
 TN-Image Help File 
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 This help file is is ordinary ASCII format. New comments or corrections
 can be added as needed, provided that the following format is adhered to:

 (1) Line length can not exceed 80 characters.
 (2) The first character of each line is either a digit (indicating the
     help topic) or a space.
 (3) A maximum of 40 lines per help topic.

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1 General Help - (F1)

  Unless you select a region, most operations will be applied to the 
  entire image. To select a region, click on one corner and drag to the 
  other corner with the mouse.

  To add text - move to the desired location and begin typing.

  To move the image around - Click on one of the 4 arrows in the menu bar.
     The amount of movement can be changed by pressing the gray (+) or (-)
     keys. These keys also change the distance the cursor will travel when
     it is moved with the arrow keys.
  
  There are also shortcut methods for some operations:
     Selecting foreground color - click on desired color in the displayed
       palette with the left mouse button.
     Selecting background color - click on desired color in the displayed
       palette with the right mouse button.
     Drawing lines - Press F2 to toggle line drawing mode on/off.
     Clicking on the menu bar also turns off line drawing, box drawing,
       densitometry, region scanning, and most other operations.

  See the manual TNIMAGE.DOC for more detailed information.

2 Help - Pixel interaction mode
  Determines how 2 pixels will interact when an image is copied
  over another or loaded from disk. You can subtract 2 images, or
  offset the same image by a small amount and then subtract it (to create a
  3D effect). 
     Overwrite ( default )  - This is the normal, fast mode.
     Maximum                - Pixel is set to the larger of the 2 values.
     Minimum                - Pixel is set to the smaller of the 2 values.
     Add                    - The 2 values are added.
     Subtract               - The 2 values are subtracted.
     XOR                    - The 2 values are XOR'd.
     Average                - The 2 values are averaged.
  For the pixel values to become permanent, you must create a new image by
  selecting "Create image" from the 'Files' menu. Otherwise, they will revert
  back to their original values when the image is redrawn.

3 Help - Save image
  Transfers an image or selected region to disk.
  
  Save entire image - This option will cause the currently-selected image 
    to be saved in its entirety.
  Save selected region - Causes the selected screen region (which may contain
    parts of 1 or more images) to be saved. If multiple images overlap,
    the pixels from the foreground image are saved. 
  TIFF/PCX/GIF/IMG/Custom - Selects the image file format.
  Color/gray scale vs. monochrome - Select monochrome for black-and-white
    images. Monochrome images will be much smaller than color/gray scale
    images but contain no color or gray. Color and gray scale images are
    treated identically. 
  Filename - Click on this box, and type in the desired filename, then press
    <Enter> or click the mouse when finished.
  Image number - Not normally changed. This indicates which image is currently
    selected in case you want to save the entire image.
  Extra TIF param.(for `Other') - Selects non-standard color depths. Only
    used if file format is TIF or Custom and Image Type is `Other'.

4 Help - Print
  Prints an image or selected region on a PCL printer.
  
  Resolution - Enter a value such as 150, 300, 600, or 1200 dots/inch, 
    depending on the resolution of your Laserjet-compatible printer.
  Positive/negative - Positive prints the image exactly as it appears on
    your screen, negative prints the inverse.
  B/W, RGB, CMY, CMYK - Select the desired print mode. For RGB, the printer
    automatically fills the entire page with black. Use B/W unless you
    have a color printer. CMY or CMYK is recommended for color printing.
  Print entire image/ print selected region - Select whether you wish to print
    the entire image, or only the screen region which you selected most
    recently (if no region was selected, it will print the entire image).
  Dither size - This determines the number of gray or color levels which 
    appear in the print-out. For example, dither size of 8x8 corresponds 
    to 64 different possible levels. A larger dither size also means the 
    print-out becomes larger.

5 Help - Change palette
  Changes the color values for 8-bit images.
  
  Click on the desired palette.
  Attaching the palette to the image causes the change to be permanent.
  These pre-defined palettes are available:
       Gray scale      Spectrum           Multi-color 1,2, or 3
       RGBI            Black to green     Zebra
       Other (selects from 10,000 other pre-defined palettes).
  Brightness - changes the color saturation.
  Rotate palette - causes the color map to be shifted to lower or higher
    pixel values (depending on where you click).
  Create - Allows you to graphically create your own palette. The palette
    can also be saved on disk.

