"""RT-DC hierarchy format"""
from __future__ import annotations
import numpy as np
from ... import definitions as dfn
from ...util import hashobj
from ..config import Configuration
from ..core import RTDCBase
from .events import (
ChildContour, ChildNDArray, ChildScalar, ChildTrace, ChildTraceItem
)
from .hfilter import HierarchyFilter
[docs]
class RTDC_Hierarchy(RTDCBase):
def __init__(self, hparent, apply_filter=True, *args, **kwargs):
"""Hierarchy dataset (filtered from RTDCBase)
A few words on hierarchies:
The idea is that a subclass of RTDCBase can use the filtered
data of another subclass of RTDCBase and interpret these data
as unfiltered events. This comes in handy e.g. when the
percentage of different subpopulations need to be distinguished
without the noise in the original data.
Children in hierarchies always update their data according to
the filtered event data from their parent when `apply_filter`
is called. This makes it easier to save and load hierarchy
children with e.g. Shape-Out and it makes the handling of
hierarchies more intuitive (when the parent changes,
the child changes as well).
Parameters
----------
hparent: instance of RTDCBase
The hierarchy parent
apply_filter: bool
Whether to apply the filter during instantiation;
If set to `False`, `apply_filter` must be called
manually.
*args:
Arguments for `RTDCBase`
**kwargs:
Keyword arguments for `RTDCBase`
Attributes
----------
hparent: RTDCBase
Hierarchy parent of this instance
"""
super(RTDC_Hierarchy, self).__init__(*args, **kwargs)
self.path = hparent.path
self.title = hparent.title + "_child"
self._logs = None # lazily-loaded
self._tables = None # lazily-loaded
self._events = {}
#: hierarchy parent
self.hparent = hparent
self.config = self._create_config() # init config
self._update_config() # sets e.g. event count
if apply_filter:
# Apply the filter
# This will also populate all event attributes
self.apply_filter()
self._length = None
def __contains__(self, key):
return self.hparent.__contains__(key)
def __getitem__(self, feat):
"""Return the feature data and cache them in self._events"""
if feat in self._events:
data = self._events[feat]
elif feat in self.hparent:
if len(self.hparent[feat].shape) > 1:
# non-scalar feature
data = ChildNDArray(self, feat)
else:
# scalar feature
data = ChildScalar(self, feat)
# Cache everything, even the Young's modulus. The user is
# responsible for calling `rejuvenate` to reset everything.
self._events[feat] = data
else:
raise KeyError(
f"The dataset {self} does not contain the feature '{feat}'! "
+ "If you are attempting to access an ancillary feature "
+ "(e.g. emodulus), please make sure that the feature "
+ f"data are computed for {self.get_root_parent()} (the "
+ "root parent of this hierarchy child).")
return data
def __len__(self):
if self._length is None:
self._length = np.sum(self.hparent.filter.all)
return self._length
def _assert_filter(self):
"""Make sure filters exists
Override from base class that uses :class:`.HierarchyFilter`
instead of :class:`.Filter`.
"""
if self._ds_filter is None:
self._ds_filter = HierarchyFilter(self)
def _check_parent_filter(self):
"""Reset filter if parent changed
This will create a new HierarchyFilter for self if the
parent RTDCBase changed. We do it like this, because it
would be complicated to track all the changes in
HierarchyFilter.
"""
if self.filter.parent_changed:
manual_pidx = self.filter.retrieve_manual_indices(self)
self._ds_filter = None # forces recreation of HierarchyFilter
self._assert_filter()
self.filter.apply_manual_indices(self, manual_pidx)
def _create_config(self):
"""Return a stripped configuration from the parent"""
# create a new configuration
cfg = self.hparent.config.copy()
# Remove previously applied filters
pops = []
for key in cfg["filtering"]:
if (key.endswith(" min") or
key.endswith(" max") or
key == "polygon filters"):
pops.append(key)
[cfg["filtering"].pop(key) for key in pops]
# Add parent information in dictionary
cfg["filtering"]["hierarchy parent"] = self.hparent.identifier
return Configuration(cfg=cfg)
def _update_config(self):
"""Update varying config values from self.hparent"""
# event count
self.config["experiment"]["event count"] = np.sum(
self.hparent.filter.all)
# calculation
if "calculation" in self.hparent.config:
self.config["calculation"].clear()
self.config["calculation"].update(
self.hparent.config["calculation"])
@property
def basins(self):
return self.hparent.basins
@property
def features(self):
return self.hparent.features
@property
def features_ancillary(self):
return self.hparent.features_ancillary
@property
def features_basin(self):
return self.hparent.features_basin
@property
def features_innate(self):
return self.hparent.features_innate
@property
def features_loaded(self):
return self.hparent.features_loaded
@property
def features_scalar(self):
return self.hparent.features_scalar
@property
def hash(self):
"""Hashes of a hierarchy child changes if the parent changes"""
# Do not apply filters here (speed)
hph = self.hparent.hash
hpfilt = hashobj(self.hparent.filter.all)
dhash = hashobj(hph + hpfilt)
return dhash
@property
def logs(self):
if self._logs is None:
self._logs = self.hparent.logs
return self._logs
@logs.setter
def logs(self, value):
# to support setting `self.logs = {}` in RTDCBase
if value:
raise ValueError(
"Setting actual logs not supported for RTDC_Hierarchy")
@property
def tables(self):
if self._tables is None:
self._tables = self.hparent.tables
return self._tables
@tables.setter
def tables(self, value):
# to support setting `self.tables = {}` in RTDCBase
if value:
raise ValueError(
"Setting actual tables not supported for RTDC_Hierarchy")
[docs]
def apply_filter(self, *args, **kwargs):
"""Overridden `apply_filter` to perform tasks for hierarchy child"""
if self._ds_filter is not None:
# make sure self.filter knows about root manual indices
# (stored in self.filter._man_root_ids)
self.filter.retrieve_manual_indices(self)
# Copy event data from hierarchy parent
self.hparent.apply_filter(*args, **kwargs)
# Clear anything that has been cached until now
self._length = None
# update event index
event_count = len(self)
self._events.clear()
self._events["index"] = np.arange(1, event_count + 1)
# set non-scalar column data
for feat in ["image", "image_bg", "mask"]:
if feat in self.hparent:
self._events[feat] = ChildNDArray(self, feat)
if "contour" in self.hparent:
self._events["contour"] = ChildContour(self)
if "trace" in self.hparent:
trdict = ChildTrace()
for flname in dfn.FLUOR_TRACES:
if flname in self.hparent["trace"]:
trdict[flname] = ChildTraceItem(self, flname)
self._events["trace"] = trdict
# Update configuration
self._update_config()
# create a new filter if the parent changed
self._check_parent_filter()
super(RTDC_Hierarchy, self).apply_filter(*args, **kwargs)
[docs]
def get_root_parent(self):
"""Return the root parent of this dataset"""
if isinstance(self.hparent, RTDC_Hierarchy):
return self.hparent.get_root_parent()
else:
return self.hparent
[docs]
def rejuvenate(self):
"""Redraw the hierarchy tree, updating config and features
You should call this function whenever you change something
in the hierarchy parent(s), be it filters or metadata for computing
ancillary features.
.. versionadded: 0.47.0
This is just an alias of `apply_filter`, but with a more
accurate name (not only the filters are applied, but alot
of other things might change).
"""
self.apply_filter()