def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
os.chdir('./') # Set directory to current folder.
self.setFont(QFont("Arial"))
# self.setMinimumSize(900, 1020)
self.setWindowTitle("Screening Analysis")
self.layout = QGridLayout(self)
self.popnexttopimgcounter = 0
self.Tag_round_infor = []
self.Lib_round_infor = []
#**************************************************************************************************************************************
#-----------------------------------------------------------GUI for Billboard display------------------------------------------------------
#**************************************************************************************************************************************
ImageDisplayContainer = QGroupBox("Billboard")
ImageDisplayContainerLayout = QGridLayout()
self.GraphyDisplayTab = QTabWidget()
#----------------------------------------------------------------------
MatDsiplayPart = QWidget()
MatDsiplayPart.layout = QGridLayout()
# a figure instance to plot on
self.Matdisplay_Figure = Figure()
self.Matdisplay_Canvas = FigureCanvas(self.Matdisplay_Figure)
self.Matdisplay_toolbar = NavigationToolbar(self.Matdisplay_Canvas,
self)
MatDsiplayPart.layout.addWidget(self.Matdisplay_toolbar, 0, 0)
MatDsiplayPart.layout.addWidget(self.Matdisplay_Canvas, 1, 0)
MatDsiplayPart.setLayout(MatDsiplayPart.layout)
self.OriginalImgWidget = pg.ImageView()
self.OriginalImg_item = self.OriginalImgWidget.getImageItem(
) #setLevels
self.OriginalImg_view = self.OriginalImgWidget.getView()
self.OriginalImg_item.setAutoDownsample(True)
self.OriginalImgWidget.ui.roiBtn.hide()
self.OriginalImgWidget.ui.menuBtn.hide()
self.OriginalImgWidget.ui.normGroup.hide()
self.OriginalImgWidget.ui.roiPlot.hide()
self.GraphyDisplayTab.addTab(self.OriginalImgWidget, "Image loaded")
self.GraphyDisplayTab.addTab(MatDsiplayPart, "Scatter")
ImageDisplayContainerLayout.addWidget(self.GraphyDisplayTab, 1, 1)
#----------------------------------------------------------------------
ImageButtonContainer = QGroupBox()
ImageButtonContainerLayout = QGridLayout()
ButtonRankResetCoordImg = QPushButton('Reset coord', self)
ButtonRankResetCoordImg.clicked.connect(self.ResetRankCoord)
ImageButtonContainerLayout.addWidget(ButtonRankResetCoordImg, 0, 6)
ButtonRankPreviousCoordImg = QPushButton('Previous', self)
ButtonRankPreviousCoordImg.setShortcut('a')
ButtonRankPreviousCoordImg.clicked.connect(
lambda: self.GoThroughTopCells('previous'))
ImageButtonContainerLayout.addWidget(ButtonRankPreviousCoordImg, 1, 6)
self.ButtonShowInScatter = QPushButton('Show in scatter', self)
self.ButtonShowInScatter.setShortcut('s')
self.ButtonShowInScatter.setCheckable(True)
self.ButtonShowInScatter.clicked.connect(self.ShowScatterPos)
ImageButtonContainerLayout.addWidget(self.ButtonShowInScatter, 2, 6)
ButtonRankNextCoordImg = QPushButton('Next', self)
ButtonRankNextCoordImg.setShortcut('d')
ButtonRankNextCoordImg.clicked.connect(
lambda: self.GoThroughTopCells('next'))
ImageButtonContainerLayout.addWidget(ButtonRankNextCoordImg, 1, 7)
GoSeqButton = QPushButton('Go to IDNumber: ', self)
GoSeqButton.clicked.connect(self.GotoSequence)
ImageButtonContainerLayout.addWidget(GoSeqButton, 3, 6)
self.ShowSequenceScatterButton = QPushButton('Show this in scatter',
self)
self.ShowSequenceScatterButton.setCheckable(True)
self.ShowSequenceScatterButton.clicked.connect(
self.ShowSequenceScatter)
ImageButtonContainerLayout.addWidget(self.ShowSequenceScatterButton, 3,
8)
self.CellSequenceBox = QSpinBox(self)
self.CellSequenceBox.setMaximum(9000)
self.CellSequenceBox.setValue(0)
self.CellSequenceBox.setSingleStep(1)
ImageButtonContainerLayout.addWidget(self.CellSequenceBox, 3, 7)
ButtonRankDeleteFromList = QPushButton('Delete', self)
ButtonRankDeleteFromList.clicked.connect(self.DeleteFromTopCells)
ImageButtonContainerLayout.addWidget(ButtonRankDeleteFromList, 2, 7)
ButtonRankSaveList = QPushButton('Save array', self)
ButtonRankSaveList.clicked.connect(self.SaveCellsProArray)
ImageButtonContainerLayout.addWidget(ButtonRankSaveList, 4, 6)
self.ConsoleTextDisplay = QTextEdit()
self.ConsoleTextDisplay.setFontItalic(True)
self.ConsoleTextDisplay.setPlaceholderText(
'Notice board from console.')