6 Help - Densitometry
  
  Measures the density and area of an object on the screen.
  
  Pixel compensation -  If set to "on", the pixels are converted into 
    values proportional to the optical density originally calculated by the
    scanner. If set to "off", the results are raw intensity values.
    This only has an effect if the image contains an optical density table.
  Maximum signal - Selects whether the image is a white-on-black or
    black-on-white image. If the maximum signal is 'black', then a completely
    black region will have the strongest signal.
  Area selection -
    Automatic mode:  Click near the center of the region to be analyzed.
      The boundaries of the region will be  calculated automatically. The 
      area actually analyzed temporarily changes color. You may need to
      adjust the background level so the correct area is analyzed.
      For extremely noisy images, it may be helpful to delineate the outer
      boundary of the region to be analyzed by first drawing a black line
      around it.
    Manual mode: You must select a rectangular region each time.
    Fixed size mode: You must select a rectangular region for the first 
      measurement. This is used as a template so that all subsequent 
      measurements use the same number of pixels.
  See also `Scan region...' for an alternative method of densitometry.

7 Help - Filter -  Filters an image or selected region.
       Low pass  - Blurring filter
       High pass - Sharpening filter
       Laplace   - Edge detection
       Sobel     - Sobel edge enhancement
       Background subtract - Removes only low spatial frequencies.
         Eliminates slow gradients and broad smudges from image. The entire
         image will probably get lighter or darker, depending on whether the
         "maximum signal" is set to "white" or "black".
       Background flatten (de-trending) - Removes color gradients. 
       Noise filter - Eliminates extraneous pixels.
       Sharpen / - Adds shadow at 45ø angle (freeze-fracture effect).
       Sharpen | - Adds shadow at 90ø angle (freeze-fracture effect).
       Sharpen / - Adds shadow at 0ø angle (freeze-fracture effect).
    Kernel    - Determines the number of surrounding pixels to be
       convoluted with each pixel. In conjunction with kernel multiplier,
       this determines the size range that will be emphasized or smoothed.
    Kernel multiplier - Determines the area that is covered by the selected 
       kernel. A higher value results in filtering lower spatial frequencies.
    ñRange (median)  - Determines the maximum deviation from the median
       value that is permissible during noise filtering. If a pixel deviates 
       from the median by more than this amount, the median is substitued. 
    Amount of filtering - How much filtering is desired (10=maximum).
    Pseudo color images (such as GIF's) should be converted to 24 bits/pixel
       before filtering.

8 Help - Scan region
    Performs densitometric analysis on a screen region by scanning it from
    one side to the other.
    Select coordinates mode - In this mode, you must reselect the region to 
     be scanned each time. This is done by:
        Click on one starting corner with left mouse button.
        Drag to the other starting corner and release mouse button.
        Click on one ending corner (This can be on the left, right, above, or
          below the starting corners).
        Drag to the other ending corner and release. Scanning will then start
          in the direction of 'start' to 'end'.
    Repeat scan - In this mode, the previously-selected region is re-scanned.
    Maximum (black or white) - Determines whether black or white is to be
       regarded as the largest signal.
    Pixel compensation - If checked, converts the pixel values to O.D. 
       using the conversion table (if any) generated by your scanner.
    Diagonal / Snap to 90ø - If 'diagonal' is checked, scanning can be done
       on features that are oriented at any angle. If 'snap to 90ø'is checked,
       the starting and ending edges will automatically 'snap' to the closest
       value (0 or 90ø), causing diagonal areas to be scanned as a series
       of vertical or horizontal lines.  Snapping to 90ø is faster.
    Automatically save scan - If checked, the data will be saved in an ASCII
       file after each scan.
    Filename - Filename under which the scan will be saved. If the 1st 8
       characters are all digits, the filename will be incremented as a 
       number each time, e.g., '1000.dat' will become '1001.dat'.
    Peak area measurement - Use mouse to click and drag desired region on 
       the density profile plot.  The area is shown in the lower right. 
       Or, click on "Peak areas" to get a table of all peaks. You can save 
       this table by clicking on `save to disk'.

