PDL::Primitive - primitive operations for pdl

- NAME
- DESCRIPTION
- SYNOPSIS
- FUNCTIONS

- inner
- outer
- matmult
- innerwt
- inner2
- inner2d
- inner2t
- crossp
- norm
- indadd
- conv1d
- in
- uniq
- hclip
- lclip
- clip
- wtstat
- statsover
- stats
- histogram
- whistogram
- histogram2d
- whistogram2d
- fibonacci
- append
- axisvalues
- random
- randsym
- grandom
- vsearch
- interpolate
- interpol
- one2nd
- which
- which_both
- where
- whichND

- AUTHOR

# NAME

PDL::Primitive - primitive operations for pdl

# DESCRIPTION

This module provides some primitive and useful functions defined using PDL::PP and able to use the new indexing tricks.

See PDL::Indexing for how to use indices creatively. For explanation of the signature format, see PDL::PP.

# SYNOPSIS

     use PDL::Primitive;

# FUNCTIONS

## inner

      Signature: (a(n); b(n); [o]c())

Inner product over one dimension

     c = sum_i a_i * b_i

## outer

      Signature: (a(n); b(m); [o]c(n,m))

outer product over one dimension

Naturally, it is possible to achieve the effects of outer product simply by threading over the ```*`'' operator but this function is provided for convenience.

## matmult

     Signature: (a(x,y),b(y,z),[o]c(x,z))

Matrix multiplication

We peruse the inner product to define matrix multiplication via a threaded inner product

## innerwt

      Signature: (a(n); b(n); c(n); [o]d())

Weighted (i.e. triple) inner product

     d = sum_i a(i) b(i) c(i)

## inner2

      Signature: (a(n); b(n,m); c(m); [o]d())

Inner product of two vectors and a matrix

     d = sum_ij a(i) b(i,j) c(j)

Note that you should probably not thread over `a` and `c` since that would be very wasteful. Instead, you should use a temporary for `b*c`.

## inner2d

      Signature: (a(n,m); b(n,m); [o]c())

Inner product over 2 dimensions.

Equivalent to

     $c = inner($a->clump(2), $b->clump(2))

## inner2t

      Signature: (a(j,n); b(n,m); c(m,k); [t]tmp(n,k); [o]d(j,k)))

Efficient Triple matrix product `a*b*c`

Efficiency comes from by using the temporary `tmp`. This operation only scales as `N**3` whereas threading using inner2 would scale as `N**4`.

The reason for having this routine is that you do not need to have the same thread-dimensions for `tmp` as for the other arguments, which in case of large numbers of matrices makes this much more memory-efficient.

It is hoped that things like this could be taken care of as a kind of closures at some point.

## crossp

      Signature: (a(tri=3); b(tri); [o] c(tri))

Cross product of two 3D vectors

After

     $c = crossp $a, $b

the inner product `$c*$a` and `$c*$b` will be zero, i.e. `$c` is orthogonal to `$a` and `$b`

## norm

      Signature: (vec(n); [o] norm(n))

Normalises a vector to unit Euclidean length

## indadd

      Signature: (a(); int ind(); [o] sum(m))

Threaded Index Add: Add `a` to the `ind` element of `sum`, i.e:

     sum(ind) += a

Simple Example:

      $a = 2;
      $ind = 3;
      $sum = zeroes(10);
      indadd($a,$ind, $sum);
      print $sum
      #Result: ( 2 added to element 3 of $sum)
      # [0 0 0 2 0 0 0 0 0 0]

Threaded Example:

      $a = pdl( 1,2,3);
      $ind = pdl( 1,4,6);
      $sum = zeroes(10);
      indadd($a,$ind, $sum);
      print $sum."\n";
      #Result: ( 1, 2, and 3 added to elements 1,4,6 $sum)
      # [0 1 0 0 2 0 3 0 0 0]

## conv1d

      Signature: (a(m); kern(p); [o]b(m); int reflect)

1d convolution along first dimension

      $con = conv1d sequence(10), pdl(-1,0,1), {Boundary => 'reflect'};

By default, periodic boundary conditions are assumed (i.e. wrap around). Alternatively, you can request reflective boundary conditions using the `Boundary` option:

      {Boundary => 'reflect'} # case in 'reflect' doesn't matter

The convolution is performed along the first dimension. To apply it across another dimension use the slicing routines, e.g.

      $b = $a->mv(2,0)->conv1d($kernel)->mv(0,2); # along third dim

This function is useful for threaded filtering of 1D signals.

