fixed linking issue in arping and shm test (#659)

Co-authored-by: Erik Frojdh <erik.frojdh@psi.ch>

docs/src/slsreceiver.rst

@@ -86,6 +86,145 @@ Client Commands
         sls_detector_get -h rx_framescaught
 
 
+ZMQ: Json Header Format
+------------------------
+
+
+**Change in field names from slsDetectorPackage v6.x.x to v7.0.0**
+
+* detSpec1 <- bunchId
+* detSpec2 <- reserved
+* detSpec3 <- debug
+* detSpec4 <- roundRNumber
+
+
+**Format**
+
+    .. code-block:: bash 
+
+        {
+            "jsonversion": unsigned int,
+            "bitmode": unsigned int,
+            "fileIndex": unsigned long int,
+            "detshape": [
+                unsigned int,
+                unsigned int
+            ],
+            "shape": [
+                unsigned int,
+                unsigned int
+            ],
+            "size": unsigned int,
+            "acqIndex": unsigned long int,
+            "frameIndex": unsigned long int,
+            "progress": double,
+            "fname": string,
+            "data": unsigned int,
+            "completeImage": unsigned int,
+
+            "frameNumber": unsigned long long int,
+            "expLength": unsigned int,
+            "packetNumber": unsigned int,
+            "detSpec1": unsigned long int,
+            "timestamp": unsigned long int,
+            "modId": unsigned int,
+            "row": unsigned int,
+            "column": unsigned int,
+            "detSpec2": unsigned int,
+            "detSpec3": unsigned int,
+            "detSpec4": unsigned int,
+            "detType": unsigned int,
+            "version": unsigned int,
+            
+            "flipRows": unsigned int,
+            "quad": unsigned int,
+            "addJsonHeader": {
+                string : string
+            }
+        }
+
+   +--------------+----------------------------------------------+
+   |   Field      |       Description                            |
+   +--------------+----------------------------------------------+
+   | jsonversion  | Version of the json header.                  |
+   |              | Value at 4 for v6.x.x and v7.x.x             |
+   +--------------+----------------------------------------------+
+   | bitmode      | Bits per pixel [4|8|16|32]                   |
+   +--------------+----------------------------------------------+
+   | fileIndex    | Current file acquisition index               |
+   +--------------+----------------------------------------------+
+   | detshape     | Geometry of the entire detector              |
+   +--------------+----------------------------------------------+
+   | shape        | Geometry of the current port streamed out    |
+   +--------------+----------------------------------------------+
+   | size         | Size of image of current port in bytesout    |
+   +--------------+----------------------------------------------+
+   | acqIndex     | Frame number from the detector (redundant)   |
+   +--------------+----------------------------------------------+
+   | frameIndex   | Frame number of current acquisition          |
+   |              | (Starting at 0)                              |
+   +--------------+----------------------------------------------+
+   | progress     | Progress of current acquisition in %         |
+   +--------------+----------------------------------------------+
+   | fname        | Current file name                            |
+   +--------------+----------------------------------------------+
+   | data         | 1 if there is data following                 |
+   |              | 0 if dummy header                            |
+   +--------------+----------------------------------------------+
+   | completeImage| 1 if no missing packets for this frame       |
+   |              | in this port, else 0                         |
+   +--------------+----------------------------------------------+
+   | frameNumber  | Frame number                                 |
+   |              | [From detector udp header]                   |
+   +--------------+----------------------------------------------+
+   | expLength    | subframe number (32 bit eiger)               |
+   |              | or real time exposure time in 100ns (others) |
+   |              | [From detector udp header]                   |
+   +--------------+----------------------------------------------+
+   | packetNumber | Number of packets caught for that frame      |
+   +--------------+----------------------------------------------+
+   | detSpec1     | See :ref:`here<Detector Specific Fields>`    |
+   |              | [From detector udp header]                   |
+   +--------------+----------------------------------------------+
+   | timestamp    | Timestamp with 10 MHz clock                  |
+   |              | [From detector udp header]                   |
+   +--------------+----------------------------------------------+
+   | modId        | Module Id                                    |
+   |              | [From detector udp header]                   |
+   +--------------+----------------------------------------------+
+   | row          | Row number in detector                       |
+   |              | [From detector udp header]                   |
+   +--------------+----------------------------------------------+
+   | column       | Column number in detector                    |
+   |              | [From detector udp header]                   |
+   +--------------+----------------------------------------------+
+   | detSpec2     | See :ref:`here<Detector Specific Fields>`    |
+   |              | [From detector udp header]                   |
+   +--------------+----------------------------------------------+
+   | detSpec3     | See :ref:`here<Detector Specific Fields>`    |
+   |              | [From detector udp header]                   |
+   +--------------+----------------------------------------------+
+   | detSpec4     | See :ref:`here<Detector Specific Fields>`    |
+   |              | [From detector udp header]                   |
+   +--------------+----------------------------------------------+
+   | detType      | Detector type enum                           |
+   | detSpec3     | See :ref:`Detector enum<Detector Enum>`      |
+   |              | [From detector udp header]                   |
+   +--------------+----------------------------------------------+
+   | version      | Detector header version. At 2                |
+   |              | [From detector udp header]                   |
+   +--------------+----------------------------------------------+
+   | flipRows     | 1 if rows should be flipped.                 |
+   |              | Usually for Eiger bottom.                    |
+   +--------------+----------------------------------------------+
+   | quad         | 1 if its an Eiger quad.                      |
+   +--------------+----------------------------------------------+
+   | addJsonHeader| Optional custom parameters that is required  |
+   |              | for processing code.                         |
+   +--------------+----------------------------------------------+
+
+
+
 File format
 --------------
 

examples/badchannel.txt

@@ -0,0 +1,6 @@
+0
+10, 30
+40:45 50:52
+1279
+# all bad channels are applied for all counters in deector
+

patternGenerator/plotPattern.py

@@ -31,7 +31,7 @@ alpha_wait = [0.5, 0.5, 0.5, 0.5, 0.5, 0.5]
 alpha_wait_rect = [0.2, 0.2, 0.2, 0.2, 0.2, 0.2]
 
 # Loop colors and line styles (6 needed from 0 to 5)
-colors_loop = ['tab:green', 'tab:red', 'tab:purple', 'tab:brown', 'tab:ping', 'tab:grey']
+colors_loop = ['tab:green', 'tab:red', 'tab:purple', 'tab:brown', 'tab:pink', 'tab:grey']
 linestyles_loop = ['-.', '-.', '-.', '-.', '-.', '-.']
 alpha_loop = [0.5, 0.5, 0.5, 0.5, 0.5, 0.5]
 alpha_loop_rect = [0.2, 0.2, 0.2, 0.2, 0.2, 0.2]
@@ -527,7 +527,7 @@ for idx, i in enumerate(range(nbiteff)):
                            linestyle=linestyles_loop[2], color=colors_loop[2], alpha=alpha_loop[2],
                            label="loop 2: " + str(nloop2) + " times" if idx == 0 else "", linewidth=2.0)
             axs2[idx].plot([loop2_end, loop2_end], [-10, 10],
-                           linestyle=linestyles_loop[0], color=colors_loop[0], alpha=alpha_loop[2], linewidth=2.0)
+                           linestyle=linestyles_loop[2], color=colors_loop[2], alpha=alpha_loop[2], linewidth=2.0)
 
     # Loop 3
     if nloop3 is not None:

python/slsdet/detector.py

@@ -14,7 +14,7 @@ streamingInterface = slsDetectorDefs.streamingInterface
 defs = slsDetectorDefs
 
 from .utils import element_if_equal, all_equal, get_set_bits, list_to_bitmask
-from .utils import Geometry, to_geo, element, reduce_time, is_iterable
+from .utils import Geometry, to_geo, element, reduce_time, is_iterable, hostname_list
 from _slsdet import xy
 from . import utils as ut
 from .proxy import JsonProxy, SlowAdcProxy, ClkDivProxy, MaxPhaseProxy, ClkFreqProxy, PatLoopProxy, PatNLoopProxy, PatWaitProxy, PatWaitTimeProxy 
@@ -162,12 +162,8 @@ class Detector(CppDetectorApi):
 
     @hostname.setter
     def hostname(self, hostnames):
-        if isinstance(hostnames, str):
+        args = hostname_list(hostnames)
-            hostnames = [hostnames]
+        self.setHostname(args)
-        if isinstance(hostnames, list):
-            self.setHostname(hostnames)
-        else:
-            raise ValueError("hostname needs to be string or list of strings")
 
 
     @property
@@ -271,7 +267,7 @@ class Detector(CppDetectorApi):
     @element
     def rx_threads(self):
         """
-        Get thread ids from the receiver in order of [parent, tcp, listener 0, processor 0, streamer 0, listener 1, processor 1, streamer 1, arping]. 
+        Get kernel thread ids from the receiver in order of [parent, tcp, listener 0, processor 0, streamer 0, listener 1, processor 1, streamer 1, arping]. 
         
         Note
         -----
@@ -784,7 +780,8 @@ class Detector(CppDetectorApi):
 
     @rx_hostname.setter
     def rx_hostname(self, hostname):
-        self.setRxHostname(hostname)
+        args = hostname_list(hostname)
+        self.setRxHostname(args)
 
     @property
     @element
@@ -1568,6 +1565,20 @@ class Detector(CppDetectorApi):
     def trimval(self, value):
         ut.set_using_dict(self.setAllTrimbits, value)
 
+    @property
+    @element
+    def fliprows(self):
+        """
+        [Eiger] flips rows paramater sent to slsreceiver to stream as json parameter to flip rows in gui. \n
+        [Jungfrau] flips rows in the detector itself. For bottom module and number of interfaces must be set to 2. slsReceiver and slsDetectorGui does not handle.
+        """
+        return self.getFlipRows()
+
+    @fliprows.setter
+    def fliprows(self, value):
+        ut.set_using_dict(self.setFlipRows, value)
+
+
     @property
     @element
     def master(self):
@@ -1593,6 +1604,19 @@ class Detector(CppDetectorApi):
     def sync(self, value):
         ut.set_using_dict(self.setSynchronization, value)
 
+    @property
+    @element
+    def badchannels(self):
+        """
+        [fname|none|0]\n\t[Gotthard2][Mythen3] Sets the bad channels (from file of bad channel numbers) to be masked out. None or 0 unsets all the badchannels.\n
+        [Mythen3] Also does trimming
+        """
+        return self.getBadChannels()
+
+    @badchannels.setter
+    def badchannels(self, value):
+        ut.set_using_dict(self.setBadChannels, value)
+
     @property
     @element
     def lock(self):
@@ -1802,6 +1826,15 @@ class Detector(CppDetectorApi):
 
     @property
     def versions(self):
+        if self.type == detectorType.EIGER:
+            return {'type': self.type,
+                'package': self.packageversion, 
+                'client': self.clientversion,
+                'firmware': self.firmwareversion,
+                'detectorserver': self.detectorserverversion,
+                'kernel': self.kernelversion,
+                'receiver': self.rx_version}
+
         return {'type': self.type,
                 'package': self.packageversion, 
                 'client': self.clientversion,

python/slsdet/utils.py

@@ -261,3 +261,20 @@ def merge_args(*args):
 
     else:
         raise ValueError("Multiple dictionaries passes cannot merge args")
+
+
+def hostname_list(args):
+    """
+    Generates a list from a hostname string
+    * Lists are passed through
+    * as are tuples (conversion in pybind11 to vector)
+    * if + is found it splits the string
+    """
+    if isinstance(args, (list, tuple)):
+        return args
+    elif(isinstance(args, str)):
+        hosts = args.split('+')
+        hosts = [it for it in hosts if len(it)]
+        return hosts
+    else:
+        raise ValueError("hostname needs to be string or list of strings")

python/src/detector.cpp

@@ -219,6 +219,21 @@ void init_det(py::module &m) {
         (void (Detector::*)(const std::string &, sls::Positions)) &
             Detector::setBadChannels,
         py::arg(), py::arg() = Positions{});
+    CppDetectorApi.def(
+        "getBadChannels",
+        (Result<std::vector<int>>(Detector::*)(sls::Positions) const) &
+            Detector::getBadChannels,
+        py::arg() = Positions{});
+    CppDetectorApi.def(
+        "setBadChannels",
+        (void (Detector::*)(const std::vector<int>, sls::Positions)) &
+            Detector::setBadChannels,
+        py::arg(), py::arg() = Positions{});
+    CppDetectorApi.def(
+        "setBadChannels",
+        (void (Detector::*)(const std::vector<std::vector<int>>)) &
+            Detector::setBadChannels,
+        py::arg());
     CppDetectorApi.def("isVirtualDetectorServer",
                        (Result<bool>(Detector::*)(sls::Positions) const) &
                            Detector::isVirtualDetectorServer,

python/src/duration.cpp

@@ -12,6 +12,7 @@ void init_duration(py::module &m) {
         .def("total_seconds", &DurationWrapper::total_seconds)
         .def("count", &DurationWrapper::count)
         .def("set_count", &DurationWrapper::set_count)
+        .def("__eq__", &DurationWrapper::operator==)
         .def("__repr__", [](const DurationWrapper &self) {
             std::stringstream ss;
             ss << "sls::DurationWrapper(total_seconds: " << self.total_seconds()

python/tests/test_utils.py

@@ -8,7 +8,7 @@ Testing functions from utils.py
 
 import pytest
 from slsdet.utils import *
-from slsdet import IpAddr, MacAddr
+from slsdet import IpAddr, MacAddr, DurationWrapper
 import datetime as dt
 import pathlib
 from pathlib import Path
@@ -22,7 +22,11 @@ def test_iterable():
 
 
 def test_reduce_time_to_single_value_from_list():
-    t = 3 * [dt.timedelta(seconds=1)]
+    t = [dt.timedelta(seconds=1) for i in range(3)]
+    assert reduce_time(t) == 1
+
+def test_reduce_time_to_single_value_from_list_DurationWrapper():
+    t = [DurationWrapper(1) for i in range(3)]
     assert reduce_time(t) == 1
 
 
@@ -83,6 +87,12 @@ def test_all_equal_str_fails():
     assert all_equal('aaab') == False
 
 
+def test_all_equal_DurationWrapper():
+    assert all_equal([DurationWrapper(1), DurationWrapper(1)])
+
+def test_all_equal_DurationWrapper_fail():
+    assert not all_equal([DurationWrapper(1), DurationWrapper(2)])
+
 def test_element_if_equal_int():
     assert element_if_equal([5, 5]) == 5
 
@@ -342,3 +352,32 @@ def test_merge_args_tuple():
 
 def test_merge_args_dict_with_tuple():
     assert merge_args({0: (1,2)}, 3) == ({0: (1,2,3)},)
+
+
+def test_hostname_to_list():
+    s = "localhost"
+    r = hostname_list(s)
+    assert r == [s]
+
+def test_hostname_to_list_passthrough():
+    args = ["localhost"]
+    ret = hostname_list(args)
+    assert ret == args
+
+    args = ("localhost",)
+    ret = hostname_list(args)
+    assert ret == args
+
+def test_splitting_hostname():
+    args = 'apple+banana+pear+'
+    ret = hostname_list(args)
+    assert ret == ['apple', 'banana', 'pear']
+
+    #not sensitive to trailing +
+    args = 'apple+banana+pear'
+    ret = hostname_list(args)
+    assert ret == ['apple', 'banana', 'pear']
+
+def test_hostame_throws_on_wrong_args():
+    with pytest.raises(Exception) as e:
+        hostname_list(5)

serverBin/ctbDetectorServerv7.0.0.rc1

@@ -1 +0,0 @@
-../slsDetectorServers/ctbDetectorServer/bin/ctbDetectorServerv7.0.0.rc1

serverBin/ctbDetectorServerv7.0.0.rc3

@@ -0,0 +1 @@
+../slsDetectorServers/ctbDetectorServer/bin/ctbDetectorServerv7.0.0.rc3

serverBin/eigerDetectorServerv7.0.0.rc1

@@ -1 +0,0 @@
-../slsDetectorServers/eigerDetectorServer/bin/eigerDetectorServerv7.0.0.rc1

serverBin/eigerDetectorServerv7.0.0.rc3

@@ -0,0 +1 @@
+../slsDetectorServers/eigerDetectorServer/bin/eigerDetectorServerv7.0.0.rc3

serverBin/gotthard2DetectorServerv7.0.0.rc1

@@ -1 +0,0 @@
-../slsDetectorServers/gotthard2DetectorServer/bin/gotthard2DetectorServerv7.0.0.rc1

serverBin/gotthard2DetectorServerv7.0.0.rc3

@@ -0,0 +1 @@
+../slsDetectorServers/gotthard2DetectorServer/bin/gotthard2DetectorServerv7.0.0.rc3

serverBin/gotthardDetectorServerv7.0.0.rc1

@@ -1 +0,0 @@
-../slsDetectorServers/gotthardDetectorServer/bin/gotthardDetectorServerv7.0.0.rc1

serverBin/gotthardDetectorServerv7.0.0.rc3

@@ -0,0 +1 @@
+../slsDetectorServers/gotthardDetectorServer/bin/gotthardDetectorServerv7.0.0.rc3

serverBin/jungfrauDetectorServerv7.0.0.rc1

@@ -1 +0,0 @@
-../slsDetectorServers/jungfrauDetectorServer/bin/jungfrauDetectorServerv7.0.0.rc1

serverBin/jungfrauDetectorServerv7.0.0.rc3

@@ -0,0 +1 @@
+../slsDetectorServers/jungfrauDetectorServer/bin/jungfrauDetectorServerv7.0.0.rc3

serverBin/moenchDetectorServerv7.0.0.rc1

@@ -1 +0,0 @@
-../slsDetectorServers/moenchDetectorServer/bin/moenchDetectorServerv7.0.0.rc1

serverBin/moenchDetectorServerv7.0.0.rc3

@@ -0,0 +1 @@
+../slsDetectorServers/moenchDetectorServer/bin/moenchDetectorServerv7.0.0.rc3

serverBin/mythen3DetectorServerv7.0.0.rc1

@@ -1 +0,0 @@
-../slsDetectorServers/mythen3DetectorServer/bin/mythen3DetectorServerv7.0.0.rc1

serverBin/mythen3DetectorServerv7.0.0.rc3

@@ -0,0 +1 @@
+../slsDetectorServers/mythen3DetectorServer/bin/mythen3DetectorServerv7.0.0.rc3

slsDetectorCalibration/dataStructures/jungfrauModuleData.h

@@ -40,20 +40,31 @@ class jungfrauModuleData : public slsDetectorData<uint16_t> {
        out by a module i.e. using the slsReceiver (160x160 pixels, 40 packets
        1286 large etc.) \param c crosstalk parameter for the output buffer
 
-    */
+   */
+#ifndef ZMQ
+#define off sizeof(jf_header)
+#endif
+#ifdef ZMQ
+#define off 0
+#endif
+
+
     jungfrauModuleData()
         : slsDetectorData<uint16_t>(1024, 512,
-                                    1024* 512 * 2 + sizeof(jf_header)) {
+                                    1024* 512 * 2 + off) {
   
         for (int ix = 0; ix < 1024; ix++) {
             for (int iy = 0; iy < 512; iy++) {
-                dataMap[iy][ix] = sizeof(jf_header) + (1024 * iy + ix) * 2;
+                dataMap[iy][ix] = off + (1024 * iy + ix) * 2;
 #ifdef HIGHZ
                 dataMask[iy][ix] = 0x3fff;
 #endif
             }
         }
 
+
+
+
         iframe = 0;
         //  cout << "data struct created" << endl;
     };

slsDetectorCalibration/jungfrauExecutables/Makefile.rawdataprocess

@@ -0,0 +1,64 @@
+# SPDX-License-Identifier: LGPL-3.0-or-other
+# Copyright (C) 2021 Contributors to the SLS Detector Package
+#module add CBFlib/0.9.5
+INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures  -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/ -I../tiffio/include
+
+LDFLAG= ../tiffio/src/tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++   -pthread -lrt    -ltiff -O3  -std=c++11
+
+MAIN=jungfrauClusterFinder.cpp
+
+
+all: jungfrauRawDataProcess
+
+jungfrauRawDataProcess:  jungfrauRawDataProcess.cpp  $(INCS) clean
+			 g++ -o jungfrauRawDataProcess  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  -DMODULE
+
+jungfrauRawDataProcessStrx:  jungfrauRawDataProcess.cpp  $(INCS) clean
+			 g++ -o jungfrauRawDataProcessStrx  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DJFSTRX 
+
+jungfrauRawDataProcessStrxAldo:  jungfrauRawDataProcess.cpp  $(INCS) clean
+			 g++ -o jungfrauRawDataProcessStrxAldo  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DJFSTRX -DALDO
+
+jungfrauRawDataProcessStrxOld:  jungfrauRawDataProcess.cpp  $(INCS) clean
+			 g++ -o jungfrauRawDataProcessStrxOld  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DJFSTRXOLD 
+
+jungfrauRawDataProcessStrxOldAldo:  jungfrauRawDataProcess.cpp  $(INCS) clean
+			 g++ -o jungfrauRawDataProcessStrxOldAldo  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DJFSTRXOLD -DALDO
+
+
+
+jungfrauClusterFinder:  jungfrauClusterFinder.cpp  $(INCS) clean
+			 g++ -o jungfrauClusterFinder  jungfrauClusterFinder.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  
+
+
+jungfrauClusterFinderHighZ:  jungfrauClusterFinder.cpp  $(INCS) clean
+			 g++ -o jungfrauClusterFinderHighZ  jungfrauClusterFinder.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  -DHIGHZ 
+
+
+
+
+jungfrauMakeEta:  jungfrauInterpolation.cpp  $(INCS) clean
+			 g++ -o jungfrauMakeEta jungfrauInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DFF
+
+jungfrauInterpolation:  jungfrauInterpolation.cpp  $(INCS) clean
+			 g++ -o jungfrauInterpolation jungfrauInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  
+
+jungfrauNoInterpolation:  jungfrauNoInterpolation.cpp  $(INCS) clean
+			 g++ -o jungfrauNoInterpolation jungfrauNoInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) 
+
+jungfrauPhotonCounter: jungfrauPhotonCounter.cpp   $(INCS) clean
+			 g++ -o jungfrauPhotonCounter  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER
+
+jungfrauAnalog: jungfrauPhotonCounter.cpp  $(INCS) clean
+			 g++ -o jungfrauAnalog  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DANALOG
+
+jungfrauPhotonCounterHighZ: jungfrauPhotonCounter.cpp   $(INCS) clean
+			 g++ -o jungfrauPhotonCounterHighZ  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DHIGHZ
+
+jungfrauAnalogHighZ: jungfrauPhotonCounter.cpp  $(INCS) clean
+			 g++ -o jungfrauAnalogHighZ  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DANALOG -DHIGHZ
+
+clean: 	
+	rm -f  jungfrauClusterFinder jungfrauMakeEta jungfrauInterpolation jungfrauNoInterpolation jungfrauPhotonCounter jungfrauAnalog
+
+

slsDetectorCalibration/jungfrauExecutables/Makefile.zmq

@@ -1,25 +1,19 @@
 # SPDX-License-Identifier: LGPL-3.0-or-other
 # Copyright (C) 2021 Contributors to the SLS Detector Package
 
-INCDIR=   -I. -I../dataStructures ../tiffIO.cpp -I../ -I../interpolations/ -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/ -I../../libs/rapidjson/
+INCDIR=   -I. -I../dataStructures ../tiffio/src/tiffIO.cpp -I../ -I../interpolations/ -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/ -I../../libs/rapidjson/ -I../tiffio/include
 LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt -ltiff   -O3  -std=c++11 -Wall -L../../build/bin/ -lSlsSupport
 #-L../../bin -lhdf5  -L.
 
