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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<const T,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::FullFrameV1 or ndarray<const T,3> or ndarray<const T,3>
    for source and key parameters
  • Put in the event store   ndarray<const T,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

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.

Due to specifics of pnCCD DAQ readout, it is recommended to evaluate common mode for consecutive groups of 128 pixel in the  [4][512][512] array.

 

Data corrections in module ImgAlgos.NDArrCalib

Module description: Module ImgAlgos::NDArrCalib 

List of parameters in configuration file

Module ImgAlgos::NDArrCalib is controlled by the list of parameters in the configuration file for psana, for example:

[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

Region of interest (ROI) mask can be generated by the Mask Editor.

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

 

Image of pnCCD

pnCCD image can be reconstructed from data by two methods using

  1. Module ImgAlgos::PnccdImageProducer and
  2. Module ImgAlgos::NDArrImageProducer

Examples of the first method are available in psana - Module Examples

Second method is available since release ana-0.13.14 (package PSCalib V00-02-40).

It allows to reconstruct image using generic Detector Geometry technique with geometry file. Current version of pnCCD has a solid structure without moving parts, hence the main part of the geometry file is unchanged. Example of the geometry file for pnCCD can be found in /reg/g/psdm/detector/alignment/pnccd/amo-pnccd.1-2015-01-23/calib/PNCCD::CalibV1/Camp.0:pnCCD.1/geometry/0-end.data, which essential part is

# HDR PARENT IND      OBJECT   IND    X0[um]  Y0[um]  Z0[um]   ROT-Z ROT-Y ROT-X    TILT-Z   TILT-Y   TILT-X
DETPNCCD:V1    0    PNCCD:V1     0         0       0       0       0     0     0    0.0      0.0      0.0
DETPNCCD:V1    0    PNCCD:V1     1     76725   38325       0     180     0     0    0.0      0.0      0.0
DETPNCCD:V1    0    PNCCD:V1     2     76725   77925       0     180     0     0    0.0      0.0      0.0
DETPNCCD:V1    0    PNCCD:V1     3         0   39600       0       0     0     0    0.0      0.0      0.0
#IP:V1         0    DETPNCCD:V1  0     38400   39000   10000     -90     0     0    0.0      0.0      0.0

The last commented line in this file can be un-commented in order to rotate and translate detector relative to IP.


  • The name of the segment PNCCD:V1 should be unchanged. Other names DETPNCCD:V1 and IP:V1 are optional.
  • Four segment coordinates are given in µm and it is assumed that each segment has 512x512 pixels of size 75x75µm².
  • All coordinates are given in matrix-like frame, where X axis goes from top to bottom, Y - from left to right.
  • Gap is set to 16 pixels and may be a subject of calibration.

 

 

Example of the configuration file psana-amoa1214-r0108-pnccd-NDArrImageProducer.cfg

[psana]                                                              
# psana -m EventKeys -n 3 exp=amoa1214:run=108
#calib-dir = /reg/d/psdm/AMO/amoa1214/calib
files = exp=amoa1214:run=108
events = 10
 
modules = ImgAlgos.PnccdNDArrProducer \
          ImgAlgos.NDArrCalib \
          ImgAlgos.NDArrImageProducer \
          ImgAlgos.NDArrAverage:nda \
          ImgAlgos.NDArrAverage:img-geo \
          ImgAlgos.Tahometer
 
[ImgAlgos.PnccdNDArrProducer]
source  = DetInfo(Camp.0:pnCCD.1)
key_in  =
key_out = pnccd-ndarr
outtype = asdata
print_bits = 0
 
[ImgAlgos.NDArrCalib]
source = DetInfo(Camp.0:pnCCD.1)
key_in = pnccd-ndarr
key_out = calibrated
do_peds = yes
do_cmod = yes
do_stat = yes
do_mask = no
do_bkgd = no
do_gain = no
do_nrms = no
do_thre = no
#fname_mask = pnccd-test-mask.txt
#fname_bkgd = pnccd-test-bkgd.txt
masked_value     =    0
threshold_nrms   =  4.0
threshold        =  100
below_thre_value =    0
bkgd_ind_min     = 10000
bkgd_ind_max     = 10200
bkgd_ind_inc     =    1
print_bits       =    1
 
[ImgAlgos.NDArrAverage:nda]
source       = DetInfo(Camp.0:pnCCD.1)
key          = calibrated
avefile      = pnccd-nda-ave
rmsfile      = pnccd-nda-rms
#maskfile     = pnccd-nda-msk
#hotpixfile   = pnccd-nda-hot
thr_rms_ADU  = 0
thr_min_ADU  = 2
thr_max_ADU  = 65000
print_bits   = 29

[ImgAlgos.NDArrImageProducer]
#calibdir = ./calib
calibdir = /reg/g/psdm/detector/alignment/pnccd/amo-pnccd.1-2015-01-23/calib
source       = DetInfo(Camp.0:pnCCD.1)
key_in       = calibrated
key_out      = pnccd-img-geo
print_bits   = 1

[ImgAlgos.NDArrAverage:img-geo]
source       = DetInfo(Camp.0:pnCCD.1)
key          = pnccd-img-geo
avefile      = pnccd-img-geo-ave
rmsfile      = pnccd-img-geo-rms
#maskfile     = pnccd-img-geo-msk
#hotpixfile   = pnccd-img-geo-hot
thr_rms_ADU  = 0
thr_min_ADU  = 2
thr_max_ADU  = 65000
print_bits   = 29

[ImgAlgos.Tahometer]
dn         = 100
print_bits = 7

uses psana modules

  • ImgAlgos.PnccdNDArrProducer  - gets pnCCD data and put it as ndarray in the event store
  • ImgAlgos.NDArrCalib - applys calibrations to ndarray
  • ImgAlgos.NDArrImageProducer - produces calibrated image
  • ImgAlgos.NDArrAverage:nda - averages calibrated ndarray
  • ImgAlgos.NDArrAverage:img-geo - averages calibratedimage

This script can be executed by the command

psana -c psana-amoa1214-r0108-pnccd-NDArrImageProducer.cfg

which saves averaged and RMS files for calibrated ndarray and image, which can be plotted by the command plims <file-name>. For eample

plims pnccd-nda-ave-amoa1214-r0108.dat
plims pnccd-img-geo-ave-amoa1214-r0108.dat

plot images with intensity distributions for ndarray and image, respectively:

Masks and other calibration files for pnCCD and image can be generated with calibman.

 

References

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