alphas_inslice = np.append(
0, alphas_inslice
) # To include alpha=0, and put it at the beginning of the array
inds_al = np.where(
(alphas_inslice < alpha_high) & (alphas_inslice > alpha_low)
) # we cut to this range to avoid issues with the edges of the slices.
alphas_inslice = alphas_inslice[inds_al]
for alpha_pos in alphas_inslice:
if alpha_pos == alphas_inslice[0]:
print 'Along-slice position:'
print ' {} arcsec'.format(round(alpha_pos, 2))
# Take pixel trace along specified slice, specified alpha position trace is built by taking the pixel in every detector row with alpha value closest to the one specified
ypos, xpos = funcs.detpixel_trace(band,
d2cMaps,
sliceID=islice,
alpha_pos=alpha_pos)
if band == '1C':
xpos[0] = xpos[1]
xpos[-1] = xpos[-2]
# Choose data regions
#--FM data
etalon1A_fm_data = etalon1A_img[ypos, xpos]
etalon1B_fm_data = etalon1B_img[ypos, xpos]
# Determine etalon peaks
#--FM Etalon_1A data
if user == 'yannis':
etalon1A_fm_data[np.isnan(etalon1A_fm_data)] = -1
FMetalon1A_peaks = funcs.find_peaks(etalon1A_fm_data,
sliceMap = d2cMaps['sliceMap']
lambdaMap = d2cMaps['lambdaMap']
alphaMap = d2cMaps['alphaMap']
nslices = d2cMaps['nslices']
det_dims = (1024, 1032)
# In[6]:
plt.close('all')
# reference spectral trace
if band == '2C':
lower, upper = 600, -10
else:
lower, upper = 10, -10
ypos_ref, xpos_ref = funcs.detpixel_trace(band,
d2cMaps,
sliceID=ref_slice,
alpha_pos=ref_alpha)
sci_fm_data_ref = mrs_transmission_img[ypos_ref, xpos_ref][lower:upper]
# create a finer grid
step = 0.2
fine_grid = np.arange(lower, 1023 - abs(upper) + step, step)
if band == '2C': fine_grid = fine_grid[:-2]
sci_fm_data_ref_fine = interp1d(lower + np.arange(len(sci_fm_data_ref)),
sci_fm_data_ref)(fine_grid)
if band in ['1B', '2C']:
sci_fm_data_ref_fine = savgol_filter(sci_fm_data_ref_fine, 201, 2)
pix_offsets = []
offsets = np.arange(1, 200)
wider_offsets = np.arange(-200, 200)