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.
Note that most modules have configuration parameters which are documented in tables. For example:
parameter |
default value |
description |
---|---|---|
|
"=" |
separator string |
|
80 |
number of repeats of separator string on |
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.
Example of the output produced by this module:
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)) ...
This module is useful to display the content of the events without dumping all the data. Example command which uses this module is:
% psana -m EventKeys <input-files>
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:
[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.
parameter |
default value |
description |
---|---|---|
|
"=" |
separator string |
|
80 |
number of repeats of separator string on |
Example of the output produced by this module with the default parameters (including output from PrintEventId module):
[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
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.
parameter |
default value |
description |
---|---|---|
|
"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.
parameter |
default value |
description |
---|---|---|
|
"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
).
parameter |
default value |
description |
---|---|---|
|
"BldInfo(EBeam)" |
data source address for |
|
"BldInfo(PhaseCavity)" |
data source address for |
|
"BldInfo(FEEGasDetEnergy)" |
data source address for |
|
"BldInfo(NH2-SB1-IPM-01)" |
data source address for |
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.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Opal1000)" |
data source address |
Module psana_examples.DumpControl
Extracts and dumps the content of scan control configuration (Psana::ControlData::ConfigV1
) object.
parameter |
default value |
description |
---|---|---|
|
"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.
parameter |
default value |
description |
---|---|---|
|
"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.
parameter |
default value |
description |
---|---|---|
|
"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.
parameter |
default value |
description |
---|---|---|
|
"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.
parameter |
default value |
description |
---|---|---|
|
"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.
parameter |
default value |
description |
---|---|---|
|
"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.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Tm6740)" |
data source address for |
|
"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.
parameter |
default value |
description |
---|---|---|
|
"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.
parameter |
default value |
description |
---|---|---|
|
"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.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Princeton)" |
data source address |
Module psana_examples.DumpPulnix
Extracts and dumps the content of Pulnix configuration (Psana::Pulnix::TM6740ConfigV*
) objects.
parameter |
default value |
description |
---|---|---|
|
"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.
parameter |
default value |
description |
---|---|---|
|
"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.
parameter |
default value |
description |
---|---|---|
|
"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 provided |
|
"cspad-pedestals.dat" |
name of the output file for average values, if empty file will not be written |
|
"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:
psana -m cspad_mod.CsPadPedestals input-files.xtc
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:
[psana] modules = cspad_mod.CsPadPedestals [cspad_mod.CsPadPedestals] source = DetInfo(CxiDs1.0:Cspad.0) output = pedestals.dat noise =
and then run psana:
psana input-files.xtc
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.
parameter |
default value |
description |
---|---|---|
|
"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 provided |
|
"cspad2x2-pedestals.dat" |
name of the output file for average values, if empty file will not be written |
|
"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:
psana -m cspad_mod.CsPad2x2Pedestals input-files.xtc
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:
[psana] modules = cspad_mod.CsPad2x2Pedestals [cspad_mod.CsPad2x2Pedestals] source = DetInfo(CxiSc1.0:Cspad2x2.0) output = pedestals.dat noise =
and then run psana:
psana input-files.xtc
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).
parameter |
default value |
description |
---|---|---|
|
"" |
string key used to locate uncalibrated data objects in event |
|
"calibrated" |
string key used to store calibrated data objects in event |
|
"yes" |
can be set to "no" to explicitly disable pedestal subtraction algorithm |
|
"yes" |
can be set to "no" to explicitly disable reading of pixel status data, all pixels will be used for common mode |
|
"yes" |
can be set to "no" to explicitly disable common mode algorithm |
|
"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.
parameter |
default value |
description |
---|---|---|
|
'' |
string key used to locate uncalibrated data objects in event |
|
"DetInfo(:Cspad)" |
data source address |
|
"yes" |
when set to "yes" if the module does not find CsPad data in an event then it skips event |
|
-1 |
filtering mode, see below |
|
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.
parameter |
default value |
description |
---|---|---|
|
"/reg/d/psdm/CXI/cxi35711/calib" |
directory with calibration file |
|
"CsPad::CalibV1" |
data type and group names |
|
"CxiDs1.0:Cspad.0" |
source of data |
|
32 |
run number for calibration file |
|
32 |
number of events before stop a job |
|
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
ndarray<double,2>
orImage2D<double>
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.
