Index: /trunk/PS-IPP-Config/Build.PL =================================================================== --- /trunk/PS-IPP-Config/Build.PL (revision 8310) +++ /trunk/PS-IPP-Config/Build.PL (revision 8310) @@ -0,0 +1,15 @@ +use Module::Build; +# See perldoc Module::Build for details of how this works + +Module::Build->new( + module_name => 'PS::IPP::Metadata', + dist_version => '0.01', + author => 'Paul Price and Joshua Hoblitt ', + license => 'gpl', + create_makefile_pl => 'passthrough', + requires => { + 'Carp' => 0, + 'Class::Accessor::Fast' => '0.19', + 'Statistics::Descriptive' => '2.6' + } +)->create_build_script; Index: /trunk/PS-IPP-Config/LICENSE =================================================================== --- /trunk/PS-IPP-Config/LICENSE (revision 8310) +++ /trunk/PS-IPP-Config/LICENSE (revision 8310) @@ -0,0 +1,260 @@ +The General Public License (GPL) +Version 2, June 1991 + +Copyright (C) 1989, 1991 Free Software Foundation, Inc. 675 Mass Ave, +Cambridge, MA 02139, USA. Everyone is permitted to copy and distribute +verbatim copies of this license document, but changing it is not allowed. + +Preamble + +The licenses for most software are designed to take away your freedom to share +and change it. By contrast, the GNU General Public License is intended to +guarantee your freedom to share and change free software--to make sure the +software is free for all its users. This General Public License applies to most of +the Free Software Foundation's software and to any other program whose +authors commit to using it. (Some other Free Software Foundation software is +covered by the GNU Library General Public License instead.) You can apply it to +your programs, too. + +When we speak of free software, we are referring to freedom, not price. Our +General Public Licenses are designed to make sure that you have the freedom +to distribute copies of free software (and charge for this service if you wish), that +you receive source code or can get it if you want it, that you can change the +software or use pieces of it in new free programs; and that you know you can do +these things. + +To protect your rights, we need to make restrictions that forbid anyone to deny +you these rights or to ask you to surrender the rights. These restrictions +translate to certain responsibilities for you if you distribute copies of the +software, or if you modify it. + +For example, if you distribute copies of such a program, whether gratis or for a +fee, you must give the recipients all the rights that you have. You must make +sure that they, too, receive or can get the source code. And you must show +them these terms so they know their rights. + +We protect your rights with two steps: (1) copyright the software, and (2) offer +you this license which gives you legal permission to copy, distribute and/or +modify the software. + +Also, for each author's protection and ours, we want to make certain that +everyone understands that there is no warranty for this free software. If the +software is modified by someone else and passed on, we want its recipients to +know that what they have is not the original, so that any problems introduced by +others will not reflect on the original authors' reputations. + +Finally, any free program is threatened constantly by software patents. We wish +to avoid the danger that redistributors of a free program will individually obtain +patent licenses, in effect making the program proprietary. To prevent this, we +have made it clear that any patent must be licensed for everyone's free use or +not licensed at all. + +The precise terms and conditions for copying, distribution and modification +follow. + +GNU GENERAL PUBLIC LICENSE +TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND +MODIFICATION + +0. This License applies to any program or other work which contains a notice +placed by the copyright holder saying it may be distributed under the terms of +this General Public License. The "Program", below, refers to any such program +or work, and a "work based on the Program" means either the Program or any +derivative work under copyright law: that is to say, a work containing the +Program or a portion of it, either verbatim or with modifications and/or translated +into another language. (Hereinafter, translation is included without limitation in +the term "modification".) Each licensee is addressed as "you". + +Activities other than copying, distribution and modification are not covered by +this License; they are outside its scope. The act of running the Program is not +restricted, and the output from the Program is covered only if its contents +constitute a work based on the Program (independent of having been made by +running the Program). Whether that is true depends on what the Program does. + +1. You may copy and distribute verbatim copies of the Program's source code as +you receive it, in any medium, provided that you conspicuously and appropriately +publish on each copy an appropriate copyright notice and disclaimer of warranty; +keep intact all the notices that refer to this License and to the absence of any +warranty; and give any other recipients of the Program a copy of this License +along with the Program. + +You may charge a fee for the physical act of transferring a copy, and you may at +your option offer warranty protection in exchange for a fee. + +2. You may modify your copy or copies of the Program or any portion of it, thus +forming a work based on the Program, and copy and distribute such +modifications or work under the terms of Section 1 above, provided that you also +meet all of these conditions: + +a) You must cause the modified files to carry prominent notices stating that you +changed the files and the date