Date: Tue, 17 Aug 2021 02:51:44 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: df70b7efede8 - main - biology/biosig: New port: Library for reading and writing different biosignal data format Message-ID: <202108170251.17H2pijg098280@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=df70b7efede8c1936ae5c1867aa0910b99c34ab9 commit df70b7efede8c1936ae5c1867aa0910b99c34ab9 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2021-08-17 02:50:48 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2021-08-17 02:51:36 +0000 biology/biosig: New port: Library for reading and writing different biosignal data format --- biology/Makefile | 1 + biology/biosig/Makefile | 34 +++ biology/biosig/distinfo | 3 + biology/biosig/files/patch-biosig4c++_biosig-dev.h | 21 ++ biology/biosig/files/patch-biosig4c++_biosig.c | 43 +++ .../patch-biosig4c++_t220_sopen__scp__write.c | 28 ++ biology/biosig/pkg-descr | 10 + biology/biosig/pkg-plist | 320 +++++++++++++++++++++ 8 files changed, 460 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 13f0cd294ee5..81760e9e66a3 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -13,6 +13,7 @@ SUBDIR += biococoa SUBDIR += biolibc SUBDIR += bioparser + SUBDIR += biosig SUBDIR += biosoup SUBDIR += biostar-tools SUBDIR += bolt-lmm diff --git a/biology/biosig/Makefile b/biology/biosig/Makefile new file mode 100644 index 000000000000..f77bfdbb11a7 --- /dev/null +++ b/biology/biosig/Makefile @@ -0,0 +1,34 @@ +PORTNAME= biosig +DISTVERSION= 2.3.3 +DISTVERSIONSUFFIX= .src +CATEGORIES= biology +MASTER_SITES= SF/${PORTNAME}/BioSig%20for%20C_C%2B%2B/src/ + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Library for reading and writing different biosignal data format + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/COPYING + +LIB_DEPENDS= libb64.so:converters/libb64 \ + libcholmod.so:math/suitesparse-cholmod \ + libiconv.so:converters/libiconv \ + libtinyxml.so:textproc/tinyxml + +USES= gmake iconv localbase:ldflags +USE_LDCONFIG= yes + +WRKSRC= ${WRKDIR}/${PORTNAME}-${DISTVERSION} + +GNU_CONFIGURE= yes + +CFLAGS+= -D__BYTE_ORDER=BYTE_ORDER -D__LITTLE_ENDIAN=LITTLE_ENDIAN -D__BIG_ENDIAN=BIG_ENDIAN \ + -Dbswap_16=bswap16 -Dbswap_32=bswap32 -Dbswap_64=bswap64 +LDFLAGS+= -liconv + +post-install: +.for f in bin/biosig_fhir bin/biosig2gdf bin/physicalunits bin/save2gdf lib/libbiosig.so.3 + @${STRIP_CMD} ${STAGEDIR}${PREFIX}/${f} +.endfor + +.include <bsd.port.mk> diff --git a/biology/biosig/distinfo b/biology/biosig/distinfo new file mode 100644 index 000000000000..af035532c834 --- /dev/null +++ b/biology/biosig/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1629098745 +SHA256 (biosig-2.3.3.src.tar.gz) = ecff695e912265cbb817b936209086d1b5854afeb44ed58e701feeb2e0b1b33e +SIZE (biosig-2.3.3.src.tar.gz) = 2525173 diff --git a/biology/biosig/files/patch-biosig4c++_biosig-dev.h b/biology/biosig/files/patch-biosig4c++_biosig-dev.h new file mode 100644 index 000000000000..39fedc40975c --- /dev/null +++ b/biology/biosig/files/patch-biosig4c++_biosig-dev.h @@ -0,0 +1,21 @@ +--- biosig4c++/biosig-dev.h.orig 2021-08-13 09:17:15 UTC ++++ biosig4c++/biosig-dev.h +@@ -35,6 +35,8 @@ + #include <time.h> + #include "physicalunits.h" + ++#include <sys/endian.h> ++#include <machine/endian.h> // for betoh16, etc. + + #ifdef __cplusplus + extern "C" { +@@ -549,6 +551,9 @@ HDRTYPE* sopen_extended(const char* FileName, const ch + #elif defined(__linux__) + # include <endian.h> + # include <byteswap.h> ++ ++#elif defined(__FreeBSD__) ++# include <machine/endian.h> + + #elif defined(__GLIBC__) // for Hurd + # include <endian.h> diff --git a/biology/biosig/files/patch-biosig4c++_biosig.c b/biology/biosig/files/patch-biosig4c++_biosig.c new file mode 100644 index 000000000000..06f8a056571d --- /dev/null +++ b/biology/biosig/files/patch-biosig4c++_biosig.c @@ -0,0 +1,43 @@ +--- biosig4c++/biosig.c.orig 2021-08-13 09:17:15 UTC ++++ biosig4c++/biosig.c +@@ -631,7 +631,7 @@ int ifsetpos(HDRTYPE* hdr, size_t *pos) { + // gnu linux on sparc needs this + fpos_t p; + p.__pos = *pos; +-#elif __sparc__ || __APPLE__ || __MINGW32__ || ANDROID || __NetBSD__ || __CYGWIN__ ++#elif __sparc__ || __APPLE__ || __MINGW32__ || ANDROID || __NetBSD__ || __CYGWIN__ || __FreeBSD__ + fpos_t p = *pos; + #else + fpos_t p; +@@ -652,7 +652,7 @@ int ifsetpos(HDRTYPE* hdr, size_t *pos) { + #if __gnu_linux__ + // gnu linux on sparc needs this + *pos = p.