def plot_summary(
x,
y,
xlabel,
ylabel,
legend=None,
title=None,
append_to_filename="",
ylim=(None, None),
plot_kwargs={},
**params,
):
"""Plot 1-dimensional data and save figure."""
if len(x.shape) > 1:
logger.warning(f"Failed to plot {params['labber_filename']}: "
f"data is more than 1D ({x.shape=})")
return
if x.shape[0] != y.shape[0]:
logger.warning(
f"Failed to plot {params['labber_filename']}: "
f"first dimensions of data don't match ({x.shape=}, {y.shape=})")
return
try:
fig = Figure()
ax = fig.add_subplot()
plot(
x,
y,
xlabel=xlabel,
ylabel=ylabel,
title=title,
ax=ax,
label=legend,
**plot_kwargs,
)
except Exception as e:
logger.warning(
f"Failed to plot data from {params['labber_filename']}: caught {repr(e)}"
)
logger.exception("ERROR")
return
ax.set_ylim(ylim)
scan_id = flat_clfs(params)["scan"]
stamp(ax, scan_id)
fig.savefig(out_dir(params) / (scan_id + append_to_filename + ".png"),
format="png")
def reconstruct_current(name, obj):
scan = name.split("/")[-1].split("::")[-1]
if scan not in scans.keys():
return None
print(scan, name)
params = scans[scan]
field = obj["x magnet field"]
ibias = obj["dc current bias"]
dvdi = np.abs(obj["lock-in (impedance)"])
# extract fraunhofer from data
ic = extract_switching_current(ibias, dvdi, threshold=params["threshold"])
fig, ax = plot2d(field, ibias, dvdi)
plot(
np.unique(field),
ic,
ax=ax,
title="Ic extraction",
color="k",
lw="0",
marker=".",
markersize=5,
)
ax.axis("off")
stamp(ax, scan)
fig.savefig(outdir / f"{scan}_ic-extraction.png")
field = np.unique(field)
# center fraunhofer
argmax_ic = find_fraunhofer_center(field, ic)
ic_n = extract_switching_current(ibias,
dvdi,
threshold=params["threshold"],
side="negative")
argmax_ic_n = find_fraunhofer_center(field, np.abs(ic_n))
field -= (argmax_ic + argmax_ic_n) / 2
# field = recenter_fraunhofer(np.unique(field), ic) # if just centering at argmax(Ic+)
fig, ax = plot(
field / 1e-3,
np.array([ic, ic_n]).T / 1e-6,
xlabel="field (mT)",
ylabel="critical current (μA)",
title="fraunhofer centered",
)
ax.axvline(0, color="k")
fig.savefig(outdir / f"{scan}_fraunhofer-centered.png")
# reconstruct current distribution
x, jx = extract_current_distribution(
field,
ic,
f2k=2 * np.pi * params["jj_length"] / phys_c["mag. flux quantum"][0],
jj_width=params["jj_width"],
jj_points=400,
)
fig, ax = subplots()
ax.fill_between(x / 1e-6, jx)
ax.set_xlabel("position (μA)")
ax.set_ylabel("critical current density (μA/μm)")
ax.set_title(
f"$\ell_\mathrm{{eff}}$ = {round(params['jj_length'] / 1e-6, 1)}μm")
fig.savefig(outdir / f"{scan}_current-distribution.png")
zlabel="dV/dI (Ω)",
title="raw data",
stamp=COOLDOWN_SCAN,
)
fig.savefig(str(OUTPATH) + "_raw-data.png")
# extract the switching currents
ic_n, ic_p = extract_switching_current(
ibias,
dvdi,
side="both",
threshold=RESISTANCE_THRESHOLD,
interp=True,
)
ax.set_title("$I_c$ extraction")
plot(bfield / 1e-3, ic_p / 1e-6, ax=ax, color="w", lw=0, marker=".")
plot(bfield / 1e-3, ic_n / 1e-6, ax=ax, color="w", lw=0, marker=".")
fig.savefig(str(OUTPATH) + "_ic-extraction.png")
# in vector10, positive Bx points into the daughterboard
if FRIDGE == "vector10":
bfield = np.flip(bfield) * -1
ic_p = np.flip(ic_p)
# in vector9, positive Bx points out of the daughterboard
elif FRIDGE == "vector9":
pass
else:
warnings.warn(f"I don't recognize fridge `{FRIDGE}`")
# parameterize the fit
params = Parameters()
def estimate_bfield_offset(bfield: np.ndarray, ic_p: np.ndarray, ic_n=None):
"""Estimate the coil field at which the true flux is integral.
The position of a maximum near the center of the `bfield` range is returned.
If `ic_n` is given, a better estimate is midway between a peak in `ic_p` and the
closest valley in `ic_n`.
