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  • The PHANGS-ALMA Pipeline
    • Introduction
    • What this pipeline is for
    • Pipeline and configuration files
    • Contact
  • Installation
    • Requirements
    • Install directly from GitHub
    • Install from a cloned repository
  • Key files
    • Master key
      • Key definitions
        • Directories
        • Files giving locations of input data
        • Files defining targets and algorithms
      • Example master key file
    • MS key
      • Example MS key file
    • Singledish key
      • Example singledish key file
    • Cleanmask key
      • Example cleanmask key file
    • Distance key
      • Example distance key file
    • Window key
      • Example window key file
    • Config key
      • Column Definitions
        • Column 1: Type of field
        • Column 2: Name
        • Column 3: Pameters
      • Parameter options
        • line_product
        • cont_product
        • interf_config
        • feather_config
        • singledish_config
      • Example config key file
    • Target key
      • Example target key file
    • Moment key
      • Example moment key file
    • Derived key
      • Example derived key file
    • Imaging key
      • Example imaging key file
    • Linmos key
      • Example linmos key file
    • Override key
      • Example override key file
    • Dir key
      • Example dir key file
  • Running the pipeline
    • Setting up
    • Running
  • Handlers
    • KeyHandler
    • SingleDishHandler
    • VisHandler
    • ImagingHandler
    • ImagingChunkedHandler
    • PostProcessHandler
    • DerivedHandler
  • Changelog
    • [Unreleased]
      • Added
      • Changed
      • Fixed
      • Dependencies
  • Reference/API
    • KeyHandler
      • KeyHandler
        • KeyHandler.build_key_handler()
        • KeyHandler.check_dir_existence()
        • KeyHandler.check_key_existence()
        • KeyHandler.check_ms_existence()
        • KeyHandler.check_sd_existence()
        • KeyHandler.get_all_configs()
        • KeyHandler.get_all_mosaic_targets()
        • KeyHandler.get_all_non_mosaic_targets()
        • KeyHandler.get_all_targets()
        • KeyHandler.get_alma_download_restrictions()
        • KeyHandler.get_ang_res_dict()
        • KeyHandler.get_array_tags_for_config()
        • KeyHandler.get_channel_width_for_cont_product()
        • KeyHandler.get_channel_width_for_line_product()
        • KeyHandler.get_clean_scales_for_config()
        • KeyHandler.get_cleanmask_dir_for_target()
        • KeyHandler.get_cleanmask_filename()
        • KeyHandler.get_continuum_products()
        • KeyHandler.get_contsub_combinespw()
        • KeyHandler.get_contsub_excludefreqrange()
        • KeyHandler.get_contsub_fitorder()
        • KeyHandler.get_contsub_flagedgefraction()
        • KeyHandler.get_derived_dir_for_target()
        • KeyHandler.get_derived_kwargs()
        • KeyHandler.get_distance_for_target()
        • KeyHandler.get_feather_config_for_interf_config()
        • KeyHandler.get_feather_configs()
        • KeyHandler.get_field_for_input_ms()
        • KeyHandler.get_file_for_input_ms()
        • KeyHandler.get_freq_ranges_for_cont_product()
        • KeyHandler.get_imaging_dir_for_target()
        • KeyHandler.get_imaging_recipes()
        • KeyHandler.get_interf_config_for_feather_config()
        • KeyHandler.get_interf_configs()
        • KeyHandler.get_joint_imaging_dirs_for_singledish_config()
        • KeyHandler.get_joint_imaging_suffix_for_singledish_config()
        • KeyHandler.get_line_products()
        • KeyHandler.get_line_tag_for_line_product()
        • KeyHandler.get_lines_to_flag()
        • KeyHandler.get_linked_mask_configs()
        • KeyHandler.get_linmos_targets()
        • KeyHandler.get_moment_list()
        • KeyHandler.get_mosaic_target_for_parts()
        • KeyHandler.get_overrides()
        • KeyHandler.get_params_for_moment()
        • KeyHandler.get_params_for_singledish()
        • KeyHandler.get_parts_for_linmos()
        • KeyHandler.get_path_for_casaversion()
        • KeyHandler.get_phasecenter_for_target()
        • KeyHandler.get_phys_res_dict()
        • KeyHandler.get_postprocess_dir_for_target()
        • KeyHandler.get_release_dir_for_target()
        • KeyHandler.get_require_tags_for_config()
        • KeyHandler.get_sd_filename()
        • KeyHandler.get_singledish_configs()
        • KeyHandler.get_singledish_dir_for_target()
        • KeyHandler.get_statwt_edge_for_line_product()
        • KeyHandler.get_system_velocity_and_velocity_width_for_target()
        • KeyHandler.get_targets()
        • KeyHandler.get_targets_in_ms_key()
        • KeyHandler.get_timebin_for_array_tag()
        • KeyHandler.get_vfield_dir_for_target()
        • KeyHandler.get_vfield_file_for_target()
        • KeyHandler.get_whole_targets()
