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This page provides a list of existing modules for psana framework. Only the modules that are included in the standard analysis releases appear on this page.
Package psana
Psana package
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Module psana.EventKeys
This module dumps the list of the event keys in the event or configuration store. Event key is a triplet of data type, data source address, and string key.
Example of the output produced by this module:
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Event keys:
EventKey(type=Psana::EvrData::DataV3, src=DetInfo(NoDetector.0:Evr.0))
EventKey(type=Psana::Camera::FrameV1, src=DetInfo(CxiDg1.0:Tm6740.0))
EventKey(type=Psana::Ipimb::DataV1, src=DetInfo(CxiDg1.0:Ipimb.0))
...
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This module is useful to display the content of the events without dumping all the data. Example command which uses this module is:
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% psana -m EventKeys <input-files>
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Note that one can specify EventKeys
instead of psana.EventKeys
as psana
package name is optional.
Module psana.PrintEventId
This module prints the content of the Event ID object on every event.
Example of the output produced by this module:
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[info:psana.PrintEventId] event ID: XtcEventId(run=100, time=2010-12-12 11:09:36.300506429-08)
[info:psana.PrintEventId] event ID: XtcEventId(run=100, time=2010-12-12 11:09:36.317163082-08)
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Module psana.PrintSeparator
This module prints separator line on every event. Can be used to indicate event boundaries in job's log.
Module has two configuration parameters:
separator
(default: "=") – separator stringrepeat
(default: 80) – number of repeats of separator string on a separator line
Example of the output produced by this module with the default parameters (including output from PrintEventId module):
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[info:/root/] ================================================================================
[info:psana.PrintEventId] event ID: XtcEventId(run=100, time=2010-12-12 11:09:36.300506429-08)
[info:/root/] ================================================================================
[info:psana.PrintEventId] event ID: XtcEventId(run=100, time=2010-12-12 11:09:36.317163082-08)
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Package psana_examples
This package contains modules that are meant to be used as examples of accessing different data types or framework services. Can be used by developers as templates for new modules.
Module psana_examples.DumpAcqiris
Extracts and dumps the content of Acqiris configuration (Psana::Acqiris::ConfigV1
) and event data (Psana::Acqiris::DataDescV1
) objects.
Module has one configuration parameter:
source
(default: "DetInfo(:Acqiris)") – data source address
Module psana_examples.DumpAcqTdc
Extracts and dumps the content of Acqiris TDC configuration (Psana::Acqiris::TdcConfigV1
) and event data (Psana::Acqiris::TdcDataV1
) objects.
Module has one configuration parameter:
source
(default: "DetInfo(:AcqTDC.0)") – data source address
Module psana_examples.DumpBld
Extracts and dumps the content of beamline data objects (Psana::Bld::BldDataEBeamV0
, Psana::Bld::BldDataEBeam
, Psana::Bld::BldDataPhaseCavity
, Psana::Bld::BldDataFEEGasDetEnergy
, and Psana::Bld::BldDataIpimb
).
Module has four configuration parameters:
eBeamSource
(default: "BldInfo(EBeam)") – data source address forPsana::Bld::BldDataEBeam
phaseCavSource
(default: "BldInfo(PhaseCavity)") – data source address forPsana::Bld::BldDataPhaseCavity
feeSource
(default: "BldInfo(FEEGasDetEnergy)") – data source address forPsana::Bld::BldDataFEEGasDetEnergy
ipimbSource
(default: "BldInfo(NH2-SB1-IPM-01)") – data source address forPsana::Bld::BldDataIpimb
Module psana_examples.DumpCamera
Extracts and dumps the content of camera configuration (Psana::Camera::FrameFexConfigV1
) and event data (Psana::Camera::FrameV1
and Psana::Camera::TwoDGaussianV1
) objects.
Module has one configuration parameter:
source
(default: "DetInfo(:Opal1000)") – data source address
Module psana_examples.DumpControl
Extracts and dumps the content of scan control configuration (Psana::ControlData::ConfigV1
) object.
Module has one configuration parameter:
source
(default: "ProcInfo()") – data source address
Module psana_examples.DumpCsPad
Extracts and dumps the content of CsPad configuration (Psana::CsPad::ConfigV*
) and event data (Psana::CsPad::DataV*
) objects.
Module has one configuration parameter:
source
(default: "DetInfo(:Cspad)") – data source address
Module psana_examples.DumpEncoder
Extracts and dumps the content of encoder configuration (Psana::Encoder::ConfigV1
) and event data (Psana::Encoder::DataV*
) objects.
Module has one configuration parameter:
source
(default: "DetInfo(:Encoder)") – data source address
Module psana_examples.DumpEpics
Extracts and dumps the list of EPICS PVs and their values and status information on every event.
Module psana_examples.DumpEvr
Extracts and dumps the content of Evr configuration (Psana::EvrData::ConfigV*
and Psana::EvrData::IOConfigV1
) and event data (Psana::EvrData::DataV*
) objects.
Module has one configuration parameter:
source
(default: "DetInfo(:Evr)") – data source address
Module psana_examples.DumpFccd
Extracts and dumps the content of FCCD configuration (Psana::FCCD::FccdConfigV*
) objects. To dump event data objects use psana_examples.DumpCamera module.
Module has one configuration parameter:
source
(default: "DetInfo(:Fccd)") – data source address
Module psana_examples.DumpIpimb
Extracts and dumps the content of IPIMB configuration (Psana::Ipimb::ConfigV1
) and event data (Psana::Ipimb::DataV1
) objects.
