class PiezoStageHW(HardwareComponent):
## Define name of this hardware plug-in
def setup(self):
# Define your hardware settings here.
# These settings will be displayed in the GUI and auto-saved with data files
self.name = 'piezostage'
self.settings.New('x_position', dtype=float, unit='um')
self.settings.New('y_position', dtype=float, unit='um')
self.settings.New('x_abs',
dtype=float,
initial=0,
unit='um',
vmin=0,
vmax=100)
self.settings.New('y_abs',
dtype=float,
initial=0,
unit='um',
vmin=0,
vmax=100)
self.settings.New('x_rel', dtype=float, initial=0, unit='um')
self.settings.New('y_rel', dtype=float, initial=0, unit='um')
self.add_operation('center_stage', self.center_piezo)
self.add_operation('absolute_movement', self.abs_mov)
self.add_operation('relative_movement', self.rel_mov)
def connect(self):
# Open connection to the device:
self.pi_device = GCSDevice("E-710") # Creates a Controller instant
self.pi_device.ConnectNIgpib(board=0,
device=4) # Connect to GPIB board
self.axes = self.pi_device.axes[
0:2] # selecting x and y axis of the stage
self.pi_device.INI()
self.pi_device.REF(axes=self.axes)
self.pi_device.SVO(axes=self.axes,
values=[True, True
]) # Turn on servo control for both axes
#Connect settings to hardware:
LQ = self.settings.as_dict()
LQ["x_position"].hardware_read_func = self.getX
LQ["y_position"].hardware_read_func = self.getY
LQ["x_position"].hardware_set_func = self.abs_mov
LQ["y_position"].hardware_set_func = self.abs_mov
LQ["x_position"].hardware_set_func = self.rel_mov
LQ["y_position"].hardware_set_func = self.rel_mov
#Take an initial sample of the data.
self.read_from_hardware()
def disconnect(self):
#Disconnect the device and remove connections from settings
self.settings.disconnect_all_from_hardware()
if hasattr(self, 'pi_device'):
self.pi_device.close()
del self.pi_device
self.pi_device = None
def center_piezo(self):
if hasattr(self, 'pi_device'):
self.pi_device.MOV(axes=self.axes, values=[50, 50])
self.read_from_hardware()
def abs_mov(self):
if hasattr(self, 'pi_device'):
x_abs_pos = self.settings['x_abs']
y_abs_pos = self.settings['y_abs']
self.pi_device.MOV(axes=self.axes, values=[x_abs_pos, y_abs_pos])
self.read_from_hardware()
def rel_mov(self):
if hasattr(self, 'pi_device'):
x_rel_pos = self.settings['x_rel']
y_rel_pos = self.settings['y_rel']
self.pi_device.MVR(axes=self.axes, values=[x_rel_pos, y_rel_pos])
self.read_from_hardware()
def getX(self):
return self.pi_device.qPOS(axes=self.axes)['1']
def getY(self):
return self.pi_device.qPOS(axes=self.axes)['2']
class MainWindow(TemplateBaseClass):
def __init__(self):
TemplateBaseClass.__init__(self)
# Create the main window
self.ui = WindowTemplate()
self.ui.setupUi(self)
self.ui.connect_checkBox.stateChanged.connect(
self._handle_spectrometer_connection)
self.ui.live_pushButton.clicked.connect(self.live)
self.ui.path_to_folder_pushButton.clicked.connect(
self.save_file_location)
self.ui.save_single_spec_pushButton.clicked.connect(
self.save_single_spec)
self.ui.init_stage_pushButton.clicked.connect(self.init_piezo_stage)
self.ui.show_curr_pos_pushButton.clicked.connect(
self.current_piezo_stage_pos)
self.ui.center_stage_pushButton.clicked.connect(self.center_piezo)
self.ui.abs_mov_pushButton.clicked.connect(self.abs_mov)
self.ui.rel_mov_pushButton.clicked.connect(self.rel_mov)
self.ui.estimate_scan_time_pushButton.clicked.connect(
self.estimate_scan_time)
self.ui.start_x_y_sacan_pushButton.clicked.connect(self.x_y_scan)
# self.ui.clear_pushButton.clicked.connect(self.clear_plot)
self.pi_device = None
self.spec = None
self.ui.status_textBrowser.setText("Welcome!\nGUI Initiated!")
