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authorJason W. Bacon <jwb@FreeBSD.org>2019-05-21 03:35:57 +0800
committerJason W. Bacon <jwb@FreeBSD.org>2019-05-21 03:35:57 +0800
commitade7919150a1f75b7155f56b5333b34776351526 (patch)
tree89caef674cd4202b000a03596d08be65c3c46040 /science/afni
parent5d1fd40db892e261c375f1b2d75bf9616487a7eb (diff)
downloadfreebsd-ports-gnome-ade7919150a1f75b7155f56b5333b34776351526.tar.gz
freebsd-ports-gnome-ade7919150a1f75b7155f56b5333b34776351526.tar.zst
freebsd-ports-gnome-ade7919150a1f75b7155f56b5333b34776351526.zip
science/afni: Upgrade to 19.1.08
Switch from personal dist snapshots to Github releases Improve staging procedure to preserve results of build phase Temporarily use bundled GLw pending fix of libglw port
Diffstat (limited to 'science/afni')
-rw-r--r--science/afni/Makefile159
-rw-r--r--science/afni/distinfo5
-rw-r--r--science/afni/files/Makefile8
-rw-r--r--science/afni/files/patch-Makefile.INCLUDE72
-rw-r--r--science/afni/files/patch-crorden_dcm2niix__console_makefile24
-rw-r--r--science/afni/files/patch-misc_math.c16
-rw-r--r--science/afni/files/patch-netcdf-3.5.0_src_configure4
-rw-r--r--science/afni/files/patch-prf__common__circular.c18
-rw-r--r--science/afni/pkg-descr6
-rw-r--r--science/afni/pkg-plist869
10 files changed, 702 insertions, 479 deletions
diff --git a/science/afni/Makefile b/science/afni/Makefile
index 8744258258fe..393a627ad67e 100644
--- a/science/afni/Makefile
+++ b/science/afni/Makefile
@@ -1,28 +1,21 @@
# $FreeBSD$
-############################################################################
-# http://www.neuro.mcw.edu/Ports has the latest source distribution from
-# which this port is built. It will be updated as time permits.
-#
-# afni.nimh.nih.gov is the ultimate source for AFNI, and will always
-# contain the latest source release. If this port is not up to date,
-# you can download the latest sources and build manually.
-
-PORTNAME= afni
-PORTVERSION= 2015.11.13
-PORTREVISION= 8
-CATEGORIES= science biology graphics
-MASTER_SITES= http://www.acadix.biz/Ports/distfiles/
+PORTNAME= afni
+DISTVERSIONPREFIX= AFNI_
+DISTVERSION= 19.1.08
+CATEGORIES= science biology graphics perl5 python
MAINTAINER= jwb@FreeBSD.org
COMMENT= Advanced Functional Neuro Imaging
LICENSE= GPLv2
-BUILD_DEPENDS= gm4:devel/m4
+BROKEN_sparc64= Does not compile: "undefined reference to '_mcount'"
+
+BUILD_DEPENDS= gm4:devel/m4 \
+ R:math/R
LIB_DEPENDS= libexpat.so:textproc/expat2 \
libf2c.so:lang/f2c \
- libR.so:math/R \
libgsl.so:math/gsl \
libnetcdff.so:science/netcdf-fortran \
libxml2.so:textproc/libxml2 \
@@ -30,33 +23,32 @@ LIB_DEPENDS= libexpat.so:textproc/expat2 \
RUN_DEPENDS= endian:sysutils/endian \
mpeg_encode:multimedia/mpeg_encode \
ppmtogif:graphics/netpbm \
- qhull:math/qhull5
-
-BROKEN_aarch64= fails to compile: suma_utils.c:3043:10: statement requires expression of scalar type
-BROKEN_sparc64= fails to compile: undefined reference to '_mcount'
-
-CONFLICTS= im-[0-9]* \
- nifticlib-[0-9]* \
- open-usp-tukubai-[0-9]*
+ qhull:math/qhull5 \
+ R:math/R
-USES= gettext gmake iconv jpeg:run motif perl5 python shebangfix tar:xz
-SHEBANG_FILES= suma_change_spec \
- 3dPAR2AFNI.pl \
- python_scripts/*.py \
- pkundu/meica.py \
- pkundu/meica.libs/*.py \
- pkundu/meica.libs/mdp/test/run_tests.py
+USES= compiler:openmp gettext gl gmake gnome iconv jpeg:run motif \
+ perl5 python shebangfix tar:xz
USE_GNOME= glib20
+USE_GITHUB= yes
+
+SHEBANG_FILES= scripts_install/* \
+ python_scripts/afni_python/*.py \
+ jzosky/*.py \
+ jzosky/lib_RetroTS/*.py \
+ discoraj/ClusterExplorer/*.py \
