autoemx.core.em_runtime.sample_finder module

Electron Microscope Sample Finder module.

Provides utilities for locating and managing samples within the EM, particularly for detecting carbon tape position and dimensions.

Classes

EM_Sample_Finder

Utilities for locating samples and detecting carbon tape.

Created on 2026 @author: Andrea

class autoemx.core.em_runtime.sample_finder.EM_Sample_Finder(microscope_ID: str, center_pos: ndarray | tuple | list, sample_half_width_mm: float, substrate_width_mm: float, development_mode: bool | None = False, results_dir: str | None = None, verbose: bool = False)[source]

Bases: object

Class for locating and managing samples in an electron microscope (EM).

Provides methods for detecting sample features (such as the center and size of a C tape) using the microscope’s navigation camera.

Variables:

  • microscope_ID (str) – Identifier for the target microscope.

  • center_pos (np.ndarray) – Initial center position of sample as [x, y] coordinates in mm.

  • results_dir (Optional[str]) – Directory path to save results, or None if not set.

  • verbose (bool) – If True, enables detailed debug output.

  • development_mode (bool) – If True, enables offline testing without real-time acquisition.

Example

>>> import numpy as np
>>> sample_center = np.array([0.0, 0.0])
>>> finder = EM_Sample_Finder(
...     microscope_ID='MySEM',
...     center_pos=sample_center,
...     sample_half_width_mm=3,
...     substrate_width_mm=12,
...     results_dir='./results',
...     verbose=True
... )
>>> ctape_result = finder.detect_Ctape()
>>> if ctape_result is not None:
...     center_pos, sample_hw_mm = ctape_result
...     print("C tape center (mm):", center_pos)
...     print("C tape half-width (mm):", sample_hw_mm)

Notes

  • The navigation camera image can be provided directly (for offline testing) or acquired live from the microscope.

  • For successful detection, the microscope calibration file must include: ‘navcam_im_w_mm’, ‘navcam_x_offset’, ‘navcam_y_offset’.

detect_Ctape(navcam_im: ndarray | None = None) → Tuple[ndarray, float] | None[source]

Detect the effective center position and radius of the C tape.

Uses the provided navigation camera image or acquires it from the microscope. Applies edge detection and circle fitting to locate the tape.

Parameters:

navcam_im (Optional[np.ndarray]) – Navigation camera image. If None, acquires from microscope.

Returns:

Tuple of (center_pos, sample_hw_mm) if detection successful, else None.

Return type:

Optional[Tuple[np.ndarray, float]]