Add layout files for various wafers: aepwafer, bcdwafer, fwafer, xwafer, zwafer, and zwafer_rev

- Add stability detection and threshold classification features with corresponding tests

.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"
+    ]
+}

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] },
+}

pyproject.toml

@@ -1,3 +1,8 @@
+# ===== Build System =====
+[build-system]
+requires = ["setuptools>=61"]
+build-backend = "setuptools.build_meta"
+
 # ===== Project Metadata =====
 [project]
 name = "pygui"
@@ -6,9 +11,50 @@ version = "0.1.0"
 [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/serialcomm/__init__.py",
+    "src/pygui/serialcomm/data_parser.py",
+    "src/pygui/serialcomm/device_service.py",
+    "src/pygui/serialcomm/serial_port.py",
+]
 
 [dependency-groups]
 dev = [

src/pygui/ISC/Theme.qml

@@ -92,6 +92,13 @@ QtObject {
     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 ? "#589DF5" : "#2F6FE0"
+    readonly property color waferRingColor: toneBorder
+    readonly property color waferAxisColor: softBorder
+
     // ── 11. Geometry ─────────────────────────────────────────────────────────
     // Radius
     readonly property int radiusXs: 4   // fields, tight elements

src/pygui/__main__.py

@@ -5,13 +5,14 @@ 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.device_controller import DeviceController
+from pygui.backend.local_settings import LocalSettings
+from pygui.backend.local_settings_model import LocalSettingsModel
+from pygui.backend.file_browser import FileBrowser
+
 
 # ===== Application Entry Point =====
-if __name__ == "__main__":
+def main() -> int:
     # ===== UI Style Setup =====
     # Use a non-native controls style so our custom QML button backgrounds are supported.
     QQuickStyle.setStyle("Basic")
@@ -35,11 +36,17 @@ if __name__ == "__main__":
     engine.rootContext().setContextProperty("deviceController", device_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/backend/device_controller.py

@@ -15,17 +15,17 @@ 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.data_model import TemperatureTableModel
+from pygui.backend.graph_view import GraphView
+from pygui.backend.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
 
 log = logging.getLogger(__name__)
 

src/pygui/backend/file_browser.py

@@ -8,8 +8,8 @@ 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.csv_file_metadata import CSVFileMetadata
+from pygui.backend.zwafer_parser import ZWaferParser
 
 
 # ===== File Browser Model =====

src/pygui/backend/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
+    t: float             # seconds (relative or epoch)
+    values: list[float]  # one per sensor, in sensor-layout order

src/pygui/backend/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/local_settings_model.py

@@ -6,7 +6,7 @@ from typing import Any
 
 from PySide6.QtCore import QObject, Property, QDateTime, QStandardPaths, Signal, Slot
 
-from backend.local_settings import LocalSettings
+from pygui.backend.local_settings import LocalSettings
 
 
 MASTER_FAMILIES = ("A", "B", "C", "D", "E", "F", "P", "X", "Z")

src/pygui/backend/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.contour_models import ContourLine, ContourSegment
 
 
 # ===== Contour Generation =====

src/pygui/backend/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/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/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.zwafer_models import ZWaferData, Sensor
 
 
 # ===== Z-Wafer CSV Parser =====

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.local_settings import LocalSettings
+from pygui.serialcomm.serial_port import SerialPort, WaferInfo
 
 log = logging.getLogger(__name__)
 

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_frame_stats.py

@@ -0,0 +1,22 @@
+import math
+import pytest
+from pygui.backend.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_stability__detector.py

@@ -0,0 +1,35 @@
+from pygui.backend.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_threshold_classifier.py

@@ -0,0 +1,29 @@
+import math
+
+from pygui.backend.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]
+