7.0.3.rc2 (#866) (#867)

*7.0.3.rc2
* moench: handling bug in post processing from receiver when partial_frames policy and empty frame happens, only json header without data is sent

CMakeLists.txt

@@ -2,7 +2,7 @@
 # Copyright (C) 2021 Contributors to the SLS Detector Package
 cmake_minimum_required(VERSION 3.12)
 project(slsDetectorPackage)
-set(PROJECT_VERSION 7.0.0)
+set(PROJECT_VERSION 7.0.3)
 
 set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
 

README.md

@@ -1,102 +1,233 @@
-### Note
+## Dependencies
+Before building from source make sure that you have the [software wiki](https://slsdetectorgroup.github.io/devdoc/dependencies.html) installed. If installing using conda, conda will manage the dependencies. Avoid also installing packages with pip. 
 
-Please do not update to any xxxx.xx.xx.dev0 tags. They are not releases, but tags for internal usage.
-Use only releases with tags such as x.x.x or x.x.x-rcx.
+## Documentaion
+Detailed documentation can be found in the [software wiki](https://slsdetectorgroup.github.io/devdoc/index.html) and on the [official site](https://www.psi.ch/en/detectors/software).
 
-### Documentation
-##### 5.0.0 - Latest Release
-Detailed documentation on the latest release can be found in the [software wiki](https://slsdetectorgroup.github.io/devdoc/index.html) and on the [official site](https://www.psi.ch/en/detectors/software).
+## Installation
 
-##### Older Releases
-Documentation is found in the package.
+### 1. Install binaries using conda
+Conda is not only useful to manage python environments but can also
+be used as a user space package manager. Dates in the tag (for eg. 2020.07.23.dev0) 
+are from the developer branch. Please use released tags for stability.
+
+We have three different packages available:
+* **slsdetlib** shared libraries and command line utilities 
+* **slsdetgui** GUI
+* **slsdet** Python bindings
 
-### Binaries
-Binaries for the slsDetectorPackage are available through conda. 
 ```
-#Add conda channels
+#Add channels for dependencies and our library
 conda config --add channels conda-forge
 conda config --add channels slsdetectorgroup
 conda config --set channel_priority strict
 
-conda install slsdetlib   #only shared lib and command line
-conda install slsdet      #python bindings (includes slsdetlib)
-conda install slsdetgui   #gui (includes qt4)
-
-#Install specific version
-conda install slsdet=2020.03.02.dev0 #developer version from 3 March 2020
+#create and activate an environment with our library
+#replace 6.1.1 with the required tag
+conda create -n myenv slsdetlib=6.1.1
+conda activate myenv
 
+#ready to use
+sls_detector_get exptime
+etc ...
 ```
 
-### Source code
-One can also obtain the source code from this repository and compile.
 ```
-git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git
+# List available versions
+# lib and binaries
+conda search slsdetlib
+# python
+conda search slsdet
+# gui
+conda search slsdetgui
+```
+
+### 2. Build from source
+
+##### 2.1 Download Source Code from github
+```
+git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 7.0.0
+```
+
+**Pybind for Python**<br>
+* **v7.0.0+**:
+pybind11 packaged into 'libs/pybind'. No longer a submodule. No need for "recursive" or "submodule update".
+ 
+* **Older versions**:
+   pybind11 is a submodule. Must be cloned using "recursive" and updated when switching between versions using the following commands.
 
 ```
-#### Dependencies 
+# clone using recursive to get pybind11 submodule
+git clone --recursive https://github.com/slsdetectorgroup/slsDetectorPackage.git
 
-Refer [this page](https://slsdetectorgroup.github.io/devdoc/dependencies.html)  for dependencies.
-
-
-#### Compilation 
-
-Compiling can be done in two ways. Either with the convenience script
-cmk.sh or directly with cmake for more control.
-
-**1. Compile using script cmk.sh**<br>
-
-These are mainly aimed at those not familiar with using ccmake and cmake. 
+# update submodule when switching between releases
+cd slsDetectorPackage
+git submodule update --init
 ```
-    The binaries are generated in slsDetectorPackage/build/bin directory.
 
-    Usage: ./cmk.sh [-c] [-b] [-p] [e] [t] [r] [g] [s] [u] [i] [m] [n] [-h] [z] [-d <HDF5 directory>] [-l Install directory] [-k <CMake command>] [-j <Number of threads>]
-    -[no option]: only make
-    -c: Clean
-    -b: Builds/Rebuilds CMake files normal mode
-    -p: Builds/Rebuilds Python API
-    -h: Builds/Rebuilds Cmake files with HDF5 package
-    -d: HDF5 Custom Directory
-    -k: CMake command
-    -l: Install directory
-    -t: Build/Rebuilds only text client
-    -r: Build/Rebuilds only receiver
-    -g: Build/Rebuilds only gui
-    -s: Simulator
-    -u: Chip Test Gui
-    -j: Number of threads to compile through
-    -e: Debug mode
-    -i: Builds tests
-    -m: Manuals
-    -n: Manuals without compiling doxygen (only rst)
-    -z: Moench zmq processor
+##### 2.2 Build from source
+
+
+###### Build using CMake
+
+```
+# outside slsDetecorPackage folder
+mkdir build && cd build
+
+# configure & generate Makefiles using cmake
+# by listing all your options (alternately use ccmake described below)
+# cmake3 for some systems
+cmake ../slsDetectorPackage -DCMAKE_INSTALL_PREFIX=/your/install/path
+
+# compiled to the build/bin directory
+make -j12 #or whatever number of cores you are using to build
+
+# install headers and libs in /your/install/path directory
+make install
+```
+
+Instead of the cmake command, one can use ccmake to get a list of options to configure and generate Makefiles at ease.
+
+
+```
+# ccmake3 for some systems
+ccmake ..
+ 
+# choose the options
+# first press [c] - configure
+# then press [g] - generate
+```
+
+|Example cmake options|Comment|
+|---|---|
+| -DSLS_USE_PYTHON=ON            | Python                                 |   
+| -DPython_FIND_VIRTUALENV=ONLY  | Python from only the conda environment |
+| -DZeroMQ_HINT=/usr/lib64       | Use system zmq instead                 |    
+| -DSLS_USE_GUI=ON               | GUI                                    |
+
+
+###### Build using in-built cmk.sh script
+
+```
+The binaries are generated in slsDetectorPackage/build/bin directory.
+
+Usage: ./cmk.sh [-b] [-c] [-d <HDF5 directory>] [e] [g] [-h] [i] [-j <Number of threads>] 
+[-k <CMake command>] [-l <Install directory>] [m] [n] [-p] [-q <Zmq hint directory>] 
+[r] [s] [t] [u] [z]  
+-[no option]: only make
+-b: Builds/Rebuilds CMake files normal mode
+-c: Clean
+-d: HDF5 Custom Directory
+-e: Debug mode
+-g: Build/Rebuilds gui
+-h: Builds/Rebuilds Cmake files with HDF5 package
+-i: Builds tests
+-j: Number of threads to compile through
+-k: CMake command
+-l: Install directory
+-m: Manuals
+-n: Manuals without compiling doxygen (only rst)
+-p: Builds/Rebuilds Python API
+-q: Zmq hint directory
+-r: Build/Rebuilds only receiver
+-s: Simulator
+-t: Build/Rebuilds only text client
+-u: Chip Test Gui
+-z: Moench zmq processor
 
     
-    # get all options
-    ./cmk.sh -?
+# display all options
+./cmk.sh -?
 
-    # new build  and compile in parallel:
-    ./cmk.sh -bj5
-```
- 
-**2. Compile without script**<br>
-Use cmake to create out-of-source builds, by creating a build folder parallel to source directory. This would create a debug build with address sanitizers.
-```
-    $ mkdir build
-    $ cd build
-    $ cmake ../slsDetectorPackage  -DCMAKE_BUILD_TYPE=Debug -DSLS_USE_SANITIZER=ON
-    $ make -j12 #or whatever number of threads wanted
+# new build and compile in parallel (recommended basic option):
+./cmk.sh -cbj5
+
+# new build, python and compile in parallel:
+./cmk.sh -cbpj5
+
+#To use the system zmq (/usr/lib64) instead
+./cmk.sh -cbj5 -q /usr/lib64
 ```
 
-To install binaries using CMake
+###### Build on old distributions
+
+If your linux distribution doesn't come with a C++11 compiler (gcc>4.8) then 
+it's possible to install a newer gcc using conda and build the slsDetectorPackage
+using this compiler
+
 ```
-    git clone --recursive https://github.com/slsdetectorgroup/slsDetectorPackage.git
-    mkdir build && cd build
-    cmake ../slsDetectorPackage -DCMAKE_INSTALL_PREFIX=/your/install/path
-    make -j12 #or whatever number of cores you are using to build
-    make install
+#Create an environment with the dependencies
+conda create -n myenv gxx_linux-64 cmake zmq
+conda activate myenv
+
+# outside slsDetecorPackage folder
+mkdir build && cd build
+cmake ../slsDetectorPackage -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
+make -j12
+```
+
+###### Build slsDetectorGui (Qt5)
+
+1. Using pre-built binary on conda
+```
+conda create -n myenv slsdetgui=7.0.0
+conda activate myenv
+```
+
+2. Using system installation on RHEL7
+```
+yum install qt5-qtbase-devel.x86_64
+yum install qt5-qtsvg-devel.x86_64 
+```
+
+3. Using conda
+```
+#Add channels for dependencies and our library
+conda config --add channels conda-forge
+conda config --add channels slsdetectorgroup
+conda config --set channel_priority strict
+
+# create environment to compile
+# on rhel7
+conda create -n slsgui zeromq gxx_linux-64 gxx_linux-64 mesa-libgl-devel-cos6-x86_64 qt
+# on fedora or newer systems
+conda create -n slsgui zeromq qt
+
+# when using conda compilers, would also need libgl, but no need for it on fedora unless maybe using it with ROOT
+
+# activate environment
+conda activate slsgui
+
+# compile with cmake outside slsDetecorPackage folder
+mkdir build && cd build
+cmake ../slsDetectorPackage -DSLS_USE_GUI=ON
+make -j12
+
+# or compile with cmk.sh
+cd slsDetectorPackage
+./cmk.sh -cbgj9
+```
+
+###### Build documentation from package
+The documentation for the slsDetectorPackage is build using a combination 
+of Doxygen, Sphinx and Breathe. The easiest way to install the dependencies
+is to use conda 
+
+```
+conda create -n myenv python sphinx_rtd_theme breathe
+```
+
+```
+# using cmake or ccmake to enable DSLS_BUILD_DOCS
+# outside slsDetecorPackage folder
+mkdir build && cd build
+cmake ../slsDetectorPackage -DSLS_BUILD_DOCS=ON
+
+make docs # generate API docs and build Sphinx RST
+make rst # rst only, saves time in case the API did not change
 ```
 
 
-### Support
+## Support
     dhanya.thattil@psi.ch
-    erik.frojdh@psi.ch
+    erik.frojdh@psi.ch

RELEASE.txt

@@ -1,838 +1,139 @@
-SLS Detector Package Minor Release 7.0.0.rc1 released on 12.12.2021
-===================================================================
+SLS Detector Package Major Release 7.0.3 released on 14.11.2023
+===============================================================
 
-This document describes the differences between v7.0.0.rc1 and v6.1.2   
+This document describes the differences between v7.0.3 and v7.0.2   
 
 
 
     CONTENTS
     --------
-    1.          New, Changed or Resolved Features
-        1.1.    Compilation
-        1.2.    Callback
-        1.3.    Python
-        1.4.    Client
-        1.5.    Detector Server
-        1.6.    Simulator
-        1.7.    Receiver
-    2.          On-board Detector Server Compatibility
-    3.          Firmware Requirements
-    4.          Kernel Requirements
-    5.          Download, Documentation & Support
+    1   Resolved Issues
+    2   On-board Detector Server Compatibility
+    3   Firmware Requirements
+    4   Kernel Requirements
+    5   Download, Documentation & Support
 
 
 
+1 Resolved Issues
+=================
 
-1. New or Changed Features
-==========================
 
+    Firmware
+    --------
 
-1.1. Compilation
-----------------
 
+    *   [Eiger] Blocking trigger on quad
+        Previously, blocking software trigger on a quad was not blocking. Fixed
+        with firmware v32.
 
-    General:
 
+    Client
+    ------
 
-    *   Custom location to find ZeroMQ
-        Option to provide a custom location to look for ZeroMQ, if not found 
-        using FindZeroMQ.cmake
-        
-        For example, to use the system installed zmq:
-        Using cmake: -DZeroMQ_HINT=/usr/lib64 
-        Using cmk.sh script: -q /usr/lib64
 
+    *   Limit port number max to 65535
+        Previously, one could set the port numbers (TCP, UDP, ZMQ) to values 
+        higher than 65535 and also to 0. However, it was truncated to 16 bit
+        in the background, but not relayed to the user. 
+        Now, it will throw if it is 0 or greater than 65535 (16 bit).
 
-    *   Support external build 
-        Assuming already installed version of the slsDetectorPacakge exists, 
-        external build of python bindings, gui, ctbgui and moench has been added.
 
+    *   Stopping acqusition for a single or subset of modules
+        The Detector API previously stopped all modules.
+        Now, it takes into account which modules the user wanted to stop.
 
-    *   Catch updated to latest 2.x version due to build failure in fedora
-    
 
+    *   [Jungfrau] Stop in sync mode
+        When stopping acquisition in sync mode, only the master module sometimes 
+        returns 'Idle' state instead of 'Stopped'. The software threw an 
+        exception for the different states then.
+        Now, it does not throw and a fix will be added to the next firmware 
+        release for the different states (with SW release: v8.0.0).
 
-    Gui:
 
+    *   [Eiger] Incorrect error message in Stop
+        When stopping acquisition, if a half module were to give an error in a 
+        rare case while the others succeeded, this would result in an re-attempt 
+        to stop 9 more times before throwing an incorrect exception messsage that 
+        it could not stop.
+        Now, it is handled and will throw an exception of the error status
+        immediately.
 
-    *   Qt5 and in-built compressed Qwt 6.1.5
-        Ported from Qt4 to Qt5. Minimum requirement: Qt 5.9
-        Compressed Qwt 6.1.5 added into the package in libs. It is unpacked and built
-        as a static library.This allows us to remove qwt as an external dependency
-        and reduces the risk of picking up the wrong version.
 
