def __init__(self, parent, image_class=None):
super(signalAveragingWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.image_class = image_class
self.averaging_result = None
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Signal vs. Averaging")
# Populate the panel
self.createPathSelection(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createAveragingSelection(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createGraphDisplay(self.mainLayout)
self.createSignalSelection(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
self.setMinimumSize(600, 650)
self.resize(600, 650)
# Initialise
self.initialiseDisplay()
def __init__(self, parent, image_class=None):
super(particleDetectionWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.image_class = image_class
#self.setWindowModality(qtc.Qt.ApplicationModal)
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Particle Detection")
# Populate the panel
self.createDetectionControls(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createPreviewActions(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
self.setFixedSize(self.size())
# Update the panel with image content
self.initializeDetection()
def __init__(self, parent, image_array=None):
super(backgroundCorrectionWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.image_array = image_array
self.setWindowModality(qtc.Qt.ApplicationModal)
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Background Correction")
# Populate the panel
self.createCorrectionSettings(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createCorrectionOptions(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
self.setFixedSize(self.size())
# Update the panel with image content
self.analyseStack()
def __init__(self, parent, file_path=None):
super(readMetadataWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.file_path = file_path
# Load the file
self.loadFromFile(file_path)
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Read Metadata")
# Populate the panel
self.createGeneralContentDisplay(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createContentTable(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
# Set the size
if self.data_type == 'experiment':
self.setMinimumSize(700,600)
elif self.data_type == 'fast_record':
self.setMinimumSize(500,600)
def __init__(self, name, parent):
super(TrajectoryControlsPanel, self).__init__(name, parent)
# Initialise the subwindow
self.parent = parent
self.trajectory = None
self.setAllowedAreas(qtc.Qt.LeftDockWidgetArea
| qtc.Qt.RightDockWidgetArea)
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
# Populate the panel
self.createVisualisationDisplay(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createPathSelectionDisplay(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createTrajectoryFileActions(self.mainLayout)
# Display the panel
self.mainLayout.setAlignment(qtc.Qt.AlignTop)
self.mainWidget.setLayout(self.mainLayout)
self.setWidget(self.mainWidget)
#self.show()
#self.setFixedSize(self.size())
# Add listeners
self.topLevelChanged.connect(self.detectLocationChange)
def __init__(self, parent, image_class=None):
super(contrastCorrectionWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.image_class = image_class
self.analyzed_image = image_class.image.source
self.auto_attempt = 0
self.setWindowModality(qtc.Qt.ApplicationModal)
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Brightness & Contrast")
# Populate the panel
self.createGraphDisplay(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createBrightnessControls(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createBrightnessActions(self.mainLayout)
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
self.setFixedSize(375, 600)
# Update the panel with image content
self.getDistribution()
def __init__(self, parent, image_array=None):
super(frameAveragingWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.image_array = image_array
self.max_n = self.image_array.shape[0]
self.setWindowModality(qtc.Qt.ApplicationModal)
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Frame Averaging")
# Populate the panel
self.createCorrectionSettings(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createInformationDisplay(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
self.setFixedSize(300, 350)
# Update the panel with image content
self.calculateInfos()
def __init__(self, parent, image_class=None):
super(saveSingleImageWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.image_class = image_class
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Save Single Frame(s)...")
# Populate the panel
self.createSaveFileDisplay(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createSaveContentDisplay(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
self.setFixedSize(self.size())
# Initialise the display
self.updateRadioButton()
def __init__(self, parent, image_array=None):
super(fluctuationCorrectionWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.image_array = image_array
self.setWindowModality(qtc.Qt.ApplicationModal)
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Intensity Fluctuations...")
