coseda package

Subpackages

• coseda.centerfinding package
  • Submodules
  • coseda.centerfinding.findcenters_beamstop module
    • divide_into_batches()
    • find_friedel_pairs()
    • fit_gaussian_to_largest_cluster()
    • get_frame_stack_shape()
    • get_pixels_per_meter()
    • iterative_gaussian_fitting_on_subset()
    • plot_batch_centers()
    • plot_deviation_cloud()
    • plot_linear_fit()
    • process_batch()
    • quartering()
    • quartering_batch()
    • refine_center_with_friedel()
    • resolve_frame_dataset()
    • set_center_based_on_batch()
    • set_center_based_on_line_fit()
    • update_detector_shifts()
  • coseda.centerfinding.findcenters_direct module
    • compute_auto_significance_threshold()
    • find_primary_beam_direct()
    • interpolate_centers()
    • is_within_bounds()
    • process_centers()
    • run_findcenters_direct()
    • write_centerfinderdirectsettings()
  • Module contents
• coseda.centerrefinement package
  • Submodules
  • coseda.centerrefinement.cancellation module
    • RefinementCancelled
      • RefinementCancelled.add_note()
      • RefinementCancelled.args
      • RefinementCancelled.with_traceback()
    • check_cancel()
  • coseda.centerrefinement.refinecenters_beamstop module
    • output()
    • perform_lowess()
    • plot_deviations()
    • plot_lowess_and_centers()
    • refine()
    • refine_center_with_friedel_and_update()
    • refine_center_with_friedel_batch()
    • refinecenters_batch()
  • coseda.centerrefinement.refinecenters_direct module
    • lowess_xunit()
    • output_direct()
    • quadrant_var_cost()
    • quadrant_variance_numba()
    • refine_and_update_centers()
    • refine_direct_all()
    • refine_direct_batch()
    • refine_direct_single_frame()
    • refinecenters_direct_batch()
    • refinecenters_direct_file()
    • resolve_loess_span()
    • write_centerrefinement_direct_settings()
  • Module contents
• coseda.exporters package
  • Submodules
  • coseda.exporters.hklf4 module
    • crystfel_to_hklf4()
    • main()
  • coseda.exporters.mtz module
  • coseda.exporters.p4p module
  • coseda.exporters.res module
  • Module contents
• coseda.ici package
  • Submodules
  • coseda.ici.build_early_break_from_log module
    • build_plans_from_state()
    • build_stream_for_plans()
    • chunk_key_from_slice()
    • extract_chunks_for_run()
    • load_state()
    • main()
    • map_chunk_ids_by_image_event()
    • parse_stream_chunks()
    • run_stream_path()
  • coseda.ici.build_overlays_and_list module
    • collect_latest_numeric_proposals()
    • ensure_overlay_for_run()
    • load_state()
    • main()
    • parse_log()
    • tag_overlay_with_original()
    • write_all_shifts()
    • write_event_lists()
    • write_overlay_mapping()
  • coseda.ici.create_run_sh module
    • main()
  • coseda.ici.evaluate_stream module
    • ChunkRow
      • ChunkRow.det_dx_mm
      • ChunkRow.det_dy_mm
      • ChunkRow.event
      • ChunkRow.image
      • ChunkRow.indexed
      • ChunkRow.n_kept
      • ChunkRow.n_matches
      • ChunkRow.reason
      • ChunkRow.wrmsd
    • get_chunks()
    • main()
    • parse_chunk_text()
  • coseda.ici.extract_mille_shifts module
    • iter_records()
    • main()
    • per_frame_two_globals()
  • coseda.ici.fix_stream_paths module
    • USAGE EXAMPLES
    • main()
  • coseda.ici.no_run_prep_singlelist module
    • build_argparser()
    • main()
  • coseda.ici.orchestrator module
    • OrchestratorRunLogger
    • TimestampingStream
      • TimestampingStream.flush()
      • TimestampingStream.write()
    • all_next_done_for_latest()
    • detect_latest_run_from_log()
    • do_init_sequence()
    • iterate_until_done()
    • latest_run()
    • list_run_numbers()
    • main()
    • run_py()
    • runs_dir()
  • coseda.ici.overlay_elink module
    • create_overlay()
    • write_shifts_mm()
  • coseda.ici.propose_next_shifts module
    • load_state()
    • main()
    • parse_blocks()
    • propose_event()
    • read_log()
    • save_state()
    • update_csv_with_proposals()
    • write_log()
    • wrmsd_median_convergence()
    • wrmsd_no_improvement()
    • wrmsd_recurring_convergence()
    • wrmsd_stability()
  • coseda.ici.run_contract module
    • canonical_stream_filename()
    • canonical_stream_path()
    • done_stream_path()
    • early_break_stream_path()
    • manifest_path()
    • resolve_final_stream_path()
    • run_name()
    • run_root_path()
    • update_final_stream_alias()
    • write_run_manifest()
