ratapi 0.0.0.dev10__tar.gz → 0.0.0.dev12__tar.gz

{ratapi-0.0.0.dev10/ratapi.egg-info → ratapi-0.0.0.dev12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ratapi
-Version: 0.0.0.dev10
+Version: 0.0.0.dev12
 Summary: Python extension for the Reflectivity Analysis Toolbox (RAT)
 Project-URL: Documentation, https://rascalsoftware.github.io/RAT/
 Project-URL: Repository, https://github.com/RascalSoftware/python-RAT

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/cpp/RAT/RATMain.cpp

@@ -940,10 +940,10 @@ namespace RAT
       bayesResults->confidenceIntervals.mean, bayesResults->dreamParams,
       bayesResults->dreamOutput, b_bayesResults.nestedSamplerOutput,
       bayesResults->chain);
-    bayesResults->nestedSamplerOutput.LogZ =
-      b_bayesResults.nestedSamplerOutput.LogZ;
-    bayesResults->nestedSamplerOutput.LogZErr =
-      b_bayesResults.nestedSamplerOutput.LogZErr;
+    bayesResults->nestedSamplerOutput.logZ =
+      b_bayesResults.nestedSamplerOutput.logZ;
+    bayesResults->nestedSamplerOutput.logZErr =
+      b_bayesResults.nestedSamplerOutput.logZErr;
     bayesResults->nestedSamplerOutput.nestSamples.set_size(1, 2);
     bayesResults->nestedSamplerOutput.postSamples.set_size(1, 2);
     bayesResults->nestedSamplerOutput.nestSamples[0] =
@@ -1108,10 +1108,10 @@ namespace RAT
                expl_temp.contrastParams.subRoughs,
                expl_temp.contrastParams.resample, expl_temp.fitParams,
                expl_temp.fitNames, results);
-          bayesResults->nestedSamplerOutput.LogZ =
-            b_bayesResults.nestedSamplerOutput.LogZ;
-          bayesResults->nestedSamplerOutput.LogZErr =
-            b_bayesResults.nestedSamplerOutput.LogZErr;
+          bayesResults->nestedSamplerOutput.logZ =
+            b_bayesResults.nestedSamplerOutput.logZ;
+          bayesResults->nestedSamplerOutput.logZErr =
+            b_bayesResults.nestedSamplerOutput.logZErr;
           bayesResults->nestedSamplerOutput.nestSamples.set_size(1, 2);
           bayesResults->nestedSamplerOutput.postSamples.set_size(1, 2);
           bayesResults->nestedSamplerOutput.nestSamples[0] =

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/cpp/RAT/RATMain_internal_types.h

@@ -26,8 +26,8 @@ namespace RAT
 
   struct struct_T
   {
-    double LogZ;
-    double LogZErr;
+    double logZ;
+    double logZErr;
     ::coder::bounded_array<double, 2U, 2U> nestSamples;
     ::coder::bounded_array<double, 2U, 2U> postSamples;
   };

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/cpp/RAT/RATMain_types.h

@@ -261,8 +261,8 @@ namespace RAT
 
   struct NestedSamplerOutput
   {
-    double LogZ;
-    double LogZErr;
+    double logZ;
+    double logZErr;
     ::coder::array<double, 2U> nestSamples;
     ::coder::array<double, 2U> postSamples;
   };

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/cpp/RAT/applyHydration.cpp

@@ -43,7 +43,7 @@ namespace RAT
         //  Index 6 determines what we hydrate with
         //  Hydrate the real component of the SLD.
         //  Note that we never hydrate the imaginary component of the SLD.
-        if (layers[b_i + layers.size(0) * 5] == 1.0) {
+        if (layers[b_i + layers.size(0) * 5] == 0.0) {
           d = bulkIn;
         } else {
           d = bulkOut;

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/cpp/RAT/callCppFunction.cpp

@@ -81,11 +81,11 @@ namespace RAT
     bulkOutArray = convertPtr2Vector(&(bulkOut.data())[0], static_cast<double>
       (varargin_3.size(0)));
 
