Index

A

abbrev() (in module hong2p.olf) add_abbrevs_from_odor_lists() (in module hong2p.olf) add_colorbar() (in module hong2p.viz) add_fly_id() (in module hong2p.util) add_group_id() (in module hong2p.util) add_group_labels_and_lines() (in module hong2p.viz) add_missing_odor_cols() (in module hong2p.util) add_mix_str_index_level() (in module hong2p.olf) add_norm_options() (in module hong2p.viz) add_recording_id() (in module hong2p.util) add_scalebar() (in module hong2p.viz)

addlevel() (in module hong2p.util) analysis_fly_dir() (in module hong2p.util) analysis_intermediates_root() (in module hong2p.util) analysis_output_root() (in module hong2p.util) arraylike_cols() (in module hong2p.util) assign_frame_times_to_blocks() (in module hong2p.thor) assign_frames_to_blocks() (in module hong2p.thor) assign_frames_to_odor_presentations() (in module hong2p.thor) assign_frames_to_trials() (in module hong2p.util) assign_scalar_coords_to_dim() (in module hong2p.xarray) autoroi_metadata_filename() (in module hong2p.roi)

B

baselined_normed_u8() (in module hong2p.util)

C

calculate_df_over_f() (in module hong2p.util) callable_ticklabels() (in module hong2p.viz) cell_ids() (in module hong2p.util) certain_roi_indices() (in module hong2p.roi) check_dir_exists() (in module hong2p.util) check_index_vals_unique() (in module hong2p.util) check_no_roi_jumps() (in module hong2p.roi) clean_generated_latex() (in module hong2p.latex) clustermap() (in module hong2p.viz) cnmf_metadata_from_thor() (in module hong2p.thor)

col_labels() (in module hong2p.viz) compile_tex_to_pdf() (in module hong2p.latex) const_ranges() (in module hong2p.util) constrained_layout() (in module hong2p.viz) contour2mask() (in module hong2p.roi) contour_bbox() (in module hong2p.viz) contour_center_of_mass() (in module hong2p.viz) correspond_and_renumber_rois() (in module hong2p.roi) correspond_rois() (in module hong2p.roi) crop_to_coord_bbox() (in module hong2p.roi) crop_to_nonzero() (in module hong2p.roi)

D

data_root() (in module hong2p.util) date_fly_list2paired_thor_dirs() (in module hong2p.util) db_footprints2array() (in module hong2p.roi) db_row2footprint() (in module hong2p.roi) df_to_odor_order() (in module hong2p.util) diff_dataframes() (in module hong2p.util)

diff_dicts() (in module hong2p.suite2p) dir2keys() (in module hong2p.util) downsample_movie() (in module hong2p.util) drop_incomplete_presentations() (in module hong2p.util) drop_orphaned_presentations() (in module hong2p.util) drop_scalar_coords() (in module hong2p.xarray) dtypes_equal() (in module hong2p.util)

E

euclidean_dist() (in module hong2p.util) exp_decay() (in module hong2p.util)

expand_array_cols() (in module hong2p.util) extract_traces() (in module hong2p.roi) extract_traces_bool_masks() (in module hong2p.roi)

F

find_last_true() (in module hong2p.thor) first_group() (in module hong2p.util) fit_circle_rois() (in module hong2p.roi) fit_exp_decay() (in module hong2p.util) fix_facetgrid_axis_labels() (in module hong2p.viz) footprints_to_flat_cnmf_dims() (in module hong2p.roi) format_date() (in module hong2p.util) format_index_row() (in module hong2p.viz) format_keys() (in module hong2p.util)

format_mix_from_strs() (in module hong2p.olf) format_mixture() (in module hong2p.util) format_odor() (in module hong2p.olf) format_odor_conc() (in module hong2p.util) format_odor_list() (in module hong2p.olf) format_params() (in module hong2p.util) format_timestamp() (in module hong2p.util) fps_from_thor() (in module hong2p.thor) frame_pdist() (in module hong2p.util) full_frame_avg_trace() (in module hong2p.util)

