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added try/except to scan pre-runs
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@SarthakJariwala
SarthakJariwala committed Aug 7, 2019
1 parent 4db43a8 commit b1c4bad
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279 changes: 141 additions & 138 deletions HW_OceanOptics/OceanOptics_Scan.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,141 +12,144 @@

class OceanOptics_Scan(PiezoStage_Scan):

name = "OceanOptics_Scan"

def setup(self):
PiezoStage_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)

def setup_figure(self):
PiezoStage_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 update_estimated_scan_time(self):
try:
self.overhead = self.x_range * self.y_range * .058 #determined by running scans and timing
scan_time = self.x_range * self.y_range * self.settings["intg_time"] * 1e-3 + self.overhead #s
self.ui.estimated_scan_time_label.setText("Estimated scan time: " + "%.2f" % scan_time + "s")
except:
pass

def update_display(self):
PiezoStage_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 pre_run(self):
PiezoStage_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")

def scan_measure(self):
"""
Data collection for each pixel.
"""
self._read_spectrometer()
self.data_array[self.pixels_scanned,:] = self.y
self.sum_intensities_image_map[self.index_x, self.index_y] = self.y.sum()
self.spectrum_image_map[:, self.index_x, self.index_y] = self.y

def post_run(self):
"""
Export data.
"""
PiezoStage_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 _read_spectrometer(self):
'''
Read spectrometer according to settings and update self.y (intensities array)
'''
if hasattr(self, 'spec'):
intg_time_ms = self.spec_hw.settings['intg_time']
self.spec.integration_time_micros(intg_time_ms*1e3) #seabreeze error checking

scans_to_avg = self.spec_measure.settings['scans_to_avg']
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.spec_hw.settings['correct_dark_counts'])#acquire wavelengths and intensities from spec
Int_array[:,i] = data[1]
self.y = np.mean(Int_array, axis=-1)

def save_intensities_data(self):
transposed = np.transpose(self.sum_intensities_image_map) #transpose so data visually makes sense
PiezoStage_Scan.save_intensities_data(self, transposed, 'oo')

def save_intensities_image(self):
PiezoStage_Scan.save_intensities_image(self, self.sum_intensities_image_map, 'oo')
name = "OceanOptics_Scan"

def setup(self):
PiezoStage_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)

def setup_figure(self):
PiezoStage_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 update_estimated_scan_time(self):
try:
self.overhead = self.x_range * self.y_range * .058 #determined by running scans and timing
scan_time = self.x_range * self.y_range * self.settings["intg_time"] * 1e-3 + self.overhead #s
self.ui.estimated_scan_time_label.setText("Estimated scan time: " + "%.2f" % scan_time + "s")
except:
pass

def update_display(self):
PiezoStage_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 pre_run(self):
try:
PiezoStage_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 scan_measure(self):
"""
Data collection for each pixel.
"""
self._read_spectrometer()
self.data_array[self.pixels_scanned,:] = self.y
self.sum_intensities_image_map[self.index_x, self.index_y] = self.y.sum()
self.spectrum_image_map[:, self.index_x, self.index_y] = self.y

def post_run(self):
"""
Export data.
"""
PiezoStage_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 _read_spectrometer(self):
'''
Read spectrometer according to settings and update self.y (intensities array)
'''
if hasattr(self, 'spec'):
intg_time_ms = self.spec_hw.settings['intg_time']
self.spec.integration_time_micros(intg_time_ms*1e3) #seabreeze error checking

scans_to_avg = self.spec_measure.settings['scans_to_avg']
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.spec_hw.settings['correct_dark_counts'])#acquire wavelengths and intensities from spec
Int_array[:,i] = data[1]
self.y = np.mean(Int_array, axis=-1)

def save_intensities_data(self):
transposed = np.transpose(self.sum_intensities_image_map) #transpose so data visually makes sense
PiezoStage_Scan.save_intensities_data(self, transposed, 'oo')

def save_intensities_image(self):
PiezoStage_Scan.save_intensities_image(self, self.sum_intensities_image_map, 'oo')
59 changes: 31 additions & 28 deletions HW_Picoharp/picoharp_scan.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ def setup_figure(self):
self.ui.save_image_pushButton.clicked.connect(self.save_intensities_image)
self.ui.save_array_pushButton.clicked.connect(self.save_intensities_data)

