natcap.invest.fisheries.fisheries_hst_io¶

The Fisheries Habitat Scenarios Tool IO module contains functions for handling inputs and outputs

natcap.invest.fisheries.fisheries_hst_io.fetch_args(args)¶

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 (same as Fisheries Preprocessor entry point)
Returns: dictionary containing necessary variables
Return type: vars_dict (dictionary)
Raises: ValueError – parameter mismatch between Population and Habitat CSV files

Example Returns:

vars_dict = {
    'workspace_dir': 'path/to/workspace_dir/',
    'output_dir': 'path/to/output_dir/',
    'sexsp': 2,
    'gamma': 0.5,

    # Pop Vars
    'population_csv_path': 'path/to/csv_path',
    'Surv_nat_xsa': np.array(
        [[[...], [...]], [[...], [...]], ...]),
    'Classes': np.array([...]),
    'Class_vectors': {
        'Vulnfishing': np.array([...], [...]),
        'Maturity': np.array([...], [...]),
        'Duration': np.array([...], [...]),
        'Weight': np.array([...], [...]),
        'Fecundity': np.array([...], [...]),
    },
    'Regions': np.array([...]),
    'Region_vectors': {
        'Exploitationfraction': np.array([...]),
        'Larvaldispersal': np.array([...]),
    },

    # Habitat Vars
    'habitat_chg_csv_path': 'path/to/csv',
    'habitat_dep_csv_path': 'path/to/csv',
    'Habitats': ['habitat1', 'habitat2', ...],
    'Hab_classes': ['class1', 'class2', ...],
    'Hab_regions': ['region1', 'region2', ...],
    'Hab_chg_hx': np.array(
        [[[...], [...]], [[...], [...]], ...]),
    'Hab_dep_ha': np.array(
        [[[...], [...]], [[...], [...]], ...]),
    'Hab_class_mvmt_a': np.array([...]),
    'Hab_dep_num_a': np.array([...]),
}

natcap.invest.fisheries.fisheries_hst_io.read_habitat_chg_csv(args)¶

Parses and verifies a Habitat Change Parameters CSV file and returns a dictionary of information related to the interaction between a species and the given habitats.

Parses the Habitat Change Parameters CSV file for the following vectors:

Names of Habitats and Regions

Habitat Area Change

Parameters

args (dictionary) – arguments from the user (same as Fisheries HST entry point)

Returns

dictionary containing necessary: variables

Return type

habitat_chg_dict (dictionary)

Raises

MissingParameter – required parameter not included
ValueError – values are out of bounds or of wrong type
IndexError – likely a file formatting issue

Example Returns:

habitat_chg_dict = {
    'Habitats': ['habitat1', 'habitat2', ...],
    'Hab_regions': ['region1', 'region2', ...],
    'Hab_chg_hx': np.array(
        [[[...], [...]], [[...], [...]], ...]),
}

natcap.invest.fisheries.fisheries_hst_io.read_habitat_dep_csv(args)¶

Parses and verifies a Habitat Dependency Parameters CSV file and returns a dictionary of information related to the interaction between a species and the given habitats.

Parses the Habitat Parameters CSV file for the following vectors:

Names of Habitats and Classes

Habitat-Class Dependency

The following vectors are derived from the information given in the file:

Classes where movement between habitats occurs

Number of habitats that a particular class depends upon

Parameters

args (dictionary) – arguments from the user (same as Fisheries HST entry point)

Returns

dictionary containing necessary: variables

Return type

habitat_dep_dict (dictionary)

Raises

MissingParameter - required parameter not included –
ValueError - values are out of bounds or of wrong type –
IndexError - likely a file formatting issue –

Example Returns:

habitat_dep_dict = {
    'Habitats': ['habitat1', 'habitat2', ...],
    'Hab_classes': ['class1', 'class2', ...],
    'Hab_dep_ha': np.array(
        [[[...], [...]], [[...], [...]], ...]),
    'Hab_class_mvmt_a': np.array([...]),
    'Hab_dep_num_a': np.array([...]),
}

natcap.invest.fisheries.fisheries_hst_io.read_population_csv(args)¶

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

Returns

dictionary containing verified population: arguments

Return type

pop_dict (dictionary)

Raises

MissingParameter – required parameter not included
ValueError – values are out of bounds or of wrong type

Example Returns:

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

    # Class Vectors
    'Classes': np.array([...]),
    'Class_vector_names': [...],
    'Class_vectors': {
        'Vulnfishing': np.array([...], [...]),
        'Maturity': np.array([...], [...]),
        'Duration': np.array([...], [...]),
        'Weight': np.array([...], [...]),
        'Fecundity': np.array([...], [...]),
    },

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

natcap.invest.fisheries.fisheries_hst_io.save_population_csv(vars_dict)¶

Creates a new Population Parameters CSV file based the provided inputs.

Parameters: vars_dict (dictionary) – variables generated by preprocessor arguments and run.

Example Args:

args = {
    'workspace_dir': 'path/to/workspace_dir/',
    'output_dir': 'path/to/output_dir/',
    'sexsp': 2,
    'population_csv_path': 'path/to/csv',  # original csv file
    'Surv_nat_xsa': np.ndarray([...]),
    'Surv_nat_xsa_mod': np.ndarray([...]),

    # Class Vectors
    'Classes': np.array([...]),
    'Class_vector_names': [...],
    'Class_vectors': {
        'Vulnfishing': np.array([...], [...]),
        'Maturity': np.array([...], [...]),
        'Duration': np.array([...], [...]),
        'Weight': np.array([...], [...]),
        'Fecundity': np.array([...], [...]),
    },

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

    # other arguments are ignored ...
}

Note

Creates a modified Population Parameters CSV file located in the ‘workspace/output/’ folder
Currently appends ‘_modified’ to original filename for new filename