+ roopchansinghv/PsychoPy-NeuroFeedback-Demo/*.py \
+ roopchansinghv/PsychoPy-NeuroFeedback-Demo/*/*.py \
+ pkundu/*.py \
+ pkundu/meica.libs/*.py \
+ pkundu/meica.libs/*/*.py \
+ pkundu/meica.libs/*/*/*.py
-OPTIONS_DEFINE= DOCS
-
-.include <bsd.port.options.mk>
-
-USE_GL= gl glu glw
+USE_GL= gl glu
USE_XORG= x11 xext xi xmu xp xt
MAKE_ENV= CC="${CC}" R_SHARE_DIR=${LOCALBASE}/lib/R/share
MAKE_JOBS_UNSAFE=yes
+WRKSRC_SUBDIR= src
ALL_TARGET= vastness suma
###########################################################################
@@ -65,8 +57,17 @@ ALL_TARGET= vastness suma
SUB_FILES= pkg-message afni.cshrc afni.profile
INSTALL_WRKSRC= ${WRKSRC}/BSD
+INSTALL_TMP= ${INSTALL_WRKSRC}-temp
PRESTAGE= ${WRKSRC}/prestage
+OPTIONS_DEFINE= DOCS
+
+.include <bsd.port.options.mk>
+
+CONFLICTS= im-[0-9]* \
+ nifticlib-[0-9]* \
+ open-usp-tukubai-[0-9]*
+
X11R6_FILES= coxplot/Makefile \
coxplot/Makefile.f2c \
3DEdge/src/Makefile \
@@ -86,21 +87,20 @@ post-extract:
.endfor
@${REINPLACE_CMD} \
-E 's|AFNI_[0-9_]+|${PORTVERSION}|g' ${WRKSRC}/AFNI_label.h
- @${REINPLACE_CMD} \
- -e "s|%%PREFIX%%|${PREFIX}|g" ${WRKSRC}/afni.1
@${CP} ${FILESDIR}/Makefile ${WRKSRC}
@${RM} ${WRKSRC}/3DEdge/src/Makefile.orig
# shebangfix misses /bin/python on 10.1
-post-patch:
- ${REINPLACE_CMD} -e "s|-lglib|-lglib-2.0|g" \
+# @${REINPLACE_CMD} -e "s|/bin/python|${PYTHON_CMD}|g" \
+# ${WRKSRC}/python_scripts/afni_python/lib_fat_Rfactor.py
+
+pre-configure:
+ @${REINPLACE_CMD} -e "s|-lglib|-lglib-2.0|g" \
${WRKSRC}/SUMA/SUMA_Makefile
- ${REINPLACE_CMD} -e "s|/bin/python|${PYTHON_CMD}|g" \
- ${WRKSRC}/python_scripts/lib_fat_Rfactor.py
- ${REINPLACE_CMD} \
- -e 's|os\.path\.dirname(sys\.argv\[0\])|"${PREFIX}/libexec"|g' \
+ @${REINPLACE_CMD} \
+ -e 's|os\.path\.dirname(sys\.argv\[0\])|"${DATADIR}"|g' \
${WRKSRC}/pkundu/meica.py
- ${REINPLACE_CMD} \
+ @${REINPLACE_CMD} \
-e 's|g_info|afni_g_info|g' \
${WRKSRC}/rickr/Dimon.c \
${WRKSRC}/rickr/Dimon1.c \
@@ -111,53 +111,58 @@ post-patch:
${WRKSRC}/to3d.c \
${WRKSRC}/mri_dicom_stuff.h
-post-build:
- ${MKDIR} ${PRESTAGE}/bin \
+do-install:
+ # AFNI install just dumps everything into one flat directory
+ # Preserve original install dir and make a sacrificial temp copy
+ # to be pruned and rearranged for easy staging
+ @${RM} -r ${INSTALL_TMP}
+ @${CP} -R ${INSTALL_WRKSRC} ${INSTALL_TMP}
+
+ # Clean up and organize files into ${PRESTAGE}, destroying
+ # temp copy in the process
+ @${RM} -rf ${PRESTAGE}
+ @${MKDIR} ${PRESTAGE}/bin \
${PRESTAGE}/scripts \
${PRESTAGE}/lib \
${PRESTAGE}/include \
${PRESTAGE}/trash \
${PRESTAGE}/doc \
${PRESTAGE}/share
- ${MV} ${INSTALL_WRKSRC}/libf2c.a \
- ${PRESTAGE}/trash
- ${MV} ${INSTALL_WRKSRC}/*.a \
- ${INSTALL_WRKSRC}/*.so \
- ${PRESTAGE}/lib
- ${MV} ${INSTALL_WRKSRC}/funstuff \
- ${INSTALL_WRKSRC}/AFNI.*rc \
- ${INSTALL_WRKSRC}/afnigui* \
+ @${RM} ${INSTALL_TMP}/libf2c.a
+ @${MV} ${INSTALL_TMP}/meica.libs \
+ ${INSTALL_TMP}/shiny \
+ ${INSTALL_TMP}/lib_RetroTS \
+ ${INSTALL_TMP}/afniInterfaceRT \
+ ${INSTALL_TMP}/funstuff \
+ ${INSTALL_TMP}/AFNI.*rc \
+ ${INSTALL_TMP}/afnigui* \
${PRESTAGE}/share
- ${MV} ${INSTALL_WRKSRC}/*.h \
- ${PRESTAGE}/include
- ${MV} ${INSTALL_WRKSRC}/README* \
- ${PRESTAGE}/doc
- for binary in `${FILE} ${INSTALL_WRKSRC}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \
+ @${MV} ${INSTALL_TMP}/*.a \
+ ${INSTALL_TMP}/*.so \
+ ${PRESTAGE}/lib
+ @${MV} ${INSTALL_TMP}/*.h ${PRESTAGE}/include
+ @${CP} ${WRKDIR}/afni-AFNI_${PORTVERSION}/doc/README/* ${PRESTAGE}/doc
+ @for binary in `${FILE} ${INSTALL_TMP}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \
${MV} $${binary} ${PRESTAGE}/bin ; \
