def fitTrace(self,kwidth=10,porder=3,cwidth=30,pad=False):
sh = self.sh
xr1 = (0,sh[1])
xrs = [xr1]
polys = []
for xr in xrs:
xindex = np.arange(xr[0],xr[1])
kernel = np.median(self.image[int(sh[0]/2-kwidth):int(sh[0]/2+kwidth),xindex],0)
centroids = []
totals = []
for i in np.arange(sh[0]):
row = self.image[i,xindex]
row_med = np.median(row)
total = np.abs((row-row_med).sum())
cc = fp.ifft(fp.fft(kernel)*np.conj(fp.fft(row-row_med)))
cc_sh = fp.fftshift(cc)
centroid = helpers.calc_centroid(cc_sh,cwidth=cwidth).real - xindex.shape[0]/2.
centroids.append(centroid)
totals.append(total)
centroids = np.array(centroids)
yindex = np.arange(sh[0])
gsubs = np.where((np.isnan(centroids)==False))
centroids[gsubs] = median_filter(centroids[gsubs],size=20)
coeffs = np.polyfit(yindex[gsubs],centroids[gsubs],porder)
poly = np.poly1d(coeffs)
polys.append(poly)
return xrs,polys
def _findYOffsets(self):
kernel = np.median(self.stack[:,:,0],1)
offsets = np.empty(0)
nplanes = self.stack.shape[2]
for i in np.arange(nplanes):
profile = np.median(self.stack[:,:,i],1)
cc = fp.ifft(fp.fft(kernel)*np.conj(fp.fft(profile)))
cc_sh = fp.fftshift(cc)
cen = helpers.calc_centroid(cc_sh).real - self.height/2.
offsets = np.append(offsets,cen)
return offsets
def _findYOffsets(self):
kernel = np.median(self.stack[:, :, 0], 1)
offsets = np.empty(0)
nplanes = self.stack.shape[2]
for i in np.arange(nplanes):
profile = np.median(self.stack[:, :, i], 1)
cc = fp.ifft(fp.fft(kernel) * np.conj(fp.fft(profile)))
cc_sh = fp.fftshift(cc)
cen = helpers.calc_centroid(cc_sh).real - self.height / 2.
offsets = np.append(offsets, cen)
return offsets
def fitTrace(self, kwidth=10, porder=3, cwidth=30, pad=False):
sh = self.sh
xr1 = (0, sh[1])
xrs = [xr1]
polys = []
for xr in xrs:
xindex = np.arange(xr[0], xr[1])
kernel = np.median(
self.image[int(sh[0] / 2 - kwidth):int(sh[0] / 2 + kwidth),
xindex], 0)
centroids = []
totals = []
for i in np.arange(sh[0]):
row = self.image[i, xindex]
row_med = np.median(row)
total = np.abs((row - row_med).sum())
cc = fp.ifft(fp.fft(kernel) * np.conj(fp.fft(row - row_med)))
cc_sh = fp.fftshift(cc)
centroid = helpers.calc_centroid(
cc_sh, cwidth=cwidth).real - xindex.shape[0] / 2.
centroids.append(centroid)
totals.append(total)
centroids = np.array(centroids)
yindex = np.arange(sh[0])
gsubs = np.where((np.isnan(centroids) == False))
centroids[gsubs] = median_filter(centroids[gsubs], size=20)
coeffs = np.polyfit(yindex[gsubs], centroids[gsubs], porder)
poly = np.poly1d(coeffs)
polys.append(poly)
return xrs, polys
