Module Widefield-Imaging-Acquisition.gui.interface
Expand source code
import sys
import time
import os
import matplotlib.pyplot as plt
from PyQt5.QtCore import QModelIndex, Qt, QLocale, qInstallMessageHandler
import numpy as np
from PyQt5.QtWidgets import (
QVBoxLayout,
QWidget,
QGridLayout,
QLabel,
QHBoxLayout,
QLineEdit,
QCheckBox,
QPushButton,
QStackedLayout,
QComboBox,
QMessageBox,
QFileDialog,
QApplication,
QSlider,
QHeaderView,
QDialog,
QWizard,
)
from PyQt5.QtGui import (
QIntValidator,
QDoubleValidator,
QFont,
QIcon,
QBrush,
QColor,
QPixmap,
)
from matplotlib.widgets import RectangleSelector
from threading import Thread
sys.path.append(os.path.dirname(os.path.dirname(__file__)))
from src.controls import DAQ, Instrument, Camera
from src.blocks import Experiment
from src.tree import Tree
from src.plot import PlotWindow
from src.calculations import (
get_dictionary,
shrink_array,
frames_acquired_from_camera_signal,
get_baseline_frame_indices,
average_baseline,
)
import warnings
warnings.filterwarnings("ignore")
class App(QWidget):
def __init__(self):
"""Initialize the application"""
super().__init__()
qInstallMessageHandler(self.handler)
self.cwd = os.path.dirname(os.path.dirname(__file__))
self.config = get_dictionary(os.path.join(self.cwd, "config.json"))
self.ports = self.config["Ports"]
self.elapsed_time = 0
self.files_saved = False
self.save_files_after_stop = False
self.roi_extent = None
self.max_exposure = 4096
self.slider_values = {
"Infrared": {"None": 4096, "Normal": 4096, "Logarithmic": 4096},
"Red": {"None": 4096, "Normal": 4096, "Logarithmic": 4096},
"Green": {"None": 4096, "Normal": 4096, "Logarithmic": 4096},
"Blue": {"None": 4096, "Normal": 4096, "Logarithmic": 4096},
}
self.daq_generated = False
self.onlyFloat = QDoubleValidator()
self.onlyFloat.setLocale(QLocale(QLocale.English, QLocale.UnitedStates))
self.onlyFloat.setNotation(QDoubleValidator.StandardNotation)
self.onlyFramerate = QIntValidator(1, 57, self)
self.onlyExposure = QIntValidator(1, 900, self)
self.start_container = QWidget()
self.start_layout = QVBoxLayout()
self.start_container.setLayout(self.start_layout)
self.start_title = QLabel("Welcome to WideBrain!")
self.start_title.setFont(QFont("IBM Plex Sans", 20, QFont.Bold))
self.start_title.setAlignment(Qt.AlignCenter)
self.start_image = QLabel()
self.start_image.setPixmap(
QPixmap(os.path.join(self.cwd, "assets", "logo-small.png"))
)
self.start_image.setAlignment(Qt.AlignCenter)
self.start_description = QLabel("Choose the type of experiment you want to run")
self.start_description.setFont(QFont("IBM Plex Sans", 14, QFont.Light))
self.start_description.setWordWrap(True)
self.start_description.setAlignment(Qt.AlignCenter)
self.trigger_mode_button = QPushButton("Start in Trigger Mode")
self.trigger_mode_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "bolt.png"))
)
self.trigger_mode_button.setFont(QFont("IBM Plex Sans", 15, QFont.Light))
self.trigger_mode_button.clicked.connect(self.start_in_trigger_mode)
self.acquisition_mode_button = QPushButton("Start in Acquisition Mode")
self.acquisition_mode_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "camera.png"))
)
self.acquisition_mode_button.setFont(QFont("IBM Plex Sans", 15, QFont.Light))
self.acquisition_mode_button.clicked.connect(self.start_in_acquisition_mode)
self.start_buttons = QHBoxLayout()
self.start_buttons.addWidget(self.trigger_mode_button)
self.start_buttons.addWidget(self.acquisition_mode_button)
self.start_layout.addWidget(self.start_title)
self.start_layout.addWidget(self.start_image)
self.start_layout.addWidget(self.start_description)
self.start_layout.addLayout(self.start_buttons)
self.grid_layout = QGridLayout()
self.grid_layout.addWidget(self.start_container, 0, 0)
self.setLayout(self.grid_layout)
self.show()
def start_in_trigger_mode(self):
"""Initialize the interface in trigger mode"""
self.start_container.setParent(None)
self.acquisition_mode = False
self.initUI()
def start_in_acquisition_mode(self):
"""Initialize the interface in acquisition mode"""
self.start_container.setParent(None)
self.acquisition_mode = True
self.initUI()
def closeEvent(self, *args, **kwargs):
"""Stop all processes when closing the application"""
self.video_running = False
try:
self.camera.stop_signal = True
self.camera.video_running = False
self.daq.stop_signal = True
self.daq.camera.cam.stop_acquisition()
print("Program Closed")
except Exception as err:
pass
self.check_if_thread_is_alive()
def handler(*args, **kwargs):
"""Ignore Qt messages"""
pass
def initUI(self):
"""Initialize the user interface"""
self.title = "Widefield Imaging Aquisition"
self.dimensions = (10, 10, 640, 480)
self.setWindowTitle(self.title)
self.setGeometry(*self.dimensions)
# self.grid_layout = QGridLayout()
# self.setLayout(self.grid_layout)
self.grid_layout.setAlignment(Qt.AlignTop)
self.experiment_settings_label = QLabel("Experiment Settings")
self.experiment_settings_label.setFont(QFont("IBM Plex Sans", 17))
self.grid_layout.addWidget(self.experiment_settings_label, 0, 0)
self.experiment_settings_main_window = QVBoxLayout()
self.experiment_name_window = QHBoxLayout()
self.experiment_name = QLabel("Experiment Name")
self.experiment_name_window.addWidget(self.experiment_name)
self.experiment_name_cell = QLineEdit()
self.experiment_name_window.addWidget(self.experiment_name_cell)
self.experiment_settings_main_window.addLayout(self.experiment_name_window)
self.mouse_id_window = QHBoxLayout()
self.mouse_id_label = QLabel("Mouse ID")
self.mouse_id_window.addWidget(self.mouse_id_label)
self.mouse_id_cell = QLineEdit()
self.mouse_id_window.addWidget(self.mouse_id_cell)
self.experiment_settings_main_window.addLayout(self.mouse_id_window)
self.framerate_exposure_window = QHBoxLayout()
self.exposure_window = QHBoxLayout()
self.exposure_label = QLabel("Exposure (ms)")
self.exposure_window.addWidget(self.exposure_label)
self.exposure_cell = QLineEdit("10")
self.exposure_cell.setValidator(self.onlyExposure)
self.exposure_cell.textChanged.connect(self.verify_exposure)
self.exposure_window.addWidget(self.exposure_cell)
self.framerate_exposure_window.addLayout(self.exposure_window)
self.framerate_window = QHBoxLayout()
self.framerate_label = QLabel("Framerate")
self.framerate_window.addWidget(self.framerate_label)
self.framerate_cell = QLineEdit("30")
self.framerate_cell.setValidator(self.onlyFramerate)
self.framerate_cell.textChanged.connect(self.verify_exposure)
self.framerate_window.addWidget(self.framerate_cell)
self.framerate_exposure_window.addLayout(self.framerate_window)
if self.acquisition_mode:
self.experiment_settings_main_window.addLayout(
self.framerate_exposure_window
)
self.exposure_warning_label = QLabel("Invalid Exposure / Frame Rate")
if self.acquisition_mode:
self.experiment_settings_main_window.addWidget(self.exposure_warning_label)
self.exposure_warning_label.setStyleSheet("color: red")
self.exposure_warning_label.setHidden(True)
self.directory_window = QHBoxLayout()
self.directory_save_files_checkbox = QCheckBox()
self.directory_save_files_checkbox.setText("Save")
self.directory_save_files_checkbox.stateChanged.connect(self.enable_directory)
self.directory_window.addWidget(self.directory_save_files_checkbox)
self.directory_choose_button = QPushButton("Select Directory")
self.directory_choose_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "folder-plus.png"))
)
# self.directory_choose_button.setIcon(QIcon(os.path.join("gui", "icons", "folder-plus.png")))
self.directory_choose_button.setDisabled(True)
self.directory_choose_button.clicked.connect(self.choose_directory)
self.directory_window.addWidget(self.directory_choose_button)
self.directory_cell = QLineEdit("")
self.directory_cell.setReadOnly(True)
self.directory_window.addWidget(self.directory_cell)
self.experiment_settings_main_window.addLayout(self.directory_window)
self.trigger_checkbox = QCheckBox("Wait for Trigger")
self.trigger_activated = False
self.trigger_checkbox.stateChanged.connect(self.set_trigger)
# self.experiment_settings_main_window.addWidget(self.trigger_checkbox)
self.save_config_button = QPushButton("Save Config")
self.save_config_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "save.png"))
)
self.save_config_button.clicked.connect(self.save_config)
self.save_config_button.setEnabled(False)
self.experiment_settings_main_window.addWidget(self.save_config_button)
self.experiment_settings_main_window.addStretch()
if self.acquisition_mode:
self.grid_layout.addLayout(self.experiment_settings_main_window, 1, 0)
else:
self.grid_layout.addLayout(self.experiment_settings_main_window, 1, 0, 1, 2)
self.image_settings_label = QLabel("Image Settings")
self.image_settings_label.setFont(QFont("IBM Plex Sans", 17))
if self.acquisition_mode:
self.grid_layout.addWidget(self.image_settings_label, 0, 1)
self.image_settings_main_window = QVBoxLayout()
self.image_settings_main_window.setAlignment(Qt.AlignLeft)
self.image_settings_main_window.setAlignment(Qt.AlignTop)
self.image_settings_second_window = QHBoxLayout()
self.ir_checkbox = QCheckBox("Infrared")
self.ir_checkbox.stateChanged.connect(self.actualize_lights)
self.image_settings_second_window.addWidget(self.ir_checkbox)
self.red_checkbox = QCheckBox("Red")
self.red_checkbox.stateChanged.connect(self.actualize_lights)
self.image_settings_second_window.addWidget(self.red_checkbox)
self.green_checkbox = QCheckBox("Green")
self.green_checkbox.stateChanged.connect(self.actualize_lights)
self.image_settings_second_window.addWidget(self.green_checkbox)
self.fluorescence_checkbox = QCheckBox("Blue")
self.fluorescence_checkbox.stateChanged.connect(self.actualize_lights)
self.image_settings_second_window.addWidget(self.fluorescence_checkbox)
self.light_channel_layout = QHBoxLayout()
self.preview_light_label = QLabel("Light Channel Preview")
self.light_channel_layout.addWidget(self.preview_light_label)
self.preview_light_combo = QComboBox()
self.preview_light_combo.setEnabled(False)
self.preview_light_combo.currentIndexChanged.connect(
self.change_preview_light_channel
)
self.light_channel_layout.addWidget(self.preview_light_combo)
# self.activation_map_checkbox = QCheckBox("Show Activation Map")
self.activation_map_window = QHBoxLayout()
self.activation_map_label = QLabel("Activation Map")
self.activation_map_window.addWidget(self.activation_map_label)
self.activation_map_combo = QComboBox()
self.activation_map_combo.addItem("None")
self.activation_map_combo.addItem("Normal")
self.activation_map_combo.addItem("Logarithmic")
self.activation_map_combo.currentIndexChanged.connect(self.adjust_slider)
self.activation_map_window.addWidget(self.activation_map_combo)
self.image_settings_main_window.addLayout(self.image_settings_second_window)
self.image_settings_main_window.addLayout(self.light_channel_layout)
# self.image_settings_main_window.addWidget(self.activation_map_checkbox)
self.image_settings_main_window.addLayout(self.activation_map_window)
self.roi_buttons = QStackedLayout()
self.roi_layout1 = QHBoxLayout()
self.roi_layout1.setAlignment(Qt.AlignLeft)
self.roi_layout1.setAlignment(Qt.AlignTop)
self.roi_layout1.setContentsMargins(0, 0, 0, 0)
self.reset_roi_button = QPushButton()
self.reset_roi_button.setText("Reset ROI")
self.reset_roi_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-out-area.png"))
)
# self.reset_roi_button.setIcon(QIcon("gui/icons/zoom-out-area.png"))
self.reset_roi_button.setEnabled(False)
self.reset_roi_button.clicked.connect(self.reset_roi)
self.roi_layout1.addWidget(self.reset_roi_button)
self.set_roi_button = QPushButton()
self.set_roi_button.setText("Set ROI")
self.set_roi_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-in-area.png"))
)
self.set_roi_button.clicked.connect(self.set_roi)
self.roi_layout1.addWidget(self.set_roi_button)
self.roi_layout1_container = QWidget()
self.roi_layout1_container.setLayout(self.roi_layout1)
self.roi_layout2 = QHBoxLayout()
self.roi_layout2.setAlignment(Qt.AlignLeft)
self.roi_layout2.setAlignment(Qt.AlignTop)
self.roi_layout2.setContentsMargins(0, 0, 0, 0)
self.cancel_roi_button = QPushButton()
self.cancel_roi_button.setText("Cancel")
self.cancel_roi_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-cancel.png"))
)
self.cancel_roi_button.clicked.connect(self.cancel_roi)
self.roi_layout2.addWidget(self.cancel_roi_button)
self.save_roi_button = QPushButton()
self.save_roi_button.setText("Save ROI")
self.save_roi_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-check.png"))
)
self.save_roi_button.clicked.connect(self.save_roi)
self.roi_layout2.addWidget(self.save_roi_button)
self.roi_layout2_container = QWidget()
self.roi_layout2_container.setLayout(self.roi_layout2)
if self.acquisition_mode:
self.roi_buttons.addWidget(self.roi_layout1_container)
self.roi_buttons.addWidget(self.roi_layout2_container)
self.image_settings_main_window.addLayout(self.roi_buttons)
self.exposure_slider = QSlider(Qt.Horizontal, self)
self.exposure_slider.setRange(0, 4096)
self.exposure_slider.setValue(4096)
self.exposure_slider.valueChanged.connect(self.adjust_exposure)
self.image_settings_main_window.addWidget(self.exposure_slider)
self.image_settings_main_window.addStretch()
self.activate_live_preview_button = QPushButton()
self.activate_live_preview_button.setText("Start Live Preview")
self.activate_live_preview_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "video.png"))
)
self.activate_live_preview_button.clicked.connect(self.open_live_preview_thread)
self.deactivate_live_preview_button = QPushButton()
self.deactivate_live_preview_button.setText("Stop Live Preview")
self.deactivate_live_preview_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "video-off.png"))
)
self.deactivate_live_preview_button.clicked.connect(self.stop_live)
self.image_settings_main_window.addStretch()
if self.acquisition_mode:
self.grid_layout.addLayout(self.image_settings_main_window, 1, 1)
self.live_preview_label = QLabel("Live Preview")
self.live_preview_label.setFont(QFont("IBM Plex Sans", 17))
self.image_view = PlotWindow()
self.plot_image = plt.imshow(
np.zeros(
(int(1024 / self.config["Binning"]), int(1024 / self.config["Binning"]))
),
cmap="binary_r",
vmin=0,
vmax=4096,
origin="lower",
)
self.plot_image.axes.get_xaxis().set_visible(False)
self.plot_image.axes.axes.get_yaxis().set_visible(False)
if self.acquisition_mode:
self.grid_layout.addWidget(self.live_preview_label, 0, 2)
self.grid_layout.addWidget(self.image_view, 1, 2)
self.tree_label = QLabel("Stimulation Tree")
self.tree_label.setFont(QFont("IBM Plex Sans", 17))
self.grid_layout.addWidget(self.tree_label, 2, 0)
self.tree_window = QVBoxLayout()
self.tree = Tree()
self.tree.setHeaderLabels(
[
"0 Name",
"1 Iterations",
"2 Delay",
"3 Jitter",
"4 Type",
"5 Pulses",
"6 Duration",
"7 Jitter",
"8 Width",
"9 Frequency",
"10 Duty",
"11 Type2",
"12 Pulses 2",
"13 Jitter 2",
"14 Width 2",
"15 Frequency 2",
"16 Duty 2",
"17 Baseline",
"18 Canal 1",
"19 Canal 2",
"20 Valid",
"21 Heigth",
"22 Heigth 2",
"23 Type 3",
"24 Pulses 3",
"25 Jitter 3",
"26 Width 3",
"27 Frequency 3",
"28 Duty 3",
"29 Heigth 3",
"30 Canal 3",
]
)
if not self.config["Debug"]:
for i in range(1, 20):
self.tree.header().hideSection(i)
for i in range(21, 31):
self.tree.header().hideSection(i)
self.tree.setHeaderHidden(True)
self.tree.header().setSectionResizeMode(0, QHeaderView.Stretch)
self.tree.header().setStretchLastSection(False)
self.tree.currentItemChanged.connect(self.actualize_window)
self.tree_window.addWidget(self.tree)
self.tree_switch_window = QStackedLayout()
self.tree_second_window = QHBoxLayout()
self.stim_buttons_container = QWidget()
self.delete_item_button = QPushButton("Delete")
self.delete_item_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "trash.png"))
)
self.delete_item_button.clicked.connect(self.tree.delete_item)
self.tree_second_window.addWidget(self.delete_item_button)
self.add_brother_branch_button = QPushButton("Add Sibling")
self.add_brother_branch_button.clicked.connect(self.tree.add_brother)
self.add_brother_branch_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "arrow-bar-down.png"))
)
self.tree_second_window.addWidget(self.add_brother_branch_button)
self.add_child_branch_button = QPushButton("Add Child")
self.add_child_branch_button.clicked.connect(self.tree.add_child)
self.add_child_branch_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "arrow-bar-right.png"))
)
self.tree_second_window.addWidget(self.add_child_branch_button)
self.stim_buttons_container.setLayout(self.tree_second_window)
self.tree_switch_window.addWidget(self.stim_buttons_container)
self.tree_third_window = QHBoxLayout()
self.import_button = QPushButton("Import Configuration")
self.import_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "packge-import.png"))
)
self.import_button.clicked.connect(self.import_config)
self.tree_third_window.addWidget(self.import_button)
self.new_branch_button = QPushButton("New Stimulation")
self.new_branch_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "square-plus.png"))
)
self.tree_third_window.addWidget(self.new_branch_button)
self.stim_buttons_container2 = QWidget()
self.stim_buttons_container2.setLayout(self.tree_third_window)
self.tree_switch_window.addWidget(self.stim_buttons_container2)
self.new_branch_button.clicked.connect(self.tree.first_stimulation)
self.grid_layout.addLayout(self.tree_switch_window, 4, 0)
self.tree_switch_window.setCurrentIndex(1)
self.grid_layout.addLayout(self.tree_window, 3, 0)
self.signal_adjust_label = QLabel("Signal Adjust")
self.signal_adjust_label.setFont(QFont("IBM Plex Sans", 17))
self.grid_layout.addWidget(self.signal_adjust_label, 2, 1)
self.signal_adjust_superposed = QStackedLayout()
self.stimulation_edit_layout = QVBoxLayout()
self.stimulation_edit_layout.setContentsMargins(0, 0, 0, 0)
self.canal_window = QVBoxLayout()
self.canal_window.setAlignment(Qt.AlignLeft)
self.canal_window.setAlignment(Qt.AlignTop)
self.canal_window.setContentsMargins(0, 0, 0, 0)
self.first_canal_check = QCheckBox()
self.first_canal_check.stateChanged.connect(self.canals_to_tree)
self.first_canal_check.setText("Canal 1")
self.stim_type_cell = QComboBox()
self.stim_type_cell.addItem("square")
self.stim_type_cell.addItem("random-square")
self.stim_type_cell.addItem("Third")
self.stim_type_cell.currentIndexChanged.connect(self.type_to_tree)
self.stimulation_type_window = QHBoxLayout()
self.stimulation_type_window.addWidget(self.first_canal_check)
self.stimulation_type_window.addWidget(self.stim_type_cell)
self.canal_window.addLayout(self.stimulation_type_window)
self.different_signals_window = QStackedLayout()
self.canal_window.addLayout(self.different_signals_window)
self.second_canal_check = QCheckBox()
self.second_canal_check.stateChanged.connect(self.canals_to_tree)
self.second_canal_check.setText("Canal 2")
self.stim_type_cell2 = QComboBox()
self.stim_type_cell2.addItem("square")
self.stim_type_cell2.addItem("random-square")
self.stim_type_cell2.addItem("Third")
self.stim_type_cell2.currentIndexChanged.connect(self.type_to_tree)
self.stimulation_type_window2 = QHBoxLayout()
self.stimulation_type_window2.addWidget(self.second_canal_check)
self.stimulation_type_window2.addWidget(self.stim_type_cell2)
self.canal_window.addLayout(self.stimulation_type_window2)
self.different_signals_window2 = QStackedLayout()
self.canal_window.addLayout(self.different_signals_window2)
self.third_canal_check = QCheckBox()
self.third_canal_check.stateChanged.connect(self.canals_to_tree)
self.third_canal_check.setText("Canal 3")
# self.canal_window.addWidget(self.third_canal_check)
self.stim_type_cell3 = QComboBox()
self.stim_type_cell3.addItem("square")
self.stim_type_cell3.addItem("random-square")
self.stim_type_cell3.addItem("Third")
self.stim_type_cell3.currentIndexChanged.connect(self.type_to_tree)
self.stimulation_type_window3 = QHBoxLayout()
self.stimulation_type_window3.addWidget(self.third_canal_check)
# self.stimulation_type_window3.addWidget(self.stim_type_cell3)
self.canal_window.addLayout(self.stimulation_type_window3)
self.different_signals_window3 = QStackedLayout()
self.canal_window.addLayout(self.different_signals_window3)
self.stimulation_name_label = QLabel("Stimulation Name")
self.stimulation_name_cell = QLineEdit()
self.stimulation_name_cell.textEdited.connect(self.name_to_tree)
self.stimulation_name_window = QHBoxLayout()
self.stimulation_name_window.addWidget(self.stimulation_name_label)
self.stimulation_name_window.addWidget(self.stimulation_name_cell)
self.stimulation_edit_layout.addLayout(self.stimulation_name_window)
self.duration_window = QHBoxLayout()
self.first_signal_type_duration_label = QLabel("Duration (s)")
self.duration_window.addWidget(self.first_signal_type_duration_label)
self.duration_cell = QLineEdit()
self.duration_window.addWidget(self.duration_cell)
self.duration_cell.setValidator(self.onlyFloat)
self.duration_cell.textEdited.connect(self.signal_to_tree)
self.stimulation_edit_layout.addLayout(self.duration_window)
self.baseline_checkbox = QCheckBox("Baseline")
self.baseline_checkbox.stateChanged.connect(self.canals_to_tree)
if self.acquisition_mode:
self.stimulation_edit_layout.addWidget(self.baseline_checkbox)
self.stimulation_edit_layout.addLayout(self.canal_window)
self.first_signal_type_window = QVBoxLayout()
self.first_signal_type_window.setAlignment(Qt.AlignLeft)
self.first_signal_type_window.setAlignment(Qt.AlignTop)
self.first_signal_type_window.setContentsMargins(0, 0, 0, 0)
self.first_signal_type_container = QWidget()
self.first_signal_type_container.setLayout(self.first_signal_type_window)
self.first_signal_type_window2 = QVBoxLayout()
self.first_signal_type_window2.setAlignment(Qt.AlignLeft)
self.first_signal_type_window2.setAlignment(Qt.AlignTop)
self.first_signal_type_window2.setContentsMargins(0, 0, 0, 0)
self.first_signal_type_container2 = QWidget()
self.first_signal_type_container2.setLayout(self.first_signal_type_window2)
self.first_signal_type_window3 = QVBoxLayout()
self.first_signal_type_window3.setAlignment(Qt.AlignLeft)
self.first_signal_type_window3.setAlignment(Qt.AlignTop)
self.first_signal_type_window3.setContentsMargins(0, 0, 0, 0)
self.first_signal_type_container3 = QWidget()
self.first_signal_type_container3.setLayout(self.first_signal_type_window3)
self.pulses_window = QHBoxLayout()
self.pulses_label = QLabel("Pulses")
self.pulses_window.addWidget(self.pulses_label)
self.pulses_cell = QLineEdit()
self.pulses_cell.setValidator(QIntValidator())
self.pulses_cell.textEdited.connect(self.signal_to_tree)
self.pulses_window.addWidget(self.pulses_cell)
self.pulses_window2 = QHBoxLayout()
self.pulses_label2 = QLabel("Pulses")
self.pulses_window2.addWidget(self.pulses_label2)
self.pulses_cell2 = QLineEdit()
self.pulses_cell2.setValidator(QIntValidator())
self.pulses_cell2.textEdited.connect(self.signal_to_tree)
self.pulses_window2.addWidget(self.pulses_cell2)
self.pulses_window3 = QHBoxLayout()
self.pulses_label3 = QLabel("Pulses")
self.pulses_window3.addWidget(self.pulses_label3)
self.pulses_cell3 = QLineEdit()
self.pulses_cell3.setValidator(QIntValidator())
self.pulses_cell3.textEdited.connect(self.signal_to_tree)
self.pulses_window3.addWidget(self.pulses_cell3)
self.jitter_window = QHBoxLayout()
self.jitter_label = QLabel("Jitter (s)")
self.jitter_window.addWidget(self.jitter_label)
self.jitter_cell = QLineEdit()
self.jitter_cell.setValidator(self.onlyFloat)
self.jitter_cell.setText("0")
self.jitter_cell.textEdited.connect(self.signal_to_tree)
self.jitter_window.addWidget(self.jitter_cell)
self.jitter_window2 = QHBoxLayout()
self.jitter_window2 = QHBoxLayout()
self.jitter_label2 = QLabel("Jitter (s)")
self.jitter_window2.addWidget(self.jitter_label2)
