Difference between revisions of "AntennaeBand7 for CASA 3.3"

From CASA Guides
Jump to navigationJump to search
 
(66 intermediate revisions by 8 users not shown)
Line 1: Line 1:
Draft casaguide for the Antennae at Band 7
+
[[Category:ALMA]][[Category:Calibration]][[Category:Spectral Line]]
  
[[Category:ALMA]][[Category:Calibration]][[Category:Spectral Line]]
+
'''NOTE: These guides are dynamic and will evolve as our understanding of how best to reduce ALMA data improves. Check back for updates periodically.'''
  
 
==Science Target Overview==
 
==Science Target Overview==
[[File:604px-Antennae_galaxies_xl.jpg|200px|thumb|right|Fig. 1. HST image of Antennae (Credit: NASA, ESA, and the Hubble Heritage Team STScI/AURA)-ESA/Hubble Collaboration. Acknowledgement: B. Whitmore ( Space Telescope Science Institute) and James Long (ESA/Hubble).]]
+
[[File:604px-Antennae_galaxies_xl.jpg|200px|thumb|right|'''Fig. 1.''' HST image of the Antennae. White contours correspond to the CO(1-0) intensity map in Wilson et al. (2000; see also Fig. 2). (Credit: NASA, ESA, and the Hubble Heritage Team STScI/AURA-ESA/Hubble Collaboration). Acknowledgement: B. Whitmore ( Space Telescope Science Institute) and James Long (ESA/Hubble)]]
[[File:Wilson00-antennaeco1-0.jpg|200px|thumb|right|Fig. 2. Caltech millimeter array CO(1-0) integrated intensity map from Wilson et al. (2000) overlaid on the true-color HST image from Whitmore et al. (1999). ]]
+
[[File:Wilson00-antennaeco1-0.jpg|200px|thumb|right|'''Fig. 2.''' Caltech millimeter array (OVRO) CO(1-0) integrated intensity map from Wilson et al. (2000). ]]
  
 +
The Antennae are a nearby (22 Mpc, Schweizer et al. 2008) pair of merging galaxies, NGC 4038 (RA 12h 01m 53.0s, Dec −18° 52′ 10″) in the north and NGC 4039 (RA 12h 01m 53.6s, Dec −18° 53′ 11″) in the south. These two spiral galaxies started to interact only a few hundred million years ago (Mihos et al. 1993), making the Antennae one of the nearest and youngest examples of a major galaxy merger. The yellow bright components to the south and north of the image center of Figure 1 correspond to the nuclei of the original galaxies and are composed mostly of old stars. Dust filaments, which appear brown in the image, pervade the region between the two nuclei, and star-forming regions surrounded by HII regions (blue) can be seen throughout the system. [http://adsabs.harvard.edu/abs/2000ApJ...542..120W Wilson et al. (2000)] used OVRO to map CO(1-0) emission, a tracer of the bulk molecular gas distribution, with a resolution of 3.15″ x 4.91″ (Figures 1 and 2). Molecular emission is detected throughout the system and is particularly bright in the "interaction region" between the two nuclei, where it appears concentrated in five supergiant molecular complexes (see Figure 2).
  
The Antennae galaxy is a colliding galaxy pair located at a distance of 22 Mpc in the southern sky, composed of NGC 4038 (north) and NGC 4039 (south) (Figure 1). NGC 4038 is located at RA 12h 01m 53.0s, Dec −18° 52′ 10″; and NGC 4039 at RA 12h 01m 53.6s, Dec −18° 53′ 11″. The two spiral galaxies started to interact only a few hundred million years ago, therefore, Antennae galaxies is one of the nearest and youngest examples of two galaxies merging. The yellow bright components to the south-east and north-west of the image center seem to correspond to the nuclei of the original galaxies and are composed mostly of old stars. Filaments of dust, which appears brown in the image, are also apparent, and there are abundant blue star-forming regions surrounded by HII regions (appearing in the image in pink).
+
==ALMA Data Overview==
The properties of the bulk of the molecular gas of Antennae galaxies was studied by Wilson et al. (2000), who conducted CO(1-0) observations using OVRO with resolutions of 3''.15 x 4"91 (see Figure 2).
+
[[File:antennae_foralmaCO3_2_north_withSV.png|200px|thumb|right|'''Fig. 3''' Coverage of the "Northern Mosaic" carried out for ALMA Science Verification overlaid on an HST image. Circles show individual pointings, which were observed in rapid succession during each of the "Northern" observations.]]
Molecular emission is seen toward the two nuclei. An ''overlap region'' between the two galaxies is seen to have prominent CO emission, and is concentrated in five supergiant molecular complexes (SGMC).
+
[[File:antennae_foralmaCO3_2_withSV.png|200px|thumb|right|'''fig 4.''' Coverage of the "Southern Mosaic" carried out for ALMA Science Verification overlaid on an HST image. Circles show individual pointings, which were observed in rapid succession during each of the "Southern" observations.]]
There is also a partial ring of molecular gas to the west of NGC 4038, but this structure is not covered by our observations.
 
