Re-organized directory for a facilitated workflow

TrackerMillepedeAlignment/README.md

@@ -0,0 +1,25 @@
+## Alignment Workflow ##
+### A directory containing scripts and macros for doing alignment ###
+
+Workflow:
+* Edit `scripts/alignment_setup.sh` for your environment
+	* Define `MYINSTALL` to the location of your custom-built sPHENIX libraries (if you need custom libraries--you do not necessarily need this)
+	* Define `ALIGN_DATA_DIR` to the top-level directory where you want data output (.root files, pede binaries, large .txt files)
+	* The setup script will NOT create top-level directories if they do not already exist
+	* (But it will create subdirectories for you)
+* Run `scripts/alignment_setup.sh` for the first time
+	* Check that an `iteration_0` subdirectory appears under `ALIGN_DATA_DIR`
+	* Check that an `txt/iteration.txt` file appers (which only contains "0")
+* Run `scripts/submit_fun4all_jobs.sh`
+	* Copies `localAlignmentParamsFile.txt` to `ALIGN_DATA_DIR/iteration_0` (only if this is the 0th iteration)
+	* Creates a file list with one line per segment for each run in the `RUN_NUMS` variable
+	* You can edit this variable (and will likely need to edit the `FILE_FORMAT` variable depending on the range)
+	* This creates a job file to submit a job for each segment--the job is `scripts/Fun4All_SiliconOnlyAlignment.sh`
+	* The output is under `ALIGN_DATA_DIR/iteration_0/dat`, the `out` files are in `out/`
+* Run `scripts/run_pede.sh`
+	* This runs millepede over the expansion `ALIGN_DATA_DIR/iteration_0/dat/*.bin`
+	* It creates the steering file with ls and sets the scale errors to the end of this file
+	* It then runs several macros in sequences to get the next localAlignmentParamsFile.txt and create plots
+* Run `scripts/increment.sh`
+	* This increments the contents `txt/iteration.txt` and copies the `newLocalAlignmentParamsFile.txt` to `localAlignmentParamsFile.txt` for the next iteration
+

TrackerMillepedeAlignment/detailed_alignment_parameter_plots.C

@@ -69,20 +69,21 @@ static const std::array<double,3> tpc_sector_mean[3] = {
   legvec.push_back( "Input");
   col.push_back(kRed); 
   */
-  /*
+
   finvec.push_back("tmp.root");
   legvec.push_back( "ideal");
   col.push_back(kBlue); 
-  */
 
+  /*
   finvec.push_back("/sphenix/tg/tg01/hf/frawley/residuals1/kshort_proc_25.rootseedresiduals.root");
   legvec.push_back( "ideal");
   col.push_back(kBlue); 
-
+  */
 
   for(int ifile = 0; ifile < finvec.size(); ++ifile)
     {
       TFile *fin = new TFile(finvec[ifile].c_str());      
+	  if (!fin) continue;
 
       for(unsigned int layer = 0; layer <3; ++layer)
 	{
@@ -255,4 +256,9 @@ static const std::array<double,3> tpc_sector_mean[3] = {
 	} 
 
     }  
+
+
+  cmvtx->SaveAs("cmvtx.png");
+  cintt->SaveAs("cintt.png");
+  ctpc->SaveAs("ctpc.png");
 }

TrackerMillepedeAlignment/makeAlignmentParsSumFile.C

@@ -24,13 +24,19 @@ void makeAlignmentParsSumFile()
 
   std::cout << " Add new parameters to existing ones" << std::endl;
 
-  ifstream foriginal("sumAlignmentParams_run20_iter1.txt");
-  if(!foriginal.is_open()) std::cout << "Unable to open original misalignment params file" << std::endl;
+  ifstream foriginal("localAlignmentParamsFile.txt");
+  if(!foriginal.is_open()) {
+    std::cout << "Unable to open original misalignment params file" << std::endl;
+	return;
+  }
 
   ifstream fupdated("new_alignment_corrections.txt");
-  if(!fupdated.is_open()) std::cout << "Unable to open updated params file" << std::endl;
+  if(!fupdated.is_open()) {
+    std::cout << "Unable to open updated params file" << std::endl;
+    return;
+  }
 
-  ofstream fsum("sumAlignmentParams_run20_iter2.txt");
+  ofstream fsum("newLocalAlignmentParamsFile.txt");
 
   TrkrDefs::hitsetkey key_original, key_updated;
   float pars_original[6], pars_updated[6];

TrackerMillepedeAlignment/plot_alignment_residuals.C

@@ -51,8 +51,7 @@ unsigned int getSensor(TrkrDefs::hitsetkey hitsetkey)
 
 }
 
-void plot_alignment_residuals(std::string inputfilename = "data.txt",
-			      std::string outfilename = "tmp.root")
+void plot_alignment_residuals(std::string outfilename = "tmp.root")
 {
   gStyle->SetStatW(0.3);
   gStyle->SetStatH(0.3);
@@ -68,10 +67,13 @@ void plot_alignment_residuals(std::string inputfilename = "data.txt",
   //ifstream fin("/sphenix/user/frawley/march17_2023/macros/detectors/sPHENIX/localAlignmentParamsFile.txt");
   //ifstream fin("/sphenix/user/frawley/march17_2023/macros/detectors/sPHENIX/sumAlignmentParams_run18_iter2.txt");
   //  ifstream fin("/sphenix/user/frawley/march17_2023/macros/detectors/sPHENIX/sumAlignmentParams_run18_iter6_fixed_noconstraints.txt");
-  ifstream fin("/sphenix/user/frawley/march17_2023/macros/detectors/sPHENIX/localAlignmentParamsFile.txt");
+  ifstream fin("localAlignmentParamsFile.txt");
 
 
-  if(!fin.is_open()) std::cout << "Unable to open input alignment params file" << std::endl;
+  if(!fin.is_open()) {
+    std::cout << "Unable to open input alignment params file" << std::endl;
+    return;
+  }
 
   TH2D *hpar[57][6];
   for(int ilayer=0;ilayer<57;++ilayer)