Rosenblatt transform works

.gitea/workflows/rh8-native.yml

@@ -21,9 +21,9 @@ jobs:
       - name: Build library 
         run: |
             mkdir build && cd build
-            cmake .. -DSLS_USE_PYTHON=ON -DSLS_USE_TESTS=ON -DSLS_USE_SIMULATOR=ON
+            cmake .. -DSLS_USE_PYTHON=ON -DSLS_USE_TESTS=ON 
             make -j 2 
 
       - name: C++ unit tests
         working-directory: ${{gitea.workspace}}/build
-        run: ctest -j1  --rerun-failed --output-on-failure
+        run: ctest

.gitea/workflows/rh9-native.yml

@@ -19,9 +19,9 @@ jobs:
       - name: Build library 
         run: |
             mkdir build && cd build
-            cmake .. -DSLS_USE_PYTHON=ON -DSLS_USE_TESTS=ON  -DSLS_USE_SIMULATOR=ON
+            cmake .. -DSLS_USE_PYTHON=ON -DSLS_USE_TESTS=ON
             make -j 2 
 
       - name: C++ unit tests
         working-directory: ${{gitea.workspace}}/build
-        run: ctest -j1  --rerun-failed --output-on-failure
+        run: ctest

.github/workflows/cmake.yaml

@@ -37,7 +37,7 @@ jobs:
 
       - name: C++ unit tests
         working-directory: ${{github.workspace}}/build
-        run: ctest -C ${{env.BUILD_TYPE}} -j1 --rerun-failed --output-on-failure
+        run: ctest -C ${{env.BUILD_TYPE}} -j1
 
       - name: Python unit tests
         working-directory: ${{github.workspace}}/build/bin

CMakeLists.txt

@@ -24,15 +24,6 @@ include(cmake/SlsAddFlag.cmake)
 include(cmake/helpers.cmake)
 
 
-find_package(Threads REQUIRED)
-
-# POSIX threads are required for the moment but we use CMake to find them
-# Once migrated to std::thread this can be removed
-if(NOT CMAKE_USE_PTHREADS_INIT)
-    message(FATAL_ERROR "A POSIX threads (pthread) implementation is required, but was not found.")
-endif()
-
-
 option(SLS_USE_SYSTEM_ZMQ "Use system installed libzmq" OFF)
 
 # Using FetchContent to get libzmq
@@ -341,9 +332,6 @@ if (NOT TARGET slsProjectCSettings)
                                                 -Wno-format-truncation
                                     )
     sls_disable_c_warning("-Wstringop-truncation")
-    target_link_libraries(slsProjectCSettings INTERFACE
-        Threads::Threads
-    )
 endif()
 
 

conda-recipes/main-library/build.sh

@@ -19,7 +19,6 @@ cmake .. -G Ninja \
       -DSLS_USE_PYTHON=OFF \
       -DCMAKE_BUILD_TYPE=Release \
       -DSLS_USE_HDF5=OFF \
-      -DSLS_USE_SYSTEM_ZMQ=ON \
      
 NCORES=$(getconf _NPROCESSORS_ONLN)
 echo "Building using: ${NCORES} cores"

conda-recipes/main-library/meta.yaml

@@ -29,7 +29,6 @@ requirements:
     - libtiff
     - zlib
     - expat
-    - zeromq
   
   run:
     - libstdcxx-ng

examples/rawdata.config

@@ -5,18 +5,18 @@ nsigma 5
 gainfile none
 detectorMode counting
 threshold 0
-pedestalfile none
+pedestalfile /mnt/sls_det_storage/moench_data/testNewFW20230714/cu_half_speed_d0_f0_4.raw
 nframes 0
 xMin 0
 xMax 400
 yMin 0
 yMax 400
-outdir ./
-indir ./
+outdir /mnt/sls_det_storage/moench_data/testNewFW20230714/clustNew/
+indir /mnt/sls_det_storage/moench_data/testNewFW20230714/
 flist none
-fformat none
+fformat cu_half_speed_d0_f0_4
 runmin 0
-runmax -1
+runmax 0
 readnrows 400
 eMin 0
 eMax 16000

python/scripts/generate_functions.py

@@ -33,31 +33,6 @@ def green(msg):
     return f"{GREENC}{msg}{ENDC}"
 
