* start acq for master m3 was sent twice (non blocking), removed redundant code, check that there is only one master
* m3 can have more than 1 master (when many master modules used independently)
* fix for singe mod m3 or other dets
Use already installed version of the slsDetectorPackage. Assumes that the library has already been built and installed either on a system wide location or pointed to by CMAKE_PREFIX_PATH
* inconsistent copy with generalData and implementation members, especially for m3 (non default rxr generic values), issue caught on second configure with non m3 default values, eg tengiga 0
* removing test
* wip, adding m3 functions: polarity, inerpolation, pumpprobe
* added interpol, polarity, pump probe, analog pulsing, digital pulsing
* tests
* binaries in
* update release
* added python polarity enum
* fixed python and minor readability in mythen3.c
* binarie sin
* added all the m3 funcs also in list.c and enablingall counters for enabling interpolation
* binarie sin
Fixed by checking for help action before using the detector
added test that checks that for all helps this doesn't crash
Disabled Timer tests by default since they take ~2s
# Setting DAC names for CTB
* Introduced new shared memory for CTB only
* Prepared for additional functionality
* Works from C++ and Python
Co-authored-by: Dhanya Thattil <dhanya.thattil@psi.ch>
- progress looks at activated or enabled ports, so progress does not stagnate
- (eiger) disable datastreaming also for virtual servers only for 10g
- missing packets also takes care of disabled ports
* test for rx_arping
* arping ip and interface from client interface
* apring thread added to thread ids
* clean code for thread for arping
* removing the assumption that udpip1 fill be updated along with udpip2
* review, replacing syscall(sys_gettid) with gettid()
* removed Makefile for moench and integrated the build in CMake
* broke out tiff reading and writing to its own library
* moved tiff includes to include/sls
* moved tiffio source to src
* removed incorrectly used bps
* cleanup and tests for tiffio
* removed using namespace std from header
* some fixing for moench04
* Program for offline processing renamed
Co-authored-by: Anna Bergamaschi <anna.bergamaschi@psi.ch>
A delay of 100ms has been added between the generation of the stop pulse and the resetCore function call. This should give enough time to the detector to readout and streamout the ongoing frame before the internal logic is reset (even after the transmission is delayed with txndelay_frame).
* Setting pattern from memory (#218)
* ToString accepts c-style arrays
* fixed patwait time bug in validation
* Introduced pattern class
* compile for servers too
* Python binding for Pattern
* added scanParameters in Python
* slsReceiver: avoid potential memory leak around Implementation::generalData
* additional constructors for scanPrameters in python
* bugfix: avoid potentital memory leak in receiver if called outside constructor context
* added scanParameters in Python
* additional constructors for scanPrameters in python
* M3defaultpattern (#227)
* default pattern for m3 and moench including Python bindings
* M3settings (#228)
* some changes to compile on RH7 and in the server to load the default chip status register at startup
* Updated mythen3DeectorServer_developer executable with correct initialization at startup
Co-authored-by: Erik Frojdh <erik.frojdh@gmail.com>
Co-authored-by: Anna Bergamaschi <anna.bergamaschi@psi.ch>
* Pattern.h as a public header files (#229)
* fixed buffer overflow but caused by using global instead of local enum
* replacing out of range trimbits with edge values
* replacing dac values that are out of range after interpolation
* updated pybind11 to 2.6.2
* Mythen3 improved synchronization (#231)
Disabling scans for multi module Mythen3, since there is no feedback of the detectors being ready
startDetector first starts the slaves then the master
acquire firs calls startDetector for the slaves then acquire on the master
getMaster to read back from hardware which one is master
* New server for JF to go with the new FW (#232)
* Modified Jungfrau speed settings for HW1.0 - FW fix version 1.1.1, compilation date 210218
* Corrected bug. DBIT clk phase is implemented in both HW version 1.0 and 2.0. Previous version did not update the DBIT phase shift on the configuration of a speed.
* fix for m3 scan with single module
* m3 fw version
* m3 server
* bugfix for bottom when setting quad
* new strategy for finding zmq based on cppzmq
Co-authored-by: Dhanya Thattil <dhanya.thattil@psi.ch>
Co-authored-by: Dhanya Thattil <33750417+thattil@users.noreply.github.com>
Co-authored-by: Alejandro Homs Puron <ahoms@esrf.fr>
Co-authored-by: Anna Bergamaschi <anna.bergamaschi@psi.ch>
Co-authored-by: Xiaoqiang Wang <xiaoqiangwang@gmail.com>
Co-authored-by: lopez_c <carlos.lopez-cuenca@psi.ch>
* Modified Jungfrau speed settings for HW1.0 - FW fix version 1.1.1, compilation date 210218
* Corrected bug. DBIT clk phase is implemented in both HW version 1.0 and 2.0. Previous version did not update the DBIT phase shift on the configuration of a speed.
