saoimage (1) - Linux Manuals

saoimage: X11 window based, interactive, color or halftone image display

Command to display saoimage manual in Linux: $ man 1 saoimage

NAME

SAOimage 1.23 - X11 window based, interactive, color or halftone image display program for astronomical images

SYNOPSIS

DESCRIPTION

SAOimage is a utility for displaying astronomical images which runs under the X11 window environment. Image files can be read directly, or image data may be passed through a named pipe (Unix) or a mailbox (VMS) from IRAF display tasks. SAOimage provides a large selection of options for zooming, panning, scaling, coloring, pixel readback, display blinking, and region specification. User interactions are generally performed with the mouse.

The SAOimage desktop includes, a main image display window, a button menu panel, a display magnifier, a pan and zoom reference image, and a color bar. A color table graph window can be brought up by clicking on the color bar.

WORLD COORDINATE SYSTEMS

saoimage tracks world coordinate systems as well as pixel coordinates within the image, if WCS information is present. Several single character keyboard commands have been added. c prints the world coordinate (RA and Dec as hh:mm:ss.sss dd:mm:ss.ss and Lat Long as dd.ddddd dd.ddddd) and image pixel coordinate, along with the value of that pixel to standard output. w executes the command set by -wcscom, substituting that same world coordinate string for %s. b prints the world coordinate RA and Dec in the FK4/B1950 system. j prints the world coordinate RA and Dec in the FK5/J2000 system. g prints the world coordinates as galactic longitude and latitude. e prints the world coordinates as ecliptic longitude and latitude. i prints the world coordinates as the image header defines them. h toggles between degrees and sexigesimal units for RA and Dec.