done
- ${MV} ${INSTALL_WRKSRC}/* \
- ${PRESTAGE}/scripts
- ${MV} ${PRESTAGE}/scripts/meica.libs ${PRESTAGE}
+ @${MV} ${INSTALL_TMP}/* ${PRESTAGE}/scripts
-do-install:
- ${MKDIR} ${STAGEDIR}${DATADIR} \
+ # Install to STAGEDIR using proper ports tools
+ @${MKDIR} \
+ ${STAGEDIR}${DATADIR} \
${STAGEDIR}${PREFIX}/lib/afni \
- ${STAGEDIR}${PREFIX}/include/afni
- for f in ${PRESTAGE}/lib/*; do \
- ${STRIP_CMD} $${f}; \
- done
- ${INSTALL_DATA} ${PRESTAGE}/lib/* ${STAGEDIR}${PREFIX}/lib/afni
- ${INSTALL_DATA} ${PRESTAGE}/include/* ${STAGEDIR}${PREFIX}/include/afni
- cd ${PRESTAGE}/share && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}
+ ${STAGEDIR}${PREFIX}/include/afni \
+ ${STAGEDIR}${DOCSDIR} \
+ ${STAGEDIR}${PREFIX}/etc/mri
${INSTALL_PROGRAM} ${PRESTAGE}/bin/* ${STAGEDIR}${PREFIX}/bin
${INSTALL_SCRIPT} ${PRESTAGE}/scripts/* ${STAGEDIR}${PREFIX}/bin
- cd ${PRESTAGE} && ${COPYTREE_BIN} meica.libs \
- ${STAGEDIR}${PREFIX}/libexec
- ${INSTALL_DATA} ${WRKSRC}/Atlases/* ${STAGEDIR}${DATADIR}
- ${INSTALL_MAN} ${WRKSRC}/afni.1 ${STAGEDIR}${MAN1PREFIX}/man/man1
- ${MKDIR} ${STAGEDIR}${DOCSDIR} ${STAGEDIR}${PREFIX}/etc/mri
- ${INSTALL_DATA} ${PRESTAGE}/doc/* ${STAGEDIR}${DOCSDIR}
+ ${INSTALL_DATA} ${PRESTAGE}/lib/* ${STAGEDIR}${PREFIX}/lib/afni
+ ${INSTALL_DATA} ${PRESTAGE}/include/* ${STAGEDIR}${PREFIX}/include/afni
+ (cd ${PRESTAGE}/share && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR})
${INSTALL_SCRIPT} ${WRKDIR}/afni.cshrc ${WRKDIR}/afni.profile \
${STAGEDIR}${PREFIX}/etc/mri
+do-install-DOCS-on:
+ ${INSTALL_DATA} ${PRESTAGE}/doc/* ${STAGEDIR}${DOCSDIR}
+
.include <bsd.port.mk>
diff --git a/science/afni/distinfo b/science/afni/distinfo
index 95dcb05123df..ba5c91280c59 100644
--- a/science/afni/distinfo
+++ b/science/afni/distinfo
@@ -1,2 +1,3 @@
-SHA256 (afni-2015.11.13.tar.xz) = b8647ed2f522a520d90cbfd3da70d34849cec421678ff3baf0ecbb6e9e72414b
-SIZE (afni-2015.11.13.tar.xz) = 48722840
+TIMESTAMP = 1557698397
+SHA256 (afni-afni-AFNI_19.1.08_GH0.tar.gz) = 15dcb04412c68e3ca2673eaf90cdd9bb26c1d23c09ed3346bf330ecbf18c4269
+SIZE (afni-afni-AFNI_19.1.08_GH0.tar.gz) = 38767080
diff --git a/science/afni/files/Makefile b/science/afni/files/Makefile
index db7e4f4a4f40..9c6e28e2e4d4 100644
--- a/science/afni/files/Makefile
+++ b/science/afni/files/Makefile
@@ -100,11 +100,15 @@ LLIBS = -lmri -lf2c -lXm -lXp -lXpm -lXext -lXmu -lXt -lX11 -lm $(LZLIB) $(LGIF
# vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
# For suma (NO STATIC LINKING OF GL libs)
-SUMA_INCLUDE_PATH = -I${LOCALBASE}/include/glib-2.0 -I${LOCALBASE}/lib/glib-2.0/include -I${LOCALBASE}/include -I./ -I../ -I../niml/ -Igts/src
+# Use -IGLw_local and -lGLws to avert the following suma runtime error due
+# to lack of extern modifier in GLwDrawA.h:
+# ** ERROR: glwMDrawingAreaWidgetClass is NULL
+# This may break if bundled GLw is not kept up-to-date,
+SUMA_INCLUDE_PATH = -IGLw_local -I${LOCALBASE}/include/glib-2.0 -I${LOCALBASE}/lib/glib-2.0/include -I${LOCALBASE}/include -I./ -I../ -I../niml/ -Igts/src
SUMA_LINK_PATH = -L/usr/lib -L${LOCALBASE}/lib -L../
#use -lGLw if you have libGLw.a or libGLw.so* or
# -lMesaGLw if you have Mesa's version (libMesaGLw*) of libGLw
-SUMA_LINK_LIB = -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm $(LZLIB) -lxml2 -lexpat
+SUMA_LINK_LIB = -lXm -lGLws -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm $(LZLIB) -lxml2 -lexpat
SUMA_MAKEFILE_NAME = SUMA_Makefile
SUMA_BIN_ARCHIVE = SUMA_FreeBSD.tar
SUMA_GLIB_VER = -2.0
diff --git a/science/afni/files/patch-Makefile.INCLUDE b/science/afni/files/patch-Makefile.INCLUDE
