* vicin default changed to 800, only setting vthx directly allows to set dac even if counter disabled, else disable counter, setallthresholdenergy if an energy is -1, get module value, fix that reg was repaced by isettings
* vth3 disabled for interpolation enable, interpolation disable sets counter mask to what it was before (updating old mask whn setting counter mask except for setting all counters for interpolation enable) and enabling vth3 if counter was enabled
* refactor and test for previous commit
* pump probe only has vth2 enabled, handles both pump probe mode and interpolation mode as well
* wip
* refactored pump probe and interpolation and added to setmodule
* check dacs and trimbits out of range for setmodule (not just threshold)
* binaries in
* m3: pump probe and interpolation mutually exclusive
* minor
* added the possibility to save settings file for m3 and eiger
* added save trimbits to gui
* update release notes
* python wip
* moved location of trimbits save option in gui
* python works
* updating getModule with all its parameters in the server side
* updating binaries
* roi structure expanded to have ymin and ymax
* compile with 'detector roi'
* wip
* wip, rx_roi, rx_clearroi
* wip rxroi
* rxroi wip
* wip rxroi
* merge fix
* wip
* rx_roi works, impl wip, test
* tests in, impl left
* wip, rxroi impl
* wip, rxroi impl
* wip
* setrx_Roi works, getrx_roi, wip
* rx_roi impl done
* wip, rxroi
* wip, getrx_roi rxr ports
* fix ports
* wip
* wip
* fix positions on server side
* wip
* numports wip
* wip
* jungfrau top inner interface row increment
* x, y detpos, wip
* removed eiger row indices flipping in gui (bottom flipping maintained)
* wip
* wip, jungfrau numinterfaces2
* jungfrau virtual works
* eiger, jungfrau, g2 virtual server works
* eiger positions fix, wip
* binaries in
* minor printout
* binaries in
* merge fix
* merge fix
* removing getposition
* setrxroi wip
* set upto port
* get messed, wip
* roi multi to module works, wip
* wip
* roi dont return -1
* added rxroi metadata in master file
* added rxroifromshm, not yet in detector
* rx roi in gui with box, also for gap pixels (gappixels for jungfrau mess)
* fix for segfault in gui with detaching roi box in gui
* wip
* m3 gui: slave timing modes should be discarded when squashing
* fixed m3 virtual data, and fixed counters in gui asthetics
* m3 roi works
* wip, g2
* wip
* handling g225um boards, and showing roi for gainplot as well
* udpate python functions
* fix for 1d and a2d roi written
* fixed actual roi written to file
* no virtual hdf5 when handling rx roi
* test
* minor
* binarie in
* 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
- rx_roi
- 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
- 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)
- m3 (settings dac check disabled temporarily?)
- m3 virtual server sends the right pacets now
- gap pixels in gui enabled by default
- rxr src files and classes (detectordata, ZmqSocket, helpDacs) added to sls namespace, and macros (namely from logger (logINFO etc)), slsDetectorGui (make_unique in implemtnation requires sls nemspace (points to std otherwise) but not deectorImpl.cpp)
- blackfin programing made seamless (nCE fixed which helps)
-save settings file for m3 and eiger
- m3 threshold changes
- g2 and m3 clkdiv 2 (system clock) change should affect time settings (g2: exptime, period, delayaftertrigger, burstperiod, m3: exptime, gatedelay, gateperiod, period, delayaftertrigger)
- g2 system frequency is the same irrespective of timing source
- (apparently) rxr doesnt get stuck anymore from 6.1.1
-rx_bunchsize, (default fifodepth for g2 changed to 50)
- rxr mem size changed (fifo header size from 8 to 16) due to sls rxr header = 112.. 112+ 16=128 (reduces packet losss especially for g2)
-udp_srcip and udp_Srcip2: can set to auto (for virtual or 1g data networks)
- set dataset name for all hdf5 files to "data" only
- number of storage cells is not updated in teh receiver. done. and also allowing it to be modified in running status
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 +108,22 @@ 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 +140,36 @@ 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
-------------
@ -116,106 +86,29 @@ 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
-------
@ -375,38 +223,24 @@ Download
^^^^^^^^^^^^^
- detector server corresponding to package in slsDetectorPackage/serverBin
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)
@ -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).
The choice of the level of the comparator threshold plays a very important role in counting systems since it influences the efficiency of the detector as well as its spatial resolution (for details see the paper Bergamaschi, A. et al. (2010). J. Synchrotron Rad. 17, 653-668).
Single-photon-counting detectors are sensitive to single photons and the only limitation on the fluctuations of the number of counts is given by the Poisson-like statistics of the X-ray quanta.
