diff options
Diffstat (limited to 'science/bblimage')
-rw-r--r-- | science/bblimage/Makefile | 66 | ||||
-rw-r--r-- | science/bblimage/distinfo | 5 | ||||
-rw-r--r-- | science/bblimage/files/patch-src__parray.c | 76 | ||||
-rw-r--r-- | science/bblimage/files/patch-src__pyvox.c | 20 | ||||
-rw-r--r-- | science/bblimage/files/patch-src__tkphoto.c | 11 | ||||
-rw-r--r-- | science/bblimage/pkg-descr | 22 | ||||
-rw-r--r-- | science/bblimage/pkg-plist | 33 |
7 files changed, 185 insertions, 48 deletions
diff --git a/science/bblimage/Makefile b/science/bblimage/Makefile index 9aa1805ff657..221a9bf84d7a 100644 --- a/science/bblimage/Makefile +++ b/science/bblimage/Makefile @@ -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 + +.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.mk> +.include <bsd.port.post.mk> diff --git a/science/bblimage/distinfo b/science/bblimage/distinfo index 7da85ab0f456..62547d6b3ece 100644 --- a/science/bblimage/distinfo +++ b/science/bblimage/distinfo @@ -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 diff --git a/science/bblimage/files/patch-src__parray.c b/science/bblimage/files/patch-src__parray.c new file mode 100644 index 000000000000..a84acca50fdd --- /dev/null +++ b/science/bblimage/files/patch-src__parray.c @@ -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); + } + diff --git a/science/bblimage/files/patch-src__pyvox.c b/science/bblimage/files/patch-src__pyvox.c new file mode 100644 index 000000000000..07f056943e7d --- /dev/null +++ b/science/bblimage/files/patch-src__pyvox.c @@ -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 */ + }; diff --git a/science/bblimage/files/patch-src__tkphoto.c b/science/bblimage/files/patch-src__tkphoto.c new file mode 100644 index 000000000000..9be4a5503b5f --- /dev/null +++ b/science/bblimage/files/patch-src__tkphoto.c @@ -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); + } + diff --git a/science/bblimage/pkg-descr b/science/bblimage/pkg-descr index 9753cc4f0d55..6daca94b72f2 100644 --- a/science/bblimage/pkg-descr +++ b/science/bblimage/pkg-descr @@ -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 diff --git a/science/bblimage/pkg-plist b/science/bblimage/pkg-plist index 114ca046c741..2d3ecb6c87dd 100644 --- a/science/bblimage/pkg-plist +++ b/science/bblimage/pkg-plist @@ -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 |