fill value in hdf5 according to actual datatype of dataset

* m3: clk 0 changed from 10 to 20 (100MHz to 50MHz)

* g2: startup clk div back to 10 as in firmware but setting in software startup to 20

CMakeLists.txt

@@ -2,7 +2,7 @@
 # Copyright (C) 2021 Contributors to the SLS Detector Package
 cmake_minimum_required(VERSION 3.14)
 project(slsDetectorPackage)
-set(PROJECT_VERSION 8.0.0)
+set(PROJECT_VERSION 8.0.1)
 
 set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
 
@@ -33,7 +33,7 @@ else()
     # Standard behaviour use libzmq included in this repo (libs/libzmq)
     FetchContent_Declare(
         libzmq
-        URL ${CMAKE_SOURCE_DIR}/libs/libzmq/libzmq-4.3.4.tar.gz
+        URL ${CMAKE_CURRENT_SOURCE_DIR}/libs/libzmq/libzmq-4.3.4.tar.gz
         URL_HASH MD5=cc20b769ac10afa352e5ed2769bb23b3
     )
 endif()

RELEASE.txt

@@ -1,265 +1,43 @@
-SLS Detector Package Major Release 8.0.0 released on 13.11.2023
+SLS Detector Package Major Release 8.0.1 released on 16.01.2024
 ===============================================================
 
-This document describes the differences between v8.0.0 and v7.0.3
+This document describes the differences between v8.0.1 and v8.0.0
 
 
 
     CONTENTS
     --------
-    1           Compilation Changes
-    2           New or Changed Features
-        2.1         Breaking API
-        2.2         Resolved or Changed Features
-        2.3         New Features
-    3           On-board Detector Server Compatibility
-    4           Firmware Requirements
-    5           Kernel Requirements
-    6           Download, Documentation & Support
+    1           Resolved Issues
+    2           On-board Detector Server Compatibility
+    3           Firmware Requirements
+    4           Kernel Requirements
+    5           Download, Documentation & Support
 
 
 
 
-2 Compilation Changes
-=====================
+1 Resolved Issues
+=================
 
 
-    *   Minimum CMake version changed from 3.12 to 3.14
+    Compilation
+    -----------
 
 
-    *   Internal zmq lib
-        Building zmq from tar file in repo (libs/libzmq/libzmq-4.3.4.tar.gz), 
-        but added option (SLS_FETCH_ZMQ_FROM_GITHUB) to pull zmq version (v4.3.4) 
-        from github (https://github.com/zeromq/libzmq.git)
+    *   Fixed compilation error when building without zmq-devel installed
+        and removed dependency on zeromq in conda build. 
 
 
-    *   Internal pybind11 lib
-        Building pybind11 from tar file in repo (libs/pybind11/v2.11.0.tar.gz), 
-        but added option (SLS_FETCH_PYBIND11_FROM_GITHUB) to pull pybind11 version 
-        (v2.11.0) from github (https://github.com/pybind/pybind11)        
+    *   Fixed libzmq compilation error to build the package as a submodule.
 
 
+    Calibration
+    -----------
 
-2 New, Changed or Resolved Features
-=====================================
 
+    *   [Moench] Fixed Moench calibration
 
 
-2.1 Breaking API
-==================
-
-
-    Firmware
-    --------
-
-    *   [Jungfrau] Status register and Sync mode fix
-        The regiser bit definition changed and fixes for stable control in sync mode.
-        Effect: Master and slaves give same status (previously master is sometimes 'idle' when acquisition is stopped), same #frames left and #nextframenumber.
-        Also ERROR status connected, but never noticed to occur.
-
-        For user, everything is transparent unless one touches status register
-        using advanced commands. 
-
-
-    *   [Moench] Status: Development mode
-        Moench is now being made compatible with Jungfrau v2.0 readout boards. 
-        Hence, firmware and software is in development mode. 
-        7.x.x will continue to have fixes for Moench until this version is deployed.
-
-
-    *   [Ctb] Fixes and features described later on.
-
-
-    Client
-    ======
-
-
-    *   Datatype change of port numbers from int to uint16_t   
-        API: setVirtualDetectorServers, 
-        get/setRxPort, get/setControlPort, get/setStopPort,
-        get/setDestinationUDPPort(2), get/setRxZmqPort, get/setClientZmqPort
-
-
-    *   [Eiger] versions, hardware version, febl/r firmware version 
-        Versions command modified to give more info about hardware version ['fx30', 'fx70'] and Febl/r firmware versions.
-        Command line: versions (output modified), hardwareversion (added for Eiger)
-        API added for Eiger: getHardwareVersion, getFrontEndFirmwareVersion
-        Enums added: fpgaPosition {FRONT_LEFT, FRONT_RIGHT}
-    
-
-    *   [Ctb] Voltage->Power name change
-        Command line: voltagelist ->powerlist
-        API: get/setVoltage -> get/setPower, get/setVoltageList -> get/setPowerList,
-        getMeasuredVoltage -> getMeasuredPower
-
-
-
-2.2 Resolved or Changed Features
-================================
-
-
-    Detector Server
-    ---------------
-
-
-    *   Set bit and clear bit validation
-        Previously, validation expected all the other bits in the register to 
-        not change. Now, it only validates the selected bit.
-
-    
-    *   [Jungfrau] Electron collection mode (bit 14 of 0x5D register)
-        Affected Command line: setbit, clearbit, reg
-        Affected API: setBit, clearBit, writeRegister
-        Electron collection mode and requires chip reconfiguration. 
-        Temporary fix added that touching this bit will reconfigure chip if chip 
-        is v1.1 and powered on. Permanent fix by introducing a command for the 
-        same in future release.
-    
-
-    *   [Ctb] Fixes
-
-        -   Patioctrl, patsetbit, patbitmask
-            MSB (64 bit unsigned) could not be set as a value of -1 was interpreted 
-            as a 'get'. Fixed in server. 
-
-        -   Allow dac tristate when v_limit is set. Fixed.
-
-        -   Changing fw bit from disable analog to enable analog
-
-        -   Allow adc enable for 1 GbE and 10GbE to be 0.
-
-        -   Slow ADCs previously misread (a high 5k+ value). Firmware updated 
-            and software adjusted now.
-
-        -   Allow non blocking acquire for 1GbE. Added Transmitting status when it
-            might still be reading from fifo.
-
-        -   Clean memory before reading from fifo in 1GbE mode. Read fifo then
-            RD strobe (corresponding firmware fix) fixes number of reads, but 
-            increases all pipelines by 1.
-        
-        -   Fixed pattern viewer (auto legend buf without wait and loop), allow 
-            pyat files. (/patterngenerator)
-
-
-    Simulator
-    ---------
-
-
-    *   Unique TCP port for multiple simulators
-        Checks include unique TCP port-hostname combo.
-
-
-    Receiver
-    --------
-
-
-    *   Unique TCP port for multiple receivers
-        7.x.x already has automatically increasing TCP ports in shared memory 
-        for multiple receivers. Now, checks include unique TCP port-hostname 
-        combo.
-
-
-    *   [Ctb] Fixes
-
-        -   Readout mode updated
-            'rx_hostname' should configure the receiver with parameters from detector,
-            but readout mode in receiver always configured at start up to Analog only. 
-            Fixed.
-
-        -   Incorrect image size in zmq header, which happens when dbit list is 
-            less than 64 bits. Fixed.
-
-        -   Rearranging digital data when dbit list less than 64 bits fixed.
-
-
-    Client
-    ------
-
-
-    *   [Jungfrau][Mythen3][Gotthard2] Sync mode should have at least one master
-        Multi module synced detectors should have at least one master when 
-        starting acquisition, else it will throw. Once master is done acquiring
-        (blocking mode), status of all modules checked to ensure none of the 
-        slaves in waiting due to hardware issues such as cabling.
-
-
-
-2.3 New Features
-================
-
-
-    Client
-    ------
-    
-
-    *   [Jungfrau] Pedestal mode
-        Command line: pedestalmode
-        API: get/setPedestalMode
-        Example: 
-            pedestalmode 0 # turns off pedestal mode
-            pedestalmode 50 10 # turns on pedestal mode (50 pedestal frames, 10 loops)
-        
-        In pedestal mode, number of frames/triggers
-        is overwritten by '#pedestal_frames x #pedestal_loops x 2'.
-        In auto timing mode or trigger mode with #frames > 1, #frames is overwritten
-        with #triggers is 1. Otherwise, #triggers is overwritten with #frames is 1.
-        In pedestal mode, one cannot set #frames, #triggers or timing mode (exception).
-
-        Disabling pedestal mode will set back to normal mode with normal previous
-        values of #frames and #triggers.
-
-
-    *   Source UDP IP: Auto
-        Command line: udp_srcip, udp_srcip2
-        API: get/setSourceUDPIP(2)
-        Allow 'auto' for udp_srcip to pick up IP from detector hostname. Not allowed
-        for Gotthard1.
-
-
-    *   Custom row and column for detector UDP header
-        Command line: row, column
-        API: get/setRow, get/setColumn
-        By default, row and column of module is determined in a pre-determined 
-        manner or by custom detector size (Command line: detsize).
-        This is useful if user accesses row and column in multi- detector UDP header 
-        or for the GUI to rearrange for complete image.
-        Option now added to set custom row and column. 
-
-
-    *   [Ctb] Features
-
-        -   List for ADC, signal, power, slowadc 
-            Also allow their list to set names and to obtain their indices and values.
-
-            Command line: dacname, dacindex, 
-            adclist, adcname, adcindex, 
-            signallist, signalname,signalindex, 
-            powerlist, powername, powerindex, powervalues,
-            slowadclist, slowadcname, slowadcindex, slowadcvalues
-
-            API: get/setDacName, getDacIndex, 
-            get/setAdcNames, getAdcIndex, get/setAdcName,
-            get/setSignalNames, getSignalIndex, get/setSignalName,
-            get/setPowerNames, getPowerIndex, get/setPowerName, getPowerList,
-            get/setSlowADCNames, getSlowADCIndex, get/setSlowADCName, getSlowADCList
-
-        -   Added more modes for transceiver in read out mode.
-            Allow to set number of samples and enable mask for transceiver.
-
-            Command line: romode (more modes: 'transceiver', 'digital_transceiver'),
-            tsamples, transceiverenable
-            API: get/setTransceiverEnableMask, get/setNumberOfTransceiverSamples,
-            get/setReadoutMode (more enums: TRANSCEIVER_ONLY, DIGITAL_AND_TRANSCEIVER)
-
-
-        -   Command to get file name with path of last pattern uploaded.
-            Command line: patfname
-            API: getPatterFileName
-
-
-    *   Automatic test script for all virtual simulators added.
-
 