-    //  domain should either before 0 or 1. A value less than zero indicates no domains
+    //  domain should either be 1 or 2. A value less than 1 indicates no domains
     std::mem_fn<void(std::vector<double>&, std::vector<double>&, std::vector<
                      double>&, int, int, std::vector<double>&, double*, double*)>
       (&CallbackInterface::invoke)(callback, paramsArray, bulkInArray,
-      bulkOutArray, varargin_4, 0.0, outArray, &outputSize[0], &varargout_1);
+      bulkOutArray, varargin_4, 1.0, outArray, &outputSize[0], &varargout_1);
     actualSize = getVectorSize(outArray);
     loop_ub = static_cast<int>(actualSize);
     tempOutput.set_size(1, static_cast<int>(actualSize));
@@ -193,11 +193,11 @@ namespace RAT
     bulkOutArray = convertPtr2Vector(&(bulkOut.data())[0], static_cast<double>
       (varargin_3.size(0)));
 
-    //  domain should either before 0 or 1. A value less than zero indicates no domains
+    //  domain should either be 1 or 2. A value less than 1 indicates no domains
     std::mem_fn<void(std::vector<double>&, std::vector<double>&, std::vector<
                      double>&, int, int, std::vector<double>&, double*, double*)>
       (&CallbackInterface::invoke)(callback, paramsArray, bulkInArray,
-      bulkOutArray, varargin_4, 1.0, outArray, &outputSize[0], &varargout_1);
+      bulkOutArray, varargin_4, 2.0, outArray, &outputSize[0], &varargout_1);
     actualSize = getVectorSize(outArray);
     loop_ub = static_cast<int>(actualSize);
     tempOutput.set_size(1, static_cast<int>(actualSize));
@@ -305,7 +305,7 @@ namespace RAT
     bulkOutArray = convertPtr2Vector(&(bulkOut.data())[0], static_cast<double>
       (varargin_3.size(0)));
 
-    //  domain should either before 0 or 1. A value less than zero indicates no domains
+    //  domain should either be 1 or 2. A value less than 1 indicates no domains
     std::mem_fn<void(std::vector<double>&, std::vector<double>&, std::vector<
                      double>&, int, std::vector<double>&, double*, double*)>
       (&CallbackInterface::invoke)(callback, paramsArray, bulkInArray,

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/cpp/RAT/makeEmptyBayesResultsStruct.cpp

@@ -379,8 +379,8 @@ namespace RAT
       bayesResults_dreamOutput.AR.data, bayesResults_dreamOutput.AR.size,
       bayesResults_dreamOutput.R_stat, bayesResults_dreamOutput.CR,
       bayesResults_dreamOutput.iteration);
-    bayesResults_nestedSamplerOutput.LogZ = 0.0;
-    bayesResults_nestedSamplerOutput.LogZErr = 0.0;
+    bayesResults_nestedSamplerOutput.logZ = 0.0;
+    bayesResults_nestedSamplerOutput.logZErr = 0.0;
 
     //  ------------------------------------------------------------------
     //  (6) chain
@@ -582,8 +582,8 @@ namespace RAT
       bayesResults_dreamOutput.AR.data, bayesResults_dreamOutput.AR.size,
       bayesResults_dreamOutput.R_stat, bayesResults_dreamOutput.CR,
       bayesResults_dreamOutput.iteration);
-    bayesResults_nestedSamplerOutput.LogZ = 0.0;
-    bayesResults_nestedSamplerOutput.LogZErr = 0.0;
+    bayesResults_nestedSamplerOutput.logZ = 0.0;
+    bayesResults_nestedSamplerOutput.logZErr = 0.0;
 
     //  ------------------------------------------------------------------
     //  (6) chain

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/cpp/RAT/mrdivide_helper.cpp

@@ -231,6 +231,7 @@ namespace RAT
             }
           }
         } else if (B.size(0) == 1) {
+          int Y_idx_0;
           int loop_ub;
           b_Y.set_size(A.size(0));
           loop_ub = A.size(0);
@@ -238,9 +239,9 @@ namespace RAT
             b_Y[i] = A[i] / B[0];
           }
 
