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 handleExtrapolatePict(self):
pict_x = self.pointf.x() + (self.pointf.x() - self.extrapolate_start.x())
pict_y = self.pointf.y() + (self.pointf.y() - self.extrapolate_start.y())
self.extrapolate_start = None
pic_list = [coord.Point(pict_x, pict_y, "pix")]
pic_list.extend(createSpiral(self.extrapolate_count))
self.takePictures.emit(pic_list)
def addImage(self, image):
# If image is not an object then we are done.
if not image:
self.taking_pictures = False
self.comm.commDisconnect()
return
self.view.addImage(image, self.current_objective,
self.current_magnification, self.current_offset)
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
) * self.parameters.pixels_to_um * tx / self.current_magnification
next_y_um = self.current_center.y_um + 0.95 * float(
image.height
) * self.parameters.pixels_to_um * ty / self.current_magnification
self.picture_queue = self.picture_queue[1:]
self.comm.captureStart(next_x_um, next_y_um)
else:
if self.taking_pictures:
self.taking_pictures = False
self.comm.commDisconnect()
def handleMOValueChange(self, objective, box_type, value):
if (box_type == "magnification"):
value = value / 100.0
if (objective == self.current_objective):
self.current_magnification = value
self.view.changeMagnification(objective, value)
elif (box_type == "xoffset"):
if (objective == self.current_objective):
self.current_offset = coord.Point(value,
self.current_offset.y_um,
"um")
self.view.changeXOffset(objective, coord.umToPix(value))
elif (box_type == "yoffset"):
if (objective == self.current_objective):
self.current_offset = coord.Point(self.current_offset.x_um,
value, "um")
self.view.changeYOffset(objective, coord.umToPix(value))
else:
print "unknown box type:", box_type
def handleObjectiveChange(self, mag_index):
data = self.ui.magComboBox.itemData(mag_index).toString()
if data:
data = data.split(",")
if (mag_index == 0):
[mag, x_offset, y_offset] = map(float, data[1:])
else:
[mag, x_offset, y_offset] = findMO(data[0], self.spin_boxes)
mag = mag / 100.0
self.current_objective = data[0]
self.current_magnification = mag
self.current_offset = coord.Point(x_offset, y_offset, "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 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 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 __init__(self, data, size, params):
self.camera = params.get("acquisition.camera")
self.data = data
self.height = size[0]
self.image_min = params.get(self.camera + ".scalemin")
self.image_max = params.get(self.camera + ".scalemax")
self.parameters = params
self.parameters_file = params.get("parameters_file")
self.width = size[1]
location = params.get("acquisition.stage_position")
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 movePosition(self, dx_um, dy_um):
self.a_point = coord.Point(self.a_point.x_um + dx_um,
self.a_point.y_um + dy_um, "um")
self.setLocation(self.a_point)
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 handleGoto(self, boolean):
self.gotoPosition.emit(
coord.Point(self.pointf.x(), self.pointf.y(), "pix"))
def __init__(self, parameters, parent=None):
QtGui.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.debug
self.file_filter = "\S+.dax"
self.parameters = parameters
self.picture_queue = []
self.regexp_str = ""
self.requested_stage_pos = False
self.stage_tracking_timer = QtCore.QTimer(self)
self.taking_pictures = False
self.snapshot_directory = self.parameters.directory
self.spin_boxes = []
self.stage_tracking_timer.setInterval(500)
# ui setup
self.ui = steveUi.Ui_MainWindow()
self.ui.setupUi(self)
# 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 = QtGui.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 = QtGui.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 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 handlePos(self, boolean):
self.addPosition.emit(
[coord.Point(self.pointf.x(), self.pointf.y(), "pix")])
def handlePictures(self, positions):
pic_list = [coord.Point(self.pointf.x(), self.pointf.y(), "pix")]
pic_list.extend(positions)
self.takePictures.emit(pic_list)
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 handleSec(self, boolean):
self.addSection.emit(
coord.Point(self.pointf.x(), self.pointf.y(), "pix"))
def mouseMoveEvent(self, event):
pointf = self.mapToScene(event.pos())
self.mouseMove.emit(coord.Point(pointf.x(), pointf.y(), "pix"))
def currentLocation(self):
return coord.Point(self.x_spin_box.value(), self.y_spin_box.value(),
"um")
def __init__(self, parameters, parent=None):
QtGui.QMainWindow.__init__(self, parent)
# coordinate system setup
coord.Point.pixels_to_um = parameters.pixels_to_um
# variables
self.current_center = coord.Point(0.0, 0.0, "um")
self.current_magnification = 1.0
self.current_objective = False
self.current_offset = coord.Point(0.0, 0.0, "um")
self.debug = parameters.debug
self.parameters = parameters
self.picture_queue = []
self.taking_pictures = False
# ui setup
self.ui = steveUi.Ui_MainWindow()
self.ui.setupUi(self)
