ImageD11.nbGui package¶

Submodules¶

ImageD11.nbGui.fit_geometry module¶

ImageD11.nbGui.install_ImageD11_from_git module¶

ImageD11.nbGui.install_ImageD11_from_git.guess_ImageD11_code_path()¶: Locates: scripts can hold a local installation of ImageD11 if you need one

ImageD11.nbGui.install_ImageD11_from_git.run_ImageD11_from_git(path, checkout)¶

ImageD11.nbGui.install_ImageD11_from_git.setup_ImageD11_from_git(path=None, checkout='ImageD11')¶

ImageD11.nbGui.nb_utils module¶

ImageD11.nbGui.nb_utils.assign_peaks_to_grains(grains, cf, tol)¶: Assigns peaks to the best fitting grain

ImageD11.nbGui.nb_utils.find_datasets_to_process(rawdata_path, skips_dict, dset_prefix, sample_list)¶

ImageD11.nbGui.nb_utils.get_rgbs_for_grains(grains)¶

ImageD11.nbGui.nb_utils.plot_all_ipfs(grains)¶

ImageD11.nbGui.nb_utils.plot_all_ipfs_from_meta_orien(meta_orien, ref_ucell)¶

ImageD11.nbGui.nb_utils.plot_direct_pole_figure(grains, uvw=array([1., 0., 0.]))¶

ImageD11.nbGui.nb_utils.plot_grain_positions(grains, colour='npks', centre_plot=False, size_scaling=0.5)¶: colour: choose from ‘npks’ or one of ‘x’, ‘y’, ‘z’ for IPF scaling centre_plot: choose whether to centre the plot horizontally (x and y) size_scaling: we only know relative grain sizes, adjust this to scale the diameter of the points on the plot

ImageD11.nbGui.nb_utils.plot_grain_sinograms(grains, cf, n_grains_to_plot=None)¶

ImageD11.nbGui.nb_utils.plot_index_results(ind, colfile, title)¶

ImageD11.nbGui.nb_utils.plot_inverse_pole_figure(grains, axis=array([0., 0., 1.]))¶

ImageD11.nbGui.nb_utils.plot_inverse_pole_figure_from_meta_orien(meta_orien, ref_ucell, axis=array([0., 0., 1.]))¶

ImageD11.nbGui.nb_utils.prepare_astra_bash(ds, grainsfile, id11_code_path, group_name='grains')¶

ImageD11.nbGui.nb_utils.prepare_mlem_bash(ds, grains, id11_code_path, n_simultaneous_jobs=50, cores_per_task=8)¶

ImageD11.nbGui.nb_utils.prepare_pbp_bash(pbp_object, id11_code_path, minpkint)¶

ImageD11.nbGui.nb_utils.refine_grain_positions(cf_3d, ds, grains, parfile, symmetry='cubic', cf_frac=0.85, cf_dstol=0.01, hkl_tols=(0.05, 0.025, 0.01))¶

ImageD11.nbGui.nb_utils.save_array(grp, name, ary)¶

ImageD11.nbGui.nb_utils.save_ubi_map(ds, ubi_map, eps_map, misorientation_map, ipf_x_col_map, ipf_y_col_map, ipf_z_col_map)¶

ImageD11.nbGui.nb_utils.slurm_submit_and_wait(bash_script_path, wait_time_sec=60)¶

ImageD11.nbGui.nb_utils.slurm_submit_many_and_wait(bash_script_paths, wait_time_sec=60)¶

ImageD11.nbGui.plot3d module¶

ImageD11.nbGui.segmenter_gui module¶

ImageD11.nbGui.segmenter_gui_utils module¶

ImageD11.nbGui.segmenter_gui_utils.chooseframe(dset, scan=None, idx=None, counter='_roi1', fetch_raw_image=False)¶

Locate a busy frame from the dataset and optionally fetch the raw image.

Args:: dset: Dataset object. scan: Scan to use (default is middle scan). idx: Frame index (None to auto-detect). counter: Counter to use for locating the frame. fetch_raw_image: Whether to fetch the raw image for the frame.
Returns:: scan, idx, raw_image (if fetch_raw_image is True, otherwise None)

ImageD11.nbGui.segmenter_gui_utils.guess_ESRF_paths()¶: Locates: dataroot holds raw data in folders dataroot + {sample}/{sample}_{dataset} analysisroot holds output results in folders analysisroot + {sample}/{sample}_{dataset}

ImageD11.nbGui.segmenter_gui_utils.printdatasets(dataroot, sample)¶

ImageD11.nbGui.segmenter_gui_utils.printsamples(dataroot)¶

Module contents¶

nbGui