index 11cff7353590..adbfdb0f19f6 100644
--- a/science/afni/files/patch-Makefile.INCLUDE
+++ b/science/afni/files/patch-Makefile.INCLUDE
@@ -1,16 +1,16 @@
---- Makefile.INCLUDE.orig 2015-11-06 21:25:04 UTC
+--- Makefile.INCLUDE.orig 2019-05-10 21:23:56 UTC
+++ Makefile.INCLUDE
-@@ -50,7 +50,7 @@ MISC = AFNI_atlas_spaces.niml AFNI.Xd
+@@ -64,7 +64,7 @@ MISC = AFNI_atlas_spaces.niml AFNI.Xdefaults AFNI.a
## AFNI package, but included because they are useful. Some of
## them are Open Source programs, not from the AFNI group at all.
-EXTRAS = cjpeg djpeg whirlgif mpeg_encode myget Xphace rmz aiv mycat quotize $(EXPROGS)
-+EXTRAS = 3dClustBust whirlgif myget Xphace rmz aiv mycat quotize $(EXPROGS)
++EXTRAS = whirlgif myget Xphace rmz aiv mycat quotize $(EXPROGS)
# mpegtoppm in above list
-@@ -60,7 +60,7 @@ EXTRAS = cjpeg djpeg whirlgif mpeg_enc
- PROGRAMS = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge count \
+@@ -77,7 +77,7 @@ EXTRAS = cjpeg djpeg whirlgif mpeg_encode myget Xpha
+ PROGS_1 = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge count \
sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals \
fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3daxialize \
- cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
@@ -18,7 +18,7 @@
waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \
3dNLfim 3dTSgen AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \
3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \
-@@ -72,7 +72,7 @@ PROGRAMS = afni to3d from3d abut 3dclust
+@@ -90,7 +90,7 @@ PROGS_2 = 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dn
3dWavelets 3dfim+ imcutup imcat 3dWinsor 3dZeropad 3dTagalign \
3dMean 3dAttribute cat_matvec 3dOverlap 3dClipLevel 3dZregrid \
3dEntropy 3ddelay ent16 3dRowFillin 1dgrayplot 3dToutcount 1dsum \
@@ -27,8 +27,8 @@
3dTcorrelate 3dAnatNudge 3dcopy Vecwarp 3dMINCtoAFNI 3dCM fdrval \
3dAFNItoANALYZE siemens_vision ge_header mayo_analyze 3dAFNItoNIFTI \
3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dAFNItoMINC 3dBrickStat \
-@@ -92,7 +92,7 @@ PROGRAMS = afni to3d from3d abut 3dclust
- 3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip \
+@@ -112,7 +112,7 @@ PROGS_3 = 3dDeconvolve_f 3dAnhist 3dAFNIto3D 3dUnifor
+ PROGS_4 = 3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip \
3dLocalPV 3dBandpass 3dSetupGroupInCorr 3dGroupInCorr 3dTcorr1D \
3dClustSim 3dRetinoPhase 3dMaskToASCII 3dttest++ 3dDTtoDWI \
- niccc rbox qdelaunay 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply \
@@ -36,7 +36,7 @@
1dCorrelate 3dCountSpikes 3dNwarpCalc dicom_hinfo apsearch 1dBport \
3dNormalityTest 3dmask_tool FIRdesign help_format 2perm 3dClustCount \
column_cat 3dUnifize 3dNwarpCat 3dQwarp 3dLocalHistog 3dNwarpAdjust \
-@@ -104,7 +104,7 @@ PROGRAMS = afni to3d from3d abut 3dclust
+@@ -138,7 +138,7 @@ PROGRAMS = $(PROGS_1) $(PROGS_2) $(PROGS_3) $(PROGS_4)
PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge \
sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnoise count \
fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim imupsam \
@@ -45,7 +45,7 @@
waver 3dnewid 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval \
3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \
imstack byteorder 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot \
-@@ -144,7 +144,7 @@ PROGRAMS_NOPLUG = afni to3d from3d abut
+@@ -181,7 +181,7 @@ PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize
PROGRAMS_EXE = afni.exe to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge \
sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals count \
fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3dGetrow \
@@ -54,26 +54,25 @@
waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \
3dAFNItoNIML AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \
3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \
-@@ -276,7 +276,7 @@ prog_list:
- echo "$(PROGRAMS) $(SCRIPTS) $(SUMA_PROGS) $(SUMA_GTS_PROGS) \
- $(PY_SCRIPTS)" | tr ' ' '\n' | LC_COLLATE=C sort | uniq \
- > ___prog_list.txt
-- make -s -f ptaylor/Makefile.ptaylor.INCLUDE echo_progs | \
-+ $(MAKE) -s -f ptaylor/Makefile.ptaylor.INCLUDE echo_progs | \
- tr ' ' '\n' | LC_COLLATE=C sort | uniq >> ___prog_list.txt
- cat ___prog_list.txt | LC_COLLATE=C sort | uniq >> prog_list.txt
- \rm -f ___prog_list.txt
-@@ -364,6 +364,9 @@ byteorder:byteorder.o
- 3dbuc2fim:3dbuc2fim.o
- $(CC) -o 3dbuc2fim 3dbuc2fim.o $(LFLAGS) $(LLIBS)
+@@ -303,7 +303,7 @@ echo_progs:
+ prog_list_bin:
+ echo "$(PROGRAMS) $(SUMA_PROGS) $(SUMA_GTS_PROGS)" \
+ | tr ' ' '\n' > ___plist_bin.txt
+- make -s -f ptaylor/Makefile.ptaylor.INCLUDE echo_progs \
++ $(MAKE) -s -f ptaylor/Makefile.ptaylor.INCLUDE echo_progs \
+ | tr ' ' '\n' >> ___plist_bin.txt
+ cat ___plist_bin.txt | LC_COLLATE=C sort | uniq > prog_list_bin.txt
+ \rm -f ___plist_bin.txt
+@@ -2884,7 +2884,7 @@ r_misc.o: rickr/r_misc.c rickr/r_misc.h
-+3dClustBust:3dClustBust.c
-+ $(CC) -o 3dClustBust 3dClustBust.c $(INFLAGS) $(LFLAGS) $(LLIBS)
-+
- mritopgm:mritopgm.c
- $(CC) -o mritopgm mritopgm.c $(INFLAGS) $(LFLAGS) $(LLIBS)
