natcap.invest.fisheries.fisheries_io

The Fisheries IO module contains functions for handling inputs and outputs

exception natcap.invest.fisheries.fisheries_io.MissingParameter

Bases: ValueError

An exception class that may be raised when a necessary parameter is not provided by the user.

natcap.invest.fisheries.fisheries_io.create_outputs(vars_dict)

Creates outputs from variables generated in the run_population_model() function in the fisheries_model module

Creates the following:

• Results CSV File

• Results HTML Page

• Results Shapefile (if provided)

• Intermediate CSV File

Parameters

vars_dict (dictionary) – contains variables generated by model run

natcap.invest.fisheries.fisheries_io.fetch_args(args, create_outputs=True)

Fetches input arguments from the user, verifies for correctness and completeness, and returns a list of variables dictionaries

Parameters

args (dictionary) – arguments from the user

Returns

set of variable dictionaries for each

model

Return type

model_list (list)

Example Returns:

model_list = [
    {
        'workspace_dir': 'path/to/workspace_dir',
        'results_suffix': 'scenario_name',
        'output_dir': 'path/to/output_dir',
        'aoi_vector_path': 'path/to/aoi_vector_path',
        'total_timesteps': 100,
        'population_type': 'Stage-Based',
        'sexsp': 2,
        'harvest_units': 'Individuals',
        'do_batch': False,
        'spawn_units': 'Weight',
        'total_init_recruits': 100.0,
        'recruitment_type': 'Ricker',
        'alpha': 32.4,
        'beta': 54.2,
        'total_recur_recruits': 92.1,
        'migr_cont': True,
        'val_cont': True,
        'frac_post_process': 0.5,
        'unit_price': 5.0,

        # Pop Params
        'population_csv_path': 'path/to/csv_path',
        'Survnaturalfrac': numpy.array(
            [[[...], [...]], [[...], [...]], ...]),
        'Classes': numpy.array([...]),
        'Vulnfishing': numpy.array([...], [...]),
        'Maturity': numpy.array([...], [...]),
        'Duration': numpy.array([...], [...]),
        'Weight': numpy.array([...], [...]),
        'Fecundity': numpy.array([...], [...]),
        'Regions': numpy.array([...]),
        'Exploitationfraction': numpy.array([...]),
        'Larvaldispersal': numpy.array([...]),

        # Mig Params
        'migration_dir': 'path/to/mig_dir',
        'Migration': [numpy.ndarray, numpy.ndarray, ...]
    },
    {
        ...  # additional dictionary doesn't exist when 'do_batch'
             # is false
    }
]

Note

This function receives an unmodified ‘args’ dictionary from the user

natcap.invest.fisheries.fisheries_io.read_migration_tables(args, class_list, region_list)

Parses, verifies and orders list of migration matrices necessary for program.

Parameters

• args (dictionary) – same args as model entry point

• class_list (list) – list of class names

• region_list (list) – list of region names

Returns

see example below

Return type

mig_dict (dictionary)

Example Returns:

mig_dict = {
    'Migration': [numpy.ndarray, numpy.ndarray, ...]
}

Note

If migration matrices are not provided for all classes, the function will generate identity matrices for missing classes

natcap.invest.fisheries.fisheries_io.read_population_csv(args, path)

Parses and verifies a single Population Parameters CSV file

Parses and verifies inputs from the Population Parameters CSV file. If not all necessary vectors are included, the function will raise a MissingParameter exception. Survival matrix will be arranged by class-elements, 2nd dim: sex, and 3rd dim: region. Class vectors will be arranged by class-elements, 2nd dim: sex (depending on whether model is sex-specific) Region vectors will be arraged by region-elements, sex-agnostic.

Parameters

• args (dictionary) – arguments provided by user

• path (string) – the particular Population Parameters CSV file to parse and verifiy

Returns

dictionary containing verified population

arguments

Return type

pop_dict (dictionary)

Example Returns:

pop_dict = {
    'population_csv_path': 'path/to/csv',
    'Survnaturalfrac': numpy.array(
        [[...], [...]], [[...], [...]], ...),

    # Class Vectors
    'Classes': numpy.array([...]),
    'Vulnfishing': numpy.array([...], [...]),
    'Maturity': numpy.array([...], [...]),
    'Duration': numpy.array([...], [...]),
    'Weight': numpy.array([...], [...]),
    'Fecundity': numpy.array([...], [...]),

    # Region Vectors
    'Regions': numpy.array([...]),
    'Exploitationfraction': numpy.array([...]),
    'Larvaldispersal': numpy.array([...]),
}

natcap.invest.fisheries.fisheries_io.read_population_csvs(args)

Parses and verifies the Population Parameters CSV files

Parameters

args (dictionary) – arguments provided by user

Returns

list of dictionaries containing verified population

arguments

Return type

pop_list (list)

Example Returns:

pop_list = [
    {
        'Survnaturalfrac': numpy.array(
            [[...], [...]], [[...], [...]], ...),

        # Class Vectors
        'Classes': numpy.array([...]),
        'Vulnfishing': numpy.array([...], [...]),
        'Maturity': numpy.array([...], [...]),
        'Duration': numpy.array([...], [...]),
        'Weight': numpy.array([...], [...]),
        'Fecundity': numpy.array([...], [...]),

        # Region Vectors
        'Regions': numpy.array([...]),
        'Exploitationfraction': numpy.array([...]),
        'Larvaldispersal': numpy.array([...]),
    },
    {
        ...
    }
]