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Q3 a6YzZ.Uz"Z [D{0ĞE8E/gLgxHH;'7`w֍4W*an!Z0$w簽& aܪnڮ rkTZ &k17)z/pM0EǥH7[j8iK4[g\66X*Ķx ٠qű&!3=hQM;1}(l`xj<,I lgx*@Tlm% vHdY/sYJc(3~y[h@O~\[ \=`<|M0Ξ@kBnlPxɍw nkj@L{5XGr[Z3<bO8Lm12*pև/B]?FMGo KCyLtr5}"( 1p6IK~ ^)(n15H4K X} .֪Oq?f06#Rzx'00 o%KNR bNABDv8) k"&){3fn) JQ5 d oh|["TsSaE00f;H҇aZom1ȹuRVHhf7 '~!@kEA$2y.R]G";E̾0MğSe,^`XFZ);pe+& ;%$6o qTadDs>fVh\|Is {g=O(8<e),Hgq  DOSB5΋e13l->3$bB:Xdld SntdomTѦ]|ð[x:y(v\p6):a5t>T^#VG~U]Qj~'wJj=o_*AsKz{?/E5cZn?Z>fRZ e5BI@y0=(wD%MWc+$4IyCTD]S. mRm؀VL"lz~q%5c>rLJsd+qB=$ay8"f DgGz/QYicIm{kO6dֹ'UtENO=[k`8)o pJ`^vE c]%iFl1Z!V|CgH4ۉC@p%?'ɣlE}OvAG?)z, ~dl*tS5Լ-2D]q/ex̿Ol_ !z}E{-Ur$ׅIy2-(RE).4_2f ~[O<M\xF[a2ZBh`VlI {=E7w=QOed6V{%6B>ރ;G   `tKQw0)ڿԳj?t:(kB >H`tB OagJԕw#!C\γOM eq"rXs6UXEԫ^}#HDgxmlYU~.P.cYCVbpJrW"ZuP6zU<JlmN H;۞Hz,6diRI_wlD4(; _3waiP;' ^NWwh\FjUF}Z[N~D4-Qv$F&{]U}]]{.tB857pn4ǞGK7,i#ghMu`3<RwKxB]| ^+"f ONgڒ-.RUYЩ^,@,}EAhKeG+ ze[p;aSm;\Ujj p"ڨ :4$ReW }_MNXw#r6 mq{xñ\s14] R!t{/6}ɺE  )HA3J" ]vU(Cެ1Fx`0`8T6 {%IQjEQ.@`{IN6pgSS$Bl}H {?ڻ.LF Oo"eCwX$I;Or ?\?zk-q_vqS]RV9p}K_݌-4pVR'hpPoCrD¹W6T$ u"@YxL 'գD\Y)34{K9sxLAj( JKn55P3NX+sb!8ؘ&k4.3jGL|nD~lK-8/Ds=&t=PG4~D??l.8H'y?J}-E'mFVe\Q-&>_YAKd@^%DC9-'|1s8&e֊wCIqW{{HRC?7ai@\d e?9$KF)709!)N XJ3SYV%33T#5f$8LxQXu'#y-6F2 &h|z wH{vFsomoclu/.git/info/0000755000417600011450000000000012402311153015443 5ustar pewiunix-users-shamansomoclu/.git/info/exclude0000644000417600011450000000036012402311153017016 0ustar pewiunix-users-shaman# git ls-files --others --exclude-from=.git/info/exclude # Lines that start with '#' are comments. # For a project mostly in C, the following would be a good set of # exclude patterns (uncomment them if you want to use them): # *.[oa] # *~ somoclu/.git/logs/0000755000417600011450000000000012402311155015456 5ustar pewiunix-users-shamansomoclu/.git/logs/HEAD0000644000417600011450000000027512402311155016106 0ustar pewiunix-users-shaman0000000000000000000000000000000000000000 c5ba668a942c65196e2df61a8673acee893fae03 Peter Wittek 1409913453 +0200 clone: from https://github.com/peterwittek/somoclu.git somoclu/.git/logs/refs/0000755000417600011450000000000012402311155016415 5ustar pewiunix-users-shamansomoclu/.git/logs/refs/heads/0000755000417600011450000000000012402311155017501 5ustar pewiunix-users-shamansomoclu/.git/logs/refs/heads/master0000644000417600011450000000027512402311155020723 0ustar pewiunix-users-shaman0000000000000000000000000000000000000000 c5ba668a942c65196e2df61a8673acee893fae03 Peter Wittek 1409913453 +0200 clone: from https://github.com/peterwittek/somoclu.git somoclu/.git/hooks/0000755000417600011450000000000012402311153015633 5ustar pewiunix-users-shamansomoclu/.git/hooks/applypatch-msg.sample0000755000417600011450000000070412402311153021773 0ustar pewiunix-users-shaman#!/bin/sh # # An example hook script to check the commit log message taken by # applypatch from an e-mail message. # # The hook should exit with non-zero status after issuing an # appropriate message if it wants to stop the commit. The hook is # allowed to edit the commit message file. # # To enable this hook, rename this file to "applypatch-msg". . git-sh-setup test -x "$GIT_DIR/hooks/commit-msg" && exec "$GIT_DIR/hooks/commit-msg" ${1+"$@"} : somoclu/.git/hooks/commit-msg.sample0000755000417600011450000000160012402311153021112 0ustar pewiunix-users-shaman#!/bin/sh # # An example hook script to check the commit log message. # Called by "git commit" with one argument, the name of the file # that has the commit message. The hook should exit with non-zero # status after issuing an appropriate message if it wants to stop the # commit. The hook is allowed to edit the commit message file. # # To enable this hook, rename this file to "commit-msg". # Uncomment the below to add a Signed-off-by line to the message. # Doing this in a hook is a bad idea in general, but the prepare-commit-msg # hook is more suited to it. # # SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p') # grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1" # This example catches duplicate Signed-off-by lines. test "" = "$(grep '^Signed-off-by: ' "$1" | sort | uniq -c | sed -e '/^[ ]*1[ ]/d')" || { echo >&2 Duplicate Signed-off-by lines. exit 1 } somoclu/.git/hooks/prepare-commit-msg.sample0000755000417600011450000000232712402311153022555 0ustar pewiunix-users-shaman#!/bin/sh # # An example hook script to prepare the commit log message. # Called by "git commit" with the name of the file that has the # commit message, followed by the description of the commit # message's source. The hook's purpose is to edit the commit # message file. If the hook fails with a non-zero status, # the commit is aborted. # # To enable this hook, rename this file to "prepare-commit-msg". # This hook includes three examples. The first comments out the # "Conflicts:" part of a merge commit. # # The second includes the output of "git diff --name-status -r" # into the message, just before the "git status" output. It is # commented because it doesn't cope with --amend or with squashed # commits. # # The third example adds a Signed-off-by line to the message, that can # still be edited. This is rarely a good idea. case "$2,$3" in merge,) /usr/bin/perl -i.bak -ne 's/^/# /, s/^# #/#/ if /^Conflicts/ .. /#/; print' "$1" ;; # ,|template,) # /usr/bin/perl -i.bak -pe ' # print "\n" . `git diff --cached --name-status -r` # if /^#/ && $first++ == 0' "$1" ;; *) ;; esac # SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p') # grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1" somoclu/.git/hooks/post-update.sample0000755000417600011450000000027512402311153021312 0ustar pewiunix-users-shaman#!/bin/sh # # An example hook script to prepare a packed repository for use over # dumb transports. # # To enable this hook, rename this file to "post-update". exec git update-server-info somoclu/.git/hooks/update.sample0000755000417600011450000000703312402311153020326 0ustar pewiunix-users-shaman#!/bin/sh # # An example hook script to blocks unannotated tags from entering. # Called by "git receive-pack" with arguments: refname sha1-old sha1-new # # To enable this hook, rename this file to "update". # # Config # ------ # hooks.allowunannotated # This boolean sets whether unannotated tags will be allowed into the # repository. By default they won't be. # hooks.allowdeletetag # This boolean sets whether deleting tags will be allowed in the # repository. By default they won't be. # hooks.allowmodifytag # This boolean sets whether a tag may be modified after creation. By default # it won't be. # hooks.allowdeletebranch # This boolean sets whether deleting branches will be allowed in the # repository. By default they won't be. # hooks.denycreatebranch # This boolean sets whether remotely creating branches will be denied # in the repository. By default this is allowed. # # --- Command line refname="$1" oldrev="$2" newrev="$3" # --- Safety check if [ -z "$GIT_DIR" ]; then echo "Don't run this script from the command line." >&2 echo " (if you want, you could supply GIT_DIR then run" >&2 echo " $0 )" >&2 exit 1 fi if [ -z "$refname" -o -z "$oldrev" -o -z "$newrev" ]; then echo "Usage: $0 " >&2 exit 1 fi # --- Config allowunannotated=$(git config --bool hooks.allowunannotated) allowdeletebranch=$(git config --bool hooks.allowdeletebranch) denycreatebranch=$(git config --bool hooks.denycreatebranch) allowdeletetag=$(git config --bool hooks.allowdeletetag) allowmodifytag=$(git config --bool hooks.allowmodifytag) # check for no description projectdesc=$(sed -e '1q' "$GIT_DIR/description") case "$projectdesc" in "Unnamed repository"* | "") echo "*** Project description file hasn't been set" >&2 exit 1 ;; esac # --- Check types # if $newrev is 0000...0000, it's a commit to delete a ref. zero="0000000000000000000000000000000000000000" if [ "$newrev" = "$zero" ]; then newrev_type=delete else newrev_type=$(git cat-file -t $newrev) fi case "$refname","$newrev_type" in refs/tags/*,commit) # un-annotated tag short_refname=${refname##refs/tags/} if [ "$allowunannotated" != "true" ]; then echo "*** The un-annotated tag, $short_refname, is not allowed in this repository" >&2 echo "*** Use 'git tag [ -a | -s ]' for tags you want to propagate." >&2 exit 1 fi ;; refs/tags/*,delete) # delete tag if [ "$allowdeletetag" != "true" ]; then echo "*** Deleting a tag is not allowed in this repository" >&2 exit 1 fi ;; refs/tags/*,tag) # annotated tag if [ "$allowmodifytag" != "true" ] && git rev-parse $refname > /dev/null 2>&1 then echo "*** Tag '$refname' already exists." >&2 echo "*** Modifying a tag is not allowed in this repository." >&2 exit 1 fi ;; refs/heads/*,commit) # branch if [ "$oldrev" = "$zero" -a "$denycreatebranch" = "true" ]; then echo "*** Creating a branch is not allowed in this repository" >&2 exit 1 fi ;; refs/heads/*,delete) # delete branch if [ "$allowdeletebranch" != "true" ]; then echo "*** Deleting a branch is not allowed in this repository" >&2 exit 1 fi ;; refs/remotes/*,commit) # tracking branch ;; refs/remotes/*,delete) # delete tracking branch if [ "$allowdeletebranch" != "true" ]; then echo "*** Deleting a tracking branch is not allowed in this repository" >&2 exit 1 fi ;; *) # Anything else (is there anything else?) echo "*** Update hook: unknown type of update to ref $refname of type $newrev_type" >&2 exit 1 ;; esac # --- Finished exit 0 somoclu/.git/hooks/pre-rebase.sample0000755000417600011450000001152712402311153021074 0ustar pewiunix-users-shaman#!/bin/sh # # Copyright (c) 2006, 2008 Junio C Hamano # # The "pre-rebase" hook is run just before "git rebase" starts doing # its job, and can prevent the command from running by exiting with # non-zero status. # # The hook is called with the following parameters: # # $1 -- the upstream the series was forked from. # $2 -- the branch being rebased (or empty when rebasing the current branch). # # This sample shows how to prevent topic branches that are already # merged to 'next' branch from getting rebased, because allowing it # would result in rebasing already published history. publish=next basebranch="$1" if test "$#" = 2 then topic="refs/heads/$2" else topic=`git symbolic-ref HEAD` || exit 0 ;# we do not interrupt rebasing detached HEAD fi case "$topic" in refs/heads/??/*) ;; *) exit 0 ;# we do not interrupt others. ;; esac # Now we are dealing with a topic branch being rebased # on top of master. Is it OK to rebase it? # Does the topic really exist? git show-ref -q "$topic" || { echo >&2 "No such branch $topic" exit 1 } # Is topic fully merged to master? not_in_master=`git rev-list --pretty=oneline ^master "$topic"` if test -z "$not_in_master" then echo >&2 "$topic is fully merged to master; better remove it." exit 1 ;# we could allow it, but there is no point. fi # Is topic ever merged to next? If so you should not be rebasing it. only_next_1=`git rev-list ^master "^$topic" ${publish} | sort` only_next_2=`git rev-list ^master ${publish} | sort` if test "$only_next_1" = "$only_next_2" then not_in_topic=`git rev-list "^$topic" master` if test -z "$not_in_topic" then echo >&2 "$topic is already up-to-date with master" exit 1 ;# we could allow it, but there is no point. else exit 0 fi else not_in_next=`git rev-list --pretty=oneline ^${publish} "$topic"` /usr/bin/perl -e ' my $topic = $ARGV[0]; my $msg = "* $topic has commits already merged to public branch:\n"; my (%not_in_next) = map { /^([0-9a-f]+) /; ($1 => 1); } split(/\n/, $ARGV[1]); for my $elem (map { /^([0-9a-f]+) (.*)$/; [$1 => $2]; } split(/\n/, $ARGV[2])) { if (!exists $not_in_next{$elem->[0]}) { if ($msg) { print STDERR $msg; undef $msg; } print STDERR " $elem->[1]\n"; } } ' "$topic" "$not_in_next" "$not_in_master" exit 1 fi exit 0 ################################################################ This sample hook safeguards topic branches that have been published from being rewound. The workflow assumed here is: * Once a topic branch forks from "master", "master" is never merged into it again (either directly or indirectly). * Once a topic branch is fully cooked and merged into "master", it is deleted. If you need to build on top of it to correct earlier mistakes, a new topic branch is created by forking at the tip of the "master". This is not strictly necessary, but it makes it easier to keep your history simple. * Whenever you need to test or publish your changes to topic branches, merge them into "next" branch. The script, being an example, hardcodes the publish branch name to be "next", but it is trivial to make it configurable via $GIT_DIR/config mechanism. With this workflow, you would want to know: (1) ... if a topic branch has ever been merged to "next". Young topic branches can have stupid mistakes you would rather clean up before publishing, and things that have not been merged into other branches can be easily rebased without affecting other people. But once it is published, you would not want to rewind it. (2) ... if a topic branch has been fully merged to "master". Then you can delete it. More importantly, you should not build on top of it -- other people may already want to change things related to the topic as patches against your "master", so if you need further changes, it is better to fork the topic (perhaps with the same name) afresh from the tip of "master". Let's look at this example: o---o---o---o---o---o---o---o---o---o "next" / / / / / a---a---b A / / / / / / / / c---c---c---c B / / / / \ / / / / b---b C \ / / / / / \ / ---o---o---o---o---o---o---o---o---o---o---o "master" A, B and C are topic branches. * A has one fix since it was merged up to "next". * B has finished. It has been fully merged up to "master" and "next", and is ready to be deleted. * C has not merged to "next" at all. We would want to allow C to be rebased, refuse A, and encourage B to be deleted. To compute (1): git rev-list ^master ^topic next git rev-list ^master next if these match, topic has not merged in next at all. To compute (2): git rev-list master..topic if this is empty, it is fully merged to "master". somoclu/.git/hooks/pre-applypatch.sample0000755000417600011450000000061612402311153021775 0ustar pewiunix-users-shaman#!/bin/sh # # An example hook script to verify what is about to be committed # by applypatch from an e-mail message. # # The hook should exit with non-zero status after issuing an # appropriate message if it wants to stop the commit. # # To enable this hook, rename this file to "pre-applypatch". . git-sh-setup test -x "$GIT_DIR/hooks/pre-commit" && exec "$GIT_DIR/hooks/pre-commit" ${1+"$@"} : somoclu/.git/hooks/pre-commit.sample0000755000417600011450000000325012402311153021115 0ustar pewiunix-users-shaman#!/bin/sh # # An example hook script to verify what is about to be committed. # Called by "git commit" with no arguments. The hook should # exit with non-zero status after issuing an appropriate message if # it wants to stop the commit. # # To enable this hook, rename this file to "pre-commit". if git rev-parse --verify HEAD >/dev/null 2>&1 then against=HEAD else # Initial commit: diff against an empty tree object against=4b825dc642cb6eb9a060e54bf8d69288fbee4904 fi # If you want to allow non-ascii filenames set this variable to true. allownonascii=$(git config hooks.allownonascii) # Redirect output to stderr. exec 1>&2 # Cross platform projects tend to avoid non-ascii filenames; prevent # them from being added to the repository. We exploit the fact that the # printable range starts at the space character and ends with tilde. if [ "$allownonascii" != "true" ] && # Note that the use of brackets around a tr range is ok here, (it's # even required, for portability to Solaris 10's /usr/bin/tr), since # the square bracket bytes happen to fall in the designated range. test $(git diff --cached --name-only --diff-filter=A -z $against | LC_ALL=C tr -d '[ -~]\0' | wc -c) != 0 then echo "Error: Attempt to add a non-ascii file name." echo echo "This can cause problems if you want to work" echo "with people on other platforms." echo echo "To be portable it is advisable to rename the file ..." echo echo "If you know what you are doing you can disable this" echo "check using:" echo echo " git config hooks.allownonascii true" echo exit 1 fi # If there are whitespace errors, print the offending file names and fail. exec git diff-index --check --cached $against -- somoclu/.git/index0000644000417600011450000001234012402311155015544 0ustar pewiunix-users-shamanDIRC=T mT m܀~e֍rD&94q%Zh.CHANGEST mT m܀~e큄3#Ƌ3CDd:LICENSET mT m܀~e0'&% Ru[;;Bo>k' Makefile.inT mT m܀~e%#&gz-|tSbxL README.mdT mT m܀~e{ Jh\>=STODOT mT m܀~e8qn:R0*0x autogen.shT mT m܀~e ri{1dSAm> configure.acT mT m܀~eV_sP%ܲ.)m data/rgbs.lrnT mT m܀~e|=~y4VDcGO data/rgbs.svmT mT m܀~eT. [H data/rgbs.txtT mT m܀~e ;/TiEBϕ32w m4/ax_mpi_options.m4T mT m܀~e'yY$_`zkO=m4/ax_mpi_tests.m4T mT m܀~e^S^ [dsrc/MATLAB/MexSomoclu.cppT mT m܀~e +W5 8G:<-.src/MATLAB/README.rstT mT m܀~exCêU3D |tj'8{src/MATLAB/makeMex-GPU.shT mT m܀~e}&7@'ٜڏgsrc/MATLAB/makeMex.shT mT m܀~e',f>=_`src/MATLAB/mex_interface_test.mT mT m܀~e'آ9=~###src/MATLAB/mex_interface_test_gpu.mT mT m܀~ef,[5glogosrc/Makefile.inT mT m܀~eP3Vy8XDt9 src/Python/MANIFEST.inT mT m܀~eg3 Q}ikO\src/Python/README.rstT mT m܀~euJ&P2M7}>`src/Python/makepy.shT mT m܀~eC uwlS EPsrc/Python/setup.pyT mT m܀~e M{w{!F@̧~g"`isrc/Python/setup_with_CUDA.pyT mT m܀~e5t[,m6x.src/Python/somoclu.iT mT m܀~eS'M6R~. Lsrc/Python/somoclu.pyT mT m܀~e%K^#j|Csrc/Python/somoclu_wrap.cxxT mT m܀~eF T /ݛqUZ!\[ src/Python/tests/somoclu_test.pyT mT m܀~e)y~D 6 $ָsrc/R/DESCRIPTIONT mT m܀~e8f3Lē9 sΰsrc/R/NAMESPACET mT m܀~e —:O0*j'`/src/R/R/Rsomoclu.RT mT m܀~e -\src/training.cppT mT m܀~e D:x[.&NV K4 src/uMatrix.cppm#3bД!ꙛZsomoclu/.git/branches/0000755000417600011450000000000012402311153016275 5ustar pewiunix-users-shamansomoclu/.git/config0000644000417600011450000000041312402311155015700 0ustar pewiunix-users-shaman[core] repositoryformatversion = 0 filemode = true bare = false logallrefupdates = true [remote "origin"] fetch = +refs/heads/*:refs/remotes/origin/* url = https://github.com/peterwittek/somoclu.git [branch "master"] remote = origin merge = refs/heads/master somoclu/.git/refs/0000755000417600011450000000000012402311155015451 5ustar pewiunix-users-shamansomoclu/.git/refs/remotes/0000755000417600011450000000000012402311155017127 5ustar pewiunix-users-shamansomoclu/.git/refs/remotes/origin/0000755000417600011450000000000012402311155020416 5ustar pewiunix-users-shamansomoclu/.git/refs/remotes/origin/HEAD0000644000417600011450000000004012402311155021034 0ustar pewiunix-users-shamanref: refs/remotes/origin/master somoclu/.git/refs/heads/0000755000417600011450000000000012402311155016535 5ustar pewiunix-users-shamansomoclu/.git/refs/heads/master0000644000417600011450000000005112402311155017747 0ustar pewiunix-users-shamanc5ba668a942c65196e2df61a8673acee893fae03 somoclu/.git/refs/tags/0000755000417600011450000000000012402311153016405 5ustar pewiunix-users-shamansomoclu/.git/description0000644000417600011450000000011112402311153016747 0ustar pewiunix-users-shamanUnnamed repository; edit this file 'description' to name the repository. somoclu/.git/packed-refs0000644000417600011450000000171512402311155016625 0ustar pewiunix-users-shaman# pack-refs with: peeled ba7c59aff744fe7e8ca8674d8bee5cfeb01ea918 refs/remotes/origin/gh-pages c5ba668a942c65196e2df61a8673acee893fae03 refs/remotes/origin/master ca21c2be83da66506b2b9063b38289882b01be5b refs/remotes/origin/windows 2d10cb2b5380c7fde09d7b31f7792f15eb2cbc35 refs/tags/1.0 8d5c261c399451a58ca13b83c57e85d4942d4ef0 refs/tags/1.1 ^b02af4958cec44296a8cf2e2a5d44f61db85da56 15b77a00d7caa8623e08d91b69b0518a5a6726aa refs/tags/1.1.1 ^7ea3872a00df8dd3a8b345c835c605877be1e182 37466bab28200047bdf0ed3af918d287baf049a1 refs/tags/1.1.2 ^7ea3872a00df8dd3a8b345c835c605877be1e182 8edeb64c886120b94734a01fa9fc8d1328018bed refs/tags/1.2 ^9500571f7747d9fef0edc9ff4ef9b635a9cae4fd 4f5ff03a89737e23a057a3915c2226e37384cc6c refs/tags/1.3 ^9a8dd65ba49dd3767f5489d800630bf3951a207d 373db00e1787c8bea8c567bb14c0f4caec0d4d95 refs/tags/1.3.1 ^9cfbb6fe8ddd44b0b59199731411be61d5f89abc f926a11359326da2cd03ec41d8e6a9fbbd54ab75 refs/tags/1.4 ^c5ba668a942c65196e2df61a8673acee893fae03 somoclu/TODO0000644000417600011450000000027512402311155014345 0ustar pewiunix-users-shaman - Fix MATLAB interface with CUDA support. - Python, R with CUDA support on Windows. - Integration with data structures of SOM libraries in Python and R. - Implement hexagonal grid. somoclu/configure.ac0000644000417600011450000000531112402311155016137 0ustar pewiunix-users-shaman# -*- Autoconf -*- # Process this file with autoconf to produce a configure script. AC_PREREQ([2.61]) AC_INIT([Somoclu], [1.4]) m4_include([m4/ax_mpi_options.m4]) m4_include([m4/ax_mpi_tests.m4]) AC_CONFIG_SRCDIR([src/somoclu.cpp]) AC_CONFIG_HEADERS([config.h]) # Checks for programs. CXXFLAGS="-O3 -fPIC" AC_PROG_CXX AC_PROG_INSTALL AC_OPENMP openmp_enabled=no if test x"$OPENMP_CFLAGS" != x"" ; then openmp_enabled=yes fi CXXFLAGS="${CXXFLAGS} ${OPENMP_CFLAGS}" #find out what version we are running ARCH=`uname -m` if [[ $ARCH == "x86_64" ]]; then SUFFIX="64" else SUFFIX="" fi # Setup CUDA paths # ------------------------------------------------------------------------------ CUDA_PATH=/usr/local/cuda AC_ARG_WITH([cuda], [ --with-cuda=PATH prefix where cuda is installed [default=/usr/local/cuda]]) if test x"$with_cuda" != x"no" ; then if test -n "$with_cuda" then CUDA_PATH=$with_cuda fi AC_CHECK_PROG(NVCC_CHECK,nvcc,yes,no,$CUDA_PATH/bin) if test x"$NVCC_CHECK" = x"yes" ; then cuda_enabled=yes CUDA_CFLAGS="-I$CUDA_PATH/include -use_fast_math -Xcompiler \"${CXXFLAGS}\"" CUDA_LIBS="-lcudart -lcublas" CUDA_LDFLAGS="-L$CUDA_PATH/lib$SUFFIX" NVCC="$CUDA_PATH/bin/nvcc" AC_SUBST(CUDA_CFLAGS) AC_SUBST(CUDA_LIBS) AC_SUBST(CUDA_LDFLAGS) AC_SUBST(NVCC) AC_DEFINE([CUDA], 1, [cuda enabled]) elif test -n "$with_cuda" ; then echo "---------------------------------------" echo "Unable to find CUDA in $with_cuda." echo "Building a version without CUDA. " echo "---------------------------------------" cuda_enabled=no else cuda_enabled=no fi else cuda_enabled=no fi AM_CONDITIONAL([HAVE_CUDA], [test x"$cuda_enabled" = x"yes"]) #Setup MPI Paths # ------------------------------------------------------------------------------ AC_ARG_WITH([mpi], [ --with-mpi=PATH prefix where MPI is installed]) mpi_enabled=no if test x"$with_mpi" != x"no" ; then AX_MPI_OPTIONS if test x"$MPI_CXX" != x"none"; then AX_MPI_TESTS CXX=$MPI_CXX mpi_enabled=yes fi fi AC_CONFIG_FILES([Makefile src/Makefile]) AC_OUTPUT echo \ "------------------------------------------------- ${PACKAGE_NAME} Version ${PACKAGE_VERSION} Prefix: ${prefix}. Compiler: ${CXX} ${CXXFLAGS} ${MPI_INC} ${MPI_LIBDIR} ${MPI_LIBS} Package features: OpenMP enabled: ${openmp_enabled} MPI enabled: ${mpi_enabled} CUDA enabled: ${cuda_enabled} Now type 'make @<:@@:>@' where the optional is: all - build all binaries install - install everything --------------------------------------------------" somoclu/m4/0000755000417600011450000000000012402311155014171 5ustar pewiunix-users-shamansomoclu/m4/ax_mpi_options.m40000644000417600011450000000531312402311155017465 0ustar pewiunix-users-shamanAC_DEFUN([AX_MPI_OPTIONS],[ dnl dnl Command-line options for setting up MPI dnl MPI_CXX=none ### AC_ARG_WITH(mpi-compilers, AS_HELP_STRING([--with-mpi-compilers=DIR or --with-mpi-compilers=yes], [use MPI compiler (mpicxx) found in directory DIR, or in your PATH if =yes]), [ if test "X${withval}" = "Xyes"; then # Look for MPI C++ compile script/program in user's path, set # MPI_CXX to name of program found, else set it to "none". Could # add more paths to check as 4th argument if you wanted to. # Calls AC_SUBST for MPI_CXX, etc. if test "X${MPI_CXX}" = "Xnone" ; then echo "Looking for an MPI C++ compiler in your path" AC_CHECK_PROGS([MY_CXX], [mpic++ mpicxx mpiCC mpiicpc], [none],) MPI_CXX=${MY_CXX} fi else foundCompiler=no if test "X${MPI_CXX}" = "Xnone" ; then AC_MSG_CHECKING(MPI C++ compiler in ${withval}) if test -f ${withval}/mpic++ ; then MPI_CXX=${withval}/mpic++ fi if test "X${MPI_CXX}" = "Xnone" && test -f ${withval}/mpicxx ; then MPI_CXX=${withval}/mpicxx fi if test "X${MPI_CXX}" = "Xnone" && test -f ${withval}/mpiCC ; then MPI_CXX=${withval}/mpiCC fi if test "X${MPI_CXX}" = "Xnone" && test -f ${withval}/mpiicpc ; then MPI_CXX=${withval}/mpiicpc fi AC_MSG_RESULT([${MPI_CXX}]) fi fi if test "X${MPI_CXX}" = "Xnone" ; then AC_MSG_ERROR([MPI C++ compiler script/program not found.]) fi ] ) if test "X${MPI_CXX}" = "Xnone" ; then echo "Looking for an MPI C++ compiler in your path" AC_CHECK_PROGS([MY_CXX], [mpic++ mpicxx mpiCC mpiicpc], [none],) MPI_CXX=${MY_CXX} fi AC_ARG_WITH(mpi, AS_HELP_STRING([--with-mpi=MPIROOT],[use MPI root directory.]), [ if test "X${withval}" = "Xno"; then :; else MPI_DIR=${withval} AC_MSG_CHECKING(MPI directory) AC_MSG_RESULT([${MPI_DIR}]) fi ] ) AC_ARG_WITH(mpi-libs, AS_HELP_STRING([--with-mpi-libs="LIBS"],[MPI libraries @<:@default "-lmpi"@:>@]), [ if test "X${withval}" = "Xno"; then :; else MPI_LIBS=${withval} AC_MSG_CHECKING(user-defined MPI libraries) AC_MSG_RESULT([${MPI_LIBS}]) fi ] ) AC_ARG_WITH(mpi-incdir, AS_HELP_STRING([--with-mpi-incdir=DIR],[MPI include directory @<:@default MPIROOT/include@:>@]), [ if test "X${withval}" = "Xno"; then :; else MPI_INC="-I${withval}" AC_MSG_CHECKING(user-defined MPI includes) AC_MSG_RESULT([${MPI_INC}]) fi ] ) AC_ARG_WITH(mpi-libdir, AS_HELP_STRING([--with-mpi-libdir=DIR],[MPI library directory @<:@default MPIROOT/lib@:>@]), [ if test "X${withval}" = "Xno"; then :; else MPI_LIBDIR="-L${withval}" AC_MSG_CHECKING(user-defined MPI library directory) AC_MSG_RESULT([${MPI_LIBDIR}]) fi ] ) ]) somoclu/m4/ax_mpi_tests.m40000644000417600011450000000372412402311155017140 0ustar pewiunix-users-shamandnl MPI tests dnl dnl AX_MPI_TESTS(subpackage) AC_DEFUN([AX_MPI_TESTS],[ dnl dnl Test to see if MPI compilers work properly dnl if test -n "${MPI_DIR}" && test -z "${MPI_INC}"; then MPI_INC="-I${MPI_DIR}/include" fi if test -z "${MPI_INC}"; then AC_LANG([C++]) AC_MSG_CHECKING(whether we can preprocess mpi.h) AC_PREPROC_IFELSE( [AC_LANG_SOURCE([[#include "mpi.h"]])], [ AC_MSG_RESULT(yes) ],[ AC_MSG_RESULT(no) echo "---" echo "Cannot find header file mpi.h." echo "View the mpi options with \"configure --help\", and provide a valid MPI." echo "---" AC_MSG_ERROR(cannot find mpi.h) ]) AC_MSG_CHECKING(whether we can compile mpi.h) AC_COMPILE_IFELSE( [AC_LANG_SOURCE([[#include "mpi.h"]],[[int c; char** v; MPI_Init(&c,&v);]])], [ AC_MSG_RESULT(yes) AC_DEFINE(HAVE_MPI,,[define that mpi is being used]) ],[ AC_MSG_RESULT(no) echo "---" echo "mpi.h has compile errors" echo "View the mpi options with \"configure --help\", and provide a valid MPI." echo "---" AC_MSG_ERROR(invalid mpi.h) ]) fi AC_SUBST([MPI_INC]) if test -n "${MPI_DIR}" && test -z "${MPI_LIBDIR}"; then MPI_LIBDIR="-L${MPI_DIR}/lib" fi AC_SUBST([MPI_LIBDIR]) if test -z "${MPI_LIBS}" && test -n "${MPI_LIBDIR}"; then MPI_LIBS="-lmpi" fi AC_SUBST([MPI_LIBS]) AC_LANG([C++]) AC_MSG_CHECKING(whether special compile flag for MPICH is required) AC_RUN_IFELSE( [AC_LANG_PROGRAM( [[#define MPICH_IGNORE_CXX_SEEK] [#include ]], [[#ifdef MPICH_NAME return 0; #endif return 1;]])], [AC_MSG_RESULT(yes) CXXFLAGS="${CXXFLAGS} -DMPICH_IGNORE_CXX_SEEK" echo "-----" echo "Adding -DMPICH_IGNORE_CXX_SEEK to MPICH compilations" echo "-----"], [AC_MSG_RESULT(no)], [AC_MSG_RESULT(cross compiling) CXXFLAGS="${CXXFLAGS} -DMPICH_IGNORE_CXX_SEEK" echo "-----" echo "Adding -DMPICH_IGNORE_CXX_SEEK because we can't determine whether or not it is required" echo "-----"] ) ]) somoclu/data/0000755000417600011450000000000012402311155014562 5ustar pewiunix-users-shamansomoclu/data/rgbs.lrn0000644000417600011450000000112612402311155016234 0ustar pewiunix-users-shaman# Example file for ESOM lrn format % 28 % 3 % 9 1 1 1 % Seq data1 data2 data3 1 0.01 1.00 0.0 2 0.0 0.97 0.01 3 0.0 0.99 0.02 4 0.01 0.94 0.03 5 0.0 0.91 0.01 6 0.01 1.00 0.0 7 0.0 0.98 0.02 8 1.00 0.01 0.0 9 0.97 0.01 0.0 10 0.97 0.02 0.0 11 0.99 0.02 0.0 12 0.94 0.03 0.01 13 0.91 0.0 0.01 14 1.00 0.01 0.01 15 0.98 0.02 0.01 16 0.97 0.01 0.02 17 0.92 0.03 0.01 18 0.01 0.0 1.00 19 0.01 0.0 0.97 20 0.02 0.0 0.97 21 0.02 0.0 0.99 22 0.03 0.01 0.94 23 0.0 0.01 0.91 24 0.01 0.01 1.00 25 0.02 0.01 0.98 26 0.01 0.02 0.97 27 0.03 0.01 0.92 28 0.01 0.02 0.97 somoclu/data/rgbs.svm0000644000417600011450000000076212402311155016253 0ustar pewiunix-users-shaman0:0.01 1:1.0 1:0.97 2:0.01 1:0.99 2:0.02 0:0.01 1:0.94 2:0.03 1:0.91 2:0.01 0:0.01 1:1.0 1:0.98 2:0.02 0:1.0 1:0.01 0:0.97 1:0.01 0:0.97 1:0.02 0:0.99 1:0.02 0:0.94 1:0.03 2:0.01 0:0.91 2:0.01 0:1.0 1:0.01 2:0.01 0:0.98 1:0.02 2:0.01 0:0.97 1:0.01 2:0.02 0:0.92 1:0.03 2:0.01 0:0.01 2:1.0 0:0.01 2:0.97 0:0.02 2:0.97 0:0.02 2:0.99 0:0.03 1:0.01 2:0.94 1:0.01 2:0.91 0:0.01 1:0.01 2:1.0 0:0.02 1:0.01 2:0.98 0:0.01 1:0.02 2:0.97 0:0.03 1:0.01 2:0.92 0:0.01 1:0.02 2:0.97 somoclu/data/rgbs.txt0000644000417600011450000000067012402311155016263 0ustar pewiunix-users-shaman0.01 1.00 0.0 0.0 0.97 0.01 0.0 0.99 0.02 0.01 0.94 0.03 0.0 0.91 0.01 0.01 1.00 0.0 0.0 0.98 0.02 1.00 0.01 0.0 0.97 0.01 0.0 0.97 0.02 0.0 0.99 0.02 0.0 0.94 0.03 0.01 0.91 0.0 0.01 1.00 0.01 0.01 0.98 0.02 0.01 0.97 0.01 0.02 0.92 0.03 0.01 0.01 0.0 1.00 0.01 0.0 0.97 0.02 0.0 0.97 0.02 0.0 0.99 0.03 0.01 0.94 0.0 0.01 0.91 0.01 0.01 1.00 0.02 0.01 0.98 0.01 0.02 0.97 0.03 0.01 0.92 0.01 0.02 0.97 somoclu/src/0000755000417600011450000000000012402311155014440 5ustar pewiunix-users-shamansomoclu/src/R/0000755000417600011450000000000012402311155014641 5ustar pewiunix-users-shamansomoclu/src/R/DESCRIPTION0000644000417600011450000000164612402311155016356 0ustar pewiunix-users-shamanPackage: Rsomoclu Version: 1.4 Date: 2014-09-05 Title: R package for somoclu Depends: Rcpp Imports: Suggests: Authors@R: c(person(given = "Peter", family = "Wittek", role = c("aut"), email = ""), person(given = "Shichao", family = "Gao", role = c("cre"), email = "xgdgsc@gmail.com")) Description: Somoclu is a cluster-oriented implementation of self-organizing maps. It relies on MPI for distributing the workload, and it can be accelerated by CUDA on a GPU cluster. A sparse kernel is also included, which is useful for training maps on vector spaces generated in text mining processes. URL: http://peterwittek.github.io/somoclu/ BugReports: https://github.com/peterwittek/somoclu/issues License: GPL-3 Packaged: 2014-03-16 16:55:16 UTC; Author: Peter Wittek [aut], Shichao Gao [cre] Maintainer: Shichao Gao NeedsCompilation: yes Repository: CRAN SystemRequirements: GNU make somoclu/src/R/R/0000755000417600011450000000000012402311155015042 5ustar pewiunix-users-shamansomoclu/src/R/R/Rsomoclu.R0000644000417600011450000000104012402311155016763 0ustar pewiunix-users-shaman#require(Rcpp) .onLoad <- function(lib, pkg){ library.dynam("Rsomoclu", pkg, lib) } Rsomoclu.train <- function(input_data, nEpoch, nSomX, nSomY, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType ) { res <- .Call("Rtrain", input_data, nEpoch, nSomX, nSomY, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType) res } somoclu/src/R/man/0000755000417600011450000000000012402311155015414 5ustar pewiunix-users-shamansomoclu/src/R/man/Rsomoclu.train.Rd0000644000417600011450000000445512402311155020632 0ustar pewiunix-users-shaman\name{Rsomoclu.train} \alias{Rsomoclu.train} \title{Train function for somoclu} \description{ A function call to somoclu to train the Self Organizing Map. } \usage{ Rsomoclu.train(input_data, nEpoch, nSomX, nSomY, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType ) } \arguments{ \item{input_data}{input data, matrix format} \item{nEpoch}{Maximum number of epochs} \item{nSomX}{Number of columns in map (size of SOM in direction x)} \item{nSomY}{Number of rows in map (size of SOM in direction y)} \item{radius0}{Start radius (default: half of the map in direction min(x,y))} \item{radiusN}{End radius (default: 1)} \item{radiusCooling}{Radius cooling strategy: linear or exponential (default: linear)} \item{scale0}{Starting learning rate (default: 1.0)} \item{scaleN}{Finishing learning rate (default: 0.01)} \item{scaleCooling}{Learning rate cooling strategy: linear or exponential (default: linear)} \item{snapshots}{Save interim files (default: 0): 0: Do not save interim files 1: Save U-matrix only 2: Also save codebook and best matching} \item{kernelType}{Kernel type 0: Dense CPU 1: Dense GPU 2: Sparse CPU} \item{mapType}{Map type: planar or toroid (default: planar)} %% \item{initialCodebookFilename}{Specify an initial codebook for the map} } \references{Peter Wittek (2013). Somoclu: An Efficient Distributed Library for Self-Organizing Maps. arXiv:1305.1422.