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mainCheck.py
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mainCheck.py
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# -*- coding: utf-8 -*-
"""
Created on Tue Sep 10 23:14:26 2019
@author: majaa
"""
import sys
import numpy as np
import nibabel as nib
#import matplotlib.pyplot as plt
import os
import vtk.util.colors as colors
from PyQt5 import QtCore, QtGui
from PyQt5 import Qt
from fury import window,actor
#from dipy.viz import window, actor
from PyQt5.QtWidgets import QLabel,QRadioButton,QComboBox,QPushButton, QAction, QMenu, QApplication, QFileDialog, QWidget, QSplitter, QGroupBox
from PyQt5.QtGui import QIcon
import PyQt5.QtGui
from PyQt5 import QtCore, QtWidgets
from dipy.data import fetch_bundles_2_subjects, read_bundles_2_subjects
from vtk.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
from dipy.tracking.streamline import transform_streamlines, length
from shutil import copyfile
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FingureCanvas
from matplotlib.figure import Figure
import pickle
from nibabel import trackvis
from dipy.tracking import utils
import time
from dipy.tracking.streamline import set_number_of_points
from sklearn import svm
import nibabel as nib
from joblib import Parallel, delayed
from dipy.tracking.vox2track import streamline_mapping
from pykdtree.kdtree import KDTree
from kd_tree_segmentation import kd2
from one_class_svm import ocsvm
from statistical_analysis import stat
from preprocessing import preprocessing as pre
import tkinter.font as tkFont
import tkinter as tk
######### time to import matplotlib functions ############
import matplotlib
# Make sure that we are using QT5
matplotlib.use('Qt5Agg')
from numpy import arange, sin, pi
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
progname = os.path.basename(sys.argv[0])
progversion = "0.1"
class MyMplCanvas(FigureCanvas):
"""Ultimately, this is a QWidget (as well as a FigureCanvasAgg, etc.)."""
def __init__(self, parent=None, width=5, height=4, dpi=100, x=np.random.normal(size = 1000)):
fig = Figure(figsize=(width, height), dpi=dpi)
self.axes = fig.add_subplot(111)
self.compute_initial_figure(x)
FigureCanvas.__init__(self, fig)
self.setParent(parent)
FigureCanvas.setSizePolicy(self,
QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self)
def compute_initial_figure(self):
pass
class MyStaticMplCanvas(MyMplCanvas):
"""Simple canvas with a sine plot."""
def compute_initial_figure(self,x):
# t = arange(0.0, 3.0, 0.01)
# s = sin(2*pi*t)
# self.axes.plot(t, s)
# Plot Histogram on x
#x = np.random.normal(size = 1000)
self.axes.hist(x, bins=50)
#self.axes.gca().set(title='Frequency Histogram', ylabel='Frequency')
def update_figure(self,x):
# Build a list of 4 random integers between 0 and 10 (both inclusive)
self.axes.cla()
self.axes.hist(x, bins=50)
self.draw()
class MyDynamicMplCanvas(MyMplCanvas):
"""A canvas that updates itself every second with a new plot."""
