Contents
pnCCD overview
Large area pnCCD DAQ and Elictronics, Lothar Struder & Robert Hartmann
Data for tests
On 2014-01-27 Sebastian Carron kindly provide us with data files for pnCCD experiment amoa1214:
- Dark Run: 169, rear sensors gain 1/64, front 1/1, Imaging mode exp=amoa1214:run=169
- Run With Hits: 170 Low hit rate though, so you will have to use a hit finder of sorts exp=amoa1214:run=170
Psana modules for pnCCD
Module ImgAlgos.PnccdNDArrProducer
- Get from the event store
Psana::PNCCD::FramesV1, - Put in the event store
ndarray<constT,3>, where shape=[4][512][512], T=uint16_t, int, float, double, int16_t
Performance: ~13 ms/event
Modified module ImgAlgos.PnccdImageProducer
- Get from the event store
Psana::PNCCD::FullFrameV1orndarray<const T,3>orndarray<constT,3>
forsourceandkeyparameters - Put in the event store
ndarray<constT,2>, where shape=[1024+gap][1024], T= input type
Performance: ~30 ms/event (copy involves inverse iteration for 180 degree rotation of two bottom frames)
Sequence of modules for raw image averaging
ImgAlgos.PnccdImageProducer - get Psana::PNCCD::FullFrameV1, put ndarray<const uint16_t, 2>
ImgAlgos.NDArrAverage - averages ndarray<const T, 2>, save in file
Sequence of modules for calibrated image or ndarray averaging
ImgAlgos.PnccdNDArrProducer - get Psana::PNCCD::FramesV1, put ndarray<const T, 3>
ImgAlgos.NDArrCalib - getinput (raw) ndarray<const T, Ndim>, put calibrated ndarray<const T, Ndim>
ImgAlgos.PnccdImageProducer - get ndarray<const T,3>, put ndarray<const T, 2>
ImgAlgos.NDArrAverage - averages ndarray<const T, 2> or ndarray<const T,3>, save in file
"Natural order" for common mode correction in pnCCD ndarray
pnCCD image has intensity "strips" in both dimensions;
[4][512][512] array for single event and averaged over 1000 events:
At large number of events common mode should be averaged out. For 1000 events horizontal intensity "stripes" have gone.
This proves that common mode should be evaluated for horizontal stripes.
Data corrections in module ImgAlgos.NDArrCalib
Midule description: Module ImgAlgos::NDArrCalib
List of parameters in configuration file
[ImgAlgos.NDArrCalib] source = DetInfo(Camp.0:pnCCD.0) key_in = pnccd-ndarr key_out = calibrated do_peds = yes do_cmod = no do_stat = no do_mask = no do_bkgd = no do_gain = no do_nrms = no do_thre = yes fname_bkgd = fname_mask = masked_value = 0 threshold_nrms = 0 threshold = 100.0 below_thre_value = 50 bkgd_ind_min = 0 bkgd_ind_max = 1000 bkgd_ind_inc = 2 print_bits = 11
2014-02-10 Test of the module ImgAlgos.NDArrCalib
Dark run: exp=amoa1214:run=7, all plots are shown for Camp.0:pnCCD.0 event 5
pedestals and pixel_rms are generated by the calibman for arrays of shape=[4,512,512] using the same run.
Raw data
All do_* = no - that means no correction is applied
Pedestals
do_peds = yes
file with pedestals is loaded automatically from
/reg/d/psdm/AMO/amoa1214/calib/PNCCD::CalibV1/Camp.0:pnCCD.0/pedestals/1-end.data
Common mode
do_peds = yes do_cmod = yes
files with pedestals and common_mode are loaded automatically from
/reg/d/psdm/AMO/amoa1214/calib/PNCCD::CalibV1/Camp.0:pnCCD.0/pedestals/1-end.data
/reg/d/psdm/AMO/amoa1214/calib/PNCCD::CalibV1/Camp.0:pnCCD.0/common_mode/1-end.data
where common mode parameters were set preliminary as:
echo "1 300 50 256 0.2" > /reg/d/psdm/AMO/amoa1214/calib/PNCCD::CalibV1/Camp.0:pnCCD.0/common_mode/1-end.data
Average over each consecutive group of 256 pixels
Common mode subtraction improves the width of intensity distribution.
Pixel status
do_stat = yes
masked_value=0
Calibration type: pixel_status (0-good, 1,2,4,...-bad)
File with pixel status mask was produced in Calibration Manager ROI Mask application
/reg/d/psdm/AMO/amoa1214/calib/PNCCD::CalibV1/Camp.0:pnCCD.0/pixel_status/7-7.data
Set bad pixels (1) in the half of frame[1]:
Mask
do_mask = yes
fname_mask = pnccd-test-mask.txt
masked_value=0
Background
do_bkgd = yes
fname_bkgd = pnccd-test-mask.txt
For this test the file with pedestals is used:
Gain
do_gain = yes
file with gain factors is loaded automatically from
/reg/d/psdm/AMO/amoa1214/calib/PNCCD::CalibV1/Camp.0:pnCCD.0/pixel_gain/7-7.data
Fot this test all gains for [4,512,512] pixels were set to 0.5
N*RMS Threshold
do_nrms = yes
below_thre_value = 0
threshold_nrms = 0.5
file with rms values is loaded automatically from
/reg/d/psdm/AMO/amoa1214/calib/PNCCD::CalibV1/Camp.0:pnCCD.0/pixel_rms/1-end.data
Common Threshold
do_thre = yes
below_thre_value = 0
threshold = 100
Test for amob33314 run 167
Evaluate parameters in Calibration Manager
for types
- pedestals
- pixel_status for rms threshold = 15 ADU
- pixel_rms
Camp.0.pnCCD.0
Camp.0.pnCCD.1
Raw data average and rms
Pedestals subtracted average and rms
Pedestals and common mode subtracted average and rms
echo "1 50 10 128 0.2" > /reg/d/psdm/AMO/amob3313/calib/PNCCD::CalibV1/Camp.0:pnCCD.0/common_mode/167-167.data
Support of pnCCD in Calibration Manager
In dark run processing in Calibration Manager produces pedestals and pixel_rms. Then, if thresholds on rms and averaged intensity are set correctly, the pixel_status can be also produced and deployed under the calib directory. Calibration manager works with arrays of shape=[4,512,512]. Embedded ROI Mask Editor can be used to generate the ROI mask for pnCCD.
Get latest version of calibman
Run Calibration Manager from current release (for release version ≥ ana-0.10.12):
ssh -Y psana cd <your-favorite-NON-RELEASE-directory> sit_setup calibman
If CalibManager or other packages were recently updated and these updates are wanted to be used:
ssh -Y psana cd <your-favorite-directory> newrel ana-current <release-directory> cd <release-directory> sit_setup addpkg CalibManager HEAD; addpkg <package-name-2> HEAD; addpkg <package-name-3> HEAD; ... scons; calibman
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