Content

Introduction

In this note we describe the python-based PyCSPadImage package which is intended to evaluate and provide access to the pixel coordinate arrays. In addition, it converts the CSPAD raw data from HDF5 file to the geometry-corrected 2-D image array. This package can be used in a stand-alone python code.

Please note, that LCLS main-stream data analysis framework is based on C++/python package Psana. To work with CSPad images Psana has several modules which are collected in the CSPadPixCoords package. Two of these modules, CSPadImageProducer and CSPadInterpolImageProducer, are intended to produce the 2-D array with CSPAD image from raw XTC data. Precise CSPAD geometry is accounted in Psana using the calibration parameters supplied by the PSCalib package.

Package PyCSPadImage

Content

The python-based PyCSPadImage package consists of modules:

Status

Module

For

Description

(tick)

PixCoords2x1.py

2x1

defines the 2x1 section pixel coordinates

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CSPAD2x2CalibParsDefault.py

CSPAD2x2

defines default CSPAD2x2 calibration parameters

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CSPAD2x2CalibPars.py

CSPAD2x2

provides access to the CSPAD2x2 calibration parameters

(tick)

CSPAD2x2PixCoords.py

CSPAD2x2

evaluates the CSPAD2x2 pixel coordinates

(tick)

CSPAD2x2Examples.py

CSPAD2x2

CSPAD2x2 examples

(tick)

CSPadConfigPars.py

CSPAD

defines CSPAD configuration parameters

(tick)

CalibParsDefault.py

CSPAD

defines default calibration parameters

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CSPADCalibParsEvaluated.py

CSPAD

evaluates the center_global from other quad parametes

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CalibPars.py

CSPAD

provides access to the CSPAD calibration parameters

(tick)

CSPADPixCoords.py

CSPAD

evaluates the CSPAD pixel coordinates

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Examples.py

CSPAD

CSPAD examples

(plus)

CSPadImageProducer.py

CSPAD

Depricated

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GlobalGraphics.py

Utils

Graphical utils

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GlobalMethods.py

Utils

Global methods

(tick)

HDF5Methods.py

Utils

Common methods for operations with HDF5 files

(plus)

Alignment.py

Internal

It is used for alignment purpose

How to get this package

Below we assume that all standard environment variable settings are done (otherwise see Analysis Workbook. Account Setup). In order to copy the PyCSPadImage package from SVN repository and run a simple test one has to use commands:

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

Import modules

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

External parameters

HDF5 data file:

   fname = '/reg/d/psdm/xpp/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:

   path_calib = '/reg/d/psdm/CXI/cxi80410/calib/CsPad::CalibV1/CxiDs1.0:Cspad.0/'
   path_calib = '/reg/d/psdm/xpp/xpptut13/calib/CsPad::CalibV1/XppGon.0:Cspad.0/'

HDF5 dataset names for known CSPADs:

  
   dsname = '/Configure:0000/Run:0000/CalibCycle:0000/CsPad::ElementV2/CxiDs1.0:Cspad.0/data'
   dsname = '/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'

Interface to CalibPars.py

This class provides access to the CSPAD calibration parameters.

       Regular instantiation:
           ALL parameters are OPTIONAL NAMED parameters;
           path  = '/reg/d/psdm/xpp/xpptut13/calib/CsPad::CalibV1/XppGon.0:Cspad.0/' 
           run   = 123
           calib = CalibPars(path, list_of_clib_types=['center', 'tilt', 'pedestals'])
           arr_pedestals = calib.getCalibPars('pedestals', run)
 
       Other option for instantiation:
           calib    = CalibPars()
           run      = 123  - is an optional, named
           calibdir = '/reg/d/psdm/CXI/cxi35711/calib'
           group    = 'CsPad::CalibV1'
           source   = 'CxiDs1.0:Cspad.0'
           calib.setCalibPars (run, calibdir, group, source)

       Get array of calibration parameters for specified type and run number:
           type = 'center'
           arr  = calib.getCalibPars (type[,run])

Interface to CSPadConfigPars.py

This class provides access to the CSPAD configuration parameters.