The new server has been compiled
Co-authored-by: lopez_c <carlos.lopez-cuenca@psi.ch>
Disabling scans for multi module Mythen3, since there is no feedback of the detectors being ready
startDetector first starts the slaves then the master
acquire firs calls startDetector for the slaves then acquire on the master
getMaster to read back from hardware which one is master
* added temp m3 settings files
* renames settings noise to trim
* get threshold for M3
* some changes to compile on RH7 and in the server to load the default chip status register at startup
* Updated mythen3DeectorServer_developer executable with correct initialization at startup
Co-authored-by: Erik Frojdh <erik.frojdh@gmail.com>
Co-authored-by: Anna Bergamaschi <anna.bergamaschi@psi.ch>
* ToString accepts c-style arrays
* added patternParameters to python
* fixed patwait time bug in validation
* moved load from file function to patterParameters
* server using patternparamters structure to get pattern
Co-authored-by: Erik Frojdh <erik.frojdh@gmail.com>
@ -4,7 +4,11 @@ Please do not update to any xxxx.xx.xx.dev0 tags. They are not releases, but tag
Use only releases with tags such as x.x.x or x.x.x-rcx.
### Documentation
Detailed documentation can be found on the [official site.](https://www.psi.ch/detectors/users-support)
##### 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).
##### Older Releases
Documentation is found in the package.
### Binaries
Binaries for the slsDetectorPackage are available through conda.
@ -12,6 +16,7 @@ Binaries for the slsDetectorPackage are available through conda.
#Add conda channels
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
eg. Rebuild when you switch to a new build and compile in parallel:
# get 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.
@ -71,3 +86,17 @@ Use cmake to create out-of-source builds, by creating a build folder parallel to
This document describes the differences between v7.0.0 and v6.x.x
CONTENTS
--------
1. Firmware Requirements
2. Download, Documentation & Support
1. New or Changed Features
2. Resolved Issues
3. Firmware Requirements
4. Kernel Requirements
5. Download, Documentation & Support
1. Firmware Requirements
1. New or Changed Features
==========================
- Fixed minor warnings (will fix commandline print of excess packets for missing packets)
- ctb slow adcs and any other adcs (other than temp) goes to the control Server
- number of udp interfaces is 2 for Eiger (CHANGE IN API??)
- added module id for virtual servers into the udp header
- refactoring (rxr)
- fixed patsetbit and patsetmask for moench
- changed default vref of adc9257 to 2V for moench (from 1.33V)
- moench and ctb - can set the starting frame number of next acquisition
- mythen server kernel check incompatible (cet timezone)
- rx_arping
- rx_threadsids max is now 9 (breaking api)
- fixed datastream disabling for eiger. Its only available in 10g mode.
- m3 server crash (vthrehsold dac names were not provided)
- allow vtrim to be interpolated for Eiger settings
- m3 setThresholdEnergy and setAllThresholdEnergy was overwriting gaincaps with settings enum
- can set localhost with virtual server with minimum configuration: (hostname localhost, rx_hostname localhost, udp_dstip auto)
- increases the progress according to listened index. (not processed index)
- current frame index points to listened frame index (not processed index)
- when in discard partial frames or empty mode, the frame number doesnt increase by 1, it increases to that number (so its faster)
- file write disabled by default
- eiger 12 bit mode
- start non blocking acquisition at modular level
- connect master commands to api (allow set master for eiger)
--ignore-config command line
- command line argument 'master' mainly for virtual servers (also master/top for real eiger), only one virtual server for eiger, use command lines for master/top
- stop servers also check for errors at startup( in case it was running with an older version)
- hostname cmd failed when connecting to servers in update mode (ctb, moench, jungfrau, eiger)
- missingpackets signed (negative => extra packets)
- framescaught and frameindex now returns a vector for each port
- progress looks at activated or enabled ports, so progress does not stagnate
- (eiger) disable datastreaming also for virtual servers only for 10g
- missing packets also takes care of disabled ports
- added geometry to metadata
- 10g eiger nextframenumber get fixed.