The digitized signal does not carry any information concerning the energy of the X-rays and all photons with an energy larger than the threshold are counted as one bit. This means that the choice of the correct comparator threshold level is critical in order to obtain good-quality data.\\
Figure~\ref{fig:thrscanexpl} shows the expected number of counts as a function of the threshold energy for $N_0$ monochromatic X-rays of energy $E_0$. This is often denominated S-curve and can be interpreted as the integral of the signal spectrum between the threshold level and infinity.
The dashed curve represents the behavior of an ideal counting system: nothing is counted for thresholds larger than the photon energy and all the $N_0$ X-rays are counted for thresholds lower than $E_0$.
The thick solid line represents the physical curve which also takes into account the electronic noise and the charge sharing between channels.
The intrinsic noise on the electronic signal is defined by the Equivalent Noise Charge ($ENC$). The $ENC$ describes noise in terms of the charge at the detector input needed to create the same output at the end of the analog chain and is normally expressed in electrons. For silicon sensors, it can be converted into energy units by considering 1~$e^-$=3.6~eV.
The value of the $ENC$ normally depends on the shaping settings of the analog chain and increases with shorter shaping times.
The resulting electronic signal spectrum is then given by a convolution between the radiation spectrum and the noise i.e., a Gaussian of standard deviation $ENC$.
The S-curve for a monochromatic radiation beam is well described by a Gaussian cumulative distribution $D$ with an additional increase at low threshold due to the baseline noise, as shown by the solid thin line.
Moreover, when a photon is absorbed in the region between two strips of the sensor, the generated charge is partially collected by the two nearest electronic channels. For this reason the physical S-curve is not flat but can be modeled by a decreasing straight line. The number of shared photons $N_S$ is given by the difference between the number of counts and the number of X-rays whose charge is completely collected by the strip (shown by the dotted line).
The number of counts in the physical case is equal to that in the ideal case for a threshold set at half the photon energy. This defines the optimal threshold level $E_t=E_0/2$.\\
The detector response $N$ as a function of the threshold energy $E_t$ is given by the sum of the noise counts $N_n$ and the counts originating from photons $N_\gamma$:
where $C_s$ is the fraction of photons which produce a charge cloud which is shared between neighboring strips ($N_s=C_s N_0$).\\
By assuming a noise of Gaussian type, and considering its bandwidth limited by the shaping time $\tau_s$, the number of noise counts in the acquisition time $T$ can be approximated as:
\begin{equation}
N_n(E_t) \sim\frac{T}{\tau_s} D \Big(\frac{-E_t}{ENC}\Big). \label{eq:noisescan}
\end{equation}
The choice of the comparator threshold level $E_t$ influences not only the counting efficiency and noise performances, but also the spatial resolution and the counting statistics of the detector.
If the threshold is set at values higher than the ideal value $E_t=E_0/2$, a fraction of the photons absorbed in the sensor in the region between two strips is not counted thus reducing the detector efficiency but improving its spatial resolution (narrower strip size). On the other hand, if the threshold is set at values lower than $E_t$, part of the X-rays absorbed in the region between two strips are counted by both of them, resulting in a deterioration of the spatial resolution of the detector and of the fluctuations on the number of photons because of the increased multiplicity.
Furthermore, the threshold uniformity is particularly critical with regards to fluorescent radiation emitted by the sample under investigation. Since the emission of fluorescent light is isotropic, the data quality will be improved by setting the threshold high enough in order to discard the fluorescence background (see figure~\ref{fig:thrscanfluo}). \\
Moreover, setting the threshold too close to the energy of the fluorescent light gives rise to large fluctuations between channels in the number of counts since the threshold sits on the steepest part of the threshold scan curve for the fluorescent background. These differences cannot be corrected by using a flat-field normalization since the fluorescent component is not present in the reference image. For this reason, it is extremely important that the threshold uniformity over the whole detector is optimized. The threshold level must be set at least $\Sigma>3\,ENC$ away from both the fluorescent energy level and the X-ray energy in order to remove the fluorescence background while efficiently count the diffracted photons.
The comparator threshold is given by a global level which can be set on a module basis and adds to a component which is individually adjustable for each channel. In order to optimize the uniformity of the detector response it is important to properly adjust the threshold for all channels. \\
Since both the signal amplification stages and the comparator are linear, it is necessary to calibrate the detector offset $O$ and gain $G$ in order to correctly set its comparator threshold $V_t$ at the desired energy $E_t$:
\begin{equation}
V_{t}=O+G \cdot E_t.\label{eq:encal}
\end{equation}
This is initially performed by acquiring measurements while scanning the global threshold using different X-ray energies and calculating the median of the counts at each threshold value for each module $i$. The curves obtained for one of the detector modules at three energies are shown in figure~\ref{fig:modulecalibration}. The experimental data are then fitted according to equation~\ref{eq:thrscan} and for each module a linear relation is found between the X-ray energy and the estimated inflection point, as shown in the inset of figure~\ref{fig:modulecalibration}. The resulting offset $O_i$ and gain $G_i$ are used as a conversion factor between the threshold level and the energy.