self.jitter_cell2 = QLineEdit()
self.jitter_cell2.setValidator(self.onlyFloat)
self.jitter_cell2.setText("0")
self.jitter_cell2.textEdited.connect(self.signal_to_tree)
self.jitter_window2.addWidget(self.jitter_cell2)
self.jitter_window3 = QHBoxLayout()
self.jitter_window3 = QHBoxLayout()
self.jitter_label3 = QLabel("Jitter (s)")
self.jitter_window3.addWidget(self.jitter_label3)
self.jitter_cell3 = QLineEdit()
self.jitter_cell3.setValidator(self.onlyFloat)
self.jitter_cell3.setText("0")
self.jitter_cell3.textEdited.connect(self.signal_to_tree)
self.jitter_window3.addWidget(self.jitter_cell3)
self.width_window = QHBoxLayout()
self.width_label = QLabel("Width (s)")
self.width_window.addWidget(self.width_label)
self.width_cell = QLineEdit()
self.width_cell.setValidator(self.onlyFloat)
self.width_cell.setText("0")
self.width_cell.textEdited.connect(self.signal_to_tree)
self.width_window.addWidget(self.width_cell)
self.width_window2 = QHBoxLayout()
self.width_label2 = QLabel("Width (s)")
self.width_window2.addWidget(self.width_label2)
self.width_cell2 = QLineEdit()
self.width_cell2.setValidator(self.onlyFloat)
self.width_cell2.setText("0")
self.width_cell2.textEdited.connect(self.signal_to_tree)
self.width_window2.addWidget(self.width_cell2)
self.width_window3 = QHBoxLayout()
self.width_label3 = QLabel("Width (s)")
self.width_window3.addWidget(self.width_label3)
self.width_cell3 = QLineEdit()
self.width_cell3.setValidator(self.onlyFloat)
self.width_cell3.setText("0")
self.width_cell3.textEdited.connect(self.signal_to_tree)
self.width_window3.addWidget(self.width_cell3)
self.first_signal_type_window.addLayout(self.pulses_window)
self.first_signal_type_window.addLayout(self.width_window)
self.first_signal_type_window.addLayout(self.jitter_window)
self.first_signal_type_window2.addLayout(self.pulses_window2)
self.first_signal_type_window2.addLayout(self.width_window2)
self.first_signal_type_window2.addLayout(self.jitter_window2)
self.first_signal_type_window3.addLayout(self.pulses_window3)
self.first_signal_type_window3.addLayout(self.width_window3)
self.first_signal_type_window3.addLayout(self.jitter_window3)
# -------------------
self.second_signal_type_window = QVBoxLayout()
self.second_signal_type_container = QWidget()
self.second_signal_type_window.setAlignment(Qt.AlignLeft)
self.second_signal_type_window.setAlignment(Qt.AlignTop)
self.second_signal_type_window.setContentsMargins(0, 0, 0, 0)
self.second_signal_type_container.setLayout(self.second_signal_type_window)
# self.stimulation_edit_layout.addLayout(self.different_signals_window)
self.second_signal_type_window2 = QVBoxLayout()
self.second_signal_type_container2 = QWidget()
self.second_signal_type_window2.setAlignment(Qt.AlignLeft)
self.second_signal_type_window2.setAlignment(Qt.AlignTop)
self.second_signal_type_window2.setContentsMargins(0, 0, 0, 0)
self.second_signal_type_container2.setLayout(self.second_signal_type_window2)
self.second_signal_type_window3 = QVBoxLayout()
self.second_signal_type_container3 = QWidget()
self.second_signal_type_window3.setAlignment(Qt.AlignLeft)
self.second_signal_type_window3.setAlignment(Qt.AlignTop)
self.second_signal_type_window3.setContentsMargins(0, 0, 0, 0)
self.second_signal_type_container3.setLayout(self.second_signal_type_window3)
self.heigth_window = QHBoxLayout()
self.heigth_label = QLabel("Heigth (V)")
self.heigth_window.addWidget(self.heigth_label)
self.heigth_cell = QLineEdit()
self.heigth_cell.setValidator(self.onlyFloat)
self.heigth_cell.textEdited.connect(self.signal_to_tree)
self.heigth_window.addWidget(self.heigth_cell)
self.heigth_window2 = QHBoxLayout()
self.heigth_label2 = QLabel("Heigth (V)")
self.heigth_window2.addWidget(self.heigth_label2)
self.heigth_cell2 = QLineEdit()
self.heigth_cell2.setValidator(self.onlyFloat)
self.heigth_cell2.textEdited.connect(self.signal_to_tree)
self.heigth_window2.addWidget(self.heigth_cell2)
self.heigth_window3 = QHBoxLayout()
self.heigth_label3 = QLabel("Heigth (V)")
self.heigth_window3.addWidget(self.heigth_label3)
self.heigth_cell3 = QLineEdit()
self.heigth_cell3.setValidator(self.onlyFloat)
self.heigth_cell3.textEdited.connect(self.signal_to_tree)
self.heigth_window3.addWidget(self.heigth_cell3)
self.frequency_window = QHBoxLayout()
self.frequency_label = QLabel("Frequency (Hz)")
self.frequency_window.addWidget(self.frequency_label)
self.frequency_cell = QLineEdit()
self.frequency_cell.setValidator(self.onlyFloat)
self.frequency_cell.textEdited.connect(self.signal_to_tree)
self.frequency_window.addWidget(self.frequency_cell)
self.frequency_window2 = QHBoxLayout()
self.frequency_label2 = QLabel("Frequency (Hz)")
self.frequency_window2.addWidget(self.frequency_label2)
self.frequency_cell2 = QLineEdit()
self.frequency_cell2.setValidator(self.onlyFloat)
self.frequency_cell2.textEdited.connect(self.signal_to_tree)
self.frequency_window2.addWidget(self.frequency_cell2)
self.frequency_window3 = QHBoxLayout()
self.frequency_label3 = QLabel("Frequency (Hz)")
self.frequency_window3.addWidget(self.frequency_label3)
self.frequency_cell3 = QLineEdit()
self.frequency_cell3.setValidator(self.onlyFloat)
self.frequency_cell3.textEdited.connect(self.signal_to_tree)
self.frequency_window3.addWidget(self.frequency_cell3)
self.duty_window = QHBoxLayout()
self.duty_label = QLabel("Duty (%)")
self.duty_window.addWidget(self.duty_label)
self.duty_cell = QLineEdit()
self.duty_cell.setValidator(self.onlyFloat)
self.duty_cell.textEdited.connect(self.signal_to_tree)
self.duty_window.addWidget(self.duty_cell)
self.duty_window2 = QHBoxLayout()
self.duty_label2 = QLabel("Duty (%)")
self.duty_window2.addWidget(self.duty_label2)
self.duty_cell2 = QLineEdit()
self.duty_cell2.setValidator(self.onlyFloat)
self.duty_cell2.textEdited.connect(self.signal_to_tree)
self.duty_window2.addWidget(self.duty_cell2)
self.duty_window3 = QHBoxLayout()
self.duty_label3 = QLabel("Duty (%)")
self.duty_window3.addWidget(self.duty_label3)
self.duty_cell3 = QLineEdit()
self.duty_cell3.setValidator(self.onlyFloat)
self.duty_cell3.textEdited.connect(self.signal_to_tree)
self.duty_window3.addWidget(self.duty_cell3)
self.second_signal_type_window.addLayout(self.heigth_window)
self.second_signal_type_window.addLayout(self.frequency_window)
self.second_signal_type_window.addLayout(self.duty_window)
self.second_signal_type_window2.addLayout(self.heigth_window2)
self.second_signal_type_window2.addLayout(self.frequency_window2)
self.second_signal_type_window2.addLayout(self.duty_window2)
# self.second_signal_type_window3.addLayout(self.heigth_window3)
self.second_signal_type_window3.addLayout(self.frequency_window3)
self.second_signal_type_window3.addLayout(self.duty_window3)
# -------------------
self.third_signal_type_window = QVBoxLayout()
self.third_signal_type_container = QWidget()
self.third_signal_type_container.setLayout(self.third_signal_type_window)
self.third_signal_type_window2 = QVBoxLayout()
self.third_signal_type_container2 = QWidget()
self.third_signal_type_container2.setLayout(self.third_signal_type_window2)
self.third_signal_type_window3 = QVBoxLayout()
self.third_signal_type_container3 = QWidget()
self.third_signal_type_container3.setLayout(self.third_signal_type_window3)
self.third_signal_type_name = QLabel("signal3")
self.third_signal_type_window.addWidget(self.third_signal_type_name)
self.third_signal_type_name2 = QLabel("signal3")
self.third_signal_type_window2.addWidget(self.third_signal_type_name2)
self.third_signal_type_name3 = QLabel("signal3")
self.third_signal_type_window3.addWidget(self.third_signal_type_name3)
self.different_signals_window.addWidget(self.second_signal_type_container)
self.different_signals_window.addWidget(self.first_signal_type_container)
self.different_signals_window.addWidget(self.third_signal_type_container)
self.different_signals_window2.addWidget(self.second_signal_type_container2)
self.different_signals_window2.addWidget(self.first_signal_type_container2)
self.different_signals_window2.addWidget(self.third_signal_type_container2)
self.different_signals_window3.addWidget(self.second_signal_type_container3)
self.different_signals_window3.addWidget(self.first_signal_type_container3)
self.different_signals_window3.addWidget(self.third_signal_type_container3)
self.stimulation_edit_container = QWidget()
self.stimulation_edit_container.setLayout(self.stimulation_edit_layout)
self.block_edit_layout = QVBoxLayout()
self.block_edit_layout.setContentsMargins(0, 0, 0, 0)
self.block_edit_layout.setAlignment(Qt.AlignLeft)
self.block_edit_layout.setAlignment(Qt.AlignTop)
self.block_name_label = QLabel("Block Name")
self.block_name_cell = QLineEdit()
self.block_name_cell.textEdited.connect(self.name_to_tree)
self.block_name_window = QHBoxLayout()
self.block_name_window.addWidget(self.block_name_label)
self.block_name_window.addWidget(self.block_name_cell)
self.block_edit_layout.addLayout(self.block_name_window)
self.block_iterations_window = QHBoxLayout()
self.block_iterations_label = QLabel("Iterations")
self.block_iterations_cell = QLineEdit()
self.block_iterations_cell.setValidator(QIntValidator())
self.block_iterations_cell.textEdited.connect(self.block_to_tree)
self.block_iterations_window.addWidget(self.block_iterations_label)
self.block_iterations_window.addWidget(self.block_iterations_cell)
self.block_edit_layout.addLayout(self.block_iterations_window)
self.block_delay_window = QHBoxLayout()
self.block_delay_label = QLabel("Delay")
self.block_delay_cell = QLineEdit()
self.block_delay_cell.setValidator(self.onlyFloat)
self.block_delay_cell.textEdited.connect(self.block_to_tree)
self.block_delay_window = QHBoxLayout()
self.block_delay_window.addWidget(self.block_delay_label)
self.block_delay_window.addWidget(self.block_delay_cell)
self.block_edit_layout.addLayout(self.block_delay_window)
self.block_jitter_window = QHBoxLayout()
self.block_jitter_label = QLabel("Jitter")
self.block_jitter_cell = QLineEdit()
self.block_jitter_cell.setValidator(self.onlyFloat)
self.block_jitter_cell.textEdited.connect(self.block_to_tree)
self.block_jitter_window = QHBoxLayout()
self.block_jitter_window.addWidget(self.block_jitter_label)
self.block_jitter_window.addWidget(self.block_jitter_cell)
self.block_edit_layout.addLayout(self.block_jitter_window)
self.block_edit_container = QWidget()
self.block_edit_container.setLayout(self.block_edit_layout)
self.signal_adjust_superposed.addWidget(self.stimulation_edit_container)
self.signal_adjust_superposed.addWidget(self.block_edit_container)
self.signal_adjust_superposed.addWidget(QLabel())
self.signal_adjust_superposed.setCurrentIndex(2)
self.grid_layout.addLayout(self.signal_adjust_superposed, 3, 1)
self.signal_preview_label = QLabel("Signal Preview")
self.signal_preview_label.setFont(QFont("IBM Plex Sans", 17))
if self.acquisition_mode:
self.grid_layout.addWidget(self.signal_preview_label, 2, 2)
else:
self.grid_layout.addWidget(self.signal_preview_label, 0, 2)
self.buttons_main_window = QHBoxLayout()
self.stop_button = QPushButton("Stop")
self.stop_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "player-stop.png"))
)
self.stop_button.clicked.connect(self.stop_while_running)
self.stop_button.setEnabled(False)
self.buttons_main_window.addWidget(self.stop_button)
self.run_button = QPushButton("Run")
self.run_button.setIcon(
QIcon(os.path.join(self.cwd, "gui", "icons", "player-play.png"))
)
self.run_button.clicked.connect(self.run)
self.run_button.setEnabled(False)
self.buttons_main_window.addWidget(self.run_button)
self.plot_window = PlotWindow(subplots=True)
if self.acquisition_mode:
self.grid_layout.addWidget(self.plot_window, 3, 2)
else:
self.grid_layout.addWidget(self.plot_window, 1, 2, 3, 1)
self.grid_layout.addLayout(self.buttons_main_window, 4, 2)
self.open_daq_generation_thread()
self.initialize_buttons()
self.show()
def deactivate_channels(self):
"""Deactivate canal checkboxes if the baseline checkbox is checked"""
if self.baseline_checkbox.isChecked():
self.deactivate_buttons(
[
self.first_canal_check,
self.second_canal_check,
]
)
else:
self.activate_buttons(
[
self.first_canal_check,
self.second_canal_check,
]
)
def adjust_exposure(self):
"""Match the exposure of the image preview to the slider value"""
self.max_exposure = self.exposure_slider.value()
self.slider_values[self.preview_light_combo.currentText()][
self.activation_map_combo.currentText()
] = self.max_exposure
def set_trigger(self):
"""Set the trigger for the DAQ"""
if not self.acquisition_mode:
self.run_button.setText("Run at Trigger")
self.daq.set_trigger(self.ports["trigger"])
else:
self.run_button.setText("Run")
self.daq.remove_trigger()
def import_config(self):
"""Import a configuration file"""
file = QFileDialog.getOpenFileName()[0]
try:
dictionary = get_dictionary(file)
self.framerate_cell.setText(str(dictionary["Framerate"]))
self.exposure_cell.setText(str(dictionary["Exposition"]))
self.set_lights(dictionary["Lights"])
self.tree.create_tree_item(dictionary["Blocks"])
self.enable_run(self.tree.check_global_validity())
self.tree.graph(self.tree.invisibleRootItem())
self.draw()
except Exception as err:
print(err)
def set_lights(self, lights):
"""Set the lights"""
for light in lights:
if light == "infrared":
self.ir_checkbox.setChecked(True)
elif light == "red":
self.red_checkbox.setChecked(True)
elif light == "green":
self.green_checkbox.setChecked(True)
elif light == "blue":
self.fluorescence_checkbox.setChecked(True)
def run(self):
"""Run the experiment"""
if self.check_override():
self.deactivate_buttons(buttons=self.enabled_buttons)
self.master_block = self.tree.create_blocks()
self.tree.baseline_values = []
self.tree.graph(item=self.tree.invisibleRootItem())
self.root_time, self.root_signal = (
self.tree.x_values,
[
self.tree.stim1_values,
self.tree.stim2_values,
self.tree.stim3_values,
],
)
self.draw(root=True)
if self.acquisition_mode:
self.actualize_daq()
self.open_live_saving_thread()
self.open_live_preview_thread()
self.open_baseline_check_thread()
else:
self.daq.stop_signal = False
self.open_signal_preview_thread()
self.open_start_experiment_thread()
def check_override(self):
"""Check if experiment with the same name already exists"""
if os.path.isfile(
os.path.join(
self.directory_cell.text(),
self.experiment_name_cell.text(),
f"{self.experiment_name_cell.text()}-light_signal.npy",
)
):
button = QMessageBox.question(
self,
"Files already exist",
"Files already exist. \n Do you want to override the existing files?",
)
if button == QMessageBox.Yes:
return True
else:
return False
else:
return True
def open_baseline_check_thread(self):
"""Open the thread for the baseline check"""
self.baseline_check_thread = Thread(target=self.check_baseline)
self.baseline_check_thread.start()
def check_baseline(self):
"""Monitor the incoming frames and check if the baseline is reached"""
if len(self.daq.lights) > 0:
self.camera.baseline_data = []
self.camera.adding_frames = False
self.camera.completed_baseline = False
while self.daq.camera_signal is None:
pass
frames_acquired = frames_acquired_from_camera_signal(self.daq.camera_signal)
baseline_indices = get_baseline_frame_indices(
self.tree.baseline_values, frames_acquired
)
for baseline_pair in baseline_indices:
while not self.daq.stop_signal:
try:
if (
not self.camera.adding_frames
and self.camera.frames_read >= baseline_pair[0]
):
self.camera.adding_frames = True
elif (
self.camera.adding_frames
and self.camera.frames_read >= baseline_pair[1]
):
self.camera.baseline_read_list = []
self.camera.average_baseline = average_baseline(
self.camera.baseline_data,
len(self.daq.lights),
self.camera.frames_read_list[0] % len(self.daq.lights),
)
self.camera.adding_frames = False
self.camera.baseline_frames = []
self.camera.baseline_completed = True
self.camera.frames_read_list = []
break
except Exception as err:
pass
time.sleep(0.01)
def open_start_experiment_thread(self):
"""Open the thread for the start of the experiment"""
self.start_experiment_thread = Thread(target=self.run_stimulation)
self.start_experiment_thread.start()
def save_config(self):
"""Save the current configuration to a JSON file"""
folder = str(QFileDialog.getExistingDirectory(self, "Select Directory"))
if folder != "":
self.master_block = self.tree.create_blocks()
self.experiment = Experiment(
self.master_block,
int(self.framerate_cell.text()),
int(self.exposure_cell.text()),
self.mouse_id_cell.text(),
folder,
self.daq,
name=self.experiment_name_cell.text(),
config=self.config,
)
self.experiment.save_config(
[int(1024 / self.config["Binning"]), int(1024 / self.config["Binning"])]
)
def run_stimulation(self):
"""Run the stimulation in parallel with the lights"""
self.experiment = Experiment(
self.master_block,
int(self.framerate_cell.text()),
int(self.exposure_cell.text()),
self.mouse_id_cell.text(),
self.directory_cell.text(),
self.daq,
name=self.experiment_name_cell.text(),
config=self.config,
)
self.save_files_after_stop = True
self.daq.launch(self.experiment.name, self.root_time, self.root_signal)
# if (
# not self.daq.stop_signal
# and self.save_files_after_stop
# and self.directory_save_files_checkbox.isChecked()
# ):
if (
self.save_files_after_stop
and self.directory_save_files_checkbox.isChecked()
):
try:
print("this is the extent")
print(self.roi_extent)
self.experiment.save(self.roi_extent)
except Exception as err:
print("err after saving first")
print(err)
print("err before entering")
self.experiment.save()
self.stop()
def open_live_saving_thread(self):
"""Open the thread for the live saving"""
self.live_save_thread = Thread(target=self.live_save)
self.live_save_thread.start()
def live_save(self):
"""Save NPY chunked files when the number of frames is over 1200"""
self.camera.file_index = 0
self.camera.is_saving = False
if self.directory_save_files_checkbox.isChecked():
try:
os.mkdir(
os.path.join(
self.directory_cell.text(), self.experiment_name_cell.text()
)
)
os.mkdir(
os.path.join(
self.directory_cell.text(),
self.experiment_name_cell.text(),
"data",
)
)
except Exception as err:
pass
while self.camera.video_running is False and not self.camera.stop_signal:
time.sleep(0.01)
pass
while self.camera.video_running is True:
if len(self.camera.frames) > 1200:
self.memory = self.camera.frames[:1200]
self.camera.frames = self.camera.frames[1200:]
if self.directory_save_files_checkbox.isChecked():
try:
self.memory = shrink_array(self.memory, self.roi_extent)
except Exception:
pass
self.camera.is_saving = True
np.save(
os.path.join(
self.directory_cell.text(),
self.experiment_name_cell.text(),
"data",
f"{self.camera.file_index}.npy",
),
self.memory,
)
self.memory = None
self.camera.file_index += 1
self.camera.is_saving = False
time.sleep(0.01)
def open_live_preview_thread(self):
"""Open the thread for the live preview"""
self.live_preview_thread = Thread(target=self.start_live)
self.live_preview_thread.start()
def start_live(self):
"""Start the live preview"""
plt.ion()
self.memory = []
self.camera.baseline_completed = False
if len(self.daq.lights) > 0:
try:
while self.camera.video_running is False:
time.sleep(0.01)
pass
while self.camera.video_running is True:
try:
if (
not self.camera.baseline_completed
or self.activation_map_combo.currentIndex() == 0
):
self.plot_image.set(
array=self.camera.frames[
self.live_preview_light_index :: len(
self.daq.lights
)
][-1],
clim=(0, self.max_exposure),
cmap="binary_r",
)
elif self.activation_map_combo.currentIndex() == 1:
start_index = (
self.camera.baseline_read_list[0]
+ self.live_preview_light_index
) % len(self.daq.lights)
activation_map = (
self.camera.baseline_frames[
start_index :: len(self.daq.lights)
][-1]
- self.camera.average_baseline[
self.live_preview_light_index
]
) / self.camera.average_baseline[
self.live_preview_light_index
]
self.plot_image.set(
array=activation_map,
clim=(
-self.max_exposure / 200,
self.max_exposure / 200,
),
cmap="seismic",
)
else:
start_index = (
self.camera.baseline_read_list[0]
+ self.live_preview_light_index
) % len(self.daq.lights)
activation_map = np.log(
(
(
self.camera.baseline_frames[
start_index :: len(self.daq.lights)
][-1]
- self.camera.average_baseline[
self.live_preview_light_index
]
)
/ self.camera.average_baseline[
self.live_preview_light_index
]
)
)
self.plot_image.set(
array=activation_map,
clim=(
-self.max_exposure / 2000,
self.max_exposure / 2000,
),
cmap="seismic",
)
except Exception as err:
print(err)
pass
time.sleep(0.04)
except Exception as err:
pass
def stop_live(self):
"""Stop the live preview"""
self.camera.video_running = False
def open_signal_preview_thread(self):
"""Open the thread for the signal preview"""
self.signal_preview_thread = Thread(target=self.actualize_progression)
self.signal_preview_thread.start()
def actualize_progression(self):
"""Actualize the position of the progress bar"""
plt.ion()
while self.daq.stop_signal is False:
try:
if self.acquisition_mode:
position = self.camera.frames_read / int(self.framerate_cell.text())
else:
position = time.time() - self.daq.start_time
self.plot_window.vertical_lines[0].set_xdata(position)
self.plot_window.vertical_lines[1].set_xdata(position)
self.plot_window.vertical_lines[2].set_xdata(position)
time.sleep(0.5)
except Exception as err:
time.sleep(0.5)
pass
def change_preview_light_channel(self):
"""Change the light channel for the live preview"""
self.live_preview_light_index = self.preview_light_combo.currentIndex()
self.adjust_slider()
def adjust_slider(self):
"""Adjust the saturation slider using corresponding value in dictionary"""
try:
value = self.slider_values[self.preview_light_combo.currentText()][
self.activation_map_combo.currentText()
]
self.exposure_slider.setValue(value)
except Exception:
pass
def open_daq_generation_thread(self):
"""Open the thread for the DAQ generation"""
self.daq_generation_thread = Thread(target=self.generate_daq)
self.daq_generation_thread.start()
def generate_daq(self):
"""Generate the DAQ"""
try:
self.camera = Camera(self.ports["camera"], "name")
except Exception:
self.camera = None
self.stimuli = [
Instrument(self.ports["analog0"], "air-pump"),
Instrument(self.ports["analog1"], "air-pump2"),
Instrument(self.ports["co2"], "air-pump3"),
]
self.daq = DAQ(
"dev1",
[],
self.stimuli,
self.camera,
int(self.framerate_cell.text()),
int(self.exposure_cell.text()) / 1000,
)
self.daq.close_all_lights(self.ports)
self.daq_generated = True
self.enable_run(self.tree.check_global_validity())
def actualize_daq(self):
"""Actualize the DAQ with the current settings"""
try:
self.daq.lights = []
if self.ir_checkbox.isChecked():
self.daq.lights.append(Instrument(self.ports["infrared"], "ir"))
if self.red_checkbox.isChecked():
self.daq.lights.append(Instrument(self.ports["red"], "red"))
if self.green_checkbox.isChecked():
self.daq.lights.append(Instrument(self.ports["green"], "green"))
if self.fluorescence_checkbox.isChecked():
self.daq.lights.append(Instrument(self.ports["blue"], "blue"))
self.daq.framerate = int(self.framerate_cell.text())
self.daq.exposure = int(self.exposure_cell.text()) / 1000
self.camera.frames = []
self.daq.stop_signal = False
except Exception:
pass
def stop(self):
"""Stop the experiment and reactivate the interface"""
self.stop_live()
self.activate_buttons(buttons=self.enabled_buttons)
self.tree.setCurrentItem(self.tree.topLevelItem(0))
try:
self.daq.stop_signal = True
except Exception:
pass
def stop_while_running(self):
"""Stop the experiment while it is running"""
if self.directory_save_files_checkbox.isChecked():
self.stop_stimulation_dialog()
self.stop()
def stop_stimulation_dialog(self):
"""Ask if user wants to keep the files after experiment is stopped"""
button = QMessageBox.question(
self, "Save Files", "Do you want to save the current files?"