- stop, able to set nextframenumber to a consistent (max + 1) for all modules if different (eiger/ctb/jungfrau/moench)
- ctb: can set names for all the dacs
- fpga/kernel programming, checks if drive is a special file and not a normal file
- gotthard 25 um image reconstructed in gui and virtual hdf5 (firmware updated for slave to reverse channels)
- master binary file in json format now
- fixed bug introduced in 6.0.0: hdf5 files created 1 file per frame after the initial file which had maxframesperfile
- m3 polarity, interpolation (enables all counters when enabled), pump probe, analog pulsing, digital pulsing
- updatedetectorserver - removes old server current binary pointing to for blackfin
- removing copydetectorserver using tftp
>>>>>>> developer
- registerCallBackRawDataReady and registerCallBackRawDataModifyReady now gives a sls_receiver_header* instead of a char*, and uint32_t to size_t
- registerCallBackStartAcquisition gave incorrect imagesize (+120 bytes). corrected.
- registerCallBackStartAcquisition parameter is a const string reference
- m3 (runnig config second time with tengiga 0, dr !=32, counters !=0x7) calculated incorrect image size expected
- fixed row column indexing (mainly for multi module Jungfrau 2 interfaces )
- eiger gui row indices not flipped anymore (fix in config)
2. Resolved Issues
==================
3. Firmware Requirements
========================
Eiger
=====
Compatible version : 08.09.2020 (v27)
Compatible version : 08.10.2021 (v29)
Jungfrau
========
Compatible version : 24.07.2020 (v1.1, PCB v1.0)
: 21.07.2020 (v2.1, PCB v2.0)
Compatible version : 31.08.2021 (v1.2, PCB v1.0)
: 08.10.2021 (v2.2, PCB v2.0)
Gotthard
========
@ -26,24 +93,22 @@ SLS Detector Package 5.0.0-rc2 released on 09.10.2020 (Release Candidate 2)
Mythen3
=======
Compatible version : 25.09.2020 (development)
Compatible version : 10.09.2021 (v1.1)
Gotthard2
=========
Compatible version : 25.09.2020 (development)
Compatible version : 27.05.2021 (v0.1)
Moench
======
Compatible version : 10.05.2020 (v1.0)
Compatible version : 05.10.2020 (v1.0)
Ctb
===
Compatible version : 10.05.2019 (v1.0)
Compatible version : 05.10.2020 (v1.0)
Detector Upgrade
================
The following can be upgraded remotely:
Eiger via bit files
Jungfrau via command <.pof>
@ -60,11 +125,36 @@ SLS Detector Package 5.0.0-rc2 released on 09.10.2020 (Release Candidate 2)
One can test with :ref:`detector simulators<Virtual Detector Servers>` before testing the API with a real detector or when a real detector is not at hand.
CMake: slsDetectorPackage as submodule in your project
#. Tftp must be already installed on your pc to use the bcp script.
#.Kill the on-board servers and copy new servers to the board.
#.Copy new servers to the board. See :ref:`how to upgrade detector servers<Detector Server Upgrade>` for more detals. A reboot should have started the new linked servers automatically. For Eiger, do not reboot yet as we need to program the firmware via bit files.
.. code-block:: bash
# Option 1: from detector console
# kill old server
ssh root@bebxxx
killall eigerDetectorServer
# copy new server
cd executables
scp user@pc:/path/eigerDetectorServerxxx .
chmod 777 eigerDetectorServerxxx
ln -sf eigerDetectorServerxxx eigerDetectorServer
sync
# Options 2: from client console for multiple modules
* This is crucial when registers between firmwares change. Failure to do so will result in linux on boards to crash and boards can't be pinged anymore.
* This step is crucial when registers between firmwares change. Failure to do so will result in linux on boards to crash and boards can't be pinged anymore.
#. Bring the board into programmable mode using either of the 2 ways. Both methods result in only the central LED blinking.
@ -75,8 +27,13 @@ Upgrade
Do a hard reset for each half module on back panel boards, between the LEDs, closer to each of the 1G ethernet connectors. Push until all LEDs start to blink.
* Software:
..code-block::bash
# Option 1: if the old server is still running:
sls_detector_put execcommand "./boot_recovery"
# Option 2:
ssh root@bebxxx
cd executables
./boot_recovery
@ -104,11 +61,24 @@ Upgrade
#update front right fpga
bcp download.bit bebxxx:/febr
#update kernel (only if required by the SLS Detector Group)
#update kernel (only if required by us)
bcp download.bit bebxxx:/kernel
#. Reboot the detector.