  • coseda.ici.run_sh module
    • concat_streams()
    • main()
    • run_one_event()
  • coseda.ici.step1_hillmap_wrmsd module
    • Step1Params
      • Step1Params.A0
      • Step1Params.allow_spacing_relax
      • Step1Params.drop_amp_frac
      • Step1Params.explore_floor
      • Step1Params.first_attempt_center_mm
      • Step1Params.hill_amp_frac
      • Step1Params.min_spacing_mm
      • Step1Params.n_candidates
      • Step1Params.radius_mm
      • Step1Params.rng_seed
    • Step1Result
      • Step1Result.done
      • Step1Result.proposal_xy_mm
      • Step1Result.reason
    • Trial
      • Trial.indexed
      • Trial.wrmsd
      • Trial.x_mm
      • Trial.y_mm
    • propose_step1()
  • coseda.ici.step2_dxdy module
    • Step2DxDyConfig
      • Step2DxDyConfig.col_dx
      • Step2DxDyConfig.col_dy
    • propose_step2_dxdy()
  • coseda.ici.summarize_image_run_log module
    • Trial
      • Trial.indexed
      • Trial.next_dx
      • Trial.next_dy
      • Trial.run
      • Trial.wrmsd
    • cumulative_stats()
    • first_run_stats()
    • load_sidecar()
    • main()
    • parse_log_rows()
    • proposal_counts_for_run()
  • coseda.ici.update_image_run_log_grouped module
    • main()
    • resolve_real_source()
  • Module contents
• coseda.importers package
  • Submodules
  • coseda.importers.convert_dm4 module
    • bin_chunk()
    • dm4_to_h5()
    • get_stage_position()
    • process_and_save_h5()
  • coseda.importers.gatan_metareader module
    • dm4_folder_conversion()
    • extract_frame_timestamp_from_gatan_metadata()
    • extract_info_from_gatan_metadata()
    • find_all_frames_ordered()
    • get_timestamp_from_path()
    • parse_dm4_metadata()
  • coseda.importers.h5convert module
    • bin_chunk()
    • calculate_mean_intensity_per_frame_batch()
    • calculate_total_intensity_per_frame_batch()
    • dm4_folder_conversion_batch()
    • emd_to_h5()
    • emi_to_h5()
    • velox_true_conversion_batch()
  • coseda.importers.import_h5 module
    • check_image_dataset()
    • get_dataset_chunk_info()
    • is_dataset_chunked_first_dim()
    • move_plain_h5()
  • coseda.importers.import_mrc module
    • create_insfile_mrc()
    • create_insfiles_mrc_batch()
    • extract_info_from_mrc_metadata()
    • get_mrc_files()
    • mrc_folder_conversion()
    • mrc_folder_conversion_batch()
  • coseda.importers.import_tiff module
    • create_insfiles_tiff()
    • find_tiff_frame_files()
    • set_tiffconversion_parameters()
    • stupid_tiff_folder_conversion()
    • tiff_conversion()
    • tiff_conversion_batch()
  • coseda.importers.import_velox module
    • add_intesities_batch()
    • calculate_mean_intensities()
    • calculate_mean_intensities_chunked()
    • calculate_total_intensities()
    • calculate_total_intensities_chunked()
    • decode_column()
    • export_hdf5_images_to_tiff()
    • extract_instrument_data()
    • extract_pos_data()
    • extract_stage_pos()
    • find_dataset_paths()
    • find_path_in_h5()
    • get_image_mode()
    • plot_4Dstem()
    • plot_crystamorphus()
    • refine_stagepos_x()
    • remap_framestack()
    • save_4Dstem()
    • velox_batch()
    • velox_process()
    • velox_true_conversion()
    • write_stage_pos_to_hdf5()
  • Module contents
• coseda.initialize package
  • Submodules
  • coseda.initialize.insfiles module
    • create_insfiles()
    • create_insfiles_emd()
    • create_insfiles_gatan()
    • create_plain_insfile()
  • coseda.initialize.project_files module
    • find_configfiles()
    • generate_parent_ini_file()
    • get_parent_ini_file()
    • resume_processing()
    • write_index_file()
  • coseda.initialize.settings module
    • write_centerfindersettings()
    • write_centerrefinementsettings()
    • write_gandalfiteratorsettings()
    • write_h5conversionsettings()
    • write_icisettings()
    • write_mergingsettings()
    • write_peakfindersettings()
    • write_stripsettings()
    • write_xgandalfsettings()
  • Module contents
    • config_to_paths()
    • create_insfiles()
    • create_insfiles_emd()
    • create_insfiles_gatan()
    • create_plain_insfile()
    • find_configfiles()
    • generate_parent_ini_file()
    • get_parent_ini_file()
    • handle_input()
    • is_parent_config_file()
    • log_result()
    • log_start()
    • parse_config()
    • read_config()
    • resume_processing()
    • shoutout()
    • write_centerfindersettings()
    • write_centerrefinementsettings()
    • write_gandalfiteratorsettings()
    • write_h5conversionsettings()
