Difference between revisions of "Plotbandpass"
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== Clipping off the edge channels ==
== Clipping off the edge channels ==
Revision as of 12:45, 4 January 2012
Return to Analysis Utilities
This page documents the plotbandpass function of Python module analysisUtils.
The plotbandpass function provides extended capabilities beyond those of CASA's plotcal. It was written to facilitate rapid visualization of ALMA's bandpass and spectral Tsys measurements in Science Verification and Early Science data, but it can be used on EVLA data as well. It is distributed with the analysisUtils Python module which provides numerous other Python extensions callable from within CASA. Analysis Utilities has been tested on dual-polarization ALMA data, and single-, dual-, and full-polarization EVLA data. The function parameters can always be obtained by giving parameter: help=True. For example,
# In CASA import analysisUtils as au au.plotbandpass(help=True)
$Id: plotbandpass.py,v 1.118 2011/12/13 20:12:47 thunter Exp $ Usage: plotbandpass(caltable='', antenna='', field='', spw='', yaxis='amp', xaxis='chan', figfile='', plotrange=[0,0,0,0], help=False, caltable2='', overlay='', showflagged=False, timeranges='', buildpdf=False, caltable3='', markersize=3, density=108, interactive=True, showpoints='auto', showlines='auto', subplot='22', zoom='', poln='', showatm=False, pwv='1.0', gs='gs', convert='convert', chanrange='', debug=False, vm='', solutionTimeThresholdSeconds=60.0, phase='') antenna: must be ID (int or string or list), or a single antenna name or list atm: overlay the atmospheric transmission curve for the weather and elevation buildpdf: True/False, if True and figfile is set, assemble pngs into a pdf caltable: a bandpass table, of type B or BPOLY caltable2: a second cal table, of type BPOLY or B, to overlay on a B table caltable3: a third cal table, of type BPOLY, to overlay on the first two chanrange: set xrange (e.g. '5~100') over which to autoscale y-axis for xaxis='freq' convert: full path for convert command (in case it's not found) density: dpi to use in creating PNGs and PDFs (default=108) field: must be an ID, source name, or list thereof; can use trailing *: 'J*' figfile: the base_name of the png files to save: base_name.antX.spwY.png gs: full path for ghostscript command (in case it's not found) help: print this message interactive: if False, then figfile will run to completion automatically overlay: 'antenna' or 'time', make 1 plot with different items in colors showflagged: show the values of data, even if flagged markersize: size of points (default=3) phase: the y-axis limits to use for phase plots when yaxis='both' plotrange: define axis limits: [x0,x1,y0,y1] where 0,0 means auto poln: polarizations to plot (e.g. 'XX','YY','RR','LL' or '' for both) pwv: define the pwv to use for the showatm option: 'auto' or value in mm showatm: compute and overlay the atmospheric transmission curve showlines: draw lines connecting the data (default=T for amp, F for phase) showpoints: draw points for the data (default=F for amp, T for phase) solutionTimeThresholdSeconds: consider 2 solutions simultaneous if within this interval (default=60) spw: must be single ID or list or range (e.g. 0~4, not the original ID) subplot: 11,22,32 or 42 for rows x columns; options: 11,22,32 or 42 (default=22) timeranges: show only these timeranges, the first timerange being 1 vm: a result from ValueMapping, returned from a previous call xaxis: 'chan' or 'freq' yaxis: 'amp', 'phase', or 'both' == 'ap'; append 'db' for dB zoom: 'intersect' will zoom to overlap region of caltable with caltable2
If help is not True, the return value is the ValueMapping structure for the specified MS.
Regarding the showatm=True parameter, since most people reducing ALMA data do not load the ASDM_CALWVR table into the MS, the atmospheric transmission curve will be computed by default for 1.0 mm, but you can set the PWV to any value using the pwv option. If you want the fully correct curve for ALMA, then copy the CalWVR.xml file from your ASDM to the present working directory and specify pwv='auto' .
Most of the regular CASA list syntax is accepted (commas and tildes) but negation via exclamation point is not supported, nor is channel selection within an spw. You are welcome to submit a ticket to the ALMA helpdesk if you want either of these capabilities. If you find any problems or unexpected behavior, please include the following information in your bug or enhancement request and send to helpdesk:
- the version number you are using, which is printed as the first line of output;
- the exact command; and
- a pointer to the dataset.
- 1 How to speed up the performance on large datasets
- 2 Display a simple bandpass solution
- 3 Display different (fixed) y-axis ranges for amplitude and phase
- 4 Display a bandpass solution with a BPOLY solution overlaid
- 5 Overlay a bandpass solution with a smoothed version created by smoothbandpass
- 6 Display a Tsys solution for individual times for one field
- 7 Overlay Tsys values for all antennas, one plot per timerange
- 8 Overlay Tsys values for all timeranges, one plot per antenna
- 9 Overlay Tsys from TDM and interpolated result for FDM
- 10 Compute and overlay the atmospheric transmission cure
- 11 Clipping off the edge channels
How to speed up the performance on large datasets
The plotbandpass function first needs to call ValueMapping to learn about the dataset and create a structure for future reference. If you plan to run the function many times on the same dataset, then you should store the return value of the structure from ValueMapping, like so:
# In CASA vm = au.ValueMapping(your_ms)
Now, you can pass the result back to plotbandpass via the optional vm argument to avoid having to run ValueMapping inside of plotbandpass each time. It will do a sanity check to see if the MS name in the vm structure matches the MS name stored inside the caltable.
