autoemx.runners.annotate_particle_images module

Annotate the particle and frame images of a sample with the X-ray spectrum spots and the particles found.

During acquisition, particle and frame images are saved without annotations (unless annotate_particle_images=True), while the pixel position of every spectrum spot, and of every particle found in a frame, is stored in the sample ledger. This runner draws each spot as a dot with its spectrum ID, and each particle found in a frame (particle size statistics, or frames searched for EDS particles) as a circle with its particle number, as done during acquisition, plus a scale bar when the pixel size is known.

Annotated copies are written to SEM images/annotated; the original images are not modified.

Import this module in your own code and call annotate_particle_images(), or use the script Annotate_Particle_Images.py.

Workflow

  • Loads the sample ledger and the images SEM images/<sample>_par<N>_fr<F>_xyspots.<ext> (or <sample>_fr<F>_xyspots.<ext> for grid/linescan acquisitions).

  • Finds the spectra acquired on each image: same particle (or same frame, for images without particle).

  • Draws a dot + spectrum ID at the pixel position of each spectrum, and a scale bar.

  • Annotates the frame images recorded in the ledger (particle_stats, particle_stats_progress, eds_size_scans) with their particles (particle_marks_px).

Notes

  • The un-annotated image is used: the <name>_raw.<ext> copy if present, or the raw page of a two-page TIFF. Images saved with annotations and without raw copy are annotated again.

  • The pixel size used for the scale bar is read from the ledger (image_pixel_size_um of the particle) or, for older samples and images without particle, from the image metadata. Without it, no scale bar is drawn.

Created on Mon Oct 5 2026

@author: Andrea

autoemx.runners.annotate_particle_images.annotate_particle_images(sample_path: str | None = None, sample_ID: str | None = None, results_path: str | None = None, output_dir: str | None = None, scalebar: bool = True, overwrite: bool = True, verbose: bool = True) → List[str][source]

Write copies of the particle images of a sample annotated with the X-ray spectrum spots, and of its frame images annotated with the particles found in them.

Parameters:

  • sample_path (str, optional) – Full path to the sample folder (containing ledger.json).

  • sample_ID (str, optional) – Sample identifier, used with results_path when sample_path is not given.

  • results_path (str, optional) – Directory under which the sample_ID folder is searched. Default: ./Results

  • output_dir (str, optional) – Folder for the annotated images. Default: SEM images/annotated in the sample folder.

  • scalebar (bool, optional) – Whether to draw a scale bar (when the pixel size is known). Default: True.

  • overwrite (bool, optional) – Whether to overwrite existing annotated images. Default: True.

  • verbose (bool, optional) – Whether to log progress. Default: True.

Returns:

written – Paths of the annotated images.

Return type:

list of str