transform

Transform is a tool created to do often used text / sequence transformations. I find Excel to be brilliant for making pretty sequences and sequence alignments - however each character needs to be in a separate cell.

Here are some key features of "Transform":

· Insert Tab before / after each character
· Insert Return after each character
· Keep only letters a-Z
· Format in blocks of 3, 10, 50, 100
· Remove leading / trailing / multiple spaces
· Reverse / complement/ invert DNA sequence
· Translate DNA sequence in frame 1 / 2 / 3
· Backtranslate protein into human / E. coli DNA (using the most frequently used codon)
· Convert 3-Letter AminoAcid code into 1-Letter code
· Convert 1-Letter AminoAcid code into 3-Letter code (spaced / tabbed)
· Get protein sequence info


If there are other transformations youd like just drop me a line .
Please note that this program will run as it is - there is no installation, no files will be put anywhere (registry, system, etc in the Windows version) so it should even run if you are on "managed computers" like we are in our lab (which is a pain in the neck in 99% of all cases - IT support should be there for us, not the other way round).

PDL::Transform is a Perl module that coordinate transforms, image warping, and N-D functions.

SYNOPSIS

use PDL::Transform;
my $t = new PDL::Transform:: ( )

$out = $t->apply($in) # Apply transform to some N-vectors (Transform method)
$out = $in->apply($t) # Apply transform to some N-vectors (PDL method)

$im1 = $t->map($im); # Transform image coordinates (Transform method)
$im1 = $im->map($t); # Transform image coordinates (PDL method)

$t2 = $t->compose($t1); # compose two transforms
$t2 = $t x $t1; # compose two transforms (by analogy to matrix mult.)

$t3 = $t2->inverse(); # invert a transform
$t3 = !$t2; # invert a transform (by analogy to logical "not")

PDL::Transform is a convenient way to represent coordinate transformations and resample images. It embodies functions mapping R^N -> R^M, both with and without inverses. Provision exists for parametrizing functions, and for composing them. You can use this part of the Transform object to keep track of arbitrary functions mapping R^N -> R^M with or without inverses.

The simplest way to use a Transform object is to transform vector data between coordinate systems. The apply method accepts a PDL whose 0th dimension is coordinate index (all other dimensions are threaded over) and transforms the vectors into the new coordinate system.

Transform also includes image resampling, via the map method. You define a coordinate transform using a Transform object, then use it to remap an image PDL. The output is a remapped, resampled image.

You can define and compose several transformations, then apply them all at once to an image. The image is interpolated only once, when all the composed transformations are applied.

In keeping with standard practice, but somewhat counterintuitively, the map engine uses the inverse transform to map coordinates FROM the destination dataspace (or image plane) TO the source dataspace; hence PDL::Transform keeps track of both the forward and inverse transform.

For terseness and convenience, most of the constructors are exported into the current package with the name t_ <transform> transform> , so the following (for example) are synonyms:

$t = new PDL::Transform::Radial(); # Long way

$t = t_radial(); # Short way

Several math operators are overloaded, so that you can compose and invert functions with expression syntax instead of method syntax (see below).

Atlas Transform description
Atlas Transform is able to generate custom documents that depend on the data of input fields Atlas Transform is able to generate custom documents that depend on the data of input fields.

The aXfrm engine takes prospect data as XML.The engine uses the specified templates to produce documents for each prospect.

Each template provides for a start and finish block that can wrap all the prospects. The output documents are further rendered by other programs as neccessary. Integrates with axCtx to provide customized messages.

Here are some key features of "Atlas Transform":

· XML based input
· Substitution of data fields
· Reuse of prebuilt parts
· Conditional text blocks
· Multiple output streams for the same input
· The basic operation is as follows.

Recognizing cyan, magenta and yellow (CMY) as the primary colors of the subtractive system, COLORCUBE Transform encompasses the basic fundamentals of all COLORCUBE model technology. Each of the colors seen here are the result of different combinations of these primaries. As the planes of CMY gradually convert to cubes, see how COLORCUBE coordinates can be generated for color mixing, color mapping and color space construction.

