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Text File | 1997-05-19 | 28KB | 607 lines

TN-Image Help File ------------------------------------------------------------------------ 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. No copyright restrictions apply to this file. If you pass this file to another person, please indicate in the file that you have modified it, to avoid confusion. ------------------------------------------------------------------------ 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. If image colors are wrong after some operation, try pressing Alt-R to rebuild the screen display. 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 45¯ angle (freeze-fracture effect). Sharpen | - Adds shadow at 90¯ angle (freeze-fracture effect). Sharpen / - Adds shadow at 0¯ 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. ÒRange (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 90¯ - If 'diagonal' is checked, scanning can be done on features that are oriented at any angle. If 'snap to 90¯'is checked, the starting and ending edges will automatically 'snap' to the closest value (0 or 90¯), causing diagonal areas to be scanned as a series of vertical or horizontal lines. Snapping to 90¯ 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 - Configure 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. Raise image on focus - If checked, clicking on an image or otherwise selecting it will bring it to the foreground. Multiple windows - If checked, each image will be created in a separate window. 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 and functions: () + - * (multiplication) / (division) | bitwise OR & bitwise AND ^ bitwise XOR ~ bitwise NOT sin cos tan sinh cosh tanh asin acos atan sqrt asinh acosh atanh abs log (natural logarithm) ln (natural logarithm) log10 (base 10 logarithm) exp pi cbrt (cube root) rand (random number based on specified seed) The following two-parameter functions are supported: max min pow (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. To use to data in other images, use the variables: image[ino][frame][x][y] red[ino][frame][x][y] green[ino][frame][x][y] blue[ino][frame][x][y] where "ino", "frame", "x", and "y" are expressions for the image number, frame (if image is 3D), and x and y coordinates. Complex math on Fourier-transformed data is not currently implemented. 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 "Macro Programming Guide" in 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). 34 Help on Help Click on "Help" to get help. For more information, please consult the manual. 35 Palette settings No.of colors to leave untouched - Increase this number if flashing occurs when moving the mouse. Decrease the number if colors are displayed incorrectly. 36 Font Click on the appropriate buttons to change the parameters as desired. To select a font not listed, click "other" and type the font specification (for example, *times-medium-r*240*). See your X manual for details. type "xlsfonts" for a list of fonts on your system. 37 Help - 3D Image Specify the total number of frames and the width and height of each frame in pixel units. 38 Help - Sample Palette Click left mouse button on desired color to change foreground color. Click right mouse button on desired color to change background color. Drag the '=' at right to change brightness by moving palette up/down. Drag the two '<' at right to change contrast by squeezing or expanding the palette. Depending on what other applications were running when TN-Image was started, there may be a variable number of fixed colors which belong to other programs and cannot be changed. 39 Help - Scanner Interface Click on "Preview Scan" and set the desired bits/pixsl and the approximate contrast and brightness settings. A low-resolution scan will be performed. Select the desired region and click "Image scan" to scan the image at full resolution. 40 Help - Paste threshold Select a pixel value to determine which pixels to paste. Pixels above this number will be treated as transparent and will not be pasted.