+ dcm2niix_afni:
+ ( cd crorden/dcm2niix_console ; \
+- make ; \
++ $(MAKE) ; \
+ $(MV) dcm2niix ../../dcm2niix_afni ; \
+ cd ../../ ; )
-@@ -2728,8 +2731,8 @@ cjpeg:
+@@ -3108,8 +3108,8 @@ libjpeg.a:
$(MAKE) clean ; $(RM) Makefile )
libXmHTML.a:
@@ -82,18 +81,19 @@
+ ( cd XmHTML ; $(MAKE) lib 'CC=$(CC)' 'II=$(IFLAGS)' ; \
+ $(MV) lib/libXmHTML.a .. ; $(MAKE) clean )
- thd_xwebber.o:thd_xwebber.c
- $(CC) -c thd_xwebber.c -I./XmHTML/include $(INFLAGS)
-@@ -3518,8 +3521,9 @@ toyR: toyR.c AFNI_embeddedRCall.o
+ xutil_webber.o:xutil_webber.c
+ $(CC) -c xutil_webber.c -I./XmHTML/include $(INFLAGS)
+@@ -3920,9 +3920,10 @@ toyR: toyR.c AFNI_embeddedRCall.o
####
- R_io.so:R_io.c libmri.a
+ R_io.so:R_io.c $(LIBMRI_OBJ)
( if which R >/dev/null ; then \
- echo PKG_CPPFLAGS = $(INFLAGS) > Makevars ;\
-- echo PKG_LIBS = $(LFLAGS) $(LLIBS) >> Makevars ;\
-- R CMD SHLIB R_io.c ; \
+- echo PKG_LIBS = $(LFLAGS) $(LLIBS) $(RLIB_CONVERT) >> Makevars ;\
+- R CMD SHLIB -o R_io.so R_io.c ; \
+ echo PKG_CPPFLAGS = $(INFLAGS) -I${LOCALBASE}/lib/R/include > Makevars ;\
-+ echo PKG_LIBS = $(LFLAGS) $(LLIBS) -L${LOCALBASE}/lib/R/lib >> Makevars ;\
-+ # Fails because R uses 'make' instead of gmake R CMD SHLIB -n R_io.c; \
++ echo PKG_LIBS = $(LFLAGS) $(LLIBS) $(RLIB_CONVERT) -L${LOCALBASE}/lib/R/lib >> Makevars ;\
++ # Fails because R uses 'make' instead of gmake: R CMD SHLIB -n R_io.c; \
+ $(MAKE) -f 'Makevars' -f '/usr/local/lib/R/etc/Makeconf' -f '/usr/local/lib/R/share/make/shlib.mk' SHLIB='R_io.so' OBJECTS='R_io.o';\
else echo WARNING: Cannot build R_io.so because R is not installed;\
fi ; )
+
diff --git a/science/afni/files/patch-crorden_dcm2niix__console_makefile b/science/afni/files/patch-crorden_dcm2niix__console_makefile
new file mode 100644
index 000000000000..c20e41c355ea
--- /dev/null
+++ b/science/afni/files/patch-crorden_dcm2niix__console_makefile
@@ -0,0 +1,24 @@
+--- crorden/dcm2niix_console/makefile.orig 2019-05-12 14:54:20 UTC
++++ crorden/dcm2niix_console/makefile
+@@ -1,8 +1,8 @@
+ # Regular use
+-CFLAGS=-s -O3
++CXXFLAGS?=-s -O3
+
+ # Debugging
+-#CFLAGS=-g
++#CXXFLAGS=-g
+
+ #run "make" for default build
+ #run "JPEGLS=1 make" for JPEGLS build
+@@ -14,8 +14,8 @@ endif
+ ifneq ($(OS),Windows_NT)
+ OS = $(shell uname)
+ ifeq "$(OS)" "Darwin"
+- CFLAGS=-dead_strip -O3
++ CXXFLAGS=-dead_strip -O3
+ endif
+ endif
+ all:
+- g++ $(CFLAGS) -I. $(JFLAGS) main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -o dcm2niix -DmyDisableOpenJPEG
++ $(CXX) $(CXXFLAGS) -I. $(JFLAGS) main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -o dcm2niix -DmyDisableOpenJPEG
diff --git a/science/afni/files/patch-misc_math.c b/science/afni/files/patch-misc_math.c
deleted file mode 100644
index 50623944f078..000000000000
--- a/science/afni/files/patch-misc_math.c
+++ /dev/null
@@ -1,16 +0,0 @@
---- misc_math.c.orig 2015-11-06 21:25:08 UTC
-+++ misc_math.c
-@@ -1,6 +1,13 @@
-
-+/* For older libm */
-+double log2(double n)
-+{
-+ return log(n) / log(2.0);
-+}
-+
- /* move from Deconvolve.c into libmri.a 21 Jun 2010 [rickr] */
-
-+
- double legendre( double x , int m ) /* Legendre polynomials over [-1,1] */
- {
- if( m < 0 ) return 1.0 ; /* bad input */
diff --git a/science/afni/files/patch-netcdf-3.5.0_src_configure b/science/afni/files/patch-netcdf-3.5.0_src_configure
index e7a491b4a1ac..2cea4c66380a 100644
--- a/science/afni/files/patch-netcdf-3.5.0_src_configure
+++ b/science/afni/files/patch-netcdf-3.5.0_src_configure
@@ -1,6 +1,6 @@
---- netcdf-3.5.0/src/configure.orig 2015-11-06 21:25:09 UTC
+--- netcdf-3.5.0/src/configure.orig 2019-05-10 21:23:56 UTC
+++ netcdf-3.5.0/src/configure
-@@ -933,10 +933,10 @@ echo "configure:928: checking for top-le
+@@ -933,10 +933,10 @@ echo "configure:928: checking for top-level source-dir
diff --git a/science/afni/files/patch-prf__common__circular.c b/science/afni/files/patch-prf__common__circular.c
new file mode 100644
index 000000000000..cfcaf2d3f01d
--- /dev/null
+++ b/science/afni/files/patch-prf__common__circular.c
@@ -0,0 +1,18 @@
+--- prf_common_circular.c.orig 2019-05-10 21:23:56 UTC
++++ prf_common_circular.c
+@@ -318,8 +318,14 @@ static int show_malloc_stats(char * mesg)
+
+ if( show_stats ) {
+ fprintf(stderr,"\n----- malloc stats: %s\n", mesg);
+-#ifndef DARWIN
++#if defined(__linux__)
+ malloc_stats();
++#elif defined(__FreeBSD__)
++ #include <stdlib.h>
++ #include <malloc_np.h>
++ malloc_stats_print(NULL, NULL, "g");
++#else
++ fprintf(stderr, "No malloc_stats() on this platform.\n");
+ #endif
+ }
+
diff --git a/science/afni/pkg-descr b/science/afni/pkg-descr
index 0ea153f1f534..960c4832beb5 100644
--- a/science/afni/pkg-descr
+++ b/science/afni/pkg-descr
@@ -1,5 +1,5 @@
-This is a port of AFNI, Analysis of Functional Neuro Imaging. AFNI is
-a tool for analyzing 3 dimensional images, especially functional MRI
-images used in brain mapping research.
+AFNI (Analysis of Functional Neuro Imaging) is a tool for analyzing
+3-dimensional images, especially functional MRI images used in brain mapping
+research.
