Regions in the Viewer

Using CASA CRTF Regions in the Viewer

 

Regions and the Region Manager

 


Type Figure 
ID Region
Caption Region Manager: The Region Manager Panel, which becomes active once at least one region is created. Cycle through available regions using the slider bar at the bottom and use the various tabs to adjust, analyze, load, and save regions.


CASA regions are following the CASA 'crtf' standard as described in § D. CASA regions can be used in all applications, including clean and Image Analysis Tasks.

NOTE: A leading ’ann’ (short for annotation) to a region definition indicates that it is for visual overlay purposes only.

NOTE: Whereas the region format is supported by all the data processing tasks, some aspects of the viewer implementation are still limited to rectangles, ellipses, and some markers. Full support for all region types is progressing with each CASA release.

Once one or more regions are created, the Region Manager Panel becomes active (see Region Manager). Like the Position Tracking and Animator Panels, this can be docked or detached from the main viewer display. It contains several tabs that can be used to adjust, analyze, and save or load regions.

NOTE: Moving the mouse into a region will bring it into focus for the Spectral Profile or Histogram tools.

 

Region Creation, Selection, and Deletion

Within the display area, you can draw regions or select positions using the mouse. Regions can be created with the buttons marked as 'R' in the mouse tool bar (see Viewer Display Panel and Viewer Region Positioning). The viewer currently supports creation of rectangles, ellipses, polygons, and the point. As usual, a mouse button can be assigned to each button as indicated by the small black square in each button (marking the left, middle, or right mouse button Viewer Display Panel, Viewer Region Positioning). An example is shown in Region Selection.

Regions can be selected by SHIFT+click, de-selected by pressing SHIFT+click again. The bottom of the Region Manager Panel features a slider to switch between regions in the image. Regions can be removed by hovering over and pressing ESC or by pressing the buttons to the right side of the slider where the first button (trash can icon) deletes all regions and the far right button (red circle with a white X) deletes the region that is currently displayed in the panel.


Type Figure 
ID Region selection
Caption Region Selection: Selecting an image region (done with SHIFT+click). The region can be resized by dragging the handles or deleted by hitting ESCAPE.


Once regions are selected, they will feature little, skeletal squares in the corners of their boundary boxes. Selected regions can be moved by dragging with the mouse button and manually resized by grabbing the corners as handles. If more than one region is selected, all selected regions move together.

The Rectangle Region drawing tool currently enables the full functionality of the various Region Manager tabs (see below) as well as:

  • Region statistics reporting for images via double clicking (also shown in the Statistics tab of the Region Manager),
  • Defining a region to be averaged for the spectral profile tool (accessed via the Tools:Spectral Profile drop down menu or "Open the Spectrum Profiler" icon),
  • Flagging of MeasurementSets. Note that the Rectangle Region tool’s mouse button must also be double-clicked to confirm an MS flagging edit.
  • Selecting Clean regions interactively (§ 5.3.5)

The Polygon Region and Ellipse Region drawing have the same uses, except that polygon region flagging of a MeasurementSet is not supported.

 

Region Positioning


Type Figure 
ID regio editting
Caption  Region Editing: The Properties tab in the Region Manager can be used to manually adjust the location, width, and display style of the selected region.

With at least one region drawn, the Region Manager becomes active. Using the Properties tab, one can manually adjust the position, annotation, and display style of the region. The entries labeled "frames" set which planes of the image cube the region persists through (regions can have a depth associated with them and will only appear in the frames listed in this range). One can manually adjust the width and height and the center of the box in the chosen units. The 'selected' check box is an alternative way to the SHIFT+click to select a region. The 'annotation' checkbox will place the "ann" string in front of the region ASCII output – annotation regions are not be used for processing in, e.g. data analysis tasks. In the line and text tabs, one can set the style with which the region is displayed, the associated text, and the position and style of that text.

NOTE: Updating the position of a region will update the spectral profile shown if the Spectral Profile tool is open and the histogram if the Histogram tool is open. The views are linked. Dragging a region or adjusting it manually with the Properties tab is a good way to explore an image.

