baby.tracker.core.FeatureCalculator¶
- class baby.tracker.core.FeatureCalculator(feats2use: Collection[str], trapfeats: Optional[Collection[str]] = None, extrafeats: Optional[Collection[str]] = None, aweights: Optional[bool] = None, pixel_size: Optional[float] = None)¶
Bases:
ABC
Base class for making use of regionprops-based features. If no features are offered it uses most of them.
This class is not to be used directly
- Attributes
- a_ind
- ma_ind
- x_ind
- y_ind
Methods
calc_feats_from_mask
(masks[, feats2use, ...])Calculate feature ndarray from ndarray of cell masks
calc_trapfeats
(basefeats)Calculate trap-based features using basic ones. :basefeats: (n basic outfeats) 1-D array with features outputed by skimage.measure.regionprops_table.
scale_feats
(feats, pixel_size)input
get_outfeats
load_model
set_named_ids
- __init__(feats2use: Collection[str], trapfeats: Optional[Collection[str]] = None, extrafeats: Optional[Collection[str]] = None, aweights: Optional[bool] = None, pixel_size: Optional[float] = None) None ¶
Methods
__init__
(feats2use[, trapfeats, extrafeats, ...])calc_feats_from_mask
(masks[, feats2use, ...])Calculate feature ndarray from ndarray of cell masks
calc_trapfeats
(basefeats)Calculate trap-based features using basic ones. :basefeats: (n basic outfeats) 1-D array with features outputed by skimage.measure.regionprops_table.
get_outfeats
([feats2use])load_model
(path, fname)scale_feats
(feats, pixel_size)input
set_named_ids
()Attributes
a_ind
ma_ind
x_ind
y_ind
- calc_feats_from_mask(masks: ndarray, feats2use: Optional[Tuple[str]] = None, trapfeats: Optional[Tuple[str]] = None, scale: Optional[bool] = True, pixel_size: Optional[float] = None)¶
Calculate feature ndarray from ndarray of cell masks — input
- Masks
ndarray (ncells, x_size, y_size), typically dtype bool
- Feats2use
list of strings with the feature properties to extract. If it is None it uses the ones set in self.feats2use.
- Trapfeats
List of str with additional features to use calculated immediately after basic features.
- Scale
bool, if True scales mask to a defined pixel_size.
- Pixel_size
float, used to rescale the object features.
returns
(ncells, nfeats) ndarray of features for input masks
- calc_trapfeats(basefeats)¶
Calculate trap-based features using basic ones. :basefeats: (n basic outfeats) 1-D array with features outputed by
skimage.measure.regionprops_table
- requires
self.aind self.aweights self.xind self.yind self.trapfeats
returns (ntrapfeats) 1-D array with
- scale_feats(feats: ndarray, pixel_size: float)¶
input
- Feats
np.ndarray (ncells * nfeatures)
- Pixel_size
float Value used to normalise the images.
returns Rescaled list of feature values