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ALMA-IMF Hot Core Telecon - Sep 17, 2020

9/17/2020

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Previous Agenda & minutes

Connection:
Join Zoom Meeting
https://zoom.us/j/92756103231?pwd=MTM5TStyaVM1Nmx3ZUFrUE13RmtEQT09

Meeting ID: 927 5610 3231
Password: 9Jfuq5

Attendees: Nathalie, Ana, Hongli, Adam, Allison, Amy, Mélisse, Timea, Fred (late)
Not attending: 
Document drafted by Timea, but feel free to add notes

Agenda:
  1. Current issues and limitations with line/cube cleaning
  • Status of pipeline processing of cubes
  • are there any new cubes available?
    • > previous issues with frequencies, velocities etc. resolved
    • still on auto multi-thresh
    • some issues: baselines/slopes
  • what shall we look at first as QA? (which lines, which spw?)
    • check what data product exists
    • distribute the fields
  • Auto-correlation issue: FAUST home-made script to be run after the regular ALMA calibration pipeline to correct for this does exists, Adam is going to contact the PIs

  • Contribution to cubes QA 
Roberto on the H41a cubes, result of re-running them with new parameters in Morelia?
-> PSF issues
Mélisse did the QA for G337 cubes (full spw)
https://docs.google.com/document/d/1TA7FLMqnHI4CU6K-h0WOGnAyVRONuZAwqPjiFxSKUgE/edit?usp=sharing
  1. Status of on-going projects
  • Antoine: Melanie (PhD) on shocks
  • Manuel+Estrella
  • LAB: 
    • Melisse on G337:
  • Line identification towards G337-MM1 is done (only a few lines remain unidentified in both B3&B6)
  • Compare molecular content with other positions towards G337
  • QA for G337 showed that the  baseline is not so good in continuum-subtracted cubes delivered by the pipeline → tests with STATCONT and Jordan’s method to subtract continuum from non-contsub cubes
  • Nathalie W43-MM2


  • Anyone else?
A script to download a bunch of cubes at once using Globus in command line is in:
https://github.com/ALMA-IMF/private-work/tree/master/misc
(Note: to access to /private-work you need to be added by Adam)
  1. Status of data processing tools (ADMIT, IMAGER)
    • Status of the update of the linelist for ADMIT ? 
    • Adam: Linelist  on github + google doc
    https://github.com/ALMA-IMF/hotcores <- place to put line lists, code related to hot cores, etc.  This is private, so you must request access (give Adam your username)
  • spectral-cube tutorial -> Who would be interested?
    • Manuel, Fabrice, Melisse, Ana -> see with Adam


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ALMA-IMF Hot Core Telecon - Sep 3rd, 2020

9/3/2020

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Previous Agenda & minutes

Connection:
Join Zoom Meeting
https://zoom.us/j/92756103231?pwd=MTM5TStyaVM1Nmx3ZUFrUE13RmtEQT09

Meeting ID: 927 5610 3231
Password: 9Jfuq5

Attendees: Timea, Nathalie, Sylvain, Fred, Mélisse
Not attending: 
Document drafted by Timea, but feel free to add notes

Agenda:
  1. Current issues and limitations with line/cube cleaning
  • Status of pipeline processing of cubes
- Using the continuum image as a start model for cleaning non-contsub cubes is now implemented into the pipeline. Have cubes been made using this feature?
     - only W51 test case has been started and has not been finished.
    - this is new, so the cubes already done and available on globus are probably not yet done with this new feature

- There are some recent changes to the default autoMT params in the pipeline, mainly from Manuel’s suggestions. Some of these suggestions were implemented into the defaults but some were not. See discussion in slack #lines and in the repository: 
https://github.com/ALMA-IMF/reduction/commit/330b345c2913ed851a21a5900dd09d2102a1a281
These changes are expected to make more efficient the cleaning of cubes with extended emission, but at least for the recomb lines I am returning to the params that create tighter masks. That can be done on a per-source basis in imaging_parameters.py, e.g., 
line_imaging_parameters_custom = {
    "G008.67_B3_12M_robust0_contsub": {
       "minbeamfrac": 0.3,
       "dogrowprune": True,
       "threshold": "5mJy"
    },
    "G010.62_B3_12M_robust0_contsub": {
       "minbeamfrac": 0.3,
       "dogrowprune": True,
       "threshold": "8mJy"
    },
    "G012.80_B3_12M_robust0_contsub": {
       "minbeamfrac": 0.3,
       "dogrowprune": True,
       "threshold": "12mJy"
    },
  • Contribution to cubes QA 
Roberto did the QA of a few of the H41a cubes in Florida: 
https://docs.google.com/document/d/1-opjb6RU_4W-C_5gzld0UFn9_V-lYm_DN8fsgVIzl1U/edit?usp=sharing
and with that info is re-running them in Morelia 