parameter |
default value |
description |
---|---|---|
|
|
directory with calibration files, by default it is set to .../<experiment>/calib |
|
"CsPad::CalibV1" |
calibration type and group names |
|
"CxiDs1.0:Cspad.0" |
source of data |
|
|
key for data processing stage |
|
"image" |
output key for image saved in event |
|
true |
on/off for tilt angle of 2x1-sections and quads. |
|
0 |
verbosity:
|
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 (by default) 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
ndarray<double,2>
orCSPadPixCoords::Image2D<double>
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 geometry alignment parameters
center
andtilt
from/reg/d/psdm/<inst>/<experiment>/calib/...
directory - 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).
parameter |
default value |
description |
---|---|---|
|
|
path to the |
|
"CsPad2x2::CalibV1" |
calibration software version |
|
"DetInfo(:Cspad2x2.1)" |
source of data |
|
|
key for data processing stage |
|
"Image2D" |
output key for image saved in event |
|
true |
on/off for tilt angle of 2x1-sections and quads - currently is not used |
|
0 |
verbosity:
|
Remarks:
- By default the empty
inkey
corresponds to raw data. - If the
outimgkey
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::CSPadNDArrProducer
CSPadNDArrProducer is a module for psana framework. It uses specified source
and inkey
parameters,
- gets CSPAD configuration from the environment frame
Psana::CsPad::ConfigV#
, - gets CSPAD data from the event frames
Psana::CsPad::DataV#
,Psana::CsPad::ElementV#
, - creates the data array as
ndarray<T,3>
, where T stands forouttype
, which may be double, float, int, or uint16_t, - puts the data array in the event with
outkey
tag.
The data array ndarray<T,3>
has a shape (N,185,388), where N?32.
This array is combined from data arrays for quads, ndarray<int32_t,3>
with shape (M,185,388), where M?8, taking into account the CSPAD configuration.
In real data some 2x1 may be turned off, that can be seen in configuration object.
parameter |
default value |
description |
---|---|---|
|
":Cspad.0" |
source of data |
|
|
key for data processing stage |
|
"cspad_ndarr" |
output key for image saved in event |
|
"float" |
type of output data |
|
0 |
verbosity:
|
Package ImgPixSpectra
For complete reference see the Doxygen documentation.
Package ImgPixSpectra is available since release ana-0.4.1
. It uses classes from the package CSPadPixCoords V00-02-01 or higher. To add this package in release use command:
addpkg CSPadPixCoords HEAD
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
NPIXELS 143560 NBINS 100 AMIN 500 AMAX 1000 NEVENTS 2549 ARRFNAME mini-cspad-pix-spectra.txt
This information can be used in analysis or presentation of this array.
Module ImgPixSpectra::CSPadPixSpectra
parameter |
default value |
description |
---|---|---|
|
"CxiDs1.0:Cspad.0" |
source of data for CSPad |
|
1<<31U |
number of events before stop a job |
|
|
input key for data processing stage |
|
0. |
minimal spectral amplitude |
|
1000. |
maximal spectral amplitude |
|
100 |
number of bins in spectra |
|
"..._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.
parameter |
default value |
description |
---|---|---|
|
"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.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(SxrBeamline.0:Opal1000.1)" |
source of data for Opal camera |
or:
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Princeton)" |
source of data for Princeton camera |
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.
parameter |
default value |
description |
---|---|---|
|
100 |
number of events between printout |
|
2 |
filter verbosity:
|
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.
parameter |
default value |
description |
---|---|---|
|
"1970-01-01 00:00:00.000000000 / 2100-01-01 00:00:00.000000000" |
time-stamp interval string |
|
"1970-01-01 00:00:00.000000000" |
minimal time-stamp string |
|
"2100-01-01 00:00:00.000000000" |
maximal time-stamp string |
|
true |
On/Off the filter |
|
0 |
filter verbosity:
|
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.
