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Introduction of matplotlib-independent simulating, peak-wise width values and optional region of interest (ROI) based line calculation for significant speed increase. #29

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Introduction of matplotlib-independent simulating, peak-wise width values and optional region of interest (ROI) based line calculation for significant speed increase. #29

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14 changes: 7 additions & 7 deletions src/nmrsim/_classes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
import numpy as np

from nmrsim.firstorder import first_order_spin_system, multiplet
from nmrsim.math import reduce_peaks, add_lorentzians
from nmrsim.math import reduce_peaks, add_lorentzians_limitable
from nmrsim.qm import qm_spinsystem
from nmrsim._utils import low_high

Expand Down Expand Up @@ -73,7 +73,7 @@ def __init__(self, v, I, J, w=0.5):
self.I = I
self.J = J
self.w = w
self._peaklist = multiplet((v, I), J)
self._peaklist = multiplet((v, I, w), J)

def __eq__(self, other):
if hasattr(other, "peaklist") and callable(other.peaklist):
Expand All @@ -87,7 +87,7 @@ def __add__(self, other):

def __mul__(self, scalar):
if isinstance(scalar, numbers.Real):
return Multiplet(self.v, self.I * scalar, self.J)
return Multiplet(self.v, self.I * scalar, self.J, self.w)
else:
return NotImplemented

Expand All @@ -105,7 +105,7 @@ def __itruediv__(self, scalar):
return self.__imul__(1 / scalar)

def _refresh(self):
self._peaklist = multiplet((self.v, self.I), self.J)
self._peaklist = multiplet((self.v, self.I, self.w), self.J)

def peaklist(self):
"""
Expand Down Expand Up @@ -245,9 +245,9 @@ def peaklist(self):
Array of (frequency, intensity) signals.
"""
if self._second_order:
return qm_spinsystem(self._v, self._J)
return qm_spinsystem(self._v, self._J, width=self.w)
else:
return first_order_spin_system(self._v, self._J)
return first_order_spin_system(self._v, self._J, self.w)

def __eq__(self, other):
if hasattr(other, "peaklist") and callable(other.peaklist):
Expand Down Expand Up @@ -368,7 +368,7 @@ def lineshape(self, points=800):
"""
vmin, vmax = low_high((self.vmin, self.vmax))
x = np.linspace(vmin, vmax, points)
y = [add_lorentzians(x, c.peaklist(), c.w) for c in self._components]
y = [add_lorentzians_limitable(x, c.peaklist()) for c in self._components]
y_sum = np.sum(y, 0)
return x, y_sum

Expand Down
40 changes: 22 additions & 18 deletions src/nmrsim/discrete.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,8 +55,8 @@ def AB(Jab, Vab, Vcentr, normalize=True):

Returns
-------
[(float, float)...]
A list of four (frequency, intensity) tuples.
[(float, float, float)...]
A list of four (frequency, intensity, width) tuples.
"""
J = Jab
dv = Vab
Expand All @@ -73,9 +73,10 @@ def AB(Jab, Vab, Vcentr, normalize=True):
I4 = I1
vList = [v1, v2, v3, v4]
IList = [I1, I2, I3, I4]
wList = [0.5 for _ in range(len(IList))]
if normalize:
_normalize(IList, 2)
return list(zip(vList, IList))
return list(zip(vList, IList, wList))


def AB2(Jab, Vab, Vcentr, normalize=True):
Expand All @@ -96,8 +97,8 @@ def AB2(Jab, Vab, Vcentr, normalize=True):

Returns
-------
[(float, float)...]
a list of (frequency, intensity) tuples.
[(float, float, float)...]
a list of (frequency, intensity, width) tuples.
"""
# There is a disconnect between the variable names in the WINDNMR GUI and
# the variable names in this function.
Expand Down Expand Up @@ -148,10 +149,11 @@ def AB2(Jab, Vab, Vcentr, normalize=True):
I9 = (sqrt(2) * sin_dtheta + sintheta_plus * sintheta_minus) ** 2
vList = [V1, V2, V3, V4, V5, V6, V7, V8, V9]
IList = [I1, I2, I3, I4, I5, I6, I7, I8, I9]
wList = [0.5 for _ in range(len(IList))]

if normalize:
_normalize(IList, 3)
return list(zip(vList, IList))
return list(zip(vList, IList, wList))


def ABX(Jab, Jax, Jbx, Vab, Vcentr, vx, normalize=True):
Expand Down Expand Up @@ -181,8 +183,8 @@ def ABX(Jab, Jax, Jbx, Vab, Vcentr, vx, normalize=True):

