DTI visualization software from Stanford.

WWW: http://graphics.stanford.edu/projects/dti/

PR:		ports/120129
Submitted by:	Jason W. Bacon <jwbacon at tds.net>

9 files changed, 177 insertions, 0 deletions

diff --git a/science/Makefile b/science/Makefile
index caa20ca259d5..ebe08e4306c6 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -24,6 +24,7 @@
     SUBDIR += dcl
     SUBDIR += devisor
     SUBDIR += dft++
+    SUBDIR += dtiquery
     SUBDIR += ecs
     SUBDIR += elmer-eio
     SUBDIR += elmer-fem
diff --git a/science/dtiquery/Makefile b/science/dtiquery/Makefile
new file mode 100644
index 000000000000..aae83268b75a
--- /dev/null
+++ b/science/dtiquery/Makefile
@@ -0,0 +1,65 @@
+############################################################################
+# New ports collection Makefile for:   DTI-Query
+# Date created:        10 July 2006
+# Whom:                Jason W. Bacon <jwbacon@tds.net>
+#
+# $FreeBSD$
+#
+############################################################################
+
+PORTNAME=	dtiquery
+PORTVERSION=	1.1
+CATEGORIES=	science biology
+MASTER_SITES=	http://graphics.stanford.edu/projects/dti/
+
+MAINTAINER=	jwbacon@tds.net
+COMMENT=	Stanford DTI Visualization tool
+
+BUILD_DEPENDS=	${LOCALBASE}/include/tnt/tnt.h:${PORTSDIR}/devel/tnt \
+		${LOCALBASE}/include/tnt/jama_cholesky.h:${PORTSDIR}/math/jama \
+		${LOCALBASE}/lib/libRAPID.a:${PORTSDIR}/math/rapid
+EXTRACT_DEPENDS=	dos2unix:${PORTSDIR}/converters/unix2dos
+LIB_DEPENDS=	wx_gtk2_core-2.8.0:${PORTSDIR}/x11-toolkits/wxgtk28 \
+		vtkCommon.5:${PORTSDIR}/math/vtk5
+
+CONFLICTS=	dtiquery-1.0*
+
+RESTRICTED=	Must register to download at http://graphics.stanford.edu/projects/dti/
+
+SUB_FILES=	pkg-message
+PKGMESSAGE=	${WRKDIR}/pkg-message
+
+USE_GMAKE=	yes
+
+PLIST_FILES=	bin/dtiquery \
+		bin/dtiprecompute_cmd \
+		bin/dtiprecompute_gui
+
+ALL_TARGET=
+
+MAN1=		dtiquery.1 \
+		dtiprecompute_cmd.1 \
+		dtiprecompute_gui.1
+
+.include <bsd.port.pre.mk>
+
+.if !exists(${DISTDIR}/${DISTNAME}.tar.gz)
+IGNORE=	you must manually fetch ${DISTNAME}.tar.gz from http://graphics.stanford.edu/projects/dti/, place it in ${DISTDIR}, and then run make again
+.endif
+
+post-extract:
+	dos2unix ${WRKSRC}/*/Makefile ${WRKSRC}/Makefile*
+	${REINPLACE_CMD} "s/zlib-1.2.2 RAPID201//g" ${WRKSRC}/Makefile
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/DTIQuery/dtiquery ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/precompute/dtiprecompute_cmd ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/precompute/dtiprecompute_gui ${PREFIX}/bin
+	${INSTALL_MAN} ${FILESDIR}/dtiquery.1 ${MAN1PREFIX}/man/man1
+	${INSTALL_MAN} ${FILESDIR}/dtiquery.1 ${MAN1PREFIX}/man/man1/dtiprecompute_cmd.1
+	${INSTALL_MAN} ${FILESDIR}/dtiquery.1 ${MAN1PREFIX}/man/man1/dtiprecompute_gui.1
