def main(*args, **kwargs):
print 'Running "inspect" script'
# Find all multispec (.*vms.asc) files
specfiles = spec.find_multispec()
specfiles.sort()
# Curve plotting loop
type_lkup = {'zv': spec.ZVSTSBundle, 'iv': spec.IVSTSBundle}
for file_path in specfiles:
print 'Plotting all from "{}"'.format(file_path)
path_mat = re.search(r'^(.*?)\.([zi]v)ms(?:\.asc)?$', file_path)
new_foldername = path_mat.group(1)
spectype = path_mat.group(2)
all_curves = type_lkup[spectype](file_path)
# Make new folder for saving individual plots
if not os.path.exists(new_foldername):
os.makedirs(new_foldername)
X = all_curves.X
for i in range(all_curves.N):
save_path = new_foldername + '/curve_{0:03d}.png'.format(i)
if os.path.exists(save_path): continue
Y = all_curves.allY[i]
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(X, Y)
spec.pltformat_basic(ax)
ax.set_title('Curve i={}'.format(i))
fig.savefig(save_path, dpi=100)
plt.close(fig)
# END for
# END for
print 'inspect is finished.'
def main(*args, **kwargs):
print 'Running "inspect" script'
# Find all multispec (.*vms.asc) files
specfiles = spec.find_multispec()
specfiles.sort()
# Curve plotting loop
type_lkup = {'zv': spec.ZVSTSBundle, 'iv': spec.IVSTSBundle}
for file_path in specfiles:
print 'Plotting all from "{}"'.format(file_path)
path_mat = re.search(r'^(.*?)\.([zi]v)ms(?:\.asc)?$', file_path)
new_foldername = path_mat.group(1)
spectype = path_mat.group(2)
all_curves = type_lkup[spectype](file_path)
# Make new folder for saving individual plots
if not os.path.exists(new_foldername):
os.makedirs(new_foldername)
X = all_curves.X
for i in range(all_curves.N):
save_path = new_foldername+'/curve_{0:03d}.png'.format(i)
if os.path.exists(save_path): continue
Y = all_curves.allY[i]
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(X, Y)
spec.pltformat_basic(ax)
ax.set_title( 'Curve i={}'.format(i) )
fig.savefig(save_path, dpi=100)
plt.close(fig)
# END for
# END for
print 'inspect is finished.'
def zv_subroutine(path, file_name):
log = 'z(V) spectra "{}":\n'.format(file_name)
log += ' folder: {}\n'.format(path)
allZs = spec.ZVSTSBundle(path+file_name)
rr = allZs.has_ramp_reversal
if rr:
log += ' ramp reversal detected\n'
allZs_f, allZs_r = allZs.ramp_reversal_fix(opt='split')
log += ' keeping track of ramp directions\n'
N_spec = allZs_f.N
mZ_f = allZs_f.coavg()
mZ_r = allZs_r.coavg()
V = allZs_f.X
else:
N_spec = allZs.N
mZ = allZs.coavg()
V = allZs.X
# END if
log += ' {} spectra in sample\n'.format(N_spec)
# make density plot for all the z(V) spectra
fig = plt.figure()
ax = fig.add_subplot(111)
if rr:
spec.plot_density(allZs_f, ax)
spec.plot_density(allZs_r, ax, mkrcolor='red')
ax.plot(V, mZ_f, color=(0.5,0.6,1.0), linewidth=2)
ax.plot(V, mZ_r, color=(1.0,0.5,0.5), linewidth=2)
else:
spec.plot_density(allZs, ax)
ax.plot(V, mZ, color=(0.5,0.6,1.0), linewidth=2)
# END if
ax.set_title( '{}, N={}'.format(file_name, N_spec) )
spec.pltformat_basic(ax)
save_name = re.sub(r'\.[zi]vms(?:\.asc)?$', '-zv.png', file_name)