#from mainCheck import MainWindow
def __init__(self, *args, **kwargs):
MyMplCanvas.__init__(self, *args, **kwargs)
#self.listen = MainWindow.getListener(MainWindow())
#print(listen)
# if(listen):
# print(listen)
#self.update_figure
# timer = QtCore.QTimer(self)
# timer.timeout.connect(self.update_figure)
# timer.start(1000)
def compute_initial_figure(self, x):
# from mainCheck import MainWindow
# object1 = MainWindow()
#self.object2 = None
#global object2
#self.object2 = object1
self.axes.hist(x, bins=50)
def update_figure(self):
# Build a list of 4 random integers between 0 and 10 (both inclusive)
#l = [random.randint(0, 10) for i in range(4)]
from mainCheck import MainWindow
object1 = MainWindow()
x = object1.getX()
# isUpdatable=object1.setListener()
print("Ha ami ashsi update korte")
# if(isUpdatable):
self.axes.cla()
self.axes.hist(x, bins=50)
self.draw()
interactive = False # set to True to show the interactive display window
class MainWindow(Qt.QMainWindow):
def getListener(self):
return self.listener
def setListener(self):
self.listener = False
def getX(self):
return self.whole_brain_length_info_all
def load_streamline2(self,whole_brain_tractogram,fileName2):
from fury import window
scene = window.Scene()
self.no_of_points=12
self.leafsize=10
# whole_brain_id = "100307"
# #model_tracts =[ "124422", "111312", "100408", "100307", "856766"]
# self.tract = "_af.left.trk"
test_data= pre.load(self, whole_brain_tractogram)
# print("Ki shomossha! ",whole_brain_tractogram," 2 ",fileName2)
if self.method == 1:
print(fileName2)
segmented_tract_positive, segmented_tract_negative = ocsvm.oneClassSVM(self, whole_brain_tractogram, fileName2)
color_tract = colors.blue
else:
segmented_tract_positive, segmented_tract_negative = kd2.segmentation_with_NN(self, whole_brain_tractogram, fileName2, self.no_of_points, self.leafsize)
color_tract = colors.green
affine=utils.affine_for_trackvis(voxel_size=np.array([1.25,1.25,1.25]))
########### Statistical Analysis ################
self.whole_brain_length_info_all = stat.length_info_all(self, test_data)
self.listener = True
xw = self.whole_brain_length_info_all
whole_brain_length_info= np.array(stat.length_info (self, test_data))
max_label = "\nMaximum length of tracts: " + str(whole_brain_length_info[0])
min_label = "\nMinimum length of tracts: "+ str(whole_brain_length_info[1])
streamline_count_label = "\nNo of streamlines: "+ str(len(test_data))
voxel_count_label = "\nNo of voxels:: "+ str(stat.voxel_count(self, test_data))
#dev_streamline_count_label = "\nNo of streamlines: "+ str(len(test_data))
#dev_voxel_count_label = "\nNo of voxels:: "+ str(self.voxel_count(test_data))
self.max_length_label.setText(max_label)
self.min_length_label.setText(min_label)
self.no_streamlines_label.setText(streamline_count_label)
#self.dev_no_streamlines_label.setText(dev_streamline_count_label)
self.no_voxels_label.setText(voxel_count_label)
#self.dev_no_voxels_label.setText(dev_voxel_count_label)
####### Adding Matplotlib
from mainCheck import MyDynamicMplCanvas as mp
from mainCheck import MyMplCanvas as mc
#self.main_widget.update_figure
# self.main_widget = QtWidgets.QWidget(self)
# print(self.whole_brain_length_info_all)
# l = QtWidgets.QVBoxLayout(self.main_widget)
# sc = MyStaticMplCanvas(self.main_widget, width=5, height=4, dpi=100, x=self.whole_brain_length_info_all)
# l.addWidget(sc)
# self.main_widget.setFocus()
# self.setCentralWidget(self.main_widget)
# self.predBox.addWidget(self.main_widget)
# self.predBox.addStretch(2)
# self.statBox.setLayout(self.predBox)
# main_widget = QtWidgets.QWidget(self)
# l = QtWidgets.QVBoxLayout(main_widget)
# sc = MyStaticMplCanvas(main_widget, width=5, height=4, dpi=100, x=self.whole_brain_length_info_all)
# l.addWidget(sc)
# main_widget.setFocus()
# self.setCentralWidget(main_widget)
# self.predBox.addWidget(main_widget)
# self.predBox.widget
#tract_transform = transform_streamlines(test_data, np.linalg.inv(affine))
