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Merged
alexhroom merged 1 commit into from
Nov 1, 2024
Merged

Plots no longer use x-data #84

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4 changes: 0 additions & 4 deletions RATapi/outputs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -101,8 +101,6 @@ def __str__(self):
class PredictionIntervals(RATResult):
reflectivity: list
sld: list
reflectivityXData: list
sldXData: list
sampleChi: np.ndarray


Expand Down Expand Up @@ -189,8 +187,6 @@ def make_results(
prediction_intervals = PredictionIntervals(
reflectivity=bayes_results.predictionIntervals.reflectivity,
sld=bayes_results.predictionIntervals.sld,
reflectivityXData=bayes_results.predictionIntervals.reflectivityXData,
sldXData=bayes_results.predictionIntervals.sldXData,
sampleChi=bayes_results.predictionIntervals.sampleChi,
)

Expand Down
13 changes: 3 additions & 10 deletions RATapi/utils/plotting.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -118,10 +118,8 @@ def plot_ref_sld_helper(
# Plot confidence intervals if required
if confidence_intervals is not None:
ref_min, ref_max = confidence_intervals["reflectivity"][i]
# FIXME: remove x-data once rascalsoftware/RAT#249 is merged
ref_x_data = confidence_intervals["reflectivity-x-data"][i][0]
mult = (1 if not q4 else ref_x_data**4) / div
ref_plot.fill_between(ref_x_data, ref_min * mult, ref_max * mult, alpha=0.6, color="grey")
mult = (1 if not q4 else r[:, 0] ** 4) / div
ref_plot.fill_between(r[:, 0], ref_min / div, ref_max / div, alpha=0.6, color="grey")

if data.dataPresent[i]:
sd_x = sd[:, 0]
Expand All @@ -146,9 +144,7 @@ def plot_ref_sld_helper(
# Plot confidence intervals if required
if confidence_intervals is not None:
sld_min, sld_max = confidence_intervals["sld"][i][j]
# FIXME: remove x-data once rascalsoftware/RAT#249 is merged
sld_x_data = confidence_intervals["sld-x-data"][i][j][0]
sld_plot.fill_between(sld_x_data, sld_min, sld_max, alpha=0.6, color="grey")
sld_plot.fill_between(sld[j][:, 0], sld_min, sld_max, alpha=0.6, color="grey")

if data.resample[i] == 1 or data.modelType == "custom xy":
layers = data.resampledLayers[i][0]
Expand Down Expand Up @@ -278,9 +274,6 @@ def plot_ref_sld(
[(sld_inter[interval[0]], sld_inter[interval[1]]) for sld_inter in sld]
for sld in results.predictionIntervals.sld
],
# FIXME: remove x-data once rascalsoftware/RAT#249 is merged
"reflectivity-x-data": results.predictionIntervals.reflectivityXData,
"sld-x-data": results.predictionIntervals.sldXData,
}
else:
raise ValueError(
Expand Down
2 changes: 1 addition & 1 deletion cpp/RAT
Open in desktop
Submodule RAT updated 99 files
+1 −1 DREAMWrapper.cpp
+2 −2 DREAMWrapper.h
+3 −5 RATMain.cpp
+23 −25 RATMain_internal_types.h
+1 −1 RATMain_rtwutil.cpp
+1 −1 RATMain_rtwutil.h
+4 −11 RATMain_types.h
+144 −27 SLDFunction.cpp
+2 −0 SLDFunction.h
+608 −86 adaptive.cpp
+4 −2 adaptive.h
+5 −4 allocateLayersForContrast.cpp
+2 −2 allocateLayersForContrast.h
+6 −3 allocateParamsToLayers.cpp
+2 −2 allocateParamsToLayers.h
+11 −25 coreLayersCalculation.cpp
+78 −66 customLayers.cpp
+3 −3 customLayers.h
+38 −71 customLayers1.cpp
+3 −3 customLayers1.h
+92 −65 customXY.cpp
+3 −3 customXY.h
+67 −40 customXY1.cpp
+3 −3 customXY1.h
+418 −96 deopt.cpp
+2 −2 deopt.h
+1 −1 drawMCMC.cpp
+2 −2 drawMCMC.h
+1 −1 drawMultiNest.cpp
+2 −2 drawMultiNest.h
+1 −1 evaluateModel.cpp
+2 −2 evaluateModel.h
+1 −1 fMinSearch.cpp
+2 −2 fMinSearch.h
+10 −17 find.cpp
+3 −3 find.h
+2 −2 flip.cpp
+0 −5 groupLayersMod.cpp
+6 −13 groupLayersModImaginary.cpp
+1 −3 initializeDREAM.cpp
+2 −2 initializeDREAM.h
+13 −1 interp1.cpp
+16 −52 makeCell.cpp
+4 −9 makeCell.h
+16 −96 makeEmptyBayesResultsStruct.cpp
+2 −7 makeEmptyBayesResultsStruct.h
+8 −10 makeSLDProfileXY.cpp
+5 −5 mergesort.cpp
+1 −1 mergesort.h
+1 −1 nestedSampler.cpp
+2 −2 nestedSampler.h
+2 −2 nsIntraFun.cpp
+3 −3 nsIntraFun.h
+3 −2 processBayes.cpp
+2 −2 processBayes.h
+5 −37 processCustomFunction.cpp
+2 −2 processCustomFunction.h
+5 −36 processCustomFunction1.cpp
+2 −2 processCustomFunction1.h
+1 −2 processCustomFunction2.cpp
+2 −2 processCustomFunction2.h
+8 −39 processCustomFunction3.cpp
+2 −2 processCustomFunction3.h
+1 −1 ratDREAM.cpp
+2 −2 ratDREAM.h
+169 −214 refPercentileConfidenceIntervals.cpp
+5 −4 refPercentileConfidenceIntervals.h
+112 −157 reflectivityCalculation.cpp
+3 −3 reflectivityCalculation.h
+2 −2 reflectivityCalculation1.cpp
+3 −3 reflectivityCalculation1.h
+2 −2 reflectivityCalculation2.cpp
+3 −3 reflectivityCalculation2.h
+46 −1 resampleLayers.cpp
+3 −0 resampleLayers.h
+1 −1 resampleLayersReIm.cpp
+8 −15 runDE.cpp
+3 −3 runDE.h
+1 −30 runDREAM.cpp
+2 −2 runDREAM.h
+31 −65 runNestedSampler.cpp
+2 −2 runNestedSampler.h
+1 −1 runSimplex.cpp
+2 −2 runSimplex.h
+1 −1 simplexIntrafun.cpp
+2 −2 simplexIntrafun.h
+3 −3 sortIdx.cpp
+2 −2 sortIdx.h
+7 −7 sortLE.cpp
+4 −4 sortLE.h
+2 −23 sortrows.cpp
+2 −1 sortrows.h
+10 −23 standardLayers.cpp
+3 −3 standardLayers.h
+383 −376 standardLayers1.cpp
+3 −3 standardLayers1.h
+8 −28 structConstructorHelper.cpp
+6 −12 structConstructorHelper.h
+6 −6 triggerEvent.cpp
6 changes: 0 additions & 6 deletions cpp/rat.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -302,8 +302,6 @@ struct PredictionIntervals
{
py::list reflectivity;
py::list sld;
py::list reflectivityXData;
py::list sldXData;
py::array_t<real_T> sampleChi;
};

