WEB
OVERVIEW
- INTRODUCTION
- VARIABLE INITIALIZATION
- OPERATIONS
- WHATS NEW
- EXAMPLES
- INSTALLATION
WEB is a graphical user interface for displaying
and interacting with SPIDER
images developed at the Biological Microscopy and Image Reconstruction Resource
(BMIRR) located in the Wadsworth Laboratories,
Albany, New York. WEB is written in C and runs under the X/Motif system.
WEB was developed by A. Leith with contributions from L. Odesanya,
Y.H. Li, M. Ladjadj, A. Dent, M. Radermacher, and J. Frank.
WEB has been in use since 1990 and contains more than 39,000 lines
of code.
Certain variables in Web can be initialized from the command line
or in Xt resource files.
Operations are grouped under five main menu headings:
OPTIONS,
COMMANDS,
EDIT,
INFO,
SYSTEM
- "OPTIONS" alter the way information is diplayed during a WEB session.
- "COMMANDS" provide the main display and analysis of 2D & 3D images.
- "EDIT" provides further commands which edit 2D or 3D images.
- "INFO" provides information on workstation and WEB capabilities.
- "SYSTEM" provides settings for file searching and for stopping 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.
Use the movie toggle in the Image Option menu to force all
images to be displayed at the same location.
- Surface
Does fast surface display of 3D file. User
specifies surface level and relative contribution from
depth and surface reflectivity. The movie option allows
the creation of several files representing individual
frames, which can then be played back as a movie. User
can specifies the rotation angles to rotate the volume.
This rotation can be done according to the original
system or the current system.
- 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 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.
- 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.
details.
- Dendrogram
Performs a "dendrogram" plot with input taken
from a SPIDER 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.
- 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.
- Montage from doc. file
Makes a montage of 2-D images by looking up the
image numbers in a document file. The register number
containing the image number in the doc. file is solicited.
All images must have same prefix in their name
(e.g. IMA***.DAT).
- 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.
- 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 an image 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.
- 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.
Surface Rendering and Montage Operation Output
Source: web.html
Last update: 12/311997
ArDean Leith