nanodevice-flakedetect-commit

name	nanodevice_flakedetect_commit
description	Insert detected flake polygons into KLayout as GDS geometry using the geometry skill's add_polygon.py. Use after combine completes to commit traces.json contours as polygons on the correct layers.

nanodevice_flakedetect_commit — KLayout Polygon Insertion

Pure agent workflow using existing skills and MCP tools. No custom scripts needed.

Scope: This workflow is for pre-gdsalign only. If you have already run nanodevice_gdsalign, use the contour_gds coordinates from traces_gds.json directly and do not apply the image-center transform described below.

When to Use

After the combine step completes. Requires traces.json from <out>/combine/.

Prerequisites

• KLayout running with KlayoutClaw plugin (v0.5+)
• A layout open (use create_layout MCP tool if needed)
• Background image loaded (use image skill's add_image.py)
• traces.json produced by the combine step

Commit Protocol

Step 1: Load background image

NOTE: The add_image.py script uses the MCP client which does NOT work from inside a Docker container. Instead, use execute_script directly to load the image:

filepath = "/path/to/full_stack_raw.jpg"
pixel_size = 0.087  # um/px

img = pya.Image(filepath)
img.visible = True
w_um = img.width() * pixel_size
h_um = img.height() * pixel_size
img.set_pixel_width(pixel_size)
img.set_pixel_height(pixel_size)
# Center the image at (0, 0)
img.trans = pya.DCplxTrans(1.0, 0, False, pya.DVector(-w_um / 2.0, -h_um / 2.0))
_layout_view.insert_image(img)
_refresh_view()
result = f"Image loaded: {w_um:.1f} x {h_um:.1f} um, centered at origin"

Step 2: Read traces.json

Load <out>/combine/traces.json. Extract:

• image_size_um — [w_um, h_um] for coordinate transform
• layer_map — material name → "layer/datatype" string
• materials — per-material contour lists with contour_um coordinates

Step 3: Coordinate transform

Contours in traces.json use image-origin coordinates (0,0 at top-left, y-axis pointing down, units in microns).

KLayout uses centered coordinates (0,0 at image center, y-axis pointing up, units in microns).

Transform each point:

kl_x = img_x_um - w_um / 2
kl_y = h_um / 2 - img_y_um

The y-axis sign flip (h_um/2 - img_y_um) is the most common source of errors.

Step 4: Add polygons via execute_script

NOTE: The add_polygon.py script uses the MCP client which does NOT work from inside a Docker container. Instead, use execute_script to add polygons directly:

import json

with open("<out>/combine/traces.json") as f:
    traces = json.load(f)

w_um, h_um = traces["image_size_um"]
top_cell = _layout.top_cell()

for material in traces["stack"]:
    layer_str = traces["layer_map"][material]  # e.g. "10/0"
    layer_num, dt = [int(x) for x in layer_str.split("/")]
    li = _layout.layer(layer_num, dt)

    for region in traces["materials"][material]:
        pts = []
        for x_um, y_um in region["contour_um"]:
            kl_x = x_um - w_um / 2.0
            kl_y = h_um / 2.0 - y_um  # Y-axis flip!
            pts.append(pya.DPoint(kl_x, kl_y))
        top_cell.shapes(li).insert(pya.DPolygon(pts))

_refresh_view()
result = f"Committed polygons for {len(traces['stack'])} materials"

This is faster and more reliable than calling add_polygon.py for each material, and works from inside Docker containers.

Step 5: Verify with screenshot

Use the MCP screenshot tool to capture the viewport and visually confirm polygons align with the background image:

mcp__klayoutclaw__screenshot → view the PNG

Layer Assignments

Material	Layer	Color
top_hBN	10/0	green
graphene	11/0	red
bottom_hBN	12/0	blue-ish
graphite	13/0	yellow

These defaults come from traces.json layer_map — always use the values from the JSON, not hardcoded.

Common Pitfalls

1. Y-axis flip: kl_y = h_um/2 - img_y_um — forgetting the sign flip puts polygons upside down.
2. MCP client scripts fail in Docker: add_polygon.py and add_image.py connect to KLayout MCP on localhost, which doesn't work from inside a container. Always use execute_script instead (shown above).
3. Cell name: When using execute_script, use _layout.top_cell() to get the current top cell — don't hardcode a cell name.
4. Background centering: The image must be centered at KLayout's (0,0) origin so that the coordinate transform kl_x = x_um - w_um/2 aligns correctly.
5. Large contours: Some materials (bottom_hBN) can have 5000+ contour points. Use execute_script with the full polygon — it handles large point arrays efficiently.