+    Receiver
+    --------
 
-    Python:
-
-
-    *   Install python extension
-        Option to copy the python extension (slsdet folder and _slsdet-..so)
-        to CMAKE_INSTALL_PREFIX/python using
-        -DSLS_INSTALL_PYTHONEXT
-
-
-    *   Pybind11 (v2.10.0)
-        Pybind11 is removed as a submodule and instead built into package to
-        simplify for users. Now, there is no more need to clone with the '--recursive'
-        argument or to update submodule when switching to this package version 
-        and above.
-
-
-    *   Conda packages
-        Removed conda packages for python 3.6 and 3.7. Added for python 3.11.
-
-
-
-1.2. Callback
--------------
-
-
-    *   Datatype of Metadata [registerCallBackRawDataReady, registerCallBackRawDataModifyReady]
-        Datatype changed from char* to sls_receiver_header.
-
-
-    *   Datatype of Size [registerCallBackRawDataReady, registerCallBackRawDataModifyReady]
-        Datatype changed from uint32_t to size_t
-
-
-    *   Datatype of file name and file path [registerCallBackStartAcquisition]
-        Datatype changed from string to const string reference.
-
-
-    *   Incorrect image size [registerCallBackStartAcquisition]
-        Fixed. It used to give +120 bytes.
-
-
-    *   [Gotthard2] 25um Image reconstruction for 2 modules
-        First module (master) interleaves with second modules(slave). First channel
-        of master is first channel of detector. 
-
-        Requires firmware update to reverse channels of slaves.
-
-
-
-1.3. Python
------------
-
-
-    *   Defines in sls_detector_defs
-        sls_detetor_defs parsed and #defines extracted into defines.py
-        For exmaple, one can use slsdet.LOCALHOST_IP
-
-
-    *   Python sub-microsecond resolution
-        Reading back sub-microsecond exposure times from the Python API fixed by 
-        addig Python datetime supports only micro seconds as lowest unit. 
-        
-        This is fixed by introducing a new C++ type (DurationWrapper), which 
-        holds number of nanoseconds as a uint64_t (only in python bindings) and 
-        custom typecaster to convert to and from std::chrono::nanoseconds.
-
-        A get using API now returns in DurationWrapper, instead of datetime.
-        Refer exptime help for examples.
-
-
-1.4. Client
------------
-
-
-    Breaking API:
-
-
-    *   Versioning
-        The client, receiver and detector servers now have semantic Versioning
-        along with the date and are managed with the Version class.
-
-        --version argument to the executable gives the complete versioning with date.
-
-        Using the client to get versions gives only the semantic version. An older
-        server will still give date. Hence, the return type is a string, breaking API.
-
-        Compatibility checks at hostname or rx_hostname command will only be for
-        backwards compatibility (ie. it only checks for the major version number).
-        If its an old server, then its expected to have the exact same date (as
-        before)
-
-        Setting intitialchecks to 0 also bypasses the receiver compatibility check.
-
-
-    *   Detector Specific fields
-        bunchid ->detSpec1
-        reserved->detSpec2
-        debug->detSpec3
-        roundRnumber->detSpec4
-
-        Header version number stays the same in the UDP header as there is no
-        difference in the format from the detector. Only the structure memeber names
-        have changed in sls_detector_defs.h
-
-        Further details about each detector specific field can be found at:
-        https://slsdetectorgroup.github.io/devdoc/udpdetspec.html
-
-
-    *   Namespace sls
-        All files in slsSupportLib and tests have now been moved to sls namespace 
-        including macros. Using the LOG, for example, will require the sls qualifier.
-
-
-    *   [Eiger] Number of UDP interfaces
-        Command line: numinterfaces, API: getNumberofUDPInterfaces
-        This command now reflects the actual number of udp interfaces for Eiger,
-        which is 2.
-
-
-    *   [Eiger][Jungfrau] Row column
-        [Jungfrau] Fixed row column indexing for multi module 2 interfaces
-
-        [Eiger] The row indicies were switched across the Y axis for the callback
-        only for Eiger. This is now changed and kept similar to the other detectors.
-        The row indices would be in the order of the half modules in the hostname 
-        command. Therefore, to keep the image from callback, invert the hostname
-        order in the config file.
-
-
-    *   Deprecated CopyDetectorServer 
-        Command line: copydetectorserver, API: copydetectorserver
-        Removed. Use updatedetectorserver
-
-
-    *   [Eiger][Jugfrau][Mythen3] Deprecated specific transmission delay commands
-        txndelay_frame -> txdelay_frame
-        txndelay_left -> txdelay_left
-        txndelay_right -> txdelay_right
-
-
-    *   [Eiger] Datastream only for 10GbE
-        Command line: datastream, API: getDataStream/ setDataStream
-
-        This command to enable/ disable data stream from left or right port
-        is now allowed only for 10GbE. Previously, it incorrectly allowed to do so.
-
-
-    *   [Eiger][Jungfrau][Moench][Ctb] Stop command effect on next frame number
-        Stopping acquisition sometimes results in different next frame numbers
-        for different moduels. Hence, after a stop, if the next frame numbers are
-        different, they are all set to their maximum value + 1.
-
-
-    *   Missing packets
-        Command line: rx_missingpackets, API: getNumMissingPackets
-        This now returns a signed 64 bit instead of unsigned. The negative polarity
-        depicts extra packets instead of missing packets and also takes care of
-        disabled ports.
-
-
-    *   Frames caught and frame index
-        Command line rx_framescaught, rx_frameindex, API: getFramesCaught/ getRxCurrentFrameIndex
-        They now return a vector for each port when there are 2 udp interfaces
-        in the receiver.
-
-
-    *   [Gotthard][Gotthard2] Num modules
-        Only 2 modules allowed maximum in a detector shared memory.
-
-
-    *   [Moench][Ctb][Mythen3] Deprecated commands
-        Patloopx, patnloopx, patwaitx, patwaittimex
-        Please use instead patloop, patnloop, patwait and patwaittime commands
-        with the level as an argument. 
-
-        Old commands work with warning, but the server expects the new ones
-        such as a default pattern file to be loaded at startup for Moench.
-
-        Renamed patternParameters struct member from 'loop' to 'startloop' and 
-        'stoploop'.
-
-
-    *   [Mythen3] Clock Divider 4 and 5
-        Cannot be set anymore. Only read back.
-
-
-
-    New commands:
-
-
-    *   [Eiger][Gotthard][Gotthard2][Mythen3][Jungfrau] Master
-        
-        Setting up from client:
-        [Eiger][Gotthard2][Jungfrau] 
-        Command line: master, API: getMaster/ setMaster
-        All of them can get master mode from the client.
-        
-        This can also be set up on the detector server. Please refer to notes
-        on that section.
-
-
-    *   [Eiger] Top
-        Command line: top, API: getTop/ setTop
-        Sets the half module to top or bottom from the client.
-
-        This can also be set up on the detector server. Please refer to notes
-        on that section.
-
-
-    *   [Mythen3][Eiger] Save settings file
-        Command line: trimbits (sls_detector_get), API: saveTrimbits
-        Added
-
-
-    *   [Gotthard2] Parallel readout added
-        Command line: parallel, API: getParallelMode/ setParallelMode
-        Default for Gotthard2 is parallel. Non parallel mode only works in 
-        continuous mode.
-
-
-    *   [Jungfrau] Software trigger added
-        Command line: trigger, API: sendSoftwareTrigger
-        Send software trigger instead of harware trigger.
-
-
-    *   [Eiger][Jungfrau] Blocking trigger
-        Commandline: blockingtrigger, API: sendSoftwareTrigger with argument true
-        Sends software trigger signal to detector and blocks until the frames
-        are sent out for that trigger.
-
-
-    *   [Jungfrau] Sync
-        Command line: sync, API: getSynchronization/ setSynchronization
-        Enables or disables synchronization between modules
-
-
-    *   [Gotthard2][Mythen3] Temperature readout
-        Command line: temp_fpga, API: getTemperature with TEMPERATURE_FPGA enum
-        Added
-
-
-    *   [Gotthard2][Mythen3] Round robin added
-        Command line: udp_dstlist, API: getDestinationUDPList/ setDestinationUDPList
-        Command line: udp_numdst, API: getNumberofUDPDestinations
-        One can set up to 32 (64 for Mythen3) entries in the destination list.
-
-
-    *   [Jungfrau] Module Id
-        Command line: moduleid, API: getModuleId
-        16 bit value (ideally unique) that is streamed out in the udp header of 
-        the detector. The on-board detector server picks it up from a file 
-        (if it exists) called detid_jungfrau.txt.
-    
-
-    *   [Jungfrau][[Gotthard2][Myhten3][Gotthard][Ctb][Moench] Hardware version
-        Command line: hardwareversion, API: getHardwareVersion
-        Gets the board or hardware version. 
-        For example, Jungfrau returns 1.0 or 2.0.
-        It is also printed at on-board detector server start up.
-        Also printed before starting FPGA programming.
-
-
-    *   [Eiger][Jugfrau][Mythen3] Transmission Delay   
-        Command line: tx_delay, API: getTransmissionDelay/ setTransmissionDelay
-        Sets transmission delay for all modules in the detector using the step
-        size provided. Sets up for every module:
-            [Eiger] txdelay_left to (2 * mod_index * n_delay)
-            [Eiger] txdelay_right to ((2 * mod_index + 1) * n_delay)
-            [Eiger] txdelay_frame to (2 *num_modules * n_delay)
-            [Jungfrau][Mythen3] txdelay_frame to (num_modules * n_delay)
-
-
-    *   [Mythen3] Bad channels
-        Command line: badchannels, API: getBadChannels/ setBadChannels
-        Set bad channels from file with a list of channels, which will be masked
-        out. Also does trimming. A detector level command will require the channel
-        numbers accordingly. The file also extended to include commas, colons range)
-        and removes duplicates. 
-
-
-    *   [Moench][Ctb] Starting frame number
-        Command line: nextframenumber, API: getNextFrameNumber/ setNextFrameNumber
-        Added and default set up on detector server start up.
-
-
-    *   [Ctb] DAC names
-        Command line: daclist, API: getDacNames/ setDacNames
-        Can set and get dac names in the dac list now.
-    
-    
-    *   [Mythen3] Polarity, interpolation, pump probe, analog pulsing, digital pulsing
-        Command line: polarity, interpolation, pumpprobe, apulse, dpulse
-        API: getPolarity/ setPolarity, getInterpolation/ setInterpolation,
-        getPumpProbe/ setPumpProbe, getAnalogPulsing/ setAnalogPulsing,
-        getDigitalPulsing/ setDigitalPulsing
-        
-        Added these commands. 
-       
-        Enabling interpolation will also enable all counters and disable vth3.
-        Disabling sets to previous counter mask and previous vth values.
-
-        In pump probe mode, only vth2 enabled. Disabling sets vth2 to prevevious 
-        value.
-
-        Setting counter mask will check interpolation and pump probe mode
-        requirements, else sets vthx dacs according to counter mask.
-
-        Direct overwrite of any dac (including vthx) allowed using dac command
-        (as before).
-
-
-
-    New commands for Receiver only:
-
-
-    *   Arping for 10GbE
-        Command line: rx_arping API: getRxArping/ setRxArping
-        Starts a thread in the receiver to arping the interface it is listening
-        to in 10GbE mode every 60 s. 
-        Changes NUM_RX_THREAD_IDS (sls_detector_defs.h) from 8 to 9.
-
-
-    *   Receiver Region of Interest
-        Command line: rx_roi, API: getRxROI/ setRxROI
-        Command line: rx_clearroi, API: clearRxROI
-        One can set an ROI in the receiver to write to file. 1D detectors can set
-        xmin and xmax, whereas the 2D can also set ymin and ymax. -1 values signify
-        no ROI. 
-        
-        This is not at network level and can only be used to reduce size of file.
-        Virtual HDF5 files not created when this is enabled and also no link in
-        master file. No file created if module not in ROI.
-
-        There can only be one ROI per detector. Therefore, can be set only at 
-        detector level, but can be retrieved at module level as well.
-
-        The GUI still shows the entire image, but has a yellow border around the 
-        ROI. Status bar displays a message when Rx ROI enabled.
-
-
-
-    Additonal Features:
-
-
-    *   Non-blocking start
-        Allowing non-blocking start at modular level again.
-
-
-    *   [Jungfrau][Moench][Ctb] Additional programming checks
-        Also checks if the drive to write to is a special file or a normal
-        file. If its a normal file, it throws asking to redo the command with a 
-        '--please-delete' argument to delete the normal file and create the device
-        drive and restart FPGA programming.
-
-        More readable error message insetad of "programfpga not implemented for
-        this detector'. This happens when 'hostname' command fails due to 
-        server-firmware/client compatibility and the detector type becomes
-        'GENERIC'. Fixed to suggest if 'hostname' executed properly. 
-
-
-    *   Udp Source IP
-        Command line: udp_srcip(2), API: getSourceUDPIP(2)/ setSourceUDPIP(2)
-        One can also set this to 'auto' for 1 GbE data. It will set to IP of
-        rx_hostname (as in udp_dstip)
-
-    *   Incrementing default receiver tcp port
-        Automatically incrementing the default receiver tcp port for every module
-        when creating shared memory.
 
+    *   Limit TCP port number (command line) to max of 65535
+        Refer issue under 'Client'.
 
     
-    Changes or Fixes:
+    Detector Simulator
+    ------------------
 
 
-    *   [Jungfrau][Gotthard2][Mythen3][Gotthard][Moench][Ctb] Can't stop
-        This bug was introduced in 6.1.1, when stopping an acquisition saying it 
-        cannot stop, even though it was successful. It is fixed now.
+    *   Limit TCP port number (command line) to max of 65535
+        Refer issue under 'Client'.
 
 
-    *   Free and config command fail
-        Free and config command checked mismatch of size of shared memory before 
-        freeing or loading new config. Fixed.
+    *   Some commands such as 'readnrows' would complain that it cannot be set 
+        because the detector is not idle, but was setting it anyway. Fixed.
 
 
-    *   sls_detector_help or sls_detector_get -h
-        Should not create Detector object. Fixed.
+    Gui/ Client Callback
+    --------------------
 
 
-    *   [Jungfrau] Storage cells in running receiver
-        Allowing the possibility to set this when receiver in running state.
+    *   [Jungfrau] Gui: corrected color map of gain plot
+        Previously, color on the gain plot did not update after the first image, 
+        unless there were x/y min/max changes or window resizing. Fixed.
 
 
-    *   [Eiger] Vtr
-        Allow Vtrim to be interpolated for settings.
+    *   [Jungfrau] Acquisition finished callback error status in sync mode
+        When stopping acquisition in multi module Jungfrau sync mode, 
+        different status (master 'idle' and slaves 'stopped' in 
+        firmware 2.4.1 or 1.4.1) show as 'error' in acquisition finished call 
+        back (mainly used for gui). This is fixed.
 
 
-    *   [Mythen3] Incorrect gain caps when setting threshold energy
-        Gain caps overwritten with settings enum. Fixed.
+    *   [Jungfrau] Gui: Next frame number shown as 0 for inconsistency
+        When stopping an acquisition in a multi module Jungfrau, the next 
+        frame numbers might be different, for which the Gui shows an error message
+        but keeps the number as 0. Now, it is fixed to show -1 for inconsistency 
+        and error message shown. So, setting 0 will also prompt an error message
+        that 0 is an invalid input.
 
 
-    *   [Mythen3] Non blocking start acquisition 
-        Non-blocking start acquisition was sent out twice to the master. Fixed.
+    Data Processing
+    ---------------
 
 
-    *   [Mythen3] Threshold
-        When settings trimbits or threshold, counter mask is set and hence,
-        vthx dacs are set accordingly.
+    *   [Moench] Segmentation fault with moench03RawDataPrcess
+        Previously, it crashed when nframes > 0. Fixed.
 
-        setAllThresholdEnergy takes 3 values for each counter and if one of them
-        is -1, the trimbits and setings for that counter is picked up from the 
-        detector.
 
+    *   [Moench] Interpolation issues fixed.
 
-    *   [Moench][Ctb] Pattern levels
-        Changed from 3 to 6.
 
+    *   [Moench] When receiver in discard_partial mode and gets an empty frame,
+        it sends a zmq packet with header and no data. This is handled in post
+        processing as a temporary solution.
 
-    *   [Mythen3][Moench][Ctb] Default patwait and patloop addresses
-        Set default wait and loop addresses to 0x1fff (max value) for all levels
-        before loading pattern. Please use the pattern command instead of parameters.
-        This ensures defaults are set up and is faster.
 
