# -*- coding: utf-8 -*-
"""
Created on June 20 2018
@author: kushal
Chatzigeorgiou Group
Sars International Centre for Marine Molecular Biology
GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007
"""
import abc
import numpy as np
from PyQt5 import QtWidgets
from .... import pyqtgraphCore as pg
from ....common import get_proj_config, NoProjectOpen, InheritDocs
from warnings import warn
from copy import deepcopy
from typing import Union, List
[docs]class _AbstractBaseROI(metaclass=InheritDocs):
"""
Abstract base class defining an ROI that works with the ROIList and ROI Managers.
Inherit from this or BaseROI to make a new ROI class
"""
[docs] @abc.abstractmethod
def __init__(self, curve_plot_item: pg.PlotDataItem, view_box: pg.ViewBox, state: Union[dict, None]):
"""
Minimum required attributes
:param curve_plot_item: The plot item that is used for display the curves in the viewer
:param view_box: ViewBox containing the image sequence, used for overlaying the ROIs on top of the image
:param state: ROI state, used for restoring the ROIs. Pass None is not restoring an ROI from a state dict
"""
pass
# @property
# @abc.abstractmethod
# def curve_data(self) -> tuple:
# """
# The curve data for this ROI
#
# :return: (x, y), [np.ndarray, np.ndarray]
# :rtype: tuple
# """
# pass
#
# @curve_data.setter
# @abc.abstractmethod
# def curve_data(self, data: tuple):
# """
# Set the curve data for this ROI
#
# :param data: (x, y), [np.ndarray, np.ndarray]
# """
# pass
[docs] @abc.abstractmethod
def get_roi_graphics_object(self) -> QtWidgets.QGraphicsObject:
"""Get the QGraphicsObject used for visualization of the spatial localization of the ROI"""
pass
[docs] @abc.abstractmethod
def set_roi_graphics_object(self, *args, **kwargs):
"""Set the QGraphicsObject used for visualization of the spatial localization of the ROI"""
pass
[docs] @abc.abstractmethod
def reset_color(self):
"""Reset the color of this ROI back to the original color"""
pass
[docs] @abc.abstractmethod
def set_original_color(self, color):
"""
Set the original color for this ROI
:param color: 1D numpy array of 4 floating point numbers (range 0 - 255) in RBGA format, [R, G, B, A]
"""
pass
[docs] @abc.abstractmethod
def get_color(self) -> np.ndarray:
"""
Get the current color of this ROI
:return: 1D numpy array of 4 floating point numbers (range 0 - 255) in RBGA format, [R, G, B, A]
:rtype: np.ndarray
"""
pass
[docs] @abc.abstractmethod
def set_color(self, color, *args, **kwargs):
"""
Set the current color of this ROI
:param color: 1D numpy array of 4 floating point numbers (range 0 - 255) in RBGA format, [R, G, B, A]
"""
pass
[docs] @abc.abstractmethod
def set_text(self, text: str):
"""Not implemented"""
pass
[docs] @abc.abstractmethod
def set_tag(self, roi_def: str, tag: str):
"""
Set a tag for the passed roi_def
:param roi_def: The ROI_DEF that should be tagged
:param tag: The tag to label for the passed ROI_DEF/ROI Type
"""
pass
[docs] @abc.abstractmethod
def get_tag(self, roi_def) -> str:
"""
Get the tag that is set to the passed 'roi_def'
:rtype: str
"""
pass
[docs] @abc.abstractmethod
def add_to_viewer(self):
"""Add this ROI to the viewer."""
