords = parts[1:]
+            # Parse metadata (key=value pairs) — only when not a sensor layout row
+            elif first_part != "data":
+                self._parse_header_line(wafer_data, parts)
+
             # Detect end of header section
             if first_part == "data":
                 wafer_data.csv_headers = labels or []
                 self._build_sensor_layout(wafer_data, labels, x_coords, y_coords)
                 return wafer_data
 
-            # Detect switch from metadata to sensor layout
-            # Parse metadata (key=value pairs)
-            if not self._parse_header_line(wafer_data, parts):
-                # If not metadata, it's part of sensor layout
-                label = parts[0].lower()
-                values = parts[1:]
-
-                if label == "label":
-                    labels = values
-                elif label == "x (mm)":
-                    x_coords = values
-                elif label == "y (mm)":
-                    y_coords = values
-
         return wafer_data  # Incomplete file — return partial data
 
     # ===== Metadata Parsing =====

src/pygui/serialcomm/__init__.py

@@ -1,6 +1,6 @@
 """Serial port communication layer for the temperature-sensing wafer."""
 
-from serialcomm.device_service import DeviceService
-from serialcomm.serial_port import SerialPort, WaferInfo
+from pygui.serialcomm.device_service import DeviceService
+from pygui.serialcomm.serial_port import SerialPort, WaferInfo
 
 __all__ = ["DeviceService", "SerialPort", "WaferInfo"]

src/pygui/serialcomm/device_service.py

@@ -11,8 +11,8 @@ from typing import Optional
 
 import serial.tools.list_ports
 
-from backend.local_settings import LocalSettings
-from serialcomm.serial_port import SerialPort, WaferInfo
+from pygui.backend.data.local_settings import LocalSettings
+from pygui.serialcomm.serial_port import SerialPort, WaferInfo
 
 log = logging.getLogger(__name__)
 
@@ -37,7 +37,58 @@ class DeviceService:
 
     def enumerate_ports(self) -> list[str]:
         """Return list of available serial port names."""
-        return [p.device for p in serial.tools.list_ports.comports()]
+        hardware_ports = [p.device for p in serial.tools.list_ports.comports()]
+        virtual_ports = []
+
+        # On macOS/Linux, also detect virtual loopback serial ports (PTYs) opened by socat
+        import platform
+        import subprocess
+        import re
+
+        if platform.system() in ("Darwin", "Linux"):
+            try:
+                # Find PTYs opened by socat
+                result = subprocess.run(
+                    ["lsof", "-c", "socat"],
+                    capture_output=True,
+                    text=True,
+                    check=False
+                )
+                if result.returncode == 0:
+                    for line in result.stdout.splitlines():
+                        parts = line.strip().split()
+                        if len(parts) >= 9:
+                            fd = parts[3]
+                            # Exclude standard FDs (0, 1, 2) which are typically the controlling terminal
+                            if fd.startswith(('0', '1', '2')):
+                                continue
+                            name = parts[-1]
+                            match = re.search(r'(/dev/(?:ttys\d+|pts/\d+))\b', name)
+                            if match:
+                                port = match.group(1)
+                                if port not in virtual_ports:
+                                    virtual_ports.append(port)
+            except Exception as e:
+                log.debug("Error listing virtual ports via lsof: %s", e)
+
+        # Prioritize physical USB serial interfaces first -> generic hardware -> virtual ports
+        # Virtual ports (PTYs detected via lsof) should NOT appear in hardware_ports,
+        # so we filter them out explicitly.
+        virtual_set = set(virtual_ports)
+        ordered_ports = []
+        for p in hardware_ports:
+            if "usbserial" in p.lower() or "usb" in p.lower() or "ttyusb" in p.lower():
+                if p not in ordered_ports:
+                    ordered_ports.append(p)
+        for p in hardware_ports:
+            if p not in ordered_ports and p not in virtual_set:
+                ordered_ports.append(p)
+        for p in virtual_ports:
+            if p not in ordered_ports:
+                ordered_ports.append(p)
+
+        return ordered_ports
+
 
     def detect_wafer(self, port: str) -> Optional[WaferInfo]:
         """Try to detect a wafer on the given port.

src/pygui/serialcomm/serial_port.py

@@ -46,15 +46,16 @@ class SerialPort:
         self._port_name = port_name
 
     # ------------------------------------------------------------------
-    # Context manager for scoped port access
+    # Port opening (shared between scoped and long-lived use)
     # ------------------------------------------------------------------
 
