def createStatisticsDisplay(self, parentWidget):
# Generate the widget
self.statisticsWidget = qtw.QWidget()
self.statisticsLayout = qtw.QVBoxLayout(self.statisticsWidget)
# Populate all the informations
self.statisticsGridWidget = qtw.QWidget()
self.statisticsGridLayout = qtw.QGridLayout(self.statisticsGridWidget)
# Mean PV
current_row = 0
self.statisticsGridLayout.addWidget( CLabel('Mean PV:'), current_row, 0)
self.meanValueLabel = qtw.QLabel()
self.statisticsGridLayout.addWidget( self.meanValueLabel, current_row, 1)
# Standard Deviation
current_row += 1
self.statisticsGridLayout.addWidget( CLabel('St. Dev.:'), current_row, 0)
self.standardDeviationLabel = qtw.QLabel()
self.statisticsGridLayout.addWidget( self.standardDeviationLabel, current_row, 1)
# Standard Deviation
current_row += 1
self.statisticsGridLayout.addWidget( CLabel('Variations:'), current_row, 0)
self.variationsLabel = qtw.QLabel()
self.statisticsGridLayout.addWidget( self.variationsLabel, current_row, 1)
self.statisticsGridWidget.setLayout(self.statisticsGridLayout)
self.statisticsLayout.addWidget( self.statisticsGridWidget, alignment=qtc.Qt.AlignLeft)
# Display the widget
self.statisticsWidget.setLayout(self.statisticsLayout)
parentWidget.addWidget(self.statisticsWidget)
def populateGeneral(self):
# Metadata type
if self.data_type == 'experiment':
_metadata_type = 'EXPERIMENT'
_, _file_name = os.path.split(self.file_path)
elif self.data_type == 'fast_record':
_metadata_type = 'FAST RECORD'
_file_name, _ = os.path.split(self.file_path)
_, _file_name = os.path.split(_file_name)
self.generalInfosLayout.addWidget(CLabel(_metadata_type),
alignment=qtc.Qt.AlignCenter)
self.generalInfosLayout.addWidget(qtw.QLabel(_file_name),
alignment=qtc.Qt.AlignCenter)
# Populate all the informations
self.generalGridWidget = qtw.QWidget()
self.generalGridLayout = qtw.QGridLayout(self.generalGridWidget)
for i, name in enumerate(self.data_general.keys()):
# Name of the section
self.generalGridLayout.addWidget(CLabel(name), i, 0)
# Value of the section
crt_value = qtw.QLabel(self.data_general[name])
self.generalGridLayout.addWidget(crt_value, i, 1)
self.generalGridWidget.setLayout(self.generalGridLayout)
self.generalInfosLayout.addWidget(self.generalGridWidget,
alignment=qtc.Qt.AlignLeft)
def createInformationDisplay(self, parentWidget):
# Generate the widget
self.infoDisplayWidget = qtw.QWidget()
self.infoDisplayLayout = qtw.QGridLayout(self.infoDisplayWidget)
# Display the total number of frames
current_row = 0
self.infoDisplayLayout.addWidget(CLabel("Total # frames:"),
current_row, 0)
self.infoDisplayLayout.addWidget(qtw.QLabel(str(self.max_n)),
current_row, 1)
# Display the final number of frames after average
current_row += 1
self.infoDisplayLayout.addWidget(CLabel("# frames after averaging:"),
current_row, 0)
self.frameAfterLabel = qtw.QLabel("")
self.infoDisplayLayout.addWidget(self.frameAfterLabel, current_row, 1)
# Display the final number of frames after average
current_row += 1
self.infoDisplayLayout.addWidget(CLabel("# frames lost:"), current_row,
0)
self.frameLostLabel = qtw.QLabel("")
self.infoDisplayLayout.addWidget(self.frameLostLabel, current_row, 1)
# Display the widget
self.infoDisplayWidget.setLayout(self.infoDisplayLayout)
parentWidget.addWidget(self.infoDisplayWidget,
alignment=qtc.Qt.AlignLeft)
def createResultDisplay(self, parentWidget):
# Generate the widget
self.resultDisplayWidget = qtw.QWidget()
self.resultDisplayLayout = qtw.QGridLayout(self.resultDisplayWidget)
current_row = 0
self.resultDisplayLayout.addWidget(CLabel('RESULTS'), current_row, 0,
1, 2)
# Contrast
current_row += 1
self.resultDisplayLayout.addWidget(CLabel('- Contrast:'), current_row,
0)
self.contrastLabel = qtw.QLabel("")
self.resultDisplayLayout.addWidget(self.contrastLabel, current_row, 1)
# Signal-to-noise ratio
current_row += 1
self.resultDisplayLayout.addWidget(CLabel('- SNR:'), current_row, 0)
self.snrLabel = qtw.QLabel("")
self.resultDisplayLayout.addWidget(self.snrLabel, current_row, 1)
# Noise
current_row += 1
self.resultDisplayLayout.addWidget(CLabel('- Noise:'), current_row, 0)
self.noiseLabel = qtw.QLabel("")
self.resultDisplayLayout.addWidget(self.noiseLabel, current_row, 1)
# Display the widget
self.resultDisplayWidget.setLayout(self.resultDisplayLayout)
parentWidget.addWidget(self.resultDisplayWidget,
alignment=qtc.Qt.AlignLeft)
def createScaleSettings(self, parentWidget):
# Generate the widget
self.scaleSettingsWidget = qtw.QWidget()
self.scaleSettingsLayout = qtw.QGridLayout(self.scaleSettingsWidget)
# Label for space scale
current_row = 0
self.scaleSettingsLayout.addWidget(CLabel("Space Scale:"), current_row,
0, 1, 2)
# Entry for the distance in pixel
current_row += 1
self.scaleSettingsLayout.addWidget(qtw.QLabel("Distance in pixels"),
current_row, 0)
