Welcome to VDRP¶

Version: 1.0.5.post0

VDRP the Virus Data Reduction Pipeline is a collection of scripts and FORTRAN programs for astrometry, throughput and flux limit calculation.

VDRP currently supports only python 2.7.

User documentation¶

Astrometry routines¶

Throughput routines¶

Fluxlimit routines¶

Setting up and running the fluxlimit calculations¶

To calculate the fluxlimit cube of a given night shot call:

vdrp_setup_flim night shot

This will create a subdirectory tree of the form nightvshot/flim and in there a slurm batch script named flimnightvshot.slurm and the corresponding input files. Running the script as

vdrp_setup_flim --commit night shot

the slurm script will be sent to the batch system automatically. If needed the default runtime of 06:00:00 can be modified using –runtime on the command line.

Spectral line extraction routines¶

Developer documentation¶

Contribute to VDRP¶

How To¶

The suggested workflow for implementing bug fixes and/or new features is the following:

Identify or, if necessary, add to our redmine issue tracker one or more issues to tackle. Multiple issues can be addressed together if they belong together. Assign the issues to yourself.
Create a new branch from the trunk with a name either referring to the topic or the issue to solve. E.g. if you need to add a new executable, tracked by issue #1111 do_something:
```
svn cp ^/trunk ^/branches/do_something_1111\
-m 'create branch to solve issue #1111'
```

Switch to the branch:

svn switch ^/branches/do_something_1111

Implement the required changes and don’t forget to track your progress on redmine. If the feature/bug fix requires a large amount of time, we suggest, when possible, to avoid one big commit at the end in favour of smaller commits. In this way, in case of breakages, is easier to traverse the branch history and find the offending code. For each commit you should add an entry in the Changelog file.

If you work on multiple issues on the same branch, close one issue before proceeding to the next. When closing one issue is good habit to add in the description on the redmine the revision that resolves it.
Every function or class added or modified should be adequately documented as described in Coding style.

Documentation is essential both for users and for your fellow developers to understand the scope and signature of functions and classes. If a new module is added, it should be also added to the documentation in the appropriate place. See the existing documentation for examples.

Each executable should be documented and its description should contain enough information and examples to allow users to easily run it.
Every functionality should be thoroughly tested for python 3.5 or 3.6 in order to ensure that the code behaves as expected and that future modifications will not break existing functionalities. When fixing bugs, add tests to ensure that the bug will not repeat. For more information see Testing.
Once the issue(s) are solved and the branch is ready, merge any pending change from the trunk:
```
svn merge ^/trunk
```
While doing the merge, you might be asked to manually resolve one or more conflicts. Once all the conflicts have been solved, commit the changes with a meaningful commit message, e.g.: merge ^/trunk into ^/branches/do_something_1111. Then rerun the test suite to make sure your changes do not break functionalities implemented while you were working on your branch.
Then contact the maintainer of fplaneserver and ask to merge your branch back to the trunk.

Information about branching and merging can be found in the svn book. For any questions or if you need support do not hesitate to contact the maintainer or the other developers.

Coding style¶

All the code should be compliant with the official python style guidelines described in PEP 8. To help you keep the code in spec, we suggest to install plugins that check the code for you, like Synstastic for vim or flycheck for Emacs.

The code should also be thoroughly documented using the numpy style. See the existing documentation for examples.

Testing¶

Note

Every part of the code should be tested and should run at least under python 3.5 and possibly 3.6

fplaneserver uses the testing framework provided by the robot framework package. The tests should cover every aspect of a function or method. If exceptions are explicitly raised, this should also tested to ensure that the implementation behaves as expected.

The preferred way to run the tests is using tox, an automatised test help package. If you have installed tox, with e.g. pip install tox, you can run it by typing:

tox

It will take care of creating virtual environments for every supported version of python, if it exists on the system, install fplaneserver, its dependences and the packages necessary to run the tests and runs py.test

You can run the tests for a specific python version using:

python -m robot

A code coverage report is also created and can be visualized opening into a browser cover/index.html.

Besides running the tests, the tox command also builds, by default, the documentation and collates the coverage tests from the various python interpreters and can copy then to some directory. To do the latter create, if necessary, the configuration file ~/.config/little_deploy.cfg and add to it a section called fplaneserver with either one or both of the following options:

[fplaneserver]
# if given the deploys the documentation to the given dir
doc = /path/to/dir
# if given the deploys the coverage report to the given dir
cover = /path/to/other/dir

# it's also possible to insert the project name and the type of the document
# to deploy using the {project} and {type_} placeholders. E.g
# cover = /path/to/dir/{project}_{type_}
# will be expanded to /path/to/dir/fplaneserver_cover

For more information about the configuration file check little_deploy.

Documentation¶

To build the documentation you need the additional dependences described in pydep. They can be installed by hand or during fplaneserver installation by executing one of the following commands on a local copy:

pip install /path/to/fplaneserver[doc]
pip install /path/to/fplaneserver[livedoc]

The first install sphinx, the alabaster theme and the numpydoc extension; the second also installs sphinx-autobuild.

To build the documentation in html format go to the doc directory and run:

make html

The output is saved in _doc/build/html. For the full list of available targets type make help.

If you are updating the documentation and want avoid the edit-compile-browser refresh cycle, and you have installed sphinx-autobuild, type:

make livehtml

then visit http://127.0.0.1:8000. The html documentation is automatically rebuilt after every change of the source and the browser reloaded.

Please make sure that every module in fplaneserver is present in the Code documentation.

Code documentation¶

`astrometry` - Astrometry routines¶

Astrometry routine

Module to add astrometry to HETDEX catalgoues and images Contains python translation of Karl Gebhardt

vdrp.astrometry.add_ifu_xy(wdir, offset_exposure_indices)[source]¶

Adds IFU x y information to stars used for matching, and save to xy_expNN.dat. Requires: getoff.out, radec2.dat Analogous to rastrom3.

Parameters:	wdir : str Work directory. offset_exposure_indices : list List of exposure indices to consider.

vdrp.astrometry.add_ra_dec(wdir, als_data, ra, dec, pa, fp, radec_outfile='tmp.csv')[source]¶

Call add_ra_dec to compute for detections in IFU space the corresponding RA/DEC coordinates.

New version, direct python call to pyheted.coordinates.tangent_projection.

Requires, fplane.txt Creates primarely EXPOSURE_tmp.csv but also radec.dat.

Parameters:	wdir : str Work directory. als_data : dict Dictionary with als data for each IFU slot. ra : float Focal plane center RA. dec : float Focal plane center Dec. pa : float Positions angle. fp : FPlane Focal plane object. radec_outfile : str Filename that will contain output from add_ra_dec (gets overwritten!).

vdrp.astrometry.combine_radec(wdir, dither_offsets, PLOT=True)[source]¶

Computes - based on the RA Dec information of the individual exposures (from radec2_exp0?.dat) the final RA/Dec for the shot.

