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Unifies the contrast number used by python and cpp to be same with matlab and Data points now show when show_error is False #197

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Unifies the contrast number used by python and cpp to be same with matlab and Data points now show when show_error is False #197

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2bbfb41
Unifies the contrast number used by python and cpp to be same with ma…
StephenNneji Feb 4, 2026
7c15526
Data point are shown when show error is False
StephenNneji Feb 4, 2026
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2 changes: 1 addition & 1 deletion cpp/RAT
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Submodule RAT updated 3 files
+5 −5 callCppFunction.cpp
+4 −4 processCustomFunction.cpp
+8 −8 processCustomFunction1.cpp
21 changes: 12 additions & 9 deletions ratapi/examples/absorption/volume_thiol_bilayer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,9 @@ def volume_thiol_bilayer(params, bulk_in, bulk_out, contrast):

The second output parameter should be the substrate roughness.
"""
# Note - The first contrast number is 1 (not 0) so be careful if you use
# this variable for array indexing.

subRough = params[0]
alloyThick = params[1]
alloySLDUp = params[2]
Expand Down Expand Up @@ -92,11 +95,11 @@ def volume_thiol_bilayer(params, bulk_in, bulk_out, contrast):

# Correct head SLD based on hydration
thiolHeadHydr = thiolHeadHydr / 100
sldHead = sldHead * (1 - thiolHeadHydr) + (thiolHeadHydr * bulk_out[contrast])
sldHead = sldHead * (1 - thiolHeadHydr) + (thiolHeadHydr * bulk_out[contrast - 1])

# Now correct both the SLDs for the coverage parameter
sldTail = (thiolCoverage * sldTail) + ((1 - thiolCoverage) * bulk_out[contrast])
sldHead = (thiolCoverage * sldHead) + ((1 - thiolCoverage) * bulk_out[contrast])
sldTail = (thiolCoverage * sldTail) + ((1 - thiolCoverage) * bulk_out[contrast - 1])
sldHead = (thiolCoverage * sldHead) + ((1 - thiolCoverage) * bulk_out[contrast - 1])

SAMTAILS = [thickTail, sldTail, 0, goldRough]
SAMHEAD = [thickHead, sldHead, 0, goldRough]
Expand All @@ -113,27 +116,27 @@ def volume_thiol_bilayer(params, bulk_in, bulk_out, contrast):
sldHead = sumbHead / vHead
thickHead = vHead / bilayerAPM
bilHeadHydr = bilHeadHydr / 100
sldHead = sldHead * (1 - bilHeadHydr) + (bilHeadHydr * bulk_out[contrast])
sldHead = sldHead * (1 - bilHeadHydr) + (bilHeadHydr * bulk_out[contrast - 1])

sldTail = sumbTail / vTail
thickTail = vTail / bilayerAPM

sldMe = sumbMe / vMe
thickMe = vMe / bilayerAPM

sldTail = (bilayerCoverage * sldTail) + ((1 - bilayerCoverage) * bulk_out[contrast])
sldHead = (bilayerCoverage * sldHead) + ((1 - bilayerCoverage) * bulk_out[contrast])
sldMe = (bilayerCoverage * sldMe) + ((1 - bilayerCoverage) * bulk_out[contrast])
sldTail = (bilayerCoverage * sldTail) + ((1 - bilayerCoverage) * bulk_out[contrast - 1])
sldHead = (bilayerCoverage * sldHead) + ((1 - bilayerCoverage) * bulk_out[contrast - 1])
sldMe = (bilayerCoverage * sldMe) + ((1 - bilayerCoverage) * bulk_out[contrast - 1])

BILTAILS = [thickTail, sldTail, 0, bilayerRough]
BILHEAD = [thickHead, sldHead, 0, bilayerRough]
BILME = [thickMe, sldMe, 0, bilayerRough]

BILAYER = [BILHEAD, BILTAILS, BILME, BILME, BILTAILS, BILHEAD]

CW = [cwThick, bulk_out[contrast], 0, bilayerRough]
CW = [cwThick, bulk_out[contrast - 1], 0, bilayerRough]

if contrast == 1 or contrast == 3:
if contrast == 2 or contrast == 4:
output = [alloyUp, gold, SAMTAILS, SAMHEAD, CW, *BILAYER]
else:
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@DrPaulSharp DrPaulSharp Feb 4, 2026

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Is it worth changing this line to elif contrast == 1 or contrast == 3: to improve clarity?

