def plot_pdf(scatter, gobs, atoms, save_file=None, show=True, **kwargs):
fig = plt.figure()
ax = fig.add_subplot(111)
gcalc = scatter.get_pdf(atoms)
r = scatter.get_r()
rw, scale = wrap_rw(gcalc, gobs)
print 'Rw', rw * 100, '%'
baseline = -1 * np.abs(1.5 * gobs.min())
gdiff = gobs - gcalc * scale
ax.plot(r, gobs, 'bo', label="G(r) data")
ax.plot(r, gcalc * scale, 'r-', label="G(r) fit")
ax.plot(r, gdiff + baseline, 'g-', label="G(r) diff")
ax.plot(r, np.zeros_like(r) + baseline, 'k:')
ax.set_xlabel(r"$r (\AA)$")
ax.set_ylabel(r"$G (\AA^{-2})$")
plt.legend(loc='best', prop={'size': 12})
if save_file is not None:
plt.savefig(save_file + '_pdf.eps', bbox_inches='tight',
transparent='True')
plt.savefig(save_file + '_pdf.png', bbox_inches='tight',
transparent='True')
if show is True:
plt.show()
return
def plot_waterfall_diff_pdf_2d(scatter, gobs, traj, save_file=None, show=True,
**kwargs):
fig = plt.figure()
ax = fig.add_subplot(111)
r = scatter.get_r()
# ax.plot(r, gobs, 'bo', label="G(r) data")
gcalcs = []
for i, atoms in enumerate(traj):
gcalc = scatter.get_pdf(atoms)
rw, scale = wrap_rw(gcalc, gobs)
print i, 'Rw', rw * 100, '%'
gcalcs.append(gobs - gcalc * scale)
ax.imshow(gcalcs, aspect='auto', origin='lower',
extent=(r.min(), r.max(), 0, len(traj)))
ax.set_xlabel(r"$r (\AA)$")
ax.set_ylabel("iteration")
ax.legend(loc='best', prop={'size': 12})
if save_file is not None:
plt.savefig(save_file + '_2d_water_diff_pdf.eps', bbox_inches='tight',
transparent='True')
plt.savefig(save_file + '_2d_water_diff_pdf.png', bbox_inches='tight',
transparent='True')
if show is True:
plt.show()
return
def plot_waterfall_diff_pdf(scatter,
gobs,
traj,
save_file=None,
show=True,
**kwargs):
fig = plt.figure()
ax = fig.add_subplot(111)
r = scatter.get_r()
# ax.plot(r, gobs, 'bo', label="G(r) data")
for i, atoms in enumerate(traj):
gcalc = scatter.get_pdf(atoms)
rw, scale = wrap_rw(gcalc, gobs)
print i, 'Rw', rw * 100, '%'
plt.plot(
r,
gobs - (gcalc * scale)
# - i
,
'-',
label="Fit {}".format(i))
ax.set_xlabel(r"$r (\AA)$")
ax.set_ylabel(r"$G (\AA^{-2})$")
ax.legend(loc='best', prop={'size': 12})
if save_file is not None:
plt.savefig(save_file + '_pdf.eps',
bbox_inches='tight',
transparent='True')
plt.savefig(save_file + '_pdf.png',
bbox_inches='tight',
transparent='True')
if show is True:
plt.show()
return
def plot_pdf(scatter, gobs, atoms, save_file=None, show=True, **kwargs):
fig = plt.figure()
ax = fig.add_subplot(111)
gcalc = scatter.get_pdf(atoms)
r = scatter.get_r()
rw, scale = wrap_rw(gcalc, gobs)
print 'Rw', rw * 100, '%'
baseline = -1 * np.abs(1.5 * gobs.min())
gdiff = gobs - gcalc * scale
ax.plot(r, gobs, 'bo', label="G(r) data")
ax.plot(r, gcalc * scale, 'r-', label="G(r) fit")
ax.plot(r, gdiff + baseline, 'g-', label="G(r) diff")
ax.plot(r, np.zeros_like(r) + baseline, 'k:')
ax.set_xlabel(r"$r (\AA)$")
ax.set_ylabel(r"$G (\AA^{-2})$")
plt.legend(loc='best', prop={'size': 12})
if save_file is not None:
plt.savefig(save_file + '_pdf.eps',
bbox_inches='tight',
transparent='True')
