Jf rawdataprocess txtfile (#732)

* Fix ROI mapping

* Formatting

* Minor edit

* intial draft of cmake for jungfrau executables Makefile.rawdataprocess

* added the cmake file

* missed Makefile

* added libfmt

* Fix some compiler warnings

* Fix some compiler warnings

* Create filename usining fmt::format

* Rewrite command line parsing with std::string and fmt::format

* Fix file reading

* Fix root string extraction

* Fix ifstream file reading

* Clean up comments

* Add version of rawdataprocess with bash wildcards

* Add version of rawdataprocess that reads inputs from txt-file, still buggy

* intermediate

* fix file loop

* fix const

* Circumevent bug with stuck threads

* Fix mutex bug

* cleanup

---------

Co-authored-by: vhinger182 <hinger_v@hv_home_lt1.localdomain>
Co-authored-by: Dhanya Thattil <dhanya.thattil@psi.ch>
Co-authored-by: Erik Fröjdh <erik.frojdh@gmail.com>

slsDetectorCalibration/jungfrauExecutables/CMakeLists.txt

@@ -14,7 +14,7 @@ target_compile_definitions(jungfrauRawDataProcess PRIVATE MODULE)
 list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcess)
 
 # jungfrauRawDataProcessStrx
-add_executable(jungfrauRawDataProcessStrx jungfrauRawDataProcess.cpp)
+add_executable(jungfrauRawDataProcessStrx jungfrauRawDataProcess_filetxt.cpp)
 target_compile_definitions(jungfrauRawDataProcessStrx PRIVATE JFSTRX)
 list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrx)
 

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp

@@ -59,14 +59,12 @@ std::string getRootString( const std::string& filepath ) {
 //   aindex:  acquisition index (i.e. "run number")
 
 std::string createFileName( const std::string& dir, const std::string& fprefix="run", const std::string& fsuffix="", const std::string& fext="raw", int aindex=0, int mindex=0, int findex=0, int outfilecounter=-1 ) {
-  std::string filename{};
   if (outfilecounter >= 0)
-    filename = fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}_f{:05d}.{:s}", dir, fprefix, mindex, findex, aindex, outfilecounter, fext);
+    return fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}_f{:05d}.{:s}", dir, fprefix, mindex, findex, aindex, outfilecounter, fext);
   else if (fsuffix.length()!=0)
-    filename = fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
+    return fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
   else
-    filename = fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}.{:s}", dir, fprefix, mindex, findex, aindex, fext);
-  return filename;
+    return fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}.{:s}", dir, fprefix, mindex, findex, aindex, fext);
 }
 
 int main(int argc, char *argv[]) {

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxt.cpp

@@ -41,7 +41,8 @@
 #include <ctime>
 #include <fmt/core.h>
 
-std::string getRootString( const std::string filepath ) {
+
+std::string getRootString( const std::string& filepath ) {
   size_t pos1;
   if (filepath.find("/") == std::string::npos )
     pos1 = 0;
@@ -57,15 +58,13 @@ std::string getRootString( const std::string filepath ) {
 //   fprefix:   fileprefix (without extension)
 //   fsuffix:   filesuffix (for output files, e.g. "ped")
 //   fext:    file extension (e.g. "raw")
-std::string createFileName( const std::string dir, std::string fprefix="run", std::string fsuffix="", std::string fext="raw", int outfilecounter=-1 ) {
-  std::string filename{};
+std::string createFileName( const std::string& dir, const std::string& fprefix="run", const std::string& fsuffix="", const std::string& fext="raw", int outfilecounter=-1 ) {
   if (outfilecounter >= 0)
-    filename = fmt::format("{:s}/{:s}_{:s}_f{:05d}.{:s}", dir, fprefix, fsuffix, outfilecounter, fext);
+    return fmt::format("{:s}/{:s}_{:s}_f{:05d}.{:s}", dir, fprefix, fsuffix, outfilecounter, fext);
   else if (fsuffix.length()!=0)
-    filename = fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
+    return fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
   else
-    filename = fmt::format("{:s}/{:s}.{:s}", dir, fprefix, fext);
-  return filename;
+    return fmt::format("{:s}/{:s}.{:s}", dir, fprefix, fext);
 }
 
 
@@ -104,9 +103,9 @@ int main(int argc, char *argv[]) {
     int ff, np;
     // cout << " data size is " << dsize;
 
-    std::string txtfilename(argv[1]);
-    std::string outdir(argv[2]);
-    std::string pedfilename(argv[3]);
+    const std::string txtfilename(argv[1]);
+    const std::string outdir(argv[2]);
+    const std::string pedfilename(argv[3]);
 
     int xmin = atoi(argv[4]);
     int xmax = atoi(argv[5]);
@@ -122,26 +121,31 @@ int main(int argc, char *argv[]) {
 
     //Get vector of filenames from input txt-file
     std::vector<std::string> filenames{};
+    //filenames.reserve(512);
     { //Safety scope for ifstream
       ifstream inputs( txtfilename, std::ios::in );
       if (inputs.is_open()) {
 	std::cout << "Reading imput filenames from txt-file ..." << std::endl;
+	std::string line{};
 	while (!inputs.eof()) {
-	  std::string line{};
 	  std::getline(inputs, line);
-	  filenames.push_back(line);
+	  filenames.emplace_back(line);
+	  std::cout << line << " line.max_size() " << line.max_size() << " filenames.capacity() " << filenames.capacity() << '\n';
 	}
+	inputs.close();
 	std::cout << "---- Reached end of txt-file. ----" << std::endl;
-	if (filenames.size()>0) {
-	  std::cout << filenames.size() << " filenames found in " << txtfilename << std::endl;
-	  std::cout << "The files will be processed in the same order as found in the txt-file." << std::endl;
-	} else {
-	  std::cout << "No files found in txt-file!" << std::endl;
-	  return 1;
-	}
       } else
 	std::cout << "Could not open " << txtfilename << std::endl;
+      if (filenames.size()>0) {
+	std::cout << filenames.size() << " filenames found in " << txtfilename << std::endl;
+	std::cout << "The files will be processed in the same order as found in the txt-file." << std::endl;
+      } else {
+	std::cout << "No files found in txt-file!" << std::endl;
+	return 1;
+      }
     }
+
+    std::cout << "###############" << std::endl;
     