-          loop_ub = b_Y.size(0);
+          Y_idx_0 = b_Y.size(0);
           Y.set_size(b_Y.size(0), 1);
-          for (int i{0}; i < loop_ub; i++) {
+          for (int i{0}; i < Y_idx_0; i++) {
             Y[i] = b_Y[i];
           }
         } else {

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/cpp/RAT/processCustomFunction.cpp

@@ -78,8 +78,8 @@ namespace RAT
                     static_cast<int>(d) - 1].f1)->size())[1];
           subRoughs[b_i] = callCppFunction((const char *)((::coder::array<char,
             2U> *)&customFiles[static_cast<int>(d) - 1].f1)->data(), iv,
-            paramValues, bulkIns[b_i], bulkOuts, (static_cast<double>(b_i) + 1.0)
-            - 1.0, output);
+            paramValues, bulkIns[b_i], bulkOuts, static_cast<double>(b_i) + 1.0,
+            output);
         }
 
         //  If SLD is real, add dummy imaginary column
@@ -241,8 +241,8 @@ namespace RAT
                     static_cast<int>(d) - 1].f1)->size())[1];
           subRoughs[b_i] = callCppFunction((const char *)((::coder::array<char,
             2U> *)&customFiles[static_cast<int>(d) - 1].f1)->data(), iv,
-            paramValues, bulkIns[b_i], bulkOuts, (static_cast<double>(b_i) + 1.0)
-            - 1.0, output);
+            paramValues, bulkIns[b_i], bulkOuts, static_cast<double>(b_i) + 1.0,
+            output);
         }
 
         //  If SLD is real, add dummy imaginary column

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/cpp/RAT/processCustomFunction1.cpp

@@ -83,8 +83,8 @@ namespace RAT
                     static_cast<int>(d) - 1].f1)->size())[1];
           subRoughs[b_i] = b_callCppFunction((const char *)((::coder::array<char,
             2U> *)&customFiles[static_cast<int>(d) - 1].f1)->data(), iv,
-            paramValues, bulkIns[b_i], bulkOuts, (static_cast<double>(b_i) + 1.0)
-            - 1.0, output1);
+            paramValues, bulkIns[b_i], bulkOuts, static_cast<double>(b_i) + 1.0,
+            output1);
           loop_ub = output1.size(1);
           b_output1.set_size(output1.size(0), output1.size(1));
           for (i1 = 0; i1 < loop_ub; i1++) {
@@ -103,8 +103,8 @@ namespace RAT
             [1];
           c_callCppFunction((const char *)((::coder::array<char, 2U> *)
             &customFiles[static_cast<int>(contrastCustomFiles[b_i]) - 1].f1)
-                            ->data(), iv, paramValues, bulkIns[b_i], bulkOuts, (
-            static_cast<double>(b_i) + 1.0) - 1.0, output1);
+                            ->data(), iv, paramValues, bulkIns[b_i], bulkOuts,
+                            static_cast<double>(b_i) + 1.0, output1);
         }
 
         //  If SLD is real, add dummy imaginary column
@@ -356,8 +356,8 @@ namespace RAT
                     static_cast<int>(d) - 1].f1)->size())[1];
           subRoughs[b_i] = b_callCppFunction((const char *)((::coder::array<char,
             2U> *)&customFiles[static_cast<int>(d) - 1].f1)->data(), iv,
-            paramValues, bulkIns[b_i], bulkOuts, (static_cast<double>(b_i) + 1.0)
-            - 1.0, output1);
+            paramValues, bulkIns[b_i], bulkOuts, static_cast<double>(b_i) + 1.0,
+            output1);
           loop_ub = output1.size(1);
           b_output1.set_size(output1.size(0), output1.size(1));
           for (i1 = 0; i1 < loop_ub; i1++) {
@@ -376,8 +376,8 @@ namespace RAT
             [1];
           c_callCppFunction((const char *)((::coder::array<char, 2U> *)
             &customFiles[static_cast<int>(contrastCustomFiles[b_i]) - 1].f1)
-                            ->data(), iv, paramValues, bulkIns[b_i], bulkOuts, (
-            static_cast<double>(b_i) + 1.0) - 1.0, output1);
+                            ->data(), iv, paramValues, bulkIns[b_i], bulkOuts,
+                            static_cast<double>(b_i) + 1.0, output1);
         }
 
