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Operations on measurement sets
Requires:
Synopsis
Description
The ms tool provides functions to manipulate the contents of measurement set
tables. The functions can be categorised as shown below.
Attaching to a Measurement Set
The simplest and most common way to attach an ms tool to a measurement set is to use the ms.open function which requires that you specify the name of the measurement set table.
The function ms.fromfits converts a UVFITS file to a measurement set table prior to attaching the ms tool to the newly created measurement set. The conversion step may take some time if the FITS file is large. However it only needs to be done once. The measurement set table is not deleted when you close the ms tool, using the close function, or exit CASA. And once the measurement set table is created it is much faster to attach an ms tool to it using the ms.open function.
Getting summary information
The summary function will display, in the logger, an overview of the measurement set. This will include listings of the fields, spectral windows & polarization setups used in the measurement set.
The range function will provide more quantitative information on the minimum, maximum or used values of specified parameters. When using this function you may need to do an initial selection, as described below, depending on whether the parameters you ask for change their shape. A list of parameters accepted by the range function is given in table 1.7 and this table also indicates when an initial selection is necessary.
The lister function provides a concise listing of the data in the measurement set.
The listhistory function lists the contents of the measurement set history table. The history table contains a record of changes made to the measurement set by autoflag, calibrater, imager and other tools.
Selecting data
As described in the ms module documentation a measurement set can contain data with a variety of different shapes. Some of the functions in this tool require the data to be in a fixed shape. Before you can use these functions you need to select a subset of the data in the measurement set where all the data has a fixed shape. There are two functions which can be used to do this. These are the selectinit and command functions.
The select function can be used to further refine which subset of the data will be used by the data access functions. This function allows you to select specific rows in a measurement set using a wide range of criteria.
The select function can only select whole rows in a measurement set. To select specific channels within a row you use the selectchannel function. Similarly to select specific polarizations you should use the selectpolarization function.
Reading and writing data
The getdata function is used to read data from the measurement set into casapy variables. You can select which columns of the measurement set main table you are interested in and only the subset of data specified using the selection functions described above will be retreived. Any frequency averaging (see the selectfrequency function) and polarization conversion (see the selectpolarization function) will be done when you retreive the data. The full power of casapy and other CASA tasks and tools, like plotxy, can then be used for adhoc inspection and calculations involving the data.
If the measurement set was opened for writing then the putdata function can be used to write the data back into the measurement set. When writing data back into the measurement set you cannot change the data shape or the coordinates of the data, only the numerical values. This means that you cannot write data that has been averaged in frequency or converted to different polarizations.
When using the getdata function with a large measurement set you need to be careful to not request too much data. The measurement set is stored on disk but casapy variables are stored in memory. To allow you to access large amounts of data in an ordered way the ms tool provides functions that allow you to iterate through the data in a convienient way.
If you need to step through the data in an orderly fashion, you can use the iteration functions. These allow you to set up an iteration order (iterinit), obtain the first iteration (iterorigin), go to the next iteration (iternext) and end the iteration prematurely (iterend). The iterorigin and iternext function set the currently selected table (as used by getdata and others) to the current iteration. At the end of the iteration, the original selection is restored.
You can iterate through a measurement set you have previously selected using select, but if you use select while iterating, you cannot get back the unselected iteration (without reiterating through the table until the current point).
The writehistory function allows messages to be appended to the measurement set history table should you wish to do so. The listhistory function lists your messages and those created by autoflag, calibrater, imager and other tools.
Conversions to FITS
Just as the fromfits function will convert a UVFITS file to a measurement set the tofits function will convert a measurement set to a UVFITS file. Similarly a single dish measurement set ie., one with a FLOAT_DATA column rather than a DATA column, can be converted to a single dish FITS file using the tosdfits function.
You cannot read a UVFITS file into a measurement set and write it out as a single dish FITS file or vice-versa.
Concatenation
The concatenate function can be used to append the data from one measurement set to the end of another. As all the data is copied this function may take some time if the measurement set to be copied is large. The measurement set needs to be opened for writing for this to work.
Sorting the main table by time
The timesort function permits you to sort the MS main table by time in ascending order. This can be useful after a concatenation.
