NAME

nicerl2 - Apply NICER Level2 standard calibration and filtering

USAGE

nicerl2 indir ...

DESCRIPTION

The nicerl2 task applies standard NICER-recommended calibration processes to an entire NICER observation, as well as standard screening.

This is a high level task that calls multiple sub-tasks as a convenience to the user. It performs the following standard "Level2" processing steps.

  1. nicercal - apply standard NICER calibration
  2. niprefilter2 - derive calibrated filter (MKF) file
  3. nimaketime - create standard screening good time intervals
  4. nicermergeclean - combine per-MPU data and filter/screen
  5. niautoscreen - automatically screen for problematic per-FPM and per-MPU conditions
Please see the help files for these individual tasks for more information about what they do and how they can be used.

A user wishing to have more control over the analysis process may call these tasks individually. nicerl2 simply rolls these subtasks up into a single, easy-to-run task. Many, but not all, parameters of the individual subtasks are available for nicerl2, sometimes with different parameter names to avoid conflicts.

Unlike most HEASoft tasks, this task is designed to work on an entire observation directory. It is expected that the input adheres to the standard NICER directory layout: uncalibrated event files in $INDIR/xti/event_uf; MPU housekeeping data in $INDIR/xti/hk; and auxiliary files in $INDIR/auxil/.

However, an advanced programmer can adjust these locations with the hidden parameters ufdir, cldir, ufafile, clfile, and mkfile. When using these parameters, note that the certain patterns can be used as shortcuts: "$CLDIR" for the output directory name, "$OBSID" for the observation ID number, and "$INDIR" for the input directory. Note that these patterns should appear explicitly with the dollar sign included; typically the command shell will interpret '$name' as a shell variable so appropriate quoting will be required.

OUTPUTS

Output files are placed in the directory specified by cldir, typically $INDIR/xti/event_cl. The output products are:

Normally the "cl" file would be used in further analysis.

Note that the original unfiltered event files ("uf" files) are not modified.

FILTERING EVENT FILES BY TIME OR DETECTOR

nicerl2 provides various options for filtering or selecting data. This can be roughly divided into: filtering by time, and filtering by detector. Each of these will be discussed more below.

Filtering NICER events by time is done to screen out known "bad" times that may include undesireable data. Values that can be screened are stored in NICER's filter file, which is described more below. These quantities can be divided into several categories. These categories are listed below, along with the parameters that govern them.

More information about each of these parameters can be found below, as well as in the help for nimaketime. In addition, the user can enter a custom "maketime" expression using the nimaketime_gtiexpr parameter, or by entering their own custom GTI files explicitly using the gtifiles parameter.

In addition to automatic screening by time, nicerl2 also screens on a per-FPM and per-MPU basis in order to exclude modules that may have problematic conditions, such as high noise rates or high undershoots. This filtering is done when autoscreen=YES, which is set to YES by default. nicerl2 passes the default screening thresholds to the niautoscreen task which does the actual screening, but these thresholds can be adjusted by setting them to non-default values. For more information on how these screenings are applied, please see the help page for niautoscreen.

Users may also select or deselect certain detectors manually. This choice may be based on knowledge of particular detectors' undesirable behaviors. This selection is handled by the "detlist" parameter. detlist allows to select or deselect certain detectors for the entire observation, as well as for a specific time range. The default value, detlist=launch, indicates to include all detectors enabled at launch. How this works is described in more detail in the help file for the nifpmsel task.

The nifpmsel task performs these detector selections and stores per-detector exposure information in the output event file. This information is known as FPM Selection information, and is stored in an extension named FPM_SEL. This extension, as well as various additional GTI_* extensions also stored in the file, provide complete exposure information for each detector. The FPM_SEL file also contains a columned named FPM_SEL, which is a second-by-second tally of the exposure of each detector, and this information can be used by the response tasks, nicerarf and nicerrmf, to obtain accurate ARF and RMF files.