self.show()
def _handle_spectrometer_connection(self):
if self.ui.connect_checkBox.isChecked():
self.connect_spectrometer()
else:
self.close_connection()
def connect_spectrometer(self):
if self.spec is None:
devices = sb.list_devices()
self.spec = sb.Spectrometer(devices[0])
self.ui.status_textBrowser.append(
"Ocean Optics Device Connected!\n\n Device:\n\n" +
str(sb.list_devices()[0]))
else:
self.ui.status_textBrowser.append("Already Connected")
def init_piezo_stage(self):
if self.pi_device is None:
self.pi_device = GCSDevice("E-710") # Creates a Controller instant
self.pi_device.ConnectNIgpib(board=0,
device=4) # Connect to GPIB board
self.ui.status_textBrowser.append('Connected: {}'.format(
self.pi_device.qIDN().strip()))
# print('connected: {}'.format(self.pi_device.qIDN().strip()))
self.axes = self.pi_device.axes[
0:2] # selecting x and y axis of the stage
self.pi_device.INI()
self.pi_device.REF(axes=self.axes)
self.pi_device.SVO(
axes=self.axes,
values=[True, True]) # Turn on servo control for both axes
self.ui.status_textBrowser.append(
"Current Stage Position:\n{}".format(
self.pi_device.qPOS(axes=self.axes)))
# print(self.pi_device.qPOS(axes=self.axes))
else:
self.ui.status_textBrowser.append(
"Piezo Stage Is Already Initialized!")
def center_piezo(self):
if self.pi_device is None:
self.init_piezo_stage()
self.pi_device.MOV(axes=self.axes, values=[50, 50])
self.ui.status_textBrowser.append("Piezo Stage Centered: [50x,50y]")
def current_piezo_stage_pos(self):
if self.pi_device is None:
self.init_piezo_stage()
self.ui.status_textBrowser.append("Current Stage Position:\n{}".format(
self.pi_device.qPOS(axes=self.axes)))
def abs_mov(self):
if self.pi_device is None:
self.init_piezo_stage()
x_abs_pos = self.ui.x_abs_doubleSpinBox.value()
y_abs_pos = self.ui.y_abs_doubleSpinBox.value()
self.pi_device.MOV(axes=self.axes, values=[x_abs_pos, y_abs_pos])
def rel_mov(self):
if self.pi_device is None:
self.init_piezo_stage()
x_rel_pos = self.ui.x_rel_doubleSpinBox.value()
y_rel_pos = self.ui.y_rel_doubleSpinBox.value()
self.pi_device.MVR(axes=self.axes, values=[x_rel_pos, y_rel_pos])
def estimate_scan_time(self):
x_scan_size = self.ui.x_size_doubleSpinBox.value()
y_scan_size = self.ui.y_size_doubleSpinBox.value()
x_step = self.ui.x_step_doubleSpinBox.value()
y_step = self.ui.y_step_doubleSpinBox.value()
if y_scan_size == 0:
y_scan_size = 1
if x_scan_size == 0:
x_scan_size = 1
if y_step == 0:
y_step = 1
if x_step == 0:
x_step = 1
y_range = int(np.ceil(y_scan_size / y_step))
x_range = int(np.ceil(x_scan_size / x_step))
total_points = x_range * y_range
intg_time_ms = self.ui.intg_time_spinBox.value()
scans_to_avg = self.ui.scan_to_avg_spinBox.value()
total_time = total_points * (intg_time_ms * 1e-3) * (scans_to_avg
) # in seconds
self.ui.status_textBrowser.append("Estimated scan time: " +
str(np.float16(total_time / 60)) +
" mins")
def x_y_scan(self):
if self.pi_device is None:
self.init_piezo_stage()
if self.spec is None:
self.ui.status_textBrowser.append(
"Spectrometer not connected!\nForce connecting the spectrometer..."
)
self.connect_spectrometer()
start_time = time.time()
x_start = self.ui.x_start_doubleSpinBox.value()
y_start = self.ui.y_start_doubleSpinBox.value()
x_scan_size = self.ui.x_size_doubleSpinBox.value()
y_scan_size = self.ui.y_size_doubleSpinBox.value()
x_step = self.ui.x_step_doubleSpinBox.value()
y_step = self.ui.y_step_doubleSpinBox.value()
if y_scan_size == 0:
y_scan_size = 1
if x_scan_size == 0:
x_scan_size = 1
if y_step == 0:
y_step = 1
if x_step == 0:
x_step = 1
y_range = int(np.ceil(y_scan_size / y_step))
x_range = int(np.ceil(x_scan_size / x_step))
# Define empty array for saving intensities
data_array = np.zeros(shape=(x_range * y_range, 2048))
self.ui.status_textBrowser.append("Starting Scan...")