#stream_actor = actor.line(tract_transform,(1., 0.5, 0))
tract_transform2 = transform_streamlines(segmented_tract_positive, np.linalg.inv(affine))
stream_actor2 = actor.line(tract_transform2,
colors=color_tract, linewidth=0.1)
bundle_nativeNeg = transform_streamlines(segmented_tract_negative, np.linalg.inv(affine))
stream_actorNeg = actor.line(bundle_nativeNeg, colors=colors.red,
opacity=0.01, linewidth=0.1)
#scene.add(stream_actor)
scene.add(stream_actor2)
scene.add(stream_actorNeg)
self.vtkWidget2.GetRenderWindow().AddRenderer(scene)
self.iren = self.vtkWidget2.GetRenderWindow().GetInteractor()
self.iren.Initialize()
self.iren.Start()
def action_reload(self):
Qt.QMainWindow.update(self)
def load_whole_brain(self,fileName):
from fury import window
scene = window.Scene()
affine=utils.affine_for_trackvis(voxel_size=np.array([1.25,1.25,1.25]))
wholeTract= nib.streamlines.load(fileName)
wholeTract = wholeTract.streamlines
wholeTract_transform = transform_streamlines(wholeTract, np.linalg.inv(affine))
stream_actor = actor.line(wholeTract_transform, colors=colors.white,
opacity=0.02, linewidth=0.1)
# scene.set_camera(position=(-176.42, 118.52, 128.20),
# focal_point=(113.30, 128.31, 76.56),
# view_up=(0.18, 0.00, 0.98))
scene.add(stream_actor)
self.vtkWidget.GetRenderWindow().AddRenderer(scene)
self.iren = self.vtkWidget.GetRenderWindow().GetInteractor()
self.iren.Initialize()
self.iren.Start()
def openTractFilesDialog(self):
# global Tract_fileName
# options = QFileDialog.Options()
# options |= QFileDialog.DontUseNativeDialog
# fileWithPath, _ = QFileDialog.getOpenFileName(self,"QFileDialog.getOpenFileName()", "","Track Files (*.trk)", options=options)
# Tract_fileName=os.path.basename(fileWithPath)
# splitFile=Tract_fileName.split(".")[0]
# print(splitFile)
# dest="AllPickles/"+Tract_fileName
# #copyfile(fileWithPath, dest)
self.combo.clear()
self.tract_name2 = []
root_dir = 'G:\\Thesis\\ThesisIm plementations\\Tract Segmentation Visualizer\\Tract-Segmentation-Visualizer\\Tracts\\AF\\Left'
for root, dirs, files in os.walk(root_dir, topdown=False):
for name in files:
self.tract_name2.append(os.path.join(root, name))
print(os.path.join(root, name))
self.combo.addItems(self.tract_name2)
print("done...")
def openFileNameDialog(self):
# global fileName
# options = QFileDialog.Options()
# options |= QFileDialog.DontUseNativeDialog
# fileWithPath, _ = QFileDialog.getOpenFileName(self,"QFileDialog.getOpenFileName()", "","Track Files (*.trk)", options=options)
# fileName=os.path.basename(fileWithPath)
# print(fileName)
# splitFile=fileName.split(".")[0]
# print(splitFile)
#dest="WholeBrains/"+fileName
#copyfile(fileWithPath, dest)
self.combo_box1.clear()
whole_brain = []
root_dir = 'G:\\Thesis\\ThesisIm plementations\\Tract Segmentation Visualizer\\Tract-Segmentation-Visualizer\\WholeBrains'
for root, dirs, files in os.walk(root_dir, topdown=False):
for name in files:
whole_brain.append(os.path.join(root, name))
print(os.path.join(root, name))
#print(dirs,type(dirs))
# for (dirpath, dirnames, filenames) in os.walk("."):
# print("File ki morse", filenames)
# self.whole_brain.extend(str("G:\\Thesis\\ThesisIm plementations\\Tract Segmentation Visualizer\\Tract-Segmentation-Visualizer\\WholeBrains" + filenames))
# break
print("Combo te bombo", whole_brain)
self.combo_box1.addItems(whole_brain)
print("done...")