-    @contextmanager
-    def _open(self, timeout: float | None = None) -> Iterator[pyserial.Serial]:
-        """Open the serial port, yield it, then close on exit."""
-        port = pyserial.Serial(
-            self._port_name,
-            self.BAUDRATE,
+    @staticmethod
+    def open_port(port_name: str, timeout: float | None = None) -> pyserial.Serial:
+        """Open a serial port with baud-rate fallback.
+
+        Tries SerialPort.BAUDRATE first, falls back to 115200 on failure.
+        The caller owns the lifecycle of the returned Serial object."""
+        kwargs = dict(
             parity=pyserial.PARITY_NONE,
             bytesize=8,
             stopbits=pyserial.STOPBITS_ONE,
@@ -63,7 +64,22 @@ class SerialPort:
             dsrdtr=False,
         )
         if timeout is not None:
-            port.timeout = timeout
+            kwargs["timeout"] = timeout
+
+        try:
+            return pyserial.Serial(port_name, SerialPort.BAUDRATE, **kwargs)
+        except Exception as exc:
+            log.warning("Baud rate %d failed on %s, falling back to 115200: %s", SerialPort.BAUDRATE, port_name, exc)
+            return pyserial.Serial(port_name, 115200, **kwargs)
+
+    # ------------------------------------------------------------------
+    # Context manager for scoped port access
+    # ------------------------------------------------------------------
+
+    @contextmanager
+    def _open(self, timeout: float | None = None) -> Iterator[pyserial.Serial]:
+        """Open the serial port, yield it, then close on exit."""
+        port = self.open_port(self._port_name, timeout=timeout)
         try:
             yield port
         finally:

