Setup.md

@@ -44,14 +44,18 @@ The following shows an example of a setup json file.
     "CHARGE",
     "ACCEPTED",
     "TOTAL"
+  ],
+  "function" : [
+    "clovers/fullEfficiency.json"
   ]
 }
 ```
 
-It consists of three things:
+It consists of four things:
  1. `detectors` an array of detector objects.
  2. `signals` an array of names of scaler values. 
  3. `name` optional value. Just nice to keep track of things. 
+ 4. `functions` is functions that parametrize the setup, such as an efficiency curve. 
 
 Detectors
 ---------
@@ -127,6 +131,70 @@ __Pad__
 * `upLength` Size in mm along orientation vector
 * `transverseLength` Size in mm along n x orientation vector. 
 
+Functions file
+------------------
+The function must contain a name, a formula string (written in a way that can be interpreted by a TF1), the function parameters and a covariance matrix for the parameters. An example of how to write such a file can be seen here: 
+```
+        TF1 *effFit = new TF1("effFit", "[p3] * exp([p0]*log(x/1000) + [p1]*pow(log(x/1000), 2) - [p2]/pow(x,3))", 100, 1500);
+        effFit->SetNpx(1000);
+        effFit->SetLineColor(kRed);
+        effFit->SetParameters(-6.38681e-01, 1.05816e-01, 8.41966e+05, 1.65417e-04);
+        auto ptr = totalEfficiency->Fit(effFit, "QR NS");
+        auto covar = ptr->GetCovarianceMatrix();
+        auto par = ptr->GetParams();
+        vector<double> parVector = {par[0], par[1], par[2], par[3]};
+        AUSATF1 *ausaTF1 = new AUSATF1("fullEfficiency",(string)effFit->GetExpFormula(), covar, parVector);
+        auto json = buildAUSATF1JSON(*ausaTF1);
+        ofstream outfile("calout/fullEfficiency.json");
+        rapidjson::StringBuffer buffer;
+        rapidjson::PrettyWriter<rapidjson::StringBuffer> writer(buffer);
+        writer.SetIndent(' ', 4);
+        json.Accept(writer);
+        outfile << buffer.GetString() << endl;
+
+```
+And the output json file looks like this: 
+```json
+{
+    "name": "fullEfficiency",
+    "formula": "[p3]*exp([p0]*log(x/1000)+[p1]*pow(log(x/1000),2)-[p2]/pow(x,3))",
+    "parameters": [
+        -0.7694757487972153,
+        0.06299888821949205,
+        558694.190596955,
+        0.03145986764934158
+    ],
+    "covariance": [
+        [
+            0.0013829417252703846,
+            0.001324725837104106,
+            5288.965527781921,
+            -0.0000014514547654257206
+        ],
+        [
+            0.001324725837104106,
+            0.001544332430566392,
+            7163.282818239304,
+            -0.000004619537976793716
+        ],
+        [
+            5288.965527781921,
+            7163.282818239304,
+            38425470370.68322,
+            -25.306620182992537
+        ],
+        [
+            -0.0000014514547654257206,
+            -0.000004619537976793716,
+            -25.306620182992537,
+            1.1066298354253414e-7
+        ]
+    ]
+}
+ 
+```
+
+
 Loading setup
 ==============
 This small example shows how to load setup file