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.
parameter |
default value |
description |
---|---|---|
|
true |
On/Off filter |
|
0 |
the first event from the beginning of job, starting from 0 |
|
1<<31 |
the last event from the beginning of job |
|
|
the string of events of intervals from the beginning of job |
|
0 |
filter verbosity:
|
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 asthat means the list of events:2,5,11-15,20-25,29,30
In the2 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::PnccdImageProducer
Functionality:
- gets the pnccd data from the event, based on specified
source
andinkey
parameters, - puts the
ndarray<double,2>
object with pnccd 1024x1024 image in the event using specifiedoutimgkey
parameter.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:pnCCD)" |
source of data |
|
|
key for input data |
|
"pnccdimg" |
output key for image saved in event |
|
0 |
verbosity:
|
See also Example for Module ImgAlgos::PnccdImageProducer.
Module ImgAlgos::CameraImageProducer
This module takes care about any generic camera image.
Functionality:
- gets any camera image data from the event, based on specified
source
andkey_in
parameters, - puts the
ndarray<double,2>
object with camera image in the event using specifiedkey_out
parameter.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Opal1000)" |
source of data |
|
|
key for input data |
|
"pnccdimg" |
output key for image saved in event |
|
true |
on/off the amplitude offset using configuration data |
|
0 |
verbosity:
|
See also Example for Module ImgAlgos::CameraImageProducer.
Module ImgAlgos::PrincetonImageProducer
This module gets the Princeton camera image data and put it in the event as an image.
Functionality:
- gets the Princeton camera image data from the event, based on specified
source
andkey_in
parameters, - puts the
ndarray<uint16_t,2>
object with image in the event using specifiedkey_out
parameter.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Princeton)" |
source of data |
|
|
key for input data |
|
"image" |
output key for image saved in event |
|
0 |
verbosity:
|
See also Example for Module ImgAlgos::PrincetonImageProducer.
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:
- 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 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_stage1 + evts_stage2
the pixel 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 3-stage averaging algorithm eliminates large statistical fluctuations in the pixel amplitude spectrum.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Opal1000") |
input source of data |
|
|
key for input data, for example, it might be "calibrated" |
|
"" |
out file with sum of amplitudes, saved if the name is not empty |
|
"" |
out file with averaged amplitudes, saved if the name is not empty |
|
"" |
out file with rms, saved if the name is not empty |
|
"" |
out file with hot pixel mask, saved if the name is not empty |
|
"10000." |
threshold on rms (in ADU); if rms exceeds this threshold - pixel is hot |
|
1000000 |
number of events before stage 1 |
|
0 |
additional number of events before stage 2 |
|
0 |
gate_width for stage 1 |
|
0 |
gate_width for stage 2 |
|
0 |
module verbosity:
|
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:
- saturated mask for pixels, which had an intensity above the saturation-threshold with frequency grater than specified fraction of events.
- noise mask for pixels, which estimated S/N ratio exceeds the S/N-threshold with frequency grater than specified fraction of events.
In the endJob
this module saves files (if their names are provided) of image size for:
- saturated mask
- noise mask,
- combined mask,
- fraction of noisy events,
- fraction of saturated events.
The S/N is estimated by averaging over neigbouring pixels.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Opal1000") |
input source of data |
|
|
key for input data, for example, it might be "calibrated" |
|
"img-mask-satu.dat" |
out file with saturated mask |
|
"img-mask-nois.dat" |
out file with noise mask |
|
"img-mask-comb.dat" |
out file with combined mask |
|
"img-frac-satu.dat" |
out file with fraction of saturated events |
|
"img-frac-nois.dat" |
out file with fraction of noisy events |
|
1000000 |
saturation-threshold (in ADU if the gain correction was not applied to image) |
|
0 |
allowed fraction of saturated events |
|
1 |
radial size of the area for S/N evaluation |
|
3 |
noise-threshold ( in ADU if the gain correction was not applied to image) |
|
0.5 |
allowed fraction of noisy events |
|
0 |
module verbosity:
|
See also Example for Module ImgAlgos::ImgMaskEvaluation.
