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SerialFIB_Arctis.py
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# -*- coding: utf-8 -*-
'''
################################################################
# SerialFIB #
# #
# Sven Klumpe, Sara Goetz, Herman Fung #
# #
# Julia Mahamid, Jürgen Plitzko #
# #
# Max-Planck-Institute for Biochemistry #
# Martinsried, Germany #
# #
# European Molecular Biology Laboratory #
# Heidelberg, Germany #
# #
# #
# #
# if you use SerialFIB in your work, please cite: #
# DOI: #
# #
# #
# SerialFIB: A Developer’s Tool for Automated #
# cryo-FIB Customized Workflows #
# #
# with bug reports, suggestions, etc. please contact: #
# klumpe@biochem.mpg.de #
################################################################
'''
# Form implementation generated from reading ui file 'gui17.ui'
#
# Created by: PyQt5 UI code generator 5.6
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
#############################################
# Function Import #
#############################################
#### IMPORT AUTOSCRIPT STRUCTURES
try:
from autoscript_sdb_microscope_client.structures import *
except:
print("No Autoscript installed")
### IMPROT DRIVERS AND TOOLS
from src.Arctis.ArctisDriver import fibsem
from src.Arctis.scripteditor import Ui_ScriptEditor
from src.PatternDesigner import Ui_PatternFileEditor
from src.LamellaDesigner import Ui_LamellaDesigner
from src.VolumeDesigner import Ui_VolumeDesigner
from src.Param3D import Param3D
### INITIALIZE MICROSCOPE FROM DRIVER
scope=fibsem()
###
### IMPORT EXTERNAL PACKAGES
from PyQt5.QtCore import pyqtSignal
from PyQt5.QtGui import QPainter
from PyQt5.QtWidgets import QGraphicsScene
import numpy as np
import os
import src
import logging
import datetime
import cv2
import sys
import pickle
import src.project_3dct as project_3dct
import re
###
class Stream(QtCore.QObject):
'''
This class gets the output text such as error messages etc. and puts them in the GUI message
box as well as the logfile.
It does that by getting an update from the MainWindow function onUpdateText() as oyqtSignal
'''
newText = QtCore.pyqtSignal(str)
sys.stdout = open(r'./SFIB.log', mode='a')
def write(self, text):
if str(text)==" ":
print('test')
else:
self.newText.emit(str(text).split("\n")[0])
# TestImage load for developing
try:
testimage=AdornedImage.load('./DummyImages/testimage1.tif')
testimage2=AdornedImage.load('./DummyImages/testimage2.tif')
except:
print('No testcase or "wrong" developer computer')
#############################################
class Ui_MainWindow(object):
'''
Definition of the GUI class
'''
def __init__(self):
# Scene for the GraphicsView, SceneBuffer is a list of all the scenes that have been created
self.scene=QtWidgets.QGraphicsScene()
self.sceneBuffer=[]
# Dictionary of all stage positions
self.StagePos={}
# Dictionary of all patterns defined for the images in the Image Buffer.
self.pattern_dict={}
# Image Buffer handle is a number that keeps track of which image is opened in the graphicsView
# Image buffer images is a list of all images in the ImageBuffer
self.ImageBufferHandle=0
self.ImageBufferImages=[]
# Output directory for outfiles
import os
path = r'%s' % os.getcwd().replace('\\', '/')
self.output_dir=path
try:
scope.define_output_dir(self.output_dir)
except:
print("No Microscope connected")
self.SAVparamsfile=r'./SAVparams.spf'
self.roughmillprotocol=r'./roughmill.pro'
self.finemillprotocol=r'./finemill.pro'
self.custommillprotocol=r'./testprotocol.pro'
self.custompatternfile=r'./patternfile.pf'
self.settings=r'./standard.settings'
self.number=0
self.threads=[]
# Logfile initialization
self.sysout=open(self.output_dir + r'/'+r'/SFIB.log', mode='a')
self.log_out=''
# Initialization for correlation Images and associated tools, e.g. colors for displaying overlays
self.load_image_pixel_size=1
self.corrspots={}
self.copy=[]
self.pointer_projpixmap=None
self.colordict={"green":[0,255,0], "magenta":[255,0,255], "cyan":[0,255,255], "yellow":[255,255,0], "red":[255,0,0], "white":[255,255,255]}
self.CFproj=None
def get_scene(self):
'''
A function that gets the current scene displayed in the GraphicsView
Input: MainWindow class
Output: QGraphicsScene
'''
scene=self.scene
return(scene)
def get_scenebuffer(self):
'''
A function that gets the sceneBuffer
Input: MainWindow class
Output: List of QGraphicsScenes
'''
scenebuffer=self.sceneBuffer
return(scenebuffer)
def push_scene_to_buffer(self,scene,ImageBufferHandle):
