3 files changed, 147 insertions, 0 deletions
diff --git a/sci-biology/imagej/Manifest b/sci-biology/imagej/Manifest
new file mode 100644
index 0000000..b1df94b
--- /dev/null
+++ b/sci-biology/imagej/Manifest
@@ -0,0 +1,5 @@
+AUX AutoThresholder.java.patch 444 BLAKE2B d760b59f0e1b2214f66cc4b8cadc42a7f9545957d6271010cb60d393def3f79dd58a67a44bb3bf7668700abbba20a612e903985ce35c0911c7967cfbb9118dfc SHA512 46033542bc3023356692c966a0cc84819ebd52cf6fe78d6538a3c8521e58612559bfb11eea6eea61c22e354f82647f523b74ee12fa0df0bea6d26045ee2a3c96
+DIST ImageJ.png 13012 BLAKE2B b42ee855e6214b275cbdcc722f6c7b095fe83de477a151714c4afec8e23abe12b2d0bf62ae81a4f9c4ccefc9245a9e144085b844ee3f92121a88f7d27106acf5 SHA512 60c2ff73bcfc668931c59b0dfb299723a369b741601bdd591a407302e30fc58c6c626525b3f08b955a5dab37729d3f704db689317b42a94e7a3ccbfb72abc9b3
+DIST ij150.zip 6899239 BLAKE2B 7a0c15f8a2cfb5dc672fe3edb7e0daffb0c6847cf92e0c9fefa3fc22177e73ec0736b842eb1d71c1c9de49a8887e3c2dd373a10b60c5246adca3dc14f85f8120 SHA512 a927df1ca345cff4b9aa0b6c03510103bc8fc8c21a572c3417060bcf28da8a1fbce07de5a73cd04ba4818bd715a8caa05432365460651b7b9de3f34c89e6318a
+DIST ij151k-src.zip 1580015 BLAKE2B 143fca57d38457f8264f59517890b9541ebc2838f56ccc07fdc0fec114bdc02042dc74a0c9560e7ed47e8d5e3c91f83dd725c860f823f4956c55636c30025bfc SHA512 93249fb1c186e757dde78231d3064a1179f5c10d94dc02b9b0535febd5db78cb2666e9e952380de8847339c840d4e46e857eaa982340c6e5084d1003c44791e6
+EBUILD imagej-1.51k-r1.ebuild 3855 BLAKE2B c3c55318a933a9729f37b6f1867cbdc5f995c1368eac0f17ef628c08929ddd6e75da17c6348bced7f2b6e673ef4b189fb8a9847fa9ac98b4438fe85877d361c1 SHA512 abc79769a94634996e19957a4236eda54a1f3394e964fb6591e1d62ef24c2c72f7920e0a12e7d6b981922e0d8a134ee2a9a208983d0023ef151f813f1611c049
diff --git a/sci-biology/imagej/files/AutoThresholder.java.patch b/sci-biology/imagej/files/AutoThresholder.java.patch
new file mode 100644
index 0000000..97c8932
--- /dev/null
+++ b/sci-biology/imagej/files/AutoThresholder.java.patch
@@ -0,0 +1,10 @@
+--- imagej-1.51k/work/source/ij/process/AutoThresholder.java.ori	2017-03-15 22:33:45.843801175 +0100
++++ imagej-1.51k/work/source/ij/process/AutoThresholder.java	2017-03-15 22:33:55.104053480 +0100
+@@ -650,7 +650,6 @@
+ 		}
+ 		// The threshold is the minimum between the two peaks.
+ 		for (int i=1; i<255; i++) {
+-			//IJ.log(" "+i+"  "+iHisto[i]);
+ 			if (iHisto[i-1] > iHisto[i] && iHisto[i+1] >= iHisto[i]) {
+ 				threshold = i;
+ 				break;
diff --git a/sci-biology/imagej/imagej-1.51k-r1.ebuild b/sci-biology/imagej/imagej-1.51k-r1.ebuild
new file mode 100644
index 0000000..931aef0
--- /dev/null
+++ b/sci-biology/imagej/imagej-1.51k-r1.ebuild
@@ -0,0 +1,132 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit java-pkg-2 java-ant-2 eutils versionator
+
+MY_PN="ij"
+MY_PV=$(delete_all_version_separators)
+
+# NOTE:
+# as plugins are regularly lagging behind, we use the pack released for previous
+# version instead. Change to present version locally if you are sure proper
+# version has been released.