9 Help - Fill an area

   Flood-fills a screen area with color.

   Fill type - Select between a solid color, or a gradient which changes
     in the vertical or horizontal direction.
   Fill color - The color to be used when filling with a solid color.
   Max border color _  The region that includes all contiguous pixels between
   Min border color    these two values will be filled.

   Maximum gradient color -  The color value to be used at the top (for
     vertical fills) or far left (for horizontal fills). This can be any
     integer. The gradient fill will calculate the steepness and starting 
     color by interpolating between the maximum and minimum gradient colors. 
     Thus, the 'maximum' color can be lower than the 'minimum' color to 
     create a decreasing gradient.
   Minimum gradient color - The pixel value to be used at the bottom (for
     vertical fills) or far right (for horizontal fills).

   To start filling the area, click on a point inside the region to fill.
   At any time, you can stop the fill process by pressing <ESC>.
   If no filling occurs, it may be necessary to change the border colors.

10 Help - Click box
    The minimum and maximum acceptable values are shown. Click on the
    arrows on each side of the indicator bar to increase or decrease
    the value, or click and drag the vertical position indicator until
    the desired value is obtained.
    
    You can also type the number directly, by clicking on the number field.

11 Help - Read image
  Transfers an image from disk to the screen.
  Filename selection:
  Click on the "Filename" box, then type the filename, or click again
  to select a file from the list.  Click on desired file with the mouse. 
  The TAB key toggles between the filename list, directory list, and drive 
  list. Clicking on the desired list has the same effect.

  Click on the small triangles in the upper and lower right of the list
  to scroll through the list. Or, click on and drag the indicator to
  move rapidly through the list.
  The arrow keys can also be used to scroll up and down in the
  currently-active list.
  To change drives, click on the desired drive name.

  Positive/negative: Determines whether the image should be color-inverted.
  Vertical/horizontal: Determines the screen orientation for the image.
  X-position: Left x-coordinate of the image.
  Y-position: Upper y-coordinate of the image.
  X size: Final size of the image in the x dimension, as a fraction of the
     original size (0-1). (The x or y dimension is relative to the orientation
     of the image, not the screen).
  Y size: Final size of the image in the y dimension, as a fraction of the
     original size (0-1).
  Note: Targa format images must have the extension .TGA to be readable.

12 Help - Create Palette
  Creates a new, custom palette for 8-bit images.
 
  To change Red, move the mouse cursor to the top box.
  To change Green, move the mouse cursor to the middle box.
  To change Blue, move the mouse cursor to the lower box.

  Then click and drag to create a graph of the intensity of that color
  for each color value between 0 and 255. Click on 'OK' when finished.
  
  Click on 'smooth' to make the new palette smoother.
  

13 Help - Plot
    
  Click and drag on the graph to select a range of X-values to be integrated.
  Click OK when finished.  
  BL Smoothness: Adjusts the frequency cutoff of the automatic baseline
     calculation. A higher value increases the smoothness of the calculated
     baseline.


14 Help - Color Intensity

  If the region you selected contains a monochrome region, adjust 
  the desired change in brightness from -255 to 255 (0=no change). The
  pixel values in 8-bit regions will be incremented or decremented
  by this amount.  Usually this means the image gets lighter or darker;
  but the actual effect on the appearance of the image is determined 
  by the current palette.
  
  If the region you selected contains a color (16,24, or 32 bit/pixel)
  region, adjust the change in brightness of the red, green, and blue 
  components as desired. This will adjust the colors in regions containing 
  color images.

  To individually adjust the RGB components of an 8 bit/pixel image,
  you must convert the image to color first (select `Image'...`Convert
  color depth'). 

  Intensity and contrast can also be adjusted interactively by dragging
  on the palette.  
 
  "Color/brightness" tries to use the color palette if possible whereas 
  "Change pixel value" always changes the actual image.

15 Help - Significant digits

  This selects the number of decimal places that will be displayed
  when floating-point numbers are used, such as during densitometry.  
  

