Source code for starfish.core.types._spot_attributes

import json
from typing import Collection, Sequence

import numpy as np
import pandas as pd

from starfish.core.types import Axes, Features
from ._validated_table import ValidatedTable

[docs]class SpotAttributes(ValidatedTable): required_fields = [ (Axes.X.value, int), # spot x-coordinate (Axes.Y.value, int), # spot y-coordinate (Axes.ZPLANE.value, int), # spot z-coordinate (Features.SPOT_RADIUS, float) # spot radius ] def __init__(self, spot_attributes: pd.DataFrame) -> None: """Construct a SpotAttributes instance Parameters ---------- spot_attributes : pd.DataFrame """ super().__init__(spot_attributes, {i[0] for i in SpotAttributes.required_fields})
[docs] @classmethod def empty(cls, extra_fields: Collection = tuple()) -> "SpotAttributes": """return an empty SpotAttributes object""" extra_dtypes = list(zip(extra_fields, [np.object] * len(extra_fields))) dtype = cls.required_fields + extra_dtypes return cls(pd.DataFrame(np.array([], dtype=dtype)))
@classmethod def combine(cls, spot_attribute_tables: Sequence["SpotAttributes"]) -> "SpotAttributes": return cls(pd.concat([ for spot_attribute_table in spot_attribute_tables ]))
[docs] def save_geojson(self, output_file_name: str) -> None: """Save to geojson for web visualization Parameters ---------- output_file_name : str name of output json file """ # TODO ambrosejcarr: write a test for this geojson = [ { 'properties': {'id': int(row.spot_id), 'radius': int(row.r)}, 'geometry': {'type': 'Point', 'coordinates': [int(row.x), int(row.y)]} } for index, row in ] with open(output_file_name, 'w') as f: f.write(json.dumps(geojson))