of any change. + +b) You must cause any work that you distribute or publish, that in whole or in +part contains or is derived from the Program or any part thereof, to be licensed +as a whole at no charge to all third parties under the terms of this License. + +c) If the modified program normally reads commands interactively when run, you +must cause it, when started running for such interactive use in the most ordinary +way, to print or display an announcement including an appropriate copyright +notice and a notice that there is no warranty (or else, saying that you provide a +warranty) and that users may redistribute the program under these conditions, +and telling the user how to view a copy of this License. (Exception: if the +Program itself is interactive but does not normally print such an announcement, +your work based on the Program is not required to print an announcement.) + +These requirements apply to the modified work as a whole. If identifiable +sections of that work are not derived from the Program, and can be reasonably +considered independent and separate works in themselves, then this License, +and its terms, do not apply to those sections when you distribute them as +separate works. But when you distribute the same sections as part of a whole +which is a work based on the Program, the distribution of the whole must be on +the terms of this License, whose permissions for other licensees extend to the +entire whole, and thus to each and every part regardless of who wrote it. + +Thus, it is not the intent of this section to claim rights or contest your rights to +work written entirely by you; rather, the intent is to exercise the right to control +the distribution of derivative or collective works based on the Program. + +In addition, mere aggregation of another work not based on the Program with the +Program (or with a work based on the Program) on a volume of a storage or +distribution medium does not bring the other work under the scope of this +License. + +3. You may copy and distribute the Program (or a work based on it, under +Section 2) in object code or executable form under the terms of Sections 1 and 2 +above provided that you also do one of the following: + +a) Accompany it with the complete corresponding machine-readable source +code, which must be distributed under the terms of Sections 1 and 2 above on a +medium customarily used for software interchange; or, + +b) Accompany it with a written offer, valid for at least three years, to give any +third party, for a charge no more than your cost of physically performing source +distribution, a complete machine-readable copy of the corresponding source +code, to be distributed under the terms of Sections 1 and 2 above on a medium +customarily used for software interchange; or, + +c) Accompany it with the information you received as to the offer to distribute +corresponding source code. (This alternative is allowed only for noncommercial +distribution and only if you received the program in object code or executable +form with such an offer, in accord with Subsection b above.) + +The source code for a work means the preferred form of the work for making +modifications to it. For an executable work, complete source code means all the +source code for all modules it contains, plus any associated interface definition +files, plus the scripts used to control compilation and installation of the +executable. However, as a special exception, the source code distributed need +not include anything that is normally distributed (in either source or binary form) +with the major components (compiler, kernel, and so on) of the operating system +on which the executable runs, unless that component itself accompanies the +executable. + +If distribution of executable or object code is made by offering access to copy +from a designated place, then offering equivalent access to copy the source +code from the same place counts as distribution of the source code, even though +third parties are not compelled to copy the source along with the object code. + +4. You may not copy, modify, sublicense, or distribute the Program except as +expressly provided under this License. Any attempt otherwise to copy, modify, +sublicense or distribute the Program is void, and will automatically terminate +your rights under this License. However, parties who have received copies, or +rights, from you under this License will not have their licenses terminated so long +as such parties remain in full compliance. + +5. You are not required to accept this License, since you have not signed it. +However, nothing else grants you permission to modify or distribute the Program +or its derivative works. These actions are prohibited by law if you do not accept +this License. Therefore, by modifying or distributing the Program (or any work +based on the Program), you indicate your acceptance of this License to do so, +and all its terms and conditions for copying, distributing or modifying the +Program or works based on it. + +6. Each time you redistribute the Program (or any work based on the Program), +the recipient automatically receives a license from the original licensor to copy, +distribute or modify the Program subject to these terms and conditions. You +may not impose any further restrictions on the recipients' exercise of the rights +granted herein. You are not responsible for enforcing compliance by third parties +to this License. + +7. If, as a consequence of a court judgment or allegation of patent infringement +or for any other reason (not limited to patent issues), conditions are imposed on +you (whether by court order, agreement or otherwise) that contradict the +conditions of this License, they do not excuse you