### PAIRNDF

Aligns images graphically by drag and drop

#### Description:

This routine accepts a list of images which may be aligned using simple offsets in their Current coordinate frames. By making use of a graphical user interface you can indicate how pairs of images are aligned with respect to each other, and mark image features to allow accurate alignments. Once enough pairings have been specified to register all frames completely a global merger of all the positions for each image takes place. This results in the output of one list of uniquely labelled positions for each image. These position lists can then be used in a routine such as REGISTER to produce the actual transformation between the images.

If images have been grouped into Sets for alignment purposes by using MAKESET, and the USESET parameter is true, then the program will treat each Set of images as a single image to be aligned.

The graphical interface consists of two parts: a chooser which allows you to nominate pairs of images to be aligned, and an aligner which allows you to move the pair around the screen until they are registered, and to mark points in the overlapping region where the same centroidable features exist on both images.

Operation is as follows. You must first use the chooser window to select a pair of images which have a region in common (if you only have two images this step may be skipped). Use the tabs at either side of the screen to pick the image to appear on that side. You can use the "Show FITS" button to select one or more FITS headers to be displayed alongside each image if this will make it easier to identify which is which. You can use the "Display cutoff" menu to select the percentiles controlling the brightness of each pixel; alignment is easier if the same features are of a similar brightness in different images. The images are displayed resampled into their Current coordinates, so that their orientation will be the same as in the aligner. You can only align them using this program if a simple offset (translation) maps one onto another in these coordinates (or very nearly does so). If that is not the case, you will have to set their Current coordinate system to a different value (see WCSEDIT) or align them using a different method. The whole of each image will be displayed in the chooser window, select a pair with an overlapping region which you wish to align, and click the "Use this pair" button. The aligner window will then appear, displaying the two images which you have selected. The chooser window can normally be resized in the normal way to make the images bigger or smaller. However there is currently a bug which causes this to crash in some window managers which use continuous resizing. In this case you must use the PREVX and PREVY parameters to change the image size.

In the aligner window you can drag either of these images around the display region by holding down mouse button 1 (usually the left one) as you move the mouse; the easiest way to align the pair is to "pick up" one image by an identifiable feature and "drop" it on the same feature in the other image. Where the images overlap their pixels will be averaged. If they are not correctly positioned, you can move them again. Once you are happy that they are aligned about right, then click in the overlap region to mark features which appear in both images. During this part you mark points by clicking with mouse button 1 (usually the left one) and you can remove them by clicking with button 3 (usually the right one).

When you add a point by clicking it will be centroided on both images, and two markers plotted, one for each centroided position. If a centroidable object near that point cannot be identified on both images the program will not allow you to mark a point there. However, note that the centroiding algorithm is capable of locating spurious objects from noise, so the fact that a point can be marked does not prove that a real feature exists on both images. By looking at the two markers it should be possible to see whether a real feature has been located. Though the two markers do not need to be exactly concentric (REGISTER can take care of that later), the offset between them should be similar to that of other marked objects nearby in the overlap region. If you do not think the same object has been identified in both images, you should remove this point (with mouse button 3).

The aligner window can be resized, the magnification changed using the "Zoom" control, the display region scrolled using the scrollbars, and the shape and colour of the point markers selected. When you have aligned the images and marked shared features, or if you decide that the pair cannot be satisfactorily registered, click the "Done" button.

You will then be returned to the chooser window to select another pair and repeat the process. After the first time however, you will only be allowed to select a pair of images to align if at least one of them has already been aligned. Those which have already been done are marked with a ‘$+$’ sign on their selection tabs.

Once you have made enough pairings to register the whole set, the graphical windows will disappear and the program will complete the global matching up of positions without any further user interaction.

#### Usage:

pairndf in outlist percentiles

#### Parameters:

If only two images are presented in the IN list, then this parameter determines whether they should be previewed in the chooser widget before they are presented for alignment. With only two, the chooser is not normally necessary since there is only one possible pair to select for alignment, but if you want to equalise the image brightnesses using the “Display cutoff” button or preview FITS headers you may wish to respond true to this. [FALSE]
A list of image names whose data are to be transformed. The image names should be separated by commas and may include wildcards.
Name of the CCDPACK logfile. If a null (!) value is given for this parameter then no logfile will be written, regardless of the value of the LOGTO parameter.

