def _update_plot(self, axes_list):
# fit the data and set piezo to focus spot
axis_focus, axis_image = axes_list
# if take image is running we take the data from there otherwise we use the scripts own image data
if self._current_subscript_stage['current_subscript'] is self.scripts['take_image']:
if 'image_data' in self.scripts['take_image'].data:
current_image = self.scripts['take_image'].data['image_data']
else:
current_image = None
elif self._current_subscript_stage['current_subscript'] is self.scripts['take_image_2']:
if 'image_data' in self.scripts['take_image_2'].data:
current_image = self.scripts['take_image_2'].data['image_data']
else:
current_image = None
else:
current_image = self.data['current_image']
if current_image is not None:
update_fluorescence(current_image, axis_image)
axis_focus, axis_image = axes_list
update_fluorescence(self.data['current_image'], axis_image)
focus_data = self.data['focus_function_result']
focus_data_2 = self.data['focus_function_result_2']
sweep_voltages = self.data['sweep_voltages']
if len(focus_data) > 0:
axis_focus.clear() #ER 20181016 - axis.hold removed from old version of matplotlib
axis_focus.plot(sweep_voltages[0:len(focus_data)], focus_data, sweep_voltages[0:len(focus_data_2)], focus_data_2)
def _update_plot(self, axes_list):
"""
updates the galvo scan image
Args:
axes_list: list of axes objects on which to plot plots the esr on the first axes object
"""
update_fluorescence(self.data['image_data'], axes_list[0], self.settings['max_counts_plot'])
def _update_plot(self, axes_list):
"""
updates the galvo scan image
Args:
axes_list: list of axes objects on which to plot plots the esr on the first axes object
"""
update_fluorescence(self.data['image_data'], axes_list[0],
self.settings['max_counts_plot'])
def _update_plot(self, axes_list):
extent = [
self.settings['inner_loop']['min_pos'],
self.settings['inner_loop']['max_pos'],
self.settings['outer_loop']['min_pos'],
self.settings['outer_loop']['max_pos']
]
update_fluorescence(self.data['counts'], axes_list[0])
def _update_plot(self, axes_list):
"""
updates the galvo scan image
Args:
axes_list: list of axes objects on which to plot plots the esr on the first axes object
"""
print(('axes list lenght update', len(axes_list)))
update_fluorescence(self.data['image_data'], axes_list[0])
self.scripts['get_spectrum']._plot([axes_list[1]], trace_only=True)
def _update_plot(self, axes_list):
"""
updates the galvo scan image
Args:
axes_list: list of axes objects on which to plot plots the esr on the first axes object
"""
print(('axes list lenght update', len(axes_list)))
update_fluorescence(self.data['image_data'], axes_list[0])
self.scripts['get_spectrum']._plot([axes_list[1]], trace_only = True)
def _update_plot(self, axes_list):
# fit the data and set piezo to focus spot
axis_focus, axis_image = axes_list
# if take image is running we take the data from there otherwise we use the scripts own image data
if self._current_subscript_stage['current_subscript'] is self.scripts['take_image']:
if 'image_data' in self.scripts['take_image'].data:
current_image = self.scripts['take_image'].data['image_data']
else:
current_image = None
elif self._current_subscript_stage['current_subscript'] is self.scripts['take_image_2']:
if 'image_data' in self.scripts['take_image_2'].data:
current_image = self.scripts['take_image_2'].data['image_data']
else:
current_image = None
else:
current_image = self.data['current_image']
if current_image is not None:
update_fluorescence(current_image, axis_image)
axis_focus, axis_image = axes_list
update_fluorescence(self.data['current_image'], axis_image)
focus_data = self.data['focus_function_result']
focus_data_2 = self.data['focus_function_result_2']
sweep_voltages = self.data['sweep_voltages']
if len(focus_data) > 0:
axis_focus.clear() #ER 20181016 - axis.hold removed from old version of matplotlib
axis_focus.plot(sweep_voltages[0:len(focus_data)], focus_data, 'r', label='Fluorescence')
# axis_focus.hold(True)
axis_focus.plot(sweep_voltages[0:len(focus_data_2)], focus_data_2, 'g', label='Reflection')
axis_focus.legend()
# axis_focus.hold(False)
axis_focus.set_xlabel('Piezo Voltage [V]')
if self.settings['focusing_optimizer'] == 'mean':
ylabel = 'Image Mean [kcounts]'
elif self.settings['focusing_optimizer'] == 'standard_deviation':
ylabel = 'Image Standard Deviation [kcounts]'
elif self.settings['focusing_optimizer'] == 'normalized_standard_deviation':
ylabel = 'Image Normalized Standard Deviation [arb]'
else:
ylabel = self.settings['focusing_optimizer']
axis_focus.set_ylabel(ylabel)
axis_focus.set_title('Autofocusing Routine')
def _update_plot(self, axes_list):
"""
updates the galvo scan image
Args:
axes_list: list of axes objects on which to plot plots the esr on the first axes object
"""
print(('axes list lenght update', len(axes_list)))
update_fluorescence(self.data['image_data'], axes_list[0])
last_data = self.data['point_data'][-1]
dt = self.data['meta_data']['xincrement']
freq, psd = power_spectral_density(last_data, dt)
plot_psd(freq, psd, axes_list[1], y_scaling='log', x_scaling='log')
axes_list[1].hold(False)
def _update_plot(self, axes_list):
"""
updates the galvo scan image
Args:
axes_list: list of axes objects on which to plot plots the esr on the first axes object
"""
print(('axes list lenght update', len(axes_list)))
update_fluorescence(self.data['image_data'], axes_list[0])
last_data = self.data['point_data'][-1]
dt = self.data['meta_data']['xincrement']
freq, psd = power_spectral_density(last_data, dt)
plot_psd(freq, psd, axes_list[1], y_scaling='log', x_scaling='log')
axes_list[1].hold(False)
def _update_plot(self, axes_list):
'''
Plots the newly taken galvo scan to axis 2, and the correlation image to axis 1
Args:
axes_list: list of axes to plot to. Uses two axes.
'''
if self.scripts['GalvoScan'].is_running:
self.scripts['GalvoScan']._update_plot(axes_list)
else:
if not self.data['new_image'] == [] and not self.data['image_extent'] == []:
data = self.data['new_image']
update_fluorescence(data, axes_list[1])
if not self.data['correlation_image'] == []:
axes_list[0].imshow(self.data['correlation_image'])
else:
self.scripts['GalvoScan']._update_plot(axes_list)
def _update_plot(self, axes_list):
'''
Plots the newly taken galvo scan to axis 2, and the correlation image to axis 1
Args:
axes_list: list of axes to plot to. Uses two axes.
'''
if self.scripts['GalvoScan'].is_running:
self.scripts['GalvoScan']._update_plot(axes_list)
else:
if not self.data['new_image'] == [] and not self.data[
'image_extent'] == []:
data = self.data['new_image']
update_fluorescence(data, axes_list[1])
if not self.data['correlation_image'] == []:
axes_list[0].imshow(self.data['correlation_image'])
else:
self.scripts['GalvoScan']._update_plot(axes_list)
def _update_plot(self, axes_list):
update_fluorescence(self.data['counts'], axes_list[0])