ax.figure.savefig(path+save_name, dpi=150)
plt.close(fig)
log += ' saved "{}"\n'.format(save_name)
# create a dz/dV(V) spectra bundle
x_window = 0.1 #V
poly_order = 1
deriv_order = 1
if rr:
alldZs_f = allZs_f.deriv_sg(x_window, poly_order, deriv_order)
alldZs_r = allZs_r.deriv_sg(x_window, poly_order, deriv_order)
mdZ_f = alldZs_f.coavg()
mdZ_r = alldZs_r.coavg()
else:
alldZs = allZs.deriv_sg(x_window, poly_order, deriv_order)
mdZ = alldZs.coavg()
# END if
# make density plot for all the dz/dV(V) spectra
fig = plt.figure()
ax = fig.add_subplot(111)
if rr:
spec.plot_density(alldZs_f, ax)
spec.plot_density(alldZs_r, ax, mkrcolor='red')
ax.plot(V, mdZ_f, color=(0.5,0.6,1.0), linewidth=2)
ax.plot(V, mdZ_r, color=(1.0,0.5,0.5), linewidth=2)
else:
spec.plot_density(alldZs, ax)
ax.plot(V, mdZ, color=(0.5,0.6,1.0), linewidth=2)
# END if
ax.set_title( '{}, N={}'.format(file_name, N_spec) )
spec.pltformat_basic(ax)
save_name = re.sub(r'\.[zi]vms(?:\.asc)?$', '-dzdv.png', file_name)
ax.figure.savefig(path+save_name, dpi=150)
plt.close(fig)
log += ' saved "{}"\n'.format(save_name)
print log
def iv_subroutine(path, file_name):
log = 'I(V) spectra "{}":\n'.format(file_name)
log += ' folder: {}\n'.format(path)
allIs = spec.IVSTSBundle(path+file_name)
rr = allIs.has_ramp_reversal
if rr:
log += ' ramp reversal detected\n'
allIs_f, allIs_r = allIs.ramp_reversal_fix(opt='split')
log += ' keeping track of ramp directions\n'
N_spec = allIs_f.N
mI_f = allIs_f.coavg()
mI_r = allIs_r.coavg()
V = allIs_f.X
else:
N_spec = allIs.N
mI = allIs.coavg()
V = allIs.X
# END if
log += ' {} spectra in sample\n'.format(N_spec)
# make density plot for all the I(V) spectra
fig = plt.figure()
ax = fig.add_subplot(111)
if rr:
spec.plot_density(allIs_f, ax)
spec.plot_density(allIs_r, ax, mkrcolor='red')
ax.plot(V, mI_f, color=(0.5,0.6,1.0), linewidth=2)
ax.plot(V, mI_r, color=(1.0,0.5,0.5), linewidth=2)
else:
spec.plot_density(allIs, ax)
ax.plot(V, mI, color=(0.5,0.6,1.0), linewidth=2)
# END if
ax.set_title( '{}, N={}'.format(file_name, N_spec) )
spec.pltformat_basic(ax)
save_name = re.sub(r'\.[zi]vms(?:\.asc)?$', '-iv.png', file_name)
ax.figure.savefig(path+save_name, dpi=150)
plt.close(fig)
log += ' saved "{}"\n'.format(save_name)
# create a dz/dV(V) spectra bundle
x_window = 0.1 #V
poly_order = 1
if rr:
allndIs_f = allIs_f.norm_deriv(x_window, poly_order)
allndIs_r = allIs_r.norm_deriv(x_window, poly_order)
ndmI_f = spec.norm_deriv(V, allIs_f.coavg(), x_window, poly_order)
ndmI_r = spec.norm_deriv(V, allIs_r.coavg(), x_window, poly_order)
else:
allndIs = allIs.norm_deriv(x_window, poly_order)
# END if
# make density plot for all the norm. dI/dV(V) spectra
fig = plt.figure()
ax = fig.add_subplot(111)
if rr:
spec.plot_density(allndIs_f, ax)
spec.plot_density(allndIs_r, ax, mkrcolor='red')
ax.plot(V, ndmI_f, color=(0.5,0.6,1.0), linewidth=2)
ax.plot(V, ndmI_r, color=(1.0,0.5,0.5), linewidth=2)
ax.plot(V, allndIs_f.coavg(), color=(0.5,0.5,0.6), linewidth=1)