def checkFile(self,fileName):
whole_brain = []
for (dirpath, dirnames, filenames) in os.walk("WholeBrains"):
whole_brain.extend(filenames)
break
if fileName in whole_brain:
return 1
else:
return 0
def clickMethod(self):
whole_brain = str(self.combo_box1.currentText())
print(whole_brain)
self.load_whole_brain(whole_brain)
def clickMethod2(self):
#AllPickles = []
#for (dirpath, dirnames, filenames) in os.walk("AllPickles"):
# AllPickles.extend(filenames)
# break
side = ""
if self.radio1.isChecked():
side = "Left"
elif self.radio2.isChecked():
side = "Right"
elif self.radio3.isChecked():
side = "Left"
choose_pickle = self.combo.currentText() + side + ".pickle"
Title = self.combo.currentText() + side
choosed_pickle = self.tract_name2
whole_brain = str(self.combo_box1.currentText())
self.method = 1
if self.ocsvm_radio.isChecked():
self.method = 1
elif self.kd_radio.isChecked():
self.method = 2
self.load_streamline2(whole_brain,choosed_pickle)
#if choose_pickle in AllPickles:
# choosed_pickle = "AllPickles/" + choose_pickle
# whole_brain = "WholeBrains/" + str(self.combo_box1.currentText())
# print("choosed_pickle",choosed_pickle)
# print("whole_brain", whole_brain)
def HorizontalLayout(self):
self.groupBox2 = QGroupBox("Method Visuals")
self.groupBox2.setStyleSheet("background-color: #006868")
self.vbox2 = Qt.QHBoxLayout()
self.wb_box = Qt.QVBoxLayout()
self.whole_brain_label = QLabel()
self.whole_brain_label.setText("\nWhole Brain Tractogram")
self.wb_box.addWidget(self.whole_brain_label)
self.vtkWidget = QVTKRenderWindowInteractor(self.frame)
self.wb_box.addWidget(self.vtkWidget)
self.vbox2.addLayout(self.wb_box)
# self.vl.addWidget(self.frame)
############################################
self.seg_box = Qt.QVBoxLayout()
self.vtkWidget2 = QVTKRenderWindowInteractor(self.frame)
self.segmented_label = QLabel()
self.segmented_label.setText("\nTract Segmentation")
self.seg_box.addWidget(self.segmented_label)
self.seg_box.addWidget(self.vtkWidget2)
self.vbox2.addLayout(self.seg_box)
self.groupBox2.setLayout(self.vbox2)
#verbox.addLayout(self.vbox2)
### Adding statistical bar
self.statBox = QGroupBox("Tract Insights")
self.statBox.setStyleSheet("QGroupBox {font-size: 15pt; font-weight: bold; font-family: Courier; color: white}")
self.predBox = Qt.QVBoxLayout()
# ## Creating font with QtFont
# font = QtGui.QFont()
# font.setFamily("Helvetica")
# font.setBold(True)
self.max_length_label = QLabel()
self.max_length_label.setText("\nMaximum length of tracts: ")
self.max_length_label.setStyleSheet("QLabel {font-size: 10pt; font-family: Courier; color: white}")
self.min_length_label = QLabel()
self.min_length_label.setText("\nMinimum length of tracts: ")
self.min_length_label.setStyleSheet("QLabel {font-size: 10pt; font-family: Courier; color: white}")
self.fa_label = QLabel()
self.fa_label.setText("\nFA value: ")
self.fa_label.setStyleSheet("QLabel {font-size: 10pt; font-family: Courier; color: white}")
self.dev_fa_label = QLabel()
self.dev_fa_label.setText("\nDeviation FA value: ")
self.dev_fa_label.setStyleSheet("QLabel {font-size: 10pt; font-family: Courier; color: white}")
self.no_streamlines_label = QLabel()
self.no_streamlines_label.setText("\nNo of streamlines: ")
self.no_streamlines_label.setStyleSheet("QLabel {font-size: 10pt; font-family: Courier; color: white}")
self.dev_no_streamlines_label = QLabel()
self.dev_no_streamlines_label.setText("\nDeviation No of streamlines: ")
self.dev_no_streamlines_label.setStyleSheet("QLabel {font-size: 10pt; font-family: Courier; color: white}")
self.no_voxels_label = QLabel()
self.no_voxels_label.setText("\nNo of voxels: ")
