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metno/pyaerocom: Version 0.10.0

Gliß, Jonas; Gallefoss, Eirik; Brenna, Hans; Griesfeller, Jan; Mortier, Augustin; Svennevik, Hanna; Sjur, Anna-Lina; Schulz, Michael

pyaerocom version 0.10.0

This release comes with many new features, major improvements and a more stable API. Please see the individual points below for major changes.

New feature modules

Modules that contain new features. See here for a list of all file modifications between version 0.8.0 and 0.10.0.

  • pyaerocom/combine_vardata_ungridded.py: Colocation of ungridded data.
  • pyaerocom/helpers_landsea_masks.py: Access and helpers for land-sea mask filtering.
  • pyaerocom/io/read_ghost.py: reading routine for GHOST dataset.
  • pyaerocom/io/read_mscw_ctm.py: Reading interface for EMEP data.
  • pyaerocom/molmasses.py: helpers related to access of molecular masses for species.
  • pyaerocom/trends_engine.py: Interface for computing trends using the method by Mortier et al., 2020.
  • pyaerocom/web/helpers_evaluation_iface.py: helper methods for conversion of ColocatedData to json files for Aerocom Evaluation interface.
  • pyaerocom/web/helpers_trends_iface.py: helper methods for conversion of ColocatedData to json files for Aerocom trends interface.
  • pyaerocom/web/utils.py: High-level methods based on results from standard Aerocom analysis. Currently, this contains a method compute_model_average_and_diversity which can be used to compute ensemble median or mean modeldata (e.g. used to compute AEROCOM-MEDIAN and MEAN in Gliss et al., 2020).
  • pyaerocom/scripts/cli.py: simple command line interface (currently very limited).
  • pyaerocom/scripts/highlevel_utils.py: high-level functions used in CLI.
  • pyaerocom/testdata_access.py: helpers related to initialization and access of pyaerocom testdata.

Updates related to supported observation data-sets and naming conventions

  • Support for reading GHOST data.
  • Support for reading of EMEP model data.

Below, relevant changes applied to already existing code are summarized.

Reading of data (io sub-package) Reading of gridded data

  • ReadGridded class

    • Implement logic to apply constraint reading (i.e. read AOD where AE<0.5, read scattering where RH<40%, etc.). See input arg. constraints in ReadGridded.read_var and associated new class methods listed below.
    • Improve flexibility related to multiple vert_code matches using new method get_vert_code in Variable class.
    • Improve logic associated with resolving variable names for edge cases that include usage of alias variables and auxiliary reading of derived variables.
    • Add new default auxiliary / derived variables: sc550dryaer, concox, vmrox, fmf550aer.
    • New attrs. (incl. @property decorators): vars_provided, registered_var_patterns.
    • New methods: reinit, check_constraint_valid, apply_read_constraint, __repr__.
  • New: Reading interface and support for EMEP file conventions (class ReadMscvCtm).

Reading of ungridded data

  • ReadUngridded

    • Add option only_cached in read method, to only read cached data e.g. when working offline.
    • ReadUngridded can post compute variables with merge method combine.
    • New attrs. (incl. @property decorators): data_dir, post_compute
    • New methods: read_dataset_post, get_vars_supported
  • NEW: Reading interface for GHOST data (class ReadGhost).
  • read_ebas.oy (ReadEbas and ReadEbasOptions)

    • Introduced more reading options (e.g. related to shifting of wavelengths and assumed Angstrom Exponents used for shifting).
    • NOTE: Before, data at wavelengths (wvl) within a tolerance of +/- 50nm were considered around the output wvl (e.g. 500-600nm for sc550aer) and were used as is (i.e. without converting the values to 550nm). Now, the column with wvl closest to the output wvl is used and the measurement data is shifted to the output wvl (e.g. 550nm) assuming a typical Angstrom Exponent (AE=1.5 for extinction and scattering, AAE=1 for absorption, note also upcoming changes for next major release version 0.11.0).
    • Remove filelog in ReadEbas.
    • Resolve some issues related to old variable names and aliases.
    • Implement unit check in column selection method _find_best_data_column.
    • Add framework to output data.
    • Added attrs. in ReadEbas (incl. @property methods): sqlite_database_file, file_dir.
  • ReadUngriddedBase (template metaclass for ungridded reading)

    • allow to specify dataset_path (less dependency on server access, easier to work with local datasets)
    • New attrs. (incl. @property decorators): data_id
    • New methods (implemented): var_supported

Further updates in io sub-package

  • cachehandler_ungridded.py (CacheHandlerUngridded class)

    • Modified to handle custom filenames (e.g. used in new method UngriddedData.save_as).
    • New method delete_all_cache_files
    • New option force_use_outdated
  • Add method get_ungridded_reader in io/utils.py.

