diff --git a/src/napari_spatial_correlation_plotter/_widget.py b/src/napari_spatial_correlation_plotter/_widget.py index 6ff778b..7185ad8 100644 --- a/src/napari_spatial_correlation_plotter/_widget.py +++ b/src/napari_spatial_correlation_plotter/_widget.py @@ -1,25 +1,29 @@ import os -import warnings +from pathlib import Path as PathL +from time import time + import matplotlib.pyplot as plt +import napari import numpy as np -from pathlib import Path as PathL -from magicgui.widgets import Container, create_widget, EmptyWidget -from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas -from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar +from magicgui.widgets import Container, EmptyWidget, create_widget +from matplotlib.backends.backend_qt5agg import \ + FigureCanvasQTAgg as FigureCanvas +from matplotlib.backends.backend_qt5agg import \ + NavigationToolbar2QT as NavigationToolbar from matplotlib.figure import Figure from matplotlib.path import Path from matplotlib.widgets import LassoSelector, RectangleSelector -from napari.layers import Labels, Image, Layer +from napari.layers import Image, Labels, Layer +from napari.utils import DirectLabelColormap +from napari_spatial_correlation_plotter._nice_colormap import get_nice_colormap +from organoid.analysis.spatial_correlation._spatial_correlation_plotter import \ + SpatialCorrelationPlotter +from organoid.preprocessing._smoothing import \ + gaussian_smooth_dense_two_arrays_gpu from qtpy.QtCore import Qt from qtpy.QtGui import QGuiApplication, QIcon from skimage.measure import regionprops -from organoid.analysis.spatial_correlation._spatial_correlation_plotter import SpatialCorrelationPlotter -from napari_spatial_correlation_plotter._nice_colormap import get_nice_colormap from vispy.color import Color -from napari.utils import DirectLabelColormap -from pyngs.dense_smoothing_3d_gpu import gaussian_smooth_dense_two_arrays_gpu -from time import time - ICON_ROOT = PathL(__file__).parent / "icons" @@ -556,7 +560,7 @@ def manual_clustering_method(self, inside): def run(self): # Check if all necessary layers are specified if self.quantityX_layer_combo.value is None: - warnings.warn("Please specify quantityX_layer") + napari.utils.notifications.show_warning("Please specify quantityX_layer") return else: self.quantityX = self.quantityX_layer_combo.value.data @@ -569,7 +573,7 @@ def run(self): self.quantityX_labels_choice = self.quantityX_labels_choices_combo.value if self.quantityY_layer_combo.value is None: - warnings.warn("Please specify quantityY_layer") + napari.utils.notifications.show_warning("Please specify quantityY_layer") return else: self.quantityY = self.quantityY_layer_combo.value.data