  
==ALMA Data Overview==
+
This CASA Guide steps through the reduction and imaging of ALMA Science Verification data targeting the CO 3-2 line in the Antennae galaxy. These data were obtained using the ALMA Band 7 receiver and observed in 10 separate blocks, each typically ~1 hour long, during May and June 2011. Each block observed one of two mosaic patterns, which we will refer to as the "Northern" and "Southern" mosaics. Figures 3 and 4 show the coverage of these two mosaics on an optical image of the Antennae. Within an individual observing block, the observations progress through individual pointings of the mosaic in rapid succession. One field was offset from the main body of the galaxy in each mosaic for calibration purposes.
  
The ALMA CO(3-2) data presented here is similar to the Submillimeter Array data presented in Ueda et al. 2011 (submitted).
+
The observations are broken down into ten individual data sets, as follows:
ALMA Science verification data on Antennae galaxies in Band 7 were taken in ten different
 
datasets over several nights in May and June 2011, in order to get good uv-coverage. The
 
datasets are listed next, classified as observations for the northern -NGC4038- and southern components -NGC4039- of Antennae.
 
  
NGC 4038 (Northern mosaic)
+
Northern mosaic (covering the nucleus of NGC 4038):
 
*uid://A002/X1ff7b0/Xb
 
*uid://A002/X1ff7b0/Xb
 
*uid://A002/X207fe4/X3a
 
*uid://A002/X207fe4/X3a
Line 26: Line 23:
 
*uid://A002/X2181fb/X49
 
*uid://A002/X2181fb/X49
  
NGC 4039 (Southern mosaic)
+
Southern mosaic (covering the nucleus of NGC 4039 and part of the interaction region):
 
*uid://A002/X1ff7b0/X1c8
 
*uid://A002/X1ff7b0/X1c8
 
*uid://A002/X207fe4/X1f7
 
*uid://A002/X207fe4/X1f7
Line 34: Line 31:
 
*uid://A002/X215db8/X18
 
*uid://A002/X215db8/X18
  
These Band 7 observations utilized two  
+
The observations used two basebands, each associated with one spectral window (see the [https://almascience.nrao.edu/call-for-proposals/technical-guide ALMA Technical Handbook] for a discussion of the distinction between basebands and spectral windows). The baseband in the lower sideband (LSB) is centered on the CO (3-2) transition, and the baseband in the upper sideband (USB) is used to measure continuum emission. This guide will focus on the reduction of the LSB CO (3-2) data. Each sideband was observed in both a high spectral resolution "Frequency Domain Mode" (FDM) and a lower spectral resolution "Time Domain Mode" (TDM). We will focus on reducing the FDM data, which have an effective total bandwidth of 1.875 GHz (1634 km/s) divided over 3840 channels. The channel width in FDM mode is 488.28 kHz (0.426 km/s); because the data are automatically Hanning smoothed, the actual spectral resolution is twice this. The TDM mode data were observed and used mainly for calibration purposes; we will not directly analyze them in this CASA Guide, though we will use calibration products (system temperature measurements) derived from these data.
basebands, which are associated with two different spectral windows: one
+
 
in the Upper Sideband (USB) and one in the Lower Sideband (LSB). The first spectral
+
When these observations were taken, the ALMA antennas were in a configuration that is intermediate between the Cycle 0 "Extended" and "Compact" configurations. We expect this configuration to yield an angular resolution of about 1 arcsecond near 345 GHz.
window is centered on the CO(3-2) emission line in the galaxy Antenna. The additional spectral window in the USB is used to measure the continuum emission
+
 
