* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/files/
@ 2022-01-25 15:34 Andrew Ammerlaan
0 siblings, 0 replies; 2+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 15:34 UTC (permalink / raw
To: gentoo-commits
commit: 3e155035c382ba0c3e76d69636ac6eff56d2bc35
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 15:33:21 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 15:33:21 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3e155035
sci-biology/fsl: drop unused patches
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
.../fsl/files/fsl-6.0.2-fsldir_redux-p1.patch | 240 -------------------
.../fsl/files/fsl-6.0.2-fsldir_redux-p2.patch | 255 ---------------------
2 files changed, 495 deletions(-)
diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch
deleted file mode 100644
index ca3945442..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch
+++ /dev/null
@@ -1,240 +0,0 @@
-From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001
-From: François Bissey <frp.bissey@gmail.com>
-Date: Mon, 20 Jan 2020 11:40:53 +1300
-Subject: [PATCH] Making sure fsl code and executable can find other executable
- and data in standard location.
-
----
- src/fast4/fast_two.cc | 8 ++++----
- src/feat5/feat_model.cc | 8 +++-----
- src/feat5/tsplot.cc | 7 +++----
- src/first/first_utils.cc | 4 ++--
- src/fnirt/fnirtfns.cpp | 11 ++++-------
- src/fslsurface/fslsurface_first.cc | 6 ++----
- src/fslsurface/fslsurfacemaths.cpp | 12 ------------
- src/libvis/miscpic.h | 7 +------
- src/melodic/meldata.cc | 4 ++--
- src/melodic/meloptions.cc | 8 --------
- src/melodic/meloptions.h | 1 -
- src/melodic/melreport.cc | 12 ++++++------
- src/melodic/melreport.h | 20 ++++++++++----------
- src/mm/mixture_model.cc | 4 ++--
- src/siena/siena_diff.cc | 28 +++++++++++++---------------
- src/topup/topupfns.cpp | 3 +--
- 16 files changed, 53 insertions(+), 90 deletions(-)
-
-diff --git a/src/fast4/fast_two.cc b/src/fast4/fast_two.cc
-index 592b5df..b525444 100644
---- a/src/fast4/fast_two.cc
-+++ b/src/fast4/fast_two.cc
-@@ -166,7 +166,7 @@ int prior_registration(string inname, string main_prior_vol, NEWIMAGE::volume<fl
- string csfPriorName, grayPriorName, whitePriorName;
- if(alternatePriors.unset())
- {
-- string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_";
-+ string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";
- csfPriorName = priorRootName+"csf";
- grayPriorName = priorRootName+"gray";
- whitePriorName = priorRootName+"white";
-@@ -215,15 +215,15 @@ string csfPriorName, grayPriorName, whitePriorName;
- if(bapused>0)
- {
- char reg[1024];
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout<<reg<<endl;
- system(reg);
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout<<reg<<endl;
- system(reg);
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout << reg << endl;
- system(reg);
-diff --git a/src/feat5/feat_model.cc b/src/feat5/feat_model.cc
-index 399a13e..e15e43c 100644
---- a/src/feat5/feat_model.cc
-+++ b/src/feat5/feat_model.cc
-@@ -744,7 +744,7 @@ int main(int argc, char **argv)
- vector<int> G;
- vector<string> titles;
- float tr, mult, trmult, nltffwhm=0, maxconvwin=0;
-- char fl[10000], *FSLDIR;
-+ char fl[10000];
- string fn, filename;
- FONT_DATA *font_data = new FONT_DATA[1];
-
-@@ -763,8 +763,6 @@ int main(int argc, char **argv)
- if (argc==3)
- motionparams=remmean(read_ascii_matrix(argv[2]));
-
-- FSLDIR=getenv("FSLDIR");
--
- fn = string(argv[1])+".fsf";
-
- level = atoi(find_line(fn, "fmri(level)", fl));
-@@ -1510,7 +1508,7 @@ int main(int argc, char **argv)
- writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE);
- writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);
-
-- filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite "+string(argv[1])+".ppm ";
-+ filename="wpng -q -overwrite "+string(argv[1])+".ppm ";
- system(filename.c_str());
-
- return(0);
-@@ -2161,6 +2159,6 @@ char the_string[10000];
-
- fclose(outputfile);
-
-- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename;
-+ filename="wpng -q -overwrite " + filename;
