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app.py
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# PyQt5
from PyQt5 import QtCore, QtWidgets, QtGui
from PyQt5.QtWidgets import QFileDialog
from Worker import SequenceWorker
# Matplotlib
import matplotlib.pyplot as plt
# Viewers
from PhantomViewer import PhantomViewer
from SequenceViewer import SequenceViewer
from ImageViewer import ImageViewer
from Phantom import Phantom
# Numpy
import numpy as np
import math
import warnings
warnings.filterwarnings("ignore")
# Main Window
class MainWindow(QtWidgets.QMainWindow):
# Constructor
def __init__(self):
super().__init__()
self.setWindowTitle("Magnetic Resonance Imaging Simulator")
self.setWindowIcon(QtGui.QIcon("assets/icon.ico"))
self.running = False
self.k_space = np.array([])
# Initialize the UI
self.UI_init()
# Add menu bar
self.create_menu()
# Connect signals and slots
self.connect()
# Show the window
# self.phantom_viewer.setConstant(3,0)
# self.test1()
# Initialize the UI
def UI_init(self):
# Create a central widget and set the layout
central_widget = QtWidgets.QWidget()
central_layout = QtWidgets.QHBoxLayout()
# Set up the main layout
main_splitter = QtWidgets.QSplitter(QtCore.Qt.Vertical)
##############################################################
## Top splitter
top_splitter = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
main_splitter.addWidget(top_splitter)
###############################
### Viewer Layout
viewer_layout = QtWidgets.QVBoxLayout()
viewer_widget = QtWidgets.QWidget()
viewer_widget.setLayout(viewer_layout)
#### Selector Layout
selector_layout = QtWidgets.QHBoxLayout()
##### Selector
self.mode_selector = QtWidgets.QComboBox()
self.mode_selector.addItems(["Protein Density", "T1", "T2", "T2*", "Delta B"])
selector_layout.addWidget(self.mode_selector,4)
##### Reset Button
self.reset_M_Btn = QtWidgets.QPushButton("Reset Magnetization")
selector_layout.addWidget(self.reset_M_Btn,1)
viewer_layout.addLayout(selector_layout,1)
#### Lower Layout
lower_layout = QtWidgets.QHBoxLayout()
##### Phantom Buttons Layout
self.phantom_buttons_layout = QtWidgets.QVBoxLayout()
###### Shepp Logan Button
self.shepp_logan_button = QtWidgets.QPushButton("Shepp Logan")
self.phantom_buttons_layout.addWidget(self.shepp_logan_button)
###### Gradient Button
self.gradient_button = QtWidgets.QPushButton("Gradient")
self.phantom_buttons_layout.addWidget(self.gradient_button)
###### Constant Button
self.const_button = QtWidgets.QPushButton("Constant")
self.phantom_buttons_layout.addWidget(self.const_button)
lower_layout.addLayout(self.phantom_buttons_layout, 1)
##### Phantom Viewer
self.phantom_viewer = PhantomViewer(title="Phantom")
self.phantom_viewer.setCursor(QtGui.QCursor())
self.phantom_viewer.setFocusPolicy(QtCore.Qt.ClickFocus)
lower_layout.addWidget(self.phantom_viewer, 20)
viewer_layout.addLayout(lower_layout, 20)
###############################
### Sequence Layout
sequence_layout = QtWidgets.QVBoxLayout()
sequence_widget = QtWidgets.QWidget()
sequence_widget.setLayout(sequence_layout)
#### Sequence Viewer
self.sequence_viewer = SequenceViewer(title="Sequence")
self.sequence_viewer.setCursor(QtGui.QCursor())
self.sequence_viewer.setFocusPolicy(QtCore.Qt.ClickFocus)
sequence_layout.addWidget(self.sequence_viewer)
#### Control Layout
control_layout = QtWidgets.QHBoxLayout()
sequence_layout.addLayout(control_layout)
##### Radio Buttons
self.choose_output_1 = QtWidgets.QRadioButton("Output 1",checked=True)
self.choose_output_2 = QtWidgets.QRadioButton("Output 2")
control_layout.addWidget(self.choose_output_1, 1)
control_layout.addWidget(self.choose_output_2, 1)
##### Run Button
self.run_button = QtWidgets.QPushButton("Run")
self.run_button.setIcon(QtGui.QIcon("./assets/play.ico"))
self.run_button.setStyleSheet("""background-color: #4f4f4f;
font-size:15px;
border-radius: 6px;
border: 1px solid rgba(27, 31, 35, 0.15);
padding: 5px 15px;
color: #dadada;
font-weight: bold;""")
control_layout.addWidget(self.run_button,2)
###############################
