def polish_plot(ax1,ax2,d_unpolish,d_polish,xlim,ylim,f_x,plot_components_1,i):
plt.sca(ax1)
kw_plot = dict(f_x=f_x,xlim=xlim,ylim=ylim,use_shift=True,i=i)
ProcessingUtil._aligned_plot(d_unpolish, plot_components=plot_components_1,
**kw_plot)
PlotUtilities.xlabel("")
PlotUtilities.no_x_label(ax1)
plt.sca(ax2)
ProcessingUtil._aligned_plot(d_polish, plot_components=False,
**kw_plot)
def fix_axes(ax_list):
# loop through all the axes and toss them.
xlims = get_ranges(ax_list, get_x=True)
ylims = get_ranges(ax_list, get_x=False)
for i, axs in enumerate(ax_list):
for j, ax in enumerate(axs):
if (i > 0):
# columns after the first lose their labels
PlotUtilities.no_y_label(ax)
PlotUtilities.ylabel("", ax=ax)
ax.set_ylim(ylims[j])
if (j != 0):
PlotUtilities.no_x_label(ax)
PlotUtilities.xlabel("", ax=ax)
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 _plot_fmt(ax,
xlim,
ylim,
is_bottom=False,
color=False,
is_left=True,
ylabel="$F$ (pN)",
xlabel="Extension (nm)"):
PlotUtilities.tickAxisFont(ax=ax)
ax.set_xlim(xlim)
ax.set_ylim(ylim)
PlotUtilities.title("", ax=ax)
PlotUtilities.ylabel(ylabel, ax=ax)
PlotUtilities.xlabel(xlabel, ax=ax)
if (not is_bottom):
PlotUtilities.no_x_label(ax=ax)
PlotUtilities.xlabel("", ax=ax)
if (not is_left):
PlotUtilities.no_y_label(ax=ax)
PlotUtilities.ylabel("", ax=ax)
if color:
color_kw = dict(ax=ax, color='w', label_color='k')
PlotUtilities.color_x(**color_kw)
PlotUtilities.color_y(**color_kw)
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)