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.

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See also Example for Package ImgPixSpectra.

Package ImgAlgos

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

Module ImgAlgos::Tahometer

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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.

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See also Example for TimeStampFilter and XtcOutputModule.

Module ImgAlgos::EventNumberFilter

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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::EventCounterFilter

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2 3 6 7 9 11 15
17 28 32 ...

Module ImgAlgos::EventCodeFilter

ImgAlgos::

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Functionality:

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EventCodeFilter (ImgAlgos > V00-03-80) module is created by request of Silke Nelson for dark image selection based on EvrData eventCode.

Functionality: Filter selects events which have requested evtcode in Psana::EvrData::DataV4, 3, ... data objects in the list of Psana::EvrData::FIFOEvent objects. Events which do not have the event code are skipped

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Example of configuration parameters for this module:

modules = ... ImgAlgos.EventCodeFilter ...

[ImgAlgos.EventCodeFilter]
evtcode    = 41
mode       = 1
print_bits = 5

Module ImgAlgos::

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AndorImageProducer

Functionality:

• gets Epix Andor data from the event store for specified source and key_in parameters,
• puts the ndarray<const T,2> object with camera image in the event store using specified key_out parameter, where the output type T is defined by the outtype parameter.

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Module ImgAlgos::EpixNDArrProducer

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Functionality:

• gets pnCCD Epix data from Psana::PNCCD::FramesV1 object from the event store for specified source and key_in parameters,
• puts the ndarray<const TOUTT,3> object of shape 4x512x512 2> object with image in the event store using specified key_out parameter, where the output type T is defined by the outtype parameter.

parameter	default value	description
source	"DetInfo(:pnCCDEpix)"	source of data, it needs to be replaced for real detector to :Epix100a
key_in		key for input data
key_out	"pnccdepix-ndarr"	output key for image saved in the event store
outtype	"asdata"	out data type: implemented values: asdata (default, unsigned shortuint16_t), float, double, int and int16.
print_bits	0	verbosity: =0 - print nothing +1 - input pars +2 - data from event() +4 - configuration parameters +8 - table with sizes of types+16 - warning about missing data

See also Example for Module ImgAlgos::EpixNDArrProducer.

Module ImgAlgos::

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PnccdNDArrProducer

Functionality:

• gets from the event store the object with pnCCD data of typefrom Psana::PNCCD::FullFrameV1 containing four [512][512] frames with T=uint16_t, or
• ndarray<const T,3> , where shape=[4][512][512], T=unsigned short, float, double, int, or int16,
FramesV1 object from the event for specified source and inkey key_in parameters,
• puts the ndarray<const TTOUT,2> object with pnccd [1024+gap_rows][1024+gap_cols] image in the event using specified outimgkey 3> object of shape 4x512x512 specified key_out parameter.

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Module ImgAlgos::PnccdImageProducer

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Functionality:

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This module works with any generic camera image stored in data type Camera::FrameV#:

• gets any camera image data Camera::FrameV1 from the event store for specified source and key_in parameters,puts the ndarray<const T,2> object with camera image in the event store using specified type outtype and key_out parameters.

   

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

• puts the ndarray<const T,2> object with pnccd [1024+gap_rows][1024+gap_cols] image in the event using specified outimgkey parameter NoteSpecial treatment for fccd960: if  outtype is not "asdata" the gain factor depending on gain bits is applied, See FCCD-Detector.

on/off the amplitude offset using configuration data (not applied for outtype = asdata)

parameter	default value	description
source	"DetInfo(:CamerapnCCD)"	source of data
key_ininkey		key for input datakey_out
outimgkey	"pnccdimg"	output key for image saved in event
outtype	"asdata"	out data type: implemented values: asdata (default, uint16_t), float, double, int and int16.
gap_rows	0	gap between top and bottom segments in number of pixels
gap_cols	0	gap between left and right segments in number of pixels
gap_value	0	Image effective pixel intensity value in the gap	subtract_offset	true
print_bits	0	verbosity: =0 - print nothing +1 - input pars +2 - time stamp for each eventinitial portion of pnccd array +4 - summary at the endJobconfiguration pars +8 16 - details about data format conversion and applied offset+16 - configuration data for each beginCalibCyclewarning about missing data

See also Example for Module ImgAlgos::CameraImageProducerPnccdImageProducer.