Compare also conv2d, convolve, fftconvolve, fftwconv, rfftwconv

## in

      Signature: (a(); b(n); [o] c())

test if a is in the set of values b

       $goodmsk = $labels->in($goodlabels);
       print pdl(4,3,1)->in(pdl(2,3,3));
      [0 1 0]

`in` is akin to the is an element of of set theory. In priciple, PDL threading could be used to achieve its functionality by using a construct like

       $msk = ($labels->dummy(0) == $goodlabels)->orover;

However, `in` doesn't create a (potentially large) intermediate and is generally faster.

## uniq

return all unique elements of a piddle

The unique elements are returned in ascending order.

      print pdl(2,2,2,4,0,-1,6,6)->uniq;
     [-1 0 2 4 6]

Note: The returned pdl is 1D; any structure of the input piddle is lost.

## hclip

      Signature: (a(); b(); [o] c())

clip `$a` by `$b` (`$b` is upper bound)

## lclip

      Signature: (a(); b(); [o] c())

clip `$a` by `$b` (`$b` is lower bound)

## clip

Clip a piddle by (optional) upper or lower bounds.

     $b = $a->clip(0,3);
     $c = $a->clip(undef, $x);

## wtstat

      Signature: (a(n); wt(n); avg(); [o]b(); int deg)

Weighted statistical moment of given degree

This calculates a weighted statistic over the vector `a`. The formula is

     b() = (sum_i wt_i * (a_i ** degree - avg)) / (sum_i wt_i)

## statsover

      Signature: (a(n); w(n); int+ [o]avg(); int+ [o]rms(); int+ [o]min(); int+ [o]max(); int+ [o]adev())

Calculate useful statistics over a dimension of a piddle

      ($mean, $rms, $median, $min, $max, $adev) = statover($piddle, $weights);

This utility function calculates various useful quantities of a piddle. These are the mean:

      MEAN = sum (x)/ N

with `N` being the number of elements in x, the root mean square deviation from the mean, RMS, given as,

      RMS = sqrt(sum( (x-mean(x))^2 )/(N-1));

Note the use of `N-1` which for almost all cases should be the right normalisation factor. The routine also returns the median, minimum and maximum of the piddle as well as the mean absolute deviation, defined as:

      ADEV = sqrt(sum( abs(x-mean(x)) )/N)

note here that we use the mean and not the median. This could possibly be changed in future versions of the code.

This operator is a projection operator so the calculation will take place over the final dimension. Thus if the input is N-dimensional each returned value will be N-1 dimensional, to calculate the statistics for the entire piddle either use `clump(-1)` directly on the piddle or call `stats`.

## stats

Calculates useful statistics on a piddle

     ($mean,$rms,$median,$min,$max) = stats($piddle,[$weights]);

This utility calculates all the most useful quantities in one call.

Note: The RMS value that this function returns in the RMS deviation from the mean, also known as the population standard- deviation.

## histogram

      Signature: (in(n); int+[o] hist(m); double step; double min; int msize => m)

Calculates a histogram for given stepsize and minimum.

     $h = histogram($data, $step, $min, $numbins);
     $hist = zeroes $numbins;  # Put histogram in existing piddle.
     histogram($data, $hist, $step, $min, $numbins);

The histogram will contain `$numbins` bins starting from `$min`, each `$step` wide. The value in each bin is the number of values in `$data` that lie within the bin limits.

Data below the lower limit is put in the first bin, and data above the upper limit is put in the last bin.

The output is reset in a different threadloop so that you can take a histogram of `$a(10,12)` into `$b(15)` and get the result you want.

Use hist instead for a high-level interface.

     perldl> p histogram(pdl(1,1,2),1,0,3)
     [0 2 1]

## whistogram

      Signature: (in(n); float+ wt(n);float+[o] hist(m); double step; double min; int msize => m)

Calculates a histogram from weighted data for given stepsize and minimum.

     $h = whistogram($data, $weights, $step, $min, $numbins);
     $hist = zeroes $numbins;  # Put histogram in existing piddle.
     whistogram($data, $weights, $hist, $step, $min, $numbins);

The histogram will contain `$numbins` bins starting from `$min`, each `$step` wide. The value in each bin is the sum of the values in `$weights` that correspond to values in `$data` that lie within the bin limits.

Data below the lower limit is put in the first bin, and data above the upper limit is put in the last bin.

The output is reset in a different threadloop so that you can take a histogram of `$a(10,12)` into `$b(15)` and get the result you want.

     perldl> p whistogram(pdl(1,1,2), pdl(0.1,0.1,0.5), 1, 0, 4)
     [0 0.2 0.5 0]

## histogram2d

      Signature: (ina(n); inb(n); int+[o] hist(ma,mb); double stepa; double mina; int masize => ma;
                         double stepb; double minb; int mbsize => mb;)

Calculates a 2d histogram.

