def __init__(self, data, size, params):
self.camera = params.get("acquisition.camera", "camera1")
self.data = data
self.height = size[0]
# Pre HAL2 movies.
if params.has(self.camera + ".scalemin"):
self.image_min = params.get(self.camera + ".scalemin")
self.image_max = params.get(self.camera + ".scalemax")
else:
self.image_min = params.get("display00.camera1.display_min")
self.image_max = params.get("display00.camera1.display_max")
self.parameters = params
self.parameters_file = params.get("parameters_file", "NA")
self.width = size[1]
location = list(
map(float,
params.get("acquisition.stage_position").split(",")))
self.x_um = location[0]
self.y_um = location[1]
# Calculate location in pixels.
a_point = coord.Point(self.x_um, self.y_um, "um")
self.x_pix = a_point.x_pix
self.y_pix = a_point.y_pix
def loadFromMosaicFileData(self, data, directory):
if (data[0] == "section"):
self.addSection(coord.Point(float(data[2]), float(data[3]), "um"),
float(data[4]))
return True
else:
return False
def loadPositions(self, filename):
pos_fp = open(filename, "r")
while 1:
line = pos_fp.readline()
if not line: break
[x, y] = line.split(",")
self.addPosition(coord.Point(float(x), float(y), "um"))
def __init__(self, comm=None, item_store=None, parameters=None, **kwds):
super().__init__(**kwds)
self.comm = comm
self.current_center = coord.Point(0.0, 0.0, "um")
self.current_z = 0.0
self.directory = parameters.get("directory")
self.extrapolate_count = parameters.get("extrapolate_picture_count")
self.filename = parameters.get("image_filename")
self.fractional_overlap = parameters.get("fractional_overlap", 0.05)
self.grid_size = []
self.item_store = item_store
self.last_image = None
self.movie_queue = []
self.objectives = None
self.smc = None
self.z_inc = 0.01
# The idea is that in the future other modules might want to
# change how movies are taken and loaded. This will hopefully
# make this easier.
#
# This class handles creating a SteveItem() from the movie.
self.movie_loader = None
# This class handles taking the movie.
self.movie_taker = None
def loadPositions(self, filename):
with open(filename) as fp:
for line in fp:
try:
[x, y] = line.split(",")
self.addPosition(coord.Point(float(x), float(y), "um"))
except ValueError:
pass
def handleTakeMovie(self, ignored):
"""
Handle movies triggered from the context menu and the space bar key.
"""
self.image_capture.takeMovies([
coord.Point(self.mosaic_event_coord.x_um,
self.mosaic_event_coord.y_um, "um")
])
def handleMouseMove(self, a_point):
# Not sure whether I should include the offset here.
# offset_point = coord.Point(a_point.x_um - self.current_offset.x_um,
# a_point.y_um - self.current_offset.y_um,
# "um")
offset_point = coord.Point(a_point.x_um, a_point.y_um, "um")
self.ui.mosaicLabel.setText("{0:.2f}, {1:.2f}".format(
offset_point.x_um, offset_point.y_um))
def getCurrentOffset(self):
"""
Return the offset of the current objective.
The current objective should always be the one that was used to take the
last movie and/or the one that was returned by HAL when queried.
"""
objective_name = self.getCurrentName()
if objective_name is not None:
[obj_um_per_pix, x_offset_um,
y_offset_um] = self.getData(objective_name)
return coord.Point(x_offset_um, y_offset_um, "um")
def handleGetPositionComplete(self, a_point):
if not self.requested_stage_pos:
# Update cross hair
offset_point = coord.Point(a_point.x_um + self.current_offset.x_um,
a_point.y_um + self.current_offset.y_um,
"um")
self.view.setCrosshairPosition(offset_point.x_pix,
offset_point.y_pix)
else:
self.requested_stage_pos = False
self.ui.xStartPosSpinBox.setValue(a_point.x_um)
self.ui.yStartPosSpinBox.setValue(a_point.y_um)
self.comm.commDisconnect()
def handleTakeSpiral(self, n_pictures):
"""
Handle taking a spiral pattern.