Data objects

  • GriddedData

    • Can be converted to xarray.
    • More robust and flexible time-series extraction, e.g., constraints can be applied during temporal resampling (i.e. hierarchical min_num_obs or how).
    • Improving automatic retrieval of lowest layer for profile data using CF attr. "positive".
    • Method mean now uses area weighted mean by default.
    • New methods: years_avail, split_years, mean_at_coords, filter_altitude, filter_region, apply_region_mask, aerocom_savename, to_xarray, area_weighted_mean
  • UngriddedData

    • Can be filtered by country names
    • Can now be saved as pickled objects
    • Create UngriddedData from StationData object(s)
    • Colocation of UngriddedData is now possible (relevant code is in new module combine_vardata_ungridded.py)
    • Support for wildcards in station data conversion methods.
    • New attrs. (incl. decorators): last_meta_idx, nonunique_station_names, countries_available
    • New methods: from_station_data (static method), check_set_country, check_convert_var_units, filter_altitude, filter_region, apply_region_mask, colocate_vardata, save_as, from_cache (static method).
  • ColocatedData

    • Implement method to compute regional time-series.
    • Support automatic assignments of countries for each site.
    • Support computation of area weighted statistics in calc_statistics.
    • New attributes: has_time_dim, has_latlon_dims, countries_available, country_codes_available, area_weights
    • New methods: get_country_codes, calc_area_weights, flatten_latlondim_station_name, stack, unstack, check_set_countries, filter_altitude, apply_country_filter, set_zeros_nan, apply_region_mask, filter_region, get_regional_timeseries
  • StationData

    • Computation of climatological time-series
    • Improved handling of metadata access (get_meta) and merging of metadata
    • resample_timeseries was renamed to resample_time (but old version still works.)
    • new method StationData.copy

Colocation of data Low-level colocation routines (colocation.py)

  • Outliers in gridded/gridded colocation are now removed in original resolution.
  • Gridded/gridded colocation now re-grids to the lowest of both resolutions.
  • Add option resample_how, which can also be applied hierarchical, like min_num_obs (e.g. used to resample O3max).
  • resample_how option in high level colocation routines.
  • Option to use obs climatology for gridded / ungridded colocation.
  • New helper method correct_model_stp_coldata in colocation.py which applies STP correction to a colocated data object containing obs at STP based on station altitude and temperature derived from ERA Interim data (BETA feature only working for 2010 data and with access to METNo infrastructure).
  • Some bug fixes for certain edge cases.

High-level colocation routines (colocation_auto.py)

Affects classes ColocationSetup and Colocator

  • Support new EMEP reading routine.
  • Model and obsdata directories can be specified explicitly.
  • Option model_to_stp (BETA feature which will not work in most cases, see above).
  • New attrs. obs_add_meta, resample_how.
  • New methods (Colocator): read_model_data, read_ungridded

Filtering of data

  • Implement filtering of binary masks for GriddedData, UngriddedData and ColocatedData
  • Harmonize API of spatial filtering in data classes (i.e. method filter_region that can handle rectangular and binary region masks)
  • Automatic access to HTAP binary land-sea masks
  • Handling of binary and rectangular regions in Filter class.

Other updates (in top-level modules)

  • config.py (Config class)

    • Major improvements and API changes, e.g. related to automatic setup and adding new data search directories and ungridded observations.
    • In particular, attrs. BASEDIR, MODELBASEDIR, OBSBASEDIR are deprecated.
    • Instead, methods add_data_search_dir and add_ungridded_obs can be used to register data locations.
  • geodesy.py: new methods calc_latlon_dists, find_coord_indices_within_distance, get_country_info_coords.
  • New methods in helpers.py, the most relevant ones are extract_latlon_dataarray, make_dummy_cube_latlon, numpy_to_cube, sort_ts_types, calc_climatology.
  • New methods in mathutils.py: weighted_sum, sum, weighted_mean, weighted_cov, weighted_corr, corr (which were implemented in calc_statistics), vmrx_to_concx, concx_to_vmrx.
  • New class AerocomDataID in metastandards.py (is used in ReadGridded to separate data ID into metadata based on AeroCom 3 conventions).
  • New helper classes ObsVarCombi and AuxInfoUngridded in obs_io.py.
  • region.py: New method Region.plot and support for binary regions.
  • TimeResampler: implement handling of how to specify aggregating kernel (e.g. mean, max, min, std...).
  • New and interactive tutorials, for details see pyaerocom-tutorials repo.
  • NEW: colocation routine for ungridded data, the relevant code is in ne module test_combine_vardata_ungridded.py). NOTE: currently only implemented to create colocated UngriddedData objects, a routine that outputs ColocatedData object will come in v0.11.0.
  • tstype.py (class TsType)