Module ImgAlgos::ImgCalib
ImgCalib gets the raw image from data and process it as follows:
- subtracts pedestals,
- subtracts normalized background,
- apply gain factors,
- apply mask, and
- apply threshold as a constant low level,
- apply threshold as N*RMS,
and saves the corrected image in the event.
Functionality:
- ImgCalib uses the
source
andkey_in
parameters to get the input raw image (asndarray<T,2>
object), where T stands for uint16_t, int, float, uint8_t, or double, - gets the calibration parameters from files
fname_peds
,fname_bkgd
,fname_gain
,fname_mask
, andfname_nrms
, if their names are specified, - the specified by the file name corrections are applied per-pixel to raw data image as follows:
A_cor = A_raw (1) - pedestal | if the file name is specified in the parameter "fname_peds" (2) - N*background | if the file name is specified in the parameter "fname_bkgd" (3) * gain | if the file name is specified in the parameter "fname_gain" (4) apply mask | if the file name is specified in the parameter "fname_mask" (5) apply N*RMS threshold | if the file name is specified in the parameter "fname_nrms" (6) apply threshold | if the "do_threshold" = true
- corrected image is saved in the event with key
key_out
asdouble
type.
Details:
- All files with input calibration parameters should have the same shape as image and formatted as regular text file containing 2d matrix (table) of float (or integer) values, with columns separated by space(s), ' ', and rows(lines) terminated by the '\n'.
- Background normalization is performed in window defined by the parameters
bkgd_row_min
,bkgd_row_max
,bkgd_col_min
, andbkgd_col_max
. Normalization factorN
is evaluated for pixel amplitudes in this window as:
N = sum(A_raw - pedestal) / sum(A_bkgd)
. - Masking algorithm assumes that good pixels in the
fname_mask
file should be marked by '1' (ones) and bad pixels – by '0' (zeros). Mask is applied as a last correction. The bad masked pixel amplitudes are substituted by themasked_value
.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Camera)" |
source of data |
|
|
key for input image |
|
"calibrated" |
output key for calibrated image saved in event |
|
|
input file name for pedestals, applied if the file name is specified |
|
|
input file name for background, applied if the file name is specified |
|
|
input file name for gain, applied if the file name is specified |
|
|
input file name for mask, applied if the file name is specified |
|
|
input file name for RMS, applied if the file name is specified |
|
0. |
amplitude value (in ADU) substituted for masked pixels |
|
3. |
threshold as a number of sigmas from file |
|
0. |
constant low level threshold in ADU |
|
0. |
the amplitude substituted in pixels below threshold |
|
false |
if true - low level |
|
0 |
the window in image, which is used for background normalization |
|
10 |
the window in image, which is used for background normalization |
|
0 |
the window in image, which is used for background normalization |
|
10 |
the window in image, which is used for background normalization |
|
0 |
verbosity:
|
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
andkey_in
parameters to get the input image (asndarray<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 tonumber_of_bins-1
), - saves the 2-D array of <I>(event, bin) in file
fname_int_bins
.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Camera)" |
source of data |
|
|
key for input image |
|
|
input file name for map of bin indexes |
|
|
output file name for intensity(bin,event) |
|
10 |
number of bins for output intensities, if map has bins \>= |
|
0 |
verbosity:
|
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
.
