About

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.

...

This page provides examples for selected modules in Psana Module Examples.

Package psana

Psana package include several simple modules which do generic tasks that do not need knowledge of the event data types.

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.

...

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.

...

[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)

Module psana.PrintSeparator

This module prints separator line on every event. Can be used to indicate event boundaries in job's log.

...

[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)

Package psana_examples

Anchor
psana_examples 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. To find the code:

• On the psana machines, from your release directory, one can do
  cd $SIT_REPOS/psana_examples
• Visit the link https://pswww.slac.stanford.edu/swdoc/releases/ana-current/psana-modules-doxy/html/files.html to find the files.  For instance https://pswww.slac.stanford.edu/swdoc/releases/ana-current/psana-modules-doxy/html/DumpControl_8cpp-source.html shows one how to dump control data.

Module psana_examples.DumpAcqiris

Extracts and dumps the content of Acqiris configuration (Psana::Acqiris::ConfigV1) and event data (Psana::Acqiris::DataDescV1) objects.

Module psana_examples.DumpAcqTdc

Extracts and dumps the content of Acqiris TDC configuration (Psana::Acqiris::TdcConfigV1) and event data (Psana::Acqiris::TdcDataV1) objects.

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 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 psana_examples.DumpControl

Anchor
dumpcontrol dumpcontrol

Extracts and dumps the content of scan control configuration (Psana::ControlData::ConfigV1) object.

Module psana_examples.DumpCsPad

Extracts and dumps the content of CsPad configuration (Psana::CsPad::ConfigV*) and event data (Psana::CsPad::DataV*) objects.

Module psana_examples.DumpEncoder

Extracts and dumps the content of encoder configuration (Psana::Encoder::ConfigV1) and event data (Psana::Encoder::DataV*) objects.

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 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 psana_examples.DumpIpimb

Extracts and dumps the content of IPIMB configuration (Psana::Ipimb::ConfigV1) and event data (Psana::Ipimb::DataV1) objects.

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 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 psana_examples.DumpPnccd

Extracts and dumps the content of pnCCD configuration (Psana::PNCCD::ConfigV*) and event data (Psana::PNCCD::FrameV1) objects.

Module psana_examples.DumpPrinceton

Extracts and dumps the content of Princeton configuration (Psana::Princeton::ConfigV1) and event data (Psana::Princeton::FrameV1) objects.

Module psana_examples.DumpPulnix

Extracts and dumps the content of Pulnix configuration (Psana::Pulnix::TM6740ConfigV*) objects.

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.

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.

...

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.

...

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.

...

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.

...

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 CSPadPixCoords::CSPadImageProducer

CSPadImageProducer works in psana framework. It does a few operation as follows:

...

• By default the empty key corresponds to raw data.

Module CSPadPixCoords::CSPadInterpolImageProducer

CSPadInterpolImageProducer works in psana framework. It does a few operation as follows:

...

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:

...

• By default the empty inkey corresponds to raw data.
• If the outimgkey is defined as "Image2D", the image is saved in the event as a CSPadPixCoords::Image2D<double> object, otherwise (for other names) as a ndarray<double,2> object.

See also Example for Module CSPadPixCoords::CSPad2x2ImageProducer.

Module CSPadPixCoords::CSPadNDArrProducer

CSPadNDArrProducer is a module for psana framework. It uses specified source and inkey parameters,

...

See also Example for Module CSPadPixCoords::CSPadNDArrProducer.

Module CSPadPixCoords::CSPad2x2NDArrProducer

CSPad2x2NDArrProducer is a module for psana framework. It uses specified source and inkey parameters,

...

See also Example for Module CSPadPixCoords::CSPad2x2NDArrProducer.

Package ImgPixSpectra

For complete reference see the Doxygen documentation.

...

This information can be used in analysis or presentation of this array.

Module ImgPixSpectra::CSPadPixSpectra

List of parameters:

See also: Example for Module ImgPixSpectra::CSPadPixSpectra.

Module ImgPixSpectra::CSPad2x2PixSpectra

The only difference in interface of this module from previous is in the default name for the source parameter and the output file name.

See also: Example for Module ImgPixSpectra::CSPad2x2PixSpectra.

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.

...

See also Example for Package ImgPixSpectra.

Package ImgAlgos

This packages contains a few psana modules for analysis and image processing

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.

See also Example for Module ImgAlgos::Tahometer.

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.

...

• YYYYMMDD HHMMSS.FFF
• YYYYMMDDTHHMMSS.F
• YYYY-MM-DD HH:MM:SS.FFF
  but the date field has to be presented mandatory.
  If the tsinterval is defined and is different from the default, it will be used in filter and override the tstamp_min and tstamp_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.

