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Add align profile and quick Bayesian exit #212

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1ce731d
Adds function to align profiles
StephenNneji Jun 26, 2026
27a5b06
Update cpp and fix bug with blitting support
StephenNneji Jul 13, 2026
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2 changes: 1 addition & 1 deletion cpp/RAT
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Submodule RAT updated 68 files
+438 −434 DREAM.cpp
+3 −3 DREAM.h
+2 −2 DREAMWrapper.cpp
+1 −1 DREAMWrapper.h
+529 −702 RATMain.cpp
+53 −39 RATMain_internal_types.h
+111 −0 RATMain_rtwutil.cpp
+15 −0 RATMain_rtwutil.h
+80 −64 RATMain_types.h
+174 −0 alignALProfiles.cpp
+31 −0 alignALProfiles.h
+21 −0 allOrAny.cpp
+1 −0 allOrAny.h
+33 −0 any1.cpp
+30 −0 any1.h
+0 −171 asymconvstep.cpp
+0 −31 asymconvstep.h
+2 −2 boundaryHandling.cpp
+2 −2 calcLogLikelihood.cpp
+2 −2 calcLogLikelihood.h
+7 −5 deopt.cpp
+2 −2 deopt.h
+45 −45 domainsReflectivity.cpp
+2 −2 domainsReflectivity.h
+0 −43 eml_mtimes_helper.cpp
+0 −5 eml_mtimes_helper.h
+35 −0 erfcinv.cpp
+29 −0 erfcinv.h
+6 −2 fMinSearch.cpp
+4 −4 fMinSearch.h
+5 −6 groupLayersMod.cpp
+6 −6 initializeDREAM.cpp
+4 −4 initializeDREAM.h
+158 −157 makeEmptyBayesResultsStruct.cpp
+497 −0 makeEmptyResultStruct.cpp
+37 −0 makeEmptyResultStruct.h
+405 −207 makeSLDProfile.cpp
+5 −5 makeSLDProfile.h
+1 −1 mchol.cpp
+67 −12 minOrMax.cpp
+4 −3 minOrMax.h
+19 −26 nest2pos.cpp
+341 −332 nestedSampler.cpp
+21 −21 normalReflectivity.cpp
+2 −2 normalReflectivity.h
+1 −1 nsIntraFun.cpp
+25 −9 processBayes.cpp
+7 −5 processBayes.h
+1 −436 refPercentileConfidenceIntervals.cpp
+0 −6 refPercentileConfidenceIntervals.h
+9 −9 reflectivityCalculation.cpp
+2 −2 reflectivityCalculation.h
+33 −9 repmat.cpp
+3 −1 repmat.h
+3 −3 runDE.cpp
+251 −158 runDREAM.cpp
+26 −6 runDREAM.h
+304 −239 runNestedSampler.cpp
+25 −22 runNestedSampler.h
+3 −3 runSimplex.cpp
+1 −1 setupDREAM.cpp
+2 −2 setupDREAM.h
+1 −1 simplexIntrafun.cpp
+23 −21 splitEllipsoid.cpp
+85 −0 structConstructorHelper.cpp
+11 −0 structConstructorHelper.h
+123 −63 triggerEvent.cpp
+7 −9 triggerEvent.h
84 changes: 69 additions & 15 deletions ratapi/utils/plotting.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,7 @@ def _extract_plot_data(event_data: PlotEventData, q4: bool, show_error_bar: bool
# Plot the reflectivity on plot (1,1)
results["ref"].append([r[:, 0], r[:, 1] * mult])

results["error"].append([])
if event_data.dataPresent[i]:
sd_x = data[:, 0]
sd_y, sd_e = map(lambda x: x * mult, (data[:, 1], data[:, 2]))
Expand All @@ -73,7 +74,7 @@ def _extract_plot_data(event_data: PlotEventData, q4: bool, show_error_bar: bool
valid = np.ones(len(sd_e)).astype(bool)
sd_e = errors

results["error"].append([sd_x[valid], sd_y[valid], sd_e[valid]])
results["error"][-1].extend([sd_x[valid], sd_y[valid], sd_e[valid]])

results["sld"].append([])
for j in range(len(sld)):
Expand Down Expand Up @@ -111,6 +112,7 @@ def plot_ref_sld_helper(
show_legend: bool = True,
shift_value: float = 100,
animated=False,
align_profile=False,
):
"""Clear the previous plots and updates the ref and SLD plots.

Expand Down Expand Up @@ -160,6 +162,8 @@ def plot_ref_sld_helper(
ref_plot.cla()
sld_plot.cla()

if align_profile:
_align_profiles(data, confidence_intervals)
plot_data = _extract_plot_data(data, q4, show_error_bar, shift_value)
for i, name in enumerate(data.contrastNames):
ref_plot.plot(plot_data["ref"][i][0], plot_data["ref"][i][1], label=name, linewidth=1, animated=animated)
Expand Down Expand Up @@ -234,6 +238,54 @@ def plot_ref_sld_helper(
plt.pause(0.005)


def _align_profiles(data: PlotEventData, confidence_intervals: dict | None = None):
"""Align SLD profiles and resampled layers.

Aligns the A/L SLD profiles so that the substrates line up by padding the
start of any shorter than the longest profile.