"""
movie_queue = []
# Starting point.
movie_queue.append(
coord.Point(self.mosaic_event_coord.x_um,
self.mosaic_event_coord.y_um, "um"))
# Spiral.
movie_queue += imageCapture.createSpiral(n_pictures)
self.image_capture.takeMovies(movie_queue)
def addImage(self, image):
# If image is not an object then we are done.
if not image:
self.toggleTakingPicturesStatus(False)
self.comm.commDisconnect()
return
objective = image.parameters.get(
"mosaic." + image.parameters.get("mosaic.objective")).split(",")[0]
[um_per_pixel, x_offset,
y_offset] = self.ui.objectivesGroupBox.getData(objective)
magnification = coord.Point.pixels_to_um / um_per_pixel
self.current_offset = coord.Point(x_offset, y_offset, "um")
self.view.addImage(image, objective, magnification,
self.current_offset)
self.view.setCrosshairPosition(image.x_pix, image.y_pix)
if (len(self.picture_queue) > 0):
next_item = self.picture_queue[0]
if (type(next_item) == type(coord.Point(0, 0, "um"))):
self.setCenter(next_item)
next_x_um = self.current_center.x_um
next_y_um = self.current_center.y_um
else:
[tx, ty] = next_item
next_x_um = self.current_center.x_um + 0.95 * float(
image.width) * coord.Point.pixels_to_um * tx / magnification
next_y_um = self.current_center.y_um + 0.95 * float(
image.height
) * coord.Point.pixels_to_um * ty / magnification
self.picture_queue = self.picture_queue[1:]
self.comm.captureStart(next_x_um, next_y_um)
else:
if self.taking_pictures:
self.toggleTakingPicturesStatus(False)
self.comm.commDisconnect()
def handleImageGrid(self, dummy):
if not self.taking_pictures:
# Build position list
pos_list = mosaicView.createGrid(self.ui.xSpinBox.value(),
self.ui.ySpinBox.value())
# Define first position
first_pos = coord.Point(self.ui.xStartPosSpinBox.value(),
self.ui.yStartPosSpinBox.value(), "um")
pos_list.insert(0, first_pos)
# Take pictures
self.takePictures(pos_list)
else: # Abort button
self.picture_queue = []
def mousePressEvent(self, event):
"""
If the left mouse button is pressed then the view is centered on the current cursor position.
If the right mouse button is pressed then the current location of the cursor in the scene
is recorded. If self.extrapolate_start exists then self.handleExtrapolatePict() is called,
otherwise the popup menu is displayed.
"""
if event.button() == QtCore.Qt.LeftButton:
self.centerOn(self.mapToScene(event.pos()))
elif event.button() == QtCore.Qt.RightButton:
pointf = self.mapToScene(event.pos())
a_coord = coord.Point(pointf.x(), pointf.y(), "pix")
if self.extrapolate_start:
self.extrapolateTakeMovie.emit(a_coord)
else:
self.mosaicViewContextMenuEvent.emit(event, a_coord)
def handleTakeGrid(self):
"""
Handle taking a grid pattern.
"""
movie_queue = []
# Starting point.
movie_queue.append(
coord.Point(self.mosaic_event_coord.x_um,
self.mosaic_event_coord.y_um, "um"))
# Grid.
movie_queue += imageCapture.createGrid(self.ui.xSpinBox.value(),
self.ui.ySpinBox.value())
self.image_capture.takeMovies(movie_queue)
def handleMessageReceived(self, message):
if message.hasError():
hdebug.logText("tcp error: " + message.getErrorMessage())
self.messages = []
