/ 
PDL-2.095
River stage three • 96 direct dependents • 105 total dependents
/ PDL::BadValues

NAME

PDL::BadValues - Discussion of bad value support in PDL

DESCRIPTION

What are bad values and why should I bother with them?

Sometimes it's useful to be able to specify a certain value is 'bad' or 'missing'; for example CCDs used in astronomy produce 2D images which are not perfect since certain areas contain invalid data due to imperfections in the detector. Whilst PDL's powerful index routines and all the complicated business with dataflow, slices, etc etc mean that these regions can be ignored in processing, it's awkward to do. It would be much easier to be able to say $c = $x + $y and leave all the hassle to the computer.

If you're not interested in this, then you may (rightly) be concerned with how this affects the speed of PDL, since the overhead of checking for a bad value at each operation can be large. Because of this, the code has been written to be as fast as possible - particularly when operating on ndarrays which do not contain bad values. In fact, you should notice essentially no speed difference when working with ndarrays which do not contain bad values.

You may also ask 'well, my computer supports IEEE NaN, so I already have this'. They are different things; a bad value signifies "leave this out of processing", whereas NaN is the result of a mathematically-invalid operation.

Many routines, such as y=sin(x), will propagate NaN's without the user having to code differently, but routines such as qsort, or finding the median of an array, need to be re-coded to handle bad values. For floating-point datatypes, NaN and Inf can be used to flag bad values, but by default special values are used (Default bad values).

There is one default bad value for each datatype, but as of PDL 2.040, you can have different bad values for separate ndarrays of the same type.

You can use NaN as the bad value for any floating-point type, including complex.

A quick overview

pdl> $x = sequence(4,3);
pdl> p $x
[
 [ 0  1  2  3]
 [ 4  5  6  7]
 [ 8  9 10 11]
]
pdl> $x = $x->setbadif( $x % 3 == 2 )
pdl> p $x
[
 [  0   1 BAD   3]
 [  4 BAD   6   7]
 [BAD   9  10 BAD]
]
pdl> $x *= 3
pdl> p $x
[
 [  0   3 BAD   9]
 [ 12 BAD  18  21]
 [BAD  27  30 BAD]
]
pdl> p $x->sum
120

demo bad within perldl or pdl2 gives a demonstration of some of the things possible with bad values. These are also available on PDL's web-site, at http://pdl.perl.org/demos/. See PDL::Bad for useful routines for working with bad values and t/bad.t to see them in action.

To find out if a routine supports bad values, use the badinfo command in perldl or pdl2 or the -b option to pdldoc.

Each ndarray contains a flag - accessible via $pdl->badflag - to say whether there's any bad data present:

  • If false/0, which means there's no bad data here, the code supplied by the Code option to pp_def() is executed.

  • If true/1, then this says there MAY be bad data in the ndarray, so use the code in the BadCode option (assuming that the pp_def() for this routine has been updated to have a BadCode key). You get all the advantages of broadcasting, as with the Code option, but it will run slower since you are going to have to handle the presence of bad values.

If you create an ndarray, it will have its bad-value flag set to 0. To change this, use $pdl->badflag($new_bad_status), where $new_bad_status can be 0 or 1. When a routine creates an ndarray, its bad-value flag will depend on the input ndarrays: unless over-ridden (see the CopyBadStatusCode option to pp_def), the bad-value flag will be set true if any of the input ndarrays contain bad values. To check that an ndarray really contains bad data, use the check_badflag method.

NOTE: propagation of the badflag

If you change the badflag of an ndarray, this change is propagated to all the children of an ndarray, so

pdl> $x = zeroes(20,30);
pdl> $y = $x->slice('0:10,0:10');
pdl> $c = $y->slice(',(2)');
pdl> print ">>c: ", $c->badflag, "\n";
>>c: 0
pdl> $x->badflag(1);
pdl> print ">>c: ", $c->badflag, "\n";
>>c: 1

This is also propagated to the parents of an ndarray, so

pdl> print ">>a: ", $x->badflag, "\n";
>>a: 1
pdl> $c->badflag(0);
pdl> print ">>a: ", $x->badflag, "\n";
>>a: 0

There's also the issue of what happens if you change the badvalue of an ndarray - should these propagate to children/parents (yes) or whether you should only be able to change the badvalue at the 'top' level - i.e. those ndarrays which do not have parents.