The user may wish to run the standard processing first, with detlist=launch, to obtain an event file with all detectors, and then examine the resulting output for noisy or mis-behaving detectors. If such detectors are found, it is not necessary to re-run nicerl2 from the start again. Instead, use nifpmsel to select or deselect the desired detectors and make a new screened event file. It is also possible to run nicerl2 once with the default detlist=launch, and then a second time with tasks=SCREEN and detlist the desired screening. The result will be that the "ufa" file contains all launch detectors, but the "cl" file contains only the selected/deselected detectors.

FPM Selection information is stored in the output event file. As long as any event files with FPM Selection information are manipulated by the NICER tasks nifpmsel and niextract-events, this information will be carried along and updated for the output. However, if the user uses tasks outside of the NICER tasks to manipulate event files, the FPM Selection information may be lost or become inaccurate. Thus, it is recommended to stay with the NICER tasks for merging, screening and selecting/deselecting detectors from event files.

FILTERING EVENT FILES BY EVENT TYPE

Users can specify which events to keep and which to screen out during standard processing. Generally, users will not want to modify these settings, although it is possible under special circumstances.

Event type screening is governed by the parameters keep_undershoots, keep_overshoots, keep_forced, keep_noisering, and datamode. The meanings of these keywords are:

By default, events from the slow chain are included (and optionally fast chain), which is equivalent to datamode=so+s+f. This is the setting recommended by the NICER team for almost all circumstances. In the past, it was also possible to specify an EVENT_FLAGS filtering expression using the nicerclean_args keyword, which is still documented on the nicerclean help page.

As of 2023, the NICER team is aware of a new phenomenon which is designated "noise ringers." These are events that arrive very shortly after an undershoot in the same FPM, almost always within 110 usec, and only at undershoot rates that exceed about 80 undershoots per second, per FPM. The NICER software flags these events with EVENT_FLAGS=bx1xxxxxx (i.e. bit 6).

To screen out such events above an undershoot rate of 80 ct/s/FPM, set keep_noisering=NO and noisering_under=80. This screening is applied on an FPM-by-FPM basis, and doesn't change the good-time of an FPM (although it adds roughly 110 usec of deadtime in the same FPM after an undershoot).

SELECTING FILTER FILE COLUMNS

A key output of any run of the NICER pipeline is the so-called filter file (or .mkf file). This file is produced in the original NICER pipeline run, but it is updated and augmented by nicerl2 using various NICER tasks. The filter file contains many columns which are useful for diagnosing and screening nicer data. The columns include various orbital, pointing, and housekeeping data points.

The output of nicerl2 can be tailored to specific needs by requesting certain columns. Complete documentation for these different columns cannot be reproduced here. Instead, detailed information about which columns can be produced are documented in the help files for niprefilter and niprefilter2.html.

Since there are several ways in which filter file columns are calculated, requesting them can be confusing. In versions of nicerl2 v1.13 and before, the analyst had to juggle the settings for prefilter_columns, niprefilter2_coltypes and geomag_columns. In versions of nicerl2 v1.14, these requests are centralized in a single parameter called "filtcolumns." The nicerl2 task automatically populates the specific parameters as needed. Thus, it is recommended to use the filtcolumns parameter when running nicerl2. However, for backward compatibility, the user can specify the other parameters individually and override the automatic settings.

Here is a summary of most commonly-used settings:

filtcolumns is a comma-separated list. You can add any prefilter column name to the list, as well as add any geomagterp column name, or any allowed prefilter2 coltypes entry to the list, by adding a comma, followed by the requested name.

GEOMAGNETIC QUANTITIES

As of HEASoft 6.31 (NICERDAS 10), nicerl2 requires the user to use Geomagnetic quantities to construct the NICER filter file. Since background modeling is a part of this release, and some of the models use geomagnetic quantities to inform their background estimator algorithms, the geomagnetic quantities are required. For more information, please see the Geomagnetic Quantities documentation on the NICER web page.

