Merge pull request #3 from pauldmccarthy/mnt/conda

WIP: Use conda to build FSL projects
physimals · May 11, 2022 · 99c29e6 · 99c29e6
2 parents 246b343 + 20f8fcd
commit 99c29e6
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Showing 37 changed files with 224 additions and 152 deletions.
diff --git a/.gitignore b/.gitignore
@@ -7,6 +7,7 @@ CVS
 *.o
 *~
 *.a
+*.so
 .DS_Store
 depend.mk
 testfabber

diff --git a/Makefile b/Makefile
@@ -2,29 +2,37 @@ include ${FSLCONFDIR}/default.mk
 
 PROJNAME = fabber_core
 
-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_CPROB} -I${INC_BOOST} -DFABBER_SRC_DIR="\"${PWD}\"" -DFABBER_BUILD_DIR="\"${PWD}\""
-USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L/lib64
-
-FSLVERSION= $(shell cat ${FSLDIR}/etc/fslversion | head -c 1)
-ifeq ($(FSLVERSION), 5) 
-  NIFTILIB = -lfslio -lniftiio 
-  MATLIB = -lnewmat
-else 
-  UNAME := $(shell uname -s)
-  ifeq ($(UNAME), Linux)
-    MATLIB = -lopenblas
+USRINCFLAGS = -DFABBER_SRC_DIR="\"${PWD}\"" -DFABBER_BUILD_DIR="\"${PWD}\""
+
+# The FSL build system changed
+# substantially in FSL 6.0.6
+# FSL >= 6.0.6
+ifeq (${FSL_GE_606}, true)
+  LIBS         = -lfsl-newimage -lfsl-miscmaths -lfsl-utils \
+                 -lfsl-cprob -lfsl-NewNifti -lfsl-znz -ldl
+  USRCPPFLAGS += -DFSL_GE_606
+# FSL <= 6.0.5
+else
+  ifeq ($(shell uname -s), Linux)
+    MATLIB := -lopenblas
   endif
-  NIFTILIB = -lNewNifti
+
+  USRINCFLAGS += -I${INC_NEWMAT} -I${INC_CPROB} -I${INC_BOOST} \
+                 -I${FSLDIR}/extras/include/armawrap
+  USRLDFLAGS   = -L${LIB_NEWMAT} -L${LIB_CPROB}         \
+                 -lnewimage -lmiscmaths -lutils -lcprob \
+                 -lNewNifti ${MATLIB} -lznz -lz -ldl
 endif
 
-LIBS = -lnewimage -lmiscmaths -lutils -lprob ${MATLIB} ${NIFTILIB} -lznz -lz -ldl
 TESTLIBS = -lgtest -lpthread
 
 #
-# Executables
+# Executables and libraries provided by this project
 #
 
-XFILES = fabber mvntool
+XFILES  = fabber mvntool
+SOFILES = libfsl-fabbercore.so libfsl-fabberexec.so
+AFILES  = libfabbercore.a libfabberexec.a
 SCRIPTS = fabber_var
 
 # Sets of objects separated into logical divisions
@@ -60,33 +68,55 @@ OBJS = ${BASICOBJS} ${COREOBJS} ${INFERENCEOBJS} ${NOISEOBJS} ${CONFIGOBJS}
 #OPTFLAGS = -ggdb -Wall
 
 # Pass Git revision details
-GIT_SHA1:=$(shell git describe --dirty)
-GIT_DATE:=$(shell git log -1 --format=%ad --date=local)
+GIT_SHA1 := $(shell git describe --dirty)
+GIT_DATE := $(shell git log -1 --format=%ad --date=local)
 CXXFLAGS += -DGIT_SHA1=\"${GIT_SHA1}\" -DGIT_DATE="\"${GIT_DATE}\""
 
-# Targets
+clean:
+	${RM} -f /tmp/fslgrot *.o mvn_tool/*.o *.a *.so *.exe core depend.mk fabber_test
+
+# FSL >=606 uses dynamic linking
+ifeq (${FSL_GE_606}, true)
 
