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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.  
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]]


'''ALMA and CASA links to get started:'''
{| class="wikitable"
* [http://almascience.org/ ALMA Science homepage]
* [http://casa.nrao.edu CASA homepage]: includes download and installation information
* {{casadocs_6.5.4}}
  * 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]
  * 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:Alma_logo.jpg|75px|link=https://almascience.org/]]
|
* [https://almascience.org/ ALMA Science homepage]
! [[File:CARTA_logo_text.png|100px|link=https://cartavis.org/]]
|
* [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|75px|link=https://casa.nrao.edu]]
| style="vertical-align:bottom;" |
* [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]
Production version for Cycle 11: '''CASA 6.6.1'''
! <font size = 4> [https://almascience.nrao.edu/processing/science-pipeline/ Pipeline] <!--[[File:pipeline_logo.png|75px|link=https://almascience.nrao.edu/processing/science-pipeline/]]-->
| style="vertical-align:bottom;" |
* [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]
Production version for Cycle 11: '''Pipeline 2024.1.0.8'''
|}
<!--
;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]]
* [[HTT2 | CASA Hints, Tips & Tricks]]
* [[Getting Started in CASA]]
* [[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]


'''CARTA'''
;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]


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


== First Look (TW Hydra) ==
== 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.
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 Imaging]]
{| class="wikitable"
* [[First_Look_at_Self_Calibration | Continuum Self-Calibration]]
 
* [[First_Look_at_Line_Imaging | Spectral Line Imaging]]
! [[First Look at Imaging]] (continuum)
* [[First_Look_at_Image_Analysis | Moments and Image Analysis]]
|
This guide discusses '''continuum imaging''' and demonstrates both '''interactive and non-interactive tclean''' usage. Also discusses primary beam corrections.
| style="text-align:center;" rowspan=4 | [[File:TWHya.png|150px]]
|-
! [[First Look at Self Calibration]]
|
This guide is the second in sequence. It is an in-depth exploration of '''self-calibration''', which discusses motivations and model creation, and follows a detailed step-by-step process for both '''phase self-calibration''' and '''amplitude self-calibration'''.
|-
! [[First Look at Line Imaging]]
|
This guide picks up where the self-calibration guide leaves off and demonstrates continuum range determination, '''continuum subtraction''', and imaging the molecular line.
|-
! [[First Look at Image Analysis]]
|
This guide uses the images created by the line imaging guide, and demonstrates '''image inspection''', statistics generation, moment maps, and file exporting.
|-
 
|}


Older versions of these guides are archived here: [[ALMA First Look]]
Older versions of these guides are archived here: [[ALMA First Look]]
Line 39: Line 92:
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== Restoring and Imaging Calibrated Data ==
== Advanced Imaging ==


=== Considerations before Imaging ===
{| class="wikitable"
* [[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 | Customized Pipeline Imaging]]
|
This guide describes how to use ALMA pipeline tasks to restore & modify images.
|-


* [[ALMA Imaging Pipeline Reprocessing]]
! [[Guide to the NA Imaging Template | NA Manual Imaging Templates]]
:- Create images using pipeline tasks.
| This guide describes the template scripts used to manually image data for quality assurance by the North American ALMA Science Center (NAASC).
|-


=== Manual Imaging ===
! [[Automasking Guide | Automasking]]
| This guide describes how to automatically mask clean regions during non-interactive cleaning.
|-


* [[Guide NA ImagingTemplate]]
|}
:- 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 ===
'''Jump to special imaging topics from the End to End guides:'''
* [[AntennaeBand7_Imaging | AntennaeBand7 > Mosaic Imaging]]
* [[IRAS16293_Band9_-_Imaging | IRAS16293 Band9 > Mosaic Imaging]]
* [[M100_Band3_Combine | M100 Band3 > Data Combination]]
* [[3C286_Band6Pol_Imaging | 3C286 Band6 > Full Polarization Imaging]]
* [[Sunspot_Band6_Feathering | Sunspot Band6 > Data Combination]]


* [[Automasking Guide]]
== End to End Guides (Manual Calibration) ==
:- 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.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.