pass
[docs] @abc.abstractmethod
def remove_from_viewer(self):
"""Remove this ROI from the viewer"""
pass
[docs] @abc.abstractmethod
def to_state(self):
"""Get the current state for this ROI so that it can be restored later"""
pass
[docs] @classmethod
@abc.abstractmethod
def from_state(cls, curve_plot_item: pg.PlotDataItem, view_box: pg.ViewBox, state: dict):
"""
Restore this ROI from a state
:param curve_plot_item: The plot item that is used for display the curves in the viewer
:param view_box: ViewBox containing the image sequence, used for overlaying the ROIs on top of the image
:param state: ROI state, used for restoring the ROIs. Pass None is not restoring an ROI from a state dict
"""
pass
[docs]class BaseROI(_AbstractBaseROI):
"""
A base class that is used by ManualROI and CNMFEROI
Inherit from this to make a new ROI class
"""
[docs] def __init__(self, curve_plot_item: pg.PlotDataItem, view_box: pg.ViewBox, state: Union[dict, None] = None,
metadata: dict = None):
"""
Instantiate common attributes
:param curve_plot_item: The plot item that is used for display the curves in the viewer
:param view_box: ViewBox containing the image sequence, used for overlaying the ROIs on top of the image
:param state: ROI state, used for restoring the ROIs. Pass None is not restoring an ROI from a state dict
"""
super().__init__(curve_plot_item, view_box, state)
if isinstance(curve_plot_item, pg.PlotDataItem):
self.curve_plot_item = curve_plot_item
self.curve_plot_item.setZValue(1)
else:
self.curve_plot_item = None
if state is None:
try:
# Set the Tags list from the project configuration
roi_defs = get_proj_config().options('ROI_DEFS')
self._tags = dict.fromkeys(roi_defs)
except NoProjectOpen as e:
self._tags = {}
# If a project isn't open
warn('BaseROI subclass instance cannot load ROI_DEFS, no Project open.')
else:
# Restore states
self._tags = state['tags']
self.curve_data = state['curve_data']
self.view_box = view_box
self.roi_graphics_object = None
self._color = None
self._original_color = None
self.metadata = metadata
# @property
# def curve_data(self) -> tuple:
# return self.curve_plot_item.getData()
#
# @curve_data.setter
# def curve_data(self, data: tuple):
# """
#
# :rtype: tuple
# """
# if self.curve_plot_item is None:
# return
# self.curve_plot_item.setData(x=data[0], y=data[1])
@property
def zValue(self) -> int:
"""ZValue of the curve plot graphics object and roi_graphics_object"""
return self._zValue
@zValue.setter
def zValue(self, val: int):
self._zValue = val
[docs] def get_roi_graphics_object(self) -> QtWidgets.QGraphicsObject:
pass
[docs] def set_roi_graphics_object(self, *args, **kwargs):
pass
[docs] def reset_color(self):
self.set_color(self._original_color)
[docs] def set_original_color(self, color):
self._original_color = color
self.reset_color()
[docs] def get_color(self):
return self._color
[docs] def set_color(self, color: Union[np.ndarray, str], *args, **kwargs):
pen = pg.mkPen(color, *args, **kwargs)
self.roi_graphics_object.setPen(pen)
self.curve_plot_item.setPen(pen)
if isinstance(self.roi_graphics_object, pg.ScatterPlotItem):
self.roi_graphics_object.setBrush(pg.mkBrush(color, *args, **kwargs))
self._color = color
[docs] def set_text(self, text: str):
text_item = pg.TextItem(text)
# self.view_box.addItem()
[docs] def set_tag(self, roi_def: str, tag: str):
self._tags[roi_def] = tag
[docs] def get_tag(self, roi_def) -> str:
if self._tags[roi_def] is None:
return ''
return self._tags[roi_def]
[docs] def add_to_viewer(self):
self.view_box.addItem(self.get_roi_graphics_object())
[docs] def remove_from_viewer(self):
roi = self.get_roi_graphics_object()
self.view_box.removeItem(roi)
if self.curve_plot_item is not None:
self.curve_plot_item.clear()
del self.curve_plot_item
del roi
[docs] def to_state(self):
"""Must be implemented in subclass"""
raise NotImplementedError("Must be implemented in subclasses")
[docs] @classmethod
def from_state(cls, curve_plot_item: pg.PlotDataItem, view_box: pg.ViewBox, state: dict):
raise NotImplementedError("Must be implemented in subclasses")
[docs]class ManualROI(BaseROI):
"""A class manually drawn ROIs"""
[docs] def __init__(self, curve_plot_item: pg.PlotDataItem,