Module ImgAlgos::

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CameraImageProducer

This module works with any generic camera image stored in data type Camera::FrameV#Functionality:

• gets the Princeton or Pimax any camera image data Princeton::FrameV1/2 or PimaxCamera::FrameV1 from the event store for specified source and key_in parameters,

• puts the ndarray<const T,2> object with camera image in the event store using specified type outtype and key_out parameters.

   

  Note
  Special treatment for fccd960: if  outtype is not "asdata" the gain factor depending on gain bits is applied, See FCCD-Detector.

See also Example for Module ImgAlgos::PrincetonImageProducer.

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CameraImageProducer.

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Module ImgAlgos::

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PrincetonImageProducer

Functionality:

• gets the Princeton or Pimax camera image data Princeton::FrameV1/2 or Pimax::FrameV1 from the event store for specified Gets acqiris configuration and data from Acqiris::ConfigV1 and Acqiris::DataDescV1,  objects using parameters source and key_in;
• produces ndarray<const double,2> of shape[] = {nbrChannels, nbrSamples} for waveforms and time stamps;
• saves configuration data in the file defined by fname_prefix;
• parameters,
• puts the ndarray<const T,2> object with camera image in the event using specified type outtype and key_out parameterssaves waveforms and time stamps in the event store with keys key_wform and key_wtime.

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See also Example for Module ImgAlgos::

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PrincetonImageProducer.

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Module ImgAlgos::

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AcqirisArrProducer

• Gets Acqiris waveforms from event store as ndarray<const double,2> object acqiris configuration and data from Acqiris::ConfigV1 and Acqiris::DataDescV1,  objects 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;

• produces ndarray<const 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_wtimeafter 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

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Module ImgAlgos::AcqirisCalib

• Gets Acqiris waveforms from event store as ndarray<const 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<const double,2>;
• subtract baseline from waveforms;
• save corrected waveforms in the event store as ndarray<const double,2> object using parameters source and key_out.

 Example for Module ImgAlgos::AcqirisCalib

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Module ImgAlgos::AcqirisCFD

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 Example for Module ImgAlgos::AcqirisArrProducer

Module ImgAlgos::AcqirisAverage

• Gets Acqiris waveforms from event store as ndarray<const 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<const 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<const double,2>;
• subtract baseline from waveforms;
• save corrected waveforms in the event store as ndarray<const double,2> object using parameters source and key_out.

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

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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.

 Example for Module ImgAlgos::AcqirisCalib

Module ImgAlgos::AcqirisCFD

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""

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A list of baseline values (one per channel) to subtract from the waveform in volts.

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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.

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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.

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A list of deadtimes (one per channel) in seconds. After each edge the algorithm will ignore any new hits in this time interval.

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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::NDArrImageProducer

This module converts any (detector-associated) ndarray in to image.

For any available in the event store ndarray<const T,NDim>, defined by the source and key_in parameters, and which size is equal to the number of pixels in the detector,  this module creates 2-d image ndarray<const TOUT,2> and saves it in the event store with key_out. TOUT is defined by the type_out. Pixel geometry array is retreived from the calibration file of  "geometry" type from default standard or specified in calibdir directory.

Configuration parameters:

• Gets Acqiris waveforms from event store as ndarray<const 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)"

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• Source of data

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• .

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• key_

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• wform

  "acqiris_wform"

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• Key for input

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print_bits

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0

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module verbosity:

• =0 - print nothing
• +1 - input pars
• +2 - info about (non-) availability of the calibration file
• +4 - event record
• +8 - info about produced image
• +16 - size of types table
• +32 - pixel coordinates
• +64 - detailed information about geometry file processing

• 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::NDArrImageProducer

This module converts any (detector-associated) ndarray in to image.

For any available in the event store ndarray<const T,NDim>, defined by the source and key_in parameters, and which size is equal to the number of pixels in the detector,  this module creates 2-d image ndarray<const TOUT,2> and saves it in the event store with key_out. TOUT is defined by the type_out. Pixel geometry array is retreived from the calibration file of  "geometry" type from default standard or specified in calibdir directory.

Configuration parameters:

Additional parameters which can be used for special applications like alignment:

See also Example for Module ImgAlgos::NDArrImageProducer.