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@DrPaulSharp DrPaulSharp Feb 4, 2026

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Same with elsewhere in this PR.

output = [alloyDown, gold, SAMTAILS, SAMHEAD, CW, *BILAYER]
Expand Down
11 changes: 2 additions & 9 deletions ratapi/examples/bayes_benchmark/bayes_benchmark.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -188,7 +188,7 @@
"back_param = project.background_parameters[0]\n",
"background = np.linspace(back_param.min, back_param.max, 30)\n",
"\n",
"controls = RAT.Controls(procedure=\"calculate\", calcSldDuringFit=True, display=\"off\")\n",
"controls = RAT.Controls(procedure=\"calculate\", display=\"off\")\n",
"\n",
"# function to calculate exp(-chi_squared / 2) for a given pair of roughness/background values\n",
"def calculate_posterior(roughness_index: int, background_index: int) -> float:\n",
Expand Down Expand Up @@ -339,13 +339,6 @@
"fig.tight_layout()\n",
"fig.show()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -364,7 +357,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.12"
"version": "3.10.16"
}
},
"nbformat": 4,
Expand Down
7 changes: 5 additions & 2 deletions ratapi/examples/convert_rascal_project/Model_IIb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,9 @@

def Model_IIb(params, bulk_in, bulk_out, contrast):
"""Calculate layer parameters for a monolayer volume model at two deuterations."""
# Note - The first contrast number is 1 (not 0) so be careful if you use
# this variable for array indexing. Same applies to the domain number.

# converted from matlab file Model_IIb.m

Roughness, APM, thickHead, theta = params
Expand Down Expand Up @@ -49,15 +52,15 @@ def Model_IIb(params, bulk_in, bulk_out, contrast):
vTail = 2 * (16 * vCH2) + 2 * (vCH3)

# make SLDs
thisMask = deut[contrast]
thisMask = deut[contrast - 1]

if thisMask[0] == 0:
thisWater = (H2O * 0.9249) + (D2O * 0.0871)
else:
thisWater = D2O

# Calculate mole fraction of D2O from the bulk SLD
d2o_molfr = (1 / D2O - H2O) * ((bulk_out[contrast] / 0.036182336306) - H2O)
d2o_molfr = (1 / D2O - H2O) * ((bulk_out[contrast - 1] / 0.036182336306) - H2O)
thisWater = (d2o_molfr * D2O) + ((1 - d2o_molfr) * H2O)

if thisMask[1] == 0:
Expand Down
5 changes: 4 additions & 1 deletion ratapi/examples/domains/alloy_domains.py
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Expand Up @@ -7,6 +7,9 @@ def alloy_domains(params, bulkIn, bulkOut, contrast, domain):
Simple custom model for testing incoherent summing.
Simple two layer of permalloy / gold, with up/down domains.
"""
# Note - The first contrast number is 1 (not 0) so be careful if you use
# this variable for array indexing. Same applies to the domain number.

# Split up the parameters
subRough = params[0]
alloyThick = params[1]
Expand All @@ -23,7 +26,7 @@ def alloy_domains(params, bulkIn, bulkOut, contrast, domain):
gold = [goldThick, goldSLD, goldRough]

# Make the model depending on which domain we are looking at
if domain == 0:
if domain == 1:
output = [alloyUp, gold]
else:
output = [alloyDn, gold]
Expand Down
7 changes: 5 additions & 2 deletions ratapi/examples/domains/domains_XY_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,9 @@

def domains_XY_model(params, bulk_in, bulk_out, contrast, domain):
"""Calculate the SLD profile for a domains custom XY model."""
# Note - The first contrast number is 1 (not 0) so be careful if you use
# this variable for array indexing. Same applies to the domain number.

