def __init__(self, mode, parent=None):
self.mode = mode
self.parent = parent
super().__init__(parent)
self.setWindowTitle('peakonly: models')
train_folder_label = QtWidgets.QLabel()
train_folder_label.setText('Choose a folder with train data:')
self.train_folder_getter = GetFolderWidget(os.path.join(os.getcwd(), 'data', 'train'), self)
val_folder_label = QtWidgets.QLabel()
val_folder_label.setText('Choose a folder with validation data:')
self.val_folder_getter = GetFolderWidget(os.path.join(os.getcwd(), 'data', 'val'), self)
continue_button = QtWidgets.QPushButton('Continue')
continue_button.clicked.connect(self._continue)
main_layout = QtWidgets.QVBoxLayout()
main_layout.addWidget(train_folder_label)
main_layout.addWidget(self.train_folder_getter)
main_layout.addWidget(val_folder_label)
main_layout.addWidget(self.val_folder_getter)
main_layout.addWidget(continue_button)
self.setLayout(main_layout)
def __init__(self, model, parent):
self.parent = parent
super().__init__(parent)
self.model = model
folder_label = QtWidgets.QLabel()
folder_label.setText('Choose a folder where to save:')
self.folder_getter = GetFolderWidget(os.path.join(os.getcwd(), 'data', 'weights'), self)
name_label = QtWidgets.QLabel()
name_label.setText('Set a name of file: ')
self.name_getter = QtWidgets.QLineEdit(self)
self.name_getter.setText('model.pt')
save_button = QtWidgets.QPushButton('Save')
save_button.clicked.connect(self.save)
main_layout = QtWidgets.QVBoxLayout()
main_layout.addWidget(folder_label)
main_layout.addWidget(self.folder_getter)
main_layout.addWidget(name_label)
main_layout.addWidget(self.name_getter)
main_layout.addWidget(save_button)
self.setLayout(main_layout)
class TrainingParameterWindow(QtWidgets.QDialog):
"""
Training Parameter Window, where one should choose parameters for training
Parameters
----------
mode : str
A one of two 'all in one' of 'sequential'
parent : MainWindow(QtWidgets.QMainWindow)
-
Attributes
----------
mode : str
A one of two 'all in one' of 'sequential'
parent : MainWindow(QtWidgets.QMainWindow)
-
train_folder_getter : GetFolderWidget
A getter for a path to train data
val_folder_getter : GetFolderWidget
A getter for a path to validation data
"""
def __init__(self, mode, parent=None):
self.mode = mode
self.parent = parent
super().__init__(parent)
self.setWindowTitle('peakonly: models')
train_folder_label = QtWidgets.QLabel()
train_folder_label.setText('Choose a folder with train data:')
self.train_folder_getter = GetFolderWidget(os.path.join(os.getcwd(), 'data', 'train'), self)
val_folder_label = QtWidgets.QLabel()
val_folder_label.setText('Choose a folder with validation data:')
self.val_folder_getter = GetFolderWidget(os.path.join(os.getcwd(), 'data', 'val'), self)
continue_button = QtWidgets.QPushButton('Continue')
continue_button.clicked.connect(self._continue)
main_layout = QtWidgets.QVBoxLayout()
main_layout.addWidget(train_folder_label)
main_layout.addWidget(self.train_folder_getter)
main_layout.addWidget(val_folder_label)
main_layout.addWidget(self.val_folder_getter)
main_layout.addWidget(continue_button)
self.setLayout(main_layout)
def _continue(self):
try:
train_folder = self.train_folder_getter.get_folder()
val_folder = self.val_folder_getter.get_folder()
main_window = TrainingMainWindow(self.mode, train_folder, val_folder, self.parent)
main_window.show()
self.close()
except ValueError:
# popup window with exception
msg = QtWidgets.QMessageBox(self)
msg.setText("Check parameters. Something is wrong!")