 #DESTDIR?=../bin
 
-all:  moenchZmqProcess moenchZmq04Process
+all:  jungfrauZmqProcess 
- #moenchZmqProcessCtbGui
+ #jungfrauZmqProcessCtbGui
 
-moenchZmqProcess:  moenchZmqProcess.cpp   clean
+jungfrauZmqProcess:  jungfrauZmqProcess.cpp   clean
-		      g++ -o moenchZmqProcess  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP 
+		      g++ -o jungfrauZmqProcess  jungfrauZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP
-
-moenchZmq04Process:  moenchZmqProcess.cpp   clean
-		      g++ -o moench04ZmqProcess  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP -DMOENCH04 
-
-#moenchZmqProcessCtbGui:  moenchZmqProcess.cpp   clean
-#		      g++ -o moenchZmqProcessCtbGui  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP -DCTBGUI
 
 clean: 	
-	rm -f  moenchZmqProcess  
+	rm -f   jungfrauZmqProcess  
 
 

slsDetectorCalibration/jungfrauExecutables/Makefile.zmqrootdisp

@@ -0,0 +1,26 @@
+ROOTSYS=/opt/cern/v6/root
+#/afs/psi.ch/project/sls_det_sof/roottware/root_v5.34.23_sl6_64bit
+
+
+
+LIBZMQDIR = $(PWD)
+LIBZMQ =  -L$(LIBZMQDIR) -lzmq
+SHLIB_PATH=/opt/cern/v6/root/lib
+CMAKE_PREFIX_PATH=/opt/cern/v6/root
+DYLD_LIBRARY_PATH=/opt/cern/v6/root/lib
+
+
+INCDIR=   -I. -I../dataStructures ../tiffio/src/tiffIO.cpp -I../ -I../interpolations/ -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/ -I../../libs/rapidjson/ -I../tiffio/include
+LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt -ltiff   -O3  -std=c++11 -Wall -L../../build/bin/ -lSlsSupport
+#-L../../bin -lhdf5  -L.
+
+
+
+default: onlinedisp_zmq
+
+onlinedisp_zmq: onlinedisp_zmq.cpp onlinedisp_zmq.h 
+# flags from root-config --cflags --glibs
+	g++ -o onlinedisp_zmq onlinedisp_zmq.cpp  -I. -I$(ROOTSYS)/include -Wall -g -lm  -L. -lzmq -pthread -lrt -L$(ROOTSYS)/lib -lGui -lCore  -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix  -lPhysics -lMathCore -lThread -m64 $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) 
+
+#-lCint
+

slsDetectorCalibration/jungfrauExecutables/examples.txt

@@ -0,0 +1,10 @@
+
+
+ sls_detector_put rx_jsonpara detectorMode counting 
+ sls_detector_put rx_jsonpara frameMode newPedestal 
+ sls_detector_put rx_jsonpara frameMode frame 
+ sls_detector_put rx_jsonpara detectorMode analog 
+ sls_detector_put rx_jsonpara threshold 150
+ sls_detector_put rx_jsonpara threshold 0
+ sls_detector_put rx_jsonpara threshold 300
+ sls_detector_put rx_zmqhwm 50

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp

@@ -0,0 +1,418 @@
+// SPDX-License-Identifier: LGPL-3.0-or-other
+// Copyright (C) 2021 Contributors to the SLS Detector Package
+//#include "sls/ansi.h"
+#include <iostream>
+#undef CORR
+
+#define C_GHOST 0.0004
+
+#define CM_ROWS 50
+
+#define RAWDATA
+
+#ifndef JFSTRX
+#ifndef JFSTRXOLD
+#ifndef MODULE
+#include "jungfrauHighZSingleChipData.h"
+#endif
+#ifdef MODULE
+#include "jungfrauModuleData.h"
+#endif
+#endif
+#endif
+#ifdef JFSTRX
+#include "jungfrauLGADStrixelsData.h"
+#endif
+#ifdef JFSTRXOLD
+#include "jungfrauStrixelsHalfModuleOldDesign.h"
+#endif
+
+#include "multiThreadedCountingDetector.h"
+#include "singlePhotonDetector.h"
+
+#include <fstream>
+#include <map>
+#include <stdio.h>
+#include <sys/stat.h>
+
+#include <ctime>
+using namespace std;
+
+int main(int argc, char *argv[]) {
+
+    if (argc < 5) {
+        cout << "Usage is " << argv[0]
+             << "indir outdir fname(no extension) fextension [runmin] [runmax] [pedfile (raw or tiff)] [threshold] "
+                "[nframes] [xmin xmax ymin ymax] [gainmap]"
+             << endl;
+        cout << "threshold <0 means analog; threshold=0 means cluster finder; "
+                "threshold>0 means photon counting"
+             << endl;
+        cout << "nframes <0 means sum everything; nframes=0 means one file per "
+                "run; nframes>0 means one file every nframes"
+             << endl;
+        return 1;
+    }
+
+    int fifosize = 1000;
+    int nthreads = 10;
+    int csize = 3;
+    int nsigma = 5;
+    int nped = 10000;
+
+    int cf = 0;
+
+
+#ifndef JFSTRX
+#ifndef JFSTRXOLD
+#ifndef MODULE
+    jungfrauHighZSingleChipData *decoder = new jungfrauHighZSingleChipData();
+    int nx = 256, ny = 256;
+#endif
+#ifdef MODULE
+    jungfrauModuleData *decoder = new jungfrauModuleData();
+    int nx = 1024, ny = 512;
+
+#endif
+#endif
+#endif
+#ifdef JFSTRX
+    cout << "bbb" << endl;
+    jungfrauLGADStrixelsData *decoder = new jungfrauLGADStrixelsData();
+    int nx = 1024/5, ny = 512*5;
+#endif
+#ifdef JFSTRXOLD
+    cout << "ccc" << endl;
+    jungfrauStrixelsHalfModuleOldDesign *decoder = new jungfrauStrixelsHalfModuleOldDesign();
+    int nx = 1024*3, ny = 512/3;
+#endif
+
+
+    decoder->getDetectorSize(nx, ny);
+
+
+
+
+
+    cout << "Detector size is " << nx << " " << ny << endl;
+
+
+
+
+
+
+
+
+    double *gainmap = NULL;
+    //float *gm;
+
+    int ff, np;
+    // cout << " data size is " << dsize;
+
+    ifstream filebin;
+    char *indir = argv[1];
+    char *outdir = argv[2];
+    char *fformat = argv[3];
+    char *fext = argv[4];
+    int runmin = 0;
+
+    // cout << "argc is " << argc << endl;
+    if (argc >= 6) {
+        runmin = atoi(argv[5]);
+    }
+
+    int runmax = runmin;
+
+    if (argc >= 7) {
+        runmax = atoi(argv[6]);
+    }
+
+    char *pedfile = NULL;
+    if (argc >= 8) {
+        pedfile = argv[7];
+    }
+    double thr = 0;
+    double thr1 = 1;
+
+    if (argc >= 9) {
+        thr = atof(argv[8]);
+    }
+
+    int nframes = 0;
+
+    if (argc >= 10) {
+        nframes = atoi(argv[9]);
+    }
+
+    int xmin = 0, xmax = nx, ymin = 0, ymax = ny;
+    if (argc >= 14) {
+        xmin = atoi(argv[10]);
+        xmax = atoi(argv[11]);
+        ymin = atoi(argv[12]);
+        ymax = atoi(argv[13]);
+    }
+
+    char *gainfname = NULL;
+    if (argc > 14) {
+        gainfname = argv[14];
+        cout << "Gain map file name is: " << gainfname << endl;
+    }
+
+    char ffname[10000];
+    char fname[10000];
+    char imgfname[10000];
+    char cfname[10000];
+
+    std::time_t end_time;
+
+    FILE *of = NULL;
+    cout << "input directory is " << indir << endl;
+    cout << "output directory is " << outdir << endl;
+    cout << "input file is " << fformat << endl;
+    cout << "runmin is " << runmin << endl;
+    cout << "runmax is " << runmax << endl;
+    if (pedfile)
+        cout << "pedestal file is " << pedfile << endl;
+    if (thr > 0)
+        cout << "threshold is " << thr << endl;
+    cout << "Nframes is " << nframes << endl;
+
+    uint32_t nnx, nny;
+
+    singlePhotonDetector *filter = new singlePhotonDetector(
+        decoder, csize, nsigma, 1, NULL, nped, 200, -1, -1, gainmap, NULL);
+
+    if (gainfname) {
+
+        if (filter->readGainMap(gainfname))
+            cout << "using gain map " << gainfname << endl;
+        else
+            cout << "Could not open gain map " << gainfname << endl;
+    } else
+        thr = 0.15 * thr;
+    filter->newDataSet();
+    //int dsize = decoder->getDataSize();
+
+    if (thr > 0) {
+        cout << "threshold is " << thr << endl;
+        filter->setThreshold(thr);
+        cf = 0;
+
+    } else
+        cf = 1;
+
+    filter->setROI(xmin, xmax, ymin, ymax);
+    std::time(&end_time);
+    cout << std::ctime(&end_time) << endl;
+
+    char *buff;
+
+    // multiThreadedAnalogDetector *mt=new
+    // multiThreadedAnalogDetector(filter,nthreads,fifosize);
+    multiThreadedCountingDetector *mt =
+        new multiThreadedCountingDetector(filter, nthreads, fifosize);
+#ifndef ANALOG
+    mt->setDetectorMode(ePhotonCounting);
+    cout << "Counting!" << endl;
+    if (thr > 0) {
+        cf = 0;
+    }
+#endif
+//{
+#ifdef ANALOG
+    mt->setDetectorMode(eAnalog);
+    cout << "Analog!" << endl;
+    cf = 0;
+    // thr1=thr;
+#endif
+    //  }
+
+    mt->StartThreads();
+    mt->popFree(buff);
+
+    //  cout << "mt " << endl;
+
+    int ifr = 0;
+
+    char froot[1000];
+    double *ped=new double[nx * ny];//, *ped1;
+
+    int pos,pos1;
+
+    if (pedfile) {
+
+      if (string(pedfile).find(".dat") != std::string::npos) {
+	pos1=string(pedfile).rfind("/");
+	strcpy(froot,pedfile+pos1);
+	pos=string(froot).find(".dat");
+	froot[pos]='\0';
+      }
+
+        cout << "PEDESTAL " << endl;
+	// sprintf(imgfname, "%s/pedestals.tiff", outdir);
+
+        if (string(pedfile).find(".tif") == std::string::npos) {
+            sprintf(fname, "%s", pedfile);
+            cout << fname << endl;
+            std::time(&end_time);
+            //cout << "aaa" << std::ctime(&end_time) << endl;
+
+            mt->setFrameMode(ePedestal);
+            // sprintf(fn,fformat,irun);
+            filebin.open((const char *)(fname), ios::in | ios::binary);
+            //      //open file
+            if (filebin.is_open()) {
+                ff = -1;
+                while (decoder->readNextFrame(filebin, ff, np, buff)) {
+		  // if (np == 40) {
+		  if ((ifr+1) % 100 == 0) {
+		    cout << " ****" << decoder->getValue(buff,20,20);// << endl;
+		  }
+                        mt->pushData(buff);
+                        mt->nextThread();
+                        mt->popFree(buff);
+                        ifr++;
+                        if (ifr % 100 == 0) {
+			  cout << " ****" << ifr << " " << ff << " " << np << endl;
+			} //else
+                        //cout << ifr << " " << ff << " " << np << endl;
+			if (ifr>=1000)
+			  break;
+                    ff = -1;
+                }
+                filebin.close();
+                while (mt->isBusy()) {
+                    ;
+                }
+
+		sprintf(imgfname, "%s/%s_ped.tiff", outdir, froot);
+		mt->writePedestal(imgfname);
+		sprintf(imgfname, "%s/%s_rms.tiff", outdir, froot);
+		mt->writePedestalRMS(imgfname);
+
+            } else
+                cout << "Could not open pedestal file " << fname
+                     << " for reading " << endl;
+        } else {
+            float *pp = ReadFromTiff(pedfile, nny, nnx);
+            if (pp && (int)nnx == nx && (int)nny == ny) {
+                for (int i = 0; i < nx * ny; i++) {
+                    ped[i] = pp[i];
+                }
+                delete[] pp;
+                mt->setPedestal(ped);
+                cout << "Pedestal set from tiff file " << pedfile << endl;
+            } else {
+                cout << "Could not open pedestal tiff file " << pedfile
+                     << " for reading " << endl;
+            }
+        }
+        std::time(&end_time);
+        cout << std::ctime(&end_time) << endl;
+    }
+
+    ifr = 0;
+    int ifile = 0;
+
+    mt->setFrameMode(eFrame);
+
+    for (int irun = runmin; irun <= runmax; irun++) {
+        cout << "DATA ";
+        // sprintf(fn,fformat,irun);
+        sprintf(ffname, "%s/%s.%s", indir, fformat, fext);
+        sprintf(fname, (const char*)ffname, irun);
+        sprintf(ffname, "%s/%s.tiff", outdir, fformat);
+        sprintf(imgfname, (const char*)ffname, irun);
+        sprintf(ffname, "%s/%s.clust", outdir, fformat);
+        sprintf(cfname, (const char*)ffname, irun);
+        cout << fname << " ";
+        cout << imgfname << endl;
+        std::time(&end_time);
+        cout << std::ctime(&end_time) << endl;
+        //  cout <<  fname << " " << outfname << " " << imgfname <<  endl;
+        filebin.open((const char *)(fname), ios::in | ios::binary);
+        //      //open file
+        ifile = 0;
+        if (filebin.is_open()) {
+            if (thr <= 0 && cf != 0) { // cluster finder
+                if (of == NULL) {
+                    of = fopen(cfname, "w");
+                    if (of) {
+                        mt->setFilePointer(of);
+                        cout << "file pointer set " << endl;
+                    } else {
+                        cout << "Could not open " << cfname << " for writing "
+                             << endl;
+                        mt->setFilePointer(NULL);
+                        return 1;
+                    }
+                }
+            }
+            //     //while read frame
+            ff = -1;
+            ifr = 0;
+            while (decoder->readNextFrame(filebin, ff, np, buff)) {
+              //  if (np == 40) {
+                    //         //push
+	      
+		  if ((ifr+1) % 100 == 0) {
+		    cout << " ****" << decoder->getValue(buff,20,20);// << endl;
+		  }
+                    mt->pushData(buff);
+                    // 	//         //pop
+                    mt->nextThread();
+                    mt->popFree(buff);
+
+                    ifr++;
+                    if (ifr % 100 == 0)
+		      cout << " " << ifr << " " << ff << endl;
+                    if (nframes > 0) {
+                        if (ifr % nframes == 0) {
+                            sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat,
+                                    ifile);
+                            sprintf(imgfname, (const char*)ffname, irun);
+                            mt->writeImage(imgfname, thr1);
+                            mt->clearImage();
+                            ifile++;
+                        }
+                    }
+                // } else
+                //     cout << ifr << " " << ff << " " << np << endl;
+                ff = -1;
+            }
+            cout << "--" << endl;
+            filebin.close();
+            while (mt->isBusy()) {
+                ;
+            }
+            if (nframes >= 0) {
+                if (nframes > 0) {
+                    sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat, ifile);
+                    sprintf(imgfname, (const char*)ffname, irun);
+                } else {
+                    sprintf(ffname, "%s/%s.tiff", outdir, fformat);
+                    sprintf(imgfname, (const char*)ffname, irun);
+                }
+                cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
+                mt->writeImage(imgfname, thr1);
+                mt->clearImage();
+                if (of) {
+                    fclose(of);
+                    of = NULL;
+                    mt->setFilePointer(NULL);
+                }
+            }
+            std::time(&end_time);
+            cout << std::ctime(&end_time) << endl;
+        } else
+            cout << "Could not open " << fname << " for reading " << endl;
+    }
+    if (nframes < 0) {
+        sprintf(ffname, "%s/%s.tiff", outdir, fformat);
+        strcpy(imgfname, ffname);
+        cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
+        mt->writeImage(imgfname, thr1);
+    }
+
+    return 0;
+}