'''
Function to overwrite the current scene given by the
ImageBufferHandle with the given scene
Input: scene [QGraphicsScene], ImageBufferHandle [int]
Output: None
'''
scenebuffer=self.sceneBuffer
scenebuffer[ImageBufferHandle]=scene
self.sceneBuffer=scenebuffer
return()
def get_pattern_dict(self):
'''
Function to get the pattern dictionnary for e.g. session file writing
Input: MainWindow class
Output: dictionary of patterns corresponding to the images in the ImageBuffer
'''
return(self.pattern_dict)
def push_pattern_dict(self,pattern_dict_new):
'''
Function to overwrite the pattern_dictionary if session file is read
Input: pattern_dictionary
Output: None
'''
self.pattern_dict=pattern_dict_new
return()
def get_number_imageBuffer(self):
'''
Get imageBufferHandle
Input: Ma
'''
return(self.ImageBufferHandle)
####
def setupUi(self, MainWindow):
'''
GUI Setup as created by pyuic
'''
MainWindow.setObjectName("MainWindow")
MainWindow.resize(1070, 917)
self.centralwidget = QtWidgets.QWidget(MainWindow)
self.centralwidget.setObjectName("centralwidget")
self.verticalLayoutWidget = QtWidgets.QWidget(self.centralwidget)
self.verticalLayoutWidget.setGeometry(QtCore.QRect(10, 480, 201, 263))
self.verticalLayoutWidget.setObjectName("verticalLayoutWidget")
self.verticalLayout = QtWidgets.QVBoxLayout(self.verticalLayoutWidget)
self.verticalLayout.setContentsMargins(0, 0, 0, 0)
self.verticalLayout.setObjectName("verticalLayout")
self.label = QtWidgets.QLabel(self.verticalLayoutWidget)
self.label.setAlignment(QtCore.Qt.AlignCenter)
self.label.setObjectName("label")
self.verticalLayout.addWidget(self.label)
self.Button_AddPosition = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.Button_AddPosition.setObjectName("Button_AddPosition")
self.verticalLayout.addWidget(self.Button_AddPosition)
self.Button_SaveImageForAlignment = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.Button_SaveImageForAlignment.setObjectName("Button_SaveImageForAlignment")
self.verticalLayout.addWidget(self.Button_SaveImageForAlignment)
self.Button_SavePatterns = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.Button_SavePatterns.setObjectName("Button_SavePatterns")
self.verticalLayout.addWidget(self.Button_SavePatterns)
self.Button_UpdateZ = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.Button_UpdateZ.setObjectName("Button_UpdateZ")
self.verticalLayout.addWidget(self.Button_UpdateZ)
self.Button_GoToXYZ = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.Button_GoToXYZ.setObjectName("Button_GoToXYZ")
self.verticalLayout.addWidget(self.Button_GoToXYZ)
self.Button_GoToXY = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.Button_GoToXY.setObjectName("Button_GoToXY")
self.verticalLayout.addWidget(self.Button_GoToXY)
self.Button_DeleteItem = QtWidgets.QPushButton(self.verticalLayoutWidget)
self.Button_DeleteItem.setObjectName("Button_DeleteItem")
self.verticalLayout.addWidget(self.Button_DeleteItem)
####
#self.graphicsView = QtWidgets.QGraphicsView(self.centralwidget)
# Replacing the Standard QGraphicsView with the LamellaView Class
self.graphicsView = LamellaView(self.centralwidget)
#####
self.graphicsView.setGeometry(QtCore.QRect(480, 30, 581, 461))
self.graphicsView.setObjectName("graphicsView")
self.verticalLayoutWidget_4 = QtWidgets.QWidget(self.centralwidget)
self.verticalLayoutWidget_4.setGeometry(QtCore.QRect(0, 0, 207, 396))
self.verticalLayoutWidget_4.setObjectName("verticalLayoutWidget_4")
self.verticalLayout_4 = QtWidgets.QVBoxLayout(self.verticalLayoutWidget_4)
self.verticalLayout_4.setContentsMargins(0, 0, 0, 0)
self.verticalLayout_4.setObjectName("verticalLayout_4")
self.label_2 = QtWidgets.QLabel(self.verticalLayoutWidget_4)
self.label_2.setAlignment(QtCore.Qt.AlignCenter)
self.label_2.setObjectName("label_2")
self.verticalLayout_4.addWidget(self.label_2)
self.Button_SetOutputDirectory = QtWidgets.QPushButton(self.verticalLayoutWidget_4)
self.Button_SetOutputDirectory.setObjectName("Button_SetOutputDirectory")
self.verticalLayout_4.addWidget(self.Button_SetOutputDirectory)
self.Button_TakeImageIB = QtWidgets.QPushButton(self.verticalLayoutWidget_4)
self.Button_TakeImageIB.setObjectName("Button_TakeImageIB")
self.verticalLayout_4.addWidget(self.Button_TakeImageIB)
self.Button_TakeImageEB = QtWidgets.QPushButton(self.verticalLayoutWidget_4)
self.Button_TakeImageEB.setObjectName("Button_TakeImageEB")
self.verticalLayout_4.addWidget(self.Button_TakeImageEB)