ax.plot(V, allndIs_r.coavg(), color=(0.6,0.5,0.5), linewidth=1)
else:
spec.plot_density(allndIs, ax)
ax.plot(V, allndIs.coavg(), color=(0.5,0.6,1.0), linewidth=2)
# END if
ax.set_title( '{}, N={}'.format(file_name, N_spec) )
spec.pltformat_basic(ax)
spec.tight_scale(ax)
save_name = re.sub(r'\.[zi]vms(?:\.asc)?$', '-ndidv.png', file_name)
ax.figure.savefig(path+save_name, dpi=150)
plt.close(fig)
log += ' saved "{}"\n'.format(save_name)
print log
def _giv_subroutine(path, file_name):
log = 'I(V) spectra "{}":\n'.format(file_name)
gspec_file_name = re.sub(r'\.ivms', '.gvms', file_name)
log += ' dI/dV(V) spectra: "{}"'.format(gspec_file_name)
log += ' folder: {}\n'.format(path)
allIs = spec.IVSTSBundle(path+file_name)
alldIs = spec.IVSTSBundle(path+gspec_file_name)
rr = allIs.has_ramp_reversal
if rr:
log += ' ramp reversal detected\n'
allIs_f, allIs_r = allIs.ramp_reversal_fix(opt='split')
alldIs_f, alldIs_r = alldIs.ramp_reversal_fix(opt='split')
log += ' keeping track of ramp directions\n'
N_spec = allIs_f.N
mI_f = allIs_f.coavg()
mI_r = allIs_r.coavg()
mdI_f = alldIs_f.coavg()
mdI_r = alldIs_r.coavg()
V = allIs_f.X
else:
N_spec = allIs.N
mI = allIs.coavg()
mdI = alldIs.coavg()
V = allIs.X
# END if
log += ' {} spectra in sample\n'.format(N_spec)
# make density plot for all the I(V) spectra
fig = plt.figure()
ax = fig.add_subplot(111)
if rr:
spec.plot_density(allIs_f, ax)
spec.plot_density(allIs_r, ax, mkrcolor='red')
ax.plot(V, mI_f, color=(0.5,0.6,1.0), linewidth=2)
ax.plot(V, mI_r, color=(1.0,0.5,0.5), linewidth=2)
else:
spec.plot_density(allIs, ax)
ax.plot(V, mI, color=(0.5,0.6,1.0), linewidth=2)
# END if
ax.set_title( '{}, N={}'.format(file_name, N_spec) )
ax.set_xlabel('Gap Bias ({})'.format(allIs.units[0]))
ax.set_ylabel('Tunneling Current ({})'.format(allIs.units[1]))
spec.pltformat_basic(ax)
save_name = re.sub(r'\.[zi]vms(?:\.asc)?$', '-iv.png', file_name)
ax.figure.savefig(path+save_name, dpi=150)
plt.close(fig)
log += ' saved "{}"\n'.format(save_name)
# make density plot for all the dI/dV(V) spectra
fig = plt.figure()
ax = fig.add_subplot(111)
if rr:
spec.plot_density(alldIs_f, ax)
spec.plot_density(alldIs_r, ax, mkrcolor='red')
ax.plot(V, mdI_f, color=(0.5,0.6,1.0), linewidth=2)
ax.plot(V, mdI_r, color=(1.0,0.5,0.5), linewidth=2)
else:
spec.plot_density(alldIs, ax)
ax.plot(V, mdI, color=(0.5,0.6,1.0), linewidth=2)
# END if
ax.set_title( '{}, N={}'.format(file_name, N_spec) )
ax.set_xlabel('Gap Bias ({})'.format(alldIs.units[0]))
ax.set_ylabel('Lock-in Signal ({})'.format(alldIs.units[1]))
spec.pltformat_basic(ax)
save_name = re.sub(r'\.[zi]vms(?:\.asc)?$', '-didv.png', file_name)
ax.figure.savefig(path+save_name, dpi=150)
plt.close(fig)
log += ' saved "{}"\n'.format(save_name)
# create a dz/dV(V) spectra bundle
x_window = 0.1 #V
poly_order = 1
if rr:
sIs_f = allIs_f.deriv_sg(x_window, poly_order, 0)
sIs_f.zero_y0()
sIs_r = allIs_r.deriv_sg(x_window, poly_order, 0)
sIs_r.zero_y0()
sdIs_f = alldIs_f.deriv_sg(x_window, poly_order, 0)