Module has one configuration parameter:
source
(default: "DetInfo(:Ipimb)") – data source address
Module psana_examples.DumpLusi
Extracts and dumps the content of LUSI configuration (Psana::Lusi::DiodeFexConfigV1
, Psana::Lusi::IpmFexConfigV1
, and Psana::Lusi::PimImageConfigV1
) and event data (Psana::Lusi::DiodeFexV1
and Psana::Lusi::IpmFexV1
) objects.
Module has two configuration parameters:
tmSource
(default: "DetInfo(:Tm6740)") – data source address forPsana::Lusi::PimImageConfigV1
ipimbSource
(default: "DetInfo(:Ipimb)") – data source address for other data
Module psana_examples.DumpOpal1k
Extracts and dumps the content of Opal1000 configuration (Psana::Opal1k::ConfigV1
) object. To dump event data objects use psana_examples.DumpCamera module.
Module has one configuration parameter:
source
(default: "DetInfo(:Opal1000)") – data source address
Module psana_examples.DumpPnccd
Extracts and dumps the content of pnCCD configuration (Psana::PNCCD::ConfigV*
) and event data (Psana::PNCCD::FrameV1
) objects.
Module has one configuration parameter:
source
(default: "DetInfo(:pnCCD)") – data source address
Module psana_examples.DumpPrinceton
Extracts and dumps the content of Princeton configuration (Psana::Princeton::ConfigV1
) and event data (Psana::Princeton::FrameV1
) objects.
Module has one configuration parameter:
source
(default: "DetInfo(:Princeton)") – data source address
Module psana_examples.DumpPulnix
Extracts and dumps the content of Pulnix configuration (Psana::Pulnix::TM6740ConfigV*
) objects.
Module has one configuration parameter:
source
(default: "DetInfo(:Tm6740)") – data source address
Module psana_examples.EBeamHist
This module is an example of histogramming service usage. It extracts beam line data and fills couple of histograms with the beam parameters.
Module has one configuration parameter:
eBeamSource
(default: "BldInfo(EBeam)") – data source address
Package cspad_mod
Package cspad_mod contains common modules useful for analysis of data from CsPad detector.
Module cspad_mod.CsPadPedestals
This module is supposed to run on dark cspad2x2 frame data. It calculates average and standard deviation values for each pixel and writes these values to output files in text format.
Module configuration parameters:
source
(default: "DetInfo(:Cspad)") – name of the data source; default value is adequate if there is only one CsPad device in setup, if there is more than one device then more specific value should be providedoutput
(default: "cspad-pedestals.dat") – name of the output file for average values, if empty file will not be writtennoise
(default: "cspad-noise.dat") – name of the output file for standard deviation values, if empty file will not be written
To use this module with default parameters one could use this command:
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psana -m cspad_mod.CsPadPedestals input-files.xtc
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which will produce files cspad-pedestals.dat
and cspad-noise.dat
in the current directory (if input file contains CsPad data).
To change module parameters one could create file with name psana.cfg
in the current directory with a contents like this:
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[psana]
modules = cspad_mod.CsPadPedestals
[cspad_mod.CsPadPedestals]
source = DetInfo(CxiDs1.0:Cspad.0)
output = pedestals.dat
noise =
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and then run psana:
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psana input-files.xtc
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This should produce file pedestals.dat
in the current directory. As the source address is more specific this configuration file can be used even if input data contain more than one CsPad device.
Module cspad_mod.CsPad2x2Pedestals
This module is supposed to run on cspad2x2 dark frame data. It calculates average and standard deviation values for each pixel and writes these values to output files in text format.
Module configuration parameters:
source
(default: "DetInfo(:Cspad2x2)") – name of the data source; default value is adequate if there is only one CsPad2x2 device in setup, if there is more than one device then more specific value should be providedoutput
(default: "cspad2x2-pedestals.dat") – name of the output file for average values, if empty file will not be writtennoise
(default: "cspad2x2-noise.dat") – name of the output file for standard deviation values, if empty file will not be written
To use this module with default parameters one could use this command:
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psana -m cspad_mod.CsPad2x2Pedestals input-files.xtc
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which will produce files cspad2x2-pedestals.dat
and cspad2x2-noise.dat
in the current directory (if input file contains CsPad2x2 data).
To change module parameters one could create file with name psana.cfg
in the current directory with a contents like this:
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[psana]
modules = cspad_mod.CsPad2x2Pedestals
[cspad_mod.CsPad2x2Pedestals]
source = DetInfo(CxiSc1.0:Cspad2x2.0)
output = pedestals.dat
noise =
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and then run psana:
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psana input-files.xtc
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This should produce file pedestals.dat
in the current directory. As the source address is more specific this configuration file can be used even if input data contain more than one CsPad2x2 device.
Module cspad_mod.CsPadCalib
This module performs standard CsPad calibration procedures: per-pixel pedestal subtraction and common mode correction. The algorithms used in calibrations are identical to translator algorithms, the result of calibration should be the same as the data stored in HDF5 files.
The module uses three input calibration files which should be located in the standard calibration directory of the corresponding experiment:
pedestals
– per-pixel pedestal data (produced by the CsPadPedestals module or standalone applications)pixel_status
– hot/dead status for every pixel, used by common mode algorithmcommon_mode
– file with parameters controlling common mode calculationpixel_gain
– per-pixel gain data, inverse pixel gain (1/gain) as floating number
If any of the files is missing then corresponding algorithm is not executed, if pixel_status
file is missing then all pixels are assumed to have working status. Algorithms inside module are executed following this order:
- common mode is calculated for every segment; common mode uses pedestal and pixel status values
- if common mode is calculated successfully it is subtracted from every pixel value in a segment
- if pedestals are defined pedestal values are subtracted from every pixel value
- if pixel gains are defined then each pixel value is multiplied by corresponding gain factor
- resulting pixel value is rounded to nearest integer and stored in the output image
The calibration is performed on every CsPad image (full or 2x2) found in the event and works even if there is more than one CsPad data object. The original objects are preserved in event and result of the calibration is stored in event with different string key ("calibrated" by default, can be changed with module parameter).