self.Button_RunRoughProtocol = QtWidgets.QPushButton(self.verticalLayoutWidget_4)
self.Button_RunRoughProtocol.setObjectName("Button_RunRoughProtocol")
self.verticalLayout_4.addWidget(self.Button_RunRoughProtocol)
self.Button_RunFineProtocol = QtWidgets.QPushButton(self.verticalLayoutWidget_4)
self.Button_RunFineProtocol.setObjectName("Button_RunFineProtocol")
self.verticalLayout_4.addWidget(self.Button_RunFineProtocol)
self.Button_RunTrenchMilling = QtWidgets.QPushButton(self.verticalLayoutWidget_4)
self.Button_RunTrenchMilling.setObjectName("Button_RunTrenchMilling")
self.verticalLayout_4.addWidget(self.Button_RunTrenchMilling)
#self.Button_RunRoughMilling = QtWidgets.QPushButton(self.verticalLayoutWidget_4)
#self.Button_RunRoughMilling.setObjectName("Button_RunRoughMilling")
#self.verticalLayout_4.addWidget(self.Button_RunRoughMilling)
#self.Button_RunFineMilling = QtWidgets.QPushButton(self.verticalLayoutWidget_4)
#self.Button_RunFineMilling.setObjectName("Button_RunFineMilling")
#self.verticalLayout_4.addWidget(self.Button_RunFineMilling)
self.Button_LoadCorrelationImages = QtWidgets.QPushButton(self.verticalLayoutWidget_4)
self.Button_LoadCorrelationImages.setObjectName("Button_LoadCorrelationImages")
self.verticalLayout_4.addWidget(self.Button_LoadCorrelationImages)
self.label_3 = QtWidgets.QLabel(self.centralwidget)
self.label_3.setGeometry(QtCore.QRect(710, 10, 141, 16))
self.label_3.setObjectName("label_3")
self.tableWidget = QtWidgets.QTableWidget(self.centralwidget)
self.tableWidget.setGeometry(QtCore.QRect(230, 500, 831, 241))
self.tableWidget.setMouseTracking(False)
self.tableWidget.setAlternatingRowColors(True)
self.tableWidget.setColumnCount(8)
self.tableWidget.setObjectName("tableWidget")
self.tableWidget.setRowCount(0)
item = QtWidgets.QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(0, item)
item = QtWidgets.QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(1, item)
item = QtWidgets.QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(2, item)
item = QtWidgets.QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(3, item)
item = QtWidgets.QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(4, item)
item = QtWidgets.QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(5, item)
item = QtWidgets.QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(6, item)
item = QtWidgets.QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(7, item)
self.plainTextEdit = QtWidgets.QPlainTextEdit(self.centralwidget)
self.plainTextEdit.setGeometry(QtCore.QRect(10, 760, 1051, 111))
self.plainTextEdit.setReadOnly(True)
self.plainTextEdit.setObjectName("plainTextEdit")
self.label_4 = QtWidgets.QLabel(self.centralwidget)
self.label_4.setGeometry(QtCore.QRect(490, 740, 60, 16))
self.label_4.setObjectName("label_4")
self.ImageBuffer = QtWidgets.QListWidget(self.centralwidget)
self.ImageBuffer.setGeometry(QtCore.QRect(220, 30, 251, 201))
self.ImageBuffer.setObjectName("ImageBuffer")
self.label_5 = QtWidgets.QLabel(self.centralwidget)
self.label_5.setGeometry(QtCore.QRect(300, 10, 91, 16))
self.label_5.setObjectName("label_5")
self.comboBox = QtWidgets.QComboBox(self.centralwidget)
self.comboBox.setGeometry(QtCore.QRect(260, 430, 141, 26))
self.comboBox.setObjectName("comboBox")
self.comboBox.addItem("")
self.comboBox.addItem("")
self.comboBox.addItem("")
self.comboBox.addItem("")
self.comboBox.addItem("")
self.comboBox.addItem("")
self.checkBox_fluo = QtWidgets.QCheckBox(self.centralwidget)
self.checkBox_fluo.setGeometry(QtCore.QRect(260, 400, 171, 20))
self.checkBox_fluo.setObjectName("checkBox_fluo")
self.label_6 = QtWidgets.QLabel(self.centralwidget)
self.label_6.setGeometry(QtCore.QRect(250, 470, 60, 16))
self.label_6.setObjectName("label_6")
self.label_7 = QtWidgets.QLabel(self.centralwidget)
self.label_7.setGeometry(QtCore.QRect(290, 240, 121, 16))
self.label_7.setObjectName("label_7")
self.verticalLayoutWidget_2 = QtWidgets.QWidget(self.centralwidget)
self.verticalLayoutWidget_2.setGeometry(QtCore.QRect(240, 260, 211, 134))
self.verticalLayoutWidget_2.setObjectName("verticalLayoutWidget_2")
self.verticalLayout_2 = QtWidgets.QVBoxLayout(self.verticalLayoutWidget_2)
self.verticalLayout_2.setContentsMargins(0, 0, 0, 0)
self.verticalLayout_2.setObjectName("verticalLayout_2")
self.Button_SetSAVparameters = QtWidgets.QPushButton(self.verticalLayoutWidget_2)
self.Button_SetSAVparameters.setObjectName("Button_SetSAVparameters")
self.verticalLayout_2.addWidget(self.Button_SetSAVparameters)
