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
    • Usage:
    • parse_args()
    • reg_prep()
    • main()
  • unravel.register.reg module
    • Usage for tissue registration with brain mask and bias correction:
    • Usage for tissue registration without brain mask and bias correction:
    • Usage for atlas to atlas registration:
    • Usage for template to template registration:
    • parse_args()
    • bias_correction()
    • main()
  • unravel.register.affine_initializer module
    • Python usage:
    • Usage:
    • parse_args()
    • affine_initializer_wrapper()
    • run_with_timeout()
    • main()
  • unravel.register.affine_initializer_check module
    • Usage:
    • parse_args()
    • affine_initializer_check()
    • main()
  • unravel.register.reg_check module
    • Usage:
    • parse_args()
    • main()
  • unravel.register.reg_check_fsleyes module
    • Usage:
    • parse_args()
    • main()
  • unravel.register.reg_check_brain_mask module
    • Usage:
    • parse_args()
    • main()
• unravel.warp package
  • unravel.warp.to_atlas module
    • Usage:
    • parse_args()
    • copy_nii_header()
    • to_atlas()
    • main()
  • unravel.warp.to_fixed module
    • Usage:
    • parse_args()
    • calculate_padded_dimensions()
    • forward_warp()
    • main()
  • unravel.warp.to_native module
    • Python usage:
    • Usage:
    • parse_args()
    • calculate_resampled_padded_dimensions()
    • scale_to_full_res()
    • to_native()
    • main()
  • 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
    • Usage:
    • parse_args()
    • main()
  • unravel.warp.ccf30_to_merfish module
    • Usage:
    • parse_args()
    • ccf30_to_merfish()
    • main()
• unravel.segment package
  • unravel.segment.brain_mask module
    • Usage:
    • parse_args()
    • main()
  • unravel.segment.copy_tifs module
    • Usage to prep for seg_brain_mask:
    • Usage to copy tifs for ilastik:
    • parse_args()
    • copy_specific_tifs()
    • main()
  • unravel.segment.ilastik_pixel_classification module
    • Usage:
    • parse_args()
    • count_files()
    • save_labels_as_masks()
    • main()
  • unravel.segment.labels_to_masks module
    • Usage:
    • parse_args()
    • save_labels_as_masks()
    • main()
• unravel.voxel_stats package
  • unravel.voxel_stats.apply_mask module
    • Usage:
    • Usage to zero out voxels in image where mask > 0 (e.g., to exclude voxels representing artifacts):
    • Usage to zero out voxels in image where mask < 1 (e.g., to preserve signal from segmented microglia clusters):
    • Usage to replace voxels in image with the mean intensity in the brain where mask > 0:
    • parse_args()
    • load_mask()
    • mean_intensity_in_brain()
    • dilate_mask()
    • scale_bool_to_full_res()
    • apply_mask_to_ndarray()
    • main()
  • unravel.voxel_stats.vstats_prep module
    • Usage:
    • parse_args()
    • main()
  • unravel.voxel_stats.z_score module
    • Usage:
    • Usage w/ an atlas mask:
    • Usage w/ a tissue mask:
    • Usage w/ both masks for side-specific z-scoring:
    • parse_args()
    • z_score()
    • tissue_mask_to_atlas_space()
    • z_score_mask()
    • main()
  • unravel.voxel_stats.z_score_cwd module
    • Usage:
    • parse_args()
    • z_score_img()
    • main()
  • unravel.voxel_stats.whole_to_LR_avg module
    • Usage:
    • parse_args()
    • whole_to_LR_avg()
    • main()
  • unravel.voxel_stats.hemi_to_LR_avg module
    • Usage:
    • parse_args()
    • hemi_to_LR_avg()
    • main()
  • 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.vstats_check_fsleyes module
    • Usage:
    • parse_args()
    • 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.fstat_sig_vx_mask module
    • Usage:
    • parse_args()
    • main()
  • unravel.cluster_stats.recursively_mirror_rev_cluster_indices module
    • Usage:
    • parse_args()
    • process_file()
    • main()
  • unravel.cluster_stats.validation module
    • Usage:
    • parse_args()
    • crop_outer_space()
    • cluster_bbox()
    • cluster_bbox_parallel()
    • count_cells()
    • density_in_cluster()
    • density_in_cluster_parallel()