parameter |
default value |
description |
---|---|---|
|
"DetInfo()" |
input source of data |
|
|
key for input data, by default use raw data |
|
"rad_corrected" |
output key for further image processing |
|
850 |
x coordinate of the image center |
|
850 |
y coordinate of the image center |
|
10 |
radius minimal image is not processed for r<rmin |
|
1000 |
radius maximal image is not processed for r>rmax |
|
12 |
number of angular sectors for the background averaging |
|
0 |
test event for print/save |
|
0 |
module verbosity:
|
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 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.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Cspad)" |
source of data |
|
"Image2D" |
key for input image data |
|
10 |
minimal threshold on pixel amplitude |
|
100 |
minimal number of pixels with amplitude above the threshold |
|
true |
On/Off the filter |
|
0 |
minimal column number |
|
100000 |
maximal column number |
|
0 |
minimal row number |
|
100000 |
maximal row number |
|
0 |
verbosity:
|
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
:
struct Peak{ double x; double y; double ampmax; // amplitude in the peak maximum double amptot; // total amplitude in the range of {{peak_radius}} unsigned npix; // number of pixels in the range of {{peak_radius}} } ;
parameter |
default value |
description |
---|---|---|
|
"DetInfo()" |
source of data |
|
|
key for input image data |
|
"peaks" |
key for output list of peaks |
|
10 |
low threshold on pixel amplitude |
|
100 |
high threshold on pixel amplitude |
|
1.5 |
width of the Gaussian for smearing; =0-no smearing |
|
3 |
radius in pixel for smearing - radial size of matrix of weights |
|
3 |
radius in pixel for peak finding - radial size of the region to search for local maximum |
|
0 |
minimal column number |
|
100000 |
maximal column number |
|
0 |
minimal row number |
|
100000 |
maximal row number |
|
0 |
event number to save images and print info for test purpose |
|
true |
On/Off algorithm |
|
0 |
module verbosity:
|
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 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.
parameter |
default value |
description |
---|---|---|
|
"DetInfo()" |
source of data |
|
"peaks" |
key for input list of peaks, should be the same as |
|
"SELECTION_ON" |
three possible options:
|
|
0 |
threshold on peak amplitude |
|
0 |
threshold on total peak intensity (in the matrix around peak) |
|
1 |
minimal number of peaks above all thresholds |
|
|
file name prefix; by default the prefix is empty and file is not saved |
|
0 |
filter verbosity:
|
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 Module ImgAlgos::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:
- subtracts pedestals,
- apply gain factors,
- apply mask, and
- apply one of the threshold algorithms
and saves the corrected image or hit-pixel map in the event.
Functionality:
- ImgHitFinder uses the
source
andkey_in
parameters to get the input raw image (asndarray<T,2>
object), where T stands for uint16_t, int, float, uint8_t, or double, - gets the calibration parameters from files
fname_peds
,fname_gain
,fname_mask
, andfname_thre
, if their names are specified, - the specified by the file name corrections are applied per-pixel to raw data image as follows:
A_cor = A_raw (1) - pedestal | if the file name is specified in the parameter "fname_peds" (2) * gain | if the file name is specified in the parameter "fname_gain" (3) apply mask | if the file name is specified in the parameter "fname_mask" (4) apply threshold | if the file name is specified in the parameter "fname_thre"
- corrected image is saved in the event with key
key_out
asdouble
(or unsigned for pixel map) type.
Details:
- All files with input calibration parameters should have the same shape as image and formatted as regular text file containing 2d matrix (table) of float (or integer) values, with columns separated by space(s), ' ', and rows(lines) terminated by the '\n'.
- Masking algorithm assumes that good pixels in the
fname_mask
file should be marked by '1' (ones) and bad pixels – by '0' (zeros). The bad masked pixel amplitudes are substituted by themasked_value
.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Camera)" |
source of data |
|
|
key for input image |
|
"img-hits" |
output key for calibrated image saved in event |
|
|
input file name for pedestals, applied if the file name is specified |
|
|
input file name for mask, applied if the file name is specified |
|
|
input file name for gain, applied if the file name is specified |
|
|
input file name for threshold, applied if the file name is specified and |
|
0. |
amplitude value (in ADU) substituted for masked pixels |
|
1 |
threshold mode: 0 - is not applied; 1 - constant level threshold defined by |
|
def |
threshold parameter - its meaning depends on |
|
0. |
the amplitude substituted in pixels below threshold |
|
def |
the amplitude substituted in pixels below threshold, by default - amplitude above threshold is not substituted |
|
1 |
the window in image, which is used to make hit map |
|
def |
the window in image, which is used to make hit map, by default - use all rows-1 |
|
1 |
the window in image, which is used to make hit map |
|
def |
the window in image, which is used to make hit map, by default - use all columns-1 |
|
0 |
verbosity:
|
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.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Opal1000)" |
source of data |
|
"img" |
key for input image data |
|
"spectra" |
key for output array with spectra |
|
510 |
signal band central row at column=0 |
|
550 |
reference ... |
|
0 |
signal band tilt angle |
|
0 |
reference ... |
|
10 |
signal band width in number op rows |
|
10 |
reference ... |
|
0 |
module verbosity:
|
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.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Opal1000)" |
source of data |
|
"spectra" |
key for input image data |
|
0 |
module verbosity:
|
See also Example for Module ImgAlgos::ImgSpectraProc.
