def createFileBrowsingDisplay(self, parentWidget):
# Generate the widget
self.browsingWidget = qtw.QWidget()
self.browsingLayout = qtw.QVBoxLayout(self.browsingWidget)
# Generate the radio buttons
self.imageTypeButtonGroupWidget = qtw.QWidget()
self.imageTypeButtonGroupLayout = qtw.QHBoxLayout(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.browsingLayout.addWidget(self.imageTypeButtonGroupWidget)
# Add the button to open a new file
self.browseEntry = CBrowse()
self.browseEntry.connectButton(self.browseImages)
self.browsingLayout.addWidget(self.browseEntry)
# Display the widget
self.browsingWidget.setLayout(self.browsingLayout)
parentWidget.addWidget(self.browsingWidget)
def createDirectoryBrowsingDisplay(self, parentWidget):
# Generate the widget
self.browsingWidget = qtw.QWidget()
self.browsingLayout = qtw.QVBoxLayout(self.browsingWidget)
# Add the button to open a new file
self.browseEntry = CBrowse()
self.browseEntry.connectButton(self.browseDirectory)
self.browsingLayout.addWidget(self.browseEntry)
# Display the widget
self.browsingWidget.setLayout(self.browsingLayout)
parentWidget.addWidget(self.browsingWidget)
def createTrajectorySelection(self, parentWidget):
# Generate the widget
self.trajectorySelectionWidget = qtw.QWidget()
self.trajectorySelectionLayout = qtw.QGridLayout(
self.trajectorySelectionWidget)
# Bitness selection
self.sourceSelectionGroupButton = qtw.QButtonGroup(
self.trajectorySelectionLayout)
current_row = 0
self.fromFileButton = qtw.QRadioButton("Load from File")
self.sourceSelectionGroupButton.addButton(self.fromFileButton)
self.trajectorySelectionLayout.addWidget(self.fromFileButton,
current_row,
0,
alignment=qtc.Qt.AlignLeft)
self.browseEntry = CBrowse()
self.browseEntry.lineEdit.setFixedWidth(250)
self.browseEntry.connectButton(self.browseTrajectory)
self.trajectorySelectionLayout.addWidget(self.browseEntry,
current_row,
1,
alignment=qtc.Qt.AlignRight)
current_row += 1
self.fromImageButton = qtw.QRadioButton("Load from Image")
self.fromImageButton.clicked.connect(self.getScaleFromImage)
self.sourceSelectionGroupButton.addButton(self.fromImageButton)
self.trajectorySelectionLayout.addWidget(self.fromImageButton,
current_row,
0,
alignment=qtc.Qt.AlignLeft)
self.processTrajectoryButton = qtw.QPushButton("PROCESS")
self.processTrajectoryButton.clicked.connect(self.processTrajectory)
self.processTrajectoryButton.setFixedWidth(150)
self.trajectorySelectionLayout.addWidget(self.processTrajectoryButton,
current_row,
1,
alignment=qtc.Qt.AlignRight)
# Display the widget
self.trajectorySelectionWidget.setLayout(
self.trajectorySelectionLayout)
parentWidget.addWidget(self.trajectorySelectionWidget)
class openImageWindow(qtw.QMainWindow, openImageFunctions):
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()
#self.setFixedSize(self.size())
# ---------------------------------------------------
# Reinitialise the display when the window is closed
def closeEvent(self, event=None):
event.accept()
self.parent.subWindows['open_image'] = None
##-\-\-\-\-\-\-\-\-\-\
## GENERATE THE DISPLAY
##-/-/-/-/-/-/-/-/-/-/
# ---------------------------------------
# Generate the display to browse the file
def createFileBrowsingDisplay(self, parentWidget):
# Generate the widget
self.browsingWidget = qtw.QWidget()
self.browsingLayout = qtw.QVBoxLayout(self.browsingWidget)
# Generate the radio buttons
self.imageTypeButtonGroupWidget = qtw.QWidget()
self.imageTypeButtonGroupLayout = qtw.QHBoxLayout(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.browsingLayout.addWidget(self.imageTypeButtonGroupWidget)
# Add the button to open a new file
self.browseEntry = CBrowse()
self.browseEntry.connectButton(self.browseImages)
self.browsingLayout.addWidget(self.browseEntry)
# Display the widget
self.browsingWidget.setLayout(self.browsingLayout)
parentWidget.addWidget(self.browsingWidget)
# ---------------------------------
# Generate the display of the image
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)
# ----------------------------------
# Generate the controls for the user
def createUserActions(self, parentWidget):
# Generate the widget
self.userActionsWidget = qtw.QWidget()
self.userActionsLayout = qtw.QHBoxLayout(self.userActionsWidget)
# Add the button to open a new file
self.loadButton = qtw.QPushButton("Load")
self.loadButton.clicked.connect(self.getImageFromPath)
self.loadButton.setStatusTip("Load the selected file or folder.")