slsDetectorCalibration/jungfrauExecutables/onlinedisp_zmq.cpp

@@ -0,0 +1,679 @@
+#include "onlinedisp_zmq.h"
+bool  hasallpede;
+TH1F * his102;TH1F * his101;
+int processedf;
+sls::zmqHeader zHeader;
+#define PEDEFNAME "current_pede.dat"
+#define NPRO 50
+#define NPRI 50
+
+//#define JFSTRX
+#ifdef JFSTRX
+#include "jungfrauLGADStrixelsData.h"
+#else
+#include "jungfrauModuleData.h"
+#endif
+
+
+
+int main(int argc, char* argv[]) 
+{
+  goout=1;
+  hasallpede=false;
+  dophotonmap=true;  if ((argc<3)) {printf("USAGE: command photon_energy_(peakinADC) [rx_ip]  [port] \n"); return -1  ;}
+  else { 
+    phene=atoi(argv[1]);
+    if (phene<0) dophotonmap=false;
+    threshold=float (phene/2);
+    printf( " \n");
+    printf( "phene %d  \n",phene);
+  }
+  
+  if (argc>=3) {
+    strcpy(serverip,argv[2]);
+    printf("ip is %s ",serverip);
+  }
+
+  portnum=30001;
+  if (argc>=4 ){ portnum= atoi(argv[3]);
+  }
+  printf(", port number  is %d ",portnum);  printf(". \n"); 
+
+  
+#ifdef JFSTRX
+    cout << "JFSTRX" << endl;
+    jungfrauLGADStrixelsData *decoder = new jungfrauLGADStrixelsData();
+    nx = 1024/5; ny= 512*5;
+#else
+    nx = 1024; ny= 512;
+#endif
+
+
+
+
+  gain_flag=false;
+  pede_flag=false;
+  bw_flag=false;
+ 
+  HDraw_every=20;
+  fixranges=false;
+
+  
+  hchptr = (short*) malloc(NCH*sizeof(short)); 
+
+  startsocket(); //create and connect ZMQ 
+
+  for (ipx=0;ipx<NCH;ipx++) hchptr[(ipx)]=0;
+  
+  
+  //  cout<<   decoder->getValue((char*)(hchptr),279,130)<<endl;
+
+
+  nonblock(NB_ENABLE);
+
+  cout <<"opening the rootapp" <<endl;
+ 
+  rootapp = new TApplication("Online JF display",&argc, argv);
+ 
+  LoadPaletteFalse();
+
+  char hname[100];
+
+
+
+  his1000= new TH2F("his1000","2d , ev. pede corrected",nx,-0.5,nx-0.5,ny,-0.5,ny-0.5);
+  his1000->SetOption("colz");
+  his2000= new TH2F("his2000","2d gain ",nx,-0.5,nx-0.5,ny,-0.5,ny-0.5);
+  his2000->GetZaxis()->SetRangeUser(0,4);
+
+  if (dophotonmap) {
+    his3000= new TH2F("his3000"," photon map  ",nx,-0.5,nx-0.5,ny,-0.5,ny-0.5);
+  }
+  else {
+    his3000= new TH2F("his3000"," raw adc  ",nx,-0.5,nx-0.5,ny,-0.5,ny-0.5);
+  }
+ 
+  his4500= new TH2F("his45000","L vs R",101,-50,500,101,-50,500);
+  hchip=new TH1I*[8];
+  for (i=0;i<8;i++) {
+    sprintf(hname,"hchip%d",i);
+    hchip[i] = new TH1I(hname,hname,NBIN,MIN_POS,MAX_POS);
+  }
+
+  cout <<"end of histo booking" <<endl;
+  if  (A2==NULL)  A2 = new TCanvas("A2","Plotting Canvas gain",150,10,500,250);
+  if  (A3==NULL)  A3 = new TCanvas("A3","Plotting Canvas ADC",150,360,1200,550);
+  if  (A4==NULL)  A4 = new TCanvas("A4","Plotting Canvas PHs",750,300,1000,800);
+  A4->Clear();
+  A4->Divide(4,2,0.005,0.005);
+  if  (A5==NULL)  A5 = new TCanvas("A5","Plotting Canvas Photon Map",750,300,1000,600);
+  if  (A6==NULL)  A6 = new TCanvas("A6","Plotting Canvas LvsR",650,250,650,660);
+
+  gSystem->ProcessEvents();
+  int running=0;
+  char runc[15]="*\\-/|";
+  printhelp();
+ 
+ 
+ 
+  while (1==1) { // loop on streamed frames  
+
+    if(!zmqSocket->ReceiveHeader(0,zHeader,  SLS_DETECTOR_JSON_HEADER_VERSION)){
+      cout<< "Receiver stopped, waiting for new stream" << endl; 
+      zmqSocket->Disconnect();
+      zmqSocket->Connect();
+    }
+    else {
+	
+      //   if (((icount++)%10)==0) cout <<"recived frameindex "<<zHeader.frameIndex <<endl; 
+      //cout <<"there" <<endl;
+      zmqSocket->ReceiveData(0, (char *)(&image_data), NCH*2);
+    }
+
+    {
+
+      framesinstream++;
+      running++;
+     
+      fill1Ds=true; //alway fill 1d and LR plots 
+      //if  (((framesinstream%(int(HDraw_every)))==(int (HDraw_every)-1))) {fill1Ds=true;}else{fill1Ds=false;} 
+      if  (((framesinstream%(HDraw_every))==(HDraw_every)-1)) {show2Ds=true;}else{show2Ds=false;} 
+      if  (((framesinstream%NPRI)==NPRI-1))  { cout<<"\r   "<<"frame (from start):   "<<framesinstream<<" " << runc[((running/NPRI)%5)]<<  "   discarded frames %=" << (1-float(processedf)/float(zHeader.frameIndex-frameIndex_old))*100  << " current framenumber= "  <<zHeader.frameIndex  << "       "<<std::flush; processedf=0;frameIndex_old=zHeader.frameIndex;}
+
+ 
+      npacket=0;
+      if  (show2Ds)  {
+	his1000->Reset(); 
+	his2000->Reset(); 
+	if (!dophotonmap) his3000->Reset(); //FOR RAW ADC DISPLAY 
+      }
+
+
+      if ((fill1Ds)or(show2Ds)or(dophotonmap)) { // do something, otherwise skip to the next
+	processedf++;
+
+	for (i=0 ;i<NCH;i++) {
+      
+	  adcvalue= (image_data[i]) & 0x3fff;
+     
+	  if ((image_data[i] & 0xc000)!=0){ gain = (image_data[i]>>14) & 0x3;} else {gain=0;}
+	  if (pede_flag){
+	  
+	    if (gain_flag)
+	      {
+		if ((gain==0)||(!hasallpede)) adcpedecorr=(adcvalue&0x3fff)*fgaind[i]-fpeded[i]*fgaind[i];
+	  
+		if ((gain==1)&&hasallpede)  adcpedecorr=(fpedeG1d[i]*fgaind[i]+G1Poffset-adcvalue*fgaind[i])*30.0; 
+		if ((gain==3)&&hasallpede)  adcpedecorr=(fpedeG2d[i]*fgaind[i]+G2Poffset-adcvalue*fgaind[i])*340.0;
+	      }
+	    else
+
+	      {
+		  
+		if ((gain==0)||(!hasallpede))  adcpedecorr=(adcvalue&0x3fff)-fpeded[i];
+		if ((gain==1)&&hasallpede) adcpedecorr=(fpedeG1d[i]+G1Poffset-adcvalue)*30.0; 
+		if ((gain==3)&&hasallpede) adcpedecorr=(fpedeG2d[i]+G2Poffset-adcvalue)*340.0;
+	      }
+	 
+
+	  } else {adcpedecorr=float (adcvalue);}  //end of if pede 
+       
+
+      
+
+	  if ((adcpedecorr>threshold)&&(pede_flag))  hchptr[(i)]= hchptr[(i)]+(int)((adcpedecorr+threshold)/phene); 
+
+
+	  if (fill1Ds) {
+	    if (((i%1024)<1004)&&((i%1024)>20)&&((i/1024)>20)) { //skip the pix near guardring for PH plots
+	      ichip= i/(256*256*4)*4+((i/256)%4)  ;
+	   
+	      hchip[ichip]->Fill(adcpedecorr,1);
+	    
+	      if (((i%256)<253)&&((i%256)>2)) his4500->Fill(adcpedecorrold,adcpedecorr,1);
+	      adcpedecorrold=adcpedecorr;
+	    
+	    
+	    }
+	  }//if (fill1Ds)
+
+
+	
+
+	  if ((show2Ds)) {
+	    factor=2.0;
+	    value=adcpedecorr;
+	    if ((i%256==0)||(i%256==255)) value=int(value/factor);
+	    if ((i/1024==255)||(i/1024==256)||(i/1024==767)||(i/1024==768)) value=int(value/factor);
+
+	    his1000->Fill(float(i%1024),float(int (i/1024)),value);
+
+	    if (!dophotonmap) his3000->Fill(float(i%1024),float(int (i/1024)) ,adcvalue);
+	  
+	    his2000->Fill(float(i%1024),float(int (i/1024)) ,gain);
+
+	    value=(int)(hchptr[i]);
+	 
+	    if ((i%256==0)||(i%256==255)) value=int(value/factor);
+	    if ((i/1024==255)||(i/1024==256)||(i/1024==767)||(i/1024==768)) value=int(value/factor);
+	    if (dophotonmap) his3000->Fill(float(i%1024),float(int (i/1024)),float(value));
+
+	  }
+	}//   for (i=0 ;i<NCH-0;i++)
+      }// /end of do something 
+   
+
+
+      if   ((show2Ds)) {
+
+	for (ipx=0;ipx<NCH;ipx++) hchptr[(ipx)]=0;
+
+
+
+	Plot2DHistos();  Plot1DHistos();  
+      }
+   
+ 
+      ifp=kbhit();
+      processifp(ifp);
+     
+      if  (((framesinstream%NPRO))==NPRO-1) gSystem->ProcessEvents();
+	
+
+    }
+
+   
+
+  
+
+  }// end of infinite loop 
+
+  rootapp->Run();
+  nonblock(NB_DISABLE);
+  return 0;
+   
+
+}
+void processifp(int ifp){
+
+  if (ifp!=0){
+    c=fgetc(stdin);
+    if (c=='s') {if (goout==0){goout=1;}else {myloop();}}
+    if (c=='S') SetRanges();
+    if (c=='+') { HDraw_every=HDraw_every*0.8;cout<< endl <<"Drawing every "<< HDraw_every<<" frames "<<endl; }
+    if (c=='-') { HDraw_every=HDraw_every*1.25;cout<< endl <<"Drawing every "<< HDraw_every<<" frames "<<endl;}
+    if (c=='G') {gain_flag=not gain_flag ;if (gain_flag) {cout<<"gain corr enab."<< endl;}else {cout<<"gain corr disab."<< endl;}}
+    if (c=='[') { G1Poffset=G1Poffset-10;cout<< endl <<"G1Poffset "<<G1Poffset<<endl; }
+    if (c==']') { G1Poffset=G1Poffset+10;cout<< endl <<"G1Poffset "<<G1Poffset<<endl; }
+    if (c=='{') { G2Poffset=G2Poffset-10;cout<< endl <<"G2Poffset "<<G2Poffset<<endl; }
+    if (c=='}') { G2Poffset=G2Poffset+10;cout<< endl <<"G2Poffset "<<G2Poffset<<endl; }
+    if (c=='p') { //stopsocket();
+      loadpede();//startsocket();  
+    }
+    if (c=='b') {LoadPaletteBW(1.1111);bw_flag=true; } 
+    if (c=='B') {LoadPaletteBW(0.9);bw_flag=true; }
+    if (c=='O')  savepede();
+    if (c=='o')  readpede();
+    if (c=='P')  loadallpede(); 
+    if (c=='u')  his1000->SetOption("surf2z");
+    if (c=='C')  his1000->SetOption("colz");
+
+    if (c=='q') exit(0);
+    if (c=='r') historeset();
+    if (c=='R') axisreset();
+  }
+
+}
+void loadallpede(){
+  cout <<"not implemented "<< endl;
+  // hasallpede=true;
+ 
+  // system("./sls_detector_put  setbit 0x5d 12 "); //setting to FSG1 ;
+  
+  //  loadpede();
+  //  loadpede(); 
+  //  for (i=0;i<NCH;i++) {fpedeG1d[i]=fpeded[i];}
+
+  // system("./sls_detector_put  setbit 0x5d 13 "); //setting to FSG0 ;
+  // sleep(1);
+  // loadpede(); 
+  // loadpede(); 
+  // for (i=0;i<NCH;i++) {fpedeG2d[i]=fpeded[i];}
+  //   system("./sls_detector_put clearbit 0x5d 12  "); //setting to G0;
+  //   system("./sls_detector_put clearbit 0x5d 13  "); //setting to G0;
+  // sleep(2);
+
+  // loadpede(); 
+  // loadpede();
+
+
+
+
+
+}
+void loadpede(void){
+  //startsocket(); 
+  framesinstream=0;
+  pede_flag=true;
+  nframes=0;
+ 
+
+
+  for (ipx=0;ipx<NCH;ipx++) fpeded[ipx]=0; 
+  
+
+  
+  while (framesinstream<50) { // loop on files 
+
+
+    if (!zmqSocket->ReceiveHeader(0,zHeader,  SLS_DETECTOR_JSON_HEADER_VERSION)){ 
+      return;
+    }
+
+    cout <<"received frameindex "<<zHeader.frameIndex << endl; 
+ 
+    zmqSocket->ReceiveData(0,  (char *)(&image_data), NCH*2);
+    framesinstream++;nframes++;
+    for (ipx=0;ipx<NCH;ipx++) fpeded[ipx]=(fpeded[ipx]*(nframes-1)+(float)(image_data[ipx]&0x3fff))/(float)(nframes);
+  
+
+
+  }
+
+  for (ipx=0;ipx<NCH;ipx++) { ipeded[ipx]=(short)(fpeded[ipx]);
+    if (ipx%60033==0) printf("i=%d pede= %d  %f .\n",ipx, ipeded[ipx],fpeded[ipx]);
+  }
+  printf("total frames for pede: %d \n",nframes);
+  //stopsocket(); 
+
+  printhelp();
+}
+
+int kbhit()
+{
+  struct timeval tv;
+  fd_set fds;
+  tv.tv_sec = 0;
+  tv.tv_usec = 0;
+  FD_ZERO(&fds);
+  FD_SET(STDIN_FILENO, &fds); //STDIN_FILENO is 0
+  select(STDIN_FILENO+1, &fds, NULL, NULL, &tv);
+  return FD_ISSET(STDIN_FILENO, &fds);
+}
+void myloop(void){ //wait doing nothing.    
+  goout=0;
+  int ifp;
+ 
+ 
+  while (goout==0){
+   
+    ifp=kbhit();
+    processifp(ifp);
+
+
+    gSystem->ProcessEvents();
+    usleep(5000);
+
+  }
+}
+void printhelp(){
+  cout<< endl << "s=start/pause| p/n=getnewpede/raw | o/O=read/save pede | n=nopede(raw) | r/R=rst His/Axis | +/- = faster/slower ref. |q=exit | U/C sUrf2/Colz  " <<endl;
+}
+
+void historeset(){
+ 
+  his4500->Reset();
+  his3000->Reset();
+  for (i=0;i<8;i++) {
+    hchip[i]->Reset();
+  
+  }
+  Plot2DHistos();
+  Plot1DHistos();
+
+}
+
+void SetRanges() {
+  string str;
+  std::cin.clear();
+  //cin.ignore(std::numeric_limits<std::streamsize>::max(), '\n');
+
+  cout<< endl;
+  cout<<  " adc min " <<endl;
+  //getline(cin, str);
+  // adcmin= stoi(str);
+  std::cin >> adcmin;
+  cout<<  " adc max " <<endl;
+  std::cin >> adcmax;
+  cout<<  " p.map min " <<endl;
+  std::cin >> pmmin;
+  cout<<  " p.map max " <<endl;
+  std::cin >> pmmax;
+
+  fixranges=true;
+
+
+
+}
+
+
+void axisreset(){
+  fixranges=false;
+  his1000->GetXaxis()->UnZoom();
+
+  his1000->GetYaxis()->UnZoom();
+  his1000->GetZaxis()->UnZoom();
+  his2000->GetXaxis()->UnZoom();
+  his2000->GetYaxis()->UnZoom();
+
+  his3000->GetZaxis()->UnZoom();
+  
+  for (i=0;i<8;i++) {
+    hchip[i]->GetXaxis()->UnZoom();
+    hchip[i]->GetYaxis()->UnZoom();
+  }
+
+  his4500->GetXaxis()->UnZoom(); 
+  his4500->GetYaxis()->UnZoom(); 
+  his4500->GetZaxis()->UnZoom(); 
+  
+  Plot2DHistos();
+  Plot1DHistos();
+  
+
+}
+
+
+
+
+
+void nonblock(int state)
+{
+  struct termios ttystate;
+  //get the terminal state
+  tcgetattr(STDIN_FILENO, &ttystate);
+  if (state==NB_ENABLE)
+    {
+      //turn off canonical mode
+      ttystate.c_lflag &= ~ICANON;
+      //minimum of number input read.
+      ttystate.c_cc[VMIN] = 1;
+    }
+  else if (state==NB_DISABLE)
+    { //turn on canonical mode
+      ttystate.c_lflag |= ICANON;
+    }
+  //set the terminal attributes.
+  tcsetattr(STDIN_FILENO, TCSANOW, &ttystate); 
+}
+
+
+void LoadPaletteFalse(){
+  const Int_t NRGBs = 5;
+  const Int_t NCont = 90;
+
+  Double_t stops[NRGBs] = { 0.00, 0.34, 0.61, 0.84, 1.00 };
+  Double_t red[NRGBs]   = { 0.00, 0.00, 0.87, 1.00, 0.51 };
+  Double_t green[NRGBs] = { 0.00, 0.81, 1.00, 0.20, 0.00 };
+  Double_t blue[NRGBs]  = { 0.51, 1.00, 0.12, 0.00, 0.00 };
+  TColor::CreateGradientColorTable(NRGBs, stops, red,green, blue, NCont);
+  gStyle->SetNumberContours(NCont);
+  TColor::CreateGradientColorTable(NRGBs, stops, red,green  ,blue, NCont);
+  gStyle->SetNumberContours(NCont);
+
+}
+void LoadPaletteBW(float gammatune){
+
+  vgamma=vgamma*gammatune;
+  cout<< "gamma is "<<vgamma<<endl;
+  const Int_t NRGBs = 99;
+  const Int_t NCont = 990;
+  Double_t stops[NRGBs] ;
+  Double_t red[NRGBs]  ;
+  Double_t green[NRGBs];
+  Double_t blue[NRGBs] ;
+
+  for (int iRGB=0;iRGB<NRGBs;iRGB++){
+
+
+    stops[iRGB] =(1/float(NRGBs)*float(iRGB));
+    red[iRGB]   =  pow(stops[iRGB],vgamma);
+    green[iRGB] = red[iRGB];
+    blue[iRGB]  =red[iRGB];
+    //  cout << iRGB<<"  "<< stops[iRGB] <<" " << red[iRGB]<<endl;
+
+  }
+
+
+  TColor::CreateGradientColorTable(NRGBs, stops, red, green, blue, NCont);
+  gStyle->SetNumberContours(NCont);
+
+  
+
+  // TColor::SetPalette(52,0,1);
+
+}
+
+void Plot1DHistos(void){
+
+  if (hchip[0]->GetXaxis()->GetLast()!=oldh0xlast){
+    oldh0xlast=hchip[0]->GetXaxis()->GetLast();
+    oldh0xfirst=hchip[0]->GetXaxis()->GetFirst();
+    for (int ipad=1; ipad<8;ipad++) {
+      hchip[ipad]->GetXaxis()->SetRange(oldh0xfirst,oldh0xlast);
+     
+    
+    }
+  }    
+  
+
+  for (int ipad=0; ipad<8;ipad++) {
+    A4->cd(ipad+1);  
+    gStyle->SetOptStat(1);    gPad->SetLogy();
+     hchip[ipad%4+(1-int(ipad/4))*4]->Draw();
+  
+  }
+  A4->cd();
+  A4->Update();
+}
+
+
+void Plot2DHistos(void){
+  gStyle->SetOptStat(0);
+  A3->cd();
+
+  //  if (bw_flag) LoadPaletteBW(1.0);
+
+  if (fixranges) {
+
+    his1000->GetZaxis()->SetRangeUser(float(adcmin),float(adcmax));
+    his3000->GetZaxis()->SetRangeUser(float(pmmin),float(pmmax));
+    
+
+  }
+
+  his1000->SetMinimum(-200);
+  his1000->Draw();
+
+  A3->Update();
+  A2->cd();
+  // if (bw_flag)  LoadPaletteFalse();
+  his2000->GetXaxis()->SetRange(his1000->GetXaxis()->GetFirst(),his1000->GetXaxis()->GetLast());
+  his2000->GetYaxis()->SetRange(his1000->GetYaxis()->GetFirst(),his1000->GetYaxis()->GetLast());
+
+  his2000->Draw("colz"); 
+  A2->Update(); 
+  A5->cd();
+
+  his3000->GetXaxis()->SetRange(his1000->GetXaxis()->GetFirst(),his1000->GetXaxis()->GetLast());
+  his3000->GetYaxis()->SetRange(his1000->GetYaxis()->GetFirst(),his1000->GetYaxis()->GetLast());
+  his3000->Draw("colz");
+  A5->Update();
+ 
+  A6->cd();
+  his4500->Draw("colz");
+  A6->Update();
+  
+
+
+}
+
+
+void startsocket(void) {
+
+
+
+
+  try {
+    zmqSocket = new sls::ZmqSocket(serverip, portnum);
+
+  } catch (...) {
+    cprintf(RED,
+	    "Error: Could not create Zmq socket on port %d with ip %s\n",
+	    portnum, serverip);
+    delete zmqSocket;
+    return;
+  }
+  zmqSocket->SetReceiveHighWaterMark(3);
+  zmqSocket->SetReceiveBuffer(1024*1024); 
+  zmqSocket->Connect();
+
+
+  cout<<"Zmq Client[] "<< zmqSocket->GetZmqServerAddress()<<endl;
+
+
+  haveconnection=true;
+ 
+ 
+
+
+}
+
+
+
+ 
+
+void tryconnect(void) 
+
+{
+  int itry=0;
+  cout<< endl;
+ 
+  
+
+  while (haveconnection==false) {
+    sleep(1);
+    cout<<"\r trying to (re)connect " <<itry++ << " " << endl ; 
+    startsocket();
+  }
+
+}
+
+void stopsocket(void) {
+  // cout<<" cfd " << cfd << endl;; 
+  
+   
+
+  delete zmqSocket;
+  zmqSocket=0;
+  //zmqSocket->~ZmqSocket ();
+
+    
+
+  haveconnection=false;
+
+    
+  
+
+}
+void savepede(void) {
+
+  int pfd;
+
+  pfd=open(PEDEFNAME,O_CREAT|O_WRONLY, 0666);
+  if (pfd==-1) perror("open pede file");
+   
+  write(pfd,fpeded,2*NCH*sizeof(float));
+  write(pfd,fpedeG1d,2*NCH*sizeof(float));
+  write(pfd,fpedeG2d,2*NCH*sizeof(float));
+  close(pfd);
+ 
+}
+
+void readpede(void) {
+
+  int pfd;
+
+  pfd=open(PEDEFNAME,O_RDONLY);
+  if (pfd==-1) perror("open pede file");
+   
+  read(pfd,fpeded,NCH*2*sizeof(float));
+  read(pfd,fpedeG1d,NCH*2*sizeof(float));
+  read(pfd,fpedeG2d,NCH*2*sizeof(float));
+   
+  close(pfd);
+  pede_flag=true;
+  hasallpede=true;
+
+}
+