 
-    *   [Moench] Patsetbit and patsetmask
-        Command line: patsetbit API: getPatternBitMask/ setPatternBitMask
-        Command line: patmask API: getPatternMask/ setPatternMask
-        
-        Exchanging the help and masks for patsetbit and patsetmask in the detector
-        server, especially in loading settings.
 
-
-    *   [Moench][Ctb] ADC Vpp
-        Command line: adcvpp, API: getADCVpp/ setADCVpp
-        Moved from SetDAC function into into its own. One can use mV values or
-        option numbers as before.
-
-
-    *   [Ctb] ADC command goes back to control server
-        Slow ADCs, slow ADC temperature, get measured current and voltage values
-        are requested via the control server again insetad of the stop server
-        due to configuration and definitions in the control server.
-
-
-
-1.5. Detector Server
---------------------
-
-
-    Config file:
-
-    *   [Eiger][Gotthard2][Gotthard] Master
-        Using config file with 'master' with argument (master=1, slave=0)
-
-
-    *   [Eiger] Top          
-        Using config file with 'top' with argument (top=1, bottom=0)
-    
-
-
-    Command line arguments:
-
-    *   They have precedence over config files. 
-
-
-    *   [Eiger][Gotthard2 Virtual][Mythen3 Virtual][Gotthard Virtual] Master
-        Using command line '--master = 1' or '-m = 1' with argument 
-        (master = 1, slave = 0)
-
-
-    *   [Eiger] Top
-        Using command line '--top = 1' or '-t = 1' with argument (top=1, bottom=0)
-
-
-    *   Ignore config file
-        The config files can also be ignored by an argument from the command line, 
-        '--ignore-config' or '-i'.
-                      
-
-
-    Fixes:
-
-
-    *   [Jungfrau][Eiger] Clear UDP destination
-        Command line: udp_cleardst, API: clearUDPDestinations
-        Clearing udp destination also clears it in the FPGA now. 
-
-
-    *   [Eiger] Incorrect next frame number
-        Command line: nextframenumber, API: getNextFrameNumber/ setNextFrameNumber
-        Get next frame number for 10g was connected to 1g registers and gave 
-        incorrect values. Fixed.
-
-
-    *   [Mythen3][Gotthard2] System clock change effects 
-        When changing the system clock (clkdiv 2), time settings should also be 
-        affected (exptime, period etc.). Fixed.
-
-        [Gotthard2] System frequency should be same irrespective of timing source.
-        Fixed.
-
-
-    *   [Mythen3] Kernel version compatibility test
-        Fix added to parse properly the kernel version with CET for corrected
-        version compatibility test.
-
-
-    *   [Mythen3] Server crash for setting vthrehsold
-        Fixed.
-
-    
-    *   [Mythen3] Incorrect gaincaps
-        Setting threshold energy was overwriting gaincaps with settings enum. Fixed.
-
-
-    *   [Ctb][Moench] Hostname fail in update mode. 
-        Fixed
-
-
-
-    Changes:
-
-    
-    *   [Jungfrau] Temporary fix for stop in 6.1.1
-        Temporary fix introduced in 6.1.1 for not being able to start after a
-        stop command has been issued is removed. Reset core right after also has
-        been removed. It has been fixed in firmware instead.
-
-
-    *   [Gotthard2] Clock Divider defaults
-        When chancing burst mode, clock dividers (2, 3 and 4) set to their 
-        defaults according to burst mode.
-
-
-    *   [Mythen3] DAC check for settings
-        Verify DAC values for each setting has been temporarily switched off
-
-
-    *   [Mythen3] DAC min and max values
-        Vtrim minimum of 600 has been removed.
-        The threshold dacs minimum is 200 and maximum is 2400.
-        The other DACs minimum is 0 and maximum is 2800.
-        When out of range, will not throw, just a warning.
-
-
-    *   [Mythen3] Vicin Dac changed to 800      
-
-
-    *   [Jungfrau][Moench][Ctb] PLL reset at server start up
-        PLL reset now at server start up.
-
-
-    *   [Moench] ADC9257 Vref
-        ADC Vref voltage modified from 1.33V to 2V
-
-
-
-    *   [Ctb] Allow all clock dividers for PLL
-        Fixed. For example, 133 MHz would not really be set previously. Fixed by
-        changing totaldiv from float to an integer.
-
-
-
-    Additional Features:
-
-    
-    *   Stop server startup errors
-        Stop servers now also check for errors at startup (including version
-        compatibility) and like the control server, it will translate to the 
-        client when connecting for the first time (hostname command).
-
-
-    *   [Jungfrau][Moench][Ctb] Additional server update process
-        Removes old server binary or target of linked file when updating
-        detector server for blackfin detectors as there is less space on blackfin.
-
-        Clearing up absolute and respawn path (removing double '/')
-
-        Raise error if server name to be copied is the same as final soft link name.
-
-
-    *   [Moench][Ctb] 1 GbE Non blocking acquisition
-        Previously non blocking acquisition in 1 GbE would not send data.
-        This feature added now.
-
-
-    *   [Gotthard2] Adapted to new HDI version
-        HDI module ID written to FPGA register
-
-
-
-1.6. Simulator
---------------
-
-
-    *   Command line arguments. Please refer to previous section on Detector Server.
-
-
-    *   [Eiger] Only one executable
-        Only one executable for an Eiger virtual server. Master and top mode
-        can be provided via command line or config file to the detector server,
-        as well as via the client. See in Other New Features for more details.
-
-        One can start a module using:
-            eigerDetectorServer_virtual # reads default config file (top master)
-            eigerDetectorServer_virtual -i #ignores the config file (bottom slave)
-
-
-    *   [Eiger][Junfrau][Gotthard2][Mythen3] Module Id
-        Added into udp header
-
-
-    *   Minimum Configuration
-        One can setup with just:
-            hostname localhost
-            rx_hostname localhost
-            udp_dstip auto
-
-
-    *   [Mythen3] Packet size
-        Fixed packet size calculation. Previously, sending only header with no data.
-
-
-
-1.7. Receiver
--------------
-
-
-    Breaking API:
-
-
-    *   Namespace sls
-        All the receiver source files have also been added to namespace sls.
-
-
-    *   HDF5 and Binary writer version 
-        Changed from 6.3 to 6.4
-
-
-    *   Master file format to json
-        The format has been changed from ASCII to json.
-
-
-    *   Geometry metadata
-        Added geometry (number of modules in each direction) to metadata in file.
-
-
-    *   HDF5 Dataset name
-        Changed to just "data" to simplify for user
-
-
-    *   File write
-        File write is disabled by default.
-
-
-
-    Fixes:
-
-    
-    *   Refactored and fixed minor issues
-        Including memory structure and udp sockets.
-        Fixed progress also in discard partial packaets mode and deactivated ports. 
-        Fixed 200% progress.
-        Completely padded images now have detector type or version in metadata.
-        Fixed getting stuck at stop receiver when using zmq
-        Fixed clang compiler warnings
-
-
-    *   Multiple files
-        This bug was introduced in v6.0.0, where 1 file was created per frame 
-        after the first file. Fixed by resetting the number of frames in 
-        current file when creating a new one.
-
-
-    *   [Eiger] Datastream command order
-        The order of commands to set datastream from client mattered previously.
-        Datastream had to be set before 10GbE enable. Order does not matter anymore.
-
-
-    *   Udp destination MAC
-        If it has been set before, changing udp_dstip will not update udp_dstmac.
-        Fixed to always set it in detector even if it had a value before. 
-        Udp_dstmac can still be used to overwrite again. This is useful when
-        using a router for example.
-
-
-    *   Stuck when using zmq
-        More often in 6.1.1, gets stuck at stop receiver.
-
-
-    *   [Mythen3] Incorrect number of packets calculated or tengiga not set up
-        Runnig config second time (with tengiga=0, dr !=32, counters !=0x7) 
-        calculated incorrect image size expected due to inconsistent copy of
-        detector parameters. Fixed
-
-
-    *   Storage cells in receiver
-        Previously not updated in receiver. Fixed.
-
-
-    *   Virtual HDF5 Parameter datasets
-        Corner case bug when frames caught is not a multiple of frames per file.
-        Not found in virtual image datasets. Fixed.
-
-
-
-    Changes:
-
-
-    *   Master file created at end of acquisition
-        The file is now written at the end of acquisition. So if any metadata
-        is changed during an acquisition, it will reflect the last value.
-
-
-    *   File name prefix
-        Slash '/' not allowed.
-
-
-
-    Additional Features:
-
-
-    *   [Gotthard2] 25um image reconstruction in virtual HDF5
-        Virtual HDF5 reconstructs complete image by interleaving first module 
-        (master) with second module (slave). First channel of master is first
-        channel of detector.
-
-        Requires firmware update to reverse channels of slaves.
-
-
-    *   Memory size
-        Increased an internal fifo header by 8 bytes to align memory allocated for 
-        to receive images for efficiency.
-
-
-
-1.8. Gui
---------
-    
-    *   [Jungfrau][Eiger] Gap pixels
-        Enabled by default in the gui.
-
-
-    *   High voltage moved from Developer tab to Settings tab.
-
-
-    *   Gain plot zooming
-        Zooming disabled. Instead, it automatically zooms in when you zoom in
-        the main plot or if min and max of x and y axis set up in plot tab.
-
-
-    *   [Mythen3] Inconsistent timing mode
-        Timing mode of the slaves should be discarded before squashing. Fixed.
-
-  
-    *   [Mythen3][Gotthard2] Crashes
-        Additional locking Added
-
-
-
-
-2.  On-board Detector Server Compatibility
+2  On-board Detector Server Compatibility
 ==========================================
 
 
-    Eiger       7.0.0
-    Jungfrau    7.0.0
-    Mythen3     7.0.0
-    Gotthard2   7.0.0
-    Gotthard    7.0.0
-    Moench      7.0.0
-    Ctb         7.0.0
+    Eiger       7.0.3
+    Jungfrau    7.0.3
+    Mythen3     7.0.3
+    Gotthard2   7.0.3
+    Gotthard    7.0.3
+    Moench      7.0.3
+    Ctb         7.0.3
     
 
     On-board Detector Server Upgrade
@@ -849,25 +150,25 @@ This document describes the differences between v7.0.0.rc1 and v6.1.2
 
 
 
-3. Firmware Requirements
+3 Firmware Requirements
 ========================
 
 
-    Eiger       17.02.2022 (v30)
+    Eiger       02.10.2023 (v32)                    (updated in 7.0.3)
     
-    Jungfrau    04.11.2022 (v1.4, HW v1.0) 
-                03.11.2022 (v2.4, HW v2.0)
+    Jungfrau    16.05.2023 (v1.4.1, HW v1.0)        (updated in 7.0.2)
+                15.05.2023 (v2.4.1, HW v2.0)        (updated in 7.0.2)
 
-    Mythen3     05.12.2022 (v1.4)
+    Mythen3     24.01.2023 (v1.4)                   (updated in 7.0.0)
 
-    Gotthard2   23.11.2022 (v0.3)
+    Gotthard2   23.11.2022 (v0.3)                   (updated in 7.0.0)
 
     Gotthard    08.02.2018 (50um and 25um Master)
                 09.02.2018 (25 um Slave) 
 
-    Moench      05.12.2022 (v0.3)
+    Moench      05.12.2022 (v0.3)                   (updated in 7.0.0)
 
-    Ctb         05.12.2022 (v1.1)
+    Ctb         05.12.2022 (v1.1)                   (updated in 7.0.0)
 
 
     Detector Upgrade
@@ -898,22 +199,22 @@ This document describes the differences between v7.0.0.rc1 and v6.1.2
 
 
 
-4. Kernel Requirements
+4 Kernel Requirements
 ======================
 
     Blackfin 
-    ========
+    --------
     Latest version: Fri Oct 29 00:00:00 2021
     
     Older ones will work, but might have issues with programming firmware via
     the package.
 
     Nios
-    ====
+    -----
     Compatible version: Mon May 10 18:00:21 CEST 2021
 
     Kernel Upgrade
-    ==============
+    ---------------
     Eiger   via bit files
     Others  via command
 
@@ -926,7 +227,7 @@ This document describes the differences between v7.0.0.rc1 and v6.1.2
 
 
 
-5. Download, Documentation & Support
+5 Download, Documentation & Support
 ====================================
 
     Download
@@ -982,6 +283,9 @@ This document describes the differences between v7.0.0.rc1 and v6.1.2
         https://slsdetectorgroup.github.io/devdoc/udpheader.html
         https://slsdetectorgroup.github.io/devdoc/udpdetspec.html
 
+    slsReceiver Zmq Format:
+        https://slsdetectorgroup.github.io/devdoc/slsreceiver.html#zmq-json-header-format
+
     TroubleShooting:
         https://slsdetectorgroup.github.io/devdoc/troubleshooting.html
         https://slsdetectorgroup.github.io/devdoc/troubleshooting.html#receiver-pc-tuning-options

cmk.sh

@@ -33,7 +33,7 @@ Usage: $0 [-b] [-c] [-d <HDF5 directory>] [e] [g] [-h] [i] [-j <Number of thread
  -c: Clean
  -d: HDF5 Custom Directory
  -e: Debug mode
- -g: Build/Rebuilds only gui
+ -g: Build/Rebuilds gui
  -h: Builds/Rebuilds Cmake files with HDF5 package
  -i: Builds tests
  -j: Number of threads to compile through

conda-recepie/conda_build_config.yaml

@@ -3,6 +3,5 @@ python:
     - 3.9
     - 3.10
     - 3.11
+    - 3.12
     
-numpy: 
-    - 1.17

docs/src/firmware.rst

@@ -116,12 +116,16 @@ Program from console
 
         # Always ensure that the client and server software are of the same release.
 
-        # copies server from tftp folder of pc, links new server to jungfrauDetectorServer, 
+        # copies server, links new server to jungfrauDetectorServer, 
         # removes old server from respawn, sets up new lnked server to respawn
-        # programs fpga,
-        # reboots
+        # programs fpga, reboots
+
+        # v5.0.0 - 6.0.0 (copies server from tftp folder of the pc)
         sls_detector_put update jungfrauDetectorServervxxx pcxxx xx.pof
 
+        # v6.1.1 - present (copies server from the full path provided)
+        sls_detector_put update jungfrauDetectorServervxxx xx.pof
+
         # Or only program firmware
         sls_detector_put programfpga xxx.pof
 
@@ -182,11 +186,16 @@ Program from console
 
         # Always ensure that the client and server software are of the same release.
 
-        # copies server from tftp folder of pc, links new server to mythen3DetectorServer, 
-        # programs fpga,
-        # reboots
+        # copies server, links new server to mythen3DetectorServer, 
+        # removes old server from respawn, sets up new lnked server to respawn
+        # programs fpga, reboots
+
+        # v5.0.0 - 6.0.0 (copies server from tftp folder of the pc)
         sls_detector_put update mythen3DetectorServervxxx pcxxx xxx.rbf
 
+        # v6.1.1 - present (copies server from the full path provided)
+        sls_detector_put update mythen3DetectorServervxxx xxx.rbf
+
         # Or only program firmware
         sls_detector_put programfpga xxx.rbf
 
