ALMA Tutorials draft: Difference between revisions

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== Introduction ==
== 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:
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"
'''ALMA'''
* [http://almascience.org/ ALMA Science homepage]


! [[File:Alma_logo.jpg|75px|link=https://almascience.org/]]
'''CASA'''
|
* [https://almascience.org/ ALMA Science homepage]


! [[File:CARTA_logo_text.png|100px|link=https://cartavis.org/]]
* [http://casa.nrao.edu CASA homepage]: includes download and installation information
|
* {{casadocs_6.5.4}}
* [https://cartavis.org/ CARTA website]
  * To cite CASA, please use: [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]
* [https://casadocs.readthedocs.io/en/v6.6.1/notebooks/carta.html CARTA section of the CASA docs]
  * To cite the ALMA pipeline, please use: [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:Casa_logo_full-200wide.png|75px|link=https://casa.nrao.edu]]
|
* [https://casa.nrao.edu CASA homepage]: includes download and installation information
* {{casadocs_6.6.1}}
* [[CASA Tips]]
* [[Getting Started in CASA]]
* [[Getting Started in CASA]]
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]
! <font size = 4> [https://almascience.nrao.edu/processing/science-pipeline/ Pipeline] <!--[[File:pipeline_logo.png|75px|link=https://almascience.nrao.edu/processing/science-pipeline/]]-->
|
* [https://almascience.nrao.edu/processing/science-pipeline ALMA Pipeline webpage]
* [[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]
|}
<!--
;ALMA
* [https://almascience.org/ ALMA Science homepage]
;CASA
* [https://casa.nrao.edu CASA homepage]: includes download and installation information
* {{casadocs_6.6.1}}
* [[CASA Tips]]
* [[CASA Tips]]
* [[Getting Started in CASA]]
* [[HTT2 | CASA Hints, Tips & Tricks]]
* [[How To Use A CASAGuide]]
* [[How To Use A CASAGuide]]
* [[Extracting scripts from these tutorials]]
* [[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]


;Pipeline
'''CARTA'''
* [https://almascience.nrao.edu/processing/science-pipeline ALMA Pipeline webpage]
* [[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]


;CARTA
Guides that have been updated to demonstrate the CARTA image viewer will include this statement near the top:
* [https://cartavis.org/ CARTA website]
{{CARTA_6.5.4}}
* [https://casadocs.readthedocs.io/en/v6.6.1/notebooks/carta.html CARTA section of the CASA docs]
-->


== Basic Imaging and Analysis ==
== First Look (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.
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.


{| class="wikitable"
* [[First_Look_at_Imaging | Continuum Imaging]]
 
* [[First_Look_at_Self_Calibration | Continuum Self-Calibration]]
! [[First Look at Imaging]] (continuum)
* [[First_Look_at_Line_Imaging | Spectral Line Imaging]]
|
* [[First_Look_at_Image_Analysis | Moments and 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 88: Line 43:
-->
-->


== Advanced Imaging ==
== Restoring and Imaging Calibrated Data ==
 
=== Considerations before Imaging ===
* [[ALMA Renormalization Correction]]
:- A fix for amplitude calibration issues caused by the ALMA normalization strategy for sources with strong line emission.
* [[DataWeightsAndCombination]]
:- A guide to CASA data weights and how to ensure they are correct for data combination.
 
=== Pipeline Imaging ===
 
* [[ALMA Imaging Pipeline Reprocessing]]
:- Create images using pipeline tasks.
 
=== Manual Imaging ===
 
* [[Guide to the NA Imaging Template]]
:- Create images with a manual template.
* [[TCLEAN and ALMA]]
:- Examples of using {{tclean_6.5.4}}, with emphasis on changes from the older "clean" task.
 
=== Automasking ===
 
* [[Automasking Guide]]
:- Explanation of parameters used in {{tclean_6.5.4}} to automatically mask clean regions during non-interactive cleaning.
 