G

get_axis_index() (in module hong2p.util) get_circle_ijroi_input() (in module hong2p.roi) get_col_onset_indices() (in module hong2p.thor) get_col_onset_offset_indices() (in module hong2p.thor) get_col_onset_offset_times() (in module hong2p.thor) get_default_overlay_color() (in module hong2p.viz) get_fly_dir() (in module hong2p.util) get_flyback_indices() (in module hong2p.thor) get_frame_times() (in module hong2p.thor) get_iscell_path() (in module hong2p.suite2p) get_latex_dir() (in module hong2p.latex) get_suite2p_combined_dir() (in module hong2p.suite2p) get_suite2p_dir() (in module hong2p.suite2p) get_thorimage_dims() (in module hong2p.thor) get_thorimage_fps() (in module hong2p.thor) get_thorimage_fps_xml() (in module hong2p.thor) get_thorimage_n_averaged_frames_xml() (in module hong2p.thor) get_thorimage_n_channels_xml() (in module hong2p.thor) get_thorimage_n_flyback_xml() (in module hong2p.thor) get_thorimage_n_frames() (in module hong2p.thor) get_thorimage_name() (in module hong2p.thor)

get_thorimage_notes() (in module hong2p.thor) get_thorimage_pixelsize_um() (in module hong2p.thor) get_thorimage_power_regtype_and_level() (in module hong2p.thor) get_thorimage_scannertype() (in module hong2p.thor) get_thorimage_time() (in module hong2p.thor) get_thorimage_version() (in module hong2p.thor) get_thorimage_xml_path() (in module hong2p.thor) get_thorimage_xmlroot() (in module hong2p.thor) get_thorimage_z_stream_frames() (in module hong2p.thor) get_thorimage_z_xml() (in module hong2p.thor) get_thorimage_zstage_type() (in module hong2p.thor) get_thorimage_zstep_um() (in module hong2p.thor) get_thorsync_h5() (in module hong2p.thor) get_thorsync_samplerate_hz() (in module hong2p.thor) get_thorsync_time() (in module hong2p.thor) get_thorsync_xml_path() (in module hong2p.thor) git_hash() (in module hong2p.util) greedy_roi_packing() (in module hong2p.roi) gsheet_csv_export_link() (in module hong2p.util) gsheet_to_frame() (in module hong2p.util) gui_params_equal() (in module hong2p.suite2p)

H

has_ijrois() (in module hong2p.roi) have_all_repeats() (in module hong2p.util) have_full_comparisons() (in module hong2p.util) hong2p module hong2p.err module hong2p.latex module hong2p.olf module hong2p.roi module

hong2p.suite2p module hong2p.thor module hong2p.types module hong2p.util module hong2p.viz module hong2p.xarray module

I

ijroi2cv_contour() (in module hong2p.roi) ijroi2mask() (in module hong2p.roi) ijroi_comparable_via_name() (in module hong2p.roi) ijroi_filename() (in module hong2p.roi) ijroi_masks() (in module hong2p.roi) ijroi_mtime() (in module hong2p.roi) ijroi_name_as_if_certain() (in module hong2p.roi) ijrois2masks() (in module hong2p.roi) image_grid() (in module hong2p.viz) imshow() (in module hong2p.viz) index2dict_list() (in module hong2p.util) inputs_equal() (in module hong2p.suite2p) invert_combined_view_offset() (in module hong2p.suite2p) invert_melt_symmetric() (in module hong2p.util) IOPerformanceWarning is_acquisition_host() (in module hong2p.util)

is_array_sorted() (in module hong2p.util) is_cmap_diverging() (in module hong2p.viz) is_fast_z_enabled_xml() (in module hong2p.thor) is_ijroi_certain() (in module hong2p.roi) is_ijroi_name_default() (in module hong2p.roi) is_ijroi_named() (in module hong2p.roi) is_ijroi_plane_outline() (in module hong2p.roi) is_iscell_modified() (in module hong2p.suite2p) is_odor_component_level() (in module hong2p.olf) is_odor_var() (in module hong2p.olf) is_scalar_coord() (in module hong2p.xarray) is_subrecording() (in module hong2p.util) is_subrecording_tiff() (in module hong2p.util) is_thorimage_dir() (in module hong2p.thor) is_thorimage_raw() (in module hong2p.thor) is_thorsync_dir() (in module hong2p.thor) is_thorsync_h5() (in module hong2p.thor)