self.Button_RunVolumeImaging = QtWidgets.QPushButton(self.verticalLayoutWidget_2)
self.Button_RunVolumeImaging.setObjectName("Button_RunVolumeImaging")
self.verticalLayout_2.addWidget(self.Button_RunVolumeImaging)
self.Button_RunCustomProtocol = QtWidgets.QPushButton(self.verticalLayoutWidget_2)
self.Button_RunCustomProtocol.setObjectName("Button_RunCustomProtocol")
self.verticalLayout_2.addWidget(self.Button_RunCustomProtocol)
self.Button_RunCustomPatternfile = QtWidgets.QPushButton(self.verticalLayoutWidget_2)
self.Button_RunCustomPatternfile.setObjectName("Button_RunCustomPatternfile")
self.verticalLayout_2.addWidget(self.Button_RunCustomPatternfile)
MainWindow.setCentralWidget(self.centralwidget)
self.menubar = QtWidgets.QMenuBar(MainWindow)
self.menubar.setGeometry(QtCore.QRect(0, 0, 1070, 22))
self.menubar.setObjectName("menubar")
self.menuFile = QtWidgets.QMenu(self.menubar)
self.menuFile.setObjectName("menuFile")
self.menuTools = QtWidgets.QMenu(self.menubar)
self.menuTools.setObjectName("menuTools")
self.menuCorrelation = QtWidgets.QMenu(self.menubar)
self.menuCorrelation.setObjectName("menuCorrelation")
self.menuTesting = QtWidgets.QMenu(self.menubar)
self.menuTesting.setObjectName("menuTesting")
self.menuSettings = QtWidgets.QMenu(self.menubar)
self.menuSettings.setObjectName("menuSettings")
MainWindow.setMenuBar(self.menubar)
self.statusbar = QtWidgets.QStatusBar(MainWindow)
self.statusbar.setObjectName("statusbar")
MainWindow.setStatusBar(self.statusbar)
self.actionOpen = QtWidgets.QAction(MainWindow)
self.actionOpen.setObjectName("actionOpen")
self.actionClose = QtWidgets.QAction(MainWindow)
self.actionClose.setObjectName("actionClose")
self.actionSave_Session = QtWidgets.QAction(MainWindow)
self.actionSave_Session.setObjectName("actionSave_Session")
self.actionLoad_Session = QtWidgets.QAction(MainWindow)
self.actionLoad_Session.setObjectName("actionLoad_Session")
self.actionClose_2 = QtWidgets.QAction(MainWindow)
self.actionClose_2.setObjectName("actionClose_2")
self.actionOpen_Scripting = QtWidgets.QAction(MainWindow)
self.actionOpen_Scripting.setObjectName("actionOpen_Scripting")
self.actionScripting = QtWidgets.QAction(MainWindow)
self.actionScripting.setObjectName("actionScripting")
self.actionOpen_PatternDesigner = QtWidgets.QAction(MainWindow)
self.actionOpen_PatternDesigner.setObjectName("actionOpen_PatternDesigner")
self.actionCompute_FluoProjection = QtWidgets.QAction(MainWindow)
self.actionCompute_FluoProjection.setObjectName("actionCompute_FluoProjection")
self.actionLoad_Fluo_Projection = QtWidgets.QAction(MainWindow)
self.actionLoad_Fluo_Projection.setObjectName("actionLoad_Fluo_Projection")
self.actionLoad_Correlation_Images = QtWidgets.QAction(MainWindow)
self.actionLoad_Correlation_Images.setObjectName("actionLoad_Correlation_Images")
self.actionTestbutton1 = QtWidgets.QAction(MainWindow)
self.actionTestbutton1.setObjectName("actionTestbutton1")
self.actionTestbutton2 = QtWidgets.QAction(MainWindow)
self.actionTestbutton2.setObjectName("actionTestbutton2")
self.actionTestbutton3 = QtWidgets.QAction(MainWindow)
self.actionTestbutton3.setObjectName("actionTestbutton3")
self.actionTestbutton4 = QtWidgets.QAction(MainWindow)
self.actionTestbutton4.setObjectName("actionTestbutton4")
self.actionTestbutton5 = QtWidgets.QAction(MainWindow)
self.actionTestbutton5.setObjectName("actionTestbutton5")
self.actionSaveSettings = QtWidgets.QAction(MainWindow)
self.actionSaveSettings.setObjectName("actionSaveSettings")
self.actionLoadSettings = QtWidgets.QAction(MainWindow)
self.actionLoadSettings.setObjectName("actionLoadSettings")
self.actionVolumeDesigner = QtWidgets.QAction(MainWindow)
self.actionVolumeDesigner.setObjectName("actionVolumeDesigner")
self.actionLamellaDesigner = QtWidgets.QAction(MainWindow)
self.actionLamellaDesigner.setObjectName("actionLamellaDesigner")
self.actionSet_Output_Directory = QtWidgets.QAction(MainWindow)
self.actionSet_Output_Directory.setObjectName("actionSet_Output_Directory")
self.actionSet_SAV_parameters = QtWidgets.QAction(MainWindow)
self.actionSet_SAV_parameters.setObjectName("actionSet_SAV_parameters")
self.actionSet_Output_Directory_2 = QtWidgets.QAction(MainWindow)
self.actionSet_Output_Directory_2.setObjectName("actionSet_Output_Directory_2")
self.actionSet_Rough_Mill_protocol = QtWidgets.QAction(MainWindow)
self.actionSet_Rough_Mill_protocol.setObjectName("actionSet_Rough_Mill_protocol")
self.actionSet_Fine_Mill_protocol = QtWidgets.QAction(MainWindow)