@@ -211,11 +220,16 @@ Program from console
 
         # Always ensure that the client and server software are of the same release.
         
-        # copies server from tftp folder of pc, links new server to gotthard2DetectorServer, 
-        # programs fpga,
-        # reboots
+        # copies server, links new server to gotthard2DetectorServer, 
+        # removes old server from respawn, sets up new lnked server to respawn
+        # programs fpga, reboots
+
+        # v5.0.0 - 6.0.0 (copies server from tftp folder of the pc)
         sls_detector_put update gotthard2DetectorServervxxx pcxxx xxx.rbf
 
+        # v6.1.1 - present (copies server from the full path provided)
+        sls_detector_put update gotthard2DetectorServervxxx xxx.rbf
+
         # Or only program firmware
         sls_detector_put programfpga xxx.rbf
 
@@ -257,12 +271,16 @@ Program from console
 
         # Always ensure that the client and server software are of the same release.
 
-        # copies server from tftp folder of pc, links new server to moenchDetectorServer, 
+        # copies server, links new server to moenchDetectorServer, 
         # removes old server from respawn, sets up new lnked server to respawn
-        # programs fpga,
-        # reboots
+        # programs fpga, reboots
+
+        # v5.0.0 - 6.0.0 (copies server from tftp folder of the pc)
         sls_detector_put update moenchDetectorServervxxx pcxxx xx.pof
 
+        # v6.1.1 - present (copies server from the full path provided)
+        sls_detector_put update moenchDetectorServervxxx xx.pof
+
         # Or only program firmware
         sls_detector_put programfpga xxx.pof
 
@@ -288,12 +306,16 @@ Program from console
 
         # Always ensure that the client and server software are of the same release.
         
-        # copies server from tftp folder of pc, links new server to ctbDetectorServer, 
+        # copies server, links new server to ctbDetectorServer, 
         # removes old server from respawn, sets up new lnked server to respawn
-        # programs fpga,
-        # reboots
+        # programs fpga, reboots
+
+        # v5.0.0 - 6.0.0 (copies server from tftp folder of the pc)
         sls_detector_put update ctbDetectorServervxxx pcxxx xx.pof
 
+        # v6.1.1 - present (copies server from the full path provided)
+        sls_detector_put update ctbDetectorServervxxx xx.pof
+
         # Or only program firmware
         sls_detector_put programfpga xxx.pof
 

docs/src/installation.rst

@@ -1,14 +1,3 @@
-
-
-
-.. note :: 
-
-    The default branch of our git repository is developer. It contains the 
-    latest development version. It is expected to compile and work but 
-    features might be added or tweaked. In some cases the API might also change
-    without being communicated. If absolute stability of the API is needed please
-    use one of the release versions. 
-
 .. warning ::
     
     Before building from source make sure that you have the 
@@ -161,7 +150,7 @@ Build using in-built cmk.sh script
     -c: Clean
     -d: HDF5 Custom Directory
     -e: Debug mode
-    -g: Build/Rebuilds only gui
+    -g: Build/Rebuilds gui
     -h: Builds/Rebuilds Cmake files with HDF5 package
     -i: Builds tests
     -j: Number of threads to compile through
@@ -178,17 +167,17 @@ Build using in-built cmk.sh script
     -z: Moench zmq processor
 
     
-    # get all options
+    # display all options
     ./cmk.sh -?
 
-    # new build and compile in parallel:
-    ./cmk.sh -bj5
+    # new build and compile in parallel (recommended basic option):
+    ./cmk.sh -cbj5
 
     # new build, python and compile in parallel:
-    ./cmk.sh -bpj5
+    ./cmk.sh -cbpj5
 
     #To use the system zmq (/usr/lib64) instead
-    ./cmk.sh -bj5 -q /usr/lib64
+    ./cmk.sh -cbj5 -q /usr/lib64
 
 
 

docs/src/slsreceiver.rst

@@ -86,6 +86,194 @@ 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
+            },
+            "rx_roi": [
+                unsigned int,
+                unsigned int,
+                unsigned int,
+                unsigned int
+            ]
+        }
+
+   +--------------+----------------------------------------------+
+   |   Field      |       Description                            |
+   +--------------+----------------------------------------------+
+   | jsonversion  | Version of the json header.                  |
+   |              | Value at 4 for v6.x.x - v7.0.1               | 
+   |              | Value at 5 for v7.0.2                        |
+   +--------------+----------------------------------------------+
+   | 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.                         |
+   +--------------+----------------------------------------------+
+   | rx_roi       | ROI in the receiver per port (xmin, xmax,    |
+   |              | ymin, ymax). For external guis to know       |
+   |              | what is saved                                |
+   +--------------+----------------------------------------------+
+
+SLS Receiver Header Format
+--------------------------
+
+It is 112 bytes and consists of:
+    * 48 bytes of the SLS Detector Header (described in :ref:`the current detector header <detector udp header>`)
+    * 64 bytes of packet mask
+
+.. code-block:: cpp 
+    
+    typedef struct {
+        uint64_t frameNumber;
+        uint32_t expLength;
+        uint32_t packetNumber;
+        uint64_t detSpec1;
+        uint64_t timestamp;
+        uint16_t modId;
+        uint16_t row;
+        uint16_t column;
+        uint16_t detSpec2;
+        uint32_t detSpec3;
+        uint16_t detSpec4;
+        uint8_t detType;
+        uint8_t version;
+    } sls_detector_header;
+
+    struct sls_receiver_header {
+        sls_detector_header detHeader; /**< is the detector header */
+        sls_bitset packetsMask;        /**< is the packets caught bit mask */
+    };
+
+
+.. note :: 
+
+    | The packetNumber in the SLS Receiver Header will be modified to number of packets caught by receiver for that frame. For eg. Jungfrau will have 128 packets per frame. If it is less, then this is a partial frame due to missing packets.
+    
+    | Furthermore, the bit mask will specify which packets have been received.
+
+
+
+
 File format
 --------------
 
@@ -117,8 +305,6 @@ Some file name examples:
 Each acquisition will create a master file that can be enabled/disabled using **fmaster**. This should have parameters relevant to the acquisition.
 
 
-SLS Receiver Header consist of SLS Detector Header + 64 bytes of bitmask, altogether 112 bytes. The packetNumber in the sls detector header part, will be updated to number of packets caught by receiver for that frame. Furthermore, the bit mask will specify which packets have been received.
-
 **Binary file format**
 
 This is the default file format. 

docs/src/udpheader.rst

@@ -11,7 +11,7 @@ Current Version
 
 **v2.0 (slsDetectorPackage v7.0.0+)**
 
-.. table:: <---------------------------------------------------- 8 bytes ---------------------------------------------------->
+.. table:: <---------------------------------------------------- 8 bytes per row --------------------------------------------->
     :align: center
     :widths: 30,30,30,15,15
 

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
+

examples/moench03_T1.config

@@ -3,33 +3,34 @@
 ### edit with hostname or IP address of your detector 
 ############################################
 #hostname bchip181+
-hostname bchip135 
+hostname bchip076
 
 #############################################
 ### edit with hostname or 1Gbs IP address of your server
 ############################################
-rx_hostname mpc2011
+rx_hostname mpc2011:7777
 
 #############################################
 ### edit with 10 Gbs IP of your server
 ############################################
-udp_dstip 10.1.1.102
+udp_dstip 10.1.2.102
 #############################################
 ### edit with any number in the subnet of your server (first 3 numbers as above)
 ############################################
-udp_srcip 10.1.1.19
-udp_dstport 32411
+udp_srcip 10.1.2.19
+udp_dstport 32777
+
 
 #############################################
 ### edit with 10 Gbs IP of your server
 ############################################
-rx_zmqip 10.1.1.102
-rx_zmqport 50003
+rx_zmqip 10.1.2.102
+rx_zmqport 9003
 #############################################
 ### edit with 1 Gbs IP of PC where you will run the GUI
 ############################################
 zmqip 129.129.202.57
-zmqport 50001
+zmqport 9005
 
 
 
@@ -38,7 +39,7 @@ rx_zmqstream 1
 
 
 
-frames 100000
+frames 1
 period 0.0006
 exptime 0.00035
 
@@ -49,7 +50,7 @@ fpath /mnt/moench_data/scratch1/
 
 fwrite 0
 
-rx_jsonpara frameMode frame
+rx_jsonpara frameMode newPedestal
 rx_jsonpara detectorMode counting
 rx_discardpolicy discardpartial
 

examples/virtual_ctb_moench.config

@@ -1,18 +1,18 @@
 # detector hostname
 hostname localhost:1910
 
-# receiver hostname
-rx_hostname mpc1922:2010
-
 # udp destination ports
 udp_dstport 50010
 
-# udp destination ip from rx_hostname
-udp_dstip auto
-
 # udp source ip (same subnet as udp_dstip)
 udp_srcip 192.168.1.100
 
+# receiver hostname
+rx_hostname mpc1922:2010
+
+# udp destination ip from rx_hostname
+udp_dstip auto
+
 # output file directory
 fpath /tmp
 
@@ -27,418 +27,7 @@ dbitclk 40
 
 
 # patterns
-patword 0x0000 0x0000000000000000
-patword 0x0001 0x0000000000000000
-patword 0x0002 0x0008000900080000
-patword 0x0003 0x0008000900080000
-patword 0x0004 0x0008000900080000
-patword 0x0005 0x0008000900080000
-patword 0x0006 0x0008000900080000
-patword 0x0007 0x0008000900080000
-patword 0x0008 0x0008000900080000
-patword 0x0009 0x0008000900080000
-patword 0x000a 0x0008000900080000
-patword 0x000b 0x0008000900080000
-patword 0x000c 0x0008000900080000
-patword 0x000d 0x0008000900080000
-patword 0x000e 0x0008000900080000
-patword 0x000f 0x0008000900080000
-patword 0x0010 0x0008000900080000
-patword 0x0011 0x0008000900080000
-patword 0x0012 0x0008000900080000
-patword 0x0013 0x0008000900080000
-patword 0x0014 0x0008000900080000
-patword 0x0015 0x0008000900080000
-patword 0x0016 0x0008400900080020
-patword 0x0017 0x0008400900080020
-patword 0x0018 0x0008599f0418503a
-patword 0x0019 0x0008599f0418503a
-patword 0x001a 0x0108599f0418503a
-patword 0x001b 0x0108599f0418503a
-patword 0x001c 0x0108599f0418503a
-patword 0x001d 0x0108599f0418503a
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-patword 0x0020 0x0108599f0418503a
-patword 0x0021 0x0108599f0418503a
-patword 0x0022 0x0108599f0418503a
-patword 0x0023 0x0108599f0418503a
-patword 0x0024 0x0108599f0418503a
-patword 0x0025 0x0108599f0418503a
-patword 0x0026 0x0108599f0418503a
-patword 0x0027 0x0108599f0418503a
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-patword 0x0029 0x0108599f0418503a
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-patword 0x0032 0x0108599f0418503a
-patword 0x0033 0x0108599f0418503a
-patword 0x0034 0x0108599f0418503a
-patword 0x0035 0x0108599f0418503a
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-patword 0x0039 0x0108599f0418503a
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-patword 0x009c 0x030819960418501a
-patword 0x009d 0x030819960418501a
-patword 0x009e 0x030819960418501a
-patword 0x009f 0x030819960418501a
-patword 0x00a0 0x030819960418501a
-patword 0x00a1 0x030819960418501a
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-patword 0x00aa 0x030819960418501a
-patword 0x00ab 0x030819960418501a
-patword 0x00ac 0x030819960008501a
-patword 0x00ad 0x030819960008501a
-patword 0x00ae 0x030819960008501a
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-patword 0x00cc 0x0308199f0008501a
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-patword 0x00ce 0x0308199f0008501a
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-patword 0x00d0 0x0308199f0008501a
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-patword 0x00d2 0x0308199f0008501a
-patword 0x00d3 0x0308199f0008501a
-patword 0x00d4 0x0308599f0008503a
-patword 0x00d5 0x0308599f0008503a
-patword 0x00d6 0x030c599f000850ba
-patword 0x00d7 0x030c599f000850ba
-patword 0x00d8 0x030c599f000850ba
-patword 0x00d9 0x030c599f000850ba
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-patword 0x00e3 0x030c599f000850ba
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-patword 0x00e6 0x030c599f000850ba
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-patword 0x00e8 0x030c599f000850ba
-patword 0x00e9 0x030c599f000850ba
-patword 0x00ea 0x030c799f010858ba
-patword 0x00eb 0x030c799f010858ba
-patword 0x00ec 0x030c599f000850ba
-patword 0x00ed 0x030c599f000850ba
-patword 0x00ee 0x030c599f000850ba
-patword 0x00ef 0x030c599f000850ba
-patword 0x00f0 0x030c599f000850ba
-patword 0x00f1 0x030c599f000850ba
-patword 0x00f2 0x030c599f000850ba
-patword 0x00f3 0x030c599f000850ba
-patword 0x00f4 0x030c599f000850ba
-patword 0x00f5 0x030c599f000850ba
-patword 0x00f6 0x030c599f000850ba
-patword 0x00f7 0x030c599f000850ba
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-patword 0x00f9 0x030c599f000850ba
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-patword 0x00fb 0x030c599f000850ba
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-patword 0x00fd 0x030c599f000850ba
-patword 0x00fe 0x030c599f000850ba
-patword 0x00ff 0x030c599f000850ba
-patword 0x0100 0x030c599f000850ba
-patword 0x0101 0x030c599f000850ba
-patword 0x0102 0x030c599f400850ba
-patword 0x0103 0x030c599f400850ba
-patword 0x0104 0x030c599f600850ba
-patword 0x0105 0x030c599f400850ba
-patword 0x0106 0x030c599f400850ba
-patword 0x0107 0x030c599f400850ba
-patword 0x0108 0x870c599f682e50ba
-patword 0x0109 0x870c599f482850ba
-patword 0x010a 0x870c599f000e50ba
-patword 0x010b 0x870c599f000850ba
-patword 0x010c 0x870c599f000e50ba
-patword 0x010d 0x870c599f000850ba
-patword 0x010e 0x870c599f000e50ba
-patword 0x010f 0x870c599f000850ba
-patword 0x0110 0x870c599f000e50ba
-patword 0x0111 0x870c599f000850ba
-patword 0x0112 0x870c599f000e50ba
-patword 0x0113 0x870c599f000850ba
-patword 0x0114 0x870c599f000e50ba
-patword 0x0115 0x870c599f000850ba
-patword 0x0116 0x870c599f000e50ba
-patword 0x0117 0x870c599f000850ba
-patword 0x0118 0x870c599f000e50ba
-patword 0x0119 0x870c599f000850ba
-patword 0x011a 0x870c599f000e50ba
-patword 0x011b 0x870c599f000850ba
-patword 0x011c 0x870c599f000e50ba
-patword 0x011d 0x870c599f000850ba
-patword 0x011e 0x870c599f000e50ba
-patword 0x011f 0x870c599f000850ba
-patword 0x0120 0x870c599f000e50ba
-patword 0x0121 0x870c599f000850ba
-patword 0x0122 0x870c599f200e50ba
-patword 0x0123 0x870c599f000850ba
-patword 0x0124 0x870c599f000e50ba
-patword 0x0125 0x870c599f000850ba
-patword 0x0126 0x870c599f000e50ba
-patword 0x0127 0x870c599f000850ba
-patword 0x0128 0x870c599f000e50ba
-patword 0x0129 0x870c599f000850ba
-patword 0x012a 0x870c599f000e50ba
-patword 0x012b 0x870c599f000850ba
-patword 0x012c 0x870c599f000e50ba
-patword 0x012d 0x870c599f000850ba
-patword 0x012e 0x870c599f000e50ba
-patword 0x012f 0x870c599f000850ba
-patword 0x0130 0x870c599f000e50ba
-patword 0x0131 0x870c599f000850ba
-patword 0x0132 0x870c599f000e50ba
-patword 0x0133 0x870c599f000850ba
-patword 0x0134 0x870c599f000e50ba
-patword 0x0135 0x870c599f000850ba
-patword 0x0136 0x870c599f000e50ba
-patword 0x0137 0x870c599f000850ba
-patword 0x0138 0x870c599f000e50ba
-patword 0x0139 0x870c599f000850ba
-patword 0x013a 0x870c599f282e50ba
-patword 0x013b 0x870c599f082850ba
-patword 0x013c 0x870c599f000e50ba
-patword 0x013d 0x870c599f000850ba
-patword 0x013e 0x870c599f000e50ba
-patword 0x013f 0x870c599f000850ba
-patword 0x0140 0x870c599f000e50ba
-patword 0x0141 0x870c599f000850ba
-patword 0x0142 0x870c599f000e50ba
-patword 0x0143 0x870c599f000850ba
-patword 0x0144 0x870c599f000e50ba
-patword 0x0145 0x870c599f000850ba
-patword 0x0146 0x870c599f000e50ba
-patword 0x0147 0x870c599f000850ba
-patword 0x0148 0x870c599f000e50ba
-patword 0x0149 0x870c599f000850ba
-patword 0x014a 0x870c599f000e50ba
-patword 0x014b 0x870c599f000850ba
-patword 0x014c 0x870c599f000e50ba
-patword 0x014d 0x870c599f000850ba
-patword 0x014e 0x870c599f000e50ba
-patword 0x014f 0x870c599f000850ba
-patword 0x0150 0x870c599f000e50ba
-patword 0x0151 0x870c599f000850ba
-patword 0x0152 0x870c599f000e50ba
-patword 0x0153 0x870c599f000850ba
-patword 0x0154 0x870c599f200e50ba
-patword 0x0155 0x870c599f000850ba
-patword 0x0156 0x870c599f000e50ba
-patword 0x0157 0x870c599f000850ba
-patword 0x0158 0x870c599f000e50ba
-patword 0x0159 0x870c599f000850ba
-patword 0x015a 0x870c599f000e50ba
-patword 0x015b 0x870c599f000850ba
-patword 0x015c 0x870c599f000e50ba
-patword 0x015d 0x870c599f000850ba
-patword 0x015e 0x870c599f000e50ba
-patword 0x015f 0x870c599f000850ba
-patword 0x0160 0x870c599f000e50ba
-patword 0x0161 0x870c599f000850ba
-patword 0x0162 0x870c599f000e50ba
-patword 0x0163 0x870c599f000850ba
-patword 0x0164 0x870c599f000e50ba
-patword 0x0165 0x870c599f000850ba
-patword 0x0166 0x870c599f000e50ba
-patword 0x0167 0x870c599f000850ba
-patword 0x0168 0x870c599f000e50ba
-patword 0x0169 0x870c599f000850ba
-patword 0x016a 0x870c599f000e50ba
-patword 0x016b 0x870c599f000850ba
-patword 0x016c 0x070c599f000850ba
-patword 0x016d 0x070c599f000850ba
-patword 0x016e 0x000c599f000850ba
-patword 0x016f 0x000c599f000850ba
-patword 0x0170 0x0008599f200e503a
-patword 0x0171 0x0008599f0008503a
-patword 0x0172 0x0008599f200e503a
-patword 0x0173 0x0008599f0008503a
-patword 0x0174 0x0008599f0008503a
-patword 0x0175 0x0008599f0008503a
-patword 0x0176 0x0008599f0008503a
-patword 0x0177 0x0008599f0008503a
-patword 0x0178 0x0008599f0008503a
-patword 0x0179 0x0008599f0008503a
-patword 0x017a 0x0008599f0008503a
-patword 0x017b 0x0008599f0008503a
-patword 0x017c 0x0008599f0008503a
-patword 0x017d 0x0008599f0008503a
-patword 0x017e 0x0008599f0008503a
-patword 0x017f 0x0008599f0008503a
-patword 0x0180 0x0008599f0008503a
-patword 0x0181 0x0008599f0008503a
-patword 0x0182 0x0008599f0008503a
-patword 0x0183 0x0008599f0008503a
-patword 0x0184 0x0008599f0008503a
-patword 0x0185 0x0008599f0008503a
-patword 0x0186 0x0008599f0008503a
-patword 0x0187 0x0008599f0008503a
-patword 0x0188 0x0008599f0008503a
-patword 0x0189 0x0008599f0008503a
-patword 0x018a 0x0008599f0008503a
-patword 0x018b 0x0008599f0008503a
-patword 0x018c 0x0008599f0008503a
-patword 0x018d 0x0008599f0008503a
-patioctrl 0x8f0effff6dbffdbf
-patlimits 0x0000 0x018c
-patloop 0 0x013a 0x016b
-patnloop 0 0x199
-patloop 1 0x0400 0x0400
-patnloop 1 0
-patloop 2 0x0400 0x0400
-patnloop 2 0
-patwait 0 0x00aa
-patwaittime 0 10000
-patwait 1 0x0400
-patwaittime 1 0
-patwait 2 0x0400
-patwaittime 2 0
+pattern /tmp/pattern.pat
 
