Source code for arthropod_describer.plugins.test_plugin.properties.max_feret

import copy
import typing
from typing import Optional

import numpy as np
import skimage

from arthropod_describer.common.common import Info
from arthropod_describer.common.label_image import RegionProperty, PropertyType
from arthropod_describer.common.photo import Photo
from arthropod_describer.common.plugin import PropertyComputation
from arthropod_describer.common.regions_cache import RegionsCache
from arthropod_describer.common.units import Value
from arthropod_describer.common.user_params import UserParam


[docs]class MaxFeret(PropertyComputation): """ GROUP: Basic properties NAME: Max feret diameter DESCRIPTION: Maximum Feret diameter (px or mm) KEY: max_feret """ def __init__(self, info: Optional[Info] = None): super().__init__(info) def __call__(self, photo: Photo, region_labels: typing.List[int], regions_cache: RegionsCache) -> \ typing.List[RegionProperty]: props: typing.List[RegionProperty] = [] for label in region_labels: if label not in regions_cache.regions: continue region_obj = regions_cache.regions[label] reg_props = skimage.measure.regionprops_table(region_obj.mask.astype(np.uint8), region_obj.image, properties=['label', 'feret_diameter_max']) prop = RegionProperty() prop.label = int(label) prop.info = copy.deepcopy(self.info) prop.value = Value(float(reg_props['feret_diameter_max'][0]), self._px_unit) if photo.image_scale is not None and photo.image_scale.value > 0: prop.value = prop.value / photo.image_scale prop.unit = 'mm' # TODO sync unit with the units in Photo else: prop.unit = 'px' prop.prop_type = PropertyType.Scalar prop.val_names = ['Max Feret'] prop.num_vals = 1 props.append(prop) return props @property def user_params(self) -> typing.List[UserParam]: return super().user_params @property def region_restricted(self) -> bool: return super().region_restricted @property def computes(self) -> typing.Dict[str, Info]: return {self.info.key: self.info}
[docs] def example(self, prop_name: str) -> RegionProperty: prop = RegionProperty() prop.label = 0 prop.info = copy.deepcopy(self.info) prop.value = None prop.num_vals = 1 prop.prop_type = PropertyType.Scalar prop.val_names = [] return prop
[docs] def target_worksheet(self, prop_name: str) -> str: return super(MaxFeret, self).target_worksheet(self.info.key)
@property def group(self) -> str: return super().group