Module ImgAlgos::NDArrAverage

This module averages over events the per-element data of the image array (ndarray<const 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:

• 0-stage: the pixel amplitudes are averaged without any constrains for events from 0 to evts_stage1, the preliminary averaged and rms values are defined for each pixel at the end of this stage.
• 1-stage: starting from event evts_stage1 the pixel data are collected only for abs(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_stage1 + evts_stage2 the pixel data are collected only for abs(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 the avefile and rmsfile parameters, respectively.
  This 3-stage averaging algorithm eliminates large statistical fluctuations in the pixel amplitude spectrum.

If the parameter thr_rms_ADU is set ≤0 then threshold value is defined automatically using constrained averaging of pixel rms values in 3 iterations.  The threshold value is defined as mean+5*rms.

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<const T,NDIM> object from the event store, where T stands forint16_t, 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<const T,NDIM> as follows:

1. 1. 1. 1. subtracts pedestals,
         2. subtracts common mode,
         3. subtracts normalized background,
         4. apply gain factors,
         5. apply hot/bad pixel_status mask,
         6. apply mask  (1/0 = good/bad pixels),
         7. apply threshold as a common low level,
         8. apply per-pixel threshold as N*RMS,

• and saves the corrected ndarray<const TOUT,NDim> in the event with key key_out, where TOUT is controlled by the parameter outtype, which can be set to double(default), float, int, and int16.

• In ImgAlgos V00-02-01 implemented detectors: CsPad, CsPad2x2, Pnccd, Princeton, Andor, Opal1000, Opal4000

Control on corrections

A_cor = A_raw
        (1) - pedestal             | if do_peds==true and pedestals are available in calib store
        (2) - common mode          | if do_cmod==true and common_mode parameters are available in calib store
        (3) - N*background         | if do_bkgd==true and the file name is specified in the parameter fname_bkgd and bkgd_ind_* are set
        (4) * gain                 | if do_gain==true and pixel_gain are available in calib store

Additional parameters which can be used for special applications like alignment:

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Module ImgAlgos::NDArrAverage

This module averages over events the per-element data of the image array (ndarray<const 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:

• 0-stage: the pixel amplitudes are averaged without any constrains for events from 0 to evts_stage1, the preliminary averaged and rms values are defined for each pixel at the end of this stage.
• 1-stage: starting from event evts_stage1 the pixel data are collected only for abs(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_stage1 + evts_stage2 the pixel data are collected only for abs(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 the avefile and rmsfile parameters, respectively.
  This 3-stage averaging algorithm eliminates large statistical fluctuations in the pixel amplitude spectrum.

If the parameter thr_rms_ADU is set ≤0 then threshold value is defined automatically using constrained averaging of pixel rms values in 3 iterations.  The threshold value is defined as mean+5*rms.

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<const T,NDIM> object from the event store, where T stands forint16_t, 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<const T,NDIM> as follows:

1. 1. 1. 1. subtracts pedestals,
         2. subtracts common mode,
         3. subtracts normalized background,
         4. apply gain factors,
         5. apply hot/bad pixel_status mask,
         6. apply mask  (1/0 = good/bad pixels),
         7. apply threshold as a common low level,
         8. apply per-pixel threshold as N*RMS,

• and saves the corrected ndarray<const double,NDim> in the event with key key_out
• In ImgAlgos V00-02-01 implemented detectors: CsPad, CsPad2x2, Pnccd, Princeton, Andor, Opal1000, Opal4000

Control on corrections

A_cor = A_raw
        (1) - pedestal             | if do_peds==true and pedestals are available in calib store
        (2) - common mode          | if do_cmod==true and common_mode parameters are available in calib store
        (3) - N*background         | if do_bkgd==true and the file name is specified in the parameter fname_bkgd and bkgd_ind_* are set
        (4) * gain                 | if do_gain==true and pixel_gain are available in calib store
        (5) apply bad pixel status | if do_stat==true and pixel_status are available in calib store
        (6) apply mask             | if do_mask==true and the file name is specified in the parameter fname_mask. Parameter masked_value is used to substitute masked values.
        (7) apply N*RMS threshold  | if do_nrms==true and pixel_rms are available in calib store, parameters threshold_nrms and below_thre_value are set
        (8) apply common threshold | if do_thre==true. Parameter below_thre_value is used to substitute below threshold values.

