Add the prelim ALERT timeline scripts

Author: Sangbaek

src/main/java/org/jlab/clas/timeline/analysis/alert/alert_atof_tdc.groovy

@@ -0,0 +1,70 @@
+package org.jlab.clas.timeline.analysis
+import java.util.concurrent.ConcurrentHashMap
+import org.jlab.groot.data.TDirectory
+import org.jlab.groot.data.GraphErrors
+import org.jlab.clas.timeline.fitter.ALERTFitter
+
+class alert_atof_tdc {
+
+def data = new ConcurrentHashMap()
+
+  def processRun(dir, run) {
+
+    data[run] = [run:run]
+    def trigger = dir.getObject('/TRIGGER/bits')
+    def reference_trigger_bit = 0
+    data[run].put('bits',  trigger)
+    (0..<720).collect{index->
+      int sector    = index / (12 * 4);
+      int layer     = (index % (12 * 4)) / 12;
+      int component = index % 12;
+      def file_index = '';
+      if (component <= 10) file_index = String.format('sector%d_layer%d_component%d_order0', sector, layer, component)
+      else file_index = String.format('sector%d_layer%d_component%d_order1', sector, layer, component-1)
+      def h1 = dir.getObject(String.format('/ALERT/TDC_%s', file_index))
+      data[run].put(String.format('atof_tdc_%s', file_index),  h1)
+      def f1 = ALERTFitter.tdcfitter(h1)
+      data[run].put(String.format('fit_atof_tdc_%s', file_index),  f1)
+      data[run].put(String.format('peak_location_atof_tdc_%s', file_index),  f1.getParameter(1))
+      data[run].put(String.format('sigma_atof_tdc_%s', file_index),  f1.getParameter(2))
+      data[run].put(String.format('integral_per_trigger_atof_tdc_%s', file_index),  Math.sqrt(2*3.141597f) * f1.getParameter(0) * f1.getParameter(2)/trigger.getBinContent(reference_trigger_bit) )
+    }
+  }
+
+
+
+  def write() {
+
+    TDirectory out = new TDirectory()
+    out.mkdir('/timelines')
+    ['peak_location', 'sigma', 'integral_per_trigger'].each{variable->
+      (0..<15).collect{sector->
+        (0..<4).collect{layer->
+          def names = []
+          (0..<12).collect{component->
+            def file_index = ''
+            if (component <= 10) file_index = String.format('sector%d_layer%d_component%d_order0', sector, layer, component)
+            else file_index = String.format('sector%d_layer%d_component%d_order1', sector, layer, component-1)
+            names << String.format('atof_tdc_%s', file_index)
+          }
+          names.each{ name ->
+            def gr = new GraphErrors(name)
+            gr.setTitle("ATOF TDC peak "  + variable.replace('_', ' '))
+            gr.setTitleY("ATOF TDC peak " + variable.replace('_', ' '))
+            gr.setTitleX("run number")
+            data.sort{it.key}.each{run,it->
+              out.mkdir('/'+it.run)
+              out.cd('/'+it.run)
+              out.addDataSet(it[name])
+              out.addDataSet(it['fit_'+name])
+              gr.addPoint(it.run, it[variable + '_' + name], 0, 0)
+            }
+            out.cd('/timelines')
+            out.addDataSet(gr)
+          }
+          out.writeFile(String.format('alert_atof_tdc_%s_sector%d_layer%d.hipo', variable, sector, layer))
+        }
+      }
+    }
+  }
+}

src/main/java/org/jlab/clas/timeline/fitter/ALERTFitter.groovy

@@ -0,0 +1,51 @@
+/**
+*
+* Fitter package for CND
+*
+* Writer: Sangbaek Lee
+*
+**/
+package org.jlab.clas.timeline.fitter
+import org.jlab.groot.fitter.DataFitter
+import org.jlab.groot.data.H1F
+import org.jlab.groot.math.F1D
+
+
+class ALERTFitter{
+
+	static F1D tdcfitter(H1F h1){
+		def f1 =new F1D("fit:"+h1.getName(),"[amp]*gaus(x,[mean],[sigma])+[cst]", -5.0, 5.0);
+		f1.setLineColor(33);
+		f1.setLineWidth(10);
+		f1.setOptStat("1111");
+		double maxz = h1.getBinContent(h1.getMaximumBin());
+		f1.setRange(h1.getMaximumBin() + 350.5 - 50, h1.getMaximumBin() + 350.5 + 50);
+		f1.setParameter(0,maxz);
+		f1.setParameter(1, h1.getMaximumBin() + 350.5);
+		f1.setParameter(2, 20);
+		f1.setParameter(3, 0.0);
+		if (maxz>0) f1.setParLimits(0, maxz*0.9,maxz*1.1);
+		f1.setParLimits(3, 0.0, 0.1*maxz);
+
+		double hMean, hRMS
+
+		DataFitter.fit(f1, h1, "");
+
+		def makefit = {func->
+			hMean = func.getParameter(1)
+			hRMS  = func.getParameter(2).abs()
+			func.setRange(Math.max(hMean-2.5*hRMS, 350.0),Math.min(hMean+2.5*hRMS, 550.0))
+      func.setParLimits(0, func.getParameter(0)*0.9,func.getParameter(0)*1.1);
+      f1.setParLimits(3, 0.0, 0.1*func.getParameter(0));
+			DataFitter.fit(func,h1,"Q")
+			return [func.getChiSquare(), (0..<func.getNPars()).collect{func.getParameter(it)}]
+		}
+
+		def fits1 = (0..20).collect{makefit(f1)}
+		def bestfit = fits1.sort()[0]
+		f1.setParameters(*bestfit[1])
+		//makefit(f1)
+
+		return f1
+	}
+} 

src/main/java/org/jlab/clas/timeline/run_analysis.groovy

@@ -3,6 +3,8 @@ package org.jlab.clas.timeline.analysis
 import org.jlab.groot.data.TDirectory
 
 def engines = [
+  out_ALERT: [new alert_atof_tdc(),
+  ],
   out_BAND: [new band_adccor(),
     new band_lasertime(),
     new band_meantimeadc(),