Execution

The MaNGA DAP was originally developed to analyze data from the SDSS-IV/MaNGA Survey, provided reduction products from the MaNGA data-reduction pipeline (DRP). However, it is now easy to apply the MaNGA DAP to any IFU datacube.

Below, we describe how to use the MaNGA DAP to analyze MaNGA datacubes, as well as how to execute the survey-level batch mode that analyzes all the MaNGA datacubes within a given directory structure.

Warning

Much of the survey-level execution of the code needs to be updated for the front end changes in version>4.x. If not removed outright, out of date documentation is flagged in what follows.

To analyze non-MaNGA datacubes, see both How to Fit a non-MaNGA Datacube and the description of the MaNGA DAP Analysis Plans. Also, for an example of how to fit single spectra using MaNGA DAP core algorithms, see How to Fit One Spectrum.

Input files

DAP AnalysisPlan

The DAP uses a toml file to define parameters used by its modules to analyze the provided datacube. This is described in detail by Analysis Plans.

Default AnalysisPlan

If executed without an AnalysisPlan parameter file, the command-line execution of the DAP will use a default plan; see mangadap.config.analysisplan.AnalysisPlan.default() and default_plan.toml.

The DAP Datacube Configuration File

The DAP uses a configuration (ini) file to set the datacube to be analyzed and provides some relevant metadata. These configuration files are generated at the survey-level by write_config(). However, we also provide the write_dap_config script that will generate the relevant configuration files if you have the DRPall or DRPComplete file. As with all the DAP scripts, you can use the -h command-line option to get the usage:

$ write_dap_config -h
usage: write_dap_config [-h] (-c DRPCOMPLETE | -a DRPALL) [--sres_ext SRES_EXT]
                        [--sres_fill SRES_FILL] [--covar_ext COVAR_EXT]
                        [--drpver DRPVER] [--redux_path REDUX_PATH]
                        [--directory_path DIRECTORY_PATH] [-o]
                        plate ifudesign ofile

Generate a DAP input configuration file

positional arguments:
  plate                 Plate number
  ifudesign             IFU design number
  ofile                 Output file name

optional arguments:
  -h, --help            show this help message and exit
  -c DRPCOMPLETE, --drpcomplete DRPCOMPLETE
                        DRP complete fits file (default: None)
  -a DRPALL, --drpall DRPALL
                        DRPall fits file (default: None)
  --sres_ext SRES_EXT   Spectral resolution extension to use. Default set by
                        MaNGADataCube class. (default: None)
  --sres_fill SRES_FILL
                        If present, use interpolation to fill any masked pixels
                        in the spectral resolution vectors. Default set by
                        MaNGADataCube class. (default: None)
  --covar_ext COVAR_EXT
                        Use this extension to define the spatial correlation
                        matrix. Default set by MaNGADataCube class. (default:
                        None)
  --drpver DRPVER       DRP version. Default set by MaNGADataCube class.
                        (default: None)
  --redux_path REDUX_PATH
                        Path to the top-level DRP reduction directory. Default
                        set by MaNGADataCube class. (default: None)
  --directory_path DIRECTORY_PATH
                        Exact path to the directory with the MaNGA DRP datacube.
                        The name of the file itself must match the nominal MaNGA
                        DRP naming convention. Default set by MaNGADataCube
                        class. (default: None)
  -o, --overwrite       Overwrite any existing files. (default: False)

To construct the configuration file for datacube 7815-3702, run:

write_dap_config 7815 3702 mangadap-7815-3702.ini -a drpall-v3_0_1.fits

to produce:

# Auto-generated configuration file
# Fri 28 Feb 2020 16:57:19

[default]
drpver
redux_path
directory_path
plate = 7815
ifu = 3702
log = True
sres_ext
sres_fill
covar_ext
z = 2.9382300e-02
vdisp
ell = 1.1084400e-01
pa = 1.6324500e+02
reff = 3.7749500e+00

Use the relevant keywords to change the paths or the extensions used for the spectral resolution and spatial correlation matrix (e.g., GCORREL).

Note

If the isophotal ellipticity, ell, is such that \(\epsilon < 0\) or \(\epsilon > 1\), the DAP will adopt a default value of 0. The DAP accepts any value for the position angle, pa, but imposes periodic limits (e.g., 380 deg is converted to 20 deg). If the effective radius, reff, is \(R_{\rm eff} < 0\) or undefined, the DAP uses \(R_{\rm eff} = 1\).