 # dacs
 dac 6 800

examples/virtual_eiger_1_half_module.config

@@ -1,13 +1,13 @@
 # detector hostname
 hostname localhost:1900
 
-# receiver hostname
-rx_hostname mpc1922:2000
-
 # udp destination ports
 udp_dstport 50000
 udp_dstport2 50001
 
+# receiver hostname
+rx_hostname mpc1922:2000
+
 # udp destination ip from rx_hostname
 udp_dstip auto
 

examples/virtual_eiger_2_half_modules.config

@@ -1,15 +1,15 @@
 # detector hostname
 hostname localhost:1900+localhost:1902+
 
-# receiver hostname
-rx_hostname mpc1922:2000+mpc1922:2001+
-
 # udp destination ports
 0:udp_dstport 50000
 0:udp_dstport2 50001
 1:udp_dstport 50002
 1:udp_dstport2 50003
 
+# receiver hostname
+rx_hostname mpc1922:2000+mpc1922:2001+
+
 # udp destination ip from rx_hostname
 udp_dstip auto
 

examples/virtual_gotthard.config

@@ -1,18 +1,18 @@
 # detector hostname
 hostname localhost:1904
 
-# receiver hostname
-rx_hostname mpc1922:2004
-
 # udp destination ports
 udp_dstport 50004
 
-# udp destination ip from rx_hostname
-udp_dstip auto
-
 # udp source ip (same subnet as udp_dstip)
 udp_srcip 192.168.1.100
 
+# receiver hostname
+rx_hostname mpc1922:2004
+
+# udp destination ip from rx_hostname
+udp_dstip auto
+
 # output file directory
 fpath /tmp
 

examples/virtual_gotthard2.config

@@ -1,24 +1,12 @@
 # detector hostname
 hostname localhost:1914
 
-# receiver hostname
-rx_hostname mpc1922:2014
-
 # udp destination ports
 udp_dstport 50014
 
-# udp destination ip from rx_hostname
-udp_dstip auto
-
 # udp source ip (same subnet as udp_dstip)
 udp_srcip 192.168.1.100
 
-# output file directory
-fpath /tmp
-
-# disable file writing
-fwrite 0
-
 # enable 2nd interface for veto debugging
 # udp destination port for veto
 udp_dstport2 50015
@@ -27,6 +15,18 @@ udp_dstip2 auto
 # udp source ip (same subnet as udp_dstip)
 udp_srcip2 192.168.1.100
 
+# receiver hostname
+rx_hostname mpc1922:2014
+
+# udp destination ip from rx_hostname
+udp_dstip auto
+
+# output file directory
+fpath /tmp
+
+# disable file writing
+fwrite 0
+
 # to enable 2nd interface for veto debugging
 numinterfaces 2
 

examples/virtual_jungfrau.config

@@ -1,21 +1,21 @@
 # detector hostname
 hostname localhost:1906
 
-# receiver hostname
-rx_hostname mpc1922:2006
-
 # udp destination ports
 udp_dstport 50006
 udp_dstport2 50007
 
-# udp destination ip from rx_hostname
-udp_dstip auto
-udp_dstip2 auto
-
 # udp source ip (same subnet as udp_dstip)
 udp_srcip 192.168.1.100
 udp_srcip2 192.168.1.100
 
+# receiver hostname
+rx_hostname mpc1922:2006
+
+# udp destination ip from rx_hostname
+udp_dstip auto
+udp_dstip2 auto
+
 # output file directory
 fpath /tmp
 

examples/virtual_jungfrau_4.config

@@ -4,13 +4,6 @@ detsize 2048 1024
 # detector hostname
 virtual 4 1952
 
-# receiver hostname and tcpports
-0:rx_tcpport 1970
-1:rx_tcpport 1971
-2:rx_tcpport 1972
-3:rx_tcpport 1973
-rx_hostname mpc1922
-
 # udp destination ports
 0:udp_dstport2 50001
 0:udp_dstport2 50002
@@ -21,14 +14,21 @@ rx_hostname mpc1922
 3:udp_dstport 50007
 3:udp_dstport2 50008
 
-# udp destination ip from rx_hostname
-udp_dstip auto
-udp_dstip2 auto
-
 # udp source ip (same subnet as udp_dstip)
 udp_srcip 192.168.1.100
 udp_srcip2 192.168.1.100
 
+# receiver hostname and tcpports
+0:rx_tcpport 1970
+1:rx_tcpport 1971
+2:rx_tcpport 1972
+3:rx_tcpport 1973
+rx_hostname mpc1922
+
+# udp destination ip from rx_hostname
+udp_dstip auto
+udp_dstip2 auto
+
 # transmission delay frame
 0:txndelay_frame 0
 1:txndelay_frame 1

examples/virtual_moench.config

@@ -1,18 +1,18 @@
 # detector hostname
 hostname localhost:1908
 
-# receiver hostname
-rx_hostname mpc1922:2008
-
 # udp destination ports
 udp_dstport 50008
 
-# udp destination ip from rx_hostname
-udp_dstip auto
-
 # udp source ip (same subnet as udp_dstip)
 udp_srcip 192.168.1.100
 
+# receiver hostname
+rx_hostname mpc1922:2008
+
+# udp destination ip from rx_hostname
+udp_dstip auto
+
 # output file directory
 fpath /tmp
 

examples/virtual_mythen3.config

@@ -1,18 +1,18 @@
 # detector hostname
 hostname localhost:1912
 
-# receiver hostname
-rx_hostname mpc1922:2012
-
 # udp destination ports
 udp_dstport 50012
 
-# udp destination ip from rx_hostname
-udp_dstip auto
-
 # udp source ip (same subnet as udp_dstip)
 udp_srcip 192.168.1.100
 
+# receiver hostname
+rx_hostname mpc1922:2012
+
+# udp destination ip from rx_hostname
+udp_dstip auto
+
 # output file directory
 fpath /tmp
 

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/CMakeLists.txt

@@ -34,6 +34,7 @@ set( PYTHON_FILES
     slsdet/eiger.py
     slsdet/enums.py
     slsdet/errors.py
+    slsdet/gaincaps.py
     slsdet/gotthard.py
     slsdet/pattern.py
     slsdet/gotthard2.py

python/scripts/compare_with_commandline.py

@@ -2,7 +2,7 @@
 # Copyright (C) 2021 Contributors to the SLS Detector Package
 import subprocess
 import locale
-out = subprocess.run(['g', 'list'], stdout = subprocess.PIPE, encoding=locale.getpreferredencoding())
+out = subprocess.run(['sls_detector_get', 'list'], stdout = subprocess.PIPE, encoding=locale.getpreferredencoding())
 cmd = out.stdout.splitlines()
 cmd.pop(0)
 
@@ -99,7 +99,6 @@ intentionally_missing  = [
                         'temp_slowadc',
                         'temp_sodl',
                         'temp_sodr',
-                        'trigger', #use sendSoftwareTrigger
                         'update', #use updateServerAndFirmare
                         'udp_validate', #use validateUdpConfiguration
                         'udp_reconfigure', #use reconfigureUdpDestination

python/slsdet/__init__.py

@@ -11,7 +11,7 @@ from .gotthard2 import Gotthard2
 from .gotthard import Gotthard
 from .moench import Moench
 from .pattern import Pattern, patternParameters
-
+from .gaincaps import Mythen3GainCapsWrapper
 
 import _slsdet
 xy = _slsdet.xy

python/slsdet/defines.py

@@ -26,6 +26,7 @@ SHORT_STR_LENGTH=20
 MAX_PATTERN_LENGTH=0x2000
 MAX_PATTERN_LEVELS=6
 M3_MAX_PATTERN_LEVELS=3
+MAX_NUM_COUNTERS=3
 DEFAULT_STREAMING_TIMER_IN_MS=500
 NUM_RX_THREAD_IDS=9
 MAX_NUM_PACKETS=512

python/slsdet/detector.py

@@ -14,8 +14,9 @@ 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 .gaincaps import Mythen3GainCapsWrapper
 from . import utils as ut
 from .proxy import JsonProxy, SlowAdcProxy, ClkDivProxy, MaxPhaseProxy, ClkFreqProxy, PatLoopProxy, PatNLoopProxy, PatWaitProxy, PatWaitTimeProxy 
 from .registers import Register, Adc_register
@@ -162,12 +163,8 @@ class Detector(CppDetectorApi):
 
     @hostname.setter
     def hostname(self, hostnames):
-        if isinstance(hostnames, str):
-            hostnames = [hostnames]
-        if isinstance(hostnames, list):
-            self.setHostname(hostnames)
-        else:
-            raise ValueError("hostname needs to be string or list of strings")
+        args = hostname_list(hostnames)
+        self.setHostname(args)
 
 
     @property
@@ -235,7 +232,7 @@ class Detector(CppDetectorApi):
         """
         [Jungfrau][Gotthard2][Myhten3][Gotthard][Ctb][Moench] Hardware version of detector.
         """
-        return ut.lhex(self.getHardwareVersion())
+        return self.getHardwareVersion()
 
     @property
     @element
@@ -267,11 +264,17 @@ class Detector(CppDetectorApi):
         """Receiver version """
         return self.getReceiverVersion()
 
+    @property
+    @element
+    def serialnumber(self):
+        """Jungfrau][Gotthard][Mythen3][Gotthard2][CTB][Moench] Serial number of detector """
+        return ut.lhex(self.getSerialNumber())
+
     @property
     @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
         -----
@@ -457,6 +460,56 @@ class Detector(CppDetectorApi):
     def triggers(self, n_triggers):
         self.setNumberOfTriggers(n_triggers)
 