self.pixelDistanceEntry = qtw.QLineEdit()
self.pixelDistanceEntry.setText(str(
self.image_class.scale.space_scale))
self.scaleSettingsLayout.addWidget(self.pixelDistanceEntry,
current_row, 1)
# Entry for the real distance
current_row += 1
self.scaleSettingsLayout.addWidget(qtw.QLabel("Known distance"),
current_row, 0)
self.knownDistanceEntry = qtw.QLineEdit()
self.knownDistanceEntry.setText("1")
self.scaleSettingsLayout.addWidget(self.knownDistanceEntry,
current_row, 1)
# Entry for the length unit
current_row += 1
self.scaleSettingsLayout.addWidget(qtw.QLabel("Unit of length"),
current_row, 0)
self.lengthUnitEntry = qtw.QLineEdit()
self.lengthUnitEntry.setText(self.image_class.scale.space_unit)
self.scaleSettingsLayout.addWidget(self.lengthUnitEntry, current_row,
1)
current_row += 1
self.scaleSettingsLayout.addWidget(CHorizontalSeparator(), current_row,
0, 1, 2)
# Label for time scale
current_row += 1
self.scaleSettingsLayout.addWidget(CLabel("Time Scale:"), current_row,
0, 1, 2)
# Entry for the length unit
current_row += 1
self.scaleSettingsLayout.addWidget(qtw.QLabel("Frame rate"),
current_row, 0)
self.frameRateEntry = qtw.QLineEdit()
self.frameRateEntry.setText(str(self.image_class.scale.frame_rate))
self.scaleSettingsLayout.addWidget(self.frameRateEntry, current_row, 1)
# Display the widget
self.scaleSettingsWidget.setLayout(self.scaleSettingsLayout)
parentWidget.addWidget(self.scaleSettingsWidget)
def createImageInfosDisplay(self, parentWidget):
# Generate the widget
self.imageInfoWidget = qtw.QWidget()
self.imageInfoLayout = qtw.QVBoxLayout(self.imageInfoWidget)
# Populate all the informations
self.infoGridWidget = qtw.QWidget()
self.infoGridLayout = qtw.QGridLayout(self.infoGridWidget)
# Number of images
self.imageNumberLabel = qtw.QLabel('')
self.infoGridLayout.addWidget(CLabel('Number of image(s):'), 0, 0)
self.infoGridLayout.addWidget(self.imageNumberLabel, 0, 1)
# Image size
self.imageSizeLabel = qtw.QLabel('')
self.infoGridLayout.addWidget(CLabel('Image Size:'), 1, 0)
self.infoGridLayout.addWidget(self.imageSizeLabel, 1, 1)
# Image bitness
self.imageBitsLabel = qtw.QLabel('')
self.infoGridLayout.addWidget(CLabel('Image Bitness:'), 2, 0)
self.infoGridLayout.addWidget(self.imageBitsLabel, 2, 1)
# Display the grid
self.infoGridWidget.setLayout(self.infoGridLayout)
self.imageInfoLayout.addWidget(self.infoGridWidget,
alignment=qtc.Qt.AlignLeft)
# Crop selection
self.cropCheckBox = qtw.QCheckBox('Crop the image?')
self.cropCheckBox.setEnabled(False)
self.imageInfoLayout.addWidget(self.cropCheckBox)
# Signed bit correction
self.signCorrectionCheckBox = qtw.QCheckBox('Correct signed bits?')
self.signCorrectionCheckBox.setEnabled(False)
self.imageInfoLayout.addWidget(self.signCorrectionCheckBox)
# Signed bit correction
self.backgroundCorrectionCheckBox = qtw.QCheckBox(
'Apply background correction?')
self.backgroundCorrectionCheckBox.setEnabled(False)
self.imageInfoLayout.addWidget(self.backgroundCorrectionCheckBox)
# Display the widget
self.imageInfoWidget.setLayout(self.imageInfoLayout)
parentWidget.addWidget(self.imageInfoWidget)
def createScaleSelection(self, parentWidget):
# Generate the widget
self.scaleSelectionWidget = qtw.QWidget()
self.scaleSelectionLayout = qtw.QGridLayout(self.scaleSelectionWidget)
current_row = 0
self.scaleSelectionLayout.addWidget(CLabel('Scale(s):'), current_row,
0, 1, 4)
current_row += 1
self.scaleSelectionLayout.addWidget(
qtw.QLabel('Space scale (px/unit):'), current_row, 0)
self.spaceScaleEntry = qtw.QLineEdit()
self.scaleSelectionLayout.addWidget(self.spaceScaleEntry, current_row,
1)
self.scaleSelectionLayout.addWidget(qtw.QLabel('Time scale (FPS):'),
current_row, 2)
self.timeScaleEntry = qtw.QLineEdit()
self.scaleSelectionLayout.addWidget(self.timeScaleEntry, current_row,
3)
current_row += 1
self.scaleSelectionLayout.addWidget(qtw.QLabel('Space unit:'),
current_row, 0)
self.spaceUnitEntry = qtw.QLineEdit()
self.scaleSelectionLayout.addWidget(self.spaceUnitEntry, current_row,
1)
# Display the widget
self.scaleSelectionWidget.setLayout(self.scaleSelectionLayout)
parentWidget.addWidget(self.scaleSelectionWidget)
def createCorrectionSettings(self, parentWidget):
# Generate the widget
self.correctionSettingsWidget = qtw.QWidget()
self.correctionSettingsLayout = qtw.QVBoxLayout(
self.correctionSettingsWidget)
self.correctionSettingsLayout.addWidget(CLabel("Background type:"))
# Get the background type
self.backgroundTypeComboBox = qtw.QComboBox()
self.backgroundTypeComboBox.addItem('Median')
self.backgroundTypeComboBox.addItem('Mean')
self.backgroundTypeComboBox.activated.connect(self.refreshFrameDisplay)
self.correctionSettingsLayout.addWidget(self.backgroundTypeComboBox)
# Add the checkbox for intensity fluctuations corrections
self.previewCheckBox = qtw.QCheckBox("Preview?")