- system(filename.c_str());
- }
-diff --git a/src/feat5/tsplot.cc b/src/feat5/tsplot.cc
-index ae191fd..3a02b55 100644
---- a/src/feat5/tsplot.cc
-+++ b/src/feat5/tsplot.cc
-@@ -293,7 +293,7 @@ int main(int argc, char **argv)
- ofstream outputFile;
- int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600);
- vector<double> normalisedContrasts, model, triggers;
-- string fmriFileName, fslPath, featdir, vType, indexText;
-+ string fmriFileName, featdir, vType, indexText;
- ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);
- bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false);
- bool zWeightClusters(true);
-@@ -307,7 +307,6 @@ volume<float> immask;
- if (argc<2) usage("");
- featdir=string(argv[1]);
- fmriFileName=featdir+"/filtered_func_data";
-- fslPath=string(getenv("FSLDIR"));
-
- string outputName(featdir);
-
-@@ -753,7 +752,7 @@ volume4D<float> acs;
- cerr << "Can't open output report file " << outputName << endl;
- exit(1);
- }
-- outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
-+ outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
- if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
- else outputFile << "\n</BODY></HTML>\n\n";
- outputFile.close();
-@@ -768,7 +767,7 @@ volume4D<float> acs;
- cerr << "Can't open output report file " << outputName << endl;
- exit(1);
- }
-- outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
-+ outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
- outputFile.close();
-
- /* now output same thing without start and end, for inclusion in feat report */
-diff --git a/src/first/first_utils.cc b/src/first/first_utils.cc
-index 68be44b..85960f4 100644
---- a/src/first/first_utils.cc
-+++ b/src/first/first_utils.cc
-@@ -1954,8 +1954,8 @@ void do_work_bvars(){
- if (!surfaceVAout.value()) {
- // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise)
- volume<float> refim;
-- if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
-- else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
-+ if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
-+ else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
- volume<float> maskvol(refim);
- maskvol=0.0f;
- volume4D<float> volnormals;
-diff --git a/src/fnirt/fnirtfns.cpp b/src/fnirt/fnirtfns.cpp
-index 24e26fd..77899e7 100644
---- a/src/fnirt/fnirtfns.cpp
-+++ b/src/fnirt/fnirtfns.cpp
-@@ -1203,8 +1203,7 @@ string existing_ref_fname(const string& ref_fname)
- return(string(ref_fname));
- }
- else {
-- const char *fsldir_ptr = getenv("FSLDIR");
-- string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
-+ string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
- if (NEWIMAGE::FslFileExists(eref_fname)) return(eref_fname);
- else return(string(""));
- }
-@@ -1230,9 +1229,8 @@ string existing_ref_fname(const string& ref_fname)
- NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist
- eref_fname = ref_fname;
- }
-- catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard
-- const char *fsldir_ptr = getenv("FSLDIR");
-- eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
-+ catch(...) { // Didn't exist in current directory, try in .../data/standard
-+ eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
- try {
- cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl;
- NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist
-@@ -1267,8 +1265,7 @@ string existing_conf_file(const string& cfname)
- if (check_exist(ecfname)) return(ecfname);
- }
- if (!FNIRT::path(cfname).length()) { // If no path explicitly given
-- const char *fsldir_ptr = getenv("FSLDIR");
-- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
-+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
- if (check_exist(ecfname)) return(ecfname);
- else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given
- ecfname += string(".cnf");
-diff --git a/src/fslsurface/fslsurface_first.cc b/src/fslsurface/fslsurface_first.cc
-index faec642..b2ef794 100644
---- a/src/fslsurface/fslsurface_first.cc
-+++ b/src/fslsurface/fslsurface_first.cc