)
if button == QMessageBox.Yes:
self.save_files_after_stop = True
else:
self.save_files_after_stop = False
def show_buttons(self, buttons):
"""Show the buttons in a list"""
for button in buttons:
button.setVisible(True)
def hide_buttons(self, buttons):
"""Hide the buttons in a list"""
for button in buttons:
button.setVisible(False)
def activate_buttons(self, buttons):
"""Activate the buttons in a list"""
for button in buttons:
button.setEnabled(True)
if buttons == self.enabled_buttons:
if self.directory_save_files_checkbox.isChecked():
self.directory_choose_button.setEnabled(True)
if self.roi_extent is None:
self.reset_roi_button.setEnabled(False)
else:
self.set_roi_button.setEnabled(False)
self.stop_button.setDisabled(True)
def deactivate_buttons(self, buttons):
"""Deactivate the buttons in a list"""
if buttons == self.enabled_buttons:
self.stop_button.setEnabled(True)
self.tree.clearSelection()
for button in buttons:
button.setDisabled(True)
def choose_directory(self):
"""Choose the directory where to save the files"""
folder = str(QFileDialog.getExistingDirectory(self, "Select Directory"))
self.directory_cell.setText(folder)
def enable_directory(self):
"""Enable the directory cell"""
self.files_saved = self.directory_save_files_checkbox.isChecked()
self.directory_choose_button.setEnabled(self.files_saved)
self.directory_cell.setEnabled(self.files_saved)
def actualize_window(self):
"""Actualize the 'Stimulation Edit' and 'Signal Preview' windows"""
self.activate_buttons(
[self.add_child_branch_button, self.add_brother_branch_button]
)
if self.tree.currentItem():
self.tree_switch_window.setCurrentIndex(0)
else:
self.tree_switch_window.setCurrentIndex(1)
try:
if self.tree.currentItem().childCount() > 0:
self.signal_adjust_superposed.setCurrentIndex(1)
else:
self.signal_adjust_superposed.setCurrentIndex(0)
except AttributeError:
self.signal_adjust_superposed.setCurrentIndex(2)
self.tree_to_name()
self.tree_to_block()
self.tree_to_type()
self.tree_to_signal()
self.tree_to_canal()
self.tree.graph(self.tree.currentItem(), current=True)
self.draw()
def name_to_tree(self):
"""Transfer the name of the current item from the cell to the tree"""
branch = self.tree.currentItem()
branch.setForeground(0, QBrush(QColor(0, 0, 0)))
if branch.childCount() > 0:
branch.setText(0, self.block_name_cell.text())
else:
branch.setText(0, self.stimulation_name_cell.text())
def tree_to_name(self):
"""Transfer the name of the current item from the tree to the cell"""
try:
if self.tree.currentItem().childCount() > 0:
if self.tree.currentItem().text(0) != "No Name":
self.block_name_cell.setText(self.tree.currentItem().text(0))
else:
self.block_name_cell.setText("")
else:
if self.tree.currentItem().text(0) != "No Name":
self.stimulation_name_cell.setText(self.tree.currentItem().text(0))
else:
self.stimulation_name_cell.setText("")
except AttributeError:
pass
def type_to_tree(self):
"""Transfer the type of the current item from the cell to the tree"""
self.enable_run(self.tree.check_global_validity())
self.different_signals_window.setCurrentIndex(
self.stim_type_cell.currentIndex()
)
self.different_signals_window2.setCurrentIndex(
self.stim_type_cell2.currentIndex()
)
self.different_signals_window3.setCurrentIndex(
self.stim_type_cell3.currentIndex()
)
try:
self.tree.currentItem().setText(4, str(self.stim_type_cell.currentText()))
except Exception:
pass
try:
self.tree.currentItem().setText(11, str(self.stim_type_cell2.currentText()))
except Exception:
pass
try:
self.tree.currentItem().setText(23, str(self.stim_type_cell3.currentText()))
except Exception:
pass
try:
self.tree.graph(self.tree.currentItem(), current=True)
self.draw()
except Exception:
pass
def tree_to_type(self):
"""Transfer the type of the current item from the tree to the cell"""
dico = {"square": 0, "random-square": 1, "Third": 2}
try:
self.stim_type_cell.setCurrentIndex(dico[self.tree.currentItem().text(4)])
except Exception:
self.stim_type_cell.setCurrentIndex(0)
try:
self.stim_type_cell2.setCurrentIndex(dico[self.tree.currentItem().text(11)])
except Exception:
self.stim_type_cell2.setCurrentIndex(0)
try:
self.stim_type_cell3.setCurrentIndex(dico[self.tree.currentItem().text(23)])
except Exception:
self.stim_type_cell3.setCurrentIndex(0)
def signal_to_tree(self):
"""Transfer the signal of the current item from the cell to the tree"""
self.tree.currentItem().setText(6, self.duration_cell.text())
self.tree.currentItem().setText(5, self.pulses_cell.text())
self.tree.currentItem().setText(7, self.jitter_cell.text())
self.tree.currentItem().setText(8, self.width_cell.text())
self.tree.currentItem().setText(9, self.frequency_cell.text())
self.tree.currentItem().setText(10, self.duty_cell.text())
self.tree.currentItem().setText(21, self.heigth_cell.text())
self.tree.currentItem().setText(12, self.pulses_cell2.text())
self.tree.currentItem().setText(13, self.jitter_cell2.text())
self.tree.currentItem().setText(14, self.width_cell2.text())
self.tree.currentItem().setText(15, self.frequency_cell2.text())
self.tree.currentItem().setText(16, self.duty_cell2.text())
self.tree.currentItem().setText(22, self.heigth_cell2.text())
self.tree.currentItem().setText(24, self.pulses_cell3.text())
self.tree.currentItem().setText(25, self.jitter_cell3.text())
self.tree.currentItem().setText(26, self.width_cell3.text())
self.tree.currentItem().setText(27, self.frequency_cell3.text())
self.tree.currentItem().setText(28, self.duty_cell3.text())
self.enable_run(self.tree.check_global_validity())
self.tree.graph(self.tree.currentItem(), current=True)
self.draw()
def tree_to_signal(self):
"""Transfer the signal of the current item from the tree to the cell"""
try:
self.pulses_cell.setText(self.tree.currentItem().text(5))
self.duration_cell.setText(self.tree.currentItem().text(6))
self.jitter_cell.setText(self.tree.currentItem().text(7))
self.width_cell.setText(self.tree.currentItem().text(8))
self.frequency_cell.setText(self.tree.currentItem().text(9))
self.heigth_cell.setText(self.tree.currentItem().text(21))
self.duty_cell.setText(self.tree.currentItem().text(10))
self.pulses_cell2.setText(self.tree.currentItem().text(12))
self.jitter_cell2.setText(self.tree.currentItem().text(13))
self.width_cell2.setText(self.tree.currentItem().text(14))
self.frequency_cell2.setText(self.tree.currentItem().text(15))
self.heigth_cell2.setText(self.tree.currentItem().text(22))
self.duty_cell2.setText(self.tree.currentItem().text(16))
self.pulses_cell3.setText(self.tree.currentItem().text(24))
self.jitter_cell3.setText(self.tree.currentItem().text(25))
self.width_cell3.setText(self.tree.currentItem().text(26))
self.frequency_cell3.setText(self.tree.currentItem().text(27))
self.duty_cell3.setText(self.tree.currentItem().text(28))
except Exception as err:
pass
def tree_to_block(self):
"""Transfer the block attributes from the tree to the cells"""
try:
self.block_iterations_cell.setText(self.tree.currentItem().text(1))
self.block_delay_cell.setText(self.tree.currentItem().text(2))
self.block_jitter_cell.setText(self.tree.currentItem().text(3))
except Exception:
pass
def block_to_tree(self):
"""Transfer the block attributes from the cells to the tree"""
self.tree.currentItem().setText(1, self.block_iterations_cell.text())
self.tree.currentItem().setText(2, self.block_delay_cell.text())
self.tree.currentItem().setText(3, self.block_jitter_cell.text())
self.enable_run(self.tree.check_global_validity())
self.tree.graph(self.tree.currentItem(), current=True)
self.draw()
def tree_to_canal(self):
"""Transfer the canals attributes from the tree to the cells"""
self.canal_running = True
try:
self.baseline_checkbox.setChecked(
self.boolean(self.tree.currentItem().text(17))
)
self.first_canal_check.setChecked(
self.boolean(self.tree.currentItem().text(18))
)
self.second_canal_check.setChecked(
self.boolean(self.tree.currentItem().text(19))
)
self.third_canal_check.setChecked(
self.boolean(self.tree.currentItem().text(30))
)
if self.baseline_checkbox.isChecked():
self.deactivate_buttons(self.canal1buttons + [self.first_canal_check])
self.deactivate_buttons(self.canal2buttons + [self.second_canal_check])
self.deactivate_buttons(self.canal3buttons + [self.third_canal_check])
else:
self.activate_buttons(
[
self.first_canal_check,
self.second_canal_check,
self.third_canal_check,
]
)
if self.first_canal_check.isChecked():
self.activate_buttons(self.canal1buttons)
else:
self.deactivate_buttons(self.canal1buttons)
if self.second_canal_check.isChecked():
self.activate_buttons(self.canal2buttons)
else:
self.deactivate_buttons(self.canal2buttons)
if self.third_canal_check.isChecked():
self.activate_buttons(self.canal3buttons)
else:
self.deactivate_buttons(self.canal3buttons)
except Exception as err:
pass
self.canal_running = False
def canals_to_tree(self):
"""Transfer the canals attributes from the cells to the tree"""
self.baseline_checkbox.setEnabled(True)
if not self.canal_running:
if self.baseline_checkbox.isChecked():
self.deactivate_buttons(self.canal1buttons + [self.first_canal_check])
self.deactivate_buttons(self.canal2buttons + [self.second_canal_check])
self.deactivate_buttons(self.canal3buttons + [self.third_canal_check])
else:
self.activate_buttons(self.canal1buttons + [self.first_canal_check])
self.activate_buttons(self.canal2buttons + [self.second_canal_check])
self.activate_buttons(self.canal3buttons + [self.third_canal_check])
if self.first_canal_check.isChecked():
self.baseline_checkbox.setEnabled(False)
self.activate_buttons(self.canal1buttons)
else:
self.deactivate_buttons(self.canal1buttons)
if self.second_canal_check.isChecked():
self.baseline_checkbox.setEnabled(False)
self.activate_buttons(self.canal2buttons)
else:
self.deactivate_buttons(self.canal2buttons)
if self.third_canal_check.isChecked():
self.baseline_checkbox.setEnabled(False)
self.activate_buttons(self.canal3buttons)
else:
self.deactivate_buttons(self.canal3buttons)
if (
self.first_canal_check.isChecked()
or self.second_canal_check.isChecked()
or self.third_canal_check.isChecked()
):
self.deactivate_buttons([self.baseline_checkbox])
else:
self.activate_buttons([self.baseline_checkbox])
self.tree.currentItem().setText(17, str(self.baseline_checkbox.isChecked()))
self.tree.currentItem().setText(18, str(self.first_canal_check.isChecked()))
self.tree.currentItem().setText(
19, str(self.second_canal_check.isChecked())
)
self.tree.currentItem().setText(30, str(self.third_canal_check.isChecked()))
self.enable_run(self.tree.check_global_validity())
self.tree.graph(self.tree.currentItem(), current=True)
self.draw()
def enable_run(self, boolean):
"""Enable the run button"""
if not self.daq_generated:
boolean = False
self.save_config_button.setEnabled(boolean)
self.run_button.setEnabled(boolean)
def disable_run(self):
"""Disable the run button"""
self.save_config_button.setDisabled(True)
self.run_button.setDisabled(True)
def count_lights(self):
"""Return the number of lights and a list of their names"""
count = 0
text = []
for checkbox in [
self.ir_checkbox,
self.red_checkbox,
self.green_checkbox,
self.fluorescence_checkbox,
]:
if checkbox.isChecked():
count += 1
text.append(checkbox.text())
return (count, text)
def actualize_lights(self):
"""Update the lights list in the combo box"""
self.preview_light_combo.clear()
if self.count_lights()[0] == 0:
self.preview_light_combo.setEnabled(False)
else:
self.preview_light_combo.setEnabled(True)
for i in range(4):
if i < self.count_lights()[0]:
self.preview_light_combo.addItem(self.count_lights()[1][i])
def boolean(self, string):
"""Return a boolean from a string"""
if string == "True":
return True
return False
def draw(self, root=False):
"""Draw the sitmulation channels graph
Args:
root (bool, optional): If True, the graph includes a progress bar"""
try:
self.plot_window.clear()
self.plot_window.plot(
self.tree.x_values, self.tree.stim1_values, root, index=0
)
self.plot_window.plot(
self.tree.x_values,
self.tree.stim2_values,
root,
index=1,
)
self.plot_window.plot(
self.tree.x_values,
self.tree.stim3_values,
root,
index=2,
)
self.tree.x_values = []
self.tree.stim1_values = []
self.tree.stim2_values = []
self.tree.stim3_values = []
self.elapsed_time = 0
except Exception as err:
pass
def set_roi(self):
"""Set the ROI"""
self.deactivate_buttons(buttons=self.enabled_buttons)
self.stop_button.setEnabled(False)
self.save_roi_button.setEnabled(False)
self.roi_buttons.setCurrentIndex(1)
def onselect_function(eclick, erelease):
"""Save the ROI dimensions as attributes"""
self.roi_extent = self.rect_selector.extents
self.save_roi_button.setEnabled(True)
self.rect_selector = RectangleSelector(
self.plot_image.axes,
onselect_function,
drawtype="box",
useblit=True,
button=[1, 3],
minspanx=5,
minspany=5,
spancoords="pixels",
interactive=True,
)
def reset_roi(self):
"""Reset the ROI"""
plt.figure(self.image_view.figure.number)
plt.xlim(0, int(1024 / self.config["Binning"]))
plt.ylim(0, int(1024 / self.config["Binning"]))
self.roi_extent = None
self.reset_roi_button.setEnabled(False)
def cancel_roi(self):
"""Cancel the ROI selection"""
self.activate_buttons(buttons=self.enabled_buttons)
self.roi_buttons.setCurrentIndex(0)
self.rect_selector.clear()
self.rect_selector = None
def save_roi(self):
"""Save the ROI"""
self.activate_buttons(buttons=self.enabled_buttons)
self.roi_buttons.setCurrentIndex(0)
plt.figure(self.image_view.figure.number)
plt.ion()
print(self.roi_extent)
plt.xlim(self.roi_extent[0], self.roi_extent[1])
plt.ylim(self.roi_extent[2], self.roi_extent[3])
self.rect_selector.clear()
self.rect_selector = None
self.reset_roi_button.setEnabled(True)
def verify_exposure(self):
"""Verify if the exposure/framerate combination is valid"""
try:
boolean_check = (int(self.exposure_cell.text()) / 1000 + 0.0015) * int(
self.framerate_cell.text()
) < 1 and int(self.framerate_cell.text()) <= 57
except Exception:
boolean_check = False
self.exposure_warning_label.setHidden(boolean_check)
def check_if_thread_is_alive(self):
"""Check what threads are alive"""
try:
if self.live_preview_thread.is_alive():
print("Live preview thread is alive")
else:
print("Live preview thread is dead")
except Exception as err:
print(err)
try:
if self.start_experiment_thread.is_alive():
print("Start Experiment thread is alive")
else:
print("Start experiment thread is dead")
except Exception as err:
print(err)
try:
if self.daq_generation_thread.is_alive():
print("Daq Generation thread is alive")
else:
print("Daq generation thread is dead")
except Exception as err:
print(err)
try:
if self.signal_preview_thread.is_alive():
print("Signal Preview thread is alive")
else:
print("Signal Preview thread is dead")
except Exception as err:
print(err)
try:
if self.live_save_thread.is_alive():
print("Live Save thread is alive")
else:
print("Live Save thread is dead")
except Exception as err:
print(err)
try:
if self.baseline_check_thread.is_alive():
print("Baseline check thread is alive")
else:
print("Baseline check thread is dead")
except Exception as err:
print(err)
def initialize_buttons(self):
"""Define list of buttons to activate/deactivate"""
self.canal1buttons = [
self.stim_type_cell,
self.pulses_label,
self.pulses_cell,
self.width_label,
self.width_cell,
self.jitter_label,
self.jitter_cell,
self.frequency_label,
self.frequency_cell,
self.duty_label,
self.duty_cell,
self.heigth_cell,
self.heigth_label,
]
self.canal2buttons = [
self.stim_type_cell2,
self.pulses_label2,
self.pulses_cell2,
self.width_label2,
self.width_cell2,
self.jitter_label2,
self.jitter_cell2,
self.frequency_label2,
self.frequency_cell2,
self.duty_label2,
self.duty_cell2,
self.heigth_cell2,
self.heigth_label2,
]
self.canal3buttons = [
self.stim_type_cell3,
self.pulses_label3,
self.pulses_cell3,
self.width_label3,
self.width_cell3,
self.jitter_label3,
self.jitter_cell3,
self.frequency_label3,
self.frequency_cell3,
self.duty_label3,
self.duty_cell3,
self.heigth_cell3,
self.heigth_label3,
]
self.enabled_buttons = [
self.run_button,
self.experiment_name_cell,
self.mouse_id_cell,
self.directory_choose_button,
self.set_roi_button,
self.reset_roi_button,
self.experiment_name,
self.mouse_id_label,
self.framerate_label,
self.framerate_cell,
self.exposure_cell,
self.exposure_label,
self.add_brother_branch_button,
self.add_child_branch_button,
self.delete_item_button,
self.red_checkbox,
self.ir_checkbox,
self.green_checkbox,
self.fluorescence_checkbox,
self.stimulation_name_label,
self.directory_save_files_checkbox,
self.stimulation_name_cell,
self.stim_type_cell,
self.stim_type_cell2,
self.first_canal_check,
self.second_canal_check,
self.first_signal_type_duration_label,
self.duration_cell,
self.pulses_label,
self.pulses_cell,
self.width_label,
self.width_cell,
self.jitter_label,
self.jitter_cell,
self.frequency_label,
self.frequency_cell,
self.heigth_label,
self.heigth_cell,
self.duty_label,
self.duty_cell,
self.pulses_label2,
self.pulses_cell2,
self.width_label2,
self.width_cell2,
self.jitter_label2,
self.jitter_cell2,
self.frequency_label2,
self.frequency_cell2,
self.heigth_label2,
self.heigth_cell2,
self.duty_label2,
self.duty_cell2,
self.third_canal_check,
self.stim_type_cell3,
self.pulses_label3,
self.pulses_cell3,
self.width_label3,
self.width_cell3,
self.jitter_label3,
self.jitter_cell3,
self.frequency_label3,
self.frequency_cell3,
self.duty_label3,
self.duty_cell3,
self.heigth_cell3,
self.heigth_label3,
self.block_iterations_label,
self.block_iterations_cell,
self.block_delay_label,
self.block_delay_cell,
self.block_jitter_label,
self.block_jitter_cell,
self.block_name_label,
self.block_name_cell,
self.activate_live_preview_button,
self.deactivate_live_preview_button,
self.tree,
]
if __name__ == "__main__":
app = QApplication(sys.argv)
font = QFont()
font.setFamily("IBM Plex Sans")
app.setFont(font)
ex = App()
sys.exit(app.exec_())Classes
class App-
QWidget(parent: QWidget = None, flags: Union[Qt.WindowFlags, Qt.WindowType] = Qt.WindowFlags())
Initialize the application
Expand source code
class App(QWidget): def __init__(self): """Initialize the application""" super().__init__() qInstallMessageHandler(self.handler) self.cwd = os.path.dirname(os.path.dirname(__file__)) self.config = get_dictionary(os.path.join(self.cwd, "config.json")) self.ports = self.config["Ports"] self.elapsed_time = 0 self.files_saved = False self.save_files_after_stop = False self.roi_extent = None self.max_exposure = 4096 self.slider_values = { "Infrared": {"None": 4096, "Normal": 4096, "Logarithmic": 4096}, "Red": {"None": 4096, "Normal": 4096, "Logarithmic": 4096}, "Green": {"None": 4096, "Normal": 4096, "Logarithmic": 4096}, "Blue": {"None": 4096, "Normal": 4096, "Logarithmic": 4096}, } self.daq_generated = False self.onlyFloat = QDoubleValidator() self.onlyFloat.setLocale(QLocale(QLocale.English, QLocale.UnitedStates)) self.onlyFloat.setNotation(QDoubleValidator.StandardNotation) self.onlyFramerate = QIntValidator(1, 57, self) self.onlyExposure = QIntValidator(1, 900, self) self.start_container = QWidget() self.start_layout = QVBoxLayout() self.start_container.setLayout(self.start_layout) self.start_title = QLabel("Welcome to WideBrain!") self.start_title.setFont(QFont("IBM Plex Sans", 20, QFont.Bold)) self.start_title.setAlignment(Qt.AlignCenter) self.start_image = QLabel() self.start_image.setPixmap( QPixmap(os.path.join(self.cwd, "assets", "logo-small.png")) ) self.start_image.setAlignment(Qt.AlignCenter) self.start_description = QLabel("Choose the type of experiment you want to run") self.start_description.setFont(QFont("IBM Plex Sans", 14, QFont.Light)) self.start_description.setWordWrap(True) self.start_description.setAlignment(Qt.AlignCenter) self.trigger_mode_button = QPushButton("Start in Trigger Mode") self.trigger_mode_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "bolt.png")) ) self.trigger_mode_button.setFont(QFont("IBM Plex Sans", 15, QFont.Light)) self.trigger_mode_button.clicked.connect(self.start_in_trigger_mode) self.acquisition_mode_button = QPushButton("Start in Acquisition Mode") self.acquisition_mode_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "camera.png")) ) self.acquisition_mode_button.setFont(QFont("IBM Plex Sans", 15, QFont.Light)) self.acquisition_mode_button.clicked.connect(self.start_in_acquisition_mode) self.start_buttons = QHBoxLayout() self.start_buttons.addWidget(self.trigger_mode_button) self.start_buttons.addWidget(self.acquisition_mode_button) self.start_layout.addWidget(self.start_title) self.start_layout.addWidget(self.start_image) self.start_layout.addWidget(self.start_description) self.start_layout.addLayout(self.start_buttons) self.grid_layout = QGridLayout() self.grid_layout.addWidget(self.start_container, 0, 0) self.setLayout(self.grid_layout) self.show() def start_in_trigger_mode(self): """Initialize the interface in trigger mode""" self.start_container.setParent(None) self.acquisition_mode = False self.initUI() def start_in_acquisition_mode(self): """Initialize the interface in acquisition mode""" self.start_container.setParent(None) self.acquisition_mode = True self.initUI() def closeEvent(self, *args, **kwargs): """Stop all processes when closing the application""" self.video_running = False try: self.camera.stop_signal = True self.camera.video_running = False self.daq.stop_signal = True self.daq.camera.cam.stop_acquisition() print("Program Closed") except Exception as err: pass self.check_if_thread_is_alive() def handler(*args, **kwargs): """Ignore Qt messages""" pass def initUI(self): """Initialize the user interface""" self.title = "Widefield Imaging Aquisition" self.dimensions = (10, 10, 640, 480) self.setWindowTitle(self.title) self.setGeometry(*self.dimensions) # self.grid_layout = QGridLayout() # self.setLayout(self.grid_layout) self.grid_layout.setAlignment(Qt.AlignTop) self.experiment_settings_label = QLabel("Experiment Settings") self.experiment_settings_label.setFont(QFont("IBM Plex Sans", 17)) self.grid_layout.addWidget(self.experiment_settings_label, 0, 0) self.experiment_settings_main_window = QVBoxLayout() self.experiment_name_window = QHBoxLayout() self.experiment_name = QLabel("Experiment Name") self.experiment_name_window.addWidget(self.experiment_name) self.experiment_name_cell = QLineEdit() self.experiment_name_window.addWidget(self.experiment_name_cell) self.experiment_settings_main_window.addLayout(self.experiment_name_window) self.mouse_id_window = QHBoxLayout() self.mouse_id_label = QLabel("Mouse ID") self.mouse_id_window.addWidget(self.mouse_id_label) self.mouse_id_cell = QLineEdit() self.mouse_id_window.addWidget(self.mouse_id_cell) self.experiment_settings_main_window.addLayout(self.mouse_id_window) self.framerate_exposure_window = QHBoxLayout() self.exposure_window = QHBoxLayout() self.exposure_label = QLabel("Exposure (ms)") self.exposure_window.addWidget(self.exposure_label) self.exposure_cell = QLineEdit("10") self.exposure_cell.setValidator(self.onlyExposure) self.exposure_cell.textChanged.connect(self.verify_exposure) self.exposure_window.addWidget(self.exposure_cell) self.framerate_exposure_window.addLayout(self.exposure_window) self.framerate_window = QHBoxLayout() self.framerate_label = QLabel("Framerate") self.framerate_window.addWidget(self.framerate_label) self.framerate_cell = QLineEdit("30") self.framerate_cell.setValidator(self.onlyFramerate) self.framerate_cell.textChanged.connect(self.verify_exposure) self.framerate_window.addWidget(self.framerate_cell) self.framerate_exposure_window.addLayout(self.framerate_window) if self.acquisition_mode: self.experiment_settings_main_window.addLayout( self.framerate_exposure_window ) self.exposure_warning_label = QLabel("Invalid Exposure / Frame Rate") if self.acquisition_mode: self.experiment_settings_main_window.addWidget(self.exposure_warning_label) self.exposure_warning_label.setStyleSheet("color: red") self.exposure_warning_label.setHidden(True) self.directory_window = QHBoxLayout() self.directory_save_files_checkbox = QCheckBox() self.directory_save_files_checkbox.setText("Save") self.directory_save_files_checkbox.stateChanged.connect(self.enable_directory) self.directory_window.addWidget(self.directory_save_files_checkbox) self.directory_choose_button = QPushButton("Select Directory") self.directory_choose_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "folder-plus.png")) ) # self.directory_choose_button.setIcon(QIcon(os.path.join("gui", "icons", "folder-plus.png"))) self.directory_choose_button.setDisabled(True) self.directory_choose_button.clicked.connect(self.choose_directory) self.directory_window.addWidget(self.directory_choose_button) self.directory_cell = QLineEdit("") self.directory_cell.setReadOnly(True) self.directory_window.addWidget(self.directory_cell) self.experiment_settings_main_window.addLayout(self.directory_window) self.trigger_checkbox = QCheckBox("Wait for Trigger") self.trigger_activated = False