     // Define decoders...
 #if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
@@ -319,14 +323,14 @@ int main(int argc, char *argv[]) {
       std::cout << "PEDESTAL " << std::endl;
 
         if (pedfilename.find(".tif") == std::string::npos) {
-	  std::string fname = pedfilename;
+	  const std::string fname(pedfilename);
 	  std::cout << fname << std::endl;
 	  std::time(&end_time);
 	  std::cout << "aaa " << std::ctime(&end_time) << std::endl;
 
 	  mt->setFrameMode(ePedestal);
 
-	  ifstream pedefile(fname, ios::in | ios::binary);
+	  std::ifstream pedefile(fname, ios::in | ios::binary);
 	  //      //open file
 	  if (pedefile.is_open()) {
 	    std::cout << "bbbb " << std::ctime(&end_time) << std::endl;
@@ -392,15 +396,15 @@ int main(int argc, char *argv[]) {
     mt->setFrameMode(eFrame);
 
     FILE *of = NULL;
+    std::ifstream filebin{};
     
     //NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS!
     for (unsigned int ifile = 0; ifile != filenames.size(); ++ifile) {
       std::cout << "DATA ";
-      //std::string fname(argv[iargc]);
       std::string fsuffix{};
-      std::string fprefix = getRootString(filenames[ifile]);
-      std::string imgfname = createFileName( outdir, fprefix, fsuffix, "tiff" );
-      std::string cfname = createFileName( outdir, fprefix, fsuffix, "clust" );
+      const std::string fprefix( getRootString(filenames[ifile]) );
+      std::string imgfname( createFileName( outdir, fprefix, fsuffix, "tiff" ) );
+      const std::string cfname( createFileName( outdir, fprefix, fsuffix, "clust" ) );
       std::cout << filenames[ifile] << " ";
       std::cout << imgfname << std::endl;
       std::time(&end_time);
@@ -408,7 +412,7 @@ int main(int argc, char *argv[]) {
 
       ifstream filebin(filenames[ifile], ios::in | ios::binary);
       //      //open file
-      ifile = 0;
+      ioutfile = 0;
       if (filebin.is_open()) {
 	if (thr <= 0 && cf != 0) { // cluster finder
 	  if (of == NULL) {
@@ -448,21 +452,23 @@ int main(int argc, char *argv[]) {
 	      imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", ioutfile );
 	      mt->writeImage(imgfname.c_str(), thr1);
 	      mt->clearImage();
-	      ioutfile++;
+	      ++ioutfile;
 	    }
 	  }
 	  // } else
 	  //std::cout << ifr << " " << ff << " " << np << std::endl;
 	  ff = -1;
 	}
-	std::cout << "--" << std::endl;
+	std::cout << "aa --" << std::endl;
 	filebin.close();
+	std::cout << "bb --" << std::endl;
 	while (mt->isBusy()) {
 	  ;
 	}
+	std::cout << "cc --" << std::endl;
 	if (nframes >= 0) {
 	  if (nframes > 0)
-	    imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", ifile );
+	    imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", ioutfile );
 	  std::cout << "Writing tiff to " << imgfname << " " << thr1
 		    << std::endl;
 	  mt->writeImage(imgfname.c_str(), thr1);
@@ -481,8 +487,8 @@ int main(int argc, char *argv[]) {
     }
     if (nframes < 0) {
       //std::string fname(argv[10]);
-      auto fprefix = getRootString(filenames[0]); //This might by a non-ideal name choice for that file
-      auto imgfname = createFileName( outdir, fprefix, "sum", "tiff" );
+      std::string fprefix( getRootString(filenames[0]) ); //This might by a non-ideal name choice for that file
+      std::string imgfname( createFileName( outdir, fprefix, "sum", "tiff" ) );
       std::cout << "Writing tiff to " << imgfname << " " << thr1 << std::endl;
       mt->writeImage(imgfname.c_str(), thr1);
     }

slsDetectorCalibration/multiThreadedAnalogDetector.h

@@ -130,6 +130,7 @@ class threadedAnalogDetector {
     // return 1;}
 
     virtual int isBusy() {
+      //std::cout << busy << " " << fifoData->isEmpty() << " " << fifoData->getDataValue() << " " << fifoData->getFreeValue() <<  std::endl;
         if (busy == 0) {
             usleep(100);
             if (busy == 0) {
@@ -447,7 +448,7 @@ class multiThreadedAnalogDetector {
         for (int i = 0; i < nThreads; i++) {
             ret1 = dets[i]->isBusy();
             ret |= ret1;
-            //   if (ret1) cout << "thread " << i <<" still busy " << endl;
+	    //if (ret1) cout << "thread " << i <<" still busy " << endl;
         }
         return ret;
     }

slsDetectorCalibration/singlePhotonDetector.h

@@ -63,7 +63,7 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
           quad(UNDEFINED_QUADRANT), tot(0), quadTot(0) {
 
         fm = new pthread_mutex_t;
-        pthread_mutex_init(fm, NULL);
+	pthread_mutex_init(fm, NULL);
 
         eventMask = new eventType *[ny];
         //  val=new double*[ny];