msg.setIcon(QtWidgets.QMessageBox.Warning)
msg.exec_()
class ReAnnotationParameterWindow(QtWidgets.QDialog):
def __init__(self, parent: AbtractMainWindow):
self.mode = 'reannotation'
self.parent = parent
super().__init__(parent)
self.setWindowTitle('peakonly: reannotation')
save_to_label = QtWidgets.QLabel()
save_to_label.setText('Choose a folder with annotated ROIs:')
self.folder_widget = GetFolderWidget()
self.run_button = QtWidgets.QPushButton('Run reannotation')
self.run_button.clicked.connect(self.start_reannotation)
main_layout = QtWidgets.QVBoxLayout()
main_layout.addWidget(save_to_label)
main_layout.addWidget(self.folder_widget)
main_layout.addWidget(self.run_button)
self.setLayout(main_layout)
def start_reannotation(self):
folder = self.folder_widget.get_folder()
subwindow = AnnotationMainWindow([],
folder,
None,
None,
None,
self.mode,
None,
parent=self.parent)
subwindow.show()
self.close()
class SaveModelWindow(QtWidgets.QDialog):
def __init__(self, model, parent):
self.parent = parent
super().__init__(parent)
self.model = model
folder_label = QtWidgets.QLabel()
folder_label.setText('Choose a folder where to save:')
self.folder_getter = GetFolderWidget(os.path.join(os.getcwd(), 'data', 'weights'), self)
name_label = QtWidgets.QLabel()
name_label.setText('Set a name of file: ')
self.name_getter = QtWidgets.QLineEdit(self)
self.name_getter.setText('model.pt')
save_button = QtWidgets.QPushButton('Save')
save_button.clicked.connect(self.save)
main_layout = QtWidgets.QVBoxLayout()
main_layout.addWidget(folder_label)
main_layout.addWidget(self.folder_getter)
main_layout.addWidget(name_label)
main_layout.addWidget(self.name_getter)
main_layout.addWidget(save_button)
self.setLayout(main_layout)
def save(self):
folder = self.folder_getter.get_folder()
name = self.name_getter.text()
shutil.copyfile(os.path.join('data/tmp_weights', self.model.__class__.__name__),
os.path.join(folder, name))
def __init__(self, parent: AbtractMainWindow):
self.mode = 'reannotation'
self.parent = parent
super().__init__(parent)
self.setWindowTitle('peakonly: reannotation')
save_to_label = QtWidgets.QLabel()
save_to_label.setText('Choose a folder with annotated ROIs:')
self.folder_widget = GetFolderWidget()
self.run_button = QtWidgets.QPushButton('Run reannotation')
self.run_button.clicked.connect(self.start_reannotation)
main_layout = QtWidgets.QVBoxLayout()
main_layout.addWidget(save_to_label)
main_layout.addWidget(self.folder_widget)
main_layout.addWidget(self.run_button)
self.setLayout(main_layout)
def _init_ui(self):
# file and folder selection
choose_file_label = QtWidgets.QLabel()
choose_file_label.setText('Choose a file to annotate:')
self.list_of_files = FileListWidget()
for file in self.files:
self.list_of_files.addFile(file)
save_to_label = QtWidgets.QLabel()
save_to_label.setText('Choose a folder where to save annotated ROIs:')
self.folder_widget = GetFolderWidget()
file_layout = QtWidgets.QVBoxLayout()
file_layout.addWidget(choose_file_label)
file_layout.addWidget(self.list_of_files)
file_layout.addWidget(save_to_label)
file_layout.addWidget(self.folder_widget)
# parameters selection
instrumental_label = QtWidgets.QLabel()
instrumental_label.setText('Instrumentals description')
self.instrumental_getter = QtWidgets.QLineEdit(self)