-@@ -500,8 +500,7 @@ namespace fslsurface_name {
-
- volume<float>* immni = new volume<float>();
-
-- char* fsldir = getenv("FSLDIR");
-- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
-+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
-
- //read_volume_hdr_only(*immni, template_name);
-
-@@ -699,8 +698,7 @@ namespace fslsurface_name {
-
- volume<float>* immni = new volume<float>();
-
-- char* fsldir = getenv("FSLDIR");
-- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
-+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
-
- //read_volume_hdr_only(*immni, template_name);
-
-diff --git a/src/fslsurface/fslsurfacemaths.cpp b/src/fslsurface/fslsurfacemaths.cpp
-index eaf55eb..3dc184d 100644
---- a/src/fslsurface/fslsurfacemaths.cpp
-+++ b/src/fslsurface/fslsurfacemaths.cpp
-@@ -598,12 +598,6 @@ int main (int argc, char * argv[])
-
- }else if (command == "-reconFromBvars"){
- cout<<"do recon "<<endl;
-- char* fsldir = getenv("FSLDIR");
-- if (fsldir == NULL)
-- {
-- cerr<<"FSLDIR has not been set. "<<endl;
-- exit(EXIT_FAILURE);
-- }
- //file.bvars,mni_template.nii.gz
- // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
- reconSurface_from_bvars( surf, string(argv[i_arg+1]));
-@@ -612,12 +606,6 @@ int main (int argc, char * argv[])
-
- }else if (command == "-reconAllFromBvarsAndSave"){
- cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
-- char* fsldir = getenv("FSLDIR");
-- if (fsldir == NULL)
-- {
-- cerr<<"FSLDIR has not been set. "<<endl;
-- exit(EXIT_FAILURE);
-- }
- //file.bvars,mni_template.nii.gz
- // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
- cout<<"recon "<< string(argv[i_arg+1])<<endl;
diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch
deleted file mode 100644
index 74bf19169..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch
+++ /dev/null
@@ -1,255 +0,0 @@
-diff --git a/src/libvis/miscpic.h b/src/libvis/miscpic.h
-index a2f3855..5f440f2 100644
---- a/src/libvis/miscpic.h
-+++ b/src/libvis/miscpic.h
-@@ -90,12 +90,7 @@ namespace MISCPIC{
- markRight=false;
- trans= -10;
- edgethresh = 0.0;
-- if(getenv("FSLDIR")!=0){
-- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
-- }
-- else{
-- lutbase = string("/");
-- }
-+ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
- title = string("");
- cbartype = string("");
- cbarptr = NULL;
-diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
-index 1749a45..c4ad234 100644
---- a/src/melodic/meldata.cc
-+++ b/src/melodic/meldata.cc
-@@ -992,7 +992,7 @@ namespace Melodic{
- void MelodicData::est_smoothness()
- {
- if(Resels == 0){
-- string SM_path = opts.binpath + "smoothest";
-+ string SM_path = "smoothest";
- string Mask_fname = logger.appendDir("mask");
-
- if(opts.segment.value().length()>0){
-@@ -1157,7 +1157,7 @@ namespace Melodic{
- // set up all strings
- string BET_outputfname = string(Mean_fname)+"_brain";
-
-- string BET_path = opts.binpath + "bet";
-+ string BET_path = "bet";
- string BET_optarg = "-m -f 0.4"; // see man bet
- string Mask_fname = BET_outputfname+"_mask";
-
-diff --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc
-index 08170c7..252e72b 100644
---- a/src/melodic/meloptions.cc
-+++ b/src/melodic/meloptions.cc
-@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL;
- explicitnums = false;
- logfname = string("log.txt");
-
-- // work out the path to the $FSLDIR/bin directory
-- if(getenv("FSLDIR")!=0){
-- binpath = (string) getenv("FSLDIR") + "/bin/";
-- } else{
-- binpath = argv[0];
-- binpath = binpath.substr(0,binpath.length()-7);
-- }
--
- // parse once to establish log directory name
- for(int a = options.parse_command_line(argc, argv); a < argc; a++);
-
-diff --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h
-index f546125..b964b7d 100644
---- a/src/melodic/meloptions.h
-+++ b/src/melodic/meloptions.h
-@@ -93,7 +93,6 @@ class MelodicOptions {
- ~MelodicOptions() { delete gopt; }
-
- string version;
-- string binpath;
- string logfname;
- bool filtermode;
- bool explicitnums;
-diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc
-index 141b6c2..2625059 100644
---- a/src/melodic/melreport.cc
-+++ b/src/melodic/melreport.cc
-@@ -84,8 +84,8 @@ namespace Melodic{
- IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
-
- {//start IC page
-- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50
-@@ -486,8 +486,8 @@ namespace Melodic{
-
- {//start IC2 page
- IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
-- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50
-@@ -665,8 +665,8 @@ namespace Melodic{
- IChtml << "<HTML> " << endl
- << "<TITLE>MELODIC Component " << num2str(cnum)
- << "</TITLE>" << endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
- << "</H1>"<< endl;
-
-diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h
-index 574fc4c..e444681 100644
---- a/src/melodic/melreport.h
-+++ b/src/melodic/melreport.h
-@@ -104,21 +104,21 @@ namespace Melodic{
- const time_t tmptime = time(NULL);
- system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
- report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
-- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>"
-+ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- << endl <<endl;
- loghtml.setDir(report.getDir(),"log.html");
-- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>"
-+ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- << endl <<endl;
- navigator.setDir(report.getDir(),"nav.html");
- head.setDir(report.getDir(),"head.html");
-- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-- head << "<link REL=stylesheet TYPE=text/css href=file:"+
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-+ navigator << "<link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
-+ head << "<link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
- head <<"<TABLE BORDER=0><TR>" << endl
- <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
- <<"<TABLE BORDER=0>"<< endl
-@@ -130,8 +130,8 @@ namespace Melodic{
- << "</tr></table>" << endl
- << "<TD ALIGN=RIGHT>" << endl
- << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
-- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
-- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
-+ << "<IMG BORDER=0 SRC=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
- << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
- if(opts.guireport.value()==""){
- report <<"<OBJECT data=head.html></OBJECT>" << endl;
-diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc
-index b8e6167..5f00693 100644
---- a/src/mm/mixture_model.cc
-+++ b/src/mm/mixture_model.cc
-@@ -2224,8 +2224,8 @@ namespace Mm {
-
- htmllog << "<HTML> " << endl
- << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
-
- htmllog << "<hr><p>" << endl;
-diff --git a/src/siena/siena_diff.cc b/src/siena/siena_diff.cc
-index e19193a..17d8701 100644
---- a/src/siena/siena_diff.cc
-+++ b/src/siena/siena_diff.cc
-@@ -107,7 +107,7 @@ int main(int argc,char *argv[])
- {
- // {{{ vars
-
--char thestring[10000], segoptions[10000], fsldir[10000];
-+char thestring[10000], segoptions[10000];
- int x_size, y_size, z_size, size, x, y, z, i, count,
- seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
- ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
-@@ -124,8 +124,6 @@ if (argc<3)
-
- string argv1(argv[1]), argv2(argv[2]);
-
--sprintf(fsldir,"%s",getenv("FSLDIR"));
--
- for (i = 3; i < argc; i++) {
- if (!strcmp(argv[i], "-i"))
- ignore_z=1;
-@@ -209,26 +207,26 @@ for (i = 3; i < argc; i++) {
- // }}}
- // {{{ transform images and masks
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
- if (edge_masking)
- {
-- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
- }
-
-@@ -287,8 +285,8 @@ if(1) // always done unless the above uncommented and used instead of this test
- cout << "saving image 1 to disk prior to segmentation" << endl;
- save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
- in1.destroy();
-- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
-+ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-+ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
- cout << thestring << endl;
- system(thestring);