from the conditions of this +License. If you cannot distribute so as to satisfy simultaneously your obligations +under this License and any other pertinent obligations, then as a consequence +you may not distribute the Program at all. For example, if a patent license would +not permit royalty-free redistribution of the Program by all those who receive +copies directly or indirectly through you, then the only way you could satisfy +both it and this License would be to refrain entirely from distribution of the +Program. + +If any portion of this section is held invalid or unenforceable under any particular +circumstance, the balance of the section is intended to apply and the section as +a whole is intended to apply in other circumstances. + +It is not the purpose of this section to induce you to infringe any patents or other +property right claims or to contest validity of any such claims; this section has +the sole purpose of protecting the integrity of the free software distribution +system, which is implemented by public license practices. Many people have +made generous contributions to the wide range of software distributed through +that system in reliance on consistent application of that system; it is up to the +author/donor to decide if he or she is willing to distribute software through any +other system and a licensee cannot impose that choice. + +This section is intended to make thoroughly clear what is believed to be a +consequence of the rest of this License. + +8. If the distribution and/or use of the Program is restricted in certain countries +either by patents or by copyrighted interfaces, the original copyright holder who +places the Program under this License may add an explicit geographical +distribution limitation excluding those countries, so that distribution is permitted +only in or among countries not thus excluded. In such case, this License +incorporates the limitation as if written in the body of this License. + +9. The Free Software Foundation may publish revised and/or new versions of the +General Public License from time to time. Such new versions will be similar in +spirit to the present version, but may differ in detail to address new problems or +concerns. + +Each version is given a distinguishing version number. If the Program specifies a +version number of this License which applies to it and "any later version", you +have the option of following the terms and conditions either of that version or of +any later version published by the Free Software Foundation. If the Program does +not specify a version number of this License, you may choose any version ever +published by the Free Software Foundation. + +10. If you wish to incorporate parts of the Program into other free programs +whose distribution conditions are different, write to the author to ask for +permission. For software which is copyrighted by the Free Software Foundation, +write to the Free Software Foundation; we sometimes make exceptions for this. +Our decision will be guided by the two goals of preserving the free status of all +derivatives of our free software and of promoting the sharing and reuse of +software generally. + +NO WARRANTY + +11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS +NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE +COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM +"AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR +IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE +ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE +PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, +YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR +CORRECTION. + +12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED +TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY +WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS +PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES +ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM +(INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING +RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY +OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS +BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + +END OF TERMS AND CONDITIONS Index: /trunk/PS-IPP-Config/lib/PS/IPP/Metadata/List.pm =================================================================== --- /trunk/PS-IPP-Config/lib/PS/IPP/Metadata/List.pm (revision 8310) +++ /trunk/PS-IPP-Config/lib/PS/IPP/Metadata/List.pm (revision 8310) @@ -0,0 +1,46 @@ +# Copyright (c) 2006 Paul Price, Joshua Hoblitt +# +# $Id: List.pm,v 1.1 2006-08-12 04:26:12 price Exp $ + +package PS::IPP::Metadata::List; + +use strict; +use warnings FATAL => qw( all ); + +our $VERSION = '0.01'; + +use Carp qw( carp ); + +# Allow exporting of function +use base qw( Exporter ); +our @EXPORT_OK = qw( parse_md_list ); + +#$::RD_TRACE = 1; +#$::RD_HINT = 1; +#use Data::Dumper; + +# Given a parsed metadata, parse it into an array of hashes +sub parse_md_list { + my $md = shift; # Parsed metadata, from PS::IPP::Metadata::Config + + my @array; # The array of hashes, to be returned + foreach my $mdItem (@$md) { + if ($mdItem->{class} ne "metadata") { + carp "MD element ", $mdItem->{name}, " isn't of type METADATA --- ignored.