Parameters:	wdir : str Work directory.

Notes

Creates radec2_final.dat. Optionally create a plot indicating the individual exposure positions.

vdrp.astrometry.compute_offset(wdir, prefixes, getoff2_radii, add_radec_angoff_trial, add_radec_angoff, add_radec_angoff_trial_dir, offset_exposure_indices, final_ang_offset=None, shout_ifustars='shout.ifustars', ra0=None, dec0=None)[source]¶

Requires, fplane.txt and radec.orig. If not ra, dec are passed explicitly then the values from radec.orig are used. The pa value from radec.orig is used in any case. Creates primarely EXPOSURE_tmp.csv but also radec2.dat.

Compute offset in RA DEC by matching detected stars in IFUs against the shuffle profived RA DEC coordinates.

Parameters:

wdir : str: Work directory.
prefixes : list: List file name prefixes for the collapsed IFU images.
getoff2_radii : list: List of matching radii for astrometric offset measurement.
add_radec_angoff_trial : list: Trial values for angular offsets.
add_radec_angoff : float: Angular offset to add during conversion of x/y coordinate to RA/Dec.
add_radec_angoff_trial_dir : str: Directory to save results of angular offset trials.
offset_exposure_indices : list: Exposure indices.
final_ang_offset : float: Final angular offset to use. This overwrites the values in add_radec_angoff and add_radec_angoff_trial
shout_ifustars : str: Shuffle output catalog of IFU stars.
ra0 : float: Optionally allows to overwrite use of RA from radec.orig
dec0 : float: Optionally allows to overwrite use of DEC from radec.orig

Notes

Analogous to rastrom3. Creates radec.dat, radec2.dat and radec_TRIAL_OFFSET_ANGLE.dat, radec_TRIAL_OFFSET_ANGLE2.dat.

vdrp.astrometry.compute_optimal_ang_off(wdir, smoothing=0.05, PLOT=True)[source]¶

Computes the optimal angular offset angle by findin the minimal RMS of a set of different trial angles.

Takes (if exist) all three different exposures into account and computes weighted average ange (weighted by number of stars that went into the fit).

The RMS(ang_off) are interpolate with a smoothing spline. The smoothing value is a parameter to this function.

Parameters:	wdir : str Directory that holds the angular offset trials (e.g. 20180611v017/add_radec_angoff_trial)
Returns:	float : Optimal offset angle.

vdrp.astrometry.cp_addin_files(wdir, addin_dir, subdir='coords')[source]¶

Copies addin files. These are essentially the IFUcen files in a different format.

Parameters:	addin_dir : str Directory where the .addin files are stored. wdir* : str Work directory.

vdrp.astrometry.cp_ixy_files(wdir, ixy_dir, subdir='coords')[source]¶

Copies ixy files. These are essentially the IFUcen files in a different format.

Parameters:	ixy_dir_dir :str Directory where the .ixy files are stored. wdir* : str Work directory.

vdrp.astrometry.cp_post_stamps(wdir, reduction_dir, night, shotid)[source]¶

Copy CoFeS (collapsed IFU images).

Parameters:	wdir : str Work directory. reduction_dir : str Directory that holds panacea reductions. night : str Night (e.g. 20180611) shotid : str ID of shot (e.g. 017)
Raises:	Exception

vdrp.astrometry.cp_results(tmp_dir, results_dir)[source]¶

Copies all relevant result files from tmp_dir results_dir.

Parameters:	tmp_dir : str Temporary work directory. results_dir : str Final directory for results.

vdrp.astrometry.daophot_find(wdir, prefixes, daophot_opt, daophot_sigma, daophot_xmin, daophot_xmax, daophot_ymin, daophot_ymix)[source]¶

Run initial daophot find.

Parameters:

wdir : str: Work directory.
prefixes : list: List file name prefixes for the collapsed IFU images.
daophot_opt : str: Daphot sigma value.
daophot_sigma : float: Filename for daophot configuration.
daophot_xmin : float: X limit for daophot detections.
daophot_xmax : float: X limit for daophot detections.
daophot_ymin : float: Y limit for daophot detections.
daophot_ymix : float: Y limit for daophot detections.

vdrp.astrometry.daophot_phot_and_allstar(wdir, prefixes, daophot_photo_opt, daophot_allstar_opt, daophot_phot_psf)[source]¶

Runs daophot photo and allstar on all IFU postage stamps. Produces *.ap and *.als files. Analogous to run4a.

Parameters:	wdir : str Work directory. prefixes : list List file name prefixes for the collapsed IFU images. daophot_opt : str Filename for daophot configuration. daophot_photo_opt : str Filename for daophot photo task configuration. daophot_allstar_opt : str Filename for daophot allstar task configuration.

vdrp.astrometry.flux_norm(wdir, mag_max, infile='all.raw', outfile='norm.dat')[source]¶

Reads all.raw and compute relative flux normalisation for the three exposures.

Parameters:	wdir : str Work directory. mag_max : float Magnitude limit for flux normalisation. infile : str Output file of daomaster. outfile : str Filename for result file.

Notes

Analogous to run9.

vdrp.astrometry.getDefaults()[source]¶

vdrp.astrometry.getNorm(all_raw, mag_max)[source]¶

Comutes the actual normalisation for flux_norm.

Parameters:	all_raw : str Output file name of daomaster, usuall all.raw. mag_max : float Magnitude cutoff for normalisation. Fainter objects will be ignored.

Notes

Analogous to run9.

vdrp.astrometry.get_active_slots(wdir, reduction_dir, exposures, night, shotid)[source]¶: Figures out which IFU slots actually delivered data, by checking if a corresponding multifits exists for all exposures in a shot.

vdrp.astrometry.get_als_files(fp, exp_prefixes)[source]¶

Derives for a list of exposure prefixes a list of *.als files, but rejects any that refer to an IFU slot which is not contained in the fplane.

Parameters:	fp : pyhetdex.het.fplane.FPlane Fplane object. exp_prefixes : list List of epxosure prefixes.
Returns:	*(list): List of .als files.**

vdrp.astrometry.get_exposures(prefixes)[source]¶

Computes unique list of exposures from prefixes.

Parameters:	args : argparse.Namespace Parsed configuration parameters. prefixes : list List file name prefixes for the collapsed IFU images
Returns:	(list): Unique list of exposure strings.

vdrp.astrometry.get_exposures_files(basedir)[source]¶

Create list of all file prefixes based on the existing collapsed IFU files in the current directory.

