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:


{| 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|75px|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]]
* [[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]
! [[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.
! rowspan=4 | [[File:TWHya.png|150px]]
|-  
! [[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 ==


{| class="wikitable"
=== 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.


! [[ALMA Imaging Pipeline Reprocessing | Modified Pipeline Imaging]]
=== 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.
|-


! [[Guide to the NA Imaging Template | NA Manual Imaging Templates]]
* [[ALMA Imaging Pipeline Reprocessing]]
| description
:- Create images using pipeline tasks.
|-


! [[Automasking Guide | Automasking]]
=== Manual Imaging ===
| description
|-


|}
* [[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.


{| class="wikitable"
== Manual Calibration and Imaging ==


! style="text-align:left;" | Jump to special imaging topics from the End to End guides:
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.
|-
|
* [[AntennaeBand7_Imaging | AntennaeBand7 > Mosaic Imaging]]
* [[IRAS16293_Band9_-_Imaging | IRAS16293 Band9 > Mosaic Imaging]]
* [[M100_Band3_Combine | M100 Band3 > Image Combination]]
* [[3C286_Band6Pol_Imaging | 3C286 Band6 > Full Polarization Imaging]]
* [[Sunspot_Band6_Feathering | Sunspot Band6 > Image Combination]]


|}
=== Mosaic Imaging ===


== End to End Guides (Manual Calibration) ==
* [[AntennaeBand7]]
:- Band 7 (345 GHz, 0.87 mm)
:- CO 3-2 spectral line
:- Antennae Galaxy Merger (NGC 4038/4039)
:- North and South mosaics


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.
=== High Frequency Calibration ===


{| class="wikitable"
* [[IRAS16293Band9]]
:- Band 9 (650 GHz, 0.46 mm)
:- Protostellar Cluster
:- High frequency techniques
:- Mosaic


! style="text-align:left;" | [[AntennaeBand7]]
=== Single Dish and Array Image Combination  ===
! rowspan=2 | [[File:604px-Antennae_galaxies_xl.jpg|150px]]
|-
|
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)
* CO 3-2 spectral line
* Antennae Galaxy Merger (NGC 4038/4039)
* North and South mosaics
|-


! style="text-align:left;" | [[IRAS16293Band9]]
* [[M100_Band3]]
! rowspan=2 | [[File:Intro.jpg|250px]]
:- Band 3 (100 GHz, 3 mm)
|-
:- Total Power (Single Dish) calibration and imaging
|
:- Combining 12m-array, 7m-array, and Total Power data
* Band 9 (650 GHz, 0.46 mm)
* Protostellar Cluster
* High frequency techniques
* Mosaic
|-


! style="text-align:left;" | [[M100 Band3]]
=== Full Polarization ===
! rowspan=2 | [[File:M100_NASA.jpg|150px]]
|-
|
Band 3 (100 GHz, 3 mm) on M100 demonstrates Single Dish (Total Power) data reduction and 12m , 7m, Total Power combination procedures.
|-


! style="text-align:left;" | [[3C286 Polarization]]
* [[3C286_Polarization]]
! rowspan=2 | [[File:VLA_3c286.png|250px]]
:- Band 6 (230 GHz, 1.3 mm)
|-
:- Continuum polarization
|
* Band 6 (230 GHz, 1.3 mm)
* Continuum polarization calibration and imaging
|-


! style="text-align:left;" | [[Sunspot Band6]]
=== Solar Observing ===
! rowspan=2 | [[File:Sunspot_SolarMonitor.png|250px]]
|-
|
* Band 6 (230 GHz, 1.3 mm)
* Solar observing techniques
* Calibration and imaging
* Helper scripts
|-


|}
* [[Sunspot_Band6]]
:- Band 6 (230 GHz, 1.3 mm)
:- Solar observing techniques
:- Calibration and imaging
:- Helper scripts


== Special Topics ==
== Simulation ==


* [[ALMA Renormalization Correction | Renormalization]]
* [[Guide To Simulating ALMA Data]]
* [[DataWeightsAndCombination | Data Weights]]  
:- An overview of simulation as it pertains to ALMA.
:- relevant for data from Cycles 0, 1, and 2
* [[Simulating Observations in CASA]]
* [[Simulating Observations in CASA | Simulating Observations]]
:- All simulation guides (for ALMA, VLA, ngVLA, etc.)
:- Also see: [[Guide To Simulating ALMA Data]]


== Legacy Guides ==
== 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:
* [[Archived ALMA CASAguides]]
* [[Archived ALMA CASAguides]]
* [[TCLEAN and ALMA]]


* [[Guide To Processing ALMA Data for Cycle 0 | Cycle 0]]
=== Cycle 0 ===
 
* [[Guide To Processing ALMA Data for Cycle 0]]
:- Last checked in CASA 4.2
:- Last checked in CASA 4.2
:- Helpful hints for downloading the data
:- Helpful hints for downloading the data
:- Imaging, self-calibration, and image analysis
:- 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)
Example data calibration scripts used for Cycle 0 data (CASA 3.4):
:* [[File:FDM.example.ms.scriptForCalibration.py]]: FDM (3840 channels/spw)
* [[File:TDM.example.ms.scriptForCalibration.py]]: TDM (128 channels/spw)
:* [[Updating a script to work with CASA 4.2]]: Update 3.4 scripts to 4.2 or later.
* [[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 ==
=== 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]
* [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.  
=== Other Telescopes ===
* [[Karl G. Jansky VLA Tutorials]]
* [[Karl G. Jansky VLA Tutorials]]
* [[Past MM/Submm Guides]]: These are not currently being maintained.
* [[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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