Merge branch 'mnt/conda' into 'master'

Mnt/conda

See merge request !1

Makefile

 include $(FSLCONFDIR)/default.mk
 
 PROJNAME = slicetimer
+XFILES   = slicetimer
+LIBS     = -lfsl-newimage -lfsl-miscmaths -lfsl-NewNifti \
+           -lfsl-znz -lfsl-cprob -lfsl-utils
 
-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB}
-USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
-
-OBJS = slicetimer.o
-
-LIBS = -lnewimage -lmiscmaths -lNewNifti -lznz -lnewmat -lprob -lm -lutils -lz
-
-XFILES = slicetimer
-
-all:	${XFILES}
-
-slicetimer:${OBJS}
-	${CXX}  ${CXXFLAGS} ${LDFLAGS} -o $@  ${OBJS} ${LIBS}
+all: ${XFILES}
 
+slicetimer: slicetimer.o
+	${CXX}  ${CXXFLAGS} -o $@  $^ ${LDFLAGS}

branchname.log

-Initial creation of branchname log file

slicetimer.cc

 /*  slicetimer.cc - FMRIB's Slice Timing Utility
-    
+
     Peter Bannister, Stephen Smith and