Module configuration parameters:
inputKey
(default is empty) – string key used to locate uncalibrated data objects in eventoutputKey
(default is "calibrated") – string key used to store calibrated data objects in eventdoPedestals
(default is "yes") – can be set to "no" to explicitly disable pedestal subtraction algorithmdoPixelStatus
(default is "yes") – can be set to "no" to explicitly disable reading of pixel status data, all pixels will be used for common modedoCommonMode
(default is "yes") – can be set to "no" to explicitly disable common mode algorithmdoPixelGain
(default is "yes") – can be set to "no" to explicitly disable pixel gain correction algorithm
Module cspad_mod.CsPadFilter
This is a filter module which implements skipping for the events which have too low signal in CsPad. filtering algorithm can be controlled trough the module parameter and/or parameters in calibration file. The name of the calibration file is "filter" and it will be searched in the standard calibration directories of the experiment.
Module configuration parameters:
inputKey
(default is empty) – string key used to locate uncalibrated data objects in eventsource
(default is "DetInfo(:Cspad)") – data source addressskipIfNoData
(default is "yes") – when set to "yes" if the module does not find CsPad data in an event then it skips eventmode
(default is -1) – filtering mode, see belowparameters
(default is all 0) – list of parameters for filtering algorithm, up to 16 floating numbers
Parameter mode
defines where the filter get its parameters and how it works. If set to -1 (default) then it reads parameters and actual mode value from a calibration text file which should contain one integer number for mode and up to 16 floating point parameters. If parameter is set to 0 or if the value read from file is 0 then no filtering is done, all events are passed through. If mode is set to 1 (from parameter or file) then filter calculates the number of pixels above certain threshold. Filter expects two values in parameter array: threshold for pixel value and minimum number of pixels above threshold. If second parameter is negative then it's assumed to be a percentage of the full number of pixels.
Filter works on individual image arrays (quadrants). Module checks for CsPad::DataV1, CsPad::DataV2, and CsPad::MiniElementV1 objects in that order. If any object is found then module runs filter on images in that object. If any one image passes the filter then module returns and event is passed to downstream modules, otherwise framework skips this event.
With the default parameters module works with non-calibrated data, to switch to calibrated data add the module cspad_mod.CsPadCalib before filter and change inputKey
parameter to calibrated
.
Package CSPadPixCoords
Package CSPadPixCoords calculates the 2x1 section, quad, and CSPad pixel coordinates and produces the image.
For complete reference select Doxygen documentation.
Module CSPadPixCoords::PixCoordsTest
This module demonstrates of how to use the PixCoords2x1, PixCoordsQuad, and PixCoordsCSPad classes
in order to pre-calculate pixel coordinates, taking into account the calibration parameters.
Relevant images are produced in combination of the pixel coordinates with event data and saved in text files.
Module configuration parameters:
calibDir
(default: "/reg/d/psdm/CXI/cxi35711/calib") – directory with calibration files,typeGroupName
(default: "CsPad::CalibV1") – data type and group names,source
(default: "CxiDs1.0:Cspad.0") – source of data,runNumber
(default: 32U) – run number for calibration file,events
(default: 32U) – number of events before stop a job,filter
(default: false) – on/off for potential selection filter.
Module CSPadPixCoords::CSPadImageProducer
CSPadImageProducer works in psana framework. It does a few operation as follows:
- gets the pixel coordinates from PixCoords2x1, PixCoordsQuad, and PixCoordsCSPad classes,
- gets data from the event,
- produces the
Image2D<double>
orndarray<double,2>
object with CSPad image for each event, - adds the image object in the event for processing in other modules.
Time consumed to fill the CSPad image array (currently 1750x1750) is measured to be about 40 msec/event on psana0105.
Module configuration parameters:
calibDir
(default: "") – directory with calibration files, by default it is set to .../<experiment>/calibtypeGroupName
(default: "CsPad::CalibV1") – calibration type and group names,source
(default: "CxiDs1.0:Cspad.0") – source of data,key
(default: "") – key for data processing stage,imgkey
(default: "Image2D") – output key for image saved in event,events
(default: 1<<31U) – number of events before stop a job,tiltIsApplied
(default: true) – on/off for tilt angle of 2x1-sections and quads.print_bits
(default: 0) – verbosity:- =0 - print nothing,
- +1 - calib pars,
- +2 - consumed time per event.
Remarks:
- By default the
key
corresponds to raw data. - If the
imgkey
is defined as "Image2D", the image is saved in the event as aCSPadPixCoords::Image2D<double>
object, otherwise (for other names) as andarray<double,2>
object.
Module CSPadPixCoords::CSPadInterpolImageProducer
CSPadInterpolImageProducer works in psana framework. It does a few operation as follows:
- gets the pixel coordinates from PixCoords2x1, PixCoordsQuad, and PixCoordsCSPad classes,
- makes the arrays of neighbour addresses (quad, section, row, column) and weights as a function of the bin indexes (ix, iy) of the CSPad image,
- gets data from the event,
- produces the Image2D object with interpolated CSPad image for each event,
- adds the
CSPadPixCoords::Image2D<double>
orndarray<double,2>
object in the event for processing in other modules.