 
 2  On-board Detector Server Compatibility

conda-recepie/meta.yaml

@@ -18,7 +18,6 @@ requirements:
     - {{compiler('cxx')}}
     - cmake
     - qt 5.*
-    - zeromq
     - xorg-libx11
     - xorg-libice
     - xorg-libxext
@@ -37,7 +36,6 @@ requirements:
   host:
     - libstdcxx-ng
     - libgcc-ng
-    - zeromq
     - xorg-libx11
     - xorg-libice
     - xorg-libxext
@@ -48,7 +46,6 @@ requirements:
     - expat
 
   run:
-    - zeromq
     - libstdcxx-ng
     - libgcc-ng 
 
@@ -63,15 +60,11 @@ outputs:
         - {{compiler('cxx')}}
         - libstdcxx-ng
         - libgcc-ng
-        - zeromq
 
-      host:
-        - zeromq
 
       run: 
         - libstdcxx-ng
         - libgcc-ng
-        - zeromq
 
   - name: slsdet
 
@@ -84,10 +77,12 @@ outputs:
         - {{compiler('cxx')}}
         - {{ pin_subpackage('slsdetlib', exact=True) }}
         - setuptools
+        - pybind11=2.11
 
       host:
         - python
         - {{ pin_subpackage('slsdetlib', exact=True) }}
+        - pybind11=2.11
 
 
       run:

examples/rawdata.config

@@ -0,0 +1,22 @@
+numfiles 1
+nthreads 5,
+fifosize 5000
+nsigma 5
+gainfile none
+detectorMode counting
+threshold 0
+pedestalfile none
+nframes 0
+xMin 0
+xMax 400
+yMin 0
+yMax 400
+outdir ./
+indir ./
+flist none
+fformat none
+runmin 0
+runmax -1
+readnrows 400
+eMin 0
+eMax 16000

examples/zmq.config

@@ -0,0 +1,16 @@
+numinterfaces 1
+rx_zmqip 10.1.2.102
+rx_zmqport 1978
+zmqip 129.129.202.57
+zmqport 1979
+nthreads 6
+fifosize 5000
+nsigma 5
+gainfile none
+nbinsx 5
+nbinsy 5
+etafile none
+etabinsx 1000
+etabinsy 1000
+etamin -1
+etamax 2

libs/rapidjson/rapidjson/document.h

@@ -316,7 +316,8 @@ struct GenericStringRef {
 
     GenericStringRef(const GenericStringRef& rhs) : s(rhs.s), length(rhs.length) {}
 
-    GenericStringRef& operator=(const GenericStringRef& rhs) { s = rhs.s; length = rhs.length; }
+    // Removed to fix failing build in GCC 14
+    // GenericStringRef& operator=(const GenericStringRef& rhs) { s = rhs.s; length = rhs.length; }
 
     //! implicit conversion to plain CharType pointer
     operator const Ch *() const { return s; }

python/setup.py

@@ -7,7 +7,6 @@ Build upon the pybind11 example found here: https://github.com/pybind/python_exa
 
 import os
 import sys
-sys.path.append('../libs/pybind')
 from setuptools import setup, find_packages
 from pybind11.setup_helpers import Pybind11Extension, build_ext
 
@@ -41,11 +40,10 @@ ext_modules = [
         
         ,
         include_dirs=[
-            os.path.join('../libs/pybind/include'),
             os.path.join(get_conda_path(), 'include'),
 
         ],
-        libraries=['SlsDetector', 'SlsSupport', 'SlsReceiver', 'zmq'],
+        libraries=['SlsDetector', 'SlsSupport', 'SlsReceiver'],
         library_dirs=[
             os.path.join(get_conda_path(), 'lib'),
         ],

serverBin/moenchDetectorServerv8.0.0

@@ -1 +0,0 @@
-../slsDetectorServers/moenchDetectorServer/bin/moenchDetectorServerv8.0.0

serverBin/moenchDetectorServerv8.0.2

@@ -0,0 +1 @@
+../slsDetectorServers/moenchDetectorServer/bin/moenchDetectorServerv8.0.2

serverBin/mythen3DetectorServerv8.0.0

@@ -1 +0,0 @@
-../slsDetectorServers/mythen3DetectorServer/bin/mythen3DetectorServerv8.0.0

serverBin/mythen3DetectorServerv8.0.2

@@ -0,0 +1 @@
+../slsDetectorServers/mythen3DetectorServer/bin/mythen3DetectorServerv8.0.2

slsDetectorCalibration/dataStructures/moench03v2Data.h

@@ -0,0 +1,240 @@
+// SPDX-License-Identifier: LGPL-3.0-or-other
+// Copyright (C) 2021 Contributors to the SLS Detector Package
+#ifndef MOENCH03v2DATA_H
+#define MOENCH03v2DATA_H
+//#define MYROOT
+
+#ifndef MYROOT
+#include "sls/sls_detector_defs.h"
+#endif
+
+
+
+
+#ifdef MYROOT
+
+    typedef struct {
+        uint64_t frameNumber;
+        uint32_t expLength;
+        uint32_t packetNumber;
+        uint64_t bunchId;
+        uint64_t timestamp;
+        uint16_t modId;
+        uint16_t row;
+        uint16_t column;
+        uint16_t reserved;
+        uint32_t debug;
+        uint16_t roundRNumber;
+        uint8_t detType;
+        uint8_t version;
+    } sls_detector_header;
+#define MAX_NUM_PACKETS 512
+// using sls_bitset = std::bitset<MAX_NUM_PACKETS>;
+//  using bitset_storage = uint8_t[MAX_NUM_PACKETS / 8];
+  struct sls_receiver_header {
+        sls_detector_header detHeader; /**< is the detector header */
+        uint8_t packetsMask[64];        /**< is the packets caught bit mask */
+    };
+#endif
+
+#include "slsDetectorData.h"
+#ifdef RAWDATA
+#define DATA_OFFSET sizeof(header)
+#endif
+#ifndef RAWDATA
+#define DATA_OFFSET 0
+#endif
+
+
+class moench03v2Data : public slsDetectorData<uint16_t> {
+
+  private:
+    int iframe;
+    const int nRows;
+    
+    
+
+    double ghost[200][25];
+
+    // Single point of definition if we need to customize
+#ifndef MYROOT
+    using header = sls::defs::sls_receiver_header;
+#endif
+#ifdef MYROOT
+    sls_receiver_header header;
+#endif
+  public:
+    /**
+       Implements the slsReceiverData structure for the moench02 prototype read
+       out by a module i.e. using the slsReceiver (160x160 pixels, 40 packets
+       1286 large etc.) \param c crosstalk parameter for the output buffer
+
+    */
+    moench03v2Data(int nrows = 200)
+        : slsDetectorData<uint16_t>(400, nrows*2,2* 400*nrows*2 + DATA_OFFSET),
+      nRows(nrows) {
+	
+	std::cout << "MOENCH width new firmware " << dataSize << std::endl;
+	
+	int off=DATA_OFFSET;
+	    for (int ix = 0; ix < 400; ix++) {
+	      for (int iy = 0; iy < nRows*2; iy++) {
+		dataMap[iy][ix]=off+2*(iy*400+ix);
+	      }
+	    }
+	    
+        iframe = 0;
+        //  cout << "data struct created" << endl;
+      };
+
+    /**
+       Returns the value of the selected channel for the given dataset as
+       double. \param data pointer to the dataset (including headers etc) \param
+       ix pixel number in the x direction \param iy pixel number in the y
+       direction \returns data for the selected channel, with inversion if
+       required as double
+
+    */
+    double getValue(char *data, int ix, int iy = 0) override {
+        uint16_t val = getChannel(data, ix, iy) & 0x3fff;
+        return val;
+    };
+
+    virtual void calcGhost(char *data, int ix, int iy) {
+        double val = 0;
+        /* for (int ix=0; ix<25; ix++){ */
+        /*   for (int iy=0; iy<200; iy++) { */
+        val = 0;
+        //	cout << "** ";
+        for (int isc = 0; isc < 16; isc++) {
+            //  for (int ii=0; ii<2; ii++) {
+            val += getChannel(data, ix + 25 * isc, iy);
+            //  cout << "(" << isc << "," << val << " " ;
+            val += getChannel(data, ix + 25 * isc, 399 - iy);
+            // cout << val << " " ;
+            // }
+        }
+        ghost[iy][ix] = val; //-6224;
+                             //	cout << " --"<< endl;
+                             /*   }  */
+                             /* } */
+                             // cout << "*" << endl;
+    }
+
+    virtual void calcGhost(char *data) {
+        for (int ix = 0; ix < 25; ix++) {
+            for (int iy = 0; iy < 200; iy++) {
+                calcGhost(data, ix, iy);
+            }
+        }
+        // cout << "*" << endl;
+    }
+
+    double getGhost(int ix, int iy) {
+        if (iy < 200)
+            return ghost[iy][ix % 25];
+        if (iy < 400)
+            return ghost[399 - iy][ix % 25];
+        return 0;
+    };
+
+    /**
+
+    Returns the frame number for the given dataset. Purely virtual func.
+    \param buff pointer to the dataset
+    \returns frame number
+
+ */
+
+    int getFrameNumber(char *buff) {
+#ifdef RAWDATA
+      return ((sls::defs::sls_receiver_header *)buff)->detHeader.frameNumber;
+#endif
+#ifndef RAWDATA
+      return 1;
+#endif
+
+    }
+
+    /**
+
+       Returns the packet number for the given dataset. purely virtual func
+       \param buff pointer to the dataset
+       \returns packet number number
+
+
+
+    */
+    int getPacketNumber(char *buff) {
+#ifdef RAWDATA
+      return ((sls::defs::sls_receiver_header  *)buff)->detHeader.packetNumber;
+#endif
+#ifndef RAWDATA
+      return 0;
+#endif
+      
+    }
+
+    char *readNextFrame(std::ifstream &filebin) override {
+        int ff = -1, np = -1;
+        return readNextFrame(filebin, ff, np);
+    }
+
+    // not present in base class
+    virtual char *readNextFrame(std::ifstream &filebin, int &ff) {
+        int np = -1;
+        return readNextFrame(filebin, ff, np);
+    };
+
+    // not present in base class
+    virtual char *readNextFrame(std::ifstream &filebin, int &ff, int &np) {
+        char *data = new char[dataSize];
+        char *d = readNextFrame(filebin, ff, np, data);
+        if (d == NULL) {
+            delete[] data;
+            data = NULL;
+        }
+        return data;
+    }
+
+    // not present in base class
+    virtual char *readNextFrame(std::ifstream &filebin, int &ff, int &np,
+                                char *data) {
+        np = 0;
+        if (filebin.is_open()) {
+            if (filebin.read(data, dataSize)) {
+                ff = getFrameNumber(data);
+                np = getPacketNumber(data);
+		//	std::cout << "**" << ff << " " << dataSize << " " << ff << " " << np << std::endl;
+
+                return data;
+            }
+        }
+	std::cout << "**" << ff << " " << dataSize << " " << ff << " " << np << std::endl;
+        return nullptr;
+    }
+
+    /**
+
+       Loops over a memory slot until a complete frame is found (i.e. all
+       packets 0 to nPackets, same frame number). purely virtual func \param
+       data pointer to the memory to be analyzed \param ndata reference to the
+       amount of data found for the frame, in case the frame is incomplete at
+       the end of the memory slot \param dsize size of the memory slot to be
+       analyzed \returns pointer to the beginning of the last good frame (might
+       be incomplete if ndata smaller than dataSize), or NULL if no frame is
+       found
+
+    */
+    char *findNextFrame(char *data, int &ndata, int dsize) override {
+        if (dsize < dataSize)
+            ndata = dsize;
+        else
+            ndata = dataSize;
+        return data;
+    }
+
+    // int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+};
+
+#endif

