Polarization Vector Plotting Toolbox

Displaying a vector map

Select a catalogue using the "Open" item in the "File" menu (or click on one of the recently accessed file names in the "File" menu). The catalogue must be either a FITS binary table, or any of the other formats readable by the POLPACK package. The catalogue must contain columns containing Cartesian X and Y coordinates for each vector. If the names of these column are not "X" and "Y", then the names should be specified in a text file called $HOME/.polpackrc as in the following example (where the names of the two columns are "PIXEL_X" and "PIXEL_Y"):

% cat $HOME/.polpackrc
Column X PIXEL_X
Column Y PIXEL_Y
This file can also contain the names of other columns; in particular the names of columns containing RA and DEC values can be supplied if these are not just "RA" and "DEC" (the defaults). RA and DEC values are qualified by EPOCH and EQUINOX parameters supplied with the catalogue, but these both default to J2000 if not supplied.

If an image is displayed in the main image window, an attempt will be made to align the vectors with the image. If the image is displaying celestial coordinates and the catalogue contains RA and DEC values, then alignment will be in RA and DEC. Otherwise alignment will be in pixel coordinates (based on the X and Y columns in the catalogue). No other type of coordinate system is supported.

If no image is displayed in the main window, a blank image will be created covering the area of the catalogue. The colour of this image can be controlled as usual using the colour maps and intensity scaling controls in the main image control panel.

The columns to use for the length and orientation of each vector are specified on the "Rendering" tab, and default to "P" and "ANG". This tab also contains controls for setting the appearance of vectors. The appearance of selected vectors and unselected vectors can be controlled separately. Note, entering a blank value in the "Vector scale" box will cause a default vector scale to be calculated and used. If a blank value is entered in the "Thickness" box for selected vectors, then selected vectors are rendered with the same thickness as unselected vectors.

Binning vectors

Click on the "Binning" tab, select the required binning parameters and press the "Bin now" button. This will replace the displayed vector map with a map formed by binning all the previously displayed vectors (both selected and unselected). If you do not like the results, press the "Un-do" item in the "Edit" menu to re-instate the original map!

Removing vectors

Select the vectors to be removed using any of the techniques in the "How to select vectors" section of this help, and then press the "Cut" item in the "Edit" menu. The selected vectors will be removed from the map. To re-instate the original map, press the "Un-do" button in the "Edit" menu.

Saving the currently displayed vectors

Click the "Save as" item in the "File" menu.

Selecting vectors

Various operations within the toolbox require some vectors to be selected in order for the operation to complete. Vectors can be selected in several ways:

  1. By clicking and dragging with the left mouse button over the displayed vector map. The shape of the region dragged out by the pointer can be either a rectangle or a circle, and is set on the "Selecting" tab. If the control and shift keys are pressed when the button is clicked, any selected vectors are added to the previous selection.
  2. By pointing at an individual vector and clicking with the left button. This will select the single vector under the pointer. Again, if the control and shift buttons are pressed, the selected vector is added to the current selection.
  3. By clicking and dragging in the table of vectors in the Polarimetry toolbox window. Again, if the control and shift buttons are pressed, the selected vectors are added to the current selection.
  4. By entering an algebraic expression into the "Expression:" box on the "Selecting" tab, and pressing <Return>. The variables within this expression should be the names of catalogue columns, preceded by a dollar sign ($). The expression should be a legal Tcl expression. The expression is evaluated for each row in the catalogue, and if the result is non-zero the row is selected. For example, "$P > 50" selects vectors which have a value larger than 50 in the P column; "$P > 2*$DP" selects vectors with a signal to noise ratio better than 2. If the control and shift buttons are pressed when the <Return> button is pressed, the selected vectors are added to the current selection.
  5. Pressing the "Select all" button in the "Selecting" tab, will select all vectors.

De-selecting vectors

The "Selecting" tab contains a menu labelled "Operation:", which is set to "Select" by default. In this mode, the vectors chosen using the techniques described in the previous section are selected, and all other vectors are de-selected (unless control and shift are pressed, in which case the states of other vectors are left unchanged). If the "Operation:" value is set to "De-select", then this is reversed, i.e. the chosen vectors are de-selected, and all other vectors are selected (unless control and shift are pressed, in which case the states of other vectors are left unchanged).