         //  If SLD is real, add dummy imaginary column

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/cpp/RAT/runNestedSampler.cpp

@@ -132,8 +132,8 @@ namespace RAT
 
     t1_dreamParams = t0_dreamParams;
     t1_dreamOutput = t0_dreamOutput;
-    t1_nestedSamplerOutput.LogZ = t0_nestedSamplerOutput.LogZ;
-    t1_nestedSamplerOutput.LogZErr = t0_nestedSamplerOutput.LogZErr;
+    t1_nestedSamplerOutput.logZ = t0_nestedSamplerOutput.logZ;
+    t1_nestedSamplerOutput.logZErr = t0_nestedSamplerOutput.logZErr;
     t1_nestedSamplerOutput.nestSamples.set_size(1, 2);
     t1_nestedSamplerOutput.postSamples.set_size(1, 2);
     t1_nestedSamplerOutput.nestSamples[0] =
@@ -287,7 +287,7 @@ namespace RAT
 
     getFittedPriors(fitNames, problemStruct.priorNames,
                     problemStruct.priorValues, problemStruct.fitLimits, r);
-    bayesResults_nestedSamplerOutput.LogZ = nestedSampler(problemStruct,
+    bayesResults_nestedSamplerOutput.logZ = nestedSampler(problemStruct,
       expl_temp, controls_nLive, controls_nMCMC, controls_nsTolerance, r,
       bayesResults_nestedSamplerOutput.nestSamples,
       bayesResults_nestedSamplerOutput.postSamples, H);
@@ -377,7 +377,7 @@ namespace RAT
       }
     }
 
-    bayesResults_nestedSamplerOutput.LogZErr = std::sqrt(H / controls_nLive);
+    bayesResults_nestedSamplerOutput.logZErr = std::sqrt(H / controls_nLive);
     return bayesResults_predictionIntervals_sampleChi_size;
   }
 }

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/cpp/rat.cpp

@@ -525,8 +525,8 @@ OutputBayesResult OutputBayesResultsFromStruct(const RAT::BayesResults results)
     bayesResults.confidenceIntervals.percentile65 = pyArrayFromRatArray2d(results.confidenceIntervals.percentile65);
     bayesResults.confidenceIntervals.mean = pyArrayFromRatArray2d(results.confidenceIntervals.mean);
 
-    bayesResults.nestedSamplerOutput.logZ = results.nestedSamplerOutput.LogZ;
-    bayesResults.nestedSamplerOutput.logZErr = results.nestedSamplerOutput.LogZErr;
+    bayesResults.nestedSamplerOutput.logZ = results.nestedSamplerOutput.logZ;
+    bayesResults.nestedSamplerOutput.logZErr = results.nestedSamplerOutput.logZErr;
     bayesResults.nestedSamplerOutput.nestSamples = pyArrayFromRatArray2d(results.nestedSamplerOutput.nestSamples);
     bayesResults.nestedSamplerOutput.postSamples = pyArrayFromRatArray2d(results.nestedSamplerOutput.postSamples);
 

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = 'setuptools.build_meta'
 
 [project]
 name = "ratapi"
-version = "0.0.0.dev10"
+version = "0.0.0.dev12"
 description = "Python extension for the Reflectivity Analysis Toolbox (RAT)"
 readme = "README.md"
 requires-python = ">=3.10"

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/ratapi/examples/absorption/volume_thiol_bilayer.py