In this module we use 4-node bi-linear interpolation algorithm.
Time consumed to fill the CSPad image array (currently 1750x1750) is measured to be about 200 msec/event on psana0106. We consider options for acceleration using GPU or multi-core processing.
Module configuration parameters are the same as for the CSPadPixCoords::CSPadImageProducer.
Module CSPadPixCoords::CSPad2x2ImageProducer
CSPad2x2ImageProducer works in psana framework. It does a few operation as follows:
- gets the pixel coordinates from PixCoords2x1 and PixCoordsCSPad2x2 classes,
- gets data from the event,
- produces the
Image2D<double>
orndarray<double,2>
object with CSPad image for each event, - adds the image object in the event for processing in other modules.
The CSPad2x2 image array is currently shaped as (400,400).
Module configuration parameters:
source
(default: "DetInfo(:Cspad2x2)") – source of data,inkey
(default: "") – key for data processing stage,outimgkey
(default: "Image2D") – output key for image saved in event,tiltIsApplied
(default: false) – on/off for tilt angle of 2x1-sections and quads - currently is not used,print_bits
(default: 0) – verbosity:- =0 - print nothing,
- +1 - calib pars,
- +2 - eventID.
Remarks:
- By default the
key
corresponds to raw data. - If the
imgkey
is defined as "Image2D", the image is saved in the event as aCSPadPixCoords::Image2D<double>
object, otherwise (for other names) as andarray<double,2>
object.
See also Example for Module CSPadPixCoords::CSPad2x2ImageProducer.
Module CSPadPixCoords::SaveImageInFile
(Re-named from deprecated module CSPadPixCoords::CSPadImageGetTest)
SaveImageInFile is a psana module class, which works after the CSPadImageProducer or CSPadInterpolImageProducer. It receives the CSPadPixCoords::Image2D<double>
or ndarray<double,2>
image object from the event. (This image object may be used in further data processing.) For test purpose, the image of particular event, defined by the eventSave
parameter in configuration file, is saved in the text file with standard predefined name like cspad_image_ev<number>.txt
.
Module configuration parameters:
source
(default: "CxiDs1.0:Cspad.0") – source of data,key
(default: "Image2D") – input image key,eventSave
(default: 0) – event number to save the CSPad image file,saveAll
(default: false) – save or not all selected events,fname
(default: "cspad_image_ev") – common part of the output file name, event number with extension ".txt" will be added at the end.
Package ImgPixSpectra
For complete reference see the Doxygen documentation.
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Package ImgPixSpectra is available since release |
Package ImgPixSpectra is intended to accumulate the spectra for all pixels of the image array.
Different modules of this package work with different data types for detectors like CSPad, mini-CSPad, Opal, Princeton camera, etc. All modules have the same interface and the same functionality.
In the loop over events from beginJob
to endJob
the image pixel amplitudes are accumulated in the 2-d array,
of the shape (<number-of-pixels>, <number-of-spectral-bins>). The first parameter is defined by the image size. The second is passed as an external parameter of the psana configuration file (psana.cfg
) along with minimal and maximal amplitudes. At the endJob
the spectral array is saved in file with specified name. Auxiliary file with the name extension *.sha
is created in order to save the shape parameters. For example, the "mini-cspad-pix-spectra.txt.sha" outpuit file contains
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NPIXELS 143560
NBINS 100
AMIN 500
AMAX 1000
NEVENTS 2549
ARRFNAME mini-cspad-pix-spectra.txt
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This information can be used in analysis or presentation of this array.
Module ImgPixSpectra::CSPadPixSpectra
Module configuration parameters:
source
(default: "CxiDs1.0:Cspad.0" ) – source of data for CSPadevents
(default: 1<<31U ) – number of events before stop a jobinputKey
(default: "" ) – input key for data processing stageamin
(default: 0. ) – minimal spectral amplitudeamax
(default: 1000. ) – maximal spectral amplitudenbins
(default: 100 ) – number of bins in spectraarr_fname
(default: "..._spectral_array.txt" ) – output file name
Module ImgPixSpectra::MiniCSPadPixSpectra
The only difference in interface of this module from previous is in the default name for the source parameter and the output file name.
source
(default: "DetInfo(:Cspad2x2)" ) – source of data for MiniCSPad
Module ImgPixSpectra::CameraPixSpectra
The only difference in interface of this module from previous is in the default name for the source parameter and the output file name.
source
(default: "DetInfo(SxrBeamline.0:Opal1000.1)" ) – source of data for Opal camera
orsource
(default: "DetInfo(:Princeton)" ) – source of data for Princeton camera
See also Example for Package ImgPixSpectra.
Package ImgAlgos
This packages contains a few psana
modules for image processing
Module ImgAlgos::CSPadCommonModeCorrection
Alternative to the cspad_mod.CsPadCalib
algorithm for the common mode correction.
Takes the CSPad data array with subtracted pedestals, evaluate the average amplitude for each 2x1 section for amplitudes below the threshold, and subtract it from all pixel amplitudes. This algorithm consumes about 30 ms/event on psana0205.
Module configuration parameters:
source
(default: "DetInfo(:Cspad)" ) – source of data for CSPadinputKey
(default: "calibrated" ) – key for input data, by default expects data fromcspad_mod.CsPadCalib
outputKey
(default: "cm_subtracted" ) – output key for the next data processing stageampthr
(default: 30 ) – threshold to exclude the large pixel amplitudes in average
Module ImgAlgos::ImgPixAmpFilter
The ImgAlgos::ImgPixAmpFilter is a filter for event selection.