self.loadButton.setFixedWidth(150)
self.loadButton.setEnabled(False)
self.userActionsLayout.addWidget(self.loadButton, alignment=qtc.Qt.AlignLeft)
# Add the button to close
self.closeButton = qtw.QPushButton("Close")
self.closeButton.clicked.connect(self.close)
self.closeButton.setStatusTip("Close the current window.")
self.closeButton.setFixedWidth(150)
self.userActionsLayout.addWidget(self.closeButton, alignment=qtc.Qt.AlignRight)
# Display the widget
self.userActionsWidget.setLayout(self.userActionsLayout)
parentWidget.addWidget(self.userActionsWidget)
class convertStackWindow(qtw.QMainWindow, convertStackFunctions):
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)
# ---------------------------------------------------
# Reinitialise the display when the window is closed
def closeEvent(self, event=None):
event.accept()
self.parent.subWindows['convert_stacks'] = None
##-\-\-\-\-\-\-\-\-\-\
## GENERATE THE DISPLAY
##-/-/-/-/-/-/-/-/-/-/
# ---------------------------------------
# Generate the display to browse the file
def createDirectoryBrowsingDisplay(self, parentWidget):
# Generate the widget
self.browsingWidget = qtw.QWidget()
self.browsingLayout = qtw.QVBoxLayout(self.browsingWidget)
# Add the button to open a new file
self.browseEntry = CBrowse()
self.browseEntry.connectButton(self.browseDirectory)
self.browsingLayout.addWidget(self.browseEntry)
# Display the widget
self.browsingWidget.setLayout(self.browsingLayout)
parentWidget.addWidget(self.browsingWidget)
# ---------------------------------
# Generate the display of the image
def createStackSelectionDisplay(self, parentWidget):
# Generate the widget
self.folderInfoWidget = qtw.QWidget()
self.folderInfoLayout = qtw.QVBoxLayout(self.folderInfoWidget)
# Generate the table of folders
self.foldersTable = qtw.QTableWidget(0, 4)
self.foldersTable.setHorizontalHeaderLabels(
['', 'Name', '# Images', 'Bitness'])
self.foldersTable.setSelectionMode(qtw.QAbstractItemView.NoSelection)
self.foldersTable.setEditTriggers(qtw.QAbstractItemView.NoEditTriggers)
self.foldersTable.setShowGrid(False)
self.foldersTable.setMinimumHeight(100)
self.folderInfoLayout.addWidget(self.foldersTable)
# Add the delete folder checkbox
self.deleteFoldersCheckbox = qtw.QCheckBox(
'Delete folder(s) after convertion?')
self.deleteFoldersCheckbox.setChecked(True)
self.folderInfoLayout.addWidget(self.deleteFoldersCheckbox)
# Display the widget
self.folderInfoWidget.setLayout(self.folderInfoLayout)
parentWidget.addWidget(self.folderInfoWidget)
# ----------------------------------
# Generate the controls for the user
def createUserActions(self, parentWidget):
# Generate the widget
self.userActionsWidget = qtw.QWidget()
self.userActionsLayout = qtw.QHBoxLayout(self.userActionsWidget)
# Add the button to open a new file
self.loadButton = qtw.QPushButton("Convert")
self.loadButton.clicked.connect(self.convertFolders)
self.loadButton.setStatusTip(
"Convert the selected image folders into image stacks.")
