## examples/pca/pca_aucyano.lar
# note that this is similar to examples/fitting/doc_example3

auproject = read_athena('cyanobacteria.prj', do_fft=False, do_bkg=False)

d_720       = extract_athenagroup(auproject.d_720)
au_foil     = extract_athenagroup(auproject.Au_foil)
au_cl3aq    = extract_athenagroup(auproject.Au3_Cl_aq)
au_hydrox   = extract_athenagroup(auproject.Au_hydroxide)
au_sulfide  = extract_athenagroup(auproject.Au_sulphide)
au_thiocyan = extract_athenagroup(auproject.Au_thiocyanide)
au_thiosulf = extract_athenagroup(auproject.Au_thiosulphate_aq)

# make sure pre_edge() is run with the same params for all groups
for g in (d_720, au_foil, au_cl3aq, au_hydrox, au_sulfide, au_thiocyan, au_thiosulf):
    pre_edge(g, pre1=-150, pre2=-30, nnorm=1, norm1=150, norm2=850)
#endfor

standards = (au_foil, au_cl3aq, au_hydrox, au_sulfide, au_thiocyan, au_thiosulf)

# train model with standards
au_pcamodel = pca_train(standards, arrayname='norm', xmin=11870, xmax=12030)


# plot components and weights
plot_pca_components(au_pcamodel, min_weight=0.005)
plot_pca_weights(au_pcamodel, win=2, min_weight=0.005, ylog_scale=True)

# print out weights
total = 0
print(" Comp #  |  Weight   |  Cumulative Total")
for i, weight in enumerate(au_pcamodel.variances):
    total = total + weight
    print("  %3i    | %8.5f  | %8.5f " % (i+1, weight, total))
#endfor

# fit unknown data to model
pca_fit(d_720, au_pcamodel, ncomps=4)

# plot
plot_pca_fit(d_720, win=3)


## end of examples/pca/pca_aucyano.lar