self.ConsoleTextDisplay.setMaximumHeight(300)
ImageButtonContainerLayout.addWidget(self.ConsoleTextDisplay, 5, 6, 3,
2)
ImageButtonContainer.setLayout(ImageButtonContainerLayout)
ImageDisplayContainer.setLayout(ImageDisplayContainerLayout)
ImageDisplayContainer.setMinimumHeight(700)
ImageDisplayContainer.setMinimumWidth(700)
self.layout.addWidget(ImageDisplayContainer, 0, 0, 2, 2)
self.layout.addWidget(ImageButtonContainer, 0, 2)
#**************************************************************************************************************************************
#-----------------------------------------------------------GUI for Image processing settings------------------------------------------
#**************************************************************************************************************************************
self.PostProcessTab = QTabWidget()
self.PostProcessTab.setMaximumWidth(400)
self.PostProcessTab.setFixedHeight(250)
ImageProcessingContainer = QGroupBox()
IPLayout = QGridLayout()
self.IPsizetextbox = QSpinBox(self)
self.IPsizetextbox.setMaximum(2000)
self.IPsizetextbox.setValue(800)
self.IPsizetextbox.setSingleStep(1)
IPLayout.addWidget(self.IPsizetextbox, 1, 7)
IPLayout.addWidget(QLabel("Cell smallest size:"), 1, 6)
self.opening_factorBox = QSpinBox(self)
self.opening_factorBox.setMaximum(2000)
self.opening_factorBox.setValue(2)
self.opening_factorBox.setSingleStep(1)
IPLayout.addWidget(self.opening_factorBox, 2, 5)
IPLayout.addWidget(QLabel("Mask opening factor:"), 2, 4)
self.closing_factorBox = QSpinBox(self)
self.closing_factorBox.setMaximum(2000)
self.closing_factorBox.setValue(3)
self.closing_factorBox.setSingleStep(1)
IPLayout.addWidget(self.closing_factorBox, 2, 7)
IPLayout.addWidget(QLabel("Mask closing factor:"), 2, 6)
self.binary_adaptive_block_sizeBox = QSpinBox(self)
self.binary_adaptive_block_sizeBox.setMaximum(2000)
self.binary_adaptive_block_sizeBox.setValue(335)
self.binary_adaptive_block_sizeBox.setSingleStep(50)
IPLayout.addWidget(self.binary_adaptive_block_sizeBox, 1, 1)
IPLayout.addWidget(QLabel("Adaptive mask size:"), 1, 0)
self.contour_dilation_box = QSpinBox(self)
self.contour_dilation_box.setMaximum(2000)
self.contour_dilation_box.setValue(11)
self.contour_dilation_box.setSingleStep(1)
IPLayout.addWidget(self.contour_dilation_box, 1, 3)
IPLayout.addWidget(QLabel("Contour thickness:"), 1, 2)
IPLayout.addWidget(QLabel("Threshold-contour:"), 1, 4)
self.find_contour_thres_box = QDoubleSpinBox(self)
self.find_contour_thres_box.setDecimals(4)
self.find_contour_thres_box.setMinimum(-10)
self.find_contour_thres_box.setMaximum(10)
self.find_contour_thres_box.setValue(0.001)
self.find_contour_thres_box.setSingleStep(0.0001)
IPLayout.addWidget(self.find_contour_thres_box, 1, 5)
self.cellopening_factorBox = QSpinBox(self)
self.cellopening_factorBox.setMaximum(2000)
self.cellopening_factorBox.setValue(1)
self.cellopening_factorBox.setSingleStep(1)
IPLayout.addWidget(self.cellopening_factorBox, 2, 1)
IPLayout.addWidget(QLabel("Cell opening factor:"), 2, 0)
self.cellclosing_factorBox = QSpinBox(self)
self.cellclosing_factorBox.setMaximum(20000)
self.cellclosing_factorBox.setValue(2)
self.cellclosing_factorBox.setSingleStep(1)
IPLayout.addWidget(self.cellclosing_factorBox, 2, 3)
IPLayout.addWidget(QLabel("Cell closing factor:"), 2, 2)
ImageProcessingContainer.setLayout(IPLayout)
#---------------------------Loading------------------------------------
LoadSettingContainer = QGroupBox()
LoadSettingLayout = QGridLayout()
