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

7 files changed, 459 insertions, 0 deletions

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
+man/man1/sigviewer.1.gz
+%%DATADIR%%/matlab/Contents.m
+%%DATADIR%%/matlab/INDEX
+%%DATADIR%%/matlab/INSTALL
+%%DATADIR%%/matlab/LICENSE
+%%DATADIR%%/matlab/PKG_ADD
+%%DATADIR%%/matlab/PKG_DEL
+%%DATADIR%%/matlab/README
+%%DATADIR%%/matlab/demo/Contents.m
+%%DATADIR%%/matlab/demo/batch.m
+%%DATADIR%%/matlab/demo/bench_biosig.m
+%%DATADIR%%/matlab/demo/demo1.m
+%%DATADIR%%/matlab/demo/demo10.m
+%%DATADIR%%/matlab/demo/demo11.m
+%%DATADIR%%/matlab/demo/demo2.m
+%%DATADIR%%/matlab/demo/demo3.m
+%%DATADIR%%/matlab/demo/demo4.m
+%%DATADIR%%/matlab/demo/demo5.m
+%%DATADIR%%/matlab/demo/demo6.m
+%%DATADIR%%/matlab/demo/demo7.m
+%%DATADIR%%/matlab/demo/demo8.m
+%%DATADIR%%/matlab/demo/demo9.m
+%%DATADIR%%/matlab/demo/make_cc7.m
+%%DATADIR%%/matlab/demo/scptest.m
+%%DATADIR%%/matlab/demo/simulate_epsp.m
+%%DATADIR%%/matlab/demo/slope_evaluation.m
+%%DATADIR%%/matlab/doc/11073-10102-AnnexB.txt
+%%DATADIR%%/matlab/doc/Contents.m
+%%DATADIR%%/matlab/doc/DecimalFactors.txt
+%%DATADIR%%/matlab/doc/ManufacturerInformation.cfg
+%%DATADIR%%/matlab/doc/elecpos.txt
+%%DATADIR%%/matlab/doc/eventcodes.txt
+%%DATADIR%%/matlab/doc/header.txt
+%%DATADIR%%/matlab/doc/leadidtable_scpecg.txt
+%%DATADIR%%/matlab/doc/units.csv
+%%DATADIR%%/matlab/eeglab/1ST_README.txt
+%%DATADIR%%/matlab/eeglab/eegplugin_biosig.m
+%%DATADIR%%/matlab/eeglab/pop_biosig.m
+%%DATADIR%%/matlab/eeglab/pop_readbdf.m
+%%DATADIR%%/matlab/eeglab/pop_readedf.m
+%%DATADIR%%/matlab/install.m
+%%DATADIR%%/matlab/t200_FileAccess/Contents.m
+%%DATADIR%%/matlab/t200_FileAccess/adb2event.m
+%%DATADIR%%/matlab/t200_FileAccess/bdf2biosig_events.m
+%%DATADIR%%/matlab/t200_FileAccess/biosig_str2double.m
+%%DATADIR%%/matlab/t200_FileAccess/bkropen.m
+%%DATADIR%%/matlab/t200_FileAccess/bni2hdr.m
+%%DATADIR%%/matlab/t200_FileAccess/bv2biosig_events.m
+%%DATADIR%%/matlab/t200_FileAccess/cntopen.m
+%%DATADIR%%/matlab/t200_FileAccess/convert2single_sweep_atf.m
+%%DATADIR%%/matlab/t200_FileAccess/edfannot2evt.m
+%%DATADIR%%/matlab/t200_FileAccess/eload.m
+%%DATADIR%%/matlab/t200_FileAccess/famosopen.m
+%%DATADIR%%/matlab/t200_FileAccess/fefopen.m
+%%DATADIR%%/matlab/t200_FileAccess/fepi2gdf.m
+%%DATADIR%%/matlab/t200_FileAccess/fltopen.m
+%%DATADIR%%/matlab/t200_FileAccess/gdfdatatype.m
+%%DATADIR%%/matlab/t200_FileAccess/get_current_username.m
+%%DATADIR%%/matlab/t200_FileAccess/getfiletype.m
+%%DATADIR%%/matlab/t200_FileAccess/gtfopen.m
+%%DATADIR%%/matlab/t200_FileAccess/hdr2ascii.m
+%%DATADIR%%/matlab/t200_FileAccess/iopen.m
+%%DATADIR%%/matlab/t200_FileAccess/iread.m
+%%DATADIR%%/matlab/t200_FileAccess/leadidcodexyz.m
+%%DATADIR%%/matlab/t200_FileAccess/loadlexi.m
+%%DATADIR%%/matlab/t200_FileAccess/mat2sel.m
+%%DATADIR%%/matlab/t200_FileAccess/matread.m
+%%DATADIR%%/matlab/t200_FileAccess/mwfopen.m
+%%DATADIR%%/matlab/t200_FileAccess/nk2hyp.m
+%%DATADIR%%/matlab/t200_FileAccess/opendicom.m
+%%DATADIR%%/matlab/t200_FileAccess/openeep.m
+%%DATADIR%%/matlab/t200_FileAccess/openiff.m
+%%DATADIR%%/matlab/t200_FileAccess/openldr.m
+%%DATADIR%%/matlab/t200_FileAccess/openxlt.m
+%%DATADIR%%/matlab/t200_FileAccess/openxml.m
+%%DATADIR%%/matlab/t200_FileAccess/physicalunits.m
+%%DATADIR%%/matlab/t200_FileAccess/save2bkr.m