If "Operation" is set to "Select", then clicking over a blank part of the vector map will de-select all vectors (if "Operation" is set to "De-select", then clicking over a blank part of the vector map will select all vectors).

To remove some vectors from the current selection (i.e. to de-select them), set "Operation" to "De-select" and then use one of the techniques described in the previous section to choose the vectors to be de-selected. Be careful to press control and shift while choosing them, otherwise the sates of all other vectors will be reset to "selected".

Performing aperture polarimetry

The "Integrate" tab displays a single row of values formed by binning all the currently selected vectors into a single vector. This is done by combining the Stokes parameters using the selected method, and recalculating the other columns on the basis of the combined Stokes parameters. The table is updated automatically when new vectors are selected. So to perform simple aperture polarimetry, select all vectors within the aperture, and then read off the integrated values from the table in the "Integrate" tab. No facilities currently exist for removing any "background" Stokes parameters (caused by inter-stellar polarization for instance). Sky subtraction should normally be performed prior to forming the catalogue of Stokes vectors.

Note, if the catalogue contains error information in the form of columns of standard deviations for the Stokes parameters, then there is a limit of 100 on the number of vectors which can be integrated into a single measurement. This limit does not apply though if the Stokes parameters are combined using a simple mean (selected using the "Method" menu on the "Integrate" tab).

Specifying columns containing Stokes parameters

In order to use the "Bin" or "Integrate" tabs, assumptions must be made about which catalogue columns contain Stokes parameters. By default, it is assumed that the Stokes parameters are contained in columns names "I", "Q", "U" and "V", with standard deviations in columns "DI", "DQ", "DU" and "DV". To select other columns to use for these quantities, either use the "Column Names" tab, or create a file called $HOME/.polpackrc containing column names prior to using the polarimetry toolbox. This file defines columns as in the following example:

% cat $HOME/.polpackrc

The second word in each line is the standard column name, and the third word is the column name you wish to use. The standard column names are I, Q, U, V, DI, DQ, DU, DV, P, DP , ANG, DANG, PI, DPI, X, Y, RA and DEC. So the above example uses column "STOKES_I" in place of "I", and "STOKES_DI" in place of "DI". If no entry is included for a given column, then the standard column name is used. If a catalogue does not contain a given parameter, then a blank column name can be given in the .polpackrc file. Thus, the line

Column V
implies that the catalogue does not contain any V values.

Displaying vector statistics

The "Statistics" tab displays a table of statistics for the currently selected vectors. The table is updated automatically when new vectors are selected. These statistics are simple statistics of the values in each column, and do not make any assumptions about the content of each column. For instance, if column "P" contains polarization values, the "mean P" displayed in the table is literally the mean of the P values. It is not the P value implied by the mean of the Stokes vectors. Use the "Integrate" tab for such "Stokes-aware" statistics.

Control the key

A key to the vector scale can be produced, and is controlled using the controls on the "Key" tab. The position of the key can be changed by clicking and dragging over the key.

Display a plane from a spectropolarimetry cube

A catalogue containing spectropolarimetry data is assumed to have an extra column containing some indication of the spectral channel for each vector (this may be velocity, wavelength, frequency, integer channel number, etc). By default, it is assumed that this column is named "Z", but an alternative column name may be specified by including a line in a text file called $HOME/.polpackrc as in the following example, which indicates that the column named "VEL" should be used as the spectral channel column:

% cat $HOME/.polpackrc
Column Z VEL
Only a single spectral channel may be displayed at any one time. The spectral channel to use is selected using the "SpecPol" tab. The channel may be specified in two ways:
  1. as a Z column value - only rows which have the specified value in the Z column are displayed.
  2. as an Z axis value - this is only available if your catalogue has suitable WCS information which can be used to transform the column values into some other physically meaningful system of units such as Angstroms, Hertz, etc.
If available, the units required by each box will be displayed to the right of the box. Entering a value into either box will result in the corresponding value being displayed in the other box (if possible). If no vectors have the specified Z value, the nearest value for which some vectors exist will be used instead of the specified value. If the catalogue contains no Z column, or if the Z column value is the same for all rows, the entry boxes will be disabled so that nothing can be typed in them.

All subsequent operations act only on the displayed vectors (i.e. vectors for other spectral channels are ignored). Thus, for instance, dragging a box over the map will only select vectors in the specified channel, not in any other channel. If you save or bin the displayed map, the resulting map will contain only vectors for the specified spectral channel.