def post_run(self):
"""
Export data.
"""
StepperMotor_Scan.post_run(self)
save_dict = {
"Wavelengths": self.spec.wavelengths(),
"Intensities": self.data_array,
"Scan Parameters": {
"X scan start (um)": self.x_start,
"Y scan start (um)": self.y_start,
"X scan size (um)": self.x_scan_size,
"Y scan size (um)": self.y_scan_size,
"X step size (um)": self.x_step,
"Y step size (um)": self.y_step
},
"OceanOptics Parameters": {
"Integration Time (ms)": self.spec_hw.settings['intg_time'],
"Scans Averages": self.spec_measure.settings['scans_to_avg'],
"Correct Dark Counts":
self.spec_hw.settings['correct_dark_counts']
}
}
pickle.dump(
save_dict,
open(
self.app.settings['save_dir'] + "/" +
self.app.settings['sample'] + "_raw_PL_spectra_data.pkl",
"wb"))
def update_display(self):
StepperMotor_Scan.update_display(self)
if hasattr(self, 'spec') and hasattr(self, 'pi_device') and hasattr(
self, 'y'): #first, check if setup has happened
if not self.interrupt_measurement_called:
seconds_left = (
(self.x_range * self.y_range) - self.pixels_scanned
) * self.settings["intg_time"] * 1e-3 + self.overhead
self.ui.estimated_time_label.setText(
"Estimated time remaining: " + "%.2f" % seconds_left + "s")
#plot wavelengths vs intensity
self.plot.plot(self.spec.wavelengths(),
self.y,
pen='r',
clear=True) #plot wavelength vs intensity
self.graph_layout.show()
self.graph_layout.window().setWindowFlag(
QtCore.Qt.WindowCloseButtonHint,
False) #disable closing image view window
self.img_item.setImage(
self.sum_intensities_image_map) #update stage image
#update imageview
self.imv.setImage(
img=self.spectrum_image_map,
autoRange=False,
autoLevels=True,
xvals=self.spec.wavelengths()) #adjust roi plot x axis
self.imv.show()
self.imv.window().setWindowFlag(
QtCore.Qt.WindowCloseButtonHint,
False) #disable closing image view window
#update progress bar
progress = 100 * ((self.pixels_scanned + 1) /
np.abs(self.x_range * self.y_range))
self.ui.progressBar.setValue(progress)
self.set_progress(progress)
pg.QtGui.QApplication.processEvents()
def setup_figure(self):
StepperMotor_Scan.setup_figure(self)
#setup ui for ocean optics specific settings
spec_hw = self.app.hardware['oceanoptics']
details_groupBox = self.set_details_widget(widget=self.settings.New_UI(
include=["intg_time", "correct_dark_counts", "scans_to_avg"]))
widgets = details_groupBox.findChildren(QtGui.QWidget)
intg_time_spinBox = widgets[1]
correct_dark_counts_checkBox = widgets[4]
#scans_to_avg_spinBox = widgets[6]
#connect settings to ui
spec_hw.settings.intg_time.connect_to_widget(intg_time_spinBox)
spec_hw.settings.correct_dark_counts.connect_to_widget(
correct_dark_counts_checkBox)
intg_time_spinBox.valueChanged.connect(self.update_estimated_scan_time)
#save data buttons
self.ui.save_image_pushButton.clicked.connect(
self.save_intensities_image)
self.ui.save_array_pushButton.clicked.connect(
self.save_intensities_data)
#spectrometer plot
self.graph_layout = pg.GraphicsLayoutWidget()
self.plot = self.graph_layout.addPlot(
title="Spectrometer Live Reading")
self.plot.setLabel('left', 'Intensity', unit='a.u.')
self.plot.setLabel('bottom', 'Wavelength', unit='nm')
# # Create PlotDataItem object ( a scatter plot on the axes )
self.optimize_plot_line = self.plot.plot([0])
#setup imageview
self.imv = pg.ImageView()
self.imv.getView().setAspectLocked(lock=False, ratio=1)
self.imv.getView().setMouseEnabled(x=True, y=True)
self.imv.getView().invertY(False)
roi_plot = self.imv.getRoiPlot().getPlotItem()
roi_plot.getAxis("bottom").setLabel(text="Wavelength (nm)")
def pre_run(self):
try:
StepperMotor_Scan.pre_run(self) #setup scan parameters
self.spec = self.spec_hw.spec
self.check_filename("_raw_PL_spectra_data.pkl")
# Define empty array for saving intensities
self.data_array = np.zeros(shape=(self.x_range * self.y_range,
2048))
# Define empty array for image map
self.sum_intensities_image_map = np.zeros(
(self.x_range, self.y_range),
dtype=float) #store sum of intensities for each pixel
self.spectrum_image_map = np.zeros(
(2048, self.x_range, self.y_range),
dtype=float) #Store spectrum for each pixel
scan_time = self.x_range * self.y_range * self.settings[
"intg_time"] * 1e-3 #s
self.ui.estimated_scan_time_label.setText("Estimated scan time: " +
"%.2f" % scan_time + "s")
except:
pass
def save_intensities_image(self):
StepperMotor_Scan.save_intensities_image(
self, self.sum_intensities_image_map, 'oo')
def save_intensities_data(self):
transposed = np.transpose(self.sum_intensities_image_map
) #transpose so data visually makes sense
StepperMotor_Scan.save_intensities_data(self, transposed, 'oo')
def setup(self):
StepperMotor_Scan.setup(self)
self.settings.New("intg_time", dtype=int, unit='ms', initial=3, vmin=3)
self.settings.New('correct_dark_counts', dtype=bool, initial=True)
self.settings.New("scans_to_avg", dtype=int, initial=1, vmin=1)