def feather_single(d,force_no_adhesion=False,**kw):
"""
:param d: FEC to get FJC+WLC fit of
:param min_F_N: minimum force, in Newtons, for fitting event. helps avoid
occasional small force events
:param kw: keywords to use for fitting...
:return:
"""
force_N = d.Force
where_above_surface = np.where(force_N >= 0)[0]
assert where_above_surface.size > 0, "Force never above surface "
# use FEATHER; fit to the first event, don't look for adhesion
d_pred_only = d._slice(slice(0,None,1))
# first, try removing surface adhesions
is_600 = _is_PEG600(d)
skip_adhesion = force_no_adhesion or is_600
f_refs_initial = [Detector.delta_mask_function] if skip_adhesion else None
feather_kw = dict(d=d_pred_only,**kw)
pred_info,tau_n = _detect_retract_FEATHER(f_refs=f_refs_initial,
**feather_kw)
# if we removed more than 20nm or we didnt find any events, then
# FEATHER got confused by a near-surface BR. Tell it not to look for
# surface adhesions
expected_surface_m = d.Separation[pred_info.slice_fit.start]
expected_gf_m = 20e-9
if ((len(pred_info.event_idx) == 0) or (expected_surface_m > expected_gf_m)):
f_refs = [Detector.delta_mask_function]
pred_info,tau_n = _detect_retract_FEATHER(f_refs=f_refs,
**feather_kw)
pred_info.tau_n = tau_n
assert len(pred_info.event_idx) > 0 , "FEATHER can't find an event..."
# POST: found at least one event.
to_ret = ProcessingUtil.AlignedFEC(d,info_fit=None,feather_info=pred_info)
return to_ret
def align_single(d,min_F_N,**kw):
"""
:param d: FEC to get FJC+WLC fit of
:param min_F_N: minimum force, in Newtons, for fitting event. helps avoid
occasional small force events
:param kw: keywords to use for fitting...
:return:
"""
force_N = d.Force
pred_info = d.info_feather
max_fit_idx = GF2_event_idx(d,min_F_N)
# determine the minimum fit index by the maximum of...
# (1) the surface
where_above_surface = np.where(force_N >= 0)[0]
assert where_above_surface.size > 0 , "Never above surface"
first_time_above_surface = where_above_surface[0]
assert first_time_above_surface < max_fit_idx , \
"Couldn't find fitting region"
# (2) the last event *before* the current, if it exists
event_idx = pred_info.event_idx
idx_last_event_before = np.where(event_idx < max_fit_idx)[0]
start_idx = first_time_above_surface
if idx_last_event_before.size > 0:
# then we have an event *before* the final GC helix one.
# make that the start idx, if it is later (it should be!)
new_start = event_idx[idx_last_event_before[-1]]
assert new_start > start_idx , "First event is less than surface?!"
start_idx = new_start
# start the fit after any potential adhesions
fit_start = max(start_idx,pred_info.slice_fit.start)
fit_slice = slice(fit_start,max_fit_idx,1)
# slice the object to just the region we want
obj_slice = d._slice(fit_slice)
# fit wlc to the f vs x of that slice
info_fit = WLCHao.hao_fit(obj_slice.Separation,obj_slice.Force,**kw)
info_fit.fit_slice = fit_slice
to_ret = ProcessingUtil.AlignedFEC(d,info_fit,feather_info=pred_info)
return to_ret