gentoo-related/TheChymera-overlay
gentoo-related/TheChymera-overlay
1
0
Fork 0
mirror of synced 2024-12-22 12:50:33 +01:00
Code Releases Activity

sci-biology/fsl: patch porting to deal with cifti

Browse Source 
Package-Manager: Portage-2.3.76, Repoman-2.3.16
This commit is contained in:
François Bissey 2019-11-08 10:20:38 +13:00
parent 304ee84ff0
commit 6dfe74edc7
No known key found for this signature in database
GPG Key ID: 9FA0518057258AF6
4 changed files with 99 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
sci-biology/fsl/ChangeLog
View File

@ -1,3 +1,8 @@
07 Nov 2019; François Bissey <frp.bissey@gmail.com>
+files/fsl-6.0.2-no_xmlpp.patch, +files/fsl-6.0.2-qstring_compat.patch,
fsl-6.0.2.ebuild:
sci-biology/fsl: patch porting to deal with cifti
07 Nov 2019; François Bissey <frp.bissey@gmail.com> fsl-6.0.2.ebuild:
sci-biology/fsl: tcl/tk is needed at build time

44
sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch Normal file
View File

@ -0,0 +1,44 @@
diff --git a/src/flameo/Makefile b/src/flameo/Makefile
index d22eb965..e967e682 100644
--- a/src/flameo/Makefile
+++ b/src/flameo/Makefile
@@ -2,7 +2,7 @@ include ${FSLCONFDIR}/default.mk
PROJNAME = flame
-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
+USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
UNAME := $(shell uname)
@@ -10,7 +10,7 @@ ifeq (${UNAME},Darwin)
LIBS = -liconv
endif
-LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lprob -lz
+LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lNewNifti ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lprob -lz
XFILES = flameo
diff --git a/src/melodic/Makefile b/src/melodic/Makefile
index 50666517..0c356a2d 100644
--- a/src/melodic/Makefile
+++ b/src/melodic/Makefile
@@ -7,7 +7,7 @@ OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui
PROJNAME = melodic
-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
+USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
UNAME := $(shell uname)
@@ -15,7 +15,7 @@ ifeq (${UNAME},Darwin)
LIBS = -liconv
endif
-LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm -lgdc -lgd -lpng -lz
+LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lNewNifti ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm -lgdc -lgd -lpng -lz
TEST_OBJS = test.o

48
sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch Normal file
View File

@ -0,0 +1,48 @@
diff --git a/src/flameo/gsa.cc b/src/flameo/gsa.cc
index 70f8f385..16167abe 100644
--- a/src/flameo/gsa.cc
+++ b/src/flameo/gsa.cc
@@ -74,7 +74,7 @@ namespace GSA {
sourceType=mode;
if ( sourceType.compare("CIFTI") == 0 ) {
cifti::CiftiFile inputCifti;
- inputCifti.openFile(make_basename(filename)+".nii");
+ inputCifti.openFile((make_basename(filename)+".nii").c_str());
ciftiExemplar=inputCifti.getCiftiXML();
cerr << "ndim " << ciftiExemplar.getNumberOfDimensions() << endl;
cerr << "type1 " << ciftiExemplar.getMappingType(0) << endl;
@@ -194,7 +194,7 @@ namespace GSA {
scalarsMap.setLength(data.Nrows());
ciftiExemplar.setMap(0, scalarsMap);
CiftiFile outputFile;
- outputFile.setWritingFile(make_basename(filename)+extension+".nii");//sets up on-disk writing with default writing version
+ outputFile.setWritingFile((make_basename(filename)+extension+".nii").c_str());//sets up on-disk writing with default writing version
outputFile.setCiftiXML(ciftiExemplar,false);
vector<float> scratchRow(data.Nrows());//read/write a row at a time
for (int64_t row=0;row<data.Ncols();row++) {
diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
index 1749a459..b76f052d 100644
--- a/src/melodic/meldata.cc
+++ b/src/melodic/meldata.cc
@@ -118,7 +118,7 @@ namespace Melodic{
tmpData = RawData.matrix(Mask);
memmsg(" after reshape ");
} else { //Read in Cifti
- inputCifti.openFile(fname+".nii");
+ inputCifti.openFile((fname+".nii").c_str());
const vector<int64_t>& dims = inputCifti.getDimensions();
tmpData.ReSize(dims[0],dims[1]); //swapped compared to cifti
vector<float> scratchRow(dims[0]);//read/write a row at a time
diff --git a/src/melodic/meldata.h b/src/melodic/meldata.h
index 49774003..f5326bdd 100644
--- a/src/melodic/meldata.h
+++ b/src/melodic/meldata.h
@@ -109,7 +109,7 @@ namespace Melodic{
message(" " << logger.appendDir(fname) << endl);
} else { //Process CIFTI save ICs as float
cifti::CiftiFile outputFile;
- outputFile.setWritingFile(logger.appendDir(fname)+".nii");//sets up on-disk writing with default writing version
+ outputFile.setWritingFile((logger.appendDir(fname)+".nii").c_str());//sets up on-disk writing with default writing version
cifti::CiftiXML xml(inputCifti.getCiftiXML());
cifti::CiftiScalarsMap scalarsMap;
std::vector<char> foo = xml.writeXMLToVector();

4
sci-biology/fsl/fsl-6.0.2.ebuild
View File

@ -33,11 +33,11 @@ UPSTREAM_FSLDIR="/usr/share/fsl"
PATCHES=(
"${FILESDIR}/${PN}"-6.0.2-setup.patch
#"${FILESDIR}/${PN}"-5.0.11-no_xmlpp.patch
"${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
"${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
#"${FILESDIR}/${PN}"-5.0.11-qstring_compat.patch
"${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
"${FILESDIR}/${PN}"-5.0.9-headers.patch
#"${FILESDIR}/${PN}"-5.0.9-fsldir_redux.patch
)