Activating geomagnetic quantities works in the following way.

SELECTING WHICH TASKS THAT NICERL2 PERFORMS

By default, nicerl2 runs all calibration and screening steps each time when processing data in order to obtain the most up to date and recommend processing strategies.

When starting a project, it is recommended to fully run nicerl2 to completion. While this may take a significant amount of processing time to complete, it does mean that the user can be confident that all products are up to date before proceeding with science analysis.

However, there are some times when the user may want to "reprocess" their data. Usually they want to make small variations on data selections, and don't need to re-run the entire pipeline from scratch. In that case, re-running "nicerl2" may be overkill and incur significant (and unneeded) processing overhead. The NICER software has several ways to speed up execution in this case.

The 'incremental=YES' parameter

As of HEASoft 6.31, nicerl2 has a parameter 'incremental' which causes nicerl2 to only perform some processing processing if necessary.

Specifically, before calibrating the data, nicerl2 will check any existing output files and if the calibration metadata indicates that the files have current calibration, they will be used as-is without reprocessing.

Similarly, the existing filter file is checked before processing. If it has been processed with an up-to-date version of nicerl2 (niprefilter2) with the same requested columns, regeneration of the filter file is not necessary.

Some steps, such as extracting a merged "ufa" file and screening of data, are always performed regardless of the incremental=YES setting.

If you want to force full processing, set incremental=NO, which is the default. The NICER team recommends that you do this when upgrading software or calibration, or when starting a new project.

The 'tasks' parameter

nicerl2 has a parameter called "tasks" which can give the analyst more fine-grained control over which tasks the pipeline performs. These tasks are largely separable, which means that the user can run the time-consuming processes once, and then for small variations or iterations, only run the needed tasks. The "tasks" parameter is a comma-separated list of task items, which can be any one of the following,

Although the items can be listed in any order in the parameter, they are performed in the order described above.

You can use both the 'incremental' and the 'tasks' parameters simultaneously, although it is not recommended. When you do this, nicerl2 will perform the more restrictive set of operations. For, example if you set "tasks=MKF incremental=YES", nicerl2 will skip the filter file (MKF file) generation step if the MKF file is already up to date.

Strategies for reducing nicerl2 execution time

Here are some strategy to save processing time.

One strategy is to rely upon the incremental parameter. In this strategy, run nicerl2 once at the start of your project with incremental=NO. Setting incremental=NO is also recommended if you update your software or calibration mid-project. Example: 

  nicerl2 NNNNNNNNNN clobber=YES incremental=NO

Then, if you run nicerl2 again with minor variations in settings, set incremental=YES. For example, 

  nicerl2 NNNNNNNNNN clobber=YES incremental=YES

Another strategy relies upon using the tasks parameter to explicitly direct nicerl2 which operations to perform. In this example we will apply calibrations and generate the MKF file once, followed by several different screening variations. First, run nicerl2 to do the first two steps, 

   nicerl2 NNNNNNNNNN clobber=YES tasks=CALMERGE,MKF
After this run, updated filter file and event files are present in the locations described above, but the screening steps have not yet been performed. Now, run nicerl2 several different times with different screening settings, 
   nicerl2 NNNNNNNNNN clobber=YES tasks=SCREEN overonly_range=0-2.0 
   ... examine output ...
   nicerl2 NNNNNNNNNN clobber=YES tasks=SCREEN overonly_range=0-1.5
   ... examine output ...
   nicerl2 NNNNNNNNNN clobber=YES tasks=SCREEN overonly_range=0-1.0
In this example, different overonly_range parameter settings were attempted, but any of the screening-related settings could be varied at this step. The key point is that since tasks=SCREEN, the calibration and MKF steps are not performed each time.

Of course, if the analyst wishes to vary a filter-file-related setting, then one must also at least add MKF to the lists of tasks to perform. Otherwise, the requested changes will not take effect. Thus, while the tasks parameter can save significant amounts of processing time, it also requires more logistics to keep track of which parts of the tasks have been performed or need to be performed, depending on the desired parameter settings.

