def update_fit_R3(db_read, db_rds, sample, mesa='%', commit=False):
"""
:type db_read: Database
:type X: int or str
:type Y: int or str
"""
q = ('SELECT device_id, mesa, X, Y, area FROM v04_device '
'WHERE sample=%s AND mesa LIKE %s')
params = db_rds.q_all(q, (sample, mesa,))
for devid, mesa, X, Y, area in params:
print('update_fit_R3: devid{} {} {} X{} Y{} querying...'.
format(devid, sample, mesa, X, Y), end=' ', flush=True)
q = 'SELECT V, I FROM v_py_fitR3 WHERE device_id=%s'
vis = db_read.pdq(q, (devid,))
vis_100meV = vis[(-0.1 <= vis.V) & (vis.V <= 0.1)]
if vis_100meV.empty:
print('VIs (100meV) empty. skip.')
continue
c1, _, _, _ = fit_R3(vis_100meV)
_, _, _, R2 = fit_R3(vis)
R0 = 1/c1
RA0 = area/c1
oper = ('UPDATE device SET suss_R0=%s, suss_RA0=%s, suss_R2=%s '
'WHERE device_id=%s')
db_rds.cursor.execute(oper, (R0, RA0, R2, devid,))
if commit:
db_rds.cnx.commit()
print('Updated.')
def update_fit_R3(db_read, db_rds, sample, mesa='%', commit=False):
"""
:type db_read: Database
:type X: int or str
:type Y: int or str
"""
q = ('SELECT device_id, mesa, X, Y, area FROM v04_device '
'WHERE sample=%s AND mesa LIKE %s')
params = db_rds.q_all(q, (
sample,
mesa,
))
for devid, mesa, X, Y, area in params:
print('update_fit_R3: devid{} {} {} X{} Y{} querying...'.format(
devid, sample, mesa, X, Y),
end=' ',
flush=True)
q = 'SELECT V, I FROM v_py_fitR3 WHERE device_id=%s'
vis = db_read.pdq(q, (devid, ))
vis_100meV = vis[(-0.1 <= vis.V) & (vis.V <= 0.1)]
if vis_100meV.empty:
print('VIs (100meV) empty. skip.')
continue
c1, _, _, _ = fit_R3(vis_100meV)
_, _, _, R2 = fit_R3(vis)
R0 = 1 / c1
RA0 = area / c1
oper = ('UPDATE device SET suss_R0=%s, suss_RA0=%s, suss_R2=%s '
'WHERE device_id=%s')
db_rds.cursor.execute(oper, (
R0,
RA0,
R2,
devid,
))
if commit:
db_rds.cnx.commit()
print('Updated.')
def iv_matrix(db, sample, mesa, xlim=(-1.0, 1.0),
XXYY=None, inst='%', save_path=None,
R2_9th_lim=1.5, v_fit=(-0.1, 0.1),
grayout_remarks={'i', 'lin', 'c', 'bd'},
edit_remarks=False, db_rds=None, remarks_path=None, commit=False):
"""
:param XXYY: (X_min, X_max, Y_min, Y_max). if is None -> all XYs
"""
plt.close()
sns.set_style("white")
sql = ('SELECT device_id AS did, X, Y, area, suss_R0 AS R0, suss_RA0 AS RA0, '
'VI_remarks as rem '
'FROM v04_device WHERE sample=%s AND mesa=%s')
df = db.pdq(sql, (sample, mesa,))
if XXYY is None:
X_min, X_max, Y_min, Y_max = \
df.X.min(), df.X.max(), df.Y.min(), df.Y.max()
else:
X_min, X_max, Y_min, Y_max = XXYY
# Number of columns and rows in matrix plot.
numX = X_max - X_min + 1
numY = Y_max - Y_min + 1
if edit_remarks:
devid_matrix = [[None for x in range(numX)] for y in range(numY)]
remarks_matrix = [['NULL' for x in range(numX)] for y in range(numY)]
# Takes long time.
print('Making subplots frame...')
