def measureTau(abf: pyabf.ABF,
sweep: int,
epoch: int = 3,
percentile: float = .05,
ax: plt.Axes = None):
abf.setSweep(sweep)
# use epoch table to determine puff times
puffTimeStart = abf.sweepEpochs.p1s[epoch] / abf.sampleRate
puffTimeEnd = abf.sweepEpochs.p2s[epoch] / abf.sampleRate
# calculate baseline level
baselineStart = puffTimeStart - .1
baselineEnd = puffTimeStart
baselineMean = getMean(abf, baselineStart, baselineEnd)
# find antipeak
antipeakIndex = getAntiPeakIndex(abf.sweepY, abf.sampleRate, puffTimeStart,
puffTimeStart + .5)
antipeakLevel = abf.sweepY[antipeakIndex]
# find portion of curve to fit
curveIndex1, curveIndex2 = getCurveIndexes(abf.sweepY, antipeakIndex,
baselineMean, percentile)
curveYs = -abf.sweepY[curveIndex1:curveIndex2]
curveXs = np.arange(len(curveYs)) / abf.sampleRate
try:
p0 = (500, 15, 0) # start with values near those we expect
params, cv = scipy.optimize.curve_fit(monoExp, curveXs, curveYs, p0)
except:
print(f"FIT FAILED (sweep {sweep})")
return None
m, t, b = params
curveYsIdeal = monoExp(curveXs, m, t, b)
tauMS = 1000 / t
if (tauMS < 0):
return None
if ax:
yPad = abs(antipeakLevel - baselineMean) * .1
ax.plot(abf.sweepX, abf.sweepY, alpha=.5)
ax.grid(alpha=.5, ls='--')
ax.axhline(baselineMean, ls='--', color='k')
ax.plot(abf.sweepX[curveIndex1:curveIndex2], -curveYsIdeal, color='k')
ax.set(title=f"first sweep tau = {tauMS:.02f} ms")
ax.axis([
baselineStart - .1, baselineStart + 1, antipeakLevel - yPad,
baselineMean + yPad
])
ax.axvspan(puffTimeEnd, puffTimeEnd + .5, color='g', alpha=.1)
ax.axvspan(puffTimeEnd + .5, puffTimeEnd + .6, color='m', alpha=.1)
return tauMS
def plot_signal_span(self, ax: plt.Axes) -> plt.Line2D:
return ax.axvspan(
xmin=self.time_exp_start[self.index_signal_first, 0].to_datetime(),
xmax=self.time_exp_end[self.index_signal_last, 0].to_datetime(),
alpha=0.3,
color='green',
label='light frames',
)
def plot_dark_down_span(self, ax: plt.Axes) -> plt.Line2D:
return ax.axvspan(
xmin=self.time_exp_start[self.index_dark_down_first, 0].to_datetime(),
xmax=self.time_exp_end[self.index_dark_down_last, 0].to_datetime(),
alpha=0.4,
color='gray',
label='downleg dark frames',
)
def _plot_cluster(ax: plt.Axes, cluster: pd.Series) -> None:
if len(cluster) >= 2:
ax.axvspan(
xmin=cluster.index[0],
xmax=cluster.index[-1],
alpha=0.25,
edgecolor="None",
facecolor="#D1D3D4",
zorder=2.5,
)
for cluster_boundary in [cluster.index[0], cluster.index[-1]]:
ax.axvline(
cluster_boundary,
ls="--",
lw=0.5,
color="#D1D3D4",
zorder=5,
)
def histogram(
mesh: BaseMesh,
*,
metric: str,
ax: plt.Axes = None,
**kwargs,
) -> plt.Axes:
"""Create a mesh plot with the cells are colored by the cell quality.
Parameters
----------
mesh : BaseMesh
Input mesh
metric : str
Metric to calculate.
ax : `matplotlib.Axes`
If specified, `ax` will be used to create the subplot.
vmin, vmax : int, float
Set the lower/upper boundary for the color value.
cmap : str
Set the color map.
**kwargs
Keyword arguments passed on to `ax.hist`.
Returns
-------
ax : `matplotlib.Axes`
"""
kwargs.setdefault('bins', 50)
kwargs.setdefault('rwidth', 0.8)
descriptor = _metric_dispatch[metric]
quality = descriptor.func(mesh) # type: ignore
fig, ax = plt.subplots()
n, bins, patches = ax.hist(quality, **kwargs)
ax.set_title(f'Histogram of {descriptor.name.lower()}')
if optimal_range := descriptor.optimal:
ax.axvspan(*optimal_range, color='limegreen', zorder=0, alpha=0.1)
def _add_shading_to_axes(self, ax: Axes) -> None:
"""
Adds any required shading.
"""
common_args = dict(zorder=-10, alpha=0.3, color="grey", linewidth=0)
# First do horizontal
if self.x_shade[0] is not None:
ax.axvspan(self.x_lim[0], self.x_shade[0], **common_args)
if self.x_shade[1] is not None:
ax.axvspan(self.x_shade[1], self.x_lim[1], **common_args)
# Vertical
if self.y_shade[0] is not None:
ax.axhspan(self.y_lim[0], self.y_shade[0], **common_args)
if self.y_shade[1] is not None:
ax.axhspan(self.y_shade[1], self.y_lim[1], **common_args)
return
def add_tukey_marks(
data: pd.Series,
ax: plt.Axes,
annot: bool = True,
iqr_color: str = "r",
fence_color: str = "k",
fence_style: str = "--",
annot_quarts: bool = False,
) -> plt.Axes:
"""Add IQR box and fences to a histogram-like plot.