Grid::Transform is a Perl module with fast grid transformations.

SYNOPSIS

use Grid::Transform;

$g = Grid::Transform->new([a..o], rows=>5);
$g->rotate_270->flip_vertical;
print join( , $g->grid), "n";

The Grid::Transform module provides fast methods to transform a grid of arbitrary data types.

METHODS

$g = Grid::Transform->new( @grid, rows=>num, columns=>num )

Creates a new Grid::Transform object. The first argument is a reference to a 1-dimensional array representing a 2-dimensional "row major" (row by row) grid. (A column major grid is simply the counter transpose of a row major one.) The grid may be composed of arbitrary data types. The original array is never modified- all transformations operate on a copy.

At least one dimension must be specified. If the grid and dimensions do not produce a rectangular grid extra empty elements ("") will be added to the grid.

$g2 = $g->copy

Returns a copy of the original Grid::Transform object.

These methods get or set the grid attributes:

@grid = $g->grid
$grid = $g->grid
@grid = $g->grid( @grid )

In list context, returns an array representing the current grid. In scalar context, returns a reference to the array. Accepts an array reference representing a new grid. The new grid will be resized if the dimensions of the previous grid do not match.

$g->rows
$g->rows( $num )

Returns the current number of rows.

$g->columns
$g->cols
$g->columns( $num )

Returns the current number of columns.

All transform methods return the Grid::Transform object, so transforms can be chained.

$g->rotate_90
$g->rotate90

Rotates the grid 90 degrees clock-wise.

a b c d e f g h i j k l a b c d i e a
| e f g h -> j f b
i e a j f b k g c l h d i j k l k g c
l h d

$g->rotate_180
$g->rotate180

Rotates the grid 180 degrees clock-wise.

a b c d e f g h i j k l a b c d l k j i
| e f g h -> h g f e
l k j i h g f e d c b a i j k l d c b a

$g->rotate_270
$g->rotate270

Rotates the grid 270 degrees clock-wise.

a b c d e f g h i j k l a b c d d h l
| e f g h -> c g k
d h l c g k b f j a e i i j k l b f j
a e i

$g->flip_horizontal
$g->mirror_horizontal

Flips the grid across the horizontal axis.

a b c d e f g h i j k l a b c d i j k l
| e f g h -> e f g h
i j k l e f g h a b c d i j k l a b c d

$g->flip_vertical
$g->mirror_vertical

Flips the grid across the vertical axis.

a b c d e f g h i j k l a b c d d c b a
| e f g h -> h g f e
d c b a h g f e l k j i i j k l l k j i

$g->transpose

Flips the grid across the vertical axis and then rotates it 90 degress clock-wise.

a b c d e f g h i j k l a b c d l h d
| e f g h -> k g c
l h d k g c j f b i e a i j k l j f b
i e a

$g->counter_transpose
$g->countertranspose

Flips the grid across the horizontal axis and then rotates it 90 degrees clock-wise.

a b c d e f g h i j k l a b c d a e i
| e f g h -> b f j
a e i b f j c g k d h l i j k l c g k
d h l

$g->fold_right

Folds the columns to the right.

a b c d e f g h i j k l a b c d b c d a
| e f g h -> f g e h
b c a d f g e h j k i l i j k l j k i l

$g->fold_left

Folds the columns to the left.

a b c d e f g h i j k l a b c d d a c b
| e f g h -> h e g f
d a c b h e g f l i k j i j k l l i k j

Fourier transform library is a dll that contains functions which calculate the fast fourier transform (FFT) and the inverse FFT (IFFT).

This FFT implementation accepts only real numbers as input and produces complex numbers as output (spectrum). Analogously, IFFT accepts complex numbers and produces real ones.

Therefore, IFFT requires only half of the spectrum as input (the other half can be reconstructed on the basis of symmetry, since we know that it is a spectrum of a real signal). Summarizing:

real ̈ FFT ̈ complex
complex ̈ IFFT ̈ real
The functions contain implementation of Cooley-Tukey algorithm, which requires that the number of samples be a power of 2. The algorithm used here is optimized for real input.