self.previewCheckBox.setChecked(True)
self.previewCheckBox.clicked.connect(self.refreshFrameDisplay)
self.correctionSettingsLayout.addWidget(self.previewCheckBox)
# Display the widget
self.correctionSettingsWidget.setLayout(self.correctionSettingsLayout)
parentWidget.addWidget(self.correctionSettingsWidget)
def createCorrectionSettings(self, parentWidget):
# Generate the widget
self.correctionSettingsWidget = qtw.QWidget()
self.correctionSettingsLayout = qtw.QVBoxLayout(
self.correctionSettingsWidget)
self.correctionSettingsLayout.addWidget(CLabel("Correction settings:"))
# Get the correction type
self.correctionTypeComboBox = qtw.QComboBox()
self.correctionTypeComboBox.addItem('Division')
self.correctionTypeComboBox.addItem('Subtraction')
self.correctionSettingsLayout.addWidget(self.correctionTypeComboBox)
# Get the background type
self.backgroundTypeComboBox = qtw.QComboBox()
self.backgroundTypeComboBox.addItem('Median')
self.backgroundTypeComboBox.addItem('Mean')
self.correctionSettingsLayout.addWidget(self.backgroundTypeComboBox)
# Add the checkbox for intensity fluctuations corrections
self.correctFluctuationsCheckBox = qtw.QCheckBox(
"Correct intensity fluctuations")
self.correctFluctuationsCheckBox.setChecked(True)
self.correctionSettingsLayout.addWidget(
self.correctFluctuationsCheckBox)
# Display the widget
self.correctionSettingsWidget.setLayout(self.correctionSettingsLayout)
parentWidget.addWidget(self.correctionSettingsWidget)
def createCorrectionOptions(self, parentWidget):
# Generate the widget
self.correctionOptionsWidget = qtw.QWidget()
self.correctionOptionsLayout = qtw.QVBoxLayout(
self.correctionOptionsWidget)
self.correctionOptionsLayout.addWidget(CLabel("Options:"))
# Crop selection
self.cropCheckBox = qtw.QCheckBox('Crop the image?')
self.cropCheckBox.setEnabled(False)
self.correctionOptionsLayout.addWidget(self.cropCheckBox)
# Crop size selection
cropSizeEntry_l, self.cropSizeEntry = CLabelledLineEdit(
"Crop size (px):", bold=False)
self.cropSizeEntry.setText(str(self.parent.config.crop_size))
self.correctionOptionsLayout.addWidget(cropSizeEntry_l)
# Signed bit correction
self.signCorrectionCheckBox = qtw.QCheckBox('Correct signed bits?')
#self.signCorrectionCheckBox.setEnabled(False)
self.correctionOptionsLayout.addWidget(self.signCorrectionCheckBox)
# Signed bit correction
self.replaceTabCheckBox = qtw.QCheckBox('Replace current tab?')
self.replaceTabCheckBox.setChecked(True)
self.correctionOptionsLayout.addWidget(self.replaceTabCheckBox)
# Display the widget
self.correctionOptionsWidget.setLayout(self.correctionOptionsLayout)
parentWidget.addWidget(self.correctionOptionsWidget)
def createProgressDisplay(self, parentWidget):
# Show the progress bar text
self.progressTopLabel = CLabel('Signal analysis in progress.')
parentWidget.addWidget(self.progressTopLabel, alignment=qtc.Qt.AlignCenter)
self.progressBottomLabel = qtw.QLabel('This operation can take several minutes.')
parentWidget.addWidget(self.progressBottomLabel, alignment=qtc.Qt.AlignCenter)
def createDetectionControls(self, parentWidget):
# Make the grid for values
self.settingsGridWidget = qtw.QWidget()
self.settingsGridLayout = qtw.QGridLayout(self.settingsGridWidget)
# Minimum intensity input
current_row = 0
self.settingsGridLayout.addWidget(CLabel("Intensity Min."),
current_row, 0)
self.minIntensityEntry = qtw.QLineEdit()
#self.minIntensityEntry.setValidator(qtg.QDoubleValidator(999999,0,3))
self.minIntensityEntry.editingFinished.connect(self.doLiveUpdate)
self.settingsGridLayout.addWidget(self.minIntensityEntry, current_row,
1)
current_row += 1
self.settingsGridLayout.addWidget(CLabel("Diameter"), current_row, 0)
self.diameterEntry = qtw.QLineEdit()
#self.diameterEntry.setValidator(qtg.QIntValidator(999999,1))
self.diameterEntry.editingFinished.connect(self.doLiveUpdate)
self.settingsGridLayout.addWidget(self.diameterEntry, current_row, 1)
current_row += 1
self.darkSpotCheckBox = qtw.QCheckBox("Dark particles?")
self.darkSpotCheckBox.clicked.connect(self.doLiveUpdate)
self.settingsGridLayout.addWidget(self.darkSpotCheckBox, current_row,
0)
current_row += 1
self.manageTrackerButton = qtw.QPushButton("Tracker...")