self.trigger_checkbox.stateChanged.connect(self.set_trigger) # self.experiment_settings_main_window.addWidget(self.trigger_checkbox) self.save_config_button = QPushButton("Save Config") self.save_config_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "save.png")) ) self.save_config_button.clicked.connect(self.save_config) self.save_config_button.setEnabled(False) self.experiment_settings_main_window.addWidget(self.save_config_button) self.experiment_settings_main_window.addStretch() if self.acquisition_mode: self.grid_layout.addLayout(self.experiment_settings_main_window, 1, 0) else: self.grid_layout.addLayout(self.experiment_settings_main_window, 1, 0, 1, 2) self.image_settings_label = QLabel("Image Settings") self.image_settings_label.setFont(QFont("IBM Plex Sans", 17)) if self.acquisition_mode: self.grid_layout.addWidget(self.image_settings_label, 0, 1) self.image_settings_main_window = QVBoxLayout() self.image_settings_main_window.setAlignment(Qt.AlignLeft) self.image_settings_main_window.setAlignment(Qt.AlignTop) self.image_settings_second_window = QHBoxLayout() self.ir_checkbox = QCheckBox("Infrared") self.ir_checkbox.stateChanged.connect(self.actualize_lights) self.image_settings_second_window.addWidget(self.ir_checkbox) self.red_checkbox = QCheckBox("Red") self.red_checkbox.stateChanged.connect(self.actualize_lights) self.image_settings_second_window.addWidget(self.red_checkbox) self.green_checkbox = QCheckBox("Green") self.green_checkbox.stateChanged.connect(self.actualize_lights) self.image_settings_second_window.addWidget(self.green_checkbox) self.fluorescence_checkbox = QCheckBox("Blue") self.fluorescence_checkbox.stateChanged.connect(self.actualize_lights) self.image_settings_second_window.addWidget(self.fluorescence_checkbox) self.light_channel_layout = QHBoxLayout() self.preview_light_label = QLabel("Light Channel Preview") self.light_channel_layout.addWidget(self.preview_light_label) self.preview_light_combo = QComboBox() self.preview_light_combo.setEnabled(False) self.preview_light_combo.currentIndexChanged.connect( self.change_preview_light_channel ) self.light_channel_layout.addWidget(self.preview_light_combo) # self.activation_map_checkbox = QCheckBox("Show Activation Map") self.activation_map_window = QHBoxLayout() self.activation_map_label = QLabel("Activation Map") self.activation_map_window.addWidget(self.activation_map_label) self.activation_map_combo = QComboBox() self.activation_map_combo.addItem("None") self.activation_map_combo.addItem("Normal") self.activation_map_combo.addItem("Logarithmic") self.activation_map_combo.currentIndexChanged.connect(self.adjust_slider) self.activation_map_window.addWidget(self.activation_map_combo) self.image_settings_main_window.addLayout(self.image_settings_second_window) self.image_settings_main_window.addLayout(self.light_channel_layout) # self.image_settings_main_window.addWidget(self.activation_map_checkbox) self.image_settings_main_window.addLayout(self.activation_map_window) self.roi_buttons = QStackedLayout() self.roi_layout1 = QHBoxLayout() self.roi_layout1.setAlignment(Qt.AlignLeft) self.roi_layout1.setAlignment(Qt.AlignTop) self.roi_layout1.setContentsMargins(0, 0, 0, 0) self.reset_roi_button = QPushButton() self.reset_roi_button.setText("Reset ROI") self.reset_roi_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-out-area.png")) ) # self.reset_roi_button.setIcon(QIcon("gui/icons/zoom-out-area.png")) self.reset_roi_button.setEnabled(False) self.reset_roi_button.clicked.connect(self.reset_roi) self.roi_layout1.addWidget(self.reset_roi_button) self.set_roi_button = QPushButton() self.set_roi_button.setText("Set ROI") self.set_roi_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-in-area.png")) ) self.set_roi_button.clicked.connect(self.set_roi) self.roi_layout1.addWidget(self.set_roi_button) self.roi_layout1_container = QWidget() self.roi_layout1_container.setLayout(self.roi_layout1) self.roi_layout2 = QHBoxLayout() self.roi_layout2.setAlignment(Qt.AlignLeft) self.roi_layout2.setAlignment(Qt.AlignTop) self.roi_layout2.setContentsMargins(0, 0, 0, 0) self.cancel_roi_button = QPushButton() self.cancel_roi_button.setText("Cancel") self.cancel_roi_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-cancel.png")) ) self.cancel_roi_button.clicked.connect(self.cancel_roi) self.roi_layout2.addWidget(self.cancel_roi_button) self.save_roi_button = QPushButton() self.save_roi_button.setText("Save ROI") self.save_roi_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-check.png")) ) self.save_roi_button.clicked.connect(self.save_roi) self.roi_layout2.addWidget(self.save_roi_button) self.roi_layout2_container = QWidget() self.roi_layout2_container.setLayout(self.roi_layout2) if self.acquisition_mode: self.roi_buttons.addWidget(self.roi_layout1_container) self.roi_buttons.addWidget(self.roi_layout2_container) self.image_settings_main_window.addLayout(self.roi_buttons) self.exposure_slider = QSlider(Qt.Horizontal, self) self.exposure_slider.setRange(0, 4096) self.exposure_slider.setValue(4096) self.exposure_slider.valueChanged.connect(self.adjust_exposure) self.image_settings_main_window.addWidget(self.exposure_slider) self.image_settings_main_window.addStretch() self.activate_live_preview_button = QPushButton() self.activate_live_preview_button.setText("Start Live Preview") self.activate_live_preview_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "video.png")) ) self.activate_live_preview_button.clicked.connect(self.open_live_preview_thread) self.deactivate_live_preview_button = QPushButton() self.deactivate_live_preview_button.setText("Stop Live Preview") self.deactivate_live_preview_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "video-off.png")) ) self.deactivate_live_preview_button.clicked.connect(self.stop_live) self.image_settings_main_window.addStretch() if self.acquisition_mode: self.grid_layout.addLayout(self.image_settings_main_window, 1, 1) self.live_preview_label = QLabel("Live Preview") self.live_preview_label.setFont(QFont("IBM Plex Sans", 17)) self.image_view = PlotWindow() self.plot_image = plt.imshow( np.zeros( (int(1024 / self.config["Binning"]), int(1024 / self.config["Binning"])) ), cmap="binary_r", vmin=0, vmax=4096, origin="lower", ) self.plot_image.axes.get_xaxis().set_visible(False) self.plot_image.axes.axes.get_yaxis().set_visible(False) if self.acquisition_mode: self.grid_layout.addWidget(self.live_preview_label, 0, 2) self.grid_layout.addWidget(self.image_view, 1, 2) self.tree_label = QLabel("Stimulation Tree") self.tree_label.setFont(QFont("IBM Plex Sans", 17)) self.grid_layout.addWidget(self.tree_label, 2, 0) self.tree_window = QVBoxLayout() self.tree = Tree() self.tree.setHeaderLabels( [ "0 Name", "1 Iterations", "2 Delay", "3 Jitter", "4 Type", "5 Pulses", "6 Duration", "7 Jitter", "8 Width", "9 Frequency", "10 Duty", "11 Type2", "12 Pulses 2", "13 Jitter 2", "14 Width 2", "15 Frequency 2", "16 Duty 2", "17 Baseline", "18 Canal 1", "19 Canal 2", "20 Valid", "21 Heigth", "22 Heigth 2", "23 Type 3", "24 Pulses 3", "25 Jitter 3", "26 Width 3", "27 Frequency 3", "28 Duty 3", "29 Heigth 3", "30 Canal 3", ] ) if not self.config["Debug"]: for i in range(1, 20): self.tree.header().hideSection(i) for i in range(21, 31): self.tree.header().hideSection(i) self.tree.setHeaderHidden(True) self.tree.header().setSectionResizeMode(0, QHeaderView.Stretch) self.tree.header().setStretchLastSection(False) self.tree.currentItemChanged.connect(self.actualize_window) self.tree_window.addWidget(self.tree) self.tree_switch_window = QStackedLayout() self.tree_second_window = QHBoxLayout() self.stim_buttons_container = QWidget() self.delete_item_button = QPushButton("Delete") self.delete_item_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "trash.png")) ) self.delete_item_button.clicked.connect(self.tree.delete_item) self.tree_second_window.addWidget(self.delete_item_button) self.add_brother_branch_button = QPushButton("Add Sibling") self.add_brother_branch_button.clicked.connect(self.tree.add_brother) self.add_brother_branch_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "arrow-bar-down.png")) ) self.tree_second_window.addWidget(self.add_brother_branch_button) self.add_child_branch_button = QPushButton("Add Child") self.add_child_branch_button.clicked.connect(self.tree.add_child) self.add_child_branch_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "arrow-bar-right.png")) ) self.tree_second_window.addWidget(self.add_child_branch_button) self.stim_buttons_container.setLayout(self.tree_second_window) self.tree_switch_window.addWidget(self.stim_buttons_container) self.tree_third_window = QHBoxLayout() self.import_button = QPushButton("Import Configuration") self.import_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "packge-import.png")) ) self.import_button.clicked.connect(self.import_config) self.tree_third_window.addWidget(self.import_button) self.new_branch_button = QPushButton("New Stimulation") self.new_branch_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "square-plus.png")) ) self.tree_third_window.addWidget(self.new_branch_button) self.stim_buttons_container2 = QWidget() self.stim_buttons_container2.setLayout(self.tree_third_window) self.tree_switch_window.addWidget(self.stim_buttons_container2) self.new_branch_button.clicked.connect(self.tree.first_stimulation) self.grid_layout.addLayout(self.tree_switch_window, 4, 0) self.tree_switch_window.setCurrentIndex(1) self.grid_layout.addLayout(self.tree_window, 3, 0) self.signal_adjust_label = QLabel("Signal Adjust") self.signal_adjust_label.setFont(QFont("IBM Plex Sans", 17)) self.grid_layout.addWidget(self.signal_adjust_label, 2, 1) self.signal_adjust_superposed = QStackedLayout() self.stimulation_edit_layout = QVBoxLayout() self.stimulation_edit_layout.setContentsMargins(0, 0, 0, 0) self.canal_window = QVBoxLayout() self.canal_window.setAlignment(Qt.AlignLeft) self.canal_window.setAlignment(Qt.AlignTop) self.canal_window.setContentsMargins(0, 0, 0, 0) self.first_canal_check = QCheckBox() self.first_canal_check.stateChanged.connect(self.canals_to_tree) self.first_canal_check.setText("Canal 1") self.stim_type_cell = QComboBox() self.stim_type_cell.addItem("square") self.stim_type_cell.addItem("random-square") self.stim_type_cell.addItem("Third") self.stim_type_cell.currentIndexChanged.connect(self.type_to_tree) self.stimulation_type_window = QHBoxLayout() self.stimulation_type_window.addWidget(self.first_canal_check) self.stimulation_type_window.addWidget(self.stim_type_cell) self.canal_window.addLayout(self.stimulation_type_window) self.different_signals_window = QStackedLayout() self.canal_window.addLayout(self.different_signals_window) self.second_canal_check = QCheckBox() self.second_canal_check.stateChanged.connect(self.canals_to_tree) self.second_canal_check.setText("Canal 2") self.stim_type_cell2 = QComboBox() self.stim_type_cell2.addItem("square") self.stim_type_cell2.addItem("random-square") self.stim_type_cell2.addItem("Third") self.stim_type_cell2.currentIndexChanged.connect(self.type_to_tree) self.stimulation_type_window2 = QHBoxLayout() self.stimulation_type_window2.addWidget(self.second_canal_check) self.stimulation_type_window2.addWidget(self.stim_type_cell2) self.canal_window.addLayout(self.stimulation_type_window2) self.different_signals_window2 = QStackedLayout() self.canal_window.addLayout(self.different_signals_window2) self.third_canal_check = QCheckBox() self.third_canal_check.stateChanged.connect(self.canals_to_tree) self.third_canal_check.setText("Canal 3") # self.canal_window.addWidget(self.third_canal_check) self.stim_type_cell3 = QComboBox() self.stim_type_cell3.addItem("square") self.stim_type_cell3.addItem("random-square") self.stim_type_cell3.addItem("Third") self.stim_type_cell3.currentIndexChanged.connect(self.type_to_tree) self.stimulation_type_window3 = QHBoxLayout() self.stimulation_type_window3.addWidget(self.third_canal_check) # self.stimulation_type_window3.addWidget(self.stim_type_cell3) self.canal_window.addLayout(self.stimulation_type_window3) self.different_signals_window3 = QStackedLayout() self.canal_window.addLayout(self.different_signals_window3) self.stimulation_name_label = QLabel("Stimulation Name") self.stimulation_name_cell = QLineEdit() self.stimulation_name_cell.textEdited.connect(self.name_to_tree) self.stimulation_name_window = QHBoxLayout() self.stimulation_name_window.addWidget(self.stimulation_name_label) self.stimulation_name_window.addWidget(self.stimulation_name_cell) self.stimulation_edit_layout.addLayout(self.stimulation_name_window) self.duration_window = QHBoxLayout() self.first_signal_type_duration_label = QLabel("Duration (s)") self.duration_window.addWidget(self.first_signal_type_duration_label) self.duration_cell = QLineEdit() self.duration_window.addWidget(self.duration_cell) self.duration_cell.setValidator(self.onlyFloat) self.duration_cell.textEdited.connect(self.signal_to_tree) self.stimulation_edit_layout.addLayout(self.duration_window) self.baseline_checkbox = QCheckBox("Baseline") self.baseline_checkbox.stateChanged.connect(self.canals_to_tree) if self.acquisition_mode: self.stimulation_edit_layout.addWidget(self.baseline_checkbox) self.stimulation_edit_layout.addLayout(self.canal_window) self.first_signal_type_window = QVBoxLayout() self.first_signal_type_window.setAlignment(Qt.AlignLeft) self.first_signal_type_window.setAlignment(Qt.AlignTop) self.first_signal_type_window.setContentsMargins(0, 0, 0, 0) self.first_signal_type_container = QWidget() self.first_signal_type_container.setLayout(self.first_signal_type_window) self.first_signal_type_window2 = QVBoxLayout() self.first_signal_type_window2.setAlignment(Qt.AlignLeft) self.first_signal_type_window2.setAlignment(Qt.AlignTop) self.first_signal_type_window2.setContentsMargins(0, 0, 0, 0) self.first_signal_type_container2 = QWidget() self.first_signal_type_container2.setLayout(self.first_signal_type_window2) self.first_signal_type_window3 = QVBoxLayout() self.first_signal_type_window3.setAlignment(Qt.AlignLeft) self.first_signal_type_window3.setAlignment(Qt.AlignTop) self.first_signal_type_window3.setContentsMargins(0, 0, 0, 0) self.first_signal_type_container3 = QWidget() self.first_signal_type_container3.setLayout(self.first_signal_type_window3) self.pulses_window = QHBoxLayout() self.pulses_label = QLabel("Pulses") self.pulses_window.addWidget(self.pulses_label) self.pulses_cell = QLineEdit() self.pulses_cell.setValidator(QIntValidator()) self.pulses_cell.textEdited.connect(self.signal_to_tree) self.pulses_window.addWidget(self.pulses_cell) self.pulses_window2 = QHBoxLayout() self.pulses_label2 = QLabel("Pulses") self.pulses_window2.addWidget(self.pulses_label2) self.pulses_cell2 = QLineEdit() self.pulses_cell2.setValidator(QIntValidator()) self.pulses_cell2.textEdited.connect(self.signal_to_tree) self.pulses_window2.addWidget(self.pulses_cell2) self.pulses_window3 = QHBoxLayout() self.pulses_label3 = QLabel("Pulses") self.pulses_window3.addWidget(self.pulses_label3) self.pulses_cell3 = QLineEdit() self.pulses_cell3.setValidator(QIntValidator()) self.pulses_cell3.textEdited.connect(self.signal_to_tree) self.pulses_window3.addWidget(self.pulses_cell3) self.jitter_window = QHBoxLayout() self.jitter_label = QLabel("Jitter (s)") self.jitter_window.addWidget(self.jitter_label) self.jitter_cell = QLineEdit() self.jitter_cell.setValidator(self.onlyFloat) self.jitter_cell.setText("0") self.jitter_cell.textEdited.connect(self.signal_to_tree) self.jitter_window.addWidget(self.jitter_cell) self.jitter_window2 = QHBoxLayout() self.jitter_window2 = QHBoxLayout() self.jitter_label2 = QLabel("Jitter (s)") self.jitter_window2.addWidget(self.jitter_label2) self.jitter_cell2 = QLineEdit() self.jitter_cell2.setValidator(self.onlyFloat) self.jitter_cell2.setText("0") self.jitter_cell2.textEdited.connect(self.signal_to_tree) self.jitter_window2.addWidget(self.jitter_cell2) self.jitter_window3 = QHBoxLayout() self.jitter_window3 = QHBoxLayout() self.jitter_label3 = QLabel("Jitter (s)") self.jitter_window3.addWidget(self.jitter_label3) self.jitter_cell3 = QLineEdit() self.jitter_cell3.setValidator(self.onlyFloat) self.jitter_cell3.setText("0") self.jitter_cell3.textEdited.connect(self.signal_to_tree) self.jitter_window3.addWidget(self.jitter_cell3) self.width_window = QHBoxLayout() self.width_label = QLabel("Width (s)") self.width_window.addWidget(self.width_label) self.width_cell = QLineEdit() self.width_cell.setValidator(self.onlyFloat) self.width_cell.setText("0") self.width_cell.textEdited.connect(self.signal_to_tree) self.width_window.addWidget(self.width_cell) self.width_window2 = QHBoxLayout() self.width_label2 = QLabel("Width (s)") self.width_window2.addWidget(self.width_label2) self.width_cell2 = QLineEdit() self.width_cell2.setValidator(self.onlyFloat) self.width_cell2.setText("0") self.width_cell2.textEdited.connect(self.signal_to_tree) self.width_window2.addWidget(self.width_cell2) self.width_window3 = QHBoxLayout() self.width_label3 = QLabel("Width (s)") self.width_window3.addWidget(self.width_label3) self.width_cell3 = QLineEdit() self.width_cell3.setValidator(self.onlyFloat) self.width_cell3.setText("0") self.width_cell3.textEdited.connect(self.signal_to_tree) self.width_window3.addWidget(self.width_cell3) self.first_signal_type_window.addLayout(self.pulses_window) self.first_signal_type_window.addLayout(self.width_window) self.first_signal_type_window.addLayout(self.jitter_window) self.first_signal_type_window2.addLayout(self.pulses_window2) self.first_signal_type_window2.addLayout(self.width_window2) self.first_signal_type_window2.addLayout(self.jitter_window2) self.first_signal_type_window3.addLayout(self.pulses_window3) self.first_signal_type_window3.addLayout(self.width_window3) self.first_signal_type_window3.addLayout(self.jitter_window3) # ------------------- self.second_signal_type_window = QVBoxLayout() self.second_signal_type_container = QWidget() self.second_signal_type_window.setAlignment(Qt.AlignLeft) self.second_signal_type_window.setAlignment(Qt.AlignTop) self.second_signal_type_window.setContentsMargins(0, 0, 0, 0) self.second_signal_type_container.setLayout(self.second_signal_type_window) # self.stimulation_edit_layout.addLayout(self.different_signals_window) self.second_signal_type_window2 = QVBoxLayout() self.second_signal_type_container2 = QWidget() self.second_signal_type_window2.setAlignment(Qt.AlignLeft) self.second_signal_type_window2.setAlignment(Qt.AlignTop) self.second_signal_type_window2.setContentsMargins(0, 0, 0, 0) self.second_signal_type_container2.setLayout(self.second_signal_type_window2) self.second_signal_type_window3 = QVBoxLayout() self.second_signal_type_container3 = QWidget() self.second_signal_type_window3.setAlignment(Qt.AlignLeft) self.second_signal_type_window3.setAlignment(Qt.AlignTop) self.second_signal_type_window3.setContentsMargins(0, 0, 0, 0) self.second_signal_type_container3.setLayout(self.second_signal_type_window3) self.heigth_window = QHBoxLayout() self.heigth_label = QLabel("Heigth (V)") self.heigth_window.addWidget(self.heigth_label) self.heigth_cell = QLineEdit() self.heigth_cell.setValidator(self.onlyFloat) self.heigth_cell.textEdited.connect(self.signal_to_tree) self.heigth_window.addWidget(self.heigth_cell) self.heigth_window2 = QHBoxLayout() self.heigth_label2 = QLabel("Heigth (V)") self.heigth_window2.addWidget(self.heigth_label2) self.heigth_cell2 = QLineEdit() self.heigth_cell2.setValidator(self.onlyFloat) self.heigth_cell2.textEdited.connect(self.signal_to_tree) self.heigth_window2.addWidget(self.heigth_cell2) self.heigth_window3 = QHBoxLayout() self.heigth_label3 = QLabel("Heigth (V)") self.heigth_window3.addWidget(self.heigth_label3) self.heigth_cell3 = QLineEdit() self.heigth_cell3.setValidator(self.onlyFloat) self.heigth_cell3.textEdited.connect(self.signal_to_tree) self.heigth_window3.addWidget(self.heigth_cell3) self.frequency_window = QHBoxLayout() self.frequency_label = QLabel("Frequency (Hz)") self.frequency_window.addWidget(self.frequency_label) self.frequency_cell = QLineEdit() self.frequency_cell.setValidator(self.onlyFloat) self.frequency_cell.textEdited.connect(self.signal_to_tree) self.frequency_window.addWidget(self.frequency_cell) self.frequency_window2 = QHBoxLayout() self.frequency_label2 = QLabel("Frequency (Hz)") self.frequency_window2.addWidget(self.frequency_label2) self.frequency_cell2 = QLineEdit() self.frequency_cell2.setValidator(self.onlyFloat) self.frequency_cell2.textEdited.connect(self.signal_to_tree) self.frequency_window2.addWidget(self.frequency_cell2) self.frequency_window3 = QHBoxLayout() self.frequency_label3 = QLabel("Frequency (Hz)") self.frequency_window3.addWidget(self.frequency_label3) self.frequency_cell3 = QLineEdit() self.frequency_cell3.setValidator(self.onlyFloat) self.frequency_cell3.textEdited.connect(self.signal_to_tree) self.frequency_window3.addWidget(self.frequency_cell3) self.duty_window = QHBoxLayout() self.duty_label = QLabel("Duty (%)") self.duty_window.addWidget(self.duty_label) self.duty_cell = QLineEdit() self.duty_cell.setValidator(self.onlyFloat) self.duty_cell.textEdited.connect(self.signal_to_tree) self.duty_window.addWidget(self.duty_cell) self.duty_window2 = QHBoxLayout() self.duty_label2 = QLabel("Duty (%)") self.duty_window2.addWidget(self.duty_label2) self.duty_cell2 = QLineEdit() self.duty_cell2.setValidator(self.onlyFloat) self.duty_cell2.textEdited.connect(self.signal_to_tree) self.duty_window2.addWidget(self.duty_cell2) self.duty_window3 = QHBoxLayout() self.duty_label3 = QLabel("Duty (%)") self.duty_window3.addWidget(self.duty_label3) self.duty_cell3 = QLineEdit() self.duty_cell3.setValidator(self.onlyFloat) self.duty_cell3.textEdited.connect(self.signal_to_tree) self.duty_window3.addWidget(self.duty_cell3) self.second_signal_type_window.addLayout(self.heigth_window) self.second_signal_type_window.addLayout(self.frequency_window) self.second_signal_type_window.addLayout(self.duty_window) self.second_signal_type_window2.addLayout(self.heigth_window2) self.second_signal_type_window2.addLayout(self.frequency_window2) self.second_signal_type_window2.addLayout(self.duty_window2) # self.second_signal_type_window3.addLayout(self.heigth_window3) self.second_signal_type_window3.addLayout(self.frequency_window3) self.second_signal_type_window3.addLayout(self.duty_window3) # ------------------- self.third_signal_type_window = QVBoxLayout() self.third_signal_type_container = QWidget() self.third_signal_type_container.setLayout(self.third_signal_type_window) self.third_signal_type_window2 = QVBoxLayout() self.third_signal_type_container2 = QWidget() self.third_signal_type_container2.setLayout(self.third_signal_type_window2) self.third_signal_type_window3 = QVBoxLayout() self.third_signal_type_container3 = QWidget() self.third_signal_type_container3.setLayout(self.third_signal_type_window3) self.third_signal_type_name = QLabel("signal3") self.third_signal_type_window.addWidget(self.third_signal_type_name) self.third_signal_type_name2 = QLabel("signal3") self.third_signal_type_window2.addWidget(self.third_signal_type_name2) self.third_signal_type_name3 = QLabel("signal3") self.third_signal_type_window3.addWidget(self.third_signal_type_name3) self.different_signals_window.addWidget(self.second_signal_type_container) self.different_signals_window.addWidget(self.first_signal_type_container) self.different_signals_window.addWidget(self.third_signal_type_container) self.different_signals_window2.addWidget(self.second_signal_type_container2) self.different_signals_window2.addWidget(self.first_signal_type_container2) self.different_signals_window2.addWidget(self.third_signal_type_container2) self.different_signals_window3.addWidget(self.second_signal_type_container3) self.different_signals_window3.addWidget(self.first_signal_type_container3) self.different_signals_window3.addWidget(self.third_signal_type_container3) self.stimulation_edit_container = QWidget() self.stimulation_edit_container.setLayout(self.stimulation_edit_layout) self.block_edit_layout = QVBoxLayout() self.block_edit_layout.setContentsMargins(0, 0, 0, 0) self.block_edit_layout.setAlignment(Qt.AlignLeft) self.block_edit_layout.setAlignment(Qt.AlignTop) self.block_name_label = QLabel("Block Name") self.block_name_cell = QLineEdit() self.block_name_cell.textEdited.connect(self.name_to_tree) self.block_name_window = QHBoxLayout() self.block_name_window.addWidget(self.block_name_label) self.block_name_window.addWidget(self.block_name_cell) self.block_edit_layout.addLayout(self.block_name_window) self.block_iterations_window = QHBoxLayout() self.block_iterations_label = QLabel("Iterations") self.block_iterations_cell = QLineEdit() self.block_iterations_cell.setValidator(QIntValidator()) self.block_iterations_cell.textEdited.connect(self.block_to_tree) self.block_iterations_window.addWidget(self.block_iterations_label) self.block_iterations_window.addWidget(self.block_iterations_cell) self.block_edit_layout.addLayout(self.block_iterations_window) self.block_delay_window = QHBoxLayout() self.block_delay_label = QLabel("Delay") self.block_delay_cell = QLineEdit() self.block_delay_cell.setValidator(self.onlyFloat) self.block_delay_cell.textEdited.connect(self.block_to_tree) self.block_delay_window = QHBoxLayout() self.block_delay_window.addWidget(self.block_delay_label) self.block_delay_window.addWidget(self.block_delay_cell) self.block_edit_layout.addLayout(self.block_delay_window) self.block_jitter_window = QHBoxLayout() self.block_jitter_label = QLabel("Jitter") self.block_jitter_cell = QLineEdit() self.block_jitter_cell.setValidator(self.onlyFloat) self.block_jitter_cell.textEdited.connect(self.block_to_tree) self.block_jitter_window = QHBoxLayout() self.block_jitter_window.addWidget(self.block_jitter_label) self.block_jitter_window.addWidget(self.block_jitter_cell) self.block_edit_layout.addLayout(self.block_jitter_window) self.block_edit_container = QWidget() self.block_edit_container.setLayout(self.block_edit_layout) self.signal_adjust_superposed.addWidget(self.stimulation_edit_container) self.signal_adjust_superposed.addWidget(self.block_edit_container) self.signal_adjust_superposed.addWidget(QLabel()) self.signal_adjust_superposed.setCurrentIndex(2) self.grid_layout.addLayout(self.signal_adjust_superposed, 3, 1) self.signal_preview_label = QLabel("Signal Preview") self.signal_preview_label.setFont(QFont("IBM Plex Sans", 17)) if self.acquisition_mode: self.grid_layout.addWidget(self.signal_preview_label, 2, 2) else: self.grid_layout.addWidget(self.signal_preview_label, 0, 2) self.buttons_main_window = QHBoxLayout() self.stop_button = QPushButton("Stop") self.stop_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "player-stop.png")) ) self.stop_button.clicked.connect(self.stop_while_running) self.stop_button.setEnabled(False) self.buttons_main_window.addWidget(self.stop_button) self.run_button = QPushButton("Run") self.run_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "player-play.png")) ) self.run_button.clicked.connect(self.run) self.run_button.setEnabled(False) self.buttons_main_window.addWidget(self.run_button) self.plot_window = PlotWindow(subplots=True) if self.acquisition_mode: self.grid_layout.addWidget(self.plot_window, 3, 2) else: self.grid_layout.addWidget(self.plot_window, 1, 2, 3, 1) self.grid_layout.addLayout(self.buttons_main_window, 4, 2) self.open_daq_generation_thread() self.initialize_buttons() self.show() def deactivate_channels(self): """Deactivate canal checkboxes if the baseline checkbox is checked""" if self.baseline_checkbox.isChecked(): self.deactivate_buttons( [ self.first_canal_check, self.second_canal_check, ] ) else: self.activate_buttons( [ self.first_canal_check, self.second_canal_check, ] ) def adjust_exposure(self): """Match the exposure of the image preview to the slider value""" self.max_exposure = self.exposure_slider.value() self.slider_values[self.preview_light_combo.currentText()][ self.activation_map_combo.currentText() ] = self.max_exposure def set_trigger(self): """Set the trigger for the DAQ""" if not self.acquisition_mode: self.run_button.setText("Run at Trigger") self.daq.set_trigger(self.ports["trigger"]) else: self.run_button.setText("Run") self.daq.remove_trigger() def import_config(self): """Import a configuration file""" file = QFileDialog.getOpenFileName()[0] try: dictionary = get_dictionary(file) self.framerate_cell.setText(str(dictionary["Framerate"])) self.exposure_cell.setText(str(dictionary["Exposition"])) self.set_lights(dictionary["Lights"]) self.tree.create_tree_item(dictionary["Blocks"]) self.enable_run(self.tree.check_global_validity()) self.tree.graph(self.tree.invisibleRootItem()) self.draw() except Exception as err: print(err) def set_lights(self, lights): """Set the lights""" for light in lights: if light == "infrared": self.ir_checkbox.setChecked(True) elif light == "red": self.red_checkbox.setChecked(True) elif light == "green": self.green_checkbox.setChecked(True) elif light == "blue": self.fluorescence_checkbox.setChecked(True) def run(self): """Run the experiment""" if self.check_override(): self.deactivate_buttons(buttons=self.enabled_buttons) self.master_block = self.tree.create_blocks() self.tree.baseline_values = [] self.tree.graph(item=self.tree.invisibleRootItem()) self.root_time, self.root_signal = ( self.tree.x_values, [ self.tree.stim1_values, self.tree.stim2_values, self.tree.stim3_values, ], ) self.draw(root=True) if self.acquisition_mode: self.actualize_daq() self.open_live_saving_thread() self.open_live_preview_thread() self.open_baseline_check_thread() else: self.daq.stop_signal = False self.open_signal_preview_thread() self.open_start_experiment_thread() def check_override(self): """Check if experiment with the same name already exists""" if os.path.isfile( os.path.join( self.directory_cell.text(), self.experiment_name_cell.text(), f"{self.experiment_name_cell.text()}-light_signal.npy", ) ): button = QMessageBox.question( self, "Files already exist", "Files already exist. \n Do you want to override the existing files?", ) if button == QMessageBox.Yes: return True else: return False else: return True def open_baseline_check_thread(self): """Open the thread for the baseline check""" self.baseline_check_thread = Thread(target=self.check_baseline) self.baseline_check_thread.start() def check_baseline(self): """Monitor the incoming frames and check if the baseline is reached""" if len(self.daq.lights) > 0: self.camera.baseline_data = [] self.camera.adding_frames = False self.camera.completed_baseline = False while self.daq.camera_signal is None: pass frames_acquired = frames_acquired_from_camera_signal(self.daq.camera_signal) baseline_indices = get_baseline_frame_indices( self.tree.baseline_values, frames_acquired ) for baseline_pair in baseline_indices: while not self.daq.stop_signal: try: if ( not self.camera.adding_frames and self.camera.frames_read >= baseline_pair[0] ): self.camera.adding_frames = True elif ( self.camera.adding_frames and self.camera.frames_read >= baseline_pair[1] ): self.camera.baseline_read_list = [] self.camera.average_baseline = average_baseline( self.camera.baseline_data, len(self.daq.lights), self.camera.frames_read_list[0] % len(self.daq.lights), ) self.camera.adding_frames = False self.camera.baseline_frames = [] self.camera.baseline_completed = True self.camera.frames_read_list = [] break except Exception as err: pass time.sleep(0.01) def open_start_experiment_thread(self): """Open the thread for the start of the experiment""" self.start_experiment_thread = Thread(target=self.run_stimulation) self.start_experiment_thread.start() def save_config(self): """Save the current configuration to a JSON file""" folder = str(QFileDialog.getExistingDirectory(self, "Select Directory")) if folder != "": self.master_block = self.tree.create_blocks() self.experiment = Experiment( self.master_block, int(self.framerate_cell.text()), int(self.exposure_cell.text()), self.mouse_id_cell.text(), folder, self.daq, name=self.experiment_name_cell.text(), config=self.config, ) self.experiment.save_config( [int(1024 / self.config["Binning"]), int(1024 / self.config["Binning"])] ) def run_stimulation(self): """Run the stimulation in parallel with the lights""" self.experiment = Experiment( self.master_block, int(self.framerate_cell.text()), int(self.exposure_cell.text()), self.mouse_id_cell.text(), self.directory_cell.text(), self.daq, name=self.experiment_name_cell.text(), config=self.config, ) self.save_files_after_stop = True self.daq.launch(self.experiment.name, self.root_time, self.root_signal) # if ( # not self.daq.stop_signal # and self.save_files_after_stop # and self.directory_save_files_checkbox.isChecked() # ): if ( self.save_files_after_stop and self.directory_save_files_checkbox.isChecked() ): try: print("this is the extent") print(self.roi_extent) self.experiment.save(self.roi_extent) except Exception as err: print("err after saving first") print(err) print("err before entering") self.experiment.save() self.stop() def open_live_saving_thread(self): """Open the thread for the live saving""" self.live_save_thread = Thread(target=self.live_save) self.live_save_thread.start() def live_save(self): """Save NPY chunked files when the number of frames is over 1200""" self.camera.file_index = 0 self.camera.is_saving = False if self.directory_save_files_checkbox.isChecked(): try: os.mkdir( os.path.join( self.directory_cell.text(), self.experiment_name_cell.text() ) ) os.mkdir( os.path.join( self.directory_cell.text(), self.experiment_name_cell.text(), "data", ) ) except Exception as err: pass while self.camera.video_running is False and not self.camera.stop_signal: time.sleep(0.01) pass while self.camera.video_running is True: if len(self.camera.frames) > 1200: self.memory = self.camera.frames[:1200] self.camera.frames = self.camera.frames[1200:] if self.directory_save_files_checkbox.isChecked(): try: self.memory = shrink_array(self.memory, self.roi_extent) except Exception: pass self.camera.is_saving = True np.save( os.path.join( self.directory_cell.text(), self.experiment_name_cell.text(), "data", f"{self.camera.file_index}.npy", ), self.memory, ) self.memory = None self.camera.file_index += 1 self.camera.is_saving = False time.sleep(0.01) def open_live_preview_thread(self): """Open the thread for the live preview""" self.live_preview_thread = Thread(target=self.start_live) self.live_preview_thread.start() def start_live(self): """Start the live preview""" plt.ion() self.memory = [] self.camera.baseline_completed = False if len(self.daq.lights) > 0: try: while self.camera.video_running is False: time.sleep(0.01) pass while self.camera.video_running is True: try: if ( not self.camera.baseline_completed or self.activation_map_combo.currentIndex() == 0 ): self.plot_image.set( array=self.camera.frames[ self.live_preview_light_index :: len( self.daq.lights ) ][-1], clim=(0, self.max_exposure), cmap="binary_r", ) elif self.activation_map_combo.currentIndex() == 1: start_index = ( self.camera.baseline_read_list[0] + self.live_preview_light_index ) % len(self.daq.lights) activation_map = ( self.camera.baseline_frames[ start_index :: len(self.daq.lights) ][-1] - self.camera.average_baseline[ self.live_preview_light_index ] ) / self.camera.average_baseline[ self.live_preview_light_index ] self.plot_image.set( array=activation_map, clim=( -self.max_exposure / 200, self.max_exposure / 200, ), cmap="seismic", ) else: start_index = ( self.camera.baseline_read_list[0] + self.live_preview_light_index ) % len(self.daq.lights) activation_map = np.log( ( ( self.camera.baseline_frames[ start_index :: len(self.daq.lights) ][-1] - self.camera.average_baseline[ self.live_preview_light_index ] ) / self.camera.average_baseline[ self.live_preview_light_index ] ) ) self.plot_image.set( array=activation_map, clim=( -self.max_exposure / 2000, self.max_exposure / 2000, ), cmap="seismic", ) except Exception as err: print(err) pass time.sleep(0.04) except Exception as err: pass def stop_live(self): """Stop the live preview""" self.camera.video_running = False def open_signal_preview_thread(self): """Open the thread for the signal preview""" self.signal_preview_thread = Thread(target=self.actualize_progression) self.signal_preview_thread.start() def actualize_progression(self): """Actualize the position of the progress bar""" plt.ion() while self.daq.stop_signal is False: try: if self.acquisition_mode: position = self.camera.frames_read / int(self.framerate_cell.text()) else: position = time.time() - self.daq.start_time self.plot_window.vertical_lines[0].set_xdata(position) self.plot_window.vertical_lines[1].set_xdata(position) self.plot_window.vertical_lines[2].set_xdata(position) time.sleep(0.5) except Exception as err: time.sleep(0.5) pass def change_preview_light_channel(self): """Change the light channel for the live preview""" self.live_preview_light_index = self.preview_light_combo.currentIndex() self.adjust_slider() def adjust_slider(self): """Adjust the saturation slider using corresponding value in dictionary""" try: value = self.slider_values[self.preview_light_combo.currentText()][ self.activation_map_combo.currentText() ] self.exposure_slider.setValue(value) except Exception: pass def open_daq_generation_thread(self): """Open the thread for the DAQ generation""" self.daq_generation_thread = Thread(target=self.generate_daq) self.daq_generation_thread.start() def generate_daq(self): """Generate the DAQ""" try: self.camera = Camera(self.ports["camera"], "name") except Exception: self.camera = None self.stimuli = [ Instrument(self.ports["analog0"], "air-pump"), Instrument(self.ports["analog1"], "air-pump2"), Instrument(self.ports["co2"], "air-pump3"), ] self.daq = DAQ( "dev1", [], self.stimuli, self.camera, int(self.framerate_cell.text()), int(self.exposure_cell.text()) / 1000, ) self.daq.close_all_lights(self.ports) self.daq_generated = True self.enable_run(self.tree.check_global_validity()) def actualize_daq(self): """Actualize the DAQ with the current settings""" try: self.daq.lights = [] if self.ir_checkbox.isChecked(): self.daq.lights.append(Instrument(self.ports["infrared"], "ir")) if self.red_checkbox.isChecked(): self.daq.lights.append(Instrument(self.ports["red"], "red")) if self.green_checkbox.isChecked(): self.daq.lights.append(Instrument(self.ports["green"], "green")) if self.fluorescence_checkbox.isChecked(): self.daq.lights.append(Instrument(self.ports["blue"], "blue")) self.daq.framerate = int(self.framerate_cell.text()) self.daq.exposure = int(self.exposure_cell.text()) / 1000 self.camera.frames = [] self.daq.stop_signal = False except Exception: pass def stop(self): """Stop the experiment and reactivate the interface""" self.stop_live() self.activate_buttons(buttons=self.enabled_buttons) self.tree.setCurrentItem(self.tree.topLevelItem(0)) try: self.daq.stop_signal = True except Exception: pass def stop_while_running(self): """Stop the experiment while it is running""" if self.directory_save_files_checkbox.isChecked(): self.stop_stimulation_dialog() self.stop() def stop_stimulation_dialog(self): """Ask if user wants to keep the files after experiment is stopped""" button = QMessageBox.question( self, "Save Files", "Do you want to save the current files?" ) if button == QMessageBox.Yes: self.save_files_after_stop = True else: self.save_files_after_stop = False def show_buttons(self, buttons): """Show the buttons in a list""" for button in buttons: button.setVisible(True) def hide_buttons(self, buttons): """Hide the buttons in a list""" for button in buttons: button.setVisible(False) def activate_buttons(self, buttons): """Activate the buttons in a list""" for button in buttons: button.setEnabled(True) if buttons == self.enabled_buttons: if self.directory_save_files_checkbox.isChecked(): self.directory_choose_button.setEnabled(True) if self.roi_extent is None: self.reset_roi_button.setEnabled(False) else: self.set_roi_button.setEnabled(False) self.stop_button.setDisabled(True) def deactivate_buttons(self, buttons): """Deactivate the buttons in a list""" if buttons == self.enabled_buttons: self.stop_button.setEnabled(True) self.tree.clearSelection() for button in buttons: button.setDisabled(True) def choose_directory(self): """Choose the directory where to save the files""" folder = str(QFileDialog.getExistingDirectory(self, "Select Directory")) self.directory_cell.setText(folder) def enable_directory(self): """Enable the directory cell""" self.files_saved = self.directory_save_files_checkbox.isChecked() self.directory_choose_button.setEnabled(self.files_saved) self.directory_cell.setEnabled(self.files_saved) def actualize_window(self): """Actualize the 'Stimulation Edit' and 'Signal Preview' windows""" self.activate_buttons( [self.add_child_branch_button, self.add_brother_branch_button] ) if self.tree.currentItem(): self.tree_switch_window.setCurrentIndex(0) else: self.tree_switch_window.setCurrentIndex(1) try: if self.tree.currentItem().childCount() > 0: self.signal_adjust_superposed.setCurrentIndex(1) else: self.signal_adjust_superposed.setCurrentIndex(0) except AttributeError: self.signal_adjust_superposed.setCurrentIndex(2) self.tree_to_name() self.tree_to_block() self.tree_to_type() self.tree_to_signal() self.tree_to_canal() self.tree.graph(self.tree.currentItem(), current=True) self.draw() def name_to_tree(self): """Transfer the name of the current item from the cell to the tree""" branch = self.tree.currentItem() branch.setForeground(0, QBrush(QColor(0, 0, 0))) if branch.childCount() > 0: branch.setText(0, self.block_name_cell.text()) else: branch.setText(0, self.stimulation_name_cell.text()) def tree_to_name(self): """Transfer the name of the current item from the tree to the cell""" try: if self.tree.currentItem().childCount() > 0: if self.tree.currentItem().text(0) != "No Name": self.block_name_cell.setText(self.tree.currentItem().text(0)) else: self.block_name_cell.setText("") else: if self.tree.currentItem().text(0) != "No Name": self.stimulation_name_cell.setText(self.tree.currentItem().text(0)) else: self.stimulation_name_cell.setText("") except AttributeError: pass def type_to_tree(self): """Transfer the type of the current item from the cell to the tree""" self.enable_run(self.tree.check_global_validity()) self.different_signals_window.setCurrentIndex( self.stim_type_cell.currentIndex() ) self.different_signals_window2.setCurrentIndex( self.stim_type_cell2.currentIndex() ) self.different_signals_window3.setCurrentIndex( self.stim_type_cell3.currentIndex() ) try: self.tree.currentItem().setText(4, str(self.stim_type_cell.currentText())) except Exception: pass try: self.tree.currentItem().setText(11, str(self.stim_type_cell2.currentText())) except Exception: pass try: self.tree.currentItem().setText(23, str(self.stim_type_cell3.currentText())) except Exception: pass try: self.tree.graph(self.tree.currentItem(), current=True) self.draw() except Exception: pass def tree_to_type(self): """Transfer the type of the current item from the tree to the cell""" dico = {"square": 0, "random-square": 1, "Third": 2} try: self.stim_type_cell.setCurrentIndex(dico[self.tree.currentItem().text(4)]) except Exception: self.stim_type_cell.setCurrentIndex(0) try: self.stim_type_cell2.setCurrentIndex(dico[self.tree.currentItem().text(11)]) except Exception: self.stim_type_cell2.setCurrentIndex(0) try: self.stim_type_cell3.setCurrentIndex(dico[self.tree.currentItem().text(23)]) except Exception: self.stim_type_cell3.setCurrentIndex(0) def signal_to_tree(self): """Transfer the signal of the current item from the cell to the tree""" self.tree.currentItem().setText(6, self.duration_cell.text()) self.tree.currentItem().setText(5, self.pulses_cell.text()) self.tree.currentItem().setText(7, self.jitter_cell.text()) self.tree.currentItem().setText(8, self.width_cell.text()) self.tree.currentItem().setText(9, self.frequency_cell.text()) self.tree.currentItem().setText(10, self.duty_cell.text()) self.tree.currentItem().setText(21, self.heigth_cell.text()) self.tree.currentItem().setText(12, self.pulses_cell2.text()) self.tree.currentItem().setText(13, self.jitter_cell2.text()) self.tree.currentItem().setText(14, self.width_cell2.text()) self.tree.currentItem().setText(15, self.frequency_cell2.text()) self.tree.currentItem().setText(16, self.duty_cell2.text()) self.tree.currentItem().setText(22, self.heigth_cell2.text()) self.tree.currentItem().setText(24, self.pulses_cell3.text()) self.tree.currentItem().setText(25, self.jitter_cell3.text()) self.tree.currentItem().setText(26, self.width_cell3.text()) self.tree.currentItem().setText(27, self.frequency_cell3.text()) self.tree.currentItem().setText(28, self.duty_cell3.text()) self.enable_run(self.tree.check_global_validity()) self.tree.graph(self.tree.currentItem(), current=True) self.draw() def tree_to_signal(self): """Transfer the signal of the current item from the tree to the cell""" try: self.pulses_cell.setText(self.tree.currentItem().text(5)) self.duration_cell.setText(self.tree.currentItem().text(6)) self.jitter_cell.setText(self.tree.currentItem().text(7)) self.width_cell.setText(self.tree.currentItem().text(8)) self.frequency_cell.setText(self.tree.currentItem().text(9)) self.heigth_cell.setText(self.tree.currentItem().text(21)) self.duty_cell.setText(self.tree.currentItem().text(10)) self.pulses_cell2.setText(self.tree.currentItem().text(12)) self.jitter_cell2.setText(self.tree.currentItem().text(13)) self.width_cell2.setText(self.tree.currentItem().text(14)) self.frequency_cell2.setText(self.tree.currentItem().text(15)) self.heigth_cell2.setText(self.tree.currentItem().text(22)) self.duty_cell2.setText(self.tree.currentItem().text(16)) self.pulses_cell3.setText(self.tree.currentItem().text(24)) self.jitter_cell3.setText(self.tree.currentItem().text(25)) self.width_cell3.setText(self.tree.currentItem().text(26)) self.frequency_cell3.setText(self.tree.currentItem().text(27)) self.duty_cell3.setText(self.tree.currentItem().text(28)) except Exception as err: pass def tree_to_block(self): """Transfer the block attributes from the tree to the cells""" try: self.block_iterations_cell.setText(self.tree.currentItem().text(1)) self.block_delay_cell.setText(self.tree.currentItem().text(2)) self.block_jitter_cell.setText(self.tree.currentItem().text(3)) except Exception: pass def block_to_tree(self): """Transfer the block attributes from the cells to the tree""" self.tree.currentItem().setText(1, self.block_iterations_cell.text()) self.tree.currentItem().setText(2, self.block_delay_cell.text()) self.tree.currentItem().setText(3, self.block_jitter_cell.text()) self.enable_run(self.tree.check_global_validity()) self.tree.graph(self.tree.currentItem(), current=True) self.draw() def tree_to_canal(self): """Transfer the canals attributes from the tree to the cells""" self.canal_running = True try: self.baseline_checkbox.setChecked( self.boolean(self.tree.currentItem().text(17)) ) self.first_canal_check.setChecked( self.boolean(self.tree.currentItem().text(18)) ) self.second_canal_check.setChecked( self.boolean(self.tree.currentItem().text(19)) ) self.third_canal_check.setChecked( self.boolean(self.tree.currentItem().text(30)) ) if self.baseline_checkbox.isChecked(): self.deactivate_buttons(self.canal1buttons + [self.first_canal_check]) self.deactivate_buttons(self.canal2buttons + [self.second_canal_check]) self.deactivate_buttons(self.canal3buttons + [self.third_canal_check]) else: self.activate_buttons( [ self.first_canal_check, self.second_canal_check, self.third_canal_check, ] ) if self.first_canal_check.isChecked(): self.activate_buttons(self.canal1buttons) else: self.deactivate_buttons(self.canal1buttons) if self.second_canal_check.isChecked(): self.activate_buttons(self.canal2buttons) else: self.deactivate_buttons(self.canal2buttons) if self.third_canal_check.isChecked(): self.activate_buttons(self.canal3buttons) else: self.deactivate_buttons(self.canal3buttons) except Exception as err: pass self.canal_running = False def canals_to_tree(self): """Transfer the canals attributes from the cells to the tree""" self.baseline_checkbox.setEnabled(True) if not self.canal_running: if self.baseline_checkbox.isChecked(): self.deactivate_buttons(self.canal1buttons + [self.first_canal_check]) self.deactivate_buttons(self.canal2buttons + [self.second_canal_check]) self.deactivate_buttons(self.canal3buttons + [self.third_canal_check]) else: self.activate_buttons(self.canal1buttons + [self.first_canal_check]) self.activate_buttons(self.canal2buttons + [self.second_canal_check]) self.activate_buttons(self.canal3buttons + [self.third_canal_check]) if self.first_canal_check.isChecked(): self.baseline_checkbox.setEnabled(False) self.activate_buttons(self.canal1buttons) else: self.deactivate_buttons(self.canal1buttons) if self.second_canal_check.isChecked(): self.baseline_checkbox.setEnabled(False) self.activate_buttons(self.canal2buttons) else: self.deactivate_buttons(self.canal2buttons) if self.third_canal_check.isChecked(): self.baseline_checkbox.setEnabled(False) self.activate_buttons(self.canal3buttons) else: self.deactivate_buttons(self.canal3buttons) if ( self.first_canal_check.isChecked() or self.second_canal_check.isChecked() or self.third_canal_check.isChecked() ): self.deactivate_buttons([self.baseline_checkbox]) else: self.activate_buttons([self.baseline_checkbox]) self.tree.currentItem().setText(17, str(self.baseline_checkbox.isChecked())) self.tree.currentItem().setText(18, str(self.first_canal_check.isChecked())) self.tree.currentItem().setText( 