+# see https://bugs.gentoo.org/show_bug.cgi?id=112275
+# https://github.com/imagej/imagej1/issues/28
+IJ_PV=$((${MY_PV::3}-1))
+
+DESCRIPTION="Image Processing and Analysis in Java"
+HOMEPAGE="http://rsb.info.nih.gov/ij/"
+
+SRC_URI="http://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
+	http://rsb.info.nih.gov/ij/images/ImageJ.png
+	plugins? ( http://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )"
+# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins
+#	plugins? ( http://rsb.info.nih.gov/ij/download/zips/${MY_PN}${IJ_PV}.zip )"
+
+RESTRICT=""
+LICENSE="public-domain" # http://imagej.net/disclaimer.html
+SLOT="0"
+
+KEYWORDS=""
+
+IUSE="doc plugins debug"
+
+RDEPEND=">=virtual/jre-1.6:*
+	dev-java/java-config
+	dev-java/jython"
+DEPEND=">=virtual/jdk-1.6:*
+	dev-java/ant-core
+	${RDEPEND}"
+
+S=${WORKDIR}/source
+IJ_S=${WORKDIR}/ImageJ
+
+src_prepare() {
+	cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die
+
+	if ! use debug ; then
+		sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die
+	fi
+	epatch "${FILESDIR}"/AutoThresholder.java.patch
+	eapply_user
+}
+
+# in src_compile we get: !!! ERROR: Package jython was not found!
+# TODO: overwrite calls to jython ? See
+#   ij/plugin/frame/Editor.java
+#   plugin/PlugInInterpreter.java
+#   plugin/Macro_Runner.java
+
+src_compile() {
+	local antflags="build"
+	use doc && antflags="${antflags} javadocs"
+
+	ant ${antflags} || die  "ant build failed"
+
+	# Max memory usage depends on available memory and CPU type
+	MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*)
+	IJ_MAX_MEM=$(expr ${MEM} / 1024)
+	if use x86 && $IJ_MAX_MEM -gt 2048 ; then
+		IJ_MAX_MEM=2048
+	fi
+	# build finished, generate startup wrapper
+	cat <<EOF > "${T}/${PN}"
+#!${EPREFIX}/bin/bash
+IJ_LIB=${EPREFIX}/usr/share/${PN}/lib
+if !([ "\${IJ_HOME}" ]) ; then
+	IJ_HOME=\${HOME}/.imagej
+fi
+if [ -d \${IJ_HOME}/plugins ] ; then
+	IJ_PLG=\${IJ_HOME}
+else
+	IJ_PLG=${EPREFIX}/usr/share/${PN}/lib
+fi
+if !([ "\$IJ_MEM" ]) ; then
+	IJ_MEM=${IJ_MAX_MEM}
+fi
+if !([ "\$IJ_CP" ]) ; then
+	IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar
+else
+	IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar:\${IJ_CP}
+fi
+\$(java-config --java) \\
+	-Xmx\${IJ_MEM}m -Dswing.aatext=true \\
+	-Dawt.useSystemAAFontSettings=on\\
+	-cp \${IJ_CP} \\
+	-Duser.home=\${IJ_HOME} \\
+	-Dplugins.dir=\${IJ_PLG} \\
+	ij.ImageJ "\$@"
+EOF
+}
+
+src_install() {
+	java-pkg_dojar *.jar
+	dobin "${T}/${PN}"
+
+	if use plugins ; then
+		cp -R "${IJ_S}"/plugins "${ED}"/usr/share/"${PN}"/lib/
+		cp -R "${IJ_S}"/macros "${ED}"/usr/share/"${PN}"/lib/
+	fi
+
+	use doc && java-pkg_dohtml -r "${WORKDIR}"/api
+
+	insinto /usr/share/pixmaps
+	doins "${WORKDIR}/${PN}".png
+	make_desktop_entry "${PN}" ImageJ "${PN}".png Graphics
+}
+
+pkg_postinst() {
+	einfo ""
+	einfo "You can configure the path of a folder, which contains \"plugins\" directory and IJ_Prefs.txt,"
+	einfo "by setting the environmental variable, \$IJ_HOME."
+	einfo "Default setting is \$IJ_HOME=\${HOME}/.imagej, i.e. \${HOME}/.imagej/plugins and \${HOME}/.imagej/IJ_Prefs.txt."
+	einfo ""
+	einfo "You can also configure the memory size by setting the environmental variable, \$IJ_MEM,"
+	einfo "and the class path by setting the environmental variable, \$IJ_CP."
+	einfo ""
+	einfo "If you want to use much more plugins, please see http://rsb.info.nih.gov/ij/plugins/index.html"
+	einfo "and add *.class files to \$IJ_HOME/plugins folder"
+	einfo ""
+}