plt.savefig(save_file + '_pdf.png',
bbox_inches='tight',
transparent='True')
if show is True:
plt.show()
return
def plot_waterfall_diff_pdf_2d(scatter,
gobs,
traj,
save_file=None,
show=True,
**kwargs):
fig = plt.figure()
ax = fig.add_subplot(111)
r = scatter.get_r()
# ax.plot(r, gobs, 'bo', label="G(r) data")
gcalcs = []
for i, atoms in enumerate(traj):
gcalc = scatter.get_pdf(atoms)
rw, scale = wrap_rw(gcalc, gobs)
print i, 'Rw', rw * 100, '%'
gcalcs.append(gobs - gcalc * scale)
ax.imshow(gcalcs,
aspect='auto',
origin='lower',
extent=(r.min(), r.max(), 0, len(traj)))
ax.set_xlabel(r"$r (\AA)$")
ax.set_ylabel("iteration")
ax.legend(loc='best', prop={'size': 12})
if save_file is not None:
plt.savefig(save_file + '_2d_water_diff_pdf.eps',
bbox_inches='tight',
transparent='True')
plt.savefig(save_file + '_2d_water_diff_pdf.png',
bbox_inches='tight',
transparent='True')
if show is True:
plt.show()
return
def plot_waterfall_pdf(scatter, gobs, traj, save_file=None, show=True,
**kwargs):
fig = plt.figure()
ax = fig.add_subplot(111)
r = scatter.get_r()
# ax.plot(r, gobs, 'bo', label="G(r) data")
for i, atoms in enumerate(traj):
gcalc = scatter.get_pdf(atoms)
rw, scale = wrap_rw(gcalc, gobs)
print i, 'Rw', rw * 100, '%'
plt.plot(r, gcalc * scale + i, '-', label="Fit {}".format(i))
ax.set_xlabel(r"$r (\AA)$")
ax.set_ylabel(r"$G (\AA^{-2})$")
ax.legend(loc='best', prop={'size': 12})
if save_file is not None:
plt.savefig(save_file + '_pdf.eps', bbox_inches='tight',
transparent='True')
plt.savefig(save_file + '_pdf.png', bbox_inches='tight',
transparent='True')
if show is True:
plt.show()
return
os.makedirs(save_folder)
# '''
plot_temp_1d_data(Ts, data_list=data_list, x_lims=xlims,
save_path=save_folder,
plot_type=plot_type,
save=True,
plot=False,
offset=offset
)
# '''
# '''
rws = np.zeros((len(data_list), len(data_list)))
print(Ts.shape)
for i in range(len(data_list)):
for j in range(len(data_list)):
rws[i, j] = wrap_rw(data_list[i][1], data_list[j][1])[0] * 100
fig, ax = plt.subplots()
im = ax.imshow(rws, interpolation='none', cmap='viridis',
# aspect='auto',
origin='lower left')
xticks = np.asarray(ax.get_xticks(), dtype=int)
tsxt = Ts[xticks[1:-1]]
tsxt = np.reshape(tsxt, len(tsxt))
for s in range(len(tsxt)):
tsxt[s] = float(Decimal(np.round(tsxt[s], 0)).quantize(Decimal('1.')))
xtl = ['']
xtl.extend(tsxt.astype(int).tolist())
xtl.append('')
ax.set_xticklabels(xtl)
ax.set_yticklabels(xtl)
fig.savefig(
os.path.join(
dest,
"S{}-{}_{}_{}_{}{}.{}".format(
min(ns), max(ns), length, event_name, output, zz, fmt
),
)
)
if plot:
plt.show()
else:
plt.close(fig)
rws = np.zeros((len(datas), len(datas)))
for i in range(len(datas)):
for j in range(len(datas)):
rws[i, j] = wrap_rw(np.nan_to_num(datas[i][1]), np.nan_to_num(datas[j][1]))[0] * 100
fig, ax = plt.subplots()
im = ax.imshow(
rws,
interpolation="none",
cmap="viridis",
# aspect='auto',
origin="lower left",
)
xtl = [""]
xtl.extend(names)
xtl.append("")
ax.set_xticklabels([""] * len(xtl))
ax.set_yticklabels(xtl)
cbar = fig.colorbar(im)
print(event_name)