self.instrumental_getter.setText(
'Q-oa-TOF, total time=10 min, scan frequency=10Hz')
prefix_label = QtWidgets.QLabel()
prefix_label.setText('Prefix of filename: ')
self.prefix_getter = QtWidgets.QLineEdit(self)
self.prefix_getter.setText('Example')
suffix_label = QtWidgets.QLabel()
suffix_label.setText(
'Code of file (suffix, will be increased during annotation): ')
self.suffix_getter = QtWidgets.QLineEdit(self)
self.suffix_getter.setText('0')
mz_label = QtWidgets.QLabel()
mz_label.setText('m/z deviation:')
self.mz_getter = QtWidgets.QLineEdit(self)
self.mz_getter.setText('0.005')
roi_points_label = QtWidgets.QLabel()
roi_points_label.setText('Minimal length of ROI:')
self.roi_points_getter = QtWidgets.QLineEdit(self)
self.roi_points_getter.setText('15')
if self.mode == 'semi-automatic':
peak_points_label = QtWidgets.QLabel()
peak_points_label.setText('Minimal length of peak:')
self.peak_points_getter = QtWidgets.QLineEdit(self)
self.peak_points_getter.setText('8')
dropped_points_label = QtWidgets.QLabel()
dropped_points_label.setText('Maximal number of zero points in a row:')
self.dropped_points_getter = QtWidgets.QLineEdit(self)
self.dropped_points_getter.setText('3')
run_button = QtWidgets.QPushButton('Run annotation')
run_button.clicked.connect(self._run_button)
parameter_layout = QtWidgets.QVBoxLayout()
parameter_layout.addWidget(instrumental_label)
parameter_layout.addWidget(self.instrumental_getter)
parameter_layout.addWidget(prefix_label)
parameter_layout.addWidget(self.prefix_getter)
parameter_layout.addWidget(suffix_label)
parameter_layout.addWidget(self.suffix_getter)
parameter_layout.addWidget(mz_label)
parameter_layout.addWidget(self.mz_getter)
parameter_layout.addWidget(roi_points_label)
parameter_layout.addWidget(self.roi_points_getter)
# if self.mode == 'semi-automatic':
# parameter_layout.addWidget(peak_points_label)
# parameter_layout.addWidget(self.peak_points_getter)
parameter_layout.addWidget(dropped_points_label)
parameter_layout.addWidget(self.dropped_points_getter)
parameter_layout.addWidget(run_button)
# main layout
main_layout = QtWidgets.QHBoxLayout()
main_layout.addLayout(file_layout)
main_layout.addLayout(parameter_layout)
self.setLayout(main_layout)
class AnnotationParameterWindow(QtWidgets.QDialog):
def __init__(self, files, mode, parent: AbtractMainWindow):
self.mode = mode
self.parent = parent
super().__init__(parent)
self.setWindowTitle('peakonly: manual annotation')
self.files = files
self.description = None
self.file_prefix = None
self.file_suffix = None
self.minimum_peak_points = None
self.folder = None
self._init_ui()
def _init_ui(self):
# file and folder selection
choose_file_label = QtWidgets.QLabel()
choose_file_label.setText('Choose a file to annotate:')
self.list_of_files = FileListWidget()
for file in self.files:
self.list_of_files.addFile(file)
save_to_label = QtWidgets.QLabel()
save_to_label.setText('Choose a folder where to save annotated ROIs:')
self.folder_widget = GetFolderWidget()
file_layout = QtWidgets.QVBoxLayout()
file_layout.addWidget(choose_file_label)
file_layout.addWidget(self.list_of_files)
file_layout.addWidget(save_to_label)
file_layout.addWidget(self.folder_widget)
# parameters selection
instrumental_label = QtWidgets.QLabel()
