hexrd.grainmap.nfutil module

Refactor of simulate_nf so that an experiment is mocked up.

Also trying to minimize imports

class hexrd.grainmap.nfutil.ProcessController(result_handler=None, progress_observer=None, ncpus=1, chunk_size=100)

Bases: object

This is a ‘controller’ that provides the necessary hooks to track the results of the process as well as to provide clues of the progress of the process

finish(name)

get_chunk_size()

get_process_count()

handle_result(key, value)

limit(key, value)

set_limit(key, limit_function)

start(name, count)

update(value)

hexrd.grainmap.nfutil.build_controller(check=None, generate=None, ncpus=2, chunk_size=10, limit=None)

hexrd.grainmap.nfutil.checking_result_handler(filename)

returns a return handler that checks the results against a reference file.

The Check will consider a FAIL either a result not present in the reference file (saved as a numpy savez or savez_compressed) or a result that differs. It will consider a PARTIAL PASS if the reference file has a shorter result, but the existing results match. A FULL PASS will happen when all existing results match

hexrd.grainmap.nfutil.dilate_image_stack(image_stack, experiment, controller)

hexrd.grainmap.nfutil.evaluate_diffraction_angles(experiment, controller=None)

Uses simulateGVecs to generate the angles used per each grain. returns a list containg one array per grain.

experiment – a bag of experiment values, including the grains specs

and other required parameters.

hexrd.grainmap.nfutil.forgetful_result_handler()

hexrd.grainmap.nfutil.gather_confidence(controller, confidence, n_grains, n_coords)

hexrd.grainmap.nfutil.gen_nf_cleaned_image_stack(data_folder, img_nums, dark, nrows, ncols, process_type='gaussian', process_args=[4.5, 5], threshold=1.5, ome_dilation_iter=1, stem='nf_', num_digits=5, ext='.tif')

hexrd.grainmap.nfutil.gen_nf_dark(data_folder, img_nums, num_for_dark, nrows, ncols, dark_type='median', stem='nf_', num_digits=5, ext='.tif')

hexrd.grainmap.nfutil.gen_nf_test_grid(cross_sectional_dim, v_bnds, voxel_spacing)

hexrd.grainmap.nfutil.gen_nf_test_grid_tomo(x_dim_pnts, z_dim_pnts, v_bnds, voxel_spacing)

hexrd.grainmap.nfutil.gen_trial_exp_data(grain_out_file, det_file, mat_file, mat_name, max_tth, comp_thresh, chi2_thresh, misorientation_bnd, misorientation_spacing, ome_range_deg, nframes, beam_stop_parms)

hexrd.grainmap.nfutil.generate_test_grid(low, top, samples)

generates a test grid of coordinates

hexrd.grainmap.nfutil.get_dilated_image_stack(image_stack, experiment, controller, cache_file='gold_cubes_dilated.npy')

hexrd.grainmap.nfutil.get_offset_size(n_coords)

hexrd.grainmap.nfutil.get_simulate_diffractions(grain_params, experiment, cache_file='gold_cubes.npy', controller=None)

getter functions that handles the caching of the simulation

hexrd.grainmap.nfutil.grand_loop_pool(ncpus, state)

function that handles the initialization of multiprocessing. It handles properly the use of spawned vs forked multiprocessing. The multiprocessing can be either ‘fork’ or ‘spawn’, with ‘spawn’ being required in non-fork platforms (like Windows) and ‘fork’ being preferred on fork platforms due to its efficiency.

hexrd.grainmap.nfutil.load_instrument(yml)

hexrd.grainmap.nfutil.multiproc_inner_loop(chunk)

function to use in multiprocessing that computes the simulation over the task’s alloted chunk of data

hexrd.grainmap.nfutil.null_progress_observer()

hexrd.grainmap.nfutil.output_grain_map(data_location, data_stems, output_stem, vol_spacing, top_down=True, save_type=['npz'])

hexrd.grainmap.nfutil.plot_ori_map(grain_map, confidence_map, exp_maps, layer_no, mat, id_remap=None)

hexrd.grainmap.nfutil.process_raw_confidence(raw_confidence, vol_shape=None, id_remap=None, min_thresh=0.0)

hexrd.grainmap.nfutil.progressbar_progress_observer()

hexrd.grainmap.nfutil.save_nf_data(save_dir, save_stem, grain_map, confidence_map, Xs, Ys, Zs, ori_list, id_remap=None)

hexrd.grainmap.nfutil.save_raw_confidence(save_dir, save_stem, raw_confidence, id_remap=None)

hexrd.grainmap.nfutil.saving_result_handler(filename)

returns a result handler that saves the resulting arrays into a file with name filename

hexrd.grainmap.nfutil.scan_detector_parm(image_stack, experiment, test_crds, controller, parm_to_opt, parm_range, slice_shape, ang='deg')

hexrd.grainmap.nfutil.simulate_diffractions(grain_params, experiment, controller)

actual forward simulation of the diffraction

hexrd.grainmap.nfutil.test_orientations(image_stack, experiment, test_crds, controller, multiprocessing_start_method='fork')

grand loop precomputing the grown image stack

image-stack – is the dilated image stack to be tested against.

experiment – A bunch of experiment related parameters.

test_crds – Coordinates to test orientations on, units mm.

controller – An external object implementing the hooks to notify progress

as well as figuring out what to do with results.

hexrd.grainmap.nfutil.worker_init(id_state, id_exp)

process initialization function. This function is only used when the child processes are spawned (instead of forked). When using the fork model of multiprocessing the data is just inherited in process memory.