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

This module is designed for parallel image processing for correlation analysis.
Functionality:

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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

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The translator package include the H5Output module which translates xtc to hdf5. For more  information see the page Outdated: The XTC - to - HDF5 Translator

Package psana_test

Anchor
psana_test psana_test

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==================
=== begin job ====
# first the epics aliases are printed during begin job.
Epics Aliases: total = 240
  Be_xpos
  Be_ypos
  Be_zpos
  ... 
# next the epics pv, as they appear during beginJob.
# This corresponds to the xtc configure transition. 
# At this point, these are ctrl pvs.
Epics PV
  pvName=HX2:DVD:GCC:01:PMON  pvid=106 dbrtype=34 isCtrl=1 pvName=HX2:DVD:GCC:01:PMON numElements=1 status=0 severity=0 units=T upper_disp_limit=1.0000e-02 lower_disp_limit=0.0000e+00 upper_alarm_limit=0.0000e+00 upper_warning_limit=0.0000e+00 lower_warning_limit=0.0000e+00 lower_alarm_limit=0.0000e+00 upper_ctrl_limit=1.0000e-02 lower_ctrl_limit=0.0000e+00 data=5.0000e-09
  ...
# After epics, we get the content of the psana env configStore. 
# The dump module is getting all keys from the configStore(), 
# then retrieving each object. Objects that have a xtc type id, or are
# an numpy array will be printed.

# For each object, we first get a string describing the even key:

type=psana.ControlData.ConfigV2, src=ProcInfo(0.0.0.0, pid=7670)

  # then we get the data of the object.
  # most all data for a Psana object is obtained through accessor methods.
  # methods that return unsigned ints print in hex. 
  # methods that return signed ints print in decimal.
  # methods that return floats print in scientific format with 4 decimals of precision.

  npvControls: 0x1      
  npvMonitors: 0x0    
  npvLabels: 0x0
  events: 0x1E0
  uses_duration: 0x0
  uses_events: 0x1

# methods that return a compound type, like duration() that returns the compound type time
# are printed as follows:
  duration:
    nanoseconds: 0x0
    seconds: 0x0

# some methods return a python list. Each element in the list is printed separately:
  pvControls[0]:
    name: las_lensh
    index: 0xFFFFFFFF
    value: 0.0000e+00
    array: 0x0
  ...

# epics config is not dumped, see the EPICS alias list for how Psana stores this data
type=psana.Epics.ConfigV1, src=DetInfo(EpicsArch.0:NoDevice.0)
  epicsConfig not dumped

# cspad config is an example which has methods that return ndarrays
type=psana.CsPad.ConfigV4, src=DetInfo(XppGon.0:Cspad.0)
  ...
  numSect: 0x20
  # some methods return a list of simple types, these are printed in one line
  roiMask [0]=0xFF [1]=0xFF [2]=0xFF [3]=0xFF
  numAsicsStored [0]=0x10 [1]=0x10 [2]=0x10 [3]=0x10
  ...
  quads[0]:
    ...    
    dp:
      # for an ndarray, we print the type, dimensions, adler32 checksum, and quartile
      # statistics (min, 25th percentile, median, 75th percentile, and max):
      pots: ndarray_uint8_1: dim=[ 80 ] adler32=0x231B31F5 min=0x0 25th=0x3F median=0xB0 75th=0xFF max=0xFF
    gm:
      gainMap: ndarray_uint16_2: dim=[ 185 x 194 ] adler32=0x18730001 min=0x0 25th=0x0 median=0x0 75th=0x0 max=0x0
   ...

===============================================================
=== beginrun 0 ===            # typically, there is nothing new in beginrun
===============================================================
=== begincalibcycle run=0 step=0 ===

# having dumped the entire initial contents of epics and the config store, 
# the dump module will now only print changes to epics or the config.
# That is it remembers how each epics pv and config object printed the last 
# time it saw it. With each new transition, it looks at all the epics pv and
# config objects. If any change, they are dumped.

# The control data changed in the calib cycle:

type=psana.ControlData.ConfigV2, src=ProcInfo(0.0.0.0, pid=7670)
  npvControls: 0x1
  npvMonitors: 0x0
  npvLabels: 0x0
  events: 0x1E0
  uses_duration: 0x0
  uses_events: 0x1
  duration:
    nanoseconds: 0x0
    seconds: 0x0
  pvControls[0]:
    name: las_lensh
    index: 0xFFFFFFFF
    value: -4.9997e-01
    array: 0x0 are dumped.