    • write_icisettings()
    • write_index_file()
    • write_mergingsettings()
    • write_peakfindersettings()
    • write_stripsettings()
    • write_xgandalfsettings()
• coseda.map package
  • Submodules
  • coseda.map.findscanlines module
    • compare_strokes()
    • cross_correlate_lines()
    • find_closest_minimum()
    • find_closest_stroke()
    • find_line_breaks()
    • find_strokes_by_xpos()
    • find_strokes_by_ypos()
    • get_line_bounds_from_index()
    • get_three_line_bounds()
    • moving_average()
    • plot_correlation()
    • plot_line_profiles()
    • plot_stagepos_y_with_breaks()
    • plot_stagepos_y_with_breaks_debug()
    • write_combined_stroke_info()
  • coseda.map.mapping module
    • Disk
    • are_touching()
    • cluster_segments()
    • distance()
    • find_clusters()
    • find_matrix()
    • find_seeds()
    • find_touching_disks()
    • get_line_bounds()
    • has_common_angle()
    • interlacecorrection()
    • linearize_map()
    • plot_clusters()
    • plot_crystamorphusvac()
    • plot_crystamorphusvac_overlap()
    • plot_map_peaks()
    • plot_nPeaks_histogram()
    • refine_clusters()
    • write_cluster_ids()
  • coseda.map.streaks module
    • add_scalebar()
    • assign_streaks()
    • find_sweeps()
    • load_atlas()
    • plot_rasterized_map()
    • rasterize_arrays()
    • rasterize_map()
    • save_atlas()
    • write_atlas()
  • Module contents
• coseda.nexus package
  • Submodules
  • coseda.nexus.detector module
    • write_detector_geometry()
  • coseda.nexus.goniometer module
    • ensure_goniometer_transforms()
    • get_goniometer_transform_order()
  • coseda.nexus.groups module
    • ensure_nexus_parents()
  • coseda.nexus.images module
    • ensure_image_nxdata()
  • coseda.nexus.indices module
    • ensure_image_key()
  • coseda.nexus.logs module
    • ensure_dense_logs()
  • coseda.nexus.paths module
    • get_first_existing_path()
    • get_mask_dataset()
    • normalize_dataset_path()
  • coseda.nexus.peaks module
    • ensure_peak_nxdata()
  • coseda.nexus.process module
    • write_beam_incident_energy()
    • write_nxprocess_centerfinding()
    • write_nxprocess_centerrefinement()
    • write_nxprocess_import()
    • write_nxprocess_indexing()
    • write_nxprocess_merging()
    • write_nxprocess_peakfinding()
    • write_nxprocess_stripping()
  • Module contents
• coseda.peakfinding package
  • Submodules
  • coseda.peakfinding.aurora module
    • aurora_points_cache_path()
    • compute_aurora_histogram()
    • compute_aurora_histogram_for_files()
    • compute_aurora_points()
    • image_bit_depth_label()
    • load_or_compute_aurora_points()
  • coseda.peakfinding.findpeaks module
    • findpeaks8_batch()
    • process_batch()
    • process_file()
    • process_image()
    • process_single_frame()
  • coseda.peakfinding.findpeaks_dask module
    • findpeaks_dask_batch()
    • findpeaks_dask_file()
    • load_and_process_batch()
    • peakfinding_stats()
  • coseda.peakfinding.maxres module
    • write_maxres_dataset()
    • write_maxres_from_config()
  • coseda.peakfinding.peakfinder9 module
    • Algorithm
    • Implementation
    • find_peaks_pf9()
    • find_peaks_pf9_multiscale()
    • findpeaks9_dask_batch()
    • findpeaks9_dask_file()
  • Module contents
    • findpeaks8_batch()
    • findpeaks_dask_batch()
    • findpeaks_dask_file()
    • process_single_frame()
    • write_maxres_dataset()
    • write_maxres_from_config()
• coseda.pipeline package
  • Submodules
  • coseda.pipeline.frame_intensities module
    • calculate_mean_intensities_batch()
    • calculate_mean_intensities_dask_batch()
    • calculate_mean_intensities_dask_file()
    • calculate_mean_intensities_dask_file_inprocess()
    • calculate_radial_profiles_batch()
    • calculate_radial_profiles_dask_file()
    • calculate_radial_profiles_dask_file_inprocess()
  • coseda.pipeline.processimage module
    • process_image()
  • coseda.pipeline.strip_h5 module
    • check_disk_space()
    • check_if_index_dataset_exists()
    • check_if_peaks_and_intensities_datasets_exist()
    • check_if_stripped()
    • create_index_dataset()
    • repack_hdf5_with_backup()
    • strip_h5()
    • strip_h5_batch()
    • translate_to_stripped_index()
  • Module contents
    • calculate_mean_intensities_dask_batch()
    • calculate_mean_intensities_dask_file()
    • calculate_mean_intensities_dask_file_inprocess()
    • check_if_stripped()
    • process_image()
    • strip_h5()
    • strip_h5_batch()