+    def resetdacs(self, use_hardware_values):
+        self.resetToDefaultDacs(use_hardware_values)
+
+    def trigger(self):
+        self.sendSoftwareTrigger()
+
+    def blockingtrigger(self):
+        self.sendSoftwareTrigger(True)
+
+    @property
+    @element
+    def gaincaps(self):
+        """
+        [Mythen3] Gain caps. Enum: M3_GainCaps \n
+        
+        Note
+        ----
+        Options: M3_GainCaps, M3_C15sh, M3_C30sh, M3_C50sh, M3_C225ACsh, M3_C15pre
+
+        Example
+        -------
+        >>> d.gaincaps
+        C15pre, C30sh
+        >>> d.gaincaps = M3_GainCaps.M3_C30sh
+        >>> d.gaincaps
+        C30sh
+        >>> d.gaincaps = M3_GainCaps.M3_C30sh | M3_GainCaps.M3_C15sh
+        >>> d.gaincaps
+        C15sh, C30sh
+        """
+        res = [Mythen3GainCapsWrapper(it) for it in self.getGainCaps()]
+        return res
+
+    @gaincaps.setter
+    def gaincaps(self, caps):
+        #convert to int if called with Wrapper
+        if isinstance(caps, Mythen3GainCapsWrapper):
+            self.setGainCaps(caps.value)
+        elif isinstance(caps, dict):
+            corr = {}
+            for key, value in caps.items():
+                if isinstance(value, Mythen3GainCapsWrapper):
+                    corr[key] = value.value
+                else:
+                    corr[key] = value
+            ut.set_using_dict(self.setGainCaps, corr)
+        else:
+            self.setGainCaps(caps)
+
+
     @property
     def exptime(self):
         """
@@ -504,7 +557,7 @@ class Detector(CppDetectorApi):
 
     @exptime.setter
     def exptime(self, t):
-        if self.type == detectorType.MYTHEN3 and is_iterable(t):
+        if self.type == detectorType.MYTHEN3 and is_iterable(t) and not isinstance(t,dict):
             for i, v in enumerate(t):
                 if isinstance(v, int):
                     v = float(v)
@@ -513,8 +566,6 @@ class Detector(CppDetectorApi):
             ut.set_time_using_dict(self.setExptime, t)
 
 
-
-
     @property
     def period(self):
         """
@@ -653,6 +704,10 @@ class Detector(CppDetectorApi):
         """Start detector acquisition. Status changes to RUNNING or WAITING and automatically returns to idle at the end of acquisition."""
         self.startDetector()
 
+    def clearbusy(self):
+        """If acquisition aborted during acquire command, use this to clear acquiring flag in shared memory before starting next acquisition"""
+        self.clearAcquiringFlag()
+
     def rx_start(self):
         """Starts receiver listener for detector data packets and create a data file (if file write enabled)."""
         self.startReceiver()
@@ -784,7 +839,8 @@ 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 +1624,20 @@ 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 +1663,19 @@ 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):
@@ -1701,6 +1784,11 @@ class Detector(CppDetectorApi):
         """Gets the list of timing modes (timingMode) for this detector."""
         return self.getTimingModeList()
 
+    @property
+    def readoutspeedlist(self):
+        """List of readout speed levels implemented for this detector."""
+        return self.getReadoutSpeedList()
+
     @property
     def templist(self):
         """List of temperature enums (dacIndex) implemented for this detector."""
@@ -1802,14 +1890,17 @@ class Detector(CppDetectorApi):
 
     @property
     def versions(self):
-        return {'type': self.type,
+        version_list = {'type': self.type,
                 'package': self.packageversion, 
                 'client': self.clientversion,
                 'firmware': self.firmwareversion,
                 'detectorserver': self.detectorserverversion,
-                'hardware':self.hardwareversion,
-                'kernel': self.kernelversion,
-                'receiver': self.rx_version}
+                'kernel': self.kernelversion}
+        if self.type != detectorType.EIGER:
+            version_list ['hardware'] = self.hardwareversion
+        if self.use_receiver:
+            version_list ['receiver'] = self.rx_version
+        return version_list
 
     @property
     def virtual(self):
@@ -3098,6 +3189,17 @@ class Detector(CppDetectorApi):
     def dbitclk(self, value):
         ut.set_using_dict(self.setDBITClock, value)
 
+    @property
+    @element
+    def adcvpp(self):
+        """[Ctb][Moench] Vpp of ADC. [0 -> 1V | 1 -> 1.14V | 2 -> 1.33V | 3 -> 1.6V | 4 -> 2V] \n
+            Advanced User function!"""
+        return self.getADCVpp(False)
+
+    @adcvpp.setter
+    def adcvpp(self, value):
+        ut.set_using_dict(self.setADCVpp, value, False)
+
     @property
     @element
     def dbitpipeline(self):
@@ -3708,6 +3810,23 @@ class Detector(CppDetectorApi):
         """
         return self.getMeasuredCurrent(dacIndex.I_POWER_IO)
 
+    @property
+    def clkphase(self):
+        """
+        [Gotthard2][Mythen3] Phase shift of all clocks.
+        
+        Example
+        -------
+        >>> d.clkphase[0] = 20
+        >>> d.clkphase
+        0: 20
+        1: 10
+        2: 20
+        3: 10
+        4: 10
+        5: 5
+        """
+        return ClkPhaseProxy(self)
 
     @property
     def clkdiv(self):

python/slsdet/gaincaps.py

@@ -0,0 +1,42 @@
+
+
+import _slsdet
+gc = _slsdet.slsDetectorDefs.M3_GainCaps
+
+
+class Mythen3GainCapsWrapper:
+    """Holds M3_GainCaps enums and facilitates printing"""
+    # 'M3_C10pre', 'M3_C15pre', 'M3_C15sh', 'M3_C225ACsh', 'M3_C30sh', 'M3_C50sh'
+    all_bits = gc.M3_C10pre | gc.M3_C15pre | gc.M3_C15sh | gc.M3_C225ACsh | gc.M3_C30sh | gc.M3_C50sh
+    all_caps = (gc.M3_C10pre, gc.M3_C15pre, gc.M3_C15sh, gc.M3_C225ACsh, gc.M3_C30sh, gc.M3_C50sh)
+    def __init__(self, value = 0):
+        self._validate(value)
+        self.value = value
+
+
+    def __eq__(self, other) -> bool:
+        if isinstance(other, Mythen3GainCapsWrapper):
+            return self.value == other.value
+        else:
+            return self.value == other
+
+    
+    def __ne__(self, other) -> bool:
+        return not self.__eq__(other)
+
+    def __str__(self) -> str:
+        s = ', '.join(str(c).rsplit('_', 1)[1] for c in self.all_caps if self.value & c)
+        return s
+    
+    def __repr__(self) -> str:
+        return self.__str__()
+    
+    def _validate(self, value):
+        """Check that only bits representing real capacitors are set"""
+        if isinstance(value, gc):
+            return True
+        elif isinstance(value, int):
+            if value & (~self.all_bits):
+                raise ValueError(f"The value: {value} is not allowed for Mythen3GainCapsWrapper")
+        else:
+            raise ValueError("GainCaps can only be initialized from int or M3_GainCaps enum")

python/slsdet/mythen3.py

@@ -13,6 +13,7 @@ from .detector import Detector, freeze
 from .dacs import DetectorDacs
 import _slsdet
 dacIndex = _slsdet.slsDetectorDefs.dacIndex
+gc_enums = _slsdet.slsDetectorDefs.M3_GainCaps
 from .detector_property import DetectorProperty
 
 
@@ -62,4 +63,6 @@ class Mythen3(Detector):
     
     @property
     def dacs(self):
-        return self._dacs
+        return self._dacs
+    
+

python/slsdet/proxy.py

@@ -4,6 +4,7 @@ from .utils import element_if_equal
 from .enums import dacIndex
 from .defines import M3_MAX_PATTERN_LEVELS, MAX_PATTERN_LEVELS
 from _slsdet import slsDetectorDefs
+detectorType = slsDetectorDefs.detectorType
 
 
 def set_proxy_using_dict(func, key, value, unpack = False):
@@ -87,7 +88,10 @@ class ClkDivProxy:
 
     def __repr__(self):
         rstr = ''
-        for i in range(6):
+        num_clocks = 6
+        if self.det.type == detectorType.MYTHEN3:
+            num_clocks = 5
+        for i in range(num_clocks):
             r = element_if_equal(self.__getitem__(i))
             if isinstance(r, list):
                 rstr += ' '.join(f'{item}' for item in r)
@@ -96,10 +100,35 @@ class ClkDivProxy:
         
         return rstr.strip('\n')
 
+class ClkPhaseProxy:
+    """
+    Proxy class to allow for more intuitive reading clock phase
+    """
+    def __init__(self, det):
+        self.det = det
+
+    def __getitem__(self, key):
+        return element_if_equal(self.det.getClockPhase(key))
+
+    def __setitem__(self, key, value):
+        set_proxy_using_dict(self.det.setClockPhase, key, value)
+
+    def __repr__(self):
+        rstr = ''
+        if self.det.type == detectorType.MYTHEN3:
+            num_clocks = 5
+        for i in range(num_clocks):
+            r = element_if_equal(self.__getitem__(i))
+            if isinstance(r, list):
+                rstr += ' '.join(f'{item}' for item in r)
+            else:
+                rstr += f'{i}: {r}\n'
+        
+        return rstr.strip('\n')
 
 class MaxPhaseProxy:
     """
-    Proxy class to allow for more intuitive reading clockdivider
+    Proxy class to allow for more intuitive reading max clock phase shift
     """
     def __init__(self, det):
         self.det = det
@@ -109,7 +138,9 @@ class MaxPhaseProxy:
 
     def __repr__(self):
         rstr = ''
-        for i in range(5):
+        if self.det.type == detectorType.MYTHEN3:
+            num_clocks = 5
+        for i in range(num_clocks):
             r = element_if_equal(self.__getitem__(i))
             if isinstance(r, list):
                 rstr += ' '.join(f'{item}' for item in r)
@@ -120,7 +151,7 @@ class MaxPhaseProxy:
 
 class ClkFreqProxy:
     """
-    Proxy class to allow for more intuitive reading clockdivider
+    Proxy class to allow for more intuitive reading clock frequency
     """
     def __init__(self, det):
         self.det = det
@@ -130,7 +161,9 @@ class ClkFreqProxy:
 
     def __repr__(self):
         rstr = ''
-        for i in range(5):
+        if self.det.type == detectorType.MYTHEN3:
+            num_clocks = 5
+        for i in range(num_clocks):
             r = element_if_equal(self.__getitem__(i))
             if isinstance(r, list):
                 rstr += ' '.join(f'{item}' for item in r)

python/slsdet/utils.py

@@ -260,4 +260,21 @@ def merge_args(*args):
         return (ret,)
 
     else:
-        raise ValueError("Multiple dictionaries passes cannot merge args")
+        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_m3gaincaps.py

@@ -0,0 +1,24 @@
+import pytest
+
+from slsdet import Mythen3GainCapsWrapper
+from slsdet.enums import M3_GainCaps #this is the c++ enum
+
+
+def test_comapre_with_int():
+    c = Mythen3GainCapsWrapper(128) #C10pre
+    assert c == 128
+    assert c != 5
+    assert c != 1280
+
+def test_compare_with_other():
+    a = Mythen3GainCapsWrapper(128)
+    b = Mythen3GainCapsWrapper(1<<10)
+    c = Mythen3GainCapsWrapper(128)
+    assert a!=b
+    assert (a==b) == False
+    assert a==c
+
+def test_can_be_default_constructed():
+    c = Mythen3GainCapsWrapper() 
+    assert c == 0
+

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
 
@@ -341,4 +351,33 @@ def test_merge_args_tuple():
     assert merge_args(*("a", "b"), 5) == ("a", "b", 5)
 
 def test_merge_args_dict_with_tuple():
-    assert merge_args({0: (1,2)}, 3) == ({0: (1,2,3)},)
+    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/ctbDetectorServerv7.0.3

@@ -0,0 +1 @@
+../slsDetectorServers/ctbDetectorServer/bin/ctbDetectorServerv7.0.3

serverBin/eigerDetectorServerv7.0.0.rc1

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

serverBin/eigerDetectorServerv7.0.3

@@ -0,0 +1 @@
+../slsDetectorServers/eigerDetectorServer/bin/eigerDetectorServerv7.0.3

serverBin/gotthard2DetectorServerv7.0.0.rc1

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

serverBin/gotthard2DetectorServerv7.0.3

@@ -0,0 +1 @@
+../slsDetectorServers/gotthard2DetectorServer/bin/gotthard2DetectorServerv7.0.3

serverBin/gotthardDetectorServerv7.0.0.rc1

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

serverBin/gotthardDetectorServerv7.0.3

@@ -0,0 +1 @@
+../slsDetectorServers/gotthardDetectorServer/bin/gotthardDetectorServerv7.0.3

serverBin/jungfrauDetectorServerv7.0.0.rc1

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

serverBin/jungfrauDetectorServerv7.0.3

@@ -0,0 +1 @@
+../slsDetectorServers/jungfrauDetectorServer/bin/jungfrauDetectorServerv7.0.3

serverBin/moenchDetectorServerv7.0.0.rc1

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

serverBin/moenchDetectorServerv7.0.3

@@ -0,0 +1 @@
+../slsDetectorServers/moenchDetectorServer/bin/moenchDetectorServerv7.0.3

serverBin/mythen3DetectorServerv7.0.0.rc1

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

serverBin/mythen3DetectorServerv7.0.3

@@ -0,0 +1 @@
+../slsDetectorServers/mythen3DetectorServer/bin/mythen3DetectorServerv7.0.3

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/dataStructures/moench03T1ReceiverDataNew.h

@@ -42,7 +42,7 @@ class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
     int sc_width;
     int sc_height;
     const int nSamples;
-
+    int headerSize;
     double ghost[200][25];
 
     // Single point of definition if we need to customize
@@ -62,7 +62,7 @@ class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
     moench03T1ReceiverDataNew(int ns = 5000)
         : slsDetectorData<uint16_t>(400, 400, ns * 2 * 32 + sizeof(header)),
           nSamples(ns) {
-
+	    headerSize=112;
         int nadc = 32;
         int sc_width = 25;
         int sc_height = 200;
@@ -250,13 +250,22 @@ class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
     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);
-                return data;
-            }
-        }
+        if (filebin.is_open()) { 
+	    
+	  if (filebin.read(data, headerSize)) {
+	    ff = getFrameNumber(data);
+	    np = getPacketNumber(data);
+	    if (np>0)
+	      filebin.read(data+headerSize, dataSize-headerSize);
+	    return data;
+	  }
+	  /* if (filebin.read(data, dataSize)) { */
+	  /*   ff = getFrameNumber(data); */
+	  /*   np = getPacketNumber(data); */
+	  /*   return data; */
+	  /* } */
+	}
+    
         return nullptr;
     }
 

slsDetectorCalibration/interpolations/etaInterpolationGlobal.h

@@ -13,22 +13,7 @@ class etaInterpolationGlobal : public etaInterpolationBase {
 
     virtual void prepareInterpolation(int &ok) {
         ok = 1;
-#ifdef MYROOT1
-        if (hhx)
-            delete hhx;
-        if (hhy)
-            delete hhy;
 
-        hhx = new TH2D("hhx", "hhx", heta->GetNbinsX(),
-                       heta->GetXaxis()->GetXmin(), heta->GetXaxis()->GetXmax(),
-                       heta->GetNbinsY(), heta->GetYaxis()->GetXmin(),
-                       heta->GetYaxis()->GetXmax());
-        hhy = new TH2D("hhy", "hhy", heta->GetNbinsX(),
-                       heta->GetXaxis()->GetXmin(), heta->GetXaxis()->GetXmax(),
-                       heta->GetNbinsY(), heta->GetYaxis()->GetXmin(),
-                       heta->GetYaxis()->GetXmax());
-
-#endif
 