  1. Status of on-going projects
  • Antoine: Melanie (PhD) on shocks
  • Manuel+Estrella: 
            status of the data? -> QA on W51
            status of the project?
  • LAB: 
    • Melisse on G337: 
      • line identification done (B3+B6) towards G337-MM1
      • B6 one spw1 missing? (Adam is going to look into it) 
    • Nathalie W43-MM2: 


  • Anyone else?
A script to download a bunch of cubes at once using Globus in command line is in:
https://github.com/ALMA-IMF/private-work/tree/master/misc
(Note: to access to /private-work you need to be added by Adam)
  1. Status of data processing tools (ADMIT, IMAGER)
    • Status of the update of the linelist for ADMIT ? 
    • Adam: Linelist  on github + google doc
    https://github.com/ALMA-IMF/hotcores <- place to put line lists, code related to hot cores, etc.  This is private, so you must request access (give Adam your username)
  • spectral-cube tutorial -> Who would be interested?
    • Manuel, Fabrice, Melisse -> see with Adam


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ALMA-IMF Hot Core Telecon - July 23, 2020

7/23/2020

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Previous Agenda & minutes

Connection:
Join Zoom Meeting
https://zoom.us/j/92756103231?pwd=MTM5TStyaVM1Nmx3ZUFrUE13RmtEQT09

Meeting ID: 927 5610 3231
Password: 9Jfuq5

Attendees: Nathalie, Adam, Timea, Mélisse, Manuel, Lee, Ana, Roberto
Not attending: Gemma, Fred
Document drafted by Timea, but feel free to add notes

Agenda:
  1. Status of data cubes and the quality assessment

  • Cubes: what is the current status?
  • https://docs.google.com/spreadsheets/d/1tla-8sBogz1IW-GCXYC1neGA5Vz9o6fg_8HvMiuw5fc/edit?usp=sharing

Link for the QA sheet:
https://docs.google.com/spreadsheets/d/1tla-8sBogz1IW-GCXYC1neGA5Vz9o6fg_8HvMiuw5fc/edit#gid=0 

  • https://bio.rc.ufl.edu/secure/adamginsburg/ALMA-IMF/cube_quicklooks

  1. Status of data processing tools (ADMIT, IMAGER)
    • Progress with  ADMIT ? 

    https://github.com/ALMA-IMF/hotcores <- place to put line lists, code related to hot cores, etc.  This is private, so you must request access (give Adam your username)


  1. Status of projects
  • Any updates? (Manuel, Melisse, Nathalie, Gemma, Antoine?)
    • Melisse: maps of 13CH3OH, C2H5CN
    • Sgr B2 (Orion KL/BN): direct comparison of the spectra, about 50% of the lines remains unidentified in W43-MM1, brightest source
  • Status of post-processing for continuum over-subtraction 
Comment from roberto: is this continuum over-subtraction widespread? My hope would be that it’s not. If that is the case, I think uv-continuum subtracted cubes can be used for science in many cases. Some cases will still need to use non uv-continuum subtracted cubes, but as we have seen this is more difficult and we are still figuring out how to deal with them. 

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ALMA-IMF Hot Core Telecon - July 9, 2020

7/9/2020

0 Comments

 
Previous Agenda & minutes

Connection:
Join Zoom Meeting
https://zoom.us/j/92756103231?pwd=MTM5TStyaVM1Nmx3ZUFrUE13RmtEQT09

Meeting ID: 927 5610 3231
Password: 9Jfuq5

Attendees: Timea, Adam, Nathalie, Manuel, Ana Lee, Mélisse, Fred, Roberto, Vivien, Nichol
Not attending: Gemma, Amy, 
Document drafted by Timea, but feel free to add notes

Agenda:
  1. Status of on-going projects
  • Antoine: Melanie (PhD) starting in September to work on shock models. Predictions for species that are “easy” (?) to model. Shocked objects? Accretion shocks, filament formation, outflows. Currently: 140 species, the goal is to deliver a set of diagnostics based on the ALMA-IMF data to see to which extent they can distinguish between different shock models (fish out molecules sensitive to shocks).
  • Manuel+Estrella: baseline issues towards W51E resolved:
    • baseline issue produced by a shallow cleaning
    • CO spw: lots of absorption features
    • Reminder of a previous issue with Jordan’s field?
  • LAB: 
    • Melisse on G337: 
      • previous issues on B6 spw39 partly solved
      • cube seems to be intrinsically different than others?
    • Nathalie W43-MM2: 
      • imaging problem with the TM1-TM2 data
        • suggestions: concatenation, chanweight True/False?
        • Ana takes a look spw39
  • Anyone else?
 