roi_graphics_object: pg.ROI,
view_box: pg.ViewBox,
state: Union[dict, None] = None,
spike_data: np.ndarray = None,
dfof_data: np.ndarray = None,):
"""
:type state: dict
"""
assert isinstance(roi_graphics_object, pg.ROI)
super(ManualROI, self).__init__(curve_plot_item, view_box, state)
self.set_roi_graphics_object(roi_graphics_object)
if state is not None:
self.add_to_viewer()
self._set_roi_graphics_object_state(state['roi_graphics_object_state'])
@property
def curve_data(self) -> tuple:
"""
:return: tuple of (xs, ys)
"""
return self.curve_plot_item.getData()
@curve_data.setter
def curve_data(self, data: tuple):
"""
Curve data as (xs, ys)
"""
if self.curve_plot_item is None:
return
if data is None:
self.curve_plot_item.clear()
self.curve_plot_item.setData(x=data[0], y=data[1])
[docs] def get_roi_graphics_object(self) -> pg.ROI:
return self.roi_graphics_object
[docs] def set_roi_graphics_object(self, graphics_object: pg.ROI):
self.roi_graphics_object = graphics_object
def _set_roi_graphics_object_state(self, state):
self.roi_graphics_object.setState(state)
[docs] def to_state(self):
if isinstance(self.roi_graphics_object, pg.PolyLineROI):
shape = 'PolyLineROI'
elif isinstance(self.roi_graphics_object, pg.EllipseROI):
shape = 'EllipseROI'
state = {'curve_data': self.curve_data,
'shape': shape,
'roi_graphics_object_state': self.roi_graphics_object.saveState(),
'tags': self.get_all_tags(),
'roi_type': 'ManualROI'
}
return state
@staticmethod
def get_generic_roi_graphics_object(shape: str, dims: tuple) -> pg.ROI:
"""Get a generic pg.ROI instance to add to the viewer. Its state can later be set from a saved state or it can be modified by the user"""
x = dims[0]
y = dims[1]
if shape == 'PolyLineROI':
roi_graphics_object = pg.PolyLineROI([[0, 0],
[int(0.1 * x), 0],
[int(0.1 * x), int(0.1 * y)],
[0, int(0.1 * y)]],
closed=True, pos=[0, 0], removable=True)
return roi_graphics_object
elif shape == 'EllipseROI':
roi_graphics_object = pg.EllipseROI(pos=[0, 0], size=[int(x * 0.1), int(y * 0.1)], removable=True)
return roi_graphics_object
[docs] @classmethod
def from_state(cls, curve_plot_item: pg.PlotDataItem, view_box: pg.ViewBox, state: dict):
roi_graphics_object = ManualROI.get_generic_roi_graphics_object(state['shape'], (10, 10))
return cls(curve_plot_item=curve_plot_item, roi_graphics_object=roi_graphics_object, view_box=view_box, state=state)
@classmethod
def from_positions(cls, curve_plot_item: pg.PlotDataItem, view_box: pg.ViewBox, positions: list):
"""
From a list of positions. Used if importing ImageJ ROIs, can be used for other purposes as well.
:param positions: list of (x, y) tuples; [(x1, y1), (x2, y2), ... (xn, yn)]
"""
roi_graphics_object = pg.PolyLineROI(positions=positions, closed=True, removable=True)
return cls(curve_plot_item=curve_plot_item, roi_graphics_object=roi_graphics_object, view_box=view_box)
[docs]class ScatterROI(BaseROI):
"""A class for unmoveable ROIs drawn using scatter points"""
[docs] def __init__(self, curve_plot_item: pg.PlotDataItem, view_box: pg.ViewBox, state: Union[dict, None] = None,
curve_data: np.ndarray = None, xs: np.ndarray = None, ys: np.ndarray = None, metadata: dict = None,
spike_data: np.ndarray = None, dfof_data: np.ndarray = None,
**kwargs):
"""
:param curve_plot_item:
:param view_box:
:param state:
:param curve_data: 1D numpy array of y values
:param kwargs:
"""
self.spot_size = 1
self.curve_data: List[np.ndarray, np.ndarray] = None #: list of [xs, ys], xs and ys are 1D numpy arrays
self._curve_data = None
self.spike_data = None
self.dfof_data = None
super(ScatterROI, self).__init__(curve_plot_item, view_box, state, metadata=metadata)
if (xs is not None) and (ys is not None):
self.set_roi_graphics_object(xs, ys)
if state is None:
self.set_curve_data(curve_data)
# set spikes
if spike_data is not None:
xs = np.arange(len(spike_data))
self.spike_data = [xs, spike_data]
# set dfof
if dfof_data is not None:
xs = np.arange(len(dfof_data))
self.dfof_data = [xs, dfof_data]
else:
self.restore_state(state)
self.curve_data_type = 'curve'