Module ImgAlgos::ImgSaveInFile
Aka depricated modules: CSPadPixCoords::CSPadImageGetTest, CSPadPixCoords::SaveImageInFile, and ImgAlgos::SaveImageInFile.
Module ImgSaveInFile receives from the event the image object using source
and key
parameters and saves it in the ftype
format with prefix file name fname
for event(s) specified by the parameters eventSave
or saveAll
. Currently implemented file formats: txt
, bin
, tiff
, and png
.
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.
parameter |
default value |
description |
---|---|---|
|
"CxiDs1.0:Cspad.0" |
source of data |
|
"Image2D" |
input image key |
|
0 |
event number to save the CSPad image file |
|
false |
save or not all selected events |
|
"txt" |
output file format; currently implemented formats |
|
"img" |
prefix of the output file name. Entire file name is formed as |
|
0 |
verbosity:
|
Saving in PNG currently works for uint8_t and uint16_t formats only...
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.
This module is designed for parallel image processing for correlation analysis.
Functionality:
- get image for each event as an
ndarray<T,2>
object, - splits it for
nfiles_out
equal parts, - saves each part of the image for all events in the job in a separate file with name
<fname_prefix>-<fname-common>-b<block-number>.<file_type>
, - saves metadata in the text file with name:
<fname_prefix>-<fname-common>-med.txt
, - saves counter number and the time records in file:
<fname_prefix>-<fname-common>-time.txt
.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Princeton)" |
source of data |
|
"img" |
input image key |
|
"my-exp" |
output files common prefix |
|
"bin" |
output files type: "bin", "txt" |
|
true |
add time stamp to the output file names |
|
8 |
number of output files (or number of parts to split image), it works tested and works for |
|
1 |
pixel amplitude threshold in image amplitude units |
|
1 |
default pixel amplitude if it is below |
|
0 |
verbosity:
|
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++ moduleImgAlgos/app/corana.cpp (or ImgAlgos/test/corana.cpp)
whereNote, 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>\
<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:
- saves counter number and the time records in file
fname
. - print summary parameters for parser, for example:
ImgTimeStampList: Summary for parser BATCH_RUN_NUMBER 0020 BATCH_NUMBER_OF_EVENTS 75 BATCH_FRAME_TIME_INTERVAL_AVE 8.086934 BATCH_FRAME_TIME_INTERVAL_RMS 0.120381 BATCH_FRAME_TIME_INDEX_MAX 74
parameter |
default value |
description |
---|---|---|
|
"tstamp-list.txt" |
output files common prefix |
|
0 |
verbosity:
|
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.
