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  • CSPadConfigPars.py - provides access to the CSPad configuration parameters
  • CSPadImageProducer.py - receives raw CSPad data 3-D (32, 185, 388) array, uses calibration parameters, produces the 2-D image array
  • CalibPars.py - provides access to the CSPad calibration parameters
  • CalibParsDefault.py - defines the default CSPad calibration parameters
  • CalibParsEvaluated.py - defines the evaluated CSPad parameters such as pixel coordinates
  • Examples.py - contains examples of how to get the CSPad 2-D image array with corrected geometry
  • Alignment.py - similar to the Examples.py, but is used for alignment purpose, its content is not guaranteed
  • GlobalGraphics.py - a set of useful global methods for interactive graphic
  • GlobalMethods.py - a set of miscellaneous global methods
  • HDF5Methods.py - a set of global methods to work with HDF5 files
  • CSPadPixCoordsWODB.py - contains the most efficient way to get CSPad pixel x,y-coordinate arrays.

Functionality

The PyCSPadImage package is intended to convert the CSPad raw data from HDF5 file to the geometry-corrected 2-D image array. Methods of this package provide basic functionality as follows.

...

  • Methods of the class CSPadImageProducer allows to get the geometry-corrected CSPad image or its part for specified 2x1 or quad.

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:

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

cd PyCSPadImage/src/          <==== All source-code files are located here
python Examples.py

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 this:

Code Block

    path_calib = '/reg/d/psdm/CXI/cxi80410/calib/CsPad::CalibV1/CxiDs1.0:Cspad.0'
  • Methods of the class CSPadPixCoordsWODB provide the most efficient way to get CSPad pixel x,y-coordinate arrays. It works without data base access (WODB). User has to provide four 4,8 arrays for 2x1 sensor alignment: x,y-coordinate of the center, orientation, and tilt angle of each 2x1 in the "global" coordinate system of the detector. Test example inside the CSPadPixCoordsWODB.py module also shows how to generate CSPad image from x,y-coordinate arrays using numpy.histogram2d(...) method.
    This class strongly rely on numpy, has no dependency from other classes in this package. For test purpose only it uses a couple of graphical methods from GlobalGraphics.py.

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:

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

cd PyCSPadImage/src/          <==== All source-code files are located here
python Examples.py

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 this: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

Code Block
    runnum = 628
path_calib = '/reg/d/psdm/CXI/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, Data for CSPAD image and the detector configuration can be obtained from the HDF5 file, dataset name, and event number for example

Code Block
    fnamerunnum = 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  =  = '/reg/d/psdm/CXI/cxi80410/hdf5/cxi80410-r0628.h5'
    dsname = '/Configure:0000/Run:0000/CalibCycle:0000/CsPad::ElementV2/CxiDs1.0:Cspad.0/data'
    event  = 34

...

There are two equivalent examples defined by the methods main_example_xpp() and main_example_cxi()
for XPP and CXI experimental data, respectively.

The essential part of these examples can be presented as:

the methods main_example_xpp() and main_example_cxi()
for XPP and CXI experimental data, respectively.

The essential part of these examples can be presented as:

Code Block

import sys
import os
import CalibPars          as calp
import CSPadConfigPars    as ccp
import CSPadImageProducer as cip
import GlobalGraphics     as gg # For test purpose in main only
import HDF5Methods        as hm # For test purpose in main only
#----------------------------------------------
def main_example_xpp() :

    print 'Start test in main_example_xpp()'

    path_calib    = '/reg/d/psdm/xpp/xpp47712/calib/CsPad::CalibV1/XppGon.0:Cspad.0'
    fname, runnum = '/reg/d/psdm/xpp/xpp47712/hdf5/xpp47712-r0043.h5', 43
    dsname        = '/Configure:0000/Run:0000/CalibCycle:0000/CsPad::ElementV2/XppGon.0:Cspad.0/data'
    event         = 0

    print 'Load calibration parameters from', path_calib
    calp.calibpars.setCalibParsForPath ( run=runnum, path=path_calib )

    print 'Get raw CSPad event %d from file %s \ndataset %s' % (event, fname, dsname)
    ds1ev = hm.getOneCSPadEventForTest( fname, dsname, event )
    print 'ds1ev.shape = ',ds1ev.shape