# # override to get diff behavior from ManualROI
# @property
# def curve_data(self) -> tuple:
# return self._curve_data
#
# @curve_data.setter
# def curve_data(self, y_vals: np.ndarray):
# xs = np.arange(len(y_vals))
# self._curve_data = [xs, y_vals]
[docs] def set_curve_data(self, y_vals: np.ndarray, set_plot: bool = True):
"""Set the curve data"""
xs = np.arange(len(y_vals))
self.curve_data = [xs, y_vals]
if set_plot:
self.set_viewer_curveplot('curve')
# sets the plot in the viewer
def set_viewer_curveplot(self, data_type: str = 'curve'):
"""
:param data_type: one of "curve", "spike", or "dfof"
"""
if self.curve_plot_item is None:
return
data = getattr(self, f'{data_type}_data')
if data is not None:
self.curve_plot_item.setData(x=data[0], y=data[1])
else:
self.curve_plot_item.clear()
warn(f'ROI does not contain the following '
f'data attribute: {data_type}_data')
def restore_state(self, state: dict):
if 'spike_data' in state.keys():
self.spike_data = state['spike_data']
if 'dfof_data' in state.keys():
self.dfof_data = state['dfof_data']
self.roi_xs = state['roi_xs']
self.roi_ys = state['roi_ys']
self._draw()
[docs] def to_state(self) -> dict:
state = {'roi_xs': self.roi_xs,
'roi_ys': self.roi_ys,
'curve_data': self.curve_data,
'spike_data': self.spike_data,
'dfof_data': self.dfof_data,
'tags': self.get_all_tags(),
'roi_type': self.__class__.__name__,}
return state
[docs] def set_roi_graphics_object(self, xs: np.ndarray, ys: np.ndarray):
self.roi_xs = xs.astype(int)
self.roi_ys = ys.astype(int)
self._draw()
[docs] def get_roi_graphics_object(self) -> pg.ScatterPlotItem:
if self.roi_graphics_object is None:
raise AttributeError('Must call set_roi_graphics_object() first')
return self.roi_graphics_object
def _draw(self):
"""Create the scatter plot that is used for visualization of the spatial localization"""
self.roi_graphics_object = pg.ScatterPlotItem(
self.roi_xs, self.roi_ys, symbol='s', size=self.spot_size, pxMode=True
)
[docs] @classmethod
def from_state(cls, curve_plot_item: pg.PlotDataItem, view_box: pg.ViewBox, state: dict, **kwargs):
return cls(curve_plot_item=curve_plot_item, view_box=view_box, state=state, **kwargs)
[docs]class VolCNMF(ScatterROI):
"""3D ROI for CNMF data"""
[docs] def __init__(self, curve_plot_item: pg.PlotDataItem , view_box: pg.ViewBox, cnmf_idx: int = None,
curve_data: np.ndarray = None, contour: dict = None, state: Union[dict, None] = None,
spike_data: np.ndarray = None, dfof_data: np.ndarray = None, metadata: dict = None,
zlevel: int = 0):
self.zlevel: int = zlevel #: z-level of the ROI that is currently visible, different from zValue!!
self.zcenter: int = None #: z-level where this ROI has its center
super(VolCNMF, self).__init__(curve_plot_item, view_box, state, curve_data,
spike_data=spike_data, dfof_data=dfof_data,
metadata=metadata)
if state is None:
# get the outline from the cnmf output
self.coors = contour['coordinates']
self.zcenter = int(contour['CoM'][0])
self.set_roi_graphics_object()
self.set_curve_data(curve_data)
self.cnmf_idx = cnmf_idx #: original index of the ROI from cnmf idx_components
else:
self.restore_state(state)
self.visible = False
def restore_state(self, state: dict):
self.coors = state['coors']
self.cnmf_idx = state['cnmf_idx']
self.zcenter = state['zcenter']
self.set_roi_graphics_object()
[docs] def to_state(self) -> dict:
state = {'curve_data': self.curve_data,
'spike_data': self.spike_data,
'dfof_data': self.dfof_data,
'tags': self.get_all_tags(),
'roi_type': self.__class__.__name__,
'coors': self.coors,
'cnmf_idx': self.cnmf_idx,
'zcenter': self.zcenter}
return state
[docs] def set_roi_graphics_object(self):
coors = self.coors[self.zlevel]
self.current_coors = coors[~np.isnan(coors).any(axis=1)]
self.check_visible()
self.roi_xs = self.current_coors[:, 1].flatten().astype(int)
self.roi_ys = self.current_coors[:, 0].flatten().astype(int)
self._draw()
def check_visible(self):
if self.current_coors.size > 0:
self.visible = True
else:
self.visible = False
def _draw(self):
"""Create the scatter plot that is used for visualization of the spatial localization"""
self.roi_graphics_object = pg.ScatterPlotItem(
self.roi_xs,
self.roi_ys,
symbol='s',
size=self.spot_size
)
[docs] def set_zlevel(self, z: int):
"""
Set the z-level of the ROI to correspond with the
z-level of the image.