- }
-diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp
-index 6873758..9e8b956 100644
---- a/src/topup/topupfns.cpp
-+++ b/src/topup/topupfns.cpp
-@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname)
- if (TOPUP::check_exist(ecfname)) return(ecfname);
- }
- if (!TOPUP::path(cfname).length()) { // If no path explicitly given
-- const char *fsldir_ptr = getenv("FSLDIR");
-- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
-+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
- if (TOPUP::check_exist(ecfname)) return(ecfname);
- else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
- ecfname += string(".cnf");
---
-2.24.1
-
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/files/
@ 2023-12-31 8:53 Andrew Ammerlaan
0 siblings, 0 replies; 2+ messages in thread
From: Andrew Ammerlaan @ 2023-12-31 8:53 UTC (permalink / raw
To: gentoo-commits
commit: e70a178d1f25d4a537db84f43c78e03ca855ed21
Author: Michael Mair-Keimberger <mmk <AT> levelnine <DOT> at>
AuthorDate: Sat Dec 30 17:52:36 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sun Dec 31 08:50:19 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e70a178d
sci-biology/fsl: remove unused patches
Signed-off-by: Michael Mair-Keimberger <mmk <AT> levelnine.at>
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
.../fsl/files/fsl-6.0.2-cuda_buildsettings.patch | 12 --
sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch | 21 ---
.../fsl/files/fsl-6.0.2-gcc10_include.patch | 10 --
sci-biology/fsl/files/fsl-6.0.2-setup.patch | 198 ---------------------
4 files changed, 241 deletions(-)
diff --git a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch
deleted file mode 100644
index a3872acf0..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
---- fsl.orig/config/buildSettings.mk 2020-07-23 15:43:42.277064365 -0400
-+++ fsl/config/buildSettings.mk 2020-07-23 15:45:17.705069496 -0400
-@@ -141,7 +141,7 @@
- # CUDA development environment
- CUDAVER := $(or $(CUDAVER),9.1)
- #$(info $$CUDAVER is [${CUDAVER}])
--CUDA_INSTALLATION = /opt/cuda-${CUDAVER}
-+CUDA_INSTALLATION = /opt/cuda
- GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INSTALLATION})
- LIB_CUDA = ${CUDA_INSTALLATION}/lib64
- INC_CUDA = ${CUDA_INSTALLATION}/include
diff --git a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch
deleted file mode 100644
index 40409ec08..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile
---- fsl.orig/src/eddy/Makefile 2020-07-30 14:30:06.414884410 -0400
-+++ fsl/src/eddy/Makefile 2020-07-30 14:33:03.400889914 -0400
-@@ -29,6 +29,8 @@
- TMPCXXFLAGS_2=
- TMPNAME_1=
- TMPNAME_2=
-+cuda=1
-+cpu=1
-
- ifndef cuda
- ifndef cpu #Default single cpu, no threading
-@@ -74,7 +75,7 @@
- ifdef NVCC11
- NVCC=${NVCC11}
- endif
--NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11
-+NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 @@GENTOO_NVCC_FLAGS@@
- ifeq ($(CLOBBER_CLANG),1)
- NVCCFLAGS+= -DCLOBBER_CLANG
- endif
diff --git a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch
deleted file mode 100644
index 9ddb11a2b..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/src/newimage/newimageio.h 2020-06-18 06:05:51.287864975 -0400
-+++ b/src/newimage/newimageio.h 2020-06-18 06:06:27.535129711 -0400
-@@ -75,6 +75,7 @@
- #include <iostream>
- #include <fstream>
- #include <sstream>
-+#include <stdexcept>
- #include "NewNifti/NewNifti.h"
- #include "newmatio.h"
- #include "newimage.h"
diff --git a/sci-biology/fsl/files/fsl-6.0.2-setup.patch b/sci-biology/fsl/files/fsl-6.0.2-setup.patch
deleted file mode 100644
index 39737fd85..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-setup.patch
+++ /dev/null
@@ -1,198 +0,0 @@
-From baae97cc3c8d0cadcabb7ed16559f4e4de26ddbe Mon Sep 17 00:00:00 2001
-From: François Bissey <frp.bissey@gmail.com>
-Date: Mon, 20 Jan 2020 11:54:37 +1300
-Subject: [PATCH] Adjust the build system so it doesnt build packages
- externally provided by portage. Make the compilation flags more generic and
- easily adjustable. Make the build system stop at the first fault.