"""
peak_locs, _ = find_peaks(ic_p,
prominence=(np.max(ic_p) - np.min(ic_p)) / 2)
guess_loc = peak_locs[len(peak_locs) // 2]
bfield_guess = bfield[guess_loc]
if ic_n is not None:
peak_locs_n, _ = find_peaks(-ic_n,
prominence=(np.max(ic_n) - np.min(ic_n)) /
2)
guess_loc_n = peak_locs_n[len(peak_locs_n) // 2]
bfield_guess_n = bfield[guess_loc_n]
bfield_guess = (bfield_guess + bfield_guess_n) / 2
# plot the guess
if ic_n is None:
fig, ax = plt.subplots()
ax.set_xlabel("x coil field [mT]")
else:
fig, (ax, ax2) = plt.subplots(2, 1, sharex=True)
ax2.set_xlabel("x coil field [mT]")
plot(
bfield / 1e-3,
ic_n / 1e-6,
ylabel="supercurrent [μA]",
ax=ax2,
marker=".",
)
ax2.plot(
bfield[peak_locs_n] / 1e-3,
ic_n[peak_locs_n] / 1e-6,
lw=0,
marker="*",
label="$I_{c-}$ peaks",
)
ax2.plot(
bfield[guess_loc_n] / 1e-3,
ic_n[guess_loc_n] / 1e-6,
lw=0,
marker="*",
label="$I_{c-}$ guess",
)
ax2.axvline(bfield_guess / 1e-3, color="k")
ax2.legend()
plot(
bfield / 1e-3,
ic_p / 1e-6,
ylabel="supercurrent [μA]",
title="bfield offset guess",
stamp=config["COOLDOWN"] + "_" + config["SCAN"],
ax=ax,
marker=".",
)
ax.axvline(bfield_guess / 1e-3, color="k")
ax.plot(
bfield[peak_locs] / 1e-3,
ic_p[peak_locs] / 1e-6,
lw=0,
marker="*",
label="$I_{c+}$ peaks",
)
ax.plot(
bfield[guess_loc] / 1e-3,
ic_p[guess_loc] / 1e-6,
lw=0,
marker="*",
label="$I_{c+}$ guess",
)
ax.text(
0.5,
0.5,
f"bfield offset $\\approx$ {np.round(bfield_guess / 1e-3, 3)} mT",
va="center",
ha="center",
transform=ax.transAxes,
)
ax.legend()
fig.savefig(str(OUTPATH) + "_bfield-offset.png")
return bfield_guess
zlabel="dV/dI (Ω)",
title="raw data",
stamp=config["COOLDOWN"] + "_" + config["SCAN"],
)
fig.savefig(str(OUTPATH) + "_raw-data.png")
# extract the switching currents
ic_n, ic_p = extract_switching_current(
ibias,
dvdi,
side="both",
threshold=config.getfloat("RESISTANCE_THRESHOLD", fallback=None),
interp=True,
)
ax.set_title("$I_c$ extraction")
plot(bfield / 1e-3, ic_p / 1e-6, ax=ax, color="k", lw=1)
plot(bfield / 1e-3, ic_n / 1e-6, ax=ax, color="k", lw=1)
fig.savefig(str(OUTPATH) + "_ic-extraction.png")
# in vector10, positive Bx points into the daughterboard (depends on mount orientation)
if config["FRIDGE"] == "vector10":
bfield = np.flip(bfield) * -1
ic_p = np.flip(ic_p)
ic_n = np.flip(ic_n)
# in vector9, positive Bx points out of the daughterboard
elif config["FRIDGE"] == "vector9":
pass
else:
warnings.warn(f"I don't recognize fridge `{config['FRIDGE']}`")
# from vector9 fridge
FILENAME = "JS602-SE1_4xFlQpcSq-v1_N_WFSBHE01-071"
PATH = get_data_dir() / f"2021/10/Data_1030/{FILENAME}.hdf5"
with LabberData(PATH) as f:
bfield = f.get_data("Vector Magnet - Field X")
ibias, dc_volts = f.get_data("VITracer - VI curve", get_x=True)
dc_volts /= 100 # amplifier gain 100x
iflux = f.get_data("circleFL 6 - Source current")
# plot extracted switching current for a few flux current values
ic = extract_switching_current(ibias, dc_volts, threshold=3.5e-5)
fig, ax = plot(
np.unique(bfield) / 1e-6,
ic[::2].T / 1e-6,
label=[f"{int(i / 1e-6)} μA" for i in np.unique(iflux[::2])],
xlabel="Vector Magnet Field (μT)",
ylabel="Current Bias (μA)",
)
fig.savefig(OUTDIR / f"{FILENAME}_Ic.png")
# broadcast scalar data over vectorial data to have same shape
iflux, bfield, ibias, dc_volts = np.broadcast_arrays(iflux[..., np.newaxis],
bfield[..., np.newaxis],
ibias, dc_volts)
# plot the first CPR
fig, ax = plot2d(
bfield[0] / 1e-6,
ibias[0] / 1e-6,
np.diff(dc_volts[0]) / np.diff(ibias[0]),