slsDetectorCalibration/jungfrauExecutables/onlinedisp_zmq.h

@@ -0,0 +1,204 @@
+
+/**************************************************************************/
+/* Header files   section needs cleanup                     */
+/**************************************************************************/
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/socket.h>
+#include "sls/ZmqSocket.h"
+
+#include "sls/tiffIO.h"
+#include <netinet/in.h>
+#include <arpa/inet.h>
+#include <stdlib.h>  /* exit() */
+#include <string.h>  /* memset(), memcpy() */
+#include <sys/utsname.h>   /* uname() */
+#include <sys/types.h>
+#include <sys/socket.h>   /* socket(), bind(),
+			     listen(), accept() */
+#include <sys/time.h>
+#include <sys/types.h>
+#include <netinet/in.h>
+#include <netinet/tcp.h>
+#include <arpa/inet.h>
+#include <netdb.h>
+#include <unistd.h>  /* fork(), write(), close() */
+#include <time.h> 
+#include <sys/time.h>
+#include <sys/mman.h>
+#include <sys/socket.h>
+#include <sys/types.h>
+#include <cmath>
+#include <sys/stat.h>
+#include <errno.h>
+#include <fcntl.h>
+#include <stdarg.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <rapidjson/document.h> //json header in zmq stream
+#include <omp.h>
+#define NTHREADS 2
+
+#include <chrono>
+#include <cstdio>
+#include <ctime> // time_t
+
+using namespace std;
+using namespace std::chrono;
+using namespace sls;
+
+#include "TCanvas.h"
+#include "TH1F.h"
+#include "TF1.h"
+#include "TH2F.h"
+#include "TMath.h"
+#include "TFile.h"
+#include "TStyle.h"
+#include "TSystem.h"
+#include "TTimer.h"
+#include "TProfile.h"
+#include "TColor.h"
+#include <iostream>
+#include <fstream> 
+#include <termios.h>
+#include <TApplication.h>
+#include <stdio.h>
+#include <math.h>
+#include <fstream>
+#include <iomanip>
+#include <sstream>
+#include <string>
+#include <vector>
+#include <iostream>
+#include "sls/ansi.h"
+#define SLS_DETECTOR_JSON_HEADER_VERSION 0x4
+
+#define PI 3.14159265
+
+#define FALSE              0
+#define OFFSET 0
+#define NBIN 500  
+#define MIN_POS  -500.5   // 400.5   
+#define MAX_POS 3499.5   //-100.5
+
+
+#define NCH 524288
+// #define NCH 262144 in case of half_frames 
+
+char serverip[256];
+int portnum;
+FILE * sfilefd;
+
+short* hchptr; // photon counted map "histogram"
+int value;
+float factor=1.84;
+int npacket=0;
+int totalnpacket=0;
+float vgamma;
+ 
+struct sockaddr_in serveraddr;
+struct sockaddr_in clientaddr;
+struct in_addr      inadr;
+struct hostent      *server;
+ 
+int i=0;
+int ipx=0;
+bool haveconnection;
+
+
+TStyle *gStyle;
+TApplication* rootapp;
+TCanvas *A2;
+TCanvas *A3;
+TCanvas *A4;
+TCanvas *A5;
+TCanvas *A6;
+
+TH1I **hchip;
+TH2F **h4500chip;
+short image_data[NCH*2];
+short imaged[NCH*2];
+float fpeded[NCH*2];
+float fpedeG2d[NCH*2];
+float fpedeG1d[NCH*2];
+short ipeded[NCH*2];
+short pcimaged[NCH*2];
+
+float fgaind[NCH*2];
+
+
+float  adcpedecorr,adcpedecorrold;
+
+bool gain_flag;
+bool bw_flag;
+bool fill2Ds;
+bool show2Ds;
+bool fill1Ds;
+bool pede_flag;
+bool dophotonmap;
+
+int nx, ny;
+int nframes;
+int goout;
+int framesinstream;
+int ifp;
+float threshold;
+int phene;
+int  adcvalue;
+int gain;
+int ichip;
+int frameIndex_old;
+
+char pedefilename[128];
+int  framenum,bunchid;
+
+TH2F* his1000;
+TH2F* his2000;
+TH2F* his3000;
+TH2F* his4500;
+TH1I* hproj;
+TH1I* hchcum;
+
+
+using namespace std;
+void printhelp(void);
+void processifp(int ifp);
+void historeset(void);
+void SetRanges(void);
+void startsocket(void);
+void stopsocket(void);
+void axisreset(void);
+int kbhit(void);
+void myloop(void);   
+void loadpede(void);
+void loadallpede(void);
+void loadgain(void);
+void nonblock(int state);
+void LoadPaletteFalse(void);
+void LoadPaletteBW(float);
+void Plot1DHistos(void);
+void Plot2DHistos(void);
+void savepede(void);
+void readpede(void);
+int findinterpoindex(int startindex);
+int findclumax(int startindex);
+void tryconnect(void) ;
+
+#define NB_ENABLE 1 
+#define NB_DISABLE 0
+char c; 
+int HDraw_every;
+
+
+float  oldh0xfirst,oldh0xlast;
+int idx;
+int GXPoffset,G1Poffset,G2Poffset;
+int ix,iy;
+int adcmin,adcmax;
+int pmmin,pmmax; //min/mnx for the photon map
+bool fixranges;
+
+
+sls::ZmqSocket *zmqSocket= NULL;

slsDetectorGui/include/qDrawPlot.h

@@ -59,6 +59,7 @@ class qDrawPlot : public QWidget, private Ui::PlotObject {
     void ClonePlot();
     void SavePlot();
     void SetGapPixels(bool enable);
+    void UpdatePlot();
 
   protected:
     void resizeEvent(QResizeEvent *event);
@@ -67,7 +68,7 @@ class qDrawPlot : public QWidget, private Ui::PlotObject {
     void Zoom1DGainPlot(const QRectF &rect);
     void Zoom2DGainPlot(const QRectF &rect);
     void SetSaveFileName(QString val);
-    void UpdatePlot();
+    //    void UpdatePlot();
 
   signals:
     void AcquireFinishedSignal();

slsDetectorGui/include/qTabPlot.h

@@ -47,6 +47,7 @@ class qTabPlot : public QWidget, private Ui::TabPlotObject {
   private:
     void SetupWidgetWindow();
     void Initialization();
+    bool VerifyGapPixelsAllowed();
     void Select1DPlot(bool enable);
     void GetGapPixels();
     void GetStreamingFrequency();
@@ -60,7 +61,8 @@ class qTabPlot : public QWidget, private Ui::TabPlotObject {
 
     Detector *det;
     qDrawPlot *plot;
-    bool is1d;
+    bool is1d{false};
+    bool isGapPixelsAllowed{false};
 
     /** default plot and axis titles */
     static QString defaultPlotTitle;

slsDetectorGui/src/qTabPlot.cpp

@@ -16,7 +16,7 @@ QString qTabPlot::defaultImageYAxisTitle("Pixel");
 QString qTabPlot::defaultImageZAxisTitle("Intensity");
 
 qTabPlot::qTabPlot(QWidget *parent, Detector *detector, qDrawPlot *p)
-    : QWidget(parent), det(detector), plot(p), is1d(false) {
+    : QWidget(parent), det(detector), plot(p) {
     setupUi(this);
     SetupWidgetWindow();
     LOG(logDEBUG) << "Plot ready";
@@ -57,11 +57,7 @@ void qTabPlot::SetupWidgetWindow() {
         chkGainPlot1D->setChecked(true);
         plot->EnableGainPlot(true);
         break;
-    case slsDetectorDefs::EIGER:
-        chkGapPixels->setEnabled(true);
-        break;
     case slsDetectorDefs::JUNGFRAU:
-        chkGapPixels->setEnabled(true);
         chkGainPlot->setEnabled(true);
         chkGainPlot->setChecked(true);
         plot->EnableGainPlot(true);
@@ -69,6 +65,8 @@ void qTabPlot::SetupWidgetWindow() {
     default:
         break;
     }
+    isGapPixelsAllowed = VerifyGapPixelsAllowed();
+    chkGapPixels->setEnabled(isGapPixelsAllowed);
 
     Select1DPlot(is1d);
     Initialization();
@@ -195,6 +193,29 @@ void qTabPlot::Initialization() {
     connect(dispZMax, SIGNAL(editingFinished()), this, SLOT(isZMaxModified()));
 }
 
+bool qTabPlot::VerifyGapPixelsAllowed() {
+    try {
+        switch (det->getDetectorType().squash()) {
+        case slsDetectorDefs::JUNGFRAU:
+            return true;
+        case slsDetectorDefs::EIGER:
+            if (det->getQuad().squash(false)) {
+                return true;
+            }
+            // full modules
+            if (det->getModuleGeometry().y % 2 == 0) {
+                return true;
+            }
+            return false;
+        default:
+            return false;
+        }
+    }
+    CATCH_DISPLAY("Could not verify if gap pixels allowed.",
+                  "qTabPlot::VerifyGapPixelsAllowed")
+    return false;
+}
+
 void qTabPlot::Select1DPlot(bool enable) {
     LOG(logDEBUG) << "Selecting " << (enable ? "1" : "2") << "D Plot";
     is1d = enable;
@@ -487,6 +508,7 @@ void qTabPlot::SetXYRange() {
     }
 
     plot->SetXYRangeChanged(disablezoom, xyRange, isRange);
+    plot->UpdatePlot();
     emit DisableZoomSignal(disablezoom);
 }
 
@@ -624,6 +646,7 @@ void qTabPlot::SetZRange() {
         zRange[1] = val;
     }
     plot->SetZRange(zRange, isZRange);
+    plot->UpdatePlot();
 }
 
 void qTabPlot::GetStreamingFrequency() {
@@ -770,15 +793,10 @@ void qTabPlot::Refresh() {
         boxFrequency->setEnabled(true);
         GetStreamingFrequency();
         GetHwm();
-        // gain plot, gap pixels enable
+        // gain plot
         switch (det->getDetectorType().squash()) {
-        case slsDetectorDefs::EIGER:
-            chkGapPixels->setEnabled(true);
-            GetGapPixels();
-            break;
         case slsDetectorDefs::JUNGFRAU:
             chkGainPlot->setEnabled(true);
-            chkGapPixels->setEnabled(true);
             GetGapPixels();
             break;
         case slsDetectorDefs::GOTTHARD2:
@@ -787,6 +805,11 @@ void qTabPlot::Refresh() {
         default:
             break;
         }
+        // gap pixels
+        if (isGapPixelsAllowed) {
+            chkGapPixels->setEnabled(true);
+            GetGapPixels();
+        }
     } else {
         boxFrequency->setEnabled(false);
         chkGainPlot->setEnabled(false);

slsDetectorServers/eigerDetectorServer/Beb.c

@@ -1106,7 +1106,9 @@ int Beb_SetDetectorPosition(int pos[]) {
     int posRight[2] = {Beb_top ? pos[X] + 1 : pos[X], pos[Y]};
 
     if (Beb_quadEnable) {
-        posRight[Y] = 1; // right is next row
+        posLeft[Y] = 1;  // left is next row
+        posLeft[X] = 0;  // left same first row
+        posRight[Y] = 0; // right same first row
         posRight[X] = 0; // right same first column
     }
 

slsDetectorServers/eigerDetectorServer/CMakeLists.txt

@@ -25,7 +25,7 @@ target_include_directories(eigerDetectorServer_virtual
 )
 
 target_compile_definitions(eigerDetectorServer_virtual
-    PUBLIC EIGERD PCCOMPILE STOP_SERVER
+    PUBLIC EIGERD PCCOMPILE STOP_SERVER #TEST_MOD_GEOMETRY
     PUBLIC VIRTUAL #VIRTUAL_9M
 )
 

slsDetectorServers/eigerDetectorServer/FebControl.c

@@ -1240,19 +1240,16 @@ int Feb_Control_GetDynamicRange(int *retval) {
 
 int Feb_Control_Disable16bitConversion(int disable) {
     LOG(logINFO, ("%s 16 bit expansion\n", disable ? "Disabling" : "Enabling"));
+
+    uint32_t bitmask = DAQ_REG_HRDWRE_DSBL_16BIT_MSK;
     unsigned int regval = 0;
-    if (!Feb_Control_ReadRegister(DAQ_REG_HRDWRE, &regval)) {
-        LOG(logERROR, ("Could not %s 16 bit expansion (bit mode)\n",
-                       (disable ? "disable" : "enable")));
-        return 0;
-    }
     if (disable) {
-        regval |= DAQ_REG_HRDWRE_DSBL_16BIT_MSK;
+        regval |= bitmask;
     } else {
-        regval &= ~DAQ_REG_HRDWRE_DSBL_16BIT_MSK;
+        regval &= ~bitmask;
     }
 
-    if (!Feb_Control_WriteRegister(DAQ_REG_HRDWRE, regval)) {
+    if (!Feb_Control_WriteRegister_BitMask(DAQ_REG_HRDWRE, regval, bitmask)) {
         LOG(logERROR, ("Could not %s 16 bit expansion (bit mode)\n",
                        (disable ? "disable" : "enable")));
         return 0;
@@ -1262,11 +1259,12 @@ int Feb_Control_Disable16bitConversion(int disable) {
 
 int Feb_Control_Get16bitConversionDisabled(int *ret) {
     unsigned int regval = 0;
-    if (!Feb_Control_ReadRegister(DAQ_REG_HRDWRE, &regval)) {
+    if (!Feb_Control_ReadRegister_BitMask(DAQ_REG_HRDWRE, &regval,
+                                          DAQ_REG_HRDWRE_DSBL_16BIT_MSK)) {
         LOG(logERROR, ("Could not get 16 bit expansion (bit mode)\n"));
         return 0;
     }
-    if (regval & DAQ_REG_HRDWRE_DSBL_16BIT_MSK) {
+    if (regval) {
         *ret = 1;
     } else {
         *ret = 0;
@@ -1667,6 +1665,15 @@ int Feb_Control_GetReadNRows() {
 }
 
 int Feb_Control_WriteRegister(uint32_t offset, uint32_t data) {
+    return Feb_Control_WriteRegister_BitMask(offset, data, BIT32_MSK);
+}
+
+int Feb_Control_ReadRegister(uint32_t offset, uint32_t *retval) {
+    return Feb_Control_ReadRegister_BitMask(offset, retval, BIT32_MASK);
+}
+
+int Feb_Control_WriteRegister_BitMask(uint32_t offset, uint32_t data,
+                                      uint32_t bitmask) {
     uint32_t actualOffset = offset;
     char side[2][10] = {"right", "left"};
     unsigned int addr[2] = {Feb_Control_rightAddress, Feb_Control_leftAddress};
@@ -1690,24 +1697,41 @@ int Feb_Control_WriteRegister(uint32_t offset, uint32_t data) {
 
     for (int iloop = 0; iloop < 2; ++iloop) {
         if (run[iloop]) {
-            LOG(logDEBUG1,
+            LOG(logDEBUG1, ("Writing 0x%x to %s 0x%x (mask:0x%x)\n", data,
-                ("Writing 0x%x to %s 0x%x\n", data, side[iloop], actualOffset));
+                            side[iloop], actualOffset, bitmask));
-            if (!Feb_Interface_WriteRegister(addr[iloop], actualOffset, data, 0,
+
-                                             0)) {
+            uint32_t writeVal = 0;
-                LOG(logERROR, ("Could not write 0x%x to %s addr 0x%x\n", data,
+            if (!Feb_Interface_ReadRegister(addr[iloop], actualOffset,
+                                            &writeVal)) {
+                LOG(logERROR, ("Could not read %s addr 0x%x register\n",
                                side[iloop], actualOffset));
                 return 0;
             }
-            uint32_t regVal = 0;
+            // set only the bits in the mask
-            if (!Feb_Interface_ReadRegister(addr[iloop], actualOffset,
+            writeVal &= ~(bitmask);
-                                            &regVal)) {
+            writeVal |= (data & bitmask);
-                LOG(logERROR, ("Could not read %s register\n", addr[iloop]));
+
+            LOG(logDEBUG1, ("writing 0x%x to 0x%x\n", writeVal, actualOffset));
+            if (!Feb_Interface_WriteRegister(addr[iloop], actualOffset,
+                                             writeVal, 0, 0)) {
+                LOG(logERROR, ("Could not write 0x%x to %s addr 0x%x\n",
+                               writeVal, side[iloop], actualOffset));
                 return 0;
             }
-            if (regVal != data) {
+            writeVal &= bitmask;
+
+            uint32_t readVal = 0;
+            if (!Feb_Interface_ReadRegister(addr[iloop], actualOffset,
+                                            &readVal)) {
+                return 0;
+            }
+            readVal &= bitmask;
+
+            if (writeVal != readVal) {
                 LOG(logERROR,
-                    ("Could not write %s register. Write 0x%x, read 0x%x\n",
+                    ("Could not write %s addr 0x%x register. Wrote "
-                     addr[iloop], data, regVal));
+                     "0x%x, read 0x%x (mask:0x%x)\n",
+                     side[iloop], actualOffset, writeVal, readVal, bitmask));
                 return 0;
             }
         }
@@ -1716,7 +1740,8 @@ int Feb_Control_WriteRegister(uint32_t offset, uint32_t data) {
     return 1;
 }
 
-int Feb_Control_ReadRegister(uint32_t offset, uint32_t *retval) {
+int Feb_Control_ReadRegister_BitMask(uint32_t offset, uint32_t *retval,
+                                     uint32_t bitmask) {
     uint32_t actualOffset = offset;
     char side[2][10] = {"right", "left"};
     unsigned int addr[2] = {Feb_Control_rightAddress, Feb_Control_leftAddress};
@@ -1746,8 +1771,9 @@ int Feb_Control_ReadRegister(uint32_t offset, uint32_t *retval) {
                                side[iloop], actualOffset));
                 return 0;
             }
-            LOG(logDEBUG1, ("Read 0x%x from %s 0x%x\n", value[iloop],
+            value[iloop] &= bitmask;
-                            side[iloop], actualOffset));
+            LOG(logDEBUG1, ("Read 0x%x from %s 0x%x (mask:0x%x)\n",
+                            value[iloop], side[iloop], actualOffset, bitmask));
             *retval = value[iloop];
             // if not the other (left, not right OR right, not left), return the
             // value
@@ -1758,7 +1784,7 @@ int Feb_Control_ReadRegister(uint32_t offset, uint32_t *retval) {
     }
     // Inconsistent values when reading both registers
     if ((run[0] & run[1]) & (value[0] != value[1])) {
-        LOG(logERROR, ("Inconsistent values read from %s 0x%x and %s 0x%x\n",
+        LOG(logERROR, ("Inconsistent values read from %s: 0x%x and %s: 0x%x\n",
                        side[0], value[0], side[1], value[1]));
         return 0;
     }

slsDetectorServers/eigerDetectorServer/FebControl.h

@@ -95,7 +95,10 @@ int Feb_Control_SetReadNRows(int value);
 int Feb_Control_GetReadNRows();
 int Feb_Control_WriteRegister(uint32_t offset, uint32_t data);
 int Feb_Control_ReadRegister(uint32_t offset, uint32_t *retval);
-
+int Feb_Control_WriteRegister_BitMask(uint32_t offset, uint32_t data,
+                                      uint32_t bitmask);
+int Feb_Control_ReadRegister_BitMask(uint32_t offset, uint32_t *retval,
+                                     uint32_t bitmask);
 // pulsing
 int Feb_Control_Pulse_Pixel(int npulses, int x, int y);
 int Feb_Control_PulsePixelNMove(int npulses, int inc_x_pos, int inc_y_pos);

slsDetectorServers/eigerDetectorServer/slsDetectorFunctionList.c

@@ -861,12 +861,15 @@ int setDynamicRange(int dr) {
     LOG(logINFO, ("Setting dynamic range: %d\n", dr));
 #else
     sharedMemory_lockLocalLink();
-    if (Feb_Control_SetDynamicRange(dr)) {
+    if (!Feb_Control_SetDynamicRange(dr)) {
-        if (!Beb_SetUpTransferParameters(dr)) {
+        LOG(logERROR, ("Could not set dynamic range in feb\n"));
-            LOG(logERROR, ("Could not set bit mode in the back end\n"));
+        sharedMemory_unlockLocalLink();
-            sharedMemory_unlockLocalLink();
+        return FAIL;
-            return eiger_dynamicrange;
+    }
-        }
+    if (!Beb_SetUpTransferParameters(dr)) {
+        LOG(logERROR, ("Could not set bit mode in the back end\n"));
+        sharedMemory_unlockLocalLink();
+        return eiger_dynamicrange;
     }
     sharedMemory_unlockLocalLink();
 #endif
@@ -2664,6 +2667,10 @@ void *start_timer(void *arg) {
                 header->modId = eiger_virtual_module_id;
                 header->row = row;
                 header->column = colLeft;
+                if (eiger_virtual_quad_mode) {
+                    header->row = 1;    // left is next row
+                    header->column = 0; // left same first column
+                }
 
                 char packetData2[packetsize];
                 memset(packetData2, 0, packetsize);
@@ -2672,11 +2679,11 @@ void *start_timer(void *arg) {
                 header->version = SLS_DETECTOR_HEADER_VERSION;
                 header->frameNumber = frameNr + iframes;
                 header->packetNumber = i;
-                header->modId = eiger_virtual_module_id;
+                header->modId = eiger_virtual_module_id + 1;
                 header->row = row;
                 header->column = colRight;
                 if (eiger_virtual_quad_mode) {
-                    header->row = 1;    // right is next row
+                    header->row = 0;    // right is next row
                     header->column = 0; // right same first column
                 }
 

slsDetectorServers/eigerDetectorServer/slsDetectorServer_defs.h

@@ -137,6 +137,7 @@ enum MASTERINDEX { MASTER_HARDWARE, OW_MASTER, OW_SLAVE };
 #define UDP_HEADER_MAX_FRAME_VALUE (0xFFFFFFFFFFFF)
 
 #define BIT16_MASK (0xFFFF)
+#define BIT32_MSK  (0xFFFFFFFF)
 
 #define DAC_MIN_MV (0)
 #define DAC_MAX_MV (2048)

slsDetectorServers/gotthardDetectorServer/slsDetectorFunctionList.c

@@ -1007,7 +1007,9 @@ int setDelayAfterTrigger(int64_t val) {
     // validate for tolerance
     int64_t retval = getDelayAfterTrigger();
     val /= (1E-9 * CLK_FREQ);
-    val -= masterdefaultdelay;
+    if (master) {
+        val -= masterdefaultdelay;
+    }
     if (val != retval) {
         return FAIL;
     }

slsDetectorServers/mythen3DetectorServer/mythen3.c

@@ -313,7 +313,7 @@ patternParameters *setChannelRegisterChip(int ichip, char *mask,
                  chanReg, ichip * NCHAN + ich * NCOUNTERS,
                  ichip * NCHAN_1_COUNTER + ich, ichip, ich));
         }
-        for (int i = 0; i < 24; i++) {
+        for (int i = 0; i < 23; i++) {
             patword = clearBit(SIGNAL_clk, patword);
             pat->word[iaddr++] = patword;
 

slsDetectorServers/mythen3DetectorServer/slsDetectorServer_defs.h

@@ -3,7 +3,7 @@
 #pragma once
 #include "sls/sls_detector_defs.h"
 
-#define REQRD_FRMWRE_VRSN (0x221205)
+#define REQRD_FRMWRE_VRSN (0x230124)
 #define KERNEL_DATE_VRSN  "Mon May 10 18:00:21 CEST 2021"
 #define ID_FILE           "detid_mythen3.txt"
 
@@ -57,10 +57,10 @@
 #define DEFAULT_TRIMBIT_VALUE            (0)
 #define DEFAULT_COUNTER_DISABLED_VTH_VAL (2800)
 
