3 files changed, 947 insertions, 0 deletions

diff --git a/lib/ffts/java/Makefile.am b/lib/ffts/java/Makefile.am
new file mode 100644
index 0000000..83ff5d8
--- /dev/null
+++ b/lib/ffts/java/Makefile.am
@@ -0,0 +1,33 @@
+
+# TODO: the ax_prog_javah thing doesn't work so this
+# requires javah in the path
+
+if ENABLE_JNI
+JAVA_SRC=$(shell find $(srcdir)/src -name '*.java')
+
+BUILT_SOURCES = nz_ac_waikato_ffts_FFTS.h
+
+all: ffts.jar
+
+classes ffts.jar: $(JAVA_SRC)
+	-rm -rf classes
+	mkdir classes
+	$(JAVAC) -d classes -sourcepath src $(JAVA_SRC)
+	$(JAR) -cf ffts.jar -C classes .
+
+lib_LTLIBRARIES = libffts_jni.la
+libffts_jni_la_SOURCES = jni/ffts_jni.c
+nodist_include_HEADERS = nz_ac_waikato_ffts_FFTS.h
+libffts_jni_la_LIBADD = $(top_builddir)/src/libffts.la
+libffts_jni_la_CFLAGS = @JNI_CPPFLAGS@ $(AM_CFLAGS) -I$(top_srcdir)/include
+libffts_jni_la_LDFLAGS = -shared
+
+pkgdata_DATA = ffts.jar
+
+nz_ac_waikato_ffts_FFTS.h: classes
+	javah -cp $< nz.ac.waikato.ffts.FFTS
+
+CLEANFILES=ffts.jar nz_ac_waikato_ffts_FFTS.h
+clean-local:
+	-rm -rf classes
+endif
diff --git a/lib/ffts/java/Makefile.in b/lib/ffts/java/Makefile.in
new file mode 100644
index 0000000..45d41c4
--- /dev/null
+++ b/lib/ffts/java/Makefile.in
@@ -0,0 +1,681 @@
+# Makefile.in generated by automake 1.12.4 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994-2012 Free Software Foundation, Inc.
+
+# This Makefile.in 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.
+
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+
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+
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+	  $(MKDIR_P) "$(DESTDIR)$(includedir)" || exit 1; \
+	fi; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_HEADER) $$files '$(DESTDIR)$(includedir)'"; \
+	  $(INSTALL_HEADER) $$files "$(DESTDIR)$(includedir)" || exit $$?; \
+	done
+
+uninstall-nodist_includeHEADERS:
+	@$(NORMAL_UNINSTALL)
+	@list='$(nodist_include_HEADERS)'; test -n "$(includedir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	dir='$(DESTDIR)$(includedir)'; $(am__uninstall_files_from_dir)
+
+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
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+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	mkid -fID $$unique
+tags: TAGS
+
+TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	set x; \
+	here=`pwd`; \
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+	  test -n "$$unique" || unique=$$empty_fix; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
+	fi
+ctags: CTAGS
+CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	test -z "$(CTAGS_ARGS)$$unique" \
+	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+	     $$unique
+
+GTAGS:
+	here=`$(am__cd) $(top_builddir) && pwd` \
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
+
+cscopelist:  $(HEADERS) $(SOURCES) $(LISP)
+	list='$(SOURCES) $(HEADERS) $(LISP)'; \
+	case "$(srcdir)" in \
+	  [\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
+	  *) sdir=$(subdir)/$(srcdir) ;; \
+	esac; \
+	for i in $$list; do \
+	  if test -f "$$i"; then \
+	    echo "$(subdir)/$$i"; \
+	  else \
+	    echo "$$sdir/$$i"; \
+	  fi; \
+	done >> $(top_builddir)/cscope.files
+
+distclean-tags:
+	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: $(BUILT_SOURCES)
+	$(MAKE) $(AM_MAKEFLAGS) check-am
+all-am: Makefile $(LTLIBRARIES) $(DATA) $(HEADERS)
+installdirs:
+	for dir in "$(DESTDIR)$(libdir)" "$(DESTDIR)$(pkgdatadir)" "$(DESTDIR)$(includedir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: $(BUILT_SOURCES)
+	$(MAKE) $(AM_MAKEFLAGS) install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+	if test -z '$(STRIP)'; then \
+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	      install; \
+	else \