From files:

20180611T054545_015.fits … 20180611T054545_106.fits 20180611T055249_015.fits … 20180611T055249_106.fits 20180611T060006_015.fits … 20180611T060006_106.fits

Creates:

{: ‘exp01’ : [‘20180611T054545_015’,…,‘20180611T054545_106’] ‘exp02’ : [‘20180611T055249_015’,…,‘20180611T055249_106’] ‘exp03’ : [‘20180611T060006_015’,…,‘20180611T060006_106’]

}

Parameters:	basedir : str Directory to search.
Returns:	OrderedDict : Ordered dictionary with pairs of exposure string “exp??” and time and list of

vdrp.astrometry.get_fiber_coords(wdir, active_slots, dither_offsets, subdir='coords')[source]¶

Calls add_ra_dec for all IFU slots and all dithers.

The is the main routine for getcoord which computes the on-sky positions for all fibers.

Essentially this is a whole bunch of calls like.:

add_ra_dec –ftype line_detect –astrometry 262.496605 33.194212 262.975922: –fplane /work/00115/gebhardt/maverick/sci/panacea/shifts/fplane.txt –ihmps 015 –fout i015_1.csv –dx 0 –dy 0 015.addin

… add_ra_dec –ftype line_detect –astrometry 262.496605 33.194212 262.975922

–fplane /work/00115/gebhardt/maverick/sci/panacea/shifts/fplane.txt –ihmps 015 –fout i015_2.csv –dy 1.27 –dx -0.73 015.addin

… add_ra_dec –ftype line_detect –astrometry 262.496605 33.194212 262.975922

–fplane /work/00115/gebhardt/maverick/sci/panacea/shifts/fplane.txt –ihmps 015 –fout i015_3.csv –dy 1.27 –dx 0.73 015.addin

Parameters:	wdir : str Work directory.

Notes

This creates a list of files iIFUSLOT_DITHERNUM.csv that store the on-sky fiber coordinates.

vdrp.astrometry.get_prefixes(wdir)[source]¶

Create list of all file prefixes based on the existing collapsed IFU files in the current directory.

Parameters:	wdir : str Work directory.

vdrp.astrometry.get_ra_dec_orig(wdir, reduction_dir, night, shotid, user_pa=-999999.0)[source]¶

Reads first of the many multi* file’d headers to get the RA, DEC, PA guess from the telescope.

Parameters:	wdir : str Work directory. reduction_dir : str Directory that holds panacea reductions. night : str Night (e.g. 20180611) shotid : str ID of shot (e.g. 017)

Notes

Creates radec.orig

vdrp.astrometry.get_track(wdir, reduction_dir, night, shotid)[source]¶

Reads first of the many multi* file’d headers to get the track.

Parameters:	wdir : str Work directory. reduction_dir : str Directory that holds panacea reductions. night : str Night (e.g. 20180611) shotid : str ID of shot (e.g. 017) Returns —— (int): 0 = east track, 1 = west track

Notes

This function is so emparrisingly similar to get_ra_dec_orig that they should probably be combined.

vdrp.astrometry.load_als_data(als_files)[source]¶

Load set of als files.

Parameters:	als_files : list List of file names. Returns —— (OrderedDict): Dictionary with als data for each IFU slot.

vdrp.astrometry.main(args)[source]¶: Main function.

vdrp.astrometry.mk_dithall(wdir, active_slots, reduction_dir, night, shotid, subdir='.')[source]¶

This creates the dithall.use file that is required by the downstream processing functions like photometry and detect.

The file dithall.use contains for every exposure (1-3) and every fiber the RA/Dec on sky coordinats and the multifits file where the spectrum is stored and the fiber number.

vdrp.astrometry.mk_match_matrix(wdir, ax, exp, image_files, fplane_file, shout_ifu_file, xy_file, radec_file)[source]¶

Creates the actual match plot for a specific exposures. This is a subroutine to mk_match_plots.

Parameters:

wdir : str: Work directory.
prefixes : list: List file name prefixes for the collapsed IFU images.
ax : pyplot.axes: Axes object to plot into.
exp : str: Exposure string (e.g. exp01)
image_files : list: List of file names.
fplane_file : str: Focal plane file filename.
shout_ifu_file : str: Shuffle IFU star catalog output filename.
xy_file : str: Filename for list of matched stars, aka xy_exp??.dat.
radec_file : str: File that contains shot ra dec position.

vdrp.astrometry.mk_match_plots(wdir, prefixes)[source]¶

Creates match plots.

Parameters:	wdir : str Work directory. prefixes : list List file name prefixes for the collapsed IFU images.

vdrp.astrometry.mk_post_stamp_matrix(wdir, prefixes, cofes_vis_vmin, cofes_vis_vmax)[source]¶

Create the IFU postage stamp matrix image.

Parameters:	wdir : str Work directory. prefixes : list List file name prefixes for the collapsed IFU images. cofes_vis_vmin : float Minimum value (= black) for matrix overview plot. cofes_vis_vmax : float Maximum value (= black) for matrix overview plot.

vdrp.astrometry.mkmosaic(wdir, prefixes, night, shotid, mkmosaic_angoff)[source]¶

Creates mosaic fits image.

Parameters:	wdir : str Work directory. prefixes : list List file name prefixes for the collapsed IFU images. night : str Night (e.g. 20180611) shotid : str ID of shot (e.g. 017) mkmosaic_angoff : float Angular offset to add for creation of mosaic image.

vdrp.astrometry.mktot(wdir, prefixes, mktot_ifu_grid, mktot_magmin, mktot_magmax, mktot_xmin, mktot_xmax, mktot_ymin, mktot_ymax, dither_offsets)[source]¶

Reads all *.als files. Put detections on a grid corresponding to the IFU position in the focal plane as defined in config/ifu_grid.txt (should later become fplane.txt. Then produces all.mch.

Parameters:

wdir : str: Work directory.
prefixes : list: List file name prefixes for the collapsed IFU images.
mktot_ifu_grid : str: Name of file that holds gird of IFUs offset fit (mktot).
mktot_magmin : float: Magnitude limit for offset fit.
mktot_magmax : float: Magnitude limit for offset fit.
mktot_xmin : float: X limit for offset fit.
mktot_xmax : float: X limit for offset fit.
mktot_ymin : float: Y limit for offset fit.
mktot_ymax : float: Y limit for offset fit.

Notes

Analogous to run6 and run6b.

vdrp.astrometry.parseArgs(args)[source]¶

Parses configuration file and command line arguments. Command line arguments overwrite configuration file settiongs which in turn overwrite default values.

Parameters:	args : argparse.Namespace Return the populated namespace.

vdrp.astrometry.project_xy(wdir, radec_file, fplane_file, ra, dec)[source]¶

Translate all catalog stars to x/y to display then and to see which ones got matched. Call pyhetdex tangent_plane’s functionality to project ra,dec to x,y.