    • Implement setter method for mulfac
    • New attrs (incl. @property decorators): TO_NUMPY, RS_OFFSETS (not in use), TSTR_TO_CF, datetime64_str, timedelta64_str, cf_base_unit, next_lower, next_higher
    • New methods: to_timedelta64, valid, to_numpy_freq
    • Rename method to_pandas to to_pandas_freq
  • variable.py

    • Define wildcard based lookup of default vertical codes for variable families (in VarNameInfo) and related class method get_default_vert_code (experimental)
    • new helper function get_emep_variables
    • Variable class
      • New attrs (incl. @property decorators): var_name_aerocom, default_vert_code, var_name_input, is_3d, is_wavelength_dependent, is_dry, is_alias
      • New methods: get_default_vert_code, __eq__
    • VarCollection class
      • support adding new variables (in addition to the ones defined in an ini file)
      • New methods: add_var, get_var
  • NEW toplevel method pyaerocom.initialise_testdata(): checks access to testdataset and downloads it to directory ~/MyPyaerocom if not available (or outdated).

Web processing tools (web sub-package)

  • Better separation of modules and code for AerocomEvalation tools and AerosolTrends tools.
  • Add support for auxiliary / derived obsdatasets in web.helpers.ObsConfigEval.
  • New method to compute ensemble median or mean in web/utils.py.

Aerocom Evaluation tools

  • Store a copy of the config file in experiment output directory.
  • Option weighted_stats in AerocomEvaluation (if active, weighted statistics are applied to gridded/gridded colocated objects in heatmaps).
  • Create json files for daily and monthly heat-maps.
  • Support also country based regional statistics (AerocomEvaluation.regions_how)
  • Regional time-series are now computed automatically for all regions.
  • Support evaluation of diurnal (hourly data).
  • utility function compute_model_average_and_diversity now also outputs fields for 1. and 3. quantiles (median) and std. (mean)
  • New options --onlyjson and --warnings in CLI pyaeroeval.
  • Improved robustness and flexibility of evaluation framework.
  • New methods and attrs. in AerocomEvaluation class:
    • Attrs: only_json, weighted_stats, regions_how, region_groups, resample_how, all_obs_vars, iface_names, name_config_file, name_config_file_json,
    • Methods: get_model_name, get_diurnal_only, read_model_data, read_ungridded_obsdata,

Trends evaluation tools

No relevant changes here (only some refacturing).

Plotting (plot sub-package)

  • New method plot_nmb_map_colocateddata in plot/mapping.py for plotting bias maps from ColocatedData
  • Improve options in heatmap plot (plot/heatmaps.py) (i.e. smart automatic formatting of heatmap annotation if values span several orders of magnitude).
  • Some bug fixes associated with automatic retrieval of colorbar levels (io/helpers.py).
  • New method init_multimap_grid in plot/mapping.py
  • Annotation fontsize in plot_scatter can now be controlled now via input arg fontsize_annot

Major API changes (not backwards compatible):

  • Renamed class ReadSulphurAasEtAl to ReadAasEtal
  • StationData.resample_timeseries is deprecated (but still works) and usage of new method resample_time is recommended
  • Some AeroCom variables were renamed (e.g. scatc550aer -> sc550aer, absc550aer -> ac550aer, bscatc -> bsc, etc.)

Testing and CI

  • Most tests now uses a publicly available test dataset.
  • Implemented automatic CI testing in Github Actions.
  • Add conftest.py for defining session wide test fixtures.
  • Many more tests resulting in largely improved test coverage, see here.

Bug fixes

  • Fix bug related to merging of StationData in case of overlapping time-series (issue 106).
  • Fix bug in method GriddedData.change_base_year
  • ReadEbas: Fixed bug related to column selection for wavelength range which identified data columns as valid if there was only one column match for var of interest.
  • Fix minor bug in reordering of dimensions of GriddedData when one dimension definition was missing.
  • Fix bug in GriddedData.crop due to time bounds not removed correctly.
  • Fix bug related related to extraction of time interval in GriddedData.sel (see here for details).

Upcoming changes

See here for a list of changes planned for the next upcoming release.

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