sdIs_r = alldIs_r.deriv_sg(x_window, poly_order, 0)
allndIs_f = alldIs_f.copy()
allndIs_r = alldIs_r.copy()
for i in range(allndIs_f.N):
allndIs_f[i] = allIs_f.X * sdIs_f[i] / sIs_f[i]
allndIs_r[i] = allIs_f.X * sdIs_r[i] / sIs_r[i]
# END for
ndmI_f = spec.norm_deriv(V, allIs_f.coavg(), x_window, poly_order)
ndmI_r = spec.norm_deriv(V, allIs_r.coavg(), x_window, poly_order)
else:
sIs = allIs.deriv_sg(x_window, poly_order, 0)
sIs.zero_y0()
sdIs = alldIs.deriv_sg(x_window, poly_order, 0)
allndIs = alldIs.copy()
for i in range(allndIs.N):
allndIs[i] = allIs.X * sdIs[i] / sIs[i]
# END for
# END if
# make density plot for all the norm. dI/dV(V) spectra
fig = plt.figure()
ax = fig.add_subplot(111)
if rr:
spec.plot_density(allndIs_f, ax)
spec.plot_density(allndIs_r, ax, mkrcolor='red')
ax.plot(V, ndmI_f, color=(0.5,0.6,1.0), linewidth=2)
ax.plot(V, ndmI_r, color=(1.0,0.5,0.5), linewidth=2)
ax.plot(V, allndIs_f.coavg(), color=(0.5,0.5,0.6), linewidth=1)
ax.plot(V, allndIs_r.coavg(), color=(0.6,0.5,0.5), linewidth=1)
else:
spec.plot_density(allndIs, ax)
ax.plot(V, allndIs.coavg(), color=(0.5,0.6,1.0), linewidth=2)
# END if
ax.set_title( '{}, N={}'.format(file_name, N_spec) )
ax.set_xlabel('Gap Bias ({})'.format(alldIs.units[0]))
ax.set_ylabel('(V/I)*dI/dV')
spec.pltformat_basic(ax)
spec.tight_scale(ax)
save_name = re.sub(r'\.[zi]vms(?:\.asc)?$', '-ndidv.png', file_name)
ax.figure.savefig(path+save_name, dpi=150)
plt.close(fig)
log += ' saved "{}"\n'.format(save_name)
print log
def _iv_subroutine(path, file_name):
log = 'I(V) spectra "{}":\n'.format(file_name)
log += ' folder: {}\n'.format(path)
allIs = spec.IVSTSBundle(path+file_name)
rr = allIs.has_ramp_reversal
if rr:
log += ' ramp reversal detected\n'
allIs_f, allIs_r = allIs.ramp_reversal_fix(opt='split')
log += ' keeping track of ramp directions\n'
N_spec = allIs_f.N
mI_f = allIs_f.coavg()
mI_r = allIs_r.coavg()
V = allIs_f.X
else:
N_spec = allIs.N
mI = allIs.coavg()
V = allIs.X
# END if
log += ' {} spectra in sample\n'.format(N_spec)
# make density plot for all the I(V) spectra
fig = plt.figure()
ax = fig.add_subplot(111)
if rr:
spec.plot_density(allIs_f, ax)
spec.plot_density(allIs_r, ax, mkrcolor='red')
ax.plot(V, mI_f, color=(0.5,0.6,1.0), linewidth=2)
ax.plot(V, mI_r, color=(1.0,0.5,0.5), linewidth=2)
else:
spec.plot_density(allIs, ax)
ax.plot(V, mI, color=(0.5,0.6,1.0), linewidth=2)
# END if
ax.set_title( '{}, N={}'.format(file_name, N_spec) )
spec.pltformat_basic(ax)
save_name = re.sub(r'\.[zi]vms(?:\.asc)?$', '-iv.png', file_name)
ax.figure.savefig(path+save_name, dpi=150)
plt.close(fig)
log += ' saved "{}"\n'.format(save_name)
# create a dz/dV(V) spectra bundle
x_window = 0.1 #V
poly_order = 1
if rr:
allndIs_f = allIs_f.norm_deriv(x_window, poly_order)
allndIs_r = allIs_r.norm_deriv(x_window, poly_order)
dv = V[1] - V[0]
ndmI_f = spec.norm_deriv(V, allIs_f.coavg(), x_window, poly_order)
ndmI_r = spec.norm_deriv(V, allIs_r.coavg(), x_window, poly_order)
else:
