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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

...

Import modules

Code Block
import sys
import  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:

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:

Code Block

   fname =
Code Block

   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/'

Known dataset names

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

Path to the directory with calibration types:

Code Block

   path_calib = '/reg/d/psdm/CXI/cxi80410/calib/CsPad::CalibV1/CxiDs1Configure: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'
   dsnamepath_calib = '/Configure:0000/Run:0000/CalibCycle:0000/reg/d/psdm/xpp/xpptut13/calib/CsPad::ElementV2CalibV1/XppGon.0:Cspad.0/data'

HDF5 dataset names for known CSPADs:

Code Block
  
   dsname = '/Configure:0000/Run:0000/CalibCycle:0000/CsPad::ElementV2/XcsEndstationCxiDs1.0:Cspad.0/data'

Run and event number:

Code Block

    runnum = 628
    event  = 34

Import modules

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.

Code Block

       Regular instantiation:
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   ALL parameters as gg
import PyCSPadImage.GlobalMethodsare OPTIONAL NAMED parameters;
           path   as gm
import PyCSPadImage.HDF5Methods= '/reg/d/psdm/xpp/xpptut13/calib/CsPad::CalibV1/XppGon.0:Cspad.0/' 
           as hm

Reconstruction of CSPAD image

CSPAD pixel coordinate arrays

...

Examples

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

Get and plot CSPAD image and spectrum

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:

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 HDF5Methodsrun   = 123
           calib = CalibPars(path, list_of_clib_types=['center', 'tilt', 'pedestals'])
         as hm #arr_pedestals 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= calib.getCalibPars('pedestals', run)
 
       Other option for instantiation:
           calib    = CalibPars()
           run      = 123  - is an optional, named
           calibdir = '/reg/d/psdm/CXI/cxi80410/hdf5/cxi80410-r0628.h5',  628
cxi35711/calib'
       dsname    group    = '/Configure:0000/Run:0000/CalibCycle:0000/CsPad::ElementV2/CxiDs1.0:Cspad.0/dataCalibV1'
        path_calib   source   = '/reg/d/psdm/CXI/cxi80410/calib/CsPad::CalibV1/CxiDs1.0:Cspad.0'
    Range       calib.setCalibPars (run, =calibdir, (1000group,3500 source)

       Get array of calibration parameters for specified type and run number:
     calp.calibpars.setCalibParsForPath (run=runnum, path=path_calib)
     type = #cpe.cpeval.printCalibParsEvaluated('center_global')
    cpe       arr  = calib.getCalibPars (type[,run])

Interface to CSPadConfigPars.py

This class provides access to the CSPAD configuration parameters.

Code Block
.cpeval.evaluateCSPadPixCoordinatesShapedAsData(fname,dsname,rotation=0)
    #1. AtSets thisa pointbunch pixelof coordinatesdefault are available and can be extracted:
    xpix, ypix = cpe.cpeval.getCSPadPixCoordinatesShapedAsData_pix()
configuration parameters,
     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],   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 )

  [ 6262.78,  627.42,Access methods:

  516.03,  729.15,  198.28,  198.01,  115.31,  327.66]])

2.1 Access to indPairsInQuads and quadNumsInEvent:
        yc_umquadNums = 109.92 * np.array(config.getQuadNumsInEvent()
        indPairs = config.getIndPairsInQuads()
    [[1028.07, 1026.28, 1139.46,  926.91, 1456.78, 1457.35, 1539.71, 1327.89],  
   config.printCSPadConfigPars()

    2.2 Access to static class parameters:    
      [1180.51,  967.36, 1497.74, 1498.54, 1385.08, 1598.19, 1069.65, 1069.93],  
import CSPadConfigPars as ccp
        my_wid2x1 = ccp.CSPadConfigPars().wid2x1
       [ 664.89,etc...

  666.83,  5533.60,  Conversions 765.91,between  237.53,  236.06,  152.17,  365.47],  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 [ 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.],
      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:
   0.,    0.,  270.,  270.,  180.,  180.,  270.,  270.],
                     [  90.,   90.,    0.,    0.,  270.,  270.,    0.,    0.],
     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

Code Block

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

    [   01.,1 Instantiation with external  0.,geometry parameters:
 
  270.,  270.,  180.,  180.,  270.,  270.]])
 
    tilt_deg = np.array(
    All parameters optional. Default values will be used if parameters are not specified.
           xc     [[0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],  
        - np.array(...), shape=(3, 4, 8)) [um]
           yc    - np.array(...), shape=(3, 4, 8)) [um]
           tilt   [0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],  
- np.array(...), shape=(4, 8)) [deg]
           coord = CSPADPixCoords(xc_um=xc, yc_um=yc, tilt_deg=tilt)


       1.2 Instantiation with regular calibration parameters:

         [0.,  0.,  0.,  0.,path  0.,  0.,  0.,  0.],  
= '/reg/neh/home1/dubrovin/LCLS/CSPadAlignment-v01/calib-xpp-2013-01-29'
           run   = 123
           calib  [0.= CalibPars(path, run)
 0.,  0.,  0.,  0.,  0.,  0.,coord  0.]])
Note

ALL arrays are shown here FOR TEST PURPOSE ONLY !!! and they are not consistent with any real detector. The orient_deg is not consistent with real orientation as well...

These arrays of alignment parameters are used for initialization of the CSPadPixCoordsWODB class object, which can be used to get X,Y-coordinate arrays as shown below:

Code Block
= CSPADPixCoords(calib)

       1.2 Access methods:
           Get arrays of pixel coordinates in mu with shape: [2,185,388]
    w = CSPadPixCoordsWODB(xc_um, yc_um, orient_deg, tilt_deg)
    X, Y = wcoord.get_cspad_pix_coordinate_arrays_pixum  ()

where X.shape = Y.shape = (4, 8, 185, 388) and obviously can be re-shaped to (32, 185, 388). Then, it is easy to produce image of coordinate arrays using numpy 2D histogramming method:

Code Block
config=None)
           or in integer pixels:
    xsize       iX,iY = X.max() + 1
    ysize = Y.max() + 1
coord.get_cspad_pix_coordinate_arrays_pix (config=None)

       1.3 Get image  
         Img, Xedges, Yedgesimg = np.histogram2d(X.flatten(), Y.flatten(), bins=[xsize,ysize], range=[[0,xsize],[0,ysize]], normed=False, weights=None)

Image RemovedImage Removed

...

coord.get_cspad_image(data,config)

Examples

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

Get and plot CSPAD image and spectrum

Get CSPAD pixel coordinate arrays

Get CSPAD pixel coordinate arrays without data base.

References