def getSigma():
''' This function isn't complete. I need to cut out a 20x20 pxl window around large amplitude particles '''
from gaussianFitting import fitGaussian
I=g.m.currentWindow.image
xorigin=8
yorigin=9
sigma=2
amplitude=50
p0=[xorigin, yorigin, sigma,amplitude]
p, I_fit, _ =fitGaussian(I,p0)
xorigin, yorigin, sigma,amplitude = p
return sigma
def refine_pts(pts,Movie):
from gaussianFitting import fitGaussian
new_pts=[]
for pt in pts:
print(pt)
width=9
mid=int(np.floor(width/2))
I, corner=cutout(pt,Movie,width)
xorigin=mid; yorigin=mid; sigma=1.1; amplitude=50
p0=[xorigin,yorigin,sigma,amplitude]
fit_bounds = [(0,9), (0,9), (0,4), (0,1000)]
p, I_fit, _ = fitGaussian(I,p0, fit_bounds)
xfit=p[0]+corner[0]
yfit=p[1]+corner[1]
new_pts.append([pt[0],pt[1],pt[2],xfit,yfit,p[2],p[3]])
new_pts=np.array(new_pts)
return new_pts