self.FilepathSwitchBox = QComboBox()
self.FilepathSwitchBox.addItems(['Tag', 'Lib', 'All'])
LoadSettingLayout.addWidget(self.FilepathSwitchBox, 0, 0)
self.AnalysisRoundBox = QSpinBox(self)
self.AnalysisRoundBox.setMaximum(2000)
self.AnalysisRoundBox.setValue(1)
self.AnalysisRoundBox.setSingleStep(1)
LoadSettingLayout.addWidget(self.AnalysisRoundBox, 0, 2)
self.AddAnalysisRoundButton = QtWidgets.QPushButton('Add Round:')
self.AddAnalysisRoundButton.clicked.connect(self.SetAnalysisRound)
LoadSettingLayout.addWidget(self.AddAnalysisRoundButton, 0, 1)
self.datasavedirectorytextbox = QLineEdit(self)
self.datasavedirectorytextbox.setPlaceholderText('Data directory')
LoadSettingLayout.addWidget(self.datasavedirectorytextbox, 1, 0, 1, 2)
self.toolButtonOpenDialog = QtWidgets.QPushButton('Set path')
self.toolButtonOpenDialog.clicked.connect(self.SetAnalysisPath)
LoadSettingLayout.addWidget(self.toolButtonOpenDialog, 1, 2)
ExecuteAnalysisButton = QPushButton('Load images', self)
# ExecuteAnalysisButton.setObjectName('Startbutton')
ExecuteAnalysisButton.clicked.connect(
lambda: self.StartScreeningAnalysisThread())
LoadSettingLayout.addWidget(ExecuteAnalysisButton, 2, 1)
self.ClearAnalysisInforButton = QtWidgets.QPushButton('Clear infor')
self.ClearAnalysisInforButton.clicked.connect(self.ClearAnalysisInfor)
LoadSettingLayout.addWidget(self.ClearAnalysisInforButton, 2, 2)
LoadSettingContainer.setLayout(LoadSettingLayout)
#**************************************************************************************************************************************
#-----------------------------------------------------------GUI for Selection settings Container---------------------------------------
#**************************************************************************************************************************************
SelectionsettingTab = QWidget()
SelectionsettingTab.layout = QGridLayout()
self.SeleParaBox = QComboBox()
self.SeleParaBox.addItems(
['Mean intensity divided by tag/Contour soma ratio'])
SelectionsettingTab.layout.addWidget(self.SeleParaBox, 0, 2)
SelectionsettingTab.layout.addWidget(QLabel('Scatter axes'), 0, 1)
self.AnalysisTypeSwitchBox = QComboBox()
self.AnalysisTypeSwitchBox.addItems(['Brightness screening', 'Lib'])
SelectionsettingTab.layout.addWidget(self.AnalysisTypeSwitchBox, 0, 0)
UpdateProcessTab = QTabWidget()
UpdateProcessTab.layout = QGridLayout()
UpdateProcessTab_1 = QWidget()
UpdateProcessTab_1.layout = QGridLayout()
UpdateProcessTab_1.layout.addWidget(QLabel("Selection boundary:"), 0,
0)
self.Selection_boundaryBox = QComboBox()
self.Selection_boundaryBox.addItems(['Circular radius', 'Rank'])
UpdateProcessTab_1.layout.addWidget(self.Selection_boundaryBox, 0, 1)
UpdateScattersButton = QtWidgets.QPushButton('Update scatters')
UpdateScattersButton.clicked.connect(self.UpdateSelectionScatter)
UpdateProcessTab_1.layout.addWidget(UpdateScattersButton, 0, 4)
UpdateProcessTab_2 = QWidget()
UpdateProcessTab_2.layout = QGridLayout()
self.WeightBoxSelectionFactor_1 = QDoubleSpinBox(self)
self.WeightBoxSelectionFactor_1.setDecimals(2)
self.WeightBoxSelectionFactor_1.setMinimum(0)
self.WeightBoxSelectionFactor_1.setMaximum(1)
self.WeightBoxSelectionFactor_1.setValue(1)
self.WeightBoxSelectionFactor_1.setSingleStep(0.1)
UpdateProcessTab_2.layout.addWidget(self.WeightBoxSelectionFactor_1, 0,
1)
UpdateProcessTab_2.layout.addWidget(QLabel("Axis 1:"), 0, 0)
self.WeightBoxSelectionFactor_2 = QDoubleSpinBox(self)
self.WeightBoxSelectionFactor_2.setDecimals(2)
