def test_parameters_5():
# Load parameters.
p1 = params.parameters(test.xmlFilePathAndName("test_parameters.xml"),
recurse=True,
add_filename_param=False)
# Save.
p1.saveToFile("temp.xml")
# Re-load.
p2 = params.parameters("temp.xml", recurse=True, add_filename_param=False)
# Check that they are the same.
assert (len(params.difference(p1, p2)) == 0) and (len(
params.difference(p2, p1)) == 0)
def test_parameters_3():
# Load parameters.
p1 = params.parameters(test.xmlFilePathAndName("test_parameters.xml"), recurse = True)
# Test sub-section creation.
p2 = params.StormXMLObject()
p2s = p2.addSubSection("camera1", p1.get("camera1").copy())
p2s.add(params.ParameterInt(name = "test", value = 5))
# p2 is different then p1 because it has 'test'.
assert (params.difference(p2.get("camera1"), p1.get("camera1"))[0] == "test")
# But p1 is not different from p2 because difference() only
# checks p1 properties that exist in p1.
assert (len(params.difference(p1.get("camera1"), p2.get("camera1"))) == 0)
def test_parameters_5():
# Load parameters.
p1 = params.parameters(test.xmlFilePathAndName("test_parameters.xml"),
recurse = True,
add_filename_param = False)
# Save.
p1.saveToFile("temp.xml")
# Re-load.
p2 = params.parameters("temp.xml",
recurse = True,
add_filename_param = False)
# Check that they are the same.
assert (len(params.difference(p1, p2)) == 0) and (len(params.difference(p2, p1)) == 0)
def test_parameters_3():
# Load parameters.
p1 = params.parameters(test.xmlFilePathAndName("test_parameters.xml"),
recurse=True)
# Test sub-section creation.
p2 = params.StormXMLObject()
p2s = p2.addSubSection("camera1", p1.get("camera1").copy())
p2s.add(params.ParameterInt(name="test", value=5))
# p2 is different then p1 because it has 'test'.
assert (params.difference(p2.get("camera1"),
p1.get("camera1"))[0] == "test")
# But p1 is not different from p2 because difference() only
# checks p1 properties that exist in p1.
assert (len(params.difference(p1.get("camera1"), p2.get("camera1"))) == 0)
def newParameters(self, parameters, initialization = False):
if initialization:
changed_p_names = parameters.getAttrs()
else:
changed_p_names = params.difference(parameters, self.parameters)
p = parameters
for pname in changed_p_names:
print(pname)
# Update our current parameters.
self.parameters.setv(pname, p.get(pname))
# Configure the W1.
if (pname == "bright_field_bypass"):
if p.get("bright_field_bypass"):
self.w1.commandResponse("BF_ON", 1)
else:
self.w1.commandResponse("BF_OFF", 1)
elif (pname == "spin_disk"):
if p.get("spin_disk"):
self.w1.commandResponse("MS_RUN", 3)
else:
self.w1.commandResponse("MS_STOP", 1)
elif (pname == "disk"):
if (p.get("disk") == "50-micron pinholes"):
r = self.w1.commandResponse("DC_SLCT,1", 3)
elif (p.get("disk") == "25-micron pinholes"):
r = self.w1.commandResponse("DC_SLCT,2", 3)
print("disk")
print(r)
elif (pname == "disk_speed"):
self.w1.commandResponse("MS,"+str(p.get("disk_speed")), 1)
elif (pname == "dichroic_mirror"):
dichroic_num = self.dichroic_mirror_config[p.get("dichroic_mirror")]
r = self.w1.commandResponse("DMM_POS,1,"+str(dichroic_num), 1)
print(r)
a = self.w1.commandResponse("DMM_POS,1,?", 1)
print(a)
elif (pname == "filter_wheel_pos1"):
filter1_num = self.filter_wheel_1_config[p.get("filter_wheel_pos1")]
print("filter wheel position")
c = self.w1.commandResponse("FW_POS,1," + str(filter1_num) , 1)
print(c)
a = self.w1.commandResponse("FW_POS,1,?", 1)
print(a)
else:
print(">> Warning", str(pname), " is not a valid parameter for the W1")
def test_parameters_2():