If the logging system has been initialised using CCDSETUP then the value specified there will be used. Otherwise, the default is "CCDPACK.LOG". [CCDPACK.LOG]

Every CCDPACK application has the ability to log its output for future reference as well as for display on the terminal. This parameter controls this process, and may be set to any unique abbreviation of the following:
• TERMINAL – Send output to the terminal only

• LOGFILE – Send output to the logfile only (see the LOGFILE parameter)

• BOTH – Send output to both the terminal and the logfile

• NEITHER – Produce no output at all

If the logging system has been initialised using CCDSETUP then the value specified there will be used. Otherwise, the default is "BOTH". [BOTH]

##### MARKSTYLE1 = LITERAL (Read and Write)
A string indicating how markers are initially to be plotted in the aligner widget to represent points on the left hand image. It consists of a comma-separated list of "attribute=value" type strings. The available attributes are:
• colour – Colour of the marker in Xwindows format.

• size – Approximate height of the marker in pixels.

• thickness – Approximate thickness of lines in pixels.

• shape – One of Plus, Cross, Circle, Square, Diamond.

This parameter only gives the initial marker type; it can be changed interactively while the program is running. If specifying this value on the command line, it is not necessary to give values for all the attributes; missing ones will be given sensible defaults. ["shape=plus"]

##### MARKSTYLE2 = LITERAL (Read and Write)
A string indicating how markers are initially to be plotted in the aligner widget to represent points on the right hand image. It consists of a comma-separated list of "attribute=value" type strings. The available attributes are:
• colour – Colour of the marker in Xwindows format.

• size – Approximate height of the marker in pixels.

• thickness – Approximate thickness of lines in pixels.

• shape – One of Plus, Cross, Circle, Square, Diamond.

This parameter only gives the initial marker type; it can be changed interactively while the program is running. If specifying this value on the command line, it is not necessary to give values for all the attributes; missing ones will be given sensible defaults. ["shape=circle"]

##### MAXCANV = _INTEGER (Read and Write)
A value in pixels for the maximum initial X or Y dimension of the region in which the image is displayed. Note this is the scrolled region, and may be much bigger than the sizes given by WINX and WINY, which limit the size of the window on the X display. It can be overridden during operation by zooming in and out using the GUI controls, but it is intended to limit the size for the case when ZOOM is large (perhaps because the last image was quite small) and a large image is going to be displayed, which otherwise might lead to the program attempting to display an enormous viewing region. If set to zero, then no limit is in effect. [1280]
This parameter controls whether to continue and create an incomplete solution. Such solutions will result when only a subset of the input position lists have been paired.

In this case, any images for which matching was not achieved will have their associated position lists removed from their .MORE.CCDPACK extensions. Thus after running PAIRNDF with OVERRIDE set to TRUE, any position list associated with an image is guaranteed to be one which has been matched, and not just one left over from the previously associated unmatched list. [TRUE]

An expression which is either a list of names or expands to a list of names for the output position lists.

These may be specified as list of comma separated names, using indirection if required, OR, as a single modification element (of the input names). The simplest modification element is the asterisk "$\ast$" which means call each of the output lists the same name as the corresponding input images (but without the ".sdf" extension). So, IN $>$ $\ast$ OUTLIST $>$ $\ast$ signifies that all the images in the current directory should be used and the output lists should have the same names.

Other types of modification can also occur, such as, OUTLIST $>$ $\ast$_objs.dat which means call the position lists the same as the input images but put "_objs.dat" after the names. Replacement of a specified string with another in the output file names can also be used, OUTLIST $>$ $\ast$$|$_debias$|$_images.dat$|$ this replaces the string "_debias" with "_images.dat" in any of the output names.

If wildcarded names for the input images are used then it is recommended that wildcards are also used for the position list names as the correspondence between these may be confusing. [$\ast$.DAT]

