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biology/biosig: New port: Library for reading and writing different biosignal data format

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This commit is contained in:
Yuri Victorovich 2021-08-16 19:50:48 -07:00
parent e8ede160c0
commit df70b7efed
8 changed files with 460 additions and 0 deletions
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1
biology/Makefile
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@ -13,6 +13,7 @@
SUBDIR += biococoa
SUBDIR += biolibc
SUBDIR += bioparser
SUBDIR += biosig
SUBDIR += biosoup
SUBDIR += biostar-tools
SUBDIR += bolt-lmm

34
biology/biosig/Makefile Normal file
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@ -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>

3
biology/biosig/distinfo Normal file
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@ -0,0 +1,3 @@
TIMESTAMP = 1629098745
SHA256 (biosig-2.3.3.src.tar.gz) = ecff695e912265cbb817b936209086d1b5854afeb44ed58e701feeb2e0b1b33e
SIZE (biosig-2.3.3.src.tar.gz) = 2525173

21
biology/biosig/files/patch-biosig4c++_biosig-dev.h Normal file
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@ -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>

43
biology/biosig/files/patch-biosig4c++_biosig.c Normal file
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@ -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 ";

28
biology/biosig/files/patch-biosig4c++_t220_sopen__scp__write.c Normal file
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@ -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

10
biology/biosig/pkg-descr Normal file
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@ -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/

320
biology/biosig/pkg-plist Normal file
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@ -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
man/man1/sigviewer.1.gz
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%%DATADIR%%/matlab/INDEX
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%%DATADIR%%/matlab/LICENSE
%%DATADIR%%/matlab/PKG_ADD
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%%DATADIR%%/matlab/doc/elecpos.txt
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%%DATADIR%%/matlab/t200_FileAccess/biosig_str2double.m
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%%DATADIR%%/matlab/t200_FileAccess/get_current_username.m
%%DATADIR%%/matlab/t200_FileAccess/getfiletype.m
%%DATADIR%%/matlab/t200_FileAccess/gtfopen.m
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%%DATADIR%%/matlab/t200_FileAccess/iopen.m
%%DATADIR%%/matlab/t200_FileAccess/iread.m
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