Splitting The split function allows you to make a new ms from a subset of the actual ms.
Flagging data
The flag and buffer functions all belong together. The idea is to fill a buffer of data (fillbuffer), optionally retrieve it as a record (getbuffer) and display it in some data display tool, do operations like differencing (diffbuffer), clipping (clipbuffer) and manual edits of the displayed data (setbufferflags), and then write the flags back to the MS (writebufferflags), into the appropriate flag level, so you can choose to apply or undo them. The data is untouched by these functions.
Example:
We open the MS for writing, select an array and spectral window and then select a few antennas and a uv range. We then get out the weight values and the data. We change these values in casapy and then write them back to the measurement set. Finally, we close the ms, causing the values to be written back to disk.
| fromfits | Create a measurement set from a uvfits file |
| nrow | Returns the number of rows in the measurement set |
| iswritable | Returns True is the underlying Table is writable |
| open | Attach the ms tool to a measurement set table |
| close | Detach the ms tool from the measurement set table |
| name | Name of the measurement set table the tool is attached to. |
| tofits | Convert a measurement set to a uvfits file |
| summary | (PARTIALLY IMPLEMENTED!!!) Summarize the measurement set |
| listhistory | List history of the measurement set |
| writehistory | Add a row of arbitrary information to the measurement set history table |
| range | Get the range of values in the measurement set |
| lister | List measurement set visibilities |
| selectinit | Initialize the selection of an ms |
| select | Select a subset of the measurement set. |
| selecttaql | Select a subset of the measurement set. |
| selectchannel | Select and average frequency channels |
| selectpolarization | Selection and convertion of polarizations |
| cvel | transform spectral data to different reference frame, optionally regrid the frequency channels |
| getdata | Read values from the measurement set. |
| putdata | Write new values into the measurement set |
| concatenate | Concatenate two measurement sets |
| timesort | Sort the main table of an MS by time |
| split | make a new ms from a subset of an existing ms |
| iterinit | Initialize for iteration over an ms |
| iterorigin | Set the iterator to the start of the data. |
| iternext | Advance the iterator to the next lot of data |
| iterend | End the iteration and reset the selected table |
| fillbuffer | Fill the internal buffer with data and flags. |
| diffbuffer | Differentiate or difference the internal buffer. |
| getbuffer | Return the internal buffer as a Record for access from the intrepreter. |
| clipbuffer | (NON-FUNCTIONAL???) Clip the internal buffer with specified limits. |
| setbufferflags | Set the flags in the buffer |
| writebufferflags | Write the flags in the internal buffer back to the table. |
| clearbuffer | Clear the internal buffer. |
| continuumsub | Continuum fitting and subtraction in uv plane |
| done | Closes the ms tool |
| msseltoindex | Returns ids of the selection used |
| hanningsmooth | Hanning smooth the frequency channels to remove Gibbs ringing. |
| uvsub | Subtract model from the corrected visibility data. |
Description
The ms tool provides functions to manipulate the contents of measurement set
tables. The functions can be categorised as shown below.
Attaching to a Measurement Set
The simplest and most common way to attach an ms tool to a measurement set is to use the ms.open function which requires that you specify the name of the measurement set table.
The function ms.fromfits converts a UVFITS file to a measurement set table prior to attaching the ms tool to the newly created measurement set. The conversion step may take some time if the FITS file is large. However it only needs to be done once. The measurement set table is not deleted when you close the ms tool, using the close function, or exit CASA. And once the measurement set table is created it is much faster to attach an ms tool to it using the ms.open function.
Getting summary information
The summary function will display, in the logger, an overview of the measurement set. This will include listings of the fields, spectral windows & polarization setups used in the measurement set.
The range function will provide more quantitative information on the minimum, maximum or used values of specified parameters. When using this function you may need to do an initial selection, as described below, depending on whether the parameters you ask for change their shape. A list of parameters accepted by the range function is given in table 1.7 and this table also indicates when an initial selection is necessary.
The lister function provides a concise listing of the data in the measurement set.
The listhistory function lists the contents of the measurement set history table. The history table contains a record of changes made to the measurement set by autoflag, calibrater, imager and other tools.
