allegrosoftwarecat:index
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Table of Contents
Allegro Software Catalogue
This is a catalogue of ALMA-related software that may be useful in your work. Some of these software is currently installed on our computing facilities at Allegro. If you would like any piece of software on this list to be prioritised for installation or you would like another piece of software to be installed please contact us at alma@strw.leidenunv.nl.
Software statuses at Allegro
For each piece of software in the catalogue, a descriptor of the current status of how recently the software has been reported as working at Allegro is given in the “Status” column.
- Working recently at allegro
- Working (>1 year ago) at allegro
- Worked previously at allegro
- Not working or untested at allegro
Software with a status further down this list is less likely to be working on the allegro machines. Please contact alma@strw.leidenunv.nl if you find that any software doesn't work and we will be happy to help you with it.
Installed software
This is a searchable and sortable table of installed software. Click on the arrows next to column titles to sort by that column. You can also use the search box to filter the content, for example try searching Working recently to see only working software that is listed as working recently. Software is also tagged with a number of properties that you can search by, for example try searching #visualisation to see software that can be used for visualisation.
The full list of tags is: #analysis, #archive, #bayesian, #C, #calibration, #CASA, #datacubes, #imaging, #GILDAS, #GPU_computing, #gridding, #modelling, #moments, #noise, #observing, #polarisation, #python, #simulation, #visibilities, #visualisation, #visualization, #VLBI
Filter:
| Software | Startup procedure | Status | Tags | Notes |
|---|---|---|---|---|
| 3D-Barolo | import pyBBarolo (type within a python environment) | Not working or untested | #analysis #datacubes #modelling #python | A paper on the tool can be found at https://ui.adsabs.harvard.edu/abs/2015MNRAS.451.3021D/abstract |
| ADMIT | source admit_start.csh import admit (type within CASA) | Not working or untested | #archive #CASA #python | |
| ALMA FITS Keywords filler | AKF() (type within CASA) | Working recently | #archive #CASA #python | The AKF command functions as a normal CASA function, typing inp(AKF) will show input options. A CASA memo on the tool can be accessed at http://www.alma.inaf.it/images/AKF_v1.2.pdf |
| ALMASim | Execute python main.py –option value –option1 value1 value2 in the ALMASim folder. Check the available options by running python main.py -h | Working recently | #CASA #python #simulation #datacubes | A paper on the tool can be found at https://academic.oup.com/mnras/article/518/3/3407/6825518 |
| ALMA Observing Tool | Working recently | #observing | ||
| ALminer | import alminer (type within a python environment) | Working (>1 year ago) | #archive #python #visualisation #visualization | There is an online tutorial notebook that showcases alminer's various functions with examples. There is an I-TRAIN training available for ALminer, with recording of the session available as a YouTube video. Full details can be found on I-TRAIN website under the heading I-TRAIN #8: Exploring the ALMA Science Archive with ALminer |
| APSYNSIM | Working recently | #python #simulation | An arXiv paper on the tool can be found at https://arxiv.org/abs/1706.00936 |
|
| ARTIST | Not working or untested | #CASA #modelling #python | An arXiv paper on the tool can be found at https://arxiv.org/abs/1102.4815 |
|
| assess_ms | casa –nologger -c run_assess_ms_public.py | Working recently | #CASA #analysis #python #visibilities | There is an I-TRAIN training available for assess_ms. Full details can be found on the I-TRAIN website under the heading I-TRAIN #25: The ALMA UV coverage assessment tool (assess_ms 3.0). Two arXiv papers on this tool can be found at https://arxiv.org/abs/2406.13199 and https://arxiv.org/abs/2012.08993 |
| ASTRO | Working recently | #GILDAS #observing | ||
| Better Moments | import bettermoments (type within a python environment) | Working recently | #datacubes #moments #python | Papers on this tool can be found at https://iopscience.iop.org/article/10.3847/2515-5172/aae265 and https://iopscience.iop.org/article/10.3847/2515-5172/ab2125 |
| BLOBCAT | Not working or untested | #python #sourcefinder | A paper on this tool can be found at https://academic.oup.com/mnras/article/425/2/979/1202064 |
|
| CARTA | Terminal command: carta | Working recently | #datacubes #python #visualisation #visualization | There is an I-TRAIN training available for LineStacker, with recording of the session available as a YouTube video. Full details can be found on the I-TRAIN website under the heading I-TRAIN #12: CARTA tutorial. A paper on this tool can be found at https://www.sciencedirect.com/science/article/pii/S2213133720300433. |