         ///*Eta Distribution Rebinning*///
         double bsize = 1. / nSubPixels; // precision

slsDetectorCalibration/interpolations/slsInterpolation.h

@@ -357,6 +357,16 @@ class slsInterpolation {
             }
         }
 
+	/* cout << "(((" << totquad << "\t" << corner << endl; */
+	/* for (int iy=0; iy<3; iy++) { */
+	/*   for (int ix=0; ix<3; ix++)  */
+	/*     cout << cl[ix+iy*3] <<"\t"; */
+	/*   cout << endl; */
+
+	/* } */
+
+	/* cout << ")))" <<  endl; */
+
         return corner;
     }
 
@@ -370,6 +380,10 @@ class slsInterpolation {
             etax = r / totquad;
             etay = t / totquad;
         }
+	/* cout << "************" << endl; */
+	/* cout << sDum[0][0]<< "\t"<<sDum[0][1] << endl << sDum[1][0]<< "\t"<<sDum[1][1] << endl;  */
+	/* cout << "***************" <<endl; */
+	/* cout << etax << " " << etay << endl; */
         return 0;
     }
 

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
- #moenchZmqProcessCtbGui
+all:  jungfrauZmqProcess 
+ #jungfrauZmqProcessCtbGui
 
-moenchZmqProcess:  moenchZmqProcess.cpp   clean
-		      g++ -o moenchZmqProcess  moenchZmqProcess.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
+jungfrauZmqProcess:  jungfrauZmqProcess.cpp   clean
+		      g++ -o jungfrauZmqProcess  jungfrauZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP
 
 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;

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, 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
+	
+		
+		/*	cl.print();
+		cout << "(" << etax <<","<< etay <<")"<< quad<< endl;
+		*/
+		//#endif
 
-      if (sum > cmin && totquad / sum > 0.8 && totquad / sum < 1.2 &&
-                    sum < cmax) {
-                    nph++;
+		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

@@ -304,18 +304,38 @@ int main(int argc, char *argv[]) {
     int ifile = 0;
 
     mt->setFrameMode(eFrame);
+    int filelist=0;
+    ifstream flist;
+    flist.open (fformat, std::ifstream::in);
+    if (flist.is_open()) {
+      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);
+	if (flist.is_open()) {
+	  flist.getline(ffname,10000);
+	  cout << "file list " << ffname << endl;
+	} else {
+	  sprintf(ffname,(const char*)fformat,irun);
+	  cout << "loop " << ffname << endl;
+	}
+	cout << "ffname "<<ffname << endl;
+        sprintf(fname,  "%s/%s.raw",indir,ffname);
+        sprintf(imgfname,  "%s/%s.tiff",outdir,ffname);
+        sprintf(cfname,  "%s/%s.clust",outdir,ffname);
         cout << fname << " ";
-        cout << imgfname << endl;
+        cout << imgfname << " " << cfname << endl;
         std::time(&end_time);
         cout << std::ctime(&end_time) << endl;
         //  cout <<  fname << " " << outfname << " " << imgfname <<  endl;
@@ -349,13 +369,15 @@ int main(int argc, char *argv[]) {
                     mt->popFree(buff);
 
                     ifr++;
-		    if (ifr % 100 == 0)
+		    if (ifr % 10000 == 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);
+
+			  sprintf(imgfname,  "%s/%s_f%05d.tiff",outdir,ffname,ifile);
+
+			    while (mt->isBusy()) 
+			      ;
                             mt->writeImage(imgfname, thr1);
                             mt->clearImage();
                             ifile++;
@@ -374,13 +396,13 @@ 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,ffname,ifile);
                 } else {
-                    sprintf(ffname, "%s/%s.tiff", outdir, fformat);
-                    sprintf(imgfname, (const char*)ffname, irun);
+		  sprintf(imgfname,  "%s/%s_f%05d.tiff",outdir,ffname,ifile);
                 }
                 cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
+		while (mt->isBusy()) 
+		  ;
                 mt->writeImage(imgfname, thr1);
                 mt->clearImage();
                 if (of) {
@@ -395,11 +417,12 @@ 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(imgfname,  "%s/%s_tot.tiff",outdir,ffname);
+      cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
+      mt->writeImage(imgfname, thr1);
+    }
+    if (flist.is_open()) {
+      flist.close();
     }
-
     return 0;
 }

slsDetectorCalibration/moenchExecutables/moenchZmqProcess.cpp

@@ -720,6 +720,22 @@ int main(int argc, char *argv[]) {
                     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;
+            }
+
             cprintf(MAGENTA, "%d %d %d %d\n", xmin, xmax, ymin, ymax);
             mt->setROI(xmin, xmax, ymin, ymax);
             if (addJsonHeader.find("dynamicRange") != addJsonHeader.end()) {

slsDetectorCalibration/singlePhotonDetector.h

@@ -533,7 +533,7 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
 		      (clusters + nph)->print();
 		      cout << max << " " <<  val[iy * nx + ix] << endl;
 		    }
-                    good = 1;
+                    //good = 1;
                     if (eMin > 0 && tot < eMin)
                         good = 0;
                     if (eMax > 0 && tot > eMax)
@@ -542,7 +542,7 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
                         nph++;
                         image[iy * nx + ix]++;
                     }
-
+		    good=1;
                 } else if (ee == PEDESTAL) {
                     addToPedestal(data, ix, iy, cm);
                 } /*else {

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 +68,6 @@ class qDrawPlot : public QWidget, private Ui::PlotObject {
     void Zoom1DGainPlot(const QRectF &rect);
     void Zoom2DGainPlot(const QRectF &rect);
     void SetSaveFileName(QString val);
-    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/qDrawPlot.cpp

@@ -193,6 +193,7 @@ void qDrawPlot::SetupPlots() {
     gainplot2d = new SlsQt2DPlot(boxPlot, true);
     gainplot2d->SetData(nPixelsX, -0.5, nPixelsX - 0.5, nPixelsY, -0.5,
                         nPixelsY - 0.5, gainData);
+    gainplot2d->Update();
     gainplot2d->hide();
     connect(plot2d, SIGNAL(PlotZoomedSignal(const QRectF &)), this,
             SLOT(Zoom2DGainPlot(const QRectF &)));
@@ -1009,6 +1010,7 @@ void qDrawPlot::Update2dPlot() {
     if (isGainDataExtracted) {
         gainplot2d->SetData(nPixelsX, -0.5, nPixelsX - 0.5, nPixelsY, -0.5,
                             nPixelsY - 0.5, gainData);
+        gainplot2d->Update();
         if (!gainplot2d->isVisible()) {
             gainplot2d->setFixedWidth(plot2d->width() /
                                       qDefs::DATA_GAIN_PLOT_RATIO);

slsDetectorGui/src/qTabDataOutput.cpp

@@ -182,8 +182,10 @@ void qTabDataOutput::BrowseOutputDir() {
     LOG(logDEBUG) << "Browsing output directory";
     QString directory = QFileDialog::getExistingDirectory(
         this, tr("Choose Output Directory "), dispOutputDir->text());
-    if (!directory.isEmpty())
+    if (!directory.isEmpty()) {
         dispOutputDir->setText(directory);
+        ForceSetOutputDir();
+    }
 }
 
 void qTabDataOutput::SetOutputDir(bool force) {

slsDetectorGui/src/qTabMeasurement.cpp

@@ -849,8 +849,9 @@ void qTabMeasurement::GetNextFrameNumber() {
             "Inconsistent starting frame number for all detectors.");
         spinNextFrameNumber->setValue(retval);
     }
-    CATCH_DISPLAY("Could not get starting frame number.",
-                  "qTabMeasurement::GetNextFrameNumber")
+    CATCH_HANDLE("Could not get starting frame number.",
+                 "qTabMeasurement::GetNextFrameNumber", spinNextFrameNumber,
+                 &QSpinBox::setValue, -1)
     connect(spinNextFrameNumber, SIGNAL(valueChanged(int)), this,
             SLOT(SetNextFrameNumber(int)));
 }

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);

slsDetectorGui/src/qTabSettings.cpp

@@ -132,7 +132,7 @@ void qTabSettings::SetupWidgetWindow() {
 }
 
 void qTabSettings::SetExportMode(bool exportMode) {
-    if (comboGainMode->isVisible()) {
+    if (comboGainMode->isEnabled()) {
         ShowFixG0(exportMode);
     }
 }

slsDetectorServers/compileAllServers.sh

@@ -3,12 +3,12 @@
 
 # empty branch = developer branch in updateAPIVersion.sh
 branch=""
-det_list=("ctbDetectorServer" 
-	"gotthardDetectorServer" 
-	"gotthard2DetectorServer"
-	"jungfrauDetectorServer"
-	"mythen3DetectorServer"
-	"moenchDetectorServer"
+det_list=("ctbDetectorServer  
+	gotthardDetectorServer  
+	gotthard2DetectorServer 
+	jungfrauDetectorServer 
+	mythen3DetectorServer 
+	moenchDetectorServer" 
 	)
 usage="\nUsage: compileAllServers.sh [server|all(opt)] [branch(opt)]. \n\tNo arguments mean all servers with 'developer' branch. \n\tNo 'branch' input means 'developer branch'"
 
@@ -25,9 +25,11 @@ elif [ $# -eq 1 ] || [ $# -eq 2 ]; then
 	else
 		# only one server
 		# arg not in list
-		if [[ $det_list != *$1* ]]; then
+		echo $det_list | grep -w -q $1
+		#if [[ $det_list != *$1* ]]; then
+		if ! [[ $? ]] ; then
 			echo -e "Invalid argument 1: $1. $usage"
-			return -1
+			return 1
 		fi
 		declare -a det=("${1}")
 		#echo "Compiling only $1"
@@ -37,14 +39,14 @@ elif [ $# -eq 1 ] || [ $# -eq 2 ]; then
 		# arg in list
 		if [[ $det_list == *$2* ]]; then
 			echo -e "Invalid argument 2: $2. $usage"
-			return -1
+			return 1
 		fi
 		branch+=$2
 		#echo "with branch $branch"
 	fi
 else
 	echo -e "Too many arguments.$usage"
-	return -1
+	return 1
 fi
 
 declare -a deterror=("OK" "OK" "OK" "OK" "OK" "OK")

slsDetectorServers/ctbDetectorServer/slsDetectorFunctionList.c

@@ -99,7 +99,7 @@ void basictests() {
 #endif
     if (mapCSP0() == FAIL) {
         strcpy(initErrorMessage,
-               "Could not map to memory. Dangerous to continue.\n");
+               "Could not map to memory. Cannot proceed. Check Firmware.\n");
         LOG(logERROR, (initErrorMessage));
         initError = FAIL;
         return;
@@ -109,8 +109,10 @@ void basictests() {
     if ((!debugflag) && (!updateFlag) &&
         ((checkType() == FAIL) || (testFpga() == FAIL) ||
          (testBus() == FAIL))) {
-        strcpy(initErrorMessage, "Could not pass basic tests of FPGA and bus. "
-                                 "Dangerous to continue.\n");
+        sprintf(initErrorMessage,
+                "Could not pass basic tests of FPGA and bus. Cannot proceed. "
+                "Check Firmware. (Firmware version:0x%llx) \n",
+                getFirmwareVersion());
         LOG(logERROR, ("%s\n\n", initErrorMessage));
         initError = FAIL;
         return;
@@ -446,7 +448,7 @@ void initStopServer() {
         if (mapCSP0() == FAIL) {
             initError = FAIL;
             strcpy(initErrorMessage,
-                   "Stop Server: Map Fail. Dangerous to continue. Goodbye!\n");
+                   "Stop Server: Map Fail. Cannot proceed. Check Firmware.\n");
             LOG(logERROR, (initErrorMessage));
             initCheckDone = 1;
             return;

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,
-                ("Writing 0x%x to %s 0x%x\n", data, side[iloop], actualOffset));
-            if (!Feb_Interface_WriteRegister(addr[iloop], actualOffset, data, 0,
-                                             0)) {
-                LOG(logERROR, ("Could not write 0x%x to %s addr 0x%x\n", data,
+            LOG(logDEBUG1, ("Writing 0x%x to %s 0x%x (mask:0x%x)\n", data,
+                            side[iloop], actualOffset, bitmask));
+
+            uint32_t writeVal = 0;
+            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;
-            if (!Feb_Interface_ReadRegister(addr[iloop], actualOffset,
-                                            &regVal)) {
-                LOG(logERROR, ("Could not read %s register\n", addr[iloop]));
+            // set only the bits in the mask
+            writeVal &= ~(bitmask);
+            writeVal |= (data & bitmask);
+
+            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",
-                     addr[iloop], data, regVal));
+                    ("Could not write %s addr 0x%x register. Wrote "
+                     "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],
-                            side[iloop], actualOffset));
+            value[iloop] &= bitmask;
+            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 (!Beb_SetUpTransferParameters(dr)) {
-            LOG(logERROR, ("Could not set bit mode in the back end\n"));
-            sharedMemory_unlockLocalLink();
-            return eiger_dynamicrange;
-        }
+    if (!Feb_Control_SetDynamicRange(dr)) {
+        LOG(logERROR, ("Could not set dynamic range in feb\n"));
+        sharedMemory_unlockLocalLink();
+        return FAIL;
+    }
+    if (!Beb_SetUpTransferParameters(dr)) {
+        LOG(logERROR, ("Could not set bit mode in the back end\n"));
+        sharedMemory_unlockLocalLink();
+        return eiger_dynamicrange;
     }
     sharedMemory_unlockLocalLink();
 #endif
@@ -1454,6 +1457,12 @@ int setHighVoltage(int val) {
             sharedMemory_unlockLocalLink();
             return -3;
         }
+        // need to read the file twice to get the proper value
+        if (!Feb_Control_GetHighVoltage(&eiger_highvoltage)) {
+            LOG(logERROR, ("Could not read high voltage\n"));
+            sharedMemory_unlockLocalLink();
+            return -3;
+        }
         sharedMemory_unlockLocalLink();
 
         // tolerance of 5
@@ -2664,6 +2673,10 @@ 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 +2685,11 @@ 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

@@ -5,7 +5,7 @@
 
 #define LINKED_SERVER_NAME "eigerDetectorServer"
 
-#define REQUIRED_FIRMWARE_VERSION (30)
+#define REQUIRED_FIRMWARE_VERSION (32)
 // virtual ones renamed for consistency
 // real ones keep previous name for compatibility (already in production)
 #ifdef VIRTUAL
@@ -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/gotthard2DetectorServer/slsDetectorFunctionList.c

@@ -93,7 +93,7 @@ void basictests() {
 #endif
     if (mapCSP0() == FAIL) {
         strcpy(initErrorMessage,
-               "Could not map to memory. Dangerous to continue.\n");
+               "Could not map to memory. Cannot proceed. Check Firmware.\n");
         LOG(logERROR, (initErrorMessage));
         initError = FAIL;
         return;
@@ -105,8 +105,8 @@ void basictests() {
          (checkType() == FAIL) || (testFpga() == FAIL) ||
          (testBus() == FAIL))) {
         sprintf(initErrorMessage,
-                "Could not pass basic tests of FPGA and bus. Dangerous to "
-                "continue. (Firmware version:0x%llx) \n",
+                "Could not pass basic tests of FPGA and bus. Cannot proceed. "
+                "Check Firmware. (Firmware version:0x%llx) \n",
                 getFirmwareVersion());
         LOG(logERROR, ("%s\n\n", initErrorMessage));
         initError = FAIL;
@@ -396,7 +396,7 @@ void initStopServer() {
         if (mapCSP0() == FAIL) {
             initError = FAIL;
             strcpy(initErrorMessage,
-                   "Stop Server: Map Fail. Dangerous to continue. Goodbye!\n");
+                   "Stop Server: Map Fail. Cannot proceed. Check Firmware.\n");
             LOG(logERROR, (initErrorMessage));
             initCheckDone = 1;
             return;
@@ -3323,6 +3323,27 @@ void *start_timer(void *arg) {
                 break;
             }
 
