def run():
"""
<Description>
Args:
param1: This is the first param.
Returns:
This is a description of what is returned.
"""
model, descr = WLC.Hao_PEGModel, "Hao_Parameters",
fig = PlotUtilities.figure((4, 6))
plot_inf = WLC._make_plot_inf(ext_grid=np.linspace(0, 30, num=3000),
read_functor=WLC.read_haos_data,
base="../../FigData/")
make_model_plot(plot_inf=plot_inf, title=descr)
PlotUtilities.savefig(fig, "PEG_{:s}.png".format(descr))
# make sure what we have matches Hao.
fig = PlotUtilities.figure((2.5, 4))
make_comparison_plot()
plt.xlim([0, 35])
plt.ylim([0, 300])
PlotUtilities.legend(frameon=True)
PlotUtilities.savefig(fig, "out_compare.png")
pass
def run():
"""
<Description>
Args:
param1: This is the first param.
Returns:
This is a description of what is returned.
"""
base_dir = RetinalUtil._landscape_base()
step = Pipeline.Step.POLISH
in_dir = Pipeline._cache_dir(base=base_dir, enum=Pipeline.Step.REDUCED)
out_dir = Pipeline._cache_dir(base=base_dir, enum=step)
force = True
limit = None
functor = lambda: generate_landscape(in_dir)
energy_obj = CheckpointUtilities.\
getCheckpoint(filePath=out_dir + "energy.pkl",
orCall=functor,force=force)
data = CheckpointUtilities.lazy_multi_load(in_dir)
# also load all the data
fig = PlotUtilities.figure((3, 6))
PlotUtil.plot_landscapes(data, energy_obj)
PlotUtilities.savefig(fig, out_dir + "out_G.png")
pass
def run():
input_dir = "../../../../Data/FECs180307/"
out_dir = "./"
q_offset_nm = 100
q_interp, energy_list_arr, _ = FigureUtil.\
_read_energy_list_and_q_interp(input_dir, q_offset=q_offset_nm,
min_fecs=9)
# read in some example data
base_dir_BR = input_dir + "BR+Retinal/"
names_BR = ["/BR+Retinal/3000nms/170503FEC/landscape_"]
PEG600 = FigureUtil._read_samples(base_dir_BR,names_BR)[0]
# read in the FECs
fecs = FigureUtil._snapsnot(PEG600.base_dir,
step=Pipeline.Step.REDUCED).fec_list
args_mean = (energy_list_arr, q_interp)
mean_A = mean_A_jarzynski(*args_mean)
mean_G = mean_G_iwt(*args_mean)
mean_F_from_dot = mean_A_dot_iwt(*args_mean)[0]
ex = fecs[0]
q = q_interp * 1e-9
# xxx offset q and z... probably a little off!
z = ex.ZFunc(ex) + q[0]
k = ex.SpringConstant
beta = ex.Beta
A = mean_A[0]
G = mean_G[0]
n_iters = 5000
force =True
kw_lr = dict(G0=G, A=A, q=q, z=z, k=k, beta=beta,n_iters=n_iters)
lr = CheckpointUtilities.getCheckpoint("./lr_deconv.pkl",
_deconvoled_lr,force,**kw_lr)
diff_kT = np.array(lr.mean_diffs) * beta
min_idx = np.argmin(diff_kT)
idx_search = np.logspace(start=3,stop=np.floor(np.log2(min_idx)),
endpoint=True,num=10,base=2)
idx_to_use = [int(i) for i in idx_search]
# fit a spline to the converged G to get the mean restoring force
fig = PlotUtilities.figure((4,6))
xlim = [min(q_interp)-5, max(q_interp)]
fmt_kw = dict(xlim=xlim,ylim=[None,None])
ax1 = plt.subplot(3,1,1)
plt.plot(diff_kT)
plt.axvline(min_idx)
FigureUtil._plot_fmt(ax1,is_bottom=True,xlabel="iter #",
ylabel="diff G (kT)",xlim=[None,None],ylim=[None,None])
ax2 = plt.subplot(3,1,2)
plt.plot(q_interp,lr._G0_initial_lr.G0_kT,color='b',linewidth=3)