| CASA | Terminal command: casa | Working recently | #calibration #CASA #datacubes #moments #python #visibilities | Step-by-step tutorials on how to use CASA on ALMA data can be found in the CASA guides. The official CASA documentation can be found at https://casadocs.readthedocs.io/en/stable/ |
| CASAIRING | casairing()) (type within CASA) | Working recently | #CASA #python | The casairing command functions as a normal CASA function, typing inp(casairing) will show input options and help casairing will some some example of how to use the function. |
| CASSIS | Working recently | #modelling #simulation | Allegro has developed a simple cookbook that describes how to use CASSIS with a special emphasis on ALMA observations. It can be accessed from this link. | |
| CHECKRES | checkres()) (type within CASA) | Not working or untested | #CASA #python | The checkres command functions as a normal CASA function, typing inp(checkres) will show input options. |
| closures | closures()) (type within CASA) | Not working or untested | #CASA #python | The closures command functions as a normal CASA function, typing inp(closures) will show input options. |
| disksurf | from disksurf import observation (type within a python environment) | Not working or untested | #python #analysis | A paper on this tool can be found at https://joss.theoj.org/papers/10.21105/joss.03827 |
| DustPy | import dustpy (type within a python environment) | Not working or untested | #python #simulation | A paper on this tool can be found at https://iopscience.iop.org/article/10.3847/1538-4357/ac7d58 |
| eddy | import eddy (type within a python environment) | Not working or untested | #python #analysis #moments | A paper on this tool can be found at https://joss.theoj.org/papers/10.21105/joss.01220 |
| ESSENCE | import essence (type within a python environment) | Not working or untested | #python #analysis #noise | |
| FAKEOBS | fakeobs() (type within CASA) | Not working or untested | #CASA #python #simulation | The fakeobs command functions as a normal CASA function, typing inp(fakeobs) will show input options. |
| frank | import frank (type within a python environment) or in Terminal: python -m frank.fit [-uv uvtable_filename.npz] -p <parameter_filename.json> | Not working or untested | #bayesian #python #analysis | A paper on this tool can be found at https://academic.oup.com/mnras/article/495/3/3209/5838058?guestAccessKey=7f163a1f-c12f-4771-8e54-928636794a5b&login=true |
| galario | import galario (type within a python environment) | Working recently | #GPU_computing #modelling #python #visibilities | A paper on this tool can be found at https://academic.oup.com/mnras/article/476/4/4527/4867987. Galario works best on GPUs and is only compatible with python <3.8. |
| Glue | Terminal command: glue | Not working or untested | #python #visualisation #visualization | In addition to the documentation, there are a number of demo video on this tool. |
| GoFish | import gofish (type within a python environment) | Not working or untested | #python | A paper on this tool can be found at https://joss.theoj.org/papers/10.21105/joss.01632 |
| Interferopy | import interferopy (type within a python environment) | Working recently | #python #visualisation #visualization | |
| jackknify | import jackknify (type within a python environment) | Working recently | #python #noise | See documentation |
| jupyter-casa | Not working or untested | #CASA #python | The jupyter kernel is distributed as a Docker Image. | |
| LIME | Terminal command: lime [options…] <model file> | Not working or untested | #modelling | A paper on this tool can be found at https://www.aanda.org/articles/aa/full_html/2010/15/aa15333-10/aa15333-10.html |
| LineStacker | import LineStacker (type within a python environment) | Working (>1 year ago) | #analysis #python | There is an I-TRAIN training available for LineStacker, with a recording of the session available as a YouTube video. Full details can be found on the I-TRAIN website under the heading I-TRAIN #9: Stacking spectra in the image domain with LineStacker. |
| MAPPING | Working recently | #GILDAS #visibilities #visualisation #visualization | ||
| MADCUBA | Not working or untested | #analysis #datacubes #visualisation #visualization | A paper on this tool can be found at https://www.aanda.org/articles/aa/pdf/2019/11/aa36144-19.pdf | |
| MPoL | import mpol (type within a python environment) | Not working or untested | #analysis #python | A paper on this tool can be found at https://iopscience.iop.org/article/10.1088/1538-3873/acdf84 |
| Molecular EMissiOn IdentifieR (MEMOIR) | Terminal command: memoir | Not working or untested | #analysis #python | |
| Photutils | import photutils (type within a python environment) | Not working or untested | #analysis #python | |
| PolConvert | Not working or untested | #calibration #polarisation #python #VLBI | A paper on this tool can be found at https://www.aanda.org/articles/aa/full_html/2016/03/aa26063-15/aa26063-15.html |
|