WWW: http://afni.nimh.nih.gov/afni/
diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist
index b44514a4eec0..efc23f03605e 100644
--- a/science/afni/pkg-plist
+++ b/science/afni/pkg-plist
@@ -1,11 +1,12 @@
+bin/1dApar2mat
bin/1dAstrip
bin/1dBandpass
bin/1dBport
bin/1dCorrelate
-bin/1dDW_Grad_o_Mat
bin/1dFlagMotion
bin/1dGC.R
bin/1dMarry
+bin/1dNLfit
bin/1dRplot
bin/1dRplot.R
bin/1dSEM
@@ -23,6 +24,8 @@ bin/1dgrayplot
bin/1dmatcalc
bin/1dnorm
bin/1dplot
+bin/1dplot.py
+bin/1dsound
bin/1dsum
bin/1dsvd
bin/1dtranspose
@@ -54,11 +57,11 @@ bin/3dBRAIN_VOYAGERtoAFNI
bin/3dBandpass
bin/3dBlurInMask
bin/3dBlurToFWHM
+bin/3dBrainSync
bin/3dBrickStat
bin/3dCM
bin/3dCRUISEtoAFNI
bin/3dClipLevel
-bin/3dClustBust
bin/3dClustCount
bin/3dClustSim
bin/3dConformist
@@ -67,17 +70,17 @@ bin/3dCountSpikes
bin/3dDFT
bin/3dDTeig
bin/3dDTtoDWI
-bin/3dDTtoNoisyDWI
bin/3dDWItoDT
-bin/3dDWUncert
bin/3dDeconvolve
bin/3dDeconvolve_f
+bin/3dDegreeCentrality
bin/3dDespike
bin/3dDetrend
-bin/3dEigsToDT
+bin/3dECM
bin/3dEmpty
bin/3dEntropy
bin/3dErrtsCormat
+bin/3dExtractGroupInCorr
bin/3dExtrema
bin/3dFDR
bin/3dFFT
@@ -89,6 +92,7 @@ bin/3dGC.R
bin/3dGenFeatureDist
bin/3dGenPriors
bin/3dGetrow
+bin/3dGrayplot
bin/3dGroupInCorr
bin/3dHist
bin/3dICA.R
@@ -98,10 +102,12 @@ bin/3dIntracranial
bin/3dInvFMRI
bin/3dKS.R
bin/3dKruskalWallis
+bin/3dLFCD
bin/3dLME
bin/3dLME.R
bin/3dLRflip
bin/3dLSS
+bin/3dLocalACF
bin/3dLocalBistat
bin/3dLocalHistog
bin/3dLocalPV
@@ -109,17 +115,20 @@ bin/3dLocalSVD
bin/3dLocalstat
bin/3dMEMA
bin/3dMEMA.R
+bin/3dMEPFM
+bin/3dMEPFM.R
bin/3dMINCtoAFNI
+bin/3dMSE
bin/3dMVM
bin/3dMVM.R
+bin/3dMVM_validator
bin/3dMannWhitney
bin/3dMaskToASCII
-bin/3dMatch
bin/3dMax
bin/3dMean
bin/3dMedianFilter
+bin/3dMultiThresh
bin/3dNLfim
-bin/3dNetCorr
bin/3dNormalityTest
bin/3dNotes
bin/3dNwarpAdjust
@@ -132,18 +141,16 @@ bin/3dOverlap
bin/3dPAR2AFNI.pl
bin/3dPFM
bin/3dPFM.R
+bin/3dPVmap
bin/3dPeriodogram
bin/3dPolyfit
bin/3dProbTrackID
bin/3dPval
bin/3dQwarp
bin/3dREMLfit
-bin/3dROIMaker
bin/3dROIstats
-bin/3dRSFC
bin/3dRank
bin/3dRankizer
-bin/3dReHo
bin/3dRegAna
bin/3dRetinoPhase
bin/3dRowFillin
@@ -151,6 +158,7 @@ bin/3dRprogDemo
bin/3dRprogDemo.R
bin/3dSeg
bin/3dSetupGroupInCorr
+bin/3dSharpen
bin/3dSignatures
bin/3dSignatures.R
bin/3dSkullStrip
@@ -159,7 +167,6 @@ bin/3dStatClust
bin/3dSurf2Vol
bin/3dSurfMask
bin/3dSynthesize
-bin/3dTORTOISEtoHere
bin/3dTRfix
bin/3dTSgen
bin/3dTagalign
@@ -167,6 +174,7 @@ bin/3dTcat
bin/3dTcorr1D
bin/3dTcorrMap
bin/3dTcorrelate
+bin/3dTfilter
bin/3dTfitter
bin/3dThreetoRGB
bin/3dTnorm
@@ -178,7 +186,9 @@ bin/3dTrackID
bin/3dTshift
bin/3dTsmooth
bin/3dTsort
+bin/3dTsplit4D
bin/3dTstat
+bin/3dTto1D
bin/3dTwotoComplex
bin/3dUndump
bin/3dUnifize
@@ -190,6 +200,7 @@ bin/3dWarpDrive
bin/3dWavelets
bin/3dWilcoxon
bin/3dWinsor
+bin/3dXClustSim
bin/3dXYZcat
bin/3dZcat
bin/3dZcutup
@@ -232,6 +243,8 @@ bin/3dresample
bin/3dretroicor
bin/3drotate
bin/3dsvm
+bin/3dsvm_linpredict
+bin/3dtoXdataset
bin/3dttest
bin/3dttest++
bin/3dvolreg
@@ -249,6 +262,8 @@ bin/@Align_Centers
bin/@Atlasize
bin/@Center_Distance
bin/@CheckForAfniDset
+bin/@ClustExp_CatLab
+bin/@ClustExp_run_shiny
bin/@CommandGlobb
bin/@DO.examples
bin/@DTI_studio_reposition
@@ -271,14 +286,18 @@ bin/@GetAfniOrient
bin/@GetAfniPrefix
bin/@GetAfniRes
bin/@GetAfniView
+bin/@GradFlipTest
bin/@Install_3dPFM_Demo
bin/@Install_AfniRetinoDemo
bin/@Install_ClustScat_Demo
+bin/@Install_D99_macaque
bin/@Install_DBSproc
bin/@Install_FATCAT_DEMO
+bin/@Install_FATCAT_DEMO2
bin/@Install_FATMVM_DEMO
bin/@Install_InstaCorr_Demo
bin/@Install_MEICA_Demo
+bin/@Install_NIH_Marmoset
bin/@Install_RSFMRI_Motion_Group_Demo
bin/@Install_TSrestMovieDemo
bin/@IsoMasks
@@ -293,15 +312,18 @@ bin/@R_funclist
bin/@RenamePanga
bin/@Reorder
bin/@RetinoProc
+bin/@SSwarper
bin/@SUMA_AlignToExperiment
bin/@SUMA_FSvolToBRIK
bin/@SUMA_Make_Spec_Caret
bin/@SUMA_Make_Spec_FS
bin/@SUMA_Make_Spec_SF
+bin/@SUMA_renumber_FS
bin/@ScaleVolume
bin/@ScriptCheck
bin/@Shift_Volume
bin/@ShowDynamicRange
+bin/@SkullStrip_TouchUp
bin/@Spharm.examples
bin/@SurfSmooth.HEAT_07.examples
bin/@T1scale
@@ -310,42 +332,77 @@ bin/@ToRAI
bin/@UpdateAfni
bin/@VolCenter
bin/@afni.run.me
+bin/@afni_R_package_install
+bin/@afni_refacer_make_master
