def test2Dfit(fitType = None, verbose = False):
testDebug = 0
testOptimizer = 'levmar'
roi = [1, 325, 1, 335]
conIm = PrincetonSPEFile('testimage.spe')[0].astype(float32)
conZ = array(meshgrid(arange(roi[0], roi[0] + roi[1]), arange(roi[2], roi[2] + roi[3])))
if fitType == 'twodgauss':
guess = array([ conIm.max(), 162.5, 5, 167.5, 6])
func = [twodgauss]
elif fitType == 'twodgausslin':
guess = array([ 0.01*conIm.max(), 1e-8, 1e-8, conIm.max(), 162.5, 5, 167.5, 6])
func = [twodlin, twodgauss]
times = []
for optimizer in ['leastsq', 'levmar', 'mpfit']:
f = fit.fit(x = conZ, y = conIm, funcs = func , guess = guess,
debug = testDebug, optimizer = optimizer)
t1 = time.time()
f.go()
t2 = time.time()
times.append('Optimizer %s took %0.3f s' % (optimizer, (t2-t1)))
for t in times:
print t
def test2Dfit(fitType=None, verbose=False):
testDebug = 0
testOptimizer = 'levmar'
roi = [1, 325, 1, 335]
conIm = PrincetonSPEFile('testimage.spe')[0].astype(float32)
conZ = array(
meshgrid(arange(roi[0], roi[0] + roi[1]),
arange(roi[2], roi[2] + roi[3])))
if fitType == 'twodgauss':
guess = array([conIm.max(), 162.5, 5, 167.5, 6])
func = [twodgauss]
elif fitType == 'twodgausslin':
guess = array(
[0.01 * conIm.max(), 1e-8, 1e-8,
conIm.max(), 162.5, 5, 167.5, 6])
func = [twodlin, twodgauss]
times = []
for optimizer in ['leastsq', 'levmar', 'mpfit']:
f = fit.fit(x=conZ,
y=conIm,
funcs=func,
guess=guess,
debug=testDebug,
optimizer=optimizer)
t1 = time.time()
f.go()
t2 = time.time()
times.append('Optimizer %s took %0.3f s' % (optimizer, (t2 - t1)))
for t in times:
print t
def fittest():
data = loadtxt('testdata.dat')
times = []
for optimizer in ['leastsq', 'levmar', 'mpfit']:
f = fit.fit(x = data[:,0], y = data[:,1],
funcs = [fitfuncs.linear, fitfuncs.gauss],
optimizer = optimizer)
t1 = time.time()
f.go()
t2 = time.time()
times.append('Optimizer %s took %0.3f s' % (optimizer, (t2-t1)))
for t in times:
print t
def fittest():
data = loadtxt('testdata.dat')
times = []
for optimizer in ['leastsq', 'levmar', 'mpfit']:
f = fit.fit(x=data[:, 0],
y=data[:, 1],
funcs=[fitfuncs.linear, fitfuncs.gauss],
optimizer=optimizer)
t1 = time.time()
f.go()
t2 = time.time()
times.append('Optimizer %s took %0.3f s' % (optimizer, (t2 - t1)))
for t in times:
print t
def peak_analysis(img,
x,
y,
dxy=40,
interpolation_points=80,
show_plots=False,
center_on_max=True,
calculate_width=False):
x = int(x + 0.5)
y = int(y + 0.5)
sub_img = img[y - dxy:y + dxy, x - dxy:x + dxy].copy()
params = peak_params()
# calculate COM
COM = scipy.ndimage.measurements.center_of_mass(sub_img)
max_pos = scipy.ndimage.measurements.maximum_position(sub_img)
#TODO: check if we want to use the max pixel or the COM for the width measurements
if (center_on_max):
used_peak_pos_small = np.array((max_pos[1], max_pos[0]))
used_peak_pos_large = np.array(
(x - dxy + max_pos[1], y - dxy + max_pos[0]))
else:
used_peak_pos_small = np.array((COM[1], COM[0]))
used_peak_pos_large = np.array((x - dxy + COM[1], y - dxy + COM[0]))
params.COM = np.array((x - dxy + COM[1], y - dxy + COM[0]))
params.max_pos = np.array((x - dxy + max_pos[1], y - dxy + max_pos[0]))
r_x_para = 1024 - used_peak_pos_large[0]
r_y_para = 1024 - used_peak_pos_large[1]
r_mag = np.sqrt(r_x_para**2 + r_y_para**2)
r_x_para /= r_mag
r_y_para /= r_mag
if (r_x_para == 0 or r_y_para == 0):
r_x_perp = r_y_para
r_y_perp = r_x_para
else:
r_x_perp = 1. / r_x_para
r_y_perp = -1. / r_y_para
r_mag = np.sqrt(r_x_perp**2 + r_y_perp**2)
r_x_perp /= r_mag
r_y_perp /= r_mag
# subtract background
sub_img_bg = img[y - 2 * dxy:y + 2 * dxy, x - 2 * dxy:x + 2 * dxy].copy()
xi = np.arange(4 * dxy)
yi = np.arange(4 * dxy)
func_bg = scipy.interpolate.RectBivariateSpline(xi, yi, sub_img_bg)
d_vals = np.arange(4 * dxy) - 4 * dxy / 2.