self.no_voxels_label.setStyleSheet("QLabel {font-size: 10pt; font-family: Courier; color: white}")
self.dev_no_voxels_label = QLabel()
self.dev_no_voxels_label.setText("\nDeviation No of voxels: ")
self.dev_no_voxels_label.setStyleSheet("QLabel {font-size: 10pt; font-family: Courier; color: white}")
self.predBox.addWidget(self.max_length_label)
self.predBox.addWidget(self.min_length_label)
self.predBox.addWidget(self.fa_label)
self.predBox.addWidget(self.dev_fa_label)
self.predBox.addWidget(self.no_streamlines_label)
self.predBox.addWidget(self.dev_no_streamlines_label)
self.predBox.addWidget(self.no_voxels_label)
self.predBox.addWidget(self.dev_no_voxels_label)
####### Adding Matplotlib
self.main_widget = QtWidgets.QWidget(self)
print(self.whole_brain_length_info_all)
self.l = QtWidgets.QVBoxLayout(self.main_widget)
self.sc = MyDynamicMplCanvas(self.main_widget, width=5, height=4, dpi=100, x=self.whole_brain_length_info_all)
self.l.addWidget(self.sc)
self.main_widget.setFocus()
self.setCentralWidget(self.main_widget)
self.predBox.addWidget(self.main_widget)
self.predBox.addStretch(2)
self.statBox.setLayout(self.predBox)
def VerticalLayout(self):
# root = tk.Tk()
# helv36 = tkFont.Font(root, family = "Helvetica",size = 36,weight = "bold")
# tkFont.families()
self.vMain = Qt.QHBoxLayout() ## Added horizontal box layout
self.groupBox1 = QGroupBox("Select Whole Brain")
whole_brain = []
for (dirpath, dirnames, filenames) in os.walk("WholeBrains"):
whole_brain.extend(filenames)
break
self.combo_box1 = QComboBox()
self.combo_box1.addItems(whole_brain)
button_box1 = QPushButton('Choose Directory')
## Creating font with QtFont
# font = QtGui.QFont()
# font.setFamily("Helvetica")
# font.setBold(True)
# button_box1.setFont(font)
button_box2 = QPushButton("Load The Whole Brain")
button_box2.clicked.connect(self.clickMethod)
button_box1.clicked.connect(self.openFileNameDialog)
##### Adjusting Color and font
self.groupBox1.setStyleSheet("background-color: #006868; font-size: 13pt; font-weight: bold; font-family: Arial; color: white")
self.combo_box1.setStyleSheet("QComboBox {background-color: #005151; font-size: 12pt; font-family: Courier; color: white}")
button_box1.setStyleSheet("background-color: #00A0A0; font-size: 13pt; font-family: Arial; color: white")
button_box2.setStyleSheet("background-color: #72d874; font-size: 13pt; font-family: Arial; color: white")
vbox = Qt.QVBoxLayout()
vbox.addWidget(self.combo_box1)
vbox.addWidget(button_box1)
vbox.addWidget(button_box2)
vbox.addStretch(1)
self.groupBox1.setLayout(vbox)
#### Trying to add another GroupBox
self.createTrainingBox = QGroupBox("Make Your Own Training Set")
tract_files = []
for (dirpath, dirnames, filenames) in os.walk("Tracts/AF/Left"):
tract_files.extend(filenames)
break
self.training_tract_combo = QComboBox()
self.training_tract_combo.addItems(tract_files)
training_tract_button = QPushButton('Choose Your Tract')
training_button = QPushButton('Train Me!')
self.createTrainingBox.setStyleSheet("background-color: #006868; font-size: 13pt; font-weight: bold; font-family: Arial; color: white")
self.training_tract_combo.setStyleSheet("QComboBox {background-color: #005151; font-size: 12pt; font-family: Courier; color: white}")
training_tract_button.setStyleSheet("background-color: #00A0A0; font-size: 13pt; font-family: Arial; color: white")
training_button.setStyleSheet("background-color: #00A0AA; font-size: 13pt; font-family: Arial; color: white")
#### Method Radio Button
method_label = QLabel()
method_label.setText("\nSelect a method: ")
self.ocsvm_radio = QRadioButton("One Class SVM")
self.ocsvm_radio.setChecked(True)
self.kd_radio = QRadioButton("KD Tree")
button = QPushButton("Finish!")