DAP command-line script

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

$ manga_dap -h
usage: manga_dap [-h] (-c CONFIG | -f CUBEFILE)
                 [--cube_module [CUBE_MODULE ...]] [-p PLAN]
                 [--plan_module [PLAN_MODULE ...]] [--dbg] [--log LOG] [-v]
                 [-o OUTPUT_PATH]

Perform analysis of integral-field data.

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        Configuration file used to instantiate the relevant
                        DataCube derived class. (default: None)
  -f CUBEFILE, --cubefile CUBEFILE
                        Name of the file with the datacube data. Must be
                        possible to instantiate the relevant DataCube derived
                        class directly from the file only. (default: None)
  --cube_module [CUBE_MODULE ...]
                        The name of the module that contains the DataCube
                        derived class used to read the data. (default:
                        mangadap.datacube.MaNGADataCube)
  -p PLAN, --plan PLAN  TOML file with analysis plan. If not provided, a default
                        plan is used. (default: None)
  --plan_module [PLAN_MODULE ...]
                        The name of the module used to define the analysis plan
                        and the output paths. (default:
                        mangadap.config.manga.MaNGAAnalysisPlan)
  --dbg                 Run manga_dap in debug mode (default: False)
  --log LOG             File name for runtime log (default: None)
  -v, --verbose         Set verbosity level; can be omitted and set up to -vv
                        (default: 0)
  -o OUTPUT_PATH, --output_path OUTPUT_PATH
                        Top-level directory for the DAP output files; default
                        path is set by the provided analysis plan object (see
                        plan_module). (default: None)

The DAP allows you to define your own datacube class, as long as it is derived from DataCube. You can then specify that your data should be instantiated with that derived class using the cube_module argument; this defaults to mangadap.datacube.datacube.MaNGADataCube, expected a MaNGA datacube.

When running the DAP on a MaNGA datacube, you have to provide a configuration file; however, for derived classes, you may be able to fully instantiate the relevant data using the datacube file, which is why we’ve provided the -f option.

Note that the analysis plan file is an optional argument. If it is not given, the DAP will use the Default AnalysisPlan.

To run the DAP on a single datacube using the default analysis plan, and assuming you have the DRPall file and the relevant LOGCUBE and LOGRSS files (see the warning below) in the current directory, you could execute the DAP as follows:

write_dap_config 7815 3702 mangadap-7815-3702.ini -a drpall-v3_1_1.fits --directory_path .
manga_dap -c mangadap-7815-3702.ini -vv --log mangadap-7815-3702.log -d . -o dap_output

This will analyze the datacube for observation 7815-3702 using the default analysis plan, with verbose output and a log written to mangadap-7815-3702.log, and with the root directory for all the DAP output (except for the log) set to dap_output. These commands can be successfully run in the $MANGADAP_DIR/mangadap/data/remote directory if you’ve run the download_test_data.py script.

Warning

When running the DAP on a MaNGA datacube, you should have both the DRP LOGRSS and LOGCUBE files in the directory_path 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 likely missed.

Programmatic execution

The manga_dap executable script is simple, in that it only (1) reads the datacube, (2) sets the analysis plan, and (3) executes the main DAP analysis wrapper function, mangadap.survey.manga_dap.manga_dap(). It is straight-forward then to construct a script that executes the DAP programmatically for many datacubes.

Batch execution using automatically generated scripts

Warning

The batch execution of the DAP (even for MaNGA) is currently out-of-date. These will be fixed soon.

