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Code Issues Releases Activity

Update to 0.72, follow upstream name change, and clean up

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This commit is contained in:
Brendan Fabeny 2011-07-01 10:46:10 +00:00
parent 8372dd4ab2
commit e3e9cab790
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=276778
14 changed files with 370 additions and 96 deletions
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66
science/bblimage/Makefile
View File

@ -6,35 +6,61 @@
# $FreeBSD$
#
PORTNAME= bblimage
PORTVERSION= 0.66
PORTREVISION= 3
PORTNAME= pyvox
PORTVERSION= 0.72
CATEGORIES= science
MASTER_SITES= ${MASTER_SITE_LOCAL}
MASTER_SITE_SUBDIR= miwi
MASTER_SITES= http://www.med.upenn.edu/bbl/downloads/pyvox/
EXTRACT_SUFX= .src.tgz
MAINTAINER= ports@FreeBSD.org
COMMENT= A set of software tools for medical image processing
DEPRECATED= No more upstream, looks like an abandonware
EXPIRATION_DATE= 2011-08-01
LICENSE= MIT
LIB_DEPENDS= Xm.2:${PORTSDIR}/x11-toolkits/lesstif
LIB_DEPENDS= lapack.4:${PORTSDIR}/math/lapack
USE_XORG= x11
USE_PYTHON= yes
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --with-lapack --with-python
USE_GMAKE= yes
USE_LDCONFIG= yes
GNU_CONFIGURE= yes
LAPACK?= -llapack -lblas
CONFIGURE_ARGS = --with-lapack="${LAPACK}" --with-python="${PYTHON_CMD}"
CONFIGURE_ENV= ac_cv_header_tgmath_h=no
USE_GMAKE= yes
USE_LDCONFIG= yes
USE_PYTHON= 2.5+
MAN1= anonbblanz.1 bblimage.1 binnseg.1 conseg.1 decomment.1 dumpbblanz.1 \
imstack.1 inleav2.1 lovar.1 qdv.1 rpsamp.1 skmiv.1 swab.1 usb2uc.1 \
vibihist.1 vihist.1
MAN5= cdata.5 mri_data.5 param.5
.if defined(WITHOUT_X11)
CONFIGURE_ARGS+=--without-x
PLIST_SUB+= X11="@comment "
.else
CONFIGURE_ARGS+=--with-x
BUILD_DEPENDS+= ${PYTHON_SITELIBDIR}/Pmw/__init__.py:${PORTSDIR}/x11-toolkits/py-Pmw
RUN_DEPENDS+= ${PYTHON_SITELIBDIR}/Pmw/__init__.py:${PORTSDIR}/x11-toolkits/py-Pmw
USE_MOTIF= yes
USE_TK = 82+
CFLAGS+= -DUSE_COMPOSITELESS_PHOTO_PUT_BLOCK -I${LOCALBASE}/include \
-I${TCL_INCLUDEDIR} -I${TK_INCLUDEDIR}
PLIST_SUB+= X11=""
.endif
MAN1= affreg.1 anonavw.1 bredit.1 decomment.1 dumpavw.1 editavw.1 makeavw.1 pyvox.1 \
reged.1 regedit.1 qdv.1
MAN5= cdata.5 param.5
.include <bsd.port.pre.mk>
post-patch:
@${REINPLACE_CMD} -e "s|python1\.5|${PYTHON_VERSION}|g" ${WRKSRC}/configure ${WRKSRC}/Makefile.in
.if defined(WITHOUT_X11)
@${REINPLACE_CMD} -e '\|pmw=yes|s|yes|no|' -e '\|tkinter=yes|s|yes|no|' \
${WRKSRC}/configure
@${REINPLACE_CMD} -e '\|#include "tk.h"|d' ${WRKSRC}/include/pyvox.h
.else
@${REINPLACE_CMD} -e 's|-ltk|&${USE_TK}|' \
${WRKSRC}/Makefile.in
.endif
.include <bsd.port.mk>
.if defined(MAINTAINER_MODE)
check regress regression-test test: build
@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} \
${MAKEFILE} ${_MAKE_JOBS} ${MAKE_ARGS} regress)
.endif
.include <bsd.port.post.mk>

