def place_peaks(self, spectrum):
hc_axes = pyutil.order(('1H', '13C'), spectrum.nuclei)
if spectrum.dimension != 2 or hc_axes == None:
self.progress_report('Spectrum must 2D with H and C axes.')
return
molecule = spectrum.molecule
condition = spectrum.condition
self.stoppable_loop('resonances', 50)
for rH in condition.resonance_list():
self.check_for_stop()
if rH.atom.nucleus == '1H':
catom = atoms.attached_heavy_atom(rH.atom, molecule)
if catom and catom.nucleus == '13C':
rC = condition.find_resonance(catom)
if rC:
assignment = pyutil.permute((rH, rC), hc_axes)
if not spectrum.find_peak(assignment):
freq = pyutil.permute((rH.frequency, rC.frequency), hc_axes)
pos = sputil.alias_onto_spectrum(freq, spectrum)
peak = spectrum.place_peak(pos)
peak.assign(hc_axes[0], rH.group.name, rH.atom.name)
peak.assign(hc_axes[1], rC.group.name, rC.atom.name)
if freq != pos:
peak.alias = pyutil.subtract_tuples(freq, pos)
peak.show_assignment_label()
def move_peak_onto_spectrum(self, peak):
freq = peak.frequency
pos = sputil.alias_onto_spectrum(freq, peak.spectrum)
if pos != freq:
peak.position = pos
peak.alias = pyutil.subtract_tuples(freq, pos)
def peak_strips(self, peak, spectra_3d):
peak_xyz_axes = self.peak_strip_axes(peak, spectra_3d)
if peak_xyz_axes == None:
return []
paX, paY, paZ = peak_xyz_axes
if paY == None:
xyz_freq = (peak.frequency[paX], 0, peak.frequency[paZ])
else:
xyz_freq = pyutil.permute(peak.frequency, peak_xyz_axes)
nuclei = peak.spectrum.nuclei
xz_nuclei = (nuclei[paX], nuclei[paZ])
label = self.peak_strip_label(peak, paX, paZ)
strips = []
for spectrum in spectra_3d:
xyz_axes = self.xyz_axes(spectrum)
if xyz_axes:
aX, aY, aZ = xyz_axes
if (spectrum.nuclei[aX], spectrum.nuclei[aZ]) == xz_nuclei:
if self.spectrum_label:
label = spectrum.name + '\n' + label
center = pyutil.unpermute(xyz_freq, xyz_axes)
center = sputil.alias_onto_spectrum(center, spectrum)
strip = self.spectrum_strip(spectrum, xyz_axes, center, label)
strips.append(strip)
label = '\n\n'
return strips
def move_peak_onto_spectrum(self, peak):
freq = peak.frequency
pos = sputil.alias_onto_spectrum(freq, peak.spectrum)
if pos != freq:
peak.position = pos
peak.alias = pyutil.subtract_tuples(freq, pos)
def center_on_point(self, spectrum, point):
view_to_center = self.view_to_center
if view_to_center:
center = self.map_point(spectrum, point,
view_to_center.spectrum, view_to_center.center)
center = sputil.alias_onto_spectrum(center, view_to_center.spectrum)
view_to_center.center = center
def goto_peak_cb(self, event):
list_data = self.peak_list.event_line_data(event)
if self.is_assignment(list_data):
epeak, dpeak = list_data
sputil.show_peak(dpeak)
elif self.is_position(list_data):
spectrum, freq = list_data
pos = sputil.alias_onto_spectrum(freq, spectrum)
sputil.show_spectrum_position(spectrum, pos)
def goto_peak_cb(self, event):
list_data = self.peak_list.event_line_data(event)
if self.is_assignment(list_data):
epeak, dpeak = list_data
sputil.show_peak(dpeak)
elif self.is_position(list_data):
spectrum, freq = list_data
pos = sputil.alias_onto_spectrum(freq, spectrum)
sputil.show_spectrum_position(spectrum, pos)
def strip_center(self, epeak, xyz_axes):
aX, aY, aZ = xyz_axes
spectrum = epeak.peak_set.spectrum
rmin, rmax = spectrum.region