self.manageTrackerButton.clicked.connect(self.openTrackerMenu)
self.manageTrackerButton.setFixedWidth(125)
self.settingsGridLayout.addWidget(self.manageTrackerButton,
current_row, 0)
self.advancedSettingsButton = qtw.QPushButton("Advanced")
self.advancedSettingsButton.clicked.connect(self.openAdvancedSettings)
self.advancedSettingsButton.setFixedWidth(125)
self.settingsGridLayout.addWidget(self.advancedSettingsButton,
current_row, 1)
# Display the widget
self.settingsGridWidget.setLayout(self.settingsGridLayout)
parentWidget.addWidget(self.settingsGridWidget)
def createProgressBarDisplay(self, parentWidget):
# Show the progress bar text
self.progressBarLabel = CLabel("")
parentWidget.addWidget(self.progressBarLabel, alignment=qtc.Qt.AlignCenter)
# Show the progress bar
self.progressBarWidget = qtw.QProgressBar()
parentWidget.addWidget(self.progressBarWidget)
def createCorrectionSettings(self, parentWidget):
# Generate the widget
self.correctionSettingsWidget = qtw.QWidget()
self.correctionSettingsLayout = qtw.QGridLayout(
self.correctionSettingsWidget)
# Get the correction type
current_row = 0
self.averagingTypeComboBox = qtw.QComboBox()
self.averagingTypeComboBox.addItem('Standard Average')
self.averagingTypeComboBox.addItem('Running Average')
self.averagingTypeComboBox.currentIndexChanged.connect(
self.calculateInfos)
self.correctionSettingsLayout.addWidget(self.averagingTypeComboBox,
current_row, 0, 1, 2)
# Add the entry for the number of frames
current_row += 1
self.correctionSettingsLayout.addWidget(CLabel('Number of frames:'),
current_row, 0)
self.numberFrameEntry = qtw.QLineEdit()
self.numberFrameEntry.setText(str(2))
self.numberFrameEntry.setValidator(qtg.QIntValidator(2, self.max_n))
self.numberFrameEntry.editingFinished.connect(self.entryIsEdited)
self.correctionSettingsLayout.addWidget(self.numberFrameEntry,
current_row, 1)
# Add the slider for number of frames selection
current_row += 1
self.numberFrameSlider = qtw.QSlider(qtc.Qt.Horizontal)
self.numberFrameSlider.setMinimum(2)
self.numberFrameSlider.setMaximum(self.max_n)
self.numberFrameSlider.setValue(2)
self.numberFrameSlider.sliderMoved.connect(self.sliderIsEdited)
self.correctionSettingsLayout.addWidget(self.numberFrameSlider,
current_row, 0, 1, 2)
# Add the checkbox for processing partial data
current_row += 1
self.partialDataCheckBox = qtw.QCheckBox("Add partial data?")
self.partialDataCheckBox.setChecked(False)
self.partialDataCheckBox.clicked.connect(self.calculateInfos)
self.correctionSettingsLayout.addWidget(self.partialDataCheckBox,
current_row, 0, 1, 2)
# Add the checkbox for new tab
current_row += 1
self.replaceTabCheckBox = qtw.QCheckBox("Replace current tab?")
self.replaceTabCheckBox.setChecked(False)
self.correctionSettingsLayout.addWidget(self.replaceTabCheckBox,
current_row, 0, 1, 2)
# Display the widget
self.correctionSettingsWidget.setLayout(self.correctionSettingsLayout)
parentWidget.addWidget(self.correctionSettingsWidget)
def createSaveFileDisplay(self, parentWidget):
# Generate the widget
self.saveSettingsWidget = qtw.QWidget()
self.saveSettingsLayout = qtw.QGridLayout(self.saveSettingsWidget)
# Format selection
current_row = 0
self.saveSettingsLayout.addWidget(CLabel("Format:"), current_row, 0)
self.formatComboBox = qtw.QComboBox()
self.formatComboBox.addItems(['Tiff', 'Jpeg', 'BMP', 'PNG'])
self.formatComboBox.activated.connect(self.updateRadioButton)
self.saveSettingsLayout.addWidget(self.formatComboBox, current_row, 1)
# Bitness selection
self.bitnessSelectionGroupButton = qtw.QButtonGroup(
self.saveSettingsWidget)
current_row += 1
self.saveSettingsLayout.addWidget(CLabel("Bitness:"), current_row, 0)
self.bit16Radiobutton = qtw.QRadioButton("16-bits")
self.bit16Radiobutton.setChecked(True)
self.bitnessSelectionGroupButton.addButton(self.bit16Radiobutton)
self.saveSettingsLayout.addWidget(self.bit16Radiobutton, current_row,
1)
current_row += 1
self.bit8Radiobutton = qtw.QRadioButton("8-bits")
self.bitnessSelectionGroupButton.addButton(self.bit8Radiobutton)
self.saveSettingsLayout.addWidget(self.bit8Radiobutton, current_row, 1)
# Save all frames selection
current_row += 1
self.allFramesCheckbox = qtw.QCheckBox("Save all frames?")