Different from `setZValue`!!
"""
self.zlevel = z
coors = self.coors[self.zlevel]
self.current_coors = coors[~np.isnan(coors).any(axis=1)]
self.check_visible()
self.roi_xs = self.current_coors[:, 1].flatten().astype(int)
self.roi_ys = self.current_coors[:, 0].flatten().astype(int)
self.set_viewer_curveplot(self.curve_data_type)
self.roi_graphics_object.setData(self.roi_xs, self.roi_ys)#, symbol='s', size=self.spot_size)
class VolMultiCNMFROI(ScatterROI):
"""3D ROI for CNMF data created by runing CNMF independently on each plane"""
def __init__(self, curve_plot_item: pg.PlotDataItem, view_box: pg.ViewBox, cnmf_idx: int = None,
curve_data: np.ndarray = None, contour: dict = None, state: Union[dict, None] = None,
spike_data: np.ndarray = None, dfof_data: np.ndarray = None, metadata: dict = None,
zlevel: int = 0, zcenter: int = None, parent_manager=None, roi_ix: int = None,
scatter_plot: pg.ScatterPlotItem = None, **kwargs):
self.zlevel: int = zlevel #: z-level of the ROI that is currently visible, different from zValue!!
self.zcenter: int = zcenter #: z-level where this ROI has its center, must be specified
self.parent_manager = parent_manager
self.roi_ix = roi_ix
self.scatter_plot = scatter_plot
if self.parent_manager is not None:
ix = (self.parent_manager.roi_ixs[self.zcenter] == self.roi_ix).flatten()
roi_xys = self.parent_manager.roi_xys[self.zcenter][ix]
self.roi_xs = roi_xys[:, 0]
self.roi_ys = roi_xys[:, 1]
super(VolMultiCNMFROI, self).__init__(curve_plot_item, view_box, state, curve_data,
spike_data=spike_data, dfof_data=dfof_data,
metadata=metadata)
if self.zcenter is None:
raise ValueError(
"zcenter must not be None"
)
if 'raw_min_max' in kwargs.keys():
self.raw_min_max = kwargs.pop('raw_min_max')
else:
self.raw_min_max = None
if state is None:
self.set_curve_data(curve_data, set_plot=False)
self.cnmf_idx = cnmf_idx #: original index of the ROI from cnmf idx_components
else:
self.restore_state(state)
self.check_visible()
def get_roi_graphics_object(self) -> QtWidgets.QGraphicsObject:
return self.roi_graphics_object
def set_roi_graphics_object(self, *args, **kwargs):
pass
def get_color(self):
pass
def set_color(self, color: Union[np.ndarray, str], *args, **kwargs):
# just assume white color for now
colors = np.copy(self.parent_manager.roi_crs[self.zcenter])
color = np.array([255., 255., 255., 255.])
