Web

USAGE

Certain variables in Web can be initialized from Command Line Arguments or in your Xt Resource files.

Operations are grouped under five main menu headings: OPTIONS, COMMANDS, EDIT, INFO, SYSTEM

• "OPTIONS" alter the way information is displayed during a Web session.
• "COMMANDS" provide the main display and analysis of 2D & 3D images.
• "EDIT" provides operations which edit 2D or 3D images.
• "INFO" provides information on workstation and Web capabilities.
• "SYSTEM" provides settings for file searching and for exiting the application.

Operations are selected by pointing at the relevant menu heading and then selecting the menu sub-option (and sub-sub-option) using the left mouse button.

• OPTIONS
  • Image
    Alters image display charactaristics:
    • Left & top margin around image display area
    • X & Y margin around each image
    • Size reduction for image display (-2 is a magnification of 2X)
    • Montage movie flag (keeps next image in same location as current image)
    • List file names below images
    • Start new row or screen of images
    • Toggle for listing files in file-selector (toggle off if you have hundreds of files!)
  • Contrast
    Enhances contrast of image using thresholding.
  • Cursor
    Selects cursor style from a pallette.
  • Display
    Turns off scrolling text window.
  • Font
    
  • Selects font for drawing text.
  • Magnify
    Sets magnification area and magnification factor.
  • Color
    Selects color for graphics characteristics:
    • Foreground -- color for following graphics
    • Background -- image & graphics surround
    • Overlay -- overlay color (for masking)
    • Cursor -- cursor colors
  • Line Style
    Alters line style (in some operations only)
  • Line Width
    Alters line width (in some operations only)
  • Lut
    Applies a color look-up table to current screen
• COMMANDS
  • Clear
    Clears screen.
  • Image
    Shows an image. Will try to place the image on the screen so that it does not overlap previous images.
  • Montage
    Shows a montage of 2-D images or 3-D slices or a stack. For 3-D slices the first slice in the file is z = 1 (a right-handed coordinate system).
    • x-slices have y-axis horizontal (y=1 at left) and z-axis vertical (z=1 at top), starting with x = 1.
    • y-slices have x-axis horizontal (x=1 at left) and z-axis vertical (z=1 at top), starting with y = 1.
    • z-slices have x-axis horizontal (x=1 at left) and y-axis vertical (y=1 at top), starting with z = 1.
    Use the movie toggle in the Image Option menu to force all images to be displayed at the same location.
  • Surface
    Does a fast surface display from a 3D file. User can specify surface level (threshold), contribution from depth versus surface reflectivity, scaling, and rotation. A movie option creates frames of a rotation sequence. Further details.
  • Shift
    Pans previously displayed image within its original display area. Can be used for images too large for the Web window.
  • Annotate
    Draws circles and numerical labels on top of an image. Positions for circles and values for labels are read from a SPIDER document file. User can specify registers for x & y coordinates and label.
  • Blackout
    Blacks out screen margins. (You may have to maximize the display window before selecting this option on some machines).
  • Categorize
    Displays montage of individule or stacked images. Asks for new SPIDER document file name. User can assign a category to each image using mouse to select images. The category is toggled using the middle mouse button. Categories and file numbers are stored in a document file. Further details.
  • Colored Surface
    Does fast surface display of 3D file. Colors surface according to values found in a second 3D file. Specify surface level, contribution from depth and surface reflectivity, and number of colors. The values in the color volume are divided into the specified number of colors. A private color-map can be used to alter the correspondence between colors and intensities in the color volume. Can only handle less than six colors. Further details.
  • Convolve
    Does some discrete convolutions on an image.
  • Corr-map
    Displays correspondance map. Can then outline areas and query images found within areas. Further details.
  • CTF from Document file
    Interactively study CTF plot. Further details.
  • Dendrogram
    Performs a "dendrogram" plot with input taken from a SPIDER CL CLA operation document file. Can also display the averaged images of a given threshold setting.
  • Distance
    Interactively queries a pair of pixel locations to determine their separation distance. Can record distances in a document file. Can record up to six distances from each starting point on a line of the document file.
  • General filter
    Interactively masks a power spectrum image to create a general Fourier filter. This filter file can then be multipled by a Fourier file for filtering. The mask is Gaussian and the radius can be specified. Details.
  • Histogram
    Draws image histogram on screen.
  • Magnify
    Interactively magnifies an area of the screen.
  • Markers
    Interactively selects marker locations and stores locations relative to image in a SPIDER document file. Further details.
  • Mask
    Interactively draws polygons on screen to make a binary mask image. The mask image is stored in a file. This mask file can then be used in SPIDER for masking a grey scale image by multiplication. Will fail if the file to be masked is larger than window.
  • Montage from doc. file
    Makes a montage of individule or stacked 2-D images by looking up the image numbers in a document file. The image numbers must be in the first register (not keys) in the document file. All images must have same prefix in their name (e.g. IMA***.DAT). Further details.
  • Movie
    Displays a movie from a series of images. Further details.
  • Particle Picking / Pixel
    Queries a pixel for location and color. Can place pixel location, color index value, or file value in a document file. Also used for interactive particle selection. Color of marker for location is controlled by previous color foreground selection operation.
  • Power Spectrum
    Shows a power spectrum of enclosed area in a user drawn window. The spectrum is from screen data not file data. Does not work properly for some window sizes!
  • Profile
    Displays the profile of image intensities along a row or column. Details.
  • Reflections
    Interactively picks reflections from a diffraction pattern and places indices and locations in a document file.
  • Record Screen
    Records an area of screen in a SPIDER image file.
  • Show Recording
    Shows a screen recording (including color) made with the Record Screen operation.
  • Show Contourfile
    Displays a contour metafile.
  • SIRDS
    Creates and displays a "single image relative displacement stereogram" from a volume.
  • Tilted Particles
    Interactively selects coordinates from an untilted/tilted pair of micrographs, determines tilt angle and tilt-axis direction by a least-square fit of all selected particle locations. Further details.
• EDIT
  • Bars
    Draws horizontal or vertical bars on screen using previously set foreground color.
  • Lines
    Draws lines on screen using previously set foreground color.
  • Text
    Draws text on screen using previously set foreground color.
  • Draw Boxes
    Draws boxes on screen using previously set foreground color.
  • Move Area
    Moves or copies an area of the screen from one position to another. Useful also for editing labels, etc. for photography.
  • Window Last File
    Interactively windows a displayed file and saves window from original file in a new SPIDER image file.
  • Drill-n-fill
    Interactively edits a volume while viewing a surface view of volume. Volume is viewed along X axis. Surface view is same as surface operation. Mouse buttons control movement of a tool which drills or fills areas of the volume. Further details.
• INFO
  • X info
    Prints some debugging information in terminal window.
  • Manual
    Shows manual in a window.
• SYSTEM
  • File Extension
    Sets extension to associate with file names e.g. DAT
  • Current Directory
    Sets current working directory. File searches begin from here.
  • File Pattern
    Selects pattern to use in searching for files eg. T*ST**0
  • EXIT
    Stops Web and closes Web window.