[[base_properties[i][j]["length"][0] for i in range(0, len(names))]
for j in range(0, len(times))])
r0, f0 = es.fit_taproot_r(l[0:1, :], [times[0]], fixed_k)
k0 = fixed_k
print("k fixed, first ", r0, "cm/day", k0, "cm; error", f0)
r1, f1 = es.fit_taproot_r(l, times, fixed_k)
k1 = fixed_k
print("k fixed ", r1, "cm/day", k1, "cm; error", f1)
r2, k2, f2 = es.fit_taproot_rk(l, times)
print("fit r, k ", r2, "cm/day", k2, "cm; error", f2)
""" length plot """
t_ = np.linspace(0, times[-1], 200)
y0 = es.negexp_length(t_, r0, k0)
y1 = es.negexp_length(t_, r1, k1)
y2 = es.negexp_length(t_, r2, k2)
plt.plot([0.], [0.], "r*") # we can add that point
for i in range(0, len(names)):
for j in range(0, len(times)):
l = base_properties[i][j]["length"]
plt.plot([times[j] for k in l], l, "k*")
plt.plot(t_, y0, "b", label="first only, k fixed")
plt.plot(t_, y1, "g", label="k fixed")
plt.plot(t_, y2, "r", label="fit r, k")
plt.legend()
plt.title("Faba")
plt.xlabel("Time [days]")
# plt.ylabel("Root length at measurement time [cm]")
# plt.title("Maize seminals")
""" root age plot """
for j in range(0, len(times)):
age_flat, l_flat, c_flat = [], [], []
for i in range(0, len(names)):
for k, l_ in enumerate(l[j, i]):
age_flat.append(age[j, i][k])
l_flat.append(l[j, i][k])
plt.plot(age_flat, l_flat, col[j])
age_flat = [item for sublist in age for sublist2 in sublist for item in sublist2]
l_flat = [item for sublist in l for sublist2 in sublist for item in sublist2]
r, k, f = es.fit_taproot_rk(l_flat, age_flat)
k1 = 150.
r1, f1 = es.fit_taproot_r(l_flat, age_flat, k1)
print(r, "cm/day", k, "cm")
print(r1, "cm/day", k1, "cm")
t_ = np.linspace(0, times[-1], 200)
y0 = es.negexp_length(t_, r, k)
y1 = es.negexp_length(t_, r1, k1)
plt.plot(t_, y0, "k")
plt.plot(t_, y1, "k:")
plt.xlabel("root age [day]")
plt.ylabel("root length [cm]")
plt.show()
print("fin.")
