Skip to content

Unify save methods #180

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
StephenNneji merged 10 commits into from
Sep 18, 2025
Merged

Unify save methods #180

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
e9208d1
Unify save method for controls
StephenNneji Sep 8, 2025
62df2a9
Fixes for plots popping up in RasCAL
StephenNneji Sep 10, 2025
3211841
Fixing build
StephenNneji Sep 11, 2025
b939441
Fix ruff version
StephenNneji Sep 11, 2025
f0f9dee
fix
StephenNneji Sep 11, 2025
53c2618
fix
StephenNneji Sep 11, 2025
eb88023
Adds progress callback to corner plot and updates example to use scipy
StephenNneji Sep 15, 2025
ad2ac56
enable openmp windows
StephenNneji Sep 17, 2025
ffc53ca
Addresses review comments
StephenNneji Sep 17, 2025
3e87bf1
refactors makeLayer in example
StephenNneji Sep 18, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Adds progress callback to corner plot and updates example to use scipy
  • Loading branch information
@StephenNneji
StephenNneji committed Sep 15, 2025
commit eb88023ff510cf0803be8acb73fd4d577b9ee932
9 changes: 4 additions & 5 deletions ratapi/examples/normal_reflectivity/custom_XY_DSPC.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,7 @@
"""A custom XY model for a supported DSPC bilayer."""

import math

import numpy as np
from scipy.special import erf


def custom_XY_DSPC(params, bulk_in, bulk_out, contrast):
Expand Down Expand Up @@ -114,7 +113,7 @@ def custom_XY_DSPC(params, bulk_in, bulk_out, contrast):
totSLD = sldSilicon + sldOxide + sldHeadL + sldTails + sldHeadR + sldWat

# Make the SLD array for output
SLD = [[a, b] for (a, b) in zip(z, totSLD)]
SLD = np.column_stack((z, totSLD))

return SLD, subRough

Expand All @@ -132,8 +131,8 @@ def layer(z, prevLaySurf, thickness, height, Sigma_L, Sigma_R):
a = (z - left) / ((2**0.5) * Sigma_L)
b = (z - right) / ((2**0.5) * Sigma_R)

erf_a = np.array([math.erf(value) for value in a])
erf_b = np.array([math.erf(value) for value in b])
erf_a = erf(a)
erf_b = erf(b)

VF = np.array((height / 2) * (erf_a - erf_b))
Comment thread
StephenNneji marked this conversation as resolved.
Outdated

Expand Down
25 changes: 16 additions & 9 deletions ratapi/utils/plotting.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -652,6 +652,7 @@ def plot_corner(
return_fig: bool = False,
hist_kwargs: Union[dict, None] = None,
hist2d_kwargs: Union[dict, None] = None,
progress_callback: Union[Callable[[int, int], None], None] = None,
):
"""Create a corner plot from a Bayesian analysis.

Expand Down Expand Up @@ -697,29 +698,32 @@ def plot_corner(
hist2d_kwargs = {}

num_params = len(params)
total_count = num_params + (num_params**2 - num_params) // 2

if fig is None:
fig, axes = plt.subplots(num_params, num_params, figsize=(11, 10))
fig, axes = plt.subplots(num_params, num_params, figsize=(11, 10), subplot_kw={"visible": False})
else:
fig.clf()
axes = fig.subplots(num_params, num_params)
axes = fig.subplots(num_params, num_params, subplot_kw={"visible": False})

# i is row, j is column
for i, row_param in enumerate(params):
for j, col_param in enumerate(params):
current_axes: Axes = axes[i][j]
current_count = 0
for i in range(num_params):
for j in range(i + 1):
row_param = params[i]
col_param = params[j]
current_axes: Axes = axes if isinstance(axes, matplotlib.axes.Axes) else axes[i][j]
current_axes.tick_params(which="both", labelsize="medium")
current_axes.xaxis.offsetText.set_fontsize("small")
current_axes.yaxis.offsetText.set_fontsize("small")

current_axes.set_visible(True)
if i == j: # diagonal: histograms
plot_one_hist(results, param=row_param, smooth=smooth, axes=current_axes, **hist_kwargs)
elif i > j: # lower triangle: 2d histograms
plot_contour(
results, x_param=col_param, y_param=row_param, smooth=smooth, axes=current_axes, **hist2d_kwargs
)
elif i < j: # upper triangle: no plot
current_axes.set_visible(False)

# remove label if on inside of corner plot
if j != 0:
current_axes.get_yaxis().set_visible(False)
Expand All @@ -732,6 +736,9 @@ def plot_corner(
current_axes.yaxis.offset_text_position = "center"
current_axes.set_ylabel("")
current_axes.set_xlabel("")
if progress_callback is not None:
current_count += 1
progress_callback(current_count, total_count)
if return_fig:
return fig
plt.show(block=block)
Expand Down Expand Up @@ -1153,7 +1160,7 @@ def plot_chain(

"""
chain = results.chain
nsimulations, nplots = chain.shape
nsimulations, _ = chain.shape
# skip is to evenly distribute points plotted
# all points will be plotted if maxpoints < nsimulations
skip = max(floor(nsimulations / maxpoints), 1)
Expand Down