..code-block::bash
# In the first terminal where we saw "Succeess"
# reconfig febX is necessary only if you have flashed a new feb firmware
reconfig febl
reconfig febr
# will reboot controller
reconfig fw0
.. note ::
If the detector servers did not start up automatically after reboot, you need to add scripts to do that. See :ref:`Automatic start<Automatic start servers>` for more details.
Jungfrau
-------------
@ -116,146 +86,53 @@ Download
^^^^^^^^^^^^^
- detector server corresponding to package in slsDetectorPackage/serverBin
As it is still in developement, the rbf files must be picked up from the SLS Detector Group.
If the detector servers did not start up automatically after reboot, you need to add scripts to do that. See :ref:`Automatic start<Automatic start servers>` for more details.
Gotthard II
-------------
Download
^^^^^^^^^^^^^
- detector server corresponding to package in slsDetectorPackage/serverBin
If the detector servers did not start up automatically after reboot, you need to add scripts to do that. See :ref:`Automatic start<Automatic start servers>` for more details.
Moench
-------
@ -368,36 +223,24 @@ Download
^^^^^^^^^^^^^
- detector server corresponding to package in slsDetectorPackage/serverBin
# step 1: get the kernel image (uImage.lzma) from slsdetectorgroup
# and copy it to pc's tftp folder
# step 2: connect to the board
telnet bchipxxx
#step 3: go to directory for space
cd /var/tmp/
# step 3: copy kernel to board
tftp pcxxx -r uImage.lzma -g
# step 4: verify kernel copied properly
ls -lrt
# step 5: erase flash
flash_eraseall /dev/mtd1
# step 6: copy new image to kernel drive
cat uImage.lzma > /dev/mtd1
# step 7:
sync
# step 8:
reboot
# step 9: verification
telnet bchipxxx
uname -a # verify kernel date
more /proc/mtd # verify mtd3 is listed
Last Resort using USB Blaster
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If none of these steps work, the last resort might be physically upgrading the firmware using a USB blaster, which also requires opening up the detector. Instructions for all the blackfin detectors are the same as the one for :ref:`gotthard firmware upgrade <firmware upgrade using blaster for blackfin>`.
Receiver processes can be run on same or different machines as the client, receives the data from the detector (via UDP packets).
When using the slsReceiver/ slsMultiReceiver, they can be further configured by the client control software (via TCP/IP) to set file name, file path, progress of acquisition etc.
Detector UDP Header
---------------------
| The UDP data format for the packets consist of a common header for all detectors, followed by the data for that one packet.
#. UDP source port is hardcoded in detector server, starting at 32410.
#.**udp_dstport** : UDP destination port number. Port in receiver pc to listen to packets from the detector.
#.**udp_dstip** : IP address of UDP destination interface. IP address of interface in receiver pc to listen to packets from detector. If **auto** is used (only when using slsReceiver/ slsMultiReceiver), the IP of **rx_hostname** is picked up.
#.**udp_dstmac** : Mac address of UDP destination interface. MAC address of interface in receiver pc to list to packets from detector. Only required when using custom receiver, else slsReceiver/slsMultiReceiver picks it up from **udp_dstip**.
#.**udp_srcip** : IP address of UDP source interface. IP address of detector UDP interface to send packets from. Do not use for Eiger 1Gb interface (uses its hardware IP). For others, must be in the same subnet as **udp_dstip**.
#.**udp_srcmac** : MAC address of UDP source interface. MAC address of detector UDP interface to send packets from. Do not use for Eiger (uses hardware mac). For others, it is not necessary, but can help for switch and debugging to put unique values for each module.
Custom Receiver
----------------
| When using custom receiver with our package, ensure that **udp_dstmac** is also configured in the config file. This parameter is not required when using slsReceiver.
| Cannot use "auto" for **udp_dstip**.
| Also ensure that there are no **rx_** commands in the config file. These commands are for configuring the slsReceiver.
Example of a custom receiver config file
* The main difference is the lack of **rx_** commands or file commands (eg. fwrite, fpath) and the udp_dstmac is required in config file.
When using a blocking acquire command (sls_detector_acquire or Detector::acquire), the control server is blocked until end of acquisition. However, stop server commands could be used in parallel.
.._Automatic start servers:
Automatic start
------------------
One can start the on-board detector server automatically upon powering on the board.