+
+post-install:
+	@${CAT} ${PKGMESSAGE}
+
+.include <bsd.port.post.mk>
diff --git a/science/dtiquery/distinfo b/science/dtiquery/distinfo
new file mode 100644
index 000000000000..814db81f11bd
--- /dev/null
+++ b/science/dtiquery/distinfo
@@ -0,0 +1,3 @@
+MD5 (dtiquery-1.1.tar.gz) = 4104aece50029d9b3183a244c2bb36fe
+SHA256 (dtiquery-1.1.tar.gz) = c59f5911e633f1f364cfd03ed18c296f99963184e2c2ddea937109f45f4b456e
+SIZE (dtiquery-1.1.tar.gz) = 285780
diff --git a/science/dtiquery/files/dtiquery.1 b/science/dtiquery/files/dtiquery.1
new file mode 100644
index 000000000000..46b0516f3f0c
--- /dev/null
+++ b/science/dtiquery/files/dtiquery.1
@@ -0,0 +1,35 @@
+.TH DTIQUERY 1
+.SH NAME    \" Section header
+.PP
+
+DTIQuery - DTI Visualization Software
+
+.SH SYNOPSIS
+.PP
+.nf 
+.na 
+dtiquery
+dtiprecompute_cmd [args]
+dtiprecompute_gui
+
+.ad
+.fi
+
+.SH "DESCRIPTION"
+
+DTIQuery is a software suite for analyzing DTI (Diffusion Tensor Imaging)
+data obtained via MRI (Magnetic Resonence Imaging).  For full documentation,
+please visit 
+
+http://graphics.stanford.edu/projects/dti/software/.
+
+.SH "SEE ALSO"
+
+afni(1), caret(1), freesurfer(1), fsl(1)
+
+.SH AUTHOR
+.nf
+.na
+David Akers
+Stanford University
+
diff --git a/science/dtiquery/files/patch-DTIQuery-Makefile b/science/dtiquery/files/patch-DTIQuery-Makefile
new file mode 100644
index 000000000000..c7f205c84822
--- /dev/null
+++ b/science/dtiquery/files/patch-DTIQuery-Makefile
@@ -0,0 +1,13 @@
+--- DTIQuery/Makefile.orig	Thu Dec  6 13:48:54 2007
++++ DTIQuery/Makefile	Thu Dec  6 13:49:24 2007
+@@ -12,8 +12,8 @@
+ 
+ VTK_LIBS = -lvtkIO \
+         -lvtkRendering -lvtkGraphics -lvtkImaging \
+-        -lvtkFiltering -lvtkCommon -lvtkHybrid -lvtkpng -lvtkzlib \
+-        -lvtkftgl -lvtkfreetype -lvtkjpeg -lvtkDICOMParser \
++        -lvtkFiltering -lvtkCommon -lvtkHybrid -lpng -lz \
++        -lvtkftgl -lvtkfreetype -ljpeg -lvtkDICOMParser \
+ 
+ # for FreeBSD, need -lpng -ljpeg -lz instead of -lvtkpng -lvtkzlib -lvtkjpeg
+ 
diff --git a/science/dtiquery/files/patch-Makefile.definitions b/science/dtiquery/files/patch-Makefile.definitions
new file mode 100644
index 000000000000..593cefc32b3f
--- /dev/null
+++ b/science/dtiquery/files/patch-Makefile.definitions
@@ -0,0 +1,34 @@
+--- Makefile.definitions.orig	Wed Dec 19 10:50:50 2007
++++ Makefile.definitions	Wed Dec 19 10:51:13 2007
+@@ -1,6 +1,6 @@
+-CYGWIN = 1
++# CYGWIN = 1
+ # mac = 1
+-# FreeBSD = 1
++FreeBSD = 1
+ # linux = 1
+ 
+ # Uncomment the line above corresponding to your system. Then find the 
+@@ -46,18 +46,19 @@
+ 
+ ifdef FreeBSD
+ 
+-WX_CONFIG_BIN		?= /usr/X11R6/bin/wxgtk2-2.8-config
++WX_CONFIG_BIN		?= ${X11BASE}/bin/wxgtk2-2.8-config
+ VTK_INCLUDE_PATHS	?= -I/usr/local/include/vtk-5.0/