@@ -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]
@@ -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]
@@ -113,7 +116,7 @@ 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
@@ -121,9 +124,9 @@ def volume_thiol_bilayer(params, bulk_in, bulk_out, contrast):
     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]
@@ -131,11 +134,11 @@ def volume_thiol_bilayer(params, bulk_in, bulk_out, contrast):
 
     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:
+    elif contrast == 1 or contrast == 3:
         output = [alloyDown, gold, SAMTAILS, SAMHEAD, CW, *BILAYER]
 
     return output, subRough

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/ratapi/examples/convert_rascal_project/Model_IIb.py

@@ -5,6 +5,9 @@ from math import cos, radians
 
 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
@@ -49,7 +52,7 @@ 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)
@@ -57,7 +60,7 @@ def Model_IIb(params, bulk_in, bulk_out, contrast):
         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:

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/ratapi/examples/domains/alloy_domains.py

@@ -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]
@@ -23,9 +26,9 @@ 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:
+    elif domain == 2:
         output = [alloyDn, gold]
 
     return output, subRough

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/ratapi/examples/domains/domains_XY_model.py

@@ -8,6 +8,9 @@ from scipy.special import erf
 
 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]
@@ -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:
+    elif domain == 2:
         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

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/ratapi/examples/languages/custom_bilayer.py

@@ -5,6 +5,9 @@ import numpy as np
 
 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]
@@ -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]
 

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/ratapi/examples/normal_reflectivity/custom_XY_DSPC.py

@@ -8,6 +8,9 @@ from scipy.special import erf
 
 def custom_XY_DSPC(params, bulk_in, bulk_out, contrast):
     """Calculate the continuous SLD of a supported DSPC bilayer using volume restricted distribution functions."""
+    # Note - The first contrast number is 1 (not 0) so be careful if you use
+    # this variable for array indexing.
+
     # Split up the parameters
     subRough = params[0]
     oxideThick = params[1]
@@ -109,7 +112,7 @@ def custom_XY_DSPC(params, bulk_in, bulk_out, contrast):
     sldHeadL = vfHeadL * sld_Value_Head
     sldHeadR = vfHeadR * sld_Value_Head
     sldTails = vfTails * sld_Value_Tails
-    sldWat = vfWat * bulk_out[contrast]
+    sldWat = vfWat * bulk_out[contrast - 1]
 
     # Put this all together
     totSLD = sldSilicon + sldOxide + sldHeadL + sldTails + sldHeadR + sldWat

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/ratapi/examples/normal_reflectivity/custom_bilayer_DSPC.py

@@ -25,6 +25,8 @@ def custom_bilayer_DSPC(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.
     sub_rough = params[0]
     oxide_thick = params[1]
     oxide_hydration = params[2]
@@ -72,13 +74,13 @@ def custom_bilayer_DSPC(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]
 

{ratapi-0.0.0.dev10 → ratapi-0.0.0.dev12}/ratapi/inputs.py

@@ -77,6 +77,13 @@ class FileHandles:
         """
         custom_file = self.files[index]
         full_path = os.path.join(custom_file["path"], custom_file["filename"])
+
+        if not os.path.isfile(full_path):
+            raise FileNotFoundError(f"The custom file ({custom_file['name']}) does not have a valid path.")
+
+        if not custom_file["function_name"] and custom_file["language"] != Languages.Matlab:
+            raise ValueError(f"The custom file ({custom_file['name']}) does not have a valid function name.")
+
         if custom_file["language"] == Languages.Python:
             file_handle = get_python_handle(custom_file["filename"], custom_file["function_name"], custom_file["path"])
         elif custom_file["language"] == Languages.Matlab:
@@ -385,7 +392,7 @@ def make_problem(project: ratapi.Project) -> ProblemDefinition:
 
 def get_layer_details(project: ratapi.Project) -> list[int]:
     """Get parameter indices for all layers defined in the project."""
-    hydrate_id = {"bulk in": 1, "bulk out": 2}
+    hydrate_id = {"bulk in": 0, "bulk out": 1}
     layer_details = []
 
     # Get the thickness, SLD, roughness fields from the appropriate model