L

LabelsNotModifiedError LabelsNotSelectiveError latest_trace_pickles() (in module hong2p.util) list_motion_corrected_tifs() (in module hong2p.util) load() (in module hong2p.suite2p) load_iscell() (in module hong2p.suite2p) load_metadata() (in module hong2p.util) load_movie() (in module hong2p.util) load_odor_metadata() (in module hong2p.util) load_ops() (in module hong2p.suite2p) load_s2p_combined_outputs() (in module hong2p.suite2p)

load_s2p_masks() (in module hong2p.suite2p) load_s2p_ops() (in module hong2p.suite2p) load_s2p_outputs() (in module hong2p.suite2p) load_s2p_pickle() (in module hong2p.suite2p) load_stat() (in module hong2p.suite2p) load_stimfile() (in module hong2p.util) load_stimulus_yaml() (in module hong2p.olf) load_template_data() (in module hong2p.roi) load_thorimage_metadata() (in module hong2p.thor) load_thorsync_hdf5() (in module hong2p.thor) load_traces() (in module hong2p.suite2p)

M

make_pdf() (in module hong2p.latex) make_test_centers() (in module hong2p.roi) mark_all_suite2p_rois_good() (in module hong2p.suite2p) matlabels() (in module hong2p.viz) matshow() (in module hong2p.viz) mb_team_gsheet() (in module hong2p.util) md5() (in module hong2p.util) melt_symmetric() (in module hong2p.util) merge_ijroi_masks() (in module hong2p.roi) merge_rois() (in module hong2p.roi) merge_single_plane_rois() (in module hong2p.roi) metadata_filename() (in module hong2p.util) micrometer_depth_title() (in module hong2p.viz) missing_odor_pairs() (in module hong2p.util) missing_repeats() (in module hong2p.util) modify_iscell_in_suite2p() (in module hong2p.suite2p)

module hong2p hong2p.err hong2p.latex hong2p.olf hong2p.roi hong2p.suite2p hong2p.thor hong2p.types hong2p.util hong2p.viz hong2p.xarray most_recent_contained_file_mtime() (in module hong2p.util) motion_corrected_tiff_filename() (in module hong2p.util) move_all_coords_to_index() (in module hong2p.xarray) movie_blocks() (in module hong2p.util)

N

n_expected_repeats() (in module hong2p.util) n_odor_component_levels() (in module hong2p.olf) nan_eq() (in module hong2p.util) new_fmt_thorimage_num() (in module hong2p.thor) no_constrained_layout() (in module hong2p.viz)

no_skipped_comparisons() (in module hong2p.util) NoStimulusFile NotAllFramesAssigned num_notnull() (in module hong2p.util) num_null() (in module hong2p.util) numpy2xarray_rois() (in module hong2p.roi)

O

odor_corr_frame_to_dataarray() (in module hong2p.xarray) odor_index_sort_key() (in module hong2p.olf) odor_lists_to_multiindex() (in module hong2p.olf)

odordict_sort_key() (in module hong2p.olf) odorset_name() (in module hong2p.util) old_fmt_thorimage_num() (in module hong2p.thor) OnsetOffsetNumMismatch

P

pad_odor_index_to_n_components() (in module hong2p.olf) pad_odor_indices_to_max_components() (in module hong2p.olf) pair_ordering() (in module hong2p.util) pair_thor_dirs() (in module hong2p.thor) pair_thor_subdirs() (in module hong2p.thor) paired_thor_dirs() (in module hong2p.util) panel_odor_orders() (in module hong2p.olf) parent_recording_id() (in module hong2p.util) parse_log10_conc() (in module hong2p.olf) parse_odor() (in module hong2p.olf) parse_odor_list() (in module hong2p.olf) parse_odor_name() (in module hong2p.olf) parse_thorimage_notes() (in module hong2p.thor) pd_allclose() (in module hong2p.util) pd_indices_equal() (in module hong2p.util) pd_isclose() (in module hong2p.util)

plot_circles() (in module hong2p.roi) plot_closed_contours() (in module hong2p.viz) plot_odor_corrs() (in module hong2p.viz) plot_pair_n() (in module hong2p.viz) plot_roi() (in module hong2p.suite2p) plot_rois() (in module hong2p.viz) plot_traces() (in module hong2p.viz) point_idx() (in module hong2p.roi) print_all_stimfile_odorsets() (in module hong2p.util) print_block_frames() (in module hong2p.util) print_color() (in module hong2p.util) print_suite2p_params() (in module hong2p.suite2p) print_thor_paths() (in module hong2p.util) print_trial_odors() (in module hong2p.util) print_xml() (in module hong2p.thor) py2imagej_coords() (in module hong2p.roi)

