Execution¶
The MaNGA DAP is, of course, geared toward working at the survey-level for data produced by the MaNGA data-reduction pipeline (DRP). However, we have begun to generalize the usage of the DAP for datacubes from other instruments.
What follows below describes both how to use the current MaNGA DAP to analyze a datacube from the MaNGA survey, as well as how to execute the survey-level batch mode that analyzes all the MaNGA datacubes within a given directory structure.
Test cases for how to use the DAP to analyze datacubes from other instruments/surveys will be added soon.
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 method to use for each of the DAP’s six main
Analysis Modules. The AnalysisPlan
parameter file
allows you to analyze the same datacube multiple ways in a single
execution of the DAP; however, note that this is no different than
executing the DAP once per analysis method. The AnalysisPlan
is
required to execute the DAP; however, the DAP provides a
execution-analysis-plan-default that will be used if no file is
provided.
An example AnalysisPlan
parameter file looks like this (this is
exactly the file used for MPL-10):
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 MILESHCMPL10 0 EMOMMPL10 0 EFITMPL10 0 INDXEN 0
DAPPLAN SNRG 0 VOR10 0 MILESHCMPL10 0 EMOMMPL10 0 EFITMPL10 0 INDXEN 0
DAPPLAN SNRG 0 HYB10 0 MILESHCMPL10 0 EMOMMPL10 0 EFITMPL10DB 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 |
|
DAP object |
---|---|---|
drpqa |
|
|
bin |
|
|
continuum |
|
|
elmom |
|
|
elfit |
|
|
spindex |
|
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.
Default AnalysisPlan¶
If executed without an AnalysisPlan
parameter file, the command-line
execution of the DAP will use a default plan; see
mangadap.par.analysisplan.AnalysisPlanSet.default()
.
The current default plan uses the following keys:
Key |
Value |
---|---|
drpqa_key |
SNRG |
bin_key |
HYB10 |
continuum_key |
MILESHCMPL10 |
elmom_key |
EMOMMPL10 |
elfit_key |
EFITMPL10DB |
spindex_key |
INDXEN |
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 a combination of
mangadap.survey.drpcomplete.write_config()
and
mangadap.datacube.MaNGADataCube.write_config()
. However, we
also provide the $MANGADAP_DIR/bin/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
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, executing:
write_dap_config 7815 3702 mangadap-7815-3702.ini -a drpall-v3_0_1.fits
produces the following file:
# 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 (i.e., 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) [-p PLAN] [-m CUBE_MODULE]
[-o CUBE_OBJECT] [--dbg] [--log LOG] [-v] [--drpver DRPVER]
[-r REDUX_PATH] [-d DIRECTORY_PATH] [--dapver DAPVER]
[-a ANALYSIS_PATH]
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)
-p PLAN, --plan PLAN SDSS parameter file with analysis plan. If not
provided, a default plan is used. (default: None)
-m CUBE_MODULE, --cube_module CUBE_MODULE
The name of the module that contains the DataCube
derived class. (default: mangadap.datacube)
-o CUBE_OBJECT, --cube_object CUBE_OBJECT
The name of the DataCube derived class object.
(default: MaNGADataCube)
--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)
--drpver DRPVER DRP version (default: None)
-r REDUX_PATH, --redux_path REDUX_PATH
Top-level directory with the DRP products; defaults to
$MANGA_SPECTRO_REDUX/$MANGADRP_VER (default: None)
-d DIRECTORY_PATH, --directory_path DIRECTORY_PATH
Path directly to directory with DRP file to analyze
(default: None)
--dapver DAPVER DAP version (default: None)
-a ANALYSIS_PATH, --analysis_path ANALYSIS_PATH
Top-level output directory for the DAP results;
defaults to
$MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER
(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
and cube_object
arguments; these
default to mangadap.datacube
and MaNGADataCube
, respectively.
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_0_1.fits
manga_dap -c mangadap-7815-3702.ini -vv -log mangadap-7815-3702.log -d . -a 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
.
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¶
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 DAP Datacube Configuration File
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
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 The 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
fileexecutes
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_1/3.0.0/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_1/3.0.0/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_1/3.0.0 -p /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.0/log/27May2020T17.50.29UTC/mpl10_plan.par --log /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.0/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_1/3.0.0 --plan_file /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.0/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_1/3.0.0 --plan_file /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.0/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_1/3.0.0 --plan_file /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.0/log/27May2020T17.50.29UTC/mpl10_plan.par
touch /uufs/chpc.utah.edu/common/home/sdss/mangawork/manga/spectro/analysis/v3_0_1/3.0.0/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_1/3.0.0/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.