# Move to the starting position
self.pi_device.MOV(axes=self.axes, values=[x_start, y_start])
self.ui.status_textBrowser.append("Scan in Progress...")
k = 0
for i in range(y_range):
for j in range(x_range):
# print(self.pi_device.qPOS(axes=self.axes))
self._read_spectrometer()
data_array[k, :] = self.y
self.ui.plot.plot(self.spec.wavelengths(),
self.y,
pen='r',
clear=True)
pg.QtGui.QApplication.processEvents()
self.pi_device.MVR(axes=self.axes[0], values=[x_step])
self.ui.progressBar.setValue(100 * ((k + 1) /
(x_range * y_range)))
k += 1
# TODO
# if statement needs to be modified to keep the stage at the finish y-pos for line scans in x, and same for y
if i == y_range - 1: # this if statement is there to keep the stage at the finish position (in x) and not bring it back like we were doing during the scan
self.pi_device.MVR(axes=self.axes[1], values=[y_step])
else:
self.pi_device.MVR(axes=self.axes,
values=[-x_scan_size, y_step])
self.ui.status_textBrowser.append("Scan Complete!\nSaving Data...")
save_dict = {
"Wavelengths": self.spec.wavelengths(),
"Intensities": data_array,
"Scan Parameters": {
"X scan start (um)": x_start,
"Y scan start (um)": y_start,
"X scan size (um)": x_scan_size,
"Y scan size (um)": y_scan_size,
"X step size (um)": x_step,
"Y step size (um)": y_step
},
"OceanOptics Parameters": {
"Integration Time (ms)":
self.ui.intg_time_spinBox.value(),
"Scans Averages":
self.ui.scan_to_avg_spinBox.value(),
"Correct Dark Counts":
self.ui.correct_dark_counts_checkBox.isChecked()
}
}
pickle.dump(
save_dict,
open(
self.save_folder + "/" + self.ui.lineEdit.text() +
"_raw_PL_spectra_data.pkl", "wb"))
self.ui.status_textBrowser.append(
"Data saved!\nTotal time taken:" +
str(np.float16((time.time() - start_time) / 60)) + " mins")
def save_file_location(self):
self.save_folder = QtWidgets.QFileDialog.getExistingDirectory(
self, caption="Select Folder")
def save_single_spec(self):
save_array = np.zeros(shape=(2048, 2))
self._read_spectrometer()
save_array[:, 1] = self.y
save_array[:, 0] = self.spec.wavelengths()
np.savetxt(self.save_folder + "/" + self.ui.lineEdit.text() + ".txt",
save_array,
fmt='%.5f',
header='Wavelength (nm), Intensity (counts)',
delimiter=' ')
def live(self):
save_array = np.zeros(shape=(2048, 2))
self.ui.plot.setLabel('left', 'Intensity', units='a.u.')
self.ui.plot.setLabel('bottom', 'Wavelength', units='nm')
j = 0
while self.spec is not None: #self.ui.connect_checkBox.isChecked(): # this while loop works!
self._read_spectrometer()
save_array[:, 1] = self.y
self.ui.plot.plot(self.spec.wavelengths(),
self.y,
pen='r',
clear=True)
if self.ui.save_every_spec_checkBox.isChecked():
save_array[:, 0] = self.spec.wavelengths()
np.savetxt(self.save_folder + "/" + self.ui.lineEdit.text() +
str(j) + ".txt",
save_array,
fmt='%.5f',
header='Wavelength (nm), Intensity (counts)',
delimiter=' ')
pg.QtGui.QApplication.processEvents()
j += 1
def _read_spectrometer(self):
if self.spec is not None:
intg_time_ms = self.ui.intg_time_spinBox.value()
self.spec.integration_time_micros(intg_time_ms * 1e3)
scans_to_avg = self.ui.scan_to_avg_spinBox.value()
Int_array = np.zeros(shape=(2048, scans_to_avg))
for i in range(scans_to_avg): #software average
data = self.spec.spectrum(
correct_dark_counts=self.ui.correct_dark_counts_checkBox.
isChecked())
Int_array[:, i] = data[1]
self.y = np.mean(Int_array, axis=-1)
else:
self.ui.status_textBrowser.append("Connect to Spectrometer!")
raise Exception("Must connect to spectrometer first!")
def close_connection(self):
if self.spec is not None:
self.spec.close()
self.ui.status_textBrowser.append(
"Ocean Optics Device Disconnected")
del self.spec
self.spec = None
def close_application(self):
choice = QtGui.QMessageBox.question(
self, 'EXIT!', "Do you want to exit the app?",
QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
if choice == QtGui.QMessageBox.Yes:
sys.exit()
else:
pass