Parameters:	wdir : str Work directory. radec_file : str File that contains shot ra dec position. fplane_file : str Focal plane file filename. ra : list List of ra positions (in float, degree). dec : list List of dec positions (in float, degree).

vdrp.astrometry.redo_shuffle(wdir, ra, dec, track, acam_magadd, wfs1_magadd, wfs2_magadd, shuffle_cfg, fplane_txt, night, catalog=None)[source]¶

Reruns shuffle to obtain catalog of IFU stars.

Creates a number of output files, most importantly shout.ifustars which is used as catalog for the offset computation.

Parameters:	wdir : str Work directory. ra : float Right ascension in degrees. dec : float Declination in degrees. track : int East or west track (0, 1) acam_magadd : float do_shuffle acam magadd. wfs1_magadd : float do_shuffle wfs1 magadd. wfs2_magadd : float do_shuffle wfs2 magadd.

vdrp.astrometry.rmaster(wdir)[source]¶

Executes daomaster. This registers the sets of detections for the thre different exposrues with respec to each other.

Parameters:	wdir : str Work directory.

Notes

Analogous to run8b.

vdrp.astrometry.run()[source]¶

`calc_fluxlim` - Fluxlimit calculation routines¶

Fluxlimit routine

Contains python translation of Karl Gebhardt

vdrp.calc_fluxlim.calc_fluxlim(args, workdir)[source]¶

Equivalent of the rflim0 script and of mklistfl and the rspfl3f scripts.

Calculate the flux limit for a given night and shot, looping over a (by default) 70 x 70 arcsecond grid

Parameters:	args : struct The arguments structure

vdrp.calc_fluxlim.calc_fluxlim_entrypoint()[source]¶

vdrp.calc_fluxlim.getDefaults()[source]¶

vdrp.calc_fluxlim.get_arguments(parser)[source]¶

Add command line arguments for the photometry routines, this function can be called from another tool.

Parameters:	parser : argparse.ArgumentParser

vdrp.calc_fluxlim.main(jobnum, args)[source]¶: Main function.

vdrp.calc_fluxlim.parseArgs(argv)[source]¶

Parses configuration file and command line arguments. Command line arguments overwrite configuration file settiongs which in turn overwrite default values.

Args:: args (argparse.Namespace): Return the populated namespace.

vdrp.calc_fluxlim.update_im3d_header(ra, dec, wdir)[source]¶: Add header keywords to the image3d.fits

`cltools` - Commandine tools¶

Interface to astrometry command line tools

Module provide interface routines to the command line tools that are use in Karl Gebhardt’s astrometry procedure.

vdrp.cltools.getoff2(fnradec, fnshuffle_ifustars, radius, ra_offset, dec_offset, logging=None)[source]¶

Interface to getoff2.

Args:

fnradec (string): Filename for detections. fnshuffle_ifustars (string): Filename of catalog of stars to match to. radius (float): Matching radius. ra_offset (float): RA offset to apply to detecions in fnradec

before computing offset.

dec_offset (float): Dec offset to apply to detecions in fnradec: before computeing offset.
logging (module): Pass logging module if.: Otherwise output is passed to the screen.

Notes:

Creates files getoff.out, getoff2.out and intermediate file shout.ifu.

Retruns:

new_ra_offset (float), new_dec_offset (float): New offset after matching (input offset added).

vdrp.cltools.immosaicv(prefixes, fplane_file='fplane.txt', logging=None)[source]¶

Interface to immosaicv which creates a mosaic give a set of fits files and x y coordinates. Requires infp. This function will prepare the necessary infp file that is read by immosaicv command line tool. Format of the latter is 20180611T054545_015.fits 015 -450.0 -50.0 20180611T054545_022.fits 022 -349.743 250.336 20180611T054545_023.fits 023 -349.798 150.243 20180611T054545_024.fits 024 -350.0 50.0 …

Args:: prefixes (list): List file name prefixes for the collapsed IFU images. fplane_file (str): Fplane file name. logging (module): Pass logging module if. Otherwise output is passed to the screen.

vdrp.cltools.imrot(fitsfile, angle, logging=None)[source]¶

Interface to imrot. Rotates fits image by given angle.

Notes:: Creates file imrot.fits.
Args:: fitsfile (str): Input fits file name. angle (float): Rotation angle.

`cofes_vis` - Visualization routines¶

vdrp.cofes_vis.cofes_4x4_plots(prefix='', outfile_name='CoFeS_plots.png', vmin=-15, vmax=25, logging=None)[source]¶

dir is a string containing the directory with the CoFeS files you wish to plot. If its the local directory you can leave it as an empty string

outfile_name is a string with the output file name. This will be placed in the dir directory

the ifu order is 073 083 093 103 074 084 094 104 075 085 095 105 076 086 096 106

vdrp.cofes_vis.cofes_plots(ifunums, filename_array, outfile_name, vmin=-15, vmax=25, logging=None)[source]¶

filename_array is an array-like object that contains the filenames of fits files to plot. The output plot will be the shape of the input array.

outfile is the output file name including the extension, such as out.fits.

vmin and vmax set the stretch for the images. They are in units of counts; Pixels with vmin and below counts are black. Pixels with vmax and above counts are white.

vdrp.cofes_vis.main()[source]¶

`containers` - Container structures¶

exception vdrp.containers.NoShotsException[source]¶: Bases: exceptions.Exception

class vdrp.containers.DithAll(ra=0.0, dec=0.0, ifuslot='', x=0.0, y=0.0, x_fp=0.0, y_fp=0.0, filename='', timestamp='', expname='')[source]¶

class vdrp.containers.DithAllFile(filename=None)[source]¶

where(cond)[source]¶

class vdrp.containers.Spectrum[source]¶

This class encapsulates the content of a tmp*.dat spectrum file

Attributes:	wl : float Wavelength cnts : float Counts of the spectrum flx : float Flux of the spectrum amp_norm : float Ampliflier normalization tp_norm : float Throughput normalization ftf_norm : float Fiber to fiber normalization err_cts : float err_cts_local : float err_max_flux : float

read(fname)[source]¶

class vdrp.containers.StarObservation(num=0.0, night=-1, shot=-1, ra=-1, dec=-1, x=-1, y=-1, fname='', shotname='', expname='', offset_ra=-1, offset_dec=1)[source]¶

Data for one spectrum covering a star observation. This corresponds to the data stored in the l1 file with additions from other files

Attributes:

num : int: Star number
night : int: Night of the observation
shot : int: Shot of the observation
ra : float: Right Ascension of the fiber center
dec : float: Declination of the fiber center
x : float: Offset of fiber relative to IFU center in x direction
y : float: Offset of fiber relative to IFU center in y direction
full_fname : str: Filename of the multi extension fits file.
shotname : str: NightvShot shot name
expname : str: Name of the exposure.
dist : float: Distance of the fiber from the star position
offset_ra : float: Offset in ra of the fiber from the star position
offset_dec : float: Offset in dec of the fiber from the star position
fname : str: Basename of the fits filenname
ifuslot : str: IFU slot ID
avg : float: Average of the spectrum
avg_norm : float
avg_error : float: Error of the average of the spectrum
structaz : float: Azimuth of the telescope structure, read from the image header

set_fname(fname)[source]¶: Split the full filename into the base name and the ifuslot

`daophot` - Daophot helper routines¶

Interface to daophot routines.