# Load parameters.
p1 = params.parameters(test.xmlFilePathAndName("test_parameters.xml"), recurse = True)
# Copy.
p2 = p1.copy()
# Check that p1 and p2 store the same values and have
# the same structure.
assert (len(params.difference(p1, p2)) == 0)
# Change a value in p2.
p2.set("camera1.flip_horizontal", True)
# Check that p1 is still the same.
assert (p1.get("camera1.flip_horizontal") == False)
# Get the difference between p1 and p2.
assert (params.difference(p1, p2)[0] == 'camera1.flip_horizontal')
def test_parameters_2():
# Load parameters.
p1 = params.parameters(test.xmlFilePathAndName("test_parameters.xml"),
recurse=True)
# Copy.
p2 = p1.copy()
# Check that p1 and p2 store the same values and have
# the same structure.
assert (len(params.difference(p1, p2)) == 0)
# Change a value in p2.
p2.set("camera1.flip_horizontal", True)
# Check that p1 is still the same.
assert (p1.get("camera1.flip_horizontal") == False)
# Get the difference between p1 and p2.
assert (params.difference(p1, p2)[0] == 'camera1.flip_horizontal')
def newParameters(self, parameters, initialization = False):
if initialization:
changed_p_names = parameters.getAttrs()
else:
changed_p_names = params.difference(parameters, self.parameters)
p = parameters
for pname in changed_p_names:
# Update our current parameters.
self.parameters.setv(pname, p.get(pname))
# Configure the W1.
if (pname == "bright_field_bypass"):
if p.get("bright_field_bypass"):
self.w1.commandResponse("BF_ON", 1)
else:
self.w1.commandResponse("BF_OFF", 1)
elif (pname == "spin_disk"):
if p.get("spin_disk"):
self.w1.commandResponse("MS_RUN", 3)
else:
self.w1.commandResponse("MS_STOP", 1)
elif (pname == "disk"):
if (p.get("disk") == "50-micron pinholes"):
self.w1.commandResponse("DC_SLCT,1", 3)
elif (p.get("disk") == "25-micron pinholes"):
self.w1.commandResponse("DC_SLCT,2", 3)
elif (pname == "disk_speed"):
self.w1.commandResponse("MS,"+str(p.get("disk_speed")), 1)
elif (pname == "dichroic_mirror"):
dichroic_num = self.dichroic_mirror_config[p.get("dichroic_mirror")]
self.w1.commandResponse("DMM_POS,1,"+str(dichroic_num), 1)
elif (pname == "filter_wheel_pos1") or (pname == "filter_wheel_pos2"):
filter1_num = self.filter_wheel_1_config[p.get("filter_wheel_pos1")]
filter2_num = self.filter_wheel_2_config[p.get("filter_wheel_pos2")]
self.w1.commandResponse("FW_POS,0," + str(filter1_num) + "," + str(filter2_num), 0.1)
elif (pname == "camera_dichroic_mirror"):
camera_dichroic_num = self.camera_dichroic_config[p.get("camera_dichroic_mirror")]
self.w1.commandResponse("PT_POS,1," + str(camera_dichroic_num), 1)
elif (pname == "aperture"):
self.w1.commandResponse("AP_WIDTH,1,"+str(p.get("aperture")), 0.5)
else:
print(">> Warning", str(pname), " is not a valid parameter for the W1")
def __init__(self, configuration=None, **kwds):
super().__init__(**kwds)
self.current_mode = None
self.modes = []
self.parameters = params.StormXMLObject()
self.ui = focuslockUi.Ui_Dialog()
self.ui.setupUi(self)
# Add parameters
self.parameters.add(
params.ParameterFloat(description="Z stage jump size",
name="jump_size",
value=0.1))
# Set up lock display.
self.lock_display = lockDisplay.LockDisplay(
configuration=configuration, jump_signal=self.jump, parent=self)
layout = QtWidgets.QGridLayout(self.ui.lockDisplayWidget)
layout.setContentsMargins(0, 0, 0, 0)
layout.addWidget(self.lock_display)