== Manual Calibration and Imaging ==
 
These guides are useful tools for those who would like to learn the process of calibration and imaging in detail. They use publicly-available [https://almascience.nrao.edu/alma-data/science-verification 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.
 
=== Mosaic Imaging ===
 
* [[AntennaeBand7]]
:- Band 7 (345 GHz, 0.87 mm)
:- CO 3-2 spectral line
:- Antennae Galaxy Merger (NGC 4038/4039)
:- North and South mosaics


{| class="wikitable"
=== High Frequency Calibration ===


! [[ALMA Imaging Pipeline Reprocessing | Customized Pipeline Imaging]]
* [[IRAS16293Band9]]
|
:- Band 9 (650 GHz, 0.46 mm)
This is a really long sentence to force the table to fill the full page width otherwise it looks bad.
:- Protostellar Cluster
This is a really long sentence to force the table to fill the full page width otherwise it looks bad.
:- High frequency techniques
|-
:- Mosaic


! [[Guide to the NA Imaging Template | NA Manual Imaging Templates]]
=== Single Dish and Array Image Combination  ===
| This guide describes the template scripts used to manually image data for quality assurance by the North American ALMA Science Center (NAASC).
|-


! [[Automasking Guide | Automasking]]
* [[M100_Band3]]
| This guide describes how to automatically mask clean regions during non-interactive cleaning.
:- Band 3 (100 GHz, 3 mm)
|-
:- Total Power (Single Dish) calibration and imaging
:- Combining 12m-array, 7m-array, and Total Power data


|}
=== Full Polarization ===


'''Jump to special imaging topics from the End to End guides:'''
* [[3C286_Polarization]]
* [[AntennaeBand7_Imaging | AntennaeBand7 > Mosaic Imaging]]
:- Band 6 (230 GHz, 1.3 mm)
* [[IRAS16293_Band9_-_Imaging | IRAS16293 Band9 > Mosaic Imaging]]
:- Continuum polarization
* [[M100_Band3_Combine | M100 Band3 > Data Combination]]
* [[3C286_Band6Pol_Imaging | 3C286 Band6 > Full Polarization Imaging]]
* [[Sunspot_Band6_Feathering | Sunspot Band6 > Data Combination]]


== End to End Guides (Manual Calibration) ==
=== Solar Observing ===


These guides are useful tools for those who would like to learn the process of calibration and imaging in detail. They use publicly-available [https://almascience.org/alma-data/science-verification 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.
* [[Sunspot_Band6]]
:- Band 6 (230 GHz, 1.3 mm)
:- Solar observing techniques
:- Calibration and imaging
:- Helper scripts


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


! [[AntennaeBand7]]
* [[Guide To Simulating ALMA Data]]
|
:- An overview of simulation as it pertains to ALMA.
* Band 7 (345 GHz, 0.87 mm)
* [[Simulating Observations in CASA]]
* CO 3-2 spectral line
:- All simulation guides (for ALMA, VLA, ngVLA, etc.)
* Antennae Galaxy Merger (NGC 4038/4039)
* North and South mosaics
| style="text-align:center;" | [[File:604px-Antennae_galaxies_xl.jpg|100px]]
|-


! [[IRAS16293Band9]]
== Legacy Guides ==
|
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'''.
| style="text-align:center;" | [[File:Intro.jpg|200px]]
|-


! [[M100 Band3]]
These guides and scripts use Science Verification data and have been validated for older versions of CASA, but will not continue to be updated for new CASA releases:
|
* [[Archived ALMA CASAguides]]
Band 3 (100 GHz, 3 mm) on M100 demonstrates '''Single Dish''' (Total Power) data reduction and 12m, 7m, Total Power '''data combination''' procedures.
| style="text-align:center;" | [[File:M100_NASA.jpg|100px]]
|-


! [[3C286 Polarization]]
=== Cycle 0 ===
|
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.
| style="text-align:center;" | [[File:VLA_3c286.png|200px]]
|-


! [[Sunspot Band6]]  
* [[Guide To Processing ALMA Data for Cycle 0]]
|
:- Last checked in CASA 4.2
* Band 6 (230 GHz, 1.3 mm)
:- Helpful hints for downloading the data
* Solar observing techniques
:- Imaging, self-calibration, and image analysis
* Calibration and imaging
* Helper scripts
| style="text-align:center;" | [[File:Sunspot_SolarMonitor.png|150px]]


|}
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.