  1. Separate email list for the Hot core WG
  2. Status of data processing tools (ADMIT, IMAGER)
    • update on the  ADMIT linelist ? 
    • Lee: work in progress
    • Adam: Linelist  on github + google doc
    https://github.com/ALMA-IMF/hotcores <- place to put line lists, code related to hot cores, etc.  This is private, so you must request access (give Adam your username)
  • spectral-cube tutorial too, perhaps
  1. Current issues and limitations with line/cube cleaning
  • Cubes: what is the current status?
    • https://bio.rc.ufl.edu/secure/adamginsburg/ALMA-IMF/cube_quicklooks
  • Cubes: how well these will be useable for the most line-rich sources? Any post-processing needed? What softwares/methods will be used for their exploitation?
  • Contribution to cubes QA

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ALMA-IMF Hot Core Telecon - June 25, 2020

6/25/2020

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Connection:
Topic: ALMA-IMF Hot core WG
Time: Jun 25, 2020 02:00 PM Paris

Join Zoom Meeting
https://zoom.us/j/92270792020?pwd=b1dndW96TkI4ZlNjcWIvbE5MS1lrQT09

Meeting ID: 922 7079 2020
Password: 9Jfuq5

Attendees: fab, Nichol, Gemma, Fred , Lee, Mélisse, Tapas,Estrella, Sylvain Bontemps, Adam, Nathalie, Antoine, manuel, Ana
Not attending: B. Lefloch, Roberto
Document drafted by Timea, but feel free to add notes

Agenda:
  1. Status of data processing tools (ADMIT, IMAGER)
    • Lee:  ADMIT tool: provide initial linelist to work in into the tool.
    • Contact Lee if needed to get started
    • Adam: Linelist  on github + google doc
    https://github.com/ALMA-IMF/hotcores <- place to put line lists, code related to hot cores, etc.  This is private, so you must request access (give Adam your username)
  • spectral-cube tutorial too, perhaps
  • Hot core WG page: https://github.com/ALMA-IMF/reduction/wiki/Hot-core-WG
        Question to Adam: is this site protected in some way? Can I continue to use it for this purpose or better to move to a Google doc? Adam: this version (https://github.com/ALMA-IMF/hotcores/blob/master/README.md ->  https://github.com/ALMA-IMF/hotcores/blob/master/telecon_notes.md ) is private
  1. Status of on-going projects
  • Manuel+Estrella: current status
    • Spectra towards W51E seem to have baseline issues towards some positions (in cubes where the baseline is subtracted) -> this seems to vary from different versions
    • How to improve the continuum subtraction?
      • discussion on whether to clean cubes with or without the continuum: easier to do the clean with uvcontsub first
      • Manuel: imcontsub
    • Why is the average baseline curved? -> check the different data versions, reminder of a previous issue with Jordan’s field
  • LAB: 
    • Melisse (+Timea): presenting on G337: issue with non detection of some species?
    • Nathalie: complete the line-list for the following weeks

  1. Current issues and limitations with line/cube cleaning
  • Cubes: what is the current status?
    • https://bio.rc.ufl.edu/secure/adamginsburg/ALMA-IMF/cube_quicklooks
  • Cubes: how well these will be useable for the most line-rich sources? Any post-processing needed? What softwares/methods will be used for their exploitation?

  1. Current issues and limitations with line/cube cleaning
  • Roberto’s notes for issues with line/cube cleaning
https://docs.google.com/document/d/1nNmpEcD-axjVrHRowfcK3cImaZ0xrapBRcWnCg-HkVI/edit#heading=h.wc0r6ja4cl6f + the new issue with Tsys
  • Cubes: how well these will be useable for the most line-rich sources? Any post-processing needed? What softwares/methods will be used for their exploitation?


https://github.com/astroumd/admit => a tool to automatically analyse cubes 


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ALMA-IMF Hot Core Telecon - June 11, 2020

6/11/2020

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Connection:
https://ufl.zoom.us/j/99224867876?pwd=Y1ZWMWE0QW44aGN4bDI4QmdlZTl4Zz09

Attendees: Lee, Fred, Adam, Estrella, Nathalie, Gemma, Tapas, Roberto, Hongli, Nichol, Manuel , Mélisse