src/pygui/serialcomm/stream_reader.py

@@ -0,0 +1,259 @@
+"""Continuous serial frame reader (Live-mode source)"""
+from __future__ import annotations
+import logging
+import threading
+import time
+from typing import Callable
+
+from pygui.backend.models.frame import Frame
+from pygui.serialcomm.data_parser import _convert_hex_to_temp
+
+log = logging.getLogger(__name__)
+
+ParseFrame = Callable[[bytes, int], Frame]
+
+class StreamReader:
+    
+    def __init__(self, transport, parse_frame: ParseFrame,
+                on_frame: Callable[[Frame], None],
+                on_error: Callable[[Exception], None] | None = None,
+                family_code: str = "A") -> None:
+        self._transport = transport
+        self._parse = parse_frame
+        self._on_frame = on_frame
+        self._on_error = on_error or (lambda e: None)
+        self._family_code = family_code or "A"
+        self._thread: threading.Thread | None = None
+        self._stop = threading.Event()
+        self.error_count = 0
+        
+    def start(self) -> None:
+        self._stop.clear()
+        self._thread = threading.Thread(target=self._run, daemon = True)
+        self._thread.start()
+
+    def _read_chunk(self, min_bytes: int = 1) -> bytes:
+        """Read a chunk of available bytes from the transport.
+
+        Reads up to 256 bytes in one shot instead of byte-at-a-time,
+        falling back to single-byte reads with a yield when nothing is
+        immediately available."""
+        chunk = self._transport.read(max(min_bytes, 256))
+        if chunk:
+            return chunk
+        # Nothing available right now – yield briefly to avoid busy-spin.
+        b = self._transport.read(1)
+        if not b:
+            time.sleep(0.005)
+        return b
+
+    def _accumulate(self, needed: int) -> bytearray:
+        """Accumulate *needed* bytes using buffered reads."""
+        buf = bytearray()
+        while len(buf) < needed and not self._stop.is_set():
+            chunk = self._transport.read(needed - len(buf))
+            if not chunk:
+                time.sleep(0.005)
+                continue
+            buf.extend(chunk)
+        return buf
+
+    def _run(self) -> None:
+        try:
+            # Peek at the first few bytes to determine protocol.
+            peek_buf = bytearray()
+            while not self._stop.is_set() and len(peek_buf) < 32:
+                b = self._transport.read(1)
+                if not b:
+                    continue
+                peek_buf.extend(b)
+                if b[0] == 10:  # newline
+                    break
+
+            if self._stop.is_set() or not peek_buf:
+                return
+
+            raw = bytes(peek_buf)
+
+            # Binary sync bytes are the strongest signal.
+            if raw.startswith(b"\xaa\x88"):
+                self._run_binary(raw)
+                return
+
+            # Text-lines (CSV) requires BOTH a newline AND commas in the
+            # pre-newline content.  This avoids misclassifying a binary
+            # payload that happens to contain 0x2C as text.
+            has_newline = b"\n" in raw or b"\r" in raw
+            line_before_nl = raw.split(b"\n")[0].split(b"\r")[0]
+            if has_newline and b"," in line_before_nl:
+                self._run_text_lines(raw)
+                return
+
+            # Default: ASCII hex dump stream.
+            self._run_ascii(raw)
+        finally:
+            try:
+                self._transport.close()
+            except Exception:
+                pass
+
+    def _run_binary(self, initial_bytes: bytes) -> None:
+        log.info("StreamReader: starting binary stream parsing")
+        buf = bytearray(initial_bytes)
+
+        while not self._stop.is_set():
+            # Find sync marker in buffer.
+            idx = 0
+            synced = False
+            while idx < len(buf) - 1:
+                if buf[idx] == 0xAA and buf[idx + 1] == 0x88:
+                    synced = True
+                    break
+                idx += 1
+
+            if synced:
+                buf = buf[idx:]
+                # Accumulate header (5 bytes after sync).
+                while len(buf) < 7 and not self._stop.is_set():
+                    chunk = self._read_chunk()
+                    buf.extend(chunk)
+
+                if self._stop.is_set():
+                    return
+
+                payload_len = int.from_bytes(buf[5:7], byteorder='little')
+                total_packet_len = 2 + 5 + payload_len + 2
+
+                # Accumulate the rest of the packet in one buffered read.
+                remaining = total_packet_len - len(buf)
+                if remaining > 0:
+                    extra = self._accumulate(remaining)
+                    buf.extend(extra)
+
+                if self._stop.is_set():
+                    return
+
+                header = buf[2:7]
+                seq = int.from_bytes(header[1:3], byteorder='little')
+                payload = buf[7:7 + payload_len]
+
+                try:
+                    frame = self._parse(payload, seq)
+                    self._on_frame(frame)
+                except Exception as exc:
+                    self.error_count += 1
+                    if self.error_count <= 10:
+                        log.warning("Parse error on binary payload: %s", exc)
+                    self._on_error(exc)
+
+                buf = buf[total_packet_len:]
+            else:
+                # Resync: keep only trailing 0xAA if present, then read more.
+                if len(buf) > 0 and buf[-1] == 0xAA:
+                    buf = bytearray([0xAA])
+                else:
+                    buf.clear()
+
+                chunk = self._read_chunk()
+                buf.extend(chunk)
+
+    def _run_ascii(self, initial_bytes: bytes) -> None:
+        log.info("StreamReader: starting ASCII hex dump stream parsing")
+
+        valid_words = 80 if self._family_code == "X" else 244
+        block_words = 256
+        word_char_len = 4
+        chars_needed = block_words * word_char_len  # total hex chars per block
+
+        hex_chars = bytearray()
+        if initial_bytes:
+            for b in initial_bytes:
+                if chr(b) in "0123456789ABCDEFabcdef":
+                    hex_chars.append(b)
+                elif b == 0xAA:
+                    hex_chars.append(b)
+
+        seq = 0
+        while not self._stop.is_set():
+            # Accumulate a full block of hex characters using buffered reads.
+            while len(hex_chars) < chars_needed and not self._stop.is_set():
+                chunk = self._read_chunk(min_bytes=chars_needed - len(hex_chars))
+                for byte in chunk:
+                    if byte == 0xAA:
+                        # Sync marker appeared – hand off to binary parser.
+                        hex_chars.append(byte)
+                        break
+                    c = chr(byte)
+                    if c in "0123456789ABCDEFabcdef":
+                        hex_chars.append(c)
+                else:
+                    continue
+                break  # broke out of inner loop due to 0xAA
+
+            # Check for early termination (0xAA sync marker anywhere in buffer).
+            aa_idx = hex_chars.find(bytes([0xAA]))
+            if aa_idx >= 0:
+                log.info("StreamReader: Detected 0xAA at position %d, switching to binary mode.", aa_idx)
+                self._run_binary(hex_chars[aa_idx:])
+                return
+
+            # Parse words from the accumulated hex characters.
+            word_buffer = []
+            for i in range(0, min(len(hex_chars), chars_needed), word_char_len):
+                word_str = hex_chars[i:i + word_char_len]
+                if len(word_str) < word_char_len:
+                    break
+                word_buffer.append(bytes(word_str))
+
+            if not word_buffer:
+                time.sleep(0.01)
+                continue
+
+            hex_chars = hex_chars[len(word_buffer) * word_char_len:]
+
+            valid_hex_words = word_buffer[:valid_words]
+            values = []
+            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)
+                    values.append(t)
+                except Exception:
+                    values.append(0.0)
+
+            try:
+                frame = Frame(seq=seq, time=time.monotonic(), values=values)
+                self._on_frame(frame)
+                seq += 1
+            except Exception as exc:
+                log.error("Error emitting ASCII frame: %s", exc)
+
+    def _run_text_lines(self, initial_bytes: bytes) -> None:
+        log.info("StreamReader: starting line-by-line ASCII text parsing")
+        buf = bytearray(initial_bytes)
+        seq = 0
+
+        while not self._stop.is_set():
+            # Drain complete lines from the buffer.
+            while b"\n" in buf:
+                line_bytes, _, buf = buf.partition(b"\n")
+                line = line_bytes.decode('utf-8', errors='ignore').strip()
+                if line:
+                    try:
+                        frame = self._parse(line, seq)
+                        if frame:
+                            self._on_frame(frame)
+                            seq += 1
+                    except Exception as exc:
+                        self.error_count += 1
+                        self._on_error(exc)
+
+            # Read more data using buffered reads.
+            chunk = self._read_chunk()
+            buf.extend(chunk)
+
+    def stop(self) -> None:
+        self._stop.set()
+        if self._thread is not None and self._thread.is_alive():
+            self._thread.join(timeout = 2.0)
+            self._thread = None