**Location:** slsDetectorPackage/serverBin/ folder for every release.
.. note ::
For Mythen3, Gotthard2 and Eiger, you need to add scripts to automatically start detector server upon power on. See :ref:`Automatic start<Automatic start servers>` for more details.
.. note ::
Eiger requires a manual reboot. Or killall the servers and restart the new linked one. If you are in the process of updating firmware, then don't reboot yet.
From 6.1.1 and above (no tftp required)
---------------------------------------
#. Program from console
#. Kill old server and copy new server
.. code-block:: bash
# Option 1: from detector console
# kill old server
ssh root@bebxxx
killall eigerDetectorServer
# the following command copies new server, creates a soft link to xxxDetectorServerxxx
# [Jungfrau][CTB][Moench] also deletes the old server binary and edits initttab to respawn server on reboot
# Then, the detector controller will reboot (except Eiger)
| One has to start the slsReceiver before loading config file or using any receiver commands (prefix: **rx_** )
For a Single Module
.. code-block:: bash
# default port 1954
slsReceiver
# custom port 2012
slsReceiver -t2012
For Multiple Modules
.. code-block:: bash
# each receiver (for each module) requires a unique tcp port (if all on same machine)
# using slsReceiver in multiple consoles
slsReceiver
slsReceiver -t1955
# slsMultiReceiver [starting port] [number of receivers]
slsMultiReceiver 2012 2
# slsMultiReceiver [starting port] [number of receivers] [print each frame header for debugging]
slsMultiReceiver 2012 2 1
Client Commands
-----------------
| One can remove **udp_dstmac** from the config file, as the slsReceiver fetches this from the **udp_ip**.
| One can use "auto" for **udp_dstip** if one wants to use default ip of **rx_hostname**.
| The first command to the receiver (**rx_** commands) should be **rx_hostname**. The following are the different ways to establish contact.
..code-block::bash
# default receiver tcp port (1954)
rx_hostname xxx
# custom receiver port
rx_hostname xxx:1957
# custom receiver port
rx_tcpport 1954
rx_hostname xxx
# multi modules with custom ports
rx_hostname xxx:1955+xxx:1956+
# multi modules with custom ports on same rxr pc
0:rx_tcpport 1954
1:rx_tcpport 1955
2:rx_tcpport 1956
rx_hostname xxx
# multi modules with custom ports on different rxr pc
0:rx_tcpport 1954
0:rx_hostname xxx
1:rx_tcpport 1955
1:rx_hostname yyy
| Example commands:
..code-block::bash
# to get a list of receiver commands (these dont include file commands)
sls_detector_get list | grep rx_
# some file commands are:
fwrite
foverwrite
findex
fpath
fname
fmaster
fformat
# to get help on a single commands
sls_detector_get -h rx_framescaught
File format
--------------
* The file name format is [fpath]/[fname]_dx_fy_[findex].raw, where x is module index and y is file index. **fname** is file name prefix and by default "run". **fpath** is '/' by default.
* Each acquisition will have an increasing acquisition index or findex (if file write enabled). This can be retrieved by using **findex** command.
* Each acquisition can have multiple files (the file index number **y**), with **rx_framesperfile** being the maximum number of frames per file. The default varies for each detector type.
* Some file name examples:
.. code-block:: bash
# first file
path-to-file/run_d0_f0_0.raw
# second file after reaching max frames in first file
path-to-file/run_d0_f1_0.raw
# second acquisition, first file
path-to-file/run_d0_f0_1.raw
* 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.
* Each data file will consist of frames, each consisting of slsReceiver Header followed by data for 1 frame.
* Master file is of ASCII format and will also include the format of the slsReceiver Header.
**HDF5 file formats**
#. Compile the package with HDF5 option enabled
#. Using cmk script: ./cmk.sh -hj9 -d [path of hdf5 dir]
#. Enable using cmake **-DCMAKE_INSTALL_PREFIX=/path/to/hdf/installation** and **-DSLS_USE_HDF5=ON**
#. Start Receiver process
#. Load config file
#. Set file format from client or in config file
..code-block::bash
sls_detector_put fformat hdf5
| For multiple, modules, a virtual file linking all the modules is created. Both the data files and virtual files are linked in the master file.
Performance
-------------
Please refer to Receiver PC Tuning options and slsReceiver Tuning under `Troubleshooting <https://slsdetectorgroup.github.io/devdoc/troubleshooting.html>`_.
Using Callbacks
----------------
One can get a callback in the receiver for each frame to:
* manipulate the data that will be written to file, or
* disable file writing in slsReceiver and take care of the data for each call back
When handling callbacks, the control should be returned as soon as possible, to prevent packet loss from fifo being full.