# nextThe wecontrol seedata eventchanged data,in printingthe thecalib following:
===============================================================
=== event: run=0 step=0 event=0 seconds= 1362889345 nanoseconds= 770371931 fiducials= 19593
# at this point, all epics pv's are replaced with TIME pv's, not the stamp.sec, stamp.nsec below:
Epics PV
  pvName=HX2:DVD:GCC:01:PMON  pvid=106 dbrtype=20 isTime=1 numElements=1 status=0 severity=0 stamp.sec=731737344 stamp.nsec=134374000 data=5.2000e-09
  ...
# while most epics pv's have one value, there are some with more than one. If a EPICS pv has less than 20 values, they are all printed, otherwise the typical ndarray summary is printed.

# now we get into regular event data
type=psana.EvrData.DataV3, src=DetInfo(NoDetector.0:Evr.0)
  numFifoEvents: 0x2
  fifoEvents[0]:
    timestampHigh: 0x4C89
    timestampLow: 0x32A6
    eventCode: 0x29
  fifoEvents[1]:
    timestampHigh: 0x4C89
    timestampLow: 0x2E4C
    eventCode: 0x8C
type=psana.CsPad.DataV2, src=DetInfo(XppGon.0:Cspad.0)
  quads[0]:
    seq_count: 0x1
    ticks: 0x329D
    fiducials: 0x4C89
    sb_temp: ndarray_uint16_1: dim=[ 4 ] adler32=0x4FC00AC min=0x7 25th=0x8 median=0x9 75th=0x291 max=0x291
    frame_type: 0x4
    data: ndarray_int16_3: dim=[ 8 x 185 x 388 ] adler32=0xAD5ACF7F min=0 25th=1281 median=1346 75th=1475 max=16383
    virtual_channel: 0x0
    lane: 0x0
    tid: 0x0
    acq_count: 0x85
    op_code: 0x85
    quad: 0x0
    sectionMask: 0xFF
  quads[1cycle:

type=psana.ControlData.ConfigV2, src=ProcInfo(0.0.0.0, pid=7670)
  npvControls: 0x1
  npvMonitors: 0x0
  npvLabels: 0x0
  events: 0x1E0
  uses_duration: 0x0
  uses_events: 0x1
  duration:
    nanoseconds: 0x0
    seconds: 0x0
  pvControls[0]:
    name: las_lensh
    index: 0xFFFFFFFF
    value: -4.9997e-01
    array: 0x0

# next we see event data, printing the following:
===============================================================
=== event: run=0 step=0 event=0 seconds= 1362889345 nanoseconds= 770371931 fiducials= 19593
# at this point, all epics pv's are replaced with TIME pv's, not the stamp.sec, stamp.nsec below:
Epics PV
  pvName=HX2:DVD:GCC:01:PMON  pvid=106 dbrtype=20 isTime=1 numElements=1 status=0 severity=0 stamp.sec=731737344 stamp.nsec=134374000 data=5.2000e-09
  ...
# while most epics pv's have one value, there are some with more than one. If a EPICS pv has less than 20 values, they are all printed, otherwise the typical ndarray summary is printed.

# now we get into regular event data
type=psana.EvrData.DataV3, src=DetInfo(NoDetector.0:Evr.0)
  numFifoEvents: 0x2
  fifoEvents[0]:
    timestampHigh: 0x4C89
    timestampLow: 0x32A6
    eventCode: 0x29
  fifoEvents[1]:
    timestampHigh: 0x4C89
    timestampLow: 0x2E4C
    eventCode: 0x8C
type=psana.CsPad.DataV2, src=DetInfo(XppGon.0:Cspad.0)
  quads[0]:
    seq_count: 0x1
    ticks: 0x329D
    fiducials: 0x4C89
    sb_temp: ndarray_uint16_1: dim=[ 4 ] adler32=0x2DB006A0x4FC00AC min=0x7 25th=0xA0x8 median=0xA0x9 75th=0x34B0x291 max=0x34B0x291
    frame_type: 0x4
    data: ndarray_int16_3: dim=[ 8 x 185 x 388 ] adler32=0xD28441BE min=0 25th=1316 median=1374 75th=1504 max=16383
    virtual_channel: 0x0
    lane: 0x0
    tid: 0x0
    acq_count: 0x85
    op_code: 0x85
    quad: 0x1
    sectionMask: 0xFF