 
-QUALIFY_KINDS = {
-    cindex.CursorKind.NAMESPACE,
-    cindex.CursorKind.CLASS_DECL,
-    cindex.CursorKind.STRUCT_DECL,
-    cindex.CursorKind.CLASS_TEMPLATE,
-    cindex.CursorKind.ENUM_DECL,
-    cindex.CursorKind.UNION_DECL,
-    cindex.CursorKind.TYPE_ALIAS_DECL,
-}
-
-def qualified_name(cur: cindex.Cursor, include_leaf: bool = True) -> str:
-    """
-    Build a fully-qualified name by following semantic_parent up to the TU.
-    If include_leaf is False, returns just the enclosing scope (namespaces, classes).
-    """
-    parts = []
-    c = cur if include_leaf else cur.semantic_parent
-    while c and c.kind != cindex.CursorKind.TRANSLATION_UNIT:
-        name = c.spelling or c.displayname  # displayname helps for anonymous namespaces
-        if name and (c.kind in QUALIFY_KINDS or c is cur):
-            parts.append(name)
-        c = c.semantic_parent
-    return "::".join(reversed(parts))
-
-
 def check_libclang_version(required="12"):
     # Use already-loaded libclang, or let cindex resolve it
     lib = ctypes.CDLL(cindex.Config.library_file or ctypes.util.find_library("clang"))
@@ -101,8 +76,8 @@ def check_for_compile_commands_json(path):
         print(msg)
 
 
-default_build_path = Path("../../build/")
-fpath = Path("../../slsDetectorSoftware/src/Detector.cpp")
+default_build_path = "/home/l_frojdh/sls/build/"
+fpath = "../../slsDetectorSoftware/src/Detector.cpp"
 
 
 m = []
@@ -112,14 +87,25 @@ ag2 = []
 cn = []
 
 
+def get_arguments(node):
+    args = [a.type.spelling for a in node.get_arguments()]
+    args = [
+        "py::arg() = Positions{}" if item == "sls::Positions" else "py::arg()"
+        for item in args
+    ]
+    args = ", ".join(args)
+    if args:
+        args = f", {args}"
+    return args
+
 
 def get_arguments_with_default(node):
     args = []
     for arg in node.get_arguments():
         tokens = [t.spelling for t in arg.get_tokens()]
+        # print(tokens)
         if "=" in tokens:
-            # if arg.type.spelling == "sls::Positions":  # TODO! automate+
-            if arg.type.spelling == "Positions":  # TODO! automate
+            if arg.type.spelling == "sls::Positions":  # TODO! automate
                 args.append("py::arg() = Positions{}")
             else:
                 args.append("py::arg()" + "".join(tokens[tokens.index("=") :]))
@@ -188,10 +174,6 @@ def visit(node):
                     m.append(child)
                     args = get_arguments_with_default(child)
                     fs = get_fdec(child)
-                    qualified_class = qualified_name(child.semantic_parent)  # "ns1::ns2::Detector"
-                    # lines.append(
-                    #     f'CppDetectorApi.def("{child.spelling}", {fs} &{qualified_class}::{child.spelling}{args});'
-                    # )
                     lines.append(
                         f'CppDetectorApi.def("{child.spelling}",{fs} &Detector::{child.spelling}{args});'
                     )
@@ -220,11 +202,8 @@ if __name__ == "__main__":
     )
     cargs = parser.parse_args()
 
-    # check_libclang_version("12")
-    # check_clang_format_version(12)
-    cargs.build_path = cargs.build_path.resolve()
-    print(f'Using build path: {cargs.build_path}')
-
+    check_libclang_version("12")
+    check_clang_format_version(12)
     check_for_compile_commands_json(cargs.build_path)
 
     print("Parsing functions in Detector.h - ", end="", flush=True)
@@ -233,17 +212,11 @@ if __name__ == "__main__":
     db = cindex.CompilationDatabase.fromDirectory(cargs.build_path)
     index = cindex.Index.create()
     args = db.getCompileCommands(fpath)
-
-    
     args = list(iter(args).__next__().arguments)[0:-1]
-    # print('\n\nUsing compile commands:', args)
-    # args = args + "-x c++ --std=c++17".split()
+    args = args + "-x c++ --std=c++11".split()
     syspath = system_include_paths("clang++")
     incargs = ["-I" + inc for inc in syspath]
     args = args + incargs
-    args = [arg for arg in args if arg.startswith("-I") or arg.startswith("-D")]
-    # args = incargs
-    # print(f"\n\nUsing compile args: {' '.join(args)}")
     tu = index.parse(fpath, args=args)
     visit(tu.cursor)
     print(green("OK"))
@@ -268,5 +241,5 @@ if __name__ == "__main__":
     subprocess.run(["clang-format", "../src/detector.cpp", "-i"])
     print(green(" OK"))
 