# All subsequent calls to plotbandpass will now run faster, as long as the vm=vm argument is passed. au.plotbandpass(caltable='bandpass.bcal', vm=vm)
Display a simple bandpass solution
# In CASA au.plotbandpass(caltable='bandpass.bcal',yaxis='both',antenna='DV07',figfile='bandpass')
Here we have specified a single antenna, but we could give a list, or leave it blank for all antennas. We have asked for both phase and amplitude which are shown in adjacent plots. Note how the ouput figfile name will be modified to include antenna number, spw, and timerange of the first panel for your convenience: bandpass.DV07.spw0.t1.png. The default style for amplitude is lines, and phase is points, but this can be changed with showpoints or showlines.
Maybe you prefer to see your phase plots on a common -180 to +180 degree scale. You can do that with plotrange and by limiting yourself to showing only the phase plots.
# In CASA au.plotbandpass(caltable='bandpass.bcal',yaxis='phase',antenna='DV07',figfile='bandpass_phase',plotrange=[0,0,-180,180])
The first 3 plots are from the 3 different time ranges. The fourth plot is the first timerange on the second spw (spw=1). Notice how the upper half of the channels are missing. This is because they were flagged prior to the solution. The x-axis range reflects both flagged and unflagged data to visually remind you of this situation.
Display different (fixed) y-axis ranges for amplitude and phase
Alternatively, if you want to show both amplitude and phase plots on the same page, you can set a fixed amplitude range with the plotrange parameter, and a different fixed phase range with phase=[-180,180].
# In CASA au.plotbandpass(caltable='bandpass.bcal',yaxis='both',antenna='DV07',figfile='bandpass_phase',plotrange=[0,0,0,5],phase=[-180,180])
Display a bandpass solution with a BPOLY solution overlaid
You can overlay a BPOLY solution on top of the regular B solution to see how well the polynomial reproduces the shape.
# In CASA au.plotbandpass('bandpass_b_skipspw19high.bcal',overlay='',yaxis='phase',field='0', xaxis='freq',caltable2='bandpass_bpoly_skipspw19high.bcal', showpoints=True,spw=0,figfile='bpoly_overlay',antenna='4~7')
Overlay a bandpass solution with a smoothed version created by smoothbandpass
# In CASA au.plotbandpass(caltable='bandpass.bcal',caltable2='bandpass.bcal_smooth',xaxis='freq', yaxis='both',overlay='',figfile='smooth',antenna='DV07')
The "c1" and "c2" labels in the legend correspond to caltable and caltable2:
Display a Tsys solution for individual times for one field
A Tsys table is simply a bandpass table with amplitude values set to the system temperature and phase set to zero. There is no inherent way in the header to differentiate a Tsys table from another bandpass table. Therefore, in order to decide whether to make the yaxis label "Amplitude" or "Tsys", we simply look for the letters "tsys" in the caltable name.
# In CASA au.plotbandpass('X3c1.tsys',yaxis='amp',field='2',xaxis='chan',figfile='tsys_chan.png')
Overlay Tsys values for all antennas, one plot per timerange
A quick way to check whether any antenna shows an anomalous system temperature is to overlay all of them together.
# In CASA au.plotbandpass('X3c1.tsys',overlay='antenna',yaxis='amp',field='2',xaxis='chan', figfile='tsys_antenna_overlay.png',subplot=11)
Overlay Tsys values for all timeranges, one plot per antenna
# In CASA au.plotbandpass('X3c1.tsys',overlay='time',yaxis='amp',field='2',xaxis='chan', figfile='tsys_overlay.png',subplot=11)
Overlay Tsys from TDM and interpolated result for FDM
# In CASA au.plotbandpass(caltable='X3c1.tsys.fdm',caltable2='X3c1.tsys',yaxis='amp', field='1',xaxis='freq',figfile='tsys.png')
The "c1" and "c2" labels in the legend correspond to caltable and caltable2:
If you would like to zoom in on the range of intersection, use the zoom='intersect' option. The example below shows that the interpolation from TDM onto FDM is working as expected:
# In CASA au.plotbandpass(caltable='X3c1.tsys.fdm',caltable2='X3c1.tsys',yaxis='amp',field='1', xaxis='freq',figfile='tsyszoom.png',zoom='intersect')
Compute and overlay the atmospheric transmission cure
Sometimes it is instructive to compare the atmospheric transmission curve to the bandpass solution, for example to confirm that absorption features are due to ozone lines. Because Juan Pardo's atm program is contained in casa, the curve can be computed with showatm=True option. By default it will use 1.0 mm as the PWV, however you can change this by entering a different value with pwv='2.0' or by setting pwv='auto' , which will use the actual values of PWV as measured by the WVRs via TelCal and written into the ASDM_CALWVR table. In this case, the median value from all antennas is used. In all cases, the transmission curve uses the airmass of the source for the scan closest to the midpoint of the solution interval. The curve is drawn such that 0% is at the bottom and 100% is at the top of the y-axis, regardless of what plotrange is set for the amplitude.
# In CASA au.plotbandpass('bandpass2_60m.bcal',showatm=True,xaxis='freq',figfile='showatm.png', subplot=11,plotrange=[230.6,232.5,0,1.2])
Clipping off the edge channels
Sometimes the edge of the band shows extreme amplitude values. In this case, it is useful to limit the xrange of the display. If you are using xaxis='chan' , you can simply use plotrange=[8,120,0,0] to clip 8 channels off each edge. But if you are using xaxis='freq' , you must set chanrange='8~120' and leave plotrange at the default. Below is an example of the full display, and the display with chanrange set.
# In CASA au.plotbandpass('bandpass2_20m.bcal',xaxis='freq',overlay='time',showatm=T, antenna='',plotrange=[0,0,0,0],subplot=11,figfile='limitedrange', chanrange='10~120')