instrumental_label.setText('Instrumentals description')
self.instrumental_getter = QtWidgets.QLineEdit(self)
self.instrumental_getter.setText(
'Q-oa-TOF, total time=10 min, scan frequency=10Hz')
prefix_label = QtWidgets.QLabel()
prefix_label.setText('Prefix of filename: ')
self.prefix_getter = QtWidgets.QLineEdit(self)
self.prefix_getter.setText('Example')
suffix_label = QtWidgets.QLabel()
suffix_label.setText(
'Code of file (suffix, will be increased during annotation): ')
self.suffix_getter = QtWidgets.QLineEdit(self)
self.suffix_getter.setText('0')
mz_label = QtWidgets.QLabel()
mz_label.setText('m/z deviation:')
self.mz_getter = QtWidgets.QLineEdit(self)
self.mz_getter.setText('0.005')
roi_points_label = QtWidgets.QLabel()
roi_points_label.setText('Minimal length of ROI:')
self.roi_points_getter = QtWidgets.QLineEdit(self)
self.roi_points_getter.setText('15')
if self.mode == 'semi-automatic':
peak_points_label = QtWidgets.QLabel()
peak_points_label.setText('Minimal length of peak:')
self.peak_points_getter = QtWidgets.QLineEdit(self)
self.peak_points_getter.setText('8')
dropped_points_label = QtWidgets.QLabel()
dropped_points_label.setText('Maximal number of zero points in a row:')
self.dropped_points_getter = QtWidgets.QLineEdit(self)
self.dropped_points_getter.setText('3')
run_button = QtWidgets.QPushButton('Run annotation')
run_button.clicked.connect(self._run_button)
parameter_layout = QtWidgets.QVBoxLayout()
parameter_layout.addWidget(instrumental_label)
parameter_layout.addWidget(self.instrumental_getter)
parameter_layout.addWidget(prefix_label)
parameter_layout.addWidget(self.prefix_getter)
parameter_layout.addWidget(suffix_label)
parameter_layout.addWidget(self.suffix_getter)
parameter_layout.addWidget(mz_label)
parameter_layout.addWidget(self.mz_getter)
parameter_layout.addWidget(roi_points_label)
parameter_layout.addWidget(self.roi_points_getter)
# if self.mode == 'semi-automatic':
# parameter_layout.addWidget(peak_points_label)
# parameter_layout.addWidget(self.peak_points_getter)
parameter_layout.addWidget(dropped_points_label)
parameter_layout.addWidget(self.dropped_points_getter)
parameter_layout.addWidget(run_button)
# main layout
main_layout = QtWidgets.QHBoxLayout()
main_layout.addLayout(file_layout)
main_layout.addLayout(parameter_layout)
self.setLayout(main_layout)
def _run_button(self):
try:
self.description = self.instrumental_getter.text()
self.file_prefix = self.prefix_getter.text()
self.file_suffix = int(self.suffix_getter.text())
delta_mz = float(self.mz_getter.text())
required_points = int(self.roi_points_getter.text())
dropped_points = int(self.dropped_points_getter.text())
if self.mode == 'semi-automatic':
self.minimum_peak_points = int(self.peak_points_getter.text())
self.folder = self.folder_widget.get_folder()
path2mzml = None
for file in self.list_of_files.selectedItems():
path2mzml = self.list_of_files.file2path[file.text()]
if path2mzml is None:
raise ValueError
worker = Worker(get_ROIs, path2mzml, delta_mz, required_points,
dropped_points)
worker.signals.result.connect(self._start_annotation)
self.parent.run_thread('ROI detection:', worker)
self.close()
except ValueError:
# popup window with exception
msg = QtWidgets.QMessageBox(self)
msg.setText("Check parameters. Something is wrong!")