OPTIONS

-blue: Set the color of all graphics to be blue. Some inexpensive systems use a monochrome monitor connected to one of the three color outputs on the computer. That color must be specified to make the graphics visible.
-bordercolor colorname: Specify the color of all subwindow borders. The color name must be a recognized X color (there are many). This is a style issue. -bc may be used instead of -bordercolor.
-byteswap: Switch the bytes order between big-endian and little-endian order. This may be needed where data has been copied from another machine or if there is some confusion about the FITS file format. This switch toggles the previous setting. -bswap may be used instead of -byteswap.
+/-coord: Set the coordinate tracking state initially on or off. In coordinate tracking, the coordinates of the mouse and value of the pixel under it are printed in the upper-left text area, above the main display window. +/-ct can be used instead of +/-coord.
-display nodename:0.0: Specify the name of the X display server. This makes it possible to run the SAOimage program on a machine other than the one connected to your display screen, with no difference in appearance or use. By default, SAOimage gets the server name from the DISPLAY environment variable. See the xhost manual page for more details. The display server cannot be changed once SAOimage is running. -display may be abbreviated -d.
-dfits: Image file is a FITS file (see -fits), but in unexpected byteswapped order. The FITS standard is not swapped, but some naive VAX applications may swap it (see -bswap).
-fbconfig filename: Specify an alternate frame buffer configuration file for use with IRAF. By default, the file installed with SAOimage (/usr/local/lib/imtoolrc) is used.
-fits: Image file is a FITS file. If the image filename ends in .fits, this switch is not necessary. Only T=SIMPLE array types are supported. The header BITPIX card must be 8 (unsigned byte), 16 (signed short), 32 (signed int), -32 (float), -64 (double), or -16 (unsigned short). (The last two are not recognized standards). IEEE floats are not converted if that is not the machine format.
-fk4: If WCS information is available in the image header, track the cursor in FK4/B1950 right ascension and declination as well as pixel coordinates. These coordinates, followed by B1950 will be fed to an external program if the w command is used.
-fk5: If WCS information is available in the image header, track the cursor in FK5/J2000 right ascension and declination as well as pixel coordinates. These coordinates, followed by J2000 will be fed to an external program if the w command is used.
-gal: If WCS information is available in the image header, track the cursor in galactic longitude and latitude as well as pixel coordinates. These coordinates, followed by galactic will be fed to an external program if the w command is used.
-gd geometry: Specify the size of the image display subwindow and/or the screen position of SAOimage. The format is a standard X geometry statement. This switch works like -geometry, except that width and height (if given) are applied to the display subwindow. The overall SAOimage window is sized accordingly.
-geometry geometry: Specify the size and/or the screen position of SAOimage. The format is a standard X geometry statement. Both size and position may be specified, or only the size or the position. Width and height refer to the dimensions of SAOimage's desktop window (see -gd for sizing just the image display window). +x and +y refer to the upper left corner in screen coordinates. -x positions the right edge from the right edge of the screen. -y would positions the lower edge from the bottom of the screen. Width and height below a minimum size are defaulted to the minimum. Specifying the default minimum size (-geometry 0x0) also triggers SAOimage to use smaller dimensions for its internal windows. Once SAOimage is running, use the window manager's normal size and move mechanisms to make adjustments to SAOimage's main window. -geometry may be abbreviated -g.
-green: Set the color of all graphics to be green. See -blue.
-histeq may be abbreviated -hi.: Set the scaling mode for histogram equalization.
-horizgraph: Use a horizontal auxiliary color graph window, with a color bar along the bottom. See -vertgraph. -hg can be used as a shorthand for -horizgraph.
-i2 width height: Image file is a signed short integer array file of the given dimensions. If the file is square and has no added padding, the dimensions are not necessary. -shortarray width height has the same function.
-i4 width height: Image file is a signed long integer array file of the given dimensions. If the file is square and has no added padding, the dimensions are not necessary. -longarray width height has the same function.
-idev pipename: Specify the name of the named pipe used for listening. The default is /dev/imt1o, which is the default used by IRAF. See -odev.
+/-imtool: Open/close the named input pipe connection and wait for input from IRAF. When open, SAOimage emulates IRAF's imtool. IRAF's image loading and cursor read-back functions are supported. Unlike imtool, SAOimage has only one frame buffer; IRAF's frame buffer numbers are ignored. Listening on the pipe is possible even while reading image files directly. The connection may be opened, closed, or re-opened at any time. When supported, the default mode is commonly to start with the IRAF connection open. See -idev, -odev, and -pros.
-lfrac [fraction of histogram numerical peak]: Set the linear scaling limits to the values where the pixel value distribution is at a given fraction of its peak
-linear: Set the scaling mode to linear.
-log [exponent for exponential curve]: Set the scaling mode to log (exponential), and set the exponent for the curve function e sup n if given.
-lowerleft: First pixel in file represents the lower left of the image, assuming the lines of input run left to right on the screen. This is the IRAF standard and the SAOimage default. See -rotate, -upperleft, and -zero. -lowerleft may be abbreviated -ll.
-lprbuttons: Include the button menu in the hardcopy image (only on color workstations). The default on color workstations includes the area above the button panel, but excludes the buttons.
-mag magnification: Set the magnification factor of the magnifier. This factor relates the magnifier to the magnification of the display window. The default is 4; the magnifier magnifies the image to 4 times the magnification of the main display window (but never less than zoom 1 of the original data).
+/-magnifier: Set the magnifier tracking state initially on or off. With magnifier tracking, the magnifier window is continuously updated to show a magnification of the image the image under the mouse. +/-mt can be used instead of +/-magnifier.
