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Table of Contents

This note describes area detector interface methods to access raw and calibrated data, reconstruct image for mutli-panel detector, retrieve calibration constants, geometry parameters, define the mask for pixel array, etc.

Set environment

Code discussed in this note works on psana nodes which have access to data in lcls2 environment described in LCLS-II psana Environment.

To run examples one has to ssh to psana node and set environment

Code Block
titleLogin to psana node and set lcls2 environment on pcds
collapsetrue
ssh -Y pslogin.slac.stanford.edu
ssh -Y psana
source /cds/sw/ds/ana/conda1/manage/bin/psconda.sh
Code Block
titleLogin to psana node and set lcls2 environment on s3df
ssh -Y s3dflogin.slac.stanford.edu
ssh -Y psana
source /sdf/group/lcls/ds/ana/sw/conda1/manage/bin/psconda.sh

Code examples

Most truthful updated description of this interface is on git : in the head of the file detector/areadetector.py

Create DataSource, Run, and Detector objects

...

Code Block
kwa = <dict-of-mask-parameters>
a = o.calib(evt, cmpars=(7,2,100,10), **kwa)
a = o.image(evt, nda=None, **kwa)

...

 # reduced shape for available segment only
a = o.image(evt, nda=None, value_for_missing_segments=800, **kwa) # full image including missing segments

Calibration constants

All detector calibration constants (np.array) and associated  metadata (dict) are available through the dictionary det.calibconst with calibration type as a key. For example:

...

Possible calibration types: pedestals, pixel_status,  pixel_rms,  pixel_gain, pixel_mask, etc.

Other useful area detector methods

Mask

See for details Area detector mask examples.

Code Block
titleInstantiation of the Mask object
from psana.detector.mask import Mask, DTYPE_MASK

kwa = {'status':True, 'status_bits':0xffff, 'stextra_bits':(1<<64)-1, 'gain_range_inds':(0,1,2,3,4),\
       'neighbors':False, 'rad':3, 'ptrn':'r',\
       'edges':False, 'width':0, 'edge_rows':10, 'edge_cols':5,\
       'center':False, 'wcenter':0, 'center_rows':5, 'center_cols':3,\
       'calib':False,\
       'umask':None,\
       'force_update':False, 'dtype':DTYPE_MASK}

m = Mask(det, **kwa)

m = Mask(det) # minimal version.
Code Block
titleCombined and separate mask methods
m.set_mask(**kwa) # forced update of cached mask.
mask = m.mask(**kwa) # returns cached mask.
mask = m.mask_default
Code Block
# access calibration constants and derived arrays
peds = o._pedestals()
gain = o._gain() # ADU/keV
gfac = o._gain_factor() # keV/ADU
rms  = o._rms()
status = o._status()

mask = o._mask_default(dtype=DTYPE_MASK)
mask = o._mask_calib()
mask = om._mask_calib_or_default(dtype=DTYPE_MASK)) # if available returns mask from "pixel_mask" calibration type, otherwise array of ones.
mask = om._mask_from_status(status_bits=0xffff, stextra_bits:(1<<64)-1, gain_range_inds=(0,1,2,3,4), dtype=DTYPE_MASK, **kwa)
mask = om._mask_neighbors(mask, rad=9, ptrn='r')
mask = o._mask_edges(width=0, edge_rows=1, edge_cols=1, dtype=DTYPE_MASK, **kwa)
mask = om._mask_center(wcenter=0, center_rows=1, center_cols=1, dtype=DTYPE_MASK, **kwa)
mask = om._mask(status=True, status_bits=0xffff, gain_range_inds=(0,1,2,3,4)\
               neighbors=False, rad=3_neighbors(mask, rad=9, ptrn='r',\
               edges)
  • default combined mask parameters (status=True,

...

  • neighbors=False, edges=False, center=False, calib=False, umask=None) are set to define mask for pixel_status only.
  • mask is used in det.raw.calib/image mask at evaluation of common mode correction, but by default it is not applied to data.
  • to apply mask to data use multiplication calib *= mask.

Other useful area detector methods

Code Block
# direct access to calibration constants and derived arrays
peds = o._pedestals()
gain = o._gain() # ADU/keV
gfac = o._gain_factor() # keV/ADU
rms  = o._rms()
status = o._status(0, edge_rows=10, edge_cols=5,\
               center=True, wcenter=0, center_rows=5, center_cols=3,\
               calib=False,\
               umask=None,\
               force_update=False)

arrx, arry, arrz = o._pixel_coords(do_tilt=True, cframe=0)
indx, indy, indz = o._pixel_coord_indexes(pix_scale_size_um=None, xy0_off_pix=None, do_tilt=True, cframe=0)
  
# array of the common mode increment
incr = o._common_mode_increment(evt, cmpars=(0,7,100,10))

References