tests/fixtures/sample_stream.csv

@@ -0,0 +1,9 @@
+Wafer ID=A12
+Acquisition Date=03/26/2025
+Label,1,2,3
+X (mm),0,10,-10
+Y (mm),10,-10,-10
+data
+0.0,149.0,148.5,150.6
+0.5,149.2,148.4,150.7
+1.0,149.1,148.6,150.5

tests/test_cluster_average.py

@@ -0,0 +1,52 @@
+"""Tests for src/pygui/backend/cluster_average.py."""
+import math
+import pytest
+from pygui.backend.cluster_average import average_clusters, group_sensors_by_radius
+from pygui.backend.wafer.zwafer_models import Sensor
+
+
+def test_members_take_cluster_mean():
+    vals = [10.0, 20.0, 100.0, 0.0]
+    clusters = [[0, 1], [2, 3]]
+    assert average_clusters(vals, clusters) == [15.0, 15.0, 50.0, 50.0]
+
+
+def test_unclustered_sensors_unchanged():
+    vals = [10.0, 20.0, 30.0]
+    assert average_clusters(vals, [[0, 1]]) == [15.0, 15.0, 30.0]
+
+
+def test_empty_clusters_is_identity():
+    assert average_clusters([1.0, 2.0], []) == [1.0, 2.0]
+
+
+def test_nan_handling_in_averaging():
+    vals = [10.0, float('nan'), 100.0, float('nan')]
+    clusters = [[0, 1], [2, 3]]
+    res = average_clusters(vals, clusters)
+    assert res[0] == 10.0
+    assert res[1] == 10.0
+    assert res[2] == 100.0
+    assert res[3] == 100.0
+
+
+def test_all_nan_cluster():
+    vals = [float('nan'), float('nan'), 5.0]
+    clusters = [[0, 1]]
+    res = average_clusters(vals, clusters)
+    assert math.isnan(res[0])
+    assert math.isnan(res[1])
+    assert res[2] == 5.0
+
+
+def test_group_by_radius():
+    sensors = [
+        Sensor(label="1", x=0.0, y=0.0),      # center (r=0)
+        Sensor(label="2", x=10.0, y=0.0),     # r=10
+        Sensor(label="3", x=0.0, y=10.5),     # r=10.5 (within 2mm)
+        Sensor(label="4", x=20.0, y=0.0),     # r=20
+    ]
+    # Center should be excluded or not grouped; other sensors grouped
+    clusters = group_sensors_by_radius(sensors, tolerance=2.0)
+    # Expected: 2 and 3 are in the same cluster because 10.5 - 10.0 <= 2.0.
+    assert [1, 2] in clusters

