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# Specimens

Generate snail specimens.

## `SpecimenParams`

Bases: `BaseModel`

Parameters for specimen generation.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`end_date` | `date` | End date for specimen collection | required
`length` | `int` | Length of specimen genomes (must be positive) | required
`max_mass` | `float` | Maximum mass for specimens (must be positive) | required
`min_mass` | `float` | Minimum mass for specimens (must be positive and less than max_mass) | required
`mut_scale` | `float` | Scale factor for mutation effect | required
`mutations` | `int` | Number of mutations in specimens (must be between 0 and length) | required
`number` | `int` | Number of specimens to generate (must be positive) | required
`seed` | `int` | Random seed for reproducibility | required
`start_date` | `date` | Start date for specimen collection | required

Source code in `src/snailz/specimens.py`

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    class SpecimenParams(BaseModel):
        """Parameters for specimen generation."""

        end_date: date = Field(description="End date for specimen collection")
        length: int = Field(
            gt=0, description="Length of specimen genomes (must be positive)"
        )
        max_mass: float = Field(
            gt=0, description="Maximum mass for specimens (must be positive)"
        )
        min_mass: float = Field(
            gt=0,
            description="Minimum mass for specimens (must be positive and less than max_mass)",
        )
        mut_scale: float = Field(ge=0, description="Scale factor for mutation effect")
        mutations: int = Field(
            ge=0,
            description="Number of mutations in specimens (must be between 0 and length)",
        )
        number: int = Field(
            gt=0, description="Number of specimens to generate (must be positive)"
        )
        seed: int = Field(ge=0, description="Random seed for reproducibility")
        start_date: date = Field(description="Start date for specimen collection")

        model_config = {"extra": "forbid"}

        @model_validator(mode="after")
        def validate_fields(self):
            """Validate requirements on fields."""
            if self.min_mass >= self.max_mass:
                raise ValueError("max_mass must be greater than min_mass")
            if self.mutations > self.length:
                raise ValueError("mutations must be between 0 and length")
            if self.end_date < self.start_date:
                raise ValueError("end_date must be greater than or equal to start_date")
            return self

### `validate_fields()`

Validate requirements on fields.

Source code in `src/snailz/specimens.py`

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    @model_validator(mode="after")
    def validate_fields(self):
        """Validate requirements on fields."""
        if self.min_mass >= self.max_mass:
            raise ValueError("max_mass must be greater than min_mass")
        if self.mutations > self.length:
            raise ValueError("mutations must be between 0 and length")
        if self.end_date < self.start_date:
            raise ValueError("end_date must be greater than or equal to start_date")
        return self

## `Specimen`

Bases: `BaseModel`

A single specimen.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`ident` | `str` | unique identifier | required
`collected_on` | `date` | date when specimen was collected | required
`genome` | `str` | bases in genome | required
`mass` | `float` | snail mass in grams | required
`site` | `Point` | grid location where specimen was collected | required
`territory` | `float` | share of the grid that belongs to this specimen | `0.0`

Source code in `src/snailz/specimens.py`

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    class Specimen(BaseModel):
        """A single specimen."""

        ident: str = Field(description="unique identifier")
        collected_on: date = Field(description="date when specimen was collected")
        genome: str = Field(description="bases in genome")
        mass: float = Field(gt=0, description="snail mass in grams")
        site: Point = Field(description="grid location where specimen was collected")
        territory: float = Field(
            default=0.0, description="share of the grid that belongs to this specimen"
        )

## `AllSpecimens`

Bases: `BaseModel`

A set of generated specimens.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`individuals` | `list[Specimen]` | list of individual specimens | required
`loci` | `list[int]` | locations where mutations can occur | required
`params` | `SpecimenParams` | parameters used to generate this data | required
`reference` | `str` | unmutated genome | required
`susceptible_base` | `str` | mutant base that induces mass changes | required
`susceptible_locus` | `int` | location of mass change mutation | required

Source code in `src/snailz/specimens.py`

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    class AllSpecimens(BaseModel):
        """A set of generated specimens."""

        individuals: list[Specimen] = Field(description="list of individual specimens")
        loci: list[int] = Field(description="locations where mutations can occur")
        params: SpecimenParams = Field(description="parameters used to generate this data")
        reference: str = Field(description="unmutated genome")
        susceptible_base: str = Field(description="mutant base that induces mass changes")
        susceptible_locus: int = Field(ge=0, description="location of mass change mutation")

        def to_csv(self) -> str:
            """Return a CSV string representation of the specimens data.

            Returns:
                A CSV-formatted string with people data (without parameters)
            """

            output = io.StringIO()
            writer = utils.csv_writer(output)
            writer.writerow(
                ["ident", "x", "y", "genome", "mass", "collected_on", "territory"]
            )
            for indiv in self.individuals:
                writer.writerow(
                    [
                        indiv.ident,
                        indiv.site.x,
                        indiv.site.y,
                        indiv.genome,
                        indiv.mass,
                        indiv.collected_on,
                        indiv.territory,
                    ]
                )
            return output.getvalue()

### `to_csv()`

Return a CSV string representation of the specimens data.