in the galaxy and may contain other emission lines as well. Each spectral window
+
Using the data for publication:
has a total bandwidth of 2 GHz divided over 3840 channels (FDM mode), for a channel width of
+
The following statement should be included in the acknowledgment of papers using the datasets listed above:
488.28 MHz, corresponding to 1634 km/s and 0.426 km/s respectively.  
+
“The Atacama Large Millimeter/submillimeter Array (ALMA), an international astronomy facility, is a partnership of Europe, North America and East Asia in cooperation with the Republic of Chile. This paper makes use of the following ALMA Science Verification data: ADS/JAO.ALMA#2011.0.00003.SV”
For the antenna configuration that was used during these observations (similar to extended configuration in cycle 0), the angular
 
resolution is expected to be about 1".
 
  
We acknowledge Junko Ueda for suggesting these observations of Antennae galaxies for ALMA Science Verification.
+
We thank the following people for suggesting NGC4038/9 for ALMA Science Verification: Francois Boulanger, Nicole Nesvadba, Cinthya Herrera.  We particularly thank Christine Wilson and Junko Ueda for providing both the suggestions and the OVRO (CO(1-0): Wilson et al. 2000)  and SMA (CO(3-2): Ueda et al., submitted) data for verification purposes.
  
 
==Obtaining the Data==
 
==Obtaining the Data==
Line 51: Line 46:
  
 
[http://almascience.nrao.edu/almadata/sciver/AntennaeBand7 North America]
 
[http://almascience.nrao.edu/almadata/sciver/AntennaeBand7 North America]
 +
 
[http://almascience.eso.org/almadata/sciver/AntennaeBand7 Europe]
 
[http://almascience.eso.org/almadata/sciver/AntennaeBand7 Europe]
 +
 
[http://almascience.nao.ac.jp/almadata/sciver/AntennaeBand7 East Asia]
 
[http://almascience.nao.ac.jp/almadata/sciver/AntennaeBand7 East Asia]
  
 
Here you will find three gzipped tar files which, after unpacking, will create three directories:
 
Here you will find three gzipped tar files which, after unpacking, will create three directories:
  
*'''Antennae_Band7_UnCalibratedMSandTablesForReduction''' - Here we provide you with "starter" datasets, where we have taken the raw data in ALMA Science Data Model (ASDM) format and converted them to CASA Measurement Sets (MS).  We did this using the {{importasdm}} task in CASA.  Along with the raw data, we also provide some tables that you will need for the calibration which cannot currently be generated inside of CASA. (This functionality will be available in CASA for Early Science.)
+
*'''Antennae_Band7_UnCalibratedMSandTablesForReduction''' - Here we provide you with "starter" datasets, where we have taken the raw data in ALMA Science Data Model (ASDM) format and converted them to CASA Measurement Sets (MS).  We did this using the {{importasdm}} task in CASA.  Along with the raw data, we provide tables that are needed to calibrate the data, but that cannot currently be generated inside of CASA (for Early Science, these tables will either be pre-applied or supplied with the data).
  
*'''Antennae_Band7_CalibratedData''' - The fully-calibrated uvdata, ready for imaging and self-calibration
+
*'''Antennae_Band7_CalibratedData''' - The fully-calibrated u-v data, ready for imaging.
  
*'''Antennae_Band7_ReferenceImages''' - The final continuum and spectral line images
+
*'''Antennae_Band7_ReferenceImages''' - The final continuum and spectral line images.
  
 
To see which files you will need, read on below. The downloads to your local computer will take some time, so you may wish to begin them now.
 
To see which files you will need, read on below. The downloads to your local computer will take some time, so you may wish to begin them now.
  
'''NOTE: CASA 3.2.1 or later is required to follow this guide.'''  For more information on obtaining the latest version of CASA, see [http://casa.nrao.edu/ http://casa.nrao.edu].
+
'''NOTE: CASA 3.3 or later is required to follow this guide.'''  For more information on obtaining the latest version of CASA, see [http://casa.nrao.edu/ http://casa.nrao.edu].
  
