From 5caf1966fb36122407b72331c48e80930d07bcdc Mon Sep 17 00:00:00 2001
From: Kirsty Paton <kirsty.paton@psi.ch>
Date: Mon, 22 Jan 2024 14:20:25 +0100
Subject: [PATCH] Introduced changes apply common mode correction - temporarily
 commented out along with other earlier changes to try an understand
 segmentation fault after one file processed.

---
 .../jungfrauRawDataProcess.cpp                  | 17 +++++++++++++----
 slsDetectorCalibration/tiffio/src/tiffIO.cpp    |  3 ++-
 2 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp b/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp
index 8eb5f9844..2cd64be9e 100644
--- a/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp
+++ b/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp
@@ -2,8 +2,12 @@
 // Copyright (C) 2021 Contributors to the SLS Detector Package
 //#include "sls/ansi.h"
 #include <iostream>
-#undef CORR
+//enable common mode subtraction
+//#define CMS
 
+//disable common mode subtraction
+//#undef CMS
+#undef CORR
 #define C_GHOST 0.0004
 
 #define CM_ROWS 50
@@ -36,6 +40,7 @@
 #include <map>
 #include <stdio.h>
 #include <sys/stat.h>
+//#include "jungfrauCommonMode.h"
 
 #include <ctime>
 using namespace std;
@@ -44,7 +49,7 @@ int main(int argc, char *argv[]) {
 
     if (argc < 6) {
         cout << "Usage is " << argv[0]
-             << "indir outdir fname(no extension) fextension csize [runmin] [runmax] [pedfile (raw or tiff)] [threshold]"
+             << " indir outdir fname(no extension) fextension csize [runmin] [runmax] [pedfile (raw or tiff)] [threshold]"
                 "[nframes] [xmin xmax ymin ymax] [gainmap]"
              << endl;
         cout << "threshold <0 means analog; threshold=0 means cluster finder; "
@@ -81,7 +86,7 @@ int main(int argc, char *argv[]) {
     cout << "Jungfrau strixel full module readout" << endl;
     jungfrauLGADStrixelsData *decoder = new jungfrauLGADStrixelsData();
     int nx = 1024/5, ny = 512*5;
-#endif
+#endif 
 #ifdef JFSTRXCHIP1
     std::cout << "Jungfrau strixel LGAD single chip 1" << std::endl;
     jungfrauLGADStrixelsDataSingleChip *decoder = new jungfrauLGADStrixelsDataSingleChip(1);
@@ -179,7 +184,11 @@ int main(int argc, char *argv[]) {
     cout << "Nframes is " << nframes << endl;
 
     uint32_t nnx, nny;
-
+//    commonModeSubtraction *cm = NULL;
+//#ifdef CMS
+//    cm = new commonModeSubtractionSuperColumnJF();
+//    std::cout << "Enabled common mode subtraction" << std::endl;
+//#endif
     singlePhotonDetector *filter = new singlePhotonDetector(
         decoder, 3, nsigma, 1, NULL, nped, 200, -1, -1, gainmap, NULL);
 
diff --git a/slsDetectorCalibration/tiffio/src/tiffIO.cpp b/slsDetectorCalibration/tiffio/src/tiffIO.cpp
index 0aa5cc786..6347ac3e3 100644
--- a/slsDetectorCalibration/tiffio/src/tiffIO.cpp
+++ b/slsDetectorCalibration/tiffio/src/tiffIO.cpp
@@ -3,7 +3,8 @@
 
 #include "sls/tiffIO.h"
 #include <iostream>
-#include <tiffio.h>
+#include "/usr/include/tiffio.h"
+//#include <tiffio.h>
 
 void *WriteToTiff(float *imgData, const char *imgname, int ncol, int nrow) {
     constexpr uint32_t sampleperpixel = 1;