\n"; + next; + } + my %hash; # Hash element + my $mdComponents = $mdItem->{value}; # Components of the metadata + foreach my $data (@$mdComponents) { + $hash{$data->{name}} = $data->{value}; + } + push @array, \%hash; + } + + return \@array; +} + +1; + +__END__; + Index: /trunk/PS-IPP-Config/lib/PS/IPP/Metadata/Stats.pm =================================================================== --- /trunk/PS-IPP-Config/lib/PS/IPP/Metadata/Stats.pm (revision 8310) +++ /trunk/PS-IPP-Config/lib/PS/IPP/Metadata/Stats.pm (revision 8310) @@ -0,0 +1,187 @@ +# Copyright (c) 2006 Paul Price, Joshua Hoblitt +# +# $Id: Stats.pm,v 1.1 2006-08-12 04:26:12 price Exp $ + +package PS::IPP::Metadata::Stats; + +use strict; +use warnings FATAL => qw( all ); + +our $VERSION = '0.01'; + +use Carp qw( carp croak ); +use Statistics::Descriptive; + +use base qw( Class::Accessor::Fast ); +__PACKAGE__->mk_accessors( qw( bg_mean bg_stdev bg_mean_stdev constants variables ) ); + +#$::RD_TRACE = 1; +#$::RD_HINT = 1; +use Data::Dumper; + +sub new { + my $class = shift; # Class name + my $constants = shift; # Array of values that should be constant through the FPA + my $variables = shift; # Array of values that may be variable through the FPA + + my $self = { bg_mean => undef, # Mean of the mean backgrounds + bg_stdev => undef, # Standard deviation of the mean backgrounds + bg_mean_stdev => undef, # Mean of the standard deviation of the backgrounds + constants => $constants, # Array of values that should be constant through the FPA + variables => $variables, # Array of values that may be variable through the FPA + data => {} # The data + }; + + # Populate object + foreach my $constant (@$constants) { + $self->{data}->{$constant} = { type => 'constant', # Type of value (constant/variable) + value => undef # The actual variable + }; + } + foreach my $variable (@$variables) { + $self->{data}->{$variable} = { type => 'variable', # Type of value (constant/variable) + data => [], # Array of data values + mean => undef, # Mean of data values + stdev => undef # Standard deviation of data values + }; + } + + # Bless and return object + bless $self, $class; + return $self; +} + +# Given a parsed metadata from ppStats, assemble summary statistics +sub parse { + my $self = shift; # Where we'll put the information + my $md = shift; # Parsed metadata, from PS::IPP::Metadata::Config + + my @backgrounds; # Array of background measurements + my @bgStdevs; # Array of background standard deviations + + # Descend the FPA hierarchy + foreach my $fpaItem (@$md) { + if ($fpaItem->{class} eq "metadata") { + my $chipName = $fpaItem->{name}; # Name of chip + my $chipData = $fpaItem->{value}; # Chip-level data + foreach my $chipItem (@$chipData) { + if ($chipItem->{class} eq "metadata") { + my $cellName = $chipItem->{name}; # Name of cell + my $cellData = $chipItem->{value}; # Cell-level data + my $bgName; # Name of the value we measured + my $bgStdevName; # Name of the stdev we measured + foreach my $cellItem (@$cellData) { + if ($cellItem->{name} =~ /^(SAMPLE|ROBUST|FITTED|CLIPPED)_/) { + # It's a statistic of some sort + if ($cellItem->{name} =~ /_STDEV$/) { + if (defined $bgStdevName) { + carp "Ignoring duplicate background stdev (", $cellItem->{name}, "). ", + "Original is ", $bgStdevName, "\n"; + next; + } + $bgStdevName = $cellItem->{name}; + push @bgStdevs, $cellItem->{value}; + } else { + if (defined $bgName) { + carp "Ignoring duplicate background value (", $cellItem->{name}, "). ", + "Original is ", $bgName, "\n"; + next; + } + $bgName = $cellItem->{name}; + push @backgrounds, $cellItem->{value}; + } + } else { + $self->_check_values($cellItem); + } + } + } else { + $self->_check_values($chipItem); + } + } + } else { + $self->_check_values($fpaItem); + } + } + + # Check that we found everything for the constants + foreach my $constant (@{$self->constants()}) { + if (not defined $self->{data}->{$constant}->{value}) { + carp "Unable to find value for ", $constant, "\n"; + } + } + + # Get mean, stdev for the variables + foreach my $variable (@{$self->variables()}) { + my $info = $self->{data}->{$variable}; # The information about this particular variable + my $array = $info->{data}; # The array of values collected + if (scalar @$array == 0) { + carp "Unable to find any values for ", $variable, "\n"; + next; + } + + # Get statistics on the value + my $stats = Statistics::Descriptive::Sparse->new(); # Statistics calculator + $stats->add_data(@$array); + $info->{mean} = $stats->mean(); + $info->{stdev} = $stats->standard_deviation(); + } + + # Get mean, stdev, mean stdev for the background + my $meanStats = Statistics::Descriptive::Sparse->new(); # Statistics for mean + $meanStats->add_data(@backgrounds); + $self->bg_mean($meanStats->mean()); + $self->bg_stdev($meanStats->standard_deviation()); + my $stdevStats = Statistics::Descriptive::Sparse->new(); # Statistics for standard deviation + $stdevStats->add_data(@bgStdevs); + $self->bg_mean_stdev($stdevStats->mean()); + + return $self; +} + + +# Private function to check a metadata item for things we're interested in +sub _check_values { + my $self = shift; + my $mdItem = shift; # Metadata item to check + + my $name = $mdItem->{name}; # Name of the item + my $value = $mdItem->{value}; # Value of the item + + my $data = $self->{data}; # The data + return if not defined $data->{$name}; # Not interested + my $type = $data->{$name}->{type}; # Type of the item: constant or variable + + if ($type eq 'constant') { + if (defined $data->{$name}->{value} && ($data->{$name}->{value} ne $value)) { + carp "Warning: different value for ", $name, " found: ", $data->{$name}->{value}, " (old) vs ", + $value, " (new). Ignoring new value.\n"; + return; + } + $data->{$name}->{value} = $value; + return; + } + + if ($type eq 'variable') { + my $array = $data->{$name}->{data}; # Array containing all the values + push @$array, $value; + return; + } + + croak "Unrecognised type (", $type, ") for value of ", $name, "\n"; + return; +} + +# Return the data structure for a particular value, or the entire hash +sub data { + my $self = shift; + my $name = shift; # Name of data to return + + return $self->{data} if (not defined $name); + return $self->{data}->{$name}; +} + + +1; + +__END__; +