 
==Antennae Band 7 Data Reduction Tutorial==
 
==Antennae Band 7 Data Reduction Tutorial==
  
In this tutorial, or "casaguide", we will guide you step-by-step through the reduction of the ALMA science verification data on the Antennae galaxies and its subsequent imaging. This casaguide consists of two parts:
+
This tutorial has been split into two parts - calibration and imaging:
 +
 +
1) '''[[Antennae Band7 - Calibration]]''' : This section of the tutorial steps you through inspection and calibration of the basic visibility (u-v) data. To complete this part, you will need the data in the first directory: Antennae_Band7_UnCalibratedMSandTablesForReduction.
  
1) '''[[Antennae Band7 - Calibration]]'''
+
2) '''[[Antennae Band7 - Imaging]]''' : This part of the tutorial focuses on constructing images from the calibrated visibility data. If you wish to skip calibration and proceed directly to this part of the tutorial, you will need the fully-calibrated visibility data in the Antennae_Band7_CalibratedData directory. 
  
2) '''[[Antennae Band7 - Imaging]]'''
+
We also provide the final continuum and spectral line images in the Antennae_Band7_ReferenceImages directory.
  
To complete the Calibration section of the tutorial, you will need the data in the first directory: Antennae_Band7_UnCalibratedMSandTablesForReduction.  For those wishing to skip the calibration section and proceed to Imaging, we also provide the fully-calibrated data in the Antennae_Band7_CalibratedData directory.  Finally, we provide the final continuum and spectral line images in the Antennae_Band7_ReferenceImages directory.  
+
For a similar tutorial on the reduction of ALMA Band 7 data on TW Hydra, and Band 3 on NGC 3256, see the casaguides '''[[TWHydraBand7]]''' and '''[[NGC3256Band3]]'''.
  
NOTE: These guides are dynamic and will evolve as our understanding of how best to reduce ALMA data improves. Check back for updates periodically.
+
==How to Use A CASA Guide==
  
For a similar tutorial on the reduction of ALMA Band 7 data on TW Hydra, and Band 3 on NGC 3256, see the casaguide '''[[TWHydraBand7]]''' and '''[[NGC3256Band3]]'''.
+
For tips on using CASA and ways CASA can be run, see [[EVLA_Spectral_Line_Calibration_IRC%2B10216#How_to_Use_This_casaguide]] page.
  
==How to use this casaguide==
+
'''To learn how to extract executable Python scripts from the tutorial, see [[Extracting_scripts_from_these_tutorials]].'''
  
For both portions of the guide, we will provide you with the full CASA commands needed to carry out each step. 
+
Within the guides:
  
 
<source lang="python">
 
<source lang="python">
 
# In CASA
 
# In CASA
The commands you need to execute
+
Regions of this color are CASA commands (or definitions) that need to be cut and
will be displayed in regions
+
pasted in sequence. Wait until one command is finished before pasting another.
like this.
+
Tabs matter in python, make sure that commands that span more than one line and
 +
"for" loops keep their spacing. Sometimes (especially "for" loops) you may need to
 +
explicitly hit enter twice to get the command going.
 
</source>
 
</source>
 
Simply copy and paste the commands in order into your CASA terminal.  You may also type the commands in by hand if desired, but be mindful of typos.  Note that you may need to hit Enter twice in order for the process to start running.  Also note that copying and pasting multiple commands at a time may not work, so only copy and paste the contents of one region at a time. 
 
 
To learn how to extract the CASA commands into an executable python script, click [http://casaguides.nrao.edu/index.php?title=Extracting_scripts_from_these_tutorials here].
 
 
Occasionally we will also show output to the CASA logger:
 
  
 
<pre style="background-color: #fffacd;">
 
<pre style="background-color: #fffacd;">
This output will be displayed
+
Information in this color shows excerpts from the CASA Logger output
in regions like this.
 
 
</pre>
 
</pre>
 
Other relevant information will be presented as follows:
 
  
 
<pre style="background-color: #E0FFFF;">
 
<pre style="background-color: #E0FFFF;">
 
This color shows you background information about the data or other types of reference material
 
This color shows you background information about the data or other types of reference material
 
</pre>
 
</pre>
 
+
{{Checked 3.3.0}}
For a brief introduction to the different ways CASA can be run, see the [[EVLA_Spectral_Line_Calibration_IRC%2B10216#How_to_Use_This_casaguide]] page. For further help getting started with CASA, see [[Getting_Started_in_CASA]].
 