-
----
- build | 6 +++---
- config/buildSettings.mk | 20 ++++++++++----------
- config/common/buildproj | 8 +++++---
- config/common/vars.mk | 10 +++++-----
- extras/build | 8 ++++----
- src/mist-clean/Makefile | 2 +-
- 6 files changed, 28 insertions(+), 26 deletions(-)
-
-diff --git a/build b/build
-index 05dac06c..d90e407b 100755
---- a/build
-+++ b/build
-@@ -3,7 +3,7 @@
- if [ $# -ge 1 ] ; then
- PROJECTS="$@";
- else
-- MASTERPROJECTS="CiftiLib-master utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \
-+ MASTERPROJECTS="utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \
- meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc fslvtkconv fslsurface libmeshutils newmesh \
- DiscreteOpt FastPDlib MSMRegLib misc_c dpm topup \
- asl_mfree \
-@@ -80,8 +80,8 @@ xtract";
- done
- fi
-
--echo "Building projects - see build.log file for progress..."
--./config/common/buildproj $PROJECTS > ./build.log 2>&1
-+echo "Building projects"
-+./config/common/buildproj $PROJECTS
- finalStatus=$?
- if [ $finalStatus -eq 0 ]; then
- echo "Build completed successfully.";
-diff --git a/config/buildSettings.mk b/config/buildSettings.mk
-index b2e1f150..04532fc2 100644
---- a/config/buildSettings.mk
-+++ b/config/buildSettings.mk
-@@ -18,7 +18,7 @@ MV = /bin/mv
- CHMOD = /bin/chmod
- MKDIR = /bin/mkdir
- INSTALL = install -p
--TCLSH = ${FSLDIR}/bin/fsltclsh
-+TCLSH = tclsh
- DEPENDFLAGS = -MM
- MACHDBGFLAGS = -g
- #####################################################################
-@@ -124,19 +124,19 @@ endif # if Darwin
- #####################################################################
- ifeq ($(SYSTYPE), Linux)
- ############### System Vars #####################################
--CC = gcc
--CXX = c++
--CXX11 = c++
-+CC = @@GENTOO_CC@@
-+CXX = @@GENTOO_CXX@@
-+CXX11 = @@GENTOO_CXX@@
- CSTATICFLAGS = -static
- CXXSTATICFLAGS = -static
--ARCHFLAGS = -m64
--ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib'
-+ARCHFLAGS =
-+ARCHLDFLAGS =
- PARALLELFLAGS = -fopenmp
--OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
-+OPTFLAGS =
- GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long
- SGI_ANSI_FLAGS = -ansi -fullwarn
- ANSI_FLAGS = ${GNU_ANSI_FLAGS}
--RANLIB = echo
-+RANLIB = @@GENTOO_RANLIB@@
- FSLML = ${FSLDIR}/bin/fslml
- # CUDA development environment
- CUDAVER := $(or $(CUDAVER),9.1)
-@@ -148,8 +148,8 @@ INC_CUDA = ${CUDA_INSTALLATION}/include
- NVCC = ${CUDA_INSTALLATION}/bin/nvcc
- ############### External Libs #####################################
- # ZLIB library
--LIB_ZLIB = /lib64
--INC_ZLIB = /usr/include
-+#LIB_ZLIB = /lib64
-+#INC_ZLIB = /usr/include
- # QT library
- QTDIR = /usr/lib/qt3
- LIB_QT = ${QTDIR}/lib
-diff --git a/config/common/buildproj b/config/common/buildproj
-index 2f0f2b8f..48624a1f 100755
---- a/config/common/buildproj
-+++ b/config/common/buildproj
-@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then
- fi
- PROJECTS="$@" ; export PROJECTS ;
-
--FSLDIR=`pwd`
