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Content
Table of Contents |
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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.
Note |
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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 |
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| 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:
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Wiki Markup |
h1. Content {toc} h1. 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. {note} Please note, that LCLS main-stream data analysis framework is based on C+\+/python package [PCDS:Psana]. To work with CSPad images [PCDS:Psana] has several modules which are collected in the [CSPadPixCoords |PCDS:Psana CSPad Geometry # Package CSPadPixCoords] package. Two of these modules, [CSPadImageProducer|PCDS:Psana CSPad Geometry # Module CSPadImageProducer] and [CSPadInterpolImageProducer|PCDS:Psana CSPad Geometry # Module CSPadInterpolImageProducer], are intended to produce the 2-D array with CSPAD image from raw XTC data. Precise CSPAD geometry is accounted in [PCDS:Psana] using the calibration parameters supplied by the [PSCalib|PCDS:Psana CSPad Geometry # Package PSCalib] package. {note} h1. Package PyCSPadImage h3. Content The {{python}}\-based *PyCSPadImage* package consists of modules: || Status || Module || For || Description || |(/) | {{PixCoords2x1.py}} | 2x1 | defines the 2x1 section pixel coordinates | |(/) | {{CSPAD2x2CalibParsDefault.py}} | CSPAD2x2 | defines default CSPAD2x2 calibration parameters | |(/) | {{CSPAD2x2CalibPars.py}} | CSPAD2x2 | provides access to the CSPAD2x2 calibration parameters | |(/) | {{CSPAD2x2PixCoords.py}} | CSPAD2x2 | evaluates the CSPAD2x2 pixel coordinates | |(/) | {{CSPAD2x2Examples.py}} | CSPAD2x2 | CSPAD2x2 examples | |(/) | {{CSPadConfigPars.py}} | CSPAD | defines CSPAD configuration parameters | |(/) | {{CalibParsDefault.py}} | CSPAD | defines default calibration parameters | |(/) | {{CSPADCalibParsEvaluated.py}} | CSPAD | evaluates the *center_global* from other quad parametes | |(/) | {{CalibPars.py}} | CSPAD | provides access to the CSPAD calibration parameters | |(/) | {{CSPADPixCoords.py}} | CSPAD | evaluates the CSPAD pixel coordinates | |(/) | {{Examples.py}} | CSPAD | CSPAD examples | |(+) | {{CSPadImageProducer.py}} | CSPAD | Depricated | |(/) | {{GlobalGraphics.py}} | Utils | Graphical utils | |(/) | {{GlobalMethods.py}} | Utils | Global methods | |(/) | {{HDF5Methods.py}} | Utils | Common methods for operations with HDF5 files | |(+) | {{Alignment.py}} | Internal | It is used for alignment purpose | h3. How to get this package Below we assume that all standard environment variable settings are done (otherwise see [PCDS: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} 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 {code} h3. Import modules {code} |
Import modules
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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
{code}
h3. External parameters
HDF5 data file:
{code}
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External parameters
HDF5 data file:
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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
{code}
Path to the directory with calibration types:
{code}
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Path to the directory with calibration types:
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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:
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{code} HDF5 dataset names for known CSPADs: {code} 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' {code} h3. Interface to {{ |
Interface to CalibPars.py
...
This
...
class
...
provides
...
access
...
to
...
the
...
CSPAD
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calibration
...
parameters.
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} 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]) {code} h3. Interface to {{ |
Interface to CSPadConfigPars.py
...
This
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class
...
provides
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access
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to
...
the
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CSPAD
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configuration
...
parameters.
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} 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 {code} h3. Interface to {{ |
Interface to CSPADPixCoords.py
...
Class
...
for
...
generation
...
of
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CSPad
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pixel
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coordinate
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array
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with
...
and
...
without
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data
...
base
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} 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 Getor imagein integer pixels: imgiX,iY = coord.get_cspad_image(data,config) {code} h1. Examples Module {{Examples.py}} contains a few examples of how to use the *PyCSPadImage* package. {html} <!-- h3. Get and plot CSPAD image and spectrum h3. Get CSPAD pixel coordinate arrays h3. Get CSPAD pixel coordinate arrays without data base. --> {html} h1. References * [PCDS:CSPad image producer in Python] - earlier version description. * [CSPad Alignment] * [CSPAD Geometry Software] * [Package CSPadPixCoords|PCDS:Psana Module Catalog # Package CSPadPixCoords] for [PCDS:Psana]_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