} \author{Peter Wittek, Shichao Gao} \examples{ library('Rsomoclu') data_file <- system.file("data", "rgbs.txt.gz", package = 'Rsomoclu') input_data <- read.table(data_file) input_data <- data.matrix(input_data) nSomX <- 50 nSomY <- 50 nEpoch <- 10 radius0 <- 0 radiusN <- 0 radiusCooling <- "linear" scale0 <- 0 scaleN <- 0.01 scaleCooling <- "linear" kernelType <- 0 mapType <- "planar" snapshots <- 0 res <- Rsomoclu.train(input_data, nEpoch, nSomX, nSomY, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType) res$codebook res$globalBmus res$uMatrix }somoclu/src/R/man/rgbs.Rd0000644000417600011450000000025612402311155016643 0ustar pewiunix-users-shaman\name{rgbs} \docType{data} \alias{rgbs} \title{tiny rgbs data} \description{ tiny rgbs data for testing } \usage{rgbs} \format{matrix in plain text form} \keyword{datasets}somoclu/src/R/src/0000755000417600011450000000000012402311155015430 5ustar pewiunix-users-shamansomoclu/src/R/src/Rsomoclu.cpp0000644000417600011450000001407512402311155017746 0ustar pewiunix-users-shaman #include //#include using namespace std; using namespace Rcpp; #include"somocluWrap.h" void trainWrapperR(float *data, int data_length, unsigned int nEpoch, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, unsigned int snapshots, unsigned int kernelType, string mapType, // string initialCodebookFilename, float *codebook, int codebook_size, int *globalBmus, int globalBmus_size, float *uMatrix, int uMatrix_size) { /// /// Codebook /// int itask = 0; svm_node ** sparseData = NULL; core_data coreData; coreData.codebook_size = nSomY*nSomX*nDimensions; coreData.codebook = new float[coreData.codebook_size]; coreData.globalBmus = NULL; coreData.uMatrix = NULL; unsigned int nVectorsPerRank = nVectors; coreData.globalBmus_size = nVectorsPerRank*int(ceil(nVectors/(double)nVectorsPerRank))*2; if (itask == 0) { coreData.globalBmus = new int[coreData.globalBmus_size]; initializeCodebook(0, coreData.codebook, nSomX, nSomY, nDimensions); } #ifdef CUDA if(kernelType==DENSE_GPU){ int rank = 0; int nProcs = 1; setDevice(rank, nProcs); initializeGpu(data, nVectorsPerRank, nDimensions, nSomX, nSomY); } #endif /// /// Parameters for SOM /// if (radius0 == 0) { radius0 = nSomX / 2.0f; /// init radius for updating neighbors } if (radiusN == 0) { radiusN = 1; } if (scale0 == 0) { scale0 = 1.0; } unsigned int currentEpoch = 0; /// 0...nEpoch-1 /// /// Training /// while ( currentEpoch < nEpoch ) { coreData = trainOneEpoch(itask, data, sparseData, coreData, nEpoch, currentEpoch, snapshots > 0, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, kernelType, mapType); currentEpoch++; } if (itask == 0) { /// /// Save U-mat /// coreData.uMatrix = calculateUMatrix(coreData.codebook, nSomX, nSomY, nDimensions, mapType); coreData.uMatrix_size = nSomX * nSomY; } #ifdef CUDA if (kernelType == DENSE_GPU) { freeGpu(); } #endif if(coreData.codebook != NULL){ memcpy(codebook, coreData.codebook, sizeof(float) * codebook_size); delete [] coreData.codebook; } if(coreData.globalBmus != NULL){ memcpy(globalBmus, coreData.globalBmus, sizeof(int) * globalBmus_size); delete [] coreData.globalBmus; } if(coreData.uMatrix != NULL){ memcpy(uMatrix, coreData.uMatrix, sizeof(float) * uMatrix_size); delete [] coreData.uMatrix; } } RcppExport SEXP Rtrain(SEXP data_p, SEXP nEpoch_p, SEXP nSomX_p, SEXP nSomY_p, SEXP radius0_p, SEXP radiusN_p, SEXP radiusCooling_p, SEXP scale0_p, SEXP scaleN_p, SEXP scaleCooling_p, SEXP snapshots_p, SEXP kernelType_p, SEXP mapType_p) { Rcpp::NumericMatrix dataMatrix(data_p); int nVectors = dataMatrix.rows(); int nDimensions = dataMatrix.cols(); int nEpoch = as(nEpoch_p); unsigned int nSomX = (unsigned int) as (nSomX_p); unsigned int nSomY = (unsigned int) as (nSomY_p); unsigned int radius0 = (unsigned int) as (radius0_p); unsigned int radiusN = (unsigned int) as (radiusN_p); string radiusCooling = as(radiusCooling_p); unsigned int scale0 = (unsigned int) as (scale0_p); unsigned int scaleN = (unsigned int) as (scaleN_p); string scaleCooling = as (scaleCooling_p); unsigned int snapshots = (unsigned int) as(snapshots_p); unsigned int kernelType = (unsigned int) as(kernelType_p); string mapType = as(mapType_p); int data_length = nVectors * nDimensions; float* data = new float[data_length]; // convert matrix to data c float array for(int i = 0; i < nVectors; i++){ for(int j = 0; j < nDimensions; j++){ data[i * nDimensions + j] = (float) dataMatrix(i,j); } } int codebook_size = nSomY * nSomX * nDimensions; int globalBmus_size = nVectors * 2; int uMatrix_size = nSomX * nSomY; float* codebook = new float[codebook_size]; int* globalBmus = new int[globalBmus_size]; float* uMatrix = new float[uMatrix_size]; trainWrapperR(data, data_length, nEpoch, nSomX, nSomY, nDimensions, nVectors, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType, codebook, codebook_size, globalBmus, globalBmus_size, uMatrix, uMatrix_size); Rcpp::NumericVector codebook_vec(codebook_size); Rcpp::NumericVector globalBmus_vec(globalBmus_size); Rcpp::NumericVector uMatrix_vec(uMatrix_size); if(codebook != NULL){ for(int i = 0; i < codebook_size; i++){ codebook_vec(i) = codebook[i]; } } if(globalBmus != NULL){ for(int i = 0; i < globalBmus_size; i++){ globalBmus_vec(i) = globalBmus[i]; } } if(uMatrix != NULL){ for(int i = 0; i < uMatrix_size; i++){ uMatrix_vec(i) = uMatrix[i]; } } delete[] codebook; delete[] globalBmus; delete[] uMatrix; return Rcpp::List::create(Rcpp::Named("codebook") = codebook_vec, Rcpp::Named("globalBmus") = globalBmus_vec, Rcpp::Named("uMatrix") = uMatrix_vec);; } RCPP_MODULE(Rsomoclu){ Rcpp::function("Rtrain", &Rtrain); } somoclu/src/R/src/Makevars.win0000644000417600011450000000026312402311155017721 0ustar pewiunix-users-shamanPKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(SHLIB_OPENMP_CXXFLAGS) PKG_CXXFLAGS = `$(R_HOME)/bin/Rscript -e "Rcpp:::CxxFlags()"` $(SHLIB_OPENMP_CXXFLAGS) -DHAVE_R somoclu/src/R/src/Makevars0000644000417600011450000000026212402311155017124 0ustar pewiunix-users-shamanPKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(SHLIB_OPENMP_CXXFLAGS) PKG_CXXFLAGS = `$(R_HOME)/bin/Rscript -e "Rcpp:::CxxFlags()"` $(SHLIB_OPENMP_CXXFLAGS) -DHAVE_R somoclu/src/R/NAMESPACE0000644000417600011450000000007012402311155016055 0ustar pewiunix-users-shamanuseDynLib(Rsomoclu) export(Rsomoclu.train) import(Rcpp) somoclu/src/R/tests/0000755000417600011450000000000012402311155016003 5ustar pewiunix-users-shamansomoclu/src/R/tests/R_interface_test.R0000644000417600011450000000117412402311155021411 0ustar pewiunix-users-shamanlibrary('Rsomoclu') data_file <- system.file("data", "rgbs.txt.gz", package = 'Rsomoclu') input_data <- read.table(data_file) input_data <- data.matrix(input_data) nSomX <- 50 nSomY <- 50 nEpoch <- 10 radius0 <- 0 radiusN <- 0 radiusCooling <- "linear" scale0 <- 0 scaleN <- 0.01 scaleCooling <- "linear" kernelType <- 0 mapType <- "planar" snapshots <- 0 res <- Rsomoclu.train(input_data, nEpoch, nSomX, nSomY, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType) res$codebook res$globalBmus res$uMatrix somoclu/src/denseGpuKernels.cu0000644000417600011450000003610012402311155020067 0ustar pewiunix-users-shaman/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #undef _GLIBCXX_ATOMIC_BUILTINS #undef _GLIBCXX_USE_INT128 #include #include #include #include #include #include #include #include #include #include "somoclu.h" #ifdef _WIN32 #define popen _popen #define pclose _pclose #endif // Error handling macro #define CUDA_CHECK(call) \ if((call) != cudaSuccess) { \ cudaError_t err = cudaGetLastError(); \ cerr << "CUDA error calling \""#call"\", code is " << err << endl; \ my_abort(err); } //Globals cublasHandle_t handle; thrust::device_vector deviceData; thrust::device_vector deviceDataNorms; thrust::device_vector deviceCodebook; thrust::device_vector deviceCodebookNorms; // convert a linear index to a row index template struct linear_index_to_row_index : public thrust::unary_function { T C; // number of columns __host__ __device__ linear_index_to_row_index(T C) : C(C) {} __host__ __device__ T operator()(T i) { return i / C; } }; // note: functor inherits from unary_function template struct square : public thrust::unary_function { __host__ __device__ T operator()(T x) const { return x*x; } }; typedef thrust::tuple argMinType; struct argMin : public thrust::binary_function { __host__ __device__ argMinType operator()(const argMinType& a, const argMinType& b) const { if (thrust::get<1>(a) < thrust::get<1>(b)) { return a; } else { return b; } } }; template thrust::device_vector normsOfRowSpace(thrust::device_vector A, int nRows, int nColumns) { // allocate storage for row sums and indices thrust::device_vector row_sums(nRows); thrust::device_vector row_indices(nRows); // compute row sums by summing values with equal row indices thrust::reduce_by_key (thrust::make_transform_iterator(thrust::counting_iterator(0), linear_index_to_row_index(nColumns)), thrust::make_transform_iterator(thrust::counting_iterator(0), linear_index_to_row_index(nColumns)) + (nRows*nColumns), thrust::make_transform_iterator(A.begin(), square()), row_indices.begin(), row_sums.begin(), thrust::equal_to(), thrust::plus()); return row_sums; } thrust::device_vector minsOfRowSpace(thrust::device_vector A, int nRows, int nColumns) { // allocate storage for row sums and indices thrust::device_vector row_sums(nRows); thrust::device_vector row_indices(nRows); // compute row sums by summing values with equal row indices thrust::reduce_by_key (thrust::make_transform_iterator(thrust::counting_iterator(0), linear_index_to_row_index(nColumns)), thrust::make_transform_iterator(thrust::counting_iterator(0), linear_index_to_row_index(nColumns)) + (nRows*nColumns), thrust::make_zip_iterator(thrust::make_tuple(thrust::counting_iterator(0),A.begin())), row_indices.begin(), row_sums.begin(), thrust::equal_to(), argMin()); return row_sums; } template __global__ void euclidean(float *anorm2, float *bnorm2, float *M, int height, int width) { unsigned int xIndex = blockIdx.x * BLOCK_DIM + threadIdx.x; unsigned int yStartIndex = blockIdx.y * BLOCK_DIM; if (xIndex < width) { float bNormForX = bnorm2[xIndex]; unsigned int yEndIndex=(yStartIndex+BLOCK_DIM < height ? yStartIndex+BLOCK_DIM : height); for (unsigned int yIndex=yStartIndex; yIndex void printMatrix(thrust::device_vector A, int nRows, int nColumns) { for (size_t i = 0; i < nRows; i++) { for (size_t j = 0; j < nColumns; j++) { std::cout << A[i*nColumns+j] << " "; } std::cout << "\n"; } std::cout << "\n"; } /** Clear the device memory and shut down CUBLAS * */ void freeGpu() { deviceData.clear(); deviceDataNorms.clear(); deviceCodebook.clear(); deviceCodebookNorms.clear(); thrust::device_vector().swap(deviceData); thrust::device_vector().swap(deviceDataNorms); thrust::device_vector().swap(deviceCodebook); thrust::device_vector().swap(deviceCodebookNorms); cublasStatus_t status = cublasDestroy(handle); if (status != CUBLAS_STATUS_SUCCESS) { cerr << "!!!! shutdown error (A)\n"; my_abort(-1); } } /** Find the best matching units -- called from the map function * @param bmus - array of best matching units * @param codebook - the codebook to save * @param nSomX - dimensions of SOM map in the x direction * @param nSomY - dimensions of SOM map in the y direction * @param nDimensions - dimensions of a data instance * @param nVectorsPerRank - the number of data points assigned to this GPU */ void getBmusOnGpu(int *bmus, float *codebook, int nSomX, int nSomY, int nDimensions, int nVectorsPerRank) { deviceCodebook = thrust::device_vector(codebook, codebook+nSomX*nSomY*nDimensions); deviceCodebookNorms = normsOfRowSpace(deviceCodebook, nSomX*nSomY, nDimensions); thrust::device_vector deviceGramMatrix(nSomX*nSomY*nVectorsPerRank, 0); //Calculate the inner products of the data vectors and the weight vectors float alpha = 1.0f; float beta = 0.0f; cublasStatus_t status = cublasSgemm(handle, CUBLAS_OP_T, CUBLAS_OP_N, nSomX*nSomY, nVectorsPerRank, nDimensions, &alpha, thrust::raw_pointer_cast(&deviceCodebook[0]), nDimensions, thrust::raw_pointer_cast(&deviceData[0]), nDimensions, &beta, thrust::raw_pointer_cast(&deviceGramMatrix[0]), nSomX*nSomY); if (status != CUBLAS_STATUS_SUCCESS) { cerr << "!!!! kernel execution error.\n"; my_abort(-1); } //All components of the vectorized Euclidean distance are available // 32 is a magic number, this is the block size that works best on Tesla C2050 int BLOCK_DIM=32; dim3 grid((nSomX*nSomY+BLOCK_DIM-1)/BLOCK_DIM, (nVectorsPerRank+BLOCK_DIM-1)/BLOCK_DIM,1); dim3 threads(BLOCK_DIM,1,1); if (BLOCK_DIM==32) { euclidean<32><<>>(thrust::raw_pointer_cast(&deviceDataNorms[0]), thrust::raw_pointer_cast(&deviceCodebookNorms[0]), thrust::raw_pointer_cast(&deviceGramMatrix[0]), nVectorsPerRank, nSomX*nSomY); } //Finding minimums thrust::host_vector minsOfA=minsOfRowSpace(deviceGramMatrix, nVectorsPerRank, nSomX*nSomY); CUDA_CHECK(cudaDeviceSynchronize()); //Getting back SOM coordinates from minimums for (int i=0; i(tmp) % (nSomX*nSomY); bmus[i*2] = somCoordinate % nSomX; bmus[i*2+1] = somCoordinate / nSomX; } } /** Initialize CUBLAS and device data * @param hostData - the data in the main memory * @param height - number of data points assigned to this GPU * @param width - dimensions of a data instance */ void initializeGpu(float *hostData, int nVectorsPerRank, int nDimensions, int nSomX, int nSomY) { /* Initialize CUBLAS */ cublasStatus_t status = cublasCreate(&handle); if (status != CUBLAS_STATUS_SUCCESS) { cerr << "!!!! CUBLAS initialization error\n"; my_abort(-1); } deviceData = thrust::device_vector(hostData, hostData+nVectorsPerRank*nDimensions); deviceDataNorms = normsOfRowSpace(deviceData, nVectorsPerRank, nDimensions); deviceCodebook = thrust::device_vector(nSomX*nSomY*nDimensions,0); deviceCodebookNorms = thrust::device_vector(nSomX*nSomY,0); } /** Check and initialize a device attached to a node * @param commRank - the MPI rank of this process * @param commSize - the size of MPI comm world */ /// Note that this function was lifted from http://code.google.com/p/gpmr/ void setDevice(int commRank, int commSize) { int devCount; int deviceNum=0; CUDA_CHECK(cudaGetDeviceCount(&devCount)); #ifdef HAVE_MPI #ifdef _WIN32 FILE * fp = popen("hostname.exe", "r"); #else FILE * fp = popen("/bin/hostname", "r"); #endif char buf[1024]; if (fgets(buf, 1023, fp) == NULL) strcpy(buf, "localhost"); pclose(fp); string host = buf; host = host.substr(0, host.size() - 1); strcpy(buf, host.c_str()); if (commRank == 0) { map > hosts; map devCounts; hosts[buf].push_back(0); devCounts[buf] = devCount; MPI_Status stat; MPI_Request req; for (int i = 1; i < commSize; ++i) { MPI_Recv(buf, 1024, MPI_CHAR, i, 0, MPI_COMM_WORLD, &stat); MPI_Recv(&devCount, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &stat); // check to make sure each process on each node reports the same number of devices. hosts[buf].push_back(i); if (devCounts.find(buf) != devCounts.end()) { if (devCounts[buf] != devCount) { printf("Error, device count mismatch %d != %d on %s\n", devCounts[buf], devCount, buf); fflush(stdout); } } else devCounts[buf] = devCount; } // check to make sure that we don't have more jobs on a node than we have GPUs. for (map >::iterator it = hosts.begin(); it != hosts.end(); ++it) { if (it->second.size() > static_cast(devCounts[it->first])) { printf("Error, more jobs running on '%s' than devices - %d jobs > %d devices.\n", it->first.c_str(), static_cast(it->second.size()), devCounts[it->first]); fflush(stdout); my_abort(1); } } // send out the device number for each process to use. MPI_Irecv(&deviceNum, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &req); for (map >::iterator it = hosts.begin(); it != hosts.end(); ++it) { for (unsigned int i = 0; i < it->second.size(); ++i) { int devID = i; MPI_Send(&devID, 1, MPI_INT, it->second[i], 0, MPI_COMM_WORLD); } } MPI_Wait(&req, &stat); } else { // send out the hostname and device count for your local node, then get back the device number you should use. MPI_Status stat; MPI_Send(buf, strlen(buf) + 1, MPI_CHAR, 0, 0, MPI_COMM_WORLD); MPI_Send(&devCount, 1, MPI_INT, 0, 0, MPI_COMM_WORLD); MPI_Recv(&deviceNum, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &stat); } MPI_Barrier(MPI_COMM_WORLD); #endif CUDA_CHECK(cudaSetDevice(deviceNum)); } /** One epoch on the GPU, dense variant */ void trainOneEpochDenseGPU(int itask, float *data, float *numerator, float *denominator, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, float radius, float scale, string mapType, int *globalBmus) { #ifdef _WIN32 int* bmus = (int *)alloca(sizeof(int) * nVectorsPerRank * 2); #else int bmus[nVectorsPerRank*2]; #endif getBmusOnGpu(bmus, codebook, nSomX, nSomY, nDimensions, nVectorsPerRank); float *localNumerator = new float[nSomY*nSomX*nDimensions]; float *localDenominator = new float[nSomY*nSomX]; #pragma omp parallel default(shared) { #pragma omp for for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { localDenominator[som_y*nSomX + som_x] = 0.0; for (unsigned int d = 0; d < nDimensions; d++) localNumerator[som_y*nSomX*nDimensions + som_x*nDimensions + d] = 0.0; } } /// Accumulate denoms and numers #pragma omp for for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { for (unsigned int n = 0; n < nVectorsPerRank; n++) { if (itask*nVectorsPerRank+n. * */ #include #include #include #include #include #include #include "somoclu.h" using namespace std; /** Save a SOM codebook * @param cbFileName - name of the file to save * @param codebook - the codebook to save * @param nSomX - dimensions of SOM map in the x direction * @param nSomY - dimensions of SOM map in the y direction * @param nDimensions - dimensions of a data instance */ int saveCodebook(string cbFilename, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions) { FILE* file = fopen(cbFilename.c_str(), "wt"); cout << " Saving Codebook " << cbFilename << endl; fprintf(file, "%%%d %d\n", nSomY, nSomX); fprintf(file, "%%%d\n", nDimensions); if (file!=0) { for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { for (unsigned int d = 0; d < nDimensions; d++) { fprintf(file, "%0.10f ", codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d]); } fprintf(file, "\n"); } } fclose(file); return 0; } else { return 1; } } /** Save best matching units * @param filename - name of the file to save * @param bmus - the best matching units to save * @param nSomX - dimensions of SOM map in the x direction * @param nSomY - dimensions of SOM map in the y direction * @param nVectors - the number of vectors */ int saveBmus(string filename, int *bmus, unsigned int nSomX, unsigned int nSomY, unsigned int nVectors) { FILE* file = fopen(filename.c_str(), "wt"); cout << " Saving best matching units " << filename << endl; fprintf(file, "%%%d %d\n", nSomY, nSomX); fprintf(file, "%%%d\n", nVectors); if (file!=0) { for (unsigned int i = 0; i < nVectors; ++i) { // ESOM Tools swaps x and y! fprintf(file, "%d %d %d\n", i, bmus[2*i+1], bmus[2*i]); } fclose(file); return 0; } else { return 1; } } /** Save u-matrix * @param fname * @param codebook - the codebook to save * @param nSomX - dimensions of SOM map in the x direction * @param nSomY - dimensions of SOM map in the y direction * @param nDimensions - dimensions of a data instance */ int saveUMatrix(string fname, float *uMatrix, unsigned int nSomX, unsigned int nSomY) { FILE* fp = fopen(fname.c_str(), "wt"); fprintf(fp, "%%"); fprintf(fp, "%d %d", nSomY, nSomX); fprintf(fp, "\n"); if (fp != 0) { for (unsigned int som_y1 = 0; som_y1 < nSomY; som_y1++) { for (unsigned int som_x1 = 0; som_x1 < nSomX; som_x1++) { fprintf(fp, " %f", uMatrix[som_y1*nSomX+som_x1]); } fprintf(fp, "\n"); } fclose(fp); return 0; } else return -2; } void getMatrixDimensions(string inFilename, unsigned int &nRows, unsigned int &nColumns) { ifstream file; file.open(inFilename.c_str()); if (file.is_open()) { string line; float tmp; while(getline(file,line)) { if (line.substr(0,1) == "#") { continue; } std::istringstream iss(line); if (nRows == 0) { while (iss >> tmp) { nColumns++; } } nRows++; } file.close(); } else { std::cerr << "Input file could not be opened!\n"; my_abort(-1); } } unsigned int *readLrnHeader(string inFilename, unsigned int &nRows, unsigned int &nColumns) { ifstream file; file.open(inFilename.c_str()); string line; unsigned int currentColumn = 0; unsigned int nAllColumns = 0; unsigned int *columnMap = NULL; while(getline(file,line)) { if (line.substr(0,1) == "#") { continue; } if (line.substr(0,1) == "%") { std::istringstream iss(line.substr(1,line.length())); if (nRows == 0) { iss >> nRows; } else if (nAllColumns == 0) { iss >> nAllColumns; } else if (columnMap == NULL) { columnMap = new unsigned int[nAllColumns]; unsigned int itmp = 0; currentColumn = 0; while (iss >> itmp) { columnMap[currentColumn++] = itmp; if (itmp == 1) { ++nColumns; } } } else { break; } } } file.close(); return columnMap; } unsigned int *readWtsHeader(string inFilename, unsigned int &nRows, unsigned int &nColumns) { ifstream file; file.open(inFilename.c_str()); string line; while(getline(file,line)) { if (line.substr(0,1) == "#") { continue; } if (line.substr(0,1) == "%") { std::istringstream iss(line.substr(1,line.length())); if (nRows == 0) { iss >> nRows; unsigned int nSomY = 0; iss >> nSomY; nRows = nRows*nSomY; } else if (nColumns == 0) { iss >> nColumns; } else { break; } } } file.close(); unsigned int *columnMap = new unsigned int[nColumns]; for (unsigned int i = 0; i < nColumns; ++i) { columnMap[i] = 1; } return columnMap; } /** Reads a matrix * @param inFilename * @param nRows - returns the number of rows * @param nColumns - returns the number of columns * @return the matrix */ float *readMatrix(string inFilename, unsigned int &nRows, unsigned int &nColumns) { float *data = NULL; unsigned int *columnMap = NULL; if (inFilename.compare(inFilename.size()-3, 3, "lrn") == 0) { columnMap = readLrnHeader(inFilename, nRows, nColumns); } else if (inFilename.compare(inFilename.size()-3, 3, "wts") == 0) { columnMap = readWtsHeader(inFilename, nRows, nColumns); } else { getMatrixDimensions(inFilename, nRows, nColumns); columnMap = new unsigned int[nColumns]; for (unsigned int i = 0; i < nColumns; ++i) { columnMap[i] = 1; } } ifstream file; file.open(inFilename.c_str()); string line; float tmp; unsigned int j = 0; unsigned int currentColumn = 0; while(getline(file,line)) { if ( (line.substr(0,1) == "#") | (line.substr(0,1) == "%") ) { continue; } if (data == NULL) { data = new float[nRows*nColumns]; } std::istringstream iss(line); currentColumn = 0; while (iss >> tmp) { if (columnMap[currentColumn++] != 1) { continue; } data[j++] = tmp; } } file.close(); delete [] columnMap; return data; } void readSparseMatrixDimensions(string filename, unsigned int &nRows, unsigned int &nColumns) { ifstream file; file.open(filename.c_str()); if (file.is_open()) { string line; int max_index=-1; while(getline(file,line)) { if (line.substr(0,1) == "#") { continue; } stringstream linestream(line); string value; int dummy_index; while(getline(linestream,value,' ')) { int separator=value.find(":"); istringstream myStream(value.substr(0,separator)); myStream >> dummy_index; if(dummy_index > max_index) { max_index = dummy_index; } } ++nRows; } nColumns=max_index+1; file.close(); } else { std::cerr << "Input file could not be opened!\n"; my_abort(-1); } } svm_node** readSparseMatrixChunk(string filename, unsigned int nRows, unsigned int nRowsToRead, unsigned int rowOffset) { ifstream file; file.open(filename.c_str()); string line; for (unsigned int i=0; i= nRows) { nRowsToRead = nRows-rowOffset; } svm_node **x_matrix = new svm_node *[nRowsToRead]; for(unsigned int i=0; i> x_matrix[i][j].index; istringstream myStream2(value.substr(separator+1)); myStream2 >> x_matrix[i][j].value; j++; } x_matrix[i][j].index = -1; } file.close(); return x_matrix; } /** Shut down MPI cleanly if something goes wrong * @param err - error code to print */ void my_abort(int err) { cerr << "Aborted\n"; #ifdef HAVE_MPI MPI_Abort(MPI_COMM_WORLD, err); #else exit(err); #endif } somoclu/src/somoclu.cpp0000644000417600011450000003354112402311155016633 0ustar pewiunix-users-shaman/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #include #include #include #if defined(linux) || defined(__APPLE__) #include #include #endif #ifdef _WIN32 #include "Windows/unistd.h" #include "Windows/getopt.h" #endif #include "somoclu.h" using namespace std; /// For synchronized timing #ifndef MPI_WTIME_IS_GLOBAL #define MPI_WTIME_IS_GLOBAL 1 #endif // Default parameters #define N_EPOCH 10 #define N_SOM_X 50 #define N_SOM_Y 50 #define KERNEL_TYPE 0 #define SNAPSHOTS 0 void processCommandLine(int argc, char** argv, string *inFilename, string* outPrefix, unsigned int *nEpoch, unsigned int *radius0, unsigned int *radiusN, string *radiusCooling, float *scale0, float *scaleN, string *scaleCooling, unsigned int *nSomX, unsigned int *nSomY, unsigned int *kernelType, string *mapType, unsigned int *snapshots, string *initialCodebookFilename); /* -------------------------------------------------------------------------- */ int main(int argc, char** argv) /* -------------------------------------------------------------------------- */ { int rank = 0; int nProcs = 1; #ifdef HAVE_MPI /// /// MPI init /// MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &rank); MPI_Comm_size(MPI_COMM_WORLD, &nProcs); MPI_Barrier(MPI_COMM_WORLD); #endif unsigned int nEpoch = 0; unsigned int nSomX = 0; unsigned int nSomY = 0; unsigned int kernelType = 0; string mapType; unsigned int radius0 = 0; unsigned int radiusN = 0; string radiusCooling; float scale0 = 0.0; float scaleN = 0.0; string scaleCooling; unsigned int snapshots = 0; string inFilename; string initialCodebookFilename; string outPrefix; if (rank==0) { processCommandLine(argc, argv, &inFilename, &outPrefix, &nEpoch, &radius0, &radiusN, &radiusCooling, &scale0, &scaleN, &scaleCooling, &nSomX, &nSomY, &kernelType, &mapType, &snapshots, &initialCodebookFilename); #ifndef CUDA if (kernelType == DENSE_GPU) { cerr << "Somoclu was compile without GPU support!\n"; my_abort(1); } #endif } #ifdef HAVE_MPI MPI_Bcast(&nEpoch, 1, MPI_INT, 0, MPI_COMM_WORLD); MPI_Bcast(&radius0, 1, MPI_INT, 0, MPI_COMM_WORLD); MPI_Bcast(&nSomX, 1, MPI_INT, 0, MPI_COMM_WORLD); MPI_Bcast(&nSomY, 1, MPI_INT, 0, MPI_COMM_WORLD); MPI_Bcast(&kernelType, 1, MPI_INT, 0, MPI_COMM_WORLD); char *inFilenameCStr = new char[255]; if (rank == 0) { strcpy(inFilenameCStr,inFilename.c_str()); } MPI_Bcast(inFilenameCStr, 255, MPI_CHAR, 0, MPI_COMM_WORLD); inFilename = inFilenameCStr; char *mapTypeCStr = new char[255]; if (rank == 0) { strcpy(mapTypeCStr,mapType.c_str()); } MPI_Bcast(mapTypeCStr, 255, MPI_CHAR, 0, MPI_COMM_WORLD); mapType = mapTypeCStr; double profile_time = MPI_Wtime(); #endif float * dataRoot = NULL; unsigned int nDimensions = 0; unsigned int nVectors = 0; if(rank == 0 ) { if (kernelType == DENSE_CPU || kernelType == DENSE_GPU) { dataRoot = readMatrix(inFilename, nVectors, nDimensions); } else { readSparseMatrixDimensions(inFilename, nVectors, nDimensions); } } #ifdef HAVE_MPI MPI_Barrier(MPI_COMM_WORLD); MPI_Bcast(&nVectors, 1, MPI_INT, 0, MPI_COMM_WORLD); MPI_Bcast(&nDimensions, 1, MPI_INT, 0, MPI_COMM_WORLD); #endif unsigned int nVectorsPerRank = ceil(nVectors / (1.0*nProcs)); // Allocate a buffer on each node float* data = NULL; svm_node **sparseData; sparseData = NULL; if (kernelType == DENSE_CPU || kernelType == DENSE_GPU) { #ifdef HAVE_MPI // Dispatch a portion of the input data to each node data = new float[nVectorsPerRank*nDimensions]; MPI_Scatter(dataRoot, nVectorsPerRank*nDimensions, MPI_FLOAT, data, nVectorsPerRank*nDimensions, MPI_FLOAT, 0, MPI_COMM_WORLD); #else data = dataRoot; #endif } else { int currentRankProcessed = 0; while (currentRankProcessed < nProcs) { if (rank == currentRankProcessed) { sparseData=readSparseMatrixChunk(inFilename, nVectors, nVectorsPerRank, rank*nVectorsPerRank); } currentRankProcessed++; #ifdef HAVE_MPI MPI_Barrier(MPI_COMM_WORLD); #endif } } if(rank == 0) { // No need for root data any more if compiled with MPI #ifdef HAVE_MPI if (kernelType == DENSE_CPU || kernelType == DENSE_GPU) { delete [] dataRoot; } #endif cout << "nVectors: " << nVectors << " "; cout << "nVectorsPerRank: " << nVectorsPerRank << " "; cout << "nDimensions: " << nDimensions << " "; cout << endl; } #ifdef CUDA if (kernelType == DENSE_GPU) { setDevice(rank, nProcs); initializeGpu(data, nVectorsPerRank, nDimensions, nSomX, nSomY); } #endif #ifdef HAVE_MPI MPI_Barrier(MPI_COMM_WORLD); #endif // TRAINING train(rank, data, sparseData, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, nEpoch, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, outPrefix, snapshots, kernelType, mapType, initialCodebookFilename); if (kernelType == DENSE_CPU || kernelType == DENSE_GPU) { delete [] data; } else { delete [] sparseData; } #ifdef HAVE_MPI profile_time = MPI_Wtime() - profile_time; if (rank == 0) { cerr << "Total Execution Time: " << profile_time << endl; } #endif #ifdef CUDA if (kernelType == DENSE_GPU) { freeGpu(); } #endif #ifdef HAVE_MPI MPI_Finalize(); #endif return 0; } void printUsage() { cout << "Usage:\n" \ " [mpirun -np NPROC] somoclu [OPTIONs] INPUT_FILE OUTPUT_PREFIX\n" \ "Arguments:\n" \ " -c FILENAME Specify an initial codebook for the map.\n" \ " -e NUMBER Maximum number of epochs (default: " << N_EPOCH << ")\n" \ " -k NUMBER Kernel type (default: " << KERNEL_TYPE << "): \n" \ " 0: Dense CPU\n" \ " 1: Dense GPU\n" \ " 2: Sparse CPU\n" \ " -m TYPE Map type: planar or toroid (default: planar) \n" \ " -t STRATEGY Radius cooling strategy: linear or exponential (default: linear)\n" \ " -r NUMBER Start radius (default: half of the map in direction min(x,y))\n" \ " -R NUMBER End radius (default: 1)\n" \ " -T STRATEGY Learning rate cooling strategy: linear or exponential (default: linear)\n" \ " -l NUMBER Starting learning rate (default: 0.1)\n" \ " -L NUMBER Finishing learning rate (default: 0.01)\n" \ " -s NUMBER Save interim files (default: 0):\n" \ " 0: Do not save interim files\n" \ " 1: Save U-matrix only\n" \ " 2: Also save codebook and best matching neurons\n" \ " -x, --columns NUMBER Number of columns in map (size of SOM in direction x) (default: " << N_SOM_X << ")\n" \ " -y, --rows NUMBER Number of rows in map (size of SOM in direction y) (default: " << N_SOM_Y << ")\n" \ "Examples:\n" \ " somoclu data/rgbs.txt data/rgbs\n" " mpirun -np 4 somoclu -k 0 -x 20 -y 20 data/rgbs.txt data/rgbs\n"; } void processCommandLine(int argc, char** argv, string *inFilename, string* outPrefix, unsigned int *nEpoch, unsigned int *radius0, unsigned int *radiusN, string *radiusCooling, float *scale0, float *scaleN, string *scaleCooling, unsigned int *nSomX, unsigned int *nSomY, unsigned int *kernelType, string *mapType, unsigned int *snapshots, string *initialCodebookFilename) { // Setting default values *nEpoch = N_EPOCH; *nSomX = N_SOM_X; *nSomY = N_SOM_Y; *kernelType = KERNEL_TYPE; *snapshots = SNAPSHOTS; *mapType = "planar"; *radius0 = 0; *radiusN = 0; *radiusCooling = "linear"; *scale0 = 0.0; *scaleN = 0.01; *scaleCooling = "linear"; static struct option long_options[] = { {"rows", required_argument, 0, 'y'}, {"columns", required_argument, 0, 'x'}, {0, 0, 0, 0} }; int c; extern int optind, optopt; int option_index = 0; while ((c = getopt_long (argc, argv, "hx:y:e:k:l:m:r:s:t:c:L:R:T:", long_options, &option_index)) != -1) { switch (c) { case 'c': *initialCodebookFilename = optarg; break; case 'e': *nEpoch = atoi(optarg); if (*nEpoch<=0) { cerr << "The argument of option -e should be a positive integer.\n"; my_abort(1); } break; case 'h': printUsage(); my_abort(0); break; case 'k': *kernelType = atoi(optarg); if (*kernelType>SPARSE_CPU) { cerr << "The argument of option -k should be a valid kernel.\n"; my_abort(1); } break; case 'm': *mapType = optarg; if (*mapType!="planar"&&*mapType!="toroid") { cerr << "The argument of option -m should be either planar or toroid.\n"; my_abort(1); } break; case 'r': *radius0 = atoi(optarg); if (*radius0<=0) { cerr << "The argument of option -r should be a positive integer.\n"; my_abort(1); } break; case 'R': *radiusN = atoi(optarg); if (*radiusN<=0) { cerr << "The argument of option -R should be a positive integer.\n"; my_abort(1); } break; case 't': *radiusCooling = optarg; if (*radiusCooling!="linear"&&*radiusCooling!="exponential") { cerr << "The argument of option -t should be linear or exponential.\n"; my_abort(1); } break; case 'l': *scale0 = atof(optarg); if (*scale0<=0) { cerr << "The argument of option -l should be a positive float.\n"; my_abort(1); } break; case 'L': *scaleN = atof(optarg); if (*scaleN<=0) { cerr << "The argument of option -L should be a positive float.\n"; my_abort(1); } break; case 'T': *scaleCooling = optarg; if (*scaleCooling!="linear"&&*scaleCooling!="exponential") { cerr << "The argument of option -T should be linear or exponential.\n"; my_abort(1); } break; case 's': *snapshots = atoi(optarg); if (*snapshots>2) { cerr << "The argument of option -s should be 0, 1, or 2.\n"; my_abort(1); } break; case 'x': *nSomX = atoi(optarg); if (*nSomX<=0) { cerr << "The argument of option -x should be a positive integer.\n"; my_abort(1); } break; case 'y': *nSomY = atoi(optarg); if (*nSomY<=0) { cerr << "The argument of option -y should be a positive integer.\n"; my_abort(1); } break; case '?': if (optopt == 'e' || optopt == 'k' || optopt == 's' || optopt == 'x' || optopt == 'y') { cerr << "Option -" << optopt << " requires an argument.\n"; printUsage(); my_abort(1); } else if (isprint (optopt)) { cerr << "Unknown option `-" << optopt << "'.\n"; printUsage(); my_abort(1); } else { cerr << "Unknown option character `\\x" << optopt << "'.\n"; printUsage(); my_abort(1); } default: abort (); } } if (argc-optind!