self.saveSettingsLayout.addWidget(self.allFramesCheckbox, current_row,
0, 1, 2)
# Display the widget
self.saveSettingsWidget.setLayout(self.saveSettingsLayout)
parentWidget.addWidget(self.saveSettingsWidget,
alignment=qtc.Qt.AlignLeft)
def createGeneralSettings(self):
# Generate the widget
self.generalSettingsWidget = qtw.QWidget()
self.generalSettingsLayout = qtw.QVBoxLayout(self.generalSettingsWidget)
# Settings for image opening
self.generalSettingsLayout.addWidget( CLabel("Open Image(s):") )
# Default type of object
self.imageTypeButtonGroupWidget = qtw.QWidget()
self.imageTypeButtonGroupLayout = qtw.QVBoxLayout(self.imageTypeButtonGroupWidget)
self.imageTypeGroupButton = qtw.QButtonGroup(self.imageTypeButtonGroupWidget)
self.singleFileRadiobutton = qtw.QRadioButton("Single File")
self.singleFileRadiobutton.setChecked( self.parent.config.single_images )
self.imageTypeGroupButton.addButton(self.singleFileRadiobutton)
self.imageTypeButtonGroupLayout.addWidget(self.singleFileRadiobutton)
self.imageFolderRadiobutton = qtw.QRadioButton("Images Folder")
self.imageFolderRadiobutton.setChecked( not self.parent.config.single_images )
self.imageTypeGroupButton.addButton(self.imageFolderRadiobutton)
self.imageTypeButtonGroupLayout.addWidget(self.imageFolderRadiobutton)
self.imageTypeButtonGroupWidget.setLayout(self.imageTypeButtonGroupLayout)
self.imageTypeButtonGroupWidget.setContentsMargins(0, 0, 0, 0)
self.generalSettingsLayout.addWidget(self.imageTypeButtonGroupWidget)
# Load automatically with the recommandation
self.autoOpenImageCheckBox = qtw.QCheckBox("Auto-load with suggestions?")
self.autoOpenImageCheckBox.setChecked( self.parent.config.autoload_images )
self.generalSettingsLayout.addWidget(self.autoOpenImageCheckBox)
# Load automatically with the recommandation
self.autoBackgroundCorrectionCheckBox = qtw.QCheckBox("Correct background automatically?")
self.autoBackgroundCorrectionCheckBox.setChecked( self.parent.config.auto_background )
self.generalSettingsLayout.addWidget(self.autoBackgroundCorrectionCheckBox)
self.generalSettingsLayout.addWidget( CHorizontalSeparator() )
# Add dark theme checkbox
#self.darkThemeCheckBox = qtw.QCheckBox("Use dark theme?")
#self.darkThemeCheckBox.setChecked( self.parent.config.dark_theme )
#self.generalSettingsLayout.addWidget(self.darkThemeCheckBox)
# Add empty widget
for i in range(8):
self.generalSettingsLayout.addWidget(qtw.QWidget())
# Display the widget
self.generalSettingsWidget.setLayout(self.generalSettingsLayout)
return self.generalSettingsWidget
def createPathSelection(self, parentWidget):
# Generate the widget
self.pathSelectionWidget = qtw.QWidget()
self.pathSelectionLayout = qtw.QHBoxLayout(self.pathSelectionWidget)
# Add the path selection combobox
self.pathSelectionLayout.addWidget(CLabel('Analyse path:'))
self.pathSelectionBox = qtw.QComboBox()
self.pathSelectionLayout.addWidget(self.pathSelectionBox)
# Display the widget
self.pathSelectionWidget.setLayout(self.pathSelectionLayout)
parentWidget.addWidget(self.pathSelectionWidget,
alignment=qtc.Qt.AlignLeft)
def createCorrectionSelection(self, parentWidget):
# Generate the widget
self.correctionWidget = qtw.QWidget()
self.correctionLayout = qtw.QHBoxLayout(self.correctionWidget)
# Display the combo box
self.correctionLayout.addWidget(CLabel('Correction type:'))
self.correctionSelectionBox = qtw.QComboBox()
self.correctionSelectionBox.addItems(['Median', 'Mean'])
self.correctionLayout.addWidget(self.correctionSelectionBox)
# Display the widget
self.correctionWidget.setLayout(self.correctionLayout)
parentWidget.addWidget(self.correctionWidget)
def createNameSelection(self, parentWidget):
# Generate the widget
self.nameSelectionWidget = qtw.QWidget()
self.nameSelectionLayout = qtw.QHBoxLayout(self.nameSelectionWidget)
# Add the label
self.nameSelectionLayout.addWidget(CLabel('Tracker name'))
# Add the entry
self.nameSelectionEntry = qtw.QLineEdit()
self.nameSelectionLayout.addWidget(self.nameSelectionEntry)
# Display the widget
self.nameSelectionWidget.setLayout(self.nameSelectionLayout)
parentWidget.addWidget(self.nameSelectionWidget)
def createTableWidget(self, parentWidget):
# Generate the widget
self.frameDisplayWidget = qtw.QWidget()
self.frameDisplayLayout = qtw.QVBoxLayout(self.frameDisplayWidget)
# Generate the frame selection
self.frameSelectionWidget = qtw.QWidget()
self.frameSelectionLayout = qtw.QHBoxLayout(self.frameSelectionWidget)
# Label
self.frameSelectionLayout.addWidget(CLabel('Frame:'),
alignment=qtc.Qt.AlignRight)
# Selection
self.frameSelectionEntry = qtw.QLineEdit()
self.frameSelectionEntry.setText(str(self.current_frame + 1))
self.frameSelectionEntry.setFixedWidth(75)
self.frameSelectionLayout.addWidget(self.frameSelectionEntry)
# Frame number
self.totalFrameLabel = qtw.QLabel("/ " + str(self.n_frames))
self.frameSelectionLayout.addWidget(self.totalFrameLabel,
alignment=qtc.Qt.AlignLeft)