Functionality:
- ImgIntMonCorr uses the
source
andkey_in
parameters to get the input image (asndarray<double,2>
object), - gets and process the intensity monitors' data in accordance with configuration from file
fname_imon_cfg
, - intensity normalized image is saved in the event with key
key_out
. The type of output data is the same as the type of input data.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Camera)" |
source of data |
|
"calibrated" |
key for input image |
|
"imon_corrected" |
key for output calibrated image saved in event |
|
|
input file name with intensity monitors' configuration |
|
0 |
verbosity:
|
fname_imon_cfg
file content per line: source name, short name, on/off bits for 4-channels, normalization and selection, minimal, maximal and averaged intensities:
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:
IntensityMonitorsData: Summary for parser BATCH_RUN_NUMBER 0020 BATCH_NUMBER_OF_EVENTS 75
parameter |
default value |
description |
---|---|---|
|
"BldInfo(FEEGasDetEnergy)" |
source name for intensity monitor |
|
"BldInfo(XCS-IPM-02)" |
source name for intensity monitor |
|
"BldInfo(XCS-IPM-mono)" |
source name for intensity monitor |
|
"DetInfo(XcsBeamline.1:Ipimb.4)" |
source name for intensity monitor |
|
"DetInfo(XcsBeamline.1:Ipimb.5)" |
source name for intensity monitor |
|
"txt" |
file type may be "txt" or "bin" |
|
"intensity-monitor-data.txt" |
file name for data from intensity monitors |
|
"intensity-monitor-comments.txt" |
file name for comments |
|
0 |
verbosity:
|
Module ImgAlgos::CSPadArrSaveInFile
This module saves the CSPad data array formatted as [5920=4*8*185][388] in output file for each passes event.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Cspad)" |
input source of data |
|
|
key for input data, for example, it might be "calibrated" |
|
"cspad-arr" |
out file name prefix for saved array |
|
0 |
module verbosity:
|
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:
- 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_stage1 + 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.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Cspad)" |
input source of data |
|
|
key for input data, for example, it might be "calibrated" |
|
"cspad-ave.dat" |
out file with averaged amplitudes |
|
"cspad-rms.dat" |
out file with rms |
|
1<<31U |
number of events before stage 1 |
|
100 |
additional number of events before stage 2 |
|
0 |
gate_width for stage 1 |
|
0 |
gate_width for stage 2 |
|
0 |
module verbosity:
|
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.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Cspad)" |
source of data for CSPad |
|
"calibrated" |
key for input data, by default expects data from |
|
"cm_subtracted" |
output key for the next data processing stage |
|
30 |
threshold to exclude the large pixel amplitudes in average |
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.
The shape of the CSPad array in the file bkgd_fname
is [4*8*185][388] for all 2x1 sections.
The shape of the CSPad array in the event, specified by the source
and inputKey
or outputKey
,
is [number_of_sections*188][388] depends on number of available in DAQ 2x1 sections, provided by the masks in CSPad configuration, for example:
shared_ptr<Psana::CsPad::ConfigV2> config2 = env.configStore().get(m_str_src); unsigned mask = config2->roiMask(quad_number); // should be in the range from 0 to 255
parameter |
default value |
description |
||
---|---|---|---|---|
|
"DetInfo(:Cspad)" |
input source of data |
||
|
|
key for input data, by default use raw data |
||
|
"bkgd_subtracted" |
output key for the next data processing stage |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="0f2df633-39ef-439c-8b1c-7b140773b9af"><ac:plain-text-body><![CDATA[ |
|
"cspad_background.dat" |
file with CSPad array [4*8*185][388] of averaged background |
]]></ac:plain-text-body></ac:structured-macro> |
|
0 |
CSPad sector in quad from 0 to 7 |
||
|
0 |
module verbosity:
|
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].
parameter |
default value |
description |
||
---|---|---|---|---|
|
"DetInfo(:Cspad)" |
input source of data |
||
|
|
key for input data, by default use raw data |
||
|
"bkgd_subtracted" |
output key for the next data processing stage |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="5019a295-bac9-40b3-bdfe-b021d2043a0d"><ac:plain-text-body><![CDATA[ |
|
"cspad_mask.dat" |
file with CSPad mask array [4*8*185][388] |
]]></ac:plain-text-body></ac:structured-macro> |
|
0 |
this amplitude will replace the amplitude in each masked pixel |
||
|
1 |
control bits for applied mask:
|
||
|
0 |
module verbosity:
|
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].
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Cspad)" |
input source of data |
|
|
key for input data, for example, it might be "calibrated" |
|
"cspad-pix-status.dat" |
out file with pixel status: fraction of noisy images |
|
"cspad-pix-mask.dat" |
out file with pixel mask |
|
3 |
radial parameter of the area for median algorithm |
|
1 |
radial band width of the area for median algorithm |
|
3 |
S/N threshold for each pixel to be considered as noisy |
|
0.1 |
fraction of noisy images above which pixel is masked in the |
|
0 |
module verbosity:
|
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.