 

Region Statistics


 
Type Figure 
ID Statistics
Caption Region Statistics: The Statistics tab in the Region Manager.


One of the most useful features of defining a region is the ability to extract statistics characterizing the intensity distribution inside the region. You can see these in the Statistics tab of the of the Region Manager Panel (see Region Statistics). This displays statistics for the current region in the current plane of the current image. When more than a single region is drawn, you can select them one by one and the Region Panel will update the statistics to reflect the currently selected region. All values are updated on the fly when the region is dragged across the image.

A similar functionality can be achieved by double clicking inside of a region. This will send statistics information for this region in all registered images to the terminal, looking something like this:

(IRC10216.36GHzcont.image) image
          Stokes         Velocity            Frame          Doppler        Frequency
               I -2.99447e+11km/s             LSRK            RADIO      3.63499e+10
  BrightnessUnit         BeamArea             Npts              Sum             Flux
         Jy/beam          36.2521            27547     1.087686e-01     3.000336e-03
            Mean              Rms          Std dev          Minimum          Maximum
    3.948473e-06     3.723835e-04     3.723693e-04    -1.045624e-03     9.968892e-03

Listed parameters are Stokes, and the displayed channel Velocity with the associated Frame, Doppler and Frequency value. Sum, Mean, Rms, Std Deviation, Minimum, and Maximum value refer to those in the selected region and has the units as specified in BrightnessUnit. Npts is the number of pixels in the region, and BeamArea the beam size in pixels. FluxDensity is in Jy if the image is in Jy/beam. This is an easy way to copy and paste the statistical data to a program outside of CASA for further use.

Taking the RMS of the signal-free portion of an image or cube is a good way to estimate the noise. Contrasting this number with the maximum of the image gives an estimate of the dynamic range of the image. The FluxDensity measurement gives a way to use the viewer to do very basic photometry.

 

Saving and Loading Regions


Type Figure 
ID Manager
Caption Region Manager Save/Load Tabs


The File tab in the Region Manager allows one to save or load selected regions, either individually or en masse. You can choose between CASA and DS9 region format. The default is a CASA region file (saved with a '.crtf' suffix, see § D). The DS9 format does not offer the full flexibility and cannot capture Stokes and spectral axes. DS9 regions will only be usable as annotations in the viewer, they cannot be used for data processing in other CASA tasks. When saving regions, one can choose to save only the current region, all regions that were selected with SHIFT+click, or all regions that are visible on the screen.

NOTE: The load functionality for this tab will only become available once at least one region exists. To load a region when no regions exist, use the Data Manager window.

 

 

The Region Fit

The Viewer can attempt to fit a two-dimensional Gaussian to the emission distribution inside the currently selected region. To attempt the fit, go to the Fit tab of the Region Manager and click the 'gaussfit' button in the bottom left of the panel. You can choose whether or not to fit a sky level (e.g., to account for a finite background, either astronomical, sky, or instrumental). After fitting the distribution, the Fit panel shows the results of the fit, the center, major and minor axis, and position angle of the Gaussian fit in pixels (I) and in world coordinates (W, RA and Dec). The detailed results of the fit will also appear in the terminal window, including a flag showing whether the fit converged.

 

The Region Histogram


Type Figure 
ID Histogram
Caption
Histogram Tab: The histogram tab in the Region Manager. Right click to zoom. Hit SHIFT + Right Click to adjust the details of the histogram display.
 

The viewer will automatically derive a histogram of the pixel values inside the selected region. This can be viewed using the Histogram tab of the of the Region Manager Panel. This is a pared down version of the full Histogram Tool. You can manipulate the details of the histogram plot by:

  1. Using the Right Click to zoom - either to the full range, a selected percentile, or a range that you have graphically selected by dragging the mouse.
  2. Hitting SHIFT + Right Click to open the histogram options. This lets you toggle between a logarithmic and linear y-axis, choose between a line, outline, or filled histogram, and adjust the number of bins.

The histogram will update as you change the plane of the cube or shift between regions.