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.
{| class="wikitable"


=== Band 7 Mosaic ===
! [[AntennaeBand7]]
|
Discusses full calibration of '''standard 12m interferometry data''' in Band 7 (345 GHz, 0.87mm), using an extended workflow to '''calibrate multiple ASDMs''' simultaneously. Primarily focuses on inspection of the data for flagging, and plotms commands to recreate plots typically included in a QA2 weblog. Also discusses imaging of '''mosaic data''' across two separate regions, including '''continuum subtraction''', '''self-calibration''', and generation of '''image cubes''' for the CO (3-2) spectral line. It concludes with image analysis via '''moment maps''' and '''file exporting'''.
| style="text-align:center;" | [[File:604px-Antennae_galaxies_xl.jpg|100px]]
|-


* [[AntennaeBand7]]
! [[IRAS16293Band9]]
:- Band 7 (345 GHz, 0.87 mm)
|
:- CO 3-2 spectral line
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'''.
:- Antennae Galaxy Merger (NGC 4038/4039)
| style="text-align:center;" | [[File:Intro.jpg|200px]]
:- North and South mosaics
|-


=== High Frequency  ===
! [[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.
| style="text-align:center;" | [[File:M100_NASA.jpg|100px]]
|-


* [[IRAS16293Band9]]
! [[3C286 Polarization]]
:- Band 9 (650 GHz, 0.46 mm)
|
:- Protostellar Cluster
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.
:- High frequency techniques
| style="text-align:center;" | [[File:VLA_3c286.png|200px]]
:- Mosaic
|-


=== Single Dish and Array Combination  ===
! [[Sunspot Band6]]
|
Using Band 6 data (230 GHz, 1.3 mm) from a sunspot observation, this guide discusses '''solar observing techniques.''' Calibration and Imaging guides walk though the unique challenges presented by ALMA solar data. The Single Dish guide covers this process for the ALMA total power array. Finally, the Feathering guide covers '''combining interferometric images with single dish images'''.
| style="text-align:center;" | [[File:Sunspot_SolarMonitor.png|150px]]


* [[M100_Band3]]
|}
:- Band 3 (100 GHz, 3 mm)
:- Total Power (Single Dish) calibration and imaging
:- Combining 12m-array, 7m-array, and Total Power data


=== Full Polarization ===
== Special Topics ==


* [[3C286_Polarization]]
* [[ADMIT Products and Usage]]: This guide discusses how to use the ALMA Data-Mining Toolkit (ADMIT) and customize it for your data.
:- Band 6 (230 GHz, 1.3 mm)
* [[Analysis Utilities]]: A Python module containing utilities for analysis and plotting.
:- Continuum polarization
* [[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.)


=== Solar Observing ===
== Resources ==


* [[Sunspot_Band6]]
:- Band 6 (230 GHz, 1.3 mm)
:- Solar observing techniques
:- Calibration and imaging
:- Helper scripts
== Simulation ==
* [[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.)
== 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]]
 
* [https://almascience.org/about-alma/proposing/sensitivity-calculator ALMA Sensitivity Calculator]
=== Cycle 0 ===
 
* [[Guide To Processing ALMA Data for 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):
* [[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 ==
 
=== 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.
* [[Analysis Utilities]]: A Python module containing utilities for analysis and plotting.
* [[Solar System Models in CASA 4.0]]
 
=== 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]]: Old CASA guides for non-NRAO telescopes.


<!--
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[[ALMAguides_old_homepage]]
[[ALMAguides_old_homepage]]
[[ALMA_Tutorials_draft]]
-->
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Latest revision as of 21:54, 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:

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

Production version for Cycle 11: CASA 6.6.1

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

Production version for Cycle 11: Pipeline 2024.1.0.8

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 guide discusses continuum imaging and demonstrates both interactive and non-interactive tclean usage. Also discusses primary beam corrections.

First Look at Self Calibration

This guide is the second in sequence. It is an in-depth exploration of self-calibration, which discusses motivations and model creation, and follows a detailed step-by-step process for both phase self-calibration and amplitude self-calibration.

First Look at Line Imaging

This guide picks up where the self-calibration guide leaves off and demonstrates continuum range determination, continuum subtraction, and imaging the molecular line.

First Look at Image Analysis

This guide uses the images created by the line imaging guide, and demonstrates image inspection, statistics generation, moment maps, and file exporting.

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

Advanced Imaging

Customized Pipeline Imaging

This guide describes how to use ALMA pipeline tasks to restore & modify images.

NA Manual Imaging Templates This guide describes the template scripts used to manually image data for quality assurance by the North American 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

Discusses full calibration of standard 12m interferometry data in Band 7 (345 GHz, 0.87mm), using an extended workflow to calibrate multiple ASDMs simultaneously. Primarily focuses on inspection of the data for flagging, and plotms commands to recreate plots typically included in a QA2 weblog. Also discusses imaging of mosaic data across two separate regions, including continuum subtraction, self-calibration, and generation of image cubes for the CO (3-2) spectral line. It concludes with image analysis via moment maps and file exporting.

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

Using Band 6 data (230 GHz, 1.3 mm) from a sunspot observation, this guide discusses solar observing techniques. Calibration and Imaging guides walk though the unique challenges presented by ALMA solar data. The Single Dish guide covers this process for the ALMA total power array. Finally, the Feathering guide covers combining interferometric images with single dish images.

Special Topics

  • 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.
  • 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