example.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
VolPy GUI interface is used to correct outputs of Mask R-CNN or annotate new datasets.
VolPy GUI uses summary images and ROIs as the input. It outputs binary masks for the trace denoising
and spike extraction step of VolPy.
@author: @caichangjia
"""

# These imports apparently must come before importing pyqtgraph on some platforms
import PySide6
from PySide6 import QtWidgets
from PySide6.QtWidgets import QApplication
from PySide6.QtGui import QShortcut

import numpy as np
import os
from pathlib import Path
import pyqtgraph as pg
from pyqtgraph import FileDialog
from pyqtgraph.Qt import QtGui
from pyqtgraph.parametertree import Parameter, ParameterTree
import random
from skimage.draw import polygon
import sys

os.environ["QT_QPA_PLATFORM_PLUGIN_PATH"] = os.fspath(
    Path(PySide6.__file__).resolve().parent / "Qt5" / "plugins")


def release(event):
    pass

def move(event):
    pass

def add():
    pass

def remove():
    pass

def show_all():
    pass

def clear():
    pass

def show_neuron():
    pass

def load():
    pass

def load_rois():
    pass

def save():
    pass

def change(param, changes):
    pass

def down():
    pass

def up():
    pass

def adjust_contrast(img, min_value, max_value):
    pass

def overlay(all_ROIs):
    pass

if __name__ == "__main__":
    ## Always start by initializing Qt (only once per application)
    app = QApplication(sys.argv)

    ## Define a top-level widget to hold everything
    w = QtWidgets.QWidget()

    ## Create some widgets to be placed inside
    hist = pg.HistogramLUTItem()  # Contrast/color control
    win = pg.GraphicsLayoutWidget()
    win.setMaximumWidth(300)
    win.setMinimumWidth(200)
    win.addItem(hist)
    p1 = pg.PlotWidget()
    neuron_action = ParameterTree()
    neuron_list = QtWidgets.QListWidget()

    ## Create a grid layout to manage the widgets size and position
    layout = QtWidgets.QGridLayout()
    w.setLayout(layout)

    ## Add widgets to the layout in their proper positions
    layout.addWidget(win, 0, 1)
    layout.addWidget(p1, 0, 2)
    layout.addWidget(neuron_action, 0, 3)
    layout.addWidget(neuron_list, 0, 4)
    img = pg.ImageItem()
    p1.addItem(img)
    hist.setImageItem(img)

    # Add actions
    params_action = [{'name': 'LOAD DATA', 'type':'action'},
                     {'name': 'LOAD ROIS', 'type':'action'},
                     {'name': 'SAVE', 'type':'action'},
                     {'name': 'ADD', 'type': 'action'},
                     {'name': 'REMOVE', 'type': 'action'},
                     {'name': 'SHOW ALL', 'type': 'action'},
                     {'name': 'CLEAR', 'type': 'action'},
                     {'name': 'IMAGES', 'type': 'list', 'values': ['MEAN','CORR']},
                     {'name': 'DISPLAY', 'type': 'list', 'values': ['CONTOUR','SPATIAL FOOTPRINTS']},
                     {'name': 'MODE', 'type': 'list', 'values': ['POLYGON','CELL MAGIC WAND', 'CHOOSE NEURONS']},
                     {'name': 'MAGIC WAND PARAMS', 'type': 'group', 'children': [{'name': 'MIN RADIUS', 'type': 'int', 'value': 4},
                                                                        {'name': 'MAX RADIUS', 'type': 'int', 'value': 10},
                                                                        {'name': 'ROUGHNESS', 'type': 'int', 'value': 1}]}]

    pars_action = Parameter.create(name='params_action', type='group', children=params_action)
    neuron_action.setParameters(pars_action, showTop=False)
    neuron_action.setWindowTitle('Parameter Action')
    mode = pars_action.getValues()['MODE'][0]

    # Add event
    #p1.mousePressEvent = mouseClickEvent
    p1.mouseReleaseEvent = release
    p1.mouseMoveEvent = move
    pars_action.param('ADD').sigActivated.connect(add)
    pars_action.param('REMOVE').sigActivated.connect(remove)
    pars_action.param('SHOW ALL').sigActivated.connect(show_all)
    pars_action.param('CLEAR').sigActivated.connect(clear)
    pars_action.param('LOAD DATA').sigActivated.connect(load)
    pars_action.param('LOAD ROIS').sigActivated.connect(load_rois)
    pars_action.param('SAVE').sigActivated.connect(save)
    pars_action.sigTreeStateChanged.connect(change)
    shortcut_down = QShortcut(QtGui.QKeySequence("down"), w)
    shortcut_down.activated.connect(down)
    shortcut_up = QShortcut(QtGui.QKeySequence("up"), w)
    shortcut_up.activated.connect(up)
    neuron_list.itemClicked.connect(show_neuron)

    # Create dictionary for saving
    F = FileDialog()
    all_pts = {}
    all_centers = {}
    all_ROIs = {}
    pts = []
    pen = pg.mkPen(color=(255, 255, 0), width=4)#, style=Qt.DashDotLine)

    ## Display the widget as a new window
    w.show()

    ## Start the Qt event loop
    app.exec()