Source code for napari_locan.widgets.widget_render_points_2d
"""
Render 2d point cloud.
A QWidget plugin to render SMLM data in 2d.
"""
from __future__ import annotations
import logging
from typing import Any
import locan as lc
import numpy.typing as npt
from napari.utils import progress
from napari.viewer import Viewer
from qtpy.QtWidgets import (
QComboBox,
QHBoxLayout,
QLabel,
QMessageBox,
QPushButton,
QVBoxLayout,
QWidget,
)
from napari_locan import smlm_data
from napari_locan.data_model.smlm_data import SmlmData
logger = logging.getLogger(__name__)
[docs]
class RenderPoints2dQWidget(QWidget): # type: ignore
def __init__(self, napari_viewer: Viewer, smlm_data: SmlmData = smlm_data):
super().__init__()
self.viewer = napari_viewer
self.smlm_data = smlm_data
self._add_loc_properties_selection()
self._add_other_properties_selection()
self._add_points_buttons()
self._set_layout()
def _add_loc_properties_selection(self) -> None:
self._loc_properties_x_label = QLabel("x:")
self._loc_properties_x_combobox = QComboBox()
self._loc_properties_x_combobox.setToolTip(
"Choose localization property for selected SMLM dataset as x coordinate."
)
self.smlm_data.index_changed_signal.connect(
self._loc_properties_x_combobox_slot_for_smlm_data_index
)
# condition excludes smlm_data.locdata to be None in what comes:
if self.smlm_data.index != -1 and bool(self.smlm_data.locdata):
self._loc_properties_x_combobox.addItems(
self.smlm_data.locdata.data.columns # type: ignore
)
try:
key_index = list(
self.smlm_data.locdata.data.columns # type: ignore
).index(
self.smlm_data.locdata.coordinate_keys[0] # type: ignore
)
self._loc_properties_x_combobox.setCurrentIndex(key_index)
except IndexError:
self._loc_properties_x_combobox.setCurrentIndex(-1)
self._loc_properties_y_label = QLabel("y:")
self._loc_properties_y_combobox = QComboBox()
self._loc_properties_y_combobox.setToolTip(
"Choose localization property for selected SMLM dataset as y coordinate."
)
self.smlm_data.index_changed_signal.connect(
self._loc_properties_y_combobox_slot_for_smlm_data_index
)
if self.smlm_data.index != -1 and bool(self.smlm_data.locdata):
self._loc_properties_y_combobox.addItems(
self.smlm_data.locdata.data.columns # type: ignore
)
try:
key_index = list(
self.smlm_data.locdata.data.columns # type: ignore
).index(
self.smlm_data.locdata.coordinate_keys[1] # type: ignore
)
self._loc_properties_y_combobox.setCurrentIndex(key_index)
except IndexError:
self._loc_properties_y_combobox.setCurrentIndex(-1)
self._loc_properties_layout = QHBoxLayout()
self._loc_properties_layout.addWidget(self._loc_properties_x_label)
self._loc_properties_layout.addWidget(self._loc_properties_x_combobox)
self._loc_properties_layout.addWidget(self._loc_properties_y_label)
self._loc_properties_layout.addWidget(self._loc_properties_y_combobox)
def _add_other_properties_selection(self) -> None:
self._loc_properties_other_label = QLabel("other:")
self._loc_properties_other_combobox = QComboBox()
self._loc_properties_other_combobox.setToolTip(
"Choose localization property for selected SMLM dataset as pixel value."