plt.plot(q_interp,lr.G0_kT,color='r',linewidth=3)
FigureUtil._plot_fmt(ax2,is_bottom=False,ylabel="G (kT)",**fmt_kw)
ax1 = plt.subplot(3,1,3)
FigureUtil._plot_fec_list(fecs, xlim, ylim=[None,None])
for i in idx_to_use:
_plot_f_at_iter_idx(lr, i)
_plot_f_at_iter_idx(lr, 0,label="F from G0",linewidth=4)
plt.plot(q_interp,mean_F_from_dot*1e12,label="F from A_z_dot",linewidth=2)
# also plot the force we expect from the original A_z_dot
FigureUtil._plot_fmt(ax1,is_bottom=True,xlim=xlim,ylim=[None,None])
PlotUtilities.legend()
PlotUtilities.savefig(fig,"FigureS_A_z.png")
pass
def _G0_plot(plot_dir, data_sliced, landscape, fmt):
# XXX why is this necessary?? screwing up absolute values
previous_JCP = FigureUtil.read_non_peg_landscape(base="../../FigData/")
offset_s = np.mean([d.Separation[0] for d in data_sliced])
G_hao = landscape.G0_kcal_per_mol
idx_zero = np.where(landscape.q_nm <= 100)
G_hao = G_hao - landscape.G0_kcal_per_mol[0]
G_JCP = previous_JCP.G0_kcal_per_mol - previous_JCP.G0_kcal_per_mol[0] + 50
offset_jcp_nm = min(previous_JCP.q_nm)
landscape_offset_nm = min(landscape.q_nm)
q_JCP_nm = previous_JCP.q_nm - offset_jcp_nm + 5
q_Hao_nm = landscape.q_nm - landscape_offset_nm
fig = FigureUtil._fig_single(y=6)
xlim, ylim = FigureUtil._limits(data_sliced)
ax1 = plt.subplot(2, 1, 1)
FigureUtil._plot_fec_list(data_sliced, **fmt)
FigureUtil._plot_fmt(ax1, **fmt)
ax2 = plt.subplot(2, 1, 2)
plt.plot(q_Hao_nm, G_hao, label="Aligned, IWT")
plt.plot(q_JCP_nm, G_JCP, 'r--', label="JCP landscape")
FigureUtil._plot_fmt(ax2,
ylabel="G (kcal/mol)",
is_bottom=True,
xlim=xlim,
ylim=[None, None])
PlotUtilities.legend(ax=ax2, handlelength=2)
ax2.set_xlim(fmt['xlim'])
PlotUtilities.savefig(fig, plot_dir + "FigureSX_LandscapeComparison.png")
def make_aligned_plot(base_dir, step, data, xlim=None, post="", **kw):
plot_subdir = Pipeline._plot_subdir(base_dir, step)
f_x = lambda x: x.Separation
xlim_tmp, ylim = nm_and_pN_limits(data, f_x)
xlim = [xlim[0], 200] if xlim is None else xlim
name_func = FEC_Util.fec_name_func
for i, d in enumerate(data):
f = PlotUtilities.figure()
_aligned_plot(d, f_x, xlim, ylim, i=i, **kw)
PlotUtilities.savefig(f, plot_subdir + name_func(0, d) + post + ".png")
def _make_algned_plot(alignment, label):
fig = PlotUtilities.figure((3, 4))
gs = gridspec.GridSpec(3, 2)
# make the 'standard' alignment plots
axes = _heatmap_alignment(gs, alignment, 0)
_ensemble_alignment(gs, alignment, 1)
out_name = "./FigureS_Alignment_{:s}.png".format(label)
PlotUtilities.title(label, ax=axes[0])
PlotUtilities.savefig(fig,
out_name,
subplots_adjust=dict(hspace=0.12, wspace=0.02))
def _feather_plot(data,plot_subdir,f_x = lambda x: x.Separation,
xlim=[-20, 150]):
_, ylim = ProcessingUtil.nm_and_pN_limits(data, f_x=f_x)
for i,d in enumerate(data):
fig = PlotUtilities.figure()
ProcessingUtil.plot_single_fec(d, f_x, xlim, ylim, markevery=1,
i=i)
x = f_x(d) * 1e9
for i in d.info_feather.event_idx:
plt.axvline(x[i])
name = FEC_Util.fec_name_func(0,d)
PlotUtilities.savefig(fig,plot_subdir + name + ".png")
