ALMA Tutorials draft: Difference between revisions

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This page contains tutorials to guide ALMA users through some common types of data imaging and analysis using CASA with example ALMA datasets. Here are some links to get started:
This page contains tutorials to guide ALMA users through some common types of data imaging and analysis using CASA with example ALMA datasets. Here are some links to get started:
* [[How To Use A CASAGuide]]
* [[Extracting scripts from these tutorials]]


{| class="wikitable"
{| class="wikitable"


! [[File:Alma_logo.jpg|100px]]
! [[File:Alma_logo.jpg|75px|link=https://almascience.org/]]
|
* [https://almascience.org/ ALMA Science homepage]
 
! [[File:CARTA_logo_text.png|100px|link=https://cartavis.org/]]
|
|
* [http://almascience.org/ ALMA Science homepage]
* [https://cartavis.org/ CARTA website]
* [https://casadocs.readthedocs.io/en/v6.6.1/notebooks/carta.html CARTA section of the CASA docs]
|-
|-


! [[File:Casa_logo_full-200wide.png|100px]]
! [[File:Casa_logo_full-200wide.png|75px|link=https://casa.nrao.edu]]
|
|
* [http://casa.nrao.edu CASA homepage]: includes download and installation information
* [https://casa.nrao.edu CASA homepage]: includes download and installation information
* {{casadocs_6.6.1}}
* {{casadocs_6.6.1}}
* [[CASA Tips]]
* [[CASA Tips]]
* [[Getting Started in CASA]]
* [[Getting Started in CASA]]
* [[How To Use A CASAGuide]]
* [[Extracting scripts from these tutorials]]
  To cite CASA, please use:<br>[https://ui.adsabs.harvard.edu/abs/2022PASP..134k4501C/abstract \bibitem<nowiki>[CASA Team et al.(2022)]</nowiki>{2022PASP..134k4501C} CASA Team, Bean, B., Bhatnagar, S., et al.\ 2022, PASP, 134, 114501. doi:10.1088/1538-3873/ac9642]
  To cite CASA, please use:<br>[https://ui.adsabs.harvard.edu/abs/2022PASP..134k4501C/abstract \bibitem<nowiki>[CASA Team et al.(2022)]</nowiki>{2022PASP..134k4501C} CASA Team, Bean, B., Bhatnagar, S., et al.\ 2022, PASP, 134, 114501. doi:10.1088/1538-3873/ac9642]
|-


! [[File:pipeline_logo.png|100px]]
! [[File:pipeline_logo.png|75px|link=https://almascience.nrao.edu/processing/science-pipeline/]]
|
|
* [https://almascience.nrao.edu/processing/science-pipeline ALMA Pipeline webpage]
* [https://almascience.nrao.edu/processing/science-pipeline ALMA Pipeline webpage]
* [[ALMA Pipeline Known Issues]]
* [[ALMA Pipeline Known Issues]]
  To cite the ALMA pipeline, please use:<br>[https://ui.adsabs.harvard.edu/abs/2023PASP..135g4501H/abstract \bibitem<nowiki>[Hunter et al.(2023)]</nowiki>{2023PASP..135g4501H} Hunter, T.~R., Indebetouw, R., Brogan, C.~L., et al.\ 2023, PASP, 135, 074501. doi:10.1088/1538-3873/ace216]
  To cite the ALMA pipeline, please use:<br>[https://ui.adsabs.harvard.edu/abs/2023PASP..135g4501H/abstract \bibitem<nowiki>[Hunter et al.(2023)]</nowiki>{2023PASP..135g4501H} Hunter, T.~R., Indebetouw, R., Brogan, C.~L., et al.\ 2023, PASP, 135, 074501. doi:10.1088/1538-3873/ace216]
|-
! [[File:CARTA_logo_text.png|100px]]
|
* [https://cartavis.org/ CARTA website]
* [https://casadocs.readthedocs.io/en/v6.6.1/notebooks/carta.html CARTA section of the CASA docs]
|-


|}
|}
<!--
<!--
;ALMA
;ALMA
* [http://almascience.org/ ALMA Science homepage]
* [https://almascience.org/ ALMA Science homepage]


;CASA
;CASA
* [http://casa.nrao.edu CASA homepage]: includes download and installation information
* [https://casa.nrao.edu CASA homepage]: includes download and installation information
* {{casadocs_6.6.1}}
* {{casadocs_6.6.1}}
* [[CASA Tips]]
* [[CASA Tips]]
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ALMA data are delivered to users with calibrations applied and they are ready for imaging. The following "First Look" tutorials provide short examples of common next steps a user may take with their calibrated data. These guides use an example ALMA observation of TW Hydra.
ALMA data are delivered to users with calibrations applied and they are ready for imaging. The following "First Look" tutorials provide short examples of common next steps a user may take with their calibrated data. These guides use an example ALMA observation of TW Hydra.