...

1. If the first and/or last event numbers are defined, then the filter will select events in this range only.

2. If the evtstring is defined, only listed events of event ranges will be selected. For example, the evtstringparameter can be defined as

   Code Block
   bgColor #F7F7ED
   2,5,11-15,20-25,29,30

   that means the list of events:

   Code Block
   bgColor #F7F7ED
   2 5 11 12 13 14 15 20 21 22 23 24 25 29 30

   In the 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. The evtstring mode has higher priority than the 1st mode.
   The filterIsOn allows easy turn on/off this filter in *.cfg file.

Module ImgAlgos::AndorImageProducer

Functionality:

• gets Andor data from the event for specified source and key_in parameters,
• puts the ndarray<double,2> object with camera image in the event using specified key_out parameter.

Module ImgAlgos::PnccdNDArrProducer

Functionality:

• gets pnCCD data from Psana::PNCCD::FramesV1 object from the event for specified source and key_in parameters,
• puts the ndarray<TOUT,3> object of shape 4x512x512 specified key_out parameter.

Module ImgAlgos::PnccdImageProducer

Functionality:

• gets from the event store the object with pnCCD data of type
  • Psana::PNCCD::FullFrameV1 containing four [512][512] frames with T=uint16_t, or
  • ndarray<T,3> , where shape=[4][512][512], T=unsigned short, float, double, int, or int16,
  for specified source and inkey parameters

...

See also Example for Module ImgAlgos::PnccdImageProducer.

Module ImgAlgos::CameraImageProducer

This module takes care about any generic camera image.
Functionality:

...

See also Example for Module ImgAlgos::CameraImageProducer.

Module ImgAlgos::PrincetonImageProducer

Functionality:

• gets the Princeton camera image data from event for specified source and key_in parameters,
• puts the ndarray<uint16_t,2> object with image in the event using specified key_out parameter.

See also Example for Module ImgAlgos::PrincetonImageProducer.

Module ImgAlgos::AcqirisArrProducer

• Gets acqiris configuration and data from Acqiris::ConfigV1 and Acqiris::DataDescV1,  objects using parameters source and key_in;
• produces ndarray<double,2> of shape[] = {nbrChannels, nbrSamples} for waveforms and time stamps;
• saves configuration data in the file defined by fname_prefix;
• saves waveforms and time stamps in the event store with keys key_wform and key_wtime.

 Example for Module ImgAlgos::AcqirisArrProducer

Module ImgAlgos::AcqirisAverage

• Gets Acqiris waveforms from event store as ndarray<double,2> object using parameters source and key_in;
• performs waveform selection controlled by parameters: thresholds, is_postive_signal, do_inverse_selection, in the range depending on local event numbers skip_events and proc_events;

• after number of events proc_events or at the end of job (whatever happens first), saves array of averaged waveforms in the text file with name constructed from fname_ave_prefix and in the event store using parameters source and key_average.

 Example for Module ImgAlgos::AcqirisAverage

Module ImgAlgos::AcqirisCalib

• Gets Acqiris waveforms from event store as ndarray<double,2> object using parameters source and key_in;
• processes events in the range depending on local event numbers skip_events and proc_events;
• at the 1st processed event loads the fname_base_line file with baseline  ndarray<double,2>;
• subtract baseline from waveforms;
• save corrected waveforms in the event store as ndarray<double,2> object using parameters source and key_out.

 Example for Module ImgAlgos::AcqirisCalib

Module ImgAlgos::AcqirisCFD

• Gets Acqiris waveforms from event store as ndarray<double,2> object using parameters source, key_wform, key_wtime;
• runs constant-fraction discriminator algorithm on all acqiris channels using user-specified per-channel parameters;

• saves edges into the event as a set of ndarray<double,1>;

   

  parameter	default value	description
  source	"DetInfo(:Acqiris)"	Source of data.
  key_wform	"acqiris_wform"	Key for input ndarray with waveforms (either raw, or subtracted using AcqirisCalib module) from evt store.
  key_wtime	"acqiris_wtime"	Key for input ndarray with waveform times from evt store.
  key_edges	"acqiris_edges_"	Key for output ndarray<double,1> with calibrated waveforms. This key will have the acqiris channel number (1 thru 20) appended to the end of it, and the data for that channel will be added to the event only if edges were found.
  baselines	""	A list of baseline values (one per channel) to subtract from the waveform in volts.
  fractions	""	A list of fractions (one per channel) between 0 and 1. The edge-time reported will be at the time when the pulse is at this fraction of the peak value.
  thresholds	""	A list of threshold values (one per channel) in volts that indicate a new edge should be found. If this value is less than the baseline, then the algorithm will look for negative pulses, otherwise it will look for positive pulses.
  deadtimes	""	A list of deadtimes (one per channel) in seconds. After each edge the algorithm will ignore any new hits in this time interval.
  leading_edges	""	A list of 0/1 values (one per channel) indicating whether edge-times are desired for leading edges (1) or falling edges (0).