DESTRUCTIVE OVERWRITING and WORKING WITH READ-ONLY INPUT DATA

Note that this task in its default operation will attempt to write to the directory specified by cldir, typically $INDIR/xti/event_cl (the "$INDIR" is a pattern replaced by the actual input directory as described above). In addition, the filter file (.mkf file, typically in $INDIR/auxil) is modified.

Any pre-existing files in these areas will not be destructively overwritten unless clobber=YES (the default is clobber=NO). This is a reminder to the user that destructive removal of data is a possibility and that the user must explicitly allow it by setting clobber=YES.

For most typical applications, where the user is working in an existing NICER observation directory with write access, clobber=YES should be used on the command line to allow nicerl2 to overwrite existing data, with the understanding that all pre-existing contents of 'cldir' will likely be destroyed.

In some cases users may be working with a read-only archive copy of NICER observation data, with no possibility of modifying the data in place. In that case, even if clobber=YES is used, nicerl2 will be unable to run using the defaults. Another slightly similar use case would be if the user is trying different (or new) calibrations and wishes to preserve the pre-existing calibrated outputs.

To accomodate these cases, the user must still have a writable output directory, which can be kept separate from the input directory. Let's say that indir=/archive/1000010101 and the output is placed in /writable/1000010101-output.

The steps to achieve this are:

Here are the commands to be used in this case. 
     mkdir /writable/1000010101-output
     cp -p /archive/1000010101/auxil/ni*.mkf* /writable/1000010101-output/
     nicerl2 indir=/archive/1000010101 \
         cldir=/writable/1000010101-output \
         mkfile='$CLDIR/ni$OBSID.mkf'

ADJUSTING TARGET COORDINATES or DEALING WITH OFF-AXIS TARGETS

In some cases the target coordinates included in the standard NICER processing may be incorrect or need adjusting. The NICER team maintains a database of target coordinates. This database is used at the time the standard pipeline runs to set the RA_OBJ and DEC_OBJ keywords. If the database was incorrect at the time the pipeline is run, it may be necessary to adjust the target position when running nicerl2.

Another circumstance that may arise is if NICER intentionally performed an offset pointing of a target. In that case, the "target position" stored in RA_OBJ and DEC_OBJ may be the offset coordinates rather than the true target coordinates. In this case again, it is necessary to adjust the target position when running nicerl2.

Having correct target coordinates is important for NICER analysis. The coordinates are used both for screening purposes, as well as for the purpose of computing the X-ray response matrix. The X-ray throughput varies with off-axis target position, so knowing the true target coordinates can change the estimate of the response.

For screening purposes, the filter file column OFFSET is always computed using the "nominal" pointing direction (RA_NOM,DEC_NOM). This screening is appropriate because the purpose of screening on OFFSET is to remove times when the NICER observatory is not pointing at the intended pointing direction, regardless of where the target is located.

The output products will have RA_OBJ and DEC_OBJ keywords. During default operation of nicerl2 (ra=OBJ, dec=OBJ), these keywords are unchanged. However, if ra and dec are set to numerical values, these values will be written to the RA_OBJ and DEC_OBJ keywords.