    • main()
  • unravel.cluster_stats.summary_config module
    • Usage:
    • parse_args()
    • main()
  • 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
    • Usage:
    • parse_args()
    • calculate_mean_intensity_in_clusters()
    • write_to_csv()
    • main()
  • 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
    • Usage with all clusters:
    • Usage with a bounding box:
    • Usage with a cluster ID:
    • parse_args()
    • save_cropped_img()
    • main()
  • 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
    • Usage if the atlas is already in native space from warp_to_native:
    • Usage if the native atlas is not available; it is not saved (faster):
    • parse_args()
    • get_atlas_region_at_coords()
    • count_cells_in_regions()
    • calculate_regional_volumes()
    • calculate_regional_densities()
    • main()
  • 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
    • Usage:
    • parse_args()
    • calculate_mean_intensity()
    • write_to_csv()
    • main()
  • unravel.region_stats.rstats_mean_IF_in_segmented_voxels module
    • Usage
    • parse_args()
    • calculate_mean_intensity()
    • write_to_csv()
    • main()
  • 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
    • Main Functions:
    • Helper Functions:
    • return_3D_img()
    • metadata()
    • extract_resolution()
    • load_czi()
    • load_tifs()
    • load_3D_tif()
    • nii_path_or_nii()
    • nii_to_ndarray()
    • load_nii()
    • load_nii_subset()
    • load_h5()
    • load_zarr()
    • resolve_path()
    • save_metadata_to_file()
    • load_image_metadata_from_txt()
    • load_3D_img()
    • save_as_nii()
    • save_as_tifs()
    • save_as_zarr()
    • save_as_h5()
    • save_3D_img()
    • zarr_level_to_tifs()
    • nii_voxel_size()
  • unravel.core.img_tools module
    • resample()
    • reorient_axes()
    • reverse_reorient_axes()
    • pixel_classification()
    • pad()
    • reorient_ndarray()
    • reorient_ndarray2()
    • process_slice()
    • rolling_ball_subtraction_opencv_parallel()
    • label_IDs()
    • find_bounding_box()
    • crop()
  • unravel.core.utils module
    • load_config()
    • get_samples()
    • CustomMofNCompleteColumn
    • CustomTimeElapsedColumn
    • CustomTimeRemainingColumn
    • AverageTimePerIterationColumn
    • initialize_progress_bar()
    • verbose_start_msg()
    • verbose_end_msg()
    • log_command()
    • print_func_name_args_times()
    • load_text_from_file()
    • copy_files()
    • match_files()
    • get_stem()
    • get_extension()
    • get_pad_percent()
• unravel.image_io package
  • unravel.image_io.h5_to_tifs module
    • Usage:
    • parse_args()
    • load_h5()
    • metadata_from_h5()
    • save_as_tifs()
    • main()
  • unravel.image_io.img_to_npy module
    • Usage:
    • parse_args()
    • main()
  • unravel.image_io.convert_img module
    • Usage to convert a .czi file to .nii.gz:
    • Usage to convert a single .tif series to .nii.gz:
    • Usage to recursively convert all dirs with tif files to .zarr:
    • parse_args()
    • convert_img()
    • main()
  • unravel.image_io.metadata module
    • Usage for when metadata is extractable:
    • Usage for when metadata is not extractable:
    • parse_args()
    • print_metadata()
    • get_dims_from_tifs()
    • main()
  • unravel.image_io.nii_hd module
    • Usage:
    • parse_args()
    • main()
  • unravel.image_io.nii_info module
    • Usage:
    • parse_args()
    • nii_axis_codes()
    • main()
  • 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
    • Usage:
    • parse_args()
    • main()
  • 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.zarr_compress module
    • Usage for recursive compression:
    • Usage for recursive decompression:
    • parse_args()
    • compress_or_decompress_zarr()
    • run_in_parallel()
    • main()
  • unravel.image_io.points_to_img module
    • Usage:
    • parse_args()
    • threshold_points_by_region_id()
    • load_and_prepare_points()
    • points_to_img()
    • main()
  • unravel.image_io.img_to_points module
    • Usage:
    • parse_args()
