From d394f8bb1516d263863a195596182e22be6c5a41 Mon Sep 17 00:00:00 2001
From: Danilo Ferreira de Lima <danilo.enoque.ferreira.de.lima@xfel.de>
Date: Sun, 7 May 2023 11:45:50 +0200
Subject: [PATCH] Added number of observations and more plots.
---
pes_to_spec/bnn.py | 2 +-
pes_to_spec/model.py | 12 +++
pes_to_spec/test/offline_analysis.py | 142 ++++++++++++++++++++-------
3 files changed, 120 insertions(+), 36 deletions(-)
diff --git a/pes_to_spec/bnn.py b/pes_to_spec/bnn.py
index 887512e..73aca75 100644
--- a/pes_to_spec/bnn.py
+++ b/pes_to_spec/bnn.py
@@ -63,7 +63,7 @@ class BNN(nn.Module):
"""
def __init__(self, input_dimension: int=1, output_dimension: int=1):
super(BNN, self).__init__()
- hidden_dimension = 50
+ hidden_dimension = 100
# controls the aleatoric uncertainty
self.log_isigma2 = nn.Parameter(-torch.ones(1, output_dimension)*np.log(0.1**2), requires_grad=True)
# controls the weight hyperprior
diff --git a/pes_to_spec/model.py b/pes_to_spec/model.py
index 6b86d5e..1e24b05 100644
--- a/pes_to_spec/model.py
+++ b/pes_to_spec/model.py
@@ -611,6 +611,7 @@ class Model(TransformerMixin, BaseEstimator):
elif model_type == "ard":
self.fit_model = MultiOutputGenericWithStd(ARDRegression(n_iter=300, tol=1e-8, verbose=True), n_jobs=8)
self.model_type = model_type
+ self.n_obs = 0
self.kde_xgm = None
self.mu_xgm = np.nan
@@ -624,6 +625,12 @@ class Model(TransformerMixin, BaseEstimator):
# size of the test subset
self.validation_size = validation_size
+ def n_pars(self) -> float:
+ """Get number of parameters."""
+ if self.model_type == "bnn":
+ return sum(p.numel() for p in self.fit_model.model.parameters())
+ return sum(len(estimator.coef_) + 1 for estimator in self.fit_model.estimators_)
+
def get_channels(self) -> List[str]:
"""Get channels used in training."""
return self.x_select.channels
@@ -719,6 +726,7 @@ class Model(TransformerMixin, BaseEstimator):
if weights is not None:
weights = weights[inliers]
self.fit_model.fit(x_t[inliers], y_t[inliers], weights)
+ self.n_obs = len(x_t[inliers])
# calculate the effect of the PCA
print("Calculate PCA unc. on high-resolution data.")
@@ -944,6 +952,8 @@ class Model(TransformerMixin, BaseEstimator):
unc=unc.reshape((B, P, -1)),
pca=pca_unc,
total_unc=total_unc.reshape((B, P, -1)),
+ expected_pca=high_pca.reshape((B, P, -1)),
+ expected_pca_unc=high_pca_unc.reshape((B, P, -1)),
)
def deconvolve(self, expected: np.ndarray) -> np.ndarray:
@@ -986,6 +996,7 @@ class Model(TransformerMixin, BaseEstimator):
transfer_function=self.transfer_function,
impulse_response=self.impulse_response,
model_type=self.model_type,
+ n_obs=self.n_obs,
)
),
self.ood,
@@ -1023,6 +1034,7 @@ class Model(TransformerMixin, BaseEstimator):
obj.transfer_function = extra["transfer_function"]
obj.impulse_response = extra["impulse_response"]
obj.model_type = extra["model_type"]
+ obj.n_obs = extra["n_obs"]
obj.x_select = x_select
obj.x_model = x_model
diff --git a/pes_to_spec/test/offline_analysis.py b/pes_to_spec/test/offline_analysis.py
index 93c66b7..ebe3a52 100755
--- a/pes_to_spec/test/offline_analysis.py
+++ b/pes_to_spec/test/offline_analysis.py
@@ -105,15 +105,17 @@ def plot_result(filename: str,
Y = np.amax(spec_smooth)
ax.legend(frameon=False, borderaxespad=0, loc='upper left')
ax.set_title(f"Beam intensity: {intensity*1e-3:.1f} mJ", loc="left")
+ ax.spines['top'].set_visible(False)
+ ax.spines['right'].set_visible(False)
ax.set(
xlabel="Photon energy [eV]",
ylabel="Intensity",
- ylim=(0, 1.5*Y))
+ ylim=(0, 1.3*Y))
if pes is not None:
ax2 = plt.axes([0,0,1,1])
# Manually set the position and relative size of the inset axes within ax1
#ip = InsetPosition(ax, [0.65,0.6,0.35,0.4])
