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DrPaulSharpDrPaulSharp
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Modifies data for shaded plots to use the centre of the Bayes distribution (#114)
* Changes bayes plots to use mean reflectivity and SLD * Updates tests * Bug fix in q4 shaded plot * Addresses review comment
1 parent 92c6d67 commit b1a0e44

5 files changed

Lines changed: 34 additions & 28 deletions

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‎RATapi/utils/plotting.py‎

Lines changed: 13 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
11
"""Plots using the matplotlib library"""
22

3+
import copy
34
from functools import partial, wraps
45
from math import ceil, floor, sqrt
56
from statistics import stdev
@@ -119,7 +120,7 @@ def plot_ref_sld_helper(
119120
if confidence_intervals is not None:
120121
ref_min, ref_max = confidence_intervals["reflectivity"][i]
121122
mult = (1 if not q4 else r[:, 0] ** 4) / div
122-
ref_plot.fill_between(r[:, 0], ref_min / div, ref_max / div, alpha=0.6, color="grey")
123+
ref_plot.fill_between(r[:, 0], ref_min * mult, ref_max * mult, alpha=0.6, color="grey")
123124

124125
if data.dataPresent[i]:
125126
sd_x = sd[:, 0]
@@ -241,10 +242,13 @@ def plot_ref_sld(
241242
"""
242243
data = PlotEventData()
243244

245+
# We need to take a copy of reflectivity and SLD in case we are plotting a
246+
# shaded plot and will therefore change the plotted data to that from the
247+
# centre of the Bayesian distribution
244248
data.modelType = project.model
245-
data.reflectivity = results.reflectivity
249+
data.reflectivity = copy.deepcopy(results.reflectivity)
246250
data.shiftedData = results.shiftedData
247-
data.sldProfiles = results.sldProfiles
251+
data.sldProfiles = copy.deepcopy(results.sldProfiles)
248252
data.resampledLayers = results.resampledLayers
249253
data.dataPresent = RATapi.inputs.make_data_present(project)
250254
data.subRoughs = results.contrastParams.subRoughs
@@ -275,6 +279,12 @@ def plot_ref_sld(
275279
for sld in results.predictionIntervals.sld
276280
],
277281
}
282+
# For a shaded plot, use the mean values from predictionIntervals
283+
for reflectivity, mean_reflectivity in zip(data.reflectivity, results.predictionIntervals.reflectivity):
284+
reflectivity[:, 1] = mean_reflectivity[2]
285+
for sldProfile, mean_sld_profile in zip(data.sldProfiles, results.predictionIntervals.sld):
286+
for sld, mean_sld in zip(sldProfile, mean_sld_profile):
287+
sld[:, 1] = mean_sld[2]
278288
else:
279289
raise ValueError(
280290
"Shaded confidence intervals are only available for the results of Bayesian analysis (NS or DREAM)"

‎cpp/rat.cpp‎

Lines changed: 13 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -995,6 +995,18 @@ py::list pyList1DFromRatCellWrap2D(const T& values)
995995
return result;
996996
}
997997

998+
template <typename T>
999+
py::list pyList1DFromRatCellWrap1D(const T& values)
1000+
{
1001+
py::list result;
1002+
1003+
for (int32_T idx0{0}; idx0 < values.size(0); idx0++) {
1004+
result.append(pyArrayFromRatArray2d(values[idx0].f1));
1005+
}
1006+
1007+
return result;
1008+
}
1009+
9981010
template <typename T>
9991011
py::list pyList2dFromRatCellWrap(const T& values)
10001012
{
@@ -1234,7 +1246,7 @@ BayesResults bayesResultsFromStruct9T(const RAT::struct9_T results)
12341246

12351247
bayesResults.chain = pyArrayFromRatArray2d(results.chain);
12361248

1237-
bayesResults.predictionIntervals.reflectivity = pyList1DFromRatCellWrap2D<coder::array<RAT::cell_wrap_11, 1U>>(results.predictionIntervals.reflectivity);
1249+
bayesResults.predictionIntervals.reflectivity = pyList1DFromRatCellWrap1D<coder::array<RAT::cell_wrap_11, 1U>>(results.predictionIntervals.reflectivity);
12381250
bayesResults.predictionIntervals.sld = pyList2dFromRatCellWrap<coder::array<RAT::cell_wrap_11, 2U>>(results.predictionIntervals.sld);
12391251
bayesResults.predictionIntervals.sampleChi = pyArray1dFromBoundedArray<coder::bounded_array<real_T, 1000U, 1U>>(results.predictionIntervals.sampleChi);
12401252