-#define DEFAULT_READOUT_C0          (12) //(083333333) // rdo_clk, 83.33 MHz
+#define DEFAULT_READOUT_C0          (10) //(100000000) // rdo_clk, 100 MHz
-#define DEFAULT_READOUT_C1          (12) //(083333333) // rdo_smp_clk, 83.33 MHz
+#define DEFAULT_READOUT_C1          (10) //(100000000) // rdo_smp_clk, 100 MHz
-#define DEFAULT_SYSTEM_C0           (20) //(050000000) // run_clk, 20 MHz
+#define DEFAULT_SYSTEM_C0           (10) //(100000000) // run_clk, 100 MHz
-#define DEFAULT_SYSTEM_C1           (8)  //(125000000) // str_clk, 125 MHz const
+#define DEFAULT_SYSTEM_C1           (6)  //(166666666) // str_clk, 166 MHz const
 #define DEFAULT_SYSTEM_C2           (5)  //(200000000) // smp_clk, 200 MHz const
 #define DEFAULT_TRIMMING_RUN_CLKDIV (40) // (25000000) // 25 MHz
 

slsDetectorServers/slsDetectorServer/src/slsDetectorServer_funcs.c

@@ -5139,11 +5139,20 @@ int set_source_udp_mac(int file_des) {
     if (Server_VerifyLock() == OK) {
         if (check_detector_idle("configure mac") == OK) {
             if (udpDetails[0].srcmac != arg) {
-                for (int iRxEntry = 0; iRxEntry != MAX_UDP_DESTINATION;
+                // multicast (LSB of first octet = 1)
-                     ++iRxEntry) {
+                if ((arg >> 40) & 0x1) {
-                    udpDetails[iRxEntry].srcmac = arg;
+                    ret = FAIL;
+                    sprintf(mess,
+                            "Cannot set source mac address. Must be a unicast "
+                            "address (LSB of first octet should be 0).");
+                    LOG(logERROR, (mess));
+                } else {
+                    for (int iRxEntry = 0; iRxEntry != MAX_UDP_DESTINATION;
+                         ++iRxEntry) {
+                        udpDetails[iRxEntry].srcmac = arg;
+                    }
+                    configure_mac();
                 }
-                configure_mac();
             }
         }
     }

slsDetectorSoftware/include/sls/Detector.h

@@ -221,6 +221,17 @@ class Detector {
      */
     void setBadChannels(const std::string &fname, Positions pos = {});
 
+    /** [Gotthard2][Mythen3] */
+    Result<std::vector<int>> getBadChannels(Positions pos = {}) const;
+
+    /** [Gotthard2][Mythen3] Empty list resets bad channel list */
+    void setBadChannels(const std::vector<int> list, Positions pos = {});
+
+    /** [Gotthard2][Mythen3] Size of list should match number of modules. Each
+     * value is at module level and can start at 0. Empty vector resets bad
+     * channel list. */
+    void setBadChannels(const std::vector<std::vector<int>> list);
+
     Result<bool> isVirtualDetectorServer(Positions pos = {}) const;
     ///@}
 
@@ -932,9 +943,10 @@ class Detector {
     /** Client IP Address that last communicated with the receiver */
     Result<IpAddr> getRxLastClientIP(Positions pos = {}) const;
 
-    /** Get thread ids from the receiver in order of [parent, tcp, listener 0,
+    /** Get kernel thread ids from the receiver in order of [parent, tcp,
-     * processor 0, streamer 0, listener 1, processor 1, streamer 1, arping]. If
+     * listener 0, processor 0, streamer 0, listener 1, processor 1, streamer 1,
-     * no streamer yet or there is no second interface, it gives 0 in its place.
+     * arping]. If no streamer yet or there is no second interface, it gives 0
+     * in its place.
      */
     Result<std::array<pid_t, NUM_RX_THREAD_IDS>>
     getRxThreadIds(Positions pos = {}) const;

slsDetectorSoftware/src/CmdProxy.cpp

@@ -7,6 +7,7 @@
 #include "sls/ToString.h"
 #include "sls/bit_utils.h"
 #include "sls/container_utils.h"
+#include "sls/file_utils.h"
 #include "sls/logger.h"
 #include "sls/sls_detector_defs.h"
 
@@ -548,9 +549,9 @@ std::string CmdProxy::BadChannels(int action) {
     std::ostringstream os;
     os << cmd << ' ';
     if (action == defs::HELP_ACTION) {
-        os << "[fname]\n\t[Gotthard2][Mythen3] Sets the bad channels (from "
+        os << "[fname|none|0]\n\t[Gotthard2][Mythen3] Sets the bad channels "
-              "file of bad channel numbers) to be masked out."
+              "(from file of bad channel numbers) to be masked out. None or 0 "
-              "\n\t[Mythen3] Also does trimming"
+              "unsets all the badchannels.\n\t[Mythen3] Also does trimming"
            << '\n';
     } else if (action == defs::GET_ACTION) {
         if (args.size() != 1) {
@@ -559,10 +560,25 @@ std::string CmdProxy::BadChannels(int action) {
         det->getBadChannels(args[0], std::vector<int>{det_id});
         os << "successfully retrieved" << '\n';
     } else if (action == defs::PUT_ACTION) {
-        if (args.size() != 1) {
+        bool parse = false;
+        if (args.size() == 0) {
             WrongNumberOfParameters(1);
+        } else if (args.size() == 1) {
+            if (args[0] == "none" || args[0] == "0") {
+                det->setBadChannels(std::vector<int>{},
+                                    std::vector<int>{det_id});
+            } else if (args[0].find(".") != std::string::npos) {
+                det->setBadChannels(args[0], std::vector<int>{det_id});
+            } else {
+                parse = true;
+            }
+        }
+        // parse multi args or single one with range or single value
+        if (parse || args.size() > 1) {
+            // get channels
+            auto list = getChannelsFromStringList(args);
+            det->setBadChannels(list, std::vector<int>{det_id});
         }
-        det->setBadChannels(args[0], std::vector<int>{det_id});
         os << "successfully loaded" << '\n';
     } else {
         throw RuntimeError("Unknown action");
@@ -2839,6 +2855,8 @@ std::string CmdProxy::PatternLoopAddresses(int action) {
         if (cmd != "patlimits") {
             GetLevelAndUpdateArgIndex(action, "patloop", level, iArg, nGetArgs,
                                       nPutArgs);
+            if (cmd != "patloop0" && cmd != "patloop1" && cmd != "patloop2")
+                os << level << ' ';
         }
         if (action == defs::GET_ACTION) {
             auto t =
@@ -2878,6 +2896,8 @@ std::string CmdProxy::PatternLoopCycles(int action) {
         int level = -1, iArg = 0, nGetArgs = 0, nPutArgs = 1;
         GetLevelAndUpdateArgIndex(action, "patnloop", level, iArg, nGetArgs,
                                   nPutArgs);
+        if (cmd != "patnloop0" && cmd != "patnloop1" && cmd != "patnloop2")
+            os << level << ' ';
         if (action == defs::GET_ACTION) {
             auto t = det->getPatternLoopCycles(level, std::vector<int>{det_id});
             os << OutString(t) << '\n';
@@ -2912,6 +2932,8 @@ std::string CmdProxy::PatternWaitAddress(int action) {
         int level = -1, iArg = 0, nGetArgs = 0, nPutArgs = 1;
         GetLevelAndUpdateArgIndex(action, "patwait", level, iArg, nGetArgs,
                                   nPutArgs);
+        if (cmd != "patwait0" && cmd != "patwait1" && cmd != "patwait2")
+            os << level << ' ';
         if (action == defs::GET_ACTION) {
             auto t = det->getPatternWaitAddr(level, std::vector<int>{det_id});
             os << OutStringHex(t, 4) << '\n';
@@ -2945,6 +2967,9 @@ std::string CmdProxy::PatternWaitTime(int action) {
         int level = -1, iArg = 0, nGetArgs = 0, nPutArgs = 1;
         GetLevelAndUpdateArgIndex(action, "patwaittime", level, iArg, nGetArgs,
                                   nPutArgs);
+        if (cmd != "patwaittime0" && cmd != "patwaittime1" &&
+            cmd != "patwaittime2")
+            os << level << ' ';
         if (action == defs::GET_ACTION) {
             auto t = det->getPatternWaitTime(level, std::vector<int>{det_id});
             os << OutString(t) << '\n';

slsDetectorSoftware/src/CmdProxy.h

@@ -1767,11 +1767,12 @@ class CmdProxy {
         rx_lastclient, getRxLastClientIP,
         "\n\tClient IP Address that last communicated with the receiver.");
 
-    GET_COMMAND(rx_threads, getRxThreadIds,
+    GET_COMMAND(
-                "\n\tGet thread ids from the receiver in order of [parent, "
+        rx_threads, getRxThreadIds,
-                "tcp, listener 0, processor 0, streamer 0, listener 1, "
+        "\n\tGet kernel thread ids from the receiver in order of [parent, "
-                "processor 1, streamer 1, arping]. If no streamer yet or there "
+        "tcp, listener 0, processor 0, streamer 0, listener 1, "
-                "is no second interface, it gives 0 in its place.");
+        "processor 1, streamer 1, arping]. If no streamer yet or there "
+        "is no second interface, it gives 0 in its place.");
 
     INTEGER_COMMAND_VEC_ID(rx_arping, getRxArping, setRxArping, StringTo<int>,
                            "[0, 1]\n\tStarts a thread in slsReceiver to arping "

slsDetectorSoftware/src/Detector.cpp

@@ -349,6 +349,29 @@ void Detector::setBadChannels(const std::string &fname, Positions pos) {
     pimpl->setBadChannels(fname, pos);
 }
 
+Result<std::vector<int>> Detector::getBadChannels(Positions pos) const {
+    return pimpl->Parallel(&Module::getBadChannels, pos);
+}
+
+void Detector::setBadChannels(const std::vector<std::vector<int>> list) {
+
+    if (list.size() != static_cast<size_t>(size())) {
+        std::stringstream ss;
+        ss << "Number of bad channel sets (" << list.size()
+           << ") needs to match the number of modules (" << size() << ")";
+        throw RuntimeError(ss.str());
+    }
+
+    for (int idet = 0; idet < size(); ++idet) {
+        // TODO! Call in parallel since loading trimbits is slow?
+        pimpl->Parallel(&Module::setBadChannels, {idet}, list[idet]);
+    }
+}
+
+void Detector::setBadChannels(const std::vector<int> list, Positions pos) {
+    pimpl->setBadChannels(list, pos);
+}
+
 Result<bool> Detector::isVirtualDetectorServer(Positions pos) const {
     return pimpl->Parallel(&Module::isVirtualDetectorServer, pos);
 }

slsDetectorSoftware/src/DetectorImpl.cpp

@@ -253,14 +253,15 @@ void DetectorImpl::setVirtualDetectorServers(const int numdet, const int port) {
 }
 
 void DetectorImpl::setHostname(const std::vector<std::string> &name) {
-    // this check is there only to allow the previous detsizechan command
+    // do not free always to allow the previous detsize/ initialchecks command
-    if (shm()->totalNumberOfModules != 0) {
+    if (shm.exists() && shm()->totalNumberOfModules != 0) {
         LOG(logWARNING) << "There are already module(s) in shared memory."
                            "Freeing Shared memory now.";
-        bool initialChecks = shm()->initialChecks;
         freeSharedMemory();
+    }
+    // could be called after freeing shm from API
+    if (!shm.exists()) {
         setupDetector();
-        shm()->initialChecks = initialChecks;
     }
     for (const auto &hostname : name) {
         addModule(hostname);
@@ -342,28 +343,32 @@ void DetectorImpl::updateDetectorSize() {
             "updating detector size. ");
     }
 
-    int maxx = shm()->numberOfChannels.x;
-    int maxy = shm()->numberOfChannels.y;
     int nModx = 0, nMody = 0;
     // 1d, add modules along x axis
     if (modSize.y == 1) {
-        if (maxx == 0) {
+        int detSizeX = shm()->numberOfChannels.x;
-            maxx = modSize.x * size();
+        int maxChanX = modSize.x * size();
+        // user given detsizex used only within max value
+        if (detSizeX > 1 && detSizeX <= maxChanX) {
+            maxChanX = detSizeX;
         }
-        nModx = maxx / modSize.x;
+        nModx = maxChanX / modSize.x;
         nMody = size() / nModx;
-        if ((maxx % modSize.x) > 0) {
+        if ((maxChanX % modSize.x) > 0) {
             ++nMody;
         }
     }
     // 2d, add modules along y axis (due to eiger top/bottom)
     else {
-        if (maxy == 0) {
+        int detSizeY = shm()->numberOfChannels.y;
-            maxy = modSize.y * size();
+        int maxChanY = modSize.y * size();
+        // user given detsizey used only within max value
+        if (detSizeY > 1 && detSizeY <= maxChanY) {
+            maxChanY = detSizeY;
         }
-        nMody = maxy / modSize.y;
+        nMody = maxChanY / modSize.y;
         nModx = size() / nMody;
-        if ((maxy % modSize.y) > 0) {
+        if ((maxChanY % modSize.y) > 0) {
             ++nModx;
         }
     }
@@ -515,19 +520,18 @@ void DetectorImpl::setTransmissionDelay(int step) {
         f.get();
 }
 
-int DetectorImpl::destroyReceivingDataSockets() {
+void DetectorImpl::destroyReceivingDataSockets() {
     LOG(logINFO) << "Going to destroy data sockets";
     // close socket
     zmqSocket.clear();
 
     client_downstream = false;
     LOG(logINFO) << "Destroyed Receiving Data Socket(s)";
-    return OK;
 }
 
-int DetectorImpl::createReceivingDataSockets() {
+void DetectorImpl::createReceivingDataSockets() {
     if (client_downstream) {
-        return OK;
+        return;
     }
     LOG(logINFO) << "Going to create data sockets";
 
@@ -554,24 +558,22 @@ int DetectorImpl::createReceivingDataSockets() {
             int hwm = shm()->zmqHwm;
             if (hwm >= 0) {
                 zmqSocket[iSocket]->SetReceiveHighWaterMark(hwm);
-                if (zmqSocket[iSocket]->GetReceiveHighWaterMark() != hwm) {
+                // need not reconnect. cannot be connected (detector idle)
-                    throw ZmqSocketError("Could not set zmq rcv hwm to " +
-                                         std::to_string(hwm));
-                }
             }
             LOG(logINFO) << "Zmq Client[" << iSocket << "] at "
                          << zmqSocket.back()->GetZmqServerAddress() << "[hwm: "
                          << zmqSocket.back()->GetReceiveHighWaterMark() << "]";
-        } catch (...) {
+        } catch (std::exception &e) {
-            LOG(logERROR) << "Could not create Zmq socket on port " << portnum;
             destroyReceivingDataSockets();
-            return FAIL;
+            std::ostringstream oss;
+            oss << "Could not create zmq sub socket on port " << portnum;
+            oss << " [" << e.what() << ']';
+            throw RuntimeError(oss.str());
         }
     }
 
     client_downstream = true;
     LOG(logINFO) << "Receiving Data Socket(s) created";
-    return OK;
 }
 
 void DetectorImpl::readFrameFromReceiver() {
@@ -1111,9 +1113,7 @@ void DetectorImpl::setDataStreamingToClient(bool enable) {
         destroyReceivingDataSockets();
         // create data threads
     } else {
-        if (createReceivingDataSockets() == FAIL) {
+        createReceivingDataSockets();
-            throw RuntimeError("Could not create data threads in client.");
-        }
     }
 }
 
@@ -1146,11 +1146,7 @@ void DetectorImpl::setClientStreamingHwm(const int limit) {
         if (limit >= 0) {
             for (auto &it : zmqSocket) {
                 it->SetReceiveHighWaterMark(limit);
-                if (it->GetReceiveHighWaterMark() != limit) {
+                // need not reconnect. cannot be connected (detector idle)
-                    shm()->zmqHwm = -1;
-                    throw ZmqSocketError("Could not set zmq rcv hwm to " +
-                                         std::to_string(limit));
-                }
             }
             LOG(logINFO) << "Setting Client Zmq socket rcv hwm to " << limit;
         }
@@ -1774,6 +1770,10 @@ void DetectorImpl::setBadChannels(const std::string &fname, Positions pos) {
     if (list.empty()) {
         throw RuntimeError("Bad channel file is empty.");
     }
+    setBadChannels(list, pos);
+}
+
+void DetectorImpl::setBadChannels(const std::vector<int> list, Positions pos) {
 
     // update to multi values if multi modules
     if (isAllPositions(pos)) {
@@ -1790,20 +1790,24 @@ void DetectorImpl::setBadChannels(const std::string &fname, Positions pos) {
                                    " out of bounds.");
             }
             int ch = badchannel % nchan;
-            int imod = badchannel / nchan;
+            size_t imod = badchannel / nchan;
-            if (imod >= (int)modules.size()) {
+            if (imod >= modules.size()) {
                 throw RuntimeError("Invalid bad channel list. " +
                                    std::to_string(badchannel) +
                                    " out of bounds.");
             }
-
+            if (badchannels.size() != imod + 1) {
-            if ((int)badchannels.size() != imod + 1) {
                 badchannels.push_back(std::vector<int>{});
             }
             badchannels[imod].push_back(ch);
         }
-        for (int imod = 0; imod != (int)modules.size(); ++imod) {
+        for (size_t imod = 0; imod != modules.size(); ++imod) {
-            Parallel(&Module::setBadChannels, {imod}, badchannels[imod]);
+            // add empty vector if no bad channels in this module
+            if (badchannels.size() != imod + 1) {
+                badchannels.push_back(std::vector<int>{});
+            }
+            Parallel(&Module::setBadChannels, {static_cast<int>(imod)},
+                     badchannels[imod]);
         }
 
     } else if (pos.size() != 1) {

slsDetectorSoftware/src/DetectorImpl.h

@@ -306,6 +306,7 @@ class DetectorImpl : public virtual slsDetectorDefs {
 
     void getBadChannels(const std::string &fname, Positions pos) const;
     void setBadChannels(const std::string &fname, Positions pos);
+    void setBadChannels(const std::vector<int> list, Positions pos);
 
     std::vector<std::string> getCtbDacNames() const;
     std::string getCtbDacName(defs::dacIndex i) const;
@@ -348,8 +349,8 @@ class DetectorImpl : public virtual slsDetectorDefs {
 
     void updateDetectorSize();
 
-    int destroyReceivingDataSockets();
+    void destroyReceivingDataSockets();
-    int createReceivingDataSockets();
+    void createReceivingDataSockets();
 
     /**
      * Reads frames from receiver through a constant socket

slsDetectorSoftware/src/Module.cpp

@@ -76,7 +76,7 @@ void Module::setHostname(const std::string &hostname,
         initialDetectorServerChecks();
         checkDetectorVersionCompatibility();
         LOG(logINFO) << "Module Version Compatibility - Success";
-    } catch (const DetectorError &e) {
+    } catch (const RuntimeError &e) {
         if (!initialChecks) {
             LOG(logWARNING) << "Bypassing Initial Checks at your own risk!";
         } else {

slsDetectorSoftware/src/Pattern.cpp

@@ -9,7 +9,15 @@
 
 namespace sls {
 
-Pattern::Pattern() = default;
+Pattern::Pattern() {
+    // initialize pattern addresses
+    for (int i = 0; i != MAX_PATTERN_LEVELS; ++i) {
+        pat->startloop[i] = MAX_PATTERN_LENGTH - 1;
+        pat->stoploop[i] = MAX_PATTERN_LENGTH - 1;
+        pat->wait[i] = MAX_PATTERN_LENGTH - 1;
+    }
+}
+
 Pattern::~Pattern() { delete pat; }
 
 Pattern::Pattern(const Pattern &other) {

slsDetectorSoftware/src/SharedMemory.h

@@ -33,7 +33,7 @@ namespace sls {
 template <typename T> class SharedMemory {
     static constexpr int NAME_MAX_LENGTH = 255;
     std::string name;
-    T *shared_struct{};
+    T *shared_struct{nullptr};
 
   public:
     // moduleid of -1 creates a detector only shared memory
@@ -64,8 +64,18 @@ template <typename T> class SharedMemory {
             unmapSharedMemory();
     }
 
-    T *operator()() { return shared_struct; }
+    T *operator()() {
-    const T *operator()() const { return shared_struct; }
+        if (shared_struct)
+            return shared_struct;
+        throw SharedMemoryError(getNoShmAccessMessage());
+    }
+
+    const T *operator()() const {
+        if (shared_struct)
+            return shared_struct;
+        throw SharedMemoryError(getNoShmAccessMessage());
+    }
+
     std::string getName() const { return name; }
 
     bool exists() {
@@ -204,6 +214,11 @@ template <typename T> class SharedMemory {
             throw SharedMemoryError(msg);
         }
     }
+
+    const char *getNoShmAccessMessage() const {
+        return ("No shared memory to access. Create it first with "
+                "hostname or config command.");
+    };
 };
 