-    # print("Changes since last commit:")
-    # subprocess.run(["git", "diff", "../src/detector.cpp"])
+    print("Changes since last commit:")
+    subprocess.run(["git", "diff", "../src/detector.cpp"])

python/scripts/parse.py

@@ -79,10 +79,4 @@ def system_include_paths(compiler, cpp=True):
         line = line.strip()
         paths.append(line)
     paths = [p.decode('utf-8') for p in paths]
-
-    # Only keep include paths from the conda prefix 
-    # remove anything pointing to gcc
-    prefix = os.environ['CONDA_PREFIX']
-    paths = [p for p in paths if prefix in p]
-    paths = [p for p in paths if 'gcc' not in p]
     return paths 

python/src/detector_in.cpp

@@ -12,7 +12,11 @@
 #include <chrono>
 namespace py = pybind11;
 void init_det(py::module &m) {
-    using namespace sls; //TODO! qualify arguments and return types to avoid this
+    using sls::defs;
+    using sls::Detector;
+    using sls::ns;
+    using sls::Positions;
+    using sls::Result;
 
     m.def("freeSharedMemory", (void (*)(const int, const int)) &sls::freeSharedMemory, py::arg() = 0, py::arg() = -1);
 

sample/CMakeLists.txt

@@ -3,6 +3,8 @@
 add_executable(using_logger using_logger.cpp)
 target_link_libraries(using_logger 
     slsSupportShared
+    pthread
+    rt
 )  
 
 set_target_properties(using_logger PROPERTIES

slsDetectorCalibration/interpolations/etaInterpolationBase.h

@@ -200,6 +200,9 @@ class etaInterpolationBase : public slsInterpolation {
     // virtual void prepareInterpolation(int &ok)=0;
 
     void debugSaveAll(int ind = 0) {
+
+      std::cout << "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++SAVING ETAS"<< std::endl;
+      
         int ibx, iby;
         char tit[10000];
 
@@ -214,21 +217,21 @@ class etaInterpolationBase : public slsInterpolation {
             etah[ii] = heta[ii];
             tot_eta += heta[ii];
         }
-        sprintf(tit, "/scratch/eta_%d.tiff", ind);
+        sprintf(tit, "eta_%d.tiff", ind);
         WriteToTiff(etah, tit, nbetaX, nbetaY);
 
         for (int ii = 0; ii < nbetaX * nbetaY; ii++) {
             ibb = (hhx[ii] * nSubPixelsX);
             etah[ii] = ibb;
         }
-        sprintf(tit, "/scratch/eta_hhx_%d.tiff", ind);
+        sprintf(tit, "eta_hhx_%d.tiff", ind);
         WriteToTiff(etah, tit, nbetaX, nbetaY);
 
         for (int ii = 0; ii < nbetaX * nbetaY; ii++) {
             ibb = hhy[ii] * nSubPixelsY;
             etah[ii] = ibb;
         }
-        sprintf(tit, "/scratch/eta_hhy_%d.tiff", ind);
+        sprintf(tit, "eta_hhy_%d.tiff", ind);
         WriteToTiff(etah, tit, nbetaX, nbetaY);
 
         float *ftest = new float[nSubPixelsX * nSubPixelsY];
@@ -262,7 +265,7 @@ class etaInterpolationBase : public slsInterpolation {
                      << std::endl;
         }
 
-        sprintf(tit, "/scratch/ftest_%d.tiff", ind);
+        sprintf(tit, "./ftest_%d.tiff", ind);
         WriteToTiff(ftest, tit, nSubPixelsX, nSubPixelsY);
 
         // int ibx=0, iby=0;
@@ -280,7 +283,7 @@ class etaInterpolationBase : public slsInterpolation {
             } else
                 etah[ii] = 0;
         }
-        sprintf(tit, "/scratch/eta_bad_%d.tiff", ind);
+        sprintf(tit, "./eta_bad_%d.tiff", ind);
         WriteToTiff(etah, tit, nbetaX, nbetaY);
         // std::cout << "Index: " << ind << "\t Bad bins: "<< nbad << std::endl;
         // int ibx=0, iby=0;