# http://matplotlib.org/api/pyplot_api.html
subplot_kw = {'xlim': xlim, 'ylim': (-1, 1),
'xticks': [], 'yticks': [0]}
f, axarr = plt.subplots(numY, numX, squeeze=False, subplot_kw=subplot_kw,
figsize=(numX, numY), facecolor='w')
f.subplots_adjust(top=1, bottom=0, left=0, right=1, wspace=0, hspace=0)
for i, d in df.iterrows():
if not ((X_min <= d.X <= X_max) and (Y_min <= d.Y <= Y_max)):
continue
row = Y_max - d.Y
col = -X_min + d.X
ax = axarr[row, col] # row, col
ax.yaxis.set_major_formatter(plt.NullFormatter()) # Hide ticks labels
if edit_remarks:
devid_matrix[row][col] = d.did
remarks_matrix[row][col] = d.rem
tx_lb = d.rem.replace(' ', '\n') # text left bottom
ax.text(0.1, 0, tx_lb, ha='left', va='bottom',
transform=ax.transAxes, size='x-small')
print('Querying vis... (X{} Y{} {} device id: {})'.
format(d.X, d.Y, mesa, d.did), end=' ', flush=True)
sql = 'SELECT V, I FROM v_py_matrix ' \
'WHERE device_id=%s AND inst LIKE %s'
VI = db.pdq(sql, (d.did, inst,))
print('Done.', end=' ', flush=True)
if VI.empty:
print()
continue
# fit
VI_fit = VI[(v_fit[0] <= VI.V) & (VI.V <= v_fit[1])]
c1, c2, c3, R2 = al.fit_R3(VI_fit)
if not math.isclose(1/c1, d.R0, rel_tol=1e-2): # tolerance: 2 digits
print('R0 difference: db{} calc{}'.format(d.R0, 1/c1),
end=' ', flush=True)
# Vs, Is, Rs
VI['R'] = VI.V / VI.I
VI['Ifit'] = c1 * VI.V + c2 * VI.V ** 2 + c3 * VI.V ** 3
VI['Rfit'] = VI.V / VI.Ifit
# Normalize to ylim(-1, 1)
I_scale = VI.I.abs().max()
VI['In'] = VI.I / I_scale # [-1, 1]
VI['Ifitn'] = VI.Ifit / I_scale # [-1, 1]
# Intervals: assuming R > 0
R_scale = VI.R[(VI.R > 0) & (VI.R != np.inf)].max()
R_scale = VI.Rfit.max()
VI['Rn'] = (VI.R / R_scale) * 0.9 # (0, 0.9]
VI['Rn'] = VI.Rn*2 - 1 # (-1, 0.9]
VI['Rfitn'] = (VI.Rfit / R_scale)*0.9*2 - 1 # (-1, 0.9]
R2_num_9th = al.num_9th(R2)
if (R2_num_9th <= R2_9th_lim) or \
(grayout_remarks & set(d.rem.split(' ')) != set()):
blue, _, red = sns.color_palette('pastel')[:3]
else:
blue, _, red = sns.color_palette()[:3]
ax.plot(VI.V, VI.Rn, c=red, lw=0.5)
ax.plot(VI.V, VI.In, c=blue, lw=0.5)
ax.plot(VI.V, VI.Rfitn, '--', c='gray', lw=0.5)
ax.plot(VI.V, VI.Ifitn, '--', c='gray', lw=0.5)
# X Y R2-#9th R0 RA0
tx_lt = 'X{}Y{}\n{:d}'.format(d.X, d.Y, d.did)
ax.text(0, 1, tx_lt, ha='left', va='top',
transform=ax.transAxes, size='x-small')
tx_rb = 'R2 {:.2f} {:.1f}\nR{:.1e}\nRA{:.1e}'. \
format(R2, R2_num_9th, 1 / c1, d.area / c1)
ax.text(1, 0, tx_rb, ha='right', va='bottom',
transform=ax.transAxes, size='x-small')
print('') # newline
if edit_remarks:
with open(remarks_path, 'w') as f:
f.write('\n'.join([','.join(row) for row in remarks_matrix]))
if save_path is None:
plt.show()
else:
plt.savefig(save_path)
pass
if edit_remarks:
print('Edit', remarks_path, '.')
input()
with open(remarks_path, 'r') as f:
remarks_matrix2 = f.readlines()
remarks_matrix2 = [row.split(',') for row in remarks_matrix2]
pairs_remarks_devid = []
for row in range(numY):
for col in range(numX):
if devid_matrix[row][col] is None:
continue
remarks = remarks_matrix2[row][col].strip()
pairs_remarks_devid.append((remarks, devid_matrix[row][col]))
oper = 'UPDATE device SET VI_remarks=%s WHERE device_id=%s'
db_rds.exem(oper, pairs_remarks_devid)
if commit:
db_rds.cnx.commit()
print('Edit comitted.')