PARAMETERS

indir [filename]
Input directory name. The directory should be a single NICER observation directory, which in turn contains xti/{events_uf,events_cl,hk,auxil} subdirectories.
ufdir = "$INDIR/xti/event_uf" [filename]
Subdirectory containing per-MPU "uf" event files, which are the input to the task. This parameter is subject to pattern substitutions $INDIR and $CLDIR as described above.
cldir = "$INDIR/xti/event_cl" [filename]
Subdirectory where the output files as listed above are placed. This parameter is subject to pattern substitution $INDIR as described above.
ufafile = "$CLDIR/ni$OBSID_0mpu7_ufa.evt" [filename]
Name of the master "ufa" event file to be created. This parameter is subject to pattern substitutions $INDIR, $CLDIR and $OBSID as described above.
clfile = "$CLDIR/ni$OBSID_0mpu7_cl.evt" [filename]
Name of the master "cl" event file to be created. This parameter is subject to pattern substitutions $INDIR, $CLDIR and $OBSID as described above.
mkfile = "$INDIR/auxil/ni$OBSID.mkf" [filename]
Name of the MKF filter file, to be used as input. This parameter is subject to pattern substitutions $INDIR, $CLDIR and $OBSID as described above.
ra [real]
Right ascension of target in J2000 degrees. This parameter is also allowed to be "OBJ", which will use the RA_OBJ keyword from the input file.
dec [real]
Declination ascension of target in J2000 degrees. This parameter is also allowed to be "OBJ", which will use the DEC_OBJ keyword from the input file.
(mpulist = "0-6") [string]
List of MPUs to process, either as a comma-seprated list, or as a hypenated range. For example, "0,1,2,3,4,5,6" is the same as "0-6". NOTE that this parameter is deprecated and will not in fact produce the desired results of including or excluding certain MPUs from data. Use detlist instead.
gzip_thresh=50 [integer]
Optimization setting. If the observation contains at least one gzipped file larger than gzip_thresh [in megabytes], the files will be temporarily unzipped.
detlist="launch" [string]
Detector selection expression, as described in the documentation for nifpmsel.
(tasks = "ALL") [string]
Which task operations to perform, one of CALMERGE, MKF, SCREEN, or ALL. See above for more details.
(filtcolumns = "NICERV5") [string]
As described above, filtcolumns is a comma-separated list of columns to include in the NICER filter file. When using this keyword, the task automatically determines which items correspond to prefilter_columns, niprefilter2_coltypes and geomag_columns. In addition, the shorthand notation "NICERVn", where n is an integer, is allowed.
(picalfile="CALDB") [filename]
Name of PI gain calibration data file for slow chain pulse heights, or "CALDB". For standard operation, the NICER team recommends to use "CALDB".
(pifastcalfile="CALDB") [filename]
Name of PI_FAST gain calibration data file for fast chain pulse heights, or "CALDB". For standard operation, the NICER team recommends to use "CALDB".
(timebiascalfile="CALDB") [filename]
Name of clock calibration file, or "CALDB". For standard operation, the NICER team recommends to use "CALDB". A value of "NONE" disables clock calibration.
(leapinit="AUTO") [string]
Initialize LEAPINIT keyword of event extensions? An integer value indicates to use that many leap seconds. A value of "AUTO" indicates use the appropriate number of leap seconds for the given observation TSTART. A value of "NONE" indicates to not change LEAPINIT.
(nicercal_filtexpr="EVENT_FLAGS=bxxxx00") [string]
Extractor filtering expression to be used for initial screening of events. Typically this screening expression will remove over-shoot and under-shoot events, which cannot be calibrated, but keep X-ray events and forced triggers (EVENT_FLAGS=bxxxx00).
Unix wildcard matching expression to locate uncalibrated (unfiltered) events within the input directory. The default expression will locate standard NICER unfiltered ("uf") files within the xti/event_uf subdirectory. If the user has modified the directory layout this pattern can be used to point nicercal to the relevant files. The pattern "$INDIR" is replaced by the 'indir' parameter value (note that proper quoting is required by most command shells to avoid variable expansion).
