def plot_data(axes_list, data):
plot_fluorescence_new(data['image_data'], data['extent'], axes_list[0])
initial_point = data['initial_point']
patch = patches.Circle((initial_point['x'], initial_point['y']),
.001,
ec='g',
fc='none',
ls='dashed')
axes_list[0].add_patch(patch)
axes_list[0].text(initial_point['x'],
initial_point['y'] - .002,
'initial point',
color='g',
fontsize=8)
# plot marker
if data['maximum_point']:
maximum_point = data['maximum_point']
patch = patches.Circle((maximum_point['x'], maximum_point['y']),
.001,
ec='r',
fc='none',
ls='dashed')
axes_list[0].add_patch(patch)
axes_list[0].text(maximum_point['x'],
maximum_point['y'] - .002,
'found NV',
color='r',
fontsize=8)
def _plot(self, axes_list, data=None):
# fit the data and set piezo to focus spot
if data is None:
data = self.data
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']
extent = self.scripts['take_image'].data['extent']
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']
extent = self.scripts['take_image_2'].data['extent']
else:
current_image = None
else:
current_image = data['current_image']
extent = data['extent']
if current_image is not None:
plot_fluorescence_new(current_image, extent, axis_image)
if ('focus_function_result' in data) and ('focus_function_result_2' in data):
focus_data = data['focus_function_result']
focus_data_2 = data['focus_function_result_2']
sweep_voltages = data['sweep_voltages']
if len(focus_data) > 0:
axis_focus.plot(sweep_voltages[0:len(focus_data)], focus_data, sweep_voltages[0:len(focus_data_2)], focus_data_2)
if not (np.array_equal(data['fit_parameters'], [0, 0, 0, 0])):
axis_focus.plot(sweep_voltages[0:len(focus_data)],
self.gaussian(sweep_voltages[0:len(focus_data)], *self.data['fit_parameters']),
'k')
if not (np.array_equal(data['fit_parameters_2'], [0, 0, 0, 0])):
axis_focus.plot(sweep_voltages[0:len(focus_data_2)],
self.gaussian(sweep_voltages[0:len(focus_data_2)], *self.data['fit_parameters_2']),
'g')
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 _plot(self, axes_list, data=None):
"""
Plots the galvo scan image
Args:
axes_list: list of axes objects on which to plot the galvo scan on the first axes object
data: data (dictionary that contains keys image_data, extent) if not provided use self.data
"""
if data is None:
data = self.data
plot_fluorescence_new(data['image_data'],
data['extent'],
axes_list[0],
max_counts=self.settings['max_counts_plot'])
def _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']._plot(axes_list)
else:
if not self.data['new_image'] == [] and not self.data[
'image_extent'] == []:
data = self.data['new_image']
extent = self.data['image_extent']
plot_fluorescence_new(data, extent, axes_list[1])
if not self.data['correlation_image'] == []:
axes_list[0].imshow(self.data['correlation_image'])
else:
self.scripts['GalvoScan']._plot(axes_list)
def _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['take_baseline_image'].is_running:
self.scripts['take_baseline_image']._plot(axes_list)
elif self.scripts['take_new_image'].is_running:
self.scripts['take_new_image']._plot(axes_list)
else:
#when clicking on script to select it for the first time, don't attempt to plot as no data avaliable
if self.data['baseline_image'] == []:
return
if not self.settings['display_processed_images'] or self.baseline_processed_image == []:
plot_fluorescence_new(self.data['baseline_image'],
self.data['baseline_extent'],
axes_list[0])
else:
plot_fluorescence_new(self.baseline_processed_image,
self.data['baseline_extent'],
axes_list[0])
#for the first run when only the baseline is taken, plot only that image
if self.data['new_image'] == []:
return
# add patch that marks the region of interest
x, y = self.data['new_image_extent'][0], self.data[
'new_image_extent'][3]
w, h = (self.data['new_image_extent'][1] -
self.data['new_image_extent'][0]), (
self.data['new_image_extent'][2] -
self.data['new_image_extent'][3])
patch = patches.Rectangle((x, y),
w,
h,
ec='c',
fc='none',
ls='dashed')
axes_list[0].add_patch(patch)
# add patch that marks the region of interest
x, y = self.data['new_image_extent'][0] - self.data['shift'][
0], self.data['new_image_extent'][3] - self.data['shift'][1]
w, h = (self.data['new_image_extent'][1] -
self.data['new_image_extent'][0]), (