Agenda:
  • ADMIT:
    • http://github.com/astroumd/admit
    • admit.astro.umd.edu 
    • www.astro.umd.edu/~lgm/W43-MM2-cont 
    • Recording of presentation by Lee:
    • https://ufl.zoom.us/rec/share/78gpBbuv0zNIGNLcxVHCAJMCR6LBX6a823Idr_YPxBr-N68rIHxdiDyfbAvW1EqI?startTime=1591877388000 
  • GLOBUS
It needs a little bit of setup but seems to work. Some concerns about transfer speeds but might depend on endpoint connection. A few notes on installation and download script example available in #imaging slack channel. Other nodes from the DR team could download/upload data as needed. 
  • Next week: https://sites.google.com/cfa.harvard.edu/astrochemicalfrontiers/home
  • https://bio.rc.ufl.edu/secure/adamginsburg/ALMA-IMF/cube_quicklooks/maxspec_pngs/gallery.html
  • https://bio.rc.ufl.edu/secure/adamginsburg/ALMA-IMF/cube_quicklooks

Astrochemical Frontiers Meeting:
https://sites.google.com/cfa.harvard.edu/astrochemicalfrontiers/home

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ALMA-IMF Hot Core Telecon - June 4, 2020

6/4/2020

0 Comments

 
Connection:
https://us02web.zoom.us/j/81414670024?pwd=dnhMcWd5MEZHNTF6QjY5RUU0R0toUT09

Meeting ID: 814 1467 0024
Password: 9Jfuq5

Attendees: Antoine, Adam, Nathalie, Nichol, Melisse, Roberto, Gemma , Fab, Manuel, Patricio, Fred, Hongli, Bertrand, Vivien
Not attending: Fabrice Herpin, Ana López Sepulcre, Sylvain Bontemps
Document drafted by Timea, but feel free to add notes

Agenda:
  1. Main objectives and purpose of this WG.
  2. Planned projects, who is doing what
  • People working with cubes:
    • LAB: Melisse (+Timea), Nathalie
    • Manuel+Estrella: first look to general problem (beam, noise, number of channels, extended emission, convergence issues,...).

    Overlapping goals between Manuel & co and LAB team: the question is how to handle, focusing on one region? Clear desire to work with cubes. W51e2.

Adam: Linelist  on github + google doc
    https://github.com/ALMA-IMF/hotcores <- place to put line lists, code related to hot cores, etc.  This is private, so you must request access (give Adam your username)
Lee:  ADMIT tool: provide initial linelist to work in into the tool.
Tutorial from Lee for the next telecon?
spectral-cube tutorial too, perhaps

Lee: kinematics of the lines? perhaps the topic of other working groups? another common interest of several of us.

  • People interested in specific lines:
    • N2H+, CO, Halpha -> already discussed in the data reduction WG
    • Antoine: COMs or any other species to estimate N,n,T
    • Temperature measures: CH3OH, CH3CN (+isotopologue), CH3CCH lines should be added as priority?
      • CH3OH: Desmond Jeff (UF): Rotational Diagram modeling (use all transitions for a temperature measurement).
        • this is for full cubes, not to prioritize individual line imaging
      • H2CO may be a nice complementary probe to CH3OH
        • 3(0,3), 3(2,1) and 3(2,2) transitions
      • Cyanopolyynes should be targeted.
      • Gemma (chemistry) (and Patricio -> turbulence, cold sources): Deuterated species (N2D+, DCO+, DCN) + N2H+
      • Fred: SiO, 13CS, DCO+/DCN

  • interpretation of lines: 
    • LPENS: hopefully Melanie Armante will begin a PhD in October. aim = constraining the physical properties (N, T, n) and then try to apply shock models when/where applicable on a region tbd. Antoine will attend this telecon.

Roberto: image entire spw’s with auto-multithreshold seems to be possible.
From Molet et al. first line list to be compiled to identify lines for N,n,T modeling

https://ui.adsabs.harvard.edu/abs/2019A%26A...626A.132M/abstract 
  1. Current issues and limitations with line/cube cleaning
  • Roberto’s notes for issues with line/cube cleaning
https://docs.google.com/document/d/1nNmpEcD-axjVrHRowfcK3cImaZ0xrapBRcWnCg-HkVI/edit#heading=h.wc0r6ja4cl6f + the new issue with Tsys
  • Cubes: how well these will be useable for the most line-rich sources? Any post-processing needed? What softwares/methods will be used for their exploitation?


https://github.com/astroumd/admit => a tool to automatically analyse cubes 

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