5
science/bblimage/distinfo
View File

@ -1,3 +1,2 @@
MD5 (bblimage-0.66.src.tgz) = 9b01e8128c4009984300453ee00d601c
SHA256 (bblimage-0.66.src.tgz) = d645cda214076dc9977b7ed099f3643b19fe5552eab4a2ea9ddae6cec5d37f11
SIZE (bblimage-0.66.src.tgz) = 967079
SHA256 (pyvox-0.72.src.tgz) = d7a733faa323d8cdca51e8244e9c50c91bccbb77543e546125f7b251a3c75a61
SIZE (pyvox-0.72.src.tgz) = 1501027

76
science/bblimage/files/patch-src__parray.c Normal file
View File

@ -0,0 +1,76 @@
--- ./src/parray.c.orig 2006-02-24 12:18:51.000000000 -0500
+++ ./src/parray.c 2011-07-01 02:32:12.000000000 -0400
@@ -991,7 +991,7 @@
if (DEBUG_ALLOC) {
fprintf(stderr, "parray create: %p\n", self);
if (0)
- fprintf(stderr, "...reference count = %d\n",
+ fprintf(stderr, "...reference count = %zd\n",
((PyObject *)self)->ob_refcnt);
}
@@ -1171,7 +1171,7 @@
if (DEBUG_ALLOC) {
fprintf(stderr, "parray alloc: %p\n", self);
if (0)
- fprintf(stderr, "...reference count = %d\n",
+ fprintf(stderr, "...reference count = %zd\n",
((PyObject *)self)->ob_refcnt);
}
@@ -2074,7 +2074,7 @@
static PyMappingMethods
parray_as_mapping = {
- (inquiry) parray_length, /* mp_length: len(x) */
+ (lenfunc) parray_length, /* mp_length: len(x) */
(binaryfunc) parray_getitem, /* mp_subscript: x[y] */
(objobjargproc) parray_setitem, /* mp_ass_subscript: x[y] = v */
};
@@ -2204,13 +2204,13 @@
static PySequenceMethods
parray_as_sequence = {
- (inquiry) 0, /* sq_length: len(x) */
+ (lenfunc) 0, /* sq_length: len(x) */
(binaryfunc) 0, /* sq_concat: x + y */
- (intargfunc) 0, /* sq_repeat: n * x */
- (intargfunc) 0, /* sq_item: x[i] */
- (intintargfunc) parray_getslice, /* sq_slice: x[i:j] */
- (intobjargproc) 0, /* sq_ass_item: x[i] = v */
- (intintobjargproc) parray_setslice, /* sq_ass_slice: x[i:j] = v */
+ (ssizeargfunc) 0, /* sq_repeat: n * x */
+ (ssizeargfunc) 0, /* sq_item: x[i] */
+ (ssizessizeargfunc) parray_getslice, /* sq_slice: x[i:j] */
+ (ssizeobjargproc) 0, /* sq_ass_item: x[i] = v */
+ (ssizessizeobjargproc) parray_setslice, /* sq_ass_slice: x[i:j] = v */
};
@@ -7386,7 +7386,7 @@
/* DEBUG: Print ref counts of arguments */
if (0) {
- printf("Refcnts 1: %d, %d\n", self->ob_refcnt, filename->ob_refcnt);
+ printf("Refcnts 1: %zd, %zd\n", self->ob_refcnt, filename->ob_refcnt);
}
/* Paste self onto front of argument tuple. FIXME: This is really
@@ -7400,7 +7400,7 @@
/* DEBUG: Print ref counts of arguments */
if (0) {
- printf("Refcnts 2: %d, %d, %d\n", self->ob_refcnt, filename->ob_refcnt,
+ printf("Refcnts 2: %zd, %zd, %zd\n", self->ob_refcnt, filename->ob_refcnt,
newargs->ob_refcnt);
}
@@ -7418,7 +7418,7 @@
/* DEBUG: Print ref counts of arguments */
if (0) {
- printf("Refcnts 3: %d, %d, %d\n", self->ob_refcnt, filename->ob_refcnt,
+ printf("Refcnts 3: %zd, %zd, %zd\n", self->ob_refcnt, filename->ob_refcnt,
newargs->ob_refcnt);
}