-max [max val]: Set the maximum for the image value range used to compute scaling. The default is to take the maximum from the image shown in the display window. -max with no value resets the default. If the maximum value in the displayed image is lower than the given maximum, the image's maximum vale is used for the scaling range.
-min [min val]: Set the minimum for the image value range used to compute scaling. The default is to take the minimum from the image shown in the display window. -min with no value resets the default. If the minimum value in the displayed image is higher than the given minimum, the image's minimum vale is used for the scaling range.
-mtf: Give the button panel a chiseled look popularized by HP's widget set. This appearance may contrast less with other applications being used at the same time.
-name filename: This switch is only needed if the filename starts with a number or might otherwise be recognized as a switch.
-odev pipename: Specify the name of the named pipe used for sending feedback. The default is /dev/imt1i, which is the default used by IRAF. See -idev.
-oif: Image file is an IRAF image header file in OIF format. If the image filename ends in .imh, this switch is not necessary. IRAF STF and QPOE formats are not supported. Complex data cannot be handled. The data must have at least 2 dimensions. Only the first plane of multidimensional images is read. The data file is read directly by SAOimage (see -imtool and -pros).
-one: The file coordinate of the first pixel is (1,1). The real coordinates of the center of the first pixel are (1.0,1.0). This is the IRAF standard and the default for SAOimage. The second pixel is (2,1). See -zero.
-palette number: Specify the number of read/write color cells to reserve. On color workstations, SAOimage reserves color cells in the default colormap for its own use. SAOimage reserves as many color cells as it can get, up to the number given (the default is 200). If the number given is negative, SAOimage comes up in overlay mode, using 1/2 + 2 of the color cells for overlays and graphics. In verbose mode (see -verbose), SAOimage tells you how many cells it is able to use for display colors. This number can be re-entered at run-time, unless -palette 1 is given, in which case SAOimage stays in halftone mode. -p is an acceptable shorthand for -palette.
-panboxav | -panboxsum | -panboxsamp | -panboxmax: These switches select the kind of image reduction used to fit a picture of the entire image into the pan window. Each pixel is computed from a block of image pixels by averaging, summing, sampling, or taking the maximum. The default is to show the maximum from each block. When zooming in the main display involves reduction, subsampling is always used.
-pros: Virtually identical to the +imtool switch. The difference occurs when the user writes the saved regions to a disk file. imtool emulation includes writing only an IRAF list file giving center coordinates only. With -pros, SAOimage's normal region descriptor file will be written in place of the simpler list file. One may switch between this mode and +imtool, or close the IRAF connection with -imtool.
-quiet: Disable verbose mode;-q may also be used. See -verbose.
-r4 width height: Image file is a real*4 array file of the given dimensions. If the file is square and has no added padding, the dimensions are not necessary. -floatarray width height has the same function.
-r8 width height: Image file is a real*8 array file of the given dimensions. If the file is square and has no added padding, the dimensions are not necessary. -doublearray width height has the same function.
-red: Set the color of all graphics to be red. See -blue.
-rmax [max val]: Set maximum value for reading from the image file. This value is used as the maximum value when images are pre-scaled to fit the 16 bit (signed short) working buffer.
-rmin [min val]: Set minimum value for reading from the image file. This value is used as the minimum value when images are pre-scaled to fit the 16 bit (signed short) working buffer.
-rotate 1,2,or 3: Rotate the image 90, 180, or 270 degrees (respectively) before displaying it. Rotation is applied after conversion to a lower left coordinate system (-ll) if such conversion is also requested. This is useful for images when the CCD was not mounted North-up. -rot can be used as a shorthand for -rotate.
-scalebias scale bias: The data in the image file should be scaled and biased to get the true image value (TrueValue = (scale * FileValue) + bias). This cannot be used with the -fits image type (scale and bias are in the FITS header), nor with -imtool or -pros (they are passed by IRAF). -sb is a shorthand for -scalebias.
-skip bytes: Skip over the given number of bytes at the head of the file before reading data. This is used to skip header information or the first
image if two images are stored in one file. -header and -sk are aliases for -skip.
-sqrt [inverse of exponent for geometric curve]: Set the scaling function to square root (geometric), and set the inverse of the exponent for the x sup {1/n} curve, if given.
-u1 width height: Image file is an unsigned byte array file of the given dimensions. If the file is square and has no added padding, the dimensions are not necessary. -chararray width height has the same function.
-u2 width height: Image file is a unsigned short integer array file of the given dimensions. If the file is square and has no added padding, the dimensions are not necessary. -ushortarray width height has the same function.
-upperleft: First pixel in file represents the upper left of the image, assuming the lines of input run left to right on the screen (see -rotate and -lowerleft). This switch does not override IRAF WCS image coordinates. -upperleft may be abbreviated -ul.
+/-verbose: Set verbose mode on or off. In verbose mode, informative statements are printed to the terminal window when various actions are taken. The default mode is to be verbose. +/-v can be used instead of +/-verbose.
-vertgraph: Use a vertical auxiliary color graph window, with a color bar along the left side. See -horizgraph. -vg can be used as a shorthand for -vertgraph.
-wcscom [format for command to be executed]: Set the command to be executed when the w key is struck, where the world coordinates are substituted for %s in the string. Underscores should be used instead of spaces.
-wrap [number of wraps within scaling range]: Set the scaling mode to wrapped linear, and set the number of wraps for this mode, if given.
-zero: The file coordinate of the first pixel is (0,0). The real coordinates of the center of the first pixel are (0.5,0.5) which makes the very edge (0,0). This is the standard coordinate system for image displays, but not the default for SAOimage. The second pixel is indexed (1,0). See -one.
-zf zoom factor: Zoom the initial display of the image by zoom factor. A number larger than one makes the image larger by that factor, using that many display pixels per image pixel. A fractional zoom factor displays that the image with that fraction of a display pixel per image pixel.