#setup imageview
#setup imageview
self.imv = pg.ImageView()
self.imv.getView().setAspectLocked(lock=False, ratio=1)
self.imv.getView().setMouseEnabled(x=True, y=True)
Expand Down Expand Up @@ -86,43 +86,46 @@ def update_display(self):
pg.QtGui.QApplication.processEvents()

def pre_run(self):
PiezoStage_Scan.pre_run(self) #setup scan paramters
self.picoharp = self.picoharp_hw.picoharp
self.check_filename("_raw_PL_hist_data.pkl")
self.num_hist_chans = self.app.hardware['picoharp'].calc_num_hist_chans()

dirname = self.app.settings['save_dir']
self.check_filename('_histdata.dat')
sample_filename = self.app.settings['sample']
self.hist_filename = os.path.join(dirname, sample_filename + '_histdata.dat')
self.check_filename('_timedata.dat')
self.time_filename = os.path.join(dirname, sample_filename + '_timedata.dat')

hist_len = self.num_hist_chans

#Use memmaps to use less memory and store data into disk
self.hist_data= np.memmap(self.hist_filename,dtype='float32',mode='w+',shape=(hist_len, self.x_range, self.y_range))
self.time_data= np.memmap(self.time_filename,dtype='float32',mode='w+',shape=(hist_len, self.x_range, self.y_range))

#Store histogram sums for each pixel
self.sum_intensities_image_map = np.zeros((self.x_range, self.y_range), dtype=float)

scan_time = self.x_range * self.y_range * self.settings["Tacq"] #* 1e-3 #s
self.ui.estimated_scan_time_label.setText("Estimated scan time: " + "%.2f" % scan_time + "s")
try:
PiezoStage_Scan.pre_run(self) #setup scan paramters
self.picoharp = self.picoharp_hw.picoharp
self.check_filename("_raw_PL_hist_data.pkl")
self.num_hist_chans = self.app.hardware['picoharp'].calc_num_hist_chans()

dirname = self.app.settings['save_dir']
self.check_filename('_histdata.dat')
sample_filename = self.app.settings['sample']
self.hist_filename = os.path.join(dirname, sample_filename + '_histdata.dat')
self.check_filename('_timedata.dat')
self.time_filename = os.path.join(dirname, sample_filename + '_timedata.dat')

hist_len = self.num_hist_chans

#Use memmaps to use less memory and store data into disk
self.hist_data= np.memmap(self.hist_filename,dtype='float32',mode='w+',shape=(hist_len, self.x_range, self.y_range))
self.time_data= np.memmap(self.time_filename,dtype='float32',mode='w+',shape=(hist_len, self.x_range, self.y_range))

#Store histogram sums for each pixel
self.sum_intensities_image_map = np.zeros((self.x_range, self.y_range), dtype=float)

scan_time = self.x_range * self.y_range * self.settings["Tacq"] #* 1e-3 #s
self.ui.estimated_scan_time_label.setText("Estimated scan time: " + "%.2f" % scan_time + "s")
except:
pass

def scan_measure(self):
"""
Data collection for each pixel.
"""
t0 = time.time()
#t0 = time.time()
data = self.measure_hist()
print(str(time.time()-t0), " measure_hist")
t1 = time.time()
#print(str(time.time()-t0), " measure_hist")
#t1 = time.time()
self.time_data[:, self.index_x, self.index_y], self.hist_data[:, self.index_x, self.index_y] = data
self.sum_intensities_image_map[self.index_x, self.index_y] = sum(data[1])
# self.time_data.flush()
# self.hist_data.flush()
print(str(time.time()-t1), " rest of scan_measure")
#print(str(time.time()-t1), " rest of scan_measure")

def post_run(self):
"""
Expand Down

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