-all:	${XFILES} libfabbercore.a libfabberexec.a
+all: ${XFILES} ${SOFILES}
 
-clean:
-	${RM} -f /tmp/fslgrot *.o mvn_tool/*.o *.a *.exe core depend.mk fabber_test
+# Dynamically linked libraries are compiled for FSL >= 606
+libfsl-fabbercore.so : ${OBJS}
+	${CXX} ${CXXFLAGS} -shared -o $@ $^ ${LDFLAGS}
 
-mvntool: ${OBJS} mvn_tool/mvntool.o rundata_newimage.o 
-	${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} mvn_tool/mvntool.o rundata_newimage.o ${LIBS}
+libfsl-fabberexec.so : ${EXECOBJS} | libfsl-fabbercore.so
+	${CXX} ${CXXFLAGS} -shared -o $@ $^ -lfsl-fabbercore ${LDFLAGS}
+
+mvntool: mvn_tool/mvntool.o rundata_newimage.o | libfsl-fabbercore.so
+	${CXX} ${CXXFLAGS} -o $@ $^ -lfsl-fabbercore ${LDFLAGS}
 
 # Build a fabber exectuable, this will have nothing but the generic models so it not practically useful for data analysis
-fabber: ${OBJS} ${EXECOBJS} ${CLIENTOBJS}
-	${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} ${EXECOBJS} ${CLIENTOBJS} ${LIBS} 
+fabber: ${CLIENTOBJS} | libfsl-fabberexec.so libfsl-fabbercore.so
+	${CXX} ${CXXFLAGS} -o $@ $^ -lfsl-fabberexec -lfsl-fabbercore ${LDFLAGS}
+
+# Unit tests
+test: ${CLIENTOBJS} ${TESTOBJS} | libfsl-fabberexec.so libfsl-fabbercore.so
+	${CXX} ${CXXFLAGS} -o fabber_test $^ -lfsl-fabberexec -lfsl-fabbercore ${LDFLAGS} ${TESTLIBS}
+
+# FSL <=605 uses static linking
+else
+
+all: ${XFILES} ${AFILES}
 
-# Library build
 libfabbercore.a : ${OBJS}
-	${AR} -r $@ ${OBJS}
+	${AR} -r $@ $^
 
-libfabberexec.a : ${EXECOBJS} 
-	${AR} -r $@ ${EXECOBJS} 
+libfabberexec.a : ${EXECOBJS}
+	${AR} -r $@ $^
+
+mvntool: ${OBJS} mvn_tool/mvntool.o rundata_newimage.o
+	${CXX} ${CXXFLAGS} -o $@ $^ ${LDFLAGS}
+
+fabber: ${OBJS} ${EXECOBJS} ${CLIENTOBJS}
+	${CXX} ${CXXFLAGS} -o $@ $^ ${LDFLAGS}
 
-# Unit tests
 test: ${OBJS} ${EXECOBJS} ${CLIENTOBJS} ${TESTOBJS}
-	${CXX} ${CXXFLAGS} ${LDFLAGS} ${TESTINC} -o fabber_test ${OBJS} ${EXECOBJS} ${TESTOBJS} ${LIBS} ${TESTLIBS} 
+	${CXX} ${CXXFLAGS} -o fabber_test $^ ${LDFLAGS} ${TESTLIBS}
+endif
 
 # DO NOT DELETE
diff --git a/covariance_cache.cc b/covariance_cache.cc
@@ -3,7 +3,7 @@
 #include "easylog.h"
 #include "rundata.h"
 
-#include <newmat.h>
+#include "armawrap/newmat.h"
 
 #include <map>
 #include <math.h>

diff --git a/covariance_cache.h b/covariance_cache.h
@@ -9,7 +9,7 @@
 
 #include "easylog.h"
 
-#include "newmat.h"
+#include "armawrap/newmat.h"
 
 #include <map>
 #include <string>

diff --git a/dist_mvn.cc b/dist_mvn.cc
@@ -11,9 +11,10 @@
 #include "tools.h"
 
 #include <math.h>
-#include <newmatio.h>
+#include "armawrap/newmat.h"
 
 using fabber::read_matrix_file;
+using namespace std;
 using namespace NEWMAT;
 