self.waiting_for_response = False
return
#
# If the message does not involve taking a movie and there are no more
# messages then emit the otherComplete signal.
#
if (message.getData("is_other") == True) and (len(self.messages) == 0):
self.otherComplete.emit()
if (message.getType() == "Get Mosaic Settings"):
self.got_settings = True
#coord.Point.pixels_to_um = message.getResponse("pixels_to_um")
i = 1
while message.getResponse("obj" + str(i)) is not None:
self.newObjectiveData.emit(
message.getResponse("obj" + str(i)).split(","))
i += 1
if (message.getType() == "Get Objective"):
if self.curr_objective is None or (
self.curr_objective != message.getResponse("objective")):
self.curr_objective = message.getResponse("objective")
self.changeObjective.emit(self.curr_objective)
if (message.getType() == "Get Stage Position"):
a_point = coord.Point(message.getResponse("stage_x"),
message.getResponse("stage_y"), "um")
self.getPositionComplete.emit(a_point)
#
# self.loadImage() will emit the captureComplete signal.
#
if (message.getType() == "Take Movie"):
self.loadImage(self.directory + message.getData("name") + ".dax")
if (len(self.messages) > 0):
self.tcp_client.sendMessage(self.messages.pop(0))
else:
self.waiting_for_response = False
def keyPressEvent(self, event):
"""
Handles key press events. Valid events are:
'space' Take a picture.
'3' Take a 3 picture spiral.
'5' Take a 5 picture spiral.
'7' Take a 7 picture spiral.
'9' Take a 9 picture spiral.
'g' Take a grid of pictures.
'p' Add the current cursor position to the list of positions.
's' Add the current cursor position to the list of sections.
"""
event_pos = self.mapFromGlobal(QtGui.QCursor.pos())
pointf = self.mapToScene(event_pos)
a_coord = coord.Point(pointf.x(), pointf.y(), "pix")
self.mosaicViewKeyPressEvent.emit(event, a_coord)
super().keyPressEvent(event)
def handleExtrapolateTakeMovie(self, a_coord):
"""
This is called on the next right click after the extrapolate action was selected.
"""
movie_queue = []
# Starting point.
x_um = a_coord.x_um + (a_coord.x_um -
self.mosaic_view.extrapolate_start.x_um)
y_um = a_coord.y_um + (a_coord.y_um -
self.mosaic_view.extrapolate_start.y_um)
movie_queue.append(coord.Point(x_um, y_um, "um"))
# Spiral.
movie_queue += imageCapture.createSpiral(self.extrapolate_count)
self.mosaic_view.extrapolate_start = None
self.image_capture.takeMovies(movie_queue)
def handleImageGridButton(self, ignored):
"""
Handle taking a grid pattern when the 'Acquire' button is clicked.
"""
movie_queue = []
# Starting point.
x_start_um = self.ui.xStartPosSpinBox.value()
y_start_um = self.ui.yStartPosSpinBox.value()
movie_queue.append(coord.Point(x_start_um, y_start_um, "um"))
# Grid.
movie_queue += imageCapture.createGrid(self.ui.xSpinBox.value(),
self.ui.ySpinBox.value())
self.ui.imageGridButton.setText("Abort")
self.ui.imageGridButton.setStyleSheet("QPushButton { color: red }")
self.image_capture.takeMovies(movie_queue)
def takeSingleMovie(self, movie_pos):
"""
This takes a single movie as the specified position corrected
for the current offset.
Clients should not use this method, they should always takeMovies().
"""
current_offset = self.objectives.getCurrentOffset()
# Bail out if we don't have any objectives information. This
# probably means HAL is not running or we can't talk to it.
if current_offset is None:
return
pos = coord.Point(movie_pos.x_um - current_offset.x_um,
movie_pos.y_um - current_offset.y_um, "um")
self.smc = self.movie_taker(comm_instance=self.comm,
disconnect=False,
directory=self.directory,
filename=self.filename,
finalizer_fn=self.handleMovieTaken,
pos=pos)
return self.smc.start()
def nextMovie(self):
"""
Take the next movie, or disconnect if there are no more movies to take.