slsDetectorCalibration/dataStructures/moench03v2HalfData.h

@@ -0,0 +1,240 @@
+// SPDX-License-Identifier: LGPL-3.0-or-other
+// Copyright (C) 2021 Contributors to the SLS Detector Package
+#ifndef MOENCH03v2DATA_H
+#define MOENCH03v2DATA_H
+//#define MYROOT
+
+#ifndef MYROOT
+#include "sls/sls_detector_defs.h"
+#endif
+
+
+
+
+#ifdef MYROOT
+
+    typedef struct {
+        uint64_t frameNumber;
+        uint32_t expLength;
+        uint32_t packetNumber;
+        uint64_t bunchId;
+        uint64_t timestamp;
+        uint16_t modId;
+        uint16_t row;
+        uint16_t column;
+        uint16_t reserved;
+        uint32_t debug;
+        uint16_t roundRNumber;
+        uint8_t detType;
+        uint8_t version;
+    } sls_detector_header;
+#define MAX_NUM_PACKETS 512
+// using sls_bitset = std::bitset<MAX_NUM_PACKETS>;
+//  using bitset_storage = uint8_t[MAX_NUM_PACKETS / 8];
+  struct sls_receiver_header {
+        sls_detector_header detHeader; /**< is the detector header */
+        uint8_t packetsMask[64];        /**< is the packets caught bit mask */
+    };
+#endif
+
+#include "slsDetectorData.h"
+#ifdef RAWDATA
+#define DATA_OFFSET sizeof(header)
+#endif
+#ifndef RAWDATA
+#define DATA_OFFSET 0
+#endif
+
+
+class moench03v2Data : public slsDetectorData<uint16_t> {
+
+  private:
+    int iframe;
+    const int nRows;
+    
+    
+
+    double ghost[200][25];
+
+    // Single point of definition if we need to customize
+#ifndef MYROOT
+    using header = sls::defs::sls_receiver_header;
+#endif
+#ifdef MYROOT
+    sls_receiver_header header;
+#endif
+  public:
+    /**
+       Implements the slsReceiverData structure for the moench02 prototype read
+       out by a module i.e. using the slsReceiver (160x160 pixels, 40 packets
+       1286 large etc.) \param c crosstalk parameter for the output buffer
+
+    */
+    moench03v2Data(int nrows = 200)
+        : slsDetectorData<uint16_t>(400, nrows*2,2* 400*nrows*2 + DATA_OFFSET),
+      nRows(nrows) {
+	
+	std::cout << "MOENCH width new firmware " << dataSize << std::endl;
+	
+	int off=DATA_OFFSET;
+	    for (int ix = 0; ix < 400; ix++) {
+	      for (int iy = 0; iy < nRows*2; iy++) {
+		dataMap[iy][ix]=off+2*(iy*400+ix);
+	      }
+	    }
+	    
+        iframe = 0;
+        //  cout << "data struct created" << endl;
+      };
+
+    /**
+       Returns the value of the selected channel for the given dataset as
+       double. \param data pointer to the dataset (including headers etc) \param
+       ix pixel number in the x direction \param iy pixel number in the y
+       direction \returns data for the selected channel, with inversion if
+       required as double
+
+    */
+    double getValue(char *data, int ix, int iy = 0) override {
+        uint16_t val = getChannel(data, ix, iy) & 0x3fff;
+        return val;
+    };
+
+    virtual void calcGhost(char *data, int ix, int iy) {
+        double val = 0;
+        /* for (int ix=0; ix<25; ix++){ */
+        /*   for (int iy=0; iy<200; iy++) { */
+        val = 0;
+        //	cout << "** ";
+        for (int isc = 0; isc < 16; isc++) {
+            //  for (int ii=0; ii<2; ii++) {
+            val += getChannel(data, ix + 25 * isc, iy);
+            //  cout << "(" << isc << "," << val << " " ;
+            val += getChannel(data, ix + 25 * isc, 399 - iy);
+            // cout << val << " " ;
+            // }
+        }
+        ghost[iy][ix] = val; //-6224;
+                             //	cout << " --"<< endl;
+                             /*   }  */
+                             /* } */
+                             // cout << "*" << endl;
+    }
+
+    virtual void calcGhost(char *data) {
+        for (int ix = 0; ix < 25; ix++) {
+            for (int iy = 0; iy < 200; iy++) {
+                calcGhost(data, ix, iy);
+            }
+        }
+        // cout << "*" << endl;
+    }
+
+    double getGhost(int ix, int iy) {
+        if (iy < 200)
+            return ghost[iy][ix % 25];
+        if (iy < 400)
+            return ghost[399 - iy][ix % 25];
+        return 0;
+    };
+
+    /**
+
+    Returns the frame number for the given dataset. Purely virtual func.
+    \param buff pointer to the dataset
+    \returns frame number
+
+ */
+
+    int getFrameNumber(char *buff) {
+#ifdef RAWDATA
+      return ((sls::defs::sls_receiver_header *)buff)->detHeader.frameNumber;
+#endif
+#ifndef RAWDATA
+      return 1;
+#endif
+
+    }
+
+    /**
+
+       Returns the packet number for the given dataset. purely virtual func
+       \param buff pointer to the dataset
+       \returns packet number number
+
+
+
+    */
+    int getPacketNumber(char *buff) {
+#ifdef RAWDATA
+      return ((sls::defs::sls_receiver_header  *)buff)->detHeader.packetNumber;
+#endif
+#ifndef RAWDATA
+      return 0;
+#endif
+      
+    }
+
+    char *readNextFrame(std::ifstream &filebin) override {
+        int ff = -1, np = -1;
+        return readNextFrame(filebin, ff, np);
+    }
+
+    // not present in base class
+    virtual char *readNextFrame(std::ifstream &filebin, int &ff) {
+        int np = -1;
+        return readNextFrame(filebin, ff, np);
+    };
+
+    // not present in base class
+    virtual char *readNextFrame(std::ifstream &filebin, int &ff, int &np) {
+        char *data = new char[dataSize];
+        char *d = readNextFrame(filebin, ff, np, data);
+        if (d == NULL) {
+            delete[] data;
+            data = NULL;
+        }
+        return data;
+    }
+
+    // not present in base class
+    virtual char *readNextFrame(std::ifstream &filebin, int &ff, int &np,
+                                char *data) {
+        np = 0;
+        if (filebin.is_open()) {
+            if (filebin.read(data, dataSize)) {
+                ff = getFrameNumber(data);
+                np = getPacketNumber(data);
+	std::cout << "**" << ff << " " << dataSize << " " << ff << " " << np << std::endl;
+
+                return data;
+            }
+        }
+	std::cout << "**" << ff << " " << dataSize << " " << ff << " " << np << std::endl;
+        return nullptr;
+    }
+
+    /**
+
+       Loops over a memory slot until a complete frame is found (i.e. all
+       packets 0 to nPackets, same frame number). purely virtual func \param
+       data pointer to the memory to be analyzed \param ndata reference to the
+       amount of data found for the frame, in case the frame is incomplete at
+       the end of the memory slot \param dsize size of the memory slot to be
+       analyzed \returns pointer to the beginning of the last good frame (might
+       be incomplete if ndata smaller than dataSize), or NULL if no frame is
+       found
+
+    */
+    char *findNextFrame(char *data, int &ndata, int dsize) override {
+        if (dsize < dataSize)
+            ndata = dsize;
+        else
+            ndata = dataSize;
+        return data;
+    }
+
+    // int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+};
+
+#endif

