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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

...

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.

...

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