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.FILTERED
in_dir = Pipeline._cache_dir(base=base_dir, enum=Pipeline.Step.READ)
out_dir = Pipeline._cache_dir(base=base_dir, enum=step)
force = True
limit = None
f_filter_Hz = 5e3
# filter to X s
t_filter_s = 1 / f_filter_Hz
# t_filter -> n_filter_points
# after filtering, take every N points, where
# N = f_decimate * n_filter_points
# in other words, we oversample by 1/f_decimate
f_decimate = 0.33
assert f_decimate < 1 and f_decimate > 0
data = filter_data(in_dir, out_dir, force, t_filter_s, f_decimate)
ProcessingUtil.plot_data(base_dir, step, data, markevery=1)
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.ALIGNED
in_dir = Pipeline._cache_dir(base=base_dir, enum=Pipeline.Step.SANITIZED)
out_dir = Pipeline._cache_dir(base=base_dir, enum=step)
force = True
max_n_pool = multiprocessing.cpu_count() - 1
n_pool = 6
N_fit_pts = 20
min_F_N = 175e-12 if "+Retinal" in base_dir else 90e-12
data = RetinalUtil.align_data(in_dir,
out_dir,
force=force,
n_pool=n_pool,
min_F_N=min_F_N,
N_fit_pts=N_fit_pts)
plot_subdir = Pipeline._plot_subdir(base_dir, step)
xlim_heatmap_nm = [-40, 100]
ProcessingUtil.heatmap_ensemble_plot(data,
xlim=xlim_heatmap_nm,
out_name=plot_subdir + "heatmap.png")
# get the post-blacklist heapmap, too..
data_filtered = ProcessingUtil._filter_by_bl(data, in_dir)
# align the data...
data_aligned = [RetinalUtil._polish_helper(d) for d in data_filtered]
out_name = plot_subdir + "heatmap_bl.png"
ProcessingUtil.heatmap_ensemble_plot(data_aligned,
xlim=xlim_heatmap_nm,
out_name=out_name)
# make individual plots
ProcessingUtil.make_aligned_plot(base_dir,
step,
data,
xlim=[-30, 150],
use_shift=True)
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.CORRECTED
in_dir = Pipeline._cache_dir(base=base_dir, enum=Pipeline.Step.FILTERED)
out_dir = Pipeline._cache_dir(base=base_dir, enum=step)
force = True
n_filter = 10
data = filter_data(in_dir, out_dir, force, n_filter)
ProcessingUtil.plot_data(base_dir, step, data, markevery=1)
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.READ
cache_dir = Pipeline._cache_dir(base=base_dir, enum=step)
force = True
limit = None
functor = lambda: read_all_data(base_dir)
data = CheckpointUtilities.multi_load(cache_dir=cache_dir,
load_func=functor,
force=force,
limit=limit,
name_func=FEC_Util.fec_name_func)
ProcessingUtil.plot_data(base_dir, step, data, markevery=100)
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.SANITIZED
in_dir = Pipeline._cache_dir(base=base_dir, enum=Pipeline.Step.CORRECTED)
out_dir = Pipeline._cache_dir(base=base_dir,enum=step)
force = True
max_n_pool = 6
n_pool = max_n_pool
kw_feather = RetinalUtil._def_kw_FEATHER()
data = align_data(in_dir,out_dir,force=force,n_pool=n_pool,
**kw_feather)
# plot all of the FEATHER information
plot_subdir = Pipeline._plot_subdir(base_dir, step)
PlotUtil._feather_plot(data,plot_subdir)
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)
def _processing_base(default_base="../../../Data/BR+Retinal/170321FEC/",**kw):
return Pipeline._base_dir_from_cmd(default=default_base,**kw)