allndIs = allIs.norm_deriv(x_window, poly_order)
# END if
# make density plot for all the norm. dI/dV(V) spectra
fig = plt.figure()
ax = fig.add_subplot(111)
if rr:
spec.plot_density(allndIs_f, ax)
spec.plot_density(allndIs_r, ax, mkrcolor='red')
ax.plot(V, ndmI_f, color=(0.5,0.6,1.0), linewidth=2)
ax.plot(V, ndmI_r, color=(1.0,0.5,0.5), linewidth=2)
ax.plot(V, allndIs_f.coavg(), color=(0.5,0.5,0.6), linewidth=1)
ax.plot(V, allndIs_r.coavg(), color=(0.6,0.5,0.5), linewidth=1)
else:
spec.plot_density(allndIs, ax)
ax.plot(V, allndIs.coavg(), color=(0.5,0.6,1.0), linewidth=2)
# END if
ax.set_title( '{}, N={}'.format(file_name, N_spec) )
spec.pltformat_basic(ax)
spec.tight_scale(ax)
save_name = re.sub(r'\.[zi]vms(?:\.asc)?$', '-ndidv.png', file_name)
ax.figure.savefig(path+save_name, dpi=150)
plt.close(fig)
log += ' saved "{}"\n'.format(save_name)
print log
def _zv_subroutine(path, file_name):
log = 'z(V) spectra "{}":\n'.format(file_name)
log += ' folder: {}\n'.format(path)
allZs = spec.ZVSTSBundle(path+file_name)
rr = allZs.has_ramp_reversal
if rr:
log += ' ramp reversal detected\n'
allZs_f, allZs_r = allZs.ramp_reversal_fix(opt='split')
log += ' keeping track of ramp directions\n'
N_spec = allZs_f.N
mZ_f = allZs_f.coavg()
mZ_r = allZs_r.coavg()
V = allZs_f.X
else:
N_spec = allZs.N
mZ = allZs.coavg()
V = allZs.X
# END if
log += ' {} spectra in sample\n'.format(N_spec)
# make density plot for all the z(V) spectra
fig = plt.figure()
ax = fig.add_subplot(111)
if rr:
spec.plot_density(allZs_f, ax)
spec.plot_density(allZs_r, ax, mkrcolor='red')
ax.plot(V, mZ_f, color=(0.5,0.6,1.0), linewidth=2)
ax.plot(V, mZ_r, color=(1.0,0.5,0.5), linewidth=2)
else:
spec.plot_density(allZs, ax)
ax.plot(V, mZ, color=(0.5,0.6,1.0), linewidth=2)
# END if
ax.set_title( '{}, N={}'.format(file_name, N_spec) )
spec.pltformat_basic(ax)
save_name = re.sub(r'\.[zi]vms(?:\.asc)?$', '-zv.png', file_name)
ax.figure.savefig(path+save_name, dpi=150)
plt.close(fig)
log += ' saved "{}"\n'.format(save_name)
# create a dz/dV(V) spectra bundle
x_window = 0.1 #V
poly_order = 1
deriv_order = 1
if rr:
alldZs_f = allZs_f.deriv_sg(x_window, poly_order, deriv_order)
alldZs_r = allZs_r.deriv_sg(x_window, poly_order, deriv_order)
mdZ_f = alldZs_f.coavg()
mdZ_r = alldZs_r.coavg()
else:
alldZs = allZs.deriv_sg(x_window, poly_order, deriv_order)
mdZ = alldZs.coavg()
# END if
# make density plot for all the dz/dV(V) spectra
fig = plt.figure()
ax = fig.add_subplot(111)
if rr:
spec.plot_density(alldZs_f, ax)
spec.plot_density(alldZs_r, ax, mkrcolor='red')
ax.plot(V, mdZ_f, color=(0.5,0.6,1.0), linewidth=2)
ax.plot(V, mdZ_r, color=(1.0,0.5,0.5), linewidth=2)
else:
spec.plot_density(alldZs, ax)
ax.plot(V, mdZ, color=(0.5,0.6,1.0), linewidth=2)
# END if
ax.set_title( '{}, N={}'.format(file_name, N_spec) )
spec.pltformat_basic(ax)
save_name = re.sub(r'\.[zi]vms(?:\.asc)?$', '-dzdv.png', file_name)
ax.figure.savefig(path+save_name, dpi=150)
plt.close(fig)
log += ' saved "{}"\n'.format(save_name)
print log
