Execution

At the moment, the DAP execution is tailored toward its execution at the survey level. On a best effort basis, we are trying to simplify the inputs to the main executable, as well as abstracting the DAP front-end to more easily work with non-MaNGA data.

Input files

The DAP AnalysisPlan

The DAP uses an SDSS parameter file to define one or more methods to use when analyzing any given MaNGA datacube. Each method, or “analysis plan”, is defined by a set of six keywords that identify the configuration to use for each of the DAP’s six main Analysis Modules. To execute the DAP, you must construct this parameter file with at least one analysis plan. For example, the MPL-9 analysis-plan parameter file is:

typedef struct {
    char drpqa_key[8];
    int drpqa_clobber;
    char bin_key[8];
    int bin_clobber;
    char continuum_key[8];
    int continuum_clobber;
    char elmom_key[8];
    int elmom_clobber;
    char elfit_key[8];
    int elfit_clobber;
    char spindex_key[8];
    int spindex_clobber;
} DAPPLAN;

#           DRP QA    BINNING        CONTINUUM      MOMENTS       LINEPROF   SPECINDEX
#        ---------  ---------  ---------------  -----------  -------------  ----------
DAPPLAN    SNRG  0     SPX  0   MILESHCMPL9  0  EMOMMPL9  0    EFITMPL9  0   INDXEN  0
DAPPLAN    SNRG  0   VOR10  0   MILESHCMPL9  0  EMOMMPL9  0    EFITMPL9  0   INDXEN  0
DAPPLAN    SNRG  0   HYB10  0   MILESHCMPL9  0  EMOMMPL9  0  EFITMPL9DB  0   INDXEN  0

The configuration of each module is set by two values: a configuration key and a flag indicating if any existing results should be overwritten (0 = False, 1 = True). Each keyword points to a unique configuration file, and each of these keywords produce a unique instance of a parameter set that drives the relevant analysis module. The link between the relevant structure element root (e.g., drpqa), the location of its configuration files, and the object used to read the configurations are as follows:

struct	$MANGADAP_DIR/python/mangadap/config/	DAP object
drpqa	reduction_assessments	mangadap.proc.reductionassessments.ReductionAssessmentDef
bin	spatial_binning	mangadap.proc.spatiallybinnedspectra.SpatiallyBinnedSpectraDef
continuum	stellar_continuum_modeling	mangadap.proc.stellarcontinuummodel.StellarContinuumModelDef
elmom	emission_line_moments	mangadap.proc.emissionlinemoments.EmissionLineMomentsDef
elfit	emission_line_modeling	mangadap.proc.emissionlinemodel.EmissionLineModelDef
spindex	spectral_indices	mangadap.proc.spectralindices.SpectralIndicesDef

When setting the keyword values in the analysis-plan file, they must be recognized as a method defined in the relevant configuration directory. The DAP will only execute properly if at least the first three steps have valid keywords. The remaining three modules can be skipped (i.e., the emission-line moments, emission-line-model parameters, and spectral indices are not measured) by setting their keyword to None; the primary DAP output will still be produced but with empty arrays for those extensions/channels that would normally be populated by the skipped analysis steps.

The DAP ObsInputPar

The DAP uses another SDSS parameter file to set the observation it is to analyze, as well as some input parameters that it uses during its execution. Specifically, it requires:

Parameter	Description
plate	The MaNGA plate number
ifudesign	The MaNGA IFU number
mode	The MaNGA DRP output mode (should always be CUBE)
vel	Guess systemic velocity, \(cz\), in km/s
vdisp	Guess stellar velocity dispersion; if less than 0, the DAP assumes 100 km/s.
ell	Isophotal ellipticity (\(\epsilon = 1-b/a\)).
pa	Position angle, \(0 \leq \phi_0 < 360\), of the isophotal ellipse defined as the angle (deg) from N through E.
reff	Effective (half-light) radius, \(R_{\rm eff}\).