 Example for Module ImgAlgos::AcqirisCFD

Module ImgAlgos::NDArrAverage

This module averages over events the per-element data of the image array (ndarray<T,NDim>, where T is implemented for almost all types: int, int16, uint, float, double etc., NDim≤5) and saves files for sum, averaged, rms values, mask, and, the hot pixel map. Input ndarray can be specified by the source and key parameters. Averaging may have up to three stages, depending on configuration parameters:

...

If all file names are empty (by default), the files with pre-defined names "arr-ave-<exp>-r<run>.dat" and "arr-rms-<exp>-r<run>.dat" will be saved for averaged and rms arrays, respectively. Otherwise, the files with specified names will be saved.
Default parameters are set for regular single-stage averaging without any constrains.
See also Example for Module ImgAlgos::NDArrAverage.

Module ImgAlgos::NDArrCalib

Functionality

• NDArrCalib uses the source and key_in parameters to get any ndarray<T,NDIM> object from the event store, where T stands for uint16_t, int, float, uint8_t, or double, 1≤NDim≤5,
• automaticly gets parameters from calibration store for types pedestals, common_mode, pixel_status, pixel_gain, and pixel_rms,
• gets parameters from user-defined files fname_bkgd and  fname_mask, if their names are specified,

• the specified by the do_... parameter corrections are applied to raw data  ndarray<T,NDIM> as follows:

...

See also Example for Module ImgAlgos::NDArrCalib.

Module ImgAlgos::ImgAverage

This module averages over events the per-pixel data of the image array (ndarray<double,2>) and saves files for averaged, rms values, and, if requested, the hot pixel mask. Input data can be specified by the source and key parameters. Averaging may have up to three stages, depending on configuration parameters:

...

If all file names are empty (by default), the files with pre-defined names "img-ave-r####.dat" and "img-rms-r####.dat" (where #### stands for run number) will be saved for averaged and rms images, respectively. Otherwise, the files with specified names will be saved.
Default parameters are set for regular single-stage averaging without any constrains.
See also Example for Module ImgAlgos::ImgAverage.

Module ImgAlgos::ImgMaskEvaluation

This module gets the image data array (ndarray<T,2>), where T stands for double, float, int, uint8_t, or uint16_t, and evaluates two masks:

...

See also Example for Module ImgAlgos::ImgMaskEvaluation.

Module ImgAlgos::ImgCalib

ImgCalib gets the raw image from data and process it as follows:

...

The pedestal, background, gain, mask, and N*RMS corrections are applied if associated file name is specified.
The constant low level threshold is applied if do_threshold is true.
Corrections are not applied by default or with empty file names.

See also Example for Module ImgAlgos::ImgCalib.

Module ImgAlgos::ImgIntForBins

Functionality:

• ImgIntForBins uses the source and key_in parameters to get the input image (as ndarray<T,2> object), where T stands for uint16_t, int, float, uint8_t, or double,
• gets the pixel-bin indexes from files fname_map_bins, which has a size of image,
• calculates average per pixel intensity for each of number_of_bins bin (from 0 to number_of_bins-1),
• saves the 2-D array of <I>(event, bin) in file fname_int_bins.

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.

See also Example for Module ImgAlgos::ImgRadialCorrection.

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 default key ("Image2D") stands for the CSPadPixCoords::Image2D<double> image object. Other key names work for the ndarray<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:

...

• 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 selection_mode is "SELECTION_ON" and the number of found peaks exceeds the n_peaks_min the event is passed for further analysis/processing,
the table of found peaks may be saved in file with prefix defined by the fname parameter.

See also Example for Module ImgAlgos::ImgPeakFilter.

Module ImgAlgos::ImgPeakFinderAB

This module finds peaks in the ndarray<double,2> image object. Algorithm and the list of parameters are the same as described is section Psana Module CatalogImgAlgos::CSPadArrPeakFinder. The only difference is that the image size is defined by the ndarray<double,2> object.

See also Example for Module ImgAlgos::ImgPeakFinderAB.