+ VTK_LIB_PATHS		?= -L/usr/local/lib/vtk-5.0/
+ WX_INCLUDE_PATHS	?= `$(WX_CONFIG_BIN) --cxxflags`
+ WX_LIB_PATHS		?= `$(WX_CONFIG_BIN) --libs` `$(WX_CONFIG_BIN) \
+ 				--gl-libs`
+-RAPID_INCLUDE_PATH	?= -I/usr/local/include
++RAPID_INCLUDE_PATH	?= -I/usr/local/include/RAPID
+ RAPID_LIB_PATH		?= -L/usr/local/lib
+ TNT_INCLUDE_PATH	?= -I/usr/local/include/tnt/
+ JAMA_INCLUDE_PATH	?= -I/usr/local/include/
+ ZLIB_INCLUDE_PATH	?= -I/usr/include
+-SYS_INCLUDE_PATHS	?= -I/usr/include -I/usr/X11R6/include -I/usr/local/include/gtk-2.0 -I/usr/X11R6/include/gtk-2.0 -I/usr/local/include/glib-2.0 -I/usr/local/include/cairo -I/usr/local/include/pango-1.0 -I/usr/X11R6/include/pango-1.0 -I/usr/local/include/atk-1.0 
++SYS_INCLUDE_PATHS	?= -I/usr/include -I${X11BASE}/include -I/usr/local/include/gtk-2.0 -I${X11BASE}/include/gtk-2.0 -I/usr/local/include/glib-2.0 -I/usr/local/include/cairo -I/usr/local/include/pango-1.0 -I${X11BASE}/include/pango-1.0 -I/usr/local/include/atk-1.0 
++SYS_CXXFLAGS 		?= -g
+ SYS_LIBS		?= -L/usr/local/lib -lXt -lGL -lpng
+ 
+ else
diff --git a/science/dtiquery/files/patch-precompute-Makefile b/science/dtiquery/files/patch-precompute-Makefile
new file mode 100644
index 000000000000..c6ce2354c1ac
--- /dev/null
+++ b/science/dtiquery/files/patch-precompute-Makefile
@@ -0,0 +1,13 @@
+--- precompute/Makefile.orig	Thu Dec  6 13:51:44 2007
++++ precompute/Makefile	Thu Dec  6 13:52:16 2007
+@@ -21,8 +21,8 @@
+ 
+ VTK_LIBS = -lvtkIO \
+         -lvtkRendering -lvtkGraphics -lvtkImaging \
+-        -lvtkFiltering -lvtkCommon -lvtkHybrid -lvtkpng -lvtkzlib \
+-        -lvtkftgl -lvtkfreetype -lvtkjpeg -lvtkDICOMParser \
++        -lvtkFiltering -lvtkCommon -lvtkHybrid -lpng -lz \
++        -lvtkftgl -lvtkfreetype -ljpeg -lvtkDICOMParser \
+ 
+ # for FreeBSD, need -lpng -ljpeg -lz instead of -lvtkpng -lvtkzlib -lvtkjpeg
+ 
diff --git a/science/dtiquery/files/pkg-message.in b/science/dtiquery/files/pkg-message.in
new file mode 100644
index 000000000000..eb6f29e44f07
--- /dev/null
+++ b/science/dtiquery/files/pkg-message.in
@@ -0,0 +1,10 @@
+=============================================================================
+DTI Query users will need %%PREFIX%%/bin in their PATH.
+
+For questions or comments regarding this port, please contact the
+port maintainer.
+
+For dtiquery usage, please visit the WEB site at
+
+http://graphics.stanford.edu/projects/dti/
+=============================================================================
diff --git a/science/dtiquery/pkg-descr b/science/dtiquery/pkg-descr
new file mode 100644
index 000000000000..0791de735e9c
--- /dev/null
+++ b/science/dtiquery/pkg-descr
@@ -0,0 +1,3 @@
+DTI visualization software from Stanford.
+
+WWW: http://graphics.stanford.edu/projects/dti/