‎tests/conftest.py‎

Lines changed: 0 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -1827,7 +1827,6 @@ def dream_bayes():
18271827
9.14706158e-07,
18281828
9.14597081e-07,
18291829
9.14576711e-07,
1830-
9.14569865e-07,
18311830
],
18321831
[
18331832
-2.26996619e-06,
@@ -1859,7 +1858,6 @@ def dream_bayes():
18591858
9.14706158e-07,
18601859
9.14597081e-07,
18611860
9.14576711e-07,
1862-
9.14569865e-07,
18631861
],
18641862
[
18651863
-1.50598689e-07,
@@ -1891,7 +1889,6 @@ def dream_bayes():
18911889
3.33756709e-06,
18921890
3.33751126e-06,
18931891
3.33750083e-06,
1894-
3.33749733e-06,
18951892
],
18961893
[
18971894
2.07300000e-06,
@@ -1923,7 +1920,6 @@ def dream_bayes():
19231920
5.87958511e-06,
19241921
5.87958515e-06,
19251922
5.87958515e-06,
1926-
5.87958515e-06,
19271923
],
19281924
[
19291925
2.07300000e-06,
@@ -1955,7 +1951,6 @@ def dream_bayes():
19551951
5.87958511e-06,
19561952
5.87958515e-06,
19571953
5.87958515e-06,
1958-
5.87958515e-06,
19591954
],
19601955
],
19611956
),
@@ -1991,7 +1986,6 @@ def dream_bayes():
19911986
4.65378471e-06,
19921987
4.65378475e-06,
19931988
4.65378475e-06,
1994-
4.65378475e-06,
19951989
],
19961990
[
19971991
-1.35107208e-06,
@@ -2023,7 +2017,6 @@ def dream_bayes():
20232017
4.65378471e-06,
20242018
4.65378475e-06,
20252019
4.65378475e-06,
2026-
4.65378475e-06,
20272020
],
20282021
[
20292022
3.19875093e-07,
@@ -2055,7 +2048,6 @@ def dream_bayes():
20552048
4.92196879e-06,
20562049
4.92248720e-06,
20572050
4.92261931e-06,
2058-
4.92266441e-06,
20592051
],
20602052
[
20612053
2.07300000e-06,
@@ -2087,7 +2079,6 @@ def dream_bayes():
20872079
5.17758173e-06,
20882080
5.17859423e-06,
20892081
5.17885226e-06,
2090-
5.17894035e-06,
20912082
],
20922083
[
20932084
2.07300000e-06,
@@ -2119,7 +2110,6 @@ def dream_bayes():
21192110
5.17758173e-06,
21202111
5.17859423e-06,
21212112
5.17885226e-06,
2122-
5.17894035e-06,
21232113
],
21242114
],
21252115
),
@@ -4140,7 +4130,6 @@ def dream_results():
41404130
9.14706158e-07,
41414131
9.14597081e-07,
41424132
9.14576711e-07,
4143-
9.14569865e-07,
41444133
],
41454134
[
41464135
-2.26996619e-06,
@@ -4172,7 +4161,6 @@ def dream_results():
41724161
9.14706158e-07,
41734162
9.14597081e-07,
41744163
9.14576711e-07,
4175-
9.14569865e-07,
41764164
],
41774165
[
41784166
-1.50598689e-07,
@@ -4204,7 +4192,6 @@ def dream_results():
42044192
3.33756709e-06,
42054193
3.33751126e-06,
42064194
3.33750083e-06,
4207-
3.33749733e-06,
42084195
],
42094196
[
42104197
2.07300000e-06,
@@ -4236,7 +4223,6 @@ def dream_results():
42364223
5.87958511e-06,
42374224
5.87958515e-06,
42384225
5.87958515e-06,
4239-
5.87958515e-06,
42404226
],
42414227
[
42424228
2.07300000e-06,
@@ -4268,7 +4254,6 @@ def dream_results():
42684254
5.87958511e-06,
42694255
5.87958515e-06,
42704256
5.87958515e-06,
4271-
5.87958515e-06,
42724257
],
42734258
]
42744259
),
@@ -4304,7 +4289,6 @@ def dream_results():
43044289
4.65378471e-06,
43054290
4.65378475e-06,
43064291
4.65378475e-06,
4307-
4.65378475e-06,
43084292
],
43094293
[
43104294
-1.35107208e-06,
@@ -4336,7 +4320,6 @@ def dream_results():
43364320
4.65378471e-06,
43374321
4.65378475e-06,
43384322
4.65378475e-06,
4339-
4.65378475e-06,
43404323
],
43414324
[
43424325
3.19875093e-07,
@@ -4368,7 +4351,6 @@ def dream_results():
43684351
4.92196879e-06,
43694352
4.92248720e-06,
43704353
4.92261931e-06,
4371-
4.92266441e-06,
43724354
],
43734355
[
43744356
2.07300000e-06,
@@ -4400,7 +4382,6 @@ def dream_results():
44004382
5.17758173e-06,
44014383
5.17859423e-06,
44024384
5.17885226e-06,
4403-
5.17894035e-06,
44044385
],
44054386
[
44064387
2.07300000e-06,
@@ -4432,7 +4413,6 @@ def dream_results():
44324413
5.17758173e-06,
44334414
5.17859423e-06,
44344415
5.17885226e-06,
4435-
5.17894035e-06,
44364416
],
44374417
]
44384418
),