-+#FSLDIR=`pwd`
- FSLDEVDIR=${FSLDIR}
- FSLCONFDIR=${FSLDIR}/config
--FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
-+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
- FSLMASTERBUILD=1
- export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD
-
-@@ -67,7 +67,7 @@ for projname in $PROJECTS; do
- if [ -x ./fslconfig ] ; then
- . ./fslconfig ;
- fi
-- if ${MAKE} -k ${MAKEOPTIONS} ; then
-+ if ${MAKE} ${MAKEOPTIONS} ; then
- if ${MAKE} ${MAKEOPTIONS} install ; then
- installok=true;
- # Clean up after ourselves
-@@ -82,6 +82,7 @@ for projname in $PROJECTS; do
- if [ $installok = false ] ; then
- echo " "
- echo "ERROR::Could not install $projname successfully" ;
-+ exit 1
- fi
- else
- echo " "
-@@ -90,6 +91,7 @@ for projname in $PROJECTS; do
- echo " "
- echo " "
- errorprojs="$errorprojs $projname" ; export errorprojs ;
-+ exit 1
- fi
- fi
- done
-diff --git a/config/common/vars.mk b/config/common/vars.mk
-index b027b010..aeeae67c 100755
---- a/config/common/vars.mk
-+++ b/config/common/vars.mk
-@@ -24,15 +24,15 @@ USRINCFLAGS =
- USRCFLAGS =
- USRCXXFLAGS =
-
--LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
-+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
-
--AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
-+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
-
- CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
-- ${AccumulatedIncFlags}
-+ ${AccumulatedIncFlags} ${USERCFLAGS}
-
--CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
-- ${AccumulatedIncFlags}
-+CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
-+ ${AccumulatedIncFlags} ${USERCXXFLAGS}
-
- HFILES = *.h
- AFILES = *.a
-diff --git a/extras/build b/extras/build
-index 59e7a2ed..0d68232e 100755
---- a/extras/build
-+++ b/extras/build
-@@ -96,16 +96,16 @@ if [ X"${OS}" = "XDarwin" ]; then
- BUILDICONV=1
- fi
- fi
--PROJECTS="tcl tk"
-+#PROJECTS="tcl tk"
- if [ ${BUILDZLIB} -eq 1 ]; then
- PROJECTS="${PROJECTS} zlib"
- fi
--PROJECTS="${PROJECTS} libpng"
-+#PROJECTS="${PROJECTS} libpng"
- if [ ${BUILDICONV} -eq 1 ]; then
- PROJECTS="${PROJECTS} libiconv"
- fi
--PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
--PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat"
-+PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran"
-+PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat"
- for projname in $PROJECTS; do
- if [ -d $FSLESRCDIR/$projname ] ; then
- buildIt $FSLESRCDIR $projname 1
-diff --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile
-index 20402cca..6918bee4 100755
---- a/src/mist-clean/Makefile
-+++ b/src/mist-clean/Makefile
-@@ -52,6 +52,6 @@ installpython:
- cp -r python/* ${DESTDIR}/python/mist
-
- clean:
-- rm -f ${OBJS} mist/mist.o mist/mist
-+ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion."
-
- .PHONY: all clean installdata
---
-2.24.1
-
^ permalink raw reply related [flat|nested] 2+ messages in thread
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