slsDetectorCalibration/interpolations/etaInterpolationRosenblatt.h

@@ -0,0 +1,232 @@
+// SPDX-License-Identifier: LGPL-3.0-or-other
+// Copyright (C) 2021 Contributors to the SLS Detector Package
+#ifndef ETA_INTERPOLATION_POSXY_H
+#define ETA_INTERPOLATION_POSXY_H
+//#define SAVE_ALL
+//#include "sls/tiffIO.h"
+#include "eta2InterpolationBase.h"
+#include "eta3InterpolationBase.h"
+#include "etaInterpolationBase.h"
+
+
+class etaInterpolationRosenblatt : public virtual etaInterpolationBase {
+  public:
+    etaInterpolationRosenblatt(int nx = 400, int ny = 400, int ns = 25, int nsy = 25,
+                          int nb = -1, int nby = -1, double emin = 1,
+                          double emax = 0)
+        : etaInterpolationBase(nx, ny, ns, nsy, nb, nby, emin, emax){
+              //  std::cout << "epxy " << nb << " " << emin << " " << emax << std::endl;
+              //  std::cout << nbeta << " " << etamin << " " << etamax << std::endl;
+          };
+
+    etaInterpolationRosenblatt(etaInterpolationRosenblatt *orig)
+        : etaInterpolationBase(orig){};
+
+    virtual etaInterpolationRosenblatt *Clone() = 0; /* { */
+
+    /* return new etaInterpolationPosXY(this); */
+
+    /* }; */
+
+    virtual void prepareInterpolation(int &ok) {
+        ok = 1;
+
+        ///*Eta Distribution Rebinning*///
+        // double bsize=1./nSubPixels; //precision
+        // std::cout<<"nPixelsX = "<<nPixelsX<<" nPixelsY = "<<nPixelsY<<" nSubPixels
+        // = "<<nSubPixels<<endl;
+        double tot_eta = 0;
+        double tot_eta_x = 0;
+        double tot_eta_y = 0;
+        for (int ip = 0; ip < nbetaX * nbetaY; ip++)
+            tot_eta += heta[ip];
+        std::cout << "total eta entries is :" << tot_eta << std::endl;
+        if (tot_eta <= 0) {
+            ok = 0;
+            return;
+        };
+
+        double *hx = new double[nbetaX];  // profile x
+        double *hy = new double[nbetaY];  // profile y
+        double *hix = new double[nbetaX]; // integral of projection x
+        double *hiy = new double[nbetaY]; // integral of projection y
+        //  int ii=0;
+        double etax, etay;
+        for (int ib = 0; ib < nbetaX; ib++) {
+
+            // tot_eta_y=0;
+
+            for (int iby = 0; iby < nbetaY; iby++) {
+                etay = etamin + iby * etastepY;
+                // std::cout << etax << std::endl;
+
+                // tot_eta_x+=hx[iby];
+                if (etay >= 0 && etay <= 1)
+                    hy[iby] = heta[ib + iby * nbetaX];
+                else
+                    hy[iby] = 0;
+                // tot_eta_y+=hy[iby];
+            }
+
+            hiy[0] = hy[0];
+
+            for (int iby = 1; iby < nbetaY; iby++) {
+                hiy[iby] = hiy[iby - 1] + hy[iby];
+            }
+
+            tot_eta_y = hiy[nbetaY - 1] + 1;
+
+            for (int iby = 0; iby < nbetaY; iby++) {
+                if (tot_eta_y <= 0) {
+                    hhy[ib + iby * nbetaX] = -1;
+                    // ii=(ibx*nSubPixels)/nbeta;
+                } else {
+                    // if (hiy[ibx]>tot_eta_y*(ii+1)/nSubPixels) ii++;
+                    hhy[ib + iby * nbetaX] = hiy[iby] / tot_eta_y;
+                }
+            }
+        }
+
+        for (int ib = 0; ib < nbetaY; ib++) {
+
+            for (int ibx = 0; ibx < nbetaX; ibx++) {
+                etax = etamin + ibx * etastepX;
+                // std::cout << etax << std::endl;
+                if (etax >= 0 && etax <= 1)
+                    hx[ibx] = heta[ibx + ib * nbetaX];
+                else {
+                    hx[ibx] = 0;
+                }
+            }
+            hix[0] = hx[0];
+
+            for (int ibx = 1; ibx < nbetaX; ibx++) {
+                hix[ibx] = hix[ibx - 1] + hx[ibx];
+            }
+
+	    // tot_eta_x = hix[nbetaX - 1] + 1;
+
+            for (int ibx = 0; ibx < nbetaX; ibx++) {
+	      //if (tot_eta_x <= 0) {
+              //      hhx[ibx + ib * nbetaX] = -1;
+              //  } else {
+	      hhx[ibx + ib * nbetaX] = hix[ibx];// / tot_eta_x;