 // Constructors
@@ -66,9 +67,9 @@ MVNDist::MVNDist(const MVNDist &from1, const MVNDist &from2)
     // Always duplicate the covariances (even if this means some recalculation)
     // Otherwise if we use precisions.i(), zeros won't stay exactly zero
     covariance = 0;
-    for (int row=1; row <= from1.m_size; row++) 
+    for (int row=1; row <= from1.m_size; row++)
     {
-        for (int col=1; col <= from1.m_size; col++) 
+        for (int col=1; col <= from1.m_size; col++)
         {
             try
             {
@@ -80,9 +81,9 @@ MVNDist::MVNDist(const MVNDist &from1, const MVNDist &from2)
             }
         }
     }
-    for (int row=1; row <= from2.m_size; row++) 
+    for (int row=1; row <= from2.m_size; row++)
     {
-        for (int col=1; col <= from2.m_size; col++) 
+        for (int col=1; col <= from2.m_size; col++)
         {
             try
             {
@@ -417,9 +418,9 @@ void MVNDist::Save(const vector<MVNDist *> &mvns, const string &filename, Fabber
         // required by NIFTI_INTENT_SYMMATRIX
         ColumnVector cov(nCov);
         int idx=1;
-        for (int row=1; row <=nParams; row++) 
+        for (int row=1; row <=nParams; row++)
         {
-            for (int col=1; col<=row; col++) 
+            for (int col=1; col<=row; col++)
             {
                 cov(idx++) = mvns.at(vox - 1)->GetCovariance()(row, col);
             }

diff --git a/dist_mvn.h b/dist_mvn.h
@@ -11,7 +11,7 @@
 #include "easylog.h"
 #include "rundata.h"
 
-#include <newmat.h>
+#include "armawrap/newmat.h"
 #include <ostream>
 #include <string>
 #include <vector>
@@ -68,7 +68,7 @@ class MVNDist : public Loggable
      *
      * @param mvns One MVN for each voxel
      */
-    static void Save(const vector<MVNDist *> &mvns, const string &filename, FabberRunData &data);
+    static void Save(const std::vector<MVNDist *> &mvns, const std::string &filename, FabberRunData &data);
 
     /**
      * Default constructor
@@ -96,7 +96,7 @@ class MVNDist : public Loggable
     /**
      * Create from matrix file (VEST or ASCII)
      */
-    MVNDist(const string filename, EasyLog *log = 0);
+    MVNDist(const std::string filename, EasyLog *log = 0);
 
     /**
      * Copy using a subset of another MVN distribution's parameters

diff --git a/examples/fwdmodel_exp.h b/examples/fwdmodel_exp.h
@@ -3,7 +3,7 @@
 
 #include "fabber_core/fwdmodel.h"
 
-#include "newmat.h"
+#include "armawrap/newmat.h"
 
 #include <string>
 #include <vector>
@@ -22,10 +22,10 @@ class ExpFwdModel : public FwdModel {
     void GetOptions(std::vector<OptionSpec> &opts) const;
 
     void Initialize(FabberRunData &args);
-    void EvaluateModel(const NEWMAT::ColumnVector &params, 
-                       NEWMAT::ColumnVector &result, 
+    void EvaluateModel(const NEWMAT::ColumnVector &params,
+                       NEWMAT::ColumnVector &result,
                        const std::string &key="") const;
-    
+
     void InitVoxelPosterior(MVNDist &posterior) const;
 
 protected:
@@ -36,4 +36,3 @@ class ExpFwdModel : public FwdModel {
     double m_dt;
     static FactoryRegistration<FwdModelFactory, ExpFwdModel> registration;
 };
-
diff --git a/fabber_capi.cc b/fabber_capi.cc
@@ -16,7 +16,7 @@
 #include "rundata_array.h"
 #include "setup.h"
 
-#include "newmat.h"
+#include "armawrap/newmat.h"
 