+bin/@afni_refacer_make_onebigA12
+bin/@afni_refacer_run
bin/@align_partial_oblique
bin/@auto_align
bin/@auto_tlrc
bin/@build_afni_Xlib
+bin/@chauffeur_afni
bin/@clean_help_dir
bin/@clip_volume
+bin/@compute_OC_weights
bin/@compute_gcor
bin/@demo_prompt
bin/@diff.files
bin/@diff.tree
+bin/@djunct_4d_imager
+bin/@djunct_4d_slices_to_3d_vol
+bin/@djunct_calc_mont_dims.py
+bin/@djunct_combine_str.py
+bin/@djunct_dwi_selector.tcsh
+bin/@djunct_edgy_align_check
+bin/@djunct_is_label.py
+bin/@djunct_montage_coordinator
+bin/@djunct_select_str.py
+bin/@djunct_slice_space
+bin/@djunct_vol_3slice_select
bin/@escape-
+bin/@extract_meica_ortvec
bin/@fast_roi
+bin/@fat_tract_colorize
bin/@fix_FSsphere
bin/@float_fix
+bin/@get.afni.version
bin/@global_parse
+bin/@grayplot
bin/@help.AFNI
bin/@isOblique
bin/@make_plug_diff
bin/@make_stim_file
+bin/@measure_bb_thick
+bin/@measure_erosion_thick
+bin/@measure_in2out
bin/@move.to.series.dirs
bin/@np
bin/@parse_afni_name
bin/@parse_name
bin/@radial_correlate
bin/@simulate_motion
+bin/@snapshot_volreg
+bin/@snapshot_volreg3
bin/@statauxcode
+bin/@suma_reprefixize_spec
+bin/@surf_to_vol_spackle
+bin/@thickness_master
bin/@toMNI_Awarp
bin/@toMNI_Qwarpar
bin/@update.afni.binaries
+bin/@xyz_to_ijk
bin/AFNI_Batch_R
bin/AFNI_atlas_spaces.niml
+bin/AFNI_version.txt
bin/AFNIio.R
bin/AFNIplot.R
bin/AlphaSim
bin/AnalyzeTrace
+bin/BayesianGroupAna.R
+bin/BayesianGroupAna.py
bin/BrainSkin
+bin/ClustExp_HistTable.py
+bin/ClustExp_StatParse.py
bin/CompareSurfaces
bin/ConvertDset
bin/ConvertSurface
@@ -357,6 +414,7 @@ bin/Dimon1
bin/DriveSuma
bin/ExamineXmat
bin/ExamineXmat.R
+bin/FATCAT_matplot
bin/FD2
bin/FIRdesign
bin/FSread_annot
@@ -366,12 +424,17 @@ bin/Ifile
bin/InstaTract
bin/IsoSurface
bin/Level2.R
+bin/MBA
+bin/MBA.R
bin/MakeColorMap
bin/MapIcosahedron
bin/ParseName
+bin/RBA
+bin/RBA.R
bin/ROI2dataset
bin/ROIgrow
bin/RSFgen
+bin/RetroTS.py
bin/SUMA_glxdino
bin/SUMA_paperplane
bin/SUMA_pixmap2eps
@@ -396,10 +459,17 @@ bin/SurfToSurf
bin/SurfaceMetrics
bin/Vecwarp
bin/Xphace
+bin/abids_json_info.py
+bin/abids_json_tool.py
+bin/abids_lib.py
+bin/abids_tool.py
bin/abut
bin/adwarp
bin/afni
bin/afni_base.py
+bin/afni_check_omp
+bin/afni_fs_aparc+aseg_2000.txt
+bin/afni_fs_aparc+aseg_2009.txt
bin/afni_history
bin/afni_open
bin/afni_proc.py
@@ -412,6 +482,8 @@ bin/afni_vcheck
bin/afni_xmat.py
bin/aiv
bin/align_epi_anat.py
+bin/apqc_make_html.py
+bin/apqc_make_tcsh.py
bin/apsearch
bin/ask_me.py
bin/auto_warp.py
@@ -422,8 +494,10 @@ bin/cifti_tool
bin/column_cat
bin/count
bin/db_mod.py
+bin/dcm2niix_afni
bin/demo.fixed.niml.do
bin/demo.mobile.niml.do
+bin/demoExpt.py
bin/dicom_hdr
bin/dicom_hinfo
bin/dicom_to_raw
@@ -435,6 +509,18 @@ bin/fat_mvm_gridconv.py
bin/fat_mvm_prep.py
bin/fat_mvm_review.py
bin/fat_mvm_scripter.py
+bin/fat_proc_align_anat_pair
+bin/fat_proc_axialize_anat
+bin/fat_proc_connec_vis
+bin/fat_proc_convert_dcm_anat
+bin/fat_proc_convert_dcm_dwis
+bin/fat_proc_decmap
+bin/fat_proc_dwi_to_dt
+bin/fat_proc_filter_dwis
+bin/fat_proc_grad_plot
+bin/fat_proc_imit2w_from_t1w
+bin/fat_proc_map_to_dti
+bin/fat_proc_select_vols
bin/fat_roi_row.py
bin/fdrval
bin/fftest
@@ -448,6 +534,9 @@ bin/gen_epi_review.py
bin/gen_group_command.py
bin/gen_ss_review_scripts.py
bin/gen_ss_review_table.py
+bin/get_afni_model_PRF
+bin/get_afni_model_PRF_6
+bin/get_afni_model_PRF_6_BAD
bin/gifti_tool
bin/gui_uber_align_test.py
bin/gui_uber_skel.py
@@ -472,12 +561,22 @@ bin/imupsam
bin/inspec
bin/lib_RR_plot.py
bin/lib_afni1D.py
+bin/lib_apqc_html.py
+bin/lib_apqc_html_css.py
+bin/lib_apqc_html_helps.py
+bin/lib_apqc_io.py
+bin/lib_apqc_tcsh.py
+bin/lib_decay_timing.py
+bin/lib_dti_sundry.py
bin/lib_fat_Rfactor.py
bin/lib_fat_funcs.py
bin/lib_fat_plot_sel.py
bin/lib_matplot.py
+bin/lib_plot_1D.py
bin/lib_qt_gui.py
+bin/lib_rand_timing.py
bin/lib_realtime.py
+bin/lib_ss_review.py
bin/lib_subjects.py
bin/lib_surf_clustsim.py
bin/lib_system_check.py
@@ -493,7 +592,6 @@ bin/lpc_align.py
bin/make_pq_script.py
bin/make_random_timing.py
bin/make_stim_times.py
-bin/map_TrackID
bin/mayo_analyze
bin/meica.py
bin/module_test_lib.py
@@ -503,17 +601,19 @@ bin/myget
bin/neuro_deconvolve.py
bin/nicat
bin/niccc
-bin/nifti1_test