Notes: If \(\epsilon < 0\) or \(\epsilon > 1\), the DAP will adopt a default value of 0. The DAP accepts any value for \(\phi_0\) but imposes the periodic limits (i.e., 380 deg is converted set to 20 deg). If \(R_{\rm eff} < 0\), the DAP uses \(R_{\rm eff} = 1\).

An example file looks like this:

typedef struct {
    long plate;
    long ifudesign;
    char mode[4];
    double vel;
    double vdisp;
    double ell;
    double pa;
    double reff;
} DAPPAR;

DAPPAR 7443 12701 CUBE  6.1391504e+03  1.0000000e+02  3.4162802e-01  1.5024400e+02  5.7011299e+00

DAP command-line script

The main DAP script is $MANGADAP_DIR/bin/manga_dap, which is a simple wrapper of mangadap.survey.manga_dap.manga_dap(). With the DAP installed, you can call the script directly from the command line:

$ manga_dap -h
usage: manga_dap [-h] [--dbg] [--log LOG] [-v] [--drpver DRPVER]
                 [-r REDUX_PATH] [-d DIRECTORY_PATH] [--dapver DAPVER]
                 [-s DAP_SRC] [-a ANALYSIS_PATH]
                 obs plan

positional arguments:
  obs                   SDSS parameter file with observational input
  plan                  SDSS parameter file with analysis plan

optional arguments:
  -h, --help            show this help message and exit
  --dbg                 Run manga_dap in debug mode
  --log LOG             File name for runtime log
  -v, --verbose         Set verbosity level; can be omitted and set up to -vv
  --drpver DRPVER       DRP version
  -r REDUX_PATH, --redux_path REDUX_PATH
                        Top-level directory with the DRP products; defaults to
                        $MANGA_SPECTRO_REDUX/$MANGADRP_VER
  -d DIRECTORY_PATH, --directory_path DIRECTORY_PATH
                        Path directly to directory with DRP file to analyze
  --dapver DAPVER       DAP version
  -s DAP_SRC, --dap_src DAP_SRC
                        Top-level directory with the DAP source code; defaults
                        to $MANGADAP_DIR
  -a ANALYSIS_PATH, --analysis_path ANALYSIS_PATH
                        Top-level output directory for the DAP results;
                        defaults to
                        $MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER

Warning

When running the DAP, you should have both the DRP LOGRSS and LOGCUBE files if you want to account for the Spatial Covariance! If the LOGRSS files are not present, the DAP will throw a warning and continue, which means that the warning can get buried among all the other messages and missed.

An example execution of the DAP might look like this:

manga_dap mangadap-7495-12704-LOGCUBE-input.par plan.par --log mangadap-7495-12704.log -vv

where mangadap-7495-12704-LOGCUBE-input.par and plan.par are, respectively, The DAP ObsInputPar and The DAP AnalysisPlan files.

Programmatic execution

Alternatively, $MANGADAP_DIR/examples/fit_one_cube.py (see How to Fit One Datacube) provides a programmatic approach to running the exact same script that is executed by the manga_dap command-line script. The code provides a way to generate the The DAP ObsInputPar object directly from the DRPall file, instead of from a file, and it directly defines the AnalysisPlan object with a hard-coded set of keywords. Using this script as an example, one could construct a script that programmatically analyzes a large set of MaNGA datacubes.

Batch execution using automatically generated scripts

The survey-level execution of the DAP uses the $MANGADAP_DIR/bin/rundap script, which is a simple wrapper of mangadap.survey.rundap.rundap. This script

• sets up the DAP output directory structure
• either confirms that a provided list of datacubes to analyze exist on disk or trolls the DRP directory structure to find all or some subset of available datacubes to analyze
• creates The DAP ObsInputPar parameter file for each plateifu to be analyzed,
• creates a script file for each plateifu that can be sourced to execute the DAP and the associated QA plots,
• creates scripts that execute the plate-level QA plots,
• creates scripts that build the DAPall file and its QA plots, and
• submits the scripts to the Utah cluster.