- ip = InsetPosition(ax, [0.7,0.7,0.35,0.4])
+ ip = InsetPosition(ax, [0.72,0.7,0.35,0.4])
ax2.set_axes_locator(ip)
if pes_to_show == "sum":
pes_plot = sum([pes[k][pes_bin] for k in pes.keys()])
@@ -283,6 +285,20 @@ def main():
t += [time_ns() - start]
t_names += ["Load"]
+ # transfer function
+ fig = plt.figure(figsize=(12, 8))
+ gs = GridSpec(1, 1)
+ ax = fig.add_subplot(gs[0, 0])
+ plt.plot(model.wiener_energy, np.absolute(model.impulse_response))
+ ax.set(title=f"",
+ xlabel=r"Energy [eV]",
+ ylabel="Response [a.u.]",
+ yscale='log',
+ )
+ fig.savefig(os.path.join(args.directory, "impulse.png"))
+ plt.close(fig)
+ print(f"Resolution: {model.resolution:.2f} eV")
+
# plot Wiener filter
fig = plt.figure(figsize=(12, 8))
gs = GridSpec(1, 1)
@@ -303,6 +319,7 @@ def main():
ax.set(title=f"",
xlabel=r"Energy [eV]",
ylabel="Filter value [a.u.]",
+ yscale='log',
)
fig.savefig(os.path.join(args.directory, "wiener.png"))
plt.close(fig)
@@ -335,10 +352,15 @@ def main():
showSpec = True
spec_smooth = model.preprocess_high_res(spec_raw_int_t)
+ mse = np.mean((spec_smooth[:, np.newaxis, :] - spec_pred["expected"])**2, axis=(0, 1))
+ var = np.std(spec_smooth, axis=0)**2
+ r2 = 1 - mse/var
+ print(f"MSE = {np.mean(mse):.2f}, var = {np.mean(var):.2f}, R^2 = {np.mean(r2):.2f}")
+
# chi2 w.r.t XGM intensity
- de = (spec_raw_pe_t[0,1] - spec_raw_pe_t[0,0])
chi2 = np.sum((spec_smooth[:, np.newaxis, :] - spec_pred["expected"])**2/(spec_pred["total_unc"]**2), axis=(-1, -2))
- ndof = float(spec_smooth.shape[1]) - 1.0
+ ndof = spec_smooth.shape[1]
+ print(f"Chi2 after PCA: {np.mean(chi2):.2f}, ndof: {ndof}, chi2/ndof: {np.mean(chi2/ndof):.2f}")
fig = plt.figure(figsize=(12, 8))
gs = GridSpec(1, 1)
ax = fig.add_subplot(gs[0, 0])
@@ -369,39 +391,90 @@ def main():
fig = plt.figure(figsize=(12, 8))
gs = GridSpec(1, 1)
ax = fig.add_subplot(gs[0, 0])
- sns.kdeplot(x=chi2/ndof, ax=ax)
+ sns.histplot(x=chi2/ndof, kde=True, linewidth=3, ax=ax)
ax.set(title=f"",
xlabel=r"$\chi^2/$ndof",
- ylabel="Density [a.u.]",
+ ylabel="Counts [a.u.]",
xlim=(0, 5),
)
- ax.text(0.90, 0.95, fr"$\mu = ${np.mean(chi2/ndof):.2f}",
- verticalalignment='top', horizontalalignment='right',
- transform=ax.transAxes,
- color='black', fontsize=15)
- ax.text(0.90, 0.90, fr"$\sigma = ${np.std(chi2/ndof):.2f}",
- verticalalignment='top', horizontalalignment='right',
- transform=ax.transAxes,
- color='black', fontsize=15)
+ #ax.text(0.90, 0.95, fr"$\mu = ${np.mean(chi2/ndof):.2f}",
+ # verticalalignment='top', horizontalalignment='right',
+ # transform=ax.transAxes,
+ # color='black', fontsize=15)
+ #ax.text(0.90, 0.90, fr"$\sigma = ${np.std(chi2/ndof):.2f}",
+ # verticalalignment='top', horizontalalignment='right',
+ # transform=ax.transAxes,
+ # color='black', fontsize=15)
fig.savefig(os.path.join(args.directory, "chi2.png"))
plt.close(fig)
+ spec_smooth_pca = model.y_model['pca'].transform(spec_smooth)
+ chi2_prepca = np.sum((spec_smooth_pca[:, np.newaxis, :] - spec_pred["expected_pca"])**2/(spec_pred["expected_pca_unc"]**2), axis=(-1, -2))
+ ndof_prepca = float(spec_smooth_pca.shape[-1])
+ print(f"Chi2 before PCA: {np.mean(chi2_prepca):.2f}, ndof: {ndof_prepca}, chi2/ndof: {np.mean(chi2_prepca/ndof_prepca):.2f} +/- {np.std(chi2_prepca/ndof_prepca):.2f}")
+ fig = plt.figure(figsize=(12, 8))
+ gs = GridSpec(1, 1)
+ ax = fig.add_subplot(gs[0, 0])
+ sns.histplot(x=chi2_prepca/ndof_prepca, kde=True, linewidth=3, ax=ax)
+ ax.set(title=f"",
+ xlabel=r"$\chi^2/$ndof before undoing PCA",
+ ylabel="Counts [a.u.]",
+ xlim=(0, 5),
+ )