self.data['new_image_extent'][2] -
self.data['new_image_extent'][3])
patch = patches.Rectangle((x, y),
w,
h,
ec='r',
fc='none',
ls='dashed')
axes_list[0].add_patch(patch)
# plot correlation image
if not self.data['correlation_image'] == []:
# axes_list[1].imshow(self.data['correlation_image'], interpolation="nearest")
plot_fluorescence_new(self.data['correlation_image'], [
0, self.data['correlation_image'].shape[0],
self.data['correlation_image'].shape[1], 0
], axes_list[1])
axes_list[1].set_title('correlation image')
# plot new image
if not self.data['new_image'] == []:
if not self.settings['display_processed_images']:
plot_fluorescence_new(self.data['new_image'],
self.data['new_image_extent'],
axes_list[2])
else:
plot_fluorescence_new(self.new_processed_image,
self.data['new_image_extent'],
axes_list[2])
axes_list[2].set_title(
'new image shifted by dx={:0.3f} dy={:0.3f}'.format(
self.data['shift'][0], self.data['shift'][1]))
def perform_affine_transform(img_path_old, img_path_new, done_queue,
return_queue):
import time
pt11_widget = widgets.HTML("Pt 1: 0,0")
pt12_widget = widgets.HTML("Pt 2: 0,0")
pt13_widget = widgets.HTML("Pt 3: 0,0")
pt21_widget = widgets.HTML("Pt 1: 0,0")
pt22_widget = widgets.HTML("Pt 2: 0,0")
pt23_widget = widgets.HTML("Pt 3: 0,0")
display(pt11_widget)
display(pt12_widget)
display(pt13_widget)
display(pt21_widget)
display(pt22_widget)
display(pt23_widget)
# f = plt.figure(figsize=(12, 6))
# ax0 = plt.subplot(121)
# ax1 = plt.subplot(122)
f = plt.figure(figsize=(16, 8))
gs = gridspec.GridSpec(1, 2, width_ratios=[1, 2])
ax0 = plt.subplot(gs[0])
ax1 = plt.subplot(gs[1])
def onclick_old(event):
if ax0.in_axes(event):
if event.key == '1':
pt11_widget.value = 'Pt 1: ' + str(event.xdata) + ',' + str(
event.ydata)
elif event.key == '2':
pt12_widget.value = 'Pt 2: ' + str(event.xdata) + ',' + str(
event.ydata)
elif event.key == '3':
pt13_widget.value = 'Pt 3: ' + str(event.xdata) + ',' + str(
event.ydata)
elif ax1.in_axes(event):
if event.key == '1':
pt21_widget.value = 'Pt 1: ' + str(event.xdata) + ',' + str(
event.ydata)
elif event.key == '2':
pt22_widget.value = 'Pt 2: ' + str(event.xdata) + ',' + str(
event.ydata)
elif event.key == '3':
pt23_widget.value = 'Pt 3: ' + str(event.xdata) + ',' + str(
event.ydata)
cid = f.canvas.mpl_connect('button_press_event', onclick_old)
data_im_old = Script.load_data(img_path_old)
image_old = data_im_old['image_data']
extent_old = data_im_old['extent']
nv_pts_old = data_im_old['nv_locations']
plot_fluorescence_new(image_old, extent_old, ax0)
f.get_axes()[2].remove()
data_im_new = Script.load_data(img_path_new)
image_new = data_im_new['image_data']
extent_new = data_im_new['extent']
nv_pts_new = data_im_new['nv_locations']
plot_fluorescence_new(image_new, extent_new, ax1)
f.get_axes()[2].remove()
plt.show()
while done_queue.empty():
time.sleep(.5)
pt11 = map(
float,
pt11_widget.value.replace(" ", "").replace(':', ',').split(',')[1:3])
pt12 = map(
float,
pt12_widget.value.replace(" ", "").replace(':', ',').split(',')[1:3])
pt13 = map(
float,
pt13_widget.value.replace(" ", "").replace(':', ',').split(',')[1:3])
pt21 = map(
float,
pt21_widget.value.replace(" ", "").replace(':', ',').split(',')[1:3])
pt22 = map(
float,
pt22_widget.value.replace(" ", "").replace(':', ',').split(',')[1:3])
pt23 = map(
float,
pt23_widget.value.replace(" ", "").replace(':', ',').split(',')[1:3])
Avec = calc_transform_matrix((pt11, pt12, pt13), (pt21, pt22, pt23))
Amat = [[Avec[0], Avec[1], Avec[2]], [Avec[3], Avec[4], Avec[5]],
[0, 0, 1]]
shifted_nv_pts_old = []
for pt in nv_pts_old:
circ = patches.Circle((pt[0], pt[1]), .0005, fc='k', ec='k')
ax0.add_patch(circ)
vec = [pt[0], pt[1], 1]
vec_prime = np.dot(Amat, vec)
circ = patches.Circle((vec_prime[0], vec_prime[1]),
.0005,
fc='k',
ec='k')
ax1.add_patch(circ)
shifted_nv_pts_old.append([vec_prime[0], vec_prime[1]])
for pt in nv_pts_new:
circ = patches.Circle((pt[0], pt[1]), .0005, fc='g', ec='g')
ax1.add_patch(circ)
tree = scipy.spatial.KDTree(shifted_nv_pts_old)
_, new_to_old_map = tree.query(nv_pts_new, distance_upper_bound=.005)
#kd tree returns value of len(new_to_old_map) if no match found, change this to -1
new_to_old_map = [
x if x != len(nv_pts_old) else -1 for x in new_to_old_map
]
return_queue.put(new_to_old_map)