Args:
data (pd.Series): Data for calculating IQR and fences.
ax (plt.Axes): Axes to annotate.
iqr_color (str, optional): Color of shaded IQR box. Defaults to "r".
fence_color (str, optional): Fence line color. Defaults to "k".
fence_style (str, optional): Fence line style. Defaults to "--".
annot_quarts (bool, optional): Annotate Q1 and Q3. Defaults to False.
Returns:
plt.Axes: Annotated Axes object.
"""
q1 = data.quantile(0.25)
q3 = data.quantile(0.75)
ax.axvspan(q1, q3, color=iqr_color, alpha=0.2)
iqr_mp = q1 + ((q3 - q1) / 2)
lower, upper = outliers.tukey_fences(data)
ax.axvline(lower, c=fence_color, ls=fence_style)
ax.axvline(upper, c=fence_color, ls=fence_style)
text_yval = ax.get_ylim()[1]
text_yval *= 1.01
if annot:
ax.text(iqr_mp, text_yval, "IQR", ha="center")
if annot_quarts:
ax.text(q1, text_yval, "Q1", ha="center")
ax.text(q3, text_yval, "Q3", ha="center")
ax.text(upper, text_yval, "Fence", ha="center")
ax.text(lower, text_yval, "Fence", ha="center")
return ax
def plot_expression_by_distance(
ax: plt.Axes,
data: Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray],
feature: Optional[str] = None,
include_background: bool = True,
curve_label: Optional[str] = None,
flavor: str = "normal",
color_scheme: Optional[Dict[str, str]] = None,
ratio_order: List[str] = ["central", "portal"],
list_flavor_choices: bool = False,
feature_type: str = "Feature",
distance_scale_factor: float = 1.0,
**kwargs,
) -> None:
"""Generate feature by distance plots
Function for seamless production of feature
by distance plots.
Parameters:
----------
ax : plt.Axes
axes object to plot data in
data : Tuple[np.ndarray,np.ndarray,np.ndarray,np.ndarray]
Tuple of data to plot, should be in form :
(xs,ys,y_hat,std_err), the output which
utils.smooth_fit produces.
feature : Optional[str] (None)
Name of plotted feature, set to None to exclude this
information.
include_background : bool (True)
Set to True to include data points used
to fit the smoothed data
curve_label : Optional[str] (None)
label of plotted data. Set to None to exclude
legend.
flavor : str = "normal",
flavor of data, choose between 'normal' or
'logodds'.
color_scheme : Optional[Dict[str,str]] (None)
dictionary providing the color scheme to be used.
Include 'background':'color' to change color
original data, include 'envelope':'color' to set
color of envelope, include 'feature_class':'color' to
set color of class.
ratio_order : List[str] (["central","portal"])
if logodds flavor is used, then specify which
element was nominator (first element) and
denominator (second element).
list_flavor_choices : bool (False)
set to True to list flavor choices
feature_type : str ("Feature")
Name of feature to plot, will be prepended to title
as Feature : X. Set to None to only plot name X. Set
to None to exclude feature type from being indicated
in title and y-axis.
distance_scale_factor : float (1.0)
scaling factor to multiply distances with
Returns:
-------
Tuple with Matplotlib Figure and Axes object, containing
feature by distance plots.
"""
flavors = ["normal", "logodds", "single_vein"]
if list_flavor_choices:
print("Flavors to choose from are : {}".format(', '.join(flavors)))
return None
if flavor not in flavors:
raise ValueError("Not a valid flavor")
if len(data) != 4:
raise ValueError("Data must be (xs,ys,ys_hat,stderr)")
if color_scheme is None:
color_scheme = {}
scaled_distances = data[0] * (distance_scale_factor if \
flavor != "logodds" else 1.0)
if include_background:
ax.scatter(
scaled_distances,
data[1],
s=1,
c=color_scheme.get("background", "gray"),
alpha=0.4,
)
ax.fill_between(
scaled_distances,
data[2] - data[3],
data[2] + data[3],
alpha=0.2,
color=color_scheme.get("envelope", "grey"),
)
ax.set_title(
"{} : {}".format(("" if feature_type is None else feature_type),
("" if feature is None else feature)),
fontsize=kwargs.get("title_font_size", kwargs.get("fontsize", 15)),
)
ax.set_ylabel(
"{} Value".format(("" if feature_type is None else feature_type)),
fontsize=kwargs.get("label_font_size", kwargs.get("fontsize", 15)),
)
if flavor == "normal":
unit = ("" if "distance_unit" not in\
kwargs.keys() else " [{}]".format(kwargs["distance_unit"]))
ax.set_xlabel(
"Distance to vein{}".format(unit),
fontsize=kwargs.get("label_font_size", kwargs.get("fontsize", 15)),
)
if flavor == "logodds":
x_min, x_max = ax.get_xlim()
ax.axvspan(
xmin=x_min,
xmax=0,
color=color_scheme.get(ratio_order[0], "red"),
alpha=0.2,
)
ax.axvspan(
xmin=0,
xmax=x_max,
color=color_scheme.get(ratio_order[1], "blue"),
alpha=0.2,
)
d1 = ratio_order[0][0]
d2 = ratio_order[1][0]
ax.set_xlabel(
r"$\log(d_{}) - \log(d_{})$".format(d1, d2),
fontsize=kwargs.get("label_font_size", kwargs.get("fontsize", 15)),
)
ax.plot(
scaled_distances,
data[2],
c=color_scheme.get("fitted", "black"),
linewidth=2,
label=("none" if curve_label is None else curve_label),
)
if "tick_fontsize" in kwargs.keys():
ax.tick_params(axis="both",
which="major",
labelsize=kwargs["tick_fontsize"])