self.actionSet_Fine_Mill_protocol.setObjectName("actionSet_Fine_Mill_protocol")
self.actionSet_Custom_Protocol = QtWidgets.QAction(MainWindow)
self.actionSet_Custom_Protocol.setObjectName("actionSet_Custom_Protocol")
self.actionSet_Custom_Milling = QtWidgets.QAction(MainWindow)
self.actionSet_Custom_Milling.setObjectName("actionSet_Custom_Milling")
self.menuFile.addAction(self.actionOpen)
self.menuFile.addAction(self.actionSave_Session)
self.menuFile.addAction(self.actionLoad_Session)
self.menuTools.addAction(self.actionLamellaDesigner)
self.menuTools.addAction(self.actionVolumeDesigner)
self.menuTools.addAction(self.actionOpen_PatternDesigner)
self.menuTools.addAction(self.actionScripting)
self.menuCorrelation.addAction(self.actionLoad_Correlation_Images)
self.menuCorrelation.addAction(self.actionCompute_FluoProjection)
self.menuCorrelation.addAction(self.actionLoad_Fluo_Projection)
self.menuTesting.addAction(self.actionTestbutton1)
self.menuTesting.addAction(self.actionTestbutton2)
self.menuTesting.addAction(self.actionTestbutton3)
self.menuTesting.addAction(self.actionTestbutton4)
self.menuTesting.addAction(self.actionTestbutton5)
self.menuSettings.addAction(self.actionSaveSettings)
self.menuSettings.addAction(self.actionLoadSettings)
self.menuSettings.addAction(self.actionSet_Output_Directory_2)
self.menuSettings.addAction(self.actionSet_SAV_parameters)
self.menuSettings.addAction(self.actionSet_Rough_Mill_protocol)
self.menuSettings.addAction(self.actionSet_Fine_Mill_protocol)
self.menuSettings.addAction(self.actionSet_Custom_Protocol)
self.menuSettings.addAction(self.actionSet_Custom_Milling)
self.menubar.addAction(self.menuFile.menuAction())
self.menubar.addAction(self.menuTools.menuAction())
self.menubar.addAction(self.menuCorrelation.menuAction())
self.menubar.addAction(self.menuSettings.menuAction())
self.menubar.addAction(self.menuTesting.menuAction())
#self.actionTestbutton3.triggered.connect(self.roughprotocol)
self.retranslateUi(MainWindow)
QtCore.QMetaObject.connectSlotsByName(MainWindow)
def retranslateUi(self, MainWindow):
'''
GUI Translate as created by pyuic5
'''
_translate = QtCore.QCoreApplication.translate
MainWindow.setWindowTitle(_translate("MainWindow", "Serial FIB"))
self.label.setText(_translate("MainWindow", "Lamellae"))
self.Button_AddPosition.setText(_translate("MainWindow", "Add Position"))
self.Button_SaveImageForAlignment.setText(_translate("MainWindow", "Save Image for Alignment"))
self.Button_SavePatterns.setText(_translate("MainWindow", "Save Patterns"))
self.Button_UpdateZ.setText(_translate("MainWindow", "Update Z"))
self.Button_GoToXYZ.setText(_translate("MainWindow", "Go To XYZ"))
self.Button_GoToXY.setText(_translate("MainWindow", "Go To XY"))
self.Button_DeleteItem.setText(_translate("MainWindow", "Delete Item"))
self.label_2.setText(_translate("MainWindow", "Main Functions"))
self.Button_SetOutputDirectory.setText(_translate("MainWindow", "Set Output Directory"))
self.Button_TakeImageIB.setText(_translate("MainWindow", "Take Image IB"))
self.Button_TakeImageEB.setText(_translate("MainWindow", "Take Image EB"))
self.Button_RunRoughProtocol.setText(_translate("MainWindow", "Run Rough Protocol"))
self.Button_RunFineProtocol.setText(_translate("MainWindow", "Run Fine Protocol"))
self.Button_RunTrenchMilling.setText(_translate("MainWindow", "Run Trench Milling"))
#self.Button_RunRoughMilling.setText(_translate("MainWindow", "Run Rough Milling"))
#self.Button_RunFineMilling.setText(_translate("MainWindow", "Run Fine Milling"))
self.Button_LoadCorrelationImages.setText(_translate("MainWindow", "Load Correlation Images"))
self.label_3.setText(_translate("MainWindow", "Alignment Image"))
item = self.tableWidget.horizontalHeaderItem(0)
item.setText(_translate("MainWindow", "Label"))
item = self.tableWidget.horizontalHeaderItem(1)
item.setText(_translate("MainWindow", "X"))
item = self.tableWidget.horizontalHeaderItem(2)
item.setText(_translate("MainWindow", "Y"))
item = self.tableWidget.horizontalHeaderItem(3)
item.setText(_translate("MainWindow", "Z"))
item = self.tableWidget.horizontalHeaderItem(4)
item.setText(_translate("MainWindow", "R"))
item = self.tableWidget.horizontalHeaderItem(5)
item.setText(_translate("MainWindow", "T"))
item = self.tableWidget.horizontalHeaderItem(6)
item.setText(_translate("MainWindow", "Alignment Image?"))
item = self.tableWidget.horizontalHeaderItem(7)
item.setText(_translate("MainWindow", "Patterns?"))
