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Table of Contents

 

pnCCD overview

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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

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Common mode correction in pnCCD ndarray

pnCCD image has intensity "strips" in both dimensions;

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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

Midule 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:

Code Block
[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

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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

...

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.

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Code Block
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

Code Block
# 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.

Note

  • 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

Code Block
[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

Code Block
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

Code Block
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:

Image AddedImage Added

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

 

References