    • img_to_points()
    • main()
• unravel.image_tools package
  • unravel.image_tools.math module
    • Usage to add two images and binarize the result:
    • Usage multiply three images and save as Zarr:
    • Usage to binarize a single image and set to 8 bit:
    • parse_args()
    • apply_operation()
    • threshold_image()
    • main()
  • unravel.image_tools.avg module
    • Usage:
    • parse_args()
    • main()
  • unravel.image_tools.bbox module
    • Usage:
    • parse_args()
    • main()
  • unravel.image_tools.extend module
    • parse_args()
    • extend_one_side_3d_array()
    • main()
  • unravel.image_tools.max module
    • Usage:
    • parse_args()
    • find_max_intensity()
    • main()
  • unravel.image_tools.pad module
    • Usage:
    • parse_args()
    • main()
  • unravel.image_tools.resample module
    • Usage:
    • Usage for isotropic resampling:
    • Usage for anisotropic resampling:
    • Usage for resampling by scale factor:
    • Usage to resample using a reference image:
    • parse_args()
    • main()
  • unravel.image_tools.spatial_averaging module
    • Usage:
    • parse_args()
    • spatial_average_3D()
    • apply_2D_mean_filter()
    • spatial_average_2D()
    • main()
  • unravel.image_tools.DoG module
    • Usage:
    • parse_args()
    • load_tif()
    • difference_of_gaussians()
    • save_tif()
    • main()
  • unravel.image_tools.rb module
    • Usage:
    • parse_args()
    • load_tif()
    • rolling_ball_subtraction()
    • save_tif()
    • main()
  • unravel.image_tools.transpose_axes module
    • Usage:
    • parse_args()
    • transpose_img()
    • main()
  • unravel.image_tools.unique_intensities module
    • Usage for printing all non-zero intensities:
    • Usage for printing the number of voxels for each intensity that is present:
    • Usage for printing unique intensities w/ a min cluster size > 100 voxels:
    • parse_args()
    • main()
  • unravel.image_tools.resample_points module
    • Usage:
    • parse_args()
    • resample_and_convert_points()
    • main()
  • 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.process_samples module
    • Usage:
    • parse_args()
    • process_samples()
    • 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()
• unravel.segment package
  • unravel.tabular.columns module
    • Usage:
    • parse_args()
    • main()
  • unravel.tabular.edit_columns module
    • Usage:
    • parse_args()
    • edit_columns()
    • main()
  • unravel.tabular.filter_rows module
    • Usage to keep rows where ‘region’ contains ‘AUDp’:
    • Usage to exclude rows where ‘region’ contains ‘layer1’:
    • parse_args()
    • filter_table()
    • main()
  • unravel.tabular.key_value_to_table module
    • Usage:
    • parse_args()
    • reshape_key_value_blocks()
    • main()
  • unravel.tabular.unique_values module
    • Usage:
    • parse_args()
    • filter_values()
    • print_values()
    • main()
  • unravel.tabular.utils module
    • load_tabular_file()
    • save_tabular_file()
• unravel.allen_institute package
  • unravel.allen_institute.abca package
    • unravel.allen_institute.abca.cache module
    • unravel.allen_institute.abca.merfish package
    • unravel.allen_institute.abca.sunburst package
    • unravel.allen_institute.abca.scRNA_seq package
  • unravel.allen_institute.genetic_tools_atlas package
    • unravel.allen_institute.genetic_tools_atlas.download module
    • unravel.allen_institute.genetic_tools_atlas.simplify_metadata module
    • unravel.allen_institute.genetic_tools_atlas.org_samples module
    • unravel.allen_institute.genetic_tools_atlas.auto_crop module
    • unravel.allen_institute.genetic_tools_atlas.bbox_crop module
  • unravel.allen_institute.mapmysections package
    • unravel.allen_institute.mapmysections.cell_type_proportions_concat module
    • unravel.allen_institute.mapmysections.cell_type_proportions module
    • unravel.allen_institute.mapmysections.csv_concat_with_source module
    • unravel.allen_institute.mapmysections.segmentation_summary module
    • unravel.allen_institute.mapmysections.soma_ratio module

Module contents