src aliases

If a source alias has been defined, it will show up when the event key is printed:

type=psana.Pimax.FrameV1, src=DetInfo(AmoEndstation.0:Pimax.0) alias=pimax
 

Options

Several options allow you to control the output of psana_test.dump

The most useful are

include = term1 term2
exclude = term1 term2

These are used to filter the key strings. For example, running

psana -m psana_test.dump -o psana_test.dump.include=10k exp=mob30114:run=145

Would only dump event keys that had 10k in them, effectively giving you only Epix::Config10KV1 and psana.Epix.ElementV1 since these are the only types coming from the source DetInfo(NoDetector.0:Epix10k.0).

Other options one could set are:

...

 dim=[ 8 x 185 x 388 ] adler32=0xAD5ACF7F min=0 25th=1281 median=1346 75th=1475 max=16383
    virtual_channel: 0x0
    lane: 0x0
    tid: 0x0
    acq_count: 0x85
    op_code: 0x85
    quad: 0x0
    sectionMask: 0xFF
  quads[1]:
    seq_count: 0x1
    ticks: 0x329D
    fiducials: 0x4C89
    sb_temp: ndarray_uint16_1: dim=[ 4 ] adler32=0x2DB006A min=0x7 25th=0xA median=0xA 75th=0x34B max=0x34B
    frame_type: 0x4
    data: ndarray_int16_3: dim=[ 8 x 185 x 388 ] adler32=0xD28441BE min=0 25th=1316 median=1374 75th=1504 max=16383
    virtual_channel: 0x0
    lane: 0x0
    tid: 0x0
    acq_count: 0x85
    op_code: 0x85
    quad: 0x1
    sectionMask: 0xFF

src aliases

If a source alias has been defined, it will show up when the event key is printed:

type=psana.Pimax.FrameV1, src=DetInfo(AmoEndstation.0:Pimax.0) alias=pimax
 

Options

Several options allow you to control the output of psana_test.dump

The most useful are

include = term1 term2
exclude = term1 term2

These are used to filter the key strings. For example, running

psana -m psana_test.dump -o psana_test.dump.include=10k exp=mob30114:run=145

Would only dump event keys that had 10k in them, effectively giving you only Epix::Config10KV1 and psana.Epix.ElementV1 since these are the only types coming from the source DetInfo(NoDetector.0:Epix10k.0).

Other options one could set are:

epics = False       do not print epics
aliases = False     do not print the EPICS alias list
dump_aliases=True   follow EPICS aliases to print the EPICS pv's they point to
dump_sml=True       dump the small data type (if found, psana should automatically replace these proxies)
regress_dump=True   do not print the DAQ assigned pvId when printing EPICS
dump_beginjob_evt=False   do not dump begin job data
output_file = filename   write output to filename
config = False      do not print the contents of the configStore, only regular event data
counter = False     do not print the counter string that labels event numbers and calib cycle numbers
header = False
indent = 4          change the indent from the default of 2 to 4

Library Usage

Two functions are provided in the Python psana_test package that allow Python scripts to turn Psana objects into strings. A Python script could include the following function to build dictionaries describing the state of the event, configStore, and epicsStore:

from psana_test import obj2str, epicsPvToStr

def getPsanaState(event, configStore, epicsStore):
    evtDict = {}
    cfgDict = {}
    epicsDict = {}
    for key in event.keys():

Library Usage

Two functions are provided in the Python psana_test package that allow Python scripts to turn Psana objects into strings. A Python script could include the following function to build dictionaries describing the state of the event, configStore, and epicsStore:

from psana_test import obj2str, epicsPvToStr

def getPsanaState(event, configStore, epicsStore):
    evtDict = {}
    cfgDict = {}
    epicsDict = {}
    for key in event.keys():
        if key.type() is None: continue
        obj = event.get(key.type(), key.src(), key.key())
        if (obj is None): continue
        if not hasattr(obj,'TypeId'):  continue
        evtDict[str(key)]=obj2str(obj)
    for key in configStore.keys():
        if key.type() is None: continue
        obj = configStore.get(key.type(), key.src())
        if (obj is None): continue
        if not hasattr(obj,'TypeId'):  continue
        cfgDict[str(key)]=obj2str(obj)
    for pvName in epicsStore.pvNames():
        pv = epicsStore.getPV(pvName)
        if not pv: continue
        epicsDict[pvName] = epicsPvToStr(pv)
    return evtDict, cfgDict, epicsDict