Submodules

coseda.crystfel_cell module

CrystFEL unit-cell naming helpers.

coseda.crystfel_cell.crystfel_unique_axis_allowed(lattice_type)

Return whether CrystFEL accepts unique_axis for this lattice type.

coseda.crystfel_cell.normalize_crystfel_lattice_type(lattice_type, centering='')

Return a CrystFEL-accepted lattice_type value.

coseda.dask_client_manager module

Singleton-style helpers to start/reuse Dask clusters for COSEDA tasks.

class coseda.dask_client_manager.DaskClientManager

Bases: object

Create or reuse a LocalCluster, honoring optional override scheduler addresses.

classmethod close_client()

Close the active client handle (does not kill external clusters).

classmethod get_client()

Return the singleton Dask client, preferring reuse over new clusters.

Preference order: 1) explicit override address 2) existing scheduler file in temp dir 3) brand new LocalCluster

If an existing client reports zero workers, it is discarded and rebuilt.

classmethod get_client_info()

Return dashboard URL, worker count, threads per worker, and memory per worker.

classmethod kill_all_dask_clusters()

Terminate all local Dask worker/scheduler processes (last resort).

classmethod kill_current_cluster()

Gracefully shutdown the current Dask cluster via the client API and clean up.

Removes any persisted scheduler file so the next run does not attempt to reuse a stale cluster.

classmethod log_client_info(logfile_path)

Log current worker counts, thread counts, and memory per worker to a logfile.

If no client is running, writes a short note instead of raising.

classmethod set_scheduler_address(address)

Force all new Dask connections to use this scheduler address.