tests/test_csv_recorder.py

@@ -0,0 +1,40 @@
+from pygui.backend.data.csv_recorder import CsvRecorder
+from pygui.backend.data.data_records import read_data_records
+from pygui.backend.models.frame import Frame
+from pygui.backend.wafer.zwafer_models import Sensor
+from pygui.backend.wafer.zwafer_parser import ZWaferParser
+
+
+def test_recording_roundtrips_through_parser(tmp_path):
+    sensors = [Sensor("1", 0.0, 1.0), Sensor("2", 1.0, 0.0)]
+    path = tmp_path / "rec.csv"
+
+    rec = CsvRecorder()
+    rec.start(str(path), sensors, serial="A12")
+    rec.write(Frame(seq=0, time=0.0, values=[149.0, 148.0]))
+    rec.write(Frame(seq=1, time=0.5, values=[149.5, 148.5]))
+    rec.stop()
+
+    assert path.exists()
+    data, _ = ZWaferParser().parse(str(path))
+    assert data is not None
+    assert[s.label for s in data.sensors] == ["1", "2"]
+    assert len(data.csv_headers) == 2
+
+
+def test_recorded_data_rows_are_readable(tmp_path):
+    sensors = [Sensor("1", 0.0, 1.0), Sensor("2", 1.0, 0.0)]
+    path = tmp_path / "rec.csv"
+
+    rec = CsvRecorder()
+    rec.start(str(path), sensors, serial="A12")
+    rec.write(Frame(seq=0, time=0.0, values=[149.0, 148.0]))
+    rec.write(Frame(seq=1, time=0.5, values=[149.5, 148.5]))
+    rec.stop()
+
+    records = read_data_records(str(path))
+    assert len(records) == 2
+    assert records[0].time == 0.0
+    assert records[0].values == [149.0, 148.0]
+    assert records[1].time == 0.5
+    assert records[1].values == [149.5, 148.5]

tests/test_data_parser.py

@@ -1,7 +1,7 @@
 """Tests for serialcomm/data_parser.py binary parsing pipeline."""
 
 import pytest
-from serialcomm.data_parser import (
+from pygui.serialcomm.data_parser import (
     csv_column_count,
     parse_binary_data,
     convert_to_temperatures,
@@ -12,7 +12,6 @@ from serialcomm.data_parser import (
     MAXDUT_X,
 )
 
-
 # ── csv_column_count ──────────────────────────────────────────────────────────
 
 
@@ -203,6 +202,7 @@ class TestConvertToTemperatures:
     def test_p_family_single_block(self):
         data = _make_p_block(1, value=0x0100)
         hex_data = parse_binary_data(data, "P")
+        assert hex_data is not None
         result = convert_to_temperatures(hex_data, "P")
         assert len(result) == 1
         assert all(isinstance(v, str) for v in result[0])
@@ -270,9 +270,9 @@ class TestSaveToCsv:
             result = save_to_csv(data, family, f"{family}00001", str(tmp_path))
             assert result is not None, f"save_to_csv returned None for {family}"
             headers = open(result).readline().strip().split(",")
-            assert len(headers) == expected_cols, (
-                f"{family}: expected {expected_cols} headers, got {len(headers)}"
-            )
+            assert (
+                len(headers) == expected_cols
+            ), f"{family}: expected {expected_cols} headers, got {len(headers)}"
             assert headers[0] == "Sensor1"
             assert headers[-1] == f"Sensor{expected_cols}"
 

tests/test_data_records.py

@@ -0,0 +1,19 @@
+"""Tests for src/pygui/backend/data_records.py."""
+from pygui.backend.data.data_records import read_data_records
+
+
+def test_reads_rows_after_data_marker(tmp_path):
+    p = tmp_path / "s.csv"
+    p.write_text(
+        "Wafer ID=A12\n"
+        "Label,1,2\nX (mm),0,10\nY (mm),10,-10\n"
+        "data\n"
+        "0.0,149.0,148.5\n"
+        "0.5,149.2,148.4\n",
+        encoding="utf-8",
+    )
+    recs = read_data_records(str(p))
+    assert len(recs) == 2
+    assert recs[0].time == 0.0
+    assert recs[0].values == [149.0, 148.5]
+    assert recs[1].values == [149.2, 148.4]

