for numspec in range(len(yobs)):
cc_numspec = []
for seg_num in range(int(segment)):
y_temp_order = h5f_temp[
str(ccd) + "vmr-" + str(vmr) + "-order-" +
str(order) + "-segment-" +
str(seg_num
)][:] #Loading template of vmr, v= -55., 355
low_lim = int(((seg_num) / segment) * len(yobs[0]))
up_lim = int(((seg_num + 1.) / segment) * len(yobs[0]))
fluxsegment = yobs[numspec][low_lim:up_lim]
cc_each_seg = []
for rv in range(len(drvs)):
cc_rv = crossco(fluxsegment, y_temp_order[rv])
cc_each_seg.append(cc_rv)
cc_numspec.append(np.array(cc_each_seg))
cc_numspec = np.array(
cc_numspec)[~np.isnan(np.mean(cc_numspec, axis=1))]
cc_numspec_SA = np.mean(cc_numspec, axis=0)
cc_order_SA[numspec] = cc_numspec_SA
cc_svd_collect_SA.append(cc_order_SA)
cc_map_full_SA.append(cc_svd_collect_SA)
h5f_cc.create_dataset(
str(ccd) + "_cc_vmr_" + str(vmr),
data=cc_map_full_SA) #Writing the template of the specific vmr
# h5f_reduced.close()
h5f_reduced.close()
h5f_cc.close()
h5f_temp.close()
for var in tqdm(range(len_sv),ascii="True",desc=str(vari)+"="+str(va)+" R"+str(varname)):
cc_svd_collect=[] #Different SV are saved in this matrix
for order in tqdm (range(1,len_order),ascii="True",desc="Order"):
# y_temp_order=h5f_temp[str(ccd)+"-vmr-"+str(va)+"-order-"+str(order)][:]
yobs=h5f_reduced[str(ccd)+"-flux"+str(vari)+"-"+str(va)+"-order-"+str(order)+"sysrem"][:][var]
# yobs=h5f_reduced[str(ccd)+"-flux-"+str(vari)+"-"+str(va)+"-order-"+str(order)+"sysrem"][:][var]
y_temp_order=h5f_temp[str(ccd)+"-vmr-9-order-"+str(order)][:]
# yobs= h5f_reduced[str(ccd)+"-flux-"+str(vari)+"-7-order-"+str(order)+str(varname)+"-"+str(var+1)][:]
for filenum in range (len(yobs)):
sm = pyasl.smooth(yobs[filenum], 25, 'flat')
sm1 = pyasl.smooth(sm, 51, 'flat')
yobs[filenum]=(yobs[filenum]+1.)/(sm1+1.)-1.
std_frames=[]
std_pix=[]
for wvbin in range (len(yobs[1])):
std_pix.append(np.std(yobs[:,wvbin]))
for filenum in range (len(yobs)):
std_frames.append(np.std(yobs[filenum,:]))
std_frames=np.array(std_frames,dtype="float")
yobs=divstd_prime(yobs,std_pix,std_frames)
cc_order=np.zeros((len(yobs),len(drvs)),dtype="float")
for numspec in range(len(yobs)):
for rv in range(len(drvs)):
cc_order[numspec][rv]=crossco(yobs[numspec],y_temp_order[rv])
# cc_order[numspec][rv]=cc_sp(yobs[numspec],y_temp_order[rv])
cc_svd_collect.append(cc_order)
cc_map_full.append(np.array(cc_svd_collect))
h5f_cc.create_dataset(str(ccd)+"_cc_"+str(vari)+"_"+str(va), data= np.array(cc_map_full)) #Writing the template of the specific vmr
h5f_cc.close()
h5f_reduced.close()