__pos; +-#elif __sparc__ || __APPLE__ || __MINGW32__ || ANDROID || __NetBSD__ || __CYGWIN__ ++#elif __sparc__ || __APPLE__ || __MINGW32__ || ANDROID || __NetBSD__ || __CYGWIN__ || __FreeBSD__ + *pos = p; + #else + *pos = p.__pos; +@@ -678,7 +678,7 @@ int ifgetpos(HDRTYPE* hdr, size_t *pos) { + #if __gnu_linux__ + // gnu linux on sparc needs this + *pos = p.__pos; // ugly hack but working +-#elif __sparc__ || __APPLE__ || __MINGW32__ || ANDROID || __NetBSD__ || __CYGWIN__ ++#elif __sparc__ || __APPLE__ || __MINGW32__ || ANDROID || __NetBSD__ || __CYGWIN__ || __FreeBSD__ + *pos = p; + #else + *pos = p.__pos; // ugly hack but working +@@ -1219,8 +1219,11 @@ HDRTYPE* constructHDR(const unsigned NS, const unsigne + hdr->data.size[0] = 0; // rows + hdr->data.size[1] = 0; // columns + hdr->data.block = NULL; +- hdr->T0 = t_time2gdf_time(time(NULL)-timezone); // localtime +- hdr->tzmin = -timezone/60; // convert from seconds west of UTC to minutes east; ++ ++ time_t t=time(NULL); ++ struct tm *tt = localtime(&t); ++ hdr->tzmin = tt->tm_gmtoff/60; ++ hdr->T0 = t_time2gdf_time(time(NULL)-tt->tm_gmtoff); // localtime + + { + uint8_t Equipment[8] = "b4c_1.5 "; diff --git a/biology/biosig/files/patch-biosig4c++_t220_sopen__scp__write.c b/biology/biosig/files/patch-biosig4c++_t220_sopen__scp__write.c new file mode 100644 index 000000000000..20cb7ed4f3b8 --- /dev/null +++ b/biology/biosig/files/patch-biosig4c++_t220_sopen__scp__write.c @@ -0,0 +1,28 @@ +--- biosig4c++/t220/sopen_scp_write.c.orig 2021-08-13 09:17:15 UTC ++++ biosig4c++/t220/sopen_scp_write.c +@@ -388,10 +388,8 @@ int sopen_SCP_write(HDRTYPE* hdr) { + if (VERBOSE_LEVEL>7) fprintf(stdout,"Section 1 Tag 25 \n"); + + gdf_time T1 = hdr->T0; +-#ifndef __APPLE__ +- T1 += (int32_t)ldexp(timezone/86400.0,32); +-#endif +- T0_tm = gdf_time2tm_time(T1); ++ T0_tm = gdf_time2tm_time(hdr->T0); ++ T0_tm->tm_gmtoff = hdr->tzmin*60; + + *(ptr+sectionStart+curSectLen) = 25; // tag + leu16a(4, ptr+sectionStart+curSectLen+1); // length +@@ -719,10 +717,8 @@ int sopen_SCP_write(HDRTYPE* hdr) { + + // Recording Date and Time + gdf_time T1 = hdr->T0; +-#ifndef __APPLE__ +- T1 += (int32_t)ldexp(timezone/86400.0,32); +-#endif +- T0_tm = gdf_time2tm_time(T1); ++ T0_tm = gdf_time2tm_time(hdr->T0); ++ T0_tm->tm_gmtoff = hdr->tzmin*60; + + leu16a(T0_tm->tm_year+1900, PtrCurSect+10); // year + PtrCurSect[12] = (uint8_t)(T0_tm->tm_mon + 1); // month diff --git a/biology/biosig/pkg-descr b/biology/biosig/pkg-descr new file mode 100644 index 000000000000..5a12322fe229 --- /dev/null +++ b/biology/biosig/pkg-descr @@ -0,0 +1,10 @@ +BioSig is an open source software library for biomedical signal processing, +featuring for example the analysis of biosignals such as the +electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), +electrooculogram (EOG), electromyogram (EMG), respiration, and so on. Major +application areas are: Neuroinformatics, brain-computer interfaces, +neurophysiology, psychology, cardiovascular systems and sleep research. The aim +of the BioSig project is to foster research in biomedical signal processing by +providing open source software tools for many different applications. + +WWW: http://biosig.sourceforge.net/ diff --git a/biology/biosig/pkg-plist b/biology/biosig/pkg-plist new file mode 100644 index 000000000000..fca3a09eb6fe --- /dev/null +++ b/biology/biosig/pkg-plist @@ -0,0 +1,320 @@ +bin/bin2rec +bin/biosig2gdf +bin/biosig_fhir +bin/heka2itx +bin/physicalunits +bin/rec2bin +bin/save2aecg +bin/save2gdf +bin/save2scp +include/biosig-dev.h +include/biosig.h +include/biosig2.h +include/gdftime.h +include/physicalunits.h +lib/libbiosig.a +lib/libbiosig.so +lib/libbiosig.so.3 +lib/libphysicalunits.a +libdata/pkgconfig/libbiosig.pc +man/man1/bin2rec.1.gz +man/man1/biosig2gdf.1.gz +man/man1/biosig_fhir.1.gz +man/man1/heka2itx.1.gz +man/man1/mexSLOAD.1.gz +man/man1/physicalunits.1.gz +man/man1/rec2bin.1.gz +man/man1/save2aecg.1.gz +man/man1/save2gdf.1.gz +man/man1/save2scp.1.gz 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