coseda.centerrefinement package

Submodules

coseda.centerrefinement.cancellation module

Shared helpers for cooperative cancellation of long-running refinement jobs.

exception coseda.centerrefinement.cancellation.RefinementCancelled

Bases: Exception

Raised when a user requests to stop an in-flight refinement.

add_note()

Exception.add_note(note) – add a note to the exception

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

coseda.centerrefinement.cancellation.check_cancel(stop_event, where='')

Raise RefinementCancelled if the provided stop_event is set.

Parameters:

• stop_event (threading.Event or None) – Event used to request cancellation. If None, no check is performed.

• where (str) – Optional string describing the current phase, helpful for logging.

coseda.centerrefinement.refinecenters_beamstop module

coseda.centerrefinement.refinecenters_beamstop.output(indices, deviations, graphicsfolder_path, logfile_path, itcount, index_length=None)

Save deviations for GUI.

coseda.centerrefinement.refinecenters_beamstop.perform_lowess(indices, deviations, frac=0.1)

Perform LOWESS smoothing on deviations.

coseda.centerrefinement.refinecenters_beamstop.plot_deviations(indices, deviations, graphicsfolder_path, itcount, lowess_frac=0.1)

Plot deviations with LOWESS fit.

coseda.centerrefinement.refinecenters_beamstop.plot_lowess_and_centers(lowess_fit_x, lowess_fit_y, original_center_x, original_center_y, existing_indices, itcount, graphicsfolder_path)

Plot LOWESS fits and original centers.

coseda.centerrefinement.refinecenters_beamstop.refine(configfile, client, batch_size=500, stop_event=None)

Main center refinement function.

coseda.centerrefinement.refinecenters_beamstop.refine_center_with_friedel_and_update(h5file_path, min_peaks, tolerance, resolution_limit, itcount, convergence_threshold, converged, graphicsfolder_path, logfile_path, client, lowess_frac=0.1, lowess_window=None, batch_size=500, stop_event=None, detector_geometry=None, max_pairs_per_frame=None, deviation_aggregation='median')

Refine centers using Friedel pairs and update the HDF5 file.

coseda.centerrefinement.refinecenters_beamstop.refine_center_with_friedel_batch(h5file_path, min_peaks, tolerance, resolution_limit, indices_subset, centers_x, centers_y, index_map, detector_geometry=None, max_pairs_per_frame=None)

Process a subset of frames (indices_subset, which are original frame numbers) to find deviations.

coseda.centerrefinement.refinecenters_beamstop.refinecenters_batch(input_path, usedask=False, batch_size=500, stop_event=None)

Process all configuration files for center refinement.

coseda.centerrefinement.refinecenters_direct module

coseda.centerrefinement.refinecenters_direct.lowess_xunit(x, y, xout, span)

Custom LOESS smoothing using a fixed window span in x-units. x, y: original data arrays. xout: points at which to evaluate the fit (subset of x). span: half-window width in the same units as x. Returns array of shape (len(xout), 2) with columns (xout, smoothed y).

coseda.centerrefinement.refinecenters_direct.output_direct(indices, coarse, fine, outputfolder_path, logfile_path, loess_span=None, loess_frac=None, total_frames=None, iteration=0)

Outputs direct refinement results to numpy files.

Parameters:

• loess_span (float)

• loess_frac (float)

• total_frames (int)

• iteration (int)

coseda.centerrefinement.refinecenters_direct.quadrant_var_cost(img, xc, yc, half, dxs, dys)

coseda.centerrefinement.refinecenters_direct.quadrant_variance_numba(img, cx, cy, half, deltas_x, deltas_y)

coseda.centerrefinement.refinecenters_direct.refine_and_update_centers(h5file_path, sigma_x, sigma_y, threshold_frac, box1_half, step1, step2, batch_size=500, R_min=None, R_max=None, debug_plot_dir=None, logfile_path=None, loess_span=None, loess_frac=None, usedask=False, convergence_threshold=None, skip_fit=False, stop_event=None)

Runs refine_direct_all over all frames, updates center_x and center_y datasets with the new fine centers (for all valid frames).

Parameters:

• h5file_path (str)

• sigma_x (float)

• sigma_y (float)

• threshold_frac (float)

• box1_half (int)

• step1 (float)

• step2 (float)

• batch_size (int)

• R_min (float)

• R_max (float)

• debug_plot_dir (str)

• logfile_path (str)

• loess_span (float)

• loess_frac (float)

• usedask (bool)

• convergence_threshold (float)

• skip_fit (bool)

coseda.centerrefinement.refinecenters_direct.refine_direct_all(h5file_path, all_indices, sigma_x, sigma_y, threshold_frac, box1_half, step1, step2, batch_size=500, R_min=None, R_max=None, debug_plot_dir=None, usedask=False, stop_event=None)

Driver: divides frames into batches, optionally calls refine_direct_batch for each batch in parallel with Dask. Collects and returns all valid results.

Parameters:

• h5file_path (str)

• all_indices (numpy.ndarray)

• sigma_x (float)

• sigma_y (float)

• threshold_frac (float)

• box1_half (int)

• step1 (float)

• step2 (float)

• batch_size (int)

• R_min (float)

• R_max (float)

• debug_plot_dir (str)

• usedask (bool)

coseda.centerrefinement.refinecenters_direct.refine_direct_batch(h5file_path, frame_indices, sigma_x, sigma_y, threshold_frac, box1_half, step1, step2, R_min=None, R_max=None, debug_plot_dir=None, stop_event=None)

Parameters:

• h5file_path (str)

• frame_indices (numpy.ndarray)

• sigma_x (float)

• sigma_y (float)

• threshold_frac (float)

• box1_half (int)

• step1 (float)

• step2 (float)

• R_min (float)

• R_max (float)

• debug_plot_dir (str)

coseda.centerrefinement.refinecenters_direct.refine_direct_single_frame(frameindex, frame, x0, y0, sigma_x, sigma_y, threshold_frac, box1_half, step1, step2, R_min=None, R_max=None, debug_plot_path=None)

Perform adaptive two-stage quadrant-variance refinement on a single frame. Returns a dict with keys ‘coarse’ and ‘fine’ containing (x,y) tuples.

Parameters:

• frameindex (int)

• frame (numpy.ndarray)

• x0 (float)

• y0 (float)

• sigma_x (float)

• sigma_y (float)

• threshold_frac (float)

• box1_half (int)

• step1 (float)

• step2 (float)

• R_min (float)

• R_max (float)

• debug_plot_path (str)

Return type:

dict

coseda.centerrefinement.refinecenters_direct.refinecenters_direct_batch(input_path, usedask=True, batch_size=50, stop_event=None)

Process all configuration files for center refinement.

coseda.centerrefinement.refinecenters_direct.refinecenters_direct_file(configfile, client=None, batch_size=50, stop_event=None)

coseda.centerrefinement.refinecenters_direct.resolve_loess_span(loess_span, loess_frac, total_frames, default_frac=0.1)

Determine the LOESS span (in frame units) from either an explicit span or a fraction. Returns a tuple (span, fraction_used). If both are missing and default_frac is None or <=0, span will be None to indicate smoothing should be skipped.

coseda.centerrefinement.refinecenters_direct.write_centerrefinement_direct_settings(input_path, threshold_frac, box1_half, step1, step2, sigma_x, sigma_y, loess_span=None, loess_frac=None, batch_size=None, cycles=None, convergence_threshold=None)

Update .ini files to set parameters for direct center refinement.

Module contents

Center refinement workflows.