The last step uses an SDSS python package called pbs, which isn’t required for the more general-purpose use of the rundap script discussed here. With the DAP installed, you can call the script directly from the command line:

$ rundap -h
usage: rundap [-h] [--clobber] [-v] [--quiet] [--print_version] [--loose]
              [--mplver MPLVER] [--redux_path REDUX_PATH] [--dapver DAPVER]
              [--analysis_path ANALYSIS_PATH] [--plan_file PLAN_FILE]
              [--platelist PLATELIST] [--ifudesignlist IFUDESIGNLIST]
              [--list_file LIST_FILE] [--combinatorics] [--use_plttargets]
              [--plttargets PLTTARGETS] [--on_disk] [--log] [--no_proc]
              [--no_plots] [--post] [--post_plots] [--dapall] [--label LABEL]
              [--nodes NODES] [--cpus CPUS] [--fast QOS] [--umask UMASK]
              [--walltime WALLTIME] [--toughness] [--create] [--submit]
              [--progress] [--queue QUEUE]

optional arguments:
  -h, --help            show this help message and exit
  --clobber             if all selected, will run dap for all
                        plates/ifudesigns/modes regardless of state
  -v, --verbose         Set verbosity level for manga_dap; can be omitted and
                        set up to -vv
  --quiet               suppress screen output
  --print_version       print DAP version and stop
  --loose               Only throw warnings if the versioning is not
                        identically as it should be for the designated MPL
  --mplver MPLVER       select MPL version to analyze
  --redux_path REDUX_PATH
                        main DRP output path
  --dapver DAPVER       optional output version, different from product
                        version
  --analysis_path ANALYSIS_PATH
                        main DAP output path
  --plan_file PLAN_FILE
                        parameter file with the MaNGA DAP execution plan to
                        use instead of the default
  --platelist PLATELIST
                        set list of plates to reduce
  --ifudesignlist IFUDESIGNLIST
                        set list of ifus to reduce
  --list_file LIST_FILE
                        a file with the list of plates, ifudesigns, and modes
                        to analyze
  --combinatorics       force execution of all permutations of the provided
                        lists
  --use_plttargets      Use platetargets files instead of the DRPall file to
                        generate the DRP complete database
  --plttargets PLTTARGETS
                        path to plateTargets file(s); if provided will force
                        update to drpcomplete fits file
  --on_disk             When using the DRPall file to collate the data for
                        input to the DAP, search for available DRP files on
                        disk instead of using the DRPall file content.
  --log                 Have the main DAP executable produce a log file
  --no_proc             Do NOT perform the main DAP processing steps
  --no_plots            Do NOT create QA plots
  --post                Create/Submit the post-processing scripts
  --post_plots          Create/Submit the post-processing plotting scripts
  --dapall              Wait for any individual plate-ifu processes to finish
                        and then update the DAPall file
  --label LABEL         label for cluster job
  --nodes NODES         number of nodes to use in cluster
  --cpus CPUS           number of cpus to use per node. Default is to use all
                        available; otherwise, set to minimum of provided
                        number and number of processors per node
  --fast QOS            qos state
  --umask UMASK         umask bit for cluster job
  --walltime WALLTIME   walltime for cluster job
  --toughness           turn off hard keyword for cluster submission
  --create              use the pbs package to create the cluster scripts
  --submit              submit the scripts to the cluster
  --progress            instead of closing the script, report the progress of
                        the analysis on the cluster; this is required if you
                        want to submit the DAPall script immediately after
                        completing the individual cube analysis
  --queue QUEUE         set the destination queue

Note that you still need a parameter file with The DAP AnalysisPlan details; all datacubes selected by the rundap execution will be analyzed with the same AnalysisPlan. An example call of this script that will only construct scripts for the analysis of observation 7443-12701 is:

rundap --platelist 7443 --ifudesignlist 12701 --redux_path /path/with/drp/output/ --analysis_path /path/for/dap/output/ --plan_file /path/to/plan/file/plan.par -vv --log

In this call, I’ve specified that the DRP data is in /path/with/drp/output/ and that the DAP output should be placed in /path/for/dap/output/ instead of using the default DAP Directory Structure.