### K Space Layout
k_space_layout = QtWidgets.QVBoxLayout()
k_space_widget = QtWidgets.QWidget()
k_space_widget.setLayout(k_space_layout)
#### K Space Viewer
self.k_space_viewer = ImageViewer(title="K Space")
self.k_space_viewer.setCursor(QtGui.QCursor())
self.k_space_viewer.setFocusPolicy(QtCore.Qt.ClickFocus)
k_space_layout.addWidget(self.k_space_viewer)
#### Progress Bar
self.progress_bar = QtWidgets.QProgressBar()
self.progress_bar.setRange(0,100)
self.progress_bar.setValue(0)
k_space_layout.addWidget(self.progress_bar)
###############################
# Add widgets to the layout
top_splitter.addWidget(viewer_widget)
top_splitter.addWidget(sequence_widget)
top_splitter.addWidget(k_space_widget)
##############################################################
## Bottom Splitter
bottom_splitter = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
main_splitter.addWidget(bottom_splitter)
###############################
### Output 1 Layout
output_layout_1 = QtWidgets.QVBoxLayout()
output_widget_1 = QtWidgets.QWidget()
output_widget_1.setLayout(output_layout_1)
#### Output 1 Viewer
self.output_viewer_1 = ImageViewer(title="Output 1")
self.output_viewer_1.setCursor(QtGui.QCursor())
self.output_viewer_1.setFocusPolicy(QtCore.Qt.ClickFocus)
output_layout_1.addWidget(self.output_viewer_1)
###############################
### Output 2 Layout
output_layout_2 = QtWidgets.QVBoxLayout()
output_widget_2 = QtWidgets.QWidget()
output_widget_2.setLayout(output_layout_2)
#### Output 2 Viewer
self.output_viewer_2 = ImageViewer(title="Output 2")
self.output_viewer_2.setCursor(QtGui.QCursor())
self.output_viewer_2.setFocusPolicy(QtCore.Qt.ClickFocus)
output_layout_2.addWidget(self.output_viewer_2)
###############################
# Add widgets to the layout
bottom_splitter.addWidget(output_widget_1)
bottom_splitter.addWidget(output_widget_2)
##############################################################
# Set the central widget
central_layout.addWidget(main_splitter)
central_widget.setLayout(central_layout)
self.setCentralWidget(central_widget)
# Connect signals and slots
def connect(self):
# Mode Selector
self.mode_selector.currentIndexChanged.connect(self.change_mode)
# Run Button
self.run_button.clicked.connect(self.run_button_event)
# Phantom Buttons
self.shepp_logan_button.clicked.connect(lambda: self.phantom_viewer.setSheppLogan(32))
self.gradient_button.clicked.connect(lambda: self.phantom_viewer.setGradient(32))
self.const_button.clicked.connect(lambda: self.phantom_viewer.setConstant(32,120))
# Reset Mag. Button
self.reset_M_Btn.clicked.connect(self.phantom_viewer.resetM)
# Create the menu bar
def create_menu(self):
menu_bar = self.menuBar()
file_menu = menu_bar.addMenu("File")
open_phantom_action = QtWidgets.QAction("Open Phantom", self)
open_phantom_action.setShortcut("Ctrl+p")
open_phantom_action.triggered.connect(self.open_phantom)
open_sequence_action = QtWidgets.QAction("Open Sequence", self)
open_sequence_action.setShortcut("Ctrl+s")
open_sequence_action.triggered.connect(self.open_sequence)
file_menu.addAction(open_phantom_action)
file_menu.addAction(open_sequence_action)
# Open Phantom
def open_phantom(self):
file_dialog = QFileDialog()
file_dialog.setFileMode(QFileDialog.ExistingFile)
file_dialog.setNameFilter("Image Files (*.png *.jpg *.jpeg *.svg *.webp);;Numpy files (*.npy)")
if file_dialog.exec_():
filenames = file_dialog.selectedFiles()
if len(filenames) > 0:
filename = filenames[0]
ext = filename.split('.')[1]
# try:
self.phantom_viewer.setData(filename, ext)
# except Exception as e:
# print(e)
# QtWidgets.QMessageBox.critical(self, "Error", "Unable to open the phantom file.")
# Open Sequence
def open_sequence(self):
file_dialog = QFileDialog()
file_dialog.setFileMode(QFileDialog.ExistingFile)
file_dialog.setNameFilter("Json Files (*.json)")
if file_dialog.exec_():
filenames = file_dialog.selectedFiles()
if len(filenames) > 0:
filename = filenames[0]
try:
self.sequence_viewer.setData(filename)
except Exception as e:
print(e)
QtWidgets.QMessageBox.critical(self, "Error", "Unable to open the sequence file.")