+            // change gain and data for every frame
+            {
+                const int nchannels = NCHIP * NCHAN;
+                int gainVal = 0;
+                for (int i = 0; i < nchannels; ++i) {
+                    if ((i % nchannels) < 400) {
+                        gainVal = 1 + frameNr;
+                    } else if ((i % nchannels) < 800) {
+                        gainVal = 2 + frameNr;
+                    } else {
+                        gainVal = 3 + frameNr;
+                    }
+                    int dataVal =
+                        *((uint16_t *)(imageData + i * sizeof(uint16_t)));
+                    dataVal += frameNr;
+                    int channelVal =
+                        (dataVal & ~GAIN_VAL_MSK) | (gainVal << GAIN_VAL_OFST);
+                    *((uint16_t *)(imageData + i * sizeof(uint16_t))) =
+                        (uint16_t)channelVal;
+                }
+            }
             // sleep for exposure time
             struct timespec begin, end;
             clock_gettime(CLOCK_REALTIME, &begin);

slsDetectorServers/gotthardDetectorServer/slsDetectorFunctionList.c

@@ -87,7 +87,7 @@ void basictests() {
 #endif
     if (mapCSP0() == FAIL) {
         strcpy(initErrorMessage,
-               "Could not map to memory. Dangerous to continue.\n");
+               "Could not map to memory. Cannot proceed. Check Firmware.\n");
         LOG(logERROR, (initErrorMessage));
         initError = FAIL;
     }
@@ -97,7 +97,7 @@ void basictests() {
         ((checkType() == FAIL) || (testFpga() == FAIL) ||
          (testBus() == FAIL))) {
         strcpy(initErrorMessage, "Could not pass basic tests of FPGA and bus. "
-                                 "Dangerous to continue.\n");
+                                 "Cannot proceed. Check Firmware.\n");
         LOG(logERROR, ("%s\n\n", initErrorMessage));
         initError = FAIL;
         return;
@@ -381,7 +381,7 @@ void initStopServer() {
         if (mapCSP0() == FAIL) {
             initError = FAIL;
             strcpy(initErrorMessage,
-                   "Stop Server: Map Fail. Dangerous to continue. Goodbye!\n");
+                   "Stop Server: Map Fail. Cannot proceed. Check Firmware.\n");
             LOG(logERROR, (initErrorMessage));
             initCheckDone = 1;
             return;
@@ -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/jungfrauDetectorServer/slsDetectorFunctionList.c

@@ -82,7 +82,7 @@ void basictests() {
 #endif
     if (mapCSP0() == FAIL) {
         strcpy(initErrorMessage,
-               "Could not map to memory. Dangerous to continue.\n");
+               "Could not map to memory. Cannot proceed. Check Firmware.\n");
         LOG(logERROR, (initErrorMessage));
         initError = FAIL;
     }
@@ -91,8 +91,10 @@ void basictests() {
     if ((!debugflag) && (!updateFlag) &&
         ((checkType() == FAIL) || (testFpga() == FAIL) ||
          (testBus() == FAIL))) {
-        strcpy(initErrorMessage, "Could not pass basic tests of FPGA and bus. "
-                                 "Dangerous to continue.\n");
+        sprintf(initErrorMessage,
+                "Could not pass basic tests of FPGA and bus. Cannot proceed. "
+                "Check Firmware. (Firmware version:0x%llx) \n",
+                getFirmwareVersion());
         LOG(logERROR, ("%s\n\n", initErrorMessage));
         initError = FAIL;
         return;
@@ -428,7 +430,7 @@ void initStopServer() {
         if (mapCSP0() == FAIL) {
             initError = FAIL;
             strcpy(initErrorMessage,
-                   "Stop Server: Map Fail. Dangerous to continue. Goodbye!\n");
+                   "Stop Server: Map Fail. Cannot proceed. Check Firmware.\n");
             LOG(logERROR, (initErrorMessage));
             initCheckDone = 1;
             return;
@@ -1386,14 +1388,18 @@ int setMaster(enum MASTERINDEX m) {
     char *master_names[] = {MASTER_NAMES};
     LOG(logINFOBLUE, ("Setting up as %s in (%s server)\n", master_names[m],
                       (isControlServer ? "control" : "stop")));
+
+    int prevSync = getSynchronization();
+    setSynchronization(0);
     int retval = -1;
+    int retMaster = OK;
     switch (m) {
     case OW_MASTER:
         bus_w(CONTROL_REG, bus_r(CONTROL_REG) | CONTROL_MASTER_MSK);
         isMaster(&retval);
         if (retval != 1) {
             LOG(logERROR, ("Could not set master\n"));
-            return FAIL;
+            retMaster = FAIL;
         }
         break;
     case OW_SLAVE:
@@ -1401,15 +1407,16 @@ int setMaster(enum MASTERINDEX m) {
         isMaster(&retval);
         if (retval != 0) {
             LOG(logERROR, ("Could not set slave\n"));
-            return FAIL;
+            retMaster = FAIL;
         }
         break;
     default:
         LOG(logERROR, ("Cannot reset to hardware settings from client. Restart "
                        "detector server.\n"));
-        return FAIL;
+        retMaster = FAIL;
     }
-    return OK;
+    setSynchronization(prevSync);
+    return retMaster;
 }
 
 int isMaster(int *retval) {
@@ -1447,7 +1454,7 @@ void setTiming(enum timingMode arg) {
 }
 
 enum timingMode getTiming() {
-    if (bus_r(EXT_SIGNAL_REG) == EXT_SIGNAL_MSK)
+    if ((bus_r(EXT_SIGNAL_REG) & EXT_SIGNAL_MSK) >> EXT_SIGNAL_OFST)
         return TRIGGER_EXPOSURE;
     return AUTO_TIMING;
 }
@@ -1734,40 +1741,40 @@ int setDetectorPosition(int pos[]) {
     detPos[2] = outerPos[X];
     detPos[3] = outerPos[Y];
 
-    // row
+    // row [Y]
     // outer
     uint32_t addr = COORD_ROW_REG;
     bus_w(addr,
           (bus_r(addr) & ~COORD_ROW_OUTER_MSK) |
-              ((outerPos[X] << COORD_ROW_OUTER_OFST) & COORD_ROW_OUTER_MSK));
+              ((outerPos[Y] << COORD_ROW_OUTER_OFST) & COORD_ROW_OUTER_MSK));
     if (((bus_r(addr) & COORD_ROW_OUTER_MSK) >> COORD_ROW_OUTER_OFST) !=
-        outerPos[X])
-        ret = FAIL;
-    // inner
-    bus_w(addr,
-          (bus_r(addr) & ~COORD_ROW_INNER_MSK) |
-              ((innerPos[X] << COORD_ROW_INNER_OFST) & COORD_ROW_INNER_MSK));
-    if (((bus_r(addr) & COORD_ROW_INNER_MSK) >> COORD_ROW_INNER_OFST) !=
-        innerPos[X])
-        ret = FAIL;
-
-    // col
-    // outer
-    addr = COORD_COL_REG;
-    bus_w(addr,
-          (bus_r(addr) & ~COORD_COL_OUTER_MSK) |
-              ((outerPos[Y] << COORD_COL_OUTER_OFST) & COORD_COL_OUTER_MSK));
-    if (((bus_r(addr) & COORD_COL_OUTER_MSK) >> COORD_COL_OUTER_OFST) !=
         outerPos[Y])
         ret = FAIL;
     // inner
     bus_w(addr,
-          (bus_r(addr) & ~COORD_COL_INNER_MSK) |
-              ((innerPos[Y] << COORD_COL_INNER_OFST) & COORD_COL_INNER_MSK));
-    if (((bus_r(addr) & COORD_COL_INNER_MSK) >> COORD_COL_INNER_OFST) !=
+          (bus_r(addr) & ~COORD_ROW_INNER_MSK) |
+              ((innerPos[Y] << COORD_ROW_INNER_OFST) & COORD_ROW_INNER_MSK));
+    if (((bus_r(addr) & COORD_ROW_INNER_MSK) >> COORD_ROW_INNER_OFST) !=
         innerPos[Y])
         ret = FAIL;
 
+    // col [X]
+    // outer
+    addr = COORD_COL_REG;
+    bus_w(addr,
+          (bus_r(addr) & ~COORD_COL_OUTER_MSK) |
+              ((outerPos[X] << COORD_COL_OUTER_OFST) & COORD_COL_OUTER_MSK));
+    if (((bus_r(addr) & COORD_COL_OUTER_MSK) >> COORD_COL_OUTER_OFST) !=
+        outerPos[X])
+        ret = FAIL;
+    // inner
+    bus_w(addr,
+          (bus_r(addr) & ~COORD_COL_INNER_MSK) |
+              ((innerPos[X] << COORD_COL_INNER_OFST) & COORD_COL_INNER_MSK));
+    if (((bus_r(addr) & COORD_COL_INNER_MSK) >> COORD_COL_INNER_OFST) !=
+        innerPos[X])
+        ret = FAIL;
+
     if (ret == OK) {
         if (getNumberofUDPInterfaces() == 1) {
             LOG(logINFOBLUE, ("Position set to [%d, %d] #(col, row)\n",
@@ -2625,6 +2632,7 @@ void *start_timer(void *arg) {
             if (i % pixelsPerPacket == 0) {
                 ++dataVal;
             }
+
             if ((i % 1024) < 300) {
                 gainVal = 1;
             } else if ((i % 1024) < 600) {
@@ -2665,6 +2673,28 @@ void *start_timer(void *arg) {
             clock_gettime(CLOCK_REALTIME, &begin);
             usleep(expUs);
 
+            // change gain and data for every frame
+            {
+                const int npixels = (NCHAN * NCHIP);
+                for (int i = 0; i < npixels; ++i) {
+                    int gainVal = 0;
+                    if ((i % 1024) < 300) {
+                        gainVal = 1 + iframes;
+                    } else if ((i % 1024) < 600) {
+                        gainVal = 2 + iframes;
+                    } else {
+                        gainVal = 3 + iframes;
+                    }
+                    int dataVal =
+                        *((uint16_t *)(imageData + i * sizeof(uint16_t)));
+                    dataVal += iframes;
+                    int pixelVal =
+                        (dataVal & ~GAIN_VAL_MSK) | (gainVal << GAIN_VAL_OFST);
+                    *((uint16_t *)(imageData + i * sizeof(uint16_t))) =
+                        (uint16_t)pixelVal;
+                }
+            }
+
             int srcOffset = 0;
             int srcOffset2 = DATA_BYTES / 2;
             int row0 = (numInterfaces == 1 ? detPos[1] : detPos[3]);
@@ -2798,6 +2828,7 @@ int softwareTrigger(int block) {
 
     LOG(logINFO, ("Sending Software Trigger\n"));
     bus_w(CONTROL_REG, bus_r(CONTROL_REG) | CONTROL_SOFTWARE_TRIGGER_MSK);
+    bus_w(CONTROL_REG, bus_r(CONTROL_REG) & ~CONTROL_SOFTWARE_TRIGGER_MSK);
 
 #ifndef VIRTUAL
     // block till frame is sent out

slsDetectorServers/jungfrauDetectorServer/slsDetectorServer_defs.h

@@ -5,8 +5,8 @@
 #include "sls/sls_detector_defs.h"
 
 #define MIN_REQRD_VRSN_T_RD_API  0x171220
-#define REQRD_FRMWRE_VRSN_BOARD2 0x221104 // 1.0 pcb (version = 010)
-#define REQRD_FRMWRE_VRSN        0x221103 // 2.0 pcb (version = 011)
+#define REQRD_FRMWRE_VRSN_BOARD2 0x230516 // 1.0 pcb (version = 010)
+#define REQRD_FRMWRE_VRSN        0x230515 // 2.0 pcb (version = 011)
 
 #define NUM_HARDWARE_VERSIONS (2)
 #define HARDWARE_VERSION_NUMBERS                                               \

slsDetectorServers/moenchDetectorServer/slsDetectorFunctionList.c

@@ -103,7 +103,7 @@ void basictests() {
 #endif
     if (mapCSP0() == FAIL) {
         strcpy(initErrorMessage,
-               "Could not map to memory. Dangerous to continue.\n");
+               "Could not map to memory. Cannot proceed. Check Firmware.\n");
         LOG(logERROR, ("%s\n\n", initErrorMessage));
         initError = FAIL;
         return;
@@ -113,8 +113,10 @@ void basictests() {
     if ((!debugflag) && (!updateFlag) &&
         ((checkType() == FAIL) || (testFpga() == FAIL) ||
          (testBus() == FAIL))) {
-        strcpy(initErrorMessage, "Could not pass basic tests of FPGA and bus. "
-                                 "Dangerous to continue.\n");
+        sprintf(initErrorMessage,
+                "Could not pass basic tests of FPGA and bus. Cannot proceed. "
+                "Check Firmware. (Firmware version:0x%llx) \n",
+                getFirmwareVersion());
         LOG(logERROR, ("%s\n\n", initErrorMessage));
         initError = FAIL;
         return;
@@ -451,7 +453,7 @@ void initStopServer() {
         if (mapCSP0() == FAIL) {
             initError = FAIL;
             strcpy(initErrorMessage,
-                   "Stop Server: Map Fail. Dangerous to continue. Goodbye!\n");
+                   "Stop Server: Map Fail. Cannot proceed. Check Firmware.\n");
             LOG(logERROR, (initErrorMessage));
             initCheckDone = 1;
             return;

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/slsDetectorFunctionList.c

@@ -89,7 +89,7 @@ void basictests() {
 #endif
     if (mapCSP0() == FAIL) {
         strcpy(initErrorMessage,
-               "Could not map to memory. Dangerous to continue.\n");
+               "Could not map to memory. Cannot proceed. Check Firmware.\n");
         LOG(logERROR, (initErrorMessage));
         initError = FAIL;
     }
@@ -99,8 +99,10 @@ void basictests() {
         ((validateKernelVersion(KERNEL_DATE_VRSN) == FAIL) ||
          (checkType() == FAIL) || (testFpga() == FAIL) ||
          (testBus() == FAIL))) {
-        strcpy(initErrorMessage, "Could not pass basic tests of FPGA and bus. "
-                                 "Dangerous to continue.\n");
+        sprintf(initErrorMessage,
+                "Could not pass basic tests of FPGA and bus. Cannot proceed. "
+                "Check Firmware. (Firmware version:0x%llx) \n",
+                getFirmwareVersion());
         LOG(logERROR, ("%s\n\n", initErrorMessage));
         initError = FAIL;
         return;
@@ -388,7 +390,7 @@ void initStopServer() {
         if (mapCSP0() == FAIL) {
             initError = FAIL;
             strcpy(initErrorMessage,
-                   "Stop Server: Map Fail. Dangerous to continue. Goodbye!\n");
+                   "Stop Server: Map Fail. Cannot proceed. Check Firmware. \n");
             LOG(logERROR, (initErrorMessage));
             initCheckDone = 1;
             return;