Useful when pointing the UI/CLI to a remote or pre-existing cluster instead of spawning a LocalCluster.

Parameters:

address (str)

temp_dir = '/tmp'

coseda.detector_geometry module

Helpers to parse and apply optional detector panel geometry.

coseda.detector_geometry.corrected_to_raw(corrected_xy, geometry, panel_hint=None)

Map one corrected coordinate back to raw coordinates.

Parameters:

• corrected_xy (Sequence[float])

• geometry (dict | None)

• panel_hint (str | None)

Return type:

Tuple[numpy.ndarray, str | None]

coseda.detector_geometry.corrected_to_raw_points(corrected_points, geometry, panel_hints=None)

Map N corrected points back to raw coordinates.

Parameters:

• corrected_points (numpy.ndarray)

• geometry (dict | None)

• panel_hints (Sequence[str | None] | None)

Return type:

Tuple[numpy.ndarray, List[str | None]]

coseda.detector_geometry.load_detector_geometry(config)

Parse optional [DetectorGeometry] section from a ConfigParser.

Return type:

dict | None

coseda.detector_geometry.raw_to_corrected(raw_xy, geometry, panel_hint=None)

Map one raw coordinate to corrected coordinates.

Parameters:

• raw_xy (Sequence[float])

• geometry (dict | None)

• panel_hint (str | None)

Return type:

Tuple[numpy.ndarray, str | None]

coseda.detector_geometry.raw_to_corrected_points(raw_points, geometry)

Map N raw points to corrected coordinates.

Parameters:

• raw_points (numpy.ndarray)

• geometry (dict | None)

Return type:

Tuple[numpy.ndarray, List[str | None]]

coseda.detector_geometry.validate_geometry_for_frame(geometry, frame_size_x, frame_size_y)

Validate detector geometry against actual frame shape.

Returns (errors, warnings).

Parameters:

• geometry (dict | None)

• frame_size_x (int)

• frame_size_y (int)

Return type:

Tuple[List[str], List[str]]

coseda.export module

coseda.export.hkl2mtz(input_hkl, output_dir, cellfile_path)

Convert a .hkl file to .mtz using get_hkl. All outputs (MTZ, logs) will be written into a new export_<timestamp> folder under output_dir.

Parameters:

• input_hkl (str) – Path to the input CrystFEL .hkl file (absolute or relative).

• output_dir (str) – Directory under which to create export_<timestamp> folder.

• cellfile_path (str) – Path to the cell file (.cell or .inp) for get_hkl (absolute or relative).

coseda.geomfile module

coseda.geomfile.build_geomfile_from_ini(ini_path)

Build a dictionary of geometry file parameters from an ini file. Returns a tuple (geomfile_dict, missing_values).

coseda.geomfile.write_geomfile(output_path, wavelength, adu_per_photon, clen, res, data, dim0, dim1, dim2, peak_list, peak_list_type, detector_shift_x, detector_shift_y, min_ss, max_ss, min_fs, max_fs, corner_x, corner_y, fs_axis, ss_axis, mask, mask_file, mask_good, mask_bad)

Write a CrystFEL-style geometry file with the specified parameters.

coseda.indexintegrate module

coseda.indexintegrate.run_index_and_integrate(geom_file, list_file, output_stream, threads, cell_file, push_res, integration_mode, int_radius, min_peaks, xgandalf_tolerance, xgandalf_pitch, xgandalf_min_len, xgandalf_max_len, xgandalf_iter, tolerance, profile_radius, use_cell=True)

coseda.io module

Shared INI/path helpers used across the COSEDA pipeline.

coseda.io.config_to_paths(configfile)

Given the path to a .ini configfile, determine and return: outputfolder, outputfolder_path, logfile, logfile_path, h5file, h5file_path

Path A: if <basename>.h5 exists in the same directory as the .ini:

• outputfolder: basename of the ini (without extension)

• outputfolder_path: same directory as ini

• logfile: <basename>.log

• logfile_path: same directory as ini

• h5file: <basename>.h5

• h5file_path: same directory as ini

Path B: otherwise, read the [Paths] section of the INI:

• outputfolder: config.get(‘Paths’,’outputfolder’)

• outputfolder_path: parent_dir/outputfolder

• logfile: config.get(‘Paths’,’logfile’)

• logfile_path: parent_dir/logfile

• h5file: config.get(‘Paths’,’h5file’)

• h5file_path: outputfolder_path/h5file

Parameters:

configfile (str)

coseda.io.get_dir_size(directory)

Calculate total size of a directory tree, skipping symlinks.

coseda.io.get_free_space_unix(path)

Return available bytes for a Unix path via statvfs.

coseda.io.get_free_space_windows(path)

Return available bytes for a Windows path via GetDiskFreeSpaceEx.

coseda.io.handle_input(input_path)

Normalize user input (folder, INI file, or list of INIs) into child INI paths.

• Rejects hidden files and parent configs

• Enforces a single directory when a list is provided

• Returns (configfiles, base_path) where base_path is the containing folder

Raises ValueError when the input is invalid or yields no child INIs.

coseda.io.is_parent_config_file(file_path)

Return True if the INI declares [General] config_type = parent.

coseda.io.parse_config(configfile)

Parse an INI file (UTF-8 with latin-1 fallback) and resolve common paths.

Returns: (config, outputfolder, originalfile, logfile, path, outputfolder_path, originalfile_path, logfile_path, framepath, h5file, h5file_path)

coseda.io.read_config(configfile)

Read an INI file and return the ConfigParser, tolerating legacy encodings.

Attempts UTF-8 first, then falls back to latin-1 so older datasets do not fail early when metadata contains non-UTF characters.

coseda.io.update_paths_old(configfile_path)

Legacy helper to rebuild logfile path from an INI location and [Paths].

coseda.logging_utils module

Logging helpers for consistent stdout formatting.

coseda.logging_utils.configure_logging(level=None)

Configure the root COSEDA logger once.

Parameters:

level (str | None)

Return type:

None

coseda.logging_utils.get_logger(name=None)

Return a configured logger for the given module or the root COSEDA logger.

Parameters:

name (str | None)

Return type:

Logger

coseda.logging_utils.log_print(*args, sep=' ', end='', file=None, flush=False, level=None)

Drop-in replacement for print() that routes through the COSEDA logger.

level can be one of: “debug”, “info”, “warning”, “error”.

Parameters:

• sep (str)

• end (str)

• flush (bool)

• level (str | None)

coseda.logging_utils.log_result(logfile_path, message, error)

Log a success or failure message to stdout and, when available, to the logfile.

coseda.logging_utils.log_start(logfile_path, message)

Print a message and append it (timestamped) to the logfile if a path is provided.

coseda.logging_utils.shoutout(configfile_path)

Print which config file is being processed (tiny UX helper for loops).

coseda.merge module

coseda.merge.parse_scaling_file(input_filepath, output_filepath)

Parse the scaling/refinement log output from partialator and save a CSV summary.

coseda.merge.run_merging(input_path)

Read merging parameters from the INI file and execute partialator merging. If ‘merging_threads’ is not set, defaults to the number of available CPU cores.

coseda.pixmask module

coseda.pixmask.generate_full_mask(shape)

Generate a binary mask with all pixels valid (1) for a given 2D shape.

Parameters: shape : tuple of (height, width)

The dimensions of the mask to create.

Returns: mask : np.ndarray of uint8

2D array of ones with the specified shape.

Parameters:

shape (Tuple[int, int])

Return type:

numpy.ndarray

coseda.pixmask.generate_full_mask_hdf5(hdf5_path, image_dataset='entry/data/images', mask_dataset='mask')

Inspect the given HDF5 file, read the shape of the specified 2D image stack dataset, generate a full-valid (all ones) mask of the same [height, width], and save it to the file. Overwrites any existing mask dataset at mask_dataset.

Parameters:

• hdf5_path (Path) – Path Path to the HDF5 file containing the image stack.

• image_dataset (str) – str Name of the dataset in the HDF5 file that contains the image stack (expected shape: (n_frames, height, width) or (height, width)).

• mask_dataset (str) – str Name of the dataset under which to store the generated mask.