##### PERCENTILES( 2 ) = _DOUBLE (Read)
The default low and high percentiles of the data range to use when displaying the images; any pixels with a value lower than the first element will have the same colour, and any with a value higher than the second will have the same colour. This parameter gives the default value - the percentile settings can be set for each image individually from within the GUI to accomodate the situation where images have different brightnesses. Must be in the range 0 $<$= PERCENTILES( 1 ) $<$= PERCENTILES( 2 ) $<$= 100. [2,98]
##### PREVX = _INTEGER (Read and Write)
The initial width in pixels of the preview display for each image; two images will be displayed side by side at any one time at this size in the chooser window. This can be effectively changed by resizing the entire chooser window in the normal way using the window manager while the program is running. [350]
##### PREVY = _INTEGER (Read and Write)
The initial height in pixels of the preview display for each image; two images will be displayed side by side at any one time at this size in the chooser window. This can be effectively changed by resizing the entire chooser window in the normal way using the window manager while the program is running. [350]
The tolerance for deduplicating centroided points (in pixels). If two centroided objects on the same image are within this distance of each other they will be identified as the same object. For a bright elliptical object, centroiding arising from any nearby point will normally arrive at the same position, so this can be set to a small value (less than 1), but if the objects being identified cover many pixels and are close to the background noise level it may be advantageous to set it to a larger value so that centroids near to each other are identified as referring to the same object. [0.5]
This parameter determines whether Set header information should be used or not. If USESET is true, PAIRNDF will try to group images according to their Set Name attribute. All images which share the same (non-blank) Set Name attribute, and which have a CCD_SET attached coordinate system, will be grouped together and treated as a single image for alignment. In the graphical part of the program you will view and position this group of images as a single item.

If the input images have no Set headers, or if they have no Set alignment coordinate system (one with a Domain of CCD_SET) the setting of USESET will make no difference.

If a global value for this parameter has been set using CCDSETUP then that value will be used. [FALSE]

##### WINX = _INTEGER (Read and Write)
The initial width in pixels of the aligner window, which contains a space for dragging around a pair of images and associated controls. If the region required for the images is larger than the area allocated for display, it can be scrolled around within the window. The window can be resized in the normal way using the window manager while the program is running. [800]
##### WINY = _INTEGER (Read and Write)
The initial height in pixels of the aligner window, which contains space for dragging around a pair of images and associated controls. If the region required for the images is larger than the area allocated for display, it can be scrolled around within the window. The window can be resized in the normal way using the window manager while the program is running. [400]
##### ZOOM = _DOUBLE (Read and Write)
A factor giving the initial level to zoom in to the images displayed in the aligner window, that is the number of screen pixels to use for one image pixel. It will be rounded to one of the values ... 3, 2, 1, 1/2, 1/3 .... The zoom can be changed interactively from within the program. The initial value may be limited by MAXCANV. [1]

#### Examples:

pairndf $\ast$ $\ast$.dat [1,99]
This example shows the positional nature of the parameters. All the images in the current directory are presented for alignment. Their output position lists have the same name as the images except that they have a file extension of .dat. The default image display cutoff is between the 1st and 99th percentile, which shows bright detail well.
pairndf in="data1,data2" outlist="d1-pos,d2-pos" zoom=2 maxcanv=0 markstyle1="shape=circle,size=8,thickness=1,colour=HotPink"
Only the two images data1 and data2 will be aligned, and the corresponding sets of positions will be written to the files d1-pos and d2-pos. The images will initially be displayed for alignment at a magnification of two screen pixels to each data pixel, even if that results in a very large display area. During alignment, marked points on the left hand image will be shown as little pink circles.

#### Notes:

• NDF extension items.

On exit the CURRENT_LIST items in the CCDPACK extensions (.MORE.CCDPACK) of the input NDFs are set to the names of the appropriate output lists. These items will be used by other CCDPACK position list processing routines to automatically access the lists.

• Output position list format.

CCDPACK format - Position lists in CCDPACK are formatted files whose first three columns are interpreted as the following.

• Column 1: an integer identifier

• Column 2: the X position

• Column 3: the Y position

The column one value must be an integer and is used to identify positions which may have different locations but are to be considered as the same point. Comments may be included in the file using the characters # and !. Columns may be separated by the use of commas or spaces.

In all cases, the coordinates in position lists are pixel coordinates.

#### Behaviour of parameters

All parameters retain their current value as default. The "current" value is the value assigned on the last run of the application. If the application has not been run then the "intrinsic" defaults, as shown in the parameter help, apply.

Retaining parameter values has the advantage of allowing you to define the default behaviour of the application. The intrinsic default behaviour of the application may be restored by using the RESET keyword on the command line.

Certain parameters (LOGTO, LOGFILE and USESET) have global values. These global values will always take precedence, except when an assignment is made on the command line. Global values may be set and reset using the CCDSETUP and CCDCLEAR commands.

Some of the parameters (MARKSTYLE1, MARKSTYLE2, MAXCANV, PERCENTILES, PREVX, PREVY, WINX, WINY) give initial values for quantities which can be modified while the program is running. Although these may be specified on the command line, it is normally easier to start the program up and modify them using the graphical user interface. If the program exits normally, their values at the end of the run will be used as defaults next time the program starts up.

#### Implementation Status:

• Supports Bad pixel values and all non-complex data types.