slsDetectorCalibration/moenchExecutables/moench03Interpolation.cpp

@@ -33,7 +33,7 @@ int main(int argc, char *argv[]) {
 #ifndef FF
     if (argc < 9) {
         cout << "Wrong usage! Should be: " << argv[0]
-             << " infile  etafile outfile runmin runmax ns cmin cmax" << endl;
+             << " infile  etafile outfile runmin runmax ns [cmin cmax xmin xmax ymin ymax]" << endl;
         return 1;
     }
 #endif
@@ -41,7 +41,7 @@ int main(int argc, char *argv[]) {
 #ifdef FF
     if (argc < 7) {
         cout << "Wrong usage! Should be: " << argv[0]
-             << " infile  etafile runmin runmax cmin cmax" << endl;
+             << " infile  etafile runmin runmax [cmin cmax xmin xmax ymin ymax]" << endl;
         return 1;
     }
 #endif
@@ -65,13 +65,30 @@ int main(int argc, char *argv[]) {
     nsubpix = atoi(argv[iarg++]);
     cout << "Subpix: " << nsubpix << endl;
 #endif
-    float cmin = atof(argv[iarg++]);
-    float cmax = atof(argv[iarg++]);
+    
+    float cmin = 0;
+    float cmax=1000000;
+    if (argc>iarg)
+      cmin=atof(argv[iarg++]);
+    if (argc>iarg)
+      cmax= atof(argv[iarg++]);
     cout << "Energy min: " << cmin << endl;
     cout << "Energy max: " << cmax << endl;
+    int xmin=0, xmax=NC, ymin=0, ymax=NR;
+    
+    if (argc>iarg)
+      xmin=atof(argv[iarg++]);
+    if (argc>iarg)
+      xmax= atof(argv[iarg++]);
+    
+    if (argc>iarg)
+      ymin=atof(argv[iarg++]);
+    if (argc>iarg)
+      ymax= atof(argv[iarg++]);
+    
     // int etabins=500;
     int etabins = 1000; // nsubpix*2*100;
-    double etamin = -1, etamax = 2;
+    double etamin = -0.25, etamax = 1.25;
     // double etamin=-0.1, etamax=1.1;
     //   double eta3min = -2, eta3max = 2;
     double sum, totquad;
@@ -80,7 +97,7 @@ int main(int argc, char *argv[]) {
     // double eta3x, eta3y, int3_x, int3_y, noint_x, noint_y;
    
     int ix, iy, isx, isy;
-    int nframes = 0, lastframe = -1;
+    int nframes = 0, lastframe = -1, iframe, nphFrame;
     //double d_x, d_y, res = 5, xx, yy;
     int nph = 0, totph = 0;
     //badph = 0, 
@@ -98,7 +115,7 @@ int main(int argc, char *argv[]) {
     //  int nSubPixels = nsubpix;
 #ifndef NOINTERPOLATION
     eta2InterpolationPosXY *interp =
-      new eta2InterpolationPosXY(NC, NR, nsubpix, nsubpix,etabins,etabins, etamin, etamax);
+      new eta2InterpolationPosXY(NC, NR, nsubpix, nsubpix, etabins, etabins, etamin, etamax);
     // eta2InterpolationCleverAdaptiveBins *interp=new
     // eta2InterpolationCleverAdaptiveBins(NC, NR, nsubpix, etabins, etamin,
     // etamax);
@@ -107,8 +124,8 @@ int main(int argc, char *argv[]) {
     noInterpolation *interp = new noInterpolation(NC, NR, nsubpix);
 #endif
 
-#ifndef FF
     int quad; 
+#ifndef FF
 #ifndef NOINTERPOLATION
     char fname[10000];
     int ok;
@@ -142,19 +159,26 @@ int main(int argc, char *argv[]) {
 #endif
 
     int irun;
-    for (irun = runmin; irun < runmax; irun++) {
+    for (irun = runmin; irun <= runmax; irun++) {
         sprintf(infname, argv[1], irun);
 #ifndef FF
         sprintf(outfname, argv[3], irun);
 #endif
 
+
         f = fopen(infname, "r");
         if (f) {
             cout << infname << endl;
             nframes = 0;
             //f0 = -1;
 
-            while (cl.read(f)) {
+	    //iff=0;
+	    while (fread((void*)&iframe, 1,  sizeof(int), f)) {
+	      //n=0;
+	      if (fread((void*)&nphFrame, 1,  sizeof(int), f)) {
+		for (int iph=0; iph<nphFrame; iph++) {
+		//while (cl.read(f)) {
+		  if (cl.read(f)) {
                 totph++;
                 if (lastframe != cl.iframe) {
                     lastframe = cl.iframe;
@@ -165,18 +189,28 @@ int main(int argc, char *argv[]) {
                     nframes++;
                 }
                 // quad=interp->calcQuad(cl.get_cluster(), sum, totquad, sDum);
-#ifndef FF
+// #ifndef FF
+//                 quad = interp->calcEta(cl.get_cluster(), etax, etay, sum,
+//                                        totquad, sDum);
+// #endif
+// #ifdef FF
+	
                 quad = interp->calcEta(cl.get_cluster(), etax, etay, sum,
                                        totquad, sDum);
-#endif
-#ifdef FF
-                interp->calcEta(cl.get_cluster(), etax, etay, sum,
-                                       totquad, sDum);
-#endif
 	
-      if (sum > cmin && totquad / sum > 0.8 && totquad / sum < 1.2 &&
-                    sum < cmax) {
-                    nph++;
+		
+		/*	cl.print();
+		cout << "(" << etax <<","<< etay <<")"<< quad<< endl;
+		*/
+		//#endif
+
+		if (totquad > cmin && cl.x >= xmin && cl.x <= xmax && 
+		    cl.y >= ymin && cl.y <= ymax &&
+		    totquad < cmax) {
+
+		  //	if (sum > cmin && totquad / sum > 0.8 && totquad / sum < 1.2 &&
+		  //	sum < cmax) {
+		  nph++;
                     //  if (sum>200 && sum<580) {
                     //  interp->getInterpolatedPosition(cl.x,cl.y,
                     //  totquad,quad,cl.get_cluster(),int_x, int_y);
@@ -227,9 +261,12 @@ int main(int argc, char *argv[]) {
 #ifdef FF
                         interp->writeFlatField(outfname);
 #endif
+		    }
                     }
                 }
-            }
+	      }
+	    }
+	    }
 
             fclose(f);
 #ifdef FF

slsDetectorCalibration/moenchExecutables/moenchRawDataProcess.cpp

@@ -13,7 +13,7 @@
 
 #ifndef MOENCH04
 #ifndef RECT
-#include "moench03T1ReceiverDataNew.h"
+#include "moench03v2Data.h"
 #endif
 #endif
 
@@ -41,34 +41,147 @@ using namespace std;
 
 int main(int argc, char *argv[]) {
 
-    if (argc < 4) {
+  std::map<std::string, std::string> args = {
+    {"numfiles","1"},
+    {"nthreads","5"},
+    {"fifosize","5000"},
+    {"nsigma","5"},
+    {"gainfile","none"},
+    {"detectorMode","counting"},
+    {"threshold","0"},
+    {"pedestalfile","none"},
+    {"nframes","0"},
+    {"xMin","0"},
+    {"xMax","400"},
+    {"yMin","0"},
+    {"yMax","400"},
+    {"eMin","0"},
+    {"eMax","16000"},
+    {"outdir","./"},
+    {"indir","./"},
+    {"flist","none"},
+    {"fformat","none"},
+    {"runmin","0"},
+    {"runmax","-1"},
+    {"readnrows","400"}
+  };
+  //float *gm;
+  
+  int ff, np;
+  // cout << " data size is " << dsize;
+  
+  ifstream filebin;
+  if (argc < 4) {
+    std::string name, value,sline;
+    int ic=0;
+    ifstream flist;
+    flist.open (argv[1], std::ifstream::in);
+    if (flist.is_open()) {
+      cout << "Using config file " <<argv[1] << endl;
+       while (std::getline(flist,sline)){
+	 if (sline.at(0)!='#') {
+	   ic=sline.find(' ');
+	   name = sline.substr(0,ic); 
+	   value = sline.substr(ic+1,sline.size()-ic); 
+	   args[name]=value;
+	 }
+	 
+       } 
+       flist.close();
+    } else {
         cout << "Usage is " << argv[0]
              << "indir outdir fname(no extension) [runmin] [runmax] [pedfile (raw or tiff)] [threshold] "
-                "[nframes] [xmin xmax ymin ymax] [gainmap]"
+	  "[nframes] [xmin xmax ymin ymax] [gainmap]"
              << endl;
         cout << "threshold <0 means analog; threshold=0 means cluster finder; "
-                "threshold>0 means photon counting"
+	  "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"
+	  "run; nframes>0 means one file every nframes"
              << endl;
-        return 1;
+	return EXIT_FAILURE;
+      }
+    } else {
+      args["indir"]=argv[1];
+      args["outdir"]=argv[1];
+      args["fformat"]=argv[3];
+      if (argc >= 5) {
+	args["runmin"] = argv[4];
+      }
+	args["runmax"] = args["runmin"];
+
+      if (argc >= 6) {
+	args["runmax"] = argv[5];
+      }
+      if (argc >= 7) {
+        args["pedestalfile"] = argv[6];
+      }
+      if (argc >= 8) {
+        args["threshold"] = argv[7];
+      }
+      if (argc >= 9) {
+        args["nframes"] = argv[8];
+      }
+      if (argc >= 13) {
+        args["xMin"] = argv[9];
+        args["xMax"] = argv[10];
+        args["yMin"] = argv[11];
+        args["yMax"] = argv[12];
+      }
+      if (argc > 13) {
+	args["gainfile"] = argv[13];
+      }
+      
+      if (atof(args["threshold"].c_str())<0) {
+	args["detectorMode"]="analog";
+      }
+
     }
 
