teem(1)

NAME
teem - simple command-line tools which provide fast and easy access to the functionality in the various libraries

DESCRIPTION
teem-affine: This uses air's AIR_AFFINE macro to print out the value which stands in the same relationship with the interval [<minOut>, <maxOut>] as <value> has with the interval [minIn, maxOut].

teem-deconv: Does deconvolution.

teem-airSanity:

teem-cubic:

teem-emap: Creates environment maps based on limn's "checker" normal quantization methods. By taking into account camera parameters, this allows for both lights in both world and view space. Solely out of laziness, the nrrd format is used for specifying the lights, but not to worry: you can use a simple un-adorned text file, defining one light per line, with 7 values per light: 0/1 (world/view space), R G B color, and X Y Z position.

teem-gkms: Semi-Automatic Generation of Transfer Functions

teem-idx2pos: Converts from floating-point "index" to floating-point "position", given the centering of the data (cell vs. node), the range of positions, and the number of intervals into which position has been quantized.

teem-ilk: (I)mage (L)inear Trans(X-->K)forms. Applies linear (homogenous coordinate) transforms to a given image, using the given kernel for resampling.

teem-miter: A simple but effective little volume renderer.

teem-mrender: A demonstration of hoover, gage, and nrrd measures. Uses hoover to cast rays through a volume (scalar, vector, or tensor), gage to measure one of various quantities along the rays, and a specified nrrd measure to reduce all the values along a ray down to one scalar, which is saved in the output (double) image.

teem-ninspect: Quick way of seeing what's inside a 3D volume. A color image of three axis-aligned projections is composed of histogram-equalized and quantized images of the summation (red), variance (green), and maximum (blue) intensity projections. If volume is orientation in RAS space, then a standard orientation is used for projections and projections are upsampled (with box kernel) to have isotropic pixels.

teem-ninspect: Quick way of seeing what's inside a 3D volume. A color image of three axis-aligned projections is composed of histogram-equalized and quantized images of the summation (red), variance (green), and maximum (blue) intensity projections. If volume is orientation in RAS space, then a standard orientation is used for projections and projections are upsampled (with box kernel) to have isotropic pixels.

teem-nrrdSanity:

teem-overrgb: Composites an RGBA nrrd over a background color (or image), after doing gamma correction, then quantizes to an 8-bit image. Actually, the input nrrd can have more than 4 values per pixel, but only the first four are used. If the RGBA nrrd is floating point, the values are taken at face value; if it is fixed point, the values interpreted as having been quantized (so that 8-bit RGBA images will act as you expect). When compositing with a background image, the given background image does not have to be the same size as the input image; it will be resampled (with linear interpolation) to fit.

teem-pos2idx: Converts from floating-point "position" to floating-point "index", given the centering of the data (cell vs. node), the range of positions, and the number of intervals into which position has been quantized.

teem-pprobe: Uses gageProbe() to query scalar or vector volumes at a single probe location.

teem-qbert: Generates volume datasets friendly to hardware-based volume renderers. The main value of this is a means of combining the functions of resampling a dataset to a particular size, measuring first (and optionally second) derivatives, and doing some semi-intelligent quantization of the derivative values down to 8-bits (if quantization is desired). The various up and down sampling, as well as the the VGH measurements, can be done with various nrrd kernels. Also, histogram-equalized VG and VH scatterplots can be generated at a specified resolution.

teem-talkweb: Generates HTML pages from slide images and text. This program takes multiple inputs: a template for the table of contents that will become "index.html" ("-i"), a template for the pages generated for each slide e.g. "slide000.html" ("-t"), and a script text file that contains all the information that will go into the slide pages. The format of this file is:
  - Separator line indicating slide transitions, e.g. "-------------"
  - Title of first slide (one line)
  - Filename for image to put on first slide (one line)
  - Body of HTML text to put with the slide image (multiple lines)
  - Separator followed by information for the second slide, and so forth. Textual subtitutions are performed in the template files, according to the replacement tags ("-r", see below). Within the slide pages, navigation arrows are based on remaining command-line options.

teem-tend: Diffusion Tensor Processing and Analysis

teem-undos undos: Converts from DOS text files to normal (converting LF-CR pairs to just CR), or, with the "-r" option, convert back to DOS, for whatever sick and twisted reason you'd have to do that. Can also handle legacy MAC text files (only LF). Unlike the simple sed or perl scripts for this purpose, this program is careful to be idempotent. Also, this makes an effort to not meddle with binary files (on which this may be mistakenly invoked). A message is printed to stderr for all the files actually modified.

teem-ungantry: Gantry tilt be gone! This program is actually of limited utility: it can only change the tilt by shearing with the X and Z axis fixed, by some angle "around" the X axis, assuming that (X,Y,Z) is a right-handed frame.

teem-unu: Utah Nrrd Utilities command-line interface

teem-vprobe: Shows off the functionality of the gage library. Uses gageProbe() to query various kinds of volumes to learn various measured or derived quantities. Can set environment variable TEEM_VPROBE_HACK_ZI to limit probing to a single z slice.

SEE ALSO
slicer(1)