The script file this call produces is written to /path/for/dap/output/log/[time]/7495/12704/mangadap-7495-12704, where [time] is a time stamp of when rundap was executed. (If you execute rundap multiple times, it will create new directories using new time stamps each time.) The lines of the script file for each plate-ifu:

• touches the *.started file
• executes manga_dap
• executes a series of QA plotting scripts
• touches the *.done file

The example script generated by the above command would look something like this:

# Auto-generated batch file
# Fri 01 Nov 2019 10:58:52

touch /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/7443/12701/mangadap-7443-12701.started

manga_dap /path/for/dap/output/v2_7_1/2.4.1/common/7443/12701/mangadap-7443-12701-LOGCUBE-input.par /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/plan.par -r /path/with/drp/output/v2_7_1 -a /path/for/dap/output/v2_7_1/2.4.1 --log /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/7443/12701/mangadap-7443-12701.log -vv

ppxffit_qa 7443 12701 --analysis_path /path/for/dap/output/v2_7_1/2.4.1 --plan_file /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/plan.par

spotcheck_dap_maps 7443 12701 --analysis_path /path/for/dap/output/v2_7_1/2.4.1 --plan_file /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/plan.par

dap_fit_residuals 7443 12701 --analysis_path /path/for/dap/output/v2_7_1/2.4.1 --plan_file /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/plan.par

touch /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/7443/12701/mangadap-7443-12701.done

To execute the script, you would then run:

source /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/7443/12701/mangadap-7443-12701

The rundap script allows you to construct scripts for all datacubes it can find on disk, all IFUs on a given plate, all combinations of a set of plate and IFU numbers, or for a specified list of plateifu IDs.

Note

The rundap script constructs the mangadap.survey.drpcomplete.DRPComplete object and writes its associated fits file (see DRPComplete database). The data compiled into this database can either be drawn from the DRPall file or from the plateTargets data in mangacore; the latter is the only reason the DAP has mangacore as a dependency. For general use, you should have rundap use the DRPall file. The use of the plateTargets data is only necessary in the rare case when the DAP is executed before the relevant DRPall file has been constructed.

To write the post-processing scripts, execute rundap with the --post and --post_plots options. This produces two additional types of scripts:

• Scripts to produce QA plots for all IFUs on a given plate. This file is written to, e.g., /path/for/dap/output/log/01Nov2019T16.58.40UTC/7443/7443_fitqa and looks like this:

  # Auto-generated batch file
  # Fri 01 Nov 2019 10:58:52
  
  touch /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/7443/7443_fitqa.started
  
  dap_plate_fit_qa 7443 --analysis_path /path/for/dap/output/v2_7_1/2.4.1 --plan_file /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/plan.par
  
  touch /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/7443/7443_fitqa.done
  

• A script that builds the DAPall database and writes its QA plots. This file is written to, e.g., /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/build_dapall and looks like this:

  # Auto-generated batch file
  # Fri 01 Nov 2019 10:58:52
  
  touch /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/build_dapall.started
  
  construct_dapall /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/plan.par --drpver v2_7_1 -r /path/with/drp/output/v2_7_1 --dapver 2.4.1 -a /path/for/dap/output/v2_7_1/2.4.1 -vv
  
  dap_dapall_qa --drpver v2_7_1 --redux_path /path/with/drp/output/v2_7_1 --dapver 2.4.1 --analysis_path /path/for/dap/output/v2_7_1/2.4.1 --plan_file /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/plan.par
  
  touch /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/build_dapall.done
  

In the automated run of the DAP, any entry in the DRPComplete database file with:

• MANGAID != NULL
• MANGA_TARGET1 > 0 | MANGA_TARGET3 > 0
• VEL > -500

will be analyzed.

An important consequence of the selection above is that any ancillary targets without a provided redshift will not be analyzed by the DAP, unless it has replacement redshift in the Redshift Fix File. If an ancillary target(s) were not analyzed by the DAP, it may be that this can be changed simply by supplying redshift estimates in this redshift-fix file.