# Populate the panel
self.createGraphDisplay(self.mainLayout)
self.mainLayout.addWidget( CHorizontalSeparator() )
self.createStatisticsDisplay(self.mainLayout)
self.mainLayout.addWidget( CHorizontalSeparator() )
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
self.setFixedSize(450,450)
# Update the panel with image content
self.plotFluctuations()
def __init__(self, parent, image_class=None, path_id=0):
super(cropCenterWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.image_class = image_class
self.path_id = path_id
self.setWindowModality(qtc.Qt.ApplicationModal)
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Crop and Center")
# Populate the panel
self.createMiniDisplay(self.mainLayout)
self.createSizeControl(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
#self.setFixedSize(375,600)
# Update the panel with image content
self.getCenteredPath()
def __init__(self, parent, metadata_type=None, file_contents=None):
super(seekMetadataWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.all_contents = file_contents
self.data_type = metadata_type
# Load the files
self.loadFromFolder(file_contents)
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("List Metadata")
# Populate the panel
self.createDataSelection(self.mainLayout)
self.createDataTableDisplay(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
self.setMinimumSize(650, 450)
def __init__(self, parent):
super(darkToBrightCorrectionWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
#self.setWindowModality(qtc.Qt.ApplicationModal)
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Dark Particles to Bright")
# Populate the panel
self.createCorrectionSettings(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
self.setFixedSize(self.size())
# Initialise the display
self.initialiseDisplay()
self.refreshFrameDisplay()
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 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 __init__(self, parent, image_class=None, path_id=0):
super(PathEditorWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.image_class = image_class
self.setWindowModality(qtc.Qt.ApplicationModal)
# Initialise the parameters
self.current_path = path_id
self.current_track = None
self.current_frame = self.image_class.frame
self.n_frames = self.image_class.n_frames
self.zoom = 1
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Edit Paths")
# Populate the panel
self.createPathSelection(self.mainLayout)
self.createNavigationWidget(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createTableWidget(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
#self.setFixedSize(350,275)
# Initialise the display
self.getPath(path_id=path_id)
self.populateTable()
self.initialiseDisplay()
self.current_frame = -1
self.changeFrame(frame_id=self.image_class.frame)
def __init__(self, parent, image_class=None):
super(particleDiffusionWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.trajectory = None
self.path_list = None
self.loaded_trajectory = None
self.image_class = image_class
self.space_scale = None
self.space_unit = None
self.frame_rate = None
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Mean Squared Displacement")
# Populate the panel
self.createTrajectorySelection(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createScaleSelection(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createGraphDisplay(self.mainLayout)
#self.createSignalSelection(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
self.setMinimumSize(575, 675)
self.resize(575, 675)
# Initialise
self.initialiseDisplay()
def __init__(self, parent):
super(openImageWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.image_path = None
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Open Image or Stack...")
# Populate the panel
self.createFileBrowsingDisplay(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createImageInfosDisplay(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
def __init__(self, parent, image_class=None):
super(analyseSignalWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.image_class = image_class
self.single = True
self.all_checkboxes = []
self.values = []
self.errors = []
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Measure Signals")
# Populate the panel
self.createProcessSelection(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createPropertiesTable(self.mainLayout)
self.createResultDisplay(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
self.setMinimumSize(550, 475)
# Initialise
if self.image_class.trajectory.signals is None:
self.getProperties()
else:
self.populateTable()
def __init__(self, parent):
super(convertStackWindow, self).__init__(parent)
# Initialise the subwindow
self.parent = parent
self.directory = None
# Generate the window
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
self.setWindowTitle("Folders to Stacks...")
# Populate the panel
self.createDirectoryBrowsingDisplay(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createStackSelectionDisplay(self.mainLayout)
self.mainLayout.addWidget(CHorizontalSeparator())
self.createUserActions(self.mainLayout)
# Display the panel
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
self.show()
self.setFixedSize(550, 450)
def generateCentralWidget(self):
# Define the widget
self.mainWidget = qtw.QWidget()
self.mainLayout = qtw.QVBoxLayout(self.mainWidget)
# Display the widget
self.imageTabDisplay = mainTabWidget(self)
self.mainLayout.addWidget(self.imageTabDisplay)
self.mainLayout.addWidget(CHorizontalSeparator())
# Add action widget at the bottom
self.generateButtonWidget(self.mainLayout)
# Display the widget
self.mainWidget.setLayout(self.mainLayout)
self.setCentralWidget(self.mainWidget)
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