16 Help - Color settings
   Sets various color-related items.
 
   Color reduction method determines the algorithm used when viewing
   a hi-color image (15 or 16-bits/pixel) or true color image (24 or
   32 bits/pixel) when TN-Image is in an 8 bit/pixel screen mode. This
   requires mapping the real colors into a palette.
   
   TN-Image can use quantization to find an optimal palette, or try to
   fit the image into the currently-selected palette.

   Luminosity factors are used when converting from color to gray scale.
   They should be between 0 and 1 and total to 1.0.

   Active Color Planes - Selects which colors (r,g, or b) to which 
   all image manipulations are applied.
   
17 Help - O.D. Table

   The optical density table is used to convert pixel values to optical
   density. This is also known as "gamma correction" and is only used
   for 8 bit/pixel images. Some image files contain their own O.D. table.
   
   TN-Image uses this information when "pixel compensation" is selected
   in densitometry and region-scanning modes.
   
18 Help - Histogram (indexed-color screen modes)
   Displays graphs showing the distribution of intensities and color 
   values in the image.

   The top box displays the number of pixels in the selected region
   for each of the 256 possible pixel values (intensities).

   The other 3 boxes display the palette color attributes of the same
   pixels, for each of the 64 possible red, green, and blue palette values.

   Clicking on one of the the 4 plot areas selects which plot has the
   current focus. Displayed parameters and any area measurements, 
   smoothing, etc., apply only to the plot that has the current focus.

   All 4 boxes are re-scaled whenever a change is made that affects
   the maximum or minimum values.
   
19 Help - Histogram (color screen modes)

   Displays graphs showing the distribution of color values in the image.

   The 3 boxes display the number of pixels in the selected region
   for each of the possible red, green, and blue color values. 

   Clicking on one of the the 3 plot areas selects which plot has the
   current focus. Displayed parameters and any area measurements, 
   smoothing, etc., apply only to the plot that has the current focus.
   
   All 3 boxes are re-scaled whenever a change is made that affects
   the maximum or minimum values.

20 Help - Math

   Performs a point-by-point mathematical transformation of the intensities 
   or red, green, and blue values in the selected image or region. 
   
   The decision of which formulas to apply depends on the color depth of 
   the image at each point - if the point is an 8 bit pixel, the intensity 
   is changed; otherwise, the r,g, and b values are changed.
   
   You can enter any mathematical equation using the following operators:
        ()  +  -  * (multiplication)  / (division)   ^ (exponentiation)
   You can also use these predefined variables for intensity, red, green,
   and blue, respectively:       i  r  g  b  
   
   Example:         i=i/2 + i^2
                    r=g-5
                    g=(b+r)*g-17;
                    b=b^1.23;
   Note that the r,g,and b values are bounded by 0 and 31, 63, or 255 for
   15-, 16-, and 24-bit/pixel screen modes, respectively. `i' is also 
   limited by 0 and 255.
   
   
21 Help - Fourier Transform

   Select `forward' or `reverse' to perform Fourier transform, or select
   `change display only' if you only want to change which component is
   displayed. The display can be switched between the real and imaginary 
   components of the Fourier transform.

   To perform Fourier convolution or deconvolution, you must specify two
   images. Both images will be FFT'd and the first image will be multiplied
   or divided in the frequency domain by the second image, and then 
   reverse-transformed to give the deconvoluted or convoluted result.

   Don't forget to set the display to `real' before performing a reverse 
   FFT, since the original image does not have an imaginary component and
   would otherwise appear black.
   
   FFT's are sensitive to the background and to the number of separate
   colors in the image. Improvement can sometimes be obtained by setting
   the screen background to black. See the manual for other tips.

22 Help - Calibration
   Calibrates the x and y coordinates in the image to correspond to some
   other parameter such as molecular weight.
 
   Click with the mouse at the points to use for calibration, and for each
   point, enter the corresponding calibration value. When finished, press 
   any key. The calibrated value will be continuously displayed in a window.
   To turn off the calibration window, select "Calibration" again, and
   click on "Cancel".

   2-D linear calibration multiplies the x and y coordinates by a factor
   to calibrate distance measurements. The result is the distance from the
   upper left of the image.
   