shift = self.assignments.resonance_shift
freq = [0,0,0]
freq[aX] = shift(epeak.resonances[aX])
freq[aY] = .5 * (rmin[aY] + rmax[aY])
freq[aZ] = shift(epeak.resonances[aZ])
center = sputil.alias_onto_spectrum(freq, spectrum)
return center
def strip_center(self, epeak, xyz_axes):
aX, aY, aZ = xyz_axes
spectrum = epeak.peak_set.spectrum
rmin, rmax = spectrum.region
shift = self.assignments.resonance_shift
freq = [0, 0, 0]
freq[aX] = shift(epeak.resonances[aX])
freq[aY] = .5 * (rmin[aY] + rmax[aY])
freq[aZ] = shift(epeak.resonances[aZ])
center = sputil.alias_onto_spectrum(freq, spectrum)
return center
def assigned_strip(self, spectrum, xz_assignment):
c = spectrum.condition
x_assignment, z_assignment = xz_assignment
rX = apply(c.find_resonance, x_assignment)
rZ = apply(c.find_resonance, z_assignment)
if rX and rZ:
freq = [0,0,0]
xyz_axes = self.xyz_axes(spectrum)
aX, aY, aZ = xyz_axes
freq[aX] = rX.frequency
freq[aZ] = rZ.frequency
center = sputil.alias_onto_spectrum(freq, spectrum)
group_name = x_assignment[0]
atom_name = x_assignment[1]
label = '%.4g\n%.4g\n%s %s' % (center[aX], center[aZ], group_name, atom_name)
if self.spectrum_label:
spectrum_name = spectrum.name
label = spectrum_name + '\n' + label
strip = self.spectrum_strip(spectrum, xyz_axes, center, label)
strip.xz_assignment = xz_assignment
return strip
return None
def assignment_text(self, epeak, dpeak, freq, show_assignment):
sp = epeak.peak_set.spectrum
if show_assignment:
spectrum = sp.name
assignment = epeak.assignment_text()
else:
spectrum = ''
assignment = ''
if dpeak:
position = self.position_text(freq, dpeak.frequency)
height = sputil.peak_height(dpeak) / sp.noise
assigned = dpeak.assignment
else:
position = ''
pos = sputil.alias_onto_spectrum(freq, sp)
height = sp.data_height(pos) / sp.noise
assigned = ''
text = ('%10s %20s %21s %5.1f %s'
% (spectrum, assignment, position, height, assigned))
return text
def assignment_text(self, epeak, dpeak, freq, show_assignment):
sp = epeak.peak_set.spectrum
if show_assignment:
spectrum = sp.name
assignment = epeak.assignment_text()
else:
spectrum = ''
assignment = ''
if dpeak:
position = self.position_text(freq, dpeak.frequency)
height = sputil.peak_height(dpeak) / sp.noise
assigned = dpeak.assignment
else:
position = ''
pos = sputil.alias_onto_spectrum(freq, sp)
height = sp.data_height(pos) / sp.noise
assigned = ''
text = ('%10s %20s %21s %5.1f %s' %
(spectrum, assignment, position, height, assigned))
return text
return dict(dim_list)
# place assigned peaks
from sputil import split_group_atom, alias_onto_spectrum
from pyutil import subtract_tuples
dim_dict = detect_dimension(peak_list, spec)
if dim_dict == None:
s.show_message('Error',
'Spectrum does not look the correct experiment to use.')
raise SystemExit
for peak in peak_list:
gas, freqs = peak[0], peak[1]
gas2, freqs2 = list(gas), list(freqs)
for a in range(spec.dimension):
b = dim_dict[a]
gas2[b], freqs2[b] = gas[a], freqs[a]
peak = spec.place_peak(freqs2)
# alias if edge of the spectrum
freqs3 = alias_onto_spectrum(freqs2, spec)
if freqs2 != freqs3:
peak.position = freqs3
peak.alias = subtract_tuples(freqs2, freqs3)
# attach assignment labels
for i in range(spec.dimension):
g, a = split_group_atom(gas2[i])
peak.assign(i, g, a)
peak.show_assignment_label()