# Configure modes.
lockModes.FindSumMixin.addParameters(self.parameters)
lockModes.LockedMixin.addParameters(self.parameters)
lockModes.ScanMixin.addParameters(self.parameters)
for mode_class_name in configuration.get("lock_modes").split(","):
a_class = getattr(lockModes, mode_class_name.strip())
a_object = a_class(parameters=self.parameters, parent=self)
self.ui.modeComboBox.addItem(a_object.getName())
self.modes.append(a_object)
# Set parameters values based on the config file parameters.
c_params = configuration.get("parameters")
for attr in params.difference(c_params, self.parameters):
print(attr, c_params.get(attr))
self.parameters.setv(attr, c_params.get(attr))
self.newParameters(self.parameters)
# Connect signals.
self.ui.jumpNButton.clicked.connect(self.handleJumpNButton)
self.ui.jumpPButton.clicked.connect(self.handleJumpPButton)
self.ui.lockButton.clicked.connect(self.handleLockButton)
self.ui.lockTargetSpinBox.valueChanged.connect(self.handleLockTarget)
self.ui.modeComboBox.currentIndexChanged.connect(
self.handleModeComboBox)
self.setEnabled(False)
def newParameters(self, parameters, initialization=False):
if initialization:
changed_p_names = parameters.getAttrs()
else:
changed_p_names = params.difference(parameters, self.parameters)
p = parameters
for pname in changed_p_names:
print(pname)
# Update our current parameters.
self.parameters.setv(pname, p.get(pname))
# Configure the W1.
if (pname == "bright_field_bypass"):
if p.get("bright_field_bypass"):
self.w1.commandResponse("D0", 3)
else:
self.w1.commandResponse("D1", 3)
elif (pname == "spin_disk"):
if p.get("spin_disk"):
self.w1.commandResponse("N1", 1)
else:
self.w1.commandResponse("N0", 1)
elif (pname == "disk"):
if (p.get("disk") == "70-micron pinholes"):
r = self.w1.commandResponse("D1", 3)
elif (p.get("disk") == "40-micron pinholes"):
r = self.w1.commandResponse("D2", 3)
print("changing disk")
print(r)
elif (pname == "dichroic_mirror"):
dichroic_num = self.dichroic_mirror_config[p.get(
"dichroic_mirror")]
self.w1.commandResponse("D" + str(dichroic_num), 1)
elif (pname == "filter_wheel_pos1"):
filter1_num = self.filter_wheel_1_config[p.get(
"filter_wheel_pos1")]
print("updating filter wheel position")
self.w1.commandResponse("B" + str(filter1_num), 1)
else:
print(">> Warning", str(pname),
" is not a valid parameter for the Confocal")
def __init__(self, configuration = None, **kwds):
super().__init__(**kwds)
self.current_mode = None
self.modes = []
self.parameters = params.StormXMLObject()
self.ui = focuslockUi.Ui_Dialog()
self.ui.setupUi(self)
# Add parameters
self.parameters.add(params.ParameterFloat(description = "Z stage jump size",
name = "jump_size",
value = 0.1))
# Set up lock display.
self.lock_display = lockDisplay.LockDisplay(configuration = configuration,
jump_signal = self.jump,
parent = self)
layout = QtWidgets.QGridLayout(self.ui.lockDisplayWidget)
layout.setContentsMargins(0,0,0,0)
layout.addWidget(self.lock_display)
# Configure modes.
lockModes.FindSumMixin.addParameters(self.parameters)
lockModes.LockedMixin.addParameters(self.parameters)
lockModes.ScanMixin.addParameters(self.parameters)
for mode_class_name in configuration.get("lock_modes").split(","):
a_class = getattr(lockModes, mode_class_name.strip())
a_object = a_class(parameters = self.parameters,
parent = self)
self.ui.modeComboBox.addItem(a_object.getName())
self.modes.append(a_object)
