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docker_gui.py
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docker_gui.py
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import sys
import os
import subprocess
from pathlib import Path, PurePosixPath
from PyQt5.QtWidgets import (QDialog, QVBoxLayout, QGridLayout, QLabel,
QSpinBox, QComboBox, QDialogButtonBox, QCheckBox,
QApplication, QFileDialog, QLineEdit, QListWidget,
QPushButton, QErrorMessage, QMessageBox)
from PyQt5.QtCore import Qt, pyqtSlot
from PyQt5.QtWidgets import QApplication
class LabelsDialog(QDialog):
def __init__(self,
parent=None, subject_directory=None, QApplication=None):
super().__init__(parent)
self.setWindowTitle('Label Toolbox')
vbox = QVBoxLayout(self)
grid = QGridLayout()
# Subject dir
grid.addWidget(QLabel('Subject directory:'), 0, 0)
self.QLineEdit_subject_dir = QLineEdit()
self.subject_directory = subject_directory
self.QLineEdit_subject_dir.setText(subject_directory)
grid.addWidget(self.QLineEdit_subject_dir, 0, 1)
self.QPushButton_open_subject_dir = QPushButton('Open')
self.QPushButton_open_subject_dir.clicked.connect(
self.open_subject_directory)
grid.addWidget(self.QPushButton_open_subject_dir, 0, 3)
# subject
grid.addWidget(QLabel('Subject:'), 1, 0)
self.QComboBox_subject = QListWidget()
self.set_subjects()
self.QComboBox_subject.setSelectionMode(QListWidget.ExtendedSelection)
grid.addWidget(self.QComboBox_subject, 1, 1, 1, 3)
# atlas
grid.addWidget(QLabel('Atlas:'), 2, 0)
self.QListWidget_atlas = QListWidget()
self.get_available_atlas()
self.QListWidget_atlas.insertItems(0, self.available_atlas)
self.QListWidget_atlas.setSelectionMode(QListWidget.ExtendedSelection)
grid.addWidget(self.QListWidget_atlas, 2, 1, 1, 3)
# Choose workflow
self.QCheckBox_workflow = QCheckBox()
self.QCheckBox_workflow.setText('Convert to cartool')
self.QCheckBox_workflow.setChecked(True)
self.cartool = True
grid.addWidget(self.QCheckBox_workflow, 3, 1)
# outputdir
grid.addWidget(QLabel('Output directory:'), 4, 0)
self.QLineEdit_output_dir = QLineEdit()
self.output_directory = os.getcwd()
self.QLineEdit_output_dir.setText(self.output_directory)
grid.addWidget(self.QLineEdit_output_dir, 4, 1)
self.QPushButton_open_output_dir = QPushButton('Open')
self.QPushButton_open_output_dir.clicked.connect(
self.open_output_directory)
grid.addWidget(self.QPushButton_open_output_dir, 4, 3)
# performance
grid.addWidget(QLabel('n_procs:'), 5, 0)
self.QLineEdit_output_dir = QLineEdit()
self.max_cpus = os.cpu_count()
self.QSpinBox_n_cpus = QSpinBox()
self.QSpinBox_n_cpus.setMinimum(1)
self.QSpinBox_n_cpus.setMaximum(self.max_cpus)
self.QSpinBox_n_cpus.setValue(self.max_cpus)
grid.addWidget(self.QSpinBox_n_cpus, 5, 1)
# run
self.buttonbox = QDialogButtonBox(QDialogButtonBox.Ok |
QDialogButtonBox.Cancel)
grid.addWidget(self.buttonbox, 6, 1, 1, 4)
self.buttonbox.accepted.connect(self.run_pipeline)
self.buttonbox.rejected.connect(self.reject)
vbox.addLayout(grid)
def get_subjects(self):
"Get all subject in subject_directory"
import os
self.subjects = [name for name in os.listdir(self.subject_directory)
if os.path.isdir(os.path.join(self.subject_directory,
name))]
return ()
def get_available_atlas(self):
self.available_atlas = ['desikan_killiany',
'DKTatlas40',
'Schaefer2018_100Parcels_7Networks',
'Schaefer2018_100Parcels_17Networks',
'Schaefer2018_200Parcels_7Networks',
'Schaefer2018_200Parcels_17Networks',
'Schaefer2018_300Parcels_7Networks',
'Schaefer2018_300Parcels_17Networks',
'Schaefer2018_400Parcels_7Networks',
'Schaefer2018_400Parcels_17Networks',
'Schaefer2018_500Parcels_7Networks',
'Schaefer2018_500Parcels_17Networks',
'Schaefer2018_600Parcels_7Networks',
'Schaefer2018_600Parcels_17Networks',
'Schaefer2018_700Parcels_7Networks',
'Schaefer2018_700Parcels_17Networks',
'Schaefer2018_800Parcels_7Networks',
'Schaefer2018_800Parcels_17Networks',
'Schaefer2018_900Parcels_7Networks',
'Schaefer2018_900Parcels_17Networks',
'Schaefer2018_1000Parcels_7Networks',
'Schaefer2018_1000Parcels_17Networks',
'Yeo2011_7Networks',
'Yeo2011_17Networks']
return()
def open_subject_directory(self):
self.subject_directory = QFileDialog.getExistingDirectory(self,
'OpenDir')
self.QLineEdit_subject_dir.setText(self.subject_directory)
self.set_subjects()
return()
def open_output_directory(self):
self.output_directory = QFileDialog.getExistingDirectory(self,
'OpenDir')
self.QLineEdit_output_dir.setText(self.output_directory)
return()
def set_subjects(self):
self.get_subjects()
self.QComboBox_subject.clear()
self.QComboBox_subject.insertItems(0, self.subjects)
def run_pipeline(self):
subjects = ['-s ' + item.data(0) for item in
self.QComboBox_subject.selectedItems()]
atlas = ['-a ' + item.data(0) for item in
self.QListWidget_atlas.selectedItems()]
output_path = self.output_directory
output_path = output_path.replace('\\', '/')
subjects_dir = self.subject_directory
subjects_dir = subjects_dir.replace('\\', '/')
n_cpus = self.QSpinBox_n_cpus.value()
cartool = self.QCheckBox_workflow.isChecked()
command = ['docker run -v', output_path + ':' + '/mnt/output',
'-v ' + subjects_dir + ':' + '/mnt/subjects_dir',
'vferat/labelling:latest', 'python', 'app/app.py']
command.extend(subjects)
command.extend(atlas)
command.extend(['--cpus', str(n_cpus)])
if cartool is True:
command.extend(['--cartool'])
command = ' '.join(command)
print(command)
try:
QApplication.setOverrideCursor(Qt.WaitCursor)
subprocess.run(command, check=True, shell=True)
QApplication.restoreOverrideCursor()
self.QMessageBox_finnish = QMessageBox()
self.QMessageBox_finnish.setWindowTitle("Finished")
self.QMessageBox_finnish.setText("Pipeline ran without errors.")
self.QMessageBox_finnish.exec_()
except Exception as e:
QApplication.restoreOverrideCursor()
self.QErrorMessage = QErrorMessage()
self.QErrorMessage.showMessage(str(e))
if __name__ == '__main__':
subject_directory = os.getcwd()
app = QApplication(sys.argv)
LabelsDialog = LabelsDialog(subject_directory=subject_directory,
QApplication=app)
LabelsDialog.show()
sys.exit(app.exec_())