19, str(self.second_canal_check.isChecked()) ) self.tree.currentItem().setText(30, str(self.third_canal_check.isChecked())) self.enable_run(self.tree.check_global_validity()) self.tree.graph(self.tree.currentItem(), current=True) self.draw() def enable_run(self, boolean): """Enable the run button""" if not self.daq_generated: boolean = False self.save_config_button.setEnabled(boolean) self.run_button.setEnabled(boolean) def disable_run(self): """Disable the run button""" self.save_config_button.setDisabled(True) self.run_button.setDisabled(True) def count_lights(self): """Return the number of lights and a list of their names""" count = 0 text = [] for checkbox in [ self.ir_checkbox, self.red_checkbox, self.green_checkbox, self.fluorescence_checkbox, ]: if checkbox.isChecked(): count += 1 text.append(checkbox.text()) return (count, text) def actualize_lights(self): """Update the lights list in the combo box""" self.preview_light_combo.clear() if self.count_lights()[0] == 0: self.preview_light_combo.setEnabled(False) else: self.preview_light_combo.setEnabled(True) for i in range(4): if i < self.count_lights()[0]: self.preview_light_combo.addItem(self.count_lights()[1][i]) def boolean(self, string): """Return a boolean from a string""" if string == "True": return True return False def draw(self, root=False): """Draw the sitmulation channels graph Args: root (bool, optional): If True, the graph includes a progress bar""" try: self.plot_window.clear() self.plot_window.plot( self.tree.x_values, self.tree.stim1_values, root, index=0 ) self.plot_window.plot( self.tree.x_values, self.tree.stim2_values, root, index=1, ) self.plot_window.plot( self.tree.x_values, self.tree.stim3_values, root, index=2, ) self.tree.x_values = [] self.tree.stim1_values = [] self.tree.stim2_values = [] self.tree.stim3_values = [] self.elapsed_time = 0 except Exception as err: pass def set_roi(self): """Set the ROI""" self.deactivate_buttons(buttons=self.enabled_buttons) self.stop_button.setEnabled(False) self.save_roi_button.setEnabled(False) self.roi_buttons.setCurrentIndex(1) def onselect_function(eclick, erelease): """Save the ROI dimensions as attributes""" self.roi_extent = self.rect_selector.extents self.save_roi_button.setEnabled(True) self.rect_selector = RectangleSelector( self.plot_image.axes, onselect_function, drawtype="box", useblit=True, button=[1, 3], minspanx=5, minspany=5, spancoords="pixels", interactive=True, ) def reset_roi(self): """Reset the ROI""" plt.figure(self.image_view.figure.number) plt.xlim(0, int(1024 / self.config["Binning"])) plt.ylim(0, int(1024 / self.config["Binning"])) self.roi_extent = None self.reset_roi_button.setEnabled(False) def cancel_roi(self): """Cancel the ROI selection""" self.activate_buttons(buttons=self.enabled_buttons) self.roi_buttons.setCurrentIndex(0) self.rect_selector.clear() self.rect_selector = None def save_roi(self): """Save the ROI""" self.activate_buttons(buttons=self.enabled_buttons) self.roi_buttons.setCurrentIndex(0) plt.figure(self.image_view.figure.number) plt.ion() print(self.roi_extent) plt.xlim(self.roi_extent[0], self.roi_extent[1]) plt.ylim(self.roi_extent[2], self.roi_extent[3]) self.rect_selector.clear() self.rect_selector = None self.reset_roi_button.setEnabled(True) def verify_exposure(self): """Verify if the exposure/framerate combination is valid""" try: boolean_check = (int(self.exposure_cell.text()) / 1000 + 0.0015) * int( self.framerate_cell.text() ) < 1 and int(self.framerate_cell.text()) <= 57 except Exception: boolean_check = False self.exposure_warning_label.setHidden(boolean_check) def check_if_thread_is_alive(self): """Check what threads are alive""" try: if self.live_preview_thread.is_alive(): print("Live preview thread is alive") else: print("Live preview thread is dead") except Exception as err: print(err) try: if self.start_experiment_thread.is_alive(): print("Start Experiment thread is alive") else: print("Start experiment thread is dead") except Exception as err: print(err) try: if self.daq_generation_thread.is_alive(): print("Daq Generation thread is alive") else: print("Daq generation thread is dead") except Exception as err: print(err) try: if self.signal_preview_thread.is_alive(): print("Signal Preview thread is alive") else: print("Signal Preview thread is dead") except Exception as err: print(err) try: if self.live_save_thread.is_alive(): print("Live Save thread is alive") else: print("Live Save thread is dead") except Exception as err: print(err) try: if self.baseline_check_thread.is_alive(): print("Baseline check thread is alive") else: print("Baseline check thread is dead") except Exception as err: print(err) def initialize_buttons(self): """Define list of buttons to activate/deactivate""" self.canal1buttons = [ self.stim_type_cell, self.pulses_label, self.pulses_cell, self.width_label, self.width_cell, self.jitter_label, self.jitter_cell, self.frequency_label, self.frequency_cell, self.duty_label, self.duty_cell, self.heigth_cell, self.heigth_label, ] self.canal2buttons = [ self.stim_type_cell2, self.pulses_label2, self.pulses_cell2, self.width_label2, self.width_cell2, self.jitter_label2, self.jitter_cell2, self.frequency_label2, self.frequency_cell2, self.duty_label2, self.duty_cell2, self.heigth_cell2, self.heigth_label2, ] self.canal3buttons = [ self.stim_type_cell3, self.pulses_label3, self.pulses_cell3, self.width_label3, self.width_cell3, self.jitter_label3, self.jitter_cell3, self.frequency_label3, self.frequency_cell3, self.duty_label3, self.duty_cell3, self.heigth_cell3, self.heigth_label3, ] self.enabled_buttons = [ self.run_button, self.experiment_name_cell, self.mouse_id_cell, self.directory_choose_button, self.set_roi_button, self.reset_roi_button, self.experiment_name, self.mouse_id_label, self.framerate_label, self.framerate_cell, self.exposure_cell, self.exposure_label, self.add_brother_branch_button, self.add_child_branch_button, self.delete_item_button, self.red_checkbox, self.ir_checkbox, self.green_checkbox, self.fluorescence_checkbox, self.stimulation_name_label, self.directory_save_files_checkbox, self.stimulation_name_cell, self.stim_type_cell, self.stim_type_cell2, self.first_canal_check, self.second_canal_check, self.first_signal_type_duration_label, self.duration_cell, self.pulses_label, self.pulses_cell, self.width_label, self.width_cell, self.jitter_label, self.jitter_cell, self.frequency_label, self.frequency_cell, self.heigth_label, self.heigth_cell, self.duty_label, self.duty_cell, self.pulses_label2, self.pulses_cell2, self.width_label2, self.width_cell2, self.jitter_label2, self.jitter_cell2, self.frequency_label2, self.frequency_cell2, self.heigth_label2, self.heigth_cell2, self.duty_label2, self.duty_cell2, self.third_canal_check, self.stim_type_cell3, self.pulses_label3, self.pulses_cell3, self.width_label3, self.width_cell3, self.jitter_label3, self.jitter_cell3, self.frequency_label3, self.frequency_cell3, self.duty_label3, self.duty_cell3, self.heigth_cell3, self.heigth_label3, self.block_iterations_label, self.block_iterations_cell, self.block_delay_label, self.block_delay_cell, self.block_jitter_label, self.block_jitter_cell, self.block_name_label, self.block_name_cell, self.activate_live_preview_button, self.deactivate_live_preview_button, self.tree, ]Ancestors
- PyQt5.QtWidgets.QWidget
- PyQt5.QtCore.QObject
- sip.wrapper
- PyQt5.QtGui.QPaintDevice
- sip.simplewrapper
Methods
-
Activate the buttons in a list
Expand source code
def activate_buttons(self, buttons): """Activate the buttons in a list""" for button in buttons: button.setEnabled(True) if buttons == self.enabled_buttons: if self.directory_save_files_checkbox.isChecked(): self.directory_choose_button.setEnabled(True) if self.roi_extent is None: self.reset_roi_button.setEnabled(False) else: self.set_roi_button.setEnabled(False) self.stop_button.setDisabled(True) def actualize_daq(self)-
Actualize the DAQ with the current settings
Expand source code
def actualize_daq(self): """Actualize the DAQ with the current settings""" try: self.daq.lights = [] if self.ir_checkbox.isChecked(): self.daq.lights.append(Instrument(self.ports["infrared"], "ir")) if self.red_checkbox.isChecked(): self.daq.lights.append(Instrument(self.ports["red"], "red")) if self.green_checkbox.isChecked(): self.daq.lights.append(Instrument(self.ports["green"], "green")) if self.fluorescence_checkbox.isChecked(): self.daq.lights.append(Instrument(self.ports["blue"], "blue")) self.daq.framerate = int(self.framerate_cell.text()) self.daq.exposure = int(self.exposure_cell.text()) / 1000 self.camera.frames = [] self.daq.stop_signal = False except Exception: pass def actualize_lights(self)-
Update the lights list in the combo box
Expand source code
def actualize_lights(self): """Update the lights list in the combo box""" self.preview_light_combo.clear() if self.count_lights()[0] == 0: self.preview_light_combo.setEnabled(False) else: self.preview_light_combo.setEnabled(True) for i in range(4): if i < self.count_lights()[0]: self.preview_light_combo.addItem(self.count_lights()[1][i]) def actualize_progression(self)-
Actualize the position of the progress bar
Expand source code
def actualize_progression(self): """Actualize the position of the progress bar""" plt.ion() while self.daq.stop_signal is False: try: if self.acquisition_mode: position = self.camera.frames_read / int(self.framerate_cell.text()) else: position = time.time() - self.daq.start_time self.plot_window.vertical_lines[0].set_xdata(position) self.plot_window.vertical_lines[1].set_xdata(position) self.plot_window.vertical_lines[2].set_xdata(position) time.sleep(0.5) except Exception as err: time.sleep(0.5) pass def actualize_window(self)-
Actualize the 'Stimulation Edit' and 'Signal Preview' windows
Expand source code
def actualize_window(self): """Actualize the 'Stimulation Edit' and 'Signal Preview' windows""" self.activate_buttons( [self.add_child_branch_button, self.add_brother_branch_button] ) if self.tree.currentItem(): self.tree_switch_window.setCurrentIndex(0) else: self.tree_switch_window.setCurrentIndex(1) try: if self.tree.currentItem().childCount() > 0: self.signal_adjust_superposed.setCurrentIndex(1) else: self.signal_adjust_superposed.setCurrentIndex(0) except AttributeError: self.signal_adjust_superposed.setCurrentIndex(2) self.tree_to_name() self.tree_to_block() self.tree_to_type() self.tree_to_signal() self.tree_to_canal() self.tree.graph(self.tree.currentItem(), current=True) self.draw() def adjust_exposure(self)-
Match the exposure of the image preview to the slider value
Expand source code
def adjust_exposure(self): """Match the exposure of the image preview to the slider value""" self.max_exposure = self.exposure_slider.value() self.slider_values[self.preview_light_combo.currentText()][ self.activation_map_combo.currentText() ] = self.max_exposure def adjust_slider(self)-
Adjust the saturation slider using corresponding value in dictionary
Expand source code
def adjust_slider(self): """Adjust the saturation slider using corresponding value in dictionary""" try: value = self.slider_values[self.preview_light_combo.currentText()][ self.activation_map_combo.currentText() ] self.exposure_slider.setValue(value) except Exception: pass def block_to_tree(self)-
Transfer the block attributes from the cells to the tree
Expand source code
def block_to_tree(self): """Transfer the block attributes from the cells to the tree""" self.tree.currentItem().setText(1, self.block_iterations_cell.text()) self.tree.currentItem().setText(2, self.block_delay_cell.text()) self.tree.currentItem().setText(3, self.block_jitter_cell.text()) self.enable_run(self.tree.check_global_validity()) self.tree.graph(self.tree.currentItem(), current=True) self.draw() def boolean(self, string)-
Return a boolean from a string
Expand source code
def boolean(self, string): """Return a boolean from a string""" if string == "True": return True return False def canals_to_tree(self)-
Transfer the canals attributes from the cells to the tree
Expand source code
def canals_to_tree(self): """Transfer the canals attributes from the cells to the tree""" self.baseline_checkbox.setEnabled(True) if not self.canal_running: if self.baseline_checkbox.isChecked(): self.deactivate_buttons(self.canal1buttons + [self.first_canal_check]) self.deactivate_buttons(self.canal2buttons + [self.second_canal_check]) self.deactivate_buttons(self.canal3buttons + [self.third_canal_check]) else: self.activate_buttons(self.canal1buttons + [self.first_canal_check]) self.activate_buttons(self.canal2buttons + [self.second_canal_check]) self.activate_buttons(self.canal3buttons + [self.third_canal_check]) if self.first_canal_check.isChecked(): self.baseline_checkbox.setEnabled(False) self.activate_buttons(self.canal1buttons) else: self.deactivate_buttons(self.canal1buttons) if self.second_canal_check.isChecked(): self.baseline_checkbox.setEnabled(False) self.activate_buttons(self.canal2buttons) else: self.deactivate_buttons(self.canal2buttons) if self.third_canal_check.isChecked(): self.baseline_checkbox.setEnabled(False) self.activate_buttons(self.canal3buttons) else: self.deactivate_buttons(self.canal3buttons) if ( self.first_canal_check.isChecked() or self.second_canal_check.isChecked() or self.third_canal_check.isChecked() ): self.deactivate_buttons([self.baseline_checkbox]) else: self.activate_buttons([self.baseline_checkbox]) self.tree.currentItem().setText(17, str(self.baseline_checkbox.isChecked())) self.tree.currentItem().setText(18, str(self.first_canal_check.isChecked())) self.tree.currentItem().setText( 19, str(self.second_canal_check.isChecked()) ) self.tree.currentItem().setText(30, str(self.third_canal_check.isChecked())) self.enable_run(self.tree.check_global_validity()) self.tree.graph(self.tree.currentItem(), current=True) self.draw() def cancel_roi(self)-
Cancel the ROI selection
Expand source code
def cancel_roi(self): """Cancel the ROI selection""" self.activate_buttons(buttons=self.enabled_buttons) self.roi_buttons.setCurrentIndex(0) self.rect_selector.clear() self.rect_selector = None def change_preview_light_channel(self)-
Change the light channel for the live preview
Expand source code
def change_preview_light_channel(self): """Change the light channel for the live preview""" self.live_preview_light_index = self.preview_light_combo.currentIndex() self.adjust_slider() def check_baseline(self)-
Monitor the incoming frames and check if the baseline is reached
Expand source code
def check_baseline(self): """Monitor the incoming frames and check if the baseline is reached""" if len(self.daq.lights) > 0: self.camera.baseline_data = [] self.camera.adding_frames = False self.camera.completed_baseline = False while self.daq.camera_signal is None: pass frames_acquired = frames_acquired_from_camera_signal(self.daq.camera_signal) baseline_indices = get_baseline_frame_indices( self.tree.baseline_values, frames_acquired ) for baseline_pair in baseline_indices: while not self.daq.stop_signal: try: if ( not self.camera.adding_frames and self.camera.frames_read >= baseline_pair[0] ): self.camera.adding_frames = True elif ( self.camera.adding_frames and self.camera.frames_read >= baseline_pair[1] ): self.camera.baseline_read_list = [] self.camera.average_baseline = average_baseline( self.camera.baseline_data, len(self.daq.lights), self.camera.frames_read_list[0] % len(self.daq.lights), ) self.camera.adding_frames = False self.camera.baseline_frames = [] self.camera.baseline_completed = True self.camera.frames_read_list = [] break except Exception as err: pass time.sleep(0.01) def check_if_thread_is_alive(self)-
Check what threads are alive
Expand source code
def check_if_thread_is_alive(self): """Check what threads are alive""" try: if self.live_preview_thread.is_alive(): print("Live preview thread is alive") else: print("Live preview thread is dead") except Exception as err: print(err) try: if self.start_experiment_thread.is_alive(): print("Start Experiment thread is alive") else: print("Start experiment thread is dead") except Exception as err: print(err) try: if self.daq_generation_thread.is_alive(): print("Daq Generation thread is alive") else: print("Daq generation thread is dead") except Exception as err: print(err) try: if self.signal_preview_thread.is_alive(): print("Signal Preview thread is alive") else: print("Signal Preview thread is dead") except Exception as err: print(err) try: if self.live_save_thread.is_alive(): print("Live Save thread is alive") else: print("Live Save thread is dead") except Exception as err: print(err) try: if self.baseline_check_thread.is_alive(): print("Baseline check thread is alive") else: print("Baseline check thread is dead") except Exception as err: print(err) def check_override(self)-
Check if experiment with the same name already exists
Expand source code
def check_override(self): """Check if experiment with the same name already exists""" if os.path.isfile( os.path.join( self.directory_cell.text(), self.experiment_name_cell.text(), f"{self.experiment_name_cell.text()}-light_signal.npy", ) ): button = QMessageBox.question( self, "Files already exist", "Files already exist. \n Do you want to override the existing files?", ) if button == QMessageBox.Yes: return True else: return False else: return True def choose_directory(self)-
Choose the directory where to save the files
Expand source code
def choose_directory(self): """Choose the directory where to save the files""" folder = str(QFileDialog.getExistingDirectory(self, "Select Directory")) self.directory_cell.setText(folder) def closeEvent(self, *args, **kwargs)-
Stop all processes when closing the application
Expand source code
def closeEvent(self, *args, **kwargs): """Stop all processes when closing the application""" self.video_running = False try: self.camera.stop_signal = True self.camera.video_running = False self.daq.stop_signal = True self.daq.camera.cam.stop_acquisition() print("Program Closed") except Exception as err: pass self.check_if_thread_is_alive() def count_lights(self)-
Return the number of lights and a list of their names
Expand source code
def count_lights(self): """Return the number of lights and a list of their names""" count = 0 text = [] for checkbox in [ self.ir_checkbox, self.red_checkbox, self.green_checkbox, self.fluorescence_checkbox, ]: if checkbox.isChecked(): count += 1 text.append(checkbox.text()) return (count, text) -
Deactivate the buttons in a list
Expand source code
def deactivate_buttons(self, buttons): """Deactivate the buttons in a list""" if buttons == self.enabled_buttons: self.stop_button.setEnabled(True) self.tree.clearSelection() for button in buttons: button.setDisabled(True) def deactivate_channels(self)-
Deactivate canal checkboxes if the baseline checkbox is checked
Expand source code
def deactivate_channels(self): """Deactivate canal checkboxes if the baseline checkbox is checked""" if self.baseline_checkbox.isChecked(): self.deactivate_buttons( [ self.first_canal_check, self.second_canal_check, ] ) else: self.activate_buttons( [ self.first_canal_check, self.second_canal_check, ] ) def disable_run(self)-
Disable the run button
Expand source code
def disable_run(self): """Disable the run button""" self.save_config_button.setDisabled(True) self.run_button.setDisabled(True) def draw(self, root=False)-
Draw the sitmulation channels graph
Args
root:bool, optional- If True, the graph includes a progress bar
Expand source code
def draw(self, root=False): """Draw the sitmulation channels graph Args: root (bool, optional): If True, the graph includes a progress bar""" try: self.plot_window.clear() self.plot_window.plot( self.tree.x_values, self.tree.stim1_values, root, index=0 ) self.plot_window.plot( self.tree.x_values, self.tree.stim2_values, root, index=1, ) self.plot_window.plot( self.tree.x_values, self.tree.stim3_values, root, index=2, ) self.tree.x_values = [] self.tree.stim1_values = [] self.tree.stim2_values = [] self.tree.stim3_values = [] self.elapsed_time = 0 except Exception as err: pass def enable_directory(self)-
Enable the directory cell
Expand source code
def enable_directory(self): """Enable the directory cell""" self.files_saved = self.directory_save_files_checkbox.isChecked() self.directory_choose_button.setEnabled(self.files_saved) self.directory_cell.setEnabled(self.files_saved) def enable_run(self, boolean)-
Enable the run button
Expand source code
def enable_run(self, boolean): """Enable the run button""" if not self.daq_generated: boolean = False self.save_config_button.setEnabled(boolean) self.run_button.setEnabled(boolean) def generate_daq(self)-
Generate the DAQ
Expand source code
def generate_daq(self): """Generate the DAQ""" try: self.camera = Camera(self.ports["camera"], "name") except Exception: self.camera = None self.stimuli = [ Instrument(self.ports["analog0"], "air-pump"), Instrument(self.ports["analog1"], "air-pump2"), Instrument(self.ports["co2"], "air-pump3"), ] self.daq = DAQ( "dev1", [], self.stimuli, self.camera, int(self.framerate_cell.text()), int(self.exposure_cell.text()) / 1000, ) self.daq.close_all_lights(self.ports) self.daq_generated = True self.enable_run(self.tree.check_global_validity()) def handler(*args, **kwargs)-
Ignore Qt messages
Expand source code
def handler(*args, **kwargs): """Ignore Qt messages""" pass -
Hide the buttons in a list
Expand source code
def hide_buttons(self, buttons): """Hide the buttons in a list""" for button in buttons: button.setVisible(False) def import_config(self)-
Import a configuration file
Expand source code
def import_config(self): """Import a configuration file""" file = QFileDialog.getOpenFileName()[0] try: dictionary = get_dictionary(file) self.framerate_cell.setText(str(dictionary["Framerate"])) self.exposure_cell.setText(str(dictionary["Exposition"])) self.set_lights(dictionary["Lights"]) self.tree.create_tree_item(dictionary["Blocks"]) self.enable_run(self.tree.check_global_validity()) self.tree.graph(self.tree.invisibleRootItem()) self.draw() except Exception as err: print(err) def initUI(self)-
Initialize the user interface
Expand source code