=2) { cerr << "Incorrect number of mandatory parameters\n"; printUsage(); my_abort(1); } *inFilename = argv[optind++]; *outPrefix = argv[optind++]; } /// EOF somoclu/src/uMatrix.cpp0000644000417600011450000000610412402311155016576 0ustar pewiunix-users-shaman #include"somoclu.h" #include /** Get weight vector from a codebook using x, y index * @param codebook - the codebook to save * @param som_y - y coordinate of a node in the map * @param som_x - x coordinate of a node in the map * @param nSomX - dimensions of SOM map in the x direction * @param nSomY - dimensions of SOM map in the y direction * @param nDimensions - dimensions of a data instance * @return the weight vector */ float* get_wvec(float *codebook, unsigned int som_y, unsigned int som_x, unsigned int nSomX, unsigned int nDimensions) { float* wvec = new float[nDimensions]; for (unsigned int d = 0; d < nDimensions; d++) wvec[d] = codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d]; /// CAUTION: (y,x) order return wvec; } /** Euclidean distance between vec1 and vec2 * @param vec1 * @param vec2 * @param nDimensions * @return distance */ float get_distance(const float* vec1, const float* vec2, unsigned int nDimensions) { float distance = 0.0f; float x1 = 0.0f; float x2 = 0.0f; for (unsigned int d = 0; d < nDimensions; d++) { x1 = std::min(vec1[d], vec2[d]); x2 = std::max(vec1[d], vec2[d]); distance += std::abs(x1-x2)*std::abs(x1-x2); } return sqrt(distance); } /** Calculate U-matrix * @param codebook - the codebook * @param nSomX - dimensions of SOM map in the x direction * @param nSomY - dimensions of SOM map in the y direction * @param nDimensions - dimensions of a data instance */ float *calculateUMatrix(float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, string mapType) { float *uMatrix = new float[nSomX*nSomY]; float min_dist = 1.5f; for (unsigned int som_y1 = 0; som_y1 < nSomY; som_y1++) { for (unsigned int som_x1 = 0; som_x1 < nSomX; som_x1++) { float dist = 0.0f; unsigned int nodes_number = 0; for (unsigned int som_y2 = 0; som_y2 < nSomY; som_y2++) { for (unsigned int som_x2 = 0; som_x2 < nSomX; som_x2++) { if (som_x1 == som_x2 && som_y1 == som_y2) continue; float tmp = 0.0f; if (mapType == "planar") { tmp = euclideanDistanceOnPlanarMap(som_x1, som_y1, som_x2, som_y2); } else if (mapType == "toroid") { tmp = euclideanDistanceOnToroidMap(som_x1, som_y1, som_x2, som_y2, nSomX, nSomY); } if (tmp <= min_dist) { nodes_number++; float* vec1 = get_wvec(codebook, som_y1, som_x1, nSomX, nDimensions); float* vec2 = get_wvec(codebook, som_y2, som_x2, nSomX, nDimensions); dist += get_distance(vec1, vec2, nDimensions); delete [] vec1; delete [] vec2; } } } dist /= (float)nodes_number; uMatrix[som_y1*nSomX+som_x1] = dist; } } return uMatrix; } somoclu/src/Windows/0000755000417600011450000000000012402311155016072 5ustar pewiunix-users-shamansomoclu/src/Windows/getopt.h0000644000417600011450000000600612402311155017547 0ustar pewiunix-users-shaman#ifndef __GETOPT_H__ /** * DISCLAIMER * This file has no copyright assigned and is placed in the Public Domain. * This file is a part of the w64 mingw-runtime package. * * The w64 mingw-runtime package and its code is distributed in the hope that it * will be useful but WITHOUT ANY WARRANTY. ALL WARRANTIES, EXPRESSED OR * IMPLIED ARE HEREBY DISCLAIMED. This includes but is not limited to * warranties of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. */ #define __GETOPT_H__ /* All the headers include this file. */ #include #ifdef __cplusplus extern "C" { #endif extern int optind; /* index of first non-option in argv */ extern int optopt; /* single option character, as parsed */ extern int opterr; /* flag to enable built-in diagnostics... */ /* (user may set to zero, to suppress) */ extern char *optarg; /* pointer to argument of current option */ extern int getopt(int nargc, char * const *nargv, const char *options); #ifdef _BSD_SOURCE /* * BSD adds the non-standard `optreset' feature, for reinitialisation * of `getopt' parsing. We support this feature, for applications which * proclaim their BSD heritage, before including this header; however, * to maintain portability, developers are advised to avoid it. */ # define optreset __mingw_optreset extern int optreset; #endif #ifdef __cplusplus } #endif /* * POSIX requires the `getopt' API to be specified in `unistd.h'; * thus, `unistd.h' includes this header. However, we do not want * to expose the `getopt_long' or `getopt_long_only' APIs, when * included in this manner. Thus, close the standard __GETOPT_H__ * declarations block, and open an additional __GETOPT_LONG_H__ * specific block, only when *not* __UNISTD_H_SOURCED__, in which * to declare the extended API. */ #endif /* !defined(__GETOPT_H__) */ #if !defined(__UNISTD_H_SOURCED__) && !defined(__GETOPT_LONG_H__) #define __GETOPT_LONG_H__ #ifdef __cplusplus extern "C" { #endif struct option /* specification for a long form option... */ { const char *name; /* option name, without leading hyphens */ int has_arg; /* does it take an argument? */ int *flag; /* where to save its status, or NULL */ int val; /* its associated status value */ }; enum /* permitted values for its `has_arg' field... */ { no_argument = 0, /* option never takes an argument */ required_argument, /* option always requires an argument */ optional_argument /* option may take an argument */ }; extern int getopt_long(int nargc, char * const *nargv, const char *options, const struct option *long_options, int *idx); extern int getopt_long_only(int nargc, char * const *nargv, const char *options, const struct option *long_options, int *idx); /* * Previous MinGW implementation had... */ #ifndef HAVE_DECL_GETOPT /* * ...for the long form API only; keep this for compatibility. */ # define HAVE_DECL_GETOPT 1 #endif #ifdef __cplusplus } #endif #endif /* !defined(__UNISTD_H_SOURCED__) && !defined(__GETOPT_LONG_H__) */ somoclu/src/Windows/unistd.h0000644000417600011450000000323012402311155017547 0ustar pewiunix-users-shaman#ifndef _UNISTD_H #define _UNISTD_H 1 /* This file intended to serve as a drop-in replacement for * unistd.h on Windows * Please add functionality as neeeded */ #include #include #include "getopt.h" /* getopt at: https://gist.github.com/ashelly/7776712 */ #include /* for getpid() and the exec..() family */ #include /* for _getcwd() and _chdir() */ #define srandom srand #define random rand /* Values for the second argument to access. These may be OR'd together. */ #define R_OK 4 /* Test for read permission. */ #define W_OK 2 /* Test for write permission. */ //#define X_OK 1 /* execute permission - unsupported in windows*/ #define F_OK 0 /* Test for existence. */ #define access _access #define dup2 _dup2 #define execve _execve #define ftruncate _chsize #define unlink _unlink #define fileno _fileno #define getcwd _getcwd #define chdir _chdir #define isatty _isatty #define lseek _lseek /* read, write, and close are NOT being #defined here, because while there are file handle specific versions for Windows, they probably don't work for sockets. You need to look at your app and consider whether to call e.g. closesocket(). */ #define ssize_t int #define STDIN_FILENO 0 #define STDOUT_FILENO 1 #define STDERR_FILENO 2 /* should be in some equivalent to */ typedef __int8 int8_t; typedef __int16 int16_t; typedef __int32 int32_t; typedef __int64 int64_t; typedef unsigned __int8 uint8_t; typedef unsigned __int16 uint16_t; typedef unsigned __int32 uint32_t; typedef unsigned __int64 uint64_t; #endif /* unistd.h */somoclu/src/Windows/getopt.c0000644000417600011450000003634612402311155017554 0ustar pewiunix-users-shaman/* $OpenBSD: getopt_long.c,v 1.23 2007/10/31 12:34:57 chl Exp $ */ /* $NetBSD: getopt_long.c,v 1.15 2002/01/31 22:43:40 tv Exp $ */ /* * Copyright (c) 2002 Todd C. Miller * * Permission to use, copy, modify, and distribute this software for any * purpose with or without fee is hereby granted, provided that the above * copyright notice and this permission notice appear in all copies. * * THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES * WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF * MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR * ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES * WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN * ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. * * Sponsored in part by the Defense Advanced Research Projects * Agency (DARPA) and Air Force Research Laboratory, Air Force * Materiel Command, USAF, under agreement number F39502-99-1-0512. */ /*- * Copyright (c) 2000 The NetBSD Foundation, Inc. * All rights reserved. * * This code is derived from software contributed to The NetBSD Foundation * by Dieter Baron and Thomas Klausner. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * * THIS SOFTWARE IS PROVIDED BY THE NETBSD FOUNDATION, INC. AND CONTRIBUTORS * ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE FOUNDATION OR CONTRIBUTORS * BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE * POSSIBILITY OF SUCH DAMAGE. */ #include #include #include #include "getopt.h" #include #include #include #define REPLACE_GETOPT /* use this getopt as the system getopt(3) */ #ifdef REPLACE_GETOPT int opterr = 1; /* if error message should be printed */ int optind = 1; /* index into parent argv vector */ int optopt = '?'; /* character checked for validity */ #undef optreset /* see getopt.h */ #define optreset __mingw_optreset int optreset; /* reset getopt */ char *optarg; /* argument associated with option */ #endif #define PRINT_ERROR ((opterr) && (*options != ':')) #define FLAG_PERMUTE 0x01 /* permute non-options to the end of argv */ #define FLAG_ALLARGS 0x02 /* treat non-options as args to option "-1" */ #define FLAG_LONGONLY 0x04 /* operate as getopt_long_only */ /* return values */ #define BADCH (int)'?' #define BADARG ((*options == ':') ? (int)':' : (int)'?') #define INORDER (int)1 #ifndef __CYGWIN__ #define __progname __argv[0] #else extern char __declspec(dllimport) *__progname; #endif #ifdef __CYGWIN__ static char EMSG[] = ""; #else #define EMSG "" #endif static int getopt_internal(int, char * const *, const char *, const struct option *, int *, int); static int parse_long_options(char * const *, const char *, const struct option *, int *, int); static int gcd(int, int); static void permute_args(int, int, int, char * const *); static char *place = EMSG; /* option letter processing */ /* XXX: set optreset to 1 rather than these two */ static int nonopt_start = -1; /* first non option argument (for permute) */ static int nonopt_end = -1; /* first option after non options (for permute) */ /* Error messages */ static const char recargchar[] = "option requires an argument -- %c"; static const char recargstring[] = "option requires an argument -- %s"; static const char ambig[] = "ambiguous option -- %.*s"; static const char noarg[] = "option doesn't take an argument -- %.*s"; static const char illoptchar[] = "unknown option -- %c"; static const char illoptstring[] = "unknown option -- %s"; static void _vwarnx(const char *fmt,va_list ap) { (void)fprintf(stderr,"%s: ",__progname); if (fmt != NULL) (void)vfprintf(stderr,fmt,ap); (void)fprintf(stderr,"\n"); } static void warnx(const char *fmt,...) { va_list ap; va_start(ap,fmt); _vwarnx(fmt,ap); va_end(ap); } /* * Compute the greatest common divisor of a and b. */ static int gcd(int a, int b) { int c; c = a % b; while (c != 0) { a = b; b = c; c = a % b; } return (b); } /* * Exchange the block from nonopt_start to nonopt_end with the block * from nonopt_end to opt_end (keeping the same order of arguments * in each block). */ static void permute_args(int panonopt_start, int panonopt_end, int opt_end, char * const *nargv) { int cstart, cyclelen, i, j, ncycle, nnonopts, nopts, pos; char *swap; /* * compute lengths of blocks and number and size of cycles */ nnonopts = panonopt_end - panonopt_start; nopts = opt_end - panonopt_end; ncycle = gcd(nnonopts, nopts); cyclelen = (opt_end - panonopt_start) / ncycle; for (i = 0; i < ncycle; i++) { cstart = panonopt_end+i; pos = cstart; for (j = 0; j < cyclelen; j++) { if (pos >= panonopt_end) pos -= nnonopts; else pos += nopts; swap = nargv[pos]; /* LINTED const cast */ ((char **) nargv)[pos] = nargv[cstart]; /* LINTED const cast */ ((char **)nargv)[cstart] = swap; } } } /* * parse_long_options -- * Parse long options in argc/argv argument vector. * Returns -1 if short_too is set and the option does not match long_options. */ static int parse_long_options(char * const *nargv, const char *options, const struct option *long_options, int *idx, int short_too) { char *current_argv, *has_equal; size_t current_argv_len; int i, ambiguous, match; #define IDENTICAL_INTERPRETATION(_x, _y) \ (long_options[(_x)].has_arg == long_options[(_y)].has_arg && \ long_options[(_x)].flag == long_options[(_y)].flag && \ long_options[(_x)].val == long_options[(_y)].val) current_argv = place; match = -1; ambiguous = 0; optind++; if ((has_equal = strchr(current_argv, '=')) != NULL) { /* argument found (--option=arg) */ current_argv_len = has_equal - current_argv; has_equal++; } else current_argv_len = strlen(current_argv); for (i = 0; long_options[i].name; i++) { /* find matching long option */ if (strncmp(current_argv, long_options[i].name, current_argv_len)) continue; if (strlen(long_options[i].name) == current_argv_len) { /* exact match */ match = i; ambiguous = 0; break; } /* * If this is a known short option, don't allow * a partial match of a single character. */ if (short_too && current_argv_len == 1) continue; if (match == -1) /* partial match */ match = i; else if (!IDENTICAL_INTERPRETATION(i, match)) ambiguous = 1; } if (ambiguous) { /* ambiguous abbreviation */ if (PRINT_ERROR) warnx(ambig, (int)current_argv_len, current_argv); optopt = 0; return (BADCH); } if (match != -1) { /* option found */ if (long_options[match].has_arg == no_argument && has_equal) { if (PRINT_ERROR) warnx(noarg, (int)current_argv_len, current_argv); /* * XXX: GNU sets optopt to val regardless of flag */ if (long_options[match].flag == NULL) optopt = long_options[match].val; else optopt = 0; return (BADARG); } if (long_options[match].has_arg == required_argument || long_options[match].has_arg == optional_argument) { if (has_equal) optarg = has_equal; else if (long_options[match].has_arg == required_argument) { /* * optional argument doesn't use next nargv */ optarg = nargv[optind++]; } } if ((long_options[match].has_arg == required_argument) && (optarg == NULL)) { /* * Missing argument; leading ':' indicates no error * should be generated. */ if (PRINT_ERROR) warnx(recargstring, current_argv); /* * XXX: GNU sets optopt to val regardless of flag */ if (long_options[match].flag == NULL) optopt = long_options[match].val; else optopt = 0; --optind; return (BADARG); } } else { /* unknown option */ if (short_too) { --optind; return (-1); } if (PRINT_ERROR) warnx(illoptstring, current_argv); optopt = 0; return (BADCH); } if (idx) *idx = match; if (long_options[match].flag) { *long_options[match].flag = long_options[match].val; return (0); } else return (long_options[match].val); #undef IDENTICAL_INTERPRETATION } /* * getopt_internal -- * Parse argc/argv argument vector. Called by user level routines. */ static int getopt_internal(int nargc, char * const *nargv, const char *options, const struct option *long_options, int *idx, int flags) { char *oli; /* option letter list index */ int optchar, short_too; static int posixly_correct = -1; if (options == NULL) return (-1); /* * XXX Some GNU programs (like cvs) set optind to 0 instead of * XXX using optreset. Work around this braindamage. */ if (optind == 0) optind = optreset = 1; /* * Disable GNU extensions if POSIXLY_CORRECT is set or options * string begins with a '+'. * * CV, 2009-12-14: Check POSIXLY_CORRECT anew if optind == 0 or * optreset != 0 for GNU compatibility. */ if (posixly_correct == -1 || optreset != 0) posixly_correct = (getenv("POSIXLY_CORRECT") != NULL); if (*options == '-') flags |= FLAG_ALLARGS; else if (posixly_correct || *options == '+') flags &= ~FLAG_PERMUTE; if (*options == '+' || *options == '-') options++; optarg = NULL; if (optreset) nonopt_start = nonopt_end = -1; start: if (optreset || !*place) { /* update scanning pointer */ optreset = 0; if (optind >= nargc) { /* end of argument vector */ place = EMSG; if (nonopt_end != -1) { /* do permutation, if we have to */ permute_args(nonopt_start, nonopt_end, optind, nargv); optind -= nonopt_end - nonopt_start; } else if (nonopt_start != -1) { /* * If we skipped non-options, set optind * to the first of them. */ optind = nonopt_start; } nonopt_start = nonopt_end = -1; return (-1); } if (*(place = nargv[optind]) != '-' || (place[1] == '\0' && strchr(options, '-') == NULL)) { place = EMSG; /* found non-option */ if (flags & FLAG_ALLARGS) { /* * GNU extension: * return non-option as argument to option 1 */ optarg = nargv[optind++]; return (INORDER); } if (!(flags & FLAG_PERMUTE)) { /* * If no permutation wanted, stop parsing * at first non-option. */ return (-1); } /* do permutation */ if (nonopt_start == -1) nonopt_start = optind; else if (nonopt_end != -1) { permute_args(nonopt_start, nonopt_end, optind, nargv); nonopt_start = optind - (nonopt_end - nonopt_start); nonopt_end = -1; } optind++; /* process next argument */ goto start; } if (nonopt_start != -1 && nonopt_end == -1) nonopt_end = optind; /* * If we have "-" do nothing, if "--" we are done. */ if (place[1] != '\0' && *++place == '-' && place[1] == '\0') { optind++; place = EMSG; /* * We found an option (--), so if we skipped * non-options, we have to permute. */ if (nonopt_end != -1) { permute_args(nonopt_start, nonopt_end, optind, nargv); optind -= nonopt_end - nonopt_start; } nonopt_start = nonopt_end = -1; return (-1); } } /* * Check long options if: * 1) we were passed some * 2) the arg is not just "-" * 3) either the arg starts with -- we are getopt_long_only() */ if (long_options != NULL && place != nargv[optind] && (*place == '-' || (flags & FLAG_LONGONLY))) { short_too = 0; if (*place == '-') place++; /* --foo long option */ else if (*place != ':' && strchr(options, *place) != NULL) short_too = 1; /* could be short option too */ optchar = parse_long_options(nargv, options, long_options, idx, short_too); if (optchar != -1) { place = EMSG; return (optchar); } } if ((optchar = (int)*place++) == (int)':' || (optchar == (int)'-' && *place != '\0') || (oli = strchr(options, optchar)) == NULL) { /* * If the user specified "-" and '-' isn't listed in * options, return -1 (non-option) as per POSIX. * Otherwise, it is an unknown option character (or ':'). */ if (optchar == (int)'-' && *place == '\0') return (-1); if (!*place) ++optind; if (PRINT_ERROR) warnx(illoptchar, optchar); optopt = optchar; return (BADCH); } if (long_options != NULL && optchar == 'W' && oli[1] == ';') { /* -W long-option */ if (*place) /* no space */ /* NOTHING */; else if (++optind >= nargc) { /* no arg */ place = EMSG; if (PRINT_ERROR) warnx(recargchar, optchar); optopt = optchar; return (BADARG); } else /* white space */ place = nargv[optind]; optchar = parse_long_options(nargv, options, long_options, idx, 0); place = EMSG; return (optchar); } if (*++oli != ':') { /* doesn't take argument */ if (!*place) ++optind; } else { /* takes (optional) argument */ optarg = NULL; if (*place) /* no white space */ optarg = place; else if (oli[1] != ':') { /* arg not optional */ if (++optind >= nargc) { /* no arg */ place = EMSG; if (PRINT_ERROR) warnx(recargchar, optchar); optopt = optchar; return (BADARG); } else optarg = nargv[optind]; } place = EMSG; ++optind; } /* dump back option letter */ return (optchar); } #ifdef REPLACE_GETOPT /* * getopt -- * Parse argc/argv argument vector. * * [eventually this will replace the BSD getopt] */ int getopt(int nargc, char * const *nargv, const char *options) { /* * We don't pass FLAG_PERMUTE to getopt_internal() since * the BSD getopt(3) (unlike GNU) has never done this. * * Furthermore, since many privileged programs call getopt() * before dropping privileges it makes sense to keep things * as simple (and bug-free) as possible. */ return (getopt_internal(nargc, nargv, options, NULL, NULL, 0)); } #endif /* REPLACE_GETOPT */ /* * getopt_long -- * Parse argc/argv argument vector. */ int getopt_long(int nargc, char * const *nargv, const char *options, const struct option *long_options, int *idx) { return (getopt_internal(nargc, nargv, options, long_options, idx, FLAG_PERMUTE)); } /* * getopt_long_only -- * Parse argc/argv argument vector. */ int getopt_long_only(int nargc, char * const *nargv, const char *options, const struct option *long_options, int *idx) { return (getopt_internal(nargc, nargv, options, long_options, idx, FLAG_PERMUTE|FLAG_LONGONLY)); } somoclu/src/Windows/somoclu/0000755000417600011450000000000012402311155017553 5ustar pewiunix-users-shamansomoclu/src/Windows/somoclu/somoclu.vcxproj.filters0000644000417600011450000000452512402311155024326 0ustar pewiunix-users-shaman {4FC737F1-C7A5-4376-A066-2A32D752A2FF} cpp;c;cc;cxx;def;odl;idl;hpj;bat;asm;asmx {93995380-89BD-4b04-88EB-625FBE52EBFB} h;hh;hpp;hxx;hm;inl;inc;xsd {67DA6AB6-F800-4c08-8B7A-83BB121AAD01} rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe;resx;tiff;tif;png;wav;mfcribbon-ms Header Files Header Files Header Files Header Files Source Files Source Files Source Files Source Files Source Files Source Files Source Files Source Files Source Files Source Files Source Files somoclu/src/Windows/somoclu/somoclu.vcxproj0000644000417600011450000002514412402311155022657 0ustar pewiunix-users-shaman Debug Win32 Debug x64 Release Win32 Release x64 {278ED25D-49D8-4A54-8FCC-00954022746F} Win32Proj somoclu Application true v120 Unicode Application true v120 Unicode Application false v120 true Unicode Application false v120 true Unicode true $(CUDA_INC_PATH);$(IncludePath) true $(CUDA_INC_PATH);$(IncludePath) false $(CUDA_INC_PATH);$(IncludePath) false $(CUDA_INC_PATH);$(IncludePath) Level3 Disabled CUDA;HAVE_MPI;WIN32;_DEBUG;_CONSOLE;_LIB;%(PreprocessorDefinitions) true C:\Program Files\Microsoft MPI\Inc\;%(AdditionalIncludeDirectories) Console true $(CUDA_PATH)/lib/$(PlatformName);C:\Program Files\Microsoft MPI\Lib\;C:\Program Files\Microsoft MPI\Lib\i386;%(AdditionalLibraryDirectories) cublas.lib;cudart.lib;msmpi.lib;kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;%(AdditionalDependencies) Level3 Disabled CUDA;HAVE_MPI;WIN32;_DEBUG;_CONSOLE;_LIB;%(PreprocessorDefinitions) true C:\Program Files\Microsoft MPI\Inc\;%(AdditionalIncludeDirectories) Console true $(CUDA_PATH)/lib/$(PlatformName);C:\Program Files\Microsoft MPI\Lib\amd64;C:\Program Files\Microsoft MPI\Lib\;C:\Program Files\Microsoft MPI\Lib\i386;%(AdditionalLibraryDirectories) cublas.lib;cudart.lib;msmpi.lib;kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;%(AdditionalDependencies) Level3 MaxSpeed true true CUDA;HAVE_MPI;WIN32;NDEBUG;_CONSOLE;_LIB;%(PreprocessorDefinitions) C:\Program Files\Microsoft MPI\Inc\;%(AdditionalIncludeDirectories) true Console true true true $(CUDA_PATH)/lib/$(PlatformName);C:\Program Files\Microsoft MPI\Lib\i386;C:\Program Files\Microsoft MPI\Lib\;C:\Program Files\Microsoft MPI\Lib\amd64;%(AdditionalLibraryDirectories) cublas.lib;cudart.lib;msmpi.lib;kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;%(AdditionalDependencies) Level3 MaxSpeed true true CUDA;HAVE_MPI;WIN32;NDEBUG;_CONSOLE;_LIB;%(PreprocessorDefinitions) C:\Program Files\Microsoft MPI\Inc\;%(AdditionalIncludeDirectories) true Console true true true $(CUDA_PATH)/lib/$(PlatformName);C:\Program Files\Microsoft MPI\Lib\amd64;C:\Program Files\Microsoft MPI\Lib\;%(AdditionalLibraryDirectories) cublas.lib;cudart.lib;msmpi.lib;kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;%(AdditionalDependencies) somoclu/src/Windows/somoclu/somoclu.sln0000644000417600011450000000240512402311155021753 0ustar pewiunix-users-shaman Microsoft Visual Studio Solution File, Format Version 12.00 # Visual Studio 2013 VisualStudioVersion = 12.0.30501.0 MinimumVisualStudioVersion = 10.0.40219.1 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "somoclu", "somoclu.vcxproj", "{278ED25D-49D8-4A54-8FCC-00954022746F}" EndProject Global GlobalSection(SolutionConfigurationPlatforms) = preSolution Debug|Win32 = Debug|Win32 Debug|x64 = Debug|x64 Release|Win32 = Release|Win32 Release|x64 = Release|x64 EndGlobalSection GlobalSection(ProjectConfigurationPlatforms) = postSolution {278ED25D-49D8-4A54-8FCC-00954022746F}.Debug|Win32.ActiveCfg = Debug|Win32 {278ED25D-49D8-4A54-8FCC-00954022746F}.Debug|Win32.Build.0 = Debug|Win32 {278ED25D-49D8-4A54-8FCC-00954022746F}.Debug|x64.ActiveCfg = Debug|x64 {278ED25D-49D8-4A54-8FCC-00954022746F}.Debug|x64.Build.0 = Debug|x64 {278ED25D-49D8-4A54-8FCC-00954022746F}.Release|Win32.ActiveCfg = Release|Win32 {278ED25D-49D8-4A54-8FCC-00954022746F}.Release|Win32.Build.0 = Release|Win32 {278ED25D-49D8-4A54-8FCC-00954022746F}.Release|x64.ActiveCfg = Release|x64 {278ED25D-49D8-4A54-8FCC-00954022746F}.Release|x64.Build.0 = Release|x64 EndGlobalSection GlobalSection(SolutionProperties) = preSolution HideSolutionNode = FALSE EndGlobalSection EndGlobal somoclu/src/somocluWrap.cpp0000644000417600011450000000755412402311155017472 0ustar pewiunix-users-shaman #include"somocluWrap.h" #include #include #include using namespace std; void trainWrapper(float *data, int data_length, unsigned int nEpoch, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, unsigned int snapshots, unsigned int kernelType, string mapType, string initialCodebookFilename, float *codebook, int codebook_size, int *globalBmus, int globalBmus_size, float *uMatrix, int uMatrix_size) { /// /// Codebook /// int itask = 0; svm_node ** sparseData = NULL; core_data coreData; coreData.codebook_size = nSomY*nSomX*nDimensions; coreData.codebook = new float[coreData.codebook_size]; coreData.globalBmus = NULL; coreData.uMatrix = NULL; unsigned int nVectorsPerRank = nVectors; coreData.globalBmus_size = nVectorsPerRank*int(ceil(nVectors/(double)nVectorsPerRank))*2; if (itask == 0) { coreData.globalBmus = new int[coreData.globalBmus_size]; if (initialCodebookFilename.empty()){ initializeCodebook(0, coreData.codebook, nSomX, nSomY, nDimensions); } else { unsigned int nSomXY = 0; unsigned int tmpNDimensions = 0; delete [] coreData.codebook; coreData.codebook = readMatrix(initialCodebookFilename, nSomXY, tmpNDimensions); if (tmpNDimensions != nDimensions) { cerr << "Dimension of initial codebook does not match data!\n"; // my_abort(5); } else if (nSomXY / nSomY != nSomX) { cerr << "Dimension of initial codebook does not match specified SOM grid!\n"; // my_abort(6); } cout << "Read initial codebook: " << initialCodebookFilename << "\n"; } } #ifdef CUDA if(kernelType==DENSE_GPU){ int rank = 0; int nProcs = 1; setDevice(rank, nProcs); initializeGpu(data, nVectorsPerRank, nDimensions, nSomX, nSomY); } #endif /// /// Parameters for SOM /// if (radius0 == 0) { radius0 = nSomX / 2.0f; /// init radius for updating neighbors } if (radiusN == 0) { radiusN = 1; } if (scale0 == 0) { scale0 = 1.0; } unsigned int currentEpoch = 0; /// 0...nEpoch-1 /// /// Training /// while ( currentEpoch < nEpoch ) { coreData = trainOneEpoch(itask, data, sparseData, coreData, nEpoch, currentEpoch, snapshots > 0, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, kernelType, mapType); currentEpoch++; } if (itask == 0) { /// /// Save U-mat /// coreData.uMatrix = calculateUMatrix(coreData.codebook, nSomX, nSomY, nDimensions, mapType); coreData.uMatrix_size = nSomX * nSomY; } #ifdef CUDA if (kernelType == DENSE_GPU) { freeGpu(); } #endif if(coreData.codebook != NULL){ memcpy(codebook, coreData.codebook, sizeof(float) * codebook_size); delete [] coreData.codebook; } if(coreData.globalBmus != NULL){ memcpy(globalBmus, coreData.globalBmus, sizeof(int) * globalBmus_size); delete [] coreData.globalBmus; } if(coreData.uMatrix != NULL){ memcpy(uMatrix, coreData.uMatrix, sizeof(float) * uMatrix_size); delete [] coreData.uMatrix; } } somoclu/src/MATLAB/0000755000417600011450000000000012402311155015400 5ustar pewiunix-users-shamansomoclu/src/MATLAB/mex_interface_test.m0000644000417600011450000000104712402311155021430 0ustar pewiunix-users-shamandata = importdata('../../data/rgbs.txt'); nSomX = 50; nSomY = 50; dataSize = size(data); nVectors = dataSize(1); nDimensions = dataSize(2); nEpoch = 10; radius0 = 0; radiusN = 0; radiusCooling = 'linear'; scale0 = 0; scaleN = 0.01; scaleCooling = 'linear'; kernelType = 0; mapType = 'planar'; snapshots = 0; initialCodebookFilename = ''; [codebook, globalBmus, uMatrix] = MexSomoclu(data, nEpoch, nSomX, nSomY, ... radius0, radiusN, ... radiusCooling, scale0, scaleN, ... scaleCooling, snapshots, ... kernelType, mapType, ... initialCodebookFilename);somoclu/src/MATLAB/README.rst0000644000417600011450000000445312402311155017075 0ustar pewiunix-users-shamanVersion: 1.4 Maintainer: ShichaoGao URL: http://peterwittek.github.io/somoclu/ BugReports: https://github.com/peterwittek/somoclu/issues License: GPL-3 OS_type: unix Somoclu MATLAB Extension Build Guide: ================================ 1. Follow the instructions to build Somoclu itself at: https://github.com/peterwittek/somoclu **(OS X users see the Note below first)** 2. Build MATLAB Extension by running: :: MEX_BIN="/usr/local/MATLAB/R2013a/bin/mex" ./makeMex.sh where ``MEX_BIN`` is the path to the MATLAB installation mex binary. 3. Then ``MexSomoclu.mexa64`` or ``MexSomoclu.mexa32`` is generated for use, you can test by running the ``mex_interface_test.m``. Note for Mac OS X users: ================================ As of OS X 10.9, gcc is just symlink to clang. To build somoclu and this extension correctly, it is recommended to install gcc using something like: :: $ brew install gcc48 and set environment using: :: export CC=/usr/local/bin/gcc export CXX=/usr/local/bin/g++ export CPP=/usr/local/bin/cpp export LD=/usr/local/bin/gcc alias c++=/usr/local/bin/c++ alias g++=/usr/local/bin/g++ alias gcc=/usr/local/bin/gcc alias cpp=/usr/local/bin/cpp alias ld=/usr/local/bin/gcc alias cc=/usr/local/bin/gcc Then follow the instructions at https://github.com/peterwittek/somoclu to build somoclu itself. Building Mex Extension on OS X: =============================== To build the extension on OS X, we need to make mex use gcc instead of the default clang compiler. So we need to copy ``MATLAB_ROOT/bin/mexopts.sh`` to ``~/.matlab/VERSION/mexopts.sh`` , replace ``MATLAB_ROOT`` with your installation path of MATLAB and replace ``VERSION`` with your MATLAB version in that folder. Example: :: cp /Applications/MATLAB_R2013a.app/bin/mexopts.sh ~/.matlab/R2013a/mexopts.sh Then modify ``~/.matlab/VERSION/mexopts.sh`` to use gcc as follows: 1. change ``CC='gcc'`` and comment out all ``CC=`` statements after that. 2. change ``CXX='g++'`` and comment out all ``CXX=`` statements after that. 3. change ``MACOSX_DEPLOYMENT_TARGET='10.9'`` where ``10.9`` is your OS X version number. an example is given at https://gist.github.com/xgdgsc/9832340, then you can follow the instruction step 2 at the top to build the extension and test. somoclu/src/MATLAB/makeMex-GPU.sh0000755000417600011450000000057012402311155017761 0ustar pewiunix-users-shaman#!/bin/sh if [ -z "$MEX_BIN" ] then MEX_BIN="/usr/local/MATLAB/R2013a/bin/mex" fi CUDA_LIB="/opt/cuda/lib64" $MEX_BIN -I../ MexSomoclu.cpp -DCUDA ../somocluWrap.cpp ../somoclu.o ../denseCpuKernels.o ../io.o ../sparseCpuKernels.o ../training.o ../mapDistanceFunctions.o ../trainOneEpoch.o ../uMatrix.o ../denseGpuKernels.cu.co -lgomp -L$CUDA_LIB -lcudart -lcublas -lnvblas somoclu/src/MATLAB/makeMex.sh0000755000417600011450000000042612402311155017330 0ustar pewiunix-users-shaman#!/bin/sh if [ -z "$MEX_BIN" ] then MEX_BIN="/usr/local/MATLAB/R2013a/bin/mex" fi $MEX_BIN -I../ MexSomoclu.cpp ../somocluWrap.cpp ../somoclu.o ../denseCpuKernels.o ../io.o ../sparseCpuKernels.o ../training.o ../mapDistanceFunctions.o ../trainOneEpoch.o ../uMatrix.o -lgomp somoclu/src/MATLAB/MexSomoclu.cpp0000644000417600011450000000770412402311155020207 0ustar pewiunix-users-shaman #include "mex.h" #include "somocluWrap.h" void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[]) { int i; /* Examine input (right-hand-side) arguments. */ //mexPrintf("\nThere are %d right-hand-side argument(s).", nrhs); // for (i=0; i nrhs) mexErrMsgIdAndTxt( "MATLAB:mexfunction:inputOutputMismatch", "Cannot specify more outputs than inputs.\n"); plhs[0] = mxCreateDoubleMatrix(codebook_size, 1, mxREAL); double* codebook_p = mxGetPr(plhs[0]); for(int i = 0; i < codebook_size; i++){ codebook_p[i] = (double) codebook[i]; } if(globalBmus!=NULL){ plhs[1] = mxCreateDoubleMatrix(globalBmus_size, 1, mxREAL); double* globalBmus_p = mxGetPr(plhs[1]); for(int i = 0; i < globalBmus_size; i++){ globalBmus_p[i] = (double) globalBmus[i]; } } else{ plhs[1] = mxCreateDoubleMatrix(1, 1, mxREAL); *mxGetPr(plhs[1]) = 1; } plhs[2] = mxCreateDoubleMatrix(uMatrix_size, 1, mxREAL); double* uMatrix_p = mxGetPr(plhs[2]); for(int i = 0; i < uMatrix_size; i++){ uMatrix_p[i] = (double) uMatrix[i]; } delete[] codebook; delete[] globalBmus; delete[] uMatrix; } somoclu/src/MATLAB/mex_interface_test_gpu.m0000644000417600011450000000104712402311155022303 0ustar pewiunix-users-shamandata = importdata('../../data/rgbs.txt'); nSomX = 50; nSomY = 50; dataSize = size(data); nVectors = dataSize(1); nDimensions = dataSize(2); nEpoch = 10; radius0 = 0; radiusN = 0; radiusCooling = 'linear'; scale0 = 0; scaleN = 0.01; scaleCooling = 'linear'; kernelType = 1; mapType = 'planar'; snapshots = 0; initialCodebookFilename = ''; [codebook, globalBmus, uMatrix] = MexSomoclu(data, nEpoch, nSomX, nSomY, ... radius0, radiusN, ... radiusCooling, scale0, scaleN, ... scaleCooling, snapshots, ... kernelType, mapType, ... initialCodebookFilename);somoclu/src/training.cpp0000644000417600011450000001367112402311155016767 0ustar pewiunix-users-shaman/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #include #include #include #include #include #include "somoclu.h" using namespace std; /** Main training loop * @param itask - number of work items * @param kv * @param ptr */ void train(int itask, float *data, svm_node **sparseData, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, unsigned int nEpoch, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, string outPrefix, unsigned int snapshots, unsigned int kernelType, string mapType, string initialCodebookFilename) { /// /// Codebook /// core_data coreData; coreData.codebook = new float[nSomY*nSomX*nDimensions]; coreData.globalBmus = NULL; coreData.uMatrix = NULL; if (itask == 0) { coreData.globalBmus = new int[nVectorsPerRank*int(ceil(nVectors/(double)nVectorsPerRank))*2]; if (initialCodebookFilename.empty()){ initializeCodebook(0, coreData.codebook, nSomX, nSomY, nDimensions); } else { unsigned int nSomXY = 0; unsigned int tmpNDimensions = 0; delete [] coreData.codebook; coreData.codebook = readMatrix(initialCodebookFilename, nSomXY, tmpNDimensions); if (tmpNDimensions != nDimensions) { cerr << "Dimension of initial codebook does not match data!\n"; my_abort(5); } else if (nSomXY / nSomY != nSomX) { cerr << "Dimension of initial codebook does not match specified SOM grid!