This filter counts the number of image pixels in the specified window with amplitude exceeding the threshold
. If the number of high-amplitude pixels exceed the numPixMin
, the event is passed for further analysis.
The algorithm performance was tested for CSPad images. This algorithm consumes up to 15 ms/event on psana0205 for full CSPad (1650x1650) window size. For smaller window consumed time is negligible, comparing to the image reconstruction time, which is ~70 ms/event (for cspad_mod.CsPadCalib
and CSPadPixCoords::CSPadImageProducer
) on psana0205.
Module configuration parameters:
source
(default: "DetInfo(:Cspad)") – source of datakey
(default: "Image2D") – key for input image datathreshold
(default: 10) – minimal threshold on pixel amplitudenumPixMin
(default: 100) – minimal number of pixels with amplitude above the thresholdfilterIsOn
(default: true) – On/Off the filterxmin
(default: 0) – minimal column numberxmax
(default: 100000) – maximal column numberymin
(default: 0) – minimal row numberymax
(default: 100000) – maximal row numberprint_bits
(default: 0) – verbosity:- =0 - print nothing,
- +1 - input pars,
- +2 - summary,
- +4 - per event number of pixels above the threshold,
- +8 - the same as previous, but for each 100's event,
- +16 - event ID.
Remarks:
- The default
key
("Image2D") stands for theCSPadPixCoords::Image2D<double>
image object. Otherkey
names work for thendarray<double,2>
image object. - The
xmin
,xmax
,ymin
,ymax
(in pixels) defines the window in the image for pixel counting. Default values means the entire image range. - The
threshold
,numPixMin
, and the window extents have to be adjusted for particular experiment.
Module ImgAlgos::ImgPeakFinder
This algorithm was motivated by users of amo42112:
1. Select the pixels in the window xmin
, xmax
, ymin
, ymax
with amplitudes above the threshold_low
.
2. Smear image for selected pixels, using 2-d matrix of weights over pixels
from -smear_radius
to +smear_radius
around each smeared pixel amplitude.
The matrix of weights is defined by the 2-d Gaussian function of width sigma
.
3. Find peaks as pixels with absolute-maximal amplitude above the threshold_high
in the center of the matrix -peak_radius
to +peak_radius
.
4. Put the vector of found peaks in the event with key peaksKey
. Each entry of this vector has an object of the struct Peak
, containing x, y positions, peak pixel amplitude, the total amplitude in the matrix, defined by the peak_radius
, and the number of pixels in the matrix above threshold_low
:
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struct Peak{
double x;
double y;
double ampmax; // amplitude in the peak masimum
double amptot; // total amplitude in the range of {{peak_radius}}
unsigned npix; // number of pixels in the range of {{peak_radius}}
} ;
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Module configuration parameters:
source
(default: "DetInfo()") – source of datakey
(default: "") – key for input image datapeaksKey
(default: "peaks") – key for output list of peaksthreshold_low
(default: 10) – low threshold on pixel amplitudethreshold_high
(default: 100) – high threshold on pixel amplitudesigma
(default: 1.5) – width of the Gaussian for smearingsmear_radius
(default: 1) – radius in pixel for smearingpeak_radius
(default: 3) – radius in pixel for peak findingxmin
(default: 0) – minimal column numberxmax
(default: 100000) – maximal column numberymin
(default: 0) – minimal row numberymax
(default: 100000) – maximal row numbertestEvent
(default: 0) – event number to save images and print info for test purposefinderIsOn
(default: true) – On/Off algorithmprint_bits
(default: 0) – finder verbosity:- =0 - print nothing,
- +1 - input pars,
- +2 - summary,
- +4 - number of peaks in the event,
- +8 - per event each peak parameters,
- +16- info about input image format.
Remarks:
- This algorithm consumes ~15 ms/event on psana0101 for full Opal1000 (1024x1024) camera image.
- Smearing algorithm use a "safety margin" which is currently set to 10 pixels (offset from each boarder of the full image size).
See also Example for Module ImgAlgos::ImgPeakFinder.
Module ImgAlgos::ImgPeakFilter
This module use results and should work after the ImgAlgos::ImgPeakFinder
.
It gets the vector of peaks for the source
and key
, loops over all founded peaks and counts the number of peaks above the thresholds threshold_peak
and threshold_total
. If the filterIsOn
is "on" ("true" or "yes" state) and the number of found peaks exceeds the n_peaks_min
the event is passed for further analysis/processing.
Module configuration parameters:
source
(default: "DetInfo()") – source of datakey
(default: "peaks") – key for input list of peaks, should be the same aspeaksKey
inImgPeakFinder
threshold_peak
(default: 0) – threshold on peak amplitudethreshold_total
(default: 0) – threshold on total peak intensity (in the matrix around peak)n_peaks_min
(default: 1) – minimal number of peaks above all thresholdsfilterIsOn
(default: true) – On/Off the filterprint_bits
(default: 0) – filter verbosity:- =0 - print nothing,
- +1 - input pars,
- +2 - summary,
- +4 - peaks' info,
- +8 - event ID.
Module ImgAlgos::Tahometer
This module measures the time interval for entire job and for each dn
events and prints the rate info as requested by the print_bits
parameter.
Module configuration parameters:
dn
(default: 1) – number of events between printoutprint_bits
(default: 0) – filter verbosity:- =0 - print nothing,
- +1 - input pars,
- +2 - start notice and summary at stop,
- +4 - instant rate performance after each
dn
events.
Module ImgAlgos::TimeStampFilter
This module passes only the events if their time stamp is in the requested range.
The range of allowed time stamps is defined by the configuration parameters.