"""
if (len(self.movie_queue) > 0):
# Figure out where to take the movie.
elt = self.movie_queue[0]
if isinstance(elt, list):
[dx, dy] = elt
[im_x_um, im_y_um] = self.last_image.getSizeUm()
next_x_um = self.current_center.x_um + (
1.0 - self.fractional_overlap) * im_x_um * dx
next_y_um = self.current_center.y_um + (
1.0 - self.fractional_overlap) * im_y_um * dy
movie_pos = coord.Point(next_x_um, next_y_um, "um")
else:
self.current_center = elt
movie_pos = elt
# Remove from the queue.
self.movie_queue = self.movie_queue[1:]
# Take the movie, checking for failure to communicate with HAL.
if not self.takeSingleMovie(movie_pos):
self.movie_queue = []
self.smc = None
self.sequenceComplete.emit()
else:
self.comm.stopCommunication()
self.smc = None
self.sequenceComplete.emit()
def mouseMoveEvent(self, event):
"""
Tracks mouse movements across the view.
"""
pointf = self.mapToScene(event.pos())
self.mouseMove.emit(coord.Point(pointf.x(), pointf.y(), "pix"))
def updateMosaicLabel(self, a_point):
offset_point = coord.Point(a_point.x_um - self.current_offset.x_um,
a_point.y_um - self.current_offset.y_um,
"um")
self.ui.mosaicLabel.setText("{0:.2f}, {1:.2f}".format(
offset_point.x_um, offset_point.y_um))
def __init__(self, parameters, parent=None):
QtWidgets.QMainWindow.__init__(self, parent)
# Coordinate system setup, the internal scale is 1 pixel is 100nm.
coord.Point.pixels_to_um = 0.1
# variables
self.current_center = coord.Point(0.0, 0.0, "um")
self.current_offset = coord.Point(0.0, 0.0, "um")
self.debug = parameters.get("debug")
self.file_filter = "\S+.dax"
self.parameters = parameters
self.picture_queue = []
self.regexp_str = ""
self.requested_stage_pos = False
self.settings = QtCore.QSettings("storm-control", "steve")
self.snapshot_directory = self.parameters.get("directory")
self.spin_boxes = []
self.stage_tracking_timer = QtCore.QTimer(self)
self.taking_pictures = False
self.stage_tracking_timer.setInterval(500)
# ui setup
self.ui = steveUi.Ui_MainWindow()
self.ui.setupUi(self)
self.move(self.settings.value("position", self.pos()))
self.resize(self.settings.value("size", self.size()))
# hide some things that we don't currently use & resize group-box.
self.ui.backgroundComboBox.hide()
self.ui.backgroundLabel.hide()
self.ui.moveAllSectionsCheckBox.hide()
self.ui.showFeaturesCheckBox.hide()
self.ui.thresholdLabel.hide()
self.ui.thresholdSlider.hide()
self.ui.sectionViewSettingsGroupBox.setMaximumHeight(50)
self.setWindowIcon(QtGui.QIcon("steve.ico"))
# handling file drops
self.ui.centralwidget.__class__.dragEnterEvent = self.dragEnterEvent
self.ui.centralwidget.__class__.dropEvent = self.dropEvent
self.ui.centralwidget.setAcceptDrops(True)
# Create a validator for scaleLineEdit.
self.scale_validator = QtGui.QDoubleValidator(1.0e-6, 1.0e+6, 6,
self.ui.scaleLineEdit)
self.ui.scaleLineEdit.setValidator(self.scale_validator)
# Initialize view.
self.view = mosaicView.MosaicView(parameters, self.ui.mosaicFrame)
layout = QtWidgets.QGridLayout(self.ui.mosaicFrame)
layout.addWidget(self.view)
self.ui.mosaicFrame.setLayout(layout)
self.view.show()
# Initialize positions list.
self.positions = positions.Positions(parameters, self.view.getScene(),
self.ui.positionsFrame)
layout = QtWidgets.QGridLayout(self.ui.positionsFrame)
layout.addWidget(self.positions)
self.ui.positionsFrame.setLayout(layout)
self.positions.show()
# Initialize sections.
self.sections = sections.Sections(parameters, self.view.getScene(),
self.ui.sectionsDisplayFrame,
self.ui.sectionsScrollArea,
self.ui.sectionsTab)