@ -243,6 +247,19 @@ Possible causes could be the following:
* For Jungfrau, refer to :ref:`Jungfrau Power Supply Troubleshooting<Jungfrau Troubleshooting Power Supply>`.
Cannot ping module (Nios)
^^^^^^^^^^^^^^^^^^^^^^^^^
If you executed "reboot" command on the board, you cannot ping it anymore unless you power cycle. To reboot the controller, please use the software command ("rebootcontroller"), which talks to the microcontroller.
Gotthard2
---------
Cannot get data without a module attached
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
You cannot get data without a module attached as a specific pin is floating. Attach module to get data.
# $(shell test -d $(DESTDIR)/pdf && rm -fr $(DESTDIR)/pdf)
# mv pdf $(DESTDIR)
# $(shell test -d $(DESTDIR)/html && rm -fr $(DESTDIR)/html)
# mv html $(DESTDIR)
pdf:$(PDFDIRS)
# $(shell test -d $(DESTDIR)/pdf && rm -fr $(DESTDIR)/pdf)
# mv pdf $(DESTDIR)
html:$(HTMLDIRS)
# $(shell test -d $(DESTDIR)/html && rm -fr $(DESTDIR)/html)
# mv html $(DESTDIR)
clean:$(CLEANDIRS)
rm -fr $(DESTDIR)/pdf
rm -fr $(DESTDIR)/html
all-%:
echo
cd$(@:all-%=manual-%)&& make all
pdf-%:
cd$(@:pdf-%=manual-%)&& make pdf
html-%:
cd$(@:html-%=manual-%)&& make html
clean-%:
cd$(@:clean-%=manual-%)&& make clean
#<23><>$(@D)<29><> The directory part of the file name of the target, with the trailing slash removed. If the value of <20><>$@<40><> is dir/foo.o then <20><>$(@D)<29><> is dir. This value is . if <20><>$@<40><> does not contain a slash.
#<23><>$(@F)<29><> The file-within-directory part of the file name of the target. If the value of <20><>$@<40><> is dir/foo.o then <20><>$(@F)<29><> is foo.o. <20><>$(@F)<29><> is equivalent to <20><>$(notdir $@)<29><>.
std::cout<<"Error: Could not instantiate slsDetectorUsers"<<std::endl;
returnEXIT_FAILURE;
}
/** - if specified, load configuration file (necessary at least the first time it is called to properly configure advanced settings in the shared memory) */
if(argc>=2){
pDetector->readConfigurationFile(argv[1]);
std::cout<<"Detector configured"<<std::endl;
}
/** - set detector in shared memory online (in case no config file was used) */
pDetector->setOnline(1);
/** - set receiver in shared memory online (in case no config file was used) */
In order to convert from strip number to 2$\theta$-angle, an accurate angular calibration of the detector must be performed (for details see the paper Bergamaschi, A. et al. (2010). J. Synchrotron Rad. 17, 653-668). \\
For this purpose, a series of patterns of a powder standard with symmetric peaks (e.g. silicon) must acquired while shifting the detector by an angular step of the order of about 2\% of the module size. During the measurement, a strong intensity peak (e.g. Si(111)) should pass through the field of view of every module such that it can be used as a reference angular position to perform the calibration of the modules position.\\
In a first step, the peak is fitted with a Gaussian in order to determine its position $C_{peak}$ in channel number for each of the acquired patterns.\\
In a second step, for each module $i$, the encoder position $\Theta_e$ is fitted as a function of the peak position $C_{peak}$ according to:
where the parameters $\Theta_o^i$ is the angular offset with respect to the diffractometer zero position, $C_{center}^{i}$ is the central channel and $R^i$ is the distance of the module $i$ from the diffractometer center while $p=50~\mu m$ is the strip pitch of the detector. \\
Finally, the global offset of the detector system is precisely determined by refining a silicon pattern at a well-defined energy (i.e., knowing the position of the peak).
The same function of equation~\ref{eq:angcal}, with the parameters obtained from the calibration, is used in order to convert from channel number to 2$\theta$-angle.
The parallax at the borders of the modules due to the thickness of the silicon sensor is a function of the X-ray energy (higher energy X-rays are absorbed deeper inside the sensor) and is of the order of 0.2~mdeg at 12~keV and 0.5~mdeg at 30~keV. \\
The differences in pixel size due to the different portion of solid angle covered by the strips on the border of the modules and the higher efficiency due to the longer path of the X-rays in the sensor are removed by the flat field correction. This also normalizes additional differences in pixel size between channels which are also present because of mismatches in the strip sensor fabrication and in fluctuations of the channels threshold level.