 #include <sstream>
 #include <stdexcept>
@@ -477,7 +477,7 @@ int fabber_get_model_param_descs(void *fab, unsigned int out_bufsize, char *out_
         for (iter = params.begin(); iter != params.end(); ++iter)
         {
             out << iter->name << " " << iter->desc;
-            if (iter->units != "") 
+            if (iter->units != "")
             {
                 out << " (units: " << iter->units << ")";
             }
@@ -581,7 +581,7 @@ int fabber_model_evaluate_output(void *fab, unsigned int n_params, float *params
         {
             p_vec(i + 1) = params[i];
         }
-        for (unsigned int i=0; i < n_ts; i++) 
+        for (unsigned int i=0; i < n_ts; i++)
         {
             if (indata)
                 data_vec(i + 1) = indata[i];

diff --git a/fabber_core.cc b/fabber_core.cc
@@ -13,6 +13,8 @@
 #include "version.h"
 #include "tools.h"
 
+#include "armawrap/newmat.h"
+
 #include <exception>
 #include <iostream>
 #include <map>
@@ -26,6 +28,9 @@
 
 using namespace std;
 
+using NEWMAT::Matrix;
+using NEWMAT::ColumnVector;
+
 /**
  * Print version information.
  */
@@ -154,7 +159,7 @@ int execute(int argc, char **argv)
 
             return 0;
         }
-        else if (params->GetBool("listparams")) 
+        else if (params->GetBool("listparams"))
         {
             string model = params->GetStringDefault("model", "");
             std::auto_ptr<FwdModel> fwd_model(FwdModel::NewFromName(model));
@@ -172,7 +177,7 @@ int execute(int argc, char **argv)
 
             return 0;
         }
-        else if (params->GetBool("descparams")) 
+        else if (params->GetBool("descparams"))
         {
             string model = params->GetStringDefault("model", "");
             std::auto_ptr<FwdModel> fwd_model(FwdModel::NewFromName(model));
@@ -186,7 +191,7 @@ int execute(int argc, char **argv)
             for (iter = model_params.begin(); iter != model_params.end(); ++iter)
             {
                 cout << iter->name << " " << iter->desc;
-                if (iter->units != "") 
+                if (iter->units != "")
                 {
                     cout << " (units: " << iter->units << ")";
                 }
@@ -195,7 +200,7 @@ int execute(int argc, char **argv)
 
             return 0;
         }
-        else if (params->GetBool("listoutputs")) 
+        else if (params->GetBool("listoutputs"))
         {
             string model = params->GetStringDefault("model", "");
             std::auto_ptr<FwdModel> fwd_model(FwdModel::NewFromName(model));
@@ -213,7 +218,7 @@ int execute(int argc, char **argv)
 
             return 0;
         }
-        else if (params->HaveKey("evaluate")) 
+        else if (params->HaveKey("evaluate"))
         {
             string model = params->GetStringDefault("model", "");
             std::auto_ptr<FwdModel> fwd_model(FwdModel::NewFromName(model));

diff --git a/fwdmodel.cc b/fwdmodel.cc
@@ -13,7 +13,7 @@
 #include "rundata.h"
 #include "transforms.h"
 
-#include <newmatio.h>
+#include "armawrap/newmat.h"
 
 #include <memory>
 #include <sstream>

diff --git a/fwdmodel.h b/fwdmodel.h
@@ -13,7 +13,7 @@
 #include "factories.h"
 #include "transforms.h"
 
-#include <newmat.h>
+#include "armawrap/newmat.h"
 
 #include <string>
 #include <vector>
@@ -23,9 +23,9 @@
  */
 struct Parameter
 {
-    Parameter(unsigned int idx, std::string name="", 
+    Parameter(unsigned int idx, std::string name="",
         DistParams prior=DistParams(0, 1),
-        DistParams post=DistParams(0, 1), 
+        DistParams post=DistParams(0, 1),
         char prior_type='N',
         const Transform *transform=TRANSFORM_IDENTITY(),
         std::string desc="", std::string units="")

diff --git a/fwdmodel_linear.cc b/fwdmodel_linear.cc
@@ -14,7 +14,7 @@
 #include "tools.h"
 #include "version.h"
 
-#include <newmatio.h>
+#include "armawrap/newmat.h"
 
 #include <iostream>
 #include <stdexcept>

diff --git a/fwdmodel_linear.h b/fwdmodel_linear.h
@@ -10,7 +10,7 @@
 
 #include "fwdmodel.h"
 
-#include <newmat.h>
+#include "armawrap/newmat.h"
 
 #include <string>
 #include <vector>