* [[First Look at Imaging]] (continuum)
{| class="wikitable"
* [[First Look at Self Calibration]]
 
* [[First Look at Line Imaging]]
! [[First Look at Imaging]] (continuum)
* [[First Look at Image Analysis]]
|
This is a really long sentence to force the table to fill the full page width otherwise it looks bad.
This is a really long sentence to force the table to fill the full page width otherwise it looks bad.
| style="text-align:center;" rowspan=4 | [[File:TWHya.png|100px]]
|-
! [[First Look at Self Calibration]]
| description
|-
! [[First Look at Line Imaging]]
| description
|-
! [[First Look at Image Analysis]]
| description
|-
 
|}


Older versions of these guides are archived here: [[ALMA First Look]]
Older versions of these guides are archived here: [[ALMA First Look]]
Line 79: Line 90:
== Advanced Imaging ==
== Advanced Imaging ==


* [[ALMA Imaging Pipeline Reprocessing | Modified Pipeline Imaging]]
{| class="wikitable"
* [[Guide to the NA Imaging Template | Manual Imaging Templates]]
 
* [[Automasking Guide | Automasking]]
! [[ALMA Imaging Pipeline Reprocessing | Modified Pipeline Imaging]]
The following are the portions of the End to End guides that cover special imaging topics. The full End to End guides with manual calibration are listed further down this page:
|
* [[M100_Band3_Combine | Array Combination: M100]]
This is a really long sentence to force the table to fill the full page width otherwise it looks bad.
* [[Sunspot_Band6_Feathering | Array Combination: Sunspot]]
This is a really long sentence to force the table to fill the full page width otherwise it looks bad.
* [[AntennaeBand7_Imaging | Mosaics: Antennae Galaxy Merger]]
|-
* [[IRAS16293_Band9_-_Imaging | Mosaics: IRAS16293]]
 
* [[3C286_Band6Pol_Imaging | Polarization: 3C286]]
! [[Guide to the NA Imaging Template | NA Manual Imaging Templates]]
| This guide describes the template scripts used to manually image data for quality assurance by the North America ALMA Science Center (NAASC).
|-
 
! [[Automasking Guide | Automasking]]
| This guide describes how to automatically mask clean regions during non-interactive cleaning.
|-


== Special Topics ==
|}


* [[ALMA Renormalization Correction | Renormalization]]  
'''Jump to special imaging topics from the End to End guides:'''
* [[DataWeightsAndCombination | Data Weights]]  
* [[AntennaeBand7_Imaging | AntennaeBand7 > Mosaic Imaging]]
:- relevant for data from Cycles 0, 1, and 2
* [[IRAS16293_Band9_-_Imaging | IRAS16293 Band9 > Mosaic Imaging]]
* [[Simulating Observations in CASA | Simulating Observations]]
* [[M100_Band3_Combine | M100 Band3 > Data Combination]]
:- Also see: [[Guide To Simulating ALMA Data]]
* [[3C286_Band6Pol_Imaging | 3C286 Band6 > Full Polarization Imaging]]
* [[Sunspot_Band6_Feathering | Sunspot Band6 > Data Combination]]


== End to End Guides (Manual Calibration) ==
== End to End Guides (Manual Calibration) ==
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{| class="wikitable"
{| class="wikitable"


! style="white-space:nowrap;" | Last updated for
! [[AntennaeBand7]]
|-
 
! rowspan=2 | CASA 6.6.1
! style="text-align:left;" | [[AntennaeBand7]]
! rowspan=2 | [[File:604px-Antennae_galaxies_xl.jpg|200px]]
|-
|
|
This is a really long sentence to force the table to fill the full page width otherwise it looks bad.
This is a really long sentence to force the table to fill the full page width otherwise it looks bad.
* Band 7 (345 GHz, 0.87 mm)
* Band 7 (345 GHz, 0.87 mm)
* CO 3-2 spectral line
* CO 3-2 spectral line
* Antennae Galaxy Merger (NGC 4038/4039)
* Antennae Galaxy Merger (NGC 4038/4039)
* North and South mosaics
* North and South mosaics
|-
| style="text-align:center;" | [[File:604px-Antennae_galaxies_xl.jpg|100px]]
|-
|-