self.label_4.setText(_translate("MainWindow", "Error Log"))
self.label_5.setText(_translate("MainWindow", "Image Buffer"))
self.comboBox.setItemText(0, _translate("MainWindow", "green"))
self.comboBox.setItemText(1, _translate("MainWindow", "magenta"))
self.comboBox.setItemText(2, _translate("MainWindow", "cyan"))
self.comboBox.setItemText(3, _translate("MainWindow", "yellow"))
self.comboBox.setItemText(4, _translate("MainWindow", "red"))
self.comboBox.setItemText(5, _translate("MainWindow", "white"))
self.checkBox_fluo.setText(_translate("MainWindow", "Fluorescence Overlay"))
self.label_6.setText(_translate("MainWindow", "Positions"))
self.label_7.setText(_translate("MainWindow", "Custom Functions"))
self.Button_SetSAVparameters.setText(_translate("MainWindow", "Set SAV parameters"))
self.Button_RunVolumeImaging.setText(_translate("MainWindow", "Run Volume Imaging"))
self.Button_RunCustomProtocol.setText(_translate("MainWindow", "Run Custom Protocol"))
self.Button_RunCustomPatternfile.setText(_translate("MainWindow", "Run Custom Patternfile"))
self.menuFile.setTitle(_translate("MainWindow", "File"))
self.menuTools.setTitle(_translate("MainWindow", "Tools"))
self.menuCorrelation.setTitle(_translate("MainWindow", "Correlation"))
self.menuTesting.setTitle(_translate("MainWindow", "Testing"))
self.menuSettings.setTitle(_translate("MainWindow", "Settings"))
self.actionOpen.setText(_translate("MainWindow", "Open New"))
self.actionClose.setText(_translate("MainWindow", "Close"))
self.actionSave_Session.setText(_translate("MainWindow", "Save Session"))
self.actionLoad_Session.setText(_translate("MainWindow", "Load Session"))
self.actionClose_2.setText(_translate("MainWindow", "Close"))
self.actionOpen_Scripting.setText(_translate("MainWindow", "Open Scripting"))
self.actionScripting.setText(_translate("MainWindow", "ScriptEditor"))
self.actionOpen_PatternDesigner.setText(_translate("MainWindow", "PatternDesigner"))
self.actionCompute_FluoProjection.setText(_translate("MainWindow", "Compute FluoProjection"))
self.actionLoad_Fluo_Projection.setText(_translate("MainWindow", "Load Fluo Projection"))
self.actionLoad_Correlation_Images.setText(_translate("MainWindow", "Load Correlation Images"))
self.actionTestbutton1.setText(_translate("MainWindow", "Draw Corr Pattern"))
self.actionTestbutton2.setText(_translate("MainWindow", "Align to Image Buffer"))
self.actionTestbutton3.setText(_translate("MainWindow", "Change Alignment Current"))
self.actionTestbutton4.setText(_translate("MainWindow", "Testbutton4"))
self.actionTestbutton5.setText(_translate("MainWindow", "Testbutton5"))
self.actionSaveSettings.setText(_translate("MainWindow", "SaveSettings"))
self.actionLoadSettings.setText(_translate("MainWindow", "LoadSettings"))
self.actionVolumeDesigner.setText(_translate("MainWindow", "VolumeDesigner"))
self.actionLamellaDesigner.setText(_translate("MainWindow", "LamellaDesigner"))
self.actionSet_Output_Directory.setText(_translate("MainWindow", "Set Output Directory"))
self.actionSet_SAV_parameters.setText(_translate("MainWindow", "Set SAV parameters"))
self.actionSet_Output_Directory_2.setText(_translate("MainWindow", "Set Output Directory"))
self.actionSet_Rough_Mill_protocol.setText(_translate("MainWindow", "Set Rough Mill protocol"))
self.actionSet_Fine_Mill_protocol.setText(_translate("MainWindow", "Set Fine Mill protocol"))
self.actionSet_Custom_Protocol.setText(_translate("MainWindow", "Set Custom Protocol"))
self.actionSet_Custom_Milling.setText(_translate("MainWindow", "Set Custom Milling"))
##################################
#### BUTTON DEFINITIONS #########
##################################
# Testcase defintion
self.testCase=True
self.ktest=0
# IMAGE BUFFER DEFINE
self.ImageBufferImages=[]
#self.ImageBufferHandle=0
'''
Whenever an image from the image buffer is loaded by double clicking
saving of the patterns is triggered into the pattern_dict as well as
showInGraphview, which takes the current ImageBufferHandle as changed by
double clicking and load that image into the GraphView
'''
self.ImageBuffer.itemDoubleClicked.connect(self.savePatterns)
self.ImageBuffer.itemDoubleClicked.connect(self.showInGraphview)
self.pattern_root=""
'''
ShortCut definitions for deleting patterns and fullscreenmode
'''
#### Delete Option ####
self.shortcut_backspace = QtWidgets.QShortcut(QtGui.QKeySequence("Backspace"), MainWindow)
self.shortcut_backspace.activated.connect(self.pattern_delete)
self.shortcut_delete = QtWidgets.QShortcut(QtGui.QKeySequence("Del"), MainWindow)
self.shortcut_delete.activated.connect(self.pattern_delete)
self.shortcut_fullscreen_graphview=QtWidgets.QShortcut(QtCore.Qt.Key_F5,MainWindow)
self.shortcut_fullscreen_graphview.activated.connect(self.toggleFullScreen)
self.shortcut_F6=QtWidgets.QShortcut(QtCore.Qt.Key_F6,MainWindow)
self.shortcut_F6.activated.connect(self.key_F6)
self.shortcut_copy=QtWidgets.QShortcut(QtGui.QKeySequence("Ctrl+c"),MainWindow)
self.shortcut_copy.activated.connect(self.button_savePatterns)