‎tests/test_outputs.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -85,7 +85,7 @@ def dream_str():
8585
"'Background parameter D2O', 'Background parameter SMW', 'D2O', 'SMW'],\n"
8686
"predictionIntervals = PredictionIntervals(\n"
8787
"\treflectivity = [Data array: [5 x 21], Data array: [5 x 21]],\n"
88-
"\tsld = [[Data array: [5 x 30], Data array: [5 x 30]]],\n"
88+
"\tsld = [[Data array: [5 x 29], Data array: [5 x 29]]],\n"
8989
"\tsampleChi = Data array: [1000],\n"
9090
"),\n"
9191
"confidenceIntervals = ConfidenceIntervals(\n"
@@ -191,7 +191,7 @@ def test_make_results(test_procedure, test_output_results, test_bayes, test_resu
191191
@pytest.mark.parametrize(
192192
["test_output_results", "test_str"],
193193
[
194-
# ("reflectivity_calculation_results", "reflectivity_calculation_str"),
194+
("reflectivity_calculation_results", "reflectivity_calculation_str"),
195195
("dream_results", "dream_str"),
196196
],
197197
)

‎tests/test_plotting.py‎

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -207,10 +207,14 @@ def test_plot_ref_sld(mock: MagicMock, input_project, reflectivity_calculation_r
207207
assert figure.axes[0].get_subplotspec().get_gridspec().get_geometry() == (1, 2)
208208
assert len(figure.axes) == 2
209209

210+
for reflectivity, reflectivity_results in zip(data.reflectivity, reflectivity_calculation_results.reflectivity):
211+
assert (reflectivity == reflectivity_results).all()
212+
for sldProfile, result_sld_profile in zip(data.sldProfiles, reflectivity_calculation_results.sldProfiles):
213+
for sld, sld_results in zip(sldProfile, result_sld_profile):
214+
assert (sld == sld_results).all()
215+
210216
assert data.modelType == input_project.model
211-
assert data.reflectivity == reflectivity_calculation_results.reflectivity
212217
assert data.shiftedData == reflectivity_calculation_results.shiftedData
213-
assert data.sldProfiles == reflectivity_calculation_results.sldProfiles
214218
assert data.resampledLayers == reflectivity_calculation_results.resampledLayers
215219
assert data.dataPresent.size == 0
216220
assert (data.subRoughs == reflectivity_calculation_results.contrastParams.subRoughs).all()

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