# Display the widget
self.frameSelectionWidget.setLayout(self.frameSelectionLayout)
self.frameDisplayLayout.addWidget(self.frameSelectionWidget,
alignment=qtc.Qt.AlignLeft)
# ----------
# Generate the table of servers
self.frameTable = qtw.QTableWidget(1, 6)
self.frameTable.setHorizontalHeaderLabels([''])
self.frameTable.setSelectionMode(qtw.QAbstractItemView.NoSelection)
self.frameTable.setEditTriggers(qtw.QAbstractItemView.NoEditTriggers)
self.frameTable.setShowGrid(True)
self.frameTable.setMinimumHeight(63)
self.frameTable.setMaximumHeight(63)
self.frameDisplayLayout.addWidget(self.frameTable)
# Display the widget
self.frameDisplayWidget.setLayout(self.frameDisplayLayout)
parentWidget.addWidget(self.frameDisplayWidget)
def createSaveFileDisplay(self, parentWidget):
# Generate the widget
self.saveSettingsWidget = qtw.QWidget()
self.saveSettingsLayout = qtw.QGridLayout(self.saveSettingsWidget)
# Format selection
current_row = 0
self.saveSettingsLayout.addWidget(CLabel("Frame Rate (FPS):"),
current_row, 0)
self.frameRateEntry = qtw.QLineEdit()
self.frameRateEntry.setText('25')
self.saveSettingsLayout.addWidget(self.frameRateEntry, current_row, 1)
# Display the widget
self.saveSettingsWidget.setLayout(self.saveSettingsLayout)
parentWidget.addWidget(self.saveSettingsWidget,
alignment=qtc.Qt.AlignLeft)
def createRangeSelectionDisplay(self, parentWidget):
# Generate the widget
self.imageInfoWidget = qtw.QWidget()
self.imageInfoLayout = qtw.QVBoxLayout(self.imageInfoWidget)
self.imageInfoLayout.addWidget( CLabel('Open range:') )
# Range selection
self.frameRangeSelection = CRangeSelection()
self.frameRangeSelection.setMin(1)
self.frameRangeSelection.setMax(self.n_frames)
self.frameRangeSelection.setRange(1,self.n_frames)
self.imageInfoLayout.addWidget( self.frameRangeSelection )
# Display the widget
self.imageInfoWidget.setLayout(self.imageInfoLayout)
parentWidget.addWidget(self.imageInfoWidget)
def createPathSelection(self, parentWidget):
# Generate the widget
self.pathSelectionWidget = qtw.QWidget()
self.pathSelectionLayout = qtw.QHBoxLayout(self.pathSelectionWidget)
# Add the path selection labels
self.pathSelectionLayout.addWidget(CLabel('Current path:'),
alignment=qtc.Qt.AlignRight)
self.selectedPathLabel = qtw.QLabel(str(self.current_path))
self.pathSelectionLayout.addWidget(self.selectedPathLabel,
alignment=qtc.Qt.AlignLeft)
# Add the button to save the changes
self.pathSelectionBox = qtw.QComboBox()
self.pathSelectionBox.addItems(
self.image_class.trajectory.listTracks().astype(str))
#self.pathSelectionBox.setFixedWidth(150)
self.pathSelectionLayout.addWidget(self.pathSelectionBox,
alignment=qtc.Qt.AlignRight)
# Initial the combobox settings
_index_correction = self.pathSelectionBox.findText(
str(self.current_path), qtc.Qt.MatchFixedString)
if _index_correction >= 0:
self.pathSelectionBox.setCurrentIndex(_index_correction)
# Add the button to load path
self.loadButton = qtw.QPushButton("Load path")
self.loadButton.clicked.connect(self.changePath)
self.loadButton.setFixedWidth(150)
self.pathSelectionLayout.addWidget(self.loadButton,
alignment=qtc.Qt.AlignRight)
# Add the button to create new path
self.newPathButton = qtw.QPushButton("New path")
self.newPathButton.clicked.connect(self.createNewPath)
self.newPathButton.setFixedWidth(150)
self.pathSelectionLayout.addWidget(self.newPathButton,
alignment=qtc.Qt.AlignRight)
# Display the widget
self.pathSelectionWidget.setLayout(self.pathSelectionLayout)
parentWidget.addWidget(self.pathSelectionWidget)
def __init__(self, parent):
super(aboutHelpWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.setWindowModality(qtc.Qt.ApplicationModal)
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle('About...')
# Show the logo
imageWidget = qtw.QLabel()
image = qtg.QPixmap(self.parent.appctxt.get_resource('iscan_logo.png'))
imageWidget.setPixmap(image)
self.mainLayout.addWidget(imageWidget, alignment=qtc.Qt.AlignCenter)
# Show the title
titleText = CLabel("iSCAN - v1.0")
self.mainLayout.addWidget(titleText, alignment=qtc.Qt.AlignCenter)
# Show the text
aboutText = qtw.QLabel("""Release Date: XX/XX/2020
Author: Vivien Walter
Contact: [email protected]
More information and documentation can be found on the website of the software:
https://github.com/vivien-walter/iscan""")
self.mainLayout.addWidget(aboutText) #, alignment=qtc.Qt.AlignCenter)
# Exit button
self.exitButton = qtw.QPushButton("Close")
self.exitButton.setFixedWidth(125)
self.exitButton.clicked.connect(self.close)
self.mainLayout.addWidget(self.exitButton,
alignment=qtc.Qt.AlignCenter)
# Display the panel
#self.mainLayout.setAlignment(qtc.Qt.AlignCenter)
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.resize(300, 300)
self.show()
self.setFixedSize(self.size())
def createPathSelectionDisplay(self, parentWidget):
self.pathSelectionWidget = qtw.QWidget()
self.pathSelectionLayout = qtw.QVBoxLayout(self.pathSelectionWidget)
# Add the label
self.pathSelectionLayout.addWidget(CLabel("Path selection:"))