tests/test_frame_player.py

@@ -0,0 +1,30 @@
+from pygui.backend.models.frame import Frame
+from pygui.backend.models.frame_player import FramePlayer
+
+def frames(n):
+    return [Frame(seq=i, time=float(i), values=[149.0 + i])for i in range(n)]
+
+def test_loads_and_reports_total():
+    p = FramePlayer(); p.load(frames(3))
+    assert p.total == 3 and p.index == 0 
+    current = p.current()
+    assert current is not None
+    assert current.values == [149.0]
+    
+def test_step_forward_and_back_clamps():
+    p = FramePlayer(); p.load(frames(3))
+    assert p.step(1).index == 1
+    assert p.step(1).index == 2
+    assert p.step(1).index == 2
+    assert p.step(-5).index == 0
+    
+def test_seek():
+    p = FramePlayer(); p.load(frames(5))
+    assert p.seek(3).index == 3
+    assert p.seek(99).index == 4
+    
+def test_at_end():
+    p = FramePlayer(); p.load(frames(2))
+    assert not p.at_end
+    p.seek(1)
+    assert p.at_end

tests/test_frame_stats.py

@@ -0,0 +1,22 @@
+import math
+import pytest
+from pygui.backend.models.frame_stats import compute_stats, Stats
+
+
+def test_basic_stat():
+    s = compute_stats([148.0, 150.0, 149.0])
+    assert s.min == 148.0 and s.min_index == 0
+    assert s.max == 150.0 and s.max_index == 1
+    assert s.diff == pytest.approx(2.0)
+    assert s.avg == pytest.approx(149.0)
+    assert s.sigma == pytest.approx(math.sqrt(2 / 3))
+    assert s.three_sigma == pytest.approx(3 * math.sqrt(2 / 3))
+
+
+def test_empty_values_returns_zeros():
+    s = compute_stats([])
+    assert s == Stats(0.0, -1, 0.0, -1, 0.0, 0.0, 0.0, 0.0)
+
+
+def test_ignores_nan():
+    s = compute_stats([149.0, float("nan"), 151.0])

tests/test_rbf_heatmap.py

@@ -0,0 +1,29 @@
+"""Tests for src/pygui/backend/rbf_heatmap.py."""
+import numpy as np
+from pygui.backend.visualization.rbf_heatmap import interpolate_field, BACKEND
+
+
+def test_field_shape_and_interpolates_at_sites():
+    xs = np.array([0.0, 10.0, -10.0, 0.0])
+    ys = np.array([10.0, -10.0, -10.0, 0.0])
+    vs = np.array([149.0, 150.0, 148.0, 149.5])
+    field = interpolate_field(xs, ys, vs, width=64, height=64,
+                              extent=(-15, 15, -15, 15))
+    assert field.shape == (64, 64)
+    assert np.isfinite(field).all()
+    assert field.min() <= 150.0 and field.max() >= 148.0
+
+
+def test_round_clip_produces_nans_outside_circle():
+    xs = np.array([0.0, 5.0, -5.0])
+    ys = np.array([5.0, -5.0, 0.0])
+    vs = np.array([149.0, 150.0, 148.0])
+    field = interpolate_field(xs, ys, vs, width=64, height=64,
+                              extent=(-15, 15, -15, 15), round_clip=True)
+    assert np.isnan(field).any()
+    # center pixel must be finite
+    assert np.isfinite(field[32, 32])
+
+
+def test_backend_reported():
+    assert BACKEND in ("cupy", "numpy")

tests/test_sensor_editor.py

@@ -0,0 +1,49 @@
+"""Tests for src/pygui/backend/sensor_editor.py."""
+import pytest
+from pygui.backend.models.sensor_editor import SensorEditor
+
+
+def test_replace_overrides_raw_value():
+    ed = SensorEditor()
+    ed.set_replacement(2, 150.0)     # index 2 forced to 150.0 regardless of raw
+    assert ed.apply([149.0, 149.0, 99.0]) == [149.0, 149.0, 150.0]
+
+
+def test_offset_shifts_raw_value():
+    ed = SensorEditor()
+    ed.set_offset(0, +0.5)
+    assert ed.apply([149.0, 149.0]) == [149.5, 149.0]
+
+
+def test_replace_and_offset_apply_in_order():
+    """Replacement wins over raw, then offset is added on top."""
+    ed = SensorEditor()
+    ed.set_replacement(2, 150.0)
+    ed.set_offset(2, +1.0)           # sensor 2: replace 99→150, then +1 → 151
+    ed.set_offset(0, +0.5)
+    out = ed.apply([149.0, 149.0, 99.0, 149.0])
+    assert out == [149.5, 149.0, 151.0, 149.0]
+
+
+def test_clear_single_index_restores_only_that_sensor():
+    ed = SensorEditor()
+    ed.set_replacement(0, 0.0)
+    ed.set_replacement(1, 0.0)
+    ed.clear(0)                       # clear only index 0
+    assert ed.apply([149.0, 149.0]) == [149.0, 0.0]
+
+
+def test_clear_restores_all():
+    ed = SensorEditor()
+    ed.set_offset(0, 5.0)
+    ed.set_replacement(1, 200.0)
+    ed.clear()
+    assert ed.apply([149.0, 149.0]) == [149.0, 149.0]
+
+
+def test_no_overrides_returns_copy():
+    ed = SensorEditor()
+    original = [149.0, 149.0]
+    result = ed.apply(original)
+    assert result == original
+    assert result is not original