20
science/bblimage/files/patch-src__pyvox.c Normal file
View File

@ -0,0 +1,20 @@
--- ./src/pyvox.c.orig 2006-02-24 16:33:41.000000000 -0500
+++ ./src/pyvox.c 2011-07-01 02:29:06.000000000 -0400
@@ -1850,7 +1850,7 @@
if (0) {
fprintf(stderr, "Created new kernel object at %p\n", self);
if (0)
- fprintf(stderr, "...reference count = %d\n",
+ fprintf(stderr, "...reference count = %zd\n",
((PyObject *)self)->ob_refcnt);
}
@@ -2273,7 +2273,7 @@
static PyMappingMethods
kernel_as_mapping = {
- (inquiry) kernel_length, /* mp_length: len(x) */
+ (lenfunc) kernel_length, /* mp_length: len(x) */
(binaryfunc) kernel_getitem, /* mp_subscript: x[y] */
(objobjargproc) kernel_setitem, /* mp_ass_subscript: x[y] = v */
};

11
science/bblimage/files/patch-src__tkphoto.c Normal file
View File

@ -0,0 +1,11 @@
--- ./src/tkphoto.c.orig 2005-12-29 13:33:15.000000000 -0500
+++ ./src/tkphoto.c 2011-07-01 02:28:06.000000000 -0400
@@ -632,7 +632,7 @@
if (0) {
fprintf(stderr, "Created new tkphoto object at %p\n", self);
if (0)
- fprintf(stderr, "...reference count = %d\n",
+ fprintf(stderr, "...reference count = %zd\n",
((PyObject *)pytk)->ob_refcnt);
}

22
science/bblimage/pkg-descr
View File

@ -1,10 +1,14 @@
BBLimage is a set of software tools for medical image processing, particularly
skull stripping and segmentation of MR brain images; tools to support other
applications may be added later. These tools are intended to support
researchers who need to prototype new image analysis algorithms or to develop
automated image analysis tools for specific image analysis applications. The
sequence of processing operations is specified through a scripting language
which can be used interactively or in command files; the language used is an
extension of Python.
Pyvox (formerly known as BBLimage) is a set of software tools for medical
image processing, particularly skull stripping and segmentation of MR brain
images (tools to support other applications may be added later). These tools
are intended to support researchers who need to prototype new image analysis
algorithms or to develop automated image analysis tools for specific image
analysis applications. The sequence of processing operations is specified
through the scripting language Python, which can be used interactively or in
command files.
WWW: http://www.uphs.upenn.edu/bbl/software/bblimage/
Pyvox scripts and date files are portable, easily extensible, and suitable
both for rapid prototyping of new algorithms and analysis protocols, and also
for efficient, automated processing of the finished analysis protocols.
WWW: http://www.med.upenn.edu/bbl/downloads/pyvox/index.shtml

33
science/bblimage/pkg-plist
View File

@ -1,25 +1,26 @@
bin/anonbblanz
bin/binnseg
bin/conseg
bin/affreg
bin/anonavw
bin/bredit
bin/decomment
bin/dumpbblanz
bin/imstack
bin/inleav2
bin/lovar
bin/qdv
bin/rowcol
bin/rpsamp
bin/skmiv
bin/swab
bin/usb2uc
bin/vibihist
bin/vihist
lib/libbbli.so
bin/dumpavw
bin/editavw
bin/makeavw
%%X11%%bin/qdv
bin/regedit
include/errm.h
include/exim.h
include/memm.h
include/voxel.h
lib/libpyvox.so
lib/libvoxkit.so
%%PYTHON_SITELIBDIR%%/exim.so
%%PYTHON_SITELIBDIR%%/optim.py
%%PYTHON_SITELIBDIR%%/optim.pyc
%%PYTHON_SITELIBDIR%%/pyvox.py
%%PYTHON_SITELIBDIR%%/pyvox.pyc
%%PYTHON_SITELIBDIR%%/pyvoxC.so
%%PYTHON_SITELIBDIR%%/reged.py
%%PYTHON_SITELIBDIR%%/reged.pyc
%%PYTHON_SITELIBDIR%%/regis.py
%%PYTHON_SITELIBDIR%%/regis.pyc
%%X11%%%%PYTHON_SITELIBDIR%%/tkphoto.so