# Add the checkbox for displaying trajectory
self.pathSelectionEntry = CPathSelection()
self.pathSelectionEntry.connectChange(self.refreshDisplay)
self.pathSelectionLayout.addWidget(self.pathSelectionEntry)
# Add the options
self.deletePathButton = qtw.QPushButton("Delete Path")
self.deletePathButton.setEnabled(False)
self.deletePathButton.clicked.connect(self.deleteSelectedPath)
self.pathSelectionLayout.addWidget(self.deletePathButton)
self.pathSelectionWidget.setLayout(self.pathSelectionLayout)
parentWidget.addWidget(self.pathSelectionWidget)
def createAveragingSelection(self, parentWidget):
# Generate the widget
self.averageSelectionWidget = qtw.QWidget()
self.averageSelectionLayout = qtw.QGridLayout(
self.averageSelectionWidget)
# Average type
self.averageSelectionLayout.addWidget(CLabel("Type:"), 0, 0)
self.averagingTypeComboBox = qtw.QComboBox()
self.averagingTypeComboBox.addItem('Standard Average')
self.averagingTypeComboBox.addItem('Running Average')
self.averagingTypeComboBox.setFixedWidth(200)
self.averageSelectionLayout.addWidget(self.averagingTypeComboBox, 1, 0)
# Process button
self.processButton = qtw.QPushButton("PROCESS")
self.processButton.setFixedHeight(50)
self.processButton.setFixedWidth(100)
self.processButton.clicked.connect(self.processAveraging)
self.averageSelectionLayout.addWidget(self.processButton, 0, 1, 2, 1)
# Range selection
self.averageSelectionLayout.addWidget(qtw.QLabel('Processing range:'),
2, 0, 1, 2)
self.frameRangeSelection = CRangeSelection()
self.frameRangeSelection.setMin(2)
self.frameRangeSelection.setMax(3)
self.frameRangeSelection.setRange(2, 3)
self.frameRangeSelection.setFixedWidth(550)
self.averageSelectionLayout.addWidget(self.frameRangeSelection,
3,
0,
1,
2,
alignment=qtc.Qt.AlignRight)
# Display the widget
self.averageSelectionWidget.setLayout(self.averageSelectionLayout)
parentWidget.addWidget(self.averageSelectionWidget)
def createGraphDisplay(self, parentWidget):
# Generate the widget
self.plotGraphWidget = qtw.QWidget()
self.plotGraphLayout = qtw.QVBoxLayout(self.plotGraphWidget)
# Add the graph
self.graphWidget = pg.PlotWidget()
self.plotGraphLayout.addWidget(self.graphWidget)
# Add the path selector
self.pathSelectionEntry = CPathSelection()
self.pathSelectionEntry.connectChange(self.updateGraph)
self.plotGraphLayout.addWidget(self.pathSelectionEntry,
alignment=qtc.Qt.AlignCenter)
# Add the diffusivity display
self.diffusivityValueWidget = qtw.QWidget()
self.diffusivityValueLayout = qtw.QHBoxLayout(
self.diffusivityValueWidget)
self.diffusivityValueLayout.addWidget(CLabel('Diffusivity:'))
self.diffusivityValueLabel = qtw.QLabel()
self.diffusivityValueLayout.addWidget(self.diffusivityValueLabel,
alignment=qtc.Qt.AlignLeft)
self.diffusivityValueWidget.setLayout(self.diffusivityValueLayout)
self.plotGraphLayout.addWidget(self.diffusivityValueWidget)
# Add log checkbox
self.logScaleCheckbox = qtw.QCheckBox('Log scale?')
self.logScaleCheckbox.setChecked(True)
self.logScaleCheckbox.clicked.connect(self.updateGraph)
self.plotGraphLayout.addWidget(self.logScaleCheckbox,
alignment=qtc.Qt.AlignLeft)
# Display the widget
self.plotGraphWidget.setLayout(self.plotGraphLayout)
parentWidget.addWidget(self.plotGraphWidget)
def createSizeControl(self, parentWidget):
# Generate the widget
self.sizeControlWidget = qtw.QWidget()
self.sizeControlLayout = qtw.QGridLayout(self.sizeControlWidget)
current_row = 0
self.sizeControlLayout.addWidget(CLabel('Crop size'), current_row, 0,
1, 3)
# Slider to change the size
current_row += 1
self.sizeSlider = qtw.QSlider(qtc.Qt.Horizontal)
self.sizeSlider.setMinimum(4)
self.sizeSlider.sliderMoved.connect(self.updateSlider)
self.sizeControlLayout.addWidget(self.sizeSlider, current_row, 0, 1, 3)
# Add labels and controls
current_row += 1
minLabel = qtw.QLabel('4')
minLabel.setAlignment(qtc.Qt.AlignLeft)
self.sizeControlLayout.addWidget(minLabel, current_row, 0)
self.sizeEntry = qtw.QLineEdit()
self.sizeEntry.setFixedWidth(100)
self.sizeEntry.setAlignment(qtc.Qt.AlignCenter)
self.sizeEntry.editingFinished.connect(self.updateEntry)
self.sizeControlLayout.addWidget(self.sizeEntry, current_row, 1)
self.maxLabel = qtw.QLabel('')
self.maxLabel.setAlignment(qtc.Qt.AlignRight)
self.sizeControlLayout.addWidget(self.maxLabel, current_row, 2)
# Display the widget
self.sizeControlWidget.setLayout(self.sizeControlLayout)
parentWidget.addWidget(self.sizeControlWidget)
def createImageSettings(self):
# Generate the widget
self.imageSettingsWidget = qtw.QWidget()
self.imageSettingsLayout = qtw.QVBoxLayout(self.imageSettingsWidget)
# Settings for image preparation
self.imageSettingsLayout.addWidget( CLabel("Image Preparation:") )
# Crop the image if recommended
self.cropImageCheckBox = qtw.QCheckBox("Crop the image")
self.cropImageCheckBox.setChecked( self.parent.config.crop_image )
self.imageSettingsLayout.addWidget(self.cropImageCheckBox)