\begin{figure}
\caption{Expected counts as a function of a threshold energy for a monochromatic beam of energy $E_0$=12~keV. $N_0$=10000 is the number of photons absorbed by the detector during the acquisition time. The dashed line represents the curve in an ideal case without electronic noise and charge sharing, the solid thin line with noise $ENC$=1~keV but without charge sharing and the solid thick line is the physical case with noise and $CS=$22~\% charge sharing. $N_S$ is the number of photons whose charge is shared between neighbouring strips ($CS=\frac{N_S}{N_0}$). The dotted line represents the number of photons whose charge is completely collected by a single strip.}\label{fig:thrscanexpl}
\includegraphics[width=\textwidth]{fig4.eps}
\end{figure}
\begin{figure}
\caption{Measured threshold scan at 12.5~keV with the three different settings. In the inset the fit of the experimental data with the expected curve as in function~\ref{eq:thrscan} is shown in the region of the inflection point.}\label{fig:expthrscan}
\includegraphics[width=\textwidth]{fig5.eps}
\end{figure}
\begin{figure}
\caption{Number of counts as a function of the threshold measured from a sample containing iron ($E_f$=5.9~keV) when using X-rays of energy $E_0$=12~keV. In this case, setting the threshold at $E_0/2$, which is very close to $E_f$, would give $\Delta\sim$10\% counts from the fluorescense background. Therefore the threshold should be set at an intermediate level $E_t$ between the two energy components with a distance of at least $\Sigma>3ENC$ from both $E_f$ and $E_0$.}\label{fig:thrscanfluo}
\includegraphics[width=\textwidth]{fig7.eps}
\end{figure}
Differences in gain and offset are present also between individual channels within a module and therefore the use of threshold equalization techniques (trimming) using the internal 6-bit DAC is needed in order to reduce the threshold dispersion.
Since both gain and offset have variations between channels, the optimal trimming should be performed as a function of the threshold energy.
Please not that trimming of the channels of the detector should be performed in advanced and is extremely important for a succeful energy calibration of the detector.
All energy calibration procedures should be applied to a trimmed detector and only an improvement of the existing trimbits can be performed afterwards, since it does not significatively affect the energy calibration.
\begin{figure}
\caption{Median of the number of counts as a function of the threshold for X-rays of 12.5, 17.5 and 25~keV for one of the detector modules using \textit{standard} settings. The solid line represents the fit of the experimental points with equation~\ref{eq:thrscan}. In the inset the linear fit between the X-ray energy and the position of the inflection point of the curves is shown.}\label{fig:modulecalibration}
\includegraphics[width=\textwidth]{fig8.eps}
\end{figure}
\newpage
\section{Data acquisition}
The energy calibration consists in acquiring threshold scans using the detector at at least 2 (better 3) energies. A monochromatic beam is ideal in this procedure, but beam obtained from some fluorescent sample is also good.\\
Please note that the statistic is important to succesfully analyze the data. Normally the exposure time for each step should be chosen in order to achieve at least 1000 counts per step.
If this is not possible it is better to reduce the scan range or enlarge the scan step rather than acquiring data with a too low statics.
With a quick acquisition or threshold scan it is useful to define the range of the scan and the exposure time. It is important to start from a threshold high enough that (almost) all channels of the detector have a negligible number of counts and that the plateau of the S-curve is long enough to correctly estimate the number of photons.
\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 the following the command to acquire a dataset for the energy calibration with an exposure time of 1~s, and threshold scan range between 200 and 850 with a setp of 1 DAC unit.
\begin{verbatim}
> sls_detector_put encallog 1 #setup energy calibration
> sls_detector_put exptime 1. #set exposure time to 1s
> sls_detector_put scan0range 200 850 1 #set scan range between 200 and 850, step of 1
> sls_detector_acquire #acquire the data
> sls_detector_put encallog 0 #unset energy calibration
\end{verbatim}
With the GUI you can obtain the same results by clicking on the \textit{Energy Calibration} log button in the advanced tab (see figure~\ref{fig:guiencallog}) and setting up the threshold scan in the Actions tab (see figure~\ref{fig:guithrscan}). the exposure time should also be set in the measurement tab.
This procedure should be executed at at least 2 (better 3) energies.
Additional to the data files, the acquisition will produce a .encal file containing an header and, for each step of the acquisition, the threshold value and the file name. \\
In case you forgot to enable the encallog flag in the software, you can produce the file with the syntax as follows:
\begin{verbatim}
settings standard
type Mythen+
nmod 12
modulenumber:0 000
modulenumber:1 111
modulenumber:2 222
modulenumber:3 333
modulenumber:4 444
modulenumber:5 555
modulenumber:6 666
modulenumber:7 777
modulenumber:8 888
modulenumber:9 999
modulenumber:10 aaa
modulenumber:11 bbb
450 standard_12_4keV_S450_0
460 standard_12_4keV_S460_0
470 standard_12_4keV_S470_0
480 standard_12_4keV_S480_0
490 standard_12_4keV_S490_0
500 standard_12_4keV_S500_0
510 standard_12_4keV_S510_0
520 standard_12_4keV_S520_0
...
