def FT1D(numb1, ppm_offset=0, autoph=True, ph0=0, ph1=0):
"Performs FT and corrections of experiment 'numb1' and returns data"
def phase_from_param():
"read the proc parame file, and returns phase parameters ok for spike"
#print( proc['$PHC0'], proc['$PHC1'] )
ph1 = -float(proc['$PHC1']) # First-order phase correction
ph0 = -float(proc['$PHC0']) + ph1 / 2 # Zero-order phase correction
zero = -360 * d.axis1.zerotime
#print (ph0, ph1)
return (ph0, ph1 + zero)
proc = bk.read_param(numb1[:-3] + 'pdata/1/procs')
d = bk.Import_1D(numb1)
d.apod_em(1, 1).zf(2).ft_sim()
if not autoph:
p0, p1 = phase_from_param()
d.phase(p0 + ph0, p1 + ph1) # Performs the stored phase correction
else:
d.bruker_corr().apmin() # automatic phase correction
d.unit = 'ppm'
d.axis1.offset += ppm_offset * d.axis1.frequency
spec = np.real(as_cpx(d.buffer))
# the following is a bit convoluted baseline correction,
bl = correctbaseline(spec, iterations=BC_ITER, nbchunks=d.size1 // 1000)
dd = d.copy()
dd.set_buffer(bl)
dd.unit = 'ppm'
d.real()
d -= dd # Equal to d=d-dd; Used instead of (spec-bl)
return d
def plot_2D(d, scale, numb2, resdir):
fiddir = op.dirname(numb2)
basedir, fidname = op.split(fiddir)
base, manip = op.split(basedir)
exptype = bk.read_param(bk.find_acqu(fiddir))['$PULPROG']
exptype = exptype[1:-1] # removes the <...>
d.display(scale=scale)
plt.savefig(
op.join(resdir, '2D', exptype + '_' + fidname +
'.pdf')) # Creates a PDF of the 2D spectrum without peaks
d.display_peaks(color="g")
plt.savefig(
op.join(resdir, '2D', exptype + '_' + fidname +
'_pp.pdf')) # Creates a PDF of the 2D spectrum with peaks
plt.close()
return d
def Dprocess_2D(numb2, resdir):
"Performs DOSY processing of experiment 'numb2' and produces the spectrum with and without peaks"
fiddir = op.dirname(numb2)
basedir, fidname = op.split(fiddir)
base, manip = op.split(basedir)
exptype = bk.read_param(bk.find_acqu(fiddir))['$PULPROG']
exptype = exptype[1:-1] # removes the <...>
ppm_offset, ph0, ph1 = get_config(base, manip, fidname)
d = bk.Import_2D(numb2)
d.unit = 'ppm'
if 'ste' in exptype or 'led' in exptype:
print("DOSY")
d = process_DOSY(numb2, ppm_offset, lazy=DOSY_LAZY)
scale = 50.0
else:
raise Exception("This is not a DOSY: " + numb2)
dd = analyze_2D(d, name=op.join(resdir, '2D', exptype + '_' + fidname))
d.save(op.join(fiddir, "processed.gs2"))
return dd, scale
def process_2D(xarg):
"Performs all processing of experiment 'numb2' and produces the spectrum with and without peaks"
numb2, resdir = xarg
fiddir = op.dirname(numb2)
basedir, fidname = op.split(fiddir)
base, manip = op.split(basedir)
exptype = bk.read_param(bk.find_acqu(fiddir))['$PULPROG']
exptype = exptype[1:-1] # removes the <...>
ppm_offset, ph0, ph1 = get_config(base, manip, fidname)
d = bk.Import_2D(numb2)
d.unit = 'ppm'
scale = 10.0
sanerank = SANERANK
#1. If TOCSY
if 'dipsi' in exptype:
print("TOCSY")
# print exptype
if 'dipsi2ph' in exptype:
d.apod_sin(maxi=0.5, axis=2).zf(zf2=2).ft_sim()
if sanerank != 0:
d.sane(rank=sanerank, axis=1)
d.apod_sin(maxi=0.5,
axis=1).zf(zf1=4).ft_sh_tppi().modulus().rem_ridge()
elif 'dipsi2etgpsi' in exptype:
d.apod_sin(maxi=0.5, axis=2).zf(zf2=2).ft_sim()
if sanerank != 0:
d.sane(rank=sanerank, axis=1)
d.apod_sin(maxi=0.5,
axis=1).zf(zf1=4).ft_n_p().modulus().rem_ridge()
scale = 50.0
d.axis2.offset += ppm_offset * d.axis2.frequency
if TMS:
d = autozero(d)
#2. If COSY DQF
elif 'cosy' in exptype:
print("COSY DQF")
d.apod_sin(maxi=0.5, axis=2).zf(zf2=2).ft_sim()
if sanerank != 0:
d.sane(rank=sanerank, axis=1)
d.apod_sin(maxi=0.5,
axis=1).zf(zf1=4).ft_sh_tppi().modulus().rem_ridge()
scale = 20.0
d.axis2.offset += ppm_offset * d.axis2.frequency
if TMS:
d = autozero(d)
#3. If HSQC
elif 'hsqc' in exptype:
print("HSQC")
if 'ml' in exptype:
print("TOCSY-HSQC")
d.apod_sin(maxi=0.5, axis=2).zf(zf2=2).ft_sim().conv_n_p()
if sanerank != 0:
d.sane(rank=sanerank, axis=1)
d.apod_sin(maxi=0.5, axis=1).zf(zf1=4).ft_sh().modulus().rem_ridge()
scale = 10.0
d.axis2.offset += ppm_offset * d.axis2.frequency
if TMS:
d = autozero(d, z1=(5, -5))
#4. If HMBC
elif 'hmbc' in exptype:
print("HMBC")
if 'hmbc' in exptype:
print("HMBC")
d.apod_sin(maxi=0.5, axis=2).zf(zf2=2).ft_sim()
if 'et' in exptype:
d.conv_n_p()
if sanerank != 0:
d.sane(rank=sanerank, axis=1)
d.apod_sin(maxi=0.5, axis=1).zf(
zf1=4).bk_ftF1().modulus().rem_ridge() # For Pharma MB1-X-X series
scale = 10.0
d.axis2.offset += ppm_offset * d.axis2.frequency
if TMS:
d = autozero(d, z1=(5, -5))
#5. If DOSY - Processed in process_DOSY
elif 'ste' in exptype or 'led' in exptype:
print("DOSY")
d = process_DOSY(numb2, ppm_offset, lazy=DOSY_LAZY)
scale = 50.0
analyze_2D(d, name=op.join(resdir, '2D', exptype + '_' + fidname))
d.save(op.join(fiddir, "processed.gs2"))
return d, scale