Module provides interface to daophot.

exception vdrp.daophot.DaophotException[source]¶: Bases: exceptions.Exception

class vdrp.daophot.DAOPHOT_ALS(NL, NX, NY, LOWBAD, HIGHBAD, THRESH, AP1, PH_ADU, RNOISE, FRAD, data)[source]¶

Bases: object

Reads DAOPHOT ALS files.

static read(als_file)[source]¶

Reads daophot als file.

Notes:

Creates file imrot.fits.

Args:

als_file (str): Input file name.

Returns:

(DAOPHOT_ALS): Object containing all the infromation: in the als file.

vdrp.daophot.allstar(prefix, psf='use.psf', logging=None)[source]¶

Interface to allstar.

Notes:: Replaces second part of rdsub. Requires allstar.opt and use.psf, PREFIX.ap to be in place.
Args:: prefix (str): File name prefix to call daophot phot for. psf (str): File name for PSF model. logging (module): Pass logging module if. Otherwise output is passed to the screen.

vdrp.daophot.daomaster(logging=None)[source]¶

Interface to daomaster.

Notes:: replaces “rmaster0”. Requires 20180611T054545tot.als and all.mch to be in place.
Args:: logging (module): Pass logging module if. Otherwise output is passed to the screen.

vdrp.daophot.daophot_find(prefix, sigma, logging=None)[source]¶

Interface to daophot find.

Notes:: Replaces second part of rdcoo. Requires daophot.opt to be in place.
Args:: prefix (str): File name prefix to call daophot phot for. sigma (float): Daophot phot sigma parameter. logging (module): Pass logging module if.

Otherwise output is passed to the screen.

vdrp.daophot.daophot_phot(prefix, logging=None)[source]¶

Interface to daophot phot.

Notes:: Replaces first part of rdsub. Requires photo.opt to be in place.
Args:: prefix (str): File name prefix to call daophot phot for. logging (module): Pass logging module if. Otherwise output is passed to the screen.

vdrp.daophot.filter_daophot_out(file_in, file_out, xmin, xmax, ymin, ymax)[source]¶

Filter daophot coo ouput files. For close-to-edge detections.

Read the daophot *.coo output file and rejects detections that fall outside xmin - xmax and ymin - ymax. Translated from awk ‘{s+=1; if (s<=3||($2>4&&$2<45&&$3>4&&$3<45)) print $0}’ $1.coo > $1.lst

Notes: Args:

file_in (str): Input file name. file_out (str): Output file name. xmin (float): Detection x coordinate must be larger than this vaule. xmax (float): Detection x coordinate must be smaller than this vaule. ymin (float): Detection y coordinate must be larger than this vaule. ymax (float): Detection y coordinate must be smaller than this vaule.

vdrp.daophot.mk_daophot_opt(args)[source]¶

vdrp.daophot.test_input_files_exist(input_files)[source]¶

Takes a list of files names and check if they are in place. Raises DaophotException if not.

Args:: input_files (list): List of file names to check.
Raises:: DaophotException: If not all given files are present.

`extraction` - Spectrum extraction routines¶

Spectrum extraction routines

Contains python translation of Karl Gebhardt

vdrp.extraction.extract_star_spectrum(starobs, args, wl, wlr, wdir, prefix='')[source]¶

Equivalent of the rextsp[1] and parts of the rsp1b scripts.

Extract stellar spectra, creating the tmp*.dat files. If prefix is set, it is prefixed to the tmp*dat file names.

Parameters:	starobs : list List with StarObservation objects. args : struct The arguments structure wdir : str Name of the work directory prefix : str (optional) Optional prefix for the output filenames.
Returns:	list List of tmp*dat filenames created.

vdrp.extraction.get_star_spectrum_data(ra, dec, args, nightshot, multi_shot=False, dithall=None)[source]¶

This extracts the data about the different observations of the same star on different ifus.

This is essentially the information stored in the l1 file.

Parameters:	ra : float Right Ascension of the star. dec : float Declination of the star. args : struct The arguments structure nightshot : tuple Tuple of strings with night and shot to search. if None, use all shots containing the given RA /DEC

vdrp.extraction.get_structaz(starobs, path)[source]¶: Equivalent of the rgetadc script Read the STRUCTAZ parameter from the multi extension fits files and fill in the StarObservation entries.

`file_tools` - File access routines¶

vdrp.file_tools.get_dithall_file(basedir, night, shot)[source]¶

vdrp.file_tools.get_mulitfits_file(basedir, night, shot, expname, fname)[source]¶

vdrp.file_tools.get_norm_file(path, fname)[source]¶

vdrp.file_tools.get_throughput_file(path, night, shot)[source]¶

Equivalent of rtp0 script.

Checks if a night/shot specific throughput file exists.

If true, return the filename, otherise the filename for an average throughput file.

Parameters:	path : str Path to the throughput files shotname : str Name of the shot

`fit_radec` - RA/DEC fitting routines¶

RA /DEC fitting routine, equivalent of rsp3f script

Contains python translation of Karl Gebhardt

vdrp.fit_radec.fit_radec(args)[source]¶

Equivalent of the rsp3f script

args : struct: The arguments structure

vdrp.fit_radec.fitradec_entrypoint()[source]¶

vdrp.fit_radec.getDefaults()[source]¶

vdrp.fit_radec.get_arguments(parser)[source]¶

Add command line arguments for the photometry routines, this function can be called from another tool.

Parameters:	parser : argparse.ArgumentParser

vdrp.fit_radec.main(jobnum, args)[source]¶: Main function.

vdrp.fit_radec.parseArgs(argv)[source]¶

Parses configuration file and command line arguments. Command line arguments overwrite configuration file settiongs which in turn overwrite default values.

Args:: args (argparse.Namespace): Return the populated namespace.

`fplane_client` - FPlane retrieval routines¶

vdrp.fplane_client.get_fplane(filename, datestr='', actpos=True, full=False)[source]¶

Obtains fplane file from fplane server at MPE.

Args:: filename (str) : Filename that the fplane file should be saved to. datestr (str): Datestring of format YYYYMMDD (e.g. 20180611).

vdrp.fplane_client.main()[source]¶

vdrp.fplane_client.retrieve_fplane(night, fplane_txt, wdir)[source]¶

Saves the fplane file to the target directory and names it fplane.txt.