! rowspan=2 | CASA 6.6.1
! [[IRAS16293Band9]]
! style="text-align:left;" | [[IRAS16293Band9]]
! rowspan=2 | [[File:IRAS16293_Band9.fixed.H13CN_8_7.mom0_6.5.4.png|250px]]
|-
|
|
* Band 9 (650 GHz, 0.46 mm)
Discusses full calibration of 12m interferometry Band 9 ('''high frequency''', 650 GHz, 0.46 mm) data of a protostellar cluster, including inspection of the data for flagging, and plotms commands to recreate plots typically included in a QA2 weblog.  Also discusses imaging of '''mosaic data''', including '''self-calibration''' and generation of '''image cubes''' and '''moment maps'''.
* Protostellar Cluster
| style="text-align:center;" | [[File:Intro.jpg|200px]]
* High frequency techniques
* Mosaic
|-
|-
|-


! rowspan=2 | CASA 6.6.1
! [[M100 Band3]]
! style="text-align:left;" | [[M100 Band3]]
! rowspan=2 | [[File:M100_NASA.jpg|200px]]
|-
|  
|  
* Band 3 (100 GHz, 3 mm)
Band 3 (100 GHz, 3 mm) on M100 demonstrates '''Single Dish''' (Total Power) data reduction and 12m, 7m, Total Power '''data combination''' procedures.
* Total Power (Single Dish) calibration and imaging
| style="text-align:center;" | [[File:M100_NASA.jpg|100px]]
* Combining 12m-array, 7m-array, and Total Power data
|-  
|-  
|-


! rowspan=2 | CASA 6.6.1
! [[3C286 Polarization]]
! style="text-align:left;" | [[3C286 Polarization]]
! rowspan=2 | [[File:VLA_3c286.png|250px]]
|-
|  
|  
* Band 6 (230 GHz, 1.3 mm)
Standard calibrations and '''polarization calibration''' (XX, XY, YX, YY) of 3c286 in Band 6 (230 GHz, 1.3 mm), a quasar frequently used as a flux calibrator source. '''Full Stokes imaging''' (IQUV), '''self-calibration''', and analysis of '''polarization intensity''' and '''polarization angle''' using both CARTA and numerical methods.
* Continuum polarization calibration and imaging
| style="text-align:center;" | [[File:VLA_3c286.png|200px]]
|-
|-
|-


! rowspan=2 | CASA 6.6.1
! [[Sunspot Band6]]  
! style="text-align:left;" | [[Sunspot Band6]]  
! rowspan=2 | [[File:Sunspot_singledish_regrid_CASA_6.5.4.png|250px]]
|-
|  
|  
* Band 6 (230 GHz, 1.3 mm)
* Band 6 (230 GHz, 1.3 mm)
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* Calibration and imaging
* Calibration and imaging
* Helper scripts
* Helper scripts
|-
| style="text-align:center;" | [[File:Sunspot_SolarMonitor.png|150px]]
|-


|}
|}


== Legacy Guides ==
== Special Topics ==


* [[Archived ALMA CASAguides]]
* [[ALMA Renormalization Correction | Renormalization]]: A fix for amplitude calibration issues caused by the ALMA normalization strategy for sources with strong line emission.
* [[TCLEAN and ALMA]]
* [[DataWeightsAndCombination | Data Weights]]: A guide to CASA data weights and how to ensure they are correct for data combination. Relevant for data from Cycles 0, 1, and 2.
 
* [[Guide To Simulating ALMA Data]]: An overview of simulation as it pertains to ALMA.
* [[Guide To Processing ALMA Data for Cycle 0 | Cycle 0]]
* [[Simulating Observations in CASA]]: All simulation guides (for ALMA, VLA, ngVLA, etc.)
:- Last checked in CASA 4.2
:- Helpful hints for downloading the data
:- Imaging, self-calibration, and image analysis
: Example data calibration scripts used for Cycle 0 data (CASA 3.4):
:* [[File:TDM.example.ms.scriptForCalibration.py]]: TDM (128 channels/spw)
:* [[File:FDM.example.ms.scriptForCalibration.py]]: FDM (3840 channels/spw)
:* [[Updating a script to work with CASA 4.2]]: Update 3.4 scripts to 4.2 or later.


