profile module

profile.py

Functions for extracting and fitting a Gaussian profile sparse electron datasets.

profile.extract_3x3_patches(original_frames, processed_frames)

Extract 3x3 patches from original frames based on hits identified in processed frames.

Parameters:

• original_frames (ndarray) – Array of original frames (non-baseline-subtracted, non-thresholded).

• processed_frames (ndarray) – Array of processed frames (baseline-subtracted and thresholded).

Returns:

Array of 3x3 patches centered around identified hits.

Return type:

ndarray

profile.gaussian_profile(file_path, nframes, baseline, th_single_elec, plot_results=True)

Process frames to extract the average 3x3 patch of electron hits, fit it to a Gaussian, and return the optimized Gaussian parameters and patches.

Parameters:

• file_path (str) – Path to the HDF5 file containing the frames.

• nframes (int) – Number of frames to process.

• baseline (float) – Baseline value to subtract from frames.

• th_single_elec (float) – Threshold for identifying single electron hits.

• plot_results (bool, optional) – Plot the original average patch, the optimized Gaussian, and their difference. (default: True).

Returns:

• ndarray: Average 3x3 patch from identified hits.

• ndarray: The 3x3 Gaussian patch after fitting to the Gaussian model.

• float: Optimized Gaussian amplitude (A_opt).

• float: Optimized Gaussian standard deviation (sigma_opt).

Return type:

tuple

profile.randomized_scan_order(nrows, ncols)

Generate a randomized order of pixel indices for scanning.

Parameters:

• nrows (int) – Number of rows in the frame.

• ncols (int) – Number of columns in the frame.

Returns:

List of (row, col) tuples in randomized order, excluding edges.

Return type:

list