tests/test_session_model.py

@@ -0,0 +1,28 @@
+from pygui.backend.models.frame import Frame
+from pygui.backend.models.threshold_classifier import ThresholdConfig, BAND_HIGH, BAND_IN, BAND_LOW
+from pygui.backend.models.session_model import SessionModel, SessionUpdate
+
+
+
+def test_manual_banding_and_stats():
+    model = SessionModel(ThresholdConfig(set_point=149.0, margin=1.0, auto=False))
+    update = model.process(Frame(seq=7, time=1.0, values=[151.0, 149.0, 147.0]))
+    assert update.seq == 7
+    assert update.bands == [BAND_HIGH, BAND_IN, BAND_LOW]
+    assert update.stats.avg == 149.0
+    assert (update.target, update.margin) == (149.0, 1.0)
+    assert update.state in ("idle", "ramp", "set")
+    
+def test_auto_banding_uses_mean_and_sigma():
+    model = SessionModel(ThresholdConfig(auto=True))
+    # Tight cluster around 149 -> small σ -> the 200.0 outlier reads HIGH
+    update = model.process(Frame(seq=0, time=0.0, values=[149.0, 149.0, 149.0, 200.0]))
+    assert update.bands[3] == BAND_HIGH
+    assert update.target == update.stats.avg
+    
+def test_set_thresholds_reband_on_next_frame():
+    m = SessionModel(ThresholdConfig(set_point=149.0, margin=1.0, auto=False))
+    m.set_thresholds(ThresholdConfig(set_point=149.0, margin=5.0, auto=False))
+    upd = m.process(Frame(seq=0, time=0.0, values=[151.0]))
+    assert upd.bands == [BAND_IN]
+    

tests/test_stability_detector.py

@@ -0,0 +1,35 @@
+from pygui.backend.models.stability_detector import (
+    StabilityDetector, STATE_IDLE, STATE_RAMP, STATE_SET,
+)
+
+
+SET_POINT = 149.0
+
+def make():
+    return StabilityDetector(idle_below = 50.0, tolerance=1.0, settle_seconds=2.0)
+
+def test_idle_when_cold():
+    d = make()
+    assert d.update(avg=25.0, time=0.0, set_point=SET_POINT) == STATE_IDLE
+    
+def test_ramp_while_far_from_setpoint():
+    d = make()
+    d.update(avg=100.0, time=0.0, set_point=SET_POINT)
+    
+def test_ramp_until_settle_time_elapses():
+    d = make()
+    assert d.update(avg=149.2, time=0.0, set_point=SET_POINT) == STATE_RAMP
+    assert d.update(avg=148.9, time=0.0, set_point=SET_POINT) == STATE_RAMP
+    
+def test_set_after_holding_near_setpoint():
+    d = make()
+    d.update(avg=149.2, time=0.0, set_point=SET_POINT)
+    d.update(avg=148.9, time=1.0, set_point=SET_POINT)
+    assert d.update(avg=149.0, time=2.5, set_point=SET_POINT) == STATE_SET
+
+
+def test_back_to_ramp_on_disturbance():
+    d = make()
+    for t in (0.0, 1.0, 2.5):
+        d.update(149.0, t, set_point=SET_POINT)
+    assert d.update(avg=160.0, time=3.0, set_point=SET_POINT) == STATE_RAMP