== Special Topics ==
== Resources ==


=== Pipeline ===
* [https://almascience.nrao.edu/processing/science-pipeline ALMA Pipeline webpage]
  * To cite the ALMA pipeline, please use: [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]
* [[ALMA Pipeline Known Issues]]
=== Tools ===
* [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.
* [[Analysis Utilities]]: A Python module containing utilities for analysis and plotting.
* [[Analysis Utilities]]: A Python module containing utilities for analysis and plotting.  
* [[ALMA Renormalization Correction | Renormalization]]: A fix for amplitude calibration issues caused by the ALMA normalization strategy for sources with strong line emission.
* [[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.
* [[Simulating Observations in CASA]]: All simulation guides (for ALMA, VLA, ngVLA, etc.)


== Resources ==
=== Other Telescopes ===


* [[Archived ALMA CASAguides]]
* [https://almascience.org/about-alma/proposing/sensitivity-calculator ALMA Sensitivity Calculator]
* [[Karl G. Jansky VLA Tutorials]]
* [[Karl G. Jansky VLA Tutorials]]
* [[Past MM/Submm Guides]]: Old CASA guides for non-NRAO telescopes.
* [[Past MM/Submm Guides]]: These are not currently being maintained.


<!--
<!--

Latest revision as of 21:53, 22 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:

ALMA

CASA 

  * 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
  * 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

CARTA

Guides that have been updated to demonstrate the CARTA image viewer will include this statement near the top:

This guide features CARTA, the “Cube Analysis and Rendering Tool for Astronomy,” which is the new NRAO visualization tool for images and cubes. The CASA viewer (imview) has not been maintained for a few years and will be removed from future versions of CASA. We strongly recommend using CARTA, as it provides a much more efficient, stable, and feature rich user experience. A comparison of the CASA viewer and CARTA, as well as instructions on how to use CARTA at NRAO, is provided in the CARTA section of the CASA docs.

First Look (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.

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

Restoring and Imaging Calibrated Data

Considerations before Imaging

- A fix for amplitude calibration issues caused by the ALMA normalization strategy for sources with strong line emission.
- A guide to CASA data weights and how to ensure they are correct for data combination.

Pipeline Imaging

- Create images using pipeline tasks.

Manual Imaging

- Create images with a manual template.
- Examples of using tclean, with emphasis on changes from the older "clean" task.

Automasking

- Explanation of parameters used in tclean to automatically mask clean regions during non-interactive cleaning.

Manual Calibration and Imaging

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.

Mosaic Imaging

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

High Frequency Calibration

- Band 9 (650 GHz, 0.46 mm)
- Protostellar Cluster
- High frequency techniques
- Mosaic

Single Dish and Array Image Combination

- Band 3 (100 GHz, 3 mm)
- Total Power (Single Dish) calibration and imaging
- Combining 12m-array, 7m-array, and Total Power data

Full Polarization

- Band 6 (230 GHz, 1.3 mm)
- Continuum polarization

Solar Observing

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

Simulation

- An overview of simulation as it pertains to ALMA.
- All simulation guides (for ALMA, VLA, ngVLA, etc.)

Legacy Guides

These guides and scripts use Science Verification data and have been validated for older versions of CASA, but will not continue to be updated for new CASA releases:

Cycle 0

- 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):

Resources

Pipeline

  * 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

Tools

Other Telescopes
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