 } // namespace sls

slsDetectorSoftware/tests/test-CmdProxy-pattern.cpp

@@ -186,12 +186,14 @@ TEST_CASE("patloop", "[.cmd]") {
             {
                 std::ostringstream oss;
                 proxy.Call("patloop", {sLoop, "0x20", "0x5c"}, -1, PUT, oss);
-                REQUIRE(oss.str() == "patloop [0x0020, 0x005c]\n");
+                REQUIRE(oss.str() ==
+                        "patloop " + sLoop + " [0x0020, 0x005c]\n");
             }
             {
                 std::ostringstream oss;
                 proxy.Call("patloop", {sLoop}, -1, GET, oss);
-                REQUIRE(oss.str() == "patloop [0x0020, 0x005c]\n");
+                REQUIRE(oss.str() ==
+                        "patloop " + sLoop + " [0x0020, 0x005c]\n");
             }
             for (int iDet = 0; iDet != det.size(); ++iDet) {
                 det.setPatternLoopAddresses(iLoop, prev_val[iDet][0],
@@ -233,12 +235,12 @@ TEST_CASE("patnloop", "[.cmd]") {
             {
                 std::ostringstream oss;
                 proxy.Call("patnloop", {sLoop, "5"}, -1, PUT, oss);
-                REQUIRE(oss.str() == "patnloop 5\n");
+                REQUIRE(oss.str() == "patnloop " + sLoop + " 5\n");
             }
             {
                 std::ostringstream oss;
                 proxy.Call("patnloop", {sLoop}, -1, GET, oss);
-                REQUIRE(oss.str() == "patnloop 5\n");
+                REQUIRE(oss.str() == "patnloop " + sLoop + " 5\n");
             }
             for (int iDet = 0; iDet != det.size(); ++iDet) {
                 det.setPatternLoopCycles(iLoop, prev_val[iDet], {iDet});
@@ -279,12 +281,12 @@ TEST_CASE("patwait", "[.cmd]") {
             {
                 std::ostringstream oss;
                 proxy.Call("patwait", {sLoop, "0x5c"}, -1, PUT, oss);
-                REQUIRE(oss.str() == "patwait 0x005c\n");
+                REQUIRE(oss.str() == "patwait " + sLoop + " 0x005c\n");
             }
             {
                 std::ostringstream oss;
                 proxy.Call("patwait", {sLoop}, -1, GET, oss);
-                REQUIRE(oss.str() == "patwait 0x005c\n");
+                REQUIRE(oss.str() == "patwait " + sLoop + " 0x005c\n");
             }
             for (int iDet = 0; iDet != det.size(); ++iDet) {
                 det.setPatternWaitAddr(iLoop, prev_val[iDet], {iDet});
@@ -325,12 +327,12 @@ TEST_CASE("patwaittime", "[.cmd]") {
             {
                 std::ostringstream oss;
                 proxy.Call("patwaittime", {sLoop, "8589936640"}, -1, PUT, oss);
-                REQUIRE(oss.str() == "patwaittime 8589936640\n");
+                REQUIRE(oss.str() == "patwaittime " + sLoop + " 8589936640\n");
             }
             {
                 std::ostringstream oss;
                 proxy.Call("patwaittime", {sLoop}, -1, GET, oss);
-                REQUIRE(oss.str() == "patwaittime 8589936640\n");
+                REQUIRE(oss.str() == "patwaittime " + sLoop + " 8589936640\n");
             }
             for (int iDet = 0; iDet != det.size(); ++iDet) {
                 det.setPatternWaitTime(iLoop, prev_val[iDet], {iDet});

slsDetectorSoftware/tests/test-CmdProxy.cpp

@@ -524,8 +524,10 @@ TEST_CASE("gappixels", "[.cmd]") {
     Detector det;
     CmdProxy proxy(&det);
     auto det_type = det.getDetectorType().squash();
+    bool quad = det.getQuad().squash(false);
+    bool fullModule = (det.getModuleGeometry().y % 2 == 0);
 
-    if (det_type == defs::JUNGFRAU || det_type == defs::EIGER) {
+    if (det_type == defs::JUNGFRAU || (det_type == defs::EIGER && (quad || fullModule))) {
         auto prev_val = det.getGapPixelsinCallback();
         {
             std::ostringstream oss;
@@ -644,6 +646,8 @@ TEST_CASE("badchannels", "[.cmd]") {
     auto det_type = det.getDetectorType().squash();
 
     if (det_type == defs::GOTTHARD2 || det_type == defs::MYTHEN3) {
+        auto prev = det.getBadChannels();
+
         REQUIRE_THROWS(proxy.Call("badchannels", {}, -1, GET));
 
         std::string fname_put =
@@ -656,6 +660,51 @@ TEST_CASE("badchannels", "[.cmd]") {
         std::vector<int> expected = {0, 12, 15, 40, 41, 42, 43, 44, 1279};
         REQUIRE(list == expected);
 
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {"none"}, 0, PUT));
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {fname_get}, 0, GET));
+        list = getChannelsFromFile(fname_get);
+        REQUIRE(list.empty());
+
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {fname_put}, 0, PUT));
+
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {"0"}, 0, PUT));
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {fname_get}, 0, GET));
+        list = getChannelsFromFile(fname_get);
+        REQUIRE(list.empty());
+
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {"12"}, 0, PUT));
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {fname_get}, 0, GET));
+        list = getChannelsFromFile(fname_get);
+        expected = {12};
+        REQUIRE(list == expected);
+
+        REQUIRE_NOTHROW(proxy.Call(
+            "badchannels", {"0", "12,", "15", "43", "40:45", "1279"}, 0, PUT));
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {fname_get}, 0, GET));
+        list = getChannelsFromFile(fname_get);
+        expected = {0, 12, 15, 40, 41, 42, 43, 44, 1279};
+        REQUIRE(list == expected);
+
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {"40:45"}, 0, PUT));
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {fname_get}, 0, GET));
+        list = getChannelsFromFile(fname_get);
+        expected = {40, 41, 42, 43, 44};
+        REQUIRE(list == expected);
+
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {"5,6,7"}, 0, PUT));
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {fname_get}, 0, GET));
+        list = getChannelsFromFile(fname_get);
+        expected = {5, 6, 7};
+        REQUIRE(list == expected);
+
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {"1:5,6,7"}, 0, PUT));
+        REQUIRE_NOTHROW(proxy.Call("badchannels", {fname_get}, 0, GET));
+        list = getChannelsFromFile(fname_get);
+        expected = {1, 2, 3, 4, 6, 7};
+        REQUIRE(list == expected);
+
+        det.setBadChannels(prev);
+
     } else {
         REQUIRE_THROWS(proxy.Call("badchannels", {}, -1, GET));
     }
@@ -1222,7 +1271,7 @@ TEST_CASE("clkphase", "[.cmd]") {
         }
         std::string s_deg_val = "15";
         if (det_type == defs::MYTHEN3) {
-            s_deg_val = "15";
+            s_deg_val = "14";
         } else if (det_type == defs::GOTTHARD2) {
             s_deg_val = "23";
         }

slsDetectorSoftware/tests/test-SharedMemory.cpp

@@ -101,7 +101,7 @@ TEST_CASE("Move SharedMemory", "[detector]") {
     shm2 = std::move(shm); // shm is now a moved from object!
 
     CHECK(shm2()->x == 9);
-    CHECK(shm() == nullptr);
+    REQUIRE_THROWS(shm()); // trying to access should throw instead of returning a nullptr
     CHECK(shm2.getName() == std::string("/slsDetectorPackage_detector_") +
                                 std::to_string(shm_id));
     shm2.removeSharedMemory();

slsReceiverSoftware/src/Arping.cpp

@@ -4,6 +4,8 @@
 #include "Arping.h"
 
 #include <chrono>
+#include <signal.h>
+#include <thread>
 #include <unistd.h>
 
 namespace sls {
@@ -18,7 +20,7 @@ Arping::Arping() {}
 
 Arping::~Arping() {
     if (IsRunning()) {
-        StopThread();
+        StopProcess();
     }
 }
 
@@ -33,59 +35,66 @@ void Arping::SetInterfacesAndIps(const int index, const std::string &interface,
     // create commands to arping
     std::ostringstream os;
     os << "arping -c 1 -U -I " << interface << " " << ip;
-    // to read error messages
-    os << " 2>&1";
     std::string cmd = os.str();
     commands[index] = cmd;
 }
 
-pid_t Arping::GetThreadId() const { return threadId; }
+pid_t Arping::GetProcessId() const { return childPid; }
 
 bool Arping::IsRunning() const { return runningFlag; }
 
-void Arping::StartThread() {
+void Arping::StartProcess() {
     TestCommands();
-    try {
+
-        t = std::thread(&Arping::ThreadExecution, this);
+    // to prevent zombies from child processes being killed
-    } catch (...) {
+    signal(SIGCHLD, SIG_IGN);
-        throw RuntimeError("Could not start arping thread");
+
+    // Needs to be a fork and udp socket deleted after Listening threads
+    // done running to prevent udp socket cannot bind because of popen
+    // that forks
+    childPid = fork();
+    // child process
+    if (childPid == 0) {
+        LOG(logINFOBLUE) << "Created [ Arping Process, Tid: " << gettid()
+                         << " ]";
+        ProcessExecution();
+    }
+    // parent process
+    else if (childPid > 0) {
+        runningFlag = true;
+    }
+    // error
+    else {
+        throw RuntimeError("Could not start arping Process");
     }
-    runningFlag = true;
 }
 
-void Arping::StopThread() {
+void Arping::StopProcess() {
+    LOG(logINFOBLUE) << "Exiting [ Arping Process ]";
+
+    if (kill(childPid, SIGTERM)) {
+        throw RuntimeError("Could not kill the arping Process");
+    }
     runningFlag = false;
-    t.join();
 }
 
-void Arping::ThreadExecution() {
+void Arping::ProcessExecution() {
-    threadId = gettid();
+    while (true) {
-    LOG(logINFOBLUE) << "Created [ Arping Thread, Tid: " << threadId << " ]";
-
-    while (runningFlag) {
         std::string error = ExecuteCommands();
-        // just print (was already tested at thread start)
+        // just print (was already tested at Process start)
         if (!error.empty()) {
             LOG(logERROR) << error;
         }
-
+        const auto interval = std::chrono::seconds(60);
-        // wait for 60s as long as thread not killed
+        std::this_thread::sleep_for(interval);
-        int nsecs = 0;
-        while (runningFlag && nsecs != 60) {
-            std::this_thread::sleep_for(std::chrono::seconds(1));
-            ++nsecs;
-        }
     }
-
-    LOG(logINFOBLUE) << "Exiting [ Arping Thread, Tid: " << threadId << " ]";
-    threadId = 0;
 }
 
 void Arping::TestCommands() {
     // atleast one interface must be set up
     if (commands[0].empty()) {
         throw RuntimeError(
-            "Could not arping. Interface not set up in apring thread");
+            "Could not arping. Interface not set up in arping Process");
     }
     // test if arping commands throw an error
     std::string error = ExecuteCommands();
@@ -101,7 +110,7 @@ std::string Arping::ExecuteCommands() {
         if (cmd.empty())
             continue;
 
-        LOG(logDEBUG) << "Executing Arping Command: " << cmd;
+        LOG(logDEBUG1) << "Executing Arping Command: " << cmd;
 
         // execute command
         FILE *sysFile = popen(cmd.c_str(), "r");

slsReceiverSoftware/src/Arping.h

@@ -2,15 +2,15 @@
 // Copyright (C) 2021 Contributors to the SLS Detector Package
 #pragma once
 /**
- *@short creates/destroys an ARPing thread to arping the interfaces slsReceiver
+ *@short creates/destroys an ARPing child process to arping the interfaces
-is listening to.
+slsReceiver is listening to.
  */
 
 #include "receiver_defs.h"
 #include "sls/logger.h"
 
 #include <atomic>
-#include <thread>
+#include <unistd.h>
 
 namespace sls {
 
@@ -22,21 +22,20 @@ class Arping {
 
     void SetInterfacesAndIps(const int index, const std::string &interface,
                              const std::string &ip);
-    pid_t GetThreadId() const;
+    pid_t GetProcessId() const;
     bool IsRunning() const;
-    void StartThread();
+    void StartProcess();
-    void StopThread();
+    void StopProcess();
 
   private:
     void TestCommands();
     std::string ExecuteCommands();
-    void ThreadExecution();
+    void ProcessExecution();
 
     std::vector<std::string> commands =
         std::vector<std::string>(MAX_NUMBER_OF_LISTENING_THREADS);
     std::atomic<bool> runningFlag{false};
-    std::thread t;
+    std::atomic<pid_t> childPid{0};
-    std::atomic<pid_t> threadId{0};
 };
 
 } // namespace sls

slsReceiverSoftware/src/ClientInterface.cpp

@@ -320,165 +320,122 @@ int ClientInterface::setup_receiver(Interface &socket) {
     auto arg = socket.Receive<rxParameters>();
     LOG(logDEBUG) << ToString(arg);
 
-    // if object exists, verify unlocked and idle, else only verify lock
-    // (connecting first time)
-    if (receiver != nullptr) {
-        verifyIdle(socket);
-    }
-
-    // basic setup
-    setDetectorType(arg.detType);
-    impl()->setDetectorSize(arg.numberOfModule);
-    impl()->setModulePositionId(arg.moduleIndex);
-    impl()->setDetectorHostname(arg.hostname);
-
-    // udp setup
-    // update retvals only if detmac is not the same as in detector
     MacAddr retvals[2];
-    if (arg.udp_dstip != 0) {
+    try {
-        MacAddr r = setUdpIp(IpAddr(arg.udp_dstip));
+        // if object exists, verify unlocked and idle, else only verify lock
-        MacAddr detMac{arg.udp_dstmac};
+        // (connecting first time)
-        if (detMac != r) {
+        if (receiver != nullptr) {
-            retvals[0] = r;
+            verifyIdle(socket);
         }
-    }
-    if (arg.udp_dstip2 != 0) {
-        MacAddr r = setUdpIp2(IpAddr(arg.udp_dstip2));
-        MacAddr detMac{arg.udp_dstmac2};
-        if (detMac != r) {
-            retvals[1] = r;
-        }
-    }
-    impl()->setUDPPortNumber(arg.udp_dstport);
-    impl()->setUDPPortNumber2(arg.udp_dstport2);
-    if (detType == JUNGFRAU || detType == GOTTHARD2) {
-        try {
-            impl()->setNumberofUDPInterfaces(arg.udpInterfaces);
-        } catch (const RuntimeError &e) {
-            throw RuntimeError("Failed to set number of interfaces to " +
-                               std::to_string(arg.udpInterfaces));
-        }
-    }
-    impl()->setUDPSocketBufferSize(0);
 
-    // acquisition parameters
+        // basic setup
-    impl()->setNumberOfFrames(arg.frames);
+        setDetectorType(arg.detType);
-    impl()->setNumberOfTriggers(arg.triggers);
+        impl()->setDetectorSize(arg.numberOfModule);
-    if (detType == GOTTHARD2) {
+        impl()->setModulePositionId(arg.moduleIndex);
-        impl()->setNumberOfBursts(arg.bursts);
+        impl()->setDetectorHostname(arg.hostname);
-    }
+
-    if (detType == JUNGFRAU) {
+        // udp setup
-        impl()->setNumberOfAdditionalStorageCells(arg.additionalStorageCells);
+        // update retvals only if detmac is not the same as in detector
-    }
+        if (arg.udp_dstip != 0) {
-    if (detType == MOENCH || detType == CHIPTESTBOARD) {
+            MacAddr r = setUdpIp(IpAddr(arg.udp_dstip));
-        try {
+            MacAddr detMac{arg.udp_dstmac};
+            if (detMac != r) {
+                retvals[0] = r;
+            }
+        }
+        if (arg.udp_dstip2 != 0) {
+            MacAddr r = setUdpIp2(IpAddr(arg.udp_dstip2));
+            MacAddr detMac{arg.udp_dstmac2};
+            if (detMac != r) {
+                retvals[1] = r;
+            }
+        }
+        impl()->setUDPPortNumber(arg.udp_dstport);
+        impl()->setUDPPortNumber2(arg.udp_dstport2);
+        if (detType == JUNGFRAU || detType == GOTTHARD2) {
+            impl()->setNumberofUDPInterfaces(arg.udpInterfaces);
+        }
+        impl()->setUDPSocketBufferSize(0);
+
+        // acquisition parameters
+        impl()->setNumberOfFrames(arg.frames);
+        impl()->setNumberOfTriggers(arg.triggers);
+        if (detType == GOTTHARD2) {
+            impl()->setNumberOfBursts(arg.bursts);
+        }
+        if (detType == JUNGFRAU) {
+            impl()->setNumberOfAdditionalStorageCells(
+                arg.additionalStorageCells);
+        }
+        if (detType == MOENCH || detType == CHIPTESTBOARD) {
             impl()->setNumberofAnalogSamples(arg.analogSamples);
-        } catch (const RuntimeError &e) {
-            throw RuntimeError("Could not set num analog samples to " +
-                               std::to_string(arg.analogSamples) +
-                               " due to fifo structure memory allocation.");
         }
-    }
+        if (detType == CHIPTESTBOARD) {
-    if (detType == CHIPTESTBOARD) {
-        try {
             impl()->setNumberofDigitalSamples(arg.digitalSamples);
-        } catch (const RuntimeError &e) {
-            throw RuntimeError("Could not set num digital samples to " +
-                               std::to_string(arg.analogSamples) +
-                               " due to fifo structure memory allocation.");
         }
-    }
+        if (detType != MYTHEN3) {
-    if (detType != MYTHEN3) {
+            impl()->setAcquisitionTime(std::chrono::nanoseconds(arg.expTimeNs));
-        impl()->setAcquisitionTime(std::chrono::nanoseconds(arg.expTimeNs));
+        }
-    }
+        impl()->setAcquisitionPeriod(std::chrono::nanoseconds(arg.periodNs));
-    impl()->setAcquisitionPeriod(std::chrono::nanoseconds(arg.periodNs));
+        if (detType == EIGER) {
-    if (detType == EIGER) {
+            impl()->setSubExpTime(std::chrono::nanoseconds(arg.subExpTimeNs));
-        impl()->setSubExpTime(std::chrono::nanoseconds(arg.subExpTimeNs));
+            impl()->setSubPeriod(std::chrono::nanoseconds(arg.subExpTimeNs) +
-        impl()->setSubPeriod(std::chrono::nanoseconds(arg.subExpTimeNs) +
+                                 std::chrono::nanoseconds(arg.subDeadTimeNs));
-                             std::chrono::nanoseconds(arg.subDeadTimeNs));
+            impl()->setActivate(static_cast<bool>(arg.activate));
-        impl()->setActivate(static_cast<bool>(arg.activate));
+            impl()->setDetectorDataStream(LEFT, arg.dataStreamLeft);
-        impl()->setDetectorDataStream(LEFT, arg.dataStreamLeft);
+            impl()->setDetectorDataStream(RIGHT, arg.dataStreamRight);
-        impl()->setDetectorDataStream(RIGHT, arg.dataStreamRight);
-        try {
             impl()->setQuad(arg.quad == 0 ? false : true);
-        } catch (const RuntimeError &e) {
+            impl()->setThresholdEnergy(arg.thresholdEnergyeV[0]);
-            throw RuntimeError("Could not set quad to " +
-                               std::to_string(arg.quad) +
-                               " due to fifo strucutre memory allocation");
         }
-        impl()->setThresholdEnergy(arg.thresholdEnergyeV[0]);
+        if (detType == EIGER || detType == JUNGFRAU) {
-    }
+            impl()->setReadNRows(arg.readNRows);
-    if (detType == EIGER || detType == JUNGFRAU) {
-        impl()->setReadNRows(arg.readNRows);
-    }
-    if (detType == MYTHEN3) {
-        std::array<int, 3> val;
-        for (int i = 0; i < 3; ++i) {
-            val[i] = arg.thresholdEnergyeV[i];
         }
-        impl()->setThresholdEnergy(val);
+        if (detType == MYTHEN3) {
-    }
+            std::array<int, 3> val;
-    if (detType == EIGER || detType == MYTHEN3) {
+            for (int i = 0; i < 3; ++i) {
-        try {
+                val[i] = arg.thresholdEnergyeV[i];
+            }
+            impl()->setThresholdEnergy(val);
+        }
+        if (detType == EIGER || detType == MYTHEN3) {
             impl()->setDynamicRange(arg.dynamicRange);
-        } catch (const RuntimeError &e) {
-            throw RuntimeError(
-                "Could not set dynamic range. Could not allocate "
-                "memory for fifo or could not start listening/writing threads");
         }
-    }
+        impl()->setTimingMode(arg.timMode);
-    impl()->setTimingMode(arg.timMode);
+        if (detType == EIGER || detType == MOENCH || detType == CHIPTESTBOARD ||
-    if (detType == EIGER || detType == MOENCH || detType == CHIPTESTBOARD ||
+            detType == MYTHEN3) {
-        detType == MYTHEN3) {
-        try {
             impl()->setTenGigaEnable(arg.tenGiga);
-        } catch (const RuntimeError &e) {
-            throw RuntimeError("Could not set 10GbE.");
         }
-    }
+        if (detType == CHIPTESTBOARD) {
-    if (detType == CHIPTESTBOARD) {
-        try {
             impl()->setReadoutMode(arg.roMode);
-        } catch (const RuntimeError &e) {
-            throw RuntimeError("Could not set read out mode "
-                               "due to fifo memory allocation.");
         }
-    }
+        if (detType == CHIPTESTBOARD || detType == MOENCH) {
-    if (detType == CHIPTESTBOARD || detType == MOENCH) {
-        try {
             impl()->setADCEnableMask(arg.adcMask);
-        } catch (const RuntimeError &e) {
-            throw RuntimeError("Could not set adc enable mask "
-                               "due to fifo memory allcoation");
-        }
-        try {
             impl()->setTenGigaADCEnableMask(arg.adc10gMask);
-        } catch (const RuntimeError &e) {
-            throw RuntimeError("Could not set 10Gb adc enable mask "
-                               "due to fifo memory allcoation");
         }
-    }
+        if (detType == GOTTHARD) {
-    if (detType == GOTTHARD) {
-        try {
             impl()->setDetectorROI(arg.roi);
-        } catch (const RuntimeError &e) {
-            throw RuntimeError("Could not set ROI");
         }
+        if (detType == MYTHEN3) {
+            impl()->setCounterMask(arg.countermask);
+            impl()->setAcquisitionTime1(
+                std::chrono::nanoseconds(arg.expTime1Ns));
+            impl()->setAcquisitionTime2(
+                std::chrono::nanoseconds(arg.expTime2Ns));
+            impl()->setAcquisitionTime3(
+                std::chrono::nanoseconds(arg.expTime3Ns));
+            impl()->setGateDelay1(std::chrono::nanoseconds(arg.gateDelay1Ns));
+            impl()->setGateDelay2(std::chrono::nanoseconds(arg.gateDelay2Ns));
+            impl()->setGateDelay3(std::chrono::nanoseconds(arg.gateDelay3Ns));
+            impl()->setNumberOfGates(arg.gates);
+        }
+        if (detType == GOTTHARD2) {
+            impl()->setBurstMode(arg.burstType);
+        }
+        impl()->setScan(arg.scanParams);
+    } catch (std::exception &e) {
+        throw RuntimeError("Could not setup receiver [" +
+                           std::string(e.what()) + ']');
     }
-    if (detType == MYTHEN3) {
-        impl()->setCounterMask(arg.countermask);
-        impl()->setAcquisitionTime1(std::chrono::nanoseconds(arg.expTime1Ns));
-        impl()->setAcquisitionTime2(std::chrono::nanoseconds(arg.expTime2Ns));
-        impl()->setAcquisitionTime3(std::chrono::nanoseconds(arg.expTime3Ns));
-        impl()->setGateDelay1(std::chrono::nanoseconds(arg.gateDelay1Ns));
-        impl()->setGateDelay2(std::chrono::nanoseconds(arg.gateDelay2Ns));
-        impl()->setGateDelay3(std::chrono::nanoseconds(arg.gateDelay3Ns));
-        impl()->setNumberOfGates(arg.gates);
-    }
-    if (detType == GOTTHARD2) {
-        impl()->setBurstMode(arg.burstType);
-    }
-    impl()->setScan(arg.scanParams);
 