Args: fplane_txt (str) : Either a specific fplane file is specified here, ‘DATABASE’ is passed,

or a file pattern is provided e.g. fplane_YYYYMMDD.txt. In case of the latter a substring of format YYYYMMDD is expected. The routine will then search for an fplane file of the current date or pick the next older one. E.g. if shot 2080611v017 is to be analysed and fplane files fplane_2080610.txt and fplane_2080615.txt exist, then fplane_2080610.txt will be picked. In the case of DATABASE the fplane file is retrieved from https://luna.mpe.mpg.de/fplane/.

`jobsplitter` - Jobsplitter - slurm setup tool¶

vdrp.jobsplitter.create_job_file(fname, commands, n_nodes, jobs_per_file, jobs_per_node, args)[source]¶

vdrp.jobsplitter.getDefaults()[source]¶: Get the defaults for the argument parser. Separating this out from the get_arguments routine allows us to use different defaults when using the jobsplitter from within a differen script.

vdrp.jobsplitter.get_arguments(parser)[source]¶

Add command line arguments for the jobsplitter, this function can be called from another tool, adding job splitter support.

Parameters:	parser : argparse.ArgumentParser

vdrp.jobsplitter.main(args)[source]¶

vdrp.jobsplitter.n_needed(njobs, limit)[source]¶

vdrp.jobsplitter.parse_args(argv)[source]¶

Command line parser

Parameters:	argv : list of strings list to parsed
Returns:	namespace: Parsed arguments

vdrp.jobsplitter.run()[source]¶

`mphelpers` - MPHelpers - Parallel processing routines¶

class vdrp.mphelpers.MPPool(jobnum, num_proc)[source]¶

Pool of threads consuming tasks from a queue

add_task(func, *args, **kargs)[source]¶: Add a task to the queue

wait_completion()[source]¶: Wait for completion of all the tasks in the queue

class vdrp.mphelpers.MPWorker(name, tasks)[source]¶

Bases: multiprocessing.process.Process

Thread executing tasks from a given tasks queue

run()[source]¶: Method to be run in sub-process; can be overridden in sub-class

class vdrp.mphelpers.ThreadPool(num_threads)[source]¶

Pool of threads consuming tasks from a queue

add_task(func, *args, **kargs)[source]¶: Add a task to the queue

wait_completion()[source]¶: Wait for completion of all the tasks in the queue

class vdrp.mphelpers.ThreadShutDownException[source]¶

class vdrp.mphelpers.ThreadWorker(name, tasks)[source]¶

Bases: threading.Thread

Thread executing tasks from a given tasks queue

run()[source]¶

Method representing the thread’s activity.

You may override this method in a subclass. The standard run() method invokes the callable object passed to the object’s constructor as the target argument, if any, with sequential and keyword arguments taken from the args and kwargs arguments, respectively.

vdrp.mphelpers.mp_run(func, args, rargv, parser)[source]¶

vdrp.mphelpers.shutdownThread()[source]¶

`mplog` - Mplog - Parallel process logging¶

class vdrp.mplog.MultiProcessingHandler(name, sub_handler=None)[source]¶

Bases: logging.Handler

_format_record(record)[source]¶

_receive()[source]¶

close()[source]¶

Tidy up any resources used by the handler.

This version removes the handler from an internal map of handlers, _handlers, which is used for handler lookup by name. Subclasses should ensure that this gets called from overridden close() methods.

emit(record)[source]¶

Do whatever it takes to actually log the specified logging record.

This version is intended to be implemented by subclasses and so raises a NotImplementedError.

send(s)[source]¶

setFormatter(fmt)[source]¶: Set the formatter for this handler.

vdrp.mplog.install_mp_handler(logger=None)[source]¶: Wraps the handlers in the given Logger with an MultiProcessingHandler. :param logger: whose handlers to wrap. By default, the root logger.

vdrp.mplog.setup_mp_logging(logfile, loglevel)[source]¶: Setup the logging and prepare it for use with multiprocessing

`photometry` - Throughput measurement routines¶

Photometry routine

Contains python translation of Karl Gebhardt

class vdrp.photometry.ShuffleStar(starid='', shotid='', shuffleid=-1, ra=-1.0, dec=-1.0, u=99.0, g=99.0, r=99.0, i=99.0, z=99.0, catalog='None')[source]¶

Class to store the information about one star from the shuffle output

Attributes:

starid : int: ID for the star.
shotid : int: Shot number of the star observation
shuffleid : int: ID of the star in shuffle catalog
ra : float: Right ascension
dec : float: Declination
catalog : str: Catalog name used to find these.
u : float: U-Band magnitude from the shuffle catalog
g : float: G-Band magnitude from the shuffle catalog
r : float: R-Band magnitude from the shuffle catalog
i : float: I-Band magnitude from the shuffle catalog
z : float: Z-Band magnitude from the shuffle catalog

vdrp.photometry.extract_star_single_shot(ra, dec, starid, args, dithall=None)[source]¶

Equivalent of the rsp1a2b script.

Run the stellar extraction code for a given ra / dec position.

Parameters:	ra : float Right Ascension of the star. dec : float Declination of the star. starid : int ID to give to the star / position args : struct The arguments structure

vdrp.photometry.getDefaults()[source]¶

vdrp.photometry.get_arguments(parser)[source]¶

Add command line arguments for the photometry routines, this function can be called from another tool.

Parameters:	parser : argparse.ArgumentParser

vdrp.photometry.get_g_band_throughput(args)[source]¶

Measure the throughput in the SDSS g-Band Equivalent of the rgettp0 script

Parameters:	args : struct The arguments structure

vdrp.photometry.get_sedfits(starobs, args, wdir, nomove=False)[source]¶

Run quick_fit to generate the SED fits, if available.

If quick_fit cannot be imported, fall back to copying the files from sed_fit_dir

vdrp.photometry.get_shuffle_stars(nightshot, args, wdir)[source]¶

Rerun shuffle and find the all stars for a given night / shot.

Parameters:	nightshot : str Night + shot name to work on. args : argparse.Namespace The script parameter namespace

vdrp.photometry.main(jobnum, args)[source]¶: Main function.

vdrp.photometry.mk_sed_throughput_curve(args)[source]¶

Equivalent of the rgett0b script.

Parameters:	args : struct The arguments structure

vdrp.photometry.parseArgs(argv)[source]¶

Parses configuration file and command line arguments. Command line arguments overwrite configuration file settiongs which in turn overwrite default values.

Args:: args (argparse.Namespace): Return the populated namespace.

vdrp.photometry.run()[source]¶

vdrp.photometry.run_biwt(data, outfile, wdir)[source]¶

Calculate biweight of the supplied data.