| POLSIMULATE | polsimulate() (type within CASA) | Not working or untested | #CASA #polarisation #python #simulation | The polsimulate command functions as a normal CASA function, typing inp(polsimulate) will show input options. |
| Position-Velocity Slice Extractor | import pvextractor (type within a python environment) | Working recently | #datacubes #python #visualisation #visualization | Described in https://ui.adsabs.harvard.edu/abs/2015ASPC..499..363G/abstract |
| PySpecKit | import pyspeckit
(type within a python environment) | Working recently | #datacubes #python #analysis | A paper on this tool can be found at https://iopscience.iop.org/article/10.3847/1538-3881/ac695a |
| pyuvdata | import pyuvdata (type within a python environment) | Working recently | #python #visibilities | Papers on this tool can be found at https://joss.theoj.org/papers/10.21105/joss.07482 and https://joss.theoj.org/papers/10.21105/joss.00140 |
| Qubefit | import qubefit (type within a python environment) | Not working or untested | #analysis #bayesian #datacubes #modelling #moments | |
| RADEX | Terminal command: radex | Working recently | #modelling #simulation | This tool can be used via the terminal or through the online application. A paper on this tool can be found at https://www.aanda.org/component/article?access=bibcode&bibcode=&bibcode=2007A%2526A...468..627VFUL |
| Radio Beam | import radio_beam (type within a python environment) | Not working or untested | #python #astropy | Described in this document |
| RADMC3D | Terminal command: radmc3d | Working recently | #python #simulation | |
| RATRAN | Not working or untested | #python #simulation | An arXiv paper on this tool can be found at https://arxiv.org/abs/astro-ph/0008169 |
|
| RESOLVE | Working recently | #bayesian #analysis #imaging | Papers on this tool can be found at https://www.aanda.org/articles/aa/full_html/2016/02/aa23094-13/aa23094-13.html and https://arxiv.org/abs/1605.04317 |
|
| rPICARD | Terminal command: picard | Not working or untested | #calibration #CASA | A paper on this tool can be found at https://www.aanda.org/articles/aa/full_html/2019/06/aa35181-19/aa35181-19.html |
| SD2vis | SD2vis() (type within CASA) | Not working or untested | #CASA #python #simulation #visibilities | The SD2vis command functions as a normal CASA function, typing inp(SD2vis) will show input options. |
| SUBLIME-D1DC | Compile: ./compile_sublimed1d Execute: ./sublimed1dc <inputFile.par> | Not working or untested | #C #python #modelling #simulation | A paper on this tool can be found at https://iopscience.iop.org/article/10.3847/1538-4357/ac5893 This tool also has a python interface. |
| SOFIA | Terminal command: sofia <parameter_file> <parameter>=<value> | Not working or untested | #sourcefinder #momentmaps #datacubes #analysis | See the Documentation. Papers on this tool can be found at https://academic.oup.com/mnras/article/506/3/3962/6315349?login=true and https://academic.oup.com/mnras/article/448/2/1922/1058751 |
| Spectral Cube | import spectral_cube (type within a python environment) | Working recently | #datacubes #moments #python | |
| STACKER | import stacker (type within a python environment) | Not working or untested | #analysis #python #visibilities | |
| STATCONT | import statcont (type within CASA) | Not working or untested | #python | There is an I-TRAIN training available for STATCONT, with a recording of the session available as a YouTube video. Full details can be found on the I-TRAIN website under the heading I-TRAIN #11: Statistical continuum determination with STATCONT |
| THEMIS | Working recently | #basesian #analysis #imaging #VLBI | A paper on this tool can be found at https://iopscience.iop.org/article/10.3847/1538-4357/ab91a4 |
|
| uvmultifit | AKF command within casa | Working recently | #CASA #python #visibilities | There is an I-TRAIN training available for uvmultifit, with recording of the session available as a YouTube video. Full details can be found on I-TRAIN website under the heading I-TRAIN #3: UVMultiFit |
| UVPLOT | import uvplot (type within a python environment) | Working recently | #python #visibilities | Some functionality is only available if imported within CASA |
| WSClean | Terminal command: wsclean [-options] <obs1.ms> [<obs2.ms> ..] | Working recently | #imaging #gridding #deconvolution | Papers on this tool can be found at https://academic.oup.com/mnras/article/444/1/606/1010067, https://academic.oup.com/mnras/article/471/1/301/3873955?login=true and https://www.aanda.org/articles/aa/full_html/2018/08/aa32858-18/aa32858-18.html |
| WVR Scaling Module | Not working or untested | #calibration #CASA #python | Requires astropy version 1.3.3 and CASA < 5.0 (CASA 4.7.2 is the latest working version). A paper on this tool can be found at https://www.aanda.org/articles/aa/abs/2017/09/aa31197-17/aa31197-17.html |
|
| XCLASS | Working recently | #CASA #modelling #python #visibilities | To be used in CASA. A paper on this tool can be found at https://www.aanda.org/articles/aa/full_html/2017/02/aa27203-15/aa27203-15.html |
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