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Code Block
log in to psana<XXXX>
kinit
cd <your-favorite-directory>

newrel ana-current <your-release-directory-name>
cd <your-release-directory-name>
sit_setup
addpkg PyCSPadImage HEAD

python PyCSPadImage/src/Examples.py 1

External parameters

CSPAD geometry is varying for different detectors, experiments, or even runs. In order to keep track on all these variations LCLS offline has a simple calibration data base, which works as explained in CSPad Alignment. In order to get correct CSPAD alignment parameters the pass to the calibration directory should be specified like thisHDF5 data file:

Code Block
   fname path_calib = '/reg/d/psdm/CXIxpp/cxi80410/calib/CsPad::CalibV1/CxiDs1.0:Cspad.0'

If the detector configuration was changed during the experiment, then more than one calibration file should be available for the run ranges with stable configuration.
In order to access correct calibration file the run number should be provided, for example

xpptut13/hdf5/xpptut13-r0150.h5' # to test XPP data
   fname = '/reg/d/psdm/cxi/cxitut13/hdf5/cxitut13-r1150.h5' # to test CXI data

Path to the directory with calibration types:

Code Block
    runnum = 628

Data for CSPAD image and the detector configuration can be obtained from the HDF5 file, dataset name, and event number for example

Code Block

    fname  path_calib = '/reg/d/psdm/CXI/cxi80410/calib/CsPad::CalibV1/CxiDs1.0:Cspad.0/'
   path_calib = '/reg/d/psdm/xpp/CXIxpptut13/cxi80410/hdf5/cxi80410-r0628.h5calib/CsPad::CalibV1/XppGon.0:Cspad.0/'

Known dataset names

Code Block
  
   '
    dsname = '/Configure:0000/Run:0000/CalibCycle:0000/CsPad::ElementV2/CxiDs1.0:Cspad.0/data'
   dsname  event  = 34
Note
  • In principal, the path to the calibration data types can be defined automatically, but there is a chance that user would want to keep calibration files in non-standard place.
  • The CSPad dataset can be also found automatically, but there might be more than one CSPad detector in experiment.

In further description we assume that this set of external parameters is defined.

Import modules

In code snippets below we use definitions of modules and libraries as follows

Code Block

import numpy              as np

import CalibPars          as calp
import CalibParsEvaluated as cpe
import CSPadConfigPars    as ccp
import CSPadImageProducer as cip

import GlobalGraphics     as gg
import HDF5Methods        as hm

Reconstruction of CSPAD image

Entire code example for image reconstruction is

Code Block

    calp.calibpars.setCalibParsForPath ( run=runnum, path=path_calib )
    ds1ev = hm.getOneCSPadEventForTest( fname, dsname, event )
    cspadimg = cip.CSPadImageProducer(rotation=0, tiltIsOn=True, mirror=True)
    arr = cspadimg.getCSPadImage( ds1ev )

First, one has to set the correct version of the calibration parameters

Code Block

    calp.calibpars.setCalibParsForPath ( run=runnum, path=path_calib )

Then, one need in CSPAD dataset for event,

Code Block

    ds1ev = hm.getOneCSPadEventForTest( fname, dsname, event )

this method returns the CSPAD data as a numpy array for one event, ds1ev.shape=(Nseg, 185, 388), where Nseg?32.

Note

It is recommended to use this method, which also loads correct configuration parameters from HDF5 file.
Default version of the configuration parameters can be wrong, if not all 2x1 are in use.

Then, one has to initialize the object of the class CSPadImageProducer

Code Block

    cspadimg = cip.CSPadImageProducer(rotation=0, tiltIsOn=True, mirror=True)

with optional parameters

  • rotation integer from 0 to 3 parameters for CSPAD orientation as 90*rotation degree.
  • tiltIsOn = True or False - to account or not the tiny tilt angle of 2x1 sections.
  • mirror = True or False - to mirror reflect or not the image.

Finally the method

Code Block

    arr = cspadimg.getCSPadImage( ds1ev )

returns the 2-d numpy array with CSPAD image, which can be plotted using for example matplotlib.

CSPAD pixel coordinate arrays

CSPAD pixel coordinate arrays can be evaluated/returned in two different shapes:

  1. for entire CSPAD with shape=(4,8,185,388)
  2. for data-driven shape=(Nseg,185,388), where Nseg?32 if some quads/segments are missing in data.

To get pixel coordinate arrays shaped for entire CSPAD use code:

Code Block

    calp.calibpars.setCalibParsForPath ( run=runnum, path=path_calib )
    cpe.cpeval.evaluateCSPadPixCoordinates (rotation=0, mirror=False)
    xpix, ypix = cpe.cpeval.getCSPadPixCoordinates_pix()

where the parameters rotation and mirror have the same meaning as before,
xpix and ypix are the coordinate (in pixels) arrays with shape = (4,8,185,388).
Method xpix_um, ypix_um = cpe.cpeval.getCSPadPixCoordinates_um() returns pixel coordinates in micrometer.

To get CSPAD pixel coordinate arrays shaped as in data use code:

Code Block

    calp.calibpars.setCalibParsForPath ( run=runnum, path=path_calib )
    cpe.cpeval.evaluateCSPadPixCoordinatesShapedAsData(fname,dsname,rotation=0,mirror=False)
    xpix, ypix = cpe.cpeval.getCSPadPixCoordinatesShapedAsData_pix()

where xpix and ypix are the coordinate (in pixels) arrays with shape = (Nseg,185,388).
Note that the fname and dsname need to be specified in order to get configuration of the data array.
Method xpix_um, ypix_um = cpe.cpeval.getCSPadPixCoordinatesShapedAsData_um() returns pixel coordinates in micrometer.

The coordinate arrays extracted for both shapes are tested in module Examples.py by the methods
example_of_image_built_from_pix_coordinate_array_shaped_as_data() and
example_of_image_built_from_pix_coordinate_array_for_entire_cspad(),
where images are reconstructed through the pixel coordinate arrays in
cpe.cpeval.getTestImageShapedAsData(ds1ev) and
cpe.cpeval.getTestImageForEntireArray(ds1ev), respectively.

Note

The last two methods use implicit loops over all pixels, that works pretty slow in Python. These modules are used for test only and are not recommended for real applications.

...

= '/Configure:0000/Run:0000/CalibCycle:0000/CsPad::ElementV2/CxiDsd.0:Cspad.0/data'
   dsname = '/Configure:0000/Run:0000/CalibCycle:0000/CsPad::ElementV2/XppGon.0:Cspad.0/data'
   dsname = '/Configure:0000/Run:0000/CalibCycle:0000/CsPad::ElementV2/XcsEndstation.0:Cspad.0/data'

Run and event number:

Code Block

    runnum = 628
    event  = 34

Import modules

Code Block

import sys
import os
import numpy as np

import PyCSPadImage.CalibPars          as calp
import PyCSPadImage.CSPadConfigPars    as ccp
import PyCSPadImage.CSPadImageProducer as cip
import PyCSPadImage.CSPADPixCoords     as pixcoor
import PyCSPadImage.PixCoords2x1       as pixcoor2x1

import PyCSPadImage.GlobalGraphics     as gg
import PyCSPadImage.GlobalMethods      as gm
import PyCSPadImage.HDF5Methods        as hm

Reconstruction of CSPAD image

CSPAD pixel coordinate arrays

Code Block
Examples
Module Examples.py contains a few examples of how to use the PyCSPadImage package. 
...