Module ImgAlgos::ImgHitFinder

ImgHitFinder is created by request for amo74213. It works pretty similar to ImgCalib, but the threshold algorithms are extended and background subtraction is removed.
It gets the raw image from data and process it as follows:

...

Corrections are not applied by default or with empty file names.

See also Example for Module ImgAlgos::ImgHitFinder.

Module ImgAlgos::ImgSpectra

This module is motivated by the discussion with Josef Frisch, Ryan Coffee, Nick Hartmann. In xppi0412 etc. experiments they need to extract two spectra from Opal1000 camera image for signal and reference, evaluate their relative difference, and find peak position in the differential spectrum.
Module mgAlgos::ImgSpectra works as follows:

• gets the ndarray<double,2> image object from event,
• selects two spectral band regions and integrates amplitudes for each column (it is assumed that both spectra are oriented along the rows),
• saves two spectral arrays for signal and reference bands and their relative difference as another ndarray<double,2> object with shape (3,<number-of-columns>) in the event.
• Further analytical work is assumed to be done in the next module ImgAlgos::ImgSpectraProc.

See also Example for Module ImgAlgos::ImgSpectra.

Module ImgAlgos::ImgSpectraProc

Works after module ImgAlgos::ImgSpectra.
This module is designed as an example, in order to show how to get access to spectral array.
In particular, method ImgSpectraProc::getSpectra(...) shows how to get pointer to data, and method ImgSpectraProc::printSpectra(...) iterates over array and selectively prints its elements.

See also Example for Module ImgAlgos::ImgSpectraProc.

Module ImgAlgos::ImgSaveInFile

...

ImgSaveInFile works after the CSPadImageProducer, CSPadInterpolImageProducer, CameraImageProducer, PnccdImageProducer, etc., which produce image object in formats CSPadPixCoords::Image2D<T> or ndarray<T,2>, where the T stands for one of the data types, double, float, int, uint8_t, or uint16_t.

...

See also Example for Module ImgAlgos::ImgSaveInFile

Module ImgAlgos::ImgVsTimeSplitInFiles

This module is a part of complex algorithm, described in Command Line Interface For Time Correlation Analysis.

...

See also Example for Module ImgAlgos::ImgVsTimeSplitInFiles.

Further processing of the files

• <fname_prefix>-<fname-common>-b<block-number>.<file_type>
• <fname_prefix>-<fname-common>-med.txt

• <fname_prefix>-<fname-common>-time.txt
  is implemented in stand-alone c++ module

  Code Block
  bgColor #F7F7ED
  ImgAlgos/app/corana.cpp (or ImgAlgos/test/corana.cpp)

  Note
  Note, the application in the test directory is compiled and run by the commands: scons test <path>/corana -f <fname_data> -t <fname_tau>\ -h -l <logfile>\ -b <basedir>\

  where

• <fname_data> is one of the data files: <fname_prefix>-<fname-common>-b<block-number>.<file_type>, which needs to be available;
• <fname_tau> is a file with a list of indexes of tau for evaluation of correlations. By default or if the file is missing, the list of indexes will be generated automatically, and for book-keeping is saved in the file <fname_prefix>-<fname-common>-tau.txt;
• <basedir> is a directory for all data files, which is current by default;
• <logfile> is an output log-file, or standard output by default.

Module ImgAlgos::ImgTimeStampList

This module is reduced from ImgAlgos::ImgVsTimeSplitInFiles.
Functionality is restricted to:

...

Module ImgAlgos::ImgIntMonCorr

This module is intended for CorAna project.
ImgIntMonCorr gets the image and intensity monitor data, evaluate the normalization factor, applies this factor to the image intensity, and saves the corrected image in the event.

...

 BldInfo(FEEGasDetEnergy)         FEEGasDetEnergy  1 1 1 1  0 1   3.000000  7.500000  5.250000
 BldInfo(XCS-IPM-02)              XCS-IPM-02       1 1 1 0  1 0  10.000000 13.000000 11.500000
 BldInfo(XCS-IPM-mono)            XCS-IPM-mono     1 1 1 0  0 1  14.500000 16.000000 15.250000
 DetInfo(XcsBeamline.1:Ipimb.4)   Ipimb.4          1 1 1 1  0 0  -1.000000 -1.000000  1.000000
 DetInfo(XcsBeamline.1:Ipimb.5)   Ipimb.5          1 1 1 1  0 0  -1.000000 -1.000000  1.000000

Module ImgAlgos::IntensityMonitorsData

This module is intended for CorAna project.
It gets the 5 intensity monitors data (4 channels for each) and saves them in the text or binary file file_data. Comments (or header) for this file is saved separately in file_header. It also prints the summary parameters for parser, for example:

...

