def find_peaks_automatic(self, x, y, peak_ind):
massif = Massif(self.img_data.img_data)
cur_peak_points = massif.find_peaks([x, y])
if len(cur_peak_points):
self.points.append(np.array(cur_peak_points))
self.points_index.append(peak_ind)
return np.array(cur_peak_points)
def find_peaks_automatic(self, x, y, peak_ind):
massif = Massif(self.img_data.img_data)
cur_peak_points = massif.find_peaks([x, y])
if len(cur_peak_points):
self.points.append(np.array(cur_peak_points))
self.points_index.append(peak_ind)
return np.array(cur_peak_points)
def add_points(self, x, y, phi=0.0):
xc, yc = self.parameters['xc'].value, self.parameters['yc'].value
idx, idy = self.find_peak(x, y)
points = [(idy, idx)]
circles = []
massif = Massif(self.counts)
extra_points = massif.find_peaks((idy, idx))
for point in extra_points:
points.append(point)
circles.append(self.circle(point[1], point[0], alpha=0.3))
phis = np.array([np.arctan2(p[0]-yc, p[1]-xc) for p in points])
if phi < -0.5*np.pi:
phis[np.where(phis > 0.0)] -= 2 * np.pi
self.phi_max = max(*phis, self.phi_max)
self.points.append([self.circle(idx, idy), points, circles, self.ring])
def find_peaks_automatic(self, x, y, peak_ind):
"""
Searches peaks by using the Massif algorithm
:param float x:
x-coordinate in pixel - should be from original image (not supersampled x-coordinate)
:param float y:
y-coordinate in pixel - should be from original image (not supersampled y-coordinate)
:param peak_ind:
peak/ring index to which the found points will be added
:return:
array of points found
"""
massif = Massif(self.img_model._img_data)
cur_peak_points = massif.find_peaks((int(np.round(x)), int(np.round(y))), stdout=DummyStdOut())
if len(cur_peak_points):
self.points.append(np.array(cur_peak_points))
self.points_index.append(peak_ind)
return np.array(cur_peak_points)
def find_peaks_automatic(self, x, y, peak_ind):
"""
Searches peaks by using the Massif algorithm
:param x:
x-coordinate in pixel - should be from original image (not supersampled x-coordinate)
:param y:
y-coordinate in pixel - should be from original image (not supersampled y-coordinate)
:param peak_ind:
peak/ring index to which the found points will be added
:return:
array of points found
"""
massif = Massif(self.img_model._img_data)
cur_peak_points = massif.find_peaks([x, y], stdout=DummyStdOut())
if len(cur_peak_points):
self.points.append(np.array(cur_peak_points))
self.points_index.append(peak_ind)
return np.array(cur_peak_points)
def on_button_release(self, event):
if event.inaxes:
if abs(event.x - self.xp) > 5 or abs(event.y - self.yp) > 5:
return
x, y = self.plotview.inverse_transform(event.xdata, event.ydata)
for i, point in enumerate(self.points):
circle = point[0]
if circle.contains_point(self.plotview.ax.transData.transform((x,y))):
circle.remove()
for circle in point[2]:
circle.remove()
del self.points[i]
return
idx, idy = self.find_peak(x, y)
points = [(idy, idx)]
circles = []
massif = Massif(self.counts)
extra_points = massif.find_peaks((idy, idx))
for point in extra_points:
points.append(point)
circles.append(self.circle(point[1], point[0], alpha=0.3))
self.points.append([self.circle(idx, idy), points, circles, self.ring])
def setup_peak_search_algorithm(self, algorithm, mask=None):
# init the peak search algorithm
if algorithm == 'Massif':
self.peak_search_algorithm = Massif(self.img_data.img_data)
elif algorithm == 'Blob':
if mask is not None:
self.peak_search_algorithm = BlobDetection(
self.img_data.img_data * mask)
else:
self.peak_search_algorithm = BlobDetection(
self.img_data.img_data)
self.peak_search_algorithm.process()
else:
return
def on_button_release(self, event):
if event.inaxes:
if abs(event.x - self.xp) > 5 or abs(event.y - self.yp) > 5:
return
x, y = self.plotview.inverse_transform(event.xdata, event.ydata)
for i, point in enumerate(self.points):
circle = point[0]
if circle.contains_point(
self.plotview.ax.transData.transform((x, y))):
circle.remove()
for circle in point[2]:
circle.remove()
del self.points[i]
return
idx, idy = self.find_peak(x, y)
points = [(idy, idx)]
circles = []
massif = Massif(self.counts)
extra_points = massif.find_peaks((idy, idx))
for point in extra_points:
points.append(point)
circles.append(self.circle(point[1], point[0], alpha=0.3))
self.points.append(
[self.circle(idx, idy), points, circles, self.ring])
def setup_peak_search_algorithm(self, algorithm, mask=None):
"""
Initializes the peak search algorithm on the current image
:param algorithm:
peak search algorithm used. Possible algorithms are 'Massif' and 'Blob'
:param mask:
if a mask is used during the process this is provided here as a 2d array for the image.
"""
if algorithm == 'Massif':
self.peak_search_algorithm = Massif(self.img_model.raw_img_data)
elif algorithm == 'Blob':
if mask is not None:
self.peak_search_algorithm = BlobDetection(self.img_model.raw_img_data * mask)
else:
self.peak_search_algorithm = BlobDetection(self.img_model.raw_img_data)
self.peak_search_algorithm.process()
else:
return