66
science/pyvox/Makefile
View File

@ -6,35 +6,61 @@
# $FreeBSD$
#
PORTNAME= bblimage
PORTVERSION= 0.66
PORTREVISION= 3
PORTNAME= pyvox
PORTVERSION= 0.72
CATEGORIES= science
MASTER_SITES= ${MASTER_SITE_LOCAL}
MASTER_SITE_SUBDIR= miwi
MASTER_SITES= http://www.med.upenn.edu/bbl/downloads/pyvox/
EXTRACT_SUFX= .src.tgz
MAINTAINER= ports@FreeBSD.org
COMMENT= A set of software tools for medical image processing
DEPRECATED= No more upstream, looks like an abandonware
EXPIRATION_DATE= 2011-08-01
LICENSE= MIT
LIB_DEPENDS= Xm.2:${PORTSDIR}/x11-toolkits/lesstif
LIB_DEPENDS= lapack.4:${PORTSDIR}/math/lapack
USE_XORG= x11
USE_PYTHON= yes
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --with-lapack --with-python
USE_GMAKE= yes
USE_LDCONFIG= yes
GNU_CONFIGURE= yes
LAPACK?= -llapack -lblas
CONFIGURE_ARGS = --with-lapack="${LAPACK}" --with-python="${PYTHON_CMD}"
CONFIGURE_ENV= ac_cv_header_tgmath_h=no
USE_GMAKE= yes
USE_LDCONFIG= yes
USE_PYTHON= 2.5+
MAN1= anonbblanz.1 bblimage.1 binnseg.1 conseg.1 decomment.1 dumpbblanz.1 \
imstack.1 inleav2.1 lovar.1 qdv.1 rpsamp.1 skmiv.1 swab.1 usb2uc.1 \
vibihist.1 vihist.1
MAN5= cdata.5 mri_data.5 param.5
.if defined(WITHOUT_X11)
CONFIGURE_ARGS+=--without-x
PLIST_SUB+= X11="@comment "
.else
CONFIGURE_ARGS+=--with-x
BUILD_DEPENDS+= ${PYTHON_SITELIBDIR}/Pmw/__init__.py:${PORTSDIR}/x11-toolkits/py-Pmw
RUN_DEPENDS+= ${PYTHON_SITELIBDIR}/Pmw/__init__.py:${PORTSDIR}/x11-toolkits/py-Pmw
USE_MOTIF= yes
USE_TK = 82+
CFLAGS+= -DUSE_COMPOSITELESS_PHOTO_PUT_BLOCK -I${LOCALBASE}/include \
-I${TCL_INCLUDEDIR} -I${TK_INCLUDEDIR}
PLIST_SUB+= X11=""
.endif
MAN1= affreg.1 anonavw.1 bredit.1 decomment.1 dumpavw.1 editavw.1 makeavw.1 pyvox.1 \
reged.1 regedit.1 qdv.1
MAN5= cdata.5 param.5
.include <bsd.port.pre.mk>
post-patch:
@${REINPLACE_CMD} -e "s|python1\.5|${PYTHON_VERSION}|g" ${WRKSRC}/configure ${WRKSRC}/Makefile.in
.if defined(WITHOUT_X11)
@${REINPLACE_CMD} -e '\|pmw=yes|s|yes|no|' -e '\|tkinter=yes|s|yes|no|' \
${WRKSRC}/configure
@${REINPLACE_CMD} -e '\|#include "tk.h"|d' ${WRKSRC}/include/pyvox.h
.else
@${REINPLACE_CMD} -e 's|-ltk|&${USE_TK}|' \
${WRKSRC}/Makefile.in
.endif
.include <bsd.port.mk>
.if defined(MAINTAINER_MODE)
check regress regression-test test: build
@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} \
${MAKEFILE} ${_MAKE_JOBS} ${MAKE_ARGS} regress)
.endif
.include <bsd.port.post.mk>