R

raw_data_root() (in module hong2p.util) raw_fly_dir() (in module hong2p.util) read_movie() (in module hong2p.thor) recording_df2keys() (in module hong2p.util) remerge_suite2p_merged() (in module hong2p.suite2p) remove_axes_ticks() (in module hong2p.viz) remove_consecutive_repeats() (in module hong2p.olf)

renumber_rois() (in module hong2p.roi) renumber_rois2() (in module hong2p.roi) roi_center() (in module hong2p.roi) roi_centers() (in module hong2p.roi) roi_jumps() (in module hong2p.roi) rois2best_planes_only() (in module hong2p.roi) ROIsNotLabeledError row_labels() (in module hong2p.viz)

S

save_odor2abbrev_cache() (in module hong2p.olf) scalar_coords() (in module hong2p.xarray) scale_template() (in module hong2p.roi) select_certain_rois() (in module hong2p.roi) set_data_root() (in module hong2p.util) set_facetgrid_legend() (in module hong2p.viz) set_panel2order() (in module hong2p.viz) set_suite2p_iscell_label() (in module hong2p.suite2p) shorten_path() (in module hong2p.util) shorten_stimfile_path() (in module hong2p.util) showsync() (in module hong2p.viz) skipped_comparison_nums() (in module hong2p.util) smooth_1d() (in module hong2p.util) sort_odor_list() (in module hong2p.olf) sort_odors() (in module hong2p.olf)

split_odor_w_conc() (in module hong2p.util) stable_rois() (in module hong2p.roi) start_color() (in module hong2p.util) stimfile_odorset() (in module hong2p.util) stimfile_root() (in module hong2p.util) stimulus_yaml_from_thorimage() (in module hong2p.util) stop_color() (in module hong2p.util) strip_concs_from_odor_str() (in module hong2p.olf) subrecording_tiff_blocks() (in module hong2p.util) subrecording_tiff_blocks_df() (in module hong2p.util) subset_levels() (in module hong2p.util) suffix_index_names() (in module hong2p.util) suite2p_footprint2bool_mask() (in module hong2p.suite2p) suite2p_params() (in module hong2p.suite2p) suite2p_roi_stat2roi() (in module hong2p.suite2p) suite2p_stat2rois() (in module hong2p.suite2p)

T

template_data_file() (in module hong2p.roi) template_match() (in module hong2p.roi) thor2tiff() (in module hong2p.util) thor_subdirs() (in module hong2p.thor) thorimage2yaml_info_and_odor_lists() (in module hong2p.util) thorimage_dir() (in module hong2p.util) thorimage_dir_input() (in module hong2p.util) thorimage_subdirs() (in module hong2p.thor) thorimage_xml() (in module hong2p.thor) thorsync_dir() (in module hong2p.util)

thorsync_num() (in module hong2p.thor) thorsync_subdirs() (in module hong2p.thor) threshold_crossings() (in module hong2p.thor) tif2xml_root() (in module hong2p.thor) tiff_filename2keys() (in module hong2p.util) tiff_ijroi_filename() (in module hong2p.util) tiff_thorimage_id() (in module hong2p.util) tiff_title() (in module hong2p.util) to_filename() (in module hong2p.util) TooManyStimulusFiles

U

u8_color() (in module hong2p.util)

unique_coord_value() (in module hong2p.xarray)

V

version_info() (in module hong2p.util)

W

with_panel_orders() (in module hong2p.viz)

write_tiff() (in module hong2p.util)

X

xmlroot() (in module hong2p.thor)

Y

yaml_data2odor_lists() (in module hong2p.olf)

yaml_data2pin_lists() (in module hong2p.olf)