Module configuration parameters:
tsinterval
(default: "1970-01-01 00:00:00.000000000 / 2100-01-01 00:00:00.000000000") – time-stamp interval stringtstamp_min
(default: "1970-01-01 00:00:00.000000000") – minimal time-stamp stringtstamp_max
(default: "2100-01-01 00:00:00.000000000") – maximal time-stamp stringfilterIsOn
(default: true) – On/Off the filterprint_bits
(default: 0) – filter verbosity:- =0 - print nothing,
- +1 - input pars,
- +2 - summary,
- +4 - event ID,
- +8 - time stamp variables for selected event.
The time-stamp string is accepted in various formats:
YYYYMMDD HHMMSS.FFF
YYYYMMDDTHHMMSS.F
YYYY-MM-DD HH:MM:SS.FFF
but the date field has to be presented mandatory.
If thetsinterval
is defined and is different from the default, it will be used in filter and override thetstamp_min
andtstamp_max
.
See also Example for TimeStampFilter and XtcOutputModule.
Module ImgAlgos::EventNumberFilter
This filter selects events by their number counting from the beginning of job, starting from 0. The event number is not a parameter which is associated with event. Use this filter cautiously on your own risk for debugging purpose only.
Note |
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The unique parameter associated with the event is a time-stamp. The event number is not defined in the xtc file and is not a recommended to use parameter. The events are counted locally inside this filter from the beginning of job starting from 0. Be cautious of using this filter in consecutive jobs for different runs! For example, this filter returns different subsets of events for the files with raw and selected events. |
Module configuration parameters:
filterIsOn
(default: true) – On/Off filter.first
(default: 0) – the first event from the beginning of job, starting from 0.last
(default: 1<<31) – the last event from the beginning of job.evtstring
(default: "") – the string of events of intervals from the beginning of job.print_bits
(default: 0) – filter verbosity:- =0 - print nothing,
- +1 - input pars,
- +2 - summary,
- +4 - selected event number and ID.
There are two modes of operation of this filter.
- If the
first
and/orlast
event numbers are defined, then the filter will select events in this range only. - If the
evtstring
is defined, only listed events of event ranges will be selected. For example, theevtstring
parameter can be defined as
that means the list of events:Code Block 2,5,11-15,20-25,29,30
In theCode Block 2 5 11 12 13 14 15 20 21 22 23 24 25 29 30
evtstring
parameter the comma "," and sign minus "-" as a dash are the only allowed separators. Blank spaces are also allowed. Other characters may abort the program. Theevtstring
mode has higher priority than the 1st mode.
ThefilterIsOn
allows easy turn on/off this filter in*.cfg
file.
Module ImgAlgos::CSPadArrSaveInFile
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This module saves the CSPad data array formatted as \[5920=4*8*185\]\[388\] in output file for each passes event.
Module configuration parameters: |
source
(default: "DetInfo(:Cspad)") – input source of datakey
(default: "") – key for input data, for example, it might be "calibrated"outfile
(default: "cspad-arr") – out file name prefix for saved arrayprint_bits
(default: 0) – module verbosity:- =0 - print nothing,
- +1 - input pars,
- +2 - event ID,
- +4 - time stamp,
- +8 - saved file names.
Module ImgAlgos::CSPadArrAverage
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This module averages the CSPad data array and saves two files for averaged and rms values in CSPad format \[5920=4*8*185\]\[388\]. In contrast to the [cspad_mod.CsPadPedestals|PCDS:Psana Module Catalog#Modulecspadmod.CsPadPedestals], the input data can be specified with a {{key}}, that allows to average CSPad array for already pre-processed data, for example {{"calibrated"}}. This feature can be used to evaluate the averaged signal or background event. Implemented algorithm of averaging allows to eliminate large statistical fluctuations in the pixel amplitude spectrum. In advanced case averaging may have up to three stages, depending on configuration parameters: |
- 0-stage: the 1st portion of events from 0 to
evts_stage1
is averaged without any constrains, the preliminary averaged and rms values are defined for each pixel
at the end of this stage. - 1-stage: starting from the event
evts_stage1
data are collected only forabs(amplitude-average0) < gate_width1
. At the end of this stage the preliminary averaged and rms values are defined for each pixel. - 2-stage: starting from the event
evts_stage2
data are collected only forabs(amplitude-average1) < gate_width2
. At the end of this stage the preliminary averaged and rms values are defined for each pixel and saved in the files specified by theavefile
andrmsfile
parameters, respectively.
This type of averaging algorithm may be useful for pedestal defenition in case of large amplitude fluctuations.
Module configuration parameters:
source
(default: "DetInfo(:Cspad)") – input source of datakey
(default: "") – key for input data, for example, it might be "calibrated"avefile
(default: "cspad-ave.dat") – out file with averaged amplitudesrmsfile
(default: "cspad-rms.dat") – out file with rmsevts_stage1
(default: 1<<31U) – number of events before stage 1evts_stage2
(default: 100) – additional number of events before stage 2gate_width1
(default: 0) – gate_width for stage 1gate_width2
(default: 0) – gate_width for stage 2print_bits
(default: 0) – module verbosity:- =0 - print nothing,
- +1 - input pars,
- +2 - beginning of 3 stages,
- +4 - processed statistics at the end of each stage,
- +8 - output in files,
- +16 - event ID.
Default version of the configuration parameters works the same way as cspad_mod.CsPadPedestals. In this case module gets raw events and stage 0 continues for entire input data sample.
See also Example for Module ImgAlgos::CSPadArrAverage.