-    int fifosize = 1000;
-    int nthreads = 10;
+
+
+    for (auto const& x : args)
+      {
+	std::cout << x.first  // string (key)
+		  << ':' 
+		  << x.second // string's value 
+		  << std::endl;
+      }
+
+
+    string indir=args["indir"]; 
+    string outdir = args["outdir"];
+    string fformat= args["fformat"];
+    int runmin = atoi(args["runmin"].c_str());
+    int runmax = atoi(args["runmin"].c_str());
+    string pedfile =args["pedestalfile"];
+    double thr = atof(args["threshold"].c_str());
+    double thr1 = 1;
+    
+    int nframes = atoi(args["nframes"].c_str());
+    
+    int xmin =  atoi(args["xMin"].c_str()), xmax =  atoi(args["xMax"].c_str()), ymin = atoi(args["yMin"].c_str()), ymax = atoi(args["yMax"].c_str());
+    
+    string gainfname=args["gainfile"];
+    
+    int fifosize = atoi(args["fifosize"].c_str());
+    int nthreads = atoi(args["nthreads"].c_str());
+    int nsigma = atoi(args["nsigma"].c_str());
+    int nrows = atoi(args["readnrows"].c_str());
+    float eMin = atof(args["eMin"].c_str());
+    float eMax = atof(args["eMax"].c_str());
     int csize = 3;
-    int nsigma = 5;
-    int nped = 10000;
+    int nped = 1000;
     
     int cf = 0;
-    int numberOfPackets=40;
+    int numberOfPackets=nrows/8;
+
 #ifdef RECT
     cout << "Should be rectangular but now it will crash! No data structure defined!" << endl;
 #endif
     
 #ifndef MOENCH04
-    moench03T1ReceiverDataNew *decoder = new moench03T1ReceiverDataNew();
+    moench03v2Data *decoder = new moench03v2Data(100);
     cout << "MOENCH03!" << endl;
 #endif
 
@@ -86,62 +199,10 @@ int main(int argc, char *argv[]) {
     
 #endif
 
-    //Read detector size from decoder
     int nx , ny;
     decoder->getDetectorSize(nx, ny);
 
-    //float *gm;
-
-    int ff, np;
-    // cout << " data size is " << dsize;
-
-    ifstream filebin;
-    char *indir = argv[1];
-    char *outdir = argv[2];
-    char *fformat = argv[3];
-    int runmin = 0;
-
-    // cout << "argc is " << argc << endl;
-    if (argc >= 5) {
-        runmin = atoi(argv[4]);
-    }
-
-    int runmax = runmin;
-
-    if (argc >= 6) {
-        runmax = atoi(argv[5]);
-    }
-
-    char *pedfile = NULL;
-    if (argc >= 7) {
-        pedfile = argv[6];
-    }
-    double thr = 0;
-    double thr1 = 1;
-
-    if (argc >= 8) {
-        thr = atof(argv[7]);
-    }
-
-    int nframes = 0;
-
-    if (argc >= 9) {
-        nframes = atoi(argv[8]);
-    }
-
-    int xmin = 0, xmax = nx, ymin = 0, ymax = ny;
-    if (argc >= 13) {
-        xmin = atoi(argv[9]);
-        xmax = atoi(argv[10]);
-        ymin = atoi(argv[11]);
-        ymax = atoi(argv[12]);
-    }
-
-    char *gainfname = NULL;
-    if (argc > 13) {
-        gainfname = argv[13];
-        cout << "Gain map file name is: " << gainfname << endl;
-    }
+    //Read detector size from decoder
    
     char ffname[10000];
     char fname[10000];
@@ -151,17 +212,6 @@ int main(int argc, char *argv[]) {
     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;
 
 
@@ -182,26 +232,26 @@ int main(int argc, char *argv[]) {
     singlePhotonDetector *filter = new singlePhotonDetector(
         decoder, csize, nsigma, 1, cm, nped, 200, -1, -1, gainmap, gs);
 
-    if (gainfname) {
+    //if (gainfname) {
 
-        if (filter->readGainMap(gainfname))
+    if (filter->readGainMap(gainfname.c_str()))
             cout << "using gain map " << gainfname << endl;
         else
             cout << "Could not open gain map " << gainfname << endl;
-    } else
-        thr = 0.15 * thr;
+    // } else
+    thr = 0.15 * thr;
     filter->newDataSet();
     //int dsize = decoder->getDataSize();
 
     if (thr > 0) {
-        cout << "threshold is " << thr << endl;
-        filter->setThreshold(thr);
-        cf = 0;
-
+      cout << "threshold is " << thr << endl;
+      filter->setThreshold(thr);
+      cf = 0;
     } else
-        cf = 1;
+      cf = 1;
     
     filter->setROI(xmin, xmax, ymin, ymax);
+    filter->setEnergyRange(eMin, eMax);
     std::time(&end_time);
     cout << std::ctime(&end_time) << endl;
 
@@ -211,21 +261,33 @@ int main(int argc, char *argv[]) {
     // multiThreadedAnalogDetector(filter,nthreads,fifosize);
     multiThreadedCountingDetector *mt =
         new multiThreadedCountingDetector(filter, nthreads, fifosize);
-#ifndef ANALOG
-    mt->setDetectorMode(ePhotonCounting);
-    cout << "Counting!" << endl;
-    if (thr > 0) {
+    
+    if (args["detectorMode"]=="counting") {
+      mt->setDetectorMode(ePhotonCounting);
+      if (thr > 0) {
         cf = 0;
+      }
+    } else {
+      mt->setDetectorMode(eAnalog);
+      cf = 0;
     }
-#endif
-//{
-#ifdef ANALOG
-    mt->setDetectorMode(eAnalog);
-    cout << "Analog!" << endl;
-    cf = 0;
-    // thr1=thr;
-#endif
-    //  }
+      
+      
+// #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);
@@ -236,18 +298,17 @@ int main(int argc, char *argv[]) {
     char froot[1000];
     double *ped=new double[nx * ny];//, *ped1;
     int pos,pos1;
+    //return  0;
+    if (pedfile.find(".raw") != std::string::npos) {
+      pos1=pedfile.rfind("/");
+      strcpy(froot,pedfile.substr(pos1).c_str());
+      pos=string(froot).find(".raw");
+      froot[pos]='\0';
+    }
     
-    if (pedfile) {
-      if (string(pedfile).find(".raw") != std::string::npos) {
-	pos1=string(pedfile).rfind("/");
-	strcpy(froot,pedfile+pos1);
-	pos=string(froot).find(".raw");
-	froot[pos]='\0';
-      }
-
-      cout << "PEDESTAL " << endl;
-      if (string(pedfile).find(".tif") == std::string::npos) {
-            sprintf(fname, "%s", pedfile);
+    cout << "PEDESTAL " << endl;
+    if (pedfile.find(".tif") == std::string::npos) {
+      sprintf(fname, "%s", pedfile.c_str());
             cout << fname << endl;
             std::time(&end_time);
             //cout << "aaa" << std::ctime(&end_time) << endl;
@@ -257,63 +318,97 @@ int main(int argc, char *argv[]) {
             filebin.open((const char *)(fname), ios::in | ios::binary);
             //      //open file
             if (filebin.is_open()) {
-                ff = -1;
+	      ff = -1;
                 while (decoder->readNextFrame(filebin, ff, np, buff)) {
-                    if (np == numberOfPackets) {
-                        mt->pushData(buff);
+		  if (np == numberOfPackets) {
+		    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 % 100 == 0)
+			  cout << ifr << " " << ff << " " << np << endl;
+			    //	break;
+		  } else {
+		    cout << ifr << " " << ff << " " << np << endl;
+		    break;
+		  }
                     ff = -1;
                 }
                 filebin.close();
                 while (mt->isBusy()) {
-                    ;
+		  ;
+
                 }
 		
-		sprintf(imgfname, "%s/%s_ped.tiff", outdir,froot);
+		sprintf(imgfname, "%s/%s_ped.tiff", outdir.c_str(),froot);
 		mt->writePedestal(imgfname);
-		sprintf(imgfname, "%s/%s_var.tiff", outdir,froot);
+		sprintf(imgfname, "%s/%s_var.tiff", outdir.c_str(),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++) {
+	      cout << "Could not open pedestal file " << fname
+		   << " for reading " << endl;
+    } else {
+      float *pp = ReadFromTiff(pedfile.c_str(), 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
+	}
+	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;
+      }
     }
+    std::time(&end_time);
+    cout << std::ctime(&end_time) << endl;
+
     
     ifr = 0;
     int ifile = 0;
 
     mt->setFrameMode(eFrame);
+    //t filelist=0;
+    ifstream flist;
+    flist.open (args["flist"].c_str(), std::ifstream::in);
+    if (flist.is_open()) {
+      cout << "Using file list" << endl;
+      runmin=0;
+       runmax=0;
+       while (flist.getline(ffname,10000)){
+	 cout << ffname << endl;
+	 runmax++;
+       }
+       runmax--;
+       flist.close();
+       cout << "Found " << runmax << " files " << endl;
+       flist.open (fformat, std::ifstream::in);
+    } 
 
     for (int irun = runmin; irun <= runmax; irun++) {
         cout << "DATA ";
         // sprintf(fn,fformat,irun);
-        sprintf(ffname, "%s/%s.raw", indir, fformat);
-        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);
+        // sprintf(ffname, "%s/%s.raw", indir, fformat);
+        // 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);
+	if (flist.is_open()) {
+	  flist.getline(ffname,10000);
+	  cout << "file list " << ffname << endl;
+	} else {
+	  //sprintf(ffname,(const char*)fformat,irun);
+	  sprintf(ffname,args["fformat"].c_str(),irun);
+	  cout << "loop " << ffname << endl;
+	}
+	cout << "ffname "<< ffname << endl;
+	sprintf(fname,  "%s/%s.raw",indir.c_str(),ffname);
+	sprintf(imgfname,  "%s/%s.tiff",outdir.c_str(),ffname);
+	sprintf(cfname,  "%s/%s.clust",outdir.c_str(),ffname);
+
+
         cout << fname << " ";
         cout << imgfname << endl;
         std::time(&end_time);
@@ -323,7 +418,7 @@ int main(int argc, char *argv[]) {
         //      //open file
         ifile = 0;
         if (filebin.is_open()) {
-            if (thr <= 0 && cf != 0) { // cluster finder
+            if (cf != 0) { // cluster finder
                 if (of == NULL) {
                     of = fopen(cfname, "w");
                     if (of) {
@@ -341,7 +436,7 @@ int main(int argc, char *argv[]) {
             ff = -1;
             ifr = 0;
             while (decoder->readNextFrame(filebin, ff, np, buff)) {
-                if (np == numberOfPackets) {
+	      if (np == numberOfPackets) {
                     //         //push
                     mt->pushData(buff);
                     // 	//         //pop
@@ -350,21 +445,26 @@ int main(int argc, char *argv[]) {
 