f_bg1 = np.zeros(len(d_vals))
f_bg2 = np.zeros(len(d_vals))
f_bg = np.zeros(len(d_vals))
p_1_x = np.sqrt(2) * dxy * r_x_perp + 2 * dxy
p_1_y = np.sqrt(2) * dxy * r_y_perp + 2 * dxy
p_2_x = -np.sqrt(2) * dxy * r_x_perp + 2 * dxy
p_2_y = -np.sqrt(2) * dxy * r_y_perp + 2 * dxy
line_p1_x = []
line_p1_y = []
line_p2_x = []
line_p2_y = []
for i in xrange(len(d_vals)):
f_bg1[i] = func_bg(p_1_x + d_vals[i] * r_x_para,
p_1_y + d_vals[i] * r_y_para)
f_bg2[i] = func_bg(p_2_x + d_vals[i] * r_x_para,
p_2_y + d_vals[i] * r_y_para)
f_bg[i] = (f_bg1[i] + f_bg2[i]) / 2.
#f_bg[i] /= 2.
line_p1_x.append(p_1_x + d_vals[i] * r_x_para)
line_p1_y.append(p_1_y + d_vals[i] * r_y_para)
line_p2_x.append(p_2_x + d_vals[i] * r_x_para)
line_p2_y.append(p_2_y + d_vals[i] * r_y_para)
if (show_plots):
plt.figure()
plt.plot(f_bg1)
plt.plot(f_bg2)
fig = plt.figure()
plt.title('Image with Background')
ax = fig.add_subplot(111)
im = ax.imshow(sub_img, interpolation='None')
ax.plot([used_peak_pos_small[0]], [used_peak_pos_small[1]], 'wd')
ax.format_coord = Imshow_Formatter(im)
plt.show()
dummy, bg_arr = np.meshgrid(f_bg, f_bg)
bg_arr_rot = scipy.ndimage.interpolation.rotate(
bg_arr, deg(np.arctan2(r_x_para, r_y_para)), reshape=False)
bg_arr_rot_cut = bg_arr_rot[dxy:3 * dxy, dxy:3 * dxy]
sub_img -= bg_arr_rot_cut
params.max = scipy.ndimage.measurements.maximum(sub_img)
params.integrated_intensity = np.sum(sub_img)
if (show_plots):
fig = plt.figure()
plt.title('Background subtracted')
ax = fig.add_subplot(111)
im = ax.imshow(sub_img, interpolation='None')
ax.plot([used_peak_pos_small[0]], [used_peak_pos_small[1]], 'wd')
ax.format_coord = Imshow_Formatter(im)
fig = plt.figure()
ax = fig.add_subplot(111)
im = ax.imshow(sub_img_bg, interpolation='None')
ax.plot(line_p1_x, line_p1_y, 'w')
ax.plot(line_p2_x, line_p2_y, 'w')
ax.format_coord = Imshow_Formatter(im)
# calculate peak width
if (calculate_width):
xi = np.arange(2 * dxy)
yi = np.arange(2 * dxy)
func = scipy.interpolate.RectBivariateSpline(xi, yi, sub_img)
d_vals = np.arange(interpolation_points) - int(
interpolation_points / 2.)