)
self.smlm_data.index_changed_signal.connect(
self._loc_properties_other_combobox_slot_for_smlm_data_index
)
if self.smlm_data.index != -1 and bool(self.smlm_data.locdata):
self._loc_properties_other_combobox.addItem("")
self._loc_properties_other_combobox.addItems(
self.smlm_data.locdata.data.columns # type: ignore
)
key_index = 0
self._loc_properties_other_combobox.setCurrentIndex(key_index)
self._other_properties_layout = QHBoxLayout()
self._other_properties_layout.addWidget(self._loc_properties_other_label)
self._other_properties_layout.addWidget(self._loc_properties_other_combobox)
def _loc_properties_x_combobox_slot_for_smlm_data_index(self, index: int) -> None:
key_index = self._loc_properties_x_combobox.currentIndex()
self._loc_properties_x_combobox.clear()
if index != -1:
self._loc_properties_x_combobox.addItems(
self.smlm_data.locdata.data.columns # type: ignore
)
if key_index == -1:
if bool(self.smlm_data.locdata):
new_key_index = list(
self.smlm_data.locdata.data.columns # type: ignore
).index(
self.smlm_data.locdata.coordinate_keys[0] # type: ignore
)
self._loc_properties_x_combobox.setCurrentIndex(new_key_index)
else:
self._loc_properties_x_combobox.setCurrentIndex(-1)
else:
self._loc_properties_x_combobox.setCurrentIndex(key_index)
def _loc_properties_y_combobox_slot_for_smlm_data_index(self, index: int) -> None:
key_index = self._loc_properties_y_combobox.currentIndex()
self._loc_properties_y_combobox.clear()
if index != -1:
self._loc_properties_y_combobox.addItems(
self.smlm_data.locdata.data.columns # type: ignore
)
if key_index == -1:
if bool(self.smlm_data.locdata):
new_key_index = list(
self.smlm_data.locdata.data.columns # type: ignore
).index(
self.smlm_data.locdata.coordinate_keys[1] # type: ignore
)
self._loc_properties_y_combobox.setCurrentIndex(new_key_index)
else:
self._loc_properties_y_combobox.setCurrentIndex(-1)
else:
self._loc_properties_y_combobox.setCurrentIndex(key_index)
def _loc_properties_other_combobox_slot_for_smlm_data_index(
self, index: int
) -> None:
key_index = self._loc_properties_other_combobox.currentIndex()
self._loc_properties_other_combobox.clear()
self._loc_properties_other_combobox.addItem("")
if index != -1:
self._loc_properties_other_combobox.addItems(
self.smlm_data.locdata.data.columns # type: ignore
)
if key_index == -1:
self._loc_properties_other_combobox.setCurrentIndex(0)
else:
self._loc_properties_other_combobox.setCurrentIndex(key_index)
def _add_points_buttons(self) -> None:
self._points_button = QPushButton("Render points")
self._points_button.setToolTip(
"Show point representation of SMLM data in new points layer."
)
self._points_button.clicked.connect(self._points_button_on_click)
def _set_layout(self) -> None:
layout = QVBoxLayout()
layout.addLayout(self._loc_properties_layout)
layout.addLayout(self._other_properties_layout)
layout.addWidget(self._points_button)
self.setLayout(layout)
def _points_button_on_click(self) -> None:
locdata = self.smlm_data.locdata
if locdata is None:
raise ValueError("There is no SMLM data available.")
if bool(locdata) is False:
raise ValueError("Locdata is empty.")
if self._get_message_feedback() is False:
return
loc_properties = [
self._loc_properties_x_combobox.currentText(),
self._loc_properties_y_combobox.currentText(),
]
other_property: str | None = self._loc_properties_other_combobox.currentText()
other_property = other_property if other_property != "" else None
data = locdata.data[loc_properties].to_numpy()
if other_property is None:
point_properties: dict[str, npt.NDArray[Any]] = {}
add_kwargs = {"name": self.smlm_data.locdata_name}
else:
other_property_data = locdata.data[other_property].to_numpy()
other_property_data = lc.adjust_contrast(
other_property_data, rescale=lc.Trafo.STANDARDIZE
)
point_properties = {"other_property": other_property_data}
add_kwargs = {
"name": self.smlm_data.locdata_name,
"edge_color": "",
"face_color": "other_property",
"face_colormap": "viridis",
}
with progress() as progress_bar:
progress_bar.set_description("Rendering:")
self.viewer.add_points(data=data, properties=point_properties, **add_kwargs)
def _get_message_feedback(self) -> bool:
n_localizations = len(self.smlm_data.locdata) # type: ignore
if n_localizations < 10_000:
run_computation = True
else:
msgBox = QMessageBox()
msgBox.setText(
f"There are {n_localizations} localizations. "
f"Rendering will take some time."
)
msgBox.setInformativeText("Do you want to continue?")
msgBox.setStandardButtons(QMessageBox.Ok | QMessageBox.Cancel) # type: ignore[attr-defined]
msgBox.setDefaultButton(QMessageBox.Cancel) # type: ignore[attr-defined]
return_value = msgBox.exec()
run_computation = bool(return_value == QMessageBox.Ok) # type: ignore[attr-defined]
return run_computation