The survey-level execution of the DAP uses the $MANGADAP_DIR/bin/rundap script, which is a simple wrapper of 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 Datacube Configuration 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] [--sres_ext SRES_EXT]
              [--sres_fill SRES_FILL] [--covar_ext COVAR_EXT]
              [--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 (default:
                        False)
  -v, --verbose         Set verbosity level for manga_dap; can be omitted and
                        set up to -vv (default: 0)
  --quiet               suppress screen output (default: False)
  --print_version       print DAP version and stop (default: False)
  --loose               Only throw warnings if the versioning is not
                        identically as it should be for the designated MPL
                        (default: False)
  --mplver MPLVER       select MPL version to analyze (default: None)
  --redux_path REDUX_PATH
                        main DRP output path (default: None)
  --dapver DAPVER       optional output version, different from product
                        version (default: None)
  --analysis_path ANALYSIS_PATH
                        main DAP output path (default: None)
  --plan_file PLAN_FILE
                        parameter file with the MaNGA DAP execution plan to
                        use instead of the default (default: None)
  --platelist PLATELIST
                        set list of plates to reduce (default: None)
  --ifudesignlist IFUDESIGNLIST
                        set list of ifus to reduce (default: None)
  --list_file LIST_FILE
                        A file with the list of plates and ifudesigns to
                        analyze (default: None)
  --combinatorics       force execution of all permutations of the provided
                        lists (default: False)
  --sres_ext SRES_EXT   Spectral resolution extension to use. Default set by
                        MaNGADataCube class. (default: None)
  --sres_fill SRES_FILL
                        If present, use interpolation to fill any masked
                        pixels in the spectral resolution vectors. Default set
                        by MaNGADataCube class. (default: None)
  --covar_ext COVAR_EXT
                        Use this extension to define the spatial correlation
                        matrix. Default set by MaNGADataCube class. (default:
                        None)
  --use_plttargets      Use platetargets files instead of the DRPall file to
                        generate the DRP complete database (default: False)
  --plttargets PLTTARGETS
                        path to plateTargets file(s); if provided will force
                        update to drpcomplete fits file (default: None)
  --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.
                        (default: False)
  --log                 Have the main DAP executable produce a log file
                        (default: False)
  --no_proc             Do NOT perform the main DAP processing steps (default:
                        False)
  --no_plots            Do NOT create QA plots (default: False)
  --post                Create/Submit the post-processing scripts (default:
                        False)
  --post_plots          Create/Submit the post-processing plotting scripts
                        (default: False)
  --dapall              Wait for any individual plate-ifu processes to finish
                        and thenupdate the DAPall file (default: False)
  --label LABEL         label for cluster job (default: None)
  --nodes NODES         number of nodes to use in cluster (default: 1)
  --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 (default:
                        None)
  --fast QOS            qos state (default: None)
  --umask UMASK         umask bit for cluster job (default: 0027)
  --walltime WALLTIME   walltime for cluster job (default: 240:00:00)
  --toughness           turn off hard keyword for cluster submission (default:
                        True)
  --create              use the pbs package to create the cluster scripts
                        (default: False)
  --submit              submit the scripts to the cluster (default: False)
  --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 (default:
                        False)
  --queue QUEUE         set the destination queue (default: None)

If a DAP AnalysisPlan is not provided, the scripts will use the Default AnalysisPlan.

An example call of this script that will only construct scripts for the analysis of observation 7443-12701 using the default AnalysisPlan is:

rundap --platelist 7443 --ifudesignlist 12701 --redux_path /path/with/drp/output/ --analysis_path /path/for/dap/output/ -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
# Wed 27 May 2020 11:50:45

touch /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.1/log/27May2020T17.50.29UTC/7443/12701/mangadap-7443-12701.started

OMP_NUM_THREADS=1 manga_dap -c /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.1/common/7443/12701/mangadap-7443-12701-LOGCUBE.ini -r /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/redux/v3_0_1 -a /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.1 -p /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.1/log/27May2020T17.50.29UTC/mpl10_plan.par --log /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.1/log/27May2020T17.50.29UTC/7443/12701/mangadap-7443-12701.log -vv

OMP_NUM_THREADS=1 dap_ppxffit_qa 7443 12701 --analysis_path /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.1 --plan_file /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.1/log/27May2020T17.50.29UTC/mpl10_plan.par

OMP_NUM_THREADS=1 spotcheck_dap_maps 7443 12701 --analysis_path /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.1 --plan_file /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.1/log/27May2020T17.50.29UTC/mpl10_plan.par

OMP_NUM_THREADS=1 dap_fit_residuals 7443 12701 --analysis_path /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.1 --plan_file /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.1/log/27May2020T17.50.29UTC/mpl10_plan.par

touch /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.1/log/27May2020T17.50.29UTC/7443/12701/mangadap-7443-12701.done

To execute the script, you would then run:

source /path/for/dap/output/v3_0_1/3.0.1/log/27May2020T17.50.29UTC/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 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:

Todo

update the scripts below!