                     ifr++;
 		    if (ifr % 100 == 0)
-                        cout << ifr << " " << ff << endl;
+		      cout << ifr << " " << ff << " " << np << endl;
+		    //break;
                     if (nframes > 0) {
                         if (ifr % nframes == 0) {
-                            sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat,
-                                    ifile);
-                            sprintf(imgfname, (const char*)ffname, irun);
+                            // sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat,
+                            //         ifile);
+                            // sprintf(imgfname, (const char*)ffname, irun);
+			  sprintf(imgfname,  "%s/%s_f%05d.tiff",outdir.c_str(),ffname,ifile);
+                           while (mt->isBusy()) 
+                             ;
+
                             mt->writeImage(imgfname, thr1);
                             mt->clearImage();
                             ifile++;
                         }
                     }
-                } else {
-		  cout << "bp " << ifr << " " << ff << " " << np << endl;
-		  //break;
-		}
+	      } else {
+		cout << "bp " << ifr << " " << ff << " " << np << endl;
+		//break;
+	      }
                 ff = -1;
             }
             cout << "--" << endl;
@@ -374,13 +474,17 @@ int main(int argc, char *argv[]) {
             }
             if (nframes >= 0) {
                 if (nframes > 0) {
-                    sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat, ifile);
-                    sprintf(imgfname, (const char*)ffname, irun);
+		  sprintf(imgfname,  "%s/%s_f%05d.tiff",outdir.c_str(),ffname,ifile);
+                  //  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);
+		  sprintf(imgfname,  "%s/%s.tiff",outdir.c_str(),ffname);
+                  //  sprintf(ffname, "%s/%s.tiff", outdir, fformat);
+                  //  sprintf(imgfname, (const char*)ffname, irun);
                 }
                 cout << "Writing tiff to " << imgfname << " " << thr1 << endl; 
+		while (mt->isBusy()) 
+		  ;
                 mt->writeImage(imgfname, thr1);
                 mt->clearImage();
                 if (of) {
@@ -395,11 +499,16 @@ int main(int argc, char *argv[]) {
             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);
+      //sprintf(ffname, "%s/%s.tiff", outdir, fformat);
+      //  strcpy(imgfname, ffname);
+      sprintf(imgfname,  "%s/%s_tot.tiff",outdir.c_str(),ffname);
+      cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
+      while (mt->isBusy()) 
+	;
+      mt->writeImage(imgfname, thr1);
+    }
+    if (flist.is_open()) {
+      flist.close();
     }
-
     return 0;
 }

slsDetectorCalibration/moenchExecutables/moenchZmqProcess.cpp

@@ -13,7 +13,8 @@
 #include "sls/sls_detector_defs.h"
 #ifndef MOENCH04
 //#ifndef RECT
-#include "moench03T1ZmqDataNew.h"
+#include "moench03v2Data.h"
+//#include "moench03T1ZmqDataNew.h"
 //#endif
 //#ifdef RECT
 //#include "moench03T1ZmqDataNewRect.h"
@@ -31,6 +32,7 @@
 #include <sstream>
 #include <string>
 #include <vector>
+#include <map>
 
 #include <rapidjson/document.h> //json header in zmq stream
 
@@ -64,35 +66,47 @@ int main(int argc, char *argv[]) {
      * number]
      *
      */ 
-    FILE *of = NULL;
-    int fifosize = 5000;
+  std::map<std::string, std::string> args = {
+    {"numinterfaces","1"},	
+    {"rx_zmqip","10.1.2.102"},	
+    {"rx_zmqport","7770"},
+    {"zmqip","129.129.202.153"},
+    {"zmqport","7780"},
+    {"nthreads","5"},
+    {"fifosize","5000"},
+    {"nsigma","5"},
+    {"gainfile","none"},
+    {"nbinsx","5"},
+    {"nbinsy","5"},
+    {"etafile","none"},
+    {"etabinsx","1000"},
+    {"etamin","-1"},
+    {"etamax","2"}  };
+  FILE *of = NULL;
     int etabins = 1000, etabinsy = 1000; // nsubpix*2*100;
     double etamin = -1, etamax = 2;
     int nSubPixelsX = 2;
     int emin, emax;
     int nSubPixelsY = 2;
+    int nthreads = 5;
+    int fifosize = 5000;
+    uint32_t nSigma = 5;
 
-    // help
-    if (argc < 3) {
-        cprintf(RED, "Help: ./trial [receive socket ip] [receive starting port "
-                     "number] [send_socket ip] [send starting port number] "
-                     "[nthreads] [nsubpix] [gainmap]  [etafile]\n");
-        return EXIT_FAILURE;
-    }
+    string etafname;// = NULL;
+    string gainfname;// = NULL;
 
     // receive parameters
     bool send = false;
-    char *socketip = argv[1];
-    uint32_t portnum = atoi(argv[2]);
     // send parameters if any
-    char *socketip2 = 0;
+    string socketip2;// = 0;
     uint32_t portnum2 = 0;  
+    string socketip;// = 0;
+    uint32_t portnum = 0;
 
     sls::zmqHeader zHeader, outHeader;
     zHeader.jsonversion = SLS_DETECTOR_JSON_HEADER_VERSION;
     outHeader.jsonversion = SLS_DETECTOR_JSON_HEADER_VERSION;
 
-    uint32_t nSigma = 5;
 
     int ok;
 
@@ -102,48 +116,85 @@ int main(int argc, char *argv[]) {
     // time_t begin,end,finished;
     int rms = 0;
 
-    if (argc > 4) {
-        socketip2 = argv[3];
-        portnum2 = atoi(argv[4]);
-        if (portnum2 > 0)
-            send = true;
-    }
-    cout << "\nrx socket ip : " << socketip << "\nrx port num  : " << portnum;
-    if (send) {
-        cout << "\ntx socket ip : " << socketip2
-             << "\ntx port num  : " << portnum2;
-    }
-    int nthreads = 5;
-    if (argc > 5)
-        nthreads = atoi(argv[5]);
+    send = true;
+    // help
+    if (argc < 5) {
+      std::string name, value,sline;
+      int ic=0;
+      ifstream flist;
+      flist.open (argv[1], std::ifstream::in);
+      if (flist.is_open()) {
+	cout << "Using config file " <<argv[1] << endl;
+       while (std::getline(flist,sline)){
+	 if (sline.at(0)!='#') {
+	   ic=sline.find(' ');
+	   name = sline.substr(0,ic); 
+	   value = sline.substr(ic+1,sline.size()-ic); 
+	   args[name]=value;
+	 }
 
-    cout << "Number of threads is: " << nthreads << endl;
-    if (argc > 6) {
-        nSubPixelsX = atoi(argv[6]);
-        nSubPixelsY = nSubPixelsX;
-#ifdef RECT
-        nSubPixelsX = 2;
-#endif
-    }
-    cout << "Number of subpixels is: " << nSubPixelsX << " " << nSubPixelsY
-         << endl;
+       } 
+       flist.close();
+      } else {
+        cprintf(RED, "Arguments are either: \n [config file] \n or the following list (deprecated): [receive socket ip] [receive starting port "
+		"number] [send_socket ip] [send starting port number] "
+		"[nthreads] [nsubpix] [gainmap]  [etafile]\n");
+        return EXIT_FAILURE;
+      }
+    } else {
+       args["rx_zmqip"]=argv[1];	
+       args["rx_zmqport"]=argv[2];
+
+       args["zmqip"]=argv[3];
+       args["zmqport"]=argv[4];
+       if (argc > 5)
+        args["nthreads"] = argv[5];
+       if (argc > 6) {
+	 args["nbinsx"]=argv[6];
+	 args["nbinsy"]=argv[6];
+       }
+       
+      if (argc > 7) {
+	args["gainfile"]=argv[7];
+      }
+      if (argc > 8) {
+	args["etafilefile"]=argv[8];
+      }
 
-    char *gainfname = NULL;
-    if (argc > 7) {
-        gainfname = argv[7];
-        cout << "Gain map file name is: " << gainfname << endl;
     }
 
-    char *etafname = NULL;
-    if (argc > 8) {
-        etafname = argv[8];
-        cout << "Eta file name is: " << etafname << endl;
+       for (auto const& x : args)
+	 {
+	   std::cout << x.first  // string (key)
+		     << ':' 
+		     << x.second // string's value 
+		     << std::endl;
+	 }
+
+    socketip = args["rx_zmqip"];
+    portnum = atoi(args["rx_zmqport"].c_str());
+    
+    socketip2 = args["zmqip"];
+    portnum2 = atoi(args["zmqport"].c_str());
+
+    nthreads = atoi(args["nthreads"].c_str());
+    nSubPixelsX =atoi(args["nbinsx"].c_str());
+    nSubPixelsY =atoi(args["nbinsy"].c_str());
+    gainfname = args["gainfile"];
+    etafname = args["etafilefile"];
+    
+    if (atoi(args["nuninterfaces"].c_str())>1){
+      cprintf(RED, "Sorry, at the  moment only a single interface is supported instead of %d\n",atoi(args["nuninterfaces"].c_str()));
+      return EXIT_FAILURE;
     }
 
+
     // slsDetectorData *det=new moench03T1ZmqDataNew();
 #ifndef MOENCH04
-    cout << "This is a Moench03" << endl;
-    moench03T1ZmqDataNew *det = new moench03T1ZmqDataNew();
+    cout << "This is a Moench03 v2" << endl;
+    //moench03T1ZmqDataNew *det = new moench03T1ZmqDataNew();
+    moench03v2Data *det = new moench03v2Data();
+    cout << "MOENCH03!" << endl;
 #endif
 #ifdef MOENCH04
     cout << "This is a Moench04" << endl;
@@ -177,8 +228,8 @@ int main(int argc, char *argv[]) {
     double *gmap = NULL;
 
     uint32_t nnnx, nnny;
-    if (gainfname) {
-        gm = ReadFromTiff(gainfname, nnny, nnnx);
+    //if (gainfname) {
+        gm = ReadFromTiff(gainfname.c_str(), nnny, nnnx);
         if (gm && nnnx == (uint)npx && nnny == (uint)npy) {
             gmap = new double[npx * npy];
             for (int i = 0; i < npx * npy; i++) {
@@ -187,7 +238,7 @@ int main(int argc, char *argv[]) {
             delete[] gm;
         } else
             cout << "Could not open gain map " << gainfname << endl;
-    }
+	//}
 