Module ImgAlgos::CSPadBkgdSubtract
This module uses the CSPad array, specified by the configuration parameters source
and inputKey
, subtracts the background, defined in the file bkgd_fname
, and saves the resulting array in the event with outputKey
. The subtracted background array is normalized on the sum of pixel amplitudes in the quad section norm_sector
, which can be set from 0 to 7.
Note | ||||
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Module configuration parameters:
source
(default: "DetInfo(:Cspad)") – input source of datainputKey
(default: " " ) – key for input data, by default use raw dataoutputKey
(default: "bkgd_subtracted" ) – output key for the next data processing stageWiki Markup {{bkgd_fname}} (default: "cspad_background.dat" ) -- file with CSPad array \[4*8*185\]\[388\] of averaged background
norm_sector
(default: 0) – CSPad sector in quad from 0 to 7print_bits
(default: 0) – module verbosity:- =0 - print nothing,
- +1 - input pars,
- +2 - event ID,
- +4 - normalization factor for each event,
- +8 - part of the background array.
See also Example for Module ImgAlgos::CSPadBkgdSubtract.
Module ImgAlgos::CSPadMaskApply
This module uses the CSPad array, defined by the configuration parameters source
and inkey
, apply the mask from file mask_fnname
and saves the masked data with key outkey
. For masked pixels the amplitude will be replaced by the value from masked_amp
.
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The file {{mask_fnname}} has the same structure as files for pedestals and background with dimensions \[4*8*185\]\[388\]. Masked pixels are indicated by 0-th in this file. This file can be generated, for example, from the averaged background file, using amplitude threshold. This can be done with auxiliary python script {{MakePixelMask.py}} as explained in [Example for Module ImgAlgos::CSPadMaskApply|PCDS:Psana Module Examples#Example for Module ImgAlgos::CSPadMaskApply]. |
Module configuration parameters:
source
(default: "DetInfo(:Cspad)" ) – input source of datainkey
(default: " " ) – key for input data, by default use raw dataoutkey
(default: "bkgd_subtracted" ) – output key for the next data processing stageWiki Markup {{mask_fname}} (default: "cspad_mask.dat" ) -- file with CSPad mask array \[4*8*185\]\[388\]
masked_amp
(default: 0) – this amplitude will replace the amplitude in each masked pixelmask_control_bits
(default: 1) – control bits for applied mask:- =0 - do not apply any mask,
- +1 - apply mask from file,
- +2 - mask two long edges of 2x1,
- +4 - mask two short edges of 2x1,
- +8 - mask two short rows in the middle of 2x1 (rows with wide pixels).
print_bits
(default: 0) – module verbosity:- =0 - print nothing,
- +1 - input pars (in beginJob),
- +2 - event ID (in event),
- +4 - mask statistics (in beginJob),
- +8 - part of the mask array (in beginJob).
Module ImgAlgos::ImgRadialCorrection
This module averages the image pixel amplitude in r-phi bins, normalizes it per single pixel and subtracts the average amplitude from each pixel. Image is obtained from event by its source
and inkey
values. The output corrected image is saved in the event with outkey
keyword. Carthesian to polar coordinate transformation is done with respect to center coordinates xcenter
, ycenter
. The central region (r<rmin) and edges of the image (r>rmax) pixels can be removed from further consideration by setting rmin
and rmax
. The number of radial bins is defined as an int(rmax-rmin)
. The number of angular bins is set by n_phi_bins
.
Module configuration parameters:
source
(default: "DetInfo()") – input source of datainkey
(default: " " ) – key for input data, by default use raw dataoutkey
(default: "rad_corrected" ) – output key for further image processingxcenter
(default: 850) – x coordinate of the image centerycenter
(default: 850) – y coordinate of the image centerrmin
(default: 10) – radius minimal image is not processed for r<rminrmax
(default:1000) – radius maximal image is not processed for r>rmaxn_phi_bins
(default: 12) – number of angular sectors for the background averaging.event
(default: 0) – test event for print/saveprint_bits
(default: 0) – module verbosity:- =0 - print nothing,
- +1 - input pars,
- +2 - summary,
- +4 - event ID,
- +8 - info about input image type (ndarray<double,2> or Image2D<double>).
See also Example for Module ImgAlgos::ImgRadialCorrection.
Module ImgAlgos::CSPadArrNoise
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This module works on CSPad data array (shaped as \[5920=4*8*185\]\[388\]), uses the "median algorithm" to evaluate the signal and noise for each pixel, evaluates S/N ratio for each pixel, counts the fraction of events where {{S/N > SoNThr}}, and writes the same shape arrays for pixel mask and status information in the {{maskfile}} and {{statusfile}}, respectively. The {{statusfile}} contains for each pixel the fraction of events where {{S/N > SoNThr}}. |
Module configuration parameters:
source
(default: "DetInfo(:Cspad)") – input source of datakey
(default: "") – key for input data, for example, it might be "calibrated"statusfile
(default: "cspad-pix-status.dat") – out file with pixel status: fraction of noisy imagesmaskfile
(default: "cspad-pix-mask.dat") – out file with pixel maskrmin
(default: 3) – radial parameter of the area for median algorithmdr
(default: 1) – radial band width of the area for median algorithmSoNThr
(default: 3) – S/N threshold for each pixel to be considered as noisyfrac_noisy_img
(default: 0.1) – fraction of noisy images above which pixel is masked in themaskfile
print_bits
(default: 0) – module verbosity:- =0 - print nothing,
- +1 - input pars,
- +2 - empty,
- +4 - processed statistics,
- +8 - output in files,
- +16 - event ID,
- +32 - event time stamp,
- +32 - vector of indexes and map of indexes for the median algorithm.
See also Example for Module ImgAlgos::CSPadArrNoise.
