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

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]
@@ -113,27 +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:
         output = [alloyDown, gold, SAMTAILS, SAMHEAD, CW, *BILAYER]

ratapi/examples/bayes_benchmark/bayes_benchmark.ipynb

@@ -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",
@@ -339,13 +339,6 @@
     "fig.tight_layout()\n",
     "fig.show()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -364,7 +357,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.10.16"
   }
  },
  "nbformat": 4,

ratapi/examples/convert_rascal_project/Model_IIb.py

@@ -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
@@ -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:

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]
@@ -23,7 +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]

ratapi/examples/domains/domains_XY_model.py

@@ -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]
@@ -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

ratapi/examples/languages/custom_bilayer.cpp

@@ -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];
@@ -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...
@@ -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...

ratapi/examples/languages/custom_bilayer.py

@@ -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]
@@ -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]