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fixing phase map plots #730

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Merged
smribet merged 2 commits into from
Aug 22, 2025
Merged

fixing phase map plots #730

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d65ffda
fixing phase map plots
cophus Aug 22, 2025
2c5a913
black formatting
cophus Aug 22, 2025
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73 changes: 57 additions & 16 deletions py4DSTEM/process/diffraction/crystal_phase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -966,8 +966,8 @@ def plot_phase_weights(
if total_intensity_normalize:
sub = self.int_total > 0.0
for a0 in range(self.num_fits):
phase_weights[:, :, a0][sub] /= self.int_total[sub]
phase_residuals[sub] /= self.int_total[sub]
phase_weights[:, :, a0][sub] /= self.int_total[sub] + 1e-12
phase_residuals[sub] /= self.int_total[sub] + 1e-12

# intensity range for plotting
if weight_normalize:
Expand Down Expand Up @@ -1112,7 +1112,7 @@ def plot_phase_maps(
if total_intensity_normalize:
sub = self.int_total > 0.0
for a0 in range(self.num_fits):
phase_weights[:, :, a0][sub] /= self.int_total[sub]
phase_weights[:, :, a0][sub] /= self.int_total[sub] + 1e-12

# intensity range for plotting
if weight_normalize:
Expand Down Expand Up @@ -1228,7 +1228,8 @@ def plot_phase_maps(
def plot_dominant_phase(
self,
use_correlation_scores=False,
reliability_range=(0.0, 1.0),
reliability_range=None,
correlation_range=None,
normalize_exp_intensity=True,
sigma=0.0,
phase_colors=None,
Expand All @@ -1248,7 +1249,9 @@ def plot_dominant_phase(
use_correlation_scores: bool
Set to True to use correlation scores instead of reliabiltiy from intensity residuals.
reliability_range: (float, float)
Plotting intensity range
Plotting intensity range from reliability
correlation_range: (float, float)
Plotting intensity range from correlation score
sigma: float
Smoothing in units of probe position.
phase_colors: np.array
Expand Down Expand Up @@ -1323,16 +1326,40 @@ def plot_dominant_phase(
sub = phase_sig[a0] > phase_corr
phase_map[sub] = a0
phase_corr[sub] = phase_sig[a0][sub]
self.phase_corr_total = np.sum(phase_corr, axis=0)

if self.single_phase:
phase_scale = np.clip(
(self.phase_reliability - reliability_range[0])
/ (reliability_range[1] - reliability_range[0]),
0,
1,
phase_scale = np.ones(
(
self.phase_sig.shape[1],
self.phase_sig.shape[2],
)
)
# if self.single_phase:
# if reliability_range is not None:
# phase_scale *= np.clip(
# (self.phase_reliability - reliability_range[0])
# / (reliability_range[1] - reliability_range[0]),
# 0,
# 1,
# )
# if correlation_range is not None:
# phase_scale *= np.clip(
# (self.phase_corr_total - correlation_range[0])
# / (correlation_range[1] - correlation_range[0]),
# 0,
# 1,
# )

# phase_scale = np.clip(
# (self.phase_reliability - reliability_range[0])
# / (reliability_range[1] - reliability_range[0]),
# 0,
# 1,
# )

# else:
if not self.single_phase:

else:
# find the second correlation score for each crystal and match index
for a0 in range(self.num_crystals):
corr = phase_sig[a0].copy()
Expand All @@ -1345,14 +1372,28 @@ def plot_dominant_phase(

# normalize the reliability by the intensity of each experimental pattern
if normalize_exp_intensity:
phase_rel /= self.int_total

phase_scale = np.clip(
(phase_rel - reliability_range[0])
phase_rel /= self.int_total + 1e-12

# phase_scale = np.clip(
# (phase_rel - reliability_range[0])
# / (reliability_range[1] - reliability_range[0]),
# 0,
# 1,
# )
if reliability_range is not None:
phase_scale *= np.clip(
(self.phase_reliability - reliability_range[0])
/ (reliability_range[1] - reliability_range[0]),
0,
1,
)
if correlation_range is not None:
phase_scale *= np.clip(
(self.phase_corr_total - correlation_range[0])
/ (correlation_range[1] - correlation_range[0]),
0,
1,
)

# Print the total area of fraction of each phase
if print_fractions:
Expand Down