def initUI(self): """Initialize the user interface""" self.title = "Widefield Imaging Aquisition" self.dimensions = (10, 10, 640, 480) self.setWindowTitle(self.title) self.setGeometry(*self.dimensions) # self.grid_layout = QGridLayout() # self.setLayout(self.grid_layout) self.grid_layout.setAlignment(Qt.AlignTop) self.experiment_settings_label = QLabel("Experiment Settings") self.experiment_settings_label.setFont(QFont("IBM Plex Sans", 17)) self.grid_layout.addWidget(self.experiment_settings_label, 0, 0) self.experiment_settings_main_window = QVBoxLayout() self.experiment_name_window = QHBoxLayout() self.experiment_name = QLabel("Experiment Name") self.experiment_name_window.addWidget(self.experiment_name) self.experiment_name_cell = QLineEdit() self.experiment_name_window.addWidget(self.experiment_name_cell) self.experiment_settings_main_window.addLayout(self.experiment_name_window) self.mouse_id_window = QHBoxLayout() self.mouse_id_label = QLabel("Mouse ID") self.mouse_id_window.addWidget(self.mouse_id_label) self.mouse_id_cell = QLineEdit() self.mouse_id_window.addWidget(self.mouse_id_cell) self.experiment_settings_main_window.addLayout(self.mouse_id_window) self.framerate_exposure_window = QHBoxLayout() self.exposure_window = QHBoxLayout() self.exposure_label = QLabel("Exposure (ms)") self.exposure_window.addWidget(self.exposure_label) self.exposure_cell = QLineEdit("10") self.exposure_cell.setValidator(self.onlyExposure) self.exposure_cell.textChanged.connect(self.verify_exposure) self.exposure_window.addWidget(self.exposure_cell) self.framerate_exposure_window.addLayout(self.exposure_window) self.framerate_window = QHBoxLayout() self.framerate_label = QLabel("Framerate") self.framerate_window.addWidget(self.framerate_label) self.framerate_cell = QLineEdit("30") self.framerate_cell.setValidator(self.onlyFramerate) self.framerate_cell.textChanged.connect(self.verify_exposure) self.framerate_window.addWidget(self.framerate_cell) self.framerate_exposure_window.addLayout(self.framerate_window) if self.acquisition_mode: self.experiment_settings_main_window.addLayout( self.framerate_exposure_window ) self.exposure_warning_label = QLabel("Invalid Exposure / Frame Rate") if self.acquisition_mode: self.experiment_settings_main_window.addWidget(self.exposure_warning_label) self.exposure_warning_label.setStyleSheet("color: red") self.exposure_warning_label.setHidden(True) self.directory_window = QHBoxLayout() self.directory_save_files_checkbox = QCheckBox() self.directory_save_files_checkbox.setText("Save") self.directory_save_files_checkbox.stateChanged.connect(self.enable_directory) self.directory_window.addWidget(self.directory_save_files_checkbox) self.directory_choose_button = QPushButton("Select Directory") self.directory_choose_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "folder-plus.png")) ) # self.directory_choose_button.setIcon(QIcon(os.path.join("gui", "icons", "folder-plus.png"))) self.directory_choose_button.setDisabled(True) self.directory_choose_button.clicked.connect(self.choose_directory) self.directory_window.addWidget(self.directory_choose_button) self.directory_cell = QLineEdit("") self.directory_cell.setReadOnly(True) self.directory_window.addWidget(self.directory_cell) self.experiment_settings_main_window.addLayout(self.directory_window) self.trigger_checkbox = QCheckBox("Wait for Trigger") self.trigger_activated = False self.trigger_checkbox.stateChanged.connect(self.set_trigger) # self.experiment_settings_main_window.addWidget(self.trigger_checkbox) self.save_config_button = QPushButton("Save Config") self.save_config_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "save.png")) ) self.save_config_button.clicked.connect(self.save_config) self.save_config_button.setEnabled(False) self.experiment_settings_main_window.addWidget(self.save_config_button) self.experiment_settings_main_window.addStretch() if self.acquisition_mode: self.grid_layout.addLayout(self.experiment_settings_main_window, 1, 0) else: self.grid_layout.addLayout(self.experiment_settings_main_window, 1, 0, 1, 2) self.image_settings_label = QLabel("Image Settings") self.image_settings_label.setFont(QFont("IBM Plex Sans", 17)) if self.acquisition_mode: self.grid_layout.addWidget(self.image_settings_label, 0, 1) self.image_settings_main_window = QVBoxLayout() self.image_settings_main_window.setAlignment(Qt.AlignLeft) self.image_settings_main_window.setAlignment(Qt.AlignTop) self.image_settings_second_window = QHBoxLayout() self.ir_checkbox = QCheckBox("Infrared") self.ir_checkbox.stateChanged.connect(self.actualize_lights) self.image_settings_second_window.addWidget(self.ir_checkbox) self.red_checkbox = QCheckBox("Red") self.red_checkbox.stateChanged.connect(self.actualize_lights) self.image_settings_second_window.addWidget(self.red_checkbox) self.green_checkbox = QCheckBox("Green") self.green_checkbox.stateChanged.connect(self.actualize_lights) self.image_settings_second_window.addWidget(self.green_checkbox) self.fluorescence_checkbox = QCheckBox("Blue") self.fluorescence_checkbox.stateChanged.connect(self.actualize_lights) self.image_settings_second_window.addWidget(self.fluorescence_checkbox) self.light_channel_layout = QHBoxLayout() self.preview_light_label = QLabel("Light Channel Preview") self.light_channel_layout.addWidget(self.preview_light_label) self.preview_light_combo = QComboBox() self.preview_light_combo.setEnabled(False) self.preview_light_combo.currentIndexChanged.connect( self.change_preview_light_channel ) self.light_channel_layout.addWidget(self.preview_light_combo) # self.activation_map_checkbox = QCheckBox("Show Activation Map") self.activation_map_window = QHBoxLayout() self.activation_map_label = QLabel("Activation Map") self.activation_map_window.addWidget(self.activation_map_label) self.activation_map_combo = QComboBox() self.activation_map_combo.addItem("None") self.activation_map_combo.addItem("Normal") self.activation_map_combo.addItem("Logarithmic") self.activation_map_combo.currentIndexChanged.connect(self.adjust_slider) self.activation_map_window.addWidget(self.activation_map_combo) self.image_settings_main_window.addLayout(self.image_settings_second_window) self.image_settings_main_window.addLayout(self.light_channel_layout) # self.image_settings_main_window.addWidget(self.activation_map_checkbox) self.image_settings_main_window.addLayout(self.activation_map_window) self.roi_buttons = QStackedLayout() self.roi_layout1 = QHBoxLayout() self.roi_layout1.setAlignment(Qt.AlignLeft) self.roi_layout1.setAlignment(Qt.AlignTop) self.roi_layout1.setContentsMargins(0, 0, 0, 0) self.reset_roi_button = QPushButton() self.reset_roi_button.setText("Reset ROI") self.reset_roi_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-out-area.png")) ) # self.reset_roi_button.setIcon(QIcon("gui/icons/zoom-out-area.png")) self.reset_roi_button.setEnabled(False) self.reset_roi_button.clicked.connect(self.reset_roi) self.roi_layout1.addWidget(self.reset_roi_button) self.set_roi_button = QPushButton() self.set_roi_button.setText("Set ROI") self.set_roi_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-in-area.png")) ) self.set_roi_button.clicked.connect(self.set_roi) self.roi_layout1.addWidget(self.set_roi_button) self.roi_layout1_container = QWidget() self.roi_layout1_container.setLayout(self.roi_layout1) self.roi_layout2 = QHBoxLayout() self.roi_layout2.setAlignment(Qt.AlignLeft) self.roi_layout2.setAlignment(Qt.AlignTop) self.roi_layout2.setContentsMargins(0, 0, 0, 0) self.cancel_roi_button = QPushButton() self.cancel_roi_button.setText("Cancel") self.cancel_roi_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-cancel.png")) ) self.cancel_roi_button.clicked.connect(self.cancel_roi) self.roi_layout2.addWidget(self.cancel_roi_button) self.save_roi_button = QPushButton() self.save_roi_button.setText("Save ROI") self.save_roi_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-check.png")) ) self.save_roi_button.clicked.connect(self.save_roi) self.roi_layout2.addWidget(self.save_roi_button) self.roi_layout2_container = QWidget() self.roi_layout2_container.setLayout(self.roi_layout2) if self.acquisition_mode: self.roi_buttons.addWidget(self.roi_layout1_container) self.roi_buttons.addWidget(self.roi_layout2_container) self.image_settings_main_window.addLayout(self.roi_buttons) self.exposure_slider = QSlider(Qt.Horizontal, self) self.exposure_slider.setRange(0, 4096) self.exposure_slider.setValue(4096) self.exposure_slider.valueChanged.connect(self.adjust_exposure) self.image_settings_main_window.addWidget(self.exposure_slider) self.image_settings_main_window.addStretch() self.activate_live_preview_button = QPushButton() self.activate_live_preview_button.setText("Start Live Preview") self.activate_live_preview_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "video.png")) ) self.activate_live_preview_button.clicked.connect(self.open_live_preview_thread) self.deactivate_live_preview_button = QPushButton() self.deactivate_live_preview_button.setText("Stop Live Preview") self.deactivate_live_preview_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "video-off.png")) ) self.deactivate_live_preview_button.clicked.connect(self.stop_live) self.image_settings_main_window.addStretch() if self.acquisition_mode: self.grid_layout.addLayout(self.image_settings_main_window, 1, 1) self.live_preview_label = QLabel("Live Preview") self.live_preview_label.setFont(QFont("IBM Plex Sans", 17)) self.image_view = PlotWindow() self.plot_image = plt.imshow( np.zeros( (int(1024 / self.config["Binning"]), int(1024 / self.config["Binning"])) ), cmap="binary_r", vmin=0, vmax=4096, origin="lower", ) self.plot_image.axes.get_xaxis().set_visible(False) self.plot_image.axes.axes.get_yaxis().set_visible(False) if self.acquisition_mode: self.grid_layout.addWidget(self.live_preview_label, 0, 2) self.grid_layout.addWidget(self.image_view, 1, 2) self.tree_label = QLabel("Stimulation Tree") self.tree_label.setFont(QFont("IBM Plex Sans", 17)) self.grid_layout.addWidget(self.tree_label, 2, 0) self.tree_window = QVBoxLayout() self.tree = Tree() self.tree.setHeaderLabels( [ "0 Name", "1 Iterations", "2 Delay", "3 Jitter", "4 Type", "5 Pulses", "6 Duration", "7 Jitter", "8 Width", "9 Frequency", "10 Duty", "11 Type2", "12 Pulses 2", "13 Jitter 2", "14 Width 2", "15 Frequency 2", "16 Duty 2", "17 Baseline", "18 Canal 1", "19 Canal 2", "20 Valid", "21 Heigth", "22 Heigth 2", "23 Type 3", "24 Pulses 3", "25 Jitter 3", "26 Width 3", "27 Frequency 3", "28 Duty 3", "29 Heigth 3", "30 Canal 3", ] ) if not self.config["Debug"]: for i in range(1, 20): self.tree.header().hideSection(i) for i in range(21, 31): self.tree.header().hideSection(i) self.tree.setHeaderHidden(True) self.tree.header().setSectionResizeMode(0, QHeaderView.Stretch) self.tree.header().setStretchLastSection(False) self.tree.currentItemChanged.connect(self.actualize_window) self.tree_window.addWidget(self.tree) self.tree_switch_window = QStackedLayout() self.tree_second_window = QHBoxLayout() self.stim_buttons_container = QWidget() self.delete_item_button = QPushButton("Delete") self.delete_item_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "trash.png")) ) self.delete_item_button.clicked.connect(self.tree.delete_item) self.tree_second_window.addWidget(self.delete_item_button) self.add_brother_branch_button = QPushButton("Add Sibling") self.add_brother_branch_button.clicked.connect(self.tree.add_brother) self.add_brother_branch_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "arrow-bar-down.png")) ) self.tree_second_window.addWidget(self.add_brother_branch_button) self.add_child_branch_button = QPushButton("Add Child") self.add_child_branch_button.clicked.connect(self.tree.add_child) self.add_child_branch_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "arrow-bar-right.png")) ) self.tree_second_window.addWidget(self.add_child_branch_button) self.stim_buttons_container.setLayout(self.tree_second_window) self.tree_switch_window.addWidget(self.stim_buttons_container) self.tree_third_window = QHBoxLayout() self.import_button = QPushButton("Import Configuration") self.import_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "packge-import.png")) ) self.import_button.clicked.connect(self.import_config) self.tree_third_window.addWidget(self.import_button) self.new_branch_button = QPushButton("New Stimulation") self.new_branch_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "square-plus.png")) ) self.tree_third_window.addWidget(self.new_branch_button) self.stim_buttons_container2 = QWidget() self.stim_buttons_container2.setLayout(self.tree_third_window) self.tree_switch_window.addWidget(self.stim_buttons_container2) self.new_branch_button.clicked.connect(self.tree.first_stimulation) self.grid_layout.addLayout(self.tree_switch_window, 4, 0) self.tree_switch_window.setCurrentIndex(1) self.grid_layout.addLayout(self.tree_window, 3, 0) self.signal_adjust_label = QLabel("Signal Adjust") self.signal_adjust_label.setFont(QFont("IBM Plex Sans", 17)) self.grid_layout.addWidget(self.signal_adjust_label, 2, 1) self.signal_adjust_superposed = QStackedLayout() self.stimulation_edit_layout = QVBoxLayout() self.stimulation_edit_layout.setContentsMargins(0, 0, 0, 0) self.canal_window = QVBoxLayout() self.canal_window.setAlignment(Qt.AlignLeft) self.canal_window.setAlignment(Qt.AlignTop) self.canal_window.setContentsMargins(0, 0, 0, 0) self.first_canal_check = QCheckBox() self.first_canal_check.stateChanged.connect(self.canals_to_tree) self.first_canal_check.setText("Canal 1") self.stim_type_cell = QComboBox() self.stim_type_cell.addItem("square") self.stim_type_cell.addItem("random-square") self.stim_type_cell.addItem("Third") self.stim_type_cell.currentIndexChanged.connect(self.type_to_tree) self.stimulation_type_window = QHBoxLayout() self.stimulation_type_window.addWidget(self.first_canal_check) self.stimulation_type_window.addWidget(self.stim_type_cell) self.canal_window.addLayout(self.stimulation_type_window) self.different_signals_window = QStackedLayout() self.canal_window.addLayout(self.different_signals_window) self.second_canal_check = QCheckBox() self.second_canal_check.stateChanged.connect(self.canals_to_tree) self.second_canal_check.setText("Canal 2") self.stim_type_cell2 = QComboBox() self.stim_type_cell2.addItem("square") self.stim_type_cell2.addItem("random-square") self.stim_type_cell2.addItem("Third") self.stim_type_cell2.currentIndexChanged.connect(self.type_to_tree) self.stimulation_type_window2 = QHBoxLayout() self.stimulation_type_window2.addWidget(self.second_canal_check) self.stimulation_type_window2.addWidget(self.stim_type_cell2) self.canal_window.addLayout(self.stimulation_type_window2) self.different_signals_window2 = QStackedLayout() self.canal_window.addLayout(self.different_signals_window2) self.third_canal_check = QCheckBox() self.third_canal_check.stateChanged.connect(self.canals_to_tree) self.third_canal_check.setText("Canal 3") # self.canal_window.addWidget(self.third_canal_check) self.stim_type_cell3 = QComboBox() self.stim_type_cell3.addItem("square") self.stim_type_cell3.addItem("random-square") self.stim_type_cell3.addItem("Third") self.stim_type_cell3.currentIndexChanged.connect(self.type_to_tree) self.stimulation_type_window3 = QHBoxLayout() self.stimulation_type_window3.addWidget(self.third_canal_check) # self.stimulation_type_window3.addWidget(self.stim_type_cell3) self.canal_window.addLayout(self.stimulation_type_window3) self.different_signals_window3 = QStackedLayout() self.canal_window.addLayout(self.different_signals_window3) self.stimulation_name_label = QLabel("Stimulation Name") self.stimulation_name_cell = QLineEdit() self.stimulation_name_cell.textEdited.connect(self.name_to_tree) self.stimulation_name_window = QHBoxLayout() self.stimulation_name_window.addWidget(self.stimulation_name_label) self.stimulation_name_window.addWidget(self.stimulation_name_cell) self.stimulation_edit_layout.addLayout(self.stimulation_name_window) self.duration_window = QHBoxLayout() self.first_signal_type_duration_label = QLabel("Duration (s)") self.duration_window.addWidget(self.first_signal_type_duration_label) self.duration_cell = QLineEdit() self.duration_window.addWidget(self.duration_cell) self.duration_cell.setValidator(self.onlyFloat) self.duration_cell.textEdited.connect(self.signal_to_tree) self.stimulation_edit_layout.addLayout(self.duration_window) self.baseline_checkbox = QCheckBox("Baseline") self.baseline_checkbox.stateChanged.connect(self.canals_to_tree) if self.acquisition_mode: self.stimulation_edit_layout.addWidget(self.baseline_checkbox) self.stimulation_edit_layout.addLayout(self.canal_window) self.first_signal_type_window = QVBoxLayout() self.first_signal_type_window.setAlignment(Qt.AlignLeft) self.first_signal_type_window.setAlignment(Qt.AlignTop) self.first_signal_type_window.setContentsMargins(0, 0, 0, 0) self.first_signal_type_container = QWidget() self.first_signal_type_container.setLayout(self.first_signal_type_window) self.first_signal_type_window2 = QVBoxLayout() self.first_signal_type_window2.setAlignment(Qt.AlignLeft) self.first_signal_type_window2.setAlignment(Qt.AlignTop) self.first_signal_type_window2.setContentsMargins(0, 0, 0, 0) self.first_signal_type_container2 = QWidget() self.first_signal_type_container2.setLayout(self.first_signal_type_window2) self.first_signal_type_window3 = QVBoxLayout() self.first_signal_type_window3.setAlignment(Qt.AlignLeft) self.first_signal_type_window3.setAlignment(Qt.AlignTop) self.first_signal_type_window3.setContentsMargins(0, 0, 0, 0) self.first_signal_type_container3 = QWidget() self.first_signal_type_container3.setLayout(self.first_signal_type_window3) self.pulses_window = QHBoxLayout() self.pulses_label = QLabel("Pulses") self.pulses_window.addWidget(self.pulses_label) self.pulses_cell = QLineEdit() self.pulses_cell.setValidator(QIntValidator()) self.pulses_cell.textEdited.connect(self.signal_to_tree) self.pulses_window.addWidget(self.pulses_cell) self.pulses_window2 = QHBoxLayout() self.pulses_label2 = QLabel("Pulses") self.pulses_window2.addWidget(self.pulses_label2) self.pulses_cell2 = QLineEdit() self.pulses_cell2.setValidator(QIntValidator()) self.pulses_cell2.textEdited.connect(self.signal_to_tree) self.pulses_window2.addWidget(self.pulses_cell2) self.pulses_window3 = QHBoxLayout() self.pulses_label3 = QLabel("Pulses") self.pulses_window3.addWidget(self.pulses_label3) self.pulses_cell3 = QLineEdit() self.pulses_cell3.setValidator(QIntValidator()) self.pulses_cell3.textEdited.connect(self.signal_to_tree) self.pulses_window3.addWidget(self.pulses_cell3) self.jitter_window = QHBoxLayout() self.jitter_label = QLabel("Jitter (s)") self.jitter_window.addWidget(self.jitter_label) self.jitter_cell = QLineEdit() self.jitter_cell.setValidator(self.onlyFloat) self.jitter_cell.setText("0") self.jitter_cell.textEdited.connect(self.signal_to_tree) self.jitter_window.addWidget(self.jitter_cell) self.jitter_window2 = QHBoxLayout() self.jitter_window2 = QHBoxLayout() self.jitter_label2 = QLabel("Jitter (s)") self.jitter_window2.addWidget(self.jitter_label2) self.jitter_cell2 = QLineEdit() self.jitter_cell2.setValidator(self.onlyFloat) self.jitter_cell2.setText("0") self.jitter_cell2.textEdited.connect(self.signal_to_tree) self.jitter_window2.addWidget(self.jitter_cell2) self.jitter_window3 = QHBoxLayout() self.jitter_window3 = QHBoxLayout() self.jitter_label3 = QLabel("Jitter (s)") self.jitter_window3.addWidget(self.jitter_label3) self.jitter_cell3 = QLineEdit() self.jitter_cell3.setValidator(self.onlyFloat) self.jitter_cell3.setText("0") self.jitter_cell3.textEdited.connect(self.signal_to_tree) self.jitter_window3.addWidget(self.jitter_cell3) self.width_window = QHBoxLayout() self.width_label = QLabel("Width (s)") self.width_window.addWidget(self.width_label) self.width_cell = QLineEdit() self.width_cell.setValidator(self.onlyFloat) self.width_cell.setText("0") self.width_cell.textEdited.connect(self.signal_to_tree) self.width_window.addWidget(self.width_cell) self.width_window2 = QHBoxLayout() self.width_label2 = QLabel("Width (s)") self.width_window2.addWidget(self.width_label2) self.width_cell2 = QLineEdit() self.width_cell2.setValidator(self.onlyFloat) self.width_cell2.setText("0") self.width_cell2.textEdited.connect(self.signal_to_tree) self.width_window2.addWidget(self.width_cell2) self.width_window3 = QHBoxLayout() self.width_label3 = QLabel("Width (s)") self.width_window3.addWidget(self.width_label3) self.width_cell3 = QLineEdit() self.width_cell3.setValidator(self.onlyFloat) self.width_cell3.setText("0") self.width_cell3.textEdited.connect(self.signal_to_tree) self.width_window3.addWidget(self.width_cell3) self.first_signal_type_window.addLayout(self.pulses_window) self.first_signal_type_window.addLayout(self.width_window) self.first_signal_type_window.addLayout(self.jitter_window) self.first_signal_type_window2.addLayout(self.pulses_window2) self.first_signal_type_window2.addLayout(self.width_window2) self.first_signal_type_window2.addLayout(self.jitter_window2) self.first_signal_type_window3.addLayout(self.pulses_window3) self.first_signal_type_window3.addLayout(self.width_window3) self.first_signal_type_window3.addLayout(self.jitter_window3) # ------------------- self.second_signal_type_window = QVBoxLayout() self.second_signal_type_container = QWidget() self.second_signal_type_window.setAlignment(Qt.AlignLeft) self.second_signal_type_window.setAlignment(Qt.AlignTop) self.second_signal_type_window.setContentsMargins(0, 0, 0, 0) self.second_signal_type_container.setLayout(self.second_signal_type_window) # self.stimulation_edit_layout.addLayout(self.different_signals_window) self.second_signal_type_window2 = QVBoxLayout() self.second_signal_type_container2 = QWidget() self.second_signal_type_window2.setAlignment(Qt.AlignLeft) self.second_signal_type_window2.setAlignment(Qt.AlignTop) self.second_signal_type_window2.setContentsMargins(0, 0, 0, 0) self.second_signal_type_container2.setLayout(self.second_signal_type_window2) self.second_signal_type_window3 = QVBoxLayout() self.second_signal_type_container3 = QWidget() self.second_signal_type_window3.setAlignment(Qt.AlignLeft) self.second_signal_type_window3.setAlignment(Qt.AlignTop) self.second_signal_type_window3.setContentsMargins(0, 0, 0, 0) self.second_signal_type_container3.setLayout(self.second_signal_type_window3) self.heigth_window = QHBoxLayout() self.heigth_label = QLabel("Heigth (V)") self.heigth_window.addWidget(self.heigth_label) self.heigth_cell = QLineEdit() self.heigth_cell.setValidator(self.onlyFloat) self.heigth_cell.textEdited.connect(self.signal_to_tree) self.heigth_window.addWidget(self.heigth_cell) self.heigth_window2 = QHBoxLayout() self.heigth_label2 = QLabel("Heigth (V)") self.heigth_window2.addWidget(self.heigth_label2) self.heigth_cell2 = QLineEdit() self.heigth_cell2.setValidator(self.onlyFloat) self.heigth_cell2.textEdited.connect(self.signal_to_tree) self.heigth_window2.addWidget(self.heigth_cell2) self.heigth_window3 = QHBoxLayout() self.heigth_label3 = QLabel("Heigth (V)") self.heigth_window3.addWidget(self.heigth_label3) self.heigth_cell3 = QLineEdit() self.heigth_cell3.setValidator(self.onlyFloat) self.heigth_cell3.textEdited.connect(self.signal_to_tree) self.heigth_window3.addWidget(self.heigth_cell3) self.frequency_window = QHBoxLayout() self.frequency_label = QLabel("Frequency (Hz)") self.frequency_window.addWidget(self.frequency_label) self.frequency_cell = QLineEdit() self.frequency_cell.setValidator(self.onlyFloat) self.frequency_cell.textEdited.connect(self.signal_to_tree) self.frequency_window.addWidget(self.frequency_cell) self.frequency_window2 = QHBoxLayout() self.frequency_label2 = QLabel("Frequency (Hz)") self.frequency_window2.addWidget(self.frequency_label2) self.frequency_cell2 = QLineEdit() self.frequency_cell2.setValidator(self.onlyFloat) self.frequency_cell2.textEdited.connect(self.signal_to_tree) self.frequency_window2.addWidget(self.frequency_cell2) self.frequency_window3 = QHBoxLayout() self.frequency_label3 = QLabel("Frequency (Hz)") self.frequency_window3.addWidget(self.frequency_label3) self.frequency_cell3 = QLineEdit() self.frequency_cell3.setValidator(self.onlyFloat) self.frequency_cell3.textEdited.connect(self.signal_to_tree) self.frequency_window3.addWidget(self.frequency_cell3) self.duty_window = QHBoxLayout() self.duty_label = QLabel("Duty (%)") self.duty_window.addWidget(self.duty_label) self.duty_cell = QLineEdit() self.duty_cell.setValidator(self.onlyFloat) self.duty_cell.textEdited.connect(self.signal_to_tree) self.duty_window.addWidget(self.duty_cell) self.duty_window2 = QHBoxLayout() self.duty_label2 = QLabel("Duty (%)") self.duty_window2.addWidget(self.duty_label2) self.duty_cell2 = QLineEdit() self.duty_cell2.setValidator(self.onlyFloat) self.duty_cell2.textEdited.connect(self.signal_to_tree) self.duty_window2.addWidget(self.duty_cell2) self.duty_window3 = QHBoxLayout() self.duty_label3 = QLabel("Duty (%)") self.duty_window3.addWidget(self.duty_label3) self.duty_cell3 = QLineEdit() self.duty_cell3.setValidator(self.onlyFloat) self.duty_cell3.textEdited.connect(self.signal_to_tree) self.duty_window3.addWidget(self.duty_cell3) self.second_signal_type_window.addLayout(self.heigth_window) self.second_signal_type_window.addLayout(self.frequency_window) self.second_signal_type_window.addLayout(self.duty_window) self.second_signal_type_window2.addLayout(self.heigth_window2) self.second_signal_type_window2.addLayout(self.frequency_window2) self.second_signal_type_window2.addLayout(self.duty_window2) # self.second_signal_type_window3.addLayout(self.heigth_window3) self.second_signal_type_window3.addLayout(self.frequency_window3) self.second_signal_type_window3.addLayout(self.duty_window3) # ------------------- self.third_signal_type_window = QVBoxLayout() self.third_signal_type_container = QWidget() self.third_signal_type_container.setLayout(self.third_signal_type_window) self.third_signal_type_window2 = QVBoxLayout() self.third_signal_type_container2 = QWidget() self.third_signal_type_container2.setLayout(self.third_signal_type_window2) self.third_signal_type_window3 = QVBoxLayout() self.third_signal_type_container3 = QWidget() self.third_signal_type_container3.setLayout(self.third_signal_type_window3) self.third_signal_type_name = QLabel("signal3") self.third_signal_type_window.addWidget(self.third_signal_type_name) self.third_signal_type_name2 = QLabel("signal3") self.third_signal_type_window2.addWidget(self.third_signal_type_name2) self.third_signal_type_name3 = QLabel("signal3") self.third_signal_type_window3.addWidget(self.third_signal_type_name3) self.different_signals_window.addWidget(self.second_signal_type_container) self.different_signals_window.addWidget(self.first_signal_type_container) self.different_signals_window.addWidget(self.third_signal_type_container) self.different_signals_window2.addWidget(self.second_signal_type_container2) self.different_signals_window2.addWidget(self.first_signal_type_container2) self.different_signals_window2.addWidget(self.third_signal_type_container2) self.different_signals_window3.addWidget(self.second_signal_type_container3) self.different_signals_window3.addWidget(self.first_signal_type_container3) self.different_signals_window3.addWidget(self.third_signal_type_container3) self.stimulation_edit_container = QWidget() self.stimulation_edit_container.setLayout(self.stimulation_edit_layout) self.block_edit_layout = QVBoxLayout() self.block_edit_layout.setContentsMargins(0, 0, 0, 0) self.block_edit_layout.setAlignment(Qt.AlignLeft) self.block_edit_layout.setAlignment(Qt.AlignTop) self.block_name_label = QLabel("Block Name") self.block_name_cell = QLineEdit() self.block_name_cell.textEdited.connect(self.name_to_tree) self.block_name_window = QHBoxLayout() self.block_name_window.addWidget(self.block_name_label) self.block_name_window.addWidget(self.block_name_cell) self.block_edit_layout.addLayout(self.block_name_window) self.block_iterations_window = QHBoxLayout() self.block_iterations_label = QLabel("Iterations") self.block_iterations_cell = QLineEdit() self.block_iterations_cell.setValidator(QIntValidator()) self.block_iterations_cell.textEdited.connect(self.block_to_tree) self.block_iterations_window.addWidget(self.block_iterations_label) self.block_iterations_window.addWidget(self.block_iterations_cell) self.block_edit_layout.addLayout(self.block_iterations_window) self.block_delay_window = QHBoxLayout() self.block_delay_label = QLabel("Delay") self.block_delay_cell = QLineEdit() self.block_delay_cell.setValidator(self.onlyFloat) self.block_delay_cell.textEdited.connect(self.block_to_tree) self.block_delay_window = QHBoxLayout() self.block_delay_window.addWidget(self.block_delay_label) self.block_delay_window.addWidget(self.block_delay_cell) self.block_edit_layout.addLayout(self.block_delay_window) self.block_jitter_window = QHBoxLayout() self.block_jitter_label = QLabel("Jitter") self.block_jitter_cell = QLineEdit() self.block_jitter_cell.setValidator(self.onlyFloat) self.block_jitter_cell.textEdited.connect(self.block_to_tree) self.block_jitter_window = QHBoxLayout() self.block_jitter_window.addWidget(self.block_jitter_label) self.block_jitter_window.addWidget(self.block_jitter_cell) self.block_edit_layout.addLayout(self.block_jitter_window) self.block_edit_container = QWidget() self.block_edit_container.setLayout(self.block_edit_layout) self.signal_adjust_superposed.addWidget(self.stimulation_edit_container) self.signal_adjust_superposed.addWidget(self.block_edit_container) self.signal_adjust_superposed.addWidget(QLabel()) self.signal_adjust_superposed.setCurrentIndex(2) self.grid_layout.addLayout(self.signal_adjust_superposed, 3, 1) self.signal_preview_label = QLabel("Signal Preview") self.signal_preview_label.setFont(QFont("IBM Plex Sans", 17)) if self.acquisition_mode: self.grid_layout.addWidget(self.signal_preview_label, 2, 2) else: self.grid_layout.addWidget(self.signal_preview_label, 0, 2) self.buttons_main_window = QHBoxLayout() self.stop_button = QPushButton("Stop") self.stop_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "player-stop.png")) ) self.stop_button.clicked.connect(self.stop_while_running) self.stop_button.setEnabled(False) self.buttons_main_window.addWidget(self.stop_button) self.run_button = QPushButton("Run") self.run_button.setIcon( QIcon(os.path.join(self.cwd, "gui", "icons", "player-play.png")) ) self.run_button.clicked.connect(self.run) self.run_button.setEnabled(False) self.buttons_main_window.addWidget(self.run_button) self.plot_window = PlotWindow(subplots=True) if self.acquisition_mode: self.grid_layout.addWidget(self.plot_window, 3, 2) else: self.grid_layout.addWidget(self.plot_window, 1, 2, 3, 1) self.grid_layout.addLayout(self.buttons_main_window, 4, 2) self.open_daq_generation_thread() self.initialize_buttons() self.show() -