\n"; my_abort(6); } cout << "Read initial codebook: " << initialCodebookFilename << "\n"; } } /// /// Parameters for SOM /// if (radius0 == 0) { unsigned int minDim = min(nSomX, nSomY); radius0 = minDim / 2.0f; /// init radius for updating neighbors } if (radiusN == 0) { radiusN = 1; } if (scale0 == 0) { scale0 = 0.1; } unsigned int currentEpoch = 0; /// 0...nEpoch-1 /// /// Training /// #ifdef HAVE_MPI double training_time = MPI_Wtime(); #endif while ( currentEpoch < nEpoch ) { #ifdef HAVE_MPI double epoch_time = MPI_Wtime(); #endif coreData = trainOneEpoch(itask, data, sparseData, coreData, nEpoch, currentEpoch, snapshots > 0, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, kernelType, mapType); if (snapshots > 0 && itask == 0) { cout << "Saving interim U-Matrix..." << endl; stringstream sstm; sstm << outPrefix << "." << currentEpoch + 1; saveUMatrix(sstm.str() + string(".umx"), coreData.uMatrix, nSomX, nSomY); if (snapshots == 2){ saveBmus(sstm.str() + string(".bm"), coreData.globalBmus, nSomX, nSomY, nVectors); saveCodebook(sstm.str() + string(".wts"), coreData.codebook, nSomX, nSomY, nDimensions); } } currentEpoch++; #ifdef HAVE_MPI if (itask == 0) { epoch_time = MPI_Wtime() - epoch_time; cerr << "Epoch Time: " << epoch_time << endl; if ( (currentEpoch != nEpoch) && (currentEpoch % (nEpoch/100+1) != 0) ){} else{ float ratio = currentEpoch/(float)nEpoch; int c = ratio * 50 + 1; cout << std::setw(7) << (int)(ratio*100) << "% ["; for (int x=0; x. * */ #include #include "somoclu.h" #ifdef HAVE_R #include #endif /** Distance b/w a feature vector and a weight vector * = Euclidean * @param som_y * @param som_x * @param r - row number in the input feature file */ float get_distance(float* codebook, svm_node **sparseData, unsigned int som_y, unsigned int som_x, unsigned int nSomX, unsigned int nDimensions, unsigned int r) { float distance = 0.0f; unsigned int j=0; for ( unsigned int d=0; d < nDimensions; d++ ) { if ( (int) d == sparseData[r][j].index ) { distance += (codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d]- sparseData[r][j].value) * (codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d]- sparseData[r][j].value); ++j; } else { distance += codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d]* codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d]; } } return distance; } /** Get node coords for the best matching unit (BMU) * @param coords - BMU coords * @param n - row num in the input feature file */ void get_bmu_coord(float* codebook, svm_node **sparseData, unsigned int nSomY, unsigned int nSomX, unsigned int nDimensions, int* coords, unsigned int n) { float mindist = 9999.99; float dist = 0.0f; /// Check nSomX * nSomY nodes one by one and compute the distance /// D(W_K, Fvec) and get the mindist and get the coords for the BMU. /// for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { dist = get_distance(codebook, sparseData, som_y, som_x, nSomX, nDimensions, n); if (dist < mindist) { mindist = dist; coords[0] = som_x; coords[1] = som_y; } } } } void trainOneEpochSparseCPU(int itask, svm_node **sparseData, float *numerator, float *denominator, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, float radius, float scale, string mapType, int *globalBmus) { int p1[2] = {0, 0}; int *bmus = new int[nVectorsPerRank*2]; #ifdef _OPENMP #pragma omp parallel default(shared) private(p1) #endif { #ifdef _OPENMP #pragma omp for #endif #if defined(linux) || defined(__APPLE__) for (unsigned int n = 0; n < nVectorsPerRank; n++) { #endif #ifdef _WIN32 for (int n = 0; n < nVectorsPerRank; n++) { #endif if (itask*nVectorsPerRank+n using namespace std; void trainWrapper(float *data, int data_length, unsigned int nEpoch, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, unsigned int snapshots, unsigned int kernelType, string mapType, string initialCodebookFilename, float* codebook, int codebook_size, int* globalBmus, int globalBmus_size, float* uMatrix, int uMatrix_size); void trainWrapperR(float *data, int data_length, unsigned int nEpoch, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, unsigned int snapshots, unsigned int kernelType, string mapType, float *codebook, int codebook_size, int *globalBmus, int globalBmus_size, float *uMatrix, int uMatrix_size); #endif // SOMOCLUWRAP_H somoclu/src/somoclu.h0000644000417600011450000001267012402311155016300 0ustar pewiunix-users-shaman/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #include #include using namespace std; #ifndef SOMOCLU_H #define SOMOCLU_H #if HAVE_CONFIG_H #include #endif #ifdef HAVE_MPI #include #endif #define DENSE_CPU 0 #define DENSE_GPU 1 #define SPARSE_CPU 2 /// The neighbor_fuct value below which we consider /// the impact zero for a given node in the map #define NEIGHBOR_THRESHOLD 0.05 /// Sparse structures and routines struct svm_node { int index; float value; }; /// Core data structures struct core_data { float *codebook; int *globalBmus; float *uMatrix; int codebook_size; int globalBmus_size; int uMatrix_size; }; float euclideanDistanceOnToroidMap(const unsigned int som_x, const unsigned int som_y, const unsigned int x, const unsigned int y, const unsigned int nSomX, const unsigned int nSomY); float euclideanDistanceOnPlanarMap(const unsigned int som_x, const unsigned int som_y, const unsigned int x, const unsigned int y); float getWeight(float distance, float radius, float scaling); int saveCodebook(string cbFileName, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions); float *calculateUMatrix(float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, string mapType); int saveUMatrix(string fname, float *uMatrix, unsigned int nSomX, unsigned int nSomY); int saveBmus(string filename, int *bmus, unsigned int nSomX, unsigned int nSomY, unsigned int nVectors); //void printMatrix(float *A, int nRows, int nCols); float *readMatrix(const string inFilename, unsigned int &nRows, unsigned int &nCols); void readSparseMatrixDimensions(const string filename, unsigned int &nRows, unsigned int &nColumns); svm_node** readSparseMatrixChunk(const string filename, unsigned int nRows, unsigned int nRowsToRead, unsigned int rowOffset); core_data trainOneEpoch(int itask, float *data, svm_node **sparseData, core_data coreData, unsigned int nEpoch, unsigned int currentEpoch, bool enableCalculatingUMatrix, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, unsigned int kernelType, string mapType); void train(int itask, float *data, svm_node **sparseData, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, unsigned int nEpoch, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, string outPrefix, unsigned int snapshots, unsigned int kernelType, string mapType, string initialCodebookFilename); void trainOneEpochDenseCPU(int itask, float *data, float *numerator, float *denominator, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, float radius, float scale, string mapType, int *globalBmus); void trainOneEpochSparseCPU(int itask, svm_node **sparseData, float *numerator, float *denominator, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, float radius, float scale, string mapType, int *globalBmus); void initializeCodebook(unsigned int seed, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions); extern "C" { #ifdef CUDA void setDevice(int commRank, int commSize); void freeGpu(); void initializeGpu(float *hostData, int nVectorsPerRank, int nDimensions, int nSomX, int nSomY); void trainOneEpochDenseGPU(int itask, float *data, float *numerator, float *denominator, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, float radius, float scale, string mapType, int *globalBmus); #endif void my_abort(int err); } #endif somoclu/src/trainOneEpoch.cpp0000644000417600011450000001304512402311155017705 0ustar pewiunix-users-shaman#include"somoclu.h" #include #include float linearCooling(float start, float end, float nEpoch, float epoch) { float diff = (start - end) / (nEpoch-1); return start - (epoch * diff); } float exponentialCooling(float start, float end, float nEpoch, float epoch) { float diff = 0; if (end == 0.0) { diff = -log(0.1) / nEpoch; } else { diff = -log(end / start) / nEpoch; } return start * exp(-epoch * diff); } /** Initialize SOM codebook with random values * @param seed - random seed * @param codebook - the codebook to fill in * @param nSomX - dimensions of SOM map in the currentEpoch direction * @param nSomY - dimensions of SOM map in the y direction * @param nDimensions - dimensions of a data instance */ void initializeCodebook(unsigned int seed, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions) { /// /// Fill initial random weights /// srand(seed); for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { for (unsigned int d = 0; d < nDimensions; d++) { int w = 0xFFF & rand(); w -= 0x800; codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d] = (float)w / 4096.0f; } } } } core_data trainOneEpoch(int itask, float *data, svm_node **sparseData, core_data coreData, unsigned int nEpoch, unsigned int currentEpoch, bool enableCalculatingUMatrix, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, unsigned int radius0, unsigned int radiusN, string radiusCooling, float scale0, float scaleN, string scaleCooling, unsigned int kernelType, string mapType){ float N = (float)nEpoch; float *numerator; float *denominator; float scale = scale0; float radius = radius0; if (itask == 0) { numerator = new float[nSomY*nSomX*nDimensions]; denominator = new float[nSomY*nSomX]; for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { denominator[som_y*nSomX + som_x] = 0.0; for (unsigned int d = 0; d < nDimensions; d++) { numerator[som_y*nSomX*nDimensions + som_x*nDimensions + d] = 0.0; } } } if (radiusCooling == "linear") { radius = linearCooling(float(radius0), radiusN, N, currentEpoch); } else { radius = exponentialCooling(radius0, radiusN, N, currentEpoch); } if (scaleCooling == "linear") { scale = linearCooling(scale0, scaleN, N, currentEpoch); } else { scale = exponentialCooling(scale0, scaleN, N, currentEpoch); } // cout << "Epoch: " << currentEpoch << " Radius: " << radius << endl; } #ifdef HAVE_MPI MPI_Bcast(&radius, 1, MPI_FLOAT, 0, MPI_COMM_WORLD); MPI_Bcast(&scale, 1, MPI_FLOAT, 0, MPI_COMM_WORLD); MPI_Bcast(coreData.codebook, nSomY*nSomX*nDimensions, MPI_FLOAT, 0, MPI_COMM_WORLD); #endif /// 1. Each task fills localNumerator and localDenominator /// 2. MPI_reduce sums up each tasks localNumerator and localDenominator to the root's /// numerator and denominator. switch (kernelType) { default: case DENSE_CPU: trainOneEpochDenseCPU(itask, data, numerator, denominator, coreData.codebook, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, radius, scale, mapType, coreData.globalBmus); break; #ifdef CUDA case DENSE_GPU: trainOneEpochDenseGPU(itask, data, numerator, denominator, coreData.codebook, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, radius, scale, mapType, coreData.globalBmus); break; #endif case SPARSE_CPU: trainOneEpochSparseCPU(itask, sparseData, numerator, denominator, coreData.codebook, nSomX, nSomY, nDimensions, nVectors, nVectorsPerRank, radius, scale, mapType, coreData.globalBmus); break; } /// 3. Update codebook using numerator and denominator #ifdef HAVE_MPI MPI_Barrier(MPI_COMM_WORLD); #endif if (itask == 0) { #pragma omp parallel for #if defined(linux) || defined(__APPLE__) for (unsigned int som_y = 0; som_y < nSomY; som_y++) { #endif #ifdef _WIN32 for (int som_y = 0; som_y < nSomY; som_y++) { #endif for (unsigned int som_x = 0; som_x < nSomX; som_x++) { float denom = denominator[som_y*nSomX + som_x]; for (unsigned int d = 0; d < nDimensions; d++) { float newWeight = numerator[som_y*nSomX*nDimensions + som_x*nDimensions + d] / denom; if (newWeight > 0.0) { coreData.codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d] = newWeight; } } } } } if (enableCalculatingUMatrix) { coreData.uMatrix = calculateUMatrix(coreData.codebook, nSomX, nSomY, nDimensions, mapType); } if (itask == 0) { delete [] numerator; delete [] denominator; } return coreData; } somoclu/src/mapDistanceFunctions.cpp0000644000417600011450000000441612402311155021272 0ustar pewiunix-users-shaman/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #include #include #include #include "somoclu.h" float euclideanDistanceOnToroidMap(const unsigned int som_x, const unsigned int som_y, const unsigned int x, const unsigned int y, const unsigned int nSomX, const unsigned int nSomY) { unsigned int x1 = std::min(som_x, x); unsigned int y1 = std::min(som_y, y); unsigned int x2 = std::max(som_x, x); unsigned int y2 = std::max(som_y, y); unsigned int xdist = std::min(x2-x1, x1+nSomX-x2); unsigned int ydist = std::min(y2-y1, y1+nSomY-y2); //unsigned int xdist = std::min(std::abs(x1-x2), std::abs(x1+nSomX-x2)); //unsigned int ydist = std::min(std::abs(y1-y2), std::abs(y1+nSomY-y2)); return sqrt(float(xdist*xdist+ydist*ydist)); } float euclideanDistanceOnPlanarMap(const unsigned int som_x, const unsigned int som_y, const unsigned int x, const unsigned int y) { unsigned int x1 = std::min(som_x, x); unsigned int y1 = std::min(som_y, y); unsigned int x2 = std::max(som_x, x); unsigned int y2 = std::max(som_y, y); unsigned int xdist = x2-x1; unsigned int ydist = y2-y1; return sqrt(float(xdist*xdist+ydist*ydist)); } float gaussianNeighborhood(float distance, float radius, float stddevs) { float norm = (2 * (radius + 1)*(radius + 1)) / (stddevs*stddevs); return exp((-(float) distance * distance) / norm); } float getWeight(float distance, float radius, float scaling) { if (distance <= radius) { return scaling * gaussianNeighborhood(distance, radius, 2); } else { return 0.0; } } somoclu/src/Rscript/0000755000417600011450000000000012402311155016066 5ustar pewiunix-users-shamansomoclu/src/Rscript/makeR-CUDA.sh0000755000417600011450000000101612402311155020174 0ustar pewiunix-users-shaman#!/bin/sh rm -rf ../R-CUDA cp -r ../R ../R-CUDA cp configure ../R-CUDA cp tests/R_interface_test_CUDA.R ../R-CUDA/tests cd ../R-CUDA mkdir data cp -r ../../m4/ ./src/ cp ../../autogen.sh ./src/ cp ../../configure.ac ./src/ cp ../../Makefile.in ./src/ mkdir ./src/src cp ../../src/*.cpp ./src/src cp ../../src/*.h ./src/src cp ../../src/*.cu ./src/src cp ../../src/Makefile.in ./src/src cp ../../data/rgbs.txt ./data/ gzip -f ./data/rgbs.txt cd src mv Rsomoclu.cpp src rm *.cpp rm *.h rm Makevars* cd ../../ R CMD build R-CUDA somoclu/src/Rscript/makeR.sh0000755000417600011450000000050312402311155017462 0ustar pewiunix-users-shaman#!/bin/sh cd ../R mkdir data cp ../../src/*.h ./src/ cp ../../src/mapDistanceFunctions.cpp ./src/ cp ../../src/trainOneEpoch.cpp ./src/ cp ../../src/uMatrix.cpp ./src/ cp ../../src/denseCpuKernels.cpp ./src/ cp ../../src/sparseCpuKernels.cpp ./src/ cp ../../data/rgbs.txt ./data/ gzip ./data/rgbs.txt cd ../ R CMD build R somoclu/src/Rscript/configure0000755000417600011450000000153312402311155017777 0ustar pewiunix-users-shaman#!/bin/bash cd src bash autogen.sh HAS_CUDA=FALSE if test -z "${CUDA_HOME}"; then echo "could not determine CUDA_HOME. Please see the README file for installation requirements" exit 1 else HAS_CUDA=TRUE fi ARCH=$(uname -m) # replace these five lines with # CUDA_LIB := if [ ${ARCH} = 'i386' ] ; then CUDA_LIB=${CUDA_HOME}/lib else CUDA_LIB=${CUDA_HOME}/lib64 fi ./configure --with-cuda=${CUDA_HOME} --without-mpi make export PKG_LIBS=`${R_HOME}/bin/Rscript -e "Rcpp:::LdFlags()"` export PKG_CXXFLAGS=`${R_HOME}/bin/Rscript -e "Rcpp:::CxxFlags()"`" -DHAVE_R -DCUDA" cd src ${R_HOME}/bin/R CMD SHLIB $PKG_CXXFLAGS Rsomoclu.cpp denseCpuKernels.o sparseCpuKernels.o mapDistanceFunctions.o trainOneEpoch.o uMatrix.o denseGpuKernels.cu.co io.o -lgomp -L${CUDA_LIB} -lcudart -lcublas rm somoclu cp Rsomoclu.so ../ somoclu/src/Rscript/clean.sh0000755000417600011450000000012312402311155017503 0ustar pewiunix-users-shaman#!/bin/bash cd ../R/src/ shopt -s extglob rm !(Makevars|Makevars.win|Rsomoclu.cpp) somoclu/src/Rscript/tests/0000755000417600011450000000000012402311155017230 5ustar pewiunix-users-shamansomoclu/src/Rscript/tests/R_interface_test_CUDA.R0000644000417600011450000000130612402311155023427 0ustar pewiunix-users-shamanlibrary('Rsomoclu') data_file <- system.file("data", "rgbs.txt.gz", package = 'Rsomoclu') input_data <- read.table(data_file) input_data <- data.matrix(input_data) nSomX <- 50 nSomY <- 50 nEpoch <- 10 radius0 <- 0 radiusN <- 0 radiusCooling <- "linear" scale0 <- 0 scaleN <- 0.01 scaleCooling <- "linear" kernelType <- 1 mapType <- "planar" snapshots <- 0 # initialCodebookFilename <- '' res <- Rsomoclu.train(input_data, nEpoch, nSomX, nSomY, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType) # initialCodebookFilename) res$codebook res$globalBmus res$uMatrix somoclu/src/Rscript/README.md0000644000417600011450000000111412402311155017342 0ustar pewiunix-users-shamanInstructions for building the R package with CUDA support on Linux == First after unzip the tarball, you can cd to the directory that contains the script to help you build the package with CUDA support: $ cd src/Rscript Then export the variable `CUDA_HOME` which indicates your installation: $ export CUDA_HOME=/opt/cuda or like: $ export CUDA_HOME=/usr/local/cuda then run the script to build: $ ./makeR-CUDA.sh If there isn' t error. You will then find the package `Rsomoclu_VERION.tar.gz` at the upper src folder. Install it with: $ R CMD INSTALL Rsomoclu_VERION.tar.gz somoclu/src/Python/0000755000417600011450000000000012402311155015721 5ustar pewiunix-users-shamansomoclu/src/Python/setup_with_CUDA.py0000644000417600011450000000451512402311155021267 0ustar pewiunix-users-shaman#!/usr/bin/env python2 """ setup.py file for CUDA use sudo python2 setup_with_CUDA.py install to install """ from setuptools import setup, Extension from setuptools.command.install import install from subprocess import call import numpy import os try: numpy_include = numpy.get_include() except AttributeError: numpy_include = numpy.get_numpy_include() class MyInstall(install): def run(self): #call(["src/autogen.sh"]) call(["pwd"]) os.chdir('src') call(["bash", "autogen.sh"]) ## CUDA PATH here: call(["./configure", "--without-mpi","--with-cuda=/opt/cuda/"]) call(["make"]) os.chdir('../') install.run(self) somoclu_module = Extension('_somoclu', sources=['somoclu_wrap.cxx', 'src/src/somocluWrap.cpp'], extra_objects=['src/src/somoclu.o', 'src/src/denseCpuKernels.o', 'src/src/io.o', 'src/src/sparseCpuKernels.o', 'src/src/training.o', 'src/src/mapDistanceFunctions.o', 'src/src/trainOneEpoch.o', 'src/src/uMatrix.o', 'src/src/denseGpuKernels.cu.co'], define_macros=[('CUDA', None)], #PATH to CUDA library here, 64 for 64 bit library_dirs=['/opt/cuda/lib64'], libraries=['gomp','cudart','cublas'], include_dirs=[numpy_include] ) setup(name='somoclu', version='1.4', license='GPL3', author="peterwittek", author_email="", maintainer="shichaogao", maintainer_email="xgdgsc@gmail.com", url="http://peterwittek.github.io/somoclu/", platforms="unix", description="a cluster-oriented implementation of self-organizing maps", ext_modules=[somoclu_module], py_modules=["somoclu"], install_requires=['numpy'], # test_suite="tests", cmdclass={'install': MyInstall} # , 'build_ext': MyBuildExt ) somoclu/src/Python/setup.py0000644000417600011450000000434212402311155017436 0ustar pewiunix-users-shaman#!/usr/bin/env python2 """ setup.py file for SWIG example """ from setuptools import setup, Extension from setuptools.command.install import install from subprocess import call import numpy #from setuptools.command.build_ext import build_ext import os try: numpy_include = numpy.get_include() except AttributeError: numpy_include = numpy.get_numpy_include() # class MyBuildExt(build_ext): # def run(self): # call(["pwd"]) # call(["cd", "src"]) # call(["pwd"]) # call(["bash", "autogen.sh"]) # build_ext.run(self) class MyInstall(install): def run(self): #call(["src/autogen.sh"]) call(["pwd"]) os.chdir('src') call(["bash", "autogen.sh"]) call(["./configure", "--without-mpi", "--without-cuda"]) call(["make"]) os.chdir('../') install.run(self) somoclu_module = Extension('_somoclu', sources=['somoclu_wrap.cxx', 'src/src/somocluWrap.cpp'], extra_objects=['src/src/somoclu.o', 'src/src/denseCpuKernels.o', 'src/src/io.o', 'src/src/sparseCpuKernels.o', 'src/src/training.o', 'src/src/mapDistanceFunctions.o', 'src/src/trainOneEpoch.o', 'src/src/uMatrix.o'], libraries=['gomp'], include_dirs=[numpy_include] ) setup(name='somoclu', version='1.4', license='GPL3', author="peterwittek", author_email="", maintainer="shichaogao", maintainer_email="xgdgsc@gmail.com", url="http://peterwittek.github.io/somoclu/", platforms="unix", description="a cluster-oriented implementation of self-organizing maps", ext_modules=[somoclu_module], py_modules=["somoclu"], install_requires=['numpy'], # test_suite="tests", cmdclass={'install': MyInstall} # , 'build_ext': MyBuildExt ) somoclu/src/Python/README.rst0000644000417600011450000000714712402311155017421 0ustar pewiunix-users-shamanSomoclu - python interface ================================ Somoclu is a massively parallel implementation of self-organizing maps. It relies on OpenMP for multicore execution, MPI for distributing the workload, and it can be accelerated by CUDA on a GPU cluster. A sparse kernel is also included, which is useful for training maps on vector spaces generated in text mining processes. The topology of the grid is rectangular. Currently a subset of the C++ version is supported with this package. Homepage: `https://github.com/peterwittek/somoclu `_ Example, in which the data file rgbs.txt can be found at https://github.com/peterwittek/somoclu/tree/master/data .. code-block:: python #!/usr/bin/env python2 # -*- coding: utf-8 -*- import somoclu import numpy as np data = np.loadtxt('rgbs.txt') print(data) data = np.float32(data) nSomX = 50 nSomY = 50 nVectors = data.shape[0] nDimensions = data.shape[1] data1D = np.ndarray.flatten(data) nEpoch = 10 radius0 = 0 radiusN = 0 radiusCooling = "linear" scale0 = 0 scaleN = 0.01 scaleCooling = "linear" kernelType = 0 mapType = "planar" snapshots = 0 initialCodebookFilename = '' codebook_size = nSomY * nSomX * nDimensions codebook = np.zeros(codebook_size, dtype=np.float32) globalBmus_size = int(nVectors * int(np.ceil(nVectors/nVectors))*2) globalBmus = np.zeros(globalBmus_size, dtype=np.intc) uMatrix_size = nSomX * nSomY uMatrix = np.zeros(uMatrix_size, dtype=np.float32) somoclu.trainWrapper(data1D, nEpoch, nSomX, nSomY, nDimensions, nVectors, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType, initialCodebookFilename, codebook, globalBmus, uMatrix) print codebook print globalBmus print uMatrix Get it now ---------- :: $ sudo pip install somoclu Build on Mac OS X: -------------------- Before installing using pip, gcc should be installed first. As of OS X 10.9, gcc is just symlink to clang. To build somoclu and this extension correctly, it is recommended to install gcc using something like: :: $ brew install gcc48 and set environment using: :: export CC=/usr/local/bin/gcc export CXX=/usr/local/bin/g++ export CPP=/usr/local/bin/cpp export LD=/usr/local/bin/gcc alias c++=/usr/local/bin/c++ alias g++=/usr/local/bin/g++ alias gcc=/usr/local/bin/gcc alias cpp=/usr/local/bin/cpp alias ld=/usr/local/bin/gcc alias cc=/usr/local/bin/gcc Then you can :: $ sudo pip install somoclu Build with CUDA support on Linux: -------------------------------------- You need to clone this repo or download the latest release tarball, and :: $ cd src/Python $ bash makepy.sh Then if your CUDA installation is located at /opt/cuda and 64bit, you can do the following to install: :: $ sudo python2 setup_with_CUDA.py install Otherwise, you should modify the setup_with_CUDA.py , change the path to CUDA installation accordingly: :: call(["./configure", "--without-mpi","--with-cuda=/opt/cuda/"]) and :: library_dirs=['/opt/cuda/lib64'] Then run the install command :: $ sudo python2 setup_with_CUDA.py install Then you can use the python interface like before, with CUDA support. somoclu/src/Python/somoclu.py0000644000417600011450000000432412402311155017757 0ustar pewiunix-users-shaman# This file was automatically generated by SWIG (http://www.swig.org). # Version 2.0.12 # # Do not make changes to this file unless you know what you are doing--modify # the SWIG interface file instead. from sys import version_info if version_info >= (2,6,0): def swig_import_helper(): from os.path import dirname import imp fp = None try: fp, pathname, description = imp.find_module('_somoclu', [dirname(__file__)]) except ImportError: import _somoclu return _somoclu if fp is not None: try: _mod = imp.load_module('_somoclu', fp, pathname, description) finally: fp.close() return _mod _somoclu = swig_import_helper() del swig_import_helper else: import _somoclu del version_info try: _swig_property = property except NameError: pass # Python < 2.2 doesn't have 'property'. def _swig_setattr_nondynamic(self,class_type,name,value,static=1): if (name == "thisown"): return self.this.own(value) if (name == "this"): if type(value).__name__ == 'SwigPyObject': self.__dict__[name] = value return method = class_type.__swig_setmethods__.get(name,None) if method: return method(self,value) if (not static): self.__dict__[name] = value else: raise AttributeError("You cannot add attributes to %s" % self) def _swig_setattr(self,class_type,name,value): return _swig_setattr_nondynamic(self,class_type,name,value,0) def _swig_getattr(self,class_type,name): if (name == "thisown"): return self.this.own() method = class_type.__swig_getmethods__.get(name,None) if method: return method(self) raise AttributeError(name) def _swig_repr(self): try: strthis = "proxy of " + self.this.__repr__() except: strthis = "" return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,) try: _object = object _newclass = 1 except AttributeError: class _object : pass _newclass = 0 def trainWrapper(*args): return _somoclu.trainWrapper(*args) trainWrapper = _somoclu.trainWrapper # This file is compatible with both classic and new-style classes. somoclu/src/Python/makepy.sh0000755000417600011450000000100412402311155017541 0ustar pewiunix-users-shaman#!/bin/sh # rm _somoclu.so # rm somoclu.pyc # swig -c++ -python -module somoclu somoclu.i # ./setup.py clean # ./setup.py build_ext --inplace rm -rf ./src rm -rf ./dist rm -rf ./build mkdir src mkdir src/src cp ../../autogen.sh ./src cp -r ../../m4 ./src cp ../../configure.ac ./src cp ../../Makefile.in ./src cp ../../src/*.h ./src/src cp ../../src/*.cpp ./src/src cp ../../src/*.cu ./src/src cp ../../src/Makefile.in ./src/src cp ../../data/rgbs.txt tests/ python2 setup.py sdist #sudo python2 setup.py install somoclu/src/Python/somoclu_wrap.cxx0000644000417600011450000042276212402311155021174 0ustar pewiunix-users-shaman/* ---------------------------------------------------------------------------- * This file was automatically generated by SWIG (http://www.swig.org). * Version 2.0.12 * * This file is not intended to be easily readable and contains a number of * coding conventions designed to improve portability and efficiency. Do not make * changes to this file unless you know what you are doing--modify the SWIG * interface file instead. * ----------------------------------------------------------------------------- */ #define SWIGPYTHON #define SWIG_PYTHON_DIRECTOR_NO_VTABLE #ifdef __cplusplus /* SwigValueWrapper is described in swig.swg */ template class SwigValueWrapper { struct SwigMovePointer { T *ptr; SwigMovePointer(T *p) : ptr(p) { } ~SwigMovePointer() { delete ptr; } SwigMovePointer& operator=(SwigMovePointer& rhs) { T* oldptr = ptr; ptr = 0; delete oldptr; ptr = rhs.ptr; rhs.ptr = 0; return *this; } } pointer; SwigValueWrapper& operator=(const SwigValueWrapper& rhs); SwigValueWrapper(const SwigValueWrapper& rhs); public: SwigValueWrapper() : pointer(0) { } SwigValueWrapper& operator=(const T& t) { SwigMovePointer tmp(new T(t)); pointer = tmp; return *this; } operator T&() const { return *pointer.ptr; } T *operator&() { return pointer.ptr; } }; template T SwigValueInit() { return T(); } #endif /* ----------------------------------------------------------------------------- * This section contains generic SWIG labels for method/variable * declarations/attributes, and other compiler dependent labels. * ----------------------------------------------------------------------------- */ /* template workaround for compilers that cannot correctly implement the C++ standard */ #ifndef SWIGTEMPLATEDISAMBIGUATOR # if defined(__SUNPRO_CC) && (__SUNPRO_CC <= 0x560) # define SWIGTEMPLATEDISAMBIGUATOR template # elif defined(__HP_aCC) /* Needed even with `aCC -AA' when `aCC -V' reports HP ANSI C++ B3910B A.03.55 */ /* If we find a maximum version that requires this, the test would be __HP_aCC <= 35500 for A.03.55 */ # define SWIGTEMPLATEDISAMBIGUATOR template # else # define SWIGTEMPLATEDISAMBIGUATOR # endif #endif /* inline attribute */ #ifndef SWIGINLINE # if defined(__cplusplus) || (defined(__GNUC__) && !defined(__STRICT_ANSI__)) # define SWIGINLINE inline # else # define SWIGINLINE # endif #endif /* attribute recognised by some compilers to avoid 'unused' warnings */ #ifndef SWIGUNUSED # if defined(__GNUC__) # if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) # define SWIGUNUSED __attribute__ ((__unused__)) # else # define SWIGUNUSED # endif # elif defined(__ICC) # define SWIGUNUSED __attribute__ ((__unused__)) # else # define SWIGUNUSED # endif #endif #ifndef SWIG_MSC_UNSUPPRESS_4505 # if defined(_MSC_VER) # pragma warning(disable : 4505) /* unreferenced local function has been removed */ # endif #endif #ifndef SWIGUNUSEDPARM # ifdef __cplusplus # define SWIGUNUSEDPARM(p) # else # define SWIGUNUSEDPARM(p) p SWIGUNUSED # endif #endif /* internal SWIG method */ #ifndef SWIGINTERN # define SWIGINTERN static SWIGUNUSED #endif /* internal inline SWIG method */ #ifndef SWIGINTERNINLINE # define SWIGINTERNINLINE SWIGINTERN SWIGINLINE #endif /* exporting methods */ #if (__GNUC__ >= 4) || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) # ifndef GCC_HASCLASSVISIBILITY # define GCC_HASCLASSVISIBILITY # endif #endif #ifndef SWIGEXPORT # if defined(_WIN32) || defined(__WIN32__) || defined(__CYGWIN__) # if defined(STATIC_LINKED) # define SWIGEXPORT # else # define SWIGEXPORT __declspec(dllexport) # endif # else # if defined(__GNUC__) && defined(GCC_HASCLASSVISIBILITY) # define SWIGEXPORT __attribute__ ((visibility("default"))) # else # define SWIGEXPORT # endif # endif #endif /* calling conventions for Windows */ #ifndef SWIGSTDCALL # if defined(_WIN32) || defined(__WIN32__) || defined(__CYGWIN__) # define SWIGSTDCALL __stdcall # else # define SWIGSTDCALL # endif #endif /* Deal with Microsoft's attempt at deprecating C standard runtime functions */ #if !defined(SWIG_NO_CRT_SECURE_NO_DEPRECATE) && defined(_MSC_VER) && !defined(_CRT_SECURE_NO_DEPRECATE) # define _CRT_SECURE_NO_DEPRECATE #endif /* Deal with Microsoft's attempt at deprecating methods in the standard C++ library */ #if !defined(SWIG_NO_SCL_SECURE_NO_DEPRECATE) && defined(_MSC_VER) && !defined(_SCL_SECURE_NO_DEPRECATE) # define _SCL_SECURE_NO_DEPRECATE #endif #if defined(_DEBUG) && defined(SWIG_PYTHON_INTERPRETER_NO_DEBUG) /* Use debug wrappers with the Python release dll */ # undef _DEBUG # include # define _DEBUG #else # include #endif /* ----------------------------------------------------------------------------- * swigrun.swg * * This file contains generic C API SWIG runtime support for pointer * type checking. * ----------------------------------------------------------------------------- */ /* This should only be incremented when either the layout of swig_type_info changes, or for whatever reason, the runtime changes incompatibly */ #define SWIG_RUNTIME_VERSION "4" /* define SWIG_TYPE_TABLE_NAME as "SWIG_TYPE_TABLE" */ #ifdef SWIG_TYPE_TABLE # define SWIG_QUOTE_STRING(x) #x # define SWIG_EXPAND_AND_QUOTE_STRING(x) SWIG_QUOTE_STRING(x) # define SWIG_TYPE_TABLE_NAME SWIG_EXPAND_AND_QUOTE_STRING(SWIG_TYPE_TABLE) #else # define SWIG_TYPE_TABLE_NAME #endif /* You can use the SWIGRUNTIME and SWIGRUNTIMEINLINE macros for creating a static or dynamic library from the SWIG runtime code. In 99.9% of the cases, SWIG just needs to declare them as 'static'. But only do this if strictly necessary, ie, if you have problems with your compiler or suchlike. */ #ifndef SWIGRUNTIME # define SWIGRUNTIME SWIGINTERN #endif #ifndef SWIGRUNTIMEINLINE # define SWIGRUNTIMEINLINE SWIGRUNTIME SWIGINLINE #endif /* Generic buffer size */ #ifndef SWIG_BUFFER_SIZE # define SWIG_BUFFER_SIZE 1024 #endif /* Flags for pointer conversions */ #define SWIG_POINTER_DISOWN 0x1 #define SWIG_CAST_NEW_MEMORY 0x2 /* Flags for new pointer objects */ #define SWIG_POINTER_OWN 0x1 /* Flags/methods for returning states. The SWIG conversion methods, as ConvertPtr, return an integer that tells if the conversion was successful or not. And if not, an error code can be returned (see swigerrors.swg for the codes). Use the following macros/flags to set or process the returning states. 