     return socket.sendResult(retvals);
 }
@@ -502,13 +459,10 @@ void ClientInterface::setDetectorType(detectorType arg) {
         detType = GENERIC;
         receiver = make_unique<Implementation>(arg);
         detType = arg;
-    } catch (std::exception &e) {
+    } catch (const std::exception &e) {
-        std::ostringstream os;
+        throw RuntimeError("Could not set detector type in the receiver. [" +
-        os << "Could not set detector type in the receiver. ";
+                           std::string(e.what()) + ']');
-        os << e.what();
-        throw RuntimeError(os.str());
     }
-
     // callbacks after (in setdetectortype, the object is reinitialized)
     if (startAcquisitionCallBack != nullptr)
         impl()->registerCallBackStartAcquisition(startAcquisitionCallBack,
@@ -536,8 +490,8 @@ int ClientInterface::set_detector_roi(Interface &socket) {
     verifyIdle(socket);
     try {
         impl()->setDetectorROI(arg);
-    } catch (const RuntimeError &e) {
+    } catch (const std::exception &e) {
-        throw RuntimeError("Could not set ROI");
+        throw RuntimeError("Could not set ROI [" + std::string(e.what()) + ']');
     }
     return socket.Send(OK);
 }
@@ -616,10 +570,10 @@ int ClientInterface::set_num_analog_samples(Interface &socket) {
     }
     try {
         impl()->setNumberofAnalogSamples(value);
-    } catch (const RuntimeError &e) {
+    } catch (const std::exception &e) {
-        throw RuntimeError("Could not set num analog samples to " +
+        throw RuntimeError("Could not set number of analog samples to " +
-                           std::to_string(value) +
+                           std::to_string(value) + " [" +
-                           " due to fifo structure memory allocation.");
+                           std::string(e.what()) + ']');
     }
     return socket.Send(OK);
 }
@@ -632,11 +586,12 @@ int ClientInterface::set_num_digital_samples(Interface &socket) {
     }
     try {
         impl()->setNumberofDigitalSamples(value);
-    } catch (const RuntimeError &e) {
+    } catch (const std::exception &e) {
-        throw RuntimeError("Could not set num digital samples to " +
+        throw RuntimeError("Could not set number of digital samples to " +
-                           std::to_string(value) +
+                           std::to_string(value) + " [" +
-                           " due to fifo structure memory allocation.");
+                           std::string(e.what()) + ']');
     }
+
     return socket.Send(OK);
 }
 
@@ -743,9 +698,9 @@ int ClientInterface::set_dynamic_range(Interface &socket) {
         } else {
             try {
                 impl()->setDynamicRange(dr);
-            } catch (const RuntimeError &e) {
+            } catch (const std::exception &e) {
-                throw RuntimeError("Could not allocate memory for fifo or "
+                throw RuntimeError("Could not set dynamic range [" +
-                                   "could not start listening/writing threads");
+                                   std::string(e.what()) + ']');
             }
         }
     }
@@ -781,7 +736,12 @@ int ClientInterface::get_status(Interface &socket) {
 int ClientInterface::start_receiver(Interface &socket) {
     if (impl()->getStatus() == IDLE) {
         LOG(logDEBUG1) << "Starting Receiver";
-        impl()->startReceiver();
+        try {
+            impl()->startReceiver();
+        } catch (const std::exception &e) {
+            throw RuntimeError("Could not start reciever [" +
+                               std::string(e.what()) + ']');
+        }
     }
     return socket.Send(OK);
 }
@@ -791,12 +751,16 @@ int ClientInterface::stop_receiver(Interface &socket) {
     if (impl()->getStatus() == RUNNING) {
         LOG(logDEBUG1) << "Stopping Receiver";
         impl()->setStoppedFlag(static_cast<bool>(arg));
-        impl()->stopReceiver();
+        try {
+            impl()->stopReceiver();
+        } catch (const std::exception &e) {
+            throw RuntimeError("Could not stop receiver [" +
+                               std::string(e.what()) + ']');
+        }
     }
     auto s = impl()->getStatus();
     if (s != IDLE)
-        throw RuntimeError("Could not stop receiver. It as it is: " +
+        throw RuntimeError("Could not stop receiver. Status: " + ToString(s));
-                           ToString(s));
 
     return socket.Send(OK);
 }
@@ -811,7 +775,12 @@ int ClientInterface::set_file_dir(Interface &socket) {
         throw RuntimeError("Receiver path needs to be absolute path");
 
     LOG(logDEBUG1) << "Setting file path: " << fpath;
-    impl()->setFilePath(fpath);
+    try {
+        impl()->setFilePath(fpath);
+    } catch (const std::exception &e) {
+        throw RuntimeError("Could not set file path [" + std::string(e.what()) +
+                           ']');
+    }
     return socket.Send(OK);
 }
 
@@ -893,7 +862,12 @@ int ClientInterface::set_file_write(Interface &socket) {
     }
     verifyIdle(socket);
     LOG(logDEBUG1) << "Setting File write enable:" << enable;
-    impl()->setFileWriteEnable(enable);
+    try {
+        impl()->setFileWriteEnable(enable);
+    } catch (const std::exception &e) {
+        throw RuntimeError("Could not enable/disable file write [" +
+                           std::string(e.what()) + ']');
+    }
     return socket.Send(OK);
 }
 
@@ -948,8 +922,9 @@ int ClientInterface::enable_tengiga(Interface &socket) {
         LOG(logDEBUG1) << "Setting 10GbE:" << val;
         try {
             impl()->setTenGigaEnable(val);
-        } catch (const RuntimeError &e) {
+        } catch (const std::exception &e) {
-            throw RuntimeError("Could not set 10GbE.");
+            throw RuntimeError("Could not set 10GbE. [" +
+                               std::string(e.what()) + ']');
         }
     }
     int retval = impl()->getTenGigaEnable();
@@ -965,9 +940,9 @@ int ClientInterface::set_fifo_depth(Interface &socket) {
         LOG(logDEBUG1) << "Setting fifo depth:" << value;
         try {
             impl()->setFifoDepth(value);
-        } catch (const RuntimeError &e) {
+        } catch (const std::exception &e) {
-            throw RuntimeError("Could not set fifo depth due to fifo structure "
+            throw RuntimeError("Could not set fifo depth [" +
-                               "memory allocation.");
+                               std::string(e.what()) + ']');
         }
     }
     int retval = impl()->getFifoDepth();
@@ -1002,10 +977,12 @@ int ClientInterface::set_streaming(Interface &socket) {
     LOG(logDEBUG1) << "Setting data stream enable:" << index;
     try {
         impl()->setDataStreamEnable(index);
-    } catch (const RuntimeError &e) {
+    } catch (const std::exception &e) {
         throw RuntimeError("Could not set data stream enable to " +
-                           std::to_string(index));
+                           std::to_string(index) + " [" +
+                           std::string(e.what()) + ']');
     }
+
     return socket.Send(OK);
 }
 
@@ -1064,7 +1041,12 @@ int ClientInterface::set_file_format(Interface &socket) {
     }
     verifyIdle(socket);
     LOG(logDEBUG1) << "Setting file format:" << f;
-    impl()->setFileFormat(f);
+    try {
+        impl()->setFileFormat(f);
+    } catch (const std::exception &e) {
+        throw RuntimeError("Could not set file format to " + ToString(f) +
+                           " [" + std::string(e.what()) + ']');
+    }
 
     auto retval = impl()->getFileFormat();
     validate(f, retval, "set file format", DEC);
@@ -1185,7 +1167,13 @@ int ClientInterface::set_udp_socket_buffer_size(Interface &socket) {
                 "Receiver socket buffer size exceeded max (INT_MAX/2)");
         }
         LOG(logDEBUG1) << "Setting UDP Socket Buffer size: " << size;
-        impl()->setUDPSocketBufferSize(size);
+        try {
+            impl()->setUDPSocketBufferSize(size);
+        } catch (const std::exception &e) {
+            throw RuntimeError("Could not set udp socket buffer size to " +
+                               std::to_string(size) + " [" +
+                               std::string(e.what()) + ']');
+        }
     }
     int retval = impl()->getUDPSocketBufferSize();
     if (size != 0)
@@ -1264,9 +1252,9 @@ int ClientInterface::set_readout_mode(Interface &socket) {
         LOG(logDEBUG1) << "Setting readout mode: " << arg;
         try {
             impl()->setReadoutMode(arg);
-        } catch (const RuntimeError &e) {
+        } catch (const std::exception &e) {
-            throw RuntimeError(
+            throw RuntimeError("Could not set read out mode [" +
-                "Could not set read out mode due to fifo memory allocation.");
+                               std::string(e.what()) + ']');
         }
     }
     auto retval = impl()->getReadoutMode();
@@ -1282,10 +1270,11 @@ int ClientInterface::set_adc_mask(Interface &socket) {
     LOG(logDEBUG1) << "Setting 1Gb ADC enable mask: " << arg;
     try {
         impl()->setADCEnableMask(arg);
-    } catch (const RuntimeError &e) {
+    } catch (const std::exception &e) {
-        throw RuntimeError(
+        throw RuntimeError("Could not set adc enable mask [" +
-            "Could not set adc enable mask due to fifo memory allcoation");
+                           std::string(e.what()) + ']');
     }
+
     auto retval = impl()->getADCEnableMask();
     if (retval != arg) {
         std::ostringstream os;
@@ -1349,10 +1338,10 @@ int ClientInterface::set_quad_type(Interface &socket) {
         LOG(logDEBUG1) << "Setting quad:" << quadEnable;
         try {
             impl()->setQuad(quadEnable == 0 ? false : true);
-        } catch (const RuntimeError &e) {
+        } catch (const std::exception &e) {
             throw RuntimeError("Could not set quad to " +
-                               std::to_string(quadEnable) +
+                               std::to_string(quadEnable) + " [" +
-                               " due to fifo strucutre memory allocation");
+                               std::string(e.what()) + ']');
         }
     }
     int retval = impl()->getQuad() ? 1 : 0;
@@ -1487,10 +1476,12 @@ int ClientInterface::set_num_interfaces(Interface &socket) {
     LOG(logDEBUG1) << "Setting Number of UDP Interfaces:" << arg;
     try {
         impl()->setNumberofUDPInterfaces(arg);
-    } catch (const RuntimeError &e) {
+    } catch (const std::exception &e) {
-        throw RuntimeError("Failed to set number of interfaces to " +
+        throw RuntimeError("Could not set number of interfaces to " +
-                           std::to_string(arg));
+                           std::to_string(arg) + " [" + std::string(e.what()) +
+                           ']');
     }
+
     return socket.Send(OK);
 }
 
@@ -1500,10 +1491,11 @@ int ClientInterface::set_adc_mask_10g(Interface &socket) {
     LOG(logDEBUG1) << "Setting 10Gb ADC enable mask: " << arg;
     try {
         impl()->setTenGigaADCEnableMask(arg);
-    } catch (const RuntimeError &e) {
+    } catch (const std::exception &e) {
-        throw RuntimeError(
+        throw RuntimeError("Could not set 10Gb adc enable mask [" +
-            "Could not set 10Gb adc enable mask due to fifo memory allcoation");
+                           std::string(e.what()) + ']');
     }
+
     auto retval = impl()->getTenGigaADCEnableMask();
     if (retval != arg) {
         std::ostringstream os;
@@ -1519,7 +1511,12 @@ int ClientInterface::set_counter_mask(Interface &socket) {
     auto arg = socket.Receive<uint32_t>();
     verifyIdle(socket);
     LOG(logDEBUG1) << "Setting counters: " << arg;
-    impl()->setCounterMask(arg);
+    try {
+        impl()->setCounterMask(arg);
+    } catch (const std::exception &e) {
+        throw RuntimeError("Could not set counter mask [" +
+                           std::string(e.what()) + ']');
+    }
     return socket.Send(OK);
 }
 
@@ -1715,7 +1712,12 @@ int ClientInterface::set_arping(Interface &socket) {
     }
     verifyIdle(socket);
     LOG(logDEBUG1) << "Starting/ Killing arping thread:" << value;
-    impl()->setArping(value, udpips);
+    try {
+        impl()->setArping(value, udpips);
+    } catch (const std::exception &e) {
+        throw RuntimeError("Could not start/kill arping thread [" +
+                           std::string(e.what()) + ']');
+    }
     return socket.Send(OK);
 }
 
@@ -1733,9 +1735,11 @@ int ClientInterface::set_receiver_roi(Interface &socket) {
     verifyIdle(socket);
     try {
         impl()->setReceiverROI(arg);
-    } catch (const RuntimeError &e) {
+    } catch (const std::exception &e) {
-        throw RuntimeError("Could not set ReceiverROI");
+        throw RuntimeError("Could not set Receiver ROI [" +
+                           std::string(e.what()) + ']');
     }
+
     return socket.Send(OK);
 }
 
@@ -1747,9 +1751,11 @@ int ClientInterface::set_receiver_roi_metadata(Interface &socket) {
     verifyIdle(socket);
     try {
         impl()->setReceiverROIMetadata(arg);
-    } catch (const RuntimeError &e) {
+    } catch (const std::exception &e) {
-        throw RuntimeError("Could not set ReceiverROI metadata");
+        throw RuntimeError("Could not set ReceiverROI metadata [" +
+                           std::string(e.what()) + ']');
     }
+
     return socket.Send(OK);
 }
 

slsReceiverSoftware/src/DataStreamer.cpp

@@ -87,19 +87,18 @@ void DataStreamer::CreateZmqSockets(uint32_t port, const IpAddr ip, int hwm) {
     std::string sip = ip.str();
     try {
         zmqSocket = new ZmqSocket(portnum, (ip != 0 ? sip.c_str() : nullptr));
+
         // set if custom
         if (hwm >= 0) {
             zmqSocket->SetSendHighWaterMark(hwm);
-            if (zmqSocket->GetSendHighWaterMark() != hwm) {
+            // needed, or HWL is not taken
-                throw RuntimeError(
+            zmqSocket->Rebind();
-                    "Could not set zmq send high water mark to " +
-                    std::to_string(hwm));
-            }
         }
-    } catch (...) {
+    } catch (std::exception &e) {
-        LOG(logERROR) << "Could not create Zmq socket on port " << portnum
+        std::ostringstream oss;
-                      << " for Streamer " << index;
+        oss << "Could not create zmq pub socket on port " << portnum;
-        throw;
+        oss << " [" << e.what() << ']';
+        throw RuntimeError(oss.str());
     }
     LOG(logINFO) << index << " Streamer: Zmq Server started at "
                  << zmqSocket->GetZmqServerAddress()

slsReceiverSoftware/src/Implementation.cpp

@@ -78,11 +78,12 @@ void Implementation::SetupFifoStructure() {
         try {
             fifo.push_back(
                 sls::make_unique<Fifo>(i, datasize, generalData->fifoDepth));
-        } catch (...) {
+        } catch (const std::exception &e) {
             fifo.clear();
             generalData->fifoDepth = 0;
-            throw RuntimeError("Could not allocate memory for fifo structure " +
+            std::ostringstream oss;
-                               std::to_string(i) + ". FifoDepth is now 0.");
+            oss << e.what() << ". Fifo depth is now 0";
+            throw RuntimeError(oss.str());
         }
         // set the listener & dataprocessor threads to point to the right fifo
         if (listener.size())
@@ -165,12 +166,10 @@ void Implementation::setDetectorType(const detectorType d) {
             SetupListener(i);
             dataProcessor.push_back(sls::make_unique<DataProcessor>(i));
             SetupDataProcessor(i);
-        } catch (...) {
+        } catch (const std::exception &e) {
             listener.clear();
             dataProcessor.clear();
-            throw RuntimeError(
+            throw;
-                "Could not create listener/dataprocessor threads (index:" +
-                std::to_string(i) + ")");
         }
     }
 
@@ -212,6 +211,7 @@ void Implementation::SetupDataStreamer(int i) {
                                       streamingHwm);
     dataStreamer[i]->SetAdditionalJsonHeader(additionalJsonHeader);
     dataStreamer[i]->SetFileIndex(fileIndex);
+    dataStreamer[i]->SetQuadEnable(quadEnable);
     dataStreamer[i]->SetFlipRows(flipRows);
     dataStreamer[i]->SetNumberofPorts(numPorts);
     dataStreamer[i]->SetQuadEnable(quadEnable);
@@ -351,19 +351,21 @@ std::array<pid_t, NUM_RX_THREAD_IDS> Implementation::getThreadIds() const {
             retval[id++] = 0;
         }
     }
-    retval[NUM_RX_THREAD_IDS - 1] = arping.GetThreadId();
+    retval[NUM_RX_THREAD_IDS - 1] = arping.GetProcessId();
     return retval;
 }
 
 bool Implementation::getArping() const { return arping.IsRunning(); }
 
-pid_t Implementation::getArpingThreadId() const { return arping.GetThreadId(); }
+pid_t Implementation::getArpingProcessId() const {
+    return arping.GetProcessId();
+}
 
 void Implementation::setArping(const bool i,
                                const std::vector<std::string> ips) {
     if (i != arping.IsRunning()) {
         if (!i) {
-            arping.StopThread();
+            arping.StopProcess();
         } else {
             // setup interface
             for (int i = 0; i != generalData->numUDPInterfaces; ++i) {
@@ -374,7 +376,7 @@ void Implementation::setArping(const bool i,
                 }
                 arping.SetInterfacesAndIps(i, eth[i], ips[i]);
             }
-            arping.StartThread();
+            arping.StartProcess();
         }
     }
 }
@@ -665,8 +667,9 @@ void Implementation::startReceiver() {
             startAcquisitionCallBack(filePath, fileName, fileIndex, imageSize,
                                      pStartAcquisition);
         } catch (const std::exception &e) {
-            throw RuntimeError("Start Acquisition Callback Error: " +
+            std::ostringstream oss;
-                               std::string(e.what()));
+            oss << "Start Acquisition Callback Error: " << e.what();
+            throw RuntimeError(oss.str());
         }
         if (rawDataReadyCallBack != nullptr) {
             LOG(logINFO) << "Data Write has been defined externally";
@@ -713,6 +716,10 @@ void Implementation::stopReceiver() {
         std::this_thread::sleep_for(std::chrono::milliseconds(5));
     }
 
+    // delete the udp sockets
+    for (const auto &it : listener)
+        it->DeleteUDPSocket();
+
     if (fileWriteEnable && modulePos == 0) {
         // master and virtual file (hdf5)
         StartMasterWriter();
@@ -777,8 +784,9 @@ void Implementation::stopReceiver() {
                 status = IDLE;
                 LOG(logINFO) << "Receiver Stopped";
                 LOG(logINFO) << "Status: " << ToString(status);
-                throw RuntimeError("Acquisition Finished Callback Error: " +
+                std::ostringstream oss;
-                                   std::string(e.what()));
+                oss << "Acquisition Finished Callback Error: " << e.what();
+                throw RuntimeError(oss.str());
             }
         }
     }
@@ -859,7 +867,7 @@ void Implementation::CreateUDPSockets() {
         }
     } catch (const RuntimeError &e) {
         shutDownUDPSockets();
-        throw RuntimeError("Could not create UDP Socket(s).");
+        throw;
     }
     LOG(logDEBUG) << "UDP socket(s) created successfully.";
 }
@@ -879,7 +887,9 @@ void Implementation::SetupWriter() {
         shutDownUDPSockets();
         for (const auto &it : dataProcessor)
             it->CloseFiles();
-        throw RuntimeError("Could not create first data file.");
+        std::ostringstream oss;
+        oss << "Could not set up writer: " << e.what();
+        throw RuntimeError(oss.str());
     }
 }
 
@@ -968,10 +978,9 @@ void Implementation::StartMasterWriter() {
             }
         }
 #endif
-    } catch (std::exception &e) {
+    } catch (const std::exception &e) {
         // ignore it and just print it
-        LOG(logWARNING) << "Caught exception when handling virtual hdf5 file ["
+        LOG(logWARNING) << "Error creating master/virtualfiles: " << e.what();
-                        << e.what() << "]";
     }
 }
 
@@ -1032,12 +1041,10 @@ void Implementation::setNumberofUDPInterfaces(const int n) {
                 SetupListener(i);
                 dataProcessor.push_back(sls::make_unique<DataProcessor>(i));
                 SetupDataProcessor(i);
-            } catch (...) {
+            } catch (const std::exception &e) {
                 listener.clear();
                 dataProcessor.clear();
-                throw RuntimeError(
+                throw;
-                    "Could not create listener/dataprocessor threads (index:" +
-                    std::to_string(i) + ")");
             }
 
