`diamond_utils`

This file contains a suite of utility functions for processing data acquired specifically at Diamond.

Module Contents

Classes

ProcessArgs

a class to hold all information about the processing settings requested, and provide parsing checks, then job submission

Functions

`get_im_path`
`setup_processing`	uses process configuration to create an experiment object and setup a logger if requested returns : Experiment, config, logger
`create_process_config`	creates a simplenamespace configuration settings object
`check_folder`	check individual scan folders for corrupt .h5 files
`check_folder_corruption`	check any folders associated with scan
`get_good_paths`	checks for corrupted .h5 files in scan folder
`colour_text`	return a colour string to print using chosen colour and string text
`data_corruption_warning`	give warning in terminal if corrupt scans found
`create_experiment`	creates an experiment object from process configuration settings
`initial_value_checks`	does initial checks on dps_centres, cylinder_axis, setup, output_file_size sets oop value returns: oop
`setup_dps`	adjust dps settings in scan metadata
`standard_adjustments`	carries out standard adjustments to the Experiment object keeping track of total images, calculating dps offsets, setting skipscans and skipimages, setting up slitratio values
`make_mask_lists`	takes in specific pixels and mask regions makes sure specific pixels x,y is correct way round for analysis sets up mask Region objects, and corrects region x,y
`make_new_hdf5`	makes a new hdf5 file using a process_config, scan_index, name and Experiment
`run_one_scan_process`	creates a hdf5 file and then sends off a process option to run
`run_scanlist_loop`	iterates through list of scans and runs requested process options
`run_scanlist_combined`	sends whole list of scans to run requested process together
`get_run_function`	returns a dict of functions for mapping either static or moving, depending on configuration requested
`run_process_list`	separate function for sending of jobs defined by process output list and input arguments
`run_full_map_process`	runs full reciprocal map processing using a process configuration
`save_binoviewer_hdf5`	Saves the .npy file as a binoviewer-readable hdf5 file.
`get_volume_and_bounds`	Takes the path to a .npy file. Loads the volume stored in the .npy file, and also grabs the definition of the corresponding finite differences volume from the bounds file.

API

diamond_utils.get_im_path(directorypath: str, scan_number: int, image_number: int = 0)

diamond_utils.setup_processing(exp_setup_file: pathlib.Path, job_file_path: str, scan_numbers: list, debuglogging: bool): uses process configuration to create an experiment object and setup a logger if requested returns : Experiment, config, logger

diamond_utils.create_process_config(exp_setup_file: pathlib.Path, job_file_path: str, scan_numbers: list, debuglogging: bool): creates a simplenamespace configuration settings object

diamond_utils.check_folder(folder): check individual scan folders for corrupt .h5 files

diamond_utils.check_folder_corruption(folderpath: pathlib.Path): check any folders associated with scan

diamond_utils.get_good_paths(process_config: types.SimpleNamespace): checks for corrupted .h5 files in scan folder

diamond_utils.colour_text(colour, string): return a colour string to print using chosen colour and string text

diamond_utils.data_corruption_warning(cfg: types.SimpleNamespace): give warning in terminal if corrupt scans found

diamond_utils.create_experiment(process_config: types.SimpleNamespace): creates an experiment object from process configuration settings

diamond_utils.initial_value_checks(dps_centres, cylinder_axis, setup, output_file_size): does initial checks on dps_centres, cylinder_axis, setup, output_file_size sets oop value returns: oop

diamond_utils.setup_dps(scan, process_config): adjust dps settings in scan metadata

diamond_utils.standard_adjustments(experiment, process_config): carries out standard adjustments to the Experiment object keeping track of total images, calculating dps offsets, setting skipscans and skipimages, setting up slitratio values

diamond_utils.make_mask_lists(specific_pixels, mask_regions): takes in specific pixels and mask regions makes sure specific pixels x,y is correct way round for analysis sets up mask Region objects, and corrects region x,y

diamond_utils.make_new_hdf5(cfg: types.SimpleNamespace, scan_index: int, name_start: str, experiment: fast_rsm.experiment.Experiment): makes a new hdf5 file using a process_config, scan_index, name and Experiment

diamond_utils.run_one_scan_process(cfg, i, experiment, inputscan, runoptions): creates a hdf5 file and then sends off a process option to run

diamond_utils.run_scanlist_loop(cfg, experiment, runoptions): iterates through list of scans and runs requested process options

diamond_utils.run_scanlist_combined(cfg, experiment, runoptions): sends whole list of scans to run requested process together

diamond_utils.get_run_function(map_per_image): returns a dict of functions for mapping either static or moving, depending on configuration requested

diamond_utils.run_process_list(experiment, process_config): separate function for sending of jobs defined by process output list and input arguments

diamond_utils.run_full_map_process(experiment, cfg): runs full reciprocal map processing using a process configuration

diamond_utils.save_binoviewer_hdf5(output_path: str, process_config: types.SimpleNamespace): Saves the .npy file as a binoviewer-readable hdf5 file.

diamond_utils.get_volume_and_bounds(path_to_npy: str) → Tuple[numpy.ndarray]

Takes the path to a .npy file. Loads the volume stored in the .npy file, and also grabs the definition of the corresponding finite differences volume from the bounds file.

Args:

path_to_npy:: Path to the .npy file containing the volume of interest.

Returns:

A tuple taking the form (volume, start, stop, step), where each element of the tuple is a numpy array of values. The first value returned is the full reciprocal space volume, and could be very large (up to ~GB).

class diamond_utils.ProcessArgs