Selecting data
As described in the ms module documentation a measurement set can contain data with a variety of different shapes. Some of the functions in this tool require the data to be in a fixed shape. Before you can use these functions you need to select a subset of the data in the measurement set where all the data has a fixed shape. There are two functions which can be used to do this. These are the selectinit and command functions.
The select function can be used to further refine which subset of the data will be used by the data access functions. This function allows you to select specific rows in a measurement set using a wide range of criteria.
The select function can only select whole rows in a measurement set. To select specific channels within a row you use the selectchannel function. Similarly to select specific polarizations you should use the selectpolarization function.
Reading and writing data
The getdata function is used to read data from the measurement set into casapy variables. You can select which columns of the measurement set main table you are interested in and only the subset of data specified using the selection functions described above will be retreived. Any frequency averaging (see the selectfrequency function) and polarization conversion (see the selectpolarization function) will be done when you retreive the data. The full power of casapy and other CASA tasks and tools, like plotxy, can then be used for adhoc inspection and calculations involving the data.
If the measurement set was opened for writing then the putdata function can be used to write the data back into the measurement set. When writing data back into the measurement set you cannot change the data shape or the coordinates of the data, only the numerical values. This means that you cannot write data that has been averaged in frequency or converted to different polarizations.
When using the getdata function with a large measurement set you need to be careful to not request too much data. The measurement set is stored on disk but casapy variables are stored in memory. To allow you to access large amounts of data in an ordered way the ms tool provides functions that allow you to iterate through the data in a convienient way.
If you need to step through the data in an orderly fashion, you can use the iteration functions. These allow you to set up an iteration order (iterinit), obtain the first iteration (iterorigin), go to the next iteration (iternext) and end the iteration prematurely (iterend). The iterorigin and iternext function set the currently selected table (as used by getdata and others) to the current iteration. At the end of the iteration, the original selection is restored.
You can iterate through a measurement set you have previously selected using select, but if you use select while iterating, you cannot get back the unselected iteration (without reiterating through the table until the current point).
The writehistory function allows messages to be appended to the measurement set history table should you wish to do so. The listhistory function lists your messages and those created by autoflag, calibrater, imager and other tools.
Conversions to FITS
Just as the fromfits function will convert a UVFITS file to a measurement set the tofits function will convert a measurement set to a UVFITS file. Similarly a single dish measurement set ie., one with a FLOAT_DATA column rather than a DATA column, can be converted to a single dish FITS file using the tosdfits function.
You cannot read a UVFITS file into a measurement set and write it out as a single dish FITS file or vice-versa.
Concatenation
The concatenate function can be used to append the data from one measurement set to the end of another. As all the data is copied this function may take some time if the measurement set to be copied is large. The measurement set needs to be opened for writing for this to work.
Sorting the main table by time
The timesort function permits you to sort the MS main table by time in ascending order. This can be useful after a concatenation.
Splitting The split function allows you to make a new ms from a subset of the actual ms.
Flagging data
The flag and buffer functions all belong together. The idea is to fill a buffer of data (fillbuffer), optionally retrieve it as a record (getbuffer) and display it in some data display tool, do operations like differencing (diffbuffer), clipping (clipbuffer) and manual edits of the displayed data (setbufferflags), and then write the flags back to the MS (writebufferflags), into the appropriate flag level, so you can choose to apply or undo them. The data is untouched by these functions.
| Table 1.7: | Items recognized by the range, select, getdata and putdata functions. Items marked with a † are only available in interferometric measurement sets. Items marked with a ‡ are only available in interferometric measurement sets that have been processed with calibrator or imager. Items marked with a * do not require all the data in the selected measurement set to have the same shape. |
Example:
We open the MS for writing, select an array and spectral window and then select a few antennas and a uv range. We then get out the weight values and the data. We change these values in casapy and then write them back to the measurement set. Finally, we close the ms, causing the values to be written back to disk.
Please send any comments or questions about CASA or AIPS++ to aips2-requests@nrao.edu
Copyright © 2008 Associated Universities Inc., Washington, D.C.
This code is available under the terms of the GNU General Public Lincense
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