23 Help - Draw curve 
 
   Linear - Fits a straight line through the control points.
   Bezier - Draws a Bezier curve.
   B-Spline - Draws a B spline curve.
   
   To draw a curve, click with the mouse at desired positions of control
   points. The points can be moved by dragging them to a different location.
   When you have enough control points, press a key to make the curve
   permanent.
   
24 Help - Creating custom format images
   Sets parameters for a new image format.

   `Target platform' is the type of computer that created the image.
   For most UNIX workstations, Mac's, and Cray and similar mainframes, 
   select `Mac'. For IBM and similar mainframes, select `MVS'.

   `Bit packing' selects whether bits are to be packed left to right 
   (TIF-like) or right to left (GIF-like). This is especially important 
   if the total bits/pixel is not a multiple of 8.
   
   If `Use header' is checked, specify the file containing the header
   to copy, the number of bytes to copy, and the offset in the header
   where the x (image width) and y (image length) are to be placed.
   
   `Offsets' are the positions in the image file where various information
   will be stored. Setting the offsets to -1 will cause them not to be
   stored.
   
   `Bytes to skip' must be a multiple of the no.of bytes per pixel.
   See manual for details.

25 Help - Multiple click box
    For each variable (e.g.,red, green, and blue), the minimum and maximum 
    acceptable values are shown. Click on the arrows on each side of the 
    indicator bar to increase or decrease the value, or click and drag 
    the vertical position indicator until the desired value is obtained.
    
26 Help - Calibrate
    Select "New calibration" to calibrate an image or background. 
    Select "Hide calibration" to temporarily turn off the calibration window. 
    Select "Un-hide calibration" to turn on the previous calibration window. 
    
27 Help - Grayscale adjustment
    Changes the mapping of grayscale values to the screen. The grayscale
    values are also filtered through the currently-selected palette, which
    allows pseudo-color.
    This option only has an effect on monochrome and pseudo-color images.
    It is mainly useful for displaying monochrome images greater than
    8 bits per pixel, and for enhancing contrast of low-contrast images.

    Image white value = the highest pixel value to view in the image.   
    Image black value = the lowest pixel value to view in the image.   
    Screen white level = the highest screen gray level to produce.
    Screen black level = the lowest screen gray level to produce.
        
28 Help - Rotate palette
    Click on "-1" to rotate palette downwards.
    Click on "1" to rotate palette upwards.    
    
    
29 Help - Contrast
    If the image or selected region contains monochrome pixels, select 
    the contrast factor for the monochrome portion of the image.

    If the image or selected region contains color pixels, select contrast
    factors for the red, green, and blue components of the color portion.
    
    A contrast factor of 100 = no change.

    Intensity and contrast can also be adjusted interactively by dragging
    on the palette.  

30 Help - Macros
    Enter one command per line.
    Any menu item can be part of a macro, with the following caveats:
    1. Spaces should be replaced by underlines (_)
    2. Periods and check marks should be omitted.

    In addition, the following non-menu commands can also be used:
      beep   load   save   print   fill   dos   color   brightness  size
      select_region  select_image    goto   loop   palette   exit
      messages  convert
 
    Many of these commands require string or numeric parameters. The number
    is usually the same as the order in which the item would appear in the 
    menu or dialog box.  See manual for details.
    
31 Help - Create image

    You can create an image by clicking and dragging with the mouse, setting
    a fixed size and position, or by copying or resizing another image. 
    
    For 'fixed size', you must enter the x and y size (in pixels), and 
    the x and y position for the upper left corner of the image. 
    
    For 'use mouse', use the mouse to select the region for the new image.
    
    For 'copy another image', enter the number of the image to duplicate.
    
    For 'resize another image', enter the image number of the image to 
    duplicate, the new x and y size (in pixels), and the x and y position 
    for the upper left corner of the new image. 
    
32 Help - Trace curve
 
    Click on the image at the leftmost edge of the curve to trace. 
    Curve tracing will proceed from left to right.


33 Help - Measure
  
    To measure distance - click at starting point and drag to ending point.
    To measure angles   - click and drag twice to define 2 lines. The
    angle between the lines in degrees is calculated. (The lines are
    assumed to extend indefinitely in either direction).
    
      