     $h = histogram2d($datax, $datay,
           $stepx, $minx, $nbinx, $stepy, $miny, $nbiny);
     $hist = zeroes $nbinx, $nbiny;  # Put histogram in existing piddle.
     histogram2d($datax, $datay, $hist,
           $stepx, $minx, $nbinx, $stepy, $miny, $nbiny);

The histogram will contain `$nbinx` x `$nbiny` bins, with the lower limits of the first one at `($minx, $miny)`, and with bin size `($stepx, $stepy)`. The value in each bin is the number of values in `$datax` and `$datay` that lie within the bin limits.

Data below the lower limit is put in the first bin, and data above the upper limit is put in the last bin.

     perldl> p histogram2d(pdl(1,1,1,2,2),pdl(2,1,1,1,1),1,0,3,1,0,3)
     [
      [0 0 0]
      [0 2 2]
      [0 1 0]
     ]

## whistogram2d

      Signature: (ina(n); inb(n); float+ wt(n);float+[o] hist(ma,mb); double stepa; double mina; int masize => ma;
                         double stepb; double minb; int mbsize => mb;)

Calculates a 2d histogram from weighted data.

     $h = whistogram2d($datax, $datay, $weights,
           $stepx, $minx, $nbinx, $stepy, $miny, $nbiny);
     $hist = zeroes $nbinx, $nbiny;  # Put histogram in existing piddle.
     whistogram2d($datax, $datay, $weights, $hist,
           $stepx, $minx, $nbinx, $stepy, $miny, $nbiny);

The histogram will contain `$nbinx` x `$nbiny` bins, with the lower limits of the first one at `($minx, $miny)`, and with bin size `($stepx, $stepy)`. The value in each bin is the sum of the values in `$weights` that correspond to values in `$datax` and `$datay` that lie within the bin limits.

Data below the lower limit is put in the first bin, and data above the upper limit is put in the last bin.

     perldl> p whistogram2d(pdl(1,1,1,2,2),pdl(2,1,1,1,1),pdl(0.1,0.2,0.3,0.4,0.5),1,0,3,1,0,3)
     [
      [  0   0   0]
      [  0 0.5 0.9]
      [  0 0.1   0]
     ]

## fibonacci

      Signature: ([o]x(n))

Constructor - a vector with Fibonacci's sequence

## append

      Signature: (a(n); b(m); [o] c(mn))

append two piddles by concantening along their respective first dimensions

     $a = ones(2,4,7);
     $b = sequence 5;
     $c = $a->append($b);  # size of $c is now (7,4,7) (a jumbo-piddle ;)

`append` appends two piddles along their first dims. Rest of the dimensions must be compatible in the threading sense. Resulting size of first dim is the sum of the sizes of the first dims of the two argument piddles - ie `n + m`.

## axisvalues

      Signature: ([o,nc]a(n))

Internal routine

`axisvalues` is the internal primitive that implements axisvals and alters its argument.

## random

Constructor which returns piddle of random numbers

     $a = random([type], $nx, $ny, $nz,...);
     $a = random $b;

etc (see zeroes).

This is the uniform distribution between 0 and 1 (assumedly excluding 1 itself). The arguments are the same as `zeroes` (q.v.) - i.e. one can specify dimensions, types or give a template.

You can use the perl function srand to seed the random generator. For further details consult Perl's srand documentation.

## randsym

Constructor which returns piddle of random numbers

     $a = randsym([type], $nx, $ny, $nz,...);
     $a = randsym $b;

etc (see zeroes).

This is the uniform distribution between 0 and 1 (excluding both 0 and 1, cf random). The arguments are the same as `zeroes` (q.v.) - i.e. one can specify dimensions, types or give a template.

You can use the perl function srand to seed the random generator. For further details consult Perl's srand documentation.

## grandom

Constructor which returns piddle of Gaussian random numbers

     $a = grandom([type], $nx, $ny, $nz,...);
     $a = grandom $b;

etc (see zeroes).

This is generated using the math library routine `ndtri`.

Mean = 0, Stddev = 1

You can use the perl function srand to seed the random generator. For further details consult Perl's srand documentation.

## vsearch

      Signature: (i(); x(n); int [o]ip())

routine for searching 1D values i.e. step-function interpolation.

     $inds = vsearch($vals, $xs);

Returns for each value of `$vals` the index of the least larger member of `$xs` (which need to be in increasing order). If the value is larger than any member of `$xs`, the index to the last element of `$xs` is returned.

This function is useful e.g. when you have a list of probabilities for events and want to generate indices to events:

     $a = pdl(.01,.86,.93,1); # Barnsley IFS probabilities cumulatively
     $b = random 20;
     $c = vsearch($b, $a); # Now, $c will have the appropriate distr.