     // analogDetector<uint16_t> *filter=new
     // analogDetector<uint16_t>(det,1,NULL,1000);
@@ -205,8 +256,8 @@ int main(int argc, char *argv[]) {
     eta2InterpolationPosXY *interp = new eta2InterpolationPosXY(
         npx, npy, nSubPixelsX, nSubPixelsY, etabins, etabinsy, etamin, etamax);
 
-    if (etafname)
-        interp->readFlatField(etafname);
+    //if (etafname)
+    interp->readFlatField(etafname.c_str());
 
     interpolatingDetector *filter = new interpolatingDetector(
         det, interp, nSigma, 1, cm, 1000, 10, -1, -1, gainmap, gs);
@@ -226,13 +277,13 @@ int main(int argc, char *argv[]) {
     try {
 #endif
 
-      zmqsocket = new sls::ZmqSocket(socketip, portnum);
+      zmqsocket = new sls::ZmqSocket(socketip.c_str(), portnum);
 
 #ifdef NEWZMQ
     } catch (...) {
         cprintf(RED,
                 "Error: Could not create Zmq socket on port %d with ip %s\n",
-                portnum, socketip);
+                portnum, socketip.c_str());
         delete zmqsocket;
         return EXIT_FAILURE;
     }
@@ -242,7 +293,7 @@ int main(int argc, char *argv[]) {
     if (zmqsocket->IsError()) {
         cprintf(RED,
                 "Error: Could not create Zmq socket on port %d with ip %s\n",
-                portnum, socketip);
+                portnum, socketip.c_str());
         delete zmqsocket;
         return EXIT_FAILURE;
     }
@@ -263,14 +314,14 @@ int main(int argc, char *argv[]) {
         // receive socket
         try {
 #endif
-	  zmqsocket2 = new sls::ZmqSocket(portnum2, socketip2);
+	  zmqsocket2 = new sls::ZmqSocket(portnum2, socketip2.c_str());
 
 #ifdef NEWZMQ
         } catch (...) {
             cprintf(RED,
                     "Error: Could not create Zmq socket server on port %d and "
                     "ip %s\n",
-                    portnum2, socketip2);
+                    portnum2, socketip2.c_str());
             //	delete zmqsocket2;
             //	zmqsocket2=NULL;
             //	delete zmqsocket;
@@ -284,7 +335,7 @@ int main(int argc, char *argv[]) {
             cprintf(RED,
                     "AAA Error: Could not create Zmq socket server on port %d "
                     "and ip %s\n",
-                    portnum2, socketip2);
+                    portnum2, socketip2.c_str());
             //	delete zmqsocket2;
             // delete zmqsocket;
             //	return EXIT_FAILURE;
@@ -722,6 +773,25 @@ int main(int argc, char *argv[]) {
 
             cprintf(MAGENTA, "%d %d %d %d\n", xmin, xmax, ymin, ymax);
             mt->setROI(xmin, xmax, ymin, ymax);
+
+             if (addJsonHeader.find("xMin") != addJsonHeader.end()) {
+                 istringstream(addJsonHeader.at("xMin")) >> xmin;
+             }
+ 
+             if (addJsonHeader.find("yMin") != addJsonHeader.end()) {
+                 istringstream(addJsonHeader.at("yMin")) >> ymin;
+             }
+ 
+             if (addJsonHeader.find("xMax") != addJsonHeader.end()) {
+                 istringstream(addJsonHeader.at("xMax")) >> xmax;
+             }
+ 
+             if (addJsonHeader.find("yMax") != addJsonHeader.end()) {
+                 istringstream(addJsonHeader.at("yMax")) >> ymax;
+             }
+
+
+
             if (addJsonHeader.find("dynamicRange") != addJsonHeader.end()) {
                 istringstream(addJsonHeader.at("dynamicRange")) >> dr;
                 dr = 32;
@@ -821,7 +891,7 @@ int main(int argc, char *argv[]) {
         // cout << acqIndex << " " << frameIndex << " " << subFrameIndex << "
         // "<< detSpec1 << " " << timestamp << " " << packetNumber << endl;
         // cprintf(GREEN, "frame\n");
-        if (packetNumber >= 40) {
+        if (packetNumber <= 50) {
             //*((int*)buff)=frameIndex;
             if (insubframe == 0)
                 f0 = frameIndex;

slsDetectorServers/moenchDetectorServer/slsDetectorFunctionList.c

@@ -481,7 +481,6 @@ void setupDetector() {
         return;
     }
 
-    setReadoutSpeed(DEFAULT_SPEED);
     cleanFifos();
     resetCore();
 
@@ -495,6 +494,7 @@ void setupDetector() {
     initReadoutConfiguration();
 
     // Initialization of acquistion parameters
+    setReadoutSpeed(DEFAULT_SPEED);
     setSettings(DEFAULT_SETTINGS);
     setNumFrames(DEFAULT_NUM_FRAMES);
     setNumTriggers(DEFAULT_NUM_CYCLES);
@@ -699,14 +699,12 @@ int setExpTime(int64_t val) {
     }
     LOG(logINFO, ("Setting exptime %lld ns\n", (long long int)val));
     val *= (1E-3 * CLK_RUN);
-    val -= ACQ_TIME_MIN_CLOCK;
     if (val < 0) {
         val = 0;
     }
     set64BitReg(val, SET_EXPTIME_LSB_REG, SET_EXPTIME_MSB_REG);
 
     // validate for tolerance
-    val += ACQ_TIME_MIN_CLOCK;
     int64_t retval = getExpTime();
     val /= (1E-3 * CLK_RUN);
     if (val != retval) {
@@ -716,8 +714,7 @@ int setExpTime(int64_t val) {
 }
 
 int64_t getExpTime() {
-    return (get64BitReg(SET_EXPTIME_LSB_REG, SET_EXPTIME_MSB_REG) +
-            ACQ_TIME_MIN_CLOCK) /
+    return get64BitReg(SET_EXPTIME_LSB_REG, SET_EXPTIME_MSB_REG) /
            (1E-3 * CLK_RUN);
 }
 

slsDetectorServers/moenchDetectorServer/slsDetectorServer_defs.h

@@ -5,7 +5,7 @@
 #include "sls/sls_detector_defs.h"
 
 #define REQRD_FRMWRE_VRSN_BOARD2 0x444445 // 1.0 pcb (version = 010)
-#define REQRD_FRMWRE_VRSN        0x230710 // 2.0 pcb (version = 011)
+#define REQRD_FRMWRE_VRSN        0x231026 // 2.0 pcb (version = 011)
 
 #define NUM_HARDWARE_VERSIONS (2)
 #define HARDWARE_VERSION_NUMBERS                                               \
@@ -58,11 +58,10 @@
 /* Defines in the Firmware */
 #define MAX_TIMESLOT_VAL          (0x1F)
 #define MAX_THRESHOLD_TEMP_VAL    (127999) // millidegrees
-#define ACQ_TIME_MIN_CLOCK        (2)
 #define ASIC_FILTER_MAX_RES_VALUE (1)
 #define MAX_SELECT_CHIP10_VAL     (63)
 
-#define MAX_PHASE_SHIFTS (240)
+#define MAX_PHASE_SHIFTS (200)
 #define BIT16_MASK       (0xFFFF)
 
 #define ADC_DECMT_QUARTER_SPEED (0x3)
@@ -71,7 +70,7 @@
 
 #define ADC_PHASE_DEG_QUARTER_SPEED (0)
 #define ADC_PHASE_DEG_HALF_SPEED    (0)
-#define ADC_PHASE_DEG_FULL_SPEED    (300)
+#define ADC_PHASE_DEG_FULL_SPEED    (150)
 
 #define ADC_OFST_QUARTER_SPEED (0x12)
 #define ADC_OFST_HALF_SPEED    (0x12)
@@ -134,7 +133,7 @@ enum DACINDEX {
         680,  /* MO_VB_SDA */                                                  \
         1428, /* MO_VCASC_SFP */                                               \
         1200, /* MO_VOUT_CM */                                                 \
-        800,  /* MO_VIPRE_CDS */                                               \
+        1280, /* MO_VIPRE_CDS */                                               \
         900   /* MO_IBIAS_SFP */                                               \
     };
 

slsDetectorServers/mythen3DetectorServer/slsDetectorFunctionList.c

@@ -479,6 +479,11 @@ void setupDetector() {
         READOUT_PLL_VCO_FREQ_HZ, SYSTEM_PLL_VCO_FREQ_HZ);
     ALTERA_PLL_C10_ResetPLL(READOUT_PLL);
     ALTERA_PLL_C10_ResetPLL(SYSTEM_PLL);
+    // change startup clock divider in software
+    // because firmware only sets max clock divider
+    setClockDividerWithTimeUpdateOption(READOUT_C0, DEFAULT_READOUT_C0_STARTUP,
+                                        0);
+
     // hv
     DAC6571_SetDefines(HV_HARD_MAX_VOLTAGE, HV_DRIVER_FILE_NAME);
     // dac
@@ -2331,6 +2336,7 @@ int setClockDividerWithTimeUpdateOption(enum CLKINDEX ind, int val,
         return FAIL;
     }
     if (val < 2 || val > getMaxClockDivider()) {
+        LOG(logERROR, ("Invalid clock divider %d\n", val));
         return FAIL;
     }
     char *clock_names[] = {CLK_NAMES};

slsDetectorServers/mythen3DetectorServer/slsDetectorServer_defs.h

@@ -64,6 +64,8 @@
 #define DEFAULT_SYSTEM_C2           (5)  //(200000000) // smp_clk, 200 MHz const
 #define DEFAULT_TRIMMING_RUN_CLKDIV (40) // (25000000) // 25 MHz
 
