def plot2d_summary(
x,
y,
z,
xlabel,
ylabel,
zlabel,
title=None,
append_to_filename="",
pcm_kwargs={},
rc_params={},
**params,
):
"""Plot 2-dimensional data and save figure."""
rcParams.update(rc_params)
if any(len(a.shape) > 2 for a in (x, y, z)):
logger.warning(
f"Failed to plot {params['labber_filename']}: "
f"data is more than 2D ({x.shape=} {y.shape=} {z.shape=})")
return
if len(set([x.shape[0], y.shape[0], z.shape[0]])) > 1:
logger.warning(
f"Truncating {params['labber_filename']} along first axis: "
f"scan may have been interrupted ({x.shape=} {y.shape=} {z.shape=})."
)
n = min(x.shape[0], y.shape[0], z.shape[0])
x, y, z = x[:n], y[:n], z[:n]
min_z = np.min(z)
try:
fig = Figure()
ax = fig.add_subplot()
plot2d(
x,
y,
z,
xlabel=xlabel,
ylabel=ylabel,
zlabel=zlabel,
title=title,
ax=ax,
**pcm_kwargs,
)
except Exception as e:
logger.warning(
f"Failed to plot data from {params['labber_filename']}: caught {repr(e)}"
)
return
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")
dvdi = np.abs(lockin)
temp_meas = f.get_data(CHAN_TEMP_MEAS)
# check for significant temperature deviations
MAX_TEMPERATURE_STD = 1e-3
temp_std = np.std(temp_meas)
if temp_std > MAX_TEMPERATURE_STD:
warnings.warn(
f"Temperature standard deviation {temp_std} K > {MAX_TEMPERATURE_STD} K"
)
# plot the raw data
fig, ax = plot2d(
*np.broadcast_arrays(bfield[..., np.newaxis] / 1e-3, ibias / 1e-6, dvdi),
xlabel="x coil field (mT)",
ylabel="dc bias (μA)",
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=".")
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]),
xlabel="$B_\perp^\mathrm{ext}$ (μT)",
ylabel="$I_\\mathrm{bias}$ (μA)",
zlabel="dV/dI (Ω)",
vmin=0,
vmax=500,
extend_min=False,
)
qmesh = ax.get_children()[0]
assert isinstance(qmesh,
QuadMesh), "Violated assumption that first child is QuadMesh"
line = ax.axvline(200, color="black", linestyle="--")
text = ax.text(
220,
0,
r"$I_\mathrm{flux} = " + f"{int(round(iflux[0, 0, 0])) / 1e-6}$ μA",
color="white",
size=32,