If one wants to use this library in their program, they can find function declarations in the header file, available below.

They have long comments and this is the only documentation that I have written for this library, and there will probably never be a better one, due to the authors laziness and/or lack of time.

CAD::Drawing::Manipulate::Transform is a Perl module with Matrix methods for CAD::Drawing.

Provides 3D transformation methods (based on traditional matrix algorithms) for Drawing.pm objects.

Coordinate System

All of these methods assume a RIGHT-HANDED coordinate system. If you are using a left-handed coordinate system, you are going to have trouble, trouble, trouble. We arent making video games here!

PDL::Transform::Cartography Perl module contains useful cartographic projections.

SYNOPSIS

# make a Mercator map of Earth
use PDL::Transform::Cartography;
$a = earth_coast();
$a = graticule(10,2)->glue(1,$a);
$t = t_mercator;
$w = pgwin(xs);
$w->lines($t->apply($a)->clean_lines());

PDL::Transform::Cartography includes a variety of useful cartographic and observing projections (mappings of the surface of a sphere), including reprojected observer coordinates. See PDL::Transform for more information about image transforms in general.

Cartographic transformations are used for projecting not just terrestrial maps, but also any nearly spherical surface including the Sun, the Celestial sphere, various moons and planets, distant stars, etc. They also are useful for interpreting scientific images, which are themselves generally projections of a sphere onto a flat focal plane (e.g. the t_gnomonic projection).

Unless otherwise noted, all the transformations in this file convert from (theta,phi) coordinates on the unit sphere (e.g. (lon,lat) on a planet or (RA,dec) on the celestial sphere) into some sort of projected coordinates, and have inverse transformations that convert back to (theta,phi). This is equivalent to working from the equidistant cylindrical (or "plate caree") projection, if you are a cartography wonk.

The projected coordinates are generally in units of body radii (radians), so that multiplying the output by the scale of the map yields physical units that are correct wherever the scale is correct for that projection. For example, areas should be correct everywhere in the authalic projections; and linear scales are correct along meridians in the equidistant projections and along the standard parallels in all the projections.

The transformations that are authalic (equal-area), conformal (equal-angle), azimuthal (circularly symmetric), or perspective (true perspective on a focal plane from some viewpoint) are marked. The first two categories are mutually exclusive for all but the "unit sphere" 3-D projection.

Extra dimensions tacked on to each point to be transformed are, in general, ignored. That is so that you can add on an extra index to keep track of pen color. For example, earth_coast returns a 3x< n > piddle containing (lon, lat, pen) at each list location. Transforming the vector list retains the pen value as the first index after the dimensional directions.

Fourier Bessel Transform For Face Identification is a free tool that can extract and identify face images based on polar frequency.

Fourier Bessel Transform For Face Identification - Matlab Source Code. A novel biologically motivated face recognition algorithm based on polar frequency is presented. Polar frequency descriptors are extracted from face images by Fourier-Bessel transform (FBT). Most of the current face recognition algorithms are based on feature extraction from a Cartesian perspective, typical to most analog and digital imaging systems.

The primate visual system, on the other hand, is known to process visual stimuli logarithmically. An alternative representation of an image in the polar frequency domain is the two-dimensional Fourier-Bessel Transform. This transform found several applications in analyzing patterns in a circular domain, but was seldom exploited for image recognition.

Parallel Three-Dimensional Fast Fourier Transforms, dubbed P3DFFT, is a library for computational computing in a wide range of sciences, such as physics, climatology, chemistry.

This project was developed at SDSC by Dmitry Pekurovsky as a product of a Strategic Applications Collaborations (SAC) project.

Here are some key features of "Parallel Three Dimensional Fast Fourier Transforms":

· Parallel implementation with 2D data decomposition, overcoming an important limitation to scalability of other 3D FFT libraries implementing 1D, or slab, decomposition.
· Optimized for parallel communication and single-CPU performance.
· Built on top of well-optimized and flexible 1D FFT libraries.

Whats New in This Release:

· Assorted minor bugfixes and code speedups.