# Split up the parameters for convenience
subRough = params[0]
oxideThick = params[1]
Expand Down Expand Up @@ -37,13 +40,13 @@ def domains_XY_model(params, bulk_in, bulk_out, contrast, domain):
oxSLD = vfOxide * 3.41e-6

# Layer SLD depends on whether we are calculating the domain or not
if domain == 0:
if domain == 1:
laySLD = vfLayer * layerSLD
else:
laySLD = vfLayer * domainSLD

# ... and finally the water SLD.
waterSLD = vfWater * bulk_out[contrast]
waterSLD = vfWater * bulk_out[contrast - 1]

# Make the total SLD by just adding them all up
totalSLD = siSLD + oxSLD + laySLD + waterSLD
Expand Down
10 changes: 6 additions & 4 deletions ratapi/examples/languages/custom_bilayer.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@ extern "C" {

LIB_EXPORT void custom_bilayer(std::vector<double>& params, std::vector<double>& bulkIn, std::vector<double>& bulkOut, int contrast, std::vector<double>& output, double* outputSize, double* rough)
{
// Note - The first contrast number is 1 (not 0) so be careful if you use
// this variable for array indexing.
double subRough = params[0];
double oxideThick = params[1];
double oxideHydration = params[2];
Expand Down Expand Up @@ -65,9 +67,9 @@ extern "C" {

// Manually deal with hydration for layers in
// this example.
double oxSLD = (oxideHydration * bulkOut[contrast]) + ((1 - oxideHydration) * oxideSLD);
double headSLD = (headHydration * bulkOut[contrast]) + ((1 - headHydration) * SLDhead);
double tailSLD = (bilayerHydration * bulkOut[contrast]) + ((1 - bilayerHydration) * SLDtail);
double oxSLD = (oxideHydration * bulkOut[contrast-1]) + ((1 - oxideHydration) * oxideSLD);
double headSLD = (headHydration * bulkOut[contrast-1]) + ((1 - headHydration) * SLDhead);
double tailSLD = (bilayerHydration * bulkOut[contrast-1]) + ((1 - bilayerHydration) * SLDtail);

// Make the layers
// oxide...
Expand All @@ -77,7 +79,7 @@ extern "C" {

// Water...
output.push_back(waterThick);
output.push_back(bulkOut[contrast]);
output.push_back(bulkOut[contrast-1]);
output.push_back(bilayerRough);

// Heads...
Expand Down
11 changes: 7 additions & 4 deletions ratapi/examples/languages/custom_bilayer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,9 @@

def custom_bilayer(params, bulk_in, bulk_out, contrast):
"""Calculate the layer parameters for a custom bilayer model."""
# Note - The first contrast number is 1 (not 0) so be careful if you use
# this variable for array indexing.

sub_rough = params[0]
oxide_thick = params[1]
oxide_hydration = params[2]
Expand Down Expand Up @@ -54,13 +57,13 @@ def custom_bilayer(params, bulk_in, bulk_out, contrast):
tailThick = vTail / lipidAPM

# Manually deal with hydration for layers in this example.
oxSLD = (oxide_hydration * bulk_out[contrast]) + ((1 - oxide_hydration) * oxide_SLD)
headSLD = (headHydration * bulk_out[contrast]) + ((1 - headHydration) * SLDhead)
tailSLD = (bilayerHydration * bulk_out[contrast]) + ((1 - bilayerHydration) * SLDtail)
oxSLD = (oxide_hydration * bulk_out[contrast - 1]) + ((1 - oxide_hydration) * oxide_SLD)
headSLD = (headHydration * bulk_out[contrast - 1]) + ((1 - headHydration) * SLDhead)
tailSLD = (bilayerHydration * bulk_out[contrast - 1]) + ((1 - bilayerHydration) * SLDtail)

# Make the layers
oxide = [oxide_thick, oxSLD, sub_rough]
water = [waterThick, bulk_out[contrast], bilayerRough]
water = [waterThick, bulk_out[contrast - 1], bilayerRough]
head = [headThick, headSLD, bilayerRough]
tail = [tailThick, tailSLD, bilayerRough]

Expand Down
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