5
science/pyvox/distinfo
View File

@ -1,3 +1,2 @@
MD5 (bblimage-0.66.src.tgz) = 9b01e8128c4009984300453ee00d601c
SHA256 (bblimage-0.66.src.tgz) = d645cda214076dc9977b7ed099f3643b19fe5552eab4a2ea9ddae6cec5d37f11
SIZE (bblimage-0.66.src.tgz) = 967079
SHA256 (pyvox-0.72.src.tgz) = d7a733faa323d8cdca51e8244e9c50c91bccbb77543e546125f7b251a3c75a61
SIZE (pyvox-0.72.src.tgz) = 1501027

76
science/pyvox/files/patch-src__parray.c Normal file
View File

@ -0,0 +1,76 @@
--- ./src/parray.c.orig 2006-02-24 12:18:51.000000000 -0500
+++ ./src/parray.c 2011-07-01 02:32:12.000000000 -0400
@@ -991,7 +991,7 @@
if (DEBUG_ALLOC) {
fprintf(stderr, "parray create: %p\n", self);
if (0)
- fprintf(stderr, "...reference count = %d\n",
+ fprintf(stderr, "...reference count = %zd\n",
((PyObject *)self)->ob_refcnt);
}
@@ -1171,7 +1171,7 @@
if (DEBUG_ALLOC) {
fprintf(stderr, "parray alloc: %p\n", self);
if (0)
- fprintf(stderr, "...reference count = %d\n",
+ fprintf(stderr, "...reference count = %zd\n",
((PyObject *)self)->ob_refcnt);
}
@@ -2074,7 +2074,7 @@
static PyMappingMethods
parray_as_mapping = {
- (inquiry) parray_length, /* mp_length: len(x) */
+ (lenfunc) parray_length, /* mp_length: len(x) */
(binaryfunc) parray_getitem, /* mp_subscript: x[y] */
(objobjargproc) parray_setitem, /* mp_ass_subscript: x[y] = v */
};
@@ -2204,13 +2204,13 @@
static PySequenceMethods
parray_as_sequence = {
- (inquiry) 0, /* sq_length: len(x) */
+ (lenfunc) 0, /* sq_length: len(x) */
(binaryfunc) 0, /* sq_concat: x + y */
- (intargfunc) 0, /* sq_repeat: n * x */
- (intargfunc) 0, /* sq_item: x[i] */
- (intintargfunc) parray_getslice, /* sq_slice: x[i:j] */
- (intobjargproc) 0, /* sq_ass_item: x[i] = v */
- (intintobjargproc) parray_setslice, /* sq_ass_slice: x[i:j] = v */
+ (ssizeargfunc) 0, /* sq_repeat: n * x */
+ (ssizeargfunc) 0, /* sq_item: x[i] */
+ (ssizessizeargfunc) parray_getslice, /* sq_slice: x[i:j] */
+ (ssizeobjargproc) 0, /* sq_ass_item: x[i] = v */
+ (ssizessizeobjargproc) parray_setslice, /* sq_ass_slice: x[i:j] = v */
};
@@ -7386,7 +7386,7 @@
/* DEBUG: Print ref counts of arguments */
if (0) {
- printf("Refcnts 1: %d, %d\n", self->ob_refcnt, filename->ob_refcnt);
+ printf("Refcnts 1: %zd, %zd\n", self->ob_refcnt, filename->ob_refcnt);
}
/* Paste self onto front of argument tuple. FIXME: This is really
@@ -7400,7 +7400,7 @@
/* DEBUG: Print ref counts of arguments */
if (0) {
- printf("Refcnts 2: %d, %d, %d\n", self->ob_refcnt, filename->ob_refcnt,
+ printf("Refcnts 2: %zd, %zd, %zd\n", self->ob_refcnt, filename->ob_refcnt,
newargs->ob_refcnt);
}
@@ -7418,7 +7418,7 @@
/* DEBUG: Print ref counts of arguments */
if (0) {
- printf("Refcnts 3: %d, %d, %d\n", self->ob_refcnt, filename->ob_refcnt,
+ printf("Refcnts 3: %zd, %zd, %zd\n", self->ob_refcnt, filename->ob_refcnt,
newargs->ob_refcnt);
}