== Resources ==
== Resources ==


* [[Archived ALMA CASAguides]]
* [https://almascience.nrao.edu/about-alma/proposing/sensitivity-calculator ALMA Sensitivity Calculator]
* [https://almascience.nrao.edu/about-alma/proposing/sensitivity-calculator ALMA Sensitivity Calculator]
* [[ADMIT Products and Usage]]: This guide discusses how to use the ALMA Data-Mining Toolkit (ADMIT) and customize it for your data.
* [[ADMIT Products and Usage]]: This guide discusses how to use the ALMA Data-Mining Toolkit (ADMIT) and customize it for your data.

Latest revision as of 23:39, 15 November 2024

Introduction

This page contains tutorials to guide ALMA users through some common types of data imaging and analysis using CASA with example ALMA datasets. Here are some links to get started: 

To cite CASA, please use:
\bibitem[CASA Team et al.(2022)]{2022PASP..134k4501C} CASA Team, Bean, B., Bhatnagar, S., et al.\ 2022, PASP, 134, 114501. doi:10.1088/1538-3873/ac9642
File:Pipeline logo.png 
To cite the ALMA pipeline, please use:
\bibitem[Hunter et al.(2023)]{2023PASP..135g4501H} Hunter, T.~R., Indebetouw, R., Brogan, C.~L., et al.\ 2023, PASP, 135, 074501. doi:10.1088/1538-3873/ace216

Basic Imaging and Analysis

ALMA data are delivered to users with calibrations applied and they are ready for imaging. The following "First Look" tutorials provide short examples of common next steps a user may take with their calibrated data. These guides use an example ALMA observation of TW Hydra.

First Look at Imaging (continuum)

This is a really long sentence to force the table to fill the full page width otherwise it looks bad. This is a really long sentence to force the table to fill the full page width otherwise it looks bad.

File:TWHya.png
First Look at Self Calibration description
First Look at Line Imaging description
First Look at Image Analysis description

Older versions of these guides are archived here: ALMA First Look

Advanced Imaging

Modified Pipeline Imaging

This is a really long sentence to force the table to fill the full page width otherwise it looks bad. This is a really long sentence to force the table to fill the full page width otherwise it looks bad.

NA Manual Imaging Templates This guide describes the template scripts used to manually image data for quality assurance by the North America ALMA Science Center (NAASC).
Automasking This guide describes how to automatically mask clean regions during non-interactive cleaning.

Jump to special imaging topics from the End to End guides:

End to End Guides (Manual Calibration)

These guides are useful tools for those who would like to learn the process of calibration and imaging in detail. They use publicly-available ALMA Science Verification data that illustrate several different ALMA capabilities. The links below lead to overview pages for each observation. The guides themselves are linked from the overview pages.

AntennaeBand7
  • Band 7 (345 GHz, 0.87 mm)
  • CO 3-2 spectral line
  • Antennae Galaxy Merger (NGC 4038/4039)
  • North and South mosaics
IRAS16293Band9

Discusses full calibration of 12m interferometry Band 9 (high frequency, 650 GHz, 0.46 mm) data of a protostellar cluster, including inspection of the data for flagging, and plotms commands to recreate plots typically included in a QA2 weblog. Also discusses imaging of mosaic data, including self-calibration and generation of image cubes and moment maps.

M100 Band3

Band 3 (100 GHz, 3 mm) on M100 demonstrates Single Dish (Total Power) data reduction and 12m, 7m, Total Power data combination procedures.

3C286 Polarization

Standard calibrations and polarization calibration (XX, XY, YX, YY) of 3c286 in Band 6 (230 GHz, 1.3 mm), a quasar frequently used as a flux calibrator source. Full Stokes imaging (IQUV), self-calibration, and analysis of polarization intensity and polarization angle using both CARTA and numerical methods.

Sunspot Band6
  • Band 6 (230 GHz, 1.3 mm)
  • Solar observing techniques
  • Calibration and imaging
  • Helper scripts

Special Topics

  • Renormalization: A fix for amplitude calibration issues caused by the ALMA normalization strategy for sources with strong line emission.
  • Data Weights: A guide to CASA data weights and how to ensure they are correct for data combination. Relevant for data from Cycles 0, 1, and 2.
  • Guide To Simulating ALMA Data: An overview of simulation as it pertains to ALMA.
  • Simulating Observations in CASA: All simulation guides (for ALMA, VLA, ngVLA, etc.)

Resources
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