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 |
|---|---|---|---|
|
| 2x1 | defines the 2x1 section pixel coordinates |
|
| CSPAD2x2 | defines default CSPAD2x2 calibration parameters |
|
| CSPAD2x2 | provides access to the CSPAD2x2 calibration parameters |
|
| CSPAD2x2 | evaluates the CSPAD2x2 pixel coordinates |
|
| CSPAD2x2 | CSPAD2x2 examples |
|
| CSPAD | defines CSPAD configuration parameters |
|
| CSPAD | defines default calibration parameters |
|
| CSPAD | evaluates the center_global from other quad parametes |
|
| CSPAD | provides access to the CSPAD calibration parameters |
|
| CSPAD | evaluates the CSPAD pixel coordinates |
|
| CSPAD | CSPAD examples |
|
| CSPAD | Depricated |
|
| Utils | Graphical utils |
|
| Utils | Global methods |
|
| Utils | Common methods for operations with HDF5 files |
|
| 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
- CSPad image producer in Python (DEPRICATED) - old version of this page.
- CSPAD Alignment
- CSPAD Geometry Software (depricated)
- Package CSPadPixCoords for Psana
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