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Finally, if the SWIG_CASTRANK_MODE is enabled, the result code allows to return the 'cast rank', for example, if you have this int food(double) int fooi(int); and you call food(1) // cast rank '1' (1 -> 1.0) fooi(1) // cast rank '0' just use the SWIG_AddCast()/SWIG_CheckState() */ #define SWIG_OK (0) #define SWIG_ERROR (-1) #define SWIG_IsOK(r) (r >= 0) #define SWIG_ArgError(r) ((r != SWIG_ERROR) ? r : SWIG_TypeError) /* The CastRankLimit says how many bits are used for the cast rank */ #define SWIG_CASTRANKLIMIT (1 << 8) /* The NewMask denotes the object was created (using new/malloc) */ #define SWIG_NEWOBJMASK (SWIG_CASTRANKLIMIT << 1) /* The TmpMask is for in/out typemaps that use temporal objects */ #define SWIG_TMPOBJMASK (SWIG_NEWOBJMASK << 1) /* Simple returning values */ #define SWIG_BADOBJ (SWIG_ERROR) #define SWIG_OLDOBJ (SWIG_OK) #define SWIG_NEWOBJ (SWIG_OK | SWIG_NEWOBJMASK) #define SWIG_TMPOBJ (SWIG_OK | SWIG_TMPOBJMASK) /* Check, add and del mask methods */ #define SWIG_AddNewMask(r) (SWIG_IsOK(r) ? (r | SWIG_NEWOBJMASK) : r) #define SWIG_DelNewMask(r) (SWIG_IsOK(r) ? (r & ~SWIG_NEWOBJMASK) : r) #define SWIG_IsNewObj(r) (SWIG_IsOK(r) && (r & SWIG_NEWOBJMASK)) #define SWIG_AddTmpMask(r) (SWIG_IsOK(r) ? (r | SWIG_TMPOBJMASK) : r) #define SWIG_DelTmpMask(r) (SWIG_IsOK(r) ? (r & ~SWIG_TMPOBJMASK) : r) #define SWIG_IsTmpObj(r) (SWIG_IsOK(r) && (r & SWIG_TMPOBJMASK)) /* Cast-Rank Mode */ #if defined(SWIG_CASTRANK_MODE) # ifndef SWIG_TypeRank # define SWIG_TypeRank unsigned long # endif # ifndef SWIG_MAXCASTRANK /* Default cast allowed */ # define SWIG_MAXCASTRANK (2) # endif # define SWIG_CASTRANKMASK ((SWIG_CASTRANKLIMIT) -1) # define SWIG_CastRank(r) (r & SWIG_CASTRANKMASK) SWIGINTERNINLINE int SWIG_AddCast(int r) { return SWIG_IsOK(r) ? ((SWIG_CastRank(r) < SWIG_MAXCASTRANK) ? (r + 1) : SWIG_ERROR) : r; } SWIGINTERNINLINE int SWIG_CheckState(int r) { return SWIG_IsOK(r) ? SWIG_CastRank(r) + 1 : 0; } #else /* no cast-rank mode */ # define SWIG_AddCast(r) (r) # define SWIG_CheckState(r) (SWIG_IsOK(r) ? 1 : 0) #endif #include #ifdef __cplusplus extern "C" { #endif typedef void *(*swig_converter_func)(void *, int *); typedef struct swig_type_info *(*swig_dycast_func)(void **); /* Structure to store information on one type */ typedef struct swig_type_info { const char *name; /* mangled name of this type */ const char *str; /* human readable name of this type */ swig_dycast_func dcast; /* dynamic cast function down a hierarchy */ struct swig_cast_info *cast; /* linked list of types that can cast into this type */ void *clientdata; /* language specific type data */ int owndata; /* flag if the structure owns the clientdata */ } swig_type_info; /* Structure to store a type and conversion function used for casting */ typedef struct swig_cast_info { swig_type_info *type; /* pointer to type that is equivalent to this type */ swig_converter_func converter; /* function to cast the void pointers */ struct swig_cast_info *next; /* pointer to next cast in linked list */ struct swig_cast_info *prev; /* pointer to the previous cast */ } swig_cast_info; /* Structure used to store module information * Each module generates one structure like this, and the runtime collects * all of these structures and stores them in a circularly linked list.*/ typedef struct swig_module_info { swig_type_info **types; /* Array of pointers to swig_type_info structures that are in this module */ size_t size; /* Number of types in this module */ struct swig_module_info *next; /* Pointer to next element in circularly linked list */ swig_type_info **type_initial; /* Array of initially generated type structures */ swig_cast_info **cast_initial; /* Array of initially generated casting structures */ void *clientdata; /* Language specific module data */ } swig_module_info; /* Compare two type names skipping the space characters, therefore "char*" == "char *" and "Class" == "Class", etc. Return 0 when the two name types are equivalent, as in strncmp, but skipping ' '. */ SWIGRUNTIME int SWIG_TypeNameComp(const char *f1, const char *l1, const char *f2, const char *l2) { for (;(f1 != l1) && (f2 != l2); ++f1, ++f2) { while ((*f1 == ' ') && (f1 != l1)) ++f1; while ((*f2 == ' ') && (f2 != l2)) ++f2; if (*f1 != *f2) return (*f1 > *f2) ? 1 : -1; } return (int)((l1 - f1) - (l2 - f2)); } /* Check type equivalence in a name list like ||... Return 0 if equal, -1 if nb < tb, 1 if nb > tb */ SWIGRUNTIME int SWIG_TypeCmp(const char *nb, const char *tb) { int equiv = 1; const char* te = tb + strlen(tb); const char* ne = nb; while (equiv != 0 && *ne) { for (nb = ne; *ne; ++ne) { if (*ne == '|') break; } equiv = SWIG_TypeNameComp(nb, ne, tb, te); if (*ne) ++ne; } return equiv; } /* Check type equivalence in a name list like ||... Return 0 if not equal, 1 if equal */ SWIGRUNTIME int SWIG_TypeEquiv(const char *nb, const char *tb) { return SWIG_TypeCmp(nb, tb) == 0 ? 1 : 0; } /* Check the typename */ SWIGRUNTIME swig_cast_info * SWIG_TypeCheck(const char *c, swig_type_info *ty) { if (ty) { swig_cast_info *iter = ty->cast; while (iter) { if (strcmp(iter->type->name, c) == 0) { if (iter == ty->cast) return iter; /* Move iter to the top of the linked list */ iter->prev->next = iter->next; if (iter->next) iter->next->prev = iter->prev; iter->next = ty->cast; iter->prev = 0; if (ty->cast) ty->cast->prev = iter; ty->cast = iter; return iter; } iter = iter->next; } } return 0; } /* Identical to SWIG_TypeCheck, except strcmp is replaced with a pointer comparison */ SWIGRUNTIME swig_cast_info * SWIG_TypeCheckStruct(swig_type_info *from, swig_type_info *ty) { if (ty) { swig_cast_info *iter = ty->cast; while (iter) { if (iter->type == from) { if (iter == ty->cast) return iter; /* Move iter to the top of the linked list */ iter->prev->next = iter->next; if (iter->next) iter->next->prev = iter->prev; iter->next = ty->cast; iter->prev = 0; if (ty->cast) ty->cast->prev = iter; ty->cast = iter; return iter; } iter = iter->next; } } return 0; } /* Cast a pointer up an inheritance hierarchy */ SWIGRUNTIMEINLINE void * SWIG_TypeCast(swig_cast_info *ty, void *ptr, int *newmemory) { return ((!ty) || (!ty->converter)) ? ptr : (*ty->converter)(ptr, newmemory); } /* Dynamic pointer casting. Down an inheritance hierarchy */ SWIGRUNTIME swig_type_info * SWIG_TypeDynamicCast(swig_type_info *ty, void **ptr) { swig_type_info *lastty = ty; if (!ty || !ty->dcast) return ty; while (ty && (ty->dcast)) { ty = (*ty->dcast)(ptr); if (ty) lastty = ty; } return lastty; } /* Return the name associated with this type */ SWIGRUNTIMEINLINE const char * SWIG_TypeName(const swig_type_info *ty) { return ty->name; } /* Return the pretty name associated with this type, that is an unmangled type name in a form presentable to the user. */ SWIGRUNTIME const char * SWIG_TypePrettyName(const swig_type_info *type) { /* The "str" field contains the equivalent pretty names of the type, separated by vertical-bar characters. We choose to print the last name, as it is often (?) the most specific. */ if (!type) return NULL; if (type->str != NULL) { const char *last_name = type->str; const char *s; for (s = type->str; *s; s++) if (*s == '|') last_name = s+1; return last_name; } else return type->name; } /* Set the clientdata field for a type */ SWIGRUNTIME void SWIG_TypeClientData(swig_type_info *ti, void *clientdata) { swig_cast_info *cast = ti->cast; /* if (ti->clientdata == clientdata) return; */ ti->clientdata = clientdata; while (cast) { if (!cast->converter) { swig_type_info *tc = cast->type; if (!tc->clientdata) { SWIG_TypeClientData(tc, clientdata); } } cast = cast->next; } } SWIGRUNTIME void SWIG_TypeNewClientData(swig_type_info *ti, void *clientdata) { SWIG_TypeClientData(ti, clientdata); ti->owndata = 1; } /* Search for a swig_type_info structure only by mangled name Search is a O(log #types) We start searching at module start, and finish searching when start == end. Note: if start == end at the beginning of the function, we go all the way around the circular list. */ SWIGRUNTIME swig_type_info * SWIG_MangledTypeQueryModule(swig_module_info *start, swig_module_info *end, const char *name) { swig_module_info *iter = start; do { if (iter->size) { register size_t l = 0; register size_t r = iter->size - 1; do { /* since l+r >= 0, we can (>> 1) instead (/ 2) */ register size_t i = (l + r) >> 1; const char *iname = iter->types[i]->name; if (iname) { register int compare = strcmp(name, iname); if (compare == 0) { return iter->types[i]; } else if (compare < 0) { if (i) { r = i - 1; } else { break; } } else if (compare > 0) { l = i + 1; } } else { break; /* should never happen */ } } while (l <= r); } iter = iter->next; } while (iter != end); return 0; } /* Search for a swig_type_info structure for either a mangled name or a human readable name. It first searches the mangled names of the types, which is a O(log #types) If a type is not found it then searches the human readable names, which is O(#types). We start searching at module start, and finish searching when start == end. Note: if start == end at the beginning of the function, we go all the way around the circular list. */ SWIGRUNTIME swig_type_info * SWIG_TypeQueryModule(swig_module_info *start, swig_module_info *end, const char *name) { /* STEP 1: Search the name field using binary search */ swig_type_info *ret = SWIG_MangledTypeQueryModule(start, end, name); if (ret) { return ret; } else { /* STEP 2: If the type hasn't been found, do a complete search of the str field (the human readable name) */ swig_module_info *iter = start; do { register size_t i = 0; for (; i < iter->size; ++i) { if (iter->types[i]->str && (SWIG_TypeEquiv(iter->types[i]->str, name))) return iter->types[i]; } iter = iter->next; } while (iter != end); } /* neither found a match */ return 0; } /* Pack binary data into a string */ SWIGRUNTIME char * SWIG_PackData(char *c, void *ptr, size_t sz) { static const char hex[17] = "0123456789abcdef"; register const unsigned char *u = (unsigned char *) ptr; register const unsigned char *eu = u + sz; for (; u != eu; ++u) { register unsigned char uu = *u; *(c++) = hex[(uu & 0xf0) >> 4]; *(c++) = hex[uu & 0xf]; } return c; } /* Unpack binary data from a string */ SWIGRUNTIME const char * SWIG_UnpackData(const char *c, void *ptr, size_t sz) { register unsigned char *u = (unsigned char *) ptr; register const unsigned char *eu = u + sz; for (; u != eu; ++u) { register char d = *(c++); register unsigned char uu; if ((d >= '0') && (d <= '9')) uu = ((d - '0') << 4); else if ((d >= 'a') && (d <= 'f')) uu = ((d - ('a'-10)) << 4); else return (char *) 0; d = *(c++); if ((d >= '0') && (d <= '9')) uu |= (d - '0'); else if ((d >= 'a') && (d <= 'f')) uu |= (d - ('a'-10)); else return (char *) 0; *u = uu; } return c; } /* Pack 'void *' into a string buffer. */ SWIGRUNTIME char * SWIG_PackVoidPtr(char *buff, void *ptr, const char *name, size_t bsz) { char *r = buff; if ((2*sizeof(void *) + 2) > bsz) return 0; *(r++) = '_'; r = SWIG_PackData(r,&ptr,sizeof(void *)); if (strlen(name) + 1 > (bsz - (r - buff))) return 0; strcpy(r,name); return buff; } SWIGRUNTIME const char * SWIG_UnpackVoidPtr(const char *c, void **ptr, const char *name) { if (*c != '_') { if (strcmp(c,"NULL") == 0) { *ptr = (void *) 0; return name; } else { return 0; } } return SWIG_UnpackData(++c,ptr,sizeof(void *)); } SWIGRUNTIME char * SWIG_PackDataName(char *buff, void *ptr, size_t sz, const char *name, size_t bsz) { char *r = buff; size_t lname = (name ? strlen(name) : 0); if ((2*sz + 2 + lname) > bsz) return 0; *(r++) = '_'; r = SWIG_PackData(r,ptr,sz); if (lname) { strncpy(r,name,lname+1); } else { *r = 0; } return buff; } SWIGRUNTIME const char * SWIG_UnpackDataName(const char *c, void *ptr, size_t sz, const char *name) { if (*c != '_') { if (strcmp(c,"NULL") == 0) { memset(ptr,0,sz); return name; } else { return 0; } } return SWIG_UnpackData(++c,ptr,sz); } #ifdef __cplusplus } #endif /* Errors in SWIG */ #define SWIG_UnknownError -1 #define SWIG_IOError -2 #define SWIG_RuntimeError -3 #define SWIG_IndexError -4 #define SWIG_TypeError -5 #define SWIG_DivisionByZero -6 #define SWIG_OverflowError -7 #define SWIG_SyntaxError -8 #define SWIG_ValueError -9 #define SWIG_SystemError -10 #define SWIG_AttributeError -11 #define SWIG_MemoryError -12 #define SWIG_NullReferenceError -13 /* Compatibility macros for Python 3 */ #if PY_VERSION_HEX >= 0x03000000 #define PyClass_Check(obj) PyObject_IsInstance(obj, (PyObject *)&PyType_Type) #define PyInt_Check(x) PyLong_Check(x) #define PyInt_AsLong(x) PyLong_AsLong(x) #define PyInt_FromLong(x) PyLong_FromLong(x) #define PyInt_FromSize_t(x) PyLong_FromSize_t(x) #define PyString_Check(name) PyBytes_Check(name) #define PyString_FromString(x) PyUnicode_FromString(x) #define PyString_Format(fmt, args) PyUnicode_Format(fmt, args) #define PyString_AsString(str) PyBytes_AsString(str) #define PyString_Size(str) PyBytes_Size(str) #define PyString_InternFromString(key) PyUnicode_InternFromString(key) #define Py_TPFLAGS_HAVE_CLASS Py_TPFLAGS_BASETYPE #define PyString_AS_STRING(x) PyUnicode_AS_STRING(x) #define _PyLong_FromSsize_t(x) PyLong_FromSsize_t(x) #endif #ifndef Py_TYPE # define Py_TYPE(op) ((op)->ob_type) #endif /* SWIG APIs for compatibility of both Python 2 & 3 */ #if PY_VERSION_HEX >= 0x03000000 # define SWIG_Python_str_FromFormat PyUnicode_FromFormat #else # define SWIG_Python_str_FromFormat PyString_FromFormat #endif /* Warning: This function will allocate a new string in Python 3, * so please call SWIG_Python_str_DelForPy3(x) to free the space. */ SWIGINTERN char* SWIG_Python_str_AsChar(PyObject *str) { #if PY_VERSION_HEX >= 0x03000000 char *cstr; char *newstr; Py_ssize_t len; str = PyUnicode_AsUTF8String(str); PyBytes_AsStringAndSize(str, &cstr, &len); newstr = (char *) malloc(len+1); memcpy(newstr, cstr, len+1); Py_XDECREF(str); return newstr; #else return PyString_AsString(str); #endif } #if PY_VERSION_HEX >= 0x03000000 # define SWIG_Python_str_DelForPy3(x) free( (void*) (x) ) #else # define SWIG_Python_str_DelForPy3(x) #endif SWIGINTERN PyObject* SWIG_Python_str_FromChar(const char *c) { #if PY_VERSION_HEX >= 0x03000000 return PyUnicode_FromString(c); #else return PyString_FromString(c); #endif } /* Add PyOS_snprintf for old Pythons */ #if PY_VERSION_HEX < 0x02020000 # if defined(_MSC_VER) || defined(__BORLANDC__) || defined(_WATCOM) # define PyOS_snprintf _snprintf # else # define PyOS_snprintf snprintf # endif #endif /* A crude PyString_FromFormat implementation for old Pythons */ #if PY_VERSION_HEX < 0x02020000 #ifndef SWIG_PYBUFFER_SIZE # define SWIG_PYBUFFER_SIZE 1024 #endif static PyObject * PyString_FromFormat(const char *fmt, ...) { va_list ap; char buf[SWIG_PYBUFFER_SIZE * 2]; int res; va_start(ap, fmt); res = vsnprintf(buf, sizeof(buf), fmt, ap); va_end(ap); return (res < 0 || res >= (int)sizeof(buf)) ? 0 : PyString_FromString(buf); } #endif /* Add PyObject_Del for old Pythons */ #if PY_VERSION_HEX < 0x01060000 # define PyObject_Del(op) PyMem_DEL((op)) #endif #ifndef PyObject_DEL # define PyObject_DEL PyObject_Del #endif /* A crude PyExc_StopIteration exception for old Pythons */ #if PY_VERSION_HEX < 0x02020000 # ifndef PyExc_StopIteration # define PyExc_StopIteration PyExc_RuntimeError # endif # ifndef PyObject_GenericGetAttr # define PyObject_GenericGetAttr 0 # endif #endif /* Py_NotImplemented is defined in 2.1 and up. */ #if PY_VERSION_HEX < 0x02010000 # ifndef Py_NotImplemented # define Py_NotImplemented PyExc_RuntimeError # endif #endif /* A crude PyString_AsStringAndSize implementation for old Pythons */ #if PY_VERSION_HEX < 0x02010000 # ifndef PyString_AsStringAndSize # define PyString_AsStringAndSize(obj, s, len) {*s = PyString_AsString(obj); *len = *s ? strlen(*s) : 0;} # endif #endif /* PySequence_Size for old Pythons */ #if PY_VERSION_HEX < 0x02000000 # ifndef PySequence_Size # define PySequence_Size PySequence_Length # endif #endif /* PyBool_FromLong for old Pythons */ #if PY_VERSION_HEX < 0x02030000 static PyObject *PyBool_FromLong(long ok) { PyObject *result = ok ? Py_True : Py_False; Py_INCREF(result); return result; } #endif /* Py_ssize_t for old Pythons */ /* This code is as recommended by: */ /* http://www.python.org/dev/peps/pep-0353/#conversion-guidelines */ #if PY_VERSION_HEX < 0x02050000 && !defined(PY_SSIZE_T_MIN) typedef int Py_ssize_t; # define PY_SSIZE_T_MAX INT_MAX # define PY_SSIZE_T_MIN INT_MIN typedef inquiry lenfunc; typedef intargfunc ssizeargfunc; typedef intintargfunc ssizessizeargfunc; typedef intobjargproc ssizeobjargproc; typedef intintobjargproc ssizessizeobjargproc; typedef getreadbufferproc readbufferproc; typedef getwritebufferproc writebufferproc; typedef getsegcountproc segcountproc; typedef getcharbufferproc charbufferproc; static long PyNumber_AsSsize_t (PyObject *x, void *SWIGUNUSEDPARM(exc)) { long result = 0; PyObject *i = PyNumber_Int(x); if (i) { result = PyInt_AsLong(i); Py_DECREF(i); } return result; } #endif #if PY_VERSION_HEX < 0x02050000 #define PyInt_FromSize_t(x) PyInt_FromLong((long)x) #endif #if PY_VERSION_HEX < 0x02040000 #define Py_VISIT(op) \ do { \ if (op) { \ int vret = visit((op), arg); \ if (vret) \ return vret; \ } \ } while (0) #endif #if PY_VERSION_HEX < 0x02030000 typedef struct { PyTypeObject type; PyNumberMethods as_number; PyMappingMethods as_mapping; PySequenceMethods as_sequence; PyBufferProcs as_buffer; PyObject *name, *slots; } PyHeapTypeObject; #endif #if PY_VERSION_HEX < 0x02030000 typedef destructor freefunc; #endif #if ((PY_MAJOR_VERSION == 2 && PY_MINOR_VERSION > 6) || \ (PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION > 0) || \ (PY_MAJOR_VERSION > 3)) # define SWIGPY_USE_CAPSULE # define SWIGPY_CAPSULE_NAME ((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION ".type_pointer_capsule" SWIG_TYPE_TABLE_NAME) #endif #if PY_VERSION_HEX < 0x03020000 #define PyDescr_TYPE(x) (((PyDescrObject *)(x))->d_type) #define PyDescr_NAME(x) (((PyDescrObject *)(x))->d_name) #endif /* ----------------------------------------------------------------------------- * error manipulation * ----------------------------------------------------------------------------- */ SWIGRUNTIME PyObject* SWIG_Python_ErrorType(int code) { PyObject* type = 0; switch(code) { case SWIG_MemoryError: type = PyExc_MemoryError; break; case SWIG_IOError: type = PyExc_IOError; break; case SWIG_RuntimeError: type = PyExc_RuntimeError; break; case SWIG_IndexError: type = PyExc_IndexError; break; case SWIG_TypeError: type = PyExc_TypeError; break; case SWIG_DivisionByZero: type = PyExc_ZeroDivisionError; break; case SWIG_OverflowError: type = PyExc_OverflowError; break; case SWIG_SyntaxError: type = PyExc_SyntaxError; break; case SWIG_ValueError: type = PyExc_ValueError; break; case SWIG_SystemError: type = PyExc_SystemError; break; case SWIG_AttributeError: type = PyExc_AttributeError; break; default: type = PyExc_RuntimeError; } return type; } SWIGRUNTIME void SWIG_Python_AddErrorMsg(const char* mesg) { PyObject *type = 0; PyObject *value = 0; PyObject *traceback = 0; if (PyErr_Occurred()) PyErr_Fetch(&type, &value, &traceback); if (value) { char *tmp; PyObject *old_str = PyObject_Str(value); PyErr_Clear(); Py_XINCREF(type); PyErr_Format(type, "%s %s", tmp = SWIG_Python_str_AsChar(old_str), mesg); SWIG_Python_str_DelForPy3(tmp); Py_DECREF(old_str); Py_DECREF(value); } else { PyErr_SetString(PyExc_RuntimeError, mesg); } } #if defined(SWIG_PYTHON_NO_THREADS) # if defined(SWIG_PYTHON_THREADS) # undef SWIG_PYTHON_THREADS # endif #endif #if defined(SWIG_PYTHON_THREADS) /* Threading support is enabled */ # if !defined(SWIG_PYTHON_USE_GIL) && !defined(SWIG_PYTHON_NO_USE_GIL) # if (PY_VERSION_HEX >= 0x02030000) /* For 2.3 or later, use the PyGILState calls */ # define SWIG_PYTHON_USE_GIL # endif # endif # if defined(SWIG_PYTHON_USE_GIL) /* Use PyGILState threads calls */ # ifndef SWIG_PYTHON_INITIALIZE_THREADS # define SWIG_PYTHON_INITIALIZE_THREADS PyEval_InitThreads() # endif # ifdef __cplusplus /* C++ code */ class SWIG_Python_Thread_Block { bool status; PyGILState_STATE state; public: void end() { if (status) { PyGILState_Release(state); status = false;} } SWIG_Python_Thread_Block() : status(true), state(PyGILState_Ensure()) {} ~SWIG_Python_Thread_Block() { end(); } }; class SWIG_Python_Thread_Allow { bool status; PyThreadState *save; public: void end() { if (status) { PyEval_RestoreThread(save); status = false; }} SWIG_Python_Thread_Allow() : status(true), save(PyEval_SaveThread()) {} ~SWIG_Python_Thread_Allow() { end(); } }; # define SWIG_PYTHON_THREAD_BEGIN_BLOCK SWIG_Python_Thread_Block _swig_thread_block # define SWIG_PYTHON_THREAD_END_BLOCK _swig_thread_block.end() # define SWIG_PYTHON_THREAD_BEGIN_ALLOW SWIG_Python_Thread_Allow _swig_thread_allow # define SWIG_PYTHON_THREAD_END_ALLOW _swig_thread_allow.end() # else /* C code */ # define SWIG_PYTHON_THREAD_BEGIN_BLOCK PyGILState_STATE _swig_thread_block = PyGILState_Ensure() # define SWIG_PYTHON_THREAD_END_BLOCK PyGILState_Release(_swig_thread_block) # define SWIG_PYTHON_THREAD_BEGIN_ALLOW PyThreadState *_swig_thread_allow = PyEval_SaveThread() # define SWIG_PYTHON_THREAD_END_ALLOW PyEval_RestoreThread(_swig_thread_allow) # endif # else /* Old thread way, not implemented, user must provide it */ # if !defined(SWIG_PYTHON_INITIALIZE_THREADS) # define SWIG_PYTHON_INITIALIZE_THREADS # endif # if !defined(SWIG_PYTHON_THREAD_BEGIN_BLOCK) # define SWIG_PYTHON_THREAD_BEGIN_BLOCK # endif # if !defined(SWIG_PYTHON_THREAD_END_BLOCK) # define SWIG_PYTHON_THREAD_END_BLOCK # endif # if !defined(SWIG_PYTHON_THREAD_BEGIN_ALLOW) # define SWIG_PYTHON_THREAD_BEGIN_ALLOW # endif # if !defined(SWIG_PYTHON_THREAD_END_ALLOW) # define SWIG_PYTHON_THREAD_END_ALLOW # endif # endif #else /* No thread support */ # define SWIG_PYTHON_INITIALIZE_THREADS # define SWIG_PYTHON_THREAD_BEGIN_BLOCK # define SWIG_PYTHON_THREAD_END_BLOCK # define SWIG_PYTHON_THREAD_BEGIN_ALLOW # define SWIG_PYTHON_THREAD_END_ALLOW #endif /* ----------------------------------------------------------------------------- * Python API portion that goes into the runtime * ----------------------------------------------------------------------------- */ #ifdef __cplusplus extern "C" { #endif /* ----------------------------------------------------------------------------- * Constant declarations * ----------------------------------------------------------------------------- */ /* Constant Types */ #define SWIG_PY_POINTER 4 #define SWIG_PY_BINARY 5 /* Constant information structure */ typedef struct swig_const_info { int type; char *name; long lvalue; double dvalue; void *pvalue; swig_type_info **ptype; } swig_const_info; /* ----------------------------------------------------------------------------- * Wrapper of PyInstanceMethod_New() used in Python 3 * It is exported to the generated module, used for -fastproxy * ----------------------------------------------------------------------------- */ #if PY_VERSION_HEX >= 0x03000000 SWIGRUNTIME PyObject* SWIG_PyInstanceMethod_New(PyObject *SWIGUNUSEDPARM(self), PyObject *func) { return PyInstanceMethod_New(func); } #else SWIGRUNTIME PyObject* SWIG_PyInstanceMethod_New(PyObject *SWIGUNUSEDPARM(self), PyObject *SWIGUNUSEDPARM(func)) { return NULL; } #endif #ifdef __cplusplus } #endif /* ----------------------------------------------------------------------------- * pyrun.swg * * This file contains the runtime support for Python modules * and includes code for managing global variables and pointer * type checking. * * ----------------------------------------------------------------------------- */ /* Common SWIG API */ /* for raw pointers */ #define SWIG_Python_ConvertPtr(obj, pptr, type, flags) SWIG_Python_ConvertPtrAndOwn(obj, pptr, type, flags, 0) #define SWIG_ConvertPtr(obj, pptr, type, flags) SWIG_Python_ConvertPtr(obj, pptr, type, flags) #define SWIG_ConvertPtrAndOwn(obj,pptr,type,flags,own) SWIG_Python_ConvertPtrAndOwn(obj, pptr, type, flags, own) #ifdef SWIGPYTHON_BUILTIN #define SWIG_NewPointerObj(ptr, type, flags) SWIG_Python_NewPointerObj(self, ptr, type, flags) #else #define SWIG_NewPointerObj(ptr, type, flags) SWIG_Python_NewPointerObj(NULL, ptr, type, flags) #endif #define SWIG_InternalNewPointerObj(ptr, type, flags) SWIG_Python_NewPointerObj(NULL, ptr, type, flags) #define SWIG_CheckImplicit(ty) SWIG_Python_CheckImplicit(ty) #define SWIG_AcquirePtr(ptr, src) SWIG_Python_AcquirePtr(ptr, src) #define swig_owntype int /* for raw packed data */ #define SWIG_ConvertPacked(obj, ptr, sz, ty) SWIG_Python_ConvertPacked(obj, ptr, sz, ty) #define SWIG_NewPackedObj(ptr, sz, type) SWIG_Python_NewPackedObj(ptr, sz, type) /* for class or struct pointers */ #define SWIG_ConvertInstance(obj, pptr, type, flags) SWIG_ConvertPtr(obj, pptr, type, flags) #define SWIG_NewInstanceObj(ptr, type, flags) SWIG_NewPointerObj(ptr, type, flags) /* for C or C++ function pointers */ #define SWIG_ConvertFunctionPtr(obj, pptr, type) SWIG_Python_ConvertFunctionPtr(obj, pptr, type) #define SWIG_NewFunctionPtrObj(ptr, type) SWIG_Python_NewPointerObj(NULL, ptr, type, 0) /* for C++ member pointers, ie, member methods */ #define SWIG_ConvertMember(obj, ptr, sz, ty) SWIG_Python_ConvertPacked(obj, ptr, sz, ty) #define SWIG_NewMemberObj(ptr, sz, type) SWIG_Python_NewPackedObj(ptr, sz, type) /* Runtime API */ #define SWIG_GetModule(clientdata) SWIG_Python_GetModule(clientdata) #define SWIG_SetModule(clientdata, pointer) SWIG_Python_SetModule(pointer) #define SWIG_NewClientData(obj) SwigPyClientData_New(obj) #define SWIG_SetErrorObj SWIG_Python_SetErrorObj #define SWIG_SetErrorMsg SWIG_Python_SetErrorMsg #define SWIG_ErrorType(code) SWIG_Python_ErrorType(code) #define SWIG_Error(code, msg) SWIG_Python_SetErrorMsg(SWIG_ErrorType(code), msg) #define SWIG_fail goto fail /* Runtime API implementation */ /* Error manipulation */ SWIGINTERN void SWIG_Python_SetErrorObj(PyObject *errtype, PyObject *obj) { SWIG_PYTHON_THREAD_BEGIN_BLOCK; PyErr_SetObject(errtype, obj); Py_DECREF(obj); SWIG_PYTHON_THREAD_END_BLOCK; } SWIGINTERN void SWIG_Python_SetErrorMsg(PyObject *errtype, const char *msg) { SWIG_PYTHON_THREAD_BEGIN_BLOCK; PyErr_SetString(errtype, msg); SWIG_PYTHON_THREAD_END_BLOCK; } #define SWIG_Python_Raise(obj, type, desc) SWIG_Python_SetErrorObj(SWIG_Python_ExceptionType(desc), obj) /* Set a constant value */ #if defined(SWIGPYTHON_BUILTIN) SWIGINTERN void SwigPyBuiltin_AddPublicSymbol(PyObject *seq, const char *key) { PyObject *s = PyString_InternFromString(key); PyList_Append(seq, s); Py_DECREF(s); } SWIGINTERN void SWIG_Python_SetConstant(PyObject *d, PyObject *public_interface, const char *name, PyObject *obj) { #if PY_VERSION_HEX < 0x02030000 PyDict_SetItemString(d, (char *)name, obj); #else PyDict_SetItemString(d, name, obj); #endif Py_DECREF(obj); if (public_interface) SwigPyBuiltin_AddPublicSymbol(public_interface, name); } #else SWIGINTERN void SWIG_Python_SetConstant(PyObject *d, const char *name, PyObject *obj) { #if PY_VERSION_HEX < 0x02030000 PyDict_SetItemString(d, (char *)name, obj); #else PyDict_SetItemString(d, name, obj); #endif Py_DECREF(obj); } #endif /* Append a value to the result obj */ SWIGINTERN PyObject* SWIG_Python_AppendOutput(PyObject* result, PyObject* obj) { #if !defined(SWIG_PYTHON_OUTPUT_TUPLE) if (!result) { result = obj; } else if (result == Py_None) { Py_DECREF(result); result = obj; } else { if (!PyList_Check(result)) { PyObject *o2 = result; result = PyList_New(1); PyList_SetItem(result, 0, o2); } PyList_Append(result,obj); Py_DECREF(obj); } return result; #else PyObject* o2; PyObject* o3; if (!result) { result = obj; } else if (result == Py_None) { Py_DECREF(result); result = obj; } else { if (!PyTuple_Check(result)) { o2 = result; result = PyTuple_New(1); PyTuple_SET_ITEM(result, 0, o2); } o3 = PyTuple_New(1); PyTuple_SET_ITEM(o3, 0, obj); o2 = result; result = PySequence_Concat(o2, o3); Py_DECREF(o2); Py_DECREF(o3); } return result; #endif } /* Unpack the argument tuple */ SWIGINTERN int SWIG_Python_UnpackTuple(PyObject *args, const char *name, Py_ssize_t min, Py_ssize_t max, PyObject **objs) { if (!args) { if (!min && !max) { return 1; } else { PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got none", name, (min == max ? "" : "at least "), (int)min); return 0; } } if (!PyTuple_Check(args)) { if (min <= 1 && max >= 1) { register int i; objs[0] = args; for (i = 1; i < max; ++i) { objs[i] = 0; } return 2; } PyErr_SetString(PyExc_SystemError, "UnpackTuple() argument list is not a tuple"); return 0; } else { register Py_ssize_t l = PyTuple_GET_SIZE(args); if (l < min) { PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got %d", name, (min == max ? "" : "at least "), (int)min, (int)l); return 0; } else if (l > max) { PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got %d", name, (min == max ? "" : "at most "), (int)max, (int)l); return 0; } else { register int i; for (i = 0; i < l; ++i) { objs[i] = PyTuple_GET_ITEM(args, i); } for (; l < max; ++l) { objs[l] = 0; } return i + 1; } } } /* A functor is a function object with one single object argument */ #if PY_VERSION_HEX >= 0x02020000 #define SWIG_Python_CallFunctor(functor, obj) PyObject_CallFunctionObjArgs(functor, obj, NULL); #else #define SWIG_Python_CallFunctor(functor, obj) PyObject_CallFunction(functor, "O", obj); #endif /* Helper for static pointer initialization for both C and C++ code, for example static PyObject *SWIG_STATIC_POINTER(MyVar) = NewSomething(...); */ #ifdef __cplusplus #define SWIG_STATIC_POINTER(var) var #else #define SWIG_STATIC_POINTER(var) var = 0; if (!var) var #endif /* ----------------------------------------------------------------------------- * Pointer declarations * ----------------------------------------------------------------------------- */ /* Flags for new pointer objects */ #define SWIG_POINTER_NOSHADOW (SWIG_POINTER_OWN << 1) #define SWIG_POINTER_NEW (SWIG_POINTER_NOSHADOW | SWIG_POINTER_OWN) #define SWIG_POINTER_IMPLICIT_CONV (SWIG_POINTER_DISOWN << 1) #define SWIG_BUILTIN_TP_INIT (SWIG_POINTER_OWN << 2) #define SWIG_BUILTIN_INIT (SWIG_BUILTIN_TP_INIT | SWIG_POINTER_OWN) #ifdef __cplusplus extern "C" { #endif /* How to access Py_None */ #if defined(_WIN32) || defined(__WIN32__) || defined(__CYGWIN__) # ifndef SWIG_PYTHON_NO_BUILD_NONE # ifndef SWIG_PYTHON_BUILD_NONE # define SWIG_PYTHON_BUILD_NONE # endif # endif #endif #ifdef SWIG_PYTHON_BUILD_NONE # ifdef Py_None # undef Py_None # define Py_None SWIG_Py_None() # endif SWIGRUNTIMEINLINE PyObject * _SWIG_Py_None(void) { PyObject *none = Py_BuildValue((char*)""); Py_DECREF(none); return none; } SWIGRUNTIME PyObject * SWIG_Py_None(void) { static PyObject *SWIG_STATIC_POINTER(none) = _SWIG_Py_None(); return none; } #endif /* The python void return value */ SWIGRUNTIMEINLINE PyObject * SWIG_Py_Void(void) { PyObject *none = Py_None; Py_INCREF(none); return none; } /* SwigPyClientData */ typedef struct { PyObject *klass; PyObject *newraw; PyObject *newargs; PyObject *destroy; int delargs; int implicitconv; PyTypeObject *pytype; } SwigPyClientData; SWIGRUNTIMEINLINE int SWIG_Python_CheckImplicit(swig_type_info *ty) { SwigPyClientData *data = (SwigPyClientData *)ty->clientdata; return data ? data->implicitconv : 0; } SWIGRUNTIMEINLINE PyObject * SWIG_Python_ExceptionType(swig_type_info *desc) { SwigPyClientData *data = desc ? (SwigPyClientData *) desc->clientdata : 0; PyObject *klass = data ? data->klass : 0; return (klass ? klass : PyExc_RuntimeError); } SWIGRUNTIME SwigPyClientData * SwigPyClientData_New(PyObject* obj) { if (!obj) { return 0; } else { SwigPyClientData *data = (SwigPyClientData *)malloc(sizeof(SwigPyClientData)); /* the klass element */ data->klass = obj; Py_INCREF(data->klass); /* the newraw method and newargs arguments used to create a new raw instance */ if (PyClass_Check(obj)) { data->newraw = 0; data->newargs = obj; Py_INCREF(obj); } else { #if (PY_VERSION_HEX < 0x02020000) data->newraw = 0; #else data->newraw = PyObject_GetAttrString(data->klass, (char *)"__new__"); #endif if (data->newraw) { Py_INCREF(data->newraw); data->newargs = PyTuple_New(1); PyTuple_SetItem(data->newargs, 0, obj); } else { data->newargs = obj; } Py_INCREF(data->newargs); } /* the destroy method, aka as the C++ delete method */ data->destroy = PyObject_GetAttrString(data->klass, (char *)"__swig_destroy__"); if (PyErr_Occurred()) { PyErr_Clear(); data->destroy = 0; } if (data->destroy) { int flags; Py_INCREF(data->destroy); flags = PyCFunction_GET_FLAGS(data->destroy); #ifdef METH_O data->delargs = !(flags & (METH_O)); #else data->delargs = 0; #endif } else { data->delargs = 0; } data->implicitconv = 0; data->pytype = 0; return data; } } SWIGRUNTIME void SwigPyClientData_Del(SwigPyClientData *data) { Py_XDECREF(data->newraw); Py_XDECREF(data->newargs); Py_XDECREF(data->destroy); } /* =============== SwigPyObject =====================*/ typedef struct { PyObject_HEAD void *ptr; swig_type_info *ty; int own; PyObject *next; #ifdef SWIGPYTHON_BUILTIN PyObject *dict; #endif } SwigPyObject; SWIGRUNTIME PyObject * SwigPyObject_long(SwigPyObject *v) { return PyLong_FromVoidPtr(v->ptr); } SWIGRUNTIME PyObject * SwigPyObject_format(const char* fmt, SwigPyObject *v) { PyObject *res = NULL; PyObject *args = PyTuple_New(1); if (args) { if (PyTuple_SetItem(args, 0, SwigPyObject_long(v)) == 0) { PyObject *ofmt = SWIG_Python_str_FromChar(fmt); if (ofmt) { #if PY_VERSION_HEX >= 0x03000000 res = PyUnicode_Format(ofmt,args); #else res = PyString_Format(ofmt,args); #endif Py_DECREF(ofmt); } Py_DECREF(args); } } return res; } SWIGRUNTIME PyObject * SwigPyObject_oct(SwigPyObject *v) { return SwigPyObject_format("%o",v); } SWIGRUNTIME PyObject * SwigPyObject_hex(SwigPyObject *v) { return SwigPyObject_format("%x",v); } SWIGRUNTIME PyObject * #ifdef METH_NOARGS SwigPyObject_repr(SwigPyObject *v) #else SwigPyObject_repr(SwigPyObject *v, PyObject *args) #endif { const char *name = SWIG_TypePrettyName(v->ty); PyObject *repr = SWIG_Python_str_FromFormat("", (name ? name : "unknown"), (void *)v); if (v->next) { # ifdef METH_NOARGS PyObject *nrep = SwigPyObject_repr((SwigPyObject *)v->next); # else PyObject *nrep = SwigPyObject_repr((SwigPyObject *)v->next, args); # endif # if PY_VERSION_HEX >= 0x03000000 PyObject *joined = PyUnicode_Concat(repr, nrep); Py_DecRef(repr); Py_DecRef(nrep); repr = joined; # else PyString_ConcatAndDel(&repr,nrep); # endif } return repr; } SWIGRUNTIME int SwigPyObject_compare(SwigPyObject *v, SwigPyObject *w) { void *i = v->ptr; void *j = w->ptr; return (i < j) ? -1 : ((i > j) ? 1 : 0); } /* Added for Python 3.x, would it also be useful for Python 2.x? */ SWIGRUNTIME PyObject* SwigPyObject_richcompare(SwigPyObject *v, SwigPyObject *w, int op) { PyObject* res; if( op != Py_EQ && op != Py_NE ) { Py_INCREF(Py_NotImplemented); return Py_NotImplemented; } res = PyBool_FromLong( (SwigPyObject_compare(v, w)==0) == (op == Py_EQ) ? 