cropSizeEntry_l, self.cropSizeEntry = CLabelledLineEdit("Crop size (px):", bold=False)
self.cropSizeEntry.setText( str(self.parent.config.crop_size) )
self.imageSettingsLayout.addWidget(cropSizeEntry_l)
# Correct signed bits if recommended
self.correctSignedBitsCheckBox = qtw.QCheckBox("Correct signed bits")
self.correctSignedBitsCheckBox.setChecked( self.parent.config.correct_signed )
self.imageSettingsLayout.addWidget(self.correctSignedBitsCheckBox)
self.imageSettingsLayout.addWidget( CHorizontalSeparator() )
# Settings for image correction
self.imageSettingsLayout.addWidget( CLabel("Image Correction:") )
# Settings for the background settings
self.imageSettingsLayout.addWidget( qtw.QLabel("Background correction settings") )
# Get the correction type
self.correctionTypeComboBox = qtw.QComboBox()
self.correctionTypeComboBox.addItem('Division')
self.correctionTypeComboBox.addItem('Subtraction')
_index_correction = self.correctionTypeComboBox.findText(self.parent.config.correction_type.capitalize(), qtc.Qt.MatchFixedString)
if _index_correction >= 0:
self.correctionTypeComboBox.setCurrentIndex(_index_correction)
self.imageSettingsLayout.addWidget(self.correctionTypeComboBox)
# Get the background type
self.backgroundTypeComboBox = qtw.QComboBox()
self.backgroundTypeComboBox.addItem('Median')
self.backgroundTypeComboBox.addItem('Mean')
_index_background = self.backgroundTypeComboBox.findText(self.parent.config.background_type.capitalize(), qtc.Qt.MatchFixedString)
if _index_background >= 0:
self.backgroundTypeComboBox.setCurrentIndex(_index_background)
self.imageSettingsLayout.addWidget(self.backgroundTypeComboBox)
# Correct intensity fluctuation
self.correctFluctuationsCheckBox = qtw.QCheckBox("Correct intensity fluctuations")
self.correctFluctuationsCheckBox.setChecked( self.parent.config.correct_intensity )
self.imageSettingsLayout.addWidget(self.correctFluctuationsCheckBox)
# Correct intensity fluctuation
self.newTabCheckBox = qtw.QCheckBox("Open corrected stack in a new tab")
self.newTabCheckBox.setChecked( self.parent.config.correct_newtab )
self.imageSettingsLayout.addWidget(self.newTabCheckBox)
# Display the widget
self.imageSettingsWidget.setLayout(self.imageSettingsLayout)
return self.imageSettingsWidget
def createImageInfosDisplay(self, parentWidget):
# Generate the widget
self.imageInfoWidget = qtw.QWidget()
self.imageInfoLayout = qtw.QVBoxLayout(self.imageInfoWidget)
# Populate all the informations
self.infoGridWidget = qtw.QWidget()
self.infoGridLayout = qtw.QGridLayout(self.infoGridWidget)
# Number of images
self.imageNumberLabel = qtw.QLabel('')
self.infoGridLayout.addWidget( CLabel('Number of image(s):'), 0, 0)
self.infoGridLayout.addWidget( self.imageNumberLabel, 0, 1)
# Image size
self.imageSizeLabel = qtw.QLabel('')
self.infoGridLayout.addWidget( CLabel('Image Size:'), 1, 0)
self.infoGridLayout.addWidget( self.imageSizeLabel, 1, 1)
# Image bitness
self.imageBitsLabel = qtw.QLabel('')
self.infoGridLayout.addWidget( CLabel('Image Bitness:'), 2, 0)
self.infoGridLayout.addWidget( self.imageBitsLabel, 2, 1)
# Display the grid
self.infoGridWidget.setLayout(self.infoGridLayout)
self.imageInfoLayout.addWidget( self.infoGridWidget, alignment=qtc.Qt.AlignLeft)
# Populate all the informations
self.selectionGridWidget = qtw.QWidget()
self.selectionGridLayout = qtw.QGridLayout(self.selectionGridWidget)
current_row = 0
self.selectionGridLayout.addWidget( qtw.QLabel('Open range:'), current_row, 0, 1, 3)
# Range selection
current_row += 1
self.frameRangeSelection = CRangeSelection()
self.frameRangeSelection.setMin(0)
self.frameRangeSelection.setMax(1)
self.frameRangeSelection.setRange(0,1)
self.frameRangeSelection.setEnabled(False)
self.selectionGridLayout.addWidget( self.frameRangeSelection, current_row, 0, 1, 3)
# Crop selection
current_row += 1
self.cropCheckBox = qtw.QCheckBox('Crop the image?')
self.selectionGridLayout.addWidget( self.cropCheckBox, current_row, 0)
self.selectionGridLayout.addWidget( qtw.QLabel('size (px):'), current_row, 1)
self.cropSizeEntry = qtw.QLineEdit()
self.cropSizeEntry.setText( str(self.parent.config.crop_size) )
self.selectionGridLayout.addWidget( self.cropSizeEntry, current_row, 2)
# Signed bit correction
current_row += 1
self.signCorrectionCheckBox = qtw.QCheckBox('Correct signed bits?')
#self.signCorrectionCheckBox.setEnabled(False)
self.selectionGridLayout.addWidget( self.signCorrectionCheckBox, current_row, 0, 1, 3)
# Signed bit correction
current_row += 1
self.backgroundCorrectionCheckBox = qtw.QCheckBox('Apply background correction?')
self.backgroundCorrectionCheckBox.setEnabled(False)
self.selectionGridLayout.addWidget( self.backgroundCorrectionCheckBox, current_row, 0, 1, 3)
# Display the grid
self.selectionGridWidget.setLayout(self.selectionGridLayout)
self.imageInfoLayout.addWidget( self.selectionGridWidget)
# Display the widget
self.imageInfoWidget.setLayout(self.imageInfoLayout)
parentWidget.addWidget(self.imageInfoWidget)
