3 Measuring spectral features in Specview

 

3.1 Getting started

Getting basic spectral quantities from a spectral feature can be accomplished by hitting the “Measure” button at the upper right in the plotting window:

 

 

The button will invoke a Measurement Tool, whose graphics interface is comprised of two parts:

As the measurement tool is invoked, it freezes the axis selectors (Sec. 2.2) on the plot window into their current selection. Note that, if the spectrogram currently displayed supports a rest wavelength (Sec. 4.3.1.1) scale, measurements can be taken against that scale as well.

 

3.2 The region tool

 

 

This tool consists basically of three measurement regions defined on screen by a set of vertical bars. Measurements for the spectral feature at hand are taken from the main region (depicted in red), while the two ancillary regions (depicted in blue and green) are used to define the continuum associated with the feature. The current fitted continuum is also depicted in red.

Repositioning:

Each region can be repositioned by grabbing its central handle. Handles are the little squares that are sensitive to the mouse drag action. Moving the cursor over any one of these handles causes the cursor to display a little hand. This signals that at that point the cursor drag action will not cause a display zoom (its default action) but a region reposition instead.

 

Repositioning the main region also repositions the two ancillary regions. These in turn can be repositioned independently, even to the same side of the main region.

Resizing:

Regions can be resized by dragging their lateral handles. Regions are handled independently of each other, thus they do not care if overlaps are present. It is up to the user to ensure that overlaps, if present, are actually required for the case at hand.

Zoom / screen resize:

The measurement regions are defined by default in screen coordinates, and will not follow the spectral feature when the display is rescaled or resized. Any such action will cause the regions to reposition themselves at their default locations and sizes. The purpose of this is to allow the regions to always remain visible and with a reasonable size, even when extreme zooming or panning takes place. Otherwise the regions could easily disappear from the view port, or collapse to a single degenerate vertical line, thus making impossible to grab their handles again.

 

Alternatively, the measurement regions can be defined in wavelength / frequency / energy space; see Sec. 3.4

 

Colors used to draw the measuring regions can be customized by the user through User preferences (Sec. 9).



3.3 The reporting window

Every time a measurement region changes in any way, new quantities are extracted from the spectrogram and displayed in the reporting window.

 



 

If some fields look truncated, columns can be resized by dragging their name fields at the top. Details about a particular field can be displayed using the tool tip facility, by letting the mouse cursor hover over the desired field for a few moments. Columns can also be repositioned in the table, but in this case the tool tips will not work properly.

 

Once satisfied with the current measurement, the user can record it in an output table by hitting the Record button. This output table can be examined at any time via the Output tab at the top of the reporting window.

 

Again, columns in the output table can be resized at will, and details about a particular field or column can be displayed with tool tips.

 

The Delete button can be used to delete selected table rows from the output table. Multiple selection is allowed with the Shift and Ctrl keys.

 

The output table can be saved to file at any time using the File menu at the top (Sec. 3.7).

 

Feature identification

 

The Feature ID tab gives access to text fields that enable the user to type in an optional identification text for the current feature, as well as an optional rest wavelength (in Angstrom).

 

Whenever a valid rest wavelength is provided, radial velocity quantities will be populated with radial velocity values defined based on the positional parameters of the feature.

 

3.4 Defining regions in wavelength space

The Settings tab gives access to a control panel that enables the user to define the integration regions based on wavelength / frequency / energy values.

 

 

 

The Regions tab gives access to controls for selecting the region limits. The Continuum tab gives access to a selector that enables the default continuum computation to be overridden by the actual position of the central handles in the two continuum regions. This can be used in case one needs to ignore the continuum measurements and set continuum values by hand.

 

In the Regions panel, the default and alternate modes for defining regions are selected in the Mode panel.

 

In the Region parameters panel the user types in each field the desired value for each region limit. Values should be entered in whatever

units are selected in the Units panel selector. Once entered, values can be converted to any supported units by selecting the appropriate entry in the Units selector. The units selected here act solely on the input fields, they are independent from units selected elsewhere.

 

If one or more of the region limits lies outside the range of wavelength / frequency / energy associated with the spectrogram, an error message will be issued. This usually happens the first time the alternate mode is invoked, since the fields will be initialized with arbitrary values. In this case, one can use the Repopulate button to fill in the fields based on the current location of the integration regions on screen. This button can be used any time one wants to define the regions based on the current location of the regions.

 

Once the integration regions are set, they can be dragged in the graphics window in the same way as explained in Sec. 3.2. At any time, by hitting the Reset button, the regions on screen can be moved back to the current definition in the fields.

 

Numerical values entered in the fields, and selected units, persist throughout the life of the program, thus the same values can be used for measuring different spectrograms. A future version will have the capability for saving and retrieving region settings to / from files.

3.5 Computations

Values displayed in the reporting window are computed as follows.

 

Initially the total flux in the main region is computed by integration of the data values in between the main region extremes.

 

Next, the two continuum regions are used to define average and standard deviation values in their respective wavelength ranges. These values are used to define a linear continuum, and this linear continuum is subtracted from the original values in the spectrogram.

 

The net flux in the main region is then computed by integration of the continuum-subtracted data values in between the main region extremes. The flux-weighted wavelength of the feature is also computed at this stage.

 

Finally, the equivalent width is computed from the net flux and average continuum in the main region.

 

If a rest wavelength value was provided in the Feature ID panel, radial velocity values are computed from the positional parameters.

 

Bug: the computation for the extremum position is not very reliable and may fail. Thus, the extremum RV value may also be wrong.

Errors:

Errors associated with each one of the integral quantities and their derived quantities are computed by standard error propagation from the original error information in the data. Thus, errors will be reported only if the original spectrogram carries error information. Errors for the two average continuum values are always reported since they are computed from the standard deviation within each one of the continuum regions.

 

Note that some types of spectrogram, despite originally carrying error information, will result in no error values being displayed. This happens whenever the original spectrogram is comprised of multiple data segments, such as multiple orders of an echelle spectrogram, multiple segments of certain types of ISO data, or spectrograms that result from the combination of data from multiple instruments or files.

 

The reason for that behavior is that these multiple-segmented data must be spliced or co-added together before being presented to the measurement tool, in order for the tool to be able to resolve ambiguities coming from the overlapping regions in the original data. Splicing or co-adding data requires first that the data be re-sampled to a common wavelength grid. At this re-sampling step the error information, if present, is discarded, since there is no generic way to properly resample data without introducing correlation error.

 

Note that the splicing takes place behind the scenes, and no hint that it took place surfaces to the screen.

 

Hopefully, if the error propagation in re-sampled data issue can be addressed satisfactorily in the future, this limitation of the measurement tool can be dropped.

 

Note also that errors are available if just one segment of a multiple-segment spectrogram is input, since no splicing or co-add takes place in this case.

 

3.6 Physical Units

Physical units used to report measurements can be selected from the Units menu. These units are independent from the data original units, from the Preferred Units currently selected, or from the units currently being used in the display. Flux units can also be selected from among a few options.

 

3.7 Saving measurements to file

The File menu enables the current measurements to be saved to a file in the form of a multi-table file. The first table stores the measurement values, and the second the measurement errors.

 

Both VOTable and FITS formats are supported. VOTable file names must have a .xml suffix, FITS files a .fits suffix. If no suffix is provided, .xml is used by default.

 

In a future release, it will be possible to read measurement tables from pre-existing files, for the purposes of editing and adding new measurements.

 

Bug: the FITS format does not include the measurement errors yet.