self.WeightBoxSelectionFactor_2.setMinimum(0)
self.WeightBoxSelectionFactor_2.setMaximum(1)
self.WeightBoxSelectionFactor_2.setValue(0.5)
self.WeightBoxSelectionFactor_2.setSingleStep(0.1)
UpdateProcessTab_2.layout.addWidget(self.WeightBoxSelectionFactor_2, 0,
3)
UpdateProcessTab_2.layout.addWidget(QLabel("Axis 2:"), 0, 2)
self.WeightBoxSelectionFactor_3 = QDoubleSpinBox(self)
self.WeightBoxSelectionFactor_3.setDecimals(2)
self.WeightBoxSelectionFactor_3.setMinimum(0)
self.WeightBoxSelectionFactor_3.setMaximum(1)
self.WeightBoxSelectionFactor_3.setValue(1)
self.WeightBoxSelectionFactor_3.setSingleStep(0.1)
UpdateProcessTab_2.layout.addWidget(self.WeightBoxSelectionFactor_3, 0,
5)
UpdateProcessTab_2.layout.addWidget(QLabel("Axis 3:"), 0, 4)
SelectionthresholdsettingTab = QWidget()
SelectionthresholdsettingTab.layout = QGridLayout()
SelectionthresholdsettingTab.layout.addWidget(
QLabel("Intensity threshold:"), 0, 0)
self.SelectionMeanInten_thres_box = QDoubleSpinBox(self)
self.SelectionMeanInten_thres_box.setDecimals(4)
self.SelectionMeanInten_thres_box.setMinimum(0)
self.SelectionMeanInten_thres_box.setMaximum(10)
self.SelectionMeanInten_thres_box.setValue(0.150)
self.SelectionMeanInten_thres_box.setSingleStep(0.0001)
SelectionthresholdsettingTab.layout.addWidget(
self.SelectionMeanInten_thres_box, 0, 1)
SelectionthresholdsettingTab.layout.addWidget(
QLabel("Contour/Soma threshold:"), 1, 0)
self.SelectionCSratio_thres_box = QDoubleSpinBox(self)
self.SelectionCSratio_thres_box.setDecimals(3)
self.SelectionCSratio_thres_box.setMinimum(0)
self.SelectionCSratio_thres_box.setMaximum(10)
self.SelectionCSratio_thres_box.setValue(0.80)
self.SelectionCSratio_thres_box.setSingleStep(0.0001)
SelectionthresholdsettingTab.layout.addWidget(
self.SelectionCSratio_thres_box, 1, 1)
SelectionthresholdsettingTab.layout.addWidget(
QLabel("Roundness threshold:"), 0, 2)
self.SelectionRoundness_thres_box = QDoubleSpinBox(self)
self.SelectionRoundness_thres_box.setDecimals(3)
self.SelectionRoundness_thres_box.setMinimum(0)
self.SelectionRoundness_thres_box.setMaximum(10)
self.SelectionRoundness_thres_box.setValue(1.10)
self.SelectionRoundness_thres_box.setSingleStep(0.0001)
SelectionthresholdsettingTab.layout.addWidget(
self.SelectionRoundness_thres_box, 0, 3)
SelectionthresholdsettingTab.setLayout(
SelectionthresholdsettingTab.layout)
UpdateProcessTab_2.layout.addWidget(SelectionthresholdsettingTab, 1, 0,
1, 6)
UpdateProcessTab_1.setLayout(UpdateProcessTab_1.layout)
UpdateProcessTab_2.setLayout(UpdateProcessTab_2.layout)
UpdateProcessTab.addTab(UpdateProcessTab_1, "Normalized distance")
UpdateProcessTab.addTab(UpdateProcessTab_2, "Axes weights")
SelectionsettingTab.layout.addWidget(UpdateProcessTab, 1, 0, 4, 3)
SelectionsettingTab.setLayout(SelectionsettingTab.layout)
#**************************************************************************************************************************************
#-----------------------------------------------------------GUI for Selection threshold settings---------------------------------------
#**************************************************************************************************************************************
self.PostProcessTab.addTab(LoadSettingContainer, "Loading settings")
self.PostProcessTab.addTab(SelectionsettingTab, "Analysis selection")
self.PostProcessTab.addTab(ImageProcessingContainer,
"Image analysis settings")
self.layout.addWidget(self.PostProcessTab, 1, 2)
self.setLayout(self.layout)