1 : 0); return res; } SWIGRUNTIME PyTypeObject* SwigPyObject_TypeOnce(void); #ifdef SWIGPYTHON_BUILTIN static swig_type_info *SwigPyObject_stype = 0; SWIGRUNTIME PyTypeObject* SwigPyObject_type(void) { SwigPyClientData *cd; assert(SwigPyObject_stype); cd = (SwigPyClientData*) SwigPyObject_stype->clientdata; assert(cd); assert(cd->pytype); return cd->pytype; } #else SWIGRUNTIME PyTypeObject* SwigPyObject_type(void) { static PyTypeObject *SWIG_STATIC_POINTER(type) = SwigPyObject_TypeOnce(); return type; } #endif SWIGRUNTIMEINLINE int SwigPyObject_Check(PyObject *op) { #ifdef SWIGPYTHON_BUILTIN PyTypeObject *target_tp = SwigPyObject_type(); if (PyType_IsSubtype(op->ob_type, target_tp)) return 1; return (strcmp(op->ob_type->tp_name, "SwigPyObject") == 0); #else return (Py_TYPE(op) == SwigPyObject_type()) || (strcmp(Py_TYPE(op)->tp_name,"SwigPyObject") == 0); #endif } SWIGRUNTIME PyObject * SwigPyObject_New(void *ptr, swig_type_info *ty, int own); SWIGRUNTIME void SwigPyObject_dealloc(PyObject *v) { SwigPyObject *sobj = (SwigPyObject *) v; PyObject *next = sobj->next; if (sobj->own == SWIG_POINTER_OWN) { swig_type_info *ty = sobj->ty; SwigPyClientData *data = ty ? (SwigPyClientData *) ty->clientdata : 0; PyObject *destroy = data ? data->destroy : 0; if (destroy) { /* destroy is always a VARARGS method */ PyObject *res; if (data->delargs) { /* we need to create a temporary object to carry the destroy operation */ PyObject *tmp = SwigPyObject_New(sobj->ptr, ty, 0); res = SWIG_Python_CallFunctor(destroy, tmp); Py_DECREF(tmp); } else { PyCFunction meth = PyCFunction_GET_FUNCTION(destroy); PyObject *mself = PyCFunction_GET_SELF(destroy); res = ((*meth)(mself, v)); } Py_XDECREF(res); } #if !defined(SWIG_PYTHON_SILENT_MEMLEAK) else { const char *name = SWIG_TypePrettyName(ty); printf("swig/python detected a memory leak of type '%s', no destructor found.\n", (name ? name : "unknown")); } #endif } Py_XDECREF(next); PyObject_DEL(v); } SWIGRUNTIME PyObject* SwigPyObject_append(PyObject* v, PyObject* next) { SwigPyObject *sobj = (SwigPyObject *) v; #ifndef METH_O PyObject *tmp = 0; if (!PyArg_ParseTuple(next,(char *)"O:append", &tmp)) return NULL; next = tmp; #endif if (!SwigPyObject_Check(next)) { return NULL; } sobj->next = next; Py_INCREF(next); return SWIG_Py_Void(); } SWIGRUNTIME PyObject* #ifdef METH_NOARGS SwigPyObject_next(PyObject* v) #else SwigPyObject_next(PyObject* v, PyObject *SWIGUNUSEDPARM(args)) #endif { SwigPyObject *sobj = (SwigPyObject *) v; if (sobj->next) { Py_INCREF(sobj->next); return sobj->next; } else { return SWIG_Py_Void(); } } SWIGINTERN PyObject* #ifdef METH_NOARGS SwigPyObject_disown(PyObject *v) #else SwigPyObject_disown(PyObject* v, PyObject *SWIGUNUSEDPARM(args)) #endif { SwigPyObject *sobj = (SwigPyObject *)v; sobj->own = 0; return SWIG_Py_Void(); } SWIGINTERN PyObject* #ifdef METH_NOARGS SwigPyObject_acquire(PyObject *v) #else SwigPyObject_acquire(PyObject* v, PyObject *SWIGUNUSEDPARM(args)) #endif { SwigPyObject *sobj = (SwigPyObject *)v; sobj->own = SWIG_POINTER_OWN; return SWIG_Py_Void(); } SWIGINTERN PyObject* SwigPyObject_own(PyObject *v, PyObject *args) { PyObject *val = 0; #if (PY_VERSION_HEX < 0x02020000) if (!PyArg_ParseTuple(args,(char *)"|O:own",&val)) #elif (PY_VERSION_HEX < 0x02050000) if (!PyArg_UnpackTuple(args, (char *)"own", 0, 1, &val)) #else if (!PyArg_UnpackTuple(args, "own", 0, 1, &val)) #endif { return NULL; } else { SwigPyObject *sobj = (SwigPyObject *)v; PyObject *obj = PyBool_FromLong(sobj->own); if (val) { #ifdef METH_NOARGS if (PyObject_IsTrue(val)) { SwigPyObject_acquire(v); } else { SwigPyObject_disown(v); } #else if (PyObject_IsTrue(val)) { SwigPyObject_acquire(v,args); } else { SwigPyObject_disown(v,args); } #endif } return obj; } } #ifdef METH_O static PyMethodDef swigobject_methods[] = { {(char *)"disown", (PyCFunction)SwigPyObject_disown, METH_NOARGS, (char *)"releases ownership of the pointer"}, {(char *)"acquire", (PyCFunction)SwigPyObject_acquire, METH_NOARGS, (char *)"acquires ownership of the pointer"}, {(char *)"own", (PyCFunction)SwigPyObject_own, METH_VARARGS, (char *)"returns/sets ownership of the pointer"}, {(char *)"append", (PyCFunction)SwigPyObject_append, METH_O, (char *)"appends another 'this' object"}, {(char *)"next", (PyCFunction)SwigPyObject_next, METH_NOARGS, (char *)"returns the next 'this' object"}, {(char *)"__repr__",(PyCFunction)SwigPyObject_repr, METH_NOARGS, (char *)"returns object representation"}, {0, 0, 0, 0} }; #else static PyMethodDef swigobject_methods[] = { {(char *)"disown", (PyCFunction)SwigPyObject_disown, METH_VARARGS, (char *)"releases ownership of the pointer"}, {(char *)"acquire", (PyCFunction)SwigPyObject_acquire, METH_VARARGS, (char *)"aquires ownership of the pointer"}, {(char *)"own", (PyCFunction)SwigPyObject_own, METH_VARARGS, (char *)"returns/sets ownership of the pointer"}, {(char *)"append", (PyCFunction)SwigPyObject_append, METH_VARARGS, (char *)"appends another 'this' object"}, {(char *)"next", (PyCFunction)SwigPyObject_next, METH_VARARGS, (char *)"returns the next 'this' object"}, {(char *)"__repr__",(PyCFunction)SwigPyObject_repr, METH_VARARGS, (char *)"returns object representation"}, {0, 0, 0, 0} }; #endif #if PY_VERSION_HEX < 0x02020000 SWIGINTERN PyObject * SwigPyObject_getattr(SwigPyObject *sobj,char *name) { return Py_FindMethod(swigobject_methods, (PyObject *)sobj, name); } #endif SWIGRUNTIME PyTypeObject* SwigPyObject_TypeOnce(void) { static char swigobject_doc[] = "Swig object carries a C/C++ instance pointer"; static PyNumberMethods SwigPyObject_as_number = { (binaryfunc)0, /*nb_add*/ (binaryfunc)0, /*nb_subtract*/ (binaryfunc)0, /*nb_multiply*/ /* nb_divide removed in Python 3 */ #if PY_VERSION_HEX < 0x03000000 (binaryfunc)0, /*nb_divide*/ #endif (binaryfunc)0, /*nb_remainder*/ (binaryfunc)0, /*nb_divmod*/ (ternaryfunc)0,/*nb_power*/ (unaryfunc)0, /*nb_negative*/ (unaryfunc)0, /*nb_positive*/ (unaryfunc)0, /*nb_absolute*/ (inquiry)0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_VERSION_HEX < 0x03000000 0, /*nb_coerce*/ #endif (unaryfunc)SwigPyObject_long, /*nb_int*/ #if PY_VERSION_HEX < 0x03000000 (unaryfunc)SwigPyObject_long, /*nb_long*/ #else 0, /*nb_reserved*/ #endif (unaryfunc)0, /*nb_float*/ #if PY_VERSION_HEX < 0x03000000 (unaryfunc)SwigPyObject_oct, /*nb_oct*/ (unaryfunc)SwigPyObject_hex, /*nb_hex*/ #endif #if PY_VERSION_HEX >= 0x03000000 /* 3.0 */ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_index, nb_inplace_divide removed */ #elif PY_VERSION_HEX >= 0x02050000 /* 2.5.0 */ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_index */ #elif PY_VERSION_HEX >= 0x02020000 /* 2.2.0 */ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_inplace_true_divide */ #elif PY_VERSION_HEX >= 0x02000000 /* 2.0.0 */ 0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_inplace_or */ #endif }; static PyTypeObject swigpyobject_type; static int type_init = 0; if (!type_init) { const PyTypeObject tmp = { /* PyObject header changed in Python 3 */ #if PY_VERSION_HEX >= 0x03000000 PyVarObject_HEAD_INIT(NULL, 0) #else PyObject_HEAD_INIT(NULL) 0, /* ob_size */ #endif (char *)"SwigPyObject", /* tp_name */ sizeof(SwigPyObject), /* tp_basicsize */ 0, /* tp_itemsize */ (destructor)SwigPyObject_dealloc, /* tp_dealloc */ 0, /* tp_print */ #if PY_VERSION_HEX < 0x02020000 (getattrfunc)SwigPyObject_getattr, /* tp_getattr */ #else (getattrfunc)0, /* tp_getattr */ #endif (setattrfunc)0, /* tp_setattr */ #if PY_VERSION_HEX >= 0x03000000 0, /* tp_reserved in 3.0.1, tp_compare in 3.0.0 but not used */ #else (cmpfunc)SwigPyObject_compare, /* tp_compare */ #endif (reprfunc)SwigPyObject_repr, /* tp_repr */ &SwigPyObject_as_number, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ (hashfunc)0, /* tp_hash */ (ternaryfunc)0, /* tp_call */ 0, /* tp_str */ PyObject_GenericGetAttr, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ Py_TPFLAGS_DEFAULT, /* tp_flags */ swigobject_doc, /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ (richcmpfunc)SwigPyObject_richcompare,/* tp_richcompare */ 0, /* tp_weaklistoffset */ #if PY_VERSION_HEX >= 0x02020000 0, /* tp_iter */ 0, /* tp_iternext */ swigobject_methods, /* tp_methods */ 0, /* tp_members */ 0, /* tp_getset */ 0, /* tp_base */ 0, /* tp_dict */ 0, /* tp_descr_get */ 0, /* tp_descr_set */ 0, /* tp_dictoffset */ 0, /* tp_init */ 0, /* tp_alloc */ 0, /* tp_new */ 0, /* tp_free */ 0, /* tp_is_gc */ 0, /* tp_bases */ 0, /* tp_mro */ 0, /* tp_cache */ 0, /* tp_subclasses */ 0, /* tp_weaklist */ #endif #if PY_VERSION_HEX >= 0x02030000 0, /* tp_del */ #endif #if PY_VERSION_HEX >= 0x02060000 0, /* tp_version */ #endif #ifdef COUNT_ALLOCS 0,0,0,0 /* tp_alloc -> tp_next */ #endif }; swigpyobject_type = tmp; type_init = 1; #if PY_VERSION_HEX < 0x02020000 swigpyobject_type.ob_type = &PyType_Type; #else if (PyType_Ready(&swigpyobject_type) < 0) return NULL; #endif } return &swigpyobject_type; } SWIGRUNTIME PyObject * SwigPyObject_New(void *ptr, swig_type_info *ty, int own) { SwigPyObject *sobj = PyObject_NEW(SwigPyObject, SwigPyObject_type()); if (sobj) { sobj->ptr = ptr; sobj->ty = ty; sobj->own = own; sobj->next = 0; } return (PyObject *)sobj; } /* ----------------------------------------------------------------------------- * Implements a simple Swig Packed type, and use it instead of string * ----------------------------------------------------------------------------- */ typedef struct { PyObject_HEAD void *pack; swig_type_info *ty; size_t size; } SwigPyPacked; SWIGRUNTIME int SwigPyPacked_print(SwigPyPacked *v, FILE *fp, int SWIGUNUSEDPARM(flags)) { char result[SWIG_BUFFER_SIZE]; fputs("pack, v->size, 0, sizeof(result))) { fputs("at ", fp); fputs(result, fp); } fputs(v->ty->name,fp); fputs(">", fp); return 0; } SWIGRUNTIME PyObject * SwigPyPacked_repr(SwigPyPacked *v) { char result[SWIG_BUFFER_SIZE]; if (SWIG_PackDataName(result, v->pack, v->size, 0, sizeof(result))) { return SWIG_Python_str_FromFormat("", result, v->ty->name); } else { return SWIG_Python_str_FromFormat("", v->ty->name); } } SWIGRUNTIME PyObject * SwigPyPacked_str(SwigPyPacked *v) { char result[SWIG_BUFFER_SIZE]; if (SWIG_PackDataName(result, v->pack, v->size, 0, sizeof(result))){ return SWIG_Python_str_FromFormat("%s%s", result, v->ty->name); } else { return SWIG_Python_str_FromChar(v->ty->name); } } SWIGRUNTIME int SwigPyPacked_compare(SwigPyPacked *v, SwigPyPacked *w) { size_t i = v->size; size_t j = w->size; int s = (i < j) ? -1 : ((i > j) ? 1 : 0); return s ? s : strncmp((char *)v->pack, (char *)w->pack, 2*v->size); } SWIGRUNTIME PyTypeObject* SwigPyPacked_TypeOnce(void); SWIGRUNTIME PyTypeObject* SwigPyPacked_type(void) { static PyTypeObject *SWIG_STATIC_POINTER(type) = SwigPyPacked_TypeOnce(); return type; } SWIGRUNTIMEINLINE int SwigPyPacked_Check(PyObject *op) { return ((op)->ob_type == SwigPyPacked_TypeOnce()) || (strcmp((op)->ob_type->tp_name,"SwigPyPacked") == 0); } SWIGRUNTIME void SwigPyPacked_dealloc(PyObject *v) { if (SwigPyPacked_Check(v)) { SwigPyPacked *sobj = (SwigPyPacked *) v; free(sobj->pack); } PyObject_DEL(v); } SWIGRUNTIME PyTypeObject* SwigPyPacked_TypeOnce(void) { static char swigpacked_doc[] = "Swig object carries a C/C++ instance pointer"; static PyTypeObject swigpypacked_type; static int type_init = 0; if (!type_init) { const PyTypeObject tmp = { /* PyObject header changed in Python 3 */ #if PY_VERSION_HEX>=0x03000000 PyVarObject_HEAD_INIT(NULL, 0) #else PyObject_HEAD_INIT(NULL) 0, /* ob_size */ #endif (char *)"SwigPyPacked", /* tp_name */ sizeof(SwigPyPacked), /* tp_basicsize */ 0, /* tp_itemsize */ (destructor)SwigPyPacked_dealloc, /* tp_dealloc */ (printfunc)SwigPyPacked_print, /* tp_print */ (getattrfunc)0, /* tp_getattr */ (setattrfunc)0, /* tp_setattr */ #if PY_VERSION_HEX>=0x03000000 0, /* tp_reserved in 3.0.1 */ #else (cmpfunc)SwigPyPacked_compare, /* tp_compare */ #endif (reprfunc)SwigPyPacked_repr, /* tp_repr */ 0, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ (hashfunc)0, /* tp_hash */ (ternaryfunc)0, /* tp_call */ (reprfunc)SwigPyPacked_str, /* tp_str */ PyObject_GenericGetAttr, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ Py_TPFLAGS_DEFAULT, /* tp_flags */ swigpacked_doc, /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ 0, /* tp_richcompare */ 0, /* tp_weaklistoffset */ #if PY_VERSION_HEX >= 0x02020000 0, /* tp_iter */ 0, /* tp_iternext */ 0, /* tp_methods */ 0, /* tp_members */ 0, /* tp_getset */ 0, /* tp_base */ 0, /* tp_dict */ 0, /* tp_descr_get */ 0, /* tp_descr_set */ 0, /* tp_dictoffset */ 0, /* tp_init */ 0, /* tp_alloc */ 0, /* tp_new */ 0, /* tp_free */ 0, /* tp_is_gc */ 0, /* tp_bases */ 0, /* tp_mro */ 0, /* tp_cache */ 0, /* tp_subclasses */ 0, /* tp_weaklist */ #endif #if PY_VERSION_HEX >= 0x02030000 0, /* tp_del */ #endif #if PY_VERSION_HEX >= 0x02060000 0, /* tp_version */ #endif #ifdef COUNT_ALLOCS 0,0,0,0 /* tp_alloc -> tp_next */ #endif }; swigpypacked_type = tmp; type_init = 1; #if PY_VERSION_HEX < 0x02020000 swigpypacked_type.ob_type = &PyType_Type; #else if (PyType_Ready(&swigpypacked_type) < 0) return NULL; #endif } return &swigpypacked_type; } SWIGRUNTIME PyObject * SwigPyPacked_New(void *ptr, size_t size, swig_type_info *ty) { SwigPyPacked *sobj = PyObject_NEW(SwigPyPacked, SwigPyPacked_type()); if (sobj) { void *pack = malloc(size); if (pack) { memcpy(pack, ptr, size); sobj->pack = pack; sobj->ty = ty; sobj->size = size; } else { PyObject_DEL((PyObject *) sobj); sobj = 0; } } return (PyObject *) sobj; } SWIGRUNTIME swig_type_info * SwigPyPacked_UnpackData(PyObject *obj, void *ptr, size_t size) { if (SwigPyPacked_Check(obj)) { SwigPyPacked *sobj = (SwigPyPacked *)obj; if (sobj->size != size) return 0; memcpy(ptr, sobj->pack, size); return sobj->ty; } else { return 0; } } /* ----------------------------------------------------------------------------- * pointers/data manipulation * ----------------------------------------------------------------------------- */ SWIGRUNTIMEINLINE PyObject * _SWIG_This(void) { return SWIG_Python_str_FromChar("this"); } static PyObject *swig_this = NULL; SWIGRUNTIME PyObject * SWIG_This(void) { if (swig_this == NULL) swig_this = _SWIG_This(); return swig_this; } /* #define SWIG_PYTHON_SLOW_GETSET_THIS */ /* TODO: I don't know how to implement the fast getset in Python 3 right now */ #if PY_VERSION_HEX>=0x03000000 #define SWIG_PYTHON_SLOW_GETSET_THIS #endif SWIGRUNTIME SwigPyObject * SWIG_Python_GetSwigThis(PyObject *pyobj) { PyObject *obj; if (SwigPyObject_Check(pyobj)) return (SwigPyObject *) pyobj; #ifdef SWIGPYTHON_BUILTIN (void)obj; # ifdef PyWeakref_CheckProxy if (PyWeakref_CheckProxy(pyobj)) { pyobj = PyWeakref_GET_OBJECT(pyobj); if (pyobj && SwigPyObject_Check(pyobj)) return (SwigPyObject*) pyobj; } # endif return NULL; #else obj = 0; #if (!defined(SWIG_PYTHON_SLOW_GETSET_THIS) && (PY_VERSION_HEX >= 0x02030000)) if (PyInstance_Check(pyobj)) { obj = _PyInstance_Lookup(pyobj, SWIG_This()); } else { PyObject **dictptr = _PyObject_GetDictPtr(pyobj); if (dictptr != NULL) { PyObject *dict = *dictptr; obj = dict ? PyDict_GetItem(dict, SWIG_This()) : 0; } else { #ifdef PyWeakref_CheckProxy if (PyWeakref_CheckProxy(pyobj)) { PyObject *wobj = PyWeakref_GET_OBJECT(pyobj); return wobj ? SWIG_Python_GetSwigThis(wobj) : 0; } #endif obj = PyObject_GetAttr(pyobj,SWIG_This()); if (obj) { Py_DECREF(obj); } else { if (PyErr_Occurred()) PyErr_Clear(); return 0; } } } #else obj = PyObject_GetAttr(pyobj,SWIG_This()); if (obj) { Py_DECREF(obj); } else { if (PyErr_Occurred()) PyErr_Clear(); return 0; } #endif if (obj && !SwigPyObject_Check(obj)) { /* a PyObject is called 'this', try to get the 'real this' SwigPyObject from it */ return SWIG_Python_GetSwigThis(obj); } return (SwigPyObject *)obj; #endif } /* Acquire a pointer value */ SWIGRUNTIME int SWIG_Python_AcquirePtr(PyObject *obj, int own) { if (own == SWIG_POINTER_OWN) { SwigPyObject *sobj = SWIG_Python_GetSwigThis(obj); if (sobj) { int oldown = sobj->own; sobj->own = own; return oldown; } } return 0; } /* Convert a pointer value */ SWIGRUNTIME int SWIG_Python_ConvertPtrAndOwn(PyObject *obj, void **ptr, swig_type_info *ty, int flags, int *own) { int res; SwigPyObject *sobj; int implicit_conv = (flags & SWIG_POINTER_IMPLICIT_CONV) != 0; if (!obj) return SWIG_ERROR; if (obj == Py_None && !implicit_conv) { if (ptr) *ptr = 0; return SWIG_OK; } res = SWIG_ERROR; sobj = SWIG_Python_GetSwigThis(obj); if (own) *own = 0; while (sobj) { void *vptr = sobj->ptr; if (ty) { swig_type_info *to = sobj->ty; if (to == ty) { /* no type cast needed */ if (ptr) *ptr = vptr; break; } else { swig_cast_info *tc = SWIG_TypeCheck(to->name,ty); if (!tc) { sobj = (SwigPyObject *)sobj->next; } else { if (ptr) { int newmemory = 0; *ptr = SWIG_TypeCast(tc,vptr,&newmemory); if (newmemory == SWIG_CAST_NEW_MEMORY) { assert(own); /* badly formed typemap which will lead to a memory leak - it must set and use own to delete *ptr */ if (own) *own = *own | SWIG_CAST_NEW_MEMORY; } } break; } } } else { if (ptr) *ptr = vptr; break; } } if (sobj) { if (own) *own = *own | sobj->own; if (flags & SWIG_POINTER_DISOWN) { sobj->own = 0; } res = SWIG_OK; } else { if (implicit_conv) { SwigPyClientData *data = ty ? (SwigPyClientData *) ty->clientdata : 0; if (data && !data->implicitconv) { PyObject *klass = data->klass; if (klass) { PyObject *impconv; data->implicitconv = 1; /* avoid recursion and call 'explicit' constructors*/ impconv = SWIG_Python_CallFunctor(klass, obj); data->implicitconv = 0; if (PyErr_Occurred()) { PyErr_Clear(); impconv = 0; } if (impconv) { SwigPyObject *iobj = SWIG_Python_GetSwigThis(impconv); if (iobj) { void *vptr; res = SWIG_Python_ConvertPtrAndOwn((PyObject*)iobj, &vptr, ty, 0, 0); if (SWIG_IsOK(res)) { if (ptr) { *ptr = vptr; /* transfer the ownership to 'ptr' */ iobj->own = 0; res = SWIG_AddCast(res); res = SWIG_AddNewMask(res); } else { res = SWIG_AddCast(res); } } } Py_DECREF(impconv); } } } } if (!SWIG_IsOK(res) && obj == Py_None) { if (ptr) *ptr = 0; if (PyErr_Occurred()) PyErr_Clear(); res = SWIG_OK; } } return res; } /* Convert a function ptr value */ SWIGRUNTIME int SWIG_Python_ConvertFunctionPtr(PyObject *obj, void **ptr, swig_type_info *ty) { if (!PyCFunction_Check(obj)) { return SWIG_ConvertPtr(obj, ptr, ty, 0); } else { void *vptr = 0; /* here we get the method pointer for callbacks */ const char *doc = (((PyCFunctionObject *)obj) -> m_ml -> ml_doc); const char *desc = doc ? strstr(doc, "swig_ptr: ") : 0; if (desc) desc = ty ? SWIG_UnpackVoidPtr(desc + 10, &vptr, ty->name) : 0; if (!desc) return SWIG_ERROR; if (ty) { swig_cast_info *tc = SWIG_TypeCheck(desc,ty); if (tc) { int newmemory = 0; *ptr = SWIG_TypeCast(tc,vptr,&newmemory); assert(!newmemory); /* newmemory handling not yet implemented */ } else { return SWIG_ERROR; } } else { *ptr = vptr; } return SWIG_OK; } } /* Convert a packed value value */ SWIGRUNTIME int SWIG_Python_ConvertPacked(PyObject *obj, void *ptr, size_t sz, swig_type_info *ty) { swig_type_info *to = SwigPyPacked_UnpackData(obj, ptr, sz); if (!to) return SWIG_ERROR; if (ty) { if (to != ty) { /* check type cast? */ swig_cast_info *tc = SWIG_TypeCheck(to->name,ty); if (!tc) return SWIG_ERROR; } } return SWIG_OK; } /* ----------------------------------------------------------------------------- * Create a new pointer object * ----------------------------------------------------------------------------- */ /* Create a new instance object, without calling __init__, and set the 'this' attribute. */ SWIGRUNTIME PyObject* SWIG_Python_NewShadowInstance(SwigPyClientData *data, PyObject *swig_this) { #if (PY_VERSION_HEX >= 0x02020000) PyObject *inst = 0; PyObject *newraw = data->newraw; if (newraw) { inst = PyObject_Call(newraw, data->newargs, NULL); if (inst) { #if !defined(SWIG_PYTHON_SLOW_GETSET_THIS) PyObject **dictptr = _PyObject_GetDictPtr(inst); if (dictptr != NULL) { PyObject *dict = *dictptr; if (dict == NULL) { dict = PyDict_New(); *dictptr = dict; PyDict_SetItem(dict, SWIG_This(), swig_this); } } #else PyObject *key = SWIG_This(); PyObject_SetAttr(inst, key, swig_this); #endif } } else { #if PY_VERSION_HEX >= 0x03000000 inst = PyBaseObject_Type.tp_new((PyTypeObject*) data->newargs, Py_None, Py_None); if (inst) { PyObject_SetAttr(inst, SWIG_This(), swig_this); Py_TYPE(inst)->tp_flags &= ~Py_TPFLAGS_VALID_VERSION_TAG; } #else PyObject *dict = PyDict_New(); if (dict) { PyDict_SetItem(dict, SWIG_This(), swig_this); inst = PyInstance_NewRaw(data->newargs, dict); Py_DECREF(dict); } #endif } return inst; #else #if (PY_VERSION_HEX >= 0x02010000) PyObject *inst = 0; PyObject *dict = PyDict_New(); if (dict) { PyDict_SetItem(dict, SWIG_This(), swig_this); inst = PyInstance_NewRaw(data->newargs, dict); Py_DECREF(dict); } return (PyObject *) inst; #else PyInstanceObject *inst = PyObject_NEW(PyInstanceObject, &PyInstance_Type); if (inst == NULL) { return NULL; } inst->in_class = (PyClassObject *)data->newargs; Py_INCREF(inst->in_class); inst->in_dict = PyDict_New(); if (inst->in_dict == NULL) { Py_DECREF(inst); return NULL; } #ifdef Py_TPFLAGS_HAVE_WEAKREFS inst->in_weakreflist = NULL; #endif #ifdef Py_TPFLAGS_GC PyObject_GC_Init(inst); #endif PyDict_SetItem(inst->in_dict, SWIG_This(), swig_this); return (PyObject *) inst; #endif #endif } SWIGRUNTIME void SWIG_Python_SetSwigThis(PyObject *inst, PyObject *swig_this) { PyObject *dict; #if (PY_VERSION_HEX >= 0x02020000) && !defined(SWIG_PYTHON_SLOW_GETSET_THIS) PyObject **dictptr = _PyObject_GetDictPtr(inst); if (dictptr != NULL) { dict = *dictptr; if (dict == NULL) { dict = PyDict_New(); *dictptr = dict; } PyDict_SetItem(dict, SWIG_This(), swig_this); return; } #endif dict = PyObject_GetAttrString(inst, (char*)"__dict__"); PyDict_SetItem(dict, SWIG_This(), swig_this); Py_DECREF(dict); } SWIGINTERN PyObject * SWIG_Python_InitShadowInstance(PyObject *args) { PyObject *obj[2]; if (!SWIG_Python_UnpackTuple(args, "swiginit", 2, 2, obj)) { return NULL; } else { SwigPyObject *sthis = SWIG_Python_GetSwigThis(obj[0]); if (sthis) { SwigPyObject_append((PyObject*) sthis, obj[1]); } else { SWIG_Python_SetSwigThis(obj[0], obj[1]); } return SWIG_Py_Void(); } } /* Create a new pointer object */ SWIGRUNTIME PyObject * SWIG_Python_NewPointerObj(PyObject *self, void *ptr, swig_type_info *type, int flags) { SwigPyClientData *clientdata; PyObject * robj; int own; if (!ptr) return SWIG_Py_Void(); clientdata = type ? (SwigPyClientData *)(type->clientdata) : 0; own = (flags & SWIG_POINTER_OWN) ? SWIG_POINTER_OWN : 0; if (clientdata && clientdata->pytype) { SwigPyObject *newobj; if (flags & SWIG_BUILTIN_TP_INIT) { newobj = (SwigPyObject*) self; if (newobj->ptr) { PyObject *next_self = clientdata->pytype->tp_alloc(clientdata->pytype, 0); while (newobj->next) newobj = (SwigPyObject *) newobj->next; newobj->next = next_self; newobj = (SwigPyObject *)next_self; } } else { newobj = PyObject_New(SwigPyObject, clientdata->pytype); } if (newobj) { newobj->ptr = ptr; newobj->ty = type; newobj->own = own; newobj->next = 0; #ifdef SWIGPYTHON_BUILTIN newobj->dict = 0; #endif return (PyObject*) newobj; } return SWIG_Py_Void(); } assert(!(flags & SWIG_BUILTIN_TP_INIT)); robj = SwigPyObject_New(ptr, type, own); if (robj && clientdata && !(flags & SWIG_POINTER_NOSHADOW)) { PyObject *inst = SWIG_Python_NewShadowInstance(clientdata, robj); Py_DECREF(robj); robj = inst; } return robj; } /* Create a new packed object */ SWIGRUNTIMEINLINE PyObject * SWIG_Python_NewPackedObj(void *ptr, size_t sz, swig_type_info *type) { return ptr ? SwigPyPacked_New((void *) ptr, sz, type) : SWIG_Py_Void(); } /* -----------------------------------------------------------------------------* * Get type list * -----------------------------------------------------------------------------*/ #ifdef SWIG_LINK_RUNTIME void *SWIG_ReturnGlobalTypeList(void *); #endif SWIGRUNTIME swig_module_info * SWIG_Python_GetModule(void *SWIGUNUSEDPARM(clientdata)) { static void *type_pointer = (void *)0; /* first check if module already created */ if (!type_pointer) { #ifdef SWIG_LINK_RUNTIME type_pointer = SWIG_ReturnGlobalTypeList((void *)0); #else # ifdef SWIGPY_USE_CAPSULE type_pointer = PyCapsule_Import(SWIGPY_CAPSULE_NAME, 0); # else type_pointer = PyCObject_Import((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION, (char*)"type_pointer" SWIG_TYPE_TABLE_NAME); # endif if (PyErr_Occurred()) { PyErr_Clear(); type_pointer = (void *)0; } #endif } return (swig_module_info *) type_pointer; } #if PY_MAJOR_VERSION < 2 /* PyModule_AddObject function was introduced in Python 2.0. The following function is copied out of Python/modsupport.c in python version 2.3.4 */ SWIGINTERN int PyModule_AddObject(PyObject *m, char *name, PyObject *o) { PyObject *dict; if (!PyModule_Check(m)) { PyErr_SetString(PyExc_TypeError, "PyModule_AddObject() needs module as first arg"); return SWIG_ERROR; } if (!o) { PyErr_SetString(PyExc_TypeError, "PyModule_AddObject() needs non-NULL value"); return SWIG_ERROR; } dict = PyModule_GetDict(m); if (dict == NULL) { /* Internal error -- modules must have a dict! */ PyErr_Format(PyExc_SystemError, "module '%s' has no __dict__", PyModule_GetName(m)); return SWIG_ERROR; } if (PyDict_SetItemString(dict, name, o)) return SWIG_ERROR; Py_DECREF(o); return SWIG_OK; } #endif SWIGRUNTIME void #ifdef SWIGPY_USE_CAPSULE SWIG_Python_DestroyModule(PyObject *obj) #else SWIG_Python_DestroyModule(void *vptr) #endif { #ifdef SWIGPY_USE_CAPSULE swig_module_info *swig_module = (swig_module_info *) PyCapsule_GetPointer(obj, SWIGPY_CAPSULE_NAME); #else swig_module_info *swig_module = (swig_module_info *) vptr; #endif swig_type_info **types = swig_module->types; size_t i; for (i =0; i < swig_module->size; ++i) { swig_type_info *ty = types[i]; if (ty->owndata) { SwigPyClientData *data = (SwigPyClientData *) ty->clientdata; if (data) SwigPyClientData_Del(data); } } Py_DECREF(SWIG_This()); swig_this = NULL; } SWIGRUNTIME void SWIG_Python_SetModule(swig_module_info *swig_module) { #if PY_VERSION_HEX >= 0x03000000 /* Add a dummy module object into sys.modules */ PyObject *module = PyImport_AddModule((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION); #else static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} }; /* Sentinel */ PyObject *module = Py_InitModule((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION, swig_empty_runtime_method_table); #endif #ifdef SWIGPY_USE_CAPSULE PyObject *pointer = PyCapsule_New((void *) swig_module, SWIGPY_CAPSULE_NAME, SWIG_Python_DestroyModule); if (pointer && module) { PyModule_AddObject(module, (char*)"type_pointer_capsule" SWIG_TYPE_TABLE_NAME, pointer); } else { Py_XDECREF(pointer); } #else PyObject *pointer = PyCObject_FromVoidPtr((void *) swig_module, SWIG_Python_DestroyModule); if (pointer && module) { PyModule_AddObject(module, (char*)"type_pointer" SWIG_TYPE_TABLE_NAME, pointer); } else { Py_XDECREF(pointer); } #endif } /* The python cached type query */ SWIGRUNTIME PyObject * SWIG_Python_TypeCache(void) { static PyObject *SWIG_STATIC_POINTER(cache) = PyDict_New(); return cache; } SWIGRUNTIME swig_type_info * SWIG_Python_TypeQuery(const char *type) { PyObject *cache = SWIG_Python_TypeCache(); PyObject *key = SWIG_Python_str_FromChar(type); PyObject *obj = PyDict_GetItem(cache, key); swig_type_info *descriptor; if (obj) { #ifdef SWIGPY_USE_CAPSULE descriptor = (swig_type_info *) PyCapsule_GetPointer(obj, NULL); #else descriptor = (swig_type_info *) PyCObject_AsVoidPtr(obj); #endif } else { swig_module_info *swig_module = SWIG_GetModule(0); descriptor = SWIG_TypeQueryModule(swig_module, swig_module, type); if (descriptor) { #ifdef SWIGPY_USE_CAPSULE obj = PyCapsule_New((void*) descriptor, NULL, NULL); #else obj = PyCObject_FromVoidPtr(descriptor, NULL); #endif PyDict_SetItem(cache, key, obj); Py_DECREF(obj); } } Py_DECREF(key); return descriptor; } /* For backward compatibility only */ #define SWIG_POINTER_EXCEPTION 0 #define SWIG_arg_fail(arg) SWIG_Python_ArgFail(arg) #define SWIG_MustGetPtr(p, type, argnum, flags) SWIG_Python_MustGetPtr(p, type, argnum, flags) SWIGRUNTIME int SWIG_Python_AddErrMesg(const char* mesg, int infront) { if (PyErr_Occurred()) { PyObject *type = 0; PyObject *value = 0; PyObject *traceback = 0; PyErr_Fetch(&type, &value, &traceback); if (value) { char *tmp; PyObject *old_str = PyObject_Str(value); Py_XINCREF(type); PyErr_Clear(); if (infront) { PyErr_Format(type, "%s %s", mesg, tmp = SWIG_Python_str_AsChar(old_str)); } else { PyErr_Format(type, "%s %s", tmp = SWIG_Python_str_AsChar(old_str), mesg); } SWIG_Python_str_DelForPy3(tmp); Py_DECREF(old_str); } return 1; } else { return 0; } } SWIGRUNTIME int SWIG_Python_ArgFail(int argnum) { if (PyErr_Occurred()) { /* add information about failing argument */ char mesg[256]; PyOS_snprintf(mesg, sizeof(mesg), "argument number %d:", argnum); return SWIG_Python_AddErrMesg(mesg, 1); } else { return 0; } } SWIGRUNTIMEINLINE const char * SwigPyObject_GetDesc(PyObject *self) { SwigPyObject *v = (SwigPyObject *)self; swig_type_info *ty = v ? v->ty : 0; return ty ? ty->str : ""; } SWIGRUNTIME void SWIG_Python_TypeError(const char *type, PyObject *obj) { if (type) { #if defined(SWIG_COBJECT_TYPES) if (obj && SwigPyObject_Check(obj)) { const char *otype = (const char *) SwigPyObject_GetDesc(obj); if (otype) { PyErr_Format(PyExc_TypeError, "a '%s' is expected, 'SwigPyObject(%s)' is received", type, otype); return; } } else #endif { const char *otype = (obj ? obj->ob_type->tp_name : 0); if (otype) { PyObject *str = PyObject_Str(obj); const char *cstr = str ? SWIG_Python_str_AsChar(str) : 0; if (cstr) { PyErr_Format(PyExc_TypeError, "a '%s' is expected, '%s(%s)' is received", type, otype, cstr); SWIG_Python_str_DelForPy3(cstr); } else { PyErr_Format(PyExc_TypeError, "a '%s' is expected, '%s' is received", type, otype); } Py_XDECREF(str); return; } } PyErr_Format(PyExc_TypeError, "a '%s' is expected", type); } else { PyErr_Format(PyExc_TypeError, "unexpected type is received"); } } /* Convert a pointer value, signal an exception on a type mismatch */ SWIGRUNTIME void * SWIG_Python_MustGetPtr(PyObject *obj, swig_type_info *ty, int SWIGUNUSEDPARM(argnum), int flags) { void *result; if (SWIG_Python_ConvertPtr(obj, &result, ty, flags) == -1) { PyErr_Clear(); #if SWIG_POINTER_EXCEPTION if (flags) { SWIG_Python_TypeError(SWIG_TypePrettyName(ty), obj); SWIG_Python_ArgFail(argnum); } #endif } return result; } #ifdef SWIGPYTHON_BUILTIN SWIGRUNTIME int SWIG_Python_NonDynamicSetAttr(PyObject *obj, PyObject *name, PyObject *value) { PyTypeObject *tp = obj->ob_type; PyObject *descr; PyObject *encoded_name; descrsetfunc f; int res = -1; # ifdef Py_USING_UNICODE if (PyString_Check(name)) { name = PyUnicode_Decode(PyString_AsString(name), PyString_Size(name), NULL, NULL); if (!name) return -1; } else if (!PyUnicode_Check(name)) # else if (!PyString_Check(name)) # endif { PyErr_Format(PyExc_TypeError, "attribute name must be string, not '%.200s'", name->ob_type->tp_name); return -1; } else { Py_INCREF(name); } if (!tp->tp_dict) { if (PyType_Ready(tp) < 0) goto done; } descr = _PyType_Lookup(tp, name); f = NULL; if (descr != NULL) f = descr->ob_type->tp_descr_set; if (!f) { if (PyString_Check(name)) { encoded_name = name; Py_INCREF(name); } else { encoded_name = PyUnicode_AsUTF8String(name); } PyErr_Format(PyExc_AttributeError, "'%.100s' object has no attribute '%.200s'", tp->tp_name, PyString_AsString(encoded_name)); Py_DECREF(encoded_name); } else { res = f(descr, obj, value); } done: Py_DECREF(name); return res; } #endif #ifdef __cplusplus } #endif #define SWIG_exception_fail(code, msg) do { SWIG_Error(code, msg); SWIG_fail; } while(0) #define SWIG_contract_assert(expr, msg) if (!