(hkpat = "$INDIR/xti/hk/ni??????????_?mpu?.hk{,.gz}") [string]
Unix wildcard matching expression to locate MPU housekeeping files within the input directory. The default expression will locate standard NICER housekeeping files within the xti/hk subdirectory. If the user has modified the directory layout this pattern can be used to point nicercal to the relevant files. The pattern "$INDIR" is replaced by the 'indir' parameter value (note that proper quoting is required by most command shells to avoid variable expansion).
(calstation="FLIGHT") [string]
Station where data was collected. For in-flight operations use calstation=FLIGHT. For ground-based testing, other values can be used. This parameter selects the NICSTATN keyword value in CALDB.
(niprefilter=YES) [boolean]
Run niprefilter to update the filter file? (IGNORED; use tasks=MKF instead)
(orbfile=$INDIR/auxil/ni$OBSID.orb) [string]
Name of the orbit file used by niprefilter. Both the orbfile and orbfile.gz patterns are checked, in that order. This parameter is subject to pattern substitutions $INDIR, $CLDIR and $OBSID as described above.
(attfile=$INDIR/auxil/ni$OBSID.att) [string]
Name of the attitude file used by niprefilter. Both the attfile and attfile.gz patterns are checked, in that order. This parameter is subject to pattern substitutions $INDIR, $CLDIR and $OBSID as described above.
(prefilter_columns=DEFAULT) [string]
A list of prefilter columns to compute, as a space-separated list. Please see the documentation of prefilter, parameter columns, for what values are allowed. A value of "DEFAULT" indicates to use the niprefilter task default. A value of "FILTCOLUMNS" indicates to defer to the filtcolumns parameter.
(niprefilter2=YES) [boolean]
Run niprefilter2 to update the filter file? (IGNORED: use tasks=MKF instead)
(saaregfile="CALDB") [string]
For niprefilter2, the name of the NICER South Atlantic Anomaly (SAA) region file, which will be used to replace the existint NICER_SAA column. Use "CALDB" to query CALDB. Use "NONE" to keep the existing value unchanged.
(vehiclefile="CALDB") [string]
For niprefilter2, retrieve International Space Station vehicle docking information as a function of time. If set to "NONE" then this is disabled. If set to "CALDB" or "CALDB:vehiclename", then use CALDB information for the specified vehicle (default is "SOYUZ").
(issmanfile="CALDB") [string]
For niprefilter2, retrieve International Space Station maneuver information as a function of time. If set to "NONE" then this is disabled. If set to "CALDB" then use CALDB information.
(robofile="CALDB") [string]
For niprefilter2, retrieve robotic "robo" activity information as a function of time. If set to "NONE" then this is disabled. If set to "CALDB" then use CALDB information.
(niprefilter2_coltypes="FILTCOLUMNS") [string]
For niprefilter2, specify which categories of columns to produce. See the documentation of niprefilter2 for more information. Use "DEFAULT" for the niprefilter2 task default, and "FILTCOLUMNS" (recommended) to defer to the filtcolumns parameter.
(geomag_columns="DEFAULT") [string]
For niprefilter2, the name of files containing geomagnetic quantities. More than one file can be specified using a comma-separated list. For each file on the list, the geomag_path is prepended. Use the notation "filename(COLNAME)" to specify that the output column should be named COLNAME. A value of NONE means no extra geomagnetic quantities, and a value of "DEFAULT" means to use the task default of niprefilter2. A value of "FILTCOLUMNS" means to defer to the filtcolumns parameter (recommended).
(geomag_path="DEFAULT") [string]
For niprefilter2, name of the base path for all geomagnetic files. This path is prepended to each item in the geomag_columns list. If DEFAULT, then what nicerl2 does depends on filtcolumns. If filtcolumns is NICERV4 or higher version, nicerl2 looks for geomagnetic data in the directory pointed to by the GEOMAG_PATH environment variable; if filtcolumns is NICERV3 or lower version and geomag_path=DEFAULT, no gemagnetic quantities will be included.