Parameters
----------
data : PlotEventData
The plot event data that contains all the information
to generate the ref and sld plots
confidence_intervals : dict or None, default None
The Bayesian confidence intervals for reflectivity and SLD.
Only relevant if the procedure used is Bayesian (NS or DREAM)
"""
slds = data.sldProfiles
size = (len(slds), len(slds[0]))

# Find the length of the longest profile.
lengths = [[sld.shape[0] for sld in sld_row] for sld_row in slds]
max_value = np.max(lengths)
max_index = np.unravel_index(np.argmax(lengths), shape=size)

max_x = slds[max_index[0]][max_index[1]][:, 0]
max_x_value = max_x[-1]

for i in range(size[0]):
for j in range(size[1]):
cur_sld = slds[i][j]
diff = max_value - cur_sld.shape[0]
if diff:
pad = np.zeros(diff)
max_y = np.concatenate((pad, cur_sld[:, 1]))
slds[i][j] = np.column_stack((max_x, max_y))

cur_resample_layer = data.resampledLayers[i][j]
if not np.all(cur_resample_layer):
total_length = sum(cur_resample_layer[:, 0])
offset = max_x_value - total_length
data.resampledLayers[i][j] = np.vstack(([offset, 0, 0], cur_resample_layer))

if confidence_intervals is not None:
cur_ci = confidence_intervals["sld"][i][j]
inter_a = np.concatenate((pad, cur_ci[0]))
inter_b = np.concatenate((pad, cur_ci[1]))
confidence_intervals["sld"][i][j] = (inter_a, inter_b)


def plot_ref_sld(
project: ratapi.Project,
results: ratapi.outputs.Results | ratapi.outputs.BayesResults,
Expand Down Expand Up @@ -294,7 +346,7 @@ def plot_ref_sld(
data.reflectivity = copy.deepcopy(results.reflectivity)
data.shiftedData = results.shiftedData
data.sldProfiles = copy.deepcopy(results.sldProfiles)
data.resampledLayers = results.resampledLayers
data.resampledLayers = copy.deepcopy(results.resampledLayers)
data.dataPresent = ratapi.inputs.make_data_present(project)
data.subRoughs = results.contrastParams.subRoughs
data.resample = ratapi.inputs.make_resample(project)
Expand Down Expand Up @@ -355,6 +407,7 @@ def plot_ref_sld(
show_grid=show_grid,
show_legend=show_legend,
shift_value=shift_value,
align_profile=(project.geometry == "air/substrate" and project.model != "custom xy"),
)

if return_fig:
Expand Down Expand Up @@ -533,13 +586,12 @@ def update_foreground(self, data):
self.figure.canvas.restore_region(self.bg)
plot_data = _extract_plot_data(data, self.q4, self.show_error_bar, self.shift_value)

offset = 2
for i in range(
0,
len(self.figure.axes[0].lines),
):
self.figure.axes[0].lines[i].set_data(plot_data["ref"][i // offset][0], plot_data["ref"][i // offset][1])
self.figure.axes[0].draw_artist(self.figure.axes[0].lines[i])
offset = 0
for i in range(len(data.contrastNames)):
for _ in range(int(data.dataPresent[i]) + 1):
self.figure.axes[0].lines[offset].set_data(plot_data["ref"][i][0], plot_data["ref"][i][1])
self.figure.axes[0].draw_artist(self.figure.axes[0].lines[offset])
offset += 1

i = 0
for j in range(len(plot_data["sld"])):
Expand All @@ -553,12 +605,14 @@ def update_foreground(self, data):
self.figure.axes[1].draw_artist(self.figure.axes[1].lines[i])
i += 1

for i, container in enumerate(self.figure.axes[0].containers):
self.adjust_error_bar(
container, plot_data["error"][i][0], plot_data["error"][i][1], plot_data["error"][i][2]
)
self.figure.axes[0].draw_artist(container[2][0])
self.figure.axes[0].draw_artist(container[0])
i = 0
for error in plot_data["error"]:
if error:
container = self.figure.axes[0].containers[i]
self.adjust_error_bar(container, error[0], error[1], error[2])
self.figure.axes[0].draw_artist(container[2][0])
self.figure.axes[0].draw_artist(container[0])
i += 1

self.figure.canvas.blit(self.figure.bbox)
self.figure.canvas.flush_events()
Expand Down
7 changes: 6 additions & 1 deletion tests/test_plotting.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -204,9 +204,14 @@ def test_plot_ref_sld(mock: MagicMock, input_project, reflectivity_calculation_r
for sld, sld_results in zip(sldProfile, result_sld_profile, strict=False):
assert (sld == sld_results).all()

for resampledLayers, reflectivity_results in zip(
data.resampledLayers, reflectivity_calculation_results.resampledLayers, strict=False
):
for resam, resam_results in zip(resampledLayers, reflectivity_results, strict=False):
assert (resam == resam_results).all()

assert data.modelType == input_project.model
assert data.shiftedData == reflectivity_calculation_results.shiftedData
assert data.resampledLayers == reflectivity_calculation_results.resampledLayers
assert data.dataPresent.size == 0
assert (data.subRoughs == reflectivity_calculation_results.contrastParams.subRoughs).all()
assert data.resample.size == 0
Expand Down
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