bin/nifti1_tool
bin/nifti_tool
bin/niml_feedme
bin/niprobe
bin/nsize
bin/option_list.py
+bin/p2dsetstat
+bin/parse_fs_lt_log.py
bin/plugout_drive
bin/plugout_ijk
bin/plugout_tt
bin/plugout_tta
+bin/prompt_popup
bin/prompt_user
bin/python_module_test.py
bin/quick.alpha.vals.py
@@ -532,18 +632,22 @@ bin/siemens_vision
bin/slow_surf_clustsim.py
bin/smooth.R
bin/sqwave
+bin/stimband
bin/strblast
bin/suma
bin/suma_change_spec
+bin/tedana_wrapper.py
bin/tfim
bin/timing_tool.py
bin/to3d
+bin/tokens
bin/uber_align_test.py
bin/uber_proc.py
bin/uber_skel.py
bin/uber_subject.py
bin/uber_ttest.py
bin/ui_xmat.py
+bin/unWarpEPI.py
bin/uniq_images
bin/waver
bin/whereami
@@ -577,7 +681,7 @@ include/afni/mri_warpfield.h
include/afni/mrilib.h
include/afni/multivector.h
include/afni/nifti1.h
-include/afni/nifti1_io.h
+include/afni/nifti2_io.h
include/afni/nifticdf.h
include/afni/niml.h
include/afni/r_idisp.h
@@ -593,7 +697,6 @@ include/afni/thd_ttatlas_CA_EZ.h
include/afni/thd_ttatlas_query.h
include/afni/vecmat.h
include/afni/vol2surf.h
-include/afni/volpack.h
include/afni/znzlib.h
lib/afni/R_io.so
lib/afni/libGLws.a
@@ -601,11 +704,12 @@ lib/afni/libSUMA.a
lib/afni/libcoxplot.a
lib/afni/libmri.a
lib/afni/libmrix.a
-lib/afni/libvolpack.a
lib/afni/model_beta.so
lib/afni/model_constant.so
lib/afni/model_conv_PRF.so
lib/afni/model_conv_PRF_6.so
+lib/afni/model_conv_PRF_6_BAD.so
+lib/afni/model_conv_PRF_DOG.so
lib/afni/model_conv_cosine4.so
lib/afni/model_conv_diffgamma.so
lib/afni/model_convgamma.so
@@ -666,7 +770,6 @@ lib/afni/plug_permtest.so
lib/afni/plug_power.so
lib/afni/plug_realtime.so
lib/afni/plug_rename.so
-lib/afni/plug_render.so
lib/afni/plug_reorder.so
lib/afni/plug_retroicor.so
lib/afni/plug_roiedit.so
@@ -682,330 +785,13 @@ lib/afni/plug_vol2surf.so
lib/afni/plug_volreg.so
lib/afni/plug_wavelets.so
lib/afni/plug_zeropad.so
-libexec/meica.libs/alignp_mepi_anat.py
-libexec/meica.libs/mdp/__init__.py
-libexec/meica.libs/mdp/caching/__init__.py
-libexec/meica.libs/mdp/caching/caching_extension.py
-libexec/meica.libs/mdp/classifier_node.py
-libexec/meica.libs/mdp/configuration.py
-libexec/meica.libs/mdp/extension.py
-libexec/meica.libs/mdp/graph/__init__.py
-libexec/meica.libs/mdp/graph/graph.py
-libexec/meica.libs/mdp/helper_funcs.py
-libexec/meica.libs/mdp/hinet/__init__.py
-libexec/meica.libs/mdp/hinet/flownode.py
-libexec/meica.libs/mdp/hinet/hinet.css
-libexec/meica.libs/mdp/hinet/htmlvisitor.py
-libexec/meica.libs/mdp/hinet/layer.py
-libexec/meica.libs/mdp/hinet/switchboard.py
-libexec/meica.libs/mdp/hinet/switchboard_factory.py
-libexec/meica.libs/mdp/linear_flows.py
-libexec/meica.libs/mdp/nodes/__init__.py
-libexec/meica.libs/mdp/nodes/classifier_nodes.py
-libexec/meica.libs/mdp/nodes/convolution_nodes.py
-libexec/meica.libs/mdp/nodes/em_nodes.py
-libexec/meica.libs/mdp/nodes/expansion_nodes.py
-libexec/meica.libs/mdp/nodes/fda_nodes.py
-libexec/meica.libs/mdp/nodes/ica_nodes.py
-libexec/meica.libs/mdp/nodes/ica_nodes.py~
-libexec/meica.libs/mdp/nodes/ica_nodes_old.py
-libexec/meica.libs/mdp/nodes/isfa_nodes.py
-libexec/meica.libs/mdp/nodes/jade.py
-libexec/meica.libs/mdp/nodes/libsvm_classifier.py
-libexec/meica.libs/mdp/nodes/lle_nodes.py
-libexec/meica.libs/mdp/nodes/misc_nodes.py
-libexec/meica.libs/mdp/nodes/neural_gas_nodes.py
-libexec/meica.libs/mdp/nodes/nipals.py
-libexec/meica.libs/mdp/nodes/pca_nodes.py
-libexec/meica.libs/mdp/nodes/rbm_nodes.py
-libexec/meica.libs/mdp/nodes/regression_nodes.py
-libexec/meica.libs/mdp/nodes/scikits_nodes.py
-libexec/meica.libs/mdp/nodes/sfa_nodes.py
-libexec/meica.libs/mdp/nodes/shogun_svm_classifier.py
-libexec/meica.libs/mdp/nodes/svm_classifiers.py
-libexec/meica.libs/mdp/nodes/xsfa_nodes.py
-libexec/meica.libs/mdp/parallel/__init__.py
-libexec/meica.libs/mdp/parallel/parallelclassifiers.py
-libexec/meica.libs/mdp/parallel/parallelflows.py
-libexec/meica.libs/mdp/parallel/parallelhinet.py
-libexec/meica.libs/mdp/parallel/parallelnodes.py
-libexec/meica.libs/mdp/parallel/pp_slave_script.py
-libexec/meica.libs/mdp/parallel/pp_slave_wrapper.py
-libexec/meica.libs/mdp/parallel/pp_support.py
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generated by cgit (git 2.34.1) at 2025-02-04 18:26:31 +0800