From 2b93ef4565ef9113cace2cba2cc6717261a5a80d Mon Sep 17 00:00:00 2001
From: vhinger182 <viktoria.hinger@psi.ch>
Date: Fri, 6 Oct 2023 11:55:20 +0200
Subject: [PATCH] minor

---
 .../jungfrauLGADStrixelsData_new.h            |  2 +-
 .../jungfrauExecutables/CMakeLists.txt        |  2 +-
 .../jungfrauRawDataProcess.cpp                |  2 +-
 .../jungfrauRawDataProcess_filetxt.cpp        | 19 +++++++++++++------
 4 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h b/slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h
index 58da3c570..1220fdba4 100644
--- a/slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h
+++ b/slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h
@@ -81,7 +81,7 @@ constexpr int c6g1_ystart = c6g2_yend + 1;        // 448
 constexpr int c6g1_yend = c6g2_yend + 64 - gr;    // 502
 
 // y shift due to faulty bonding (relevant for M408)
-constexpr int bond_shift_y = 1; // CHANGE IF YOU CHANGE MODULE!
+constexpr int bond_shift_y = 0; // CHANGE IF YOU CHANGE MODULE!
 
 } // namespace strixelSingleChip
 
diff --git a/slsDetectorCalibration/jungfrauExecutables/CMakeLists.txt b/slsDetectorCalibration/jungfrauExecutables/CMakeLists.txt
index bf9322db3..b6f2d2337 100644
--- a/slsDetectorCalibration/jungfrauExecutables/CMakeLists.txt
+++ b/slsDetectorCalibration/jungfrauExecutables/CMakeLists.txt
@@ -15,7 +15,7 @@ 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)
 
diff --git a/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp b/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp
index cba1a8be2..6320807ed 100644
--- a/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp
+++ b/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp
@@ -360,7 +360,7 @@ int main(int argc, char *argv[]) {
 
 	  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;
diff --git a/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxt.cpp b/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxt.cpp
index 11f0a1c6a..e12400d9e 100644
--- a/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxt.cpp
+++ b/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxt.cpp
@@ -111,11 +111,6 @@ int main(int argc, char *argv[]) {
     const std::string jsonmastername(argv[3]);
     const std::string pedfilename(argv[4]);
 
-    int xmin = atoi(argv[5]);
-    int xmax = atoi(argv[6]);
-    int ymin = atoi(argv[7]);
-    int ymax = atoi(argv[8]);
-
     double thr = 0;
     double thr1 = 1;
     thr = atof(argv[9]);
@@ -172,6 +167,8 @@ int main(int argc, char *argv[]) {
 	rxroi_ymin = j["Receiver Roi"]["ymin"];
 	rxroi_ymax = j["Receiver Roi"]["ymax"];
 	masterfile.close();
+	std::cout << "Read rxROI [" << rxroi_xmin << ", " << rxroi_xmax << ", "
+		      << rxroi_ymin << ", " << rxroi_ymax << "]" << std::endl;
       } else 
 	std::cout << "Could not open master file " << jsonmastername << std::endl;
       
@@ -254,7 +251,16 @@ int main(int argc, char *argv[]) {
     decoder->getDetectorSize(nx, ny);
     std::cout << "Detector size is " << nx << " " << ny << std::endl;
 
+    //Cluster finder ROI
+    int xmin = 0, xmax = nx-1, ymin = 0, ymax = ny-1;
+    xmin = atoi(argv[5]);
+    xmax = atoi(argv[6]);
+    ymin = atoi(argv[7]);
+    ymax = atoi(argv[8]);
+    std::cout << "Cluster finder ROI: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]"
+              << std::endl;
 
+    /* old
     if ( xmin == xmax ) {
       xmin = 0;
       xmax = nx;
@@ -265,6 +271,7 @@ int main(int argc, char *argv[]) {
     }
     std::cout << xmin << " " << xmax << " " << ymin << " " << ymax << " "
               << std::endl;
+    */
 
     /*
     char *gainfname = NULL;
@@ -436,7 +443,7 @@ int main(int argc, char *argv[]) {
       std::time(&end_time);
       std::cout << std::ctime(&end_time) << std::endl;
 
-      ifstream filebin(filenames[ifile], ios::in | ios::binary);
+      std::ifstream filebin(filenames[ifile], ios::in | ios::binary);
       //      //open file
       ioutfile = 0;
       if (filebin.is_open()) {