unravel package

Subpackages

• unravel.unravel_commands module
  • Usage to print common commands, aliases, and descriptions:
  • Usage to print all commands matching a specific string:
  • Usage to print all commands and module names:
  • parse_args()
  • main()
• unravel.register package
  • unravel.register.reg_prep module
  • unravel.register.reg module
  • unravel.register.affine_initializer module
    • Python usage:
    • Usage:
    • parse_args()
    • affine_initializer_wrapper()
    • run_with_timeout()
    • main()
  • unravel.register.reg_check module
    • Usage for copying to the current working directory:
    • parse_args()
    • main()
  • unravel.register.reg_check_brain_mask module
    • Usage for copying to the current working directory:
    • Usage for copying to a target directory:
    • parse_args()
    • main()
• unravel.warp package
  • unravel.warp.to_atlas module
  • unravel.warp.to_fixed module
  • unravel.warp.to_native module
  • unravel.warp.warp module
    • Usage for forward warping atlas to tissue space:
    • Usage for inverse warping tissue to atlas space:
    • parse_args()
    • warp()
    • main()
  • unravel.warp.points_to_atlas module
• unravel.segment package
  • unravel.segment.brain_mask module
  • unravel.segment.copy_tifs module
  • unravel.segment.ilastik_pixel_classification module
  • unravel.segment.labels_to_masks module
• unravel.voxel_stats package
  • unravel.voxel_stats.apply_mask module
  • unravel.voxel_stats.vstats_prep module
  • unravel.voxel_stats.z_score module
  • unravel.voxel_stats.whole_to_LR_avg module
  • unravel.voxel_stats.hemi_to_LR_avg module
  • unravel.voxel_stats.vstats module
    • Usage:
    • parse_args()
    • check_fdr_command()
    • create_design_ttest2()
    • get_groups_info()
    • calculate_fragments()
    • run_randomise_parallel()
    • main()
  • unravel.voxel_stats.mirror module
    • Usage:
    • parse_args()
    • mirror()
    • main()
  • unravel.voxel_stats.other package
    • unravel.voxel_stats.other.IF_outliers module
    • unravel.voxel_stats.other.r_to_p module
• unravel.cluster_stats package
  • unravel.cluster_stats.fdr_range module
    • Usage:
    • parse_args()
    • smart_float_format()
    • fdr_range()
    • main()
  • unravel.cluster_stats.fdr module
    • Usage
    • parse_args()
    • fdr()
    • cluster_index()
    • reverse_clusters()
    • split_clusters_based_on_effect()
    • process_fdr_and_clusters()
    • main()
  • unravel.cluster_stats.recursively_mirror_rev_cluster_indices module
    • Usage:
    • parse_args()
    • process_file()
    • main()
  • unravel.cluster_stats.validation module
  • unravel.cluster_stats.summary module
    • Usage if running directly after cstats_validation:
    • Usage from a cluster correction dir after cstats_validation:
    • Usage if running after cstats_validation and cstats_org_data:
    • parse_args()
    • run_script()
    • main()
  • unravel.cluster_stats.brain_model module
    • Usage:
    • parse_args()
    • main()
  • unravel.cluster_stats.find_incongruent_clusters module
    • Usage:
    • parse_args()
    • find_incongruent_clusters()
    • main()
  • unravel.cluster_stats.group_bilateral_data module
    • Usage:
    • parse_args()
    • group_hemisphere_data()
    • main()
  • unravel.cluster_stats.mean_IF module
  • unravel.cluster_stats.legend module
    • Usage:
    • parse_args()
    • extract_unique_regions_from_file()
    • apply_rgb_to_cell()
    • main()
  • unravel.cluster_stats.org_data module
    • Usage
    • parse_args()
    • find_matching_directory()
    • cp()
    • copy_stats_files()
    • organize_validation_data()
    • main()
  • unravel.cluster_stats.prism module
    • Usage:
    • parse_args()
    • sort_samples()
    • generate_summary_table()
    • main()
  • unravel.cluster_stats.cstats module
    • Usage for t-tests:
    • Usage for Tukey’s tests:
    • parse_args()
    • condition_selector()
    • cluster_validation_data_df()
    • valid_clusters_t_test()
    • perform_tukey_test()
    • main()
  • unravel.cluster_stats.stats_table module
    • Usage:
    • parse_args()
    • cluster_summary()
    • main()
  • unravel.cluster_stats.sunburst module
    • Usage:
    • parse_args()
    • calculate_regional_volumes()
    • sunburst()
    • main()
  • unravel.cluster_stats.table module
    • Sorting by hierarchy and volume:
    • Usage:
    • parse_args()
    • fill_na_with_last_known()
    • sort_sunburst_hierarchy()
    • undo_fill_with_original()
    • can_collapse()
    • collapse_hierarchy()
    • calculate_top_regions()
    • get_top_regions_and_percent_vols()
    • get_fill_color()
    • main()
  • unravel.cluster_stats.crop module
  • unravel.cluster_stats.index module
    • Usage
    • parse_args()
    • generate_sunburst()
    • main()
  • unravel.cluster_stats.mean_IF_summary module
    • Usage for t-tests:
    • Usage for Tukey’s tests w/ reordering and renaming of conditions:
    • parse_args()
    • load_data()
    • perform_t_tests()
    • plot_data()
    • main()
  • unravel.cluster_stats.clusters module
    • Usage
    • parse_args()
    • main()
  • unravel.cluster_stats.effect_sizes package
    • unravel.cluster_stats.effect_sizes.effect_sizes module
    • unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute module
    • unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative module
• unravel.region_stats package
  • unravel.region_stats.rstats module
  • unravel.region_stats.rstats_summary module
    • Usage for Tukey tests:
    • Usage for t-tests:
    • parse_args()
    • get_region_details()
    • parse_color_argument()
    • summarize_significance()
    • process_and_plot_data()
    • main()
  • unravel.region_stats.rstats_mean_IF module
  • unravel.region_stats.rstats_mean_IF_in_segmented_voxels module
  • unravel.region_stats.rstats_mean_IF_summary module
    • Usage for t-tests:
    • Usage for Tukey’s tests w/ reordering and renaming of conditions:
    • Usage with a custom atlas:
    • parse_args()
    • load_data()
    • get_max_region_id_from_csvs()
    • get_region_details()
    • get_all_region_ids()
    • filter_region_ids()
    • remove_zero_intensity_regions()
    • perform_t_tests()
    • plot_data()
    • main()
• unravel.core package
  • unravel.core.help_formatter module
    • SuppressMetavar
    • CustomHelpAction
    • RichArgumentParser
    • SM
    • format_argparse_help()
    • format_docstring_for_terminal()
  • unravel.core.config module
    • AttrDict
    • Config
    • Configuration
  • unravel.core.img_io module
  • unravel.core.img_tools module
  • unravel.core.utils module
    • load_config()
    • get_samples()
    • CustomMofNCompleteColumn
    • CustomTimeElapsedColumn
    • CustomTimeRemainingColumn
    • AverageTimePerIterationColumn
    • initialize_progress_bar()
    • verbose_start_msg()
    • verbose_end_msg()
    • log_command()
    • get_dir_name_from_args()
    • print_func_name_args_times()
    • load_text_from_file()
    • copy_files()
    • process_files_with_glob()
    • get_pad_percent()
• unravel.image_io package
  • unravel.image_io.h5_to_tifs module
    • Usage:
    • parse_args()
    • find_largest_h5_file()
    • load_h5()
    • metadata_from_h5()
    • save_as_tifs()
    • main()
  • unravel.image_io.img_to_npy module
  • unravel.image_io.io_img module
  • unravel.image_io.metadata module
  • unravel.image_io.nii_hd module
    • Usage:
    • parse_args()
    • main()
  • unravel.image_io.nii_info module
  • unravel.image_io.io_nii module
    • Usage:
    • parse_args()
    • convert_dtype()
    • main()
  • unravel.image_io.nii_to_tifs module
    • Usage:
    • parse_args()
    • nii_to_tifs()
    • main()
  • unravel.image_io.nii_to_zarr module
    • Usage:
    • parse_args()
    • nii_to_ndarray()
    • save_as_zarr()
    • main()
  • unravel.image_io.reorient_nii module
    • Usage:
    • parse_args()
    • transform_nii_affine()
    • reorient_nii()
    • main()
  • unravel.image_io.tif_to_tifs module
  • unravel.image_io.zarr_to_nii module
    • Usage:
    • parse_args()
    • zarr_to_ndarray()
    • define_zarr_to_nii_output()
    • save_as_nii()
    • main()
  • unravel.image_io.points_to_img module
  • unravel.image_io.img_to_points module
• unravel.image_tools package
  • unravel.image_tools.avg module
    • Usage:
    • parse_args()
    • main()
  • unravel.image_tools.bbox module
  • unravel.image_tools.extend module
  • unravel.image_tools.max module
    • Usage:
    • parse_args()
    • find_max_intensity()
    • main()
  • unravel.image_tools.pad module
  • unravel.image_tools.resample module
  • unravel.image_tools.spatial_averaging module
  • unravel.image_tools.DoG module
  • unravel.image_tools.rb module
  • unravel.image_tools.transpose_axes module
  • unravel.image_tools.unique_intensities module
  • unravel.image_tools.resample_points module
  • unravel.image_tools.modify_labels module
    • Usage:
    • parse_args()
    • set_labels()
    • retain_labels()
    • main()
  • unravel.image_tools.atlas package
    • unravel.image_tools.atlas.relabel_nii module
    • unravel.image_tools.atlas.wireframe module
• unravel.utilities package
  • unravel.utilities.get_samples module
    • Usage:
    • parse_args()
    • main()
  • unravel.utilities.region_info module
    • Usage:
    • parse_args()
    • filter_region_summary()
    • main()
  • unravel.utilities.aggregate_files_from_sample_dirs module
    • Usage:
    • Usage to prepend sample folder name to the name of files being copied:
    • parse_args()
    • aggregate_files_from_sample_dirs()
    • main()
  • unravel.utilities.aggregate_files_recursively module
    • Usage:
    • parse_args()
    • find_and_copy_files()
    • main()
  • unravel.utilities.clean_tif_dirs module
    • Usage:
    • parse_args()
    • clean_tifs_dir()
    • main()
  • unravel.utilities.prepend_conditions module
    • Usage for files:
    • Usage for directories:
    • parse_args()
    • rename_items()
    • prepend_conditions()
    • main()
  • unravel.utilities.rename module
    • Usage:
    • parse_args()
    • rename_files()
    • main()
  • unravel.utilities.toggle_samples module
    • Usage for toggling all sample?? dirs to active:
    • Usage for activating sample?? dirs for certain conditions:
    • parse_args()
    • main()
  • unravel.utilities.points_compressor module
    • Usage:
    • parse_args()
    • pack_points()
    • unpack_points()
    • summarize_points()
    • points_compressor()
    • main()

Module contents