+	      //}
+            }
+
+            
+        }
+
+
+	  for (int ibx = 0; ibx < nbetaX; ibx++) {
+	  int val=0;
+	for (int ib = 0; ib < nbetaY; ib++) {
+	    val+=hhx[ibx + ib * nbetaX];
+	  }
+	// for (int ibx = 0; ibx < nbetaX; ibx++) {
+	for (int ib = 0; ib < nbetaY; ib++) {
+	    hhx[ibx + ib * nbetaX]=val;
+          }    
+	}
+	tot_eta_x = hhx[nbetaX - 1] + 1;
+	for (int ib = 0; ib < nbetaY; ib++) {
+	    
+	  //tot_eta_x = hix[nbetaX - 1] + 1;
+
+            for (int ibx = 0; ibx < nbetaX; ibx++) {
+                if (tot_eta_x <= 0) {
+                    hhx[ibx + ib * nbetaX] = -1;
+                } else {
+                    hhx[ibx + ib * nbetaX] = hhx[ibx + ib * nbetaX] / tot_eta_x;
+                }
+            }
+	}
+	/*
+        int ibx, iby, ib;
+
+        iby = 0;
+        while (hhx[iby * nbetaY + nbetaY / 2] < 0)
+            iby++;
+        for (ib = 0; ib < iby; ib++) {
+            for (ibx = 0; ibx < nbetaX; ibx++)
+                hhx[ibx + nbetaX * ib] = hhx[ibx + nbetaX * iby];
+        }
+        iby = nbetaY - 1;
+
+        while (hhx[iby * nbetaY + nbetaY / 2] < 0)
+            iby--;
+        for (ib = iby + 1; ib < nbetaY; ib++) {
+            for (ibx = 0; ibx < nbetaX; ibx++)
+                hhx[ibx + nbetaX * ib] = hhx[ibx + nbetaX * iby];
+        }
+
+        iby = 0;
+        while (hhy[nbetaX / 2 * nbetaX + iby] < 0)
+            iby++;
+        for (ib = 0; ib < iby; ib++) {
+            for (ibx = 0; ibx < nbetaY; ibx++)
+                hhy[ib + nbetaX * ibx] = hhy[iby + nbetaX * ibx];
+        }
+        iby = nbetaX - 1;
+
+        while (hhy[nbetaX / 2 * nbetaX + iby] < 0)
+            iby--;
+        for (ib = iby + 1; ib < nbetaX; ib++) {
+            for (ibx = 0; ibx < nbetaY; ibx++)
+                hhy[ib + nbetaX * ibx] = hhy[iby + nbetaX * ibx];
+        }
+	*/
+	//#ifdef SAVE_ALL
+        debugSaveAll();
+	//#endif
+        delete[] hx;
+        delete[] hy;
+        delete[] hix;
+        delete[] hiy;
+
+        return;
+    }
+};
+
+class eta2InterpolationRosenblatt : public virtual eta2InterpolationBase,
+                               public virtual etaInterpolationRosenblatt {
+  public:
+    eta2InterpolationRosenblatt(int nx = 400, int ny = 400, int ns = 25,
+                           int nsy = 25, int nb = -1, int nby = -1,
+                           double emin = 1, double emax = 0)
+        : etaInterpolationBase(nx, ny, ns, nsy, nb, nby, emin, emax),
+          eta2InterpolationBase(nx, ny, ns, nsy, nb, nby, emin, emax),
+          etaInterpolationRosenblatt(nx, ny, ns, nsy, nb, nby, emin, emax){
+              //  std::cout << "e2pxy " << nb << " " << emin << " " << emax << std::endl;
+          };
+
+    eta2InterpolationRosenblatt(eta2InterpolationRosenblatt *orig)
+        : etaInterpolationBase(orig), etaInterpolationRosenblatt(orig){};
+
+    virtual eta2InterpolationRosenblatt *Clone() {
+        return new eta2InterpolationRosenblatt(this);
+    };
+};
+
+class eta3InterpolationRosenblatt : public virtual eta3InterpolationBase,
+                               public virtual etaInterpolationRosenblatt {
+  public:
+    eta3InterpolationRosenblatt(int nx = 400, int ny = 400, int ns = 25,
+                           int nsy = 25, int nb = -1, int nby = -1,
+                           double emin = 1, double emax = 0)
+        : etaInterpolationBase(nx, ny, ns, nsy, nb, nby, emin, emax),
+          eta3InterpolationBase(nx, ny, ns, nsy, nb, nby, emin, emax),
+          etaInterpolationRosenblatt(nx, ny, ns, nsy, nb, nby, emin, emax){
+              //   std::cout << "e3pxy " << nbeta << " " << etamin << " " << etamax
+              //   << " " << nSubPixels<< std::endl;
+          };
+
+    eta3InterpolationRosenblatt(eta3InterpolationRosenblatt *orig)
+        : etaInterpolationBase(orig), etaInterpolationRosenblatt(orig){};
+
+    virtual eta3InterpolationRosenblatt *Clone() {
+        return new eta3InterpolationRosenblatt(this);
+    };
+};
+
+#endif