# 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"))
# Initialize objectives.
objectives = []
for i in range(10):
mag = "mag" + str(i)
if hasattr(self.parameters, mag):
data = getattr(self.parameters, mag)
obj_name = data.split(",")[0]
objectives.append(data)
self.ui.magComboBox.addItem(obj_name, data)
# Create labels and spin boxes for objective settings.
self.spin_boxes = []
layout = QtGui.QGridLayout(self.ui.objectivesFrame)
for i, label_text in enumerate(
["Objective", "Magnification", "X Offset", "Y Offset"]):
text_item = QtGui.QLabel(label_text, self.ui.objectivesFrame)
layout.addWidget(text_item, 0, i)
# The first objective is assumed to be the 100x & is not adjustable.
data = objectives[0].split(",")
self.current_objective = data[0]
for j, datum in enumerate(data):
text_item = QtGui.QLabel(datum, self.ui.objectivesFrame)
layout.addWidget(text_item, 1, j)
# The other objectives are adjustable.
for i, obj in enumerate(objectives[1:]):
data = obj.split(",")
text_item = QtGui.QLabel(data[0], self.ui.objectivesFrame)
layout.addWidget(text_item, i + 2, 0)
for j, btype in enumerate(["magnification", "xoffset", "yoffset"]):
sbox = MagOffsetSpinBox(data[0], btype, float(data[j + 1]))
layout.addWidget(sbox, i + 2, j + 1)
sbox.moValueChange.connect(self.handleMOValueChange)
self.spin_boxes.append(sbox)
# Create a validator for scaleLineEdit.
self.sce_validator = QtGui.QDoubleValidator(1.0e-6, 1.0e+6, 6,
self.ui.scaleLineEdit)
self.ui.scaleLineEdit.setValidator(self.sce_validator)
# Initialize view.
self.view = mosaicView.MosaicView(parameters, self.ui.mosaicFrame)
layout = QtGui.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 = QtGui.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.abortButton.clicked.connect(self.handleAbort)
self.ui.actionQuit.triggered.connect(self.quit)
self.ui.actionDelete_Images.triggered.connect(self.handleDeleteImages)
self.ui.actionLoad_Dax.triggered.connect(self.handleLoadDax)
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.magComboBox.currentIndexChanged.connect(
self.handleObjectiveChange)
self.ui.scaleLineEdit.textEdited.connect(self.handleScaleChange)
self.ui.tabWidget.currentChanged.connect(self.handleTabChange)
self.ui.xSpinBox.valueChanged.connect(self.handleGridChange)
self.ui.ySpinBox.valueChanged.connect(self.handleGridChange)
self.view.addPosition.connect(self.addPositions)
self.view.addSection.connect(self.addSection)
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.disconnected.connect(self.handleDisconnected)
self.comm.gotoComplete.connect(self.handleGotoComplete)
self.handleObjectiveChange(0)