Expand Down Expand Up @@ -1160,8 +1158,6 @@ BayesResults bayesResultsFromStruct8T(const RAT::struct8_T results)

bayesResults.predictionIntervals.reflectivity = pyList1DFromRatCellWrap<coder::array<RAT::cell_wrap_11, 1U>>(results.predictionIntervals.reflectivity);
bayesResults.predictionIntervals.sld = pyList2dFromRatCellWrap<coder::array<RAT::cell_wrap_11, 2U>>(results.predictionIntervals.sld);
bayesResults.predictionIntervals.reflectivityXData = pyList1DFromRatCellWrap<coder::array<RAT::cell_wrap_12, 1U>>(results.predictionIntervals.reflectivityXData);
bayesResults.predictionIntervals.sldXData = pyList2dFromRatCellWrap<coder::array<RAT::cell_wrap_12, 2U>>(results.predictionIntervals.sldXData);
bayesResults.predictionIntervals.sampleChi = pyArray1dFromBoundedArray<coder::bounded_array<real_T, 1000U, 1U>>(results.predictionIntervals.sampleChi);

bayesResults.confidenceIntervals.percentile95 = pyArrayFromRatArray2d(results.confidenceIntervals.percentile95);
Expand Down Expand Up @@ -1283,8 +1279,6 @@ PYBIND11_MODULE(rat_core, m) {
.def(py::init<>())
.def_readwrite("reflectivity", &PredictionIntervals::reflectivity)
.def_readwrite("sld", &PredictionIntervals::sld)
.def_readwrite("reflectivityXData", &PredictionIntervals::reflectivityXData)
.def_readwrite("sldXData", &PredictionIntervals::sldXData)
.def_readwrite("sampleChi", &PredictionIntervals::sampleChi);