It is possible to use the cumusumover function to obtain cumulative probabilities from absolute probabilities.

## interpolate

      Signature: (xi(); x(n); y(n); [o] yi(); int [o] err())

routine for 1D linear interpolation

     ( $yi, $err ) = interpolate($xi, $x, $y)

Given a set of points `($x,$y)`, use linear interpolation to find the values `$yi` at a set of points `$xi`.

`interpolate` uses a binary search to find the suspects, er..., interpolation indices and therefore abscissas (ie `$x`) have to be strictly ordered (increasing or decreasing). For interpolation at lots of closely spaced abscissas an approach that uses the last index found as a start for the next search can be faster (compare Numerical Recipes `hunt` routine). Feel free to implement that on top of the binary search if you like. For out of bounds values it just does a linear extrapolation and sets the corresponding element of `$err` to 1, which is otherwise 0.

See also interpol, which uses the same routine, differing only in the handling of extrapolation - an error message is printed rather than returning an error piddle.

## interpol

     Signature: (xi(); x(n); y(n); [o] yi())

routine for 1D linear interpolation

     $yi = interpol($xi, $x, $y)

`interpol` uses the same search method as interpolate, hence `$x` must be strictly ordered (either increasing or decreasing). The difference occurs in the handling of out-of-bounds values; here an error message is printed.

## one2nd

Converts a one dimensional index piddle to a set of ND coordinates

     @coords=one2nd($a, $indices)

returns an array of piddles containing the ND indexes corresponding to the one dimensional list indices. The indices are assumed to correspond to array `$a` clumped using `clump(-1)`. This routine is used in whichND, but is useful on its own occasionally.

     perldl> $a=pdl [[[1,2],[-1,1]], [[0,-3],[3,2]]]; $c=$a->clump(-1)
     perldl> $maxind=maximum_ind($c); p $maxind;
     6
     perldl> print one2nd($a, maximum_ind($c))
     0 1 1
     perldl> p $a->at(0,1,1)
     3

## which

      Signature: (mask(n); int [o] inds(m))

Returns piddle of indices of non-zero values.

     $i = which($mask);

returns a pdl with indices for all those elements that are nonzero in the mask. Note that the returned indices will be 1D. If you want to index into the original mask or a similar piddle remember to flatten it before calling index:

      $data = random 5, 5;
      $idx = which $data > 0.5; # $idx is now 1D
      $bigsum = $data->flat->index($idx)->sum;  # flatten before indexing

Compare also where for similar functionality.

If you want to return both the indices of non-zero values and the complement, use the function which_both.

     perldl> $x = sequence(10); p $x
     [0 1 2 3 4 5 6 7 8 9]
     perldl> $indx = which($x>6); p $indx
     [7 8 9]

## which_both

      Signature: (mask(n); int [o] inds(m); int [o]notinds(q))

Returns piddle of indices of non-zero values and their complement

     ($i, $c_i) = which_both($mask);

This works just as which, but the complement of `$i` will be in `$c_i`.

     perldl> $x = sequence(10); p $x
     [0 1 2 3 4 5 6 7 8 9]
     perldl> ($small, $big) = which_both ($x >= 5); p "$small\n $big"
     [5 6 7 8 9]
     [0 1 2 3 4]

## where

Returns indices to non-zero values or those values from another piddle.

     $i = $x->where($x+5 > 0); # $i contains elements of $x
                               # where mask ($x+5 > 0) is 1

Note: `$i` is always 1-D, even if `$x` is >1-D. The first argument (the values) and the second argument (the mask) currently have to have the same initial dimensions (or horrible things happen).

It is also possible to use the same mask for several piddles with the same call:

     ($i,$j,$k) = where($x,$y,$z, $x+5>0);

## whichND

Returns the coordinates for non-zero values

     @coords=whichND($mask);

returns an array of piddles containing the coordinates of the elements that are non-zero in `$mask`.

     perldl> $a=sequence(10,10,3,4)
     perldl> ($x, $y, $z, $w)=whichND($a == 203); p $x, $y, $z, $w
     [3] [0] [2] [0]
     perldl> print $a->at(list(cat($x,$y,$z,$w)))
     203

# AUTHOR

Copyright (C) Tuomas J. Lukka 1997 (lukka@husc.harvard.edu) Contributions by Christian Soeller (c.soeller@auckland.ac.nz) and Karl Glazebrook (kgb@aaoepp.aao.gov.au) All rights reserved. There is no warranty. You are allowed to redistribute this software / documentation under certain conditions. For details, see the file COPYING in the PDL distribution. If this file is separated from the PDL distribution, the copyright notice should be included in the file.