SEGAL

Section: User Commands (1)
Updated: 1 May 1990
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NAME

segal - (SEGmentation AnaLyzer): binary mask editor/builder/analyzer for HIPS images.

SYNOPSIS

segal [-i image][-m mask] [-v] [-c NN]

DESCRIPTION

segal is an X-windows tool for interactively editing, creating, and analyzing binary mask images. In segal a mask is transparently laid over the original image, then using the mouse, one can "cut" or "fill" in the mask, exposing the image beneath. A new mask can be created by selecting the image threshold value. The user can select between various size paint/erase cursors, and select various zoom magnifications, to aid in building the mask. The image must be of type byte, and it is best if the image is contrast enhanced using a program such as mahe or hstr. A mask can also be edited/created without an image overlay. segal also does statistical measurements on objects in the binary mask image.

OPTIONS

-i image: image file name (must have HIPS header)
-m mask: binary mask image file name (must have HIPS header)
-v: sets segal to verbose mode, which prints several status/debugging messages along the way.
-c NNN: Sets the color (Hue) of the overlay blend. This number is an integer value for the hue (must be 0 to 360). Default value is 170 (dark green).

This program was coded using the xview toolkit, which follows Sun's Openwindows/ OPEN LOOK specifications. Therefore most of the standard xview windows arguments should work, as well as anything specified with OpenWindows.foo in your .Xdefaults file. In particular, use "OpenWindows.WindowColor: colorname" in the .Xdefaults file to set the background color for the control panels.

Here are some standard xview options that may be useful:
-display hostname:display: Specify the name of the display to manage. Overrides the DISPLAY environment variable, if any.
-position x y: Location of the segal control window.
-foreground_color red green blue: Sets text in the control windows to the color specified by (red, green, blue)
-help: List of all window control command arguments.

MAIN CONTROL WINDOW FUNCTIONS

Load Pop Up -

Select either image/mask. Enter the image/mask directory. Enter the image/mask filename and either press return or push the Load button.

Create Pop Up -

Enter the mask directory. Enter the mask filename to create and either press return or push the Create button.

Edit Window -

Must have a region cropped to edit anything. Do this by dragging out a rectangle in the main image window with the mouse and any button. A zoomed version of the cropped region will appear in the Edit Window. Next, select either Mask/Image for the Brush Mode. This determines what will be edited by the Edit Window Paint Brush. The Mask can be Painted or Erased with the brush. The image brush is either Additive or Subtractive by a certain Amount that can be changed.

Other things that can be selected:

Mask brush shape, Either brush size, and Zoom Magnification. The Original Button restores the image and the mask back to their original (loaded) states. The Undo undoes the last edit of the brush. Save is not currently working properly. (This, it turns out, doesn't affect the rest of Segal - the mask is automatically saved at various points). By holding down shift or control and a mouse button in the zoomed image, the pixel value at that location in the image is displayed in the main image window, the zoomed image window, and Segal's Main window. If the size of the zoomed window is larger than 500 in any direction, scroll bars appear to aid in keeping windows on the screen and accessible.

Frame Control Window -

Only is active for multi-framed images. When selected, the Frame Control Window pops up. With the Current Frame Slider allows any of the frames to be displayed in the main image window. By entering values in the Movie From and Movie To Text fields and then pressing the Start button, Segal can be made to display a series of frames.

Stack Loading:

This determines whether each time a frame is selected to be displayed Segal loads into a 3-d buffer enough frames above and below that frame to allow the application in 3-d of a gradient matrix in the growth process (see GROW under Mask Control Window). This is optional because on some computers memory or i/o constraints could seriously hinder the operation of Segal, and for most images the precision of 3-d gradient matrix application is not critical.

Display Control -

This window contains miscellaneous settings pertaining to the way Segal displays the image and the mask (or both). The frequently used features of this window are found in appropriate other windows in Segal.