def _fec_demo_plot(energy_list, out_dir):
fecs = []
energies = []
N = len(energy_list)
for e in energy_list:
data = RetinalUtil.read_fecs(e)
fecs.append(data)
energies.append(e)
n_cols = N
fig = PlotUtilities.figure((n_cols * 1, 6))
FigureUtil.data_plot(fecs, energies, xlim=[-20, 100])
PlotUtilities.savefig(fig,
out_dir + "energies.png",
subplots_adjust=dict(hspace=0.02, wspace=0.04))
def _energy_plot(energy_list, out_dir):
# interpolate all the energies to the same grid
energies_plot = [e._iwt_obj for e in energy_list]
q_interp, splines = RetinalUtil.interpolating_G0(energies_plot)
# get an average/stdev of energy
fig = PlotUtilities.figure((7, 7))
ax = plt.subplot(1, 1, 1)
PlotUtil.plot_mean_landscape(q_interp, splines, ax=ax)
min_x_show_nm = int(np.floor(min(q_interp) - 2))
max_x_show_nm = min_x_show_nm + 20
plt.xlim([min_x_show_nm, max_x_show_nm])
plt.xticks([i for i in range(min_x_show_nm, max_x_show_nm)])
ax.xaxis.set_ticks_position('both')
ax.grid(True)
PlotUtilities.savefig(fig, out_dir + "avg.png")
def _giant_debugging_plot(out_dir, energy_list_arr):
fig = PlotUtilities.figure((8, 12))
gs = gridspec.GridSpec(nrows=2, ncols=1, hspace=0.15)
n_cols = max([len(list_v) for list_v in energy_list_arr])
for i, energy_list in enumerate(energy_list_arr):
fecs = []
energies = []
for e in energy_list:
data = RetinalUtil.read_fecs(e)
fecs.append(data)
energies.append(e)
gs_tmp = gridspec.GridSpecFromSubplotSpec(nrows=3,
ncols=n_cols,
subplot_spec=gs[i])
FigureUtil.data_plot(fecs, energies, gs1=gs_tmp, xlim=[-20, 100])
PlotUtilities.savefig(fig,
out_dir + "FigureS_Mega_Debug.png",
subplots_adjust=dict(hspace=0.02, wspace=0.04))
def run():
"""
<Description>
Args:
param1: This is the first param.
Returns:
This is a description of what is returned.
"""
n = 1000
pts = np.linspace(-1,1,num=n)
f = lambda x: -1 * x**2 - 0.5 * x + 3 * x**3 + 10 * x**4 + \
np.sin(2 * np.pi * x * 3) * 0.5 / (1+abs(x/3))
f_pts = f(pts)
max_f = max(f(pts))
f_pts /= max_f
brute_sample_n = 15
dict_brute = dict(markersize=3)
brute_pts = pts[::int(n/brute_sample_n)]
brute_f_pts = f(brute_pts) / max_f
# get the 'zoom in' region
best_idx = np.argmin(brute_f_pts)
pts_zoom = np.linspace(brute_pts[best_idx-1],brute_pts[best_idx+1],
num=10,endpoint=True)
f_zoom = f(pts_zoom) / max_f
fig = PlotUtilities.figure((3,4))
ax1 = plt.subplot(2,1,1)
plt.plot(pts,f_pts)
plt.plot(brute_pts,brute_f_pts,'ro',**dict_brute)
PlotUtilities.lazyLabel("","Error","")
PlotUtilities.no_x_label(ax1)
ax2 = plt.subplot(2,1,2)
plt.plot(pts,f_pts)
xmin, xmax = min(pts_zoom),max(pts_zoom)
ymin, ymax = min(f_zoom),max(f_zoom)
y_range = ymax-ymin
plt.xlim(xmin,xmax)
plt.ylim(ymin - y_range * 0.1,ymax + y_range * 0.1)
plt.axvline(pts_zoom[np.argmin(f_zoom)],label="Found\nmin",
color='g',linestyle='--')
Annotations.zoom_effect01(ax1, ax2, xmin, xmax)
PlotUtilities.lazyLabel("X (au)","Error","")
PlotUtilities.savefig(fig,"./out.png")
def run():
"""
<Description>
Args:
param1: This is the first param.
Returns:
This is a description of what is returned.