msg.setIcon(QtWidgets.QMessageBox.Warning)
msg.exec_()
def _start_annotation(self, rois):
self.rois = rois
subwindow = AnnotationMainWindow(self.rois,
self.folder,
self.file_prefix,
self.file_suffix,
self.description,
self.mode,
self.minimum_peak_points,
parent=self.parent)
subwindow.show()
class EvaluationParameterWindow(QtWidgets.QDialog):
"""
Evaluation Parameter Window, where one should choose parameters for evaluation
Parameters
----------
mode : str
A one of two 'all in one' of 'sequential'
parent : MainWindow(QtWidgets.QMainWindow)
-
Attributes
----------
mode : str
A one of two 'all in one' of 'sequential'
parent : MainWindow(QtWidgets.QMainWindow)
-
test_folder_getter : GetFolderWidget
A getter for a path to test data
model_weights_getter : GetFileWidget
A getter for a path to weights for 'all-in-one' model (optional)
classifier_weights_getter : GetFileWidget
A getter for a path to weights for 'all-in-one' model (optional)
peak_points_getter : QtWidgets.QLineEdit
A getter for peak_minimum_points parameter
segmentator_weights_getter : GetFileWidget
A getter for a path to weights for 'all-in-one' model (optional)
"""
def __init__(self, mode, parent=None):
self.mode = mode
self.parent = parent
super().__init__(parent)
self.setWindowTitle('peakonly: evaluation')
test_folder_label = QtWidgets.QLabel()
test_folder_label.setText('Choose a folder with test data:')
self.test_folder_getter = GetFolderWidget(
os.path.join(os.getcwd(), 'data', 'test'), self)
if mode == 'all in one':
model_weights_label = QtWidgets.QLabel()
model_weights_label.setText(
"Choose weights for 'all-in-one' model")
# to do: save a pytorch script, not a model state
self.model_weights_getter = GetFileWidget(
'pt', os.path.join(os.getcwd(),
'data/weights/RecurrentCNN.pt'), self)
elif mode == 'sequential':
classifier_weights_label = QtWidgets.QLabel()
classifier_weights_label.setText('Choose weights for a classifier')
# to do: save a pytorch script, not a model state
self.classifier_weights_getter = GetFileWidget(
'pt', os.path.join(os.getcwd(), 'data/weights/Classifier.pt'),
self)
segmentator_weights_label = QtWidgets.QLabel()
segmentator_weights_label.setText(
'Choose weights for a segmentator')
# to do: save a pytorch script, not a model state
self.segmentator_weights_getter = GetFileWidget(
'pt', os.path.join(os.getcwd(), 'data/weights/Segmentator.pt'),
self)
else:
assert False, mode
peak_points_label = QtWidgets.QLabel()
peak_points_label.setText('Minimal length of peak:')
self.peak_points_getter = QtWidgets.QLineEdit(self)
self.peak_points_getter.setText('8')
run_button = QtWidgets.QPushButton('Run evaluation')
run_button.clicked.connect(self._run_evaluation)
main_layout = QtWidgets.QVBoxLayout()
main_layout.addWidget(test_folder_label)
main_layout.addWidget(self.test_folder_getter)
if mode == 'all in one':
main_layout.addWidget(model_weights_label)
main_layout.addWidget(self.model_weights_getter)
elif mode == 'sequential':
main_layout.addWidget(classifier_weights_label)
main_layout.addWidget(self.classifier_weights_getter)
main_layout.addWidget(segmentator_weights_label)
main_layout.addWidget(self.segmentator_weights_getter)
main_layout.addWidget(peak_points_label)
main_layout.addWidget(self.peak_points_getter)
main_layout.addWidget(run_button)
self.setLayout(main_layout)
def _run_evaluation(self):
try:
device = torch.device(
'cuda:0' if torch.cuda.is_available() else 'cpu')
# to do: device should be customizable parameter
test_folder = self.test_folder_getter.get_folder()
if self.mode == 'all in one':
# to do: save models as pytorch scripts
model = RecurrentCNN().to(device)
path2weights = self.model_weights_getter.get_file()
model.load_state_dict(
torch.load(path2weights, map_location=device))
model.eval()
models = [model]
elif self.mode == 'sequential':
classifier = Classifier().to(device)
path2classifier_weights = self.classifier_weights_getter.get_file(
)
classifier.load_state_dict(
torch.load(path2classifier_weights, map_location=device))
classifier.eval()
segmentator = Segmentator().to(device)
path2segmentator_weights = self.segmentator_weights_getter.get_file(
)
segmentator.load_state_dict(
torch.load(path2segmentator_weights, map_location=device))
segmentator.eval()
models = [classifier, segmentator]
else:
assert False, self.mode
minimum_peak_points = int(self.peak_points_getter.text())
runner = BasicRunner(self.mode, models, minimum_peak_points,
device)
main_window = EvaluationMainWindow(test_folder, runner,
self.parent)
main_window.show()
self.close()
except ValueError:
# popup window with exception
msg = QtWidgets.QMessageBox(self)
msg.setText("Check parameters. Something is wrong!")
msg.setIcon(QtWidgets.QMessageBox.Warning)
msg.exec_()