+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
+	fi
+mostlyclean-generic:
+
+clean-generic:
+	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+	-test -z "$(BUILT_SOURCES)" || rm -f $(BUILT_SOURCES)
+@ENABLE_JNI_FALSE@clean-local:
+clean: clean-am
+
+clean-am: clean-generic clean-libLTLIBRARIES clean-libtool clean-local \
+	mostlyclean-am
+
+distclean: distclean-am
+	-rm -rf ./$(DEPDIR)
+	-rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+	distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
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+html: html-am
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+html-am:
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+info: info-am
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+install-dvi: install-dvi-am
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+install-exec-am: install-libLTLIBRARIES
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+install-html: install-html-am
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+install-html-am:
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+install-info: install-info-am
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+install-info-am:
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+install-ps-am:
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+installcheck-am:
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+maintainer-clean: maintainer-clean-am
+	-rm -rf ./$(DEPDIR)
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
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+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic \
+	mostlyclean-libtool
+
+pdf: pdf-am
+
+pdf-am:
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+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-libLTLIBRARIES uninstall-nodist_includeHEADERS \
+	uninstall-pkgdataDATA
+
+.MAKE: all check install install-am install-strip
+
+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
+	clean-libLTLIBRARIES clean-libtool clean-local cscopelist \
+	ctags distclean distclean-compile distclean-generic \
+	distclean-libtool distclean-tags distdir dvi dvi-am html \
+	html-am info info-am install install-am install-data \
+	install-data-am install-dvi install-dvi-am install-exec \
+	install-exec-am install-html install-html-am install-info \
+	install-info-am install-libLTLIBRARIES install-man \
+	install-nodist_includeHEADERS install-pdf install-pdf-am \
+	install-pkgdataDATA install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-compile \
+	mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
+	tags uninstall uninstall-am uninstall-libLTLIBRARIES \
+	uninstall-nodist_includeHEADERS uninstall-pkgdataDATA
+
+
+@ENABLE_JNI_TRUE@all: ffts.jar
+
+@ENABLE_JNI_TRUE@classes ffts.jar: $(JAVA_SRC)
+@ENABLE_JNI_TRUE@	-rm -rf classes
+@ENABLE_JNI_TRUE@	mkdir classes
+@ENABLE_JNI_TRUE@	$(JAVAC) -d classes -sourcepath src $(JAVA_SRC)
+@ENABLE_JNI_TRUE@	$(JAR) -cf ffts.jar -C classes .
+
+@ENABLE_JNI_TRUE@nz_ac_waikato_ffts_FFTS.h: classes
+@ENABLE_JNI_TRUE@	javah -cp $< nz.ac.waikato.ffts.FFTS
+@ENABLE_JNI_TRUE@clean-local:
+@ENABLE_JNI_TRUE@	-rm -rf classes
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/lib/ffts/java/jni/ffts_jni.c b/lib/ffts/java/jni/ffts_jni.c
new file mode 100644
index 0000000..41fdf76
--- /dev/null
+++ b/lib/ffts/java/jni/ffts_jni.c
@@ -0,0 +1,233 @@
+/*
+ * This file is part of FFTS -- The Fastest Fourier Transform in the South
+ *
+ * Copyright (c) 2013, Michael Zucchi <notzed@gmail.com>
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ *   * Redistributions of source code must retain the above copyright
+ *     notice, this list of conditions and the following disclaimer.
+ *   * 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.