        • KeyHandler.get_window_for_target()
        • KeyHandler.has_data_for_config()
        • KeyHandler.has_overrides_for_key()
        • KeyHandler.has_singledish()
        • KeyHandler.is_target_in_mosaic()
        • KeyHandler.is_target_linmos()
        • KeyHandler.loop_over_input_ms()
        • KeyHandler.make_missing_directories()
        • KeyHandler.print_configs()
        • KeyHandler.print_derived()
        • KeyHandler.print_missing_distances()
        • KeyHandler.print_missing_targets()
        • KeyHandler.print_missing_window()
        • KeyHandler.print_products()
        • KeyHandler.set_dochecks()
    • SingleDishHandler
      • SingleDishHandler
        • SingleDishHandler.loop_singledish()
        • SingleDishHandler.recipe_process_one_target()
        • SingleDishHandler.task_execute_single_dish_pipeline()
    • VisHandler
      • VisHandler
        • VisHandler.loop_stage_uvdata()
        • VisHandler.remove_staged_products()
        • VisHandler.task_concat_uvdata()
        • VisHandler.task_contsub()
        • VisHandler.task_extract_continuum()
        • VisHandler.task_extract_line()
        • VisHandler.task_remove_concat()
        • VisHandler.task_run_custom_scripts()
        • VisHandler.task_split()
    • ImagingHandler
      • ImagingHandler
        • ImagingHandler.loop_imaging()
        • ImagingHandler.recipe_phangsalma_imaging()
        • ImagingHandler.task_assign_multiscales()
        • ImagingHandler.task_export_to_fits()
        • ImagingHandler.task_initialize_clean_call()
        • ImagingHandler.task_make_dirty_image()
        • ImagingHandler.task_multiscale_clean()
        • ImagingHandler.task_pick_cell_and_imsize()
        • ImagingHandler.task_read_clean_mask()
        • ImagingHandler.task_revert_to_imaging()
        • ImagingHandler.task_setup_sdintimaging()
        • ImagingHandler.task_singlescale_clean()
        • ImagingHandler.task_singlescale_mask()
    • ImagingChunkedHandler
      • ImagingChunkedHandler
        • ImagingChunkedHandler.configure_chunk_parameters()
        • ImagingChunkedHandler.recipe_phangsalma_imaging()
        • ImagingChunkedHandler.return_valid_chunks()
        • ImagingChunkedHandler.run_imaging()
        • ImagingChunkedHandler.set_channel_num()
        • ImagingChunkedHandler.set_cube_cell_and_imsize()
        • ImagingChunkedHandler.task_cleanup()
        • ImagingChunkedHandler.task_complete_gather_into_cubes()
        • ImagingChunkedHandler.task_export_to_fits()
        • ImagingChunkedHandler.task_gather_into_cube()
        • ImagingChunkedHandler.task_initialize_clean_call()
        • ImagingChunkedHandler.task_make_dirty_image()
        • ImagingChunkedHandler.task_multiscale_clean()
        • ImagingChunkedHandler.task_read_clean_mask()
        • ImagingChunkedHandler.task_revert_to_imaging()
        • ImagingChunkedHandler.task_setup_sdintimaging()
        • ImagingChunkedHandler.task_singlescale_clean()
        • ImagingChunkedHandler.task_singlescale_mask()
        • ImagingChunkedHandler.task_split_cube_to_chunks()
        • ImagingChunkedHandler.tempdir_exists
    • PostProcessHandler
      • PostProcessHandler
        • PostProcessHandler.loop_postprocess()
        • PostProcessHandler.recipe_cleanup_one_target()
        • PostProcessHandler.recipe_convolve_to_scale()
        • PostProcessHandler.recipe_mosaic_one_target()
        • PostProcessHandler.recipe_prep_one_target()
        • PostProcessHandler.task_align_for_mosaic()
        • PostProcessHandler.task_compress()
        • PostProcessHandler.task_convert_units()
        • PostProcessHandler.task_convolve_parts_for_mosaic()
        • PostProcessHandler.task_export_to_fits()
        • PostProcessHandler.task_feather()
        • PostProcessHandler.task_linear_mosaic()
        • PostProcessHandler.task_make_interf_weight()
        • PostProcessHandler.task_make_singledish_weight()
        • PostProcessHandler.task_pbcorr()
        • PostProcessHandler.task_rename_sdintimaging()
        • PostProcessHandler.task_round_beam()
        • PostProcessHandler.task_stage_interf_data()
        • PostProcessHandler.task_stage_singledish()
    • DerivedHandler
      • DerivedHandler
        • DerivedHandler.loop_derive_products()
        • DerivedHandler.task_build_broad_mask()
        • DerivedHandler.task_build_flat_broad_mask()
        • DerivedHandler.task_build_flat_strict_mask()
        • DerivedHandler.task_build_strict_mask()
        • DerivedHandler.task_build_vfield()
        • DerivedHandler.task_convolve()
        • DerivedHandler.task_estimate_noise()
        • DerivedHandler.task_generate_flatmaps()
        • DerivedHandler.task_generate_moments()
        • DerivedHandler.task_generate_secondary_moments()
        • DerivedHandler.task_shuffle_cube()
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