slsDetectorCalibration/jungfrauExecutables/CMakeLists.txt

@@ -76,8 +76,11 @@ foreach(exe ${JUNGFRAU_EXECUTABLES})
     target_link_libraries(${exe} 
         PUBLIC
         slsSupportStatic
+        pthread 
         tiffio
         fmt::fmt
+          #-L/usr/lib64/
+        #-lm  -lstdc++  -lrt
 
         PRIVATE
         slsProjectWarnings

slsDetectorCalibration/moenchExecutables/CMakeLists.txt

@@ -69,6 +69,7 @@ foreach(exe ${MOENCH_EXECUTABLES})
         PUBLIC
         slsSupportStatic
         ${ZeroMQ_LIBRARIES} 
+        pthread 
         tiffio
 
         PRIVATE

slsDetectorCalibration/moenchExecutables/moench03Interpolation.cpp

@@ -17,7 +17,7 @@
 #endif
 
 //#include "etaInterpolationPosXY.h"
-#include "etaInterpolationPosXY.h"
+#include "etaInterpolationRosenblatt.h"
 #include "noInterpolation.h"
 //#include "etaInterpolationCleverAdaptiveBins.h"
 //#include "etaInterpolationRandomBins.h"
@@ -114,8 +114,8 @@ int main(int argc, char *argv[]) {
     //int f0 = -1;
     //  int nSubPixels = nsubpix;
 #ifndef NOINTERPOLATION
-    eta2InterpolationPosXY *interp =
-      new eta2InterpolationPosXY(NC, NR, nsubpix, nsubpix, etabins, etabins, etamin, etamax);
+    eta2InterpolationRosenblatt *interp =
+      new eta2InterpolationRosenblatt(NC, NR, nsubpix, nsubpix, etabins, etabins, etamin, etamax);
     // eta2InterpolationCleverAdaptiveBins *interp=new
     // eta2InterpolationCleverAdaptiveBins(NC, NR, nsubpix, etabins, etamin,
     // etamax);
@@ -134,6 +134,7 @@ int main(int argc, char *argv[]) {
     cout << "read ff " << argv[2] << endl;
     sprintf(fname, "%s", argv[2]);
     interp->readFlatField(fname);
+    
     interp->prepareInterpolation(ok); //, MAX_ITERATIONS);
 #endif
     // return 0;

slsDetectorCalibration/moenchExecutables/moenchRawDataProcess.cpp

@@ -174,6 +174,7 @@ int main(int argc, char *argv[]) {
     int nped = 1000;
     
     int cf = 0;
+
     int numberOfPackets=nrows/8;
 #ifdef RECT
     cout << "Should be rectangular but now it will crash! No data structure defined!" << endl;
@@ -181,7 +182,7 @@ int main(int argc, char *argv[]) {
     
 #ifndef MOENCH04
     moench03v2Data *decoder = new moench03v2Data(nrows/2);
-    cout << "MOENCH03!" << endl;
+    cout << "MOENCH03 V2!" << endl;
 #endif
 
 #ifdef MOENCH04
@@ -298,7 +299,7 @@ int main(int argc, char *argv[]) {
     double *ped=new double[nx * ny];//, *ped1;
     int pos,pos1;
     //return  0;
-  
+
     if (pedfile.find(".raw") != std::string::npos) {
       pos1=pedfile.rfind("/");
       strcpy(froot,pedfile.substr(pos1).c_str());
@@ -309,6 +310,7 @@ int main(int argc, char *argv[]) {
     cout << "PEDESTAL " << endl;
     if (pedfile.find(".tif") == std::string::npos) {
       sprintf(fname, "%s", pedfile.c_str());
+
             cout << fname << endl;
             std::time(&end_time);
             //cout << "aaa" << std::ctime(&end_time) << endl;
@@ -320,24 +322,28 @@ int main(int argc, char *argv[]) {
             if (filebin.is_open()) {
 	      ff = -1;
                 while (decoder->readNextFrame(filebin, ff, np, buff)) {
+
 		  if (np == numberOfPackets) {
 		    mt->pushData(buff);
                         mt->nextThread();
                         mt->popFree(buff);
                         ifr++;
 			if (ifr % 100 == 0)
+
 			  cout << ifr << " " << ff << " " << np << endl;
 			    //	break;
 		  } else {
-		    cout << ifr << " " << ff << " " << np << endl;
+		    cout << "bp "<< ifr << " " << ff << " " << np << endl;
 		    break;
 		  }
                     ff = -1;
                 }
                 filebin.close();
                 while (mt->isBusy()) {
-		          ;
-		          }
+
+		  ;
+
+		}
 		