self.shortcut_copy.activated.connect(self.copy_patterns)
self.shortcut_paste=QtWidgets.QShortcut(QtGui.QKeySequence("Ctrl+v"),MainWindow)
self.shortcut_paste.activated.connect(self.paste_patterns)
#TextLogger
sys.stdout = Stream(newText=self.onUpdateText)
'''
Button Definitions
'''
# Button_Add_Position
self.Button_AddPosition.pressed.connect(self.AddPosition)
self.Button_AddPosition.pressed.connect(self.addRow)
# Button_DeleteItem
self.Button_DeleteItem.pressed.connect(self.removeRow)
# Button_GoToXYZ
self.Button_GoToXYZ.pressed.connect(self.GoToXYZ)
# Button_GoToXY
self.Button_GoToXY.pressed.connect(self.GoToXY)
# Button Take Image IB
self.Button_TakeImageIB.pressed.connect(self.button_savePatterns)
self.Button_TakeImageIB.pressed.connect(self.button_take_image_IB)
# Button Take Image EB
self.Button_TakeImageEB.pressed.connect(self.button_take_image_EB)
# Button Save Image for Alignment
self.Button_SaveImageForAlignment.pressed.connect(self.SaveImageForAlignment)
# Button Save Patterns
self.Button_SavePatterns.pressed.connect(self.button_savePatterns)
# Button Load Correlated Image
self.Button_LoadCorrelationImages.pressed.connect(self.load_correlated_image)
# Button Set Output Directory
self.Button_SetOutputDirectory.pressed.connect(self.define_directory)
self.Button_UpdateZ.pressed.connect(self.UpdateZ)
self.Button_SetSAVparameters.pressed.connect(self.define_SAVparams)
# Thread based implementations Button definition
self.Button_RunRoughProtocol.pressed.connect(self.roughprotocol)
self.Button_RunFineProtocol.pressed.connect(self.fineprotocol)
self.Button_RunVolumeImaging.pressed.connect(self.volumeimaging)
self.Button_RunCustomProtocol.pressed.connect(self.customprotocol)
self.Button_RunTrenchMilling.pressed.connect(self.trenchmill)
self.Button_RunCustomPatternfile.pressed.connect(self.custompatternfilerun)
'''
File Tab
'''
# Button Save Session
self.actionSave_Session.triggered.connect(self.save_session)
# Button Load Session
self.actionLoad_Session.triggered.connect(self.load_session)
# Button New Session
self.actionOpen.triggered.connect(self.new_session)
'''
Tools Tab
'''
# Button Open Scripting
self.actionScripting.triggered.connect(self.open_scripting)
# Button Open PatternEditor
self.actionOpen_PatternDesigner.triggered.connect(self.open_patterneditor)
self.actionVolumeDesigner.triggered.connect(self.open_volumedesigner)
self.actionLamellaDesigner.triggered.connect(self.open_lamelladesigner)
'''
Fluorescence Tab
'''
self.actionLoad_Correlation_Images.triggered.connect(self.load_correlated_image)
self.actionCompute_FluoProjection.triggered.connect(self.compute_fluo_proj)
self.actionLoad_Fluo_Projection.triggered.connect(self.load_fluo_proj)
self.checkBox_fluo.stateChanged.connect(self.overlay_fluo)
self.comboBox.currentIndexChanged.connect(self.overlay_fluo)
'''
Settings Tab
'''
self.actionSet_Output_Directory.triggered.connect(self.define_directory)
self.actionSet_Output_Directory_2.triggered.connect(self.define_directory)
self.actionSet_SAV_parameters.triggered.connect(self.define_SAVparams)
self.actionSet_Rough_Mill_protocol.triggered.connect(self.define_roughmillprotocol)
self.actionSet_Fine_Mill_protocol.triggered.connect(self.define_finemillprotocol)
self.actionSet_Custom_Protocol.triggered.connect(self.define_custommillprotocol)
self.actionSet_Custom_Milling.triggered.connect(self.define_custompatternfile)
self.actionSaveSettings.triggered.connect(self.save_settings)
self.actionLoadSettings.triggered.connect(self.load_settings)
'''
TestButtons
'''
# Button for Testing
self.actionTestbutton1.triggered.connect(self.draw_corr_pattern)
self.actionTestbutton2.triggered.connect(self.align_to_item)
self.actionTestbutton3.triggered.connect(self.set_alignment_current)
#### Graphics Viewer
self.graphicsView.aspectRatioMode = QtCore.Qt.KeepAspectRatio
##################################
# CODE:Button_take_image_IB #
##################################
def button_take_image_IB(self):
'''
Button to take an image at current mag etc. using the ion beam
Uses the driver function take_image_IB()
Input: None
Output: None
Action: Addition of image to ImageBuffer, showing Image in GraphicsView
'''
# ImageBufferHandle is set to the last image as given by the amount of images in the ImageBuffer
self.ImageBufferHandle=self.ImageBuffer.count()
# Image is taken using the Driver function and added as last element in the ImageBuffer
img=scope.take_image_IB()
numRows = self.ImageBuffer.count()
self.ImageBuffer.addItem(str(numRows) + " (IB Image)")
# Image Scene is grabed in order to set a new scene in the GraphicsView
scene=self.get_scene()
scene.clear()
self.graphicsView.setScene(scene)
# Check if image was taken, else add testimage
if self.testCase==True:
self.ktest=self.ktest+1
if img==():
if self.ktest%2==0:
array=testimage.data
self.ImageBufferImages.append(testimage)
else:
array=testimage2.data
self.ImageBufferImages.append(testimage2)
#print("Bla")
else:
array=img.data
self.ImageBufferImages.append(img)
else:
if img==():
print("No Microscope connected!")