The orig_badvalue() method returns the compile-time value for a given datatype. It works on ndarrays, PDL::Type objects, and numbers - eg

$pdl->orig_badvalue(), byte->orig_badvalue(), and orig_badvalue(4).

To get the current bad value, use the badvalue() method - it has the same syntax as orig_badvalue().

To change the current bad value, supply the new number to badvalue - eg

$pdl->badvalue(2.3), byte->badvalue(2), badvalue(5,-3e34).

Note: the value is silently converted to the correct C type, and returned - i.e. byte->badvalue(-26) returns 230 on my Linux machine.

Note that changes to the bad value are NOT propagated to previously-created ndarrays - they will still have the bad flag set, but suddenly the elements that were bad will become 'good', but containing the old bad value. See discussion below.

Bad values and boolean operators

For those boolean operators in PDL::Ops, evaluation on a bad value returns the bad value. This:

$mask = $img > $thresh;

correctly propagates bad values. This will omit any bad values, but return a bad value if there are no good ones:

$bool = any( $img > $thresh );

As of 2.077, a bad value used as a boolean will throw an exception.

When using one of the 'projection' functions in PDL::Ufunc - such as orover - bad values are skipped over (see the documentation of these functions for the current handling of the case when all elements are bad).

IMPLEMENTATION DETAILS

A new flag has been added to the state of an ndarray - PDL_BADVAL. If unset, then the ndarray does not contain bad values, and so all the support code can be ignored. If set, it does not guarantee that bad values are present, just that they should be checked for.

The pdl_trans structure has been extended to include an integer value, bvalflag, which acts as a switch to tell the code whether to handle bad values or not. This value is set if any of the input ndarrays have their PDL_BADVAL flag set (although this code can be replaced by setting FindBadStateCode in pp_def).

The per-ndarray badvalue is a PDL_Anyval, a struct with an integer-valued type (like an ndarray), and a union-value that can hold one of any value that PDL can handle. As of 2.086, this value must always have the same type as the ndarray, and this is enforced in the PDL core.

Default bad values

The default bad values are now stored in a structure within the Core PDL structure - PDL.bvals (eg Basic/Core/pdlcore.h); see also typedef pdl_badvals in Basic/Core/pdl.h.PL and the BOOT code of Basic/Core/Core.xs where the values are initialised to (hopefully) sensible values. See "badvalue" in PDL::Bad and "orig_badvalue" in PDL::Bad for read/write routines to the values.

The default/original bad values are set to the C type's maximum (unsigned integers) or the minimum (floating-point and signed integers).

How do I change a routine to handle bad values?

See "BadCode" in PDL::PP and "HandleBad" in PDL::PP.

If you have a routine that you want to be able to use as in-place, look at the routines in bad.pd (or ops.pd) which use the in-place option to see how the bad flag is propagated to children using the xxxBadStatusCode options. I decided not to automate this as rules would be a little complex, since not every in-place op will need to propagate the badflag (eg unary functions).

This all means that you can change (as of 2.073)

Code => '$a() = $b() + $c();'

to

Code => 'PDL_IF_BAD(if ( $ISBAD(b()) || $ISBAD(c()) ) {
              $SETBAD(a());
            } else,) {
              $a() = $b() + $c();
            }'

which means you only need to maintain the logic in one place, rather than having a separate BadCode. PDL_IF_BAD evaluates to its first argument if the badvalue flag is true, or its second if not. PDL::PP::PDLCode will then create code something like

if ( __trans->bvalflag ) {
     broadcastloop over Code with PDL_IF_BAD set appropriately
} else {
     broadcastloop over Code with PDL_IF_BAD set appropriately
}

WHAT ABOUT DOCUMENTATION?

One of the strengths of PDL is its on-line documentation. The aim is to use this system to provide information on how/if a routine supports bad values: in many cases pp_def() contains all the information anyway, so the function-writer doesn't need to do anything at all! For the cases when this is not sufficient, there's the BadDoc option. For code written at the Perl level - i.e. in a .pm file - use the =for bad pod directive.

This information will be available via man/pod2man/html documentation. It's also accessible from the perldl or pdl2 shells - using the badinfo command - and the pdldoc shell command - using the -b option.

AUTHOR

Copyright (C) Doug Burke (djburke@cpan.org), 2000, 2006.

The per-ndarray bad value support is by Heiko Klein (2006).