button.setStyleSheet("background-color: #20a949; font-size: 13pt; font-family: Arial; color: white")
button.clicked.connect(self.clickMethod2)
training_tract_box = Qt.QVBoxLayout()
training_tract_box.addWidget(self.training_tract_combo)
training_tract_box.addWidget(training_tract_button)
training_tract_box.addWidget(training_button)
training_tract_box.addWidget(method_label)
training_tract_box.addWidget(self.ocsvm_radio)
training_tract_box.addWidget(self.kd_radio)
training_tract_box.addWidget(button)
training_tract_box.addStretch(1)
##################################
self.createTrainingBox.setLayout(training_tract_box)
####################################################
groupBox3 = QGroupBox("Use Pre-Trained Tracts")
groupBox3.setStyleSheet("background-color: #006868")
self.tractsName = ["AF", "CG", "UF"]
self.tract_box = QPushButton("Done!")
self.tract_box.clicked.connect(self.openTractFilesDialog)
self.combo = QComboBox()
self.combo.addItems(self.tractsName)
self.radio1 = QRadioButton("Left tract")
self.radio1.setChecked(True)
self.radio2 = QRadioButton("Right tract")
self.radio3 = QRadioButton("None")
groupBox3.setStyleSheet("background-color: #006868; font-size: 13pt; font-weight:bold; font-family: Arial; color: white")
self.tract_box.setStyleSheet("background-color: #00A82d; font-size: 13pt; font-family: Arial; color: white")
self.combo.setStyleSheet("background-color: #005151; font-size: 13pt; font-family: Arial; color: white")
self.radio1.setStyleSheet("background-color: #006868; font-size: 12pt; font-family: Arial; color: white")
self.radio2.setStyleSheet("background-color: #006868; font-size: 12pt; font-family: Arial; color: white")
self.radio3.setStyleSheet("background-color: #006868; font-size: 12pt; font-family: Arial; color: white")
vbox3 = Qt.QVBoxLayout()
vbox3.addWidget(self.combo)
vbox3.addWidget(self.radio1)
vbox3.addWidget(self.radio2)
vbox3.addWidget(self.radio3)
vbox3.addWidget(self.tract_box)
vbox3.addStretch(1)
groupBox3.setLayout(vbox3)
self.vMain.addWidget(self.groupBox1)
self.vMain.addWidget(groupBox3)
self.vMain.addWidget(self.createTrainingBox)
#verbox.addLayout(self.vMain)
def __init__(self, parent = None):
Qt.QMainWindow.__init__(self, parent)
####################### menubar###############
title = "FastTractSeg"
########## Took screen width and height to adjust in any screen ##########
root = tk.Tk()
width = root.winfo_screenwidth()
height = root.winfo_screenheight()
#print(width, height)
top = width // 6
left = height // 6
width = (width // 6) * 4
height = (height // 6) * 4
######## Initialized hist plot for whole brain
self.whole_brain_length_info_all = np.random.normal(size = 1000)
xw = self.whole_brain_length_info_all
self.listener = False
# menubar = self.menuBar()
# fileMenu = menubar.addMenu('File ')
# newAct = QAction('New', self)
# fileMenu.addAction(newAct)
##### Set your icon
icon_path = './Tract-Segmentation-Visualizer/icon.png'
if (QtCore.QFile.exists( icon_path )):
self.setWindowIcon(QIcon(icon_path))
#self.setIconSize(QtCore.QSize(0,0))
self.setWindowTitle(title)
self.setGeometry(top,left, width, height)
# Set window background color
self.setAutoFillBackground(True)
p = self.palette()
print(QtCore.Qt.black)
p.setColor(self.backgroundRole(), QtCore.Qt.darkCyan) ## Set the background color
self.setPalette(p)
####################### Pyqt###############
########## frame##################
self.frame = Qt.QFrame()
self.VerticalLayout()
self.HorizontalLayout()
self.vl = Qt.QVBoxLayout()
self.vl.addLayout(self.vMain)
self.vl.addWidget(self.groupBox2)
###### Adding Horizontal Box
self.vbox = Qt.QHBoxLayout()
self.vbox.addLayout(self.vl)
self.vbox.addWidget(self.statBox)
self.frame.setLayout(self.vbox)
self.setCentralWidget(self.frame)
self.setLayout(self.vl)
self.show()
if __name__ == "__main__":
app = Qt.QApplication(sys.argv)
window = MainWindow()
app.exec()
#sys.exit(app.exec_())