    print 'Make the CSPad image from raw array'
    cspadimg = cip.CSPadImageProducer(rotation=0, tiltIsOn=True, mirror=False)
    arr = cspadimg.getCSPadImage( ds1ev )

    print 'Plot CSPad image'
    gg.plotImage(arr,range=(0,2000),figsize=(11.6,10))
    gg.move(200,100)
    gg.plotSpectrum(arr,range=(0,2000))
    gg.move(50,50)
    print 'To EXIT the test click on "x" in the top-right corner of each plot window.'
    gg.show()
#----------------------------------------------
if __name__ == "__main__" :
    main_example_xpp()
    sys.exit ( 'End of test.' )

This is working example, which can be copied, pasted in <file-name>.py file and executed.

Note

Appropriate permission is required to access particular experimental data.

In addition to the description above, the statements

Code Block

    gg.plotImage(arr,range=(0,2000),figsize=(11.6,10)) 
    gg.move(200,100)
    gg.plotSpectrum(arr,range=(0,2000))
    gg.move(50,50)
    gg.show()

allow to plot the CSPAD 2-d array as image and spectrum, move graphical windows to specified position and show all graphics.

Get CSPAD pixel coordinate arrays

Here we reproduce the test method
example_of_image_built_from_pix_coordinate_array_shaped_as_data()
from the module Examples.py.
This example shows how to get the CSPAD pixel coordinate arrays. In addition, it uses the getTestImageShapedAsData(ds1ev) (slow) method to produce image from the pixel coordinate arrays and data and plots this image.

Code Block

import sys
import CalibPars          as calp
import CalibParsEvaluated as cpe
import GlobalGraphics     as gg # For test purpose in main only
import HDF5Methods        as hm # For test purpose in main only
#----------------------------------------------
def example_of_image_built_from_pix_coordinate_array_shaped_as_data() :
    """Some CSPAD segments may be missing in the dataset
    """   
    fname, runnum = '/reg/d/psdm/CXI/cxi80410/hdf5/cxi80410-r0628.h5',  628
    dsname        = '/Configure:0000/Run:0000/CalibCycle:0000/CsPad::ElementV2/CxiDs1.0:Cspad.0/data'
    path_calib    = '/reg/d/psdm/CXI/cxi80410/calib/CsPad::CalibV1/CxiDs1.0:Cspad.0'
    Range         = (1000,3500)
 
    calp.calibpars.setCalibParsForPath (run=runnum, path=path_calib)
    #cpe.cpeval.printCalibParsEvaluated('center_global')
    cpe.cpeval.evaluateCSPadPixCoordinatesShapedAsData(fname,dsname,rotation=0)
    # At this point pixel coordinates are available and can be extracted:
    xpix, ypix = cpe.cpeval.getCSPadPixCoordinatesShapedAsData_pix()
    print 'xpix =\n', xpix

    # Test image from pixel coordinate and data arrays can be produced and plotted:
    ds1ev = hm.getOneCSPadEventForTest( fname, dsname, event=0 ) # returns array with shape=(29, 185, 388)
    arr = cpe.cpeval.getTestImageShapedAsData(ds1ev)
    gg.plotImage(arr,range=Range,figsize=(11.6,10))
    gg.move(200,100)
    gg.show()
#----------------------------------------------
if __name__ == "__main__" :
    example_of_image_built_from_pix_coordinate_array_shaped_as_data()
    sys.exit ( 'End of test.' )

Get CSPAD pixel coordinate arrays without data base.

Use class CSPadPixCoordsWODB.py
Essentialy user has to provide 4 arrays for 2x1 alignment. For example see
def main_test_cspad() :

Code Block

    xc_um = 109.92 * np.array(
            [[ 473.38,  685.26,  155.01,  154.08,  266.81,   53.95,  583.04,  582.15],  
             [ 989.30,  987.12, 1096.93,  884.11, 1413.16, 1414.94, 1500.83, 1288.02],  
             [1142.59,  930.23, 1459.44, 1460.67, 1347.57, 1559.93, 1032.27, 1033.44],
Code Block

import sys
import os
import CalibPars          as calp
import CSPadConfigPars    as ccp
import CSPadImageProducer as cip
import GlobalGraphics     as gg # For test purpose in main only
import HDF5Methods        as hm # For test purpose in main only
#----------------------------------------------
def main_example_xpp() :

    print 'Start test in main_example_xpp()'

    path_calib    = '/reg/d/psdm/xpp/xpp47712/calib/CsPad::CalibV1/XppGon.0:Cspad.0'
    fname, runnum = '/reg/d/psdm/xpp/xpp47712/hdf5/xpp47712-r0043.h5', 43
    dsname        = '/Configure:0000/Run:0000/CalibCycle:0000/CsPad::ElementV2/XppGon.0:Cspad.0/data'
    event         = 0