• 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
  
  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 --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
  
  touch /path/for/dap/output/v2_7_1/2.4.1/log/01Nov2019T16.58.40UTC/build_dapall.done
  

Todo

Check the details here.

In the automated run of the DAP, any entry in the DRPComplete database file that meets the criteria set by mangadap.survey.drpcomplete.DRPComplete.can_analyze() will be analyzed. Currently the relevant criteria are:

• MANGAID != NULL

• MANGA_TARGET1 > 0 | MANGA_TARGET3 > 0

• VEL > -500

An important consequence of the selection above is that any targets without a provided redshift will not be analyzed by the DAP, unless it has replacement redshift in the Redshift Fix File. Ancillary targets not analyzed by the DAP are likely because a redshift was not available.

Execution Recovery

If the code faults, all of the modules completed up until the fault occurred should have created a “reference” file that will effectively allow the code to pick up where it left off. The mechanism used to determine if it can do this relies simply on the existence of the expected output file. This means that if you change on of the parameters in your input Analysis Plans file without changing the keyword identifier for that module parameter set, the code may read in the existing file and keep going without incorporating your parameter change.

If you’re testing the performance with different parameter values, either perform the testing with different output directories, always remember to change the keyword for the relevant module parameter set, set the overwrite keyword for the relevant module (and each subsequent module!) to True, or just nuke the directory and start again.

Quality Assessment Plots

The survey-level execution of the MaNGA DAP constructs automatically generated plots that provide spotchecks of the performance of the DAP; see Quality Assessment Plots. The main QA plots for the analysis of a single datacube have a similar calling sequence as the main DAP command-line script. The three main scripts are spotcheck_dap_maps, dap_ppxffit_qa, and dap_fit_residuals. Following the example above, these can be created after analysing the test datacube as follows:

spotcheck_dap_maps -c mangadap-7815-3702.ini -vv --log mangadap-7815-3702.log -d . -o dap_output
dap_ppxffit_qa -c mangadap-7815-3702.ini -vv --log mangadap-7815-3702.log -d . -o dap_output
dap_fit_residuals -c mangadap-7815-3702.ini -vv --log mangadap-7815-3702.log -d . -o dap_output

Local Environment Setup for Survey-Level MaNGA Analysis

The DAP uses environmental variables to define the paths to specific data and other repositories, when executed for MaNGA data. If these are not defined, default values will be used; see the initialization of the mangadap.config module. The relevant environmental variables, their default, and their usage are provided below.

Variable	Default	Comments
MANGADRP_VER	v3_1_1 (i.e., MPL-11)	Version of the DRP, used for path construction
MANGA_SPECTRO_REDUX	$HOME/MaNGA/redux	Root path for the reduced data
MANGADAP_VER	mangadap.__version__	Version of the DAP, used for path construction
MANGA_SPECTRO_ANALYSIS	$HOME/MaNGA/analysis	Root path for the analysis data

These environmental variables can be added to, e.g., your .bash_profile file in your home directory or be included in a script that is sourced when you want to run the DAP. The lines added to your .bash_profile file could look something like this:

export MANGA_SPECTRO_REDUX=/Volumes/MaNGA/redux
export MANGADRP_VER=v3_1_1

export MANGA_SPECTRO_ANALYSIS=/Volumes/MaNGA/analysis
export MANGADAP_VER=3.1.0

Note

• Importantly, note that $MANGADAP_VER is only used to set the path names, not to select the specific version of the DAP that should be used. The version of the DAP used is always the one installed by your python environment.

• The DAP checks that these variables are defined every time it is imported.

• Some of these same variables are defined by Marvin. It is possible to have both Marvin and the DAP point to the same directory, but beware that this may mean that some of the files get overwritten!

• Two additional variables ($MANGACORE_VER and $MANGACORE_DIR) are used in a specific mode of survey-level execution of the DAP. However, this is a niche usage mode and is effectively never used. See Batch execution using automatically generated scripts.

• The DAP expects to find the DRP LOGCUBE and LOGRSS files in the directory $MANGA_SPECTRO_REDUX/$MANGADRP_VER/[PLATE]/stack, where [PLATE] is the desired plate number. The LOGRSS files are required if you want to properly account for Spatial Covariance. This path can be altered when executing the DAP.

• The DAP expects to find/write data to $MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER. This path can be altered when executing the DAP, but the subdirectory structure used by the DAP to organize its outputs within this root directory cannot currently be changed.