20
science/pyvox/files/patch-src__pyvox.c Normal file
View File

@ -0,0 +1,20 @@
--- ./src/pyvox.c.orig 2006-02-24 16:33:41.000000000 -0500
+++ ./src/pyvox.c 2011-07-01 02:29:06.000000000 -0400
@@ -1850,7 +1850,7 @@
if (0) {
fprintf(stderr, "Created new kernel object at %p\n", self);
if (0)
- fprintf(stderr, "...reference count = %d\n",
+ fprintf(stderr, "...reference count = %zd\n",
((PyObject *)self)->ob_refcnt);
}
@@ -2273,7 +2273,7 @@
static PyMappingMethods
kernel_as_mapping = {
- (inquiry) kernel_length, /* mp_length: len(x) */
+ (lenfunc) kernel_length, /* mp_length: len(x) */
(binaryfunc) kernel_getitem, /* mp_subscript: x[y] */
(objobjargproc) kernel_setitem, /* mp_ass_subscript: x[y] = v */
};

11
science/pyvox/files/patch-src__tkphoto.c Normal file
View File

@ -0,0 +1,11 @@
--- ./src/tkphoto.c.orig 2005-12-29 13:33:15.000000000 -0500
+++ ./src/tkphoto.c 2011-07-01 02:28:06.000000000 -0400
@@ -632,7 +632,7 @@
if (0) {
fprintf(stderr, "Created new tkphoto object at %p\n", self);
if (0)
- fprintf(stderr, "...reference count = %d\n",
+ fprintf(stderr, "...reference count = %zd\n",
((PyObject *)pytk)->ob_refcnt);
}

22
science/pyvox/pkg-descr
View File

@ -1,10 +1,14 @@
BBLimage is a set of software tools for medical image processing, particularly
skull stripping and segmentation of MR brain images; tools to support other
applications may be added later. These tools are intended to support
researchers who need to prototype new image analysis algorithms or to develop
automated image analysis tools for specific image analysis applications. The
sequence of processing operations is specified through a scripting language
which can be used interactively or in command files; the language used is an
extension of Python.
Pyvox (formerly known as BBLimage) is a set of software tools for medical
image processing, particularly skull stripping and segmentation of MR brain
images (tools to support other applications may be added later). These tools
are intended to support researchers who need to prototype new image analysis
algorithms or to develop automated image analysis tools for specific image
analysis applications. The sequence of processing operations is specified
through the scripting language Python, which can be used interactively or in
command files.
WWW: http://www.uphs.upenn.edu/bbl/software/bblimage/
Pyvox scripts and date files are portable, easily extensible, and suitable
both for rapid prototyping of new algorithms and analysis protocols, and also
for efficient, automated processing of the finished analysis protocols.
WWW: http://www.med.upenn.edu/bbl/downloads/pyvox/index.shtml

33
science/pyvox/pkg-plist
View File

@ -1,25 +1,26 @@
bin/anonbblanz
bin/binnseg
bin/conseg
bin/affreg
bin/anonavw
bin/bredit
bin/decomment
bin/dumpbblanz
bin/imstack
bin/inleav2
bin/lovar
bin/qdv
bin/rowcol
bin/rpsamp
bin/skmiv
bin/swab
bin/usb2uc
bin/vibihist
bin/vihist
lib/libbbli.so
bin/dumpavw
bin/editavw
bin/makeavw
%%X11%%bin/qdv
bin/regedit
include/errm.h
include/exim.h
include/memm.h
include/voxel.h
lib/libpyvox.so
lib/libvoxkit.so
%%PYTHON_SITELIBDIR%%/exim.so
%%PYTHON_SITELIBDIR%%/optim.py
%%PYTHON_SITELIBDIR%%/optim.pyc
%%PYTHON_SITELIBDIR%%/pyvox.py
%%PYTHON_SITELIBDIR%%/pyvox.pyc
%%PYTHON_SITELIBDIR%%/pyvoxC.so
%%PYTHON_SITELIBDIR%%/reged.py
%%PYTHON_SITELIBDIR%%/reged.pyc
%%PYTHON_SITELIBDIR%%/regis.py
%%PYTHON_SITELIBDIR%%/regis.pyc
%%X11%%%%PYTHON_SITELIBDIR%%/tkphoto.so