"""
base_dir = "../../../../Data/FECs180307/"
read_f = FigureUtil.read_sample_landscapes
gallery = CheckpointUtilities.getCheckpoint("./caches.pkl",
read_f,False,base_dir)
lab_plot = [ ["BR-PEG3400",gallery.PEG3400],
["BO-PEG3400",gallery.BO_PEG3400] ]
fig = PlotUtilities.figure(figsize=(4,6))
gs = gridspec.GridSpec(ncols=1,nrows=2,height_ratios=[3,1])
gs_pipeline= gridspec.GridSpecFromSubplotSpec(ncols=2,nrows=3,hspace=0.03,
subplot_spec=gs[0,:])
colors = ['r','rebeccapurple']
xlim,_,ylm_W = xlim_ylim()
mean_works_info = []
for i,(label,to_use) in enumerate(lab_plot):
pipeline = FigureUtil._alignment_pipeline(to_use)
fecs = pipeline.blacklisted.fec_list
# calculate all the works
x_arr = [f.Separation for f in fecs]
f_arr = [f.Force for f in fecs]
works = _calculate_work(x_arr,f_arr)
works_kcal = np.array(works) * kcal_per_mol_per_J()
c = colors[i]
_make_work_plot(fecs, x_arr, works_kcal,gs_pipeline,col=i,color=c,
title=label)
x_interp, mean_W, std_W= _mean_work(x_arr,works_kcal)
plt.subplot(gs[-1, :])
_plot_mean_works(x_interp, mean_W, std_W, color=c, title=label)
plt.xlim(xlim)
plt.ylim(ylm_W)
PlotUtilities.lazyLabel("Extension (nm)" , "$W$ (kcal/mol)","",
useLegend=False)
PlotUtilities.savefig(fig, "FigureS_Work.png".format(label))
def _plot_comparison(plot_dir, heatmap_jcp, iwt_obj, data_sliced_plot):
fmt = dict(xlim=[-20, 55], ylim=[-20, 150])
_G0_plot(plot_dir, data_sliced_plot, iwt_obj, fmt=fmt)
fig = FigureUtil._fig_single(y=6)
ax1 = plt.subplot(2, 1, 1)
extent = heatmap_jcp._extent_nm_and_pN(offset_x_nm=0)
plt.imshow(heatmap_jcp.heatmap,
origin='lower',
aspect='auto',
extent=extent,
cmap=plt.cm.afmhot)
FigureUtil._plot_fmt(is_bottom=False, ax=ax1, **fmt)
PlotUtilities.title("Top: JCP.\n Bottom: New data, - PEG3400")
ax2 = plt.subplot(2, 1, 2)
FEC_Plot.heat_map_fec(data_sliced_plot,
use_colorbar=False,
num_bins=(150, 75),
separation_max=fmt['xlim'][1])
FigureUtil._plot_fmt(is_bottom=True, ax=ax2, **fmt)
out_name = plot_dir + "FigureSX_jcp_fec_comparison.png"
PlotUtilities.savefig(fig, out_name, tight=True)
def _make_plots(galleries_labels):
alignments = [
FigureUtil._alignment_pipeline(gallery_tmp[0])
for gallery_tmp in galleries_labels
]
for i, (_, label) in enumerate(galleries_labels):
# make the standard aligning plot
alignment = alignments[i]
_make_algned_plot(alignment, label)
# plot the final curves on the same plot
xlim, ylim = FigureUtil._limits(alignment._all_fecs)
colors = ['rebeccapurple', 'g']
fig = PlotUtilities.figure((5, 3))
gs = gridspec.GridSpec(2, 2)
# reverse everything, so PEG600 is on top
galleries_labels = galleries_labels[::-1]
alignments = alignments[::-1]
for i, (_, l) in enumerate(galleries_labels):
ax = plt.subplot(gs[i, 0])
a = alignments[i]
FigureUtil._plot_fec_list(a.blacklisted.fec_list,
xlim,
ylim,
label=l,
color=colors[i])
if (i == 0):
PlotUtilities.no_x_label(ax)
PlotUtilities.xlabel("", ax=ax)
# plot them both on the last column
plt.subplot(gs[:, 1])
kw = [dict(), dict(linewidth=0.6)]
for i, (_, l) in enumerate(galleries_labels):
a = alignments[i]
FigureUtil._plot_fec_list(a.blacklisted.fec_list,
xlim,
ylim,
label=l,
color=colors[i],
**kw[i])
PlotUtilities.savefig(fig, "FigureS_3400vs600.png")
def _make_plots(pre_str,W_of_interest,beta,fit_info,ext_list,work_list):
work_all = np.array(work_list)
Ws_kT = W_of_interest * beta
min_W_kT, max_W_kT = min(Ws_kT), max(Ws_kT)
x_final = fit_info.x_final
kw_common = fit_info.kw_common
eq_5_B_REM = palassini_2011_eq_5(fit_info)
range_W_kT = (max_W_kT - min_W_kT)
model_W = np.linspace(min_W_kT - range_W_kT, max_W_kT + range_W_kT, num=50)
model_P_not_norm = unnormalized_prob(model_W, *x_final, **kw_common)
model_P = model_P_not_norm / trapz(x=model_W, y=model_P_not_norm)
fig = PlotUtilities.figure()
plt.hist(Ws_kT, normed=True)
plt.plot(model_W, model_P,label="Model")
title = "Bias = {:.2f} kT".format(eq_5_B_REM)
PlotUtilities.lazyLabel("W (kT)","$N$",title)
PlotUtilities.savefig(fig,pre_str + "outhist.png")
fig = PlotUtilities.figure()
for e,w in zip(ext_list,work_all):
plt.plot(e,w * beta)
PlotUtilities.lazyLabel("Ext (m)","W (kT)","")
PlotUtilities.savefig(fig,pre_str + "out.png")
def run():
"""
<Description>
Args:
param1: This is the first param.
