Index A | B | C | E | F | G | L | M | P | R | S | U A adapt_paths_to_output_pattern() (in module photon_mosaic_pipeline.paths_selection) B BOLD (photon_mosaic_pipeline.logging_config.ColoredFormatter attribute) build_snakemake_command() (in module photon_mosaic_pipeline.cli) C ColoredFormatter (class in photon_mosaic_pipeline.logging_config) COLORS (photon_mosaic_pipeline.logging_config.ColoredFormatter attribute) configure_slurm_execution() (in module photon_mosaic_pipeline.cli) create_argument_parser() (in module photon_mosaic_pipeline.cli) cross_platform_path() (in module photon_mosaic_pipeline.snakemake_utils) E ensure_default_config() (in module photon_mosaic_pipeline.cli) ensure_dir() (in module photon_mosaic_pipeline.logging_config) execute_pipeline_with_retry() (in module photon_mosaic_pipeline.cli) F find_raw_data_paths() (in module photon_mosaic_pipeline.paths_selection) format() (photon_mosaic_pipeline.logging_config.ColoredFormatter method) G get_edited_options() (in module photon_mosaic_pipeline.rules.suite2p_run) get_snakefile_path() (in module photon_mosaic_pipeline.snakemake_utils) L load_and_process_config() (in module photon_mosaic_pipeline.cli) log_cuda_availability() (in module photon_mosaic_pipeline.snakemake_utils) log_list_summary() (in module photon_mosaic_pipeline.logging_config) log_section_header() (in module photon_mosaic_pipeline.logging_config) log_subsection() (in module photon_mosaic_pipeline.logging_config) M main() (in module photon_mosaic_pipeline.cli) module photon_mosaic_pipeline.cli photon_mosaic_pipeline.logging_config photon_mosaic_pipeline.paths_selection photon_mosaic_pipeline.preprocessing.contrast photon_mosaic_pipeline.preprocessing.derotation photon_mosaic_pipeline.preprocessing.noop photon_mosaic_pipeline.preprocessing.stiminterpolation photon_mosaic_pipeline.rules.preprocessing photon_mosaic_pipeline.rules.suite2p_run photon_mosaic_pipeline.snakemake_utils P parse_si_metadata() (in module photon_mosaic_pipeline.preprocessing.stiminterpolation) photon_mosaic_pipeline.cli module photon_mosaic_pipeline.logging_config module photon_mosaic_pipeline.paths_selection module photon_mosaic_pipeline.preprocessing.contrast module photon_mosaic_pipeline.preprocessing.derotation module photon_mosaic_pipeline.preprocessing.noop module photon_mosaic_pipeline.preprocessing.stiminterpolation module photon_mosaic_pipeline.rules.preprocessing module photon_mosaic_pipeline.rules.suite2p_run module photon_mosaic_pipeline.snakemake_utils module R RESET (photon_mosaic_pipeline.logging_config.ColoredFormatter attribute) run() (in module photon_mosaic_pipeline.preprocessing.contrast) (in module photon_mosaic_pipeline.preprocessing.derotation) (in module photon_mosaic_pipeline.preprocessing.noop) (in module photon_mosaic_pipeline.preprocessing.stiminterpolation) run_preprocessing() (in module photon_mosaic_pipeline.rules.preprocessing) run_suite2p() (in module photon_mosaic_pipeline.rules.suite2p_run) S save_timestamped_config() (in module photon_mosaic_pipeline.cli) set_up_dff_targets() (in module photon_mosaic_pipeline.paths_selection) set_up_neuropil_targets() (in module photon_mosaic_pipeline.paths_selection) set_up_suite2p_targets() (in module photon_mosaic_pipeline.paths_selection) setup_logging() (in module photon_mosaic_pipeline.logging_config) setup_output_directories() (in module photon_mosaic_pipeline.cli) U update_default_config() (in module photon_mosaic_pipeline.cli)