self.loadButton.setFixedWidth(150)
self.userActionsLayout.addWidget(self.loadButton,
alignment=qtc.Qt.AlignLeft)
# Add the button to close
self.closeButton = qtw.QPushButton("Close")
self.closeButton.clicked.connect(self.close)
self.closeButton.setStatusTip("Close the current window.")
self.closeButton.setFixedWidth(150)
self.userActionsLayout.addWidget(self.closeButton,
alignment=qtc.Qt.AlignRight)
# Display the widget
self.userActionsWidget.setLayout(self.userActionsLayout)
parentWidget.addWidget(self.userActionsWidget)
class particleDiffusionWindow(qtw.QMainWindow, particleDiffusionFunctions):
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()
# ---------------------------------------------------
# Reinitialise the display when the window is closed
def closeEvent(self, event=None):
event.accept()
self.parent.subWindows['msd_analysis'] = None
##-\-\-\-\-\-\-\-\-\-\
## GENERATE THE DISPLAY
##-/-/-/-/-/-/-/-/-/-/
# ----------------------------------------------------
# Generate the selection widgets to process the signal
def createTrajectorySelection(self, parentWidget):
# Generate the widget
self.trajectorySelectionWidget = qtw.QWidget()
self.trajectorySelectionLayout = qtw.QGridLayout(
self.trajectorySelectionWidget)
# Bitness selection
self.sourceSelectionGroupButton = qtw.QButtonGroup(
self.trajectorySelectionLayout)
current_row = 0
self.fromFileButton = qtw.QRadioButton("Load from File")
self.sourceSelectionGroupButton.addButton(self.fromFileButton)
self.trajectorySelectionLayout.addWidget(self.fromFileButton,
current_row,
0,
alignment=qtc.Qt.AlignLeft)
self.browseEntry = CBrowse()
self.browseEntry.lineEdit.setFixedWidth(250)
self.browseEntry.connectButton(self.browseTrajectory)
self.trajectorySelectionLayout.addWidget(self.browseEntry,
current_row,
1,
alignment=qtc.Qt.AlignRight)
current_row += 1
self.fromImageButton = qtw.QRadioButton("Load from Image")
self.fromImageButton.clicked.connect(self.getScaleFromImage)
self.sourceSelectionGroupButton.addButton(self.fromImageButton)
self.trajectorySelectionLayout.addWidget(self.fromImageButton,
current_row,
0,
alignment=qtc.Qt.AlignLeft)
self.processTrajectoryButton = qtw.QPushButton("PROCESS")
self.processTrajectoryButton.clicked.connect(self.processTrajectory)
self.processTrajectoryButton.setFixedWidth(150)
self.trajectorySelectionLayout.addWidget(self.processTrajectoryButton,
current_row,
1,
alignment=qtc.Qt.AlignRight)
# Display the widget
self.trajectorySelectionWidget.setLayout(
self.trajectorySelectionLayout)
parentWidget.addWidget(self.trajectorySelectionWidget)
# ----------------------------------------------------
# Generate the selection widgets to process the signal
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)
# ----------------------------------
# Generate the display for the graph
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)
# ----------------------------------
# Generate the controls for the user
def createUserActions(self, parentWidget):
# Generate the widget
self.userActionsWidget = qtw.QWidget()
self.userActionsLayout = qtw.QHBoxLayout(self.userActionsWidget)
# Add the button to open a new file
self.saveButton = qtw.QPushButton("Save in File")
self.saveButton.clicked.connect(self.saveData)
self.saveButton.setStatusTip("Save the results in a file.")
self.saveButton.setFixedWidth(150)
self.saveButton.setEnabled(False)
self.userActionsLayout.addWidget(self.saveButton,
alignment=qtc.Qt.AlignLeft)
# Add the button to close
self.closeButton = qtw.QPushButton("Close")
self.closeButton.clicked.connect(self.close)
self.closeButton.setStatusTip("Close the current window.")
self.closeButton.setFixedWidth(150)
self.userActionsLayout.addWidget(self.closeButton,
alignment=qtc.Qt.AlignRight)
# Display the widget
self.userActionsWidget.setLayout(self.userActionsLayout)
parentWidget.addWidget(self.userActionsWidget)