Patterns acquired at different detector positions are generally merged together in order to fill the gaps between the modules and correct possibly bad functioning channels. In this procedure the data from different positions which are closer than 4~mdeg (the average pixel size) are averaged and the new position is set to the mean of the positions of the original points.
The position and width of the peaks results from a fit over several detector channels. Geometrical distortions might disturb this determination mainly because of errors in the angular calibration, fluctuations in the encoder position, variations between channels and parallax effects.\\
The resolution in locating the peak center and determining its width and integrated intensity has been estimated by acquiring several patterns of a LaB$_6$ sample in a 300~$\mu$m capillary with the detector shifted in 5~mdeg steps between 30.4 and 36.5 degrees. The 16~peaks acquired have been fitted with a Gaussian function plus background and the fluctuations on the fitted parameters have been calculated. The resulting average resolutions are 0.63$\pm$0.06~mdeg for the peak center and 0.22$\pm$0.05~mdeg for the peak Full-Width at Half-Maximum (FWHM) for an average peak FWHM of 27.0$\pm$2.5~mdeg. \\
These results show that the angular calibration allows a resolution in determining the peaks position and width which is appropriate for structural determination.
\section{Data acquisition}
The angular calibration consists in acquiring a set of diffraction patterns of a well known powder standard (e.g. Silicon) at different encoder positions. In order to facilitate the procedure, the sample should not emit fluorescent light and should present relatively symmetric peaks. \\
During the measurement, a strong intensity peak (e.g. Si(111)) should pass through the field of view of every module such that it can be used as a reference angular position to perform the calibration of the modules position. In general the highest peak will be used for the calibration, but this is not necessary in case there would be e.g. geometrical limitations for shifting the detector. \\\textbf{Do not forget to properly position the beam stopper if the detector is scanned in front of the direct beam.}\\
The detector should be shifted of an angular step of the order of about 2\% of the module size, such that about 50 patterns can contribute to the fitting of the 3 parameters necessary for the angular calibration.\\
All the angular calibration procedure should be acquired using a trimmed detector with the threshold set at half of the X-ray energy (Assuming no fluorescent element in the standard). A flat field should also be acquired in order to precisely correct the data, while the X-ray intensity should be kept lower than about 100~kHz per strip in order to avoid the need for rate corrections.
A rough angular conversion file starting from a previous calibration or from the geometric characteristics of the mechanics is an advantage. The angular conversion file should contain a line for each module of the detector with its module number $i$, center $C_{center}^{i}$ and error, conversion radius $p/R^i$ and error, offset $\Theta_o^i$ and error:
Also the \textit{global offset} value of the beamline should be approximately known i.e. the angular position of channel 0 of module 0 when the motor is set at 0. \\
All the documentation assumes that the detector is oriented in the same direction as the encoder position i.e. large channel number at higher angles (both per module and absolute). If this is not the case, the \textit{angular direction} should be set to -1.
\subsection{Software}
For the acquisition ot the data you need to install the slsDetector software package (please refere to separate documentation). The use of the GUI is optional and all operations can be performed also using the text client.\\
in order to be able to move the detector and read out its position by using the slsDetector software.
In the following the command to acquire a dataset for the angular calibration with an exposure time of 1~s, and position shift
\begin{verbatim}
#setup angular calibration log mode
> sls_detector_put angcallog 1
#set exposure time to 1s
> sls_detector_put exptime 1.
#setup threshold scan
> sls_detector_put scan0script position
#setup the precision for the scan variable in the file name
> sls_detector_put scan0prec 2
#set scan range between 20deg and -60deg, step of -0.1deg
# (at 12.4 keV the Si(111) peak is at approx 19deg
> sls_detector_put scan0range 20 -60 -0.1
#acquire the data
> sls_detector_acquire
#unset angular calibration log mode
> sls_detector_put angcallog 0
\end{verbatim}
With the GUI you can obtain the same results by clicking on the \textit{Angular calibration} log button in the advanced tab (see figure~\ref{fig:guiangcallog}) and setting up the motor position scan in the Actions tab (see figure~\ref{fig:guiposscan}). The exposure time should also be set in the measurement tab.