Returns:

Type | Description
--- | ---
`str` | A CSV-formatted string with people data (without parameters)

Source code in `src/snailz/specimens.py`

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    def to_csv(self) -> str:
        """Return a CSV string representation of the specimens data.

        Returns:
            A CSV-formatted string with people data (without parameters)
        """

        output = io.StringIO()
        writer = utils.csv_writer(output)
        writer.writerow(
            ["ident", "x", "y", "genome", "mass", "collected_on", "territory"]
        )
        for indiv in self.individuals:
            writer.writerow(
                [
                    indiv.ident,
                    indiv.site.x,
                    indiv.site.y,
                    indiv.genome,
                    indiv.mass,
                    indiv.collected_on,
                    indiv.territory,
                ]
            )
        return output.getvalue()

## `specimens_generate(params, grid=None)`

Generate specimens with random genomes and masses.

Each genome is a string of bases of the same length. One locus is randomly chosen as "significant", and a specific mutation there predisposes the snail to mass changes. Other mutations are added randomly at other loci. Specimen masses are only mutated if a grid is provided.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`params` | `SpecimenParams` | SpecimenParams object | required
`grid` | `Grid | None` | Grid object to place specimens on for mass mutation | `None`

Returns:

Type | Description
--- | ---
`AllSpecimens` | AllSpecimens object containing the generated specimens and parameters

Source code in `src/snailz/specimens.py`

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    def specimens_generate(
        params: SpecimenParams, grid: Grid | None = None
    ) -> AllSpecimens:
        """Generate specimens with random genomes and masses.

        Each genome is a string of bases of the same length. One locus is
        randomly chosen as "significant", and a specific mutation there
        predisposes the snail to mass changes. Other mutations are added
        randomly at other loci.  Specimen masses are only mutated if a
        grid is provided.

        Parameters:
            params: SpecimenParams object
            grid: Grid object to place specimens on for mass mutation

        Returns:
            AllSpecimens object containing the generated specimens and parameters

        """
        loci = _make_loci(params)
        reference = _make_reference_genome(params)
        susc_loc = _choose_one(loci)
        susc_base = reference[susc_loc]
        genomes = [_make_genome(reference, loci) for i in range(params.number)]
        masses = _make_masses(params, genomes, susc_loc, susc_base)
        identifiers = _make_idents(params.number)
        collection_dates = _make_collection_dates(params)

        individuals = [
            Specimen(genome=g, mass=m, site=Point(), ident=i, collected_on=d)
            for g, m, i, d in zip(genomes, masses, identifiers, collection_dates)
        ]

        result = AllSpecimens(
            individuals=individuals,
            loci=loci,
            params=params,
            reference=reference,
            susceptible_base=susc_base,
            susceptible_locus=susc_loc,
        )

        if grid is not None:
            mutate_masses(grid, result, params.mut_scale)
            calculate_ranges(grid.params.size, result)

        return result

## `calculate_ranges(size, specimens)`

Calculate the territory of each specimen.

Source code in `src/snailz/specimens.py`

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    def calculate_ranges(size: int, specimens: AllSpecimens) -> None:
        """Calculate the territory of each specimen."""
        # Allocate points to specimens.
        belong = {}
        for x in range(size):
            for y in range(size):
                for indiv in specimens.individuals:
                    assert indiv.site.x is not None
                    assert indiv.site.y is not None
                    dist = (x - indiv.site.x) ** 2 + (y - indiv.site.y) ** 2
                    if ((x, y) not in belong) or (dist < belong[(x, y)]["dist"]):
                        belong[(x, y)] = {"dist": dist, "indiv": {indiv.ident}}
                    elif dist == belong[(x, y)]["dist"]:
                        belong[(x, y)]["indiv"].add(indiv.ident)

        # Add up area per individual
        for indiv in specimens.individuals:
            indiv.territory = 0.0
            for b in belong.values():
                if indiv.ident in b["indiv"]:
                    indiv.territory += 1 / len(b["indiv"])
            indiv.territory = round(indiv.territory, utils.PRECISION)

## `mutate_masses(grid, specimens, mut_scale, specific_index=None)`

Mutate mass based on grid values and genetic susceptibility.