 		sprintf(imgfname, "%s/%s_ped.tiff", outdir.c_str(),froot);
 		mt->writePedestal(imgfname);
@@ -382,7 +388,7 @@ int main(int argc, char *argv[]) {
        runmax--;
        flist.close();
        cout << "Found " << runmax << " files " << endl;
-       flist.open (fformat, std::ifstream::in);
+       flist.open (args["flist"].c_str(), std::ifstream::in);
     } 
 
     for (int irun = runmin; irun <= runmax; irun++) {
@@ -435,6 +441,7 @@ int main(int argc, char *argv[]) {
             ff = -1;
             ifr = 0;
             while (decoder->readNextFrame(filebin, ff, np, buff)) {
+
 	      if (np == numberOfPackets) {
                     //         //push
                     mt->pushData(buff);
@@ -462,8 +469,19 @@ int main(int argc, char *argv[]) {
                     }
 	      } else {
 		cout << "bp " << ifr << " " << ff << " " << np << endl;
+		
 	      }
                 ff = -1;
+
+
+		if (ifr % 100 == 0){
+		  sprintf(imgfname, "%s/%s_f%05d_ped.tiff", outdir.c_str(),froot, ifile++); 
+		  while (mt->isBusy()) {
+		    ;
+		  }
+		  mt->writePedestal(imgfname);
+		}
+
             }
             cout << "--" << endl;
             filebin.close();

slsDetectorServers/ctbDetectorServer/CMakeLists.txt

@@ -37,9 +37,7 @@ target_compile_definitions(ctbDetectorServer_virtual
 )
 
 target_link_libraries(ctbDetectorServer_virtual
-    PUBLIC 
-    m 
-    slsProjectCSettings
+    PUBLIC pthread rt m slsProjectCSettings
 )
 
 set_target_properties(ctbDetectorServer_virtual PROPERTIES

slsDetectorServers/eigerDetectorServer/CMakeLists.txt

@@ -30,8 +30,7 @@ target_compile_definitions(eigerDetectorServer_virtual
 )
 
 target_link_libraries(eigerDetectorServer_virtual
-    PUBLIC 
-        slsProjectCSettings
+    PUBLIC pthread rt slsProjectCSettings
 )
 
 set_target_properties(eigerDetectorServer_virtual PROPERTIES

slsDetectorServers/gotthard2DetectorServer/CMakeLists.txt

@@ -31,8 +31,7 @@ target_compile_definitions(gotthard2DetectorServer_virtual
 )
 
 target_link_libraries(gotthard2DetectorServer_virtual
-    PUBLIC 
-        slsProjectCSettings
+    PUBLIC pthread rt slsProjectCSettings
 )
 
 set_target_properties(gotthard2DetectorServer_virtual PROPERTIES

slsDetectorServers/jungfrauDetectorServer/CMakeLists.txt

@@ -29,8 +29,7 @@ target_compile_definitions(jungfrauDetectorServer_virtual
 )
 
 target_link_libraries(jungfrauDetectorServer_virtual
-    PUBLIC 
-        slsProjectCSettings
+    PUBLIC pthread rt slsProjectCSettings
 )
 
 set_target_properties(jungfrauDetectorServer_virtual PROPERTIES

slsDetectorServers/moenchDetectorServer/CMakeLists.txt

@@ -29,8 +29,7 @@ target_compile_definitions(moenchDetectorServer_virtual
 )
 
 target_link_libraries(moenchDetectorServer_virtual
-    PUBLIC 
-        slsProjectCSettings
+    PUBLIC pthread rt slsProjectCSettings
 )
 
 set_target_properties(moenchDetectorServer_virtual PROPERTIES

slsDetectorServers/mythen3DetectorServer/CMakeLists.txt

@@ -33,8 +33,7 @@ target_compile_definitions(mythen3DetectorServer_virtual
 )
 
 target_link_libraries(mythen3DetectorServer_virtual
-    PUBLIC 
-        slsProjectCSettings
+    PUBLIC pthread rt slsProjectCSettings
 )
 
 set_target_properties(mythen3DetectorServer_virtual PROPERTIES

slsDetectorServers/xilinx_ctbDetectorServer/CMakeLists.txt

@@ -31,9 +31,7 @@ target_compile_definitions(xilinx_ctbDetectorServer_virtual
 )
 
 target_link_libraries(xilinx_ctbDetectorServer_virtual
-    PUBLIC 
-        m 
-        slsProjectCSettings
+    PUBLIC pthread rt m slsProjectCSettings
 )
 
 set_target_properties(xilinx_ctbDetectorServer_virtual PROPERTIES

slsDetectorSoftware/CMakeLists.txt

@@ -28,11 +28,11 @@ target_link_libraries(slsDetectorObject
     PUBLIC
         slsProjectOptions
         slsSupportStatic
+        pthread
     PRIVATE
         slsProjectWarnings
 )
 