Description of implemented algorithm:
- in the constructor and
beginJob(...)
method:- enter 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 the main part of "median algorithm" is implemented:fill [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: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
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Cspad)" |
input source of data |
|
|
key for input data, for example, it might be "calibrated" |
|
|
key for output signal array. If the string non-empty, the array is added in the datagram for each event (before selection). |
|
"peaks" |
key for vector of found peaks in the selected event |
|
"cspad-pix-mask-in.dat" |
in read the pixel mask from file |
|
"cspad-pix-mask-out.dat" |
out write current pixel mask in the file |
|
"cspad-pix-frac-out.dat" |
out file with per-pixel fraction of noisy images |
|
"./cspad-ev-" |
out file with signal CSPad array. Time stamp is added. |
|
3 |
radial parameter of the area for median algorithm |
|
1 |
radial band width of the area for median algorithm |
|
3 |
S/N threshold for each pixel to be considered as noisy |
|
5 |
S/N threshold for each pixel to be considered as noisy |
|
0.9 |
fraction of noisy images above which pixel will be masked |
|
4 |
minimal number of connected pixels for the good peak |
|
25 |
maximal number of connected pixels for the good peak |
|
0. |
threshold on total signal amplitude of the group of connected pixels, if =0:OFF |
|
7. |
threshold on peak S/N (S and N are sums over connected pixels) |
|
10 |
threshold on minimal number of good peaks for the event selection |
|
10000 |
threshold on maximal number of good peaks for the event selection |
|
0. |
threshold on total signal amplitude in ADU of all good peaks for the event selection, if =0:OFF |
|
0 |
number of skipped events before each mask re-evaluation cycle |
|
50 |
number of events for the mask re-evaluation |
|
SELECTION_ON |
selection mode, other allowed values are: SELECTION_OFF, or SELECTION_INV |
|
0 |
control on writing of files:
|
|
0 |
module verbosity:
|
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.
- It gets the vector of peaks defined by the
key
parameter, - fills ROOT-style histograms and ntuples, and
- saves histograms and ntuples in file defined by the
fname_root
parameter.
parameter |
default value |
description |
---|---|---|
|
"DetInfo(:Cspad)" |
input source of data |
|
"peaks" |
key for input data for peaks found in event |
|
"file.root" |
name of the output file with root histograms and ntuples |
|
0 |
module verbosity:
|
See also Example for Module ImgAlgos::CSPadArrPeakAnalysis.
Package py_img_algos
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 py_img_algos.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
.
parameter |
default value |
type |
description |
---|---|---|---|
|
*-*|Cspad-* |
string |
address of Detector-Id|Device-ID |
|
int |
string |
output array data type. Implemented types: int, int8, int16, int32, uint8, uint16, uint32, float, double. |
|
cspad_array |
string |
unique keyword for output array identification |
|
0 |
float |
intensity value substituted for missing 2x1 sections in data |
|
1 |
int |
module verbosity:
|
See also Examples for package py_img_algos.
Module py_img_algos.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
.
parameter |
default value |
type |
description |
---|---|---|---|
|
'' (empty) |
string |
path to calibration directory for ex.: |
|
cspad_array |
string |
keyword for input numpy array, shape=(4, 8, 185, 388) - for cspad or (185, 388, 2) - for cspad2x2 |
|
cspad_image |
string |
unique keyword for output 2-d image numpy array |
|
1 |
int |
module verbosity:
|
See also Examples for package py_img_algos.
Module py_img_algos.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. 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-r####-ev######.tiff
, where symbols # stands for numbers.
parameter |
default value |
type |
description |
---|---|---|---|
|
image |
string |
unique keyword for input 2-d image numpy array |
|
img.npy |
string |
output file name (type is selected by extension) supported formats: txt, tiff, gif, pdf, eps, png, jpg, jpeg, npy (default), npz |
|
1 |
int |
module verbosity:
|
See also Examples for package py_img_algos.
Module py_img_algos.tahometer
Is intended to print records showing job performance current and integrated from the beginning of job:
py_img_algos.tahometer: run:0049 evt:000005 t[sec]: 2.575 dt[sec]: 2.575 n/t[1/sec]: 1.942 dn/dt[1/sec]: 1.942
parameter |
default value |
type |
description |
---|---|---|---|
|
100 |
int |
interval in number of events to print current statistics |
|
1 |
int |
module verbosity:
|
See also Examples for package py_img_algos.