...
\end{verbatim}
\begin{figure}
\caption{Acquisition GUI window to enable the energy calibration log.}\label{fig:guiencallog}
The data analysis consists in fitting the S-curves obtained from the datasets acquired as above and then performing a linear fit between the energy values and the inflection points.
\subsection{Software}
The software used for the energy 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}
> ./energyCalibrationWizard
\end{verbatim}
To add anew energy write the energy value and select (or digit) the name of the .encal file corresponding to that energy (see figure~\ref{fig:addenergy}).\\
The software assumes that the data files (.raw) and the .encal file are in the same directory.
Press \textit{Preview} and a 2D color plot will be displayed, showing the channel numbers on the X-axis, the threshold on the Y-axis, and the number of counts as a color scale.
By (right) clicking close to the axis you are able to zoom in/out, set the scale to logarithmic etc.\\
If the plot corresponds to your expectations press \textit{Add to list}. The energy value will be shown in the combo box on top and labels will display the settings of the detector, the number of modules, the number of channels per module and the modules serial numbers.
Add then all the other energies to the calibration always by editing the energy value and .encal file name, pressing \textit{preview} and \textit{add to list}.\\
If the settings, number of modules or serial numbers do not match, you will not be llowed to add the energy.\\
By using the \textit{selected energy actions} you can navigate in the combo box with list of energies, view the plots and eventually remove the ones you don't want to use in your calibration.\\
Once you have uploaded at least 2 energies, you will be allowed to \textit{proceed to module calibration}.
\begin{figure}
\caption{Window to add energies to the calibration.}\label{fig:addenergy}
\includegraphics[width=\textwidth]{addEnergy.eps}
\end{figure}
In the module calibration window (see figure~\ref{fig:calibratemodule}), you are still able to look at the calibration summary, and eventually return to the previous windown by pressing \textit{Back to energy setup}.\\
The canvas will show the plot of the S-curves relative to the median of the selected module, fitted with equation~\ref{eq:thrscan} and the linear fit between the energy values and the fitted inflection points.
Normally the points lie on a straight line (although often not perfect), therefore it should be simple to spot if there are problems in the fitting of some of the data.\\
If \textit{Manual save} is unclicked, the calibration files will be saved locally, with the extension automatically generated by using the modules serial numbers, every time a linear fit is performed (i.e. if you mess up wiht the linear fit you overwrite a previous good file!). If you click the checkbox, you need to save the calibration by pressing \textit{Write to file} for each module once you are happy with the fit.
To change the Y scale of the plot, edit the \textit{Counts} entry. After clicking of the energy button (eventually twice) the maximum of the histogram will be set to three times the value.
To re-fit one energy with modified range or start parameters, you should press the central button with the energy value once the energy is selected. The text color tells you which curve you are referring to.\\
You should set the range of the fit. In particular the maximum should be limited in order to avoid to enter the noise range (and can be pretty different for the various modules).\\
Normally the data are acquired by collecting holes from the detector and therefore the \textit{Invert axis} check button should be ckecked. Uncheck it in case your detector collects electrons (e.g. CdTe, Si n in p)
You can change the start values of the parameters of the fits by editing the number eneries. The label nearby will show you the actual value of the fitted parameters.\\
By checking the checkboxes you can fix the values to the ones you specify.\\
Normally it can be useful to fix the pedestal and pedestal slope to 0, unless you have a lot of 3rd armnonics contribution, primary beam background or similar.\\
Changing the starting value of the inflection point or of the number of counts can often help the fit to converge.\\
Normally it is not very useful to change the starting value for the noise or charge sharing slope.
The button \textit{Finished} will be enebled only once the calibration files have been generated for all modules.
\begin{figure}
\caption{Window to calibrate the modules.}\label{fig:calibratemodule}
To use the genrated calibration files as default ones, copy them into your default \textit{caldir/settings} renaming them calibration.snxxx, where snxxx is the extension that the genrated files already have, which corresponds to the module serial number.\\
Fot this scope, a script as following can be used:
\begin{verbatim}
for i in $(ls newcal_standard.sn* | awk -F "." '{print $2}'); do \
By reloading the default detector settings, the calibration coefficients will be automatically loaded.
Some files were not shown because too many files have changed in this diff
Show More
Reference in New Issue
Block a user
Blocking a user prevents them from interacting with repositories, such as opening or commenting on pull requests or issues. Learn more about blocking a user.