d_x_para = np.zeros(len(d_vals))
d_y_para = np.zeros(len(d_vals))
d_ints_para = np.zeros(len(d_vals))
d_x_perp = np.zeros(len(d_vals))
d_y_perp = np.zeros(len(d_vals))
d_ints_perp = np.zeros(len(d_vals))
for i in xrange(len(d_vals)):
d_x_para[i] = used_peak_pos_small[0] + d_vals[i] * r_x_para
d_y_para[i] = used_peak_pos_small[1] + d_vals[i] * r_y_para
d_ints_para[i] = func(
used_peak_pos_small[0] + d_vals[i] * r_x_para,
used_peak_pos_small[1] + d_vals[i] * r_y_para)
d_x_perp[i] = used_peak_pos_small[0] + d_vals[i] * r_x_perp
d_y_perp[i] = used_peak_pos_small[1] + d_vals[i] * r_y_perp
d_ints_perp[i] = func(
used_peak_pos_small[0] + d_vals[i] * r_x_perp,
used_peak_pos_small[1] + d_vals[i] * r_y_perp)
try:
df_para = fit.fit(
x=d_vals,
y=d_ints_para,
funcs=[pyspec.fitfuncs.gauss, pyspec.fitfuncs.linear])
df_para.run()
df_perp = fit.fit(
x=d_vals,
y=d_ints_perp,
funcs=[pyspec.fitfuncs.gauss, pyspec.fitfuncs.linear])
df_perp.run()
params.FWHM_para = 2. * np.sqrt(
2. * np.log(2.)) * df_para.result[1]
params.FWHM_perp = 2. * np.sqrt(
2. * np.log(2.)) * df_perp.result[1]
if (show_plots):
fig = plt.figure()
ax = fig.add_subplot(111)
im = ax.imshow(sub_img, interpolation='None')
ax.plot([used_peak_pos_small[0]], [used_peak_pos_small[1]],
'wd')
ax.plot(d_x_para, d_y_para, 'r-')
ax.plot(d_x_perp, d_y_perp, 'b-')
ax.format_coord = Imshow_Formatter(im)
plt.figure()
plt.plot(d_vals, d_ints_para, 'r-')
plt.plot(d_vals, d_ints_perp, 'b-')
plt.plot(
d_vals,
pyspec.fitfuncs.gauss(d_vals, df_para.result[0:3]) +
pyspec.fitfuncs.linear(d_vals, df_para.result[3:]), 'r--')
plt.plot(
d_vals,
pyspec.fitfuncs.gauss(d_vals, df_perp.result[0:3]) +
pyspec.fitfuncs.linear(d_vals, df_perp.result[3:]), 'b--')
except:
return params
return params
if (do_plot):
plt.figure()
plt.imshow(img)
# Fit L cuts
L_cut_half_width = 10
L_cut_img = img[:, COM[1] - L_cut_half_width:COM[1] + L_cut_half_width +
1] #img[: , 372:408]
L_cut = np.sum(L_cut_img, axis=1)
L_cut[255:261] = (L_cut[253] + L_cut[254] + L_cut[261] +
L_cut[262]) / 4. # remove border between ccd panels
L_cut[338] = (L_cut[337] + L_cut[339]) / 2. # remove dead pixel
df = fit.fit(x=np.arange(516),
y=L_cut,
xlimits=[66, 515],
funcs=[pyspec.fitfuncs.pvoight, pyspec.fitfuncs.constant])
df.run()
_x = np.arange(800)
_y = pyspec.fitfuncs.pvoight(
_x, df.result[0:4]) + pyspec.fitfuncs.constant(_x, df.result[4:])
if (do_plot):
plt.figure()
plt.plot(L_cut)
plt.plot(_x, _y)
L_params = df.result
print df.result