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Diffstat (limited to 'examples/external/scikit/staining_colors_separation.py')
| -rw-r--r-- | examples/external/scikit/staining_colors_separation.py | 184 |
1 files changed, 184 insertions, 0 deletions
diff --git a/examples/external/scikit/staining_colors_separation.py b/examples/external/scikit/staining_colors_separation.py new file mode 100644 index 000000000..051b2bc25 --- /dev/null +++ b/examples/external/scikit/staining_colors_separation.py @@ -0,0 +1,184 @@ +############################################################################# +## +## Copyright (C) 2020 The Qt Company Ltd. +## Contact: https://www.qt.io/licensing/ +## +## This file is part of the Qt for Python examples of the Qt Toolkit. +## +## $QT_BEGIN_LICENSE:BSD$ +## You may use this file under the terms of the BSD license as follows: +## +## "Redistribution and use in source and binary forms, with or without +## modification, are permitted provided that the following conditions are +## met: +## * Redistributions of source code must retain the above copyright +## notice, this list of conditions and the following disclaimer. +## * Redistributions in binary form must reproduce the above copyright +## notice, this list of conditions and the following disclaimer in +## the documentation and/or other materials provided with the +## distribution. +## * Neither the name of The Qt Company Ltd nor the names of its +## contributors may be used to endorse or promote products derived +## from this software without specific prior written permission. +## +## +## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +## "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +## LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +## A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +## OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +## SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +## LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +## DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +## THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +## (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +## OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE." +## +## $QT_END_LICENSE$ +## +############################################################################# + +import sys + +import numpy as np +from matplotlib.backends.backend_qt5agg import FigureCanvas +from matplotlib.colors import LinearSegmentedColormap +from matplotlib.figure import Figure +from PySide2.QtCore import Qt, Slot +from PySide2.QtGui import QKeySequence +from PySide2.QtWidgets import (QAction, 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) + self.menu_file.addAction(exit) + + self.menu_about = self.menu.addMenu("&About") + about = QAction("About Qt", self, shortcut=QKeySequence(QKeySequence.HelpContents), + triggered=qApp.aboutQt) + 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_() |