(expr)) { SWIG_Error(SWIG_RuntimeError, msg); SWIG_fail; } else /* -------- TYPES TABLE (BEGIN) -------- */ #define SWIGTYPE_p_char swig_types[0] static swig_type_info *swig_types[2]; static swig_module_info swig_module = {swig_types, 1, 0, 0, 0, 0}; #define SWIG_TypeQuery(name) SWIG_TypeQueryModule(&swig_module, &swig_module, name) #define SWIG_MangledTypeQuery(name) SWIG_MangledTypeQueryModule(&swig_module, &swig_module, name) /* -------- TYPES TABLE (END) -------- */ #if (PY_VERSION_HEX <= 0x02000000) # if !defined(SWIG_PYTHON_CLASSIC) # error "This python version requires swig to be run with the '-classic' option" # endif #endif /*----------------------------------------------- @(target):= _somoclu.so ------------------------------------------------*/ #if PY_VERSION_HEX >= 0x03000000 # define SWIG_init PyInit__somoclu #else # define SWIG_init init_somoclu #endif #define SWIG_name "_somoclu" #define SWIGVERSION 0x020012 #define SWIG_VERSION SWIGVERSION #define SWIG_as_voidptr(a) const_cast< void * >(static_cast< const void * >(a)) #define SWIG_as_voidptrptr(a) ((void)SWIG_as_voidptr(*a),reinterpret_cast< void** >(a)) #include namespace swig { class SwigPtr_PyObject { protected: PyObject *_obj; public: SwigPtr_PyObject() :_obj(0) { } SwigPtr_PyObject(const SwigPtr_PyObject& item) : _obj(item._obj) { Py_XINCREF(_obj); } SwigPtr_PyObject(PyObject *obj, bool initial_ref = true) :_obj(obj) { if (initial_ref) { Py_XINCREF(_obj); } } SwigPtr_PyObject & operator=(const SwigPtr_PyObject& item) { Py_XINCREF(item._obj); Py_XDECREF(_obj); _obj = item._obj; return *this; } ~SwigPtr_PyObject() { Py_XDECREF(_obj); } operator PyObject *() const { return _obj; } PyObject *operator->() const { return _obj; } }; } namespace swig { struct SwigVar_PyObject : SwigPtr_PyObject { SwigVar_PyObject(PyObject* obj = 0) : SwigPtr_PyObject(obj, false) { } SwigVar_PyObject & operator = (PyObject* obj) { Py_XDECREF(_obj); _obj = obj; return *this; } }; } #include #define SWIG_FILE_WITH_INIT #include "src/src/somocluWrap.h" #ifndef SWIG_FILE_WITH_INIT #define NO_IMPORT_ARRAY #endif #include "stdio.h" #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION #include #if NPY_API_VERSION < 0x00000007 #define NPY_ARRAY_DEFAULT NPY_DEFAULT #define NPY_ARRAY_FARRAY NPY_FARRAY #define NPY_FORTRANORDER NPY_FORTRAN #endif /* Macros to extract array attributes. */ #if NPY_API_VERSION < 0x00000007 #define is_array(a) ((a) && PyArray_Check((PyArrayObject*)a)) #define array_type(a) (int)(PyArray_TYPE((PyArrayObject*)a)) #define array_numdims(a) (((PyArrayObject*)a)->nd) #define array_dimensions(a) (((PyArrayObject*)a)->dimensions) #define array_size(a,i) (((PyArrayObject*)a)->dimensions[i]) #define array_strides(a) (((PyArrayObject*)a)->strides) #define array_stride(a,i) (((PyArrayObject*)a)->strides[i]) #define array_data(a) (((PyArrayObject*)a)->data) #define array_descr(a) (((PyArrayObject*)a)->descr) #define array_flags(a) (((PyArrayObject*)a)->flags) #define array_enableflags(a,f) (((PyArrayObject*)a)->flags) = f #else #define is_array(a) ((a) && PyArray_Check(a)) #define array_type(a) PyArray_TYPE((PyArrayObject*)a) #define array_numdims(a) PyArray_NDIM((PyArrayObject*)a) #define array_dimensions(a) PyArray_DIMS((PyArrayObject*)a) #define array_strides(a) PyArray_STRIDES((PyArrayObject*)a) #define array_stride(a,i) PyArray_STRIDE((PyArrayObject*)a,i) #define array_size(a,i) PyArray_DIM((PyArrayObject*)a,i) #define array_data(a) PyArray_DATA((PyArrayObject*)a) #define array_descr(a) PyArray_DESCR((PyArrayObject*)a) #define array_flags(a) PyArray_FLAGS((PyArrayObject*)a) #define array_enableflags(a,f) PyArray_ENABLEFLAGS((PyArrayObject*)a,f) #endif #define array_is_contiguous(a) (PyArray_ISCONTIGUOUS((PyArrayObject*)a)) #define array_is_native(a) (PyArray_ISNOTSWAPPED((PyArrayObject*)a)) #define array_is_fortran(a) (PyArray_ISFORTRAN((PyArrayObject*)a)) /* Given a PyObject, return a string describing its type. */ const char* pytype_string(PyObject* py_obj) { if (py_obj == NULL ) return "C NULL value"; if (py_obj == Py_None ) return "Python None" ; if (PyCallable_Check(py_obj)) return "callable" ; if (PyString_Check( py_obj)) return "string" ; if (PyInt_Check( py_obj)) return "int" ; if (PyFloat_Check( py_obj)) return "float" ; if (PyDict_Check( py_obj)) return "dict" ; if (PyList_Check( py_obj)) return "list" ; if (PyTuple_Check( py_obj)) return "tuple" ; #if PY_MAJOR_VERSION < 3 if (PyFile_Check( py_obj)) return "file" ; if (PyModule_Check( py_obj)) return "module" ; if (PyInstance_Check(py_obj)) return "instance" ; #endif return "unkown type"; } /* Given a NumPy typecode, return a string describing the type. */ const char* typecode_string(int typecode) { static const char* type_names[25] = {"bool", "byte", "unsigned byte", "short", "unsigned short", "int", "unsigned int", "long", "unsigned long", "long long", "unsigned long long", "float", "double", "long double", "complex float", "complex double", "complex long double", "object", "string", "unicode", "void", "ntypes", "notype", "char", "unknown"}; return typecode < 24 ? type_names[typecode] : type_names[24]; } /* Make sure input has correct numpy type. This now just calls PyArray_EquivTypenums(). */ int type_match(int actual_type, int desired_type) { return PyArray_EquivTypenums(actual_type, desired_type); } #ifdef SWIGPY_USE_CAPSULE void free_cap(PyObject * cap) { void* array = (void*) PyCapsule_GetPointer(cap,SWIGPY_CAPSULE_NAME); if (array != NULL) free(array); } #endif /* Given a PyObject pointer, cast it to a PyArrayObject pointer if * legal. If not, set the python error string appropriately and * return NULL. */ PyArrayObject* obj_to_array_no_conversion(PyObject* input, int typecode) { PyArrayObject* ary = NULL; if (is_array(input) && (typecode == NPY_NOTYPE || PyArray_EquivTypenums(array_type(input), typecode))) { ary = (PyArrayObject*) input; } else if is_array(input) { const char* desired_type = typecode_string(typecode); const char* actual_type = typecode_string(array_type(input)); PyErr_Format(PyExc_TypeError, "Array of type '%s' required. Array of type '%s' given", desired_type, actual_type); ary = NULL; } else { const char* desired_type = typecode_string(typecode); const char* actual_type = pytype_string(input); PyErr_Format(PyExc_TypeError, "Array of type '%s' required. A '%s' was given", desired_type, actual_type); ary = NULL; } return ary; } /* Convert the given PyObject to a NumPy array with the given * typecode. On success, return a valid PyArrayObject* with the * correct type. On failure, the python error string will be set and * the routine returns NULL. */ PyArrayObject* obj_to_array_allow_conversion(PyObject* input, int typecode, int* is_new_object) { PyArrayObject* ary = NULL; PyObject* py_obj; if (is_array(input) && (typecode == NPY_NOTYPE || PyArray_EquivTypenums(array_type(input),typecode))) { ary = (PyArrayObject*) input; *is_new_object = 0; } else { py_obj = PyArray_FROMANY(input, typecode, 0, 0, NPY_ARRAY_DEFAULT); /* If NULL, PyArray_FromObject will have set python error value.*/ ary = (PyArrayObject*) py_obj; *is_new_object = 1; } return ary; } /* Given a PyArrayObject, check to see if it is contiguous. If so, * return the input pointer and flag it as not a new object. If it is * not contiguous, create a new PyArrayObject using the original data, * flag it as a new object and return the pointer. */ PyArrayObject* make_contiguous(PyArrayObject* ary, int* is_new_object, int min_dims, int max_dims) { PyArrayObject* result; if (array_is_contiguous(ary)) { result = ary; *is_new_object = 0; } else { result = (PyArrayObject*) PyArray_ContiguousFromObject((PyObject*)ary, array_type(ary), min_dims, max_dims); *is_new_object = 1; } return result; } /* Given a PyArrayObject, check to see if it is Fortran-contiguous. * If so, return the input pointer, but do not flag it as not a new * object. If it is not Fortran-contiguous, create a new * PyArrayObject using the original data, flag it as a new object * and return the pointer. */ PyArrayObject* make_fortran(PyArrayObject* ary, int* is_new_object) { PyArrayObject* result; if (array_is_fortran(ary)) { result = ary; *is_new_object = 0; } else { Py_INCREF(array_descr(ary)); result = (PyArrayObject*) PyArray_FromArray(ary, array_descr(ary), NPY_FORTRANORDER); *is_new_object = 1; } return result; } /* Convert a given PyObject to a contiguous PyArrayObject of the * specified type. If the input object is not a contiguous * PyArrayObject, a new one will be created and the new object flag * will be set. */ PyArrayObject* obj_to_array_contiguous_allow_conversion(PyObject* input, int typecode, int* is_new_object) { int is_new1 = 0; int is_new2 = 0; PyArrayObject* ary2; PyArrayObject* ary1 = obj_to_array_allow_conversion(input, typecode, &is_new1); if (ary1) { ary2 = make_contiguous(ary1, &is_new2, 0, 0); if ( is_new1 && is_new2) { Py_DECREF(ary1); } ary1 = ary2; } *is_new_object = is_new1 || is_new2; return ary1; } /* Convert a given PyObject to a Fortran-ordered PyArrayObject of the * specified type. If the input object is not a Fortran-ordered * PyArrayObject, a new one will be created and the new object flag * will be set. */ PyArrayObject* obj_to_array_fortran_allow_conversion(PyObject* input, int typecode, int* is_new_object) { int is_new1 = 0; int is_new2 = 0; PyArrayObject* ary2; PyArrayObject* ary1 = obj_to_array_allow_conversion(input, typecode, &is_new1); if (ary1) { ary2 = make_fortran(ary1, &is_new2); if (is_new1 && is_new2) { Py_DECREF(ary1); } ary1 = ary2; } *is_new_object = is_new1 || is_new2; return ary1; } /* Test whether a python object is contiguous. If array is * contiguous, return 1. Otherwise, set the python error string and * return 0. */ int require_contiguous(PyArrayObject* ary) { int contiguous = 1; if (!array_is_contiguous(ary)) { PyErr_SetString(PyExc_TypeError, "Array must be contiguous. A non-contiguous array was given"); contiguous = 0; } return contiguous; } /* Require that a numpy array is not byte-swapped. If the array is * not byte-swapped, return 1. Otherwise, set the python error string * and return 0. */ int require_native(PyArrayObject* ary) { int native = 1; if (!array_is_native(ary)) { PyErr_SetString(PyExc_TypeError, "Array must have native byteorder. " "A byte-swapped array was given"); native = 0; } return native; } /* Require the given PyArrayObject to have a specified number of * dimensions. If the array has the specified number of dimensions, * return 1. Otherwise, set the python error string and return 0. */ int require_dimensions(PyArrayObject* ary, int exact_dimensions) { int success = 1; if (array_numdims(ary) != exact_dimensions) { PyErr_Format(PyExc_TypeError, "Array must have %d dimensions. Given array has %d dimensions", exact_dimensions, array_numdims(ary)); success = 0; } return success; } /* Require the given PyArrayObject to have one of a list of specified * number of dimensions. If the array has one of the specified number * of dimensions, return 1. Otherwise, set the python error string * and return 0. */ int require_dimensions_n(PyArrayObject* ary, int* exact_dimensions, int n) { int success = 0; int i; char dims_str[255] = ""; char s[255]; for (i = 0; i < n && !success; i++) { if (array_numdims(ary) == exact_dimensions[i]) { success = 1; } } if (!success) { for (i = 0; i < n-1; i++) { sprintf(s, "%d, ", exact_dimensions[i]); strcat(dims_str,s); } sprintf(s, " or %d", exact_dimensions[n-1]); strcat(dims_str,s); PyErr_Format(PyExc_TypeError, "Array must have %s dimensions. Given array has %d dimensions", dims_str, array_numdims(ary)); } return success; } /* Require the given PyArrayObject to have a specified shape. If the * array has the specified shape, return 1. Otherwise, set the python * error string and return 0. */ int require_size(PyArrayObject* ary, npy_intp* size, int n) { int i; int success = 1; int len; char desired_dims[255] = "["; char s[255]; char actual_dims[255] = "["; for(i=0; i < n;i++) { if (size[i] != -1 && size[i] != array_size(ary,i)) { success = 0; } } if (!success) { for (i = 0; i < n; i++) { if (size[i] == -1) { sprintf(s, "*,"); } else { sprintf(s, "%ld,", (long int)size[i]); } strcat(desired_dims,s); } len = strlen(desired_dims); desired_dims[len-1] = ']'; for (i = 0; i < n; i++) { sprintf(s, "%ld,", (long int)array_size(ary,i)); strcat(actual_dims,s); } len = strlen(actual_dims); actual_dims[len-1] = ']'; PyErr_Format(PyExc_TypeError, "Array must have shape of %s. Given array has shape of %s", desired_dims, actual_dims); } return success; } /* Require the given PyArrayObject to to be Fortran ordered. If the * the PyArrayObject is already Fortran ordered, do nothing. Else, * set the Fortran ordering flag and recompute the strides. */ int require_fortran(PyArrayObject* ary) { int success = 1; int nd = array_numdims(ary); int i; npy_intp * strides = array_strides(ary); if (array_is_fortran(ary)) return success; /* Set the Fortran ordered flag */ array_enableflags(ary,NPY_ARRAY_FARRAY); /* Recompute the strides */ strides[0] = strides[nd-1]; for (i=1; i < nd; ++i) strides[i] = strides[i-1] * array_size(ary,i-1); return success; } #include #if !defined(SWIG_NO_LLONG_MAX) # if !defined(LLONG_MAX) && defined(__GNUC__) && defined (__LONG_LONG_MAX__) # define LLONG_MAX __LONG_LONG_MAX__ # define LLONG_MIN (-LLONG_MAX - 1LL) # define ULLONG_MAX (LLONG_MAX * 2ULL + 1ULL) # endif #endif SWIGINTERN int SWIG_AsVal_double (PyObject *obj, double *val) { int res = SWIG_TypeError; if (PyFloat_Check(obj)) { if (val) *val = PyFloat_AsDouble(obj); return SWIG_OK; } else if (PyInt_Check(obj)) { if (val) *val = PyInt_AsLong(obj); return SWIG_OK; } else if (PyLong_Check(obj)) { double v = PyLong_AsDouble(obj); if (!PyErr_Occurred()) { if (val) *val = v; return SWIG_OK; } else { PyErr_Clear(); } } #ifdef SWIG_PYTHON_CAST_MODE { int dispatch = 0; double d = PyFloat_AsDouble(obj); if (!PyErr_Occurred()) { if (val) *val = d; return SWIG_AddCast(SWIG_OK); } else { PyErr_Clear(); } if (!dispatch) { long v = PyLong_AsLong(obj); if (!PyErr_Occurred()) { if (val) *val = v; return SWIG_AddCast(SWIG_AddCast(SWIG_OK)); } else { PyErr_Clear(); } } } #endif return res; } #include #include SWIGINTERNINLINE int SWIG_CanCastAsInteger(double *d, double min, double max) { double x = *d; if ((min <= x && x <= max)) { double fx = floor(x); double cx = ceil(x); double rd = ((x - fx) < 0.5) ? fx : cx; /* simple rint */ if ((errno == EDOM) || (errno == ERANGE)) { errno = 0; } else { double summ, reps, diff; if (rd < x) { diff = x - rd; } else if (rd > x) { diff = rd - x; } else { return 1; } summ = rd + x; reps = diff/summ; if (reps < 8*DBL_EPSILON) { *d = rd; return 1; } } } return 0; } SWIGINTERN int SWIG_AsVal_unsigned_SS_long (PyObject *obj, unsigned long *val) { #if PY_VERSION_HEX < 0x03000000 if (PyInt_Check(obj)) { long v = PyInt_AsLong(obj); if (v >= 0) { if (val) *val = v; return SWIG_OK; } else { return SWIG_OverflowError; } } else #endif if (PyLong_Check(obj)) { unsigned long v = PyLong_AsUnsignedLong(obj); if (!PyErr_Occurred()) { if (val) *val = v; return SWIG_OK; } else { PyErr_Clear(); #if PY_VERSION_HEX >= 0x03000000 { long v = PyLong_AsLong(obj); if (!PyErr_Occurred()) { if (v < 0) { return SWIG_OverflowError; } } else { PyErr_Clear(); } } #endif } } #ifdef SWIG_PYTHON_CAST_MODE { int dispatch = 0; unsigned long v = PyLong_AsUnsignedLong(obj); if (!PyErr_Occurred()) { if (val) *val = v; return SWIG_AddCast(SWIG_OK); } else { PyErr_Clear(); } if (!dispatch) { double d; int res = SWIG_AddCast(SWIG_AsVal_double (obj,&d)); if (SWIG_IsOK(res) && SWIG_CanCastAsInteger(&d, 0, ULONG_MAX)) { if (val) *val = (unsigned long)(d); return res; } } } #endif return SWIG_TypeError; } SWIGINTERN int SWIG_AsVal_unsigned_SS_int (PyObject * obj, unsigned int *val) { unsigned long v; int res = SWIG_AsVal_unsigned_SS_long (obj, &v); if (SWIG_IsOK(res)) { if ((v > UINT_MAX)) { return SWIG_OverflowError; } else { if (val) *val = static_cast< unsigned int >(v); } } return res; } SWIGINTERN swig_type_info* SWIG_pchar_descriptor(void) { static int init = 0; static swig_type_info* info = 0; if (!init) { info = SWIG_TypeQuery("_p_char"); init = 1; } return info; } SWIGINTERN int SWIG_AsCharPtrAndSize(PyObject *obj, char** cptr, size_t* psize, int *alloc) { #if PY_VERSION_HEX>=0x03000000 if (PyUnicode_Check(obj)) #else if (PyString_Check(obj)) #endif { char *cstr; Py_ssize_t len; #if PY_VERSION_HEX>=0x03000000 if (!alloc && cptr) { /* We can't allow converting without allocation, since the internal representation of string in Python 3 is UCS-2/UCS-4 but we require a UTF-8 representation. TODO(bhy) More detailed explanation */ return SWIG_RuntimeError; } obj = PyUnicode_AsUTF8String(obj); PyBytes_AsStringAndSize(obj, &cstr, &len); if(alloc) *alloc = SWIG_NEWOBJ; #else PyString_AsStringAndSize(obj, &cstr, &len); #endif if (cptr) { if (alloc) { /* In python the user should not be able to modify the inner string representation. To warranty that, if you define SWIG_PYTHON_SAFE_CSTRINGS, a new/copy of the python string buffer is always returned. The default behavior is just to return the pointer value, so, be careful. */ #if defined(SWIG_PYTHON_SAFE_CSTRINGS) if (*alloc != SWIG_OLDOBJ) #else if (*alloc == SWIG_NEWOBJ) #endif { *cptr = reinterpret_cast< char* >(memcpy((new char[len + 1]), cstr, sizeof(char)*(len + 1))); *alloc = SWIG_NEWOBJ; } else { *cptr = cstr; *alloc = SWIG_OLDOBJ; } } else { #if PY_VERSION_HEX>=0x03000000 assert(0); /* Should never reach here in Python 3 */ #endif *cptr = SWIG_Python_str_AsChar(obj); } } if (psize) *psize = len + 1; #if PY_VERSION_HEX>=0x03000000 Py_XDECREF(obj); #endif return SWIG_OK; } else { swig_type_info* pchar_descriptor = SWIG_pchar_descriptor(); if (pchar_descriptor) { void* vptr = 0; if (SWIG_ConvertPtr(obj, &vptr, pchar_descriptor, 0) == SWIG_OK) { if (cptr) *cptr = (char *) vptr; if (psize) *psize = vptr ? (strlen((char *)vptr) + 1) : 0; if (alloc) *alloc = SWIG_OLDOBJ; return SWIG_OK; } } } return SWIG_TypeError; } SWIGINTERN int SWIG_AsPtr_std_string (PyObject * obj, std::string **val) { char* buf = 0 ; size_t size = 0; int alloc = SWIG_OLDOBJ; if (SWIG_IsOK((SWIG_AsCharPtrAndSize(obj, &buf, &size, &alloc)))) { if (buf) { if (val) *val = new std::string(buf, size - 1); if (alloc == SWIG_NEWOBJ) delete[] buf; return SWIG_NEWOBJ; } else { if (val) *val = 0; return SWIG_OLDOBJ; } } else { static int init = 0; static swig_type_info* descriptor = 0; if (!init) { descriptor = SWIG_TypeQuery("std::string" " *"); init = 1; } if (descriptor) { std::string *vptr; int res = SWIG_ConvertPtr(obj, (void**)&vptr, descriptor, 0); if (SWIG_IsOK(res) && val) *val = vptr; return res; } } return SWIG_ERROR; } /* Getting isfinite working pre C99 across multiple platforms is non-trivial. Users can provide SWIG_isfinite on older platforms. */ #ifndef SWIG_isfinite # if defined(isfinite) # define SWIG_isfinite(X) (isfinite(X)) # elif defined(_MSC_VER) # define SWIG_isfinite(X) (_finite(X)) # elif defined(__sun) && defined(__SVR4) # include # define SWIG_isfinite(X) (finite(X)) # endif #endif /* Accept infinite as a valid float value unless we are unable to check if a value is finite */ #ifdef SWIG_isfinite # define SWIG_Float_Overflow_Check(X) ((X < -FLT_MAX || X > FLT_MAX) && SWIG_isfinite(X)) #else # define SWIG_Float_Overflow_Check(X) ((X < -FLT_MAX || X > FLT_MAX)) #endif SWIGINTERN int SWIG_AsVal_float (PyObject * obj, float *val) { double v; int res = SWIG_AsVal_double (obj, &v); if (SWIG_IsOK(res)) { if (SWIG_Float_Overflow_Check(v)) { return SWIG_OverflowError; } else { if (val) *val = static_cast< float >(v); } } return res; } #ifdef __cplusplus extern "C" { #endif SWIGINTERN PyObject *_wrap_trainWrapper(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *resultobj = 0; float *arg1 = (float *) 0 ; int arg2 ; unsigned int arg3 ; unsigned int arg4 ; unsigned int arg5 ; unsigned int arg6 ; unsigned int arg7 ; unsigned int arg8 ; unsigned int arg9 ; std::string arg10 ; float arg11 ; float arg12 ; std::string arg13 ; unsigned int arg14 ; unsigned int arg15 ; std::string arg16 ; std::string arg17 ; float *arg18 = (float *) 0 ; int arg19 ; int *arg20 = (int *) 0 ; int arg21 ; float *arg22 = (float *) 0 ; int arg23 ; PyArrayObject *array1 = NULL ; int i1 = 1 ; unsigned int val3 ; int ecode3 = 0 ; unsigned int val4 ; int ecode4 = 0 ; unsigned int val5 ; int ecode5 = 0 ; unsigned int val6 ; int ecode6 = 0 ; unsigned int val7 ; int ecode7 = 0 ; unsigned int val8 ; int ecode8 = 0 ; unsigned int val9 ; int ecode9 = 0 ; float val11 ; int ecode11 = 0 ; float val12 ; int ecode12 = 0 ; unsigned int val14 ; int ecode14 = 0 ; unsigned int val15 ; int ecode15 = 0 ; PyArrayObject *array18 = NULL ; int i18 = 1 ; PyArrayObject *array20 = NULL ; int i20 = 1 ; PyArrayObject *array22 = NULL ; int i22 = 1 ; PyObject * obj0 = 0 ; PyObject * obj1 = 0 ; PyObject * obj2 = 0 ; PyObject * obj3 = 0 ; PyObject * obj4 = 0 ; PyObject * obj5 = 0 ; PyObject * obj6 = 0 ; PyObject * obj7 = 0 ; PyObject * obj8 = 0 ; PyObject * obj9 = 0 ; PyObject * obj10 = 0 ; PyObject * obj11 = 0 ; PyObject * obj12 = 0 ; PyObject * obj13 = 0 ; PyObject * obj14 = 0 ; PyObject * obj15 = 0 ; PyObject * obj16 = 0 ; PyObject * obj17 = 0 ; PyObject * obj18 = 0 ; if (!PyArg_ParseTuple(args,(char *)"OOOOOOOOOOOOOOOOOOO:trainWrapper",&obj0,&obj1,&obj2,&obj3,&obj4,&obj5,&obj6,&obj7,&obj8,&obj9,&obj10,&obj11,&obj12,&obj13,&obj14,&obj15,&obj16,&obj17,&obj18)) SWIG_fail; { array1 = obj_to_array_no_conversion(obj0, NPY_FLOAT); if (!array1 || !require_dimensions(array1,1) || !require_contiguous(array1) || !require_native(array1)) SWIG_fail; arg1 = (float*) array_data(array1); arg2 = 1; for (i1=0; i1 < array_numdims(array1); ++i1) arg2 *= array_size(array1,i1); } ecode3 = SWIG_AsVal_unsigned_SS_int(obj1, &val3); if (!SWIG_IsOK(ecode3)) { SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "trainWrapper" "', argument " "3"" of type '" "unsigned int""'"); } arg3 = static_cast< unsigned int >(val3); ecode4 = SWIG_AsVal_unsigned_SS_int(obj2, &val4); if (!SWIG_IsOK(ecode4)) { SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "trainWrapper" "', argument " "4"" of type '" "unsigned int""'"); } arg4 = static_cast< unsigned int >(val4); ecode5 = SWIG_AsVal_unsigned_SS_int(obj3, &val5); if (!SWIG_IsOK(ecode5)) { SWIG_exception_fail(SWIG_ArgError(ecode5), "in method '" "trainWrapper" "', argument " "5"" of type '" "unsigned int""'"); } arg5 = static_cast< unsigned int >(val5); ecode6 = SWIG_AsVal_unsigned_SS_int(obj4, &val6); if (!SWIG_IsOK(ecode6)) { SWIG_exception_fail(SWIG_ArgError(ecode6), "in method '" "trainWrapper" "', argument " "6"" of type '" "unsigned int""'"); } arg6 = static_cast< unsigned int >(val6); ecode7 = SWIG_AsVal_unsigned_SS_int(obj5, &val7); if (!SWIG_IsOK(ecode7)) { SWIG_exception_fail(SWIG_ArgError(ecode7), "in method '" "trainWrapper" "', argument " "7"" of type '" "unsigned int""'"); } arg7 = static_cast< unsigned int >(val7); ecode8 = SWIG_AsVal_unsigned_SS_int(obj6, &val8); if (!SWIG_IsOK(ecode8)) { SWIG_exception_fail(SWIG_ArgError(ecode8), "in method '" "trainWrapper" "', argument " "8"" of type '" "unsigned int""'"); } arg8 = static_cast< unsigned int >(val8); ecode9 = SWIG_AsVal_unsigned_SS_int(obj7, &val9); if (!SWIG_IsOK(ecode9)) { SWIG_exception_fail(SWIG_ArgError(ecode9), "in method '" "trainWrapper" "', argument " "9"" of type '" "unsigned int""'"); } arg9 = static_cast< unsigned int >(val9); { std::string *ptr = (std::string *)0; int res = SWIG_AsPtr_std_string(obj8, &ptr); if (!SWIG_IsOK(res) || !ptr) { SWIG_exception_fail(SWIG_ArgError((ptr ? res : SWIG_TypeError)), "in method '" "trainWrapper" "', argument " "10"" of type '" "std::string""'"); } arg10 = *ptr; if (SWIG_IsNewObj(res)) delete ptr; } ecode11 = SWIG_AsVal_float(obj9, &val11); if (!SWIG_IsOK(ecode11)) { SWIG_exception_fail(SWIG_ArgError(ecode11), "in method '" "trainWrapper" "', argument " "11"" of type '" "float""'"); } arg11 = static_cast< float >(val11); ecode12 = SWIG_AsVal_float(obj10, &val12); if (!SWIG_IsOK(ecode12)) { SWIG_exception_fail(SWIG_ArgError(ecode12), "in method '" "trainWrapper" "', argument " "12"" of type '" "float""'"); } arg12 = static_cast< float >(val12); { std::string *ptr = (std::string *)0; int res = SWIG_AsPtr_std_string(obj11, &ptr); if (!SWIG_IsOK(res) || !ptr) { SWIG_exception_fail(SWIG_ArgError((ptr ? res : SWIG_TypeError)), "in method '" "trainWrapper" "', argument " "13"" of type '" "std::string""'"); } arg13 = *ptr; if (SWIG_IsNewObj(res)) delete ptr; } ecode14 = SWIG_AsVal_unsigned_SS_int(obj12, &val14); if (!SWIG_IsOK(ecode14)) { SWIG_exception_fail(SWIG_ArgError(ecode14), "in method '" "trainWrapper" "', argument " "14"" of type '" "unsigned int""'"); } arg14 = static_cast< unsigned int >(val14); ecode15 = SWIG_AsVal_unsigned_SS_int(obj13, &val15); if (!SWIG_IsOK(ecode15)) { SWIG_exception_fail(SWIG_ArgError(ecode15), "in method '" "trainWrapper" "', argument " "15"" of type '" "unsigned int""'"); } arg15 = static_cast< unsigned int >(val15); { std::string *ptr = (std::string *)0; int res = SWIG_AsPtr_std_string(obj14, &ptr); if (!SWIG_IsOK(res) || !ptr) { SWIG_exception_fail(SWIG_ArgError((ptr ? res : SWIG_TypeError)), "in method '" "trainWrapper" "', argument " "16"" of type '" "std::string""'"); } arg16 = *ptr; if (SWIG_IsNewObj(res)) delete ptr; } { std::string *ptr = (std::string *)0; int res = SWIG_AsPtr_std_string(obj15, &ptr); if (!SWIG_IsOK(res) || !ptr) { SWIG_exception_fail(SWIG_ArgError((ptr ? res : SWIG_TypeError)), "in method '" "trainWrapper" "', argument " "17"" of type '" "std::string""'"); } arg17 = *ptr; if (SWIG_IsNewObj(res)) delete ptr; } { array18 = obj_to_array_no_conversion(obj16, NPY_FLOAT); if (!array18 || !require_dimensions(array18,1) || !require_contiguous(array18) || !require_native(array18)) SWIG_fail; arg18 = (float*) array_data(array18); arg19 = 1; for (i18=0; i18 < array_numdims(array18); ++i18) arg19 *= array_size(array18,i18); } { array20 = obj_to_array_no_conversion(obj17, NPY_INT); if (!array20 || !require_dimensions(array20,1) || !require_contiguous(array20) || !require_native(array20)) SWIG_fail; arg20 = (int*) array_data(array20); arg21 = 1; for (i20=0; i20 < array_numdims(array20); ++i20) arg21 *= array_size(array20,i20); } { array22 = obj_to_array_no_conversion(obj18, NPY_FLOAT); if (!array22 || !require_dimensions(array22,1) || !require_contiguous(array22) || !require_native(array22)) SWIG_fail; arg22 = (float*) array_data(array22); arg23 = 1; for (i22=0; i22 < array_numdims(array22); ++i22) arg23 *= array_size(array22,i22); } trainWrapper(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23); resultobj = SWIG_Py_Void(); return resultobj; fail: return NULL; } static PyMethodDef SwigMethods[] = { { (char *)"SWIG_PyInstanceMethod_New", (PyCFunction)SWIG_PyInstanceMethod_New, METH_O, NULL}, { (char *)"trainWrapper", _wrap_trainWrapper, METH_VARARGS, NULL}, { NULL, NULL, 0, NULL } }; /* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */ static swig_type_info _swigt__p_char = {"_p_char", "char *", 0, 0, (void*)0, 0}; static swig_type_info *swig_type_initial[] = { &_swigt__p_char, }; static swig_cast_info _swigc__p_char[] = { {&_swigt__p_char, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info *swig_cast_initial[] = { _swigc__p_char, }; /* -------- TYPE CONVERSION AND EQUIVALENCE RULES (END) -------- */ static swig_const_info swig_const_table[] = { {0, 0, 0, 0.0, 0, 0}}; #ifdef __cplusplus } #endif /* ----------------------------------------------------------------------------- * Type initialization: * This problem is tough by the requirement that no dynamic * memory is used. Also, since swig_type_info structures store pointers to * swig_cast_info structures and swig_cast_info structures store pointers back * to swig_type_info structures, we need some lookup code at initialization. * The idea is that swig generates all the structures that are needed. * The runtime then collects these partially filled structures. * The SWIG_InitializeModule function takes these initial arrays out of * swig_module, and does all the lookup, filling in the swig_module.types * array with the correct data and linking the correct swig_cast_info * structures together. * * The generated swig_type_info structures are assigned staticly to an initial * array. We just loop through that array, and handle each type individually. * First we lookup if this type has been already loaded, and if so, use the * loaded structure instead of the generated one. Then we have to fill in the * cast linked list. The cast data is initially stored in something like a * two-dimensional array. Each row corresponds to a type (there are the same * number of rows as there are in the swig_type_initial array). Each entry in * a column is one of the swig_cast_info structures for that type. * The cast_initial array is actually an array of arrays, because each row has * a variable number of columns. So to actually build the cast linked list, * we find the array of casts associated with the type, and loop through it * adding the casts to the list. The one last trick we need to do is making * sure the type pointer in the swig_cast_info struct is correct. * * First off, we lookup the cast->type name to see if it is already loaded. * There are three cases to handle: * 1) If the cast->type has already been loaded AND the type we are adding * casting info to has not been loaded (it is in this module), THEN we * replace the cast->type pointer with the type pointer that has already * been loaded. * 2) If BOTH types (the one we are adding casting info to, and the * cast->type) are loaded, THEN the cast info has already been loaded by * the previous module so we just ignore it. * 3) Finally, if cast->type has not already been loaded, then we add that * swig_cast_info to the linked list (because the cast->type) pointer will * be correct. * ----------------------------------------------------------------------------- */ #ifdef __cplusplus extern "C" { #if 0 } /* c-mode */ #endif #endif #if 0 #define SWIGRUNTIME_DEBUG #endif SWIGRUNTIME void SWIG_InitializeModule(void *clientdata) { size_t i; swig_module_info *module_head, *iter; int found, init; /* check to see if the circular list has been setup, if not, set it up */ if (swig_module.next==0) { /* Initialize the swig_module */ swig_module.type_initial = swig_type_initial; swig_module.cast_initial = swig_cast_initial; swig_module.next = &swig_module; init = 1; } else { init = 0; } /* Try and load any already created modules */ module_head = SWIG_GetModule(clientdata); if (!module_head) { /* This is the first module loaded for this interpreter */ /* so set the swig module into the interpreter */ SWIG_SetModule(clientdata, &swig_module); module_head = &swig_module; } else { /* the interpreter has loaded a SWIG module, but has it loaded this one? */ found=0; iter=module_head; do { if (iter==&swig_module) { found=1; break; } iter=iter->next; } while (iter!= module_head); /* if the is found in the list, then all is done and we may leave */ if (found) return; /* otherwise we must add out module into the list */ swig_module.next = module_head->next; module_head->next = &swig_module; } /* When multiple interpreters are used, a module could have already been initialized in a different interpreter, but not yet have a pointer in this interpreter. In this case, we do not want to continue adding types... everything should be set up already */ if (init == 0) return; /* Now work on filling in swig_module.types */ #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: size %d\n", swig_module.size); #endif for (i = 0; i < swig_module.size; ++i) { swig_type_info *type = 0; swig_type_info *ret; swig_cast_info *cast; #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: type %d %s\n", i, swig_module.type_initial[i]->name); #endif /* if there is another module already loaded */ if (swig_module.next != &swig_module) { type = SWIG_MangledTypeQueryModule(swig_module.next, &swig_module, swig_module.type_initial[i]->name); } if (type) { /* Overwrite clientdata field */ #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: found type %s\n", type->name); #endif if (swig_module.type_initial[i]->clientdata) { type->clientdata = swig_module.type_initial[i]->clientdata; #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: found and overwrite type %s \n", type->name); #endif } } else { type = swig_module.type_initial[i]; } /* Insert casting types */ cast = swig_module.cast_initial[i]; while (cast->type) { /* Don't need to add information already in the list */ ret = 0; #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: look cast %s\n", cast->type->name); #endif if (swig_module.next != &swig_module) { ret = SWIG_MangledTypeQueryModule(swig_module.next, &swig_module, cast->type->name); #ifdef SWIGRUNTIME_DEBUG if (ret) printf("SWIG_InitializeModule: found cast %s\n", ret->name); #endif } if (ret) { if (type == swig_module.type_initial[i]) { #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: skip old type %s\n", ret->name); #endif cast->type = ret; ret = 0; } else { /* Check for casting already in the list */ swig_cast_info *ocast = SWIG_TypeCheck(ret->name, type); #ifdef SWIGRUNTIME_DEBUG if (ocast) printf("SWIG_InitializeModule: skip old cast %s\n", ret->name); #endif if (!ocast) ret = 0; } } if (!ret) { #ifdef SWIGRUNTIME_DEBUG printf("SWIG_InitializeModule: adding cast %s\n", cast->type->name); #endif if (type->cast) { type->cast->prev = cast; cast->next = type->cast; } type->cast = cast; } cast++; } /* Set entry in modules->types array equal to the type */ swig_module.types[i] = type; } swig_module.types[i] = 0; #ifdef SWIGRUNTIME_DEBUG printf("**** SWIG_InitializeModule: Cast List ******\n"); for (i = 0; i < swig_module.size; ++i) { int j = 0; swig_cast_info *cast = swig_module.cast_initial[i]; printf("SWIG_InitializeModule: type %d %s\n", i, swig_module.type_initial[i]->name); while (cast->type) { printf("SWIG_InitializeModule: cast type %s\n", cast->type->name); cast++; ++j; } printf("---- Total casts: %d\n",j); } printf("**** SWIG_InitializeModule: Cast List ******\n"); #endif } /* This function will propagate the clientdata field of type to * any new swig_type_info structures that have been added into the list * of equivalent types. It is like calling * SWIG_TypeClientData(type, clientdata) a second time. */ SWIGRUNTIME void SWIG_PropagateClientData(void) { size_t i; swig_cast_info *equiv; static int init_run = 0; if (init_run) return; init_run = 1; for (i = 0; i < swig_module.size; i++) { if (swig_module.types[i]->clientdata) { equiv = swig_module.types[i]->cast; while (equiv) { if (!equiv->converter) { if (equiv->type && !equiv->type->clientdata) SWIG_TypeClientData(equiv->type, swig_module.types[i]->clientdata); } equiv = equiv->next; } } } } #ifdef __cplusplus #if 0 { /* c-mode */ #endif } #endif #ifdef __cplusplus extern "C" { #endif /* Python-specific SWIG API */ #define SWIG_newvarlink() SWIG_Python_newvarlink() #define SWIG_addvarlink(p, name, get_attr, set_attr) SWIG_Python_addvarlink(p, name, get_attr, set_attr) #define SWIG_InstallConstants(d, constants) SWIG_Python_InstallConstants(d, constants) /* ----------------------------------------------------------------------------- * global variable support code. * ----------------------------------------------------------------------------- */ typedef struct swig_globalvar { char *name; /* Name of global variable */ PyObject *(*get_attr)(void); /* Return the current value */ int (*set_attr)(PyObject *); /* Set the value */ struct swig_globalvar *next; } swig_globalvar; typedef struct swig_varlinkobject { PyObject_HEAD swig_globalvar *vars; } swig_varlinkobject; SWIGINTERN PyObject * swig_varlink_repr(swig_varlinkobject *SWIGUNUSEDPARM(v)) { #if PY_VERSION_HEX >= 0x03000000 return PyUnicode_InternFromString(""); #else return PyString_FromString(""); #endif } SWIGINTERN PyObject * swig_varlink_str(swig_varlinkobject *v) { #if PY_VERSION_HEX >= 0x03000000 PyObject *str = PyUnicode_InternFromString("("); PyObject *tail; PyObject *joined; swig_globalvar *var; for (var = v->vars; var; var=var->next) { tail = PyUnicode_FromString(var->name); joined = PyUnicode_Concat(str, tail); Py_DecRef(str); Py_DecRef(tail); str = joined; if (var->next) { tail = PyUnicode_InternFromString(", "); joined = PyUnicode_Concat(str, tail); Py_DecRef(str); Py_DecRef(tail); str = joined; } } tail = PyUnicode_InternFromString(")"); joined = PyUnicode_Concat(str, tail); Py_DecRef(str); Py_DecRef(tail); str = joined; #else PyObject *str = PyString_FromString("("); swig_globalvar *var; for (var = v->vars; var; var=var->next) { PyString_ConcatAndDel(&str,PyString_FromString(var->name)); if (var->next) PyString_ConcatAndDel(&str,PyString_FromString(", ")); } PyString_ConcatAndDel(&str,PyString_FromString(")")); #endif return str; } SWIGINTERN int swig_varlink_print(swig_varlinkobject *v, FILE *fp, int SWIGUNUSEDPARM(flags)) { char *tmp; PyObject *str = swig_varlink_str(v); fprintf(fp,"Swig global variables "); fprintf(fp,"%s\n", tmp = SWIG_Python_str_AsChar(str)); SWIG_Python_str_DelForPy3(tmp); Py_DECREF(str); return 0; } SWIGINTERN void swig_varlink_dealloc(swig_varlinkobject *v) { swig_globalvar *var = v->vars; while (var) { swig_globalvar *n = var->next; free(var->name); free(var); var = n; } } SWIGINTERN PyObject * swig_varlink_getattr(swig_varlinkobject *v, char *n) { PyObject *res = NULL; swig_globalvar *var = v->vars; while (var) { if (strcmp(var->name,n) == 0) { res = (*var->get_attr)(); break; } var = var->next; } if (res == NULL && !PyErr_Occurred()) { PyErr_SetString(PyExc_NameError,"Unknown C global variable"); } return res; } SWIGINTERN int swig_varlink_setattr(swig_varlinkobject *v, char *n, PyObject *p) { int res = 1; swig_globalvar *var = v->vars; while (var) { if (strcmp(var->name,n) == 0) { res = (*var->set_attr)(p); break; } var = var->next; } if (res == 1 && !PyErr_Occurred()) { PyErr_SetString(PyExc_NameError,"Unknown C global variable"); } return res; } SWIGINTERN PyTypeObject* swig_varlink_type(void) { static char varlink__doc__[] = "Swig var link object"; static PyTypeObject varlink_type; static int type_init = 0; if (!type_init) { const PyTypeObject tmp = { /* PyObject header changed in Python 3 */ #if PY_VERSION_HEX >= 0x03000000 PyVarObject_HEAD_INIT(NULL, 0) #else PyObject_HEAD_INIT(NULL) 0, /* ob_size */ #endif (char *)"swigvarlink", /* tp_name */ sizeof(swig_varlinkobject), /* tp_basicsize */ 0, /* tp_itemsize */ (destructor) swig_varlink_dealloc, /* tp_dealloc */ (printfunc) swig_varlink_print, /* tp_print */ (getattrfunc) swig_varlink_getattr, /* tp_getattr */ (setattrfunc) swig_varlink_setattr, /* tp_setattr */ 0, /* tp_compare */ (reprfunc) swig_varlink_repr, /* tp_repr */ 0, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ 0, /* tp_hash */ 0, /* tp_call */ (reprfunc) swig_varlink_str, /* tp_str */ 0, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ 0, /* tp_flags */ varlink__doc__, /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ 0, /* tp_richcompare */ 0, /* tp_weaklistoffset */ #if PY_VERSION_HEX >= 0x02020000 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, /* tp_iter -> tp_weaklist */ #endif #if PY_VERSION_HEX >= 0x02030000 0, /* tp_del */ #endif #if PY_VERSION_HEX >= 0x02060000 0, /* tp_version */ #endif #ifdef COUNT_ALLOCS 0,0,0,0 /* tp_alloc -> tp_next */ #endif }; varlink_type = tmp; type_init = 1; #if PY_VERSION_HEX < 0x02020000 varlink_type.ob_type = &PyType_Type; #else if (PyType_Ready(&varlink_type) < 0) return NULL; #endif } return &varlink_type; } /* Create a variable linking object for use later */ SWIGINTERN PyObject * SWIG_Python_newvarlink(void) { swig_varlinkobject *result = PyObject_NEW(swig_varlinkobject, swig_varlink_type()); if (result) { result->vars = 0; } return ((PyObject*) result); } SWIGINTERN void SWIG_Python_addvarlink(PyObject *p, char *name, PyObject *(*get_attr)(void), int (*set_attr)(PyObject *p)) { swig_varlinkobject *v = (swig_varlinkobject *) p; swig_globalvar *gv = (swig_globalvar *) malloc(sizeof(swig_globalvar)); if (gv) { size_t size = strlen(name)+1; gv->name = (char *)malloc(size); if (gv->name) { strncpy(gv->name,name,size); gv->get_attr = get_attr; gv->set_attr = set_attr; gv->next = v->vars; } } v->vars = gv; } SWIGINTERN PyObject * SWIG_globals(void) { static PyObject *_SWIG_globals = 0; if (!