    1. Sets a bunch of default configuration parameters,
       loads current coniguration parameters from hdf5 file or from external parameters.
    2. Provides access to current coniguration parameters
    3. Contains conversion methods for arrays between raw data and entire cspad.
    
    Interface
    =========
    1.  Instatiation
    1.1 Default constructor sets default parameters for indPairsInQuads & quadNumsInEvent:

        config = CSPadConfigPars()

    1.2 Initialization of configuration parameters using hdf5 file, for example:
        fname  = '/reg/d/psdm/xpp/xpp66213/hdf5/xpp66213-r0150.h5'
        dsname = '/Configure:0000/Run:0000/CalibCycle:0000/CsPad::ElementV2/XppGon.0:Cspad.0/data'

        config.setCSPadConfiguration( fname, dsname, event=0 ):

    1.3 Initialization of configuration parameters using external arrays, for example:        
        indPairs = np.arange(32)
        indPairs.shape = (4,8)
        quadNums = np.arange(4)

        config.setCSPadConfigArrays( indPairsInQuads=indPairs, quadNumsInEvent=quadNums )

   2.  Access methods:

    2.1 Access to indPairsInQuads and quadNumsInEvent:
        quadNums = config.getQuadNumsInEvent()
        indPairs = config.getIndPairsInQuads()
        config.printCSPadConfigPars()

    2.2 Access to static class parameters:    
        import CSPadConfigPars as ccp
        my_wid2x1 = ccp.CSPadConfigPars().wid2x1
        etc...

    3.  Conversions between entire (4,8,185,388) and shaped as data (N<32,185,388) cspad pixel array shapes:

    3.1 Conversion of the entire cspad pixel array arr_entire_cspad with shape (4,8,185,388)
        in to the arr_raw_data, shaped as data (N<32,185,388):
        arr_raw_data = config.getCSPadPixArrayShapedAsData(arr_entire_cspad)

    3.2 Conversion of the cspad pixel array arr_raw_data shaped as data (N<32,185,388)
        in to the entire cspad pixel array arr_entire_cspad with shape (4,8,185,388):
        arr_entire_cspad = getCSPadPixArrayFromArrayShapedAsData(arr_raw_data)

    4.  Tests
        To test CSPadConfigPars from release directory use command:
        python PyCSPadImage/src/CSPadConfigPars.py <test-number>
        where <test-number> stands for  0, 1, 2, or 3

Interface to CSPADPixCoords.py

Class for generation of CSPad pixel coordinate array with and without data base

    Interface
    =========
       1.0 Instantiation with default parameters taken from optical measurement for XPP on 2013-01-29:
           coord = CSPADPixCoords()

       1.1 Instantiation with external geometry parameters:
 
           All parameters optional. Default values will be used if parameters are not specified.
           xc    - np.array(...), shape=(3, 4, 8)) [um]
           yc    - np.array(...), shape=(3, 4, 8)) [um]
           tilt  - np.array(...), shape=(4, 8)) [deg]
           coord = CSPADPixCoords(xc_um=xc, yc_um=yc, tilt_deg=tilt)


       1.2 Instantiation with regular calibration parameters:

           path  = '/reg/neh/home1/dubrovin/LCLS/CSPadAlignment-v01/calib-xpp-2013-01-29'
           run   = 123
           calib = CalibPars(path, run)
           coord = CSPADPixCoords(calib)

       1.2 Access methods:
           Get arrays of pixel coordinates in mu with shape: [2,185,388]
            X, Y = coord.get_cspad_pix_coordinate_arrays_um  (config=None)
           or in integer pixels:
           iX,iY = coord.get_cspad_pix_coordinate_arrays_pix (config=None)

       1.3 Get image  
           img = coord.get_cspad_image(data,config)

Examples

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

References

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