 [ 626.78,  print 'Load calibration parameters from', path_calib
    calp.calibpars.setCalibParsForPath ( run=runnum, path=path_calib 627.42,  516.03,  729.15,  198.28,  198.01,  115.31,  327.66]])

    print 'Get raw CSPad event %d from file %s \ndataset %s' % (event, fname, dsname)
yc_um = 109.92 * np.array(
          ds1ev = hm.getOneCSPadEventForTest( fname, dsname, event )
    print 'ds1ev.shape = ',ds1ev.shape

[[1028.07, 1026.28, 1139.46,  926.91, 1456.78, 1457.35, 1539.71, 1327.89],  
       print 'Make the CSPad image from raw array'
    cspadimg = cip.CSPadImageProducer(rotation=0, tiltIsOn=True, mirror=False)[1180.51,  967.36, 1497.74, 1498.54, 1385.08, 1598.19, 1069.65, 1069.93],  
    arr = cspadimg.getCSPadImage( ds1ev )

    print 'Plot CSPad image'
[ 664.89,  666.83,  gg553.plotImage(arr,range=(0,2000),figsize=(11.6,10))
    gg.move(200,100)
    gg.plotSpectrum(arr,range=(0,2000))
    gg.move(50,50)
    print 'To EXIT the test click on "x" in the top-right corner of each plot window.'
    gg.show()
#----------------------------------------------
if __name__ == "__main__" :
    main_example_xpp()
    sys.exit ( 'End of test.' )

This is working example, which can be copied, pasted in <file-name>.py file and executed.

Note

Appropriate permission is required to access particular experimental data.

In addition to the description above, the statements

Code Block

    gg.plotImage(arr,range=(0,2000),figsize=(11.6,10)) 
    gg.move(200,100)
    gg.plotSpectrum(arr,range=(0,2000))
    gg.move(50,50)
    gg.show()

allow to plot the CSPAD 2-d array as image and spectrum, move graphical windows to specified position and show all graphics.

Get CSPAD pixel coordinate arrays

Here we reproduce the test method
example_of_image_built_from_pix_coordinate_array_shaped_as_data()
from the module Examples.py.
This example shows how to get the CSPAD pixel coordinate arrays. In addition, it uses the getTestImageShapedAsData(ds1ev) (slow) method to produce image from the pixel coordinate arrays and data and plots this image.

...

60,  765.91,  237.53,  236.06,  152.17,  365.47],  
             [ 510.38,  722.95,  193.33,  193.41,  308.04,   95.25,  625.28,  624.14]])

    orient_deg = np.array(
                    [[  90.,   90.,    0.,    0.,  270.,  270.,    0.,    0.],
                     [   0.,    0.,  270.,  270.,  180.,  180.,  270.,  270.],
                     [  90.,   90.,    0.,    0.,  270.,  270.,    0.,    0.],
                     [   0.,    0.,  270.,  270.,  180.,  180.,  270.,  270.]])
 
    tilt_deg = np.array(
                    [[0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],  
                     [0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],  
                     [0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],  
                     [0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.]])
Code Block

    w = CSPadPixCoordsWODB(xc_um, yc_um, orient_deg, tilt_deg)
    X,Y = w.get_cspad_pix_coordinate_arrays_pix ()

Then, it is easy to produce image of coordinate arrays:

Code Block

    xsize = X.max() + 1
    ysize = Y.max() + 1
    Img, Xedges, Yedges = np.histogram2d(X.flatten(), Y.flatten(), bins=[xsize,ysize], range=[[0,xsize],[0,ysize]], normed=False, weights=None)

In order to get an image of intensity the weights array needs to be provided.

Image Added

...

References