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+%%DATADIR%%/matlab/t200_FileAccess/sclose.m
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+%%DATADIR%%/matlab/t200_FileAccess/srewind.m
+%%DATADIR%%/matlab/t200_FileAccess/ssave.m
+%%DATADIR%%/matlab/t200_FileAccess/sseek.m
+%%DATADIR%%/matlab/t200_FileAccess/stell.m
+%%DATADIR%%/matlab/t200_FileAccess/swrite.m
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+%%DATADIR%%/matlab/t200_FileAccess/tlvread.m
+%%DATADIR%%/matlab/t200_FileAccess/wscore2event.m
+%%DATADIR%%/matlab/t210_Events/Contents.m
+%%DATADIR%%/matlab/t210_Events/add_events.m
+%%DATADIR%%/matlab/t210_Events/select_events.m
+%%DATADIR%%/matlab/t210_Events/sort_events.m
+%%DATADIR%%/matlab/t210_Events/unselect_events.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/Contents.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/artifact_selection.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/burstanalysis.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/detect_sharp_wave_ripple.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/detect_spikes_bursts.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/detectmuscle.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/eeg2hist.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/get_inter_spike_intervals.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/get_regress_eog.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/gettrigger.m
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+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/hist2res.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/identify_eog_channels.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/maxdistance.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/optimum_isi_spike_burst_separation.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/qc_histo.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/regress_eog.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/remove5060hz.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/resample_matrix.mat
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/rotary_decoder.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/rs.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/spatialfilter.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/spikes2bursts.m
+%%DATADIR%%/matlab/t250_ArtifactPreProcessingQualityControl/trigg.m
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+%%DATADIR%%/matlab/t300_FeatureExtraction/abp.m
+%%DATADIR%%/matlab/t300_FeatureExtraction/ap_detect.m
+%%DATADIR%%/matlab/t300_FeatureExtraction/arspectrum.m
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+%%DATADIR%%/matlab/t310_ERDSMaps/sample.gdf
+%%DATADIR%%/matlab/t320_Nirs/Contents.m
+%%DATADIR%%/matlab/t320_Nirs/Illustration_multichannel_spectra.m
+%%DATADIR%%/matlab/t320_Nirs/adaptPulseremove.m
+%%DATADIR%%/matlab/t320_Nirs/calcBPlin.m
+%%DATADIR%%/matlab/t320_Nirs/calcInfluence.m
+%%DATADIR%%/matlab/t320_Nirs/calcNIRSspectra.m
+%%DATADIR%%/matlab/t320_Nirs/demo_t320_nirs.m
+%%DATADIR%%/matlab/t320_Nirs/diadetect.m
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+%%DATADIR%%/matlab/t320_Nirs/remNoiseTF.m
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+%%DATADIR%%/matlab/t330_StimFit/demo_stimfit.m
+%%DATADIR%%/matlab/t330_StimFit/microstimfit.m
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