+ #ax.text(0.90, 0.95, fr"$\mu = ${np.mean(chi2/ndof):.2f}",
+ # verticalalignment='top', horizontalalignment='right',
+ # transform=ax.transAxes,
+ # color='black', fontsize=15)
+ #ax.text(0.90, 0.90, fr"$\sigma = ${np.std(chi2/ndof):.2f}",
+ # verticalalignment='top', horizontalalignment='right',
+ # transform=ax.transAxes,
+ # color='black', fontsize=15)
+ fig.savefig(os.path.join(args.directory, "chi2_prepca.png"))
+ plt.close(fig)
+
+ fig = plt.figure(figsize=(12, 8))
+ gs = GridSpec(1, 1)
+ ax = fig.add_subplot(gs[0, 0])
+ ax.scatter(chi2_prepca/ndof_prepca, xgm_flux_t[:,0], c='r', s=20)
+ ax.set(title=f"",
+ xlabel=r"$\chi^2/$ndof before undoing PCA",
+ ylabel="XGM intensity [uJ]",
+ xlim=(0, 5),
+ ylim=(0, np.mean(xgm_flux_t) + 3*np.std(xgm_flux_t))
+ )
+ fig.savefig(os.path.join(args.directory, "intensity_vs_chi2_prepca.png"))
+ plt.close(fig)
+
+ res_prepca = np.sum((spec_smooth_pca[:, np.newaxis, :] - spec_pred["expected_pca"])/spec_pred["expected_pca_unc"], axis=1)
+ fig = plt.figure(figsize=(12, 8))
+ gs = GridSpec(1, 1)
+ ax = fig.add_subplot(gs[0, 0])
+ sns.kdeplot(data={f"Dim. {k}": res_prepca[:, k] for k in range(res_prepca.shape[1])}, linewidth=3, ax=ax)
+ ax.set(title=f"",
+ xlabel=r"residue/uncertainty [a.u.]",
+ ylabel="Counts [a.u.]",
+ xlim=(-3, 3),
+ )
+ fig.savefig(os.path.join(args.directory, "res_prepca.png"))
+ plt.close(fig)
+
fig = plt.figure(figsize=(12, 8))
gs = GridSpec(1, 1)
ax = fig.add_subplot(gs[0, 0])
- sns.kdeplot(x=xgm_flux_t[:,0], ax=ax)
+ sns.histplot(x=xgm_flux_t[:,0], kde=True, linewidth=3, ax=ax)
ax.set(title=f"",
xlabel="XGM intensity [uJ]",
- ylabel="Density [a.u.]",
+ ylabel="Counts [a.u.]",
)
- ax.text(0.90, 0.95, fr"$\mu = ${np.mean(xgm_flux_t[:,0]):.2f}",
- verticalalignment='top', horizontalalignment='right',
- transform=ax.transAxes,
- color='black', fontsize=15)
- ax.text(0.90, 0.90, fr"$\sigma = ${np.std(xgm_flux_t[:,0]):.2f}",
- verticalalignment='top', horizontalalignment='right',
- transform=ax.transAxes,
- color='black', fontsize=15)
+ #ax.text(0.90, 0.95, fr"$\mu = ${np.mean(xgm_flux_t[:,0]):.2f}",
+ # verticalalignment='top', horizontalalignment='right',
+ # transform=ax.transAxes,
+ # color='black', fontsize=15)
+ #ax.text(0.90, 0.90, fr"$\sigma = ${np.std(xgm_flux_t[:,0]):.2f}",
+ # verticalalignment='top', horizontalalignment='right',
+ # transform=ax.transAxes,
+ # color='black', fontsize=15)
+ plt.tight_layout()
fig.savefig(os.path.join(args.directory, "intensity.png"))
plt.close(fig)
@@ -422,20 +495,19 @@ def main():
fig = plt.figure(figsize=(12, 8))
gs = GridSpec(1, 1)
ax = fig.add_subplot(gs[0, 0])
- sns.kdeplot(x=rmse, ax=ax)
+ sns.histplot(x=rmse, kde=True, linewidth=3, ax=ax)
ax.set(title=f"",
xlabel="Root-mean-squared error",
- ylabel="Density [a.u.]",
- xlim=(0, 20),
+ ylabel="Counts [a.u.]",
)
- ax.text(0.90, 0.95, fr"$\mu = ${np.mean(rmse):.2f}",
- verticalalignment='top', horizontalalignment='right',
- transform=ax.transAxes,
- color='black', fontsize=15)
- ax.text(0.90, 0.90, fr"$\sigma = ${np.std(rmse):.2f}",
- verticalalignment='top', horizontalalignment='right',
- transform=ax.transAxes,
- color='black', fontsize=15)
+ #ax.text(0.90, 0.95, fr"$\mu = ${np.mean(rmse):.2f}",
+ # verticalalignment='top', horizontalalignment='right',
+ # transform=ax.transAxes,
+ # color='black', fontsize=15)
+ #ax.text(0.90, 0.90, fr"$\sigma = ${np.std(rmse):.2f}",
+ # verticalalignment='top', horizontalalignment='right',
+ # transform=ax.transAxes,
+ # color='black', fontsize=15)
fig.savefig(os.path.join(args.directory, "rmse.png"))
plt.close(fig)
--
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