Module ImgAlgos::CSPadArrPeakFinder
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This module extends features of the previous {{ImgAlgos::CSPadArrNoise}} module for the case of peak finding.
It works on CSPad data array (shaped as \[5920=4*8*185\]\[388\]) as follows: |
- in the constructor and
beginJob(...)
method:- enters input parameters,
- (re)set the initial mask of noisy pixels from file
hot_pix_mask_file
(if its name is specified in the configuration file), - do necessary initialization of work arrays.
- in the
event(...)
method:- uses the "median algorithm" to evaluate the signal and noise for each pixel,
Wiki Markup fills \[4\]\[8\]\[185\]\[388\] per-pixel arrays:
m_stat
- number of events with|S/N| > SoNThr
,m_signal
- signal amplitude, or 0(zero) for masked pixels,m_proc_status
- sets 255 forS/N > SoNThr
or 0(zero) for masked pixels.
- use arrays
m_proc_status
andm_signal
to find peaks:Wiki Markup iterate over \[185\]\[388\] 2x1 pixels and find the connected regions (using recursive flood-filling algorithm)
- create vector of peaks
v_peaks
ofstruct Peak
, usingpeak_npix_min
,peak_npix_max
, andpeak_amp_tot_thr
parameters,
- loop over
v_peaks
, count total amplitude and the number of peaks in the event. - decide if the event selected or not based on
event_npeak_min
,event_amp_tot_thr
, andselection_mode
parameters. - periodically dynamically re-generate the mask, based on
m_stat
array andfrac_noisy_imgs
parameter. When to start and for how many events to update the mask is defined by thenevents_mask_update
andnevents_mask_accum
parameters, respectively. - save
m_signal
in file for selected events, depending onout_file_bits
parameter.
- put the vector with peaks
v_peaks
in the evt with key=key_peaks_out
.
- in the
endJob(...)
method, depending on bit status inout_file_bits
:- save current hot-pixel mask in the file
hot_pix_mask_out_file
- save current fraction of events with noisy/signal pixels in the file
frac_noisy_evts_file
- save current hot-pixel mask in the file
Module configuration parameters:
source
(default: "DetInfo(:Cspad)") – input source of datakey
(default: "") – key for input data, for example, it might be "calibrated"key_signal_out
(default: "") – key for output signal array. If the string non-empty, the array is added in the datagram for each event (before selection).key_peaks_out
(default: "peaks") – key for vector of found peaks in the selected eventhot_pix_mask_inp_file
(default: "cspad-pix-mask-in.dat") – in read the pixel mask from filehot_pix_mask_out_file
(default: "cspad-pix-mask-out.dat") – out write current pixel mask in the filefrac_noisy_evts_file
(default: "cspad-pix-frac-out.dat") – out file with per-pixel fraction of noisy imagesevt_file_out
(default: "./cspad-ev-") – out file with signal CSPad array. Time stamp is added.rmin
(default: 3) – radial parameter of the area for median algorithmdr
(default: 1) – radial band width of the area for median algorithmSoNThr_noise
(default: 3) – S/N threshold for each pixel to be considered as noisySoNThr_signal
(default: 5) – S/N threshold for each pixel to be considered as noisyfrac_noisy_imgs
(default: 0.9) – fraction of noisy images above which pixel will be maskedpeak_npix_min
(default: 4) – minimal number of connected pixels for the good peakpeak_npix_max
(default: 25) – maximal number of connected pixels for the good peakpeak_amp_tot_thr
(default: 0.) – threshold on total signal amplitude of the group of connected pixels, if =0:OFFpeak_SoN_thr
(default: 7.) – threshold on peak S/N (S and N are sums over connected pixels)event_npeak_min
(default: 10) – threshold on minimal number of good peaks for the event selectionevent_npeak_max
(default: 10000) – threshold on maximal number of good peaks for the event selectionevent_amp_tot_thr
(default: 0.) – threshold on total signal amplitude in ADU of all good peaks for the event selection, if =0:OFFnevents_mask_update
(default: 0) – number of skipped events before each mask re-evaluation cyclenevents_mask_accum
(default: 50) – number of events for the mask re-evaluationselection_mode
(default: SELECTION_ON) – selection mode, other allowed values are: SELECTION_OFF, or SELECTION_INVout_file_bits
(default: 0) – control on writting of files:- =0 - do not write files,
- +1 - save the
hot_pix_mask_out_file
file with current mask array in theendJob(...)
method. - +2 - save the
frac_noisy_evts_file
file with current fraction of noisy events array in theendJob(...)
method. - +4 - save the CSPad signal array for selected events in the file with name like
<evt_file_out>-<counter>-<run>-<time stamp>.txt
. - +8 - save the vector of found peaks in file
<evt_file_out>-<counter>-<run>-<time-stamp>-peaks.txt
.
print_bits
(default: 0) – module verbosity:- =0 - print nothing,
- +1 - input pars (once in
beginJob
), - +2 - initial and current mask statistics (in constructor and when mask is updated),
- +4 - event selection parameters (for each event); event no., time-stamp, mode, number of peaks, and amp_tot.
- +8 - output in files (for selected events),
- +16 - start/stop to collect data for mask re-evaluation (driven by the mode counters),
- +32 - event time stamp (for each event),
- +64 - vector of indexes and map of indexes for the median algorithm (once in
beginJob
), - +128 - peak parameters before selection (for each event),
- +256 - peak parameters saved in file (for selected events),
- +512 - selection statistics (N<5: for each event; N<50: for each 10-th; N<500: for each 100-th, then for each 1000-th),
- Always print:
- Summary at the
endJob
.
- Summary at the
|