# Set parameters values based on the config file parameters.
c_params = configuration.get("parameters")
for attr in params.difference(c_params, self.parameters):
print(attr, c_params.get(attr))
self.parameters.setv(attr, c_params.get(attr))
self.newParameters(self.parameters)
# Connect signals.
self.ui.jumpNButton.clicked.connect(self.handleJumpNButton)
self.ui.jumpPButton.clicked.connect(self.handleJumpPButton)
self.ui.lockButton.clicked.connect(self.handleLockButton)
self.ui.lockTargetSpinBox.valueChanged.connect(self.handleLockTarget)
self.ui.modeComboBox.currentIndexChanged.connect(self.handleModeComboBox)
self.setEnabled(False)
def newParameters(self, parameters, initialization = False):
size_x = parameters.get("x_end") - parameters.get("x_start") + 1
size_y = parameters.get("y_end") - parameters.get("y_start") + 1
parameters.setv("x_pixels", size_x)
parameters.setv("y_pixels", size_y)
parameters.setv("bytes_per_frame", 2 * size_x * size_y)
super().newParameters(parameters)
# Figure out which parameters have changed.
if initialization:
changed_p_names = parameters.getAttrs()
else:
changed_p_names = params.difference(parameters, self.parameters)
# Check if we actually need to do anything.
if (len(changed_p_names) > 0):
if not initialization:
time.sleep(0.5)
running = self.running
if running:
self.stopCamera()
p = self.parameters
# Update parameters.
for pname in changed_p_names:
p.set(pname, parameters.get(pname))
# Configure camera.
p = self.parameters
if (p.get("exposure_time") < 0.010):
p.set("exposure_time", 0.010)
p.set("fps", 1.0/p.get("exposure_time"))
self.fake_frame_size = [size_x, size_y]
self.fake_frame = numpy.zeros(size_x * size_y, dtype = numpy.uint16)
for i in range(size_x):
for j in range(size_y):
self.fake_frame[j*size_x+i] = i % 128 + j % 128
if running:
self.startCamera()
self.camera_functionality.parametersChanged.emit()
def newParameters(self, parameters, initialization=False):
size_x = parameters.get("x_end") - parameters.get("x_start") + 1
size_y = parameters.get("y_end") - parameters.get("y_start") + 1
parameters.setv("x_pixels", size_x)
parameters.setv("y_pixels", size_y)
parameters.setv("bytes_per_frame", 2 * size_x * size_y)
super().newParameters(parameters)
# Figure out which parameters have changed.
if initialization:
changed_p_names = parameters.getAttrs()
else:
changed_p_names = params.difference(parameters, self.parameters)
# Check if we actually need to do anything.
if (len(changed_p_names) > 0):
if not initialization:
time.sleep(0.5)
running = self.running
if running:
self.stopCamera()
p = self.parameters
# Update parameters.
for pname in changed_p_names:
p.set(pname, parameters.get(pname))
# Configure camera.
p = self.parameters
if (p.get("exposure_time") < 0.010):
p.set("exposure_time", 0.010)
p.set("fps", 1.0 / p.get("exposure_time"))
self.fake_frame_size = [size_x, size_y]
self.fake_frame = numpy.zeros(size_x * size_y, dtype=numpy.uint16)
for i in range(size_x):
for j in range(size_y):
self.fake_frame[j * size_x + i] = i % 128 + j % 128
if running:
self.startCamera()
self.camera_functionality.parametersChanged.emit()
def newParameters(self, parameters):
for attr in params.difference(parameters, self.parameters):
self.parameters.setv(attr, parameters.get(attr))
self.lock_display.newParameters(parameters)
for mode in self.modes:
mode.newParameters(self.parameters)
def newParameters(self, parameters):
for attr in params.difference(parameters, self.parameters):
self.parameters.setv(attr, parameters.get(attr))
def newParameters(self, parameters):
for attr in params.difference(parameters, self.parameters):
self.parameters.setv(attr, parameters.get(attr))
self.lock_display.newParameters(parameters)
for mode in self.modes:
mode.newParameters(self.parameters)