Parameters:	data : list List of the data to be run through biwt.
Returns:	n, biwt, error

vdrp.photometry.run_combsed(sedlist, sigmacut, rmscut, outfile, wdir, plotfile=None)[source]¶

Parameters:	sedlist : list List of filenames of SED fits sigmacut : float Cut value for sigma rmscut : float Cut value for rms outfile : str Output filename plotfile : str (optional) Optional plot output filename
Returns:	n, biwt, error

vdrp.photometry.run_getsdss(filename, sdss_file, wdir)[source]¶

Run getsdss on filename. Equivalent to rsdss file.

Parameters:	filename : str Filename with spectral data sdss_file : str Full path and filename to the sdss g-band filter curve.
Returns:	The flux in the g-Band.

vdrp.photometry.run_shuffle_photometry(args, wdir)[source]¶

Equivalent of the rsetstar script. Find all shuffle stars observed for the night / shot given on the command line, and the loop over all stars ra / dec.

Parameters:	args : struct The arguments structure

`programs` - FORTRAN program interfaces¶

vdrp.programs.call_fit2d(ra, dec, outname, wdir)[source]¶

Call fit2d. Calculate the 2D spatial fit based on fwhm, fiber locations, and ADC. This convolves the PSF over each fiber, for a given input position. It fits the ampltiude, minimizing to a chi^2.

Requires input files generated by run_fit2d

Parameters:	ra : float Right Ascension of the star. dec : float Declination of the star. outname : str Output filename. wdir : str Name of the work directory

vdrp.programs.call_fitem(wl, wdir)[source]¶

Call fitem requires input files created by run_fitem

The line fitter. It fits a gauss-hermite. input is fitghsp.in.

Parameters:	wl : float Wavelength

vdrp.programs.call_fitonevp(wave, outname, wdir)[source]¶

Call fitonevp

Requires fitghsp.in created by apply_factor_spline

Parameters:	wave : float Wavelength outname : str Output filename wdir : str Name of the work directory

vdrp.programs.call_getnormexp(nightshot, wdir)[source]¶

Call getnormexp. Get fwhm and relative normalizations for the frames.

Parameters:	name : str Observation name

vdrp.programs.call_imextsp(filename, ifuslot, wl, wlw, tpavg, norm, outfile, wdir)[source]¶

Equivalent of the rextsp script, a wrapper around the imextsp fortran routine.

Extracts the spectrum from the multi fits files and writes the tmp*dat. This also calculates the appropriate photon errors, using counting and sky residual errors. This applies the throughput and fiber to fiber.

Parameters:

filename : str: The filename to process
ifuslot : str: The ifuslot name
wl : float: The central extraction wavelength
wlw : float: The width of the extraction window around wl
tpavg : float: Throughput average for the spectrum
norm : str: File with fiber to fiber normaliztion for the spectrum
outfile : str: Name of the output filename
wdir : str: Name of the work directory

vdrp.programs.call_mkimage(ra, dec, starobs, wdir)[source]¶

Call mkimage, equivalent of rmkim

Reads the out2d file and creates three images of the emission line data, best fit model and residuals, called im[123].fits.

Parameters:	ra : float Right Ascension of the star. dec : float Declination of the star. starobs : list List of StarObservation objects for the star

vdrp.programs.call_mkimage3d(wdir)[source]¶: Run the mkimage3d command, creating an output file called image3d.fits

vdrp.programs.call_sumspec(starname, wdir)[source]¶

Call sumpspec. Sums a set of spectra, and then bins to 100AA bins. Used for SED fitting.

Parameters:	starname : str Star name used to create the outputn filename (adds specf.dat)

vdrp.programs.call_sumsplines(nspec, wdir)[source]¶

Call sumsplines, calculate a straight sum of the spectra in a list, including errors. Expects the spectra to be called tmp101 to tmp100+nspec.

Creates a file called splines.out

Parameters:	nspec : int Number of spectra to read. wdir : str Name of the work directory

vdrp.programs.run_fitradecsp(ra, dec, step, nstep, w_center, w_range, ifit1, starobs, specfiles, wdir)[source]¶

Setup and call fitradecsp. This creates a file called spec.out

Parameters:	starobs : list List of StarObservation structures one for each fiber specfiles : list List of filename of the different spec files

`setup_fluxlim` - Fluxlimit setup routines¶

Fluxlimit routine

Contains python translation of Karl Gebhardt

exception vdrp.setup_fluxlim.NoShotsException[source]¶: Bases: exceptions.Exception

vdrp.setup_fluxlim.getDefaults()[source]¶

vdrp.setup_fluxlim.parseArgs(argv)[source]¶

Parses configuration file and command line arguments. Command line arguments overwrite configuration file settiongs which in turn overwrite default values.

Args:: args (argparse.Namespace): Return the populated namespace.

vdrp.setup_fluxlim.setup_fluxlim(args, rargs)[source]¶

This is equivalent to the rflim0 and rsetfl scripts.

Determine the input values for the flux limit calculation, create the input file, create the slurm file using the jobsplitter and launch it using sbatch

vdrp.setup_fluxlim.setup_fluxlim_entrypoint()[source]¶: Entrypoint to run the flux limit calculation for one night / shot combination

`star_extraction` - Stellar Extraction routines¶

Star Extraction routine. Equivalent of rsp1 script.

Extract star at a given RA/DEC using all shots overlapping with these coordinates.

Contains python translation of Karl Gebhardt

vdrp.star_extraction.apply_factor_spline(factor, wdir)[source]¶

Equivalent of the rawksp[12] scripts

Apply the factor to the splines.out file. The factor is the number of individual shots the star was observed in.

Parameters:	factor : int The factor to apply. wdir : str Name of the work directory

vdrp.star_extraction.average_spectra(specfiles, starobs, wl, wlrange, wdir)[source]¶

Average all observed spectra and fill in the corresponding entries in the StarObservation class.

This corresponds to the ravgsp0 script

Parameters:	specfiles : list List of spectrum filenames. starobs : list List with StarObservation objects. wl : float Central wavelength for the averaging. wlrange : float Half width of the wavelength range for averaging.

vdrp.star_extraction.average_spectrum(spec, wlmin, wlmax)[source]¶

Corresponds to ravgsp0 script. Calculate the average of the spectrum in the range [wlmin, wlmax]

Parameters:	spec : Spectrum Spectrum class object wlmin : float Minimum wavelength of range to average. wlmax : float Maximum wavelength of range to average.
Returns:	*average, normaliztaion and uncertainty, equivalent to the spavg.dat files.**

vdrp.star_extraction.copy_stardata(starname, starid, wdir)[source]¶

Copies the result files from workdir results_dir as done by rspstar.