# Change mode showed
def change_mode(self, index):
self.phantom_viewer.changeAttribute(index)
# Run Button
def run_button_event(self):
# Get sequence based on time
sequence = self.sequence_viewer.get_sequence() # [(Time, Type, duration, flip_angle, Sign), ...]
if sequence == []:
QtWidgets.QMessageBox.critical(self, "Error", "Please load a sequence first.")
return
else:
print(sequence)
if self.running:
self.run_button.setText("Run")
self.run_button.setIcon(QtGui.QIcon("./assets/play.ico"))
self.pause_sequence()
else:
self.run_button.setText("Cancel")
self.run_button.setIcon(QtGui.QIcon("./assets/cancel.ico"))
self.run_sequence(sequence)
self.running = not self.running
# Run the sequence
def run_sequence(self, sequence):
# Settings before running
self.choose_output_1.setEnabled(False)
self.choose_output_2.setEnabled(False)
# Get phantom to simulate
phantom = self.phantom_viewer.getPhantom() # Phantom object [M, T1, T2, PD]
N = phantom.width
# Initialize the thread and worker
self.thread = QtCore.QThread()
self.worker = SequenceWorker(phantom, sequence, self.k_space_viewer)
# Final resets
# Move worker to the thread
self.worker.moveToThread(self.thread)
# Connect signals and slots
self.thread.started.connect(self.worker.run)
self.worker.finished.connect(self.thread.quit)
self.worker.finished.connect(self.worker.deleteLater)
self.thread.finished.connect(self.thread.deleteLater)
self.worker.k_space_update.connect(self.k_space_update)
self.worker.progress.connect(self.updateSimulatorProgress)
# Start the thread
self.thread.start()
## Generate output
### Draw the result
self.thread.finished.connect(self.output_update)
# Pause the sequence
def pause_sequence(self):
self.choose_output_1.setEnabled(True)
self.choose_output_2.setEnabled(True)
self.worker.pause()
# Update the progress bar
def updateSimulatorProgress(self, progress):
self.progress_bar.setValue(progress)
@QtCore.pyqtSlot(np.ndarray)
def k_space_update(self, k_space):
self.k_space = k_space
@QtCore.pyqtSlot()
def output_update(self):
### Make inverse fourier transform
print(self.k_space)
if self.k_space:
result_image = np.fft.ifft2(self.k_space)
if self.choose_output_1.isChecked():
self.output_viewer_1.drawData(np.abs(result_image), title="Output 1")
elif self.choose_output_2.isChecked():
self.output_viewer_2.drawData(np.abs(result_image), title="Output 2")
else:
QtWidgets.QMessageBox.critical(self, "Error", "Please, upload the phantom.")
self.run_button.setIcon(QtGui.QIcon("./assets/play.ico"))
self.run_button.setText("Run")
self.choose_output_1.setEnabled(True)
self.choose_output_2.setEnabled(True)
self.running = False
# Close the application
def closeEvent(self, QCloseEvent):
super().closeEvent(QCloseEvent)
# Exit the application
def exit(self):
self.close()
def test(self, arr):
# Draw Inverse Fourier Transform of the k-space
self.output_viewer_2.drawData(np.fft.fftshift(np.abs(np.fft.ifft2(arr))))
# Set Sequence
self.sequence_viewer.setData("./Resources/Sequences/GE_PD.json")
def test1(self):
arr = np.array([[0,1],[2,3]])
t1 = np.array([[3000, 500], [1000, 1500]])
t2 = np.array([[500, 250], [800, 1000]])
dB = np.array([[50, 100], [200, 150]])
# Set Attributes
self.phantom_viewer.setArray(arr)
self.phantom_viewer.getPhantom().set_information(t1, t2, dB)
self.test(arr)
def test2(self, N=16):
image = self.phantom_viewer.setSheppLogan(N)
self.test(image)