Returns
-------
[(float, float)...]
a list of (frequency, intensity) tuples.
[(float, float, float)...]
a list of (frequency, intensity, width) tuples.
"""
# Contradictions in naming between WINDNMR's interface, internal code, and
# Pople/Schneider/Bernstein "fixed" with these reassignments:
Expand Down Expand Up @@ -239,9 +241,10 @@ def ABX(Jab, Jax, Jbx, Vab, Vcentr, vx, normalize=True):
I14 = I13
VList = [V1, V2, V3, V4, V5, V6, V7, V8, V9, V10, V11, V12, V13, V14]
IList = [I1, I2, I3, I4, I5, I6, I7, I8, I9, I10, I11, I12, I13, I14]
wList = [0.5 for _ in range(len(IList))]
if normalize:
_normalize(IList, 3)
return list(zip(VList, IList))
return list(zip(VList, IList, wList))


def ABX3(Jab, Jax, Jbx, Vab, Vcentr):
Expand All @@ -264,14 +267,14 @@ def ABX3(Jab, Jax, Jbx, Vab, Vcentr):

Returns
-------
[(float, float)...]
a list of (frequency, intensity) tuples.
[(float, float, float)...]
a list of (frequency, intensity, width) tuples.
"""
# First: simulate two quartets for va and vb ("Jab turned off")
va = Vcentr - Vab / 2
vb = Vcentr + Vab / 2
a_quartet = multiplet((va, 1), [(Jax, 3)])
b_quartet = multiplet((vb, 1), [(Jbx, 3)])
a_quartet = multiplet((va, 1, 0.5), [(Jax, 3)])
b_quartet = multiplet((vb, 1, 0.5), [(Jbx, 3)])
res = []
# Then: for each pair of a and b singlets in the quartets, calculate an
# AB quartet ("Turn Jab on").
Expand All @@ -280,7 +283,7 @@ def ABX3(Jab, Jax, Jbx, Vab, Vcentr):
abcenter = (b_quartet[i][0] + a_quartet[i][0]) / 2
sub_abq = AB(Jab, dv, abcenter, normalize=True)
scale_factor = a_quartet[i][1]
scaled_sub_abq = [(v, i * scale_factor) for v, i in sub_abq]
scaled_sub_abq = [(v, i * scale_factor, w) for v, i, w in sub_abq]
res.extend(scaled_sub_abq)
return res

Expand All @@ -305,8 +308,8 @@ def AAXX(Jaa, Jxx, Jax, Jax_prime, Vcentr, normalize=True):

Returns
-------
[(float, float)...]
a list of (frequency, intensity) tuples.
[(float, float, float)...]
a list of (frequency, intensity, width) tuples.
"""
# Define the constants required to calculate frequencies and intensities

Expand Down Expand Up @@ -347,9 +350,10 @@ def AAXX(Jaa, Jxx, Jax, Jax_prime, Vcentr, normalize=True):

VList = [V1, V2, V3, V4, V5, V6, V7, V8, V9, V10]
IList = [I1, I2, I3, I4, I5, I6, I7, I8, I9, I10]
wList = [0.5 for _ in range(len(IList))]
if normalize:
_normalize(IList, 2)
return list(zip(VList, IList))
return list(zip(VList, IList, wList))


def AABB(Vab, Jaa, Jbb, Jab, Jab_prime, Vcentr, normalize=True, **kwargs):
Expand All @@ -374,7 +378,7 @@ def AABB(Vab, Jaa, Jbb, Jab, Jab_prime, Vcentr, normalize=True, **kwargs):

Returns
-------
[(float, float)...]
[(float, float, float)...]
a list of (frequency, intensity) tuples.
"""
from nmrsim.qm import qm_spinsystem
Expand Down
18 changes: 10 additions & 8 deletions src/nmrsim/firstorder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,9 +30,9 @@ def _doublet(plist, J):
a list of (frequency, intensity) tuples.
"""
res = []
for v, i in plist:
res.append((v - J / 2, i / 2))
res.append((v + J / 2, i / 2))
for v, i, w in plist:
res.append((v - J / 2, i / 2, w))
res.append((v + J / 2, i / 2, w))
return res


Expand All @@ -43,8 +43,8 @@ def multiplet(signal, couplings):

Parameters
---------
signal : (float, float)
a (frequency (Hz), intensity) tuple;
signal : (float, float, float)
a (frequency (Hz), intensity, width (Hz)) tuple;
couplings : [(float, int)...]
A list of (*J*, # of nuclei) tuples. The order of the tuples in
couplings does not matter.
Expand All @@ -64,7 +64,7 @@ def multiplet(signal, couplings):
return sorted(reduce_peaks(res))


def first_order_spin_system(v, J):
def first_order_spin_system(v, J, w):
"""
Create a first-order peaklist of several multiplets from the same v/J
arguments used for qm calculations.
Expand All @@ -80,16 +80,18 @@ def first_order_spin_system(v, J):
an array of frequencies
J : 2D array-like (square)
a matrix of J coupling constants
w : float or int
peak width at half height (Hz)

Returns
-------
[(float, float)...]
[(float, float, float)...]
a combined peaklist of signals for all the multiplets in the spin
system.
"""
result = []
for i, v_ in enumerate(v):
couplings = ((j, 1) for j in J[i] if j != 0)
signal = multiplet((v_, 1), couplings)
signal = multiplet((v_, 1, w), couplings)
result += signal
return reduce_peaks(sorted(result))
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