Parameters:	starname : str Star name to copy over. starid : int Star ID to use for the final filename. results_dir : str Final directory for results.

vdrp.star_extraction.extract_star(args)[source]¶

Equivalent of the rsp1a2b script.

Run the stellar extraction code for a given ra / dec position.

Parameters:	args : struct The arguments structure

vdrp.star_extraction.getDefaults()[source]¶

vdrp.star_extraction.get_arguments(parser)[source]¶

Add command line arguments for the photometry routines, this function can be called from another tool.

Parameters:	parser : argparse.ArgumentParser

vdrp.star_extraction.main(jobnum, args)[source]¶: Main function.

vdrp.star_extraction.parseArgs(argv)[source]¶

Parses configuration file and command line arguments. Command line arguments overwrite configuration file settiongs which in turn overwrite default values.

Args:: args (argparse.Namespace): Return the populated namespace.

vdrp.star_extraction.run_fit2d(ra, dec, starobs, seeing, outname, wdir)[source]¶

Prepare input files for running fit2d, and run it.

Parameters:	ra : float Right Ascension of the star. dec : float Declination of the star. starobs : list List with StarObservation objects. seeing : float Assumed seeing for the observation. outname : str Output filename.

vdrp.star_extraction.run_fitem(wl, outname, wdir)[source]¶

Prepare input file for fitem, and run it.

Parameters:	wl : float Wavelength outname : str Base output filename.

vdrp.star_extraction.run_sumlineserr(specfiles, wdir)[source]¶

Prepare input and run sumlineserr. It sums a set of spectra, and then bins to 100AA bins. Used for SED fitting.

Parameters:	specfiles : list List of spectrum filenames.

vdrp.star_extraction.star_extract_entrypoint()[source]¶

`utils` - VDRP utility routines¶

Utility functions for virus reductions

vdrp.utils.bindir()[source]¶

vdrp.utils.biweight_bin(xv, x, y)[source]¶: Compute the biweight location with a moving window of size “order”

vdrp.utils.biweight_filter(a, order, ignore_central=3, c=6.0, M=None, func=None)[source]¶

vdrp.utils.biweight_filter2d(a, Order, Ignore_central=(3, 3), c=6.0, M=None, func=None)[source]¶: Compute the biweight location with a moving window of size “order”

vdrp.utils.biweight_location(a, c=6.0, M=None, axis=None, eps=1e-08)[source]¶

Compute the biweight location for an array.

Returns the biweight location for the array elements. The biweight is a robust statistic for determining the central location of a distribution.

The biweight location is given by the following equation

where M is the sample mean or if run iterative the initial guess, and u_i is given by

where MAD is the median absolute deviation.

For more details, see Beers, Flynn, and Gebhardt, 1990, AJ, 100, 32B

Parameters:

a : array-like: Input array or object that can be converted to an array.
c : float, optional: Tuning constant for the biweight estimator. Default value is 6.0.
M : float, optional: Initial guess for the biweight location.
axis : tuple, optional: tuple of the integer axis values ot calculate over. Should be sorted.
Returns
——-
biweight_location : float: Returns the biweight location for the array elements.

`vdrp_helpers` - VDRP helper routines¶

class vdrp.vdrp_helpers.VdrpInfo(*args, **kwargs)[source]¶

Bases: collections.OrderedDict

classmethod read(dir, filename='vdrp_info.pickle')[source]¶

save(dir, filename='vdrp_info.pickle')[source]¶

vdrp.vdrp_helpers.read_data(filename)[source]¶

vdrp.vdrp_helpers.run_command(cmd, input=None, wdir=None)[source]¶

Run and fortran command sending the optional input string on stdin.

Parameters:	cmd : str The command to be run, must be full path to executable input : str, optional Input to be sent to the command through stdin.

vdrp.vdrp_helpers.save_data(d, filename)[source]¶

`vdrprunner` - VDRP batch runner¶

About¶

Authors¶

The HETDEX collaboration:

Jan Snigula <snigula@mpe.mpg.de>
Maximilian Fabricius <mxhf@mpe.mpg.de>
Daniel Farrow <dfarrow@mpe.mpg.de>

Parameters:	a : array-like Input array or object that can be converted to an array. c : float Tuning constant for the biweight estimator. Default value is 9.0. M : float, optional Initial guess for the biweight location. axis : tuple, optional tuple of the integer axis values ot calculate over. Should be sorted.
Returns:	biweight_midvariance : float Returns the biweight midvariance for the array elements.

Welcome to VDRP¶

User documentation¶

Astrometry routines¶

Throughput routines¶

Fluxlimit routines¶

Setting up and running the fluxlimit calculations¶

Spectral line extraction routines¶

Developer documentation¶

Contribute to VDRP¶

How To¶

Coding style¶

Testing¶

Documentation¶

Code documentation¶

astrometry - Astrometry routines¶

calc_fluxlim - Fluxlimit calculation routines¶

cltools - Commandine tools¶

cofes_vis - Visualization routines¶

containers - Container structures¶

daophot - Daophot helper routines¶

extraction - Spectrum extraction routines¶

file_tools - File access routines¶

fit_radec - RA/DEC fitting routines¶

fplane_client - FPlane retrieval routines¶

jobsplitter - Jobsplitter - slurm setup tool¶

mphelpers - MPHelpers - Parallel processing routines¶

mplog - Mplog - Parallel process logging¶

photometry - Throughput measurement routines¶

programs - FORTRAN program interfaces¶

setup_fluxlim - Fluxlimit setup routines¶

star_extraction - Stellar Extraction routines¶

utils - VDRP utility routines¶

vdrp_helpers - VDRP helper routines¶

vdrprunner - VDRP batch runner¶

About¶

Authors¶

Changelog¶

TODO¶

Links¶

`astrometry` - Astrometry routines¶

`calc_fluxlim` - Fluxlimit calculation routines¶

`cltools` - Commandine tools¶

`cofes_vis` - Visualization routines¶

`containers` - Container structures¶

`daophot` - Daophot helper routines¶

`extraction` - Spectrum extraction routines¶

`file_tools` - File access routines¶

`fit_radec` - RA/DEC fitting routines¶

`fplane_client` - FPlane retrieval routines¶

`jobsplitter` - Jobsplitter - slurm setup tool¶

`mphelpers` - MPHelpers - Parallel processing routines¶

`mplog` - Mplog - Parallel process logging¶

`photometry` - Throughput measurement routines¶

`programs` - FORTRAN program interfaces¶

`setup_fluxlim` - Fluxlimit setup routines¶

`star_extraction` - Stellar Extraction routines¶

`utils` - VDRP utility routines¶

`vdrp_helpers` - VDRP helper routines¶

`vdrprunner` - VDRP batch runner¶