Display Image/Mask/Both Setting:

Choose one. (Also found in Mask Control Window)

Combination Method:

Determines how mask is displayed in the Display Both mode. Color Blend gives the translucent green mask and Overlay gives a solid white mask. Mask Model: Please leave this on build or you will get confused!!! Original Check Box: Check this box and a copy of the main image window will pop up. This is useful when displaying in the Both mode. Image Contrast Slider: The higher the slider, the higher the contrast of the main image. Opacity for Image Blend and Mask Blend Sliders: Other good things to leave alone.

Mask Control Window -

This is where the real power of Segal is evident: the semi-automatic creation of segmentation masks. A simple Threshold can be obtained by pressing the Threshold Button. The Threshold Window will pop up, displaying a histogram of the selected region or the whole image, depending on the Portion Setting (see below). The Threshold Window offers a slider for both an upper and a lower threshold value. When these sliders are set, a push on the Threshold Button in the Threshold Window will perform a simple threshold on the selected Portion of the image. The mask is the result of the threshold. Other useful operations on a Portion of the image to create/delete a Portion of the mask are performed by selecting the Portion and then pushing the Fill, Clear, and Invert Buttons. The Polygon Mask Button is currently not working.

Growth Options:

The Original and Undo Buttons are the same as on the Main Window and the Edit Window. The Stop Button stops the growth during the multi-frame growing (when From is selected as "Beginning Frame to Ending Frame"). Portion: specifies what to apply growing, thresholding, filling, clearing, and inverting to. From can be set to Seed Points this Frame, Beginning Frame to Ending Frame, This Frame to Previous Frame, and This Frame to Next Frame. To see an explanation of these, see the tutorial. An explanation in simple English of the growth algorithm will simplify the meaning of each of the rest of the items in the Growth Options. First, all the edges of the mask in the Portion are found. Then, Segal attempts to grow the mask out in every direction, flood filling from the edge of the mask. The growth is stunted by one of the following:

    Candidate point:
        is already a mask point.
        has a gradient higher than the gradient slider.
        has a value > upper threshold value.
        has a value < lower threshold value.

Gradient:

When growing, specifies the highest gradient (as calculated by the particular gradient matrix selected) allowed for a candidate pixel to become part of the mask.

Matrix Type:

Simple Gradient, Sobel, Laplacian, Kasvand, etc.

Matrix Size:

The smaller the faster the growing; the larger the less image noise will affect the gradient.

Apply in:

Apply a 2-d matrix to the Current frame or (slower but more precise) apply a 3-d matrix to the stack of frames (stack loading from Frame Control must be "yes").

Upper and lower threshold values:

Set these to the highest and lowest pixel values to be included in the mask when growing. Obtain the pixel values by dragging the mouse in either the main image window or the Edit Window while pressing the shift or control key.

HIPS Filter -

Not working yet.

MOUSE BUTTON OPERATIONS

Left, middle, and right mouse buttons all have the same effect.

ENVIRONMENT

DISPLAY Specifies the screen for the program to be displayed at. To set, use setenv. For example: setenv DISPLAY unix:0.0 for your local machine.

TRADEMARKS

OPEN LOOK is a trademark of AT&T.
The X Window system is a trademark of the Massachusetts Institute of Technology.
OpenWindows is a trademark of Sun Microsystems, Inc.

AUTHOR

Brian Tierney, LBL email: bltierney@lbl.gov

DIAGNOSTICS

This program currently prints most error messages to stderr (the window in which the program was started). If nothing happens when you think something should be happening, check for an error message in that window.

BUGS

With large images, the image is sometimes only partially displayed when first bringing up the image window. The fix this, click the mouse in the button labeled 'image'. The largest paint and erase cursors sometimes 'break up' when moving on the edit window. I believe this must be a xview toolkit bug. Report all other bugs to Brian Tierney.

This document was created by man2html, using the manual pages.
Time: 01:44:50 GMT, December 05, 2024