# Initialize communications.
self.comm = capture.Capture(parameters)
# signals
self.ui.actionQuit.triggered.connect(self.quit)
self.ui.actionAdjust_Contrast.triggered.connect(
self.handleAdjustContrast)
self.ui.actionDelete_Images.triggered.connect(self.handleDeleteImages)
self.ui.actionLoad_Movie.triggered.connect(self.handleLoadMovie)
self.ui.actionLoad_Mosaic.triggered.connect(self.handleLoadMosaic)
self.ui.actionLoad_Positions.triggered.connect(
self.handleLoadPositions)
self.ui.actionSave_Mosaic.triggered.connect(self.handleSaveMosaic)
self.ui.actionSave_Positions.triggered.connect(
self.handleSavePositions)
self.ui.actionSave_Snapshot.triggered.connect(self.handleSnapshot)
self.ui.actionSet_Working_Directory.triggered.connect(
self.handleSetWorkingDirectory)
self.ui.foregroundOpacitySlider.valueChanged.connect(
self.handleOpacityChange)
self.ui.getStagePosButton.clicked.connect(self.handleGetStagePosButton)
self.ui.imageGridButton.clicked.connect(self.handleImageGrid)
self.ui.scaleLineEdit.textEdited.connect(self.handleScaleChange)
self.ui.tabWidget.currentChanged.connect(self.handleTabChange)
self.ui.trackStageCheckBox.stateChanged.connect(self.handleTrackStage)
self.ui.xSpinBox.valueChanged.connect(self.handleGridChange)
self.ui.ySpinBox.valueChanged.connect(self.handleGridChange)
self.stage_tracking_timer.timeout.connect(
self.handleStageTrackingTimer)
self.view.addPosition.connect(self.addPositions)
self.view.addSection.connect(self.addSection)
self.view.getObjective.connect(self.handleGetObjective)
self.view.gotoPosition.connect(self.gotoPosition)
self.view.mouseMove.connect(self.updateMosaicLabel)
self.view.scaleChange.connect(self.updateScaleLineEdit)
self.view.takePictures.connect(self.takePictures)
self.sections.addPositions.connect(self.addPositions)
self.sections.takePictures.connect(self.takePictures)
self.comm.captureComplete.connect(self.addImage)
self.comm.changeObjective.connect(self.handleChangeObjective)
self.comm.disconnected.connect(self.handleDisconnected)
self.comm.getPositionComplete.connect(self.handleGetPositionComplete)
self.comm.newObjectiveData.connect(self.handleNewObjectiveData)
self.comm.otherComplete.connect(self.handleOtherComplete)
self.ui.objectivesGroupBox.valueChanged.connect(
self.handleMOValueChange)
# Try and get settings from HAL.
self.comm.commConnect()
self.comm.getSettings()
def currentLocation(self):
return coord.Point(self.x_spin_box.value(), self.y_spin_box.value(),
"um")
def load(self, directory, index, x, y, angle):
section_item = SectionItem(
a_point=coord.Point(float(x), float(y), "um"))
section_item.setAngle(float(angle))
return section_item
def load(self, directory, x, y):
return PositionItem(coord.Point(float(x), float(y), "um"))
def handleChangeObjective(self, objective):
self.ui.objectivesGroupBox.changeObjective(objective)
[magnification, x_offset,
y_offset] = self.ui.objectivesGroupBox.getData(objective)
self.current_offset = coord.Point(x_offset, y_offset, "um")
def setCenter(self, a_point):
x_um = a_point.x_um - self.current_offset.x_um
y_um = a_point.y_um - self.current_offset.y_um
self.current_center = coord.Point(x_um, y_um, "um")
def movePosition(self, dx_um, dy_um):
a_point = coord.Point(self.a_point.x_um + dx_um,
self.a_point.y_um + dy_um, "um")
self.setLocation(a_point)
def handleExtrapolate(self, ignored):
"""
This is called when the extrapolate action is selected from the context menu.
"""
self.mosaic_view.extrapolate_start = coord.Point(
self.mosaic_event_coord.x_um, self.mosaic_event_coord.y_um, "um")