(nicersaafilt = "YES") [boolean]
For nimaketime, apply NICER_SAA filtering? .
(saafilt = "NO") [boolean]
For nimaketime, apply SAA filtering?
(trackfilt = "YES") [boolean]
For nimaketime, apply pointing tracking filtering?
(st_valid = "YES") [boolean]
For nimaketime, require star tracker valid solution?
(ang_dist=0.015) [real]
For nimaketime, apply ANG_DIST filtering (degrees). ANG_DIST must be less than this value.
(elv=15) [real]
For nimaketime, apply ELV filtering (degrees). ELV must be greater than this value.
(br_earth=30) [real]
For nimaketime, apply BR_EARTH filtering (degrees). BR_EARTH must be greater than this value.
(cor_range="*-*") [string]
For nimaketime, apply COR_SAX filtering (GeV/c). Specify a range A-B.
(underonly_range="0-500") [string]
For nimaketime, apply undershoot count rate range per module. Specify a range A-B.
(overonly_range="0-30") [string]
For nimaketime, apply overshoot count rate range per module. Specify a range A-B.
(overonly_expr="NONE") [string]
For nimaketime, apply curve-base overshoot filtering as an expression. The maximum value of overonly_range is substituted for OVERONOLY_NORM (or 1.0 if no maximum is specified).
(min_fpm=7) [integer]
For nimaketime, apply NUM_FPM_ON filtering.
(max_lowmem=250.0) [real]
Maximum value of TOT_LOWMEM_FIFO lost events, in units of events per second.
(thresh_range="-3.0-3.0") [string]
Range of NICER lower-level threshold settings to include. This is the array-average relative threshold setting, where 0.0 indicates the nominal threshold level, and the units correspond to the flight relative threshold offset value. For NICER optical light leak conditions, it would be typical to use a range of "-3.0-38" to include both nominal and "+35" settings, and "32-38" to include just the daytime threshold settings.
(threshfilter="NIGHT") [string]
A shortcut to select a certain desired threshold range One of "ALL", "DAY" or "NIGHT". "ALL" indicates the entire range of thresholds, "NIGHT" is -3.0-3.0 (default) and "DAY" is 32.0-38.0.
(mingti=5.0) [real]
Minimum GTI size in seconds for GTI filtering. This applies to any telemetry-selected filtering criteria (i.e. not user expressions or user GTIs).
(erodedilate=5.0) [real]
Specify the "erodedilate" parameter for GTI filtering of GTI rows. This applies to any telemetry-selected filtering criteria (i.e. not user expressions or user GTIs).
(mpugtimerge="OR") [string]
How to merge per-MPU GTIs into a single GTI. Either AND or OR. For versions of NICER software before June 2021, "AND" was the implicit default; for later versions "OR" is the default.
(gtifiles="NONE") [string]
Apply additional GTI filters. If you have done external filtering and produced a GTI file, you can merge with the nimaketime GTI. Either a comma-separated list of files or an @filelist.lis file. All GTIs (including the maketime GTI) are combined using "AND" (intersection) merge. A value of "NONE" indicates no additional GTI filtering.
(pirange="20:1500") [string]
For nicermergeclean, pulse height screening criteria to apply. To select PI values A to B use "A:B" notation. The asterisk can be used to select the endpoints. For example 20:* indicates a PI range of 20 to the maximum. Either low:high or low-high notation is allowed.
(trumpetfilt=YES) [boolean]
Apply standard background PI_RATIO filtering.
(autoscreen=YES) [boolean]
Automatically apply per-FPM and per-MPU screening criteria? If yes, then the niautoscreen task is used to deselect detectors with problematic conditions during individual pointing snapshots. If no, then niautoscreen is not used, but the other filtering criteria are used to screen out global bad times.
(underonlyscr="DEFAULT") [string]
Screening criteria for the high undershoot condition. The value is of the form "nsigma:rbuf:min:max". Set to NONE to disable, or DEFAULT to use the niautoscreen default values. See niautoscreen help file for more details.
(overonlyscr="DEFAULT") [string]
Screening criteria for the high overshoot condition. The value is of the form "nsigma:rbuf:min:max". Set to NONE to disable, or DEFAULT to use the niautoscreen default values. See niautoscreen help file for more details.