Module ImgAlgos::CSPadArrSaveInFile

This module saves the CSPad data array formatted as [5920=4*8*185][388] in output file for each passes event.

Module ImgAlgos::CSPadArrAverage

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, 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:

...

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::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 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.

...

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.

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.

Module ImgAlgos::CSPadArrNoise

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. This module presents a part of features implemented in the module ImgAlgos::CSPadArrPeakFinder.

See also Example for Module ImgAlgos::CSPadArrNoise.

Module ImgAlgos::CSPadArrPeakFinder

Module ImgAlgos::CSPadArrPeakFinder is a psana-based implementation of the "median algorithm" for peak finding in CSPad data array shaped as [5920=4*8*185][388]. This algorithm was first implemented in myana/Cheetah by Anton Barty and Co. The "median algorithm" assumes that the amplitude level of background and noise for each pixel can be estimated as a mean and RMS of the surrounding pixels, located in the ring with parameters rmin and dr around the pixel in question. The threshold SoNThr_noise on signal over noise (S/N) ratio allow to asset the pixel amplitude as a large noise fluctuation. Statistics of pixels above the S/N threshold accumulated over many images can be used to form the noisy-pixel mask. For example, if the fraction of images where pixel exceeds the S/N threshold grater than certain value (frac_noisy_imgs=0.9), the pixel is considered as noisy. The permanent bad pixel mask (see module ImgAlgos::CSPadMaskApply) and dynamically evaluated noisy pixel mask are used to get rid of bad pixels and improve the image quality. Healthy pixels with S/N above threshold (SoNThr_signal about 3-5) are treated as potential signals. Using recursive flood-filling algorithm the groups of connected signal pixels can be found and considered as a candidate for a diffraction peaks. Peak finding algorithm uses the amplitude, S/N thresholds, and limits on number of pixels in the connected region (parameters peak_amp_tot_thr, peak_SoN_thr, peak_npix_min, and peak_npix_max) in order to define the peak. Finally, the event is selected or discarded depending on number of found peaks and total amplitude threshold, defined by the parameters event_npeak_min, event_npeak_max, and event_amp_tot_thr, respectively.

...

See also Example for Module ImgAlgos::CSPadArrPeakFinder.

Module ImgAlgos::CSPadArrPeakAnalysis

This module is intended for analysis of the results obtained in the peak finding algorithm implemented in the ImgAlgos::CSPadArrPeakFinder module.

...

See also Example for Module ImgAlgos::CSPadArrPeakAnalysis.

Package pyimgalgos

This package contains python modules which work with both frameworks pyana and psana. Functionality of these modules resembles modules from C++ package ImgAlgos. The difference between two frameworks at code level is explained in Migration from pyana to psana.

Module pyimgalgos.cspad_arr_producer

This module gets data from evt store for CSAPD or CSPAD2x2 depending on unique detector name in parameter source, produce numpy array of full scale shape (4,8,185,388) or (185, 388, 2) of specified in dtype type, and saves it in the evt store with unique name key_out. In case of missing 2x1 sections, their pixel amplitudes substituted by the value form val_miss.

See also Examples for package pyimgalgos.

Module pyimgalgos.cspad_image_producer

This module gets from evt store the numpy array identified by key_in of full scale shape (4,8,185,388) or (185, 388, 2) for CSPAD or CSPAD2x2, respectively, and produces 2-d image numpy array, taking into account geometry calibration parameters specified by the path calib_dir. The output image array is saved in the evt store with unique name, specified by parameter key_out.

See also Examples for package pyimgalgos.

Module pyimgalgos.image_crop

This module gets from evt store the 2-d image numpy array identified by source and key_in, crop it using range of row and column parameters, and saves cropped 2-d image numpy array  in the evt store with unique key_out.

Module pyimgalgos.image_save_in_file

This module gets from evt store 2-d image numpy array for specified unique name in key_in and saves it in the file with name given by parameter ofname. File extension defines the output file format. Experiment, run, and event numbers are added to the name of the output file. For example, for ofname = image.tiff files will be created with names image-<experinent>-r####-ev######.tiff, where symbols # stands for numbers.

See also Examples for package pyimgalgos.

Module pyimgalgos.tahometer

Is intended to print records showing job performance current and integrated from the beginning of job:

...

See also Examples for package pyimgalgos.

References

• Psana User Manual - Old
• Psana Reference Manual - Old
• Psana psana - Module Examples
• Migration from pyana to psana
• psana - Migration from pyana

...