colors[(self.parent_manager.roi_ixs[self.zcenter] == self.roi_ix).flatten()] = color
brushes = list(map(pg.mkBrush, colors))
pens = list(map(pg.mkPen, colors))
self.scatter_plot.setBrush(brushes)
self.scatter_plot.setPen(pens)
# self.curve_plot_item.setSize(pg.mkPen('w', width=2))
def add_to_viewer(self):
if self.parent_manager is None:
super(VolMultiCNMFROI, self).add_to_viewer()
def remove_from_viewer(self):
if self.parent_manager is None:
super(VolMultiCNMFROI, self).remove_from_viewer()
return
new_ixs = (self.parent_manager.roi_ixs[self.zcenter] != self.roi_ix).flatten()
self.parent_manager.roi_ixs[self.zcenter] = self.parent_manager.roi_ixs[self.zcenter][new_ixs]
self.parent_manager.roi_xys[self.zcenter] = self.parent_manager.roi_xys[self.zcenter][new_ixs]
self.parent_manager.roi_crs[self.zcenter] = self.parent_manager.roi_crs[self.zcenter][new_ixs]
xys = self.parent_manager.roi_xys[self.zcenter]
crs = self.parent_manager.roi_crs[self.zcenter]
self.scatter_plot.setData(
xys[:, 0],
xys[:, 1],
symbol='s',
size=1,
pxMode=True,
brush=list(map(pg.mkBrush, crs)),
pen=list(map(pg.mkPen, crs))
)
if self.curve_plot_item is not None:
self.curve_plot_item.clear()
del self.curve_plot_item
def restore_state(self, state):
super(VolMultiCNMFROI, self).restore_state(state)
# self.curve_data = state['curve_data']
self.cnmf_idx = state['cnmf_idx']
if 'raw_min' in state.keys() and 'raw_max' in state.keys():
self.raw_min = state.pop('raw_min')
self.raw_max = state.pop('raw_max')
else:
self.raw_min = None
self.raw_max = None
self.zcenter = state['zcenter']
if self.parent_manager is None:
self._draw()
def to_state(self) -> dict:
state = {'cnmf_idx': self.cnmf_idx,
'zcenter': self.zcenter,
'roi_ix': self.roi_ix,
'roi_xs': self.roi_xs,
'roi_ys': self.roi_ys,
'raw_min_max': self.raw_min_max,
'curve_data': self.curve_data,
'spike_data': self.spike_data,
'dfof_data': self.dfof_data,
'tags': self.get_all_tags(),
'roi_type': self.__class__.__name__,
}
return state
def check_visible(self):
if self.zlevel == self.zcenter:
self.visible = True
self.set_viewer_curveplot(self.curve_data_type)
else:
self.visible = False
self.curve_plot_item.clear()
def set_zlevel(self, z: int):
"""
Set the z-level of the ROI to correspond with the
z-level of the image.
Different from `setZValue`!!
"""
self.zlevel = z
self.check_visible()
[docs]class CNMFROI(ScatterROI):
"""A class for ROIs imported from CNMF(E) output data"""
[docs] def __init__(self, curve_plot_item: pg.PlotDataItem, view_box: pg.ViewBox, cnmf_idx: int = None,
curve_data: np.ndarray = None, contour: dict = None, state: Union[dict, None] = None,
spike_data: np.ndarray = None, dfof_data: np.ndarray = None, metadata: dict = None,
**kwargs):
"""
Instantiate attributes.
:type: curve_data: np.ndarray
:param curve_data: 1D numpy array of y values
:type contour: np.ndarray
:type state: dict
:param cnmf_idx: original index of the ROI from cnmf idx_components
"""
super(CNMFROI, self).__init__(curve_plot_item, view_box, state, curve_data,
spike_data=spike_data, dfof_data=dfof_data,
metadata=metadata)
self.roi_xs = np.empty(0) #: numpy array of the x values of the ROI's spatial coordinates
self.roi_ys = np.empty(0) #: numpy array of the y values of the ROI's spatial coordinates
if 'raw_min_max' in kwargs.keys():
self.raw_min_max = kwargs.pop('raw_min_max')
else:
self.raw_min_max = None
if state is None:
# get the outline from the cnmf output
cors = contour['coordinates']
cors = cors[~np.isnan(cors).any(axis=1)]
xs = cors[:, 0].flatten()
ys = cors[:, 1].flatten()
self.set_roi_graphics_object(xs, ys)
self.set_curve_data(curve_data)
self.cnmf_idx = cnmf_idx #: original index of the ROI from cnmf idx_components
else:
self.restore_state(state)
# self.spot_size = 1
def restore_state(self, state):
super(CNMFROI, self).restore_state(state)
# self.curve_data = state['curve_data']
self.cnmf_idx = state['cnmf_idx']
if 'raw_min' in state.keys() and 'raw_max' in state.keys():
self.raw_min = state.pop('raw_min')
self.raw_max = state.pop('raw_max')
else:
self.raw_min = None
self.raw_max = None
[docs] def to_state(self) -> dict:
state = super(CNMFROI, self).to_state()
state = {**state,
'cnmf_idx': self.cnmf_idx,
'raw_min_max': self.raw_min_max
}
return state