xtclinedump

xtclinedump is a command line tool to dump xtc and datagram header information in a line oriented style. By keeping the output for each header to one line, it makes it easy to use grep to filter the output. The command can be run by

xtclinedump dg xtcfile.xtc
or
xtclinedump xtc xtcfile.xtc

The first just dumps datagram headers, the latter dumps xtc headers. There are some additional options, how much of the xtc payloads to print, and if you want parsed output for epics. A help string is available by typing xtclinedump with no arguments. Except for the non-default epics argument, xtclinedump does no parsing of the xtc payloads, it simply prints the first few bytes in hex. For reading through payloads, the intel architechture uses little endian, so 0x00040000 = 1024,

Package TimeTool

An example of how to use the TimeTool can be found Here.

Modules for analyzing recorded data from a timetool camera setup. The timetool camera measures the time difference between laser and FEL in one of two methods:

1. spatial encoding, where the X-rays change the reflectivity of a material and the laser probesthat change by the incident angle of its wavefront; or
2. spectral encoding, where the X-rays change the transmission of a material and the chirped laser probes it by a change in the spectral components of the transmitted laser.

Below the package modules are described. The package includes sample configuration files that describe all the options. From a psana release directory, users are encouraged to add the TimeTool package to obtain the latest source. For instance:

newrel ana-current myrel
cd myrel
kinit  if key.type() is None: continue
        obj = event.get(key.type(), key.src(), key.key())
        if (obj is None): continue
        if not hasattr(obj,'TypeId'):  continue
        evtDict[str(key)]=obj2str(obj)
    for key in configStore.keys():
        if key.type() is None: continue
        obj = configStore.get(key.type(), key.src())
        if (obj is None): continue
        if not  # get ticket to check out package from svn repository
addpkg TimeTool
sit_setup
scons
# now examine the files in TimeTool/data:  sxr_timetool.cfg  sxr_timetool_setup.cfg  timetool_setup.py  xpp_timetool.cfg  xpptut.cfg

 timetool_setup.py is a python script to calculate the digital filter weights.

Module Analyze

a module that analyzes the camera image by projecting a region of interest onto an axis and dividing by a reference projection acquired without the FEL.  The resulting projection is processed by a digital filter which yields a peak at the location of the change in reflectivity/transmission.  The resulting parameters are written into the psana event. The type of the parameter depends on the release. Starting with ana-0.13.10, a TimeTool::DataV2 object in put in the event store. ana-0.13.3 put a TimeTool::DataV1 object in the event store. This is the preferred method to retrieve the data that TimeTool.Analyze writes. The module also writes its output as a set of doubles, and can optionally be written as a set of ndarrays to help with C++ to Python conversion. To enable this, set the option

put_ndarrays=True

to the config file. However this is not neccessary in releases after ana-0.13.3.

Module Check

a module that retrieves results from the event for either the above module or from data recorded online.

Module Setup

hasattr(obj,'TypeId'):  continue
        cfgDict[str(key)]=obj2str(obj)
    for pvName in epicsStore.pvNames():
        pv = epicsStore.getPV(pvName)
        if not pv: continue
        epicsDict[pvName] = epicsPvToStr(pv)
    return evtDict, cfgDict, epicsDict

xtclinedump

xtclinedump is a command line tool to dump xtc and datagram header information in a line oriented style. By keeping the output for each header to one line, it makes it easy to use grep to filter the output. The command can be run by

xtclinedump dg xtcfile.xtc
or
xtclinedump xtc xtcfile.xtc

The first just dumps datagram headers, the latter dumps xtc headers. There are some additional options, how much of the xtc payloads to print, and if you want parsed output for epics. A help string is available by typing xtclinedump with no arguments. Except for the non-default epics argument, xtclinedump does no parsing of the xtc payloads, it simply prints the first few bytes in hex. For reading through payloads, the intel architechture uses little endian, so 0x00040000 = 1024,a module that calculates the reference autocorrelation function from events without FEL for use in the digital filter construction.

References

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

dump_sml            dump small data type