For each specimen, choose a random cell from the grid and modify the mass if the cell's value is non-zero and the genome is susceptible. Records the chosen site coordinates for each specimen regardless of whether mutation occurs. Modifies specimen masses in-place for susceptible individuals; updates site coordinates for all individuals.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`grid` | `Grid` | A Grid object containing pollution values | required
`specimens` | `AllSpecimens` | A AllSpecimens object with individuals to potentially mutate | required
`mut_scale` | `float` | Scaling factor for mutation effect | required
`specific_index` | `int | None` | Optional index to mutate only a specific specimen | `None`

Source code in `src/snailz/specimens.py`

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    def mutate_masses(
        grid: Grid,
        specimens: AllSpecimens,
        mut_scale: float,
        specific_index: int | None = None,
    ) -> None:
        """Mutate mass based on grid values and genetic susceptibility.

        For each specimen, choose a random cell from the grid and modify
        the mass if the cell's value is non-zero and the genome is
        susceptible. Records the chosen site coordinates for each specimen
        regardless of whether mutation occurs.  Modifies specimen masses
        in-place for susceptible individuals; updates site coordinates for
        all individuals.

        Parameters:
            grid: A Grid object containing pollution values
            specimens: A AllSpecimens object with individuals to potentially mutate
            mut_scale: Scaling factor for mutation effect
            specific_index: Optional index to mutate only a specific specimen
        """
        grid_size = len(grid.grid)
        susc_locus = specimens.susceptible_locus
        susc_base = specimens.susceptible_base

        if specific_index is None:
            individuals = specimens.individuals
        else:
            individuals = [specimens.individuals[specific_index]]

        locations = _make_locations(grid_size, len(individuals))
        for indiv, (x, y) in zip(individuals, locations):
            indiv.site.x = x
            indiv.site.y = y
            if grid.grid[x][y] > 0 and indiv.genome[susc_locus] == susc_base:
                indiv.mass = mutate_mass(indiv.mass, mut_scale, grid.grid[x][y])

## `mutate_mass(original, mut_scale, cell_value)`

Mutate a single specimen's mass.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`original` | `float` | The original mass value | required
`mut_scale` | `float` | Scaling factor for mutation effect | required
`cell_value` | `int` | The grid cell value affecting the mutation | required

Returns:

Type | Description
--- | ---
`float` | The mutated mass value, rounded to PRECISION decimal places

Source code in `src/snailz/specimens.py`

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    def mutate_mass(original: float, mut_scale: float, cell_value: int) -> float:
        """Mutate a single specimen's mass.

        Parameters:
            original: The original mass value
            mut_scale: Scaling factor for mutation effect
            cell_value: The grid cell value affecting the mutation

        Returns:
            The mutated mass value, rounded to PRECISION decimal places
        """
        return round(original * (1 + (mut_scale * cell_value)), utils.PRECISION)

## `_choose_one(values)`

Choose a single random item from a collection.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`values` | `list[int]` | A sequence to choose from | required

Returns:

Type | Description
--- | ---
`int` | A randomly selected item from the values sequence

Source code in `src/snailz/specimens.py`

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    def _choose_one(values: list[int]) -> int:
        """Choose a single random item from a collection.

        Parameters:
            values: A sequence to choose from

        Returns:
            A randomly selected item from the values sequence
        """
        return random.choices(values, k=1)[0]

## `_choose_other(values, exclude)`

Choose a value at random except for the excluded values.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`values` | `str` | A collection to choose from | required
`exclude` | `str` | Value or collection of values to exclude from the choice | required

Returns:

Type | Description
--- | ---
`str` | A randomly selected item from values that isn't in exclude

Source code in `src/snailz/specimens.py`

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    def _choose_other(values: str, exclude: str) -> str:
        """Choose a value at random except for the excluded values.

        Parameters:
            values: A collection to choose from
            exclude: Value or collection of values to exclude from the choice

        Returns:
            A randomly selected item from values that isn't in exclude
        """
        candidates = list(sorted(set(values) - set(exclude)))
        return candidates[random.randrange(len(candidates))]

## `_make_genome(reference, loci)`

Make an individual genome by mutating the reference genome.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`reference` | `str` | Reference genome string to base the new genome on | required
`loci` | `list[int]` | List of positions that can be mutated | required

Returns:

Type | Description
--- | ---
`str` | A new genome string with random mutations at some loci

Source code in `src/snailz/specimens.py`

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    def _make_genome(reference: str, loci: list[int]) -> str:
        """Make an individual genome by mutating the reference genome.

        Parameters:
            reference: Reference genome string to base the new genome on
            loci: List of positions that can be mutated

        Returns:
            A new genome string with random mutations at some loci
        """
        result = list(reference)
        num_mutations = random.randint(1, len(loci))
        for loc in random.sample(range(len(loci)), num_mutations):
            result[loc] = _choose_other(BASES, reference[loc])
        return "".join(result)

## `_make_idents(count)`

Create unique specimen identifiers.