return()
else:
array=img.data
self.ImageBufferImages.append(img)
### Convert 16 bit image to 8 bit to show it in the GraphicsView
array8u=cv2.convertScaleAbs(array, alpha=(255.0/65535.0))
img_8bit=np.uint8(array)
height,width=np.shape(img_8bit)
qImg=QtGui.QImage(img_8bit, width, height, QtGui.QImage.Format_Grayscale8)
pixmapImg=QtGui.QPixmap.fromImage(qImg)
# Set scene size to image size.
self.graphicsView.setSceneRect(QtCore.QRectF(pixmapImg.rect()))
self.graphicsView.fitInView(self.graphicsView.sceneRect(),self.graphicsView.aspectRatioMode)
w2=self.graphicsView.sceneRect().width()
h2=self.graphicsView.sceneRect().height()
#Add Image as pixmap to scene
scene.addPixmap(pixmapImg)
# Update SceneBuffer
self.scene=scene
self.sceneBuffer.append(self.scene)
# New Image cannot have fluorescence information, thus set checkBox to false
self.checkBox_fluo.setChecked(False)
# Adjust ImageBufferHandle to new Image
self.ImageBufferHandle=self.ImageBuffer.count()+1
return()
##################################
# /CODE:Button_take_image_IB #
##################################
def load_images(self,image):
'''
Same Setup as take_image_IB only that an image is loaded from a file
Input: Image as .tif
Output: None
Action: Addition of image to ImageBuffer, showing Image in GraphicsView
'''
numRows = self.ImageBuffer.count()
self.ImageBuffer.addItem(str(numRows) + " (IB Image)")
scene=self.get_scene()
scene.clear()
self.graphicsView.setScene(scene)
# Check if image was taken, else add testimage
if image==():
print("No Microscope connected!")
return()
else:
array=image.data
self.ImageBufferImages.append(image)
### Convert 16 bit image to 8 bit to show it in the GrahpicsView
array8u=cv2.convertScaleAbs(array, alpha=(255.0/65535.0))
img_8bit=np.uint8(array)
height,width=np.shape(img_8bit)
qImg=QtGui.QImage(img_8bit, width, height, QtGui.QImage.Format_Grayscale8)
pixmapImg=QtGui.QPixmap.fromImage(qImg)
# Set scene size to image size.
self.graphicsView.setSceneRect(QtCore.QRectF(pixmapImg.rect()))
self.graphicsView.fitInView(self.graphicsView.sceneRect(),self.graphicsView.aspectRatioMode)
w2=self.graphicsView.sceneRect().width()
h2=self.graphicsView.sceneRect().height()
#Add Image as pixmap to scene
scene.addPixmap(pixmapImg)
# Update SceneBuffer
self.scene=scene
self.sceneBuffer.append(self.scene)
# New Image cannot have fluorescence information, thus set checkBox to false
self.checkBox_fluo.setChecked(False)
return()
##################################
# CODE:Button_take_image_EB #
##################################
def button_take_image_EB(self):
'''
Button to take an image at current mag etc. using the electron beam
Uses the driver function take_image_EB()
Input: None
Output: None
Action: Addition of image to ImageBuffer, showing Image in GraphicsView
'''
img=scope.take_image_EB()
numRows = self.ImageBuffer.count()
self.ImageBuffer.addItem(str(numRows) + " (EB Image)")
scene=self.get_scene()
scene.clear()
self.graphicsView.setScene(scene)
self.ImageBufferHandle=numRows
# Check if image was taken, else add testimage
if self.testCase==True:
self.ktest=self.ktest+1
if img==():
if self.ktest%2==0:
array=testimage.data
self.ImageBufferImages.append(testimage)
else:
array=testimage2.data
self.ImageBufferImages.append(testimage2)
else:
array=img.data
self.ImageBufferImages.append(img)
else:
if img==():
print("No Microscope connected!")
return()
else:
array=img.data
self.ImageBufferImages.append(img)
### Convert 16 bit image to 8 bit to show it in the GrahpicsView
array8u=cv2.convertScaleAbs(array, alpha=(255.0/65535.0))
img_8bit=np.uint8(array)
height,width=np.shape(img_8bit)
qImg=QtGui.QImage(img_8bit, width, height, QtGui.QImage.Format_Grayscale8)
pixmapImg=QtGui.QPixmap.fromImage(qImg)
# Set scene size to image size.
self.graphicsView.setSceneRect(QtCore.QRectF(pixmapImg.rect()))
self.graphicsView.fitInView(self.graphicsView.sceneRect(),self.graphicsView.aspectRatioMode)
#Add Image as pixmap to scene
scene.addPixmap(pixmapImg)
# Update SceneBuffer
self.scene=scene
self.sceneBuffer.append(self.scene)
self.checkBox_fluo.setChecked(False)
return()
##################################
# /CODE:Button_take_image_EB #
##################################
##################################
# CODE:Button_run_rough_mill #
##################################
def Signal_Done(self,result):
print("Result: "+result)
self.progressDialog.close()
return()
def showInGraphview(self):
#self.savePatterns()
try:
number=self.ImageBuffer.currentItem().text().split(" ")[0]
except:
number=0