 
 
 
 
 
 
 
 
 
 
 
 
[[User:Despada|Daniel Espada]] 12:00 UT, 21 July 2011
 

Latest revision as of 12:08, 22 November 2011


NOTE: These guides are dynamic and will evolve as our understanding of how best to reduce ALMA data improves. Check back for updates periodically.

Science Target Overview

Fig. 1. HST image of the Antennae. White contours correspond to the CO(1-0) intensity map in Wilson et al. (2000; see also Fig. 2). (Credit: NASA, ESA, and the Hubble Heritage Team STScI/AURA-ESA/Hubble Collaboration). Acknowledgement: B. Whitmore ( Space Telescope Science Institute) and James Long (ESA/Hubble)
Fig. 2. Caltech millimeter array (OVRO) CO(1-0) integrated intensity map from Wilson et al. (2000).

The Antennae are a nearby (22 Mpc, Schweizer et al. 2008) pair of merging galaxies, NGC 4038 (RA 12h 01m 53.0s, Dec −18° 52′ 10″) in the north and NGC 4039 (RA 12h 01m 53.6s, Dec −18° 53′ 11″) in the south. These two spiral galaxies started to interact only a few hundred million years ago (Mihos et al. 1993), making the Antennae one of the nearest and youngest examples of a major galaxy merger. The yellow bright components to the south and north of the image center of Figure 1 correspond to the nuclei of the original galaxies and are composed mostly of old stars. Dust filaments, which appear brown in the image, pervade the region between the two nuclei, and star-forming regions surrounded by HII regions (blue) can be seen throughout the system. Wilson et al. (2000) used OVRO to map CO(1-0) emission, a tracer of the bulk molecular gas distribution, with a resolution of 3.15″ x 4.91″ (Figures 1 and 2). Molecular emission is detected throughout the system and is particularly bright in the "interaction region" between the two nuclei, where it appears concentrated in five supergiant molecular complexes (see Figure 2).

ALMA Data Overview

Fig. 3 Coverage of the "Northern Mosaic" carried out for ALMA Science Verification overlaid on an HST image. Circles show individual pointings, which were observed in rapid succession during each of the "Northern" observations.
fig 4. Coverage of the "Southern Mosaic" carried out for ALMA Science Verification overlaid on an HST image. Circles show individual pointings, which were observed in rapid succession during each of the "Southern" observations.

This CASA Guide steps through the reduction and imaging of ALMA Science Verification data targeting the CO 3-2 line in the Antennae galaxy. These data were obtained using the ALMA Band 7 receiver and observed in 10 separate blocks, each typically ~1 hour long, during May and June 2011. Each block observed one of two mosaic patterns, which we will refer to as the "Northern" and "Southern" mosaics. Figures 3 and 4 show the coverage of these two mosaics on an optical image of the Antennae. Within an individual observing block, the observations progress through individual pointings of the mosaic in rapid succession. One field was offset from the main body of the galaxy in each mosaic for calibration purposes.

The observations are broken down into ten individual data sets, as follows:

Northern mosaic (covering the nucleus of NGC 4038):

  • uid://A002/X1ff7b0/Xb
  • uid://A002/X207fe4/X3a
  • uid://A002/X207fe4/X3b9
  • uid://A002/X2181fb/X49

Southern mosaic (covering the nucleus of NGC 4039 and part of the interaction region):

  • uid://A002/X1ff7b0/X1c8
  • uid://A002/X207fe4/X1f7
  • uid://A002/X207fe4/X4d7
  • uid://A002/X215db8/X1d5
  • uid://A002/X215db8/X392
  • uid://A002/X215db8/X18

The observations used two basebands, each associated with one spectral window (see the ALMA Technical Handbook for a discussion of the distinction between basebands and spectral windows). The baseband in the lower sideband (LSB) is centered on the CO (3-2) transition, and the baseband in the upper sideband (USB) is used to measure continuum emission. This guide will focus on the reduction of the LSB CO (3-2) data. Each sideband was observed in both a high spectral resolution "Frequency Domain Mode" (FDM) and a lower spectral resolution "Time Domain Mode" (TDM). We will focus on reducing the FDM data, which have an effective total bandwidth of 1.875 GHz (1634 km/s) divided over 3840 channels. The channel width in FDM mode is 488.28 kHz (0.426 km/s); because the data are automatically Hanning smoothed, the actual spectral resolution is twice this. The TDM mode data were observed and used mainly for calibration purposes; we will not directly analyze them in this CASA Guide, though we will use calibration products (system temperature measurements) derived from these data.