Each identifier is a 6-character string: - First two characters are the same uppercase letters for all specimens - Remaining four chararacters are random uppercase letters and digits

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`count` | `int` | Number of identifiers to generate | required

Returns:

Type | Description
--- | ---
`list[str]` | List of unique specimen identifiers

Source code in `src/snailz/specimens.py`

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    def _make_idents(count: int) -> list[str]:
        """Create unique specimen identifiers.

        Each identifier is a 6-character string:
        - First two characters are the same uppercase letters for all specimens
        - Remaining four chararacters are random uppercase letters and digits

        Parameters:
            count: Number of identifiers to generate

        Returns:
            List of unique specimen identifiers
        """
        prefix = "".join(random.choices(string.ascii_uppercase, k=2))
        chars = string.ascii_uppercase + string.digits
        gen = utils.UniqueIdGenerator(
            "specimens", lambda: f"{prefix}{''.join(random.choices(chars, k=4))}"
        )
        return [gen.next() for _ in range(count)]

## `_make_locations(size, num)`

Generate non-adjacent locations for specimens or fail.

Source code in `src/snailz/specimens.py`

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    def _make_locations(size: int, num: int) -> list[tuple[int, int]]:
        """Generate non-adjacent locations for specimens or fail."""
        available = {(x, y) for x in range(size) for y in range(size)}
        chosen = set()
        for i in range(num):
            if not available:
                utils.fail(f"failed to select {num} points on iteration {i}")
            point = random.choice(list(available))
            chosen.add(point)
            for x in range(point[0] - 1, point[0] + 2):
                if (x < 0) or (x >= size):
                    continue
                for y in range(point[1] - 1, point[1] + 2):
                    if (y < 0) or (y >= size):
                        continue
                    available.discard((x, y))
        return list(chosen)

## `_make_loci(params)`

Make a list of mutable loci positions.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`params` | `SpecimenParams` | SpecimenParams with length and mutations attributes | required

Returns:

Type | Description
--- | ---
`list[int]` | A list of unique randomly selected positions that can be mutated

Source code in `src/snailz/specimens.py`

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    def _make_loci(params: SpecimenParams) -> list[int]:
        """Make a list of mutable loci positions.

        Parameters:
            params: SpecimenParams with length and mutations attributes

        Returns:
            A list of unique randomly selected positions that can be mutated
        """
        return random.sample(list(range(params.length)), params.mutations)

## `_make_masses(params, genomes, susceptible_locus, susceptible_base)`

Generate random masses for specimens.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`params` | `SpecimenParams` | SpecimenParams with min_mass and max_mass attributes | required
`genomes` | `list[str]` | List of genome strings | required
`susceptible_locus` | `int` | Position that determines susceptibility | required
`susceptible_base` | `str` | Base that makes a specimen susceptible | required

Returns:

Type | Description
--- | ---
`list[float]` | List of randomly generated mass values between min_mass and max_mass,
`list[float]` | rounded to PRECISION decimal places

Source code in `src/snailz/specimens.py`

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    def _make_masses(
        params: SpecimenParams,
        genomes: list[str],
        susceptible_locus: int,
        susceptible_base: str,
    ) -> list[float]:
        """Generate random masses for specimens.

        Parameters:
            params: SpecimenParams with min_mass and max_mass attributes
            genomes: List of genome strings
            susceptible_locus: Position that determines susceptibility
            susceptible_base: Base that makes a specimen susceptible

        Returns:
            List of randomly generated mass values between min_mass and max_mass,
            rounded to PRECISION decimal places
        """
        return [
            round(random.uniform(params.min_mass, params.max_mass), utils.PRECISION)
            for _ in genomes
        ]

## `_make_collection_dates(params)`

Generate random collection dates for specimens.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`params` | `SpecimenParams` | SpecimenParams with start_date, end_date, and number attributes | required

Returns:

Type | Description
--- | ---
`list[date]` | List of randomly generated collection dates between start_date and end_date

Source code in `src/snailz/specimens.py`

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    def _make_collection_dates(params: SpecimenParams) -> list[date]:
        """Generate random collection dates for specimens.

        Parameters:
            params: SpecimenParams with start_date, end_date, and number attributes

        Returns:
            List of randomly generated collection dates between start_date and end_date
        """
        start_ordinal = params.start_date.toordinal()
        end_ordinal = params.end_date.toordinal()
        return [
            date.fromordinal(random.randint(start_ordinal, end_ordinal))
            for _ in range(params.number)
        ]

## `_make_reference_genome(params)`

Make a random reference genome.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`params` | `SpecimenParams` | SpecimenParams with length attribute | required

Returns:

Type | Description
--- | ---
`str` | A randomly generated genome string of the specified length

Source code in `src/snailz/specimens.py`

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    def _make_reference_genome(params: SpecimenParams) -> str:
        """Make a random reference genome.

        Parameters:
            params: SpecimenParams with length attribute

        Returns:
            A randomly generated genome string of the specified length
        """
        return "".join(random.choices(BASES, k=params.length))