(noise25scr="DEFAULT") [string]
Screening criteria for the high noise peak rate condition. The value is of the form "nsigma:rbuf:min:max". Set to NONE to disable, or DEFAULT to use the niautoscreen default values. See niautoscreen help file for more details.
(noiseextscr="DEFAULT") [string]
Screening criteria for the 0.3-0.7 keV "X-ray" band. This band may occasionally have high count rates associated with an extended noise peak, which indicates detector problems. The value is of the form "nsigma:rbuf:min:max". Set to NONE to disable, or DEFAULT to use the niautoscreen default values. See niautoscreen help file for more details.
(mpugtiscr="DEFAULT") [string]
Screening criteria for the per-MPU shredded GTI condition. The value is of the form "nsigma:rbuf:min:max". Set to NONE to disable, or DEFAULT to use the niautoscreen default values. See niautoscreen help file for more details.
(roundrobbinscr="DEFAULT") [string]
Screening criteria for the "round robbin" condition. The value is of the form "nsigma:rbuf:min:max". Set to NONE to disable, or DEFAULT to use the niautoscreen default values. See niautoscreen help file for more details.
(lowmemscr="DEFAULT") [string]
Screening criteria for the LOWMEM FIFO loss amount. This is the number of lost events per GTI. The value is of the form "nsigma:rbuf:min:max". Set to NONE to disable, or DEFAULT to use the niautoscreen default values. See niautoscreen help file for more details.
(datamode="so+s+f") [string]
X-ray event type screening, as described in the help for nicerclean.
(keep_overshoots=NO) [boolean]
Set to NO to screen out overshoots, or to YES to permit them.
(keep_undershoots=NO) [boolean]
Set to NO to screen out undershoots, or to YES to permit them.
(keep_forced=NO) [boolean]
Set to NO to screen out forced triggers, or to YES to permit them.
(keep_noisering=NO) [boolean]
Set to NO to screen out noise ringers, or to YES to permit them. Note that if noisering_under is set, then the per-FPM undershoot rate is also required to exceed that value before a noise ringer is excluded.
(noisering_under=80) [real]
The per-FPM undershoot rate, above which events with the noise ringer bit flag set are screened out. If noisering_under=0, then keep_noisering is followed always, regardless of undershoot rate.
(nicerclean_args="NONE") [string]
Any additional arguments to nicerclean, such as "EVENT_FLAGS=bx1x000 fastsig=250.0". See the help file for nicer clean for more information. The gtifile, trumpetfilt, and pirange parameters are automatically passed and there is no need to specify them again with nicerclean_args.
(cleanup_ufa_files="NO") [boolean]
If yes, then clean up calibrated per-MPU "ufa" files.
(incremental="NO") [boolean]
If yes, then avoid calibration and other intensive processing where possible. Files are checked for their calibration status keywords and/or software version numbers, and if certain requirements are met, the existing files are used without change.
(cleanup="YES") [boolean]
If yes, then clean up temporary files. If no, temporary files remain. This is typically for debugging.
(clobber = NO) [boolean]
If the output file already exists, then setting "clobber = yes" will cause it to be overwritten.

(chatter = 2) [integer, 0 - 5]
Amount of verbosity of the task. For chatter=0, no output is printed. For chatter=5, debugging output is printed.

(history = YES) [boolean]
If history = YES, then a set of HISTORY keywords will be written to the header of the specified HDU in the output file to record the value of all the task parameters that were used to produce the output file.

EXAMPLES

1. Apply NICER calibration and screening to data from observation 1706221428. 

  nicerl2 indir=1706221428 clobber=YES

The input directory is a NICER observation number 1706221428. The output files are placed in the observation directory under 1706221428/xti/event_cl/.

SEE ALSO

nicercal

nimaketime

niprefilter2

nicermergeclean

nicerclean

nifpmsel

nicerarf

nicerrmf

niautoscreen

Geomagnetic Quantities (NICER Documentation Page)

LAST MODIFIED

Apr 2024