Define list of buttons to activate/deactivate
Expand source code
def initialize_buttons(self): """Define list of buttons to activate/deactivate""" self.canal1buttons = [ self.stim_type_cell, self.pulses_label, self.pulses_cell, self.width_label, self.width_cell, self.jitter_label, self.jitter_cell, self.frequency_label, self.frequency_cell, self.duty_label, self.duty_cell, self.heigth_cell, self.heigth_label, ] self.canal2buttons = [ self.stim_type_cell2, self.pulses_label2, self.pulses_cell2, self.width_label2, self.width_cell2, self.jitter_label2, self.jitter_cell2, self.frequency_label2, self.frequency_cell2, self.duty_label2, self.duty_cell2, self.heigth_cell2, self.heigth_label2, ] self.canal3buttons = [ self.stim_type_cell3, self.pulses_label3, self.pulses_cell3, self.width_label3, self.width_cell3, self.jitter_label3, self.jitter_cell3, self.frequency_label3, self.frequency_cell3, self.duty_label3, self.duty_cell3, self.heigth_cell3, self.heigth_label3, ] self.enabled_buttons = [ self.run_button, self.experiment_name_cell, self.mouse_id_cell, self.directory_choose_button, self.set_roi_button, self.reset_roi_button, self.experiment_name, self.mouse_id_label, self.framerate_label, self.framerate_cell, self.exposure_cell, self.exposure_label, self.add_brother_branch_button, self.add_child_branch_button, self.delete_item_button, self.red_checkbox, self.ir_checkbox, self.green_checkbox, self.fluorescence_checkbox, self.stimulation_name_label, self.directory_save_files_checkbox, self.stimulation_name_cell, self.stim_type_cell, self.stim_type_cell2, self.first_canal_check, self.second_canal_check, self.first_signal_type_duration_label, self.duration_cell, self.pulses_label, self.pulses_cell, self.width_label, self.width_cell, self.jitter_label, self.jitter_cell, self.frequency_label, self.frequency_cell, self.heigth_label, self.heigth_cell, self.duty_label, self.duty_cell, self.pulses_label2, self.pulses_cell2, self.width_label2, self.width_cell2, self.jitter_label2, self.jitter_cell2, self.frequency_label2, self.frequency_cell2, self.heigth_label2, self.heigth_cell2, self.duty_label2, self.duty_cell2, self.third_canal_check, self.stim_type_cell3, self.pulses_label3, self.pulses_cell3, self.width_label3, self.width_cell3, self.jitter_label3, self.jitter_cell3, self.frequency_label3, self.frequency_cell3, self.duty_label3, self.duty_cell3, self.heigth_cell3, self.heigth_label3, self.block_iterations_label, self.block_iterations_cell, self.block_delay_label, self.block_delay_cell, self.block_jitter_label, self.block_jitter_cell, self.block_name_label, self.block_name_cell, self.activate_live_preview_button, self.deactivate_live_preview_button, self.tree, ] def live_save(self)-
Save NPY chunked files when the number of frames is over 1200
Expand source code
def live_save(self): """Save NPY chunked files when the number of frames is over 1200""" self.camera.file_index = 0 self.camera.is_saving = False if self.directory_save_files_checkbox.isChecked(): try: os.mkdir( os.path.join( self.directory_cell.text(), self.experiment_name_cell.text() ) ) os.mkdir( os.path.join( self.directory_cell.text(), self.experiment_name_cell.text(), "data", ) ) except Exception as err: pass while self.camera.video_running is False and not self.camera.stop_signal: time.sleep(0.01) pass while self.camera.video_running is True: if len(self.camera.frames) > 1200: self.memory = self.camera.frames[:1200] self.camera.frames = self.camera.frames[1200:] if self.directory_save_files_checkbox.isChecked(): try: self.memory = shrink_array(self.memory, self.roi_extent) except Exception: pass self.camera.is_saving = True np.save( os.path.join( self.directory_cell.text(), self.experiment_name_cell.text(), "data", f"{self.camera.file_index}.npy", ), self.memory, ) self.memory = None self.camera.file_index += 1 self.camera.is_saving = False time.sleep(0.01) def name_to_tree(self)-
Transfer the name of the current item from the cell to the tree
Expand source code
def name_to_tree(self): """Transfer the name of the current item from the cell to the tree""" branch = self.tree.currentItem() branch.setForeground(0, QBrush(QColor(0, 0, 0))) if branch.childCount() > 0: branch.setText(0, self.block_name_cell.text()) else: branch.setText(0, self.stimulation_name_cell.text()) def open_baseline_check_thread(self)-
Open the thread for the baseline check
Expand source code
def open_baseline_check_thread(self): """Open the thread for the baseline check""" self.baseline_check_thread = Thread(target=self.check_baseline) self.baseline_check_thread.start() def open_daq_generation_thread(self)-
Open the thread for the DAQ generation
Expand source code
def open_daq_generation_thread(self): """Open the thread for the DAQ generation""" self.daq_generation_thread = Thread(target=self.generate_daq) self.daq_generation_thread.start() def open_live_preview_thread(self)-
Open the thread for the live preview
Expand source code
def open_live_preview_thread(self): """Open the thread for the live preview""" self.live_preview_thread = Thread(target=self.start_live) self.live_preview_thread.start() def open_live_saving_thread(self)-
Open the thread for the live saving
Expand source code
def open_live_saving_thread(self): """Open the thread for the live saving""" self.live_save_thread = Thread(target=self.live_save) self.live_save_thread.start() def open_signal_preview_thread(self)-
Open the thread for the signal preview
Expand source code
def open_signal_preview_thread(self): """Open the thread for the signal preview""" self.signal_preview_thread = Thread(target=self.actualize_progression) self.signal_preview_thread.start() def open_start_experiment_thread(self)-
Open the thread for the start of the experiment
Expand source code
def open_start_experiment_thread(self): """Open the thread for the start of the experiment""" self.start_experiment_thread = Thread(target=self.run_stimulation) self.start_experiment_thread.start() def reset_roi(self)-
Reset the ROI
Expand source code
def reset_roi(self): """Reset the ROI""" plt.figure(self.image_view.figure.number) plt.xlim(0, int(1024 / self.config["Binning"])) plt.ylim(0, int(1024 / self.config["Binning"])) self.roi_extent = None self.reset_roi_button.setEnabled(False) def run(self)-
Run the experiment
Expand source code
def run(self): """Run the experiment""" if self.check_override(): self.deactivate_buttons(buttons=self.enabled_buttons) self.master_block = self.tree.create_blocks() self.tree.baseline_values = [] self.tree.graph(item=self.tree.invisibleRootItem()) self.root_time, self.root_signal = ( self.tree.x_values, [ self.tree.stim1_values, self.tree.stim2_values, self.tree.stim3_values, ], ) self.draw(root=True) if self.acquisition_mode: self.actualize_daq() self.open_live_saving_thread() self.open_live_preview_thread() self.open_baseline_check_thread() else: self.daq.stop_signal = False self.open_signal_preview_thread() self.open_start_experiment_thread() def run_stimulation(self)-
Run the stimulation in parallel with the lights
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def run_stimulation(self): """Run the stimulation in parallel with the lights""" self.experiment = Experiment( self.master_block, int(self.framerate_cell.text()), int(self.exposure_cell.text()), self.mouse_id_cell.text(), self.directory_cell.text(), self.daq, name=self.experiment_name_cell.text(), config=self.config, ) self.save_files_after_stop = True self.daq.launch(self.experiment.name, self.root_time, self.root_signal) # if ( # not self.daq.stop_signal # and self.save_files_after_stop # and self.directory_save_files_checkbox.isChecked() # ): if ( self.save_files_after_stop and self.directory_save_files_checkbox.isChecked() ): try: print("this is the extent") print(self.roi_extent) self.experiment.save(self.roi_extent) except Exception as err: print("err after saving first") print(err) print("err before entering") self.experiment.save() self.stop() def save_config(self)-
Save the current configuration to a JSON file
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def save_config(self): """Save the current configuration to a JSON file""" folder = str(QFileDialog.getExistingDirectory(self, "Select Directory")) if folder != "": self.master_block = self.tree.create_blocks() self.experiment = Experiment( self.master_block, int(self.framerate_cell.text()), int(self.exposure_cell.text()), self.mouse_id_cell.text(), folder, self.daq, name=self.experiment_name_cell.text(), config=self.config, ) self.experiment.save_config( [int(1024 / self.config["Binning"]), int(1024 / self.config["Binning"])] ) def save_roi(self)-
Save the ROI
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def save_roi(self): """Save the ROI""" self.activate_buttons(buttons=self.enabled_buttons) self.roi_buttons.setCurrentIndex(0) plt.figure(self.image_view.figure.number) plt.ion() print(self.roi_extent) plt.xlim(self.roi_extent[0], self.roi_extent[1]) plt.ylim(self.roi_extent[2], self.roi_extent[3]) self.rect_selector.clear() self.rect_selector = None self.reset_roi_button.setEnabled(True) def set_lights(self, lights)-
Set the lights
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def set_lights(self, lights): """Set the lights""" for light in lights: if light == "infrared": self.ir_checkbox.setChecked(True) elif light == "red": self.red_checkbox.setChecked(True) elif light == "green": self.green_checkbox.setChecked(True) elif light == "blue": self.fluorescence_checkbox.setChecked(True) def set_roi(self)-
Set the ROI
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def set_roi(self): """Set the ROI""" self.deactivate_buttons(buttons=self.enabled_buttons) self.stop_button.setEnabled(False) self.save_roi_button.setEnabled(False) self.roi_buttons.setCurrentIndex(1) def onselect_function(eclick, erelease): """Save the ROI dimensions as attributes""" self.roi_extent = self.rect_selector.extents self.save_roi_button.setEnabled(True) self.rect_selector = RectangleSelector( self.plot_image.axes, onselect_function, drawtype="box", useblit=True, button=[1, 3], minspanx=5, minspany=5, spancoords="pixels", interactive=True, ) def set_trigger(self)-
Set the trigger for the DAQ
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def set_trigger(self): """Set the trigger for the DAQ""" if not self.acquisition_mode: self.run_button.setText("Run at Trigger") self.daq.set_trigger(self.ports["trigger"]) else: self.run_button.setText("Run") self.daq.remove_trigger() -
Show the buttons in a list
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def show_buttons(self, buttons): """Show the buttons in a list""" for button in buttons: button.setVisible(True) def signal_to_tree(self)-
Transfer the signal of the current item from the cell to the tree
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def signal_to_tree(self): """Transfer the signal of the current item from the cell to the tree""" self.tree.currentItem().setText(6, self.duration_cell.text()) self.tree.currentItem().setText(5, self.pulses_cell.text()) self.tree.currentItem().setText(7, self.jitter_cell.text()) self.tree.currentItem().setText(8, self.width_cell.text()) self.tree.currentItem().setText(9, self.frequency_cell.text()) self.tree.currentItem().setText(10, self.duty_cell.text()) self.tree.currentItem().setText(21, self.heigth_cell.text()) self.tree.currentItem().setText(12, self.pulses_cell2.text()) self.tree.currentItem().setText(13, self.jitter_cell2.text()) self.tree.currentItem().setText(14, self.width_cell2.text()) self.tree.currentItem().setText(15, self.frequency_cell2.text()) self.tree.currentItem().setText(16, self.duty_cell2.text()) self.tree.currentItem().setText(22, self.heigth_cell2.text()) self.tree.currentItem().setText(24, self.pulses_cell3.text()) self.tree.currentItem().setText(25, self.jitter_cell3.text()) self.tree.currentItem().setText(26, self.width_cell3.text()) self.tree.currentItem().setText(27, self.frequency_cell3.text()) self.tree.currentItem().setText(28, self.duty_cell3.text()) self.enable_run(self.tree.check_global_validity()) self.tree.graph(self.tree.currentItem(), current=True) self.draw() def start_in_acquisition_mode(self)-
Initialize the interface in acquisition mode
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def start_in_acquisition_mode(self): """Initialize the interface in acquisition mode""" self.start_container.setParent(None) self.acquisition_mode = True self.initUI() def start_in_trigger_mode(self)-
Initialize the interface in trigger mode
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def start_in_trigger_mode(self): """Initialize the interface in trigger mode""" self.start_container.setParent(None) self.acquisition_mode = False self.initUI() def start_live(self)-
Start the live preview
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def start_live(self): """Start the live preview""" plt.ion() self.memory = [] self.camera.baseline_completed = False if len(self.daq.lights) > 0: try: while self.camera.video_running is False: time.sleep(0.01) pass while self.camera.video_running is True: try: if ( not self.camera.baseline_completed or self.activation_map_combo.currentIndex() == 0 ): self.plot_image.set( array=self.camera.frames[ self.live_preview_light_index :: len( self.daq.lights ) ][-1], clim=(0, self.max_exposure), cmap="binary_r", ) elif self.activation_map_combo.currentIndex() == 1: start_index = ( self.camera.baseline_read_list[0] + self.live_preview_light_index ) % len(self.daq.lights) activation_map = ( self.camera.baseline_frames[ start_index :: len(self.daq.lights) ][-1] - self.camera.average_baseline[ self.live_preview_light_index ] ) / self.camera.average_baseline[ self.live_preview_light_index ] self.plot_image.set( array=activation_map, clim=( -self.max_exposure / 200, self.max_exposure / 200, ), cmap="seismic", ) else: start_index = ( self.camera.baseline_read_list[0] + self.live_preview_light_index ) % len(self.daq.lights) activation_map = np.log( ( ( self.camera.baseline_frames[ start_index :: len(self.daq.lights) ][-1] - self.camera.average_baseline[ self.live_preview_light_index ] ) / self.camera.average_baseline[ self.live_preview_light_index ] ) ) self.plot_image.set( array=activation_map, clim=( -self.max_exposure / 2000, self.max_exposure / 2000, ), cmap="seismic", ) except Exception as err: print(err) pass time.sleep(0.04) except Exception as err: pass def stop(self)-
Stop the experiment and reactivate the interface
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def stop(self): """Stop the experiment and reactivate the interface""" self.stop_live() self.activate_buttons(buttons=self.enabled_buttons) self.tree.setCurrentItem(self.tree.topLevelItem(0)) try: self.daq.stop_signal = True except Exception: pass def stop_live(self)-
Stop the live preview
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def stop_live(self): """Stop the live preview""" self.camera.video_running = False def stop_stimulation_dialog(self)-
Ask if user wants to keep the files after experiment is stopped
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def stop_stimulation_dialog(self): """Ask if user wants to keep the files after experiment is stopped""" button = QMessageBox.question( self, "Save Files", "Do you want to save the current files?" ) if button == QMessageBox.Yes: self.save_files_after_stop = True else: self.save_files_after_stop = False def stop_while_running(self)-
Stop the experiment while it is running
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def stop_while_running(self): """Stop the experiment while it is running""" if self.directory_save_files_checkbox.isChecked(): self.stop_stimulation_dialog() self.stop() def tree_to_block(self)-
Transfer the block attributes from the tree to the cells
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def tree_to_block(self): """Transfer the block attributes from the tree to the cells""" try: self.block_iterations_cell.setText(self.tree.currentItem().text(1)) self.block_delay_cell.setText(self.tree.currentItem().text(2)) self.block_jitter_cell.setText(self.tree.currentItem().text(3)) except Exception: pass def tree_to_canal(self)-
Transfer the canals attributes from the tree to the cells
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def tree_to_canal(self): """Transfer the canals attributes from the tree to the cells""" self.canal_running = True try: self.baseline_checkbox.setChecked( self.boolean(self.tree.currentItem().text(17)) ) self.first_canal_check.setChecked( self.boolean(self.tree.currentItem().text(18)) ) self.second_canal_check.setChecked( self.boolean(self.tree.currentItem().text(19)) ) self.third_canal_check.setChecked( self.boolean(self.tree.currentItem().text(30)) ) if self.baseline_checkbox.isChecked(): self.deactivate_buttons(self.canal1buttons + [self.first_canal_check]) self.deactivate_buttons(self.canal2buttons + [self.second_canal_check]) self.deactivate_buttons(self.canal3buttons + [self.third_canal_check]) else: self.activate_buttons( [ self.first_canal_check, self.second_canal_check, self.third_canal_check, ] ) if self.first_canal_check.isChecked(): self.activate_buttons(self.canal1buttons) else: self.deactivate_buttons(self.canal1buttons) if self.second_canal_check.isChecked(): self.activate_buttons(self.canal2buttons) else: self.deactivate_buttons(self.canal2buttons) if self.third_canal_check.isChecked(): self.activate_buttons(self.canal3buttons) else: self.deactivate_buttons(self.canal3buttons) except Exception as err: pass self.canal_running = False def tree_to_name(self)-
Transfer the name of the current item from the tree to the cell
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def tree_to_name(self): """Transfer the name of the current item from the tree to the cell""" try: if self.tree.currentItem().childCount() > 0: if self.tree.currentItem().text(0) != "No Name": self.block_name_cell.setText(self.tree.currentItem().text(0)) else: self.block_name_cell.setText("") else: if self.tree.currentItem().text(0) != "No Name": self.stimulation_name_cell.setText(self.tree.currentItem().text(0)) else: self.stimulation_name_cell.setText("") except AttributeError: pass def tree_to_signal(self)-
Transfer the signal of the current item from the tree to the cell
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def tree_to_signal(self): """Transfer the signal of the current item from the tree to the cell""" try: self.pulses_cell.setText(self.tree.currentItem().text(5)) self.duration_cell.setText(self.tree.currentItem().text(6)) self.jitter_cell.setText(self.tree.currentItem().text(7)) self.width_cell.setText(self.tree.currentItem().text(8)) self.frequency_cell.setText(self.tree.currentItem().text(9)) self.heigth_cell.setText(self.tree.currentItem().text(21)) self.duty_cell.setText(self.tree.currentItem().text(10)) self.pulses_cell2.setText(self.tree.currentItem().text(12)) self.jitter_cell2.setText(self.tree.currentItem().text(13)) self.width_cell2.setText(self.tree.currentItem().text(14)) self.frequency_cell2.setText(self.tree.currentItem().text(15)) self.heigth_cell2.setText(self.tree.currentItem().text(22)) self.duty_cell2.setText(self.tree.currentItem().text(16)) self.pulses_cell3.setText(self.tree.currentItem().text(24)) self.jitter_cell3.setText(self.tree.currentItem().text(25)) self.width_cell3.setText(self.tree.currentItem().text(26)) self.frequency_cell3.setText(self.tree.currentItem().text(27)) self.duty_cell3.setText(self.tree.currentItem().text(28)) except Exception as err: pass def tree_to_type(self)-
Transfer the type of the current item from the tree to the cell
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def tree_to_type(self): """Transfer the type of the current item from the tree to the cell""" dico = {"square": 0, "random-square": 1, "Third": 2} try: self.stim_type_cell.setCurrentIndex(dico[self.tree.currentItem().text(4)]) except Exception: self.stim_type_cell.setCurrentIndex(0) try: self.stim_type_cell2.setCurrentIndex(dico[self.tree.currentItem().text(11)]) except Exception: self.stim_type_cell2.setCurrentIndex(0) try: self.stim_type_cell3.setCurrentIndex(dico[self.tree.currentItem().text(23)]) except Exception: self.stim_type_cell3.setCurrentIndex(0) def type_to_tree(self)-
Transfer the type of the current item from the cell to the tree
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def type_to_tree(self): """Transfer the type of the current item from the cell to the tree""" self.enable_run(self.tree.check_global_validity()) self.different_signals_window.setCurrentIndex( self.stim_type_cell.currentIndex() ) self.different_signals_window2.setCurrentIndex( self.stim_type_cell2.currentIndex() ) self.different_signals_window3.setCurrentIndex( self.stim_type_cell3.currentIndex() ) try: self.tree.currentItem().setText(4, str(self.stim_type_cell.currentText())) except Exception: pass try: self.tree.currentItem().setText(11, str(self.stim_type_cell2.currentText())) except Exception: pass try: self.tree.currentItem().setText(23, str(self.stim_type_cell3.currentText())) except Exception: pass try: self.tree.graph(self.tree.currentItem(), current=True) self.draw() except Exception: pass def verify_exposure(self)-
Verify if the exposure/framerate combination is valid
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def verify_exposure(self): """Verify if the exposure/framerate combination is valid""" try: boolean_check = (int(self.exposure_cell.text()) / 1000 + 0.0015) * int( self.framerate_cell.text() ) < 1 and int(self.framerate_cell.text()) <= 57 except Exception: boolean_check = False self.exposure_warning_label.setHidden(boolean_check)