Return type:

None

coseda.pixmask.generate_mask(image_path, threshold=127)

Load an image (BMP, PNG, JPG), convert to grayscale, and create a binary mask: valid pixels (above threshold) -> 1, invalid (at or below threshold) -> 0 Returns the grayscale and mask arrays.

Parameters:

• image_path (Path)

• threshold (int)

Return type:

(numpy.ndarray, numpy.ndarray)

coseda.pixmask.load_mask_hdf5(hdf5_path)

Load the mask dataset from HDF5 file (NeXus path preferred).

Parameters:

hdf5_path (Path)

Return type:

numpy.ndarray

coseda.pixmask.plot_comparison(gray, mask)

Display original grayscale image and mask side by side for debugging.

Parameters:

• gray (numpy.ndarray)

• mask (numpy.ndarray)

coseda.pixmask.remove_mask_hdf5(hdf5_path, dataset='mask')

Remove the specified mask dataset from the HDF5 file. If the dataset does not exist, no error is raised.

Parameters:

• hdf5_path (Path)

• dataset (str)

coseda.pixmask.save_mask_hdf5(mask, hdf5_path, dataset='mask')

Add (or overwrite) a mask array in an existing HDF5 file under dataset. - If the file doesn’t exist, it will be created. - If the dataset already exists, only that dataset is replaced.

Parameters:

• mask (numpy.ndarray)

• hdf5_path (Path)

• dataset (str)

coseda.unitcell_fit module

Workspace unit-cell histogram aggregation and Gaussian fitting helpers.

class coseda.unitcell_fit.WorkspaceStreamSource(ini_path: 'str', run_dir: 'str', stream_path: 'str', cell_path: 'str')

Bases: object

Parameters:

• ini_path (str)

• run_dir (str)

• stream_path (str)

• cell_path (str)

cell_path: str

ini_path: str

run_dir: str

stream_path: str

coseda.unitcell_fit.discover_workspace_unit_cell_streams(ini_paths)

Discover one usable unit-cell stream per workspace INI.

The newest run folder with an existing stream is selected for each INI, matching the indexing UI’s “latest run per file” behavior.

Parameters:

ini_paths (Iterable[str])

Return type:

list[WorkspaceStreamSource]

coseda.unitcell_fit.fit_gaussian_to_values(values, value_range, bins=60)

Fit a Gaussian to unit-cell values inside value_range.

Parameters:

• value_range (tuple[float, float])

• bins (int)

Return type:

dict

coseda.unitcell_fit.gaussian_curve(x, amplitude, mean, sigma, baseline)

coseda.unitcell_fit.parse_workspace_cell(path)

Return workspace cell header values, including Cell.* keys.

Parameters:

path (str)

Return type:

dict[str, str]

coseda.unitcell_fit.resolve_stream_path_for_run(run_dir)

Resolve the best stream path for a simple indexamajig or ICI run.

Parameters:

run_dir (str)

Return type:

str | None

coseda.unitcell_fit.run_base_candidates_for_ini(ini_path)

Return plausible folders containing indexing runs for a workspace INI.

Parameters:

ini_path (str)

Return type:

list[str]

coseda.unitcell_fit.update_cell_file_parameter(cell_path, param, value)

Update one CrystFEL cell parameter in-place, preserving the line suffix.

Parameters:

• cell_path (str)

• param (str)

• value (float)

Return type:

bool

coseda.unitcell_fit.update_workspace_refined_cell_parameter(workspace_path, param, value)

Update one fitted cell parameter in the workspace header and mark it refined.

Parameters:

• workspace_path (str)

• param (str)

• value (float)

Return type:

bool

coseda.unitcell_fit.workspace_has_refined_cell(path)

Parameters:

path (str)

Return type:

bool

coseda.unitcell_fit.workspace_refined_cell_file_path(workspace_path)

Parameters:

workspace_path (str)

Return type:

str

coseda.unitcell_fit.write_workspace_refined_cell_file(workspace_path)

Materialize the refined workspace cell header into a CrystFEL .cell file.

Parameters:

workspace_path (str)

Return type:

str | None

Module contents