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

Package-Manager: Portage-2.3.76, Repoman-2.3.16

sci-biology/fsl/ChangeLog

@@ -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
 

sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch

@@ -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 
+ 

sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch

@@ -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();

sci-biology/fsl/fsl-6.0.2.ebuild

@@ -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
 )