+#define DEFAULT_READOUT_C0_STARTUP (20) //(50000000) // rdo_clk, 50 MHz
+
 #define DEFAULT_ASIC_LATCHING_NUM_PULSES (10)
 #define DEFAULT_MSTR_OTPT_P1_NUM_PULSES  (20)
 #define DEFAULT_ADIF_PIPELINE_VAL        (8)

slsDetectorServers/slsDetectorServer/src/slsDetectorServer_funcs.c

@@ -2533,7 +2533,7 @@ int set_exptime(int file_des) {
         if (gateIndex != -1) {
             ret = FAIL;
             sprintf(mess,
-                    "Could not get exposure time. Gate index not implemented "
+                    "Could not set exposure time. Gate index not implemented "
                     "for this detector\n");
             LOG(logERROR, (mess));
         } else {

slsDetectorSoftware/src/DetectorImpl.cpp

@@ -742,9 +742,8 @@ void DetectorImpl::readFrameFromReceiver() {
             }
         }
 
-        LOG(logDEBUG) << "Call Back Info:"
-                      << "\n\t nDetPixelsX: " << nDetPixelsX
-                      << "\n\t nDetPixelsY: " << nDetPixelsY
+        LOG(logDEBUG) << "Call Back Info:" << "\n\t nDetPixelsX: "
+                      << nDetPixelsX << "\n\t nDetPixelsY: " << nDetPixelsY
                       << "\n\t databytes: " << multisize
                       << "\n\t dynamicRange: " << dynamicRange;
 
@@ -762,8 +761,8 @@ void DetectorImpl::readFrameFromReceiver() {
                 callbackImage = multigappixels;
                 imagesize = n;
             }
-            LOG(logDEBUG) << "Image Info:"
-                          << "\n\tnDetActualPixelsX: " << nDetActualPixelsX
+            LOG(logDEBUG) << "Image Info:" << "\n\tnDetActualPixelsX: "
+                          << nDetActualPixelsX
                           << "\n\tnDetActualPixelsY: " << nDetActualPixelsY
                           << "\n\timagesize: " << imagesize
                           << "\n\tdynamicRange: " << dynamicRange;
@@ -798,8 +797,7 @@ void DetectorImpl::readFrameFromReceiver() {
 int DetectorImpl::insertGapPixels(char *image, char *&gpImage, bool quadEnable,
                                   int dr, int &nPixelsx, int &nPixelsy) {
 
-    LOG(logDEBUG) << "Insert Gap pixels:"
-                  << "\n\t nPixelsx: " << nPixelsx
+    LOG(logDEBUG) << "Insert Gap pixels:" << "\n\t nPixelsx: " << nPixelsx
                   << "\n\t nPixelsy: " << nPixelsy
                   << "\n\t quadEnable: " << quadEnable << "\n\t dr: " << dr;
 
@@ -884,12 +882,10 @@ int DetectorImpl::insertGapPixels(char *image, char *&gpImage, bool quadEnable,
                   << "nMod1Pixelsy: " << nMod1Pixelsy << "\n\t"
                   << "nMod1GapPixelsx: " << nMod1GapPixelsx << "\n\t"
                   << "nMod1GapPixelsy: " << nMod1GapPixelsy << "\n\t"
-                  << "nChipy: " << nChipy << "\n\t"
-                  << "nChipx: " << nChipx << "\n\t"
-                  << "nModx: " << nModx << "\n\t"
-                  << "nMody: " << nMody << "\n\t"
-                  << "nTotx: " << nTotx << "\n\t"
-                  << "nToty: " << nToty << "\n\t"
+                  << "nChipy: " << nChipy << "\n\t" << "nChipx: " << nChipx
+                  << "\n\t" << "nModx: " << nModx << "\n\t"
+                  << "nMody: " << nMody << "\n\t" << "nTotx: " << nTotx
+                  << "\n\t" << "nToty: " << nToty << "\n\t"
                   << "bytesPerPixel: " << bytesPerPixel << "\n\t"
                   << "imagesize: " << imagesize << "\n\t"
                   << "nChipBytesx: " << nChipBytesx << "\n\t"
@@ -1321,6 +1317,11 @@ void DetectorImpl::startAcquisition(const bool blocking, Positions pos) {
             // ensure all status normal (slaves not blocking)
             // to catch those slaves that are still 'waiting'
             auto status = Parallel(&Module::getRunStatus, pos);
+            // if any slave still waiting, wait up to 1s
+            for (int i = 0; i != 20 && status.any(WAITING); ++i) {
+                std::this_thread::sleep_for(std::chrono::milliseconds(50));
+                status = Parallel(&Module::getRunStatus, pos);
+            }
             if (!status.contains_only(IDLE, STOPPED, RUN_FINISHED)) {
                 throw RuntimeError("Acquisition not successful. "
                                    "Unexpected detector status");
@@ -1977,7 +1978,7 @@ void DetectorImpl::setBadChannels(const std::vector<int> list, Positions pos) {
 
     // update to multi values if multi modules
     if (isAllPositions(pos)) {
-        std::vector<std::vector<int>> badchannels;
+        std::vector<std::vector<int>> badchannels(modules.size());
         int nchan = modules[0]->getNumberOfChannels().x;
         if (shm()->detType == MYTHEN3) {
             // assuming single counter
@@ -1996,16 +1997,9 @@ void DetectorImpl::setBadChannels(const std::vector<int> list, Positions pos) {
                                    std::to_string(badchannel) +
                                    " out of bounds.");
             }
-            if (badchannels.size() != imod + 1) {
-                badchannels.push_back(std::vector<int>{});
-            }
             badchannels[imod].push_back(ch);
         }
         for (size_t imod = 0; imod != modules.size(); ++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]);
         }

slsDetectorSoftware/src/Module.cpp

@@ -3332,7 +3332,13 @@ void Module::initializeModuleStructure(detectorType type) {
     shm()->numberOfModule.y = 0;
     shm()->controlPort = DEFAULT_TCP_CNTRL_PORTNO;
     shm()->stopPort = DEFAULT_TCP_STOP_PORTNO;
-    strcpy_safe(shm()->settingsDir, getenv("HOME"));
+    char *home_directory = getenv("HOME");
+    if (home_directory != nullptr)
+        strcpy_safe(shm()->settingsDir, home_directory);
+    else {
+        strcpy_safe(shm()->settingsDir, "");
+        LOG(logWARNING) << "HOME directory not set";
+    }
     strcpy_safe(shm()->rxHostname, "none");
     shm()->rxTCPPort = DEFAULT_TCP_RX_PORTNO + moduleIndex;
     shm()->useReceiverFlag = false;

slsReceiverSoftware/src/MasterFileUtility.cpp

@@ -215,12 +215,42 @@ std::string CreateVirtualHDF5File(
 
         // property list
         H5::DSetCreatPropList plist;
-        int fill_value = -1;
-        plist.setFillValue(dataType, &fill_value);
+        uint8_t u8 = -1;
+        uint16_t u16 = -1;
+        uint32_t u32 = -1;
+        uint64_t u64 = -1;
+        void* fill_value;
+
+        if (dataType == H5::PredType::STD_U8LE) {
+            fill_value = &u8;
+        } else if (dataType == H5::PredType::STD_U16LE) {
+            fill_value = &u16;
+        } else if (dataType == H5::PredType::STD_U32LE) {
+            fill_value = &u32;
+        } else if (dataType == H5::PredType::STD_U64LE) {
+            fill_value = &u64;
+        } else {
+            throw RuntimeError("Unsupported data type for virtual HDF5 file");
+        }
+        plist.setFillValue(dataType, fill_value);
+
+        //uint64_t fill_value = -1;
+        //plist.setFillValue(dataType, &fill_value);
         std::vector<H5::DSetCreatPropList> plistPara(paraSize);
         // ignoring last fill (string)
         for (unsigned int i = 0; i != plistPara.size() - 1; ++i) {
-            plistPara[i].setFillValue(parameterDataTypes[i], &fill_value);
+            if (parameterDataTypes[i] == H5::PredType::STD_U8LE) {
+                fill_value = &u8;
+            } else if (parameterDataTypes[i] == H5::PredType::STD_U16LE) {
+                fill_value = &u16;
+            } else if (parameterDataTypes[i] == H5::PredType::STD_U32LE) {
+                fill_value = &u32;
+            } else if (parameterDataTypes[i] == H5::PredType::STD_U64LE) {
+                fill_value = &u64;
+            } else {
+                throw RuntimeError("Unsupported data type for virtual HDF5 file");
+            }
+            plistPara[i].setFillValue(parameterDataTypes[i], fill_value);
         }
 
         // hyperslab (files)

slsSupportLib/include/sls/ZmqSocket.h

@@ -24,8 +24,9 @@
 #include <rapidjson/document.h> //json header in zmq stream
 #pragma GCC diagnostic pop
 
-#include <zmq.h>
+//#include <zmq.h>
 
+class zmq_msg_t;
 namespace sls {
 
 #define MAX_STR_LENGTH 1000

slsSupportLib/include/sls/string_utils.h

@@ -20,6 +20,7 @@ Still this is better than strcpy and a buffer overflow...
 */
 template <size_t array_size>
 void strcpy_safe(char (&destination)[array_size], const char *source) {
+    assert(source != nullptr);
     assert(array_size > strlen(source));
     strncpy(destination, source, array_size - 1);
     destination[array_size - 1] = '\0';

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      "8.0.0"
-#define APILIB       "8.0.0 0x231108"
+#define RELEASE      "8.0.1"
 #define APIRECEIVER  "8.0.0 0x231108"
 #define APICTB       "8.0.0 0x231109"
 #define APIGOTTHARD  "8.0.0 0x231109"
 #define APIGOTTHARD2 "8.0.0 0x231109"
 #define APIJUNGFRAU  "8.0.0 0x231109"
-#define APIMYTHEN3   "8.0.0 0x231109"
-#define APIMOENCH    "8.0.0 0x231109"
 #define APIEIGER     "8.0.0 0x231109"
+#define APILIB       "8.0.1 0x240112"
+#define APIMOENCH "8.0.2 0x240703"
+#define APIMYTHEN3 "8.0.2 0x240715"

slsSupportLib/src/ZmqSocket.cpp

@@ -10,7 +10,7 @@
 #include <string.h>
 #include <thread>
 #include <vector>
-
+#include <zmq.h>
 namespace sls {
 
 using namespace rapidjson;