_SWIG_globals) _SWIG_globals = SWIG_newvarlink(); return _SWIG_globals; } /* ----------------------------------------------------------------------------- * constants/methods manipulation * ----------------------------------------------------------------------------- */ /* Install Constants */ SWIGINTERN void SWIG_Python_InstallConstants(PyObject *d, swig_const_info constants[]) { PyObject *obj = 0; size_t i; for (i = 0; constants[i].type; ++i) { switch(constants[i].type) { case SWIG_PY_POINTER: obj = SWIG_InternalNewPointerObj(constants[i].pvalue, *(constants[i]).ptype,0); break; case SWIG_PY_BINARY: obj = SWIG_NewPackedObj(constants[i].pvalue, constants[i].lvalue, *(constants[i].ptype)); break; default: obj = 0; break; } if (obj) { PyDict_SetItemString(d, constants[i].name, obj); Py_DECREF(obj); } } } /* -----------------------------------------------------------------------------*/ /* Fix SwigMethods to carry the callback ptrs when needed */ /* -----------------------------------------------------------------------------*/ SWIGINTERN void SWIG_Python_FixMethods(PyMethodDef *methods, swig_const_info *const_table, swig_type_info **types, swig_type_info **types_initial) { size_t i; for (i = 0; methods[i].ml_name; ++i) { const char *c = methods[i].ml_doc; if (c && (c = strstr(c, "swig_ptr: "))) { int j; swig_const_info *ci = 0; const char *name = c + 10; for (j = 0; const_table[j].type; ++j) { if (strncmp(const_table[j].name, name, strlen(const_table[j].name)) == 0) { ci = &(const_table[j]); break; } } if (ci) { void *ptr = (ci->type == SWIG_PY_POINTER) ? ci->pvalue : 0; if (ptr) { size_t shift = (ci->ptype) - types; swig_type_info *ty = types_initial[shift]; size_t ldoc = (c - methods[i].ml_doc); size_t lptr = strlen(ty->name)+2*sizeof(void*)+2; char *ndoc = (char*)malloc(ldoc + lptr + 10); if (ndoc) { char *buff = ndoc; strncpy(buff, methods[i].ml_doc, ldoc); buff += ldoc; strncpy(buff, "swig_ptr: ", 10); buff += 10; SWIG_PackVoidPtr(buff, ptr, ty->name, lptr); methods[i].ml_doc = ndoc; } } } } } } #ifdef __cplusplus } #endif /* -----------------------------------------------------------------------------* * Partial Init method * -----------------------------------------------------------------------------*/ #ifdef __cplusplus extern "C" #endif SWIGEXPORT #if PY_VERSION_HEX >= 0x03000000 PyObject* #else void #endif SWIG_init(void) { PyObject *m, *d, *md; #if PY_VERSION_HEX >= 0x03000000 static struct PyModuleDef SWIG_module = { # if PY_VERSION_HEX >= 0x03020000 PyModuleDef_HEAD_INIT, # else { PyObject_HEAD_INIT(NULL) NULL, /* m_init */ 0, /* m_index */ NULL, /* m_copy */ }, # endif (char *) SWIG_name, NULL, -1, SwigMethods, NULL, NULL, NULL, NULL }; #endif #if defined(SWIGPYTHON_BUILTIN) static SwigPyClientData SwigPyObject_clientdata = { 0, 0, 0, 0, 0, 0, 0 }; static PyGetSetDef this_getset_def = { (char *)"this", &SwigPyBuiltin_ThisClosure, NULL, NULL, NULL }; static SwigPyGetSet thisown_getset_closure = { (PyCFunction) SwigPyObject_own, (PyCFunction) SwigPyObject_own }; static PyGetSetDef thisown_getset_def = { (char *)"thisown", SwigPyBuiltin_GetterClosure, SwigPyBuiltin_SetterClosure, NULL, &thisown_getset_closure }; PyObject *metatype_args; PyTypeObject *builtin_pytype; int builtin_base_count; swig_type_info *builtin_basetype; PyObject *tuple; PyGetSetDescrObject *static_getset; PyTypeObject *metatype; SwigPyClientData *cd; PyObject *public_interface, *public_symbol; PyObject *this_descr; PyObject *thisown_descr; int i; (void)builtin_pytype; (void)builtin_base_count; (void)builtin_basetype; (void)tuple; (void)static_getset; /* metatype is used to implement static member variables. */ metatype_args = Py_BuildValue("(s(O){})", "SwigPyObjectType", &PyType_Type); assert(metatype_args); metatype = (PyTypeObject *) PyType_Type.tp_call((PyObject *) &PyType_Type, metatype_args, NULL); assert(metatype); Py_DECREF(metatype_args); metatype->tp_setattro = (setattrofunc) &SwigPyObjectType_setattro; assert(PyType_Ready(metatype) >= 0); #endif /* Fix SwigMethods to carry the callback ptrs when needed */ SWIG_Python_FixMethods(SwigMethods, swig_const_table, swig_types, swig_type_initial); #if PY_VERSION_HEX >= 0x03000000 m = PyModule_Create(&SWIG_module); #else m = Py_InitModule((char *) SWIG_name, SwigMethods); #endif md = d = PyModule_GetDict(m); (void)md; SWIG_InitializeModule(0); #ifdef SWIGPYTHON_BUILTIN SwigPyObject_stype = SWIG_MangledTypeQuery("_p_SwigPyObject"); assert(SwigPyObject_stype); cd = (SwigPyClientData*) SwigPyObject_stype->clientdata; if (!cd) { SwigPyObject_stype->clientdata = &SwigPyObject_clientdata; SwigPyObject_clientdata.pytype = SwigPyObject_TypeOnce(); } else if (SwigPyObject_TypeOnce()->tp_basicsize != cd->pytype->tp_basicsize) { PyErr_SetString(PyExc_RuntimeError, "Import error: attempted to load two incompatible swig-generated modules."); # if PY_VERSION_HEX >= 0x03000000 return NULL; # else return; # endif } /* All objects have a 'this' attribute */ this_descr = PyDescr_NewGetSet(SwigPyObject_type(), &this_getset_def); (void)this_descr; /* All objects have a 'thisown' attribute */ thisown_descr = PyDescr_NewGetSet(SwigPyObject_type(), &thisown_getset_def); (void)thisown_descr; public_interface = PyList_New(0); public_symbol = 0; (void)public_symbol; PyDict_SetItemString(md, "__all__", public_interface); Py_DECREF(public_interface); for (i = 0; SwigMethods[i].ml_name != NULL; ++i) SwigPyBuiltin_AddPublicSymbol(public_interface, SwigMethods[i].ml_name); for (i = 0; swig_const_table[i].name != 0; ++i) SwigPyBuiltin_AddPublicSymbol(public_interface, swig_const_table[i].name); #endif SWIG_InstallConstants(d,swig_const_table); import_array(); #if PY_VERSION_HEX >= 0x03000000 return m; #else return; #endif } somoclu/src/Python/somoclu.i0000644000417600011450000000333412402311155017557 0ustar pewiunix-users-shaman%module somoclu %include "std_string.i" %{ #define SWIG_FILE_WITH_INIT #include "src/src/somocluWrap.h" %} %include "numpy.i" %init %{ import_array(); %} %apply (float* INPLACE_ARRAY1, int DIM1) {(float* data, int data_length)} %apply (float* INPLACE_ARRAY1, int DIM1) {(float* codebook, int codebook_size)} %apply (int* INPLACE_ARRAY1, int DIM1) {(int* globalBmus, int globalBmus_size)} %apply (float* INPLACE_ARRAY1, int DIM1) {(float* uMatrix, int uMatrix_size)} /* %typemap (in,numinputs=0) core_data * (core_data temp) { */ /* $1 = &temp; */ /* } */ /* %typemap (argout) core_data * { */ /* /\* codebook *\/ */ /* { */ /* npy_intp dims[1] = { $1->codebook_size }; */ /* PyObject * array = PyArray_SimpleNewFromData(1, dims, NPY_FLOAT32, (void*)($1->codebook)); */ /* if (!array) SWIG_fail; */ /* $result = SWIG_Python_AppendOutput($result,array); */ /* } */ /* /\* globalBmus *\/ */ /* { */ /* npy_intp dims[1] = { $1->globalBmus_size }; */ /* PyObject * array = PyArray_SimpleNewFromData(1, dims, NPY_INT32, (void*)($1->globalBmus)); */ /* if (!array) SWIG_fail; */ /* $result = SWIG_Python_AppendOutput($result,array); */ /* } */ /* /\* uMatrix *\/ */ /* { */ /* npy_intp dims[1] = { $1->uMatrix_size }; */ /* PyObject * array = PyArray_SimpleNewFromData(1, dims, NPY_FLOAT32, (void*)($1->uMatrix)); */ /* if (!array) SWIG_fail; */ /* $result = SWIG_Python_AppendOutput($result,array); */ /* } */ /* } */ /* %ignore core_data; */ /* struct core_data */ /* { */ /* float *codebook; */ /* int *globalBmus; */ /* float *uMatrix; */ /* int codebook_size; */ /* int globalBmus_size; */ /* int uMatrix_size; */ /* }; */ %include "src/src/somocluWrap.h" somoclu/src/Python/MANIFEST.in0000644000417600011450000000035112402311155017456 0ustar pewiunix-users-shamaninclude src/autogen.sh include src/configure.ac include src/Makefile.in include src/m4/* include src/src/*.h include src/src/*.cpp include src/src/*.cu include src/src/Makefile.in include tests/rgbs.txt include tests/somoclu_test.py somoclu/src/Python/tests/0000755000417600011450000000000012402311155017063 5ustar pewiunix-users-shamansomoclu/src/Python/tests/somoclu_test.py0000755000417600011450000000310612402311155022160 0ustar pewiunix-users-shaman#!/usr/bin/env python2 # -*- coding: utf-8 -*- import somoclu import numpy as np #import argparse if __name__ == "__main__": #parser = argparse.ArgumentParser("Somoclu python example") #parser.add_argument('-i', '--input_file', help='Input data file path', # required=True) #args = parser.parse_args() #data = np.loadtxt(args.input_file) data = np.loadtxt('rgbs.txt') #print(data) data = np.float32(data) nSomX = 50 nSomY = 50 nVectors = data.shape[0] nDimensions = data.shape[1] data1D = np.ndarray.flatten(data) nEpoch = 10 radius0 = 0 radiusN = 0 radiusCooling = "linear" scale0 = 0 scaleN = 0.01 scaleCooling = "linear" kernelType = 0 mapType = "planar" snapshots = 0 initialCodebookFilename = '' codebook_size = nSomY * nSomX * nDimensions codebook = np.zeros(codebook_size, dtype=np.float32) globalBmus_size = int(nVectors * int(np.ceil(nVectors/nVectors))*2) globalBmus = np.zeros(globalBmus_size, dtype=np.intc) uMatrix_size = nSomX * nSomY uMatrix = np.zeros(uMatrix_size, dtype=np.float32) somoclu.trainWrapper(data1D, nEpoch, nSomX, nSomY, nDimensions, nVectors, radius0, radiusN, radiusCooling, scale0, scaleN, scaleCooling, snapshots, kernelType, mapType, initialCodebookFilename, codebook, globalBmus, uMatrix) #print codebook #print globalBmus #print uMatrix somoclu/src/Makefile.in0000644000417600011450000000354612402311155016515 0ustar pewiunix-users-shaman# @configure_input@ # Package-related substitution variables package = @PACKAGE_NAME@ version = @PACKAGE_VERSION@ tarname = @PACKAGE_TARNAME@ distdir = $(tarname)-$(version) # Prefix-related substitution variables prefix = @prefix@ exec_prefix = @exec_prefix@ bindir = @bindir@ libdir = @libdir@ # Tool-related substitution variables CXX = @CXX@ CXXFLAGS = @CXXFLAGS@ LIBS = @LIBS@ DEFS = @DEFS@ INSTALL = @INSTALL@ INSTALL_DATA = @INSTALL_DATA@ INSTALL_PROGRAM= @INSTALL_PROGRAM@ INSTALL_SCRIPT = @INSTALL_SCRIPT@ CUDA_CFLAGS = @CUDA_CFLAGS@ CUDA_LIBS = @CUDA_LIBS@ CUDA_LDFLAGS = @CUDA_LDFLAGS@ NVCC = @NVCC@ MPI_INC = @MPI_INC@ MPI_LIBDIR = @MPI_LIBDIR@ MPI_LIBS = @MPI_LIBS@ # VPATH-related substitution variables srcdir = @srcdir@ VPATH = @srcdir@ LIBOBJS=sparseCpuKernels.o io.o denseCpuKernels.o mapDistanceFunctions.o training.o uMatrix.o trainOneEpoch.o ifdef CUDA_LIBS LIBOBJS+=denseGpuKernels.cu.co endif OBJS=$(LIBOBJS) somoclu.o all: somoclu lib: $(LIBOBJS) $(CXX) $(DEFS) $(CXXFLAGS) $(CUDA_LDFLAGS) ${MPI_LIBDIR} -shared -o libsomoclu.so $^ $(LIBS) $(CUDA_LIBS) ${MPI_LIBS} somoclu: $(OBJS) $(CXX) $(DEFS) $(CXXFLAGS) $(CUDA_LDFLAGS) ${MPI_LIBDIR} -o $@ $^ $(LIBS) $(CUDA_LIBS) ${MPI_LIBS} %.o: %.cpp $(CXX) $(DEFS) $(CXXFLAGS) ${MPI_INC} -I$(srcdir) -I.. -o $@ -c $(srcdir)/$< %.cu.co: %.cu $(NVCC) $(DEFS) $(CUDA_CFLAGS) ${MPI_INC} -I$(srcdir) -I.. -o $@ -c $(srcdir)/$< clean: -rm -f somoclu libsomoclu.so $(OBJS) 1>/dev/null install: $(INSTALL) -d $(DESTDIR)$(bindir) $(INSTALL_PROGRAM) -m 0755 somoclu \ $(DESTDIR)$(bindir) uninstall: -rm $(DESTDIR)$(bindir)/somoclu &>/dev/null Makefile: Makefile.in ../config.status cd .. && ./config.status $@ ../config.status: ../configure cd .. && ./config.status --recheck .PHONY: all clean install uninstall somoclu/src/denseCpuKernels.cpp0000644000417600011450000001460112402311155020240 0ustar pewiunix-users-shaman/** * Self-Organizing Maps on a cluster * Copyright (C) 2013 Peter Wittek * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * */ #include #include #include "somoclu.h" #ifdef HAVE_R #include #endif /** Distance b/w a feature vector and a weight vector * = Euclidean * @param som_y * @param som_x * @param r - row number in the input feature file */ float get_distance(float* codebook, float* data, unsigned int som_y, unsigned int som_x, unsigned int nSomX, unsigned int nDimensions, unsigned int r) { float distance = 0.0f; for (unsigned int d = 0; d < nDimensions; d++) distance += (codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d] - *(data + r*nDimensions + d)) * (codebook[som_y*nSomX*nDimensions+som_x*nDimensions+d] - *(data + r*nDimensions + d)); return distance; } /** Get node coords for the best matching unit (BMU) * @param coords - BMU coords * @param n - row num in the input feature file */ void get_bmu_coord(float* codebook, float* data, unsigned int nSomY, unsigned int nSomX, unsigned int nDimensions, unsigned int* coords, unsigned int n) { float mindist = 9999.99; float dist = 0.0f; /// Check nSomX * nSomY nodes one by one and compute the distance /// D(W_K, Fvec) and get the mindist and get the coords for the BMU. /// for (unsigned int som_y = 0; som_y < nSomY; som_y++) { for (unsigned int som_x = 0; som_x < nSomX; som_x++) { dist = get_distance(codebook, data, som_y, som_x, nSomX, nDimensions, n); if (dist < mindist) { mindist = dist; coords[0] = som_x; coords[1] = som_y; } } } } void trainOneEpochDenseCPU(int itask, float *data, float *numerator, float *denominator, float *codebook, unsigned int nSomX, unsigned int nSomY, unsigned int nDimensions, unsigned int nVectors, unsigned int nVectorsPerRank, float radius, float scale, string mapType, int *globalBmus) { unsigned int p1[2] = {0, 0}; unsigned int *bmus = new unsigned int[nVectorsPerRank*2]; #ifdef _OPENMP #pragma omp parallel default(shared) private(p1) #endif { #ifdef _OPENMP #pragma omp for #endif #if defined(linux) || defined(__APPLE__) for (unsigned int n = 0; n < nVectorsPerRank; n++) { #endif #ifdef _WIN32 for (int n = 0; n < nVectorsPerRank; n++) { #endif if (itask*nVectorsPerRank+n/dev/null somoclu/aclocal.m40000644000417600011450000000403612402311225015512 0ustar pewiunix-users-shaman# generated automatically by aclocal 1.10.1 -*- Autoconf -*- # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, # 2005, 2006, 2007, 2008 Free Software Foundation, Inc. # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; without # even the implied warranty of MERCHANTABILITY or FITNESS FOR A # PARTICULAR PURPOSE. # AM_CONDITIONAL -*- Autoconf -*- # Copyright (C) 1997, 2000, 2001, 2003, 2004, 2005, 2006 # Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # serial 8 # AM_CONDITIONAL(NAME, SHELL-CONDITION) # ------------------------------------- # Define a conditional. AC_DEFUN([AM_CONDITIONAL], [AC_PREREQ(2.52)dnl ifelse([$1], [TRUE], [AC_FATAL([$0: invalid condition: $1])], [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl AC_SUBST([$1_TRUE])dnl AC_SUBST([$1_FALSE])dnl _AM_SUBST_NOTMAKE([$1_TRUE])dnl _AM_SUBST_NOTMAKE([$1_FALSE])dnl if $2; then $1_TRUE= $1_FALSE='#' else $1_TRUE='#' $1_FALSE= fi AC_CONFIG_COMMANDS_PRE( [if test -z "${$1_TRUE}" && test -z "${$1_FALSE}"; then AC_MSG_ERROR([[conditional "$1" was never defined. Usually this means the macro was only invoked conditionally.]]) fi])]) # Copyright (C) 2006 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # _AM_SUBST_NOTMAKE(VARIABLE) # --------------------------- # Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in. # This macro is traced by Automake. AC_DEFUN([_AM_SUBST_NOTMAKE]) somoclu/CHANGES0000644000417600011450000000334612402311155014652 0ustar pewiunix-users-shamanVersion 1.4: 2014-09-05 - Better Windows support. - Completed CUDA support for Python and R interfaces. - Faster compilation by removing unnecessary flags for nvcc and support for CUDA 6.5. - Bug fixes: R version no longer needs separate code. Version 1.3.1: 2014-04-10 - Better I/O separation for the Python, R, and MATLAB interfaces. - Initial Windows support through GCC on Windows. - Bug fixes: major MPI initialization bug fixed. Version 1.3: 2014-03-31 - Learning rate parameter included. - Linear and exponential cooling strategies added for radius and learning rate. - CLI interface made more user-friendly. - Default radius depends on both X and Y of the map. - Bug fixes: CUDA build without MPI, best matching unit passing without MPI, coordinate order in best matching unit file. - Python, R, and MATLAB interfaces added. Version 1.2: 2013-12-17 - Massive improvements in OpenMP parallelization. - MPI libraries are no longer mandatory. - Best matching units are saved. - Option for specifying an initial codebook for the map. - ESOM .lrn input format added. - Parsing of white-space characters corrected. - Long-named command line switches for specifying SOM dimensions. - Fine-grained control of which interim files to save across epochs - Option in Makefile for building shared library. Version 1.1.2: 2013-11-28 - Toroid maps were added. - Initial radius is exposed as a parameter via the command line interface. - Formats of codebook and U-matrix export are compatible with Databionic ESOM Tools for advanced visualisation. - Bug fixes: codebook update with a compact support was removed, NaN entry no longer appears in U-matrices. Version 1.0: 2013-05-14 - Initial release. somoclu/LICENSE0000644000417600011450000010575512402311155014673 0ustar pewiunix-users-shaman GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU General Public License is a free, copyleft license for software and other kinds of works. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too. 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If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. 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Curiously '\x00'!='x' always comes out true, for an array size at least. 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Create the # directory the slow way, step by step, checking for races as we go. case $dstdir in /*) prefix='/';; -*) prefix='./';; *) prefix='';; esac eval "$initialize_posix_glob" oIFS=$IFS IFS=/ $posix_glob set -f set fnord $dstdir shift $posix_glob set +f IFS=$oIFS prefixes= for d do test -z "$d" && continue prefix=$prefix$d if test -d "$prefix"; then prefixes= else if $posix_mkdir; then (umask=$mkdir_umask && $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break # Don't fail if two instances are running concurrently. test -d "$prefix" || exit 1 else case $prefix in *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;; *) qprefix=$prefix;; esac prefixes="$prefixes '$qprefix'" fi fi prefix=$prefix/ done if test -n "$prefixes"; then # Don't fail if two instances are running concurrently. (umask $mkdir_umask && eval "\$doit_exec \$mkdirprog $prefixes") || test -d "$dstdir" || exit 1 obsolete_mkdir_used=true fi fi fi if test -n "$dir_arg"; then { test -z "$chowncmd" || $doit $chowncmd "$dst"; } && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } && { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false || test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1 else # Make a couple of temp file names in the proper directory. dsttmp=$dstdir/_inst.$$_ rmtmp=$dstdir/_rm.$$_ # Trap to clean up those temp files at exit. trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0 # Copy the file name to the temp name. (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") && # and set any options; do chmod last to preserve setuid bits. # # If any of these fail, we abort the whole thing. If we want to # ignore errors from any of these, just make sure not to ignore # errors from the above "$doit $cpprog $src $dsttmp" command. # { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } && { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } && { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } && # If -C, don't bother to copy if it wouldn't change the file. if $copy_on_change && old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` && new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` && eval "$initialize_posix_glob" && $posix_glob set -f && set X $old && old=:$2:$4:$5:$6 && set X $new && new=:$2:$4:$5:$6 && $posix_glob set +f && test "$old" = "$new" && $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1 then rm -f "$dsttmp" else # Rename the file to the real destination. $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null || # The rename failed, perhaps because mv can't rename something else # to itself, or perhaps because mv is so ancient that it does not # support -f. { # Now remove or move aside any old file at destination location. # We try this two ways since rm can't unlink itself on some # systems and the destination file might be busy for other # reasons. In this case, the final cleanup might fail but the new # file should still install successfully. { test ! -f "$dst" || $doit $rmcmd -f "$dst" 2>/dev/null || { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null && { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; } } || { echo "$0: cannot unlink or rename $dst" >&2 (exit 1); exit 1 } } && # Now rename the file to the real destination. $doit $mvcmd "$dsttmp" "$dst" } fi || exit 1 trap '' 0 fi done # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-end: "$" # End: somoclu/README.md0000644000417600011450000002244312402311155015135 0ustar pewiunix-users-shamanSomoclu === Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs, it is able to rely on MPI for distributing the workload in a cluster, and it can be accelerated by CUDA. A sparse kernel is also included, which is useful for training maps on vector spaces generated in text mining processes. The topology of the grid of neurons is rectangular. Key features: * Fast execution by parallelization: OpenMP, MPI, and CUDA are supported. * Planar and toroid maps. * Both dense and sparse input data are supported. * Large maps of several hundred thousand neurons are feasible. * Integration with Databionic ESOM Tools. * Python, R, and MATLAB interfaces for the dense CPU and GPU kernels. For more information, refer to the following paper: Peter Wittek (2013). Somoclu: An Efficient Distributed Library for Self-Organizing Maps. [arXiv:1305.1422](http://arxiv.org/abs/1305.1422). Usage === Basic Use --- Somoclu takes a plain text input file -- either dense or sparse data. Example files are included. $ [mpirun -np NPROC] somoclu [OPTIONs] INPUT_FILE OUTPUT_PREFIX Arguments: -c FILENAME Specify an initial codebook for the map. -e NUMBER Maximum number of epochs -k NUMBER Kernel type 0: Dense CPU 1: Dense GPU 2: Sparse CPU -m TYPE Map type: planar or toroid (default: planar) -t STRATEGY Radius cooling strategy: linear or exponential (default: linear) -r NUMBER Start radius (default: half of the map in direction min(x,y)) -R NUMBER End radius (default: 1) -T STRATEGY Learning rate cooling strategy: linear or exponential (default: linear) -l NUMBER Starting learning rate (default: 0.1) -L NUMBER Finishing learning rate (default: 0.01) -s NUMBER Save interim files (default: 0): 0: Do not save interim files 1: Save U-matrix only 2: Also save codebook and best matching -x, --columns NUMBER Number of columns in map (size of SOM in direction x) -y, --rows NUMBER Number of rows in map (size of SOM in direction y) Examples: $ somoclu data/rgbs.txt data/rgbs $ mpirun -np 4 somoclu -k 0 --rows 20 --columns 20 data/rgbs.txt data/rgbs Efficient Parallel Execution --- The CPU kernels use OpenMP to load multicore processors. On a single node, this is more efficient than launching tasks with MPI to match the number of cores. The MPI tasks replicated the codebook, which is especially inefficient for large maps. For instance, given a single node with eight cores, the following execution will use 1/8th of the memory, and will run 10-20% faster: $ somoclu -x 200 -y 200 data/rgbs.txt data/rgbs Or, equivalently: $ OMP_NUM_THREADS=8 somoclu -x 200 -y 200 data/rgbs.txt data/rgbs Avoid the following on a single node: $ OMP_NUM_THREADS=1 mpirun -np 8 somoclu -x 200 -y 200 data/rgbs.txt data/rgbs The same caveats apply for the sparse CPU kernel. Visualisation --- The primary purpose of generating a map is visualisation. Somoclu does not come with its own functions for visualisation, since there are numerous generic tools that are capable of plotting high-quality figures. The output formats of the U-matrix and the codebook are compatible with [Databionic ESOM Tools](http://databionic-esom.sourceforge.net/) for more advanced visualisation. Input File Formats === One sparse and two dense data formats are supported. All of them are plain text files. The entries can be separated by any white-space character. One row represents one data instance across all formats. Comment lines starting with a hash mark are ignored. The sparse format follows the [libsvm](http://www.csie.ntu.edu.tw/~cjlin/libsvm/) guidelines. The first feature is zero-indexed. For instance, the vector [ 1.2 0 0 3.4] is represented as the following line in the file: 0:1.2 3:3.4. The file is parsed twice: once to get the number of instances and features, and the second time to read the data in the individual threads. The basic dense format includes the coordinates of the data vectors, separated by a white-space. Just like the sparse format, this file is parsed twice to get the basic dimensions right. The .lrn file of [Databionic ESOM Tools](http://databionic-esom.sourceforge.net/) is also accepted and it is parsed only once. The format is described as follows: % n % m % s1 s2 .. sm % var_name1 var_name2 .. var_namem x11 x12 .. x1m x21 x22 .. x2m . . . . . . . . xn1 xn2 .. xnm Here n is the number of rows in the file, that is, the number of data instances. Parameter m defines the number of columns in the file. The next row defines the column mask: the value 1 for a column means the column should be used in the training. Note that the first column in this format is always a unique key, so this should have the value 9 in the column mask. The row with the variable names is ignore by Somoclu. The elements of the matrix follow -- from here, the file is identical to the basic dense format, with the addition of the first column as the unique key. If the input file is sparse, but a dense kernel is invoked, Somoclu will execute and results will be incorrect. Invoking a sparse kernel on a dense input file is likely to lead to a segmentation fault. Interfaces === Python, R, and MATLAB interfaces are available for the dense CPU kernel. MPI, CUDA, and the sparse kernel are not support through the interfaces. The connection to the C++ library is seamless, data structures are not duplicated. For respective examples, see the folders in src. All versions require GCC to compile the code. The Python version is also available in Pypi. You can install it with $ sudo pip install somoclu The R version is available on CRAN. You can install it with install.packages("Rsomoclu") For using the MATLAB toolbox, define the location of the mex compiler in MEX_BIN. Then invoke makeMex.sh in the src/MATLAB folder. For more information on the respective interfaces, refer to the subfolders in src. Compilation & Installation === The only dependency is GCC, although other compiler chains might also work. Distributed systems and single-machine multicore execution is supported through MPI. The package was tested with OpenMPI. It should also work with other MPI flavours. CUDA support is optional. Linux or Mac OS X --- From GIT repository first run $ ./autogen.sh Then follow the standard POSIX procedure: $ ./configure [options] $ make $ make install Options for configure --prefix=PATH Set directory prefix for installation By default Somoclu is installed into /usr/local. If you prefer a different location, use this option to select an installation directory. --without-mpi Disregard any MPI installation found. --with-mpi=MPIROOT Use MPI root directory. --with-mpi-compilers=DIR or --with-mpi-compilers=yes use MPI compiler (mpicxx) found in directory DIR, or in your PATH if =yes --with-mpi-libs="LIBS" MPI libraries [default "-lmpi"] --with-mpi-incdir=DIR MPI include directory [default MPIROOT/include] --with-mpi-libdir=DIR MPI library directory [default MPIROOT/lib] The above flags allow the identification of the correct MPI library the user wishes to use. The flags are especially useful if MPI is installed in a non-standard location, or when multiple MPI libraries are available. --with-cuda=/path/to/cuda Set path for CUDA Somoclu looks for CUDA in /usr/local/cuda. If your installation is not there, then specify the path with this parameter. If you do not want CUDA enabled, set the parameter to ```--without-cuda```. Windows --- Use the `somoclu.sln` under src/Windows/somoclu as an example visual studio 2013 solution. Modify the CUDA version or VC compiler version according to your needs. The default solution enables all of OpenMP, MPI, and CUDA. The default MPI installation path is `C:\Program Files\Microsoft MPI`, modify the settings if yours is in a different path. The configuration default CUDA version is 6.5. Disable MPI by removing `HAVE_MPI` macro in the project properties (`Properties -> Configuration Properties -> C/C++ -> Preprocessor`). Disable CUDA by removing `CUDA` macro in the solution properties. The usage is identical to the linux version through command line (see the relevant section). Known Issues === The MATLAB CUDA interface crashes with unknown reasons. The maps generated by the GPU and the CPU kernels are likely to be different. For computational efficiency, Somoclu uses single-precision floats. This occasionally results in identical distances between a data instance and the neurons. The CPU version will pick the best matching unit with the lowest coordinate values. Such sequentiality cannot be guaranteed in the reduction kernel of the GPU variant. This is not a bug, but it is better to be aware of it. Acknowledgment === This work was supported by the European Commission Seventh Framework Programme under Grant Agreement Number FP7-601138 PERICLES and by the AWS in Education Machine Learning Grant award.