-
 set(DETECTOR_LIBRARY_TARGETS slsDetectorObject)
 
 
@@ -97,7 +97,8 @@ if(SLS_USE_TEXTCLIENT)
         add_executable(${val1} src/CmdApp.cpp)
 
         target_link_libraries(${val1} 
-            slsDetectorStatic
+        slsDetectorStatic
+        pthread
         )
         SET_SOURCE_FILES_PROPERTIES( src/Caller.cpp PROPERTIES COMPILE_FLAGS "-Wno-unused-variable -Wno-unused-but-set-variable")
 

slsReceiverSoftware/CMakeLists.txt

@@ -49,7 +49,7 @@ target_link_libraries(slsReceiverObject
     slsProjectOptions
     slsSupportStatic
   PRIVATE
-    slsProjectWarnings #don't propagate warnings
+    slsProjectWarnings #don't propagate warnigns 
 )
 
 target_compile_definitions(slsReceiverObject 
@@ -118,6 +118,8 @@ if (SLS_USE_RECEIVER_BINARIES)
     target_link_libraries(slsReceiver PUBLIC
     PUBLIC
         slsReceiverStatic
+        pthread
+        rt
     PRIVATE
         slsProjectWarnings
     )
@@ -136,6 +138,8 @@ if (SLS_USE_RECEIVER_BINARIES)
     target_link_libraries(slsMultiReceiver 
     PUBLIC
         slsReceiverStatic
+        pthread
+        rt
     PRIVATE
         slsProjectWarnings
     )
@@ -154,6 +158,8 @@ if (SLS_USE_RECEIVER_BINARIES)
     target_link_libraries(slsFrameSynchronizer 
     PUBLIC
         slsReceiverStatic
+        pthread
+        rt
     PRIVATE
         slsProjectWarnings
         

slsReceiverSoftware/tests/test-Apps.cpp

@@ -147,12 +147,8 @@ TEST_CASE("Parse port and uid", "[detector]") {
     for (auto app : {AppType::SingleReceiver, AppType::MultiReceiver,
                      AppType::FrameSynchronizer}) {
         CommandLineOptions s(app);
-
-        // TODO! This test fails on gitea CI probably because the user can set the uid
-        // commenting it out for now. Revisit later.
-        // REQUIRE_THROWS(
-        //     s.parse({"", "-p", "1234", "-u", invalidUidStr})); // invalid uid
-
+        REQUIRE_THROWS(
+            s.parse({"", "-p", "1234", "-u", invalidUidStr})); // invalid uid
         REQUIRE_THROWS(s.parse({"", "-p", "500"}));            // invalid port
 
         auto opts = s.parse({"", "-p", "1234", "-u", uidStr});

slsSupportLib/CMakeLists.txt

@@ -1,8 +1,5 @@
 # SPDX-License-Identifier: LGPL-3.0-or-other
 # Copyright (C) 2021 Contributors to the SLS Detector Package
-
-
-
 set(SOURCES
     src/string_utils.cpp
     src/file_utils.cpp
@@ -92,17 +89,12 @@ target_link_libraries(slsSupportObject
   PUBLIC
     slsProjectOptions 
     ${STD_FS_LIB} # from helpers.cmake
-    Threads::Threads # slsDetector and Receiver need this
     
   PRIVATE
     slsProjectWarnings
     md5sls     
 )
 
-#RH8 glibc 2.28, RH9 glibc 2.34 linking rt is only needed with glibc < 2.34
-#but we do it for all Linux builds to avoid too many conditionals
-target_link_libraries (slsSupportObject PUBLIC $<$<PLATFORM_ID:Linux>:rt>) 
-
 #Treat both vendored and system zmq as interface for receiver binaries
 if(SLS_USE_SYSTEM_ZMQ)
     message(STATUS "slsSupportLib using ZEROMQ_TARGET=${ZEROMQ_TARGET}")

tests/CMakeLists.txt

@@ -24,6 +24,7 @@ target_link_libraries(tests
     PUBLIC 
       slsProjectOptions
       slsSupportStatic
+      pthread
     PRIVATE
       slsProjectWarnings
 )