py::class_<PlotEventData>(m, "PlotEventData")
Expand Down
264 changes: 0 additions & 264 deletions tests/conftest.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1778,138 +1778,6 @@ def dream_bayes():
),
],
]
bayes.predictionIntervals.reflectivityXData = [
np.array(
[
[
0.011403,
0.013861,
0.016848,
0.020479,
0.024892,
0.030256,
0.036777,
0.044702,
0.054336,
0.066045,
0.080279,
0.097579,
0.11861,
0.14417,
0.17524,
0.213,
0.25891,
0.3147,
0.38252,
0.46496,
0.56516,
],
],
),
np.array(
[
[
0.011403,
0.013861,
0.016848,
0.020479,
0.024892,
0.030256,
0.036777,
0.044702,
0.054336,
0.066045,
0.080279,
0.097579,
0.11861,
0.14417,
0.17524,
0.213,
0.25891,
0.3147,
0.38252,
0.46496,
0.56516,
],
],
),
]
bayes.predictionIntervals.sldXData = [
[
np.array(
[
[
0.0,
11.0,
22.0,
33.0,
44.0,
55.0,
66.0,
77.0,
88.0,
99.0,
110.0,
121.0,
132.0,
143.0,
154.0,
165.0,
176.0,
187.0,
198.0,
209.0,
220.0,
231.0,
242.0,
253.0,
264.0,
275.0,
286.0,
297.0,
308.0,
319.0,
],
],
),
np.array(
[
[
0.0,
11.0,
22.0,
33.0,
44.0,
55.0,
66.0,
77.0,
88.0,
99.0,
110.0,
121.0,
132.0,
143.0,
154.0,
165.0,
176.0,
187.0,
198.0,
209.0,
220.0,
231.0,
242.0,
253.0,
264.0,
275.0,
286.0,
297.0,
308.0,
319.0,
],
],
),
],
]
bayes.predictionIntervals.sampleChi = np.array(
[
1.46133559e16,
Expand Down Expand Up @@ -4050,138 +3918,6 @@ def dream_results():
),
]
],
reflectivityXData=[
np.array(
[
[
0.011403,
0.013861,
0.016848,
0.020479,
0.024892,
0.030256,
0.036777,
0.044702,
0.054336,
0.066045,
0.080279,
0.097579,
0.118610,
0.144170,
0.175240,
0.213000,
0.258910,
0.314700,
0.382520,
0.464960,
0.565160,
],
],
),
np.array(
[
[
0.011403,
0.013861,
0.016848,
0.020479,
0.024892,
0.030256,
0.036777,
0.044702,
0.054336,
0.066045,
0.080279,
0.097579,
0.118610,
0.144170,
0.175240,
0.213000,
0.258910,
0.314700,
0.382520,
0.464960,
0.565160,
],
],
),
],
sldXData=[
[
np.array(
[
[
0.0,
11.0,
22.0,
33.0,
44.0,
55.0,
66.0,
77.0,
88.0,
99.0,
110.0,
121.0,
132.0,
143.0,
154.0,
165.0,
176.0,
187.0,
198.0,
209.0,
220.0,
231.0,
242.0,
253.0,
264.0,
275.0,
286.0,
297.0,
308.0,
319.0,
],
],
),
np.array(
[
[
0.0,
11.0,
22.0,
33.0,
44.0,
55.0,
66.0,
77.0,
88.0,
99.0,
110.0,
121.0,
132.0,
143.0,
154.0,
165.0,
176.0,
187.0,
198.0,
209.0,
220.0,
231.0,
242.0,
253.0,
264.0,
275.0,
286.0,
297.0,
308.0,
319.0,
],
],
),
],
],
sampleChi=np.array(
[
1.46133559e16,
Expand Down
2 changes: 0 additions & 2 deletions tests/test_outputs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -86,8 +86,6 @@ def dream_str():
"predictionIntervals = PredictionIntervals(\n"
"\treflectivity = [Data array: [5 x 21], Data array: [5 x 21]],\n"
"\tsld = [[Data array: [5 x 30], Data array: [5 x 30]]],\n"
"\treflectivityXData = [Data array: [1 x 21], Data array: [1 x 21]],\n"
"\tsldXData = [[Data array: [1 x 30], Data array: [1 x 30]]],\n"
"\tsampleChi = Data array: [1000],\n"
"),\n"
"confidenceIntervals = ConfidenceIntervals(\n"
Expand Down
2 changes: 0 additions & 2 deletions tests/test_plotting.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -68,8 +68,6 @@ def bayes_fig(request) -> plt.figure:
[(curve[:, 1] - curve[:, 1] * 0.1, curve[:, 1] + curve[:, 1] * 0.1) for curve in sld]
for sld in dat.sldProfiles
],
"reflectivity-x-data": [[curve[:, 0]] for curve in dat.reflectivity],
"sld-x-data": [[[profile[:, 0]] for profile in sld] for sld in dat.sldProfiles],
}
return RATplot.plot_ref_sld_helper(data=dat, fig=figure, confidence_intervals=confidence_intervals)

Expand Down
4 changes: 2 additions & 2 deletions tests/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -116,15 +116,15 @@ def check_bayes_fields_equal(actual_results, expected_results) -> None:
}

list_fields = {
"predictionIntervals": ["reflectivity", "reflectivityXData"],
"predictionIntervals": ["reflectivity"],
"confidenceIntervals": [],
"dreamParams": [],
"dreamOutput": [],
"nestedSamplerOutput": [],
}

double_list_fields = {
"predictionIntervals": ["sld", "sldXData"],
"predictionIntervals": ["sld"],
"confidenceIntervals": [],
"dreamParams": [],
"dreamOutput": [],
Expand Down