Additional to the data files, the acquisition will produce a .angcal file containing an header and, for each step of the acquisition, the exect value of the motor position and the file name. \\
In case you forgot to enable the angcallog flag in the software, you can produce the file with the syntax as follows, assuming that you know the exact values of your encoder for each frame:
\begin{verbatim}
type Mythen
maxmod 32
nmod 32
angconv /scratch/angcal20120422/ang.off
globaloff 5.088
fineoff 0.0
angdir 1
ffdir /scratch/angcal20120422/
flatfield flatfield_E12keV_T6keV_0.raw
badchannels /scratch/cal/bad.chans
19.99998 angcal_S20.00_0
19.90001 angcal_S19.90_0
19.79999 angcal_S19.80_0
19.70002 angcal_S19.70_0
......
\end{verbatim}
\begin{figure}
\caption{Acquisition GUI window to enable the angular calibration log.}\label{fig:guiangcallog}
The data analysis consists in fitting with a gaussian the selected peak of the powder pattern for each position in order to determine its position is channel number as a function of the encoder position. \\
In a second step, for each module, the channel vs. encoder curve is fitted in order to extrapolate the three parameters necessary for the angular conversion and the result is written to file
\subsection{Software}
The software used for the angular calibration data analysis is based on root (see http://root.cern.ch).\\
This can be downloaded as binary or installed from sources. The version of the software should not play an important role, but up to now everything has been implemented and tested using version 5.20.
To start the data analysis simply launch:
\begin{verbatim}
> ./angularCalibrationWizard
\end{verbatim}
\begin{figure}
\caption{Overview of the nagular calibration dataset.}\label{fig:setangcal}
To setup the angular calibration dataset, the .angcal file should be selected (or digited) and the load button should be pressed to confirm. The parameters of the angular calibration are then read to the file and the data loaded for a quick overview (see figure~\ref{fig:setangcal}).\\
The software assumes that the data files (.raw) and the .encal file are in the same directory.\\
A 2D color plot will show a rebinned overview of the dataset. The peak to be fitted should be visible as a high intensity diagonal line passing through all the channels.
\begin{figure}
\caption{Preview of the fitting of the Si(111) peak for one of the detector positions.}\label{fig:peakfit}
\includegraphics[width=\textwidth]{peakFit.eps}
\end{figure}
For a more detailed view of the data, one can select an angular calibration step from the combo box, select the plot mode (raw data or processed data as a function of channel number, processed angular converted data, flat field data, or again an overview of the whole dataset). \\
By (right) clicking close to the axis you are able to zoom in/out, set the scale to logarithmic etc.\\
If the bad channel list, angular conversion file or flat field file are changed compared to the acquisition, they can be reloaded by editing the correspondent text entries and pressing enter.
In particular, the angular converted data should be checked in order to view the position of the selected peak. In this case, the plot will be zoomed to the angular region slected in the minimum and maximum angle entries. By pressing fit, the fit of the peak in the selected angular range will be shown (see figure~\ref{fig:peakfit}). It is useful to check that it works properly in several positions such that then the sequential fitting on all steps can give good results.
To automatically fit all positions simply press \textit{Proceed to Modules Calibration} and wait until all steps are fitted. This can take sometime, depending on the number of steps.
\begin{figure}
\caption{Window for fitting the angular calibration parameters of a module.}\label{fig:anglefit}
\includegraphics[width=\textwidth]{angleFit.eps}
\end{figure}
In the module calibration window (see figure~\ref{fig:anglefit}), you will be able to fit the channel number to encoder position curve to estimate the three angular calibration parameters for each module.\\
The entries show the angular calibration parameters used for approximate angular conversion in the previous step of the calibration. These can be edited and will be used as start parameters for the fit.
By clicking on the check box next to the parameters, the selected parameter will be set and fixed during the fit. Often the center is used as a fix parameter.\\
It is possible to navigate between modules by using the Previous and Next module buttons. To refit the current module (e.g. after changing one of the parameters) simply re-click on the module number.
After fitting all modules you can click on the \textit{Write Angular Calibration} button, select the file name to write to and save the calibration angulat calibration data. Please note that the offset of module 0 will always be 0 and the other values will be rescaled to its value. Therefore the global offset of the steup will always need to be specified for a proper angular conversion unless the home of the encoder will not be redifined.
\section{Setup calibration files}
To use the generated angular calibration files, using the text client:
\begin{verbatim}
sls_detector_put angconv /scratch/ang_new.off
\end{verbatim}
while for the GUI the file name should be specified in the configuration file (works also for the text client).
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