1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
|
# Copyright (C) 2022 The Qt Company Ltd.
# SPDX-License-Identifier: LicenseRef-Qt-Commercial OR BSD-3-Clause
from __future__ import annotations
import sys
import numpy as np
from matplotlib.backends.backend_qt5agg import FigureCanvas
from matplotlib.colors import LinearSegmentedColormap
from matplotlib.figure import Figure
from PySide6.QtCore import Qt, Slot
from PySide6.QtGui import QAction, QKeySequence
from PySide6.QtWidgets import (QApplication, QHBoxLayout, QLabel,
QMainWindow, QPushButton, QSizePolicy,
QVBoxLayout, QWidget)
from skimage import data
from skimage.color import rgb2hed
from skimage.exposure import rescale_intensity
class ApplicationWindow(QMainWindow):
"""
Example based on the example by 'scikit-image' gallery:
"Immunohistochemical staining colors separation"
https://scikit-image.org/docs/stable/auto_examples/color_exposure/plot_ihc_color_separation.html
"""
def __init__(self, parent=None):
QMainWindow.__init__(self, parent)
self._main = QWidget()
self.setCentralWidget(self._main)
# Main menu bar
self.menu = self.menuBar()
self.menu_file = self.menu.addMenu("File")
exit = QAction("Exit", self, triggered=qApp.quit) # noqa: F821
self.menu_file.addAction(exit)
self.menu_about = self.menu.addMenu("&About")
about = QAction("About Qt", self, shortcut=QKeySequence(QKeySequence.HelpContents),
triggered=qApp.aboutQt) # noqa: F821
self.menu_about.addAction(about)
# Create an artificial color close to the original one
self.ihc_rgb = data.immunohistochemistry()
self.ihc_hed = rgb2hed(self.ihc_rgb)
main_layout = QVBoxLayout(self._main)
plot_layout = QHBoxLayout()
button_layout = QHBoxLayout()
label_layout = QHBoxLayout()
self.canvas1 = FigureCanvas(Figure(figsize=(5, 5)))
self.canvas2 = FigureCanvas(Figure(figsize=(5, 5)))
self._ax1 = self.canvas1.figure.subplots()
self._ax2 = self.canvas2.figure.subplots()
self._ax1.imshow(self.ihc_rgb)
plot_layout.addWidget(self.canvas1)
plot_layout.addWidget(self.canvas2)
self.button1 = QPushButton("Hematoxylin")
self.button2 = QPushButton("Eosin")
self.button3 = QPushButton("DAB")
self.button4 = QPushButton("Fluorescence")
self.button1.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Expanding)
self.button2.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Expanding)
self.button3.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Expanding)
self.button4.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Expanding)
self.button1.clicked.connect(self.plot_hematoxylin)
self.button2.clicked.connect(self.plot_eosin)
self.button3.clicked.connect(self.plot_dab)
self.button4.clicked.connect(self.plot_final)
self.label1 = QLabel("Original", alignment=Qt.AlignCenter)
self.label2 = QLabel("", alignment=Qt.AlignCenter)
font = self.label1.font()
font.setPointSize(16)
self.label1.setFont(font)
self.label2.setFont(font)
label_layout.addWidget(self.label1)
label_layout.addWidget(self.label2)
button_layout.addWidget(self.button1)
button_layout.addWidget(self.button2)
button_layout.addWidget(self.button3)
button_layout.addWidget(self.button4)
main_layout.addLayout(label_layout, 2)
main_layout.addLayout(plot_layout, 88)
main_layout.addLayout(button_layout, 10)
# Default image
self.plot_hematoxylin()
def set_buttons_state(self, states):
self.button1.setEnabled(states[0])
self.button2.setEnabled(states[1])
self.button3.setEnabled(states[2])
self.button4.setEnabled(states[3])
@Slot()
def plot_hematoxylin(self):
cmap_hema = LinearSegmentedColormap.from_list("mycmap", ["white", "navy"])
self._ax2.imshow(self.ihc_hed[:, :, 0], cmap=cmap_hema)
self.canvas2.draw()
self.label2.setText("Hematoxylin")
self.set_buttons_state((False, True, True, True))
@Slot()
def plot_eosin(self):
cmap_eosin = LinearSegmentedColormap.from_list("mycmap", ["darkviolet", "white"])
self._ax2.imshow(self.ihc_hed[:, :, 1], cmap=cmap_eosin)
self.canvas2.draw()
self.label2.setText("Eosin")
self.set_buttons_state((True, False, True, True))
@Slot()
def plot_dab(self):
cmap_dab = LinearSegmentedColormap.from_list("mycmap", ["white", "saddlebrown"])
self._ax2.imshow(self.ihc_hed[:, :, 2], cmap=cmap_dab)
self.canvas2.draw()
self.label2.setText("DAB")
self.set_buttons_state((True, True, False, True))
@Slot()
def plot_final(self):
h = rescale_intensity(self.ihc_hed[:, :, 0], out_range=(0, 1))
d = rescale_intensity(self.ihc_hed[:, :, 2], out_range=(0, 1))
zdh = np.dstack((np.zeros_like(h), d, h))
self._ax2.imshow(zdh)
self.canvas2.draw()
self.label2.setText("Stain separated image")
self.set_buttons_state((True, True, True, False))
if __name__ == "__main__":
app = QApplication(sys.argv)
w = ApplicationWindow()
w.show()
app.exec()
|