tests/test_stream_reader.py

@@ -0,0 +1,47 @@
+import time 
+from pygui.backend.models.frame import Frame
+from pygui.serialcomm.stream_reader import StreamReader
+
+class FakeTransport:
+    """Yield canned data then blocks (returns b'')."""
+    def __init__(self, lines):
+        self._data = b"".join(lines)
+        self._pos = 0
+        self.closed = False
+    def read(self, n=1):
+        time.sleep(0.001)
+        if self._pos >= len(self._data):
+            return b""
+        res = self._data[self._pos:self._pos+n]
+        self._pos += n
+        return res
+    def readline(self):
+        time.sleep(0.001)
+        if self._pos >= len(self._data):
+            return b""
+        idx = self._data.find(b"\n", self._pos)
+        if idx == -1:
+            res = self._data[self._pos:]
+            self._pos = len(self._data)
+            return res
+        res = self._data[self._pos:idx+1]
+        self._pos = idx + 1
+        return res
+    def close(self): self.closed = True
+    
+def parse_line(raw: str, seq: int) -> Frame:
+    parts = [float(x) for x in raw.split(",")]
+    return Frame(seq = seq, time = parts[0], values = parts[1:])
+
+def test_reads_frames_and_counts_errors():
+    got, errors = [], []
+    transport = FakeTransport([b"0.0,149,148\n", b"garbage\n", b"0.5,150,149\n"])
+    r = StreamReader(transport, parse_line,
+                    on_frame = got.append, on_error = lambda e: errors.append(e))
+    
+    r.start()
+    time.sleep(0.1)
+    r.stop()
+    assert [f.values for f in got] == [[149.0, 148.0], [150.0, 149.0]]
+    assert r.error_count == 1
+    assert transport.closed

tests/test_threshold_classifier.py

@@ -0,0 +1,29 @@
+import math
+
+from pygui.backend.models.threshold_classifier import (
+    ThresholdConfig, classify, classify_all, resolve_bounds,
+    BAND_IN, BAND_HIGH, BAND_LOW
+)
+
+
+def test_classify_about_target_margin():
+    assert classify(149.0, target=149.0, margin=1.0) ==BAND_IN      # exactly
+    assert classify(149.9, target=149.0, margin=1.0) ==BAND_IN      # within
+    assert classify(150.5, target=149.0, margin=1.0) ==BAND_HIGH    # 1.5 above
+    assert classify(147.5, target=149.0, margin=1.0) ==BAND_LOW     # 1.5 below
+    
+    
+def test_manual_bounds_use_set_point_and_margin():
+    cfg = ThresholdConfig(set_point=149.0, margin=1.0, auto=False)
+    assert resolve_bounds([200.0, 0.0], cfg) == (149.0, 1.0)
+    
+def test_auto_bounds_use_mean_and_sigma():
+    cfg = ThresholdConfig(auto=True)
+    target, margin = resolve_bounds([148.0, 150.0, 149.0], cfg)
+    assert target == 149.0
+    assert margin == math.sqrt(2 / 3) 
+    
+def test_classify_all_manual():
+    cfg = ThresholdConfig(set_point=149.0, margin=1.0, auto=False)
+    assert classify_all([149.0, 151.0, 147.0], cfg) == [BAND_IN, BAND_HIGH, BAND_LOW]
+    

tests/test_wafer_layouts.py

@@ -0,0 +1,21 @@
+"""Tests for src/pygui/backend/wafer_layouts.py."""
+import pytest
+from pygui.backend.wafer.wafer_layouts import load_layout, available_families
+from pygui.backend.wafer.zwafer_models import Sensor
+
+
+def test_lists_bundled_families():
+    fams = available_families()
+    assert "aep" in fams and "x" in fams
+
+
+def test_loads_sensors_in_mm():
+    sensors = load_layout("aep")
+    assert sensors and all(isinstance(s, Sensor) for s in sensors)
+    assert any(s.x < 0 for s in sensors)
+    assert max(abs(s.x) for s in sensors) < 200.0
+
+
+def test_unknown_family_raises():
+    with pytest.raises(KeyError):
+        load_layout("nope")

uv.lock

@@ -1,6 +1,19 @@
 version = 1
 revision = 3
 requires-python = ">=3.11"
+resolution-markers = [
+    "python_full_version >= '3.14' and sys_platform == 'darwin'",
+    "python_full_version < '3.14' and sys_platform == 'darwin'",
+    "python_full_version >= '3.14' and sys_platform == 'win32'",
+    "python_full_version < '3.14' and sys_platform == 'win32'",
+    "python_full_version >= '3.14' and sys_platform == 'linux'",
+    "python_full_version < '3.14' and sys_platform == 'linux'",
+]
+supported-markers = [
+    "sys_platform == 'darwin'",
+    "sys_platform == 'win32'",
+    "sys_platform == 'linux'",
+]
 
 [[package]]
 name = "colorama"
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 ]
 
+[[package]]
+name = "contourpy"
+version = "1.3.3"
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+]
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