USAGE

Refer to the SAOimage User Manual for detailed descriptions of all functions.

Most control actions take place within the context of a mode. Modes are selected by clicking on menu buttons in the top row of the button panel. Each menu mode brings up its own submenu buttons (the lower row in the button panel) for mode specific selections. Actions and submodes are selected by clicking on buttons in the submenu row of the menu panel.

The mouse controls specific functions in both the main display window and the pan/zoom window. In the main display window, the function of the mouse is determined by the mode and submode selections from the button menu. The function can also be recognized by the appearance of the mouse pointer icon.

The button interface is designed to be user friendly. The user is encouraged to try any and all buttons to become familiar with their functions. To exit, use the QUIT button in the etc submenu (click on etc, then click on QUIT).

Reading images

To read an image directly from a file, give its name anywhere on the command line. The -name switch is needed only when the image file name could be mistaken for a number or switch. SAOimage recognizes the .fits and .imh filename suffixes as belonging to FITS and IRAF OIF files. All other file types must be specified by an appropriate file type switch.

Raw array file types must be specified by an array data type switch (-u1, -u2, -i2, -i4, -r4, -r8) followed by width and height dimensions. To skip over a file header, use the -sk switch followed by the number of bytes. This can also be used to skip over entire images, if more than one are stored in the same file.

Use with IRAF

To emulate imtool and communicate with IRAF tasks, use either the -imtool or -pros switch. The two switches indicate which file format to use in recording saved cursors or regions. With -imtool, an IRAF list file containing only center coordinates is used (like that of imtool). With -pros, a file containing a full description of the saved cursors and their dimensions is used. The latter file can be read by tasks in the IRAF PROS spatial package for making image masks and performing image analyses. Both file types are ASCII and can be read and edited by the user. In either case, the file is not actually written until the user clicks on the write button in the region submenu. Both file types can be read back to reproduce the saved cursors.

New command input

A new command line can be entered at any time, by selecting the new button in the etc submenu or striking the N key on the keyboard. This allows the user to read in new images, change in and out of -imtool or pros mode, set new scaling parameters, or change the number of reserved display color cells. Most command line switches (except -d, -g, -gd, -red, -green, -blue, and -vertgraph) will be accepted at any time.

When a new command line is requested, the previous command line is presented in an emacs-like popup editor for editing. Ctrl-N clears the previous line. Striking the RETURN key enters the line in the popup window as the new command. Ctrl-C returns with no action taken.

Using the mouse

Most mouse interactions are based on mouse dragging (holding a button down while moving the mouse). The user should try clicking and/or dragging the mouse in each subwindow to become familiar with its functions. Modes selected in the button panel determine the response to the mouse buttons in the main display window.

In Scale mode, the mouse buttons control blinking of displays (saved by clicking with the same mouse button in the blink submenu button).

In Color mode, mouse dragging stretches and shifts the color map as per the contrast/bias, threshold/saturation, and gamma submenu selections.

In the color graph window, color table vertexes may be added or moved by clicking or dragging with the LEFT (red), MIDDLE (green), or RIGHT (blue) mouse buttons. The graph will update continuously only if tracking is turned on.

In Cursor mode, the mouse controls the size and locations of cursors. The rule is: LEFT button for position, MIDDLE button for size, and RIGHT button for angle or deletion (depending on the cursor).

Cursors

For box and ellipse cursors, MIDDLE button sizing is restricted depending on whether dragging started on a side or near a corner.

With the point cursor, the LEFT and MIDDLE buttons save the current mouse pointer position with a + or - indication, while the RIGHT button deletes saved points.

For the polygon cursor, the MIDDLE button adds or moves a single vertex, while the RIGHT button will delete vertexes. The LEFT button moves the whole polygon.

When annuli is set for a box, circle, or ellipse cursor, the MIDDLE button adds or resizes an annulus, while the RIGHT button deletes annuli.

For manipulating cursors, the ovlay selection in the Color submenu, enables the cursor to track smoothly as an overlay graphic. The region submenu button brings up another submenu with selections to display, review, and edit the saved regions, and read from or write to disk files.

Pan and zoom

In Pan mode, and in the pan window (regardless of mode), the LEFT button selects the center of the image, while the MIDDLE button selects the edge of the display, zoomed from the given center. When either function is dragged, the rectangle in the pan window shows the area that would appear in the display when the button is released.

Keys

In the cursor mode, the S and E keys, save the current cursor in a region list, while the D and DELETE keys can be used to forget a region. At any time, with the pointer in the display or pan windows, the T key prints a table of pixel values at the pointer position to stdout. The 4 arrow keys can be used for fine movement of the pointer in any window. The SHIFT and SHIFT LOCK keys will reverse the magnifier window, color graph window and coordinate tracking status. The N key summons the pop-up editor for new command input. The A key raises and redraws all of SAOimage's windows.

BUGS

SAOimage does not allocate its own colormap and thus fails with static color (i.e. NeWS) window managers. X resource settings of a user's default preferences are not read.

ONLINE HELP

Additional information about SAOimage is available on the World-Wide Web at http://tdc-www.harvard.edu/software/saoimage.html