+ *   * Neither the name of the organization nor the
+ *     names of its contributors may be used to endorse or promote products
+ *     derived from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS 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 ANTHONY M. BLAKE 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 "config.h"
+
+#include <ffts.h>
+#include <alloca.h>
+
+// Bit of a hack for android, as we can't build the *.h without
+// the classes ... but we can't build the project without the jni.
+#ifdef ANDROID
+#include <jni.h>
+#else
+#include "nz_ac_waikato_ffts_FFTS.h"
+#endif
+
+// TODO: feature tests instead
+#ifdef HAVE_SSE
+#define NEEDS_ALIGNED
+#endif
+
+#ifdef NEEDS_ALIGNED
+#define ALIGN_MASK 15
+
+static void *
+xmemalign(size_t align, size_t size) {
+#if defined(HAVE_DECL_POSIX_MEMALIGN)
+	void *r;
+
+	if (posix_memalign(&r, align, size) != 0)
+		return NULL;
+	return r;	
+#elif defined(HAVE_DECL_MEMALIGN)
+	return memalign(align, size);
+#else
+#error "Require an aligning malloc"
+#endif
+}
+#endif
+
+static void
+throwOutOfMemoryError(JNIEnv *env, const char *msg) {
+	jclass jc = (*env)->FindClass(env, "java/lang/OutOfMemoryError");
+
+	if (jc)
+		(*env)->ThrowNew(env, jc, msg);
+}
+
+JNIEXPORT jlong JNICALL Java_nz_ac_waikato_ffts_FFTS_complex_11d
+(JNIEnv *env, jclass jc, jint N, jint sign) {
+	ffts_plan_t *plan;
+
+	plan = ffts_init_1d(N, sign);
+	if (!plan)
+		throwOutOfMemoryError(env, NULL);
+
+	return (jlong)plan;
+}
+
+JNIEXPORT jlong JNICALL Java_nz_ac_waikato_ffts_FFTS_complex_12d
+(JNIEnv *env, jclass jc, jint N1, jint N2, jint sign) {
+	ffts_plan_t *plan;
+
+	plan = ffts_init_2d(N1, N2, sign);
+	if (!plan)
+		throwOutOfMemoryError(env, NULL);
+
+	return (jlong)plan;
+}
+
+JNIEXPORT jlong JNICALL Java_nz_ac_waikato_ffts_FFTS_complex_1nd
+(JNIEnv *env, jclass jc, jintArray jNs, jint sign) {
+	ffts_plan_t *plan;
+	int n = (*env)->GetArrayLength(env, jNs);
+	int *cNs;
+	size_t *Ns;
+	int i;
+
+	// Needs to convert java int array to size_t array
+	// Get the int elements and conver to C type
+	Ns = alloca(sizeof(*Ns) * n);
+	cNs = alloca(sizeof(int) * n);
+	(*env)->GetIntArrayRegion(env, jNs, 0, n, cNs);
+	for (i=0;i<n;i++)
+		Ns[i] = cNs[i];
+
+	plan = ffts_init_nd(n, Ns, sign);
+	if (!plan)
+		throwOutOfMemoryError(env, NULL);
+
+	return (jlong)plan;
+}
+
+JNIEXPORT jlong JNICALL Java_nz_ac_waikato_ffts_FFTS_real_11d
+(JNIEnv *env, jclass jc, jint N, jint sign) {
+	ffts_plan_t *plan;
+
+	plan = ffts_init_1d_real(N, sign);
+	if (!plan)
+		throwOutOfMemoryError(env, NULL);
+
+	return (jlong)plan;
+}
+
+JNIEXPORT jlong JNICALL Java_nz_ac_waikato_ffts_FFTS_real_12d
+(JNIEnv *env, jclass jc, jint N1, jint N2, jint sign) {
+	ffts_plan_t *plan;
+
+	plan = ffts_init_2d_real(N1, N2, sign);