When these observations were taken, the ALMA antennas were in a configuration that is intermediate between the Cycle 0 "Extended" and "Compact" configurations. We expect this configuration to yield an angular resolution of about 1 arcsecond near 345 GHz.

Using the data for publication: The following statement should be included in the acknowledgment of papers using the datasets listed above: “The Atacama Large Millimeter/submillimeter Array (ALMA), an international astronomy facility, is a partnership of Europe, North America and East Asia in cooperation with the Republic of Chile. This paper makes use of the following ALMA Science Verification data: ADS/JAO.ALMA#2011.0.00003.SV”

We thank the following people for suggesting NGC4038/9 for ALMA Science Verification: Francois Boulanger, Nicole Nesvadba, Cinthya Herrera. We particularly thank Christine Wilson and Junko Ueda for providing both the suggestions and the OVRO (CO(1-0): Wilson et al. 2000) and SMA (CO(3-2): Ueda et al., submitted) data for verification purposes.

Obtaining the Data

To download the data, click on the region closest to your location:

North America

Europe

East Asia

Here you will find three gzipped tar files which, after unpacking, will create three directories:

  • Antennae_Band7_UnCalibratedMSandTablesForReduction - Here we provide you with "starter" datasets, where we have taken the raw data in ALMA Science Data Model (ASDM) format and converted them to CASA Measurement Sets (MS). We did this using the importasdm task in CASA. Along with the raw data, we provide tables that are needed to calibrate the data, but that cannot currently be generated inside of CASA (for Early Science, these tables will either be pre-applied or supplied with the data).
  • Antennae_Band7_CalibratedData - The fully-calibrated u-v data, ready for imaging.
  • Antennae_Band7_ReferenceImages - The final continuum and spectral line images.

To see which files you will need, read on below. The downloads to your local computer will take some time, so you may wish to begin them now.

NOTE: CASA 3.3 or later is required to follow this guide. For more information on obtaining the latest version of CASA, see http://casa.nrao.edu.

Antennae Band 7 Data Reduction Tutorial

This tutorial has been split into two parts - calibration and imaging:

1) Antennae Band7 - Calibration : This section of the tutorial steps you through inspection and calibration of the basic visibility (u-v) data. To complete this part, you will need the data in the first directory: Antennae_Band7_UnCalibratedMSandTablesForReduction.

2) Antennae Band7 - Imaging : This part of the tutorial focuses on constructing images from the calibrated visibility data. If you wish to skip calibration and proceed directly to this part of the tutorial, you will need the fully-calibrated visibility data in the Antennae_Band7_CalibratedData directory.

We also provide the final continuum and spectral line images in the Antennae_Band7_ReferenceImages directory.

For a similar tutorial on the reduction of ALMA Band 7 data on TW Hydra, and Band 3 on NGC 3256, see the casaguides TWHydraBand7 and NGC3256Band3.

How to Use A CASA Guide

For tips on using CASA and ways CASA can be run, see EVLA_Spectral_Line_Calibration_IRC+10216#How_to_Use_This_casaguide page.

To learn how to extract executable Python scripts from the tutorial, see Extracting_scripts_from_these_tutorials.

Within the guides:

# In CASA
Regions of this color are CASA commands (or definitions) that need to be cut and 
pasted in sequence. Wait until one command is finished before pasting another. 
Tabs matter in python, make sure that commands that span more than one line and 
"for" loops keep their spacing. Sometimes (especially "for" loops) you may need to 
explicitly hit enter twice to get the command going.
Information in this color shows excerpts from the CASA Logger output
This color shows you background information about the data or other types of reference material

Last checked on CASA Version 3.3.0.