Returns:
This is a description of what is returned.
"""
default_base = "../../../Data/170321FEC/"
base_dir = Pipeline._base_dir_from_cmd(default=default_base)
step = Pipeline.Step.POLISH
in_dir = Pipeline._cache_dir(base=base_dir, enum=Pipeline.Step.ALIGNED)
out_dir = Pipeline._cache_dir(base=base_dir,enum=step)
plot_dir = Pipeline._plot_subdir(base=base_dir, enum=step)
force = True
limit = None
functor = lambda : polish_data(in_dir)
data =CheckpointUtilities.multi_load(cache_dir=out_dir,load_func=functor,
force=force,
limit=limit,
name_func=FEC_Util.fec_name_func)
sizes = [d.Force.size for d in data]
min_s = min(sizes)
sliced_data = [d._slice(slice(0,min_s,1)) for d in data]
for d in sliced_data:
d.Offset = d.ZSnsr[0]
d.Extension = d.Separation
d.kT = 4.1e-21
data_wham = UtilWHAM.to_wham_input(objs=sliced_data, n_ext_bins=75)
data_wham.z = np.array([d.ZSnsr for d in sliced_data])
obj_wham = WeightedHistogram.wham(data_wham)
data_unpolished = CheckpointUtilities.lazy_multi_load(in_dir)
f_x_zsnsr = lambda x: x.ZSnsr
xlim = [-40,150]
ProcessingUtil.heatmap_ensemble_plot(data,out_name=plot_dir + "heatmap.png",
xlim=xlim)
ProcessingUtil.heatmap_ensemble_plot(data,f_x=f_x_zsnsr,
out_name=plot_dir + "heatmap_Z.png",
kw_map=dict(x_func=f_x_zsnsr),
xlim=xlim)
# plot each individual
f_x = lambda x_tmp : x_tmp.Separation
plot_subdir = Pipeline._plot_subdir(base_dir, step)
name_func = FEC_Util.fec_name_func
_, ylim = ProcessingUtil.nm_and_pN_limits(data,f_x)
for i,(d_unpolish,d_polish) in enumerate(zip(data_unpolished,data)):
kw_plot = dict(d_unpolish=d_unpolish,
d_polish=d_polish,
xlim=xlim,ylim=ylim,i=i)
fig = PlotUtilities.figure((6,6))
# make the Separation column
ax1,ax2 = plt.subplot(2,2,1), plt.subplot(2,2,3)
polish_plot(ax1, ax2, f_x = lambda x: x.Separation,
plot_components_1=True,**kw_plot)
# make the ZSnsr column
ax3,ax4 = plt.subplot(2,2,2), plt.subplot(2,2,4)
polish_plot(ax3, ax4, f_x = lambda x: x.ZSnsr,plot_components_1=False,
**kw_plot)
PlotUtilities.xlabel("Stage Position (nm)", ax=ax4)
for a in [ax3,ax4]:
PlotUtilities.no_y_label(ax=a)
PlotUtilities.ylabel("",ax=a)
name = plot_subdir + name_func(0, d_polish) + ".png"
PlotUtilities.savefig(fig,name)