+	if (!plan)
+		throwOutOfMemoryError(env, NULL);
+
+	return (jlong)plan;
+}
+
+JNIEXPORT jlong JNICALL Java_nz_ac_waikato_ffts_FFTS_real_1nd
+(JNIEnv *env, jclass jc, jintArray jNs, jint sign) {
+	ffts_plan_t *plan;
+	int n = (*env)->GetArrayLength(env, jNs);
+	int *cNs;
+	size_t *Ns;
+	int i;
+
+	// Needs to convert java int array to size_t array
+	// Get the int elements and conver to C type
+	Ns = alloca(sizeof(*Ns) * n);
+	cNs = alloca(sizeof(int) * n);
+	(*env)->GetIntArrayRegion(env, jNs, 0, n, cNs);
+	for (i=0;i<n;i++)
+		Ns[i] = cNs[i];
+
+	plan = ffts_init_nd_real(n, Ns, sign);
+	if (!plan)
+		throwOutOfMemoryError(env, NULL);
+
+	return (jlong)plan;
+}
+
+JNIEXPORT void JNICALL Java_nz_ac_waikato_ffts_FFTS_execute__JJ_3FI_3FI
+(JNIEnv *env, jclass jc, jlong p, jlong size, jfloatArray jsrc, jint soff, jfloatArray jdst, jint doff) {
+	ffts_plan_t *plan = (ffts_plan_t *)p;
+
+	// TODO: check performance on android/arm
+#ifdef NEEDS_ALIGNED
+	// On oracle jvm this is faster than GetFloatArrayElements()
+	void *src, *dst;
+
+	src = xmemalign(64, size * 4);
+	if (!src) {
+		throwOutOfMemoryError(env, NULL);
+		return;
+	}
+	dst = xmemalign(64, size * 4);
+	if (!dst) {
+		free(src);
+		throwOutOfMemoryError(env, NULL);
+		return;
+	}
+
+	(*env)->GetFloatArrayRegion(env, jsrc, 0, size, src + soff);
+	ffts_execute(plan, src, dst);
+	(*env)->SetFloatArrayRegion(env, jdst, 0, size, dst + doff);
+
+	free(dst);
+	free(src);
+#else
+	// This is the fastest with oracle jvm, but doesn't work with sse ...
+	void *src = (*env)->GetPrimitiveArrayCritical(env, jsrc, NULL);
+	void *dst = (*env)->GetPrimitiveArrayCritical(env, jdst, NULL);
+
+	ffts_execute(plan, src + soff, dst + doff);
+
+	(*env)->ReleasePrimitiveArrayCritical(env, jdst, dst, 0);
+	(*env)->ReleasePrimitiveArrayCritical(env, jsrc, src, 0);
+#endif
+
+#if 0
+	// This is the slowest
+	void *src = (*env)->GetFloatArrayElements(env, jsrc, NULL);
+	void *dst = (*env)->GetFloatArrayElements(env, jdst, NULL);
+
+	ffts_execute(plan, src + soff, dst + doff);
+
+	(*env)->ReleaseFloatArrayElements(env, jdst, dst, 0);
+	(*env)->ReleaseFloatArrayElements(env, jsrc, src, 0);
+#endif
+}
+
+JNIEXPORT void JNICALL Java_nz_ac_waikato_ffts_FFTS_execute__JJLjava_nio_FloatBuffer_2Ljava_nio_FloatBuffer_2
+(JNIEnv *env, jclass jc, jlong p, jlong size, jobject jsrc, jobject jdst) {
+	ffts_plan_t *plan = (ffts_plan_t *)p;
+	void *src = (*env)->GetDirectBufferAddress(env, jsrc);
+	void *dst = (*env)->GetDirectBufferAddress(env, jdst);
+
+	// Bounds checking etc is in java side.
+
+	ffts_execute(plan, src, dst);
+}
+
+JNIEXPORT void JNICALL Java_nz_ac_waikato_ffts_FFTS_free
+(JNIEnv *env, jclass jc, jlong p) {
+	ffts_plan_t *plan = (ffts_plan_t *)p;
+
+	ffts_free(plan);
+}