             // streamer threads
@@ -1045,16 +1052,14 @@ void Implementation::setNumberofUDPInterfaces(const int n) {
                 try {
                     dataStreamer.push_back(sls::make_unique<DataStreamer>(i));
                     SetupDataStreamer(i);
-                } catch (...) {
+                } catch (const std::exception &e) {
                     if (dataStreamEnable) {
                         dataStreamer.clear();
                         dataStreamEnable = false;
                         for (const auto &it : dataProcessor)
                             it->SetDataStreamEnable(dataStreamEnable);
                     }
-                    throw RuntimeError(
+                    throw;
-                        "Could not create datastreamer threads (index:" +
-                        std::to_string(i) + ")");
                 }
             }
         }
@@ -1165,12 +1170,12 @@ void Implementation::setDataStreamEnable(const bool enable) {
                 try {
                     dataStreamer.push_back(sls::make_unique<DataStreamer>(i));
                     SetupDataStreamer(i);
-                } catch (...) {
+                } catch (const std::exception &e) {
                     dataStreamer.clear();
                     dataStreamEnable = false;
                     for (const auto &it : dataProcessor)
                         it->SetDataStreamEnable(dataStreamEnable);
-                    throw RuntimeError("Could not set data stream enable.");
+                    throw;
                 }
             }
             SetThreadPriorities();

slsReceiverSoftware/src/Implementation.h

@@ -54,7 +54,7 @@ class Implementation : private virtual slsDetectorDefs {
     void setThreadIds(const pid_t parentTid, const pid_t tcpTid);
     std::array<pid_t, NUM_RX_THREAD_IDS> getThreadIds() const;
     bool getArping() const;
-    pid_t getArpingThreadId() const;
+    pid_t getArpingProcessId() const;
     void setArping(const bool i, const std::vector<std::string> ips);
     ROI getReceiverROI() const;
     void setReceiverROI(const ROI arg);
@@ -323,7 +323,7 @@ class Implementation : private virtual slsDetectorDefs {
 
     // acquisition
     std::atomic<runStatus> status{IDLE};
-    bool stoppedFlag{false};
+    std::atomic<bool> stoppedFlag{false};
     scanParameters scanParams{};
 
     // network configuration (UDP)

slsReceiverSoftware/src/Listener.cpp

@@ -148,30 +148,34 @@ void Listener::RecordFirstIndex(uint64_t fnum) {
 }
 
 void Listener::CreateUDPSocket(int &actualSize) {
-    if (disabledPort) {
-        return;
-    }
-    uint32_t packetSize = generalData->packetSize;
-    if (generalData->detType == GOTTHARD2 && index != 0) {
-        packetSize = generalData->vetoPacketSize;
-    }
-
     try {
+        if (disabledPort) {
+            return;
+        }
+        uint32_t packetSize = generalData->packetSize;
+        if (generalData->detType == GOTTHARD2 && index != 0) {
+            packetSize = generalData->vetoPacketSize;
+        }
+
         udpSocket = nullptr;
         udpSocket = make_unique<UdpRxSocket>(
             udpPortNumber, packetSize,
             (eth.length() ? InterfaceNameToIp(eth).str().c_str() : nullptr),
             generalData->udpSocketBufferSize);
         LOG(logINFO) << index << ": UDP port opened at port " << udpPortNumber;
-    } catch (...) {
+
-        throw RuntimeError("Could not create UDP socket on port " +
+        udpSocketAlive = true;
-                           std::to_string(udpPortNumber));
+
+        // doubled due to kernel bookkeeping (could also be less due to
+        // permissions)
+        actualSize = udpSocket->getBufferSize();
+
+    } catch (std::exception &e) {
+        std::ostringstream oss;
+        oss << "Could not create UDP socket on port " << udpPortNumber << " ["
+            << e.what() << ']';
+        throw RuntimeError(oss.str());
     }
-
-    udpSocketAlive = true;
-
-    // doubled due to kernel bookkeeping (could also be less due to permissions)
-    actualSize = udpSocket->getBufferSize();
 }
 
 void Listener::ShutDownUDPSocket() {
@@ -184,6 +188,13 @@ void Listener::ShutDownUDPSocket() {
     }
 }
 
+void Listener::DeleteUDPSocket() {
+    if (udpSocket) {
+        udpSocket.reset();
+        LOG(logINFO) << "Closed UDP port " << udpPortNumber;
+    }
+}
+
 void Listener::CreateDummySocketForUDPSocketBufferSize(int s, int &actualSize) {
     // custom setup (s != 0)
     // default setup at startup (s = 0)

slsReceiverSoftware/src/Listener.h

@@ -50,6 +50,7 @@ class Listener : private virtual slsDetectorDefs, public ThreadObject {
     void ResetParametersforNewAcquisition();
     void CreateUDPSocket(int &actualSize);
     void ShutDownUDPSocket();
+    void DeleteUDPSocket();
     /** to set & get actual buffer size */
     void CreateDummySocketForUDPSocketBufferSize(int s, int &actualSize);
 

slsSupportLib/include/sls/ZmqSocket.h

@@ -31,6 +31,11 @@ namespace sls {
 // #define ZMQ_DETAIL
 #define ROIVERBOSITY
 
+// high water mark for gui
+#define DEFFAULT_LOW_ZMQ_HWM           (25)
+#define DEFAULT_LOW_ZMQ_HWM_BUFFERSIZE (1024 * 1024) // 1MB
+#define DEFAULT_ZMQ_BUFFERSIZE         (0)           // os default
+
 /** zmq header structure */
 struct zmqHeader {
     /** true if incoming data, false if end of acquisition */
@@ -108,15 +113,29 @@ class ZmqSocket {
     /** Returns high water mark for outbound messages */
     int GetSendHighWaterMark();
 
-    /** Sets high water mark for outbound messages. Default 1000 (zmqlib) */
+    /** Sets high water mark for outbound messages. Default 1000 (zmqlib). Also
+     * changes send buffer size depending on hwm. Must rebind.  */
     void SetSendHighWaterMark(int limit);
 
     /** Returns high water mark for inbound messages */
     int GetReceiveHighWaterMark();
 
-    /** Sets high water mark for inbound messages. Default 1000 (zmqlib) */
+    /** Sets high water mark for inbound messages. Default 1000 (zmqlib). Also
+     * changes receiver buffer size depending on hwm. Must reconnect */
     void SetReceiveHighWaterMark(int limit);
 
+    /** Gets kernel buffer for  outbound messages. Default 0 (os) */
+    int GetSendBuffer();
+
+    /** Sets kernel buffer for  outbound messages. Default 0 (os) */
+    void SetSendBuffer(int limit);
+
+    /** Gets kernel buffer for  inbound messages. Default 0 (os) */
+    int GetReceiveBuffer();
+
+    /** Sets kernel buffer for  inbound messages. Default 0 (os) */
+    void SetReceiveBuffer(int limit);
+
     /**
      * Returns Port Number
      * @returns Port Number
@@ -129,6 +148,9 @@ class ZmqSocket {
      */
     std::string GetZmqServerAddress() { return sockfd.serverAddress; }
 
+    /** unbinds and rebind, to apply changes of HWM  */
+    void Rebind();
+
     /**
      * Connect client socket to server socket
      * @returns 1 for fail, 0 for success

slsSupportLib/include/sls/container_utils.h

@@ -148,6 +148,18 @@ Squash(const Container &c, typename Container::value_type default_value = {}) {
     return default_value;
 }
 
+template <typename T>
+typename std::enable_if<is_container<T>::value, bool>::type
+removeDuplicates(T &c) {
+    auto containerSize = c.size();
+    std::sort(c.begin(), c.end());
+    c.erase(std::unique(c.begin(), c.end()), c.end());
+    if (c.size() != containerSize) {
+        return true;
+    }
+    return false;
+}
+
 } // namespace sls
 
 #endif // CONTAINER_UTILS_H

slsSupportLib/include/sls/file_utils.h

@@ -50,6 +50,8 @@ ssize_t getFileSize(FILE *fd, const std::string &prependErrorString);
 
 std::string getFileNameFromFilePath(const std::string &fpath);
 
+std::vector<int> getChannelsFromStringList(const std::vector<std::string> list);
+
 /** File can have # for comments.
  * Channels can be separated by spaces, commas
  * and ranges provided using ':', eg. 23:29

slsSupportLib/include/sls/versionAPI.h

@@ -1,13 +1,13 @@
 // SPDX-License-Identifier: LGPL-3.0-or-other
 // Copyright (C) 2021 Contributors to the SLS Detector Package
 /** API versions */
-#define RELEASE      "7.0.0.rc1"
+#define RELEASE      "7.0.0.rc4"
-#define APILIB       "7.0.0.rc1 0x221208"
+#define APICTB       "7.0.0.rc3 0x230130"
-#define APIRECEIVER  "7.0.0.rc1 0x221208"
+#define APIGOTTHARD  "7.0.0.rc3 0x230130"
-#define APICTB       "7.0.0.rc1 0x221212"
+#define APIGOTTHARD2 "7.0.0.rc3 0x230130"
-#define APIGOTTHARD  "7.0.0.rc1 0x221212"
+#define APIJUNGFRAU  "7.0.0.rc3 0x230130"
-#define APIGOTTHARD2 "7.0.0.rc1 0x221212"
+#define APIMYTHEN3   "7.0.0.rc3 0x230130"
-#define APIJUNGFRAU  "7.0.0.rc1 0x221212"
+#define APIMOENCH    "7.0.0.rc3 0x230130"
-#define APIMYTHEN3   "7.0.0.rc1 0x221212"
+#define APIEIGER     "7.0.0.rc3 0x230130"
-#define APIMOENCH    "7.0.0.rc1 0x221212"
+#define APILIB "7.0.0.rc4 0x230214"
-#define APIEIGER     "7.0.0.rc1 0x221212"
+#define APIRECEIVER "7.0.0.rc4 0x230214"

slsSupportLib/src/UdpRxSocket.cpp

@@ -27,15 +27,18 @@ UdpRxSocket::UdpRxSocket(int port, ssize_t packet_size, const char *hostname,
     const std::string portname = std::to_string(port);
     if (getaddrinfo(hostname, portname.c_str(), &hints, &res)) {
         throw RuntimeError("Failed at getaddrinfo with " +
-                           std::string(hostname));
+                           std::string(hostname) + " [" +
+                           std::string(strerror(errno)) + ']');
     }
     sockfd_ = socket(res->ai_family, res->ai_socktype, res->ai_protocol);
     if (sockfd_ == -1) {
-        throw RuntimeError("Failed to create UDP RX socket");
+        throw RuntimeError("Failed to create UDP RX socket [" +
+                           std::string(strerror(errno)) + ']');
     }
     if (bind(sockfd_, res->ai_addr, res->ai_addrlen) == -1) {
         close(sockfd_);
-        throw RuntimeError("Failed to bind UDP RX socket");
+        throw RuntimeError("Failed to bind UDP RX socket [" +
+                           std::string(strerror(errno)) + ']');
     }
     freeaddrinfo(res);
 
@@ -74,13 +77,15 @@ int UdpRxSocket::getBufferSize() const {
     int ret = 0;
     socklen_t optlen = sizeof(ret);
     if (getsockopt(sockfd_, SOL_SOCKET, SO_RCVBUF, &ret, &optlen) == -1)
-        throw RuntimeError("Could not get socket buffer size");
+        throw RuntimeError("Could not get socket buffer size [" +
+                           std::string(strerror(errno)) + ']');
     return ret;
 }
 
 void UdpRxSocket::setBufferSize(int size) {
     if (setsockopt(sockfd_, SOL_SOCKET, SO_RCVBUF, &size, sizeof(size)))
-        throw RuntimeError("Could not set socket buffer size");
+        throw RuntimeError("Could not set socket buffer size [" +
+                           std::string(strerror(errno)) + ']');
 }
 
 void UdpRxSocket::Shutdown() {

slsSupportLib/src/ZmqSocket.cpp

@@ -102,6 +102,16 @@ void ZmqSocket::SetSendHighWaterMark(int limit) {
         PrintError();
         throw ZmqSocketError("Could not set ZMQ_SNDHWM");
     }
+    if (GetSendHighWaterMark() != limit) {
+        throw ZmqSocketError("Could not set ZMQ_SNDHWM to " +
+                             std::to_string(limit));
+    }
+
+    int bufsize = DEFAULT_ZMQ_BUFFERSIZE;
+    if (limit < DEFFAULT_LOW_ZMQ_HWM) {
+        bufsize = DEFAULT_LOW_ZMQ_HWM_BUFFERSIZE;
+    }
+    SetSendBuffer(bufsize);
 }
 
 int ZmqSocket::GetReceiveHighWaterMark() {
@@ -110,7 +120,7 @@ int ZmqSocket::GetReceiveHighWaterMark() {
     if (zmq_getsockopt(sockfd.socketDescriptor, ZMQ_RCVHWM, &value,
                        &value_size)) {
         PrintError();
-        throw ZmqSocketError("Could not get ZMQ_SNDHWM");
+        throw ZmqSocketError("Could not get ZMQ_RCVHWM");
     }
     return value;
 }
@@ -119,7 +129,77 @@ void ZmqSocket::SetReceiveHighWaterMark(int limit) {
     if (zmq_setsockopt(sockfd.socketDescriptor, ZMQ_RCVHWM, &limit,
                        sizeof(limit))) {
         PrintError();
-        throw ZmqSocketError("Could not set ZMQ_SNDHWM");
+        throw ZmqSocketError("Could not set ZMQ_RCVHWM");
+    }
+    if (GetReceiveHighWaterMark() != limit) {
+        throw ZmqSocketError("Could not set ZMQ_RCVHWM to " +
+                             std::to_string(limit));
+    }
+    int bufsize = DEFAULT_ZMQ_BUFFERSIZE;
+    if (limit < DEFFAULT_LOW_ZMQ_HWM) {
+        bufsize = DEFAULT_LOW_ZMQ_HWM_BUFFERSIZE;
+    }
+    SetReceiveBuffer(bufsize);
+}
+
+int ZmqSocket::GetSendBuffer() {
+    int value = 0;
+    size_t value_size = sizeof(value);
+    if (zmq_getsockopt(sockfd.socketDescriptor, ZMQ_SNDBUF, &value,
+                       &value_size)) {
+        PrintError();
+        throw ZmqSocketError("Could not get ZMQ_SNDBUF");
+    }
+    return value;
+}
+
+void ZmqSocket::SetSendBuffer(int limit) {
+    if (zmq_setsockopt(sockfd.socketDescriptor, ZMQ_SNDBUF, &limit,
+                       sizeof(limit))) {
+        PrintError();
+        throw ZmqSocketError("Could not set ZMQ_SNDBUF");
+    }
+    if (GetSendBuffer() != limit) {
+        throw ZmqSocketError("Could not set ZMQ_SNDBUF to " +
+                             std::to_string(limit));
+    }
+}
+
+int ZmqSocket::GetReceiveBuffer() {
+    int value = 0;
+    size_t value_size = sizeof(value);
+    if (zmq_getsockopt(sockfd.socketDescriptor, ZMQ_RCVBUF, &value,
+                       &value_size)) {
+        PrintError();
+        throw ZmqSocketError("Could not get ZMQ_RCVBUF");
+    }
+    return value;
+}
+
+void ZmqSocket::SetReceiveBuffer(int limit) {
+    if (zmq_setsockopt(sockfd.socketDescriptor, ZMQ_RCVBUF, &limit,
+                       sizeof(limit))) {
+        PrintError();
+        throw ZmqSocketError("Could not set ZMQ_RCVBUF");
+    }
+    if (GetReceiveBuffer() != limit) {
+        throw ZmqSocketError("Could not set ZMQ_RCVBUF to " +
+                             std::to_string(limit));
+    }
+}
+
+void ZmqSocket::Rebind() { // the purpose is to apply HWL changes, which are
+                           // frozen at bind, which is in the constructor.
+
+    //    unbbind
+    if (zmq_unbind(sockfd.socketDescriptor, sockfd.serverAddress.c_str())) {
+        PrintError();
+        throw ZmqSocketError("Could not unbind socket");
+    }
+    // bind address
+    if (zmq_bind(sockfd.socketDescriptor, sockfd.serverAddress.c_str())) {
+        PrintError();
+        throw ZmqSocketError("Could not bind socket");
     }
 }
 

slsSupportLib/src/file_utils.cpp

@@ -2,6 +2,7 @@
 // Copyright (C) 2021 Contributors to the SLS Detector Package
 #include "sls/file_utils.h"
 #include "sls/ToString.h"
+#include "sls/container_utils.h"
 #include "sls/logger.h"
 #include "sls/sls_detector_exceptions.h"
 
@@ -165,6 +166,63 @@ ssize_t getFileSize(FILE *fd, const std::string &prependErrorString) {
     return fileSize;
 }
 
+std::vector<int>
+getChannelsFromStringList(const std::vector<std::string> list) {
+    std::vector<int> channels;
+    for (auto line : list) {
+
+        // replace comma with space
+        std::replace_if(
+            begin(line), end(line), [](char c) { return (c == ','); }, ' ');
+
+        // split line (delim space)
+        std::vector<std::string> vec = split(line, ' ');
+
+        // for every channel separated by space
+        for (auto it : vec) {
+            // find range and replace with sequence of x to y
+            auto result = it.find(':');
+            if (result != std::string::npos) {
+                try {
+                    int istart = StringTo<int>(it.substr(0, result));
+                    int istop = StringTo<int>(
+                        it.substr(result + 1, it.length() - result - 1));
+                    LOG(logDEBUG1) << "istart:" << istart << " istop:" << istop;
+                    std::vector<int> range(istop - istart);
+                    std::generate(range.begin(), range.end(),
+                                  [n = istart]() mutable { return n++; });
+                    for (auto range_it : range) {
+                        channels.push_back(range_it);
+                    }
+                } catch (std::exception &e) {
+                    throw RuntimeError(
+                        "Could not load channels. Invalid channel range: " +
+                        it);
+                }
+            }
+
+            // else convert to int
+            else {
+                int ival = 0;
+                try {
+                    ival = StringTo<int>(it);
+                } catch (std::exception &e) {
+                    throw RuntimeError(
+                        "Could not load channels. Invalid channel number: " +
+                        it);
+                }
+                channels.push_back(ival);
+            }
+        }
+    }
+
+    if (removeDuplicates(channels)) {
+        LOG(logWARNING) << "Removed duplicates from channel file";
+    }
+    LOG(logDEBUG1) << "list:" << ToString(channels);
+    return channels;
+}
+
 std::vector<int> getChannelsFromFile(const std::string &fname) {
     // read bad channels file
     std::ifstream input_file(fname);
@@ -172,73 +230,19 @@ std::vector<int> getChannelsFromFile(const std::string &fname) {
         throw RuntimeError("Could not open bad channels file " + fname +
                            " for reading");
     }
-    std::vector<int> list;
+    std::vector<std::string> lines;
     for (std::string line; std::getline(input_file, line);) {
         // ignore comments
         if (line.find('#') != std::string::npos) {
             line.erase(line.find('#'));
         }
-
+        // ignore empty lines
-        // replace comma with space
+        if (line.empty()) {
-        std::replace_if(
+            continue;
-            begin(line), end(line), [](char c) { return (c == ','); }, ' ');
-
-        // replace x:y with a sequence of x to y
-        auto result = line.find(':');
-        while (result != std::string::npos) {
-            auto start = line.rfind(' ', result);
-            if (start == std::string::npos) {
-                start = 0;
-            } else
-                ++start;
-            int istart = StringTo<int>(line.substr(start, result - start));
-
-            auto stop = line.find(' ', result);
-            if (stop == std::string::npos) {
-                stop = line.length();
-            }
-            int istop =
-                StringTo<int>(line.substr(result + 1, stop - result - 1));
-
-            std::vector<int> v(istop - istart);
-            std::generate(v.begin(), v.end(),
-                          [n = istart]() mutable { return n++; });
-            line.replace(start, stop - start, ToString(v));
-
-            LOG(logDEBUG1) << line;
-            result = line.find(':');
-        }
-
-        // remove punctuations including [ and ]
-        line.erase(std::remove_if(begin(line), end(line), ispunct), end(line));
-
-        LOG(logDEBUG) << "\nline: [" << line << ']';
-
-        // split line (delim space) and push to list
-        std::vector<std::string> vec = split(line, ' ');
-        for (auto it : vec) {
-            int ival = 0;
-            try {
-                ival = StringTo<int>(it);
-            } catch (std::exception &e) {
-                throw RuntimeError("Could not load channels from file. Invalid "
-                                   "channel number: " +
-                                   it);
-            }
-            list.push_back(ival);
         }
+        lines.push_back(line);
     }
-
+    return getChannelsFromStringList(lines);
-    // remove duplicates from list
-    auto listSize = list.size();
-    std::sort(list.begin(), list.end());
-    list.erase(unique(list.begin(), list.end()), list.end());
-    if (list.size() != listSize) {
-        LOG(logWARNING) << "Removed duplicates from channel file";
-    }
-
-    LOG(logDEBUG1) << "list:" << ToString(list);
-    return list;
 }
 
 std::string getAbsolutePathFromCurrentProcess(const std::string &fname) {

slsSupportLib/tests/test-container_utils.cpp

@@ -136,4 +136,18 @@ TEST_CASE("compare a vector of arrays", "[support]") {
     CHECK(minusOneIfDifferent(vec1) == arr);
 }
 
+TEST_CASE("remove duplicates from vector") {
+    std::vector<int> v{5, 6, 5, 3};
+    auto r = removeDuplicates(v);
+    CHECK(r == true); // did indeed remove elements
+    CHECK(v == std::vector<int>{3, 5, 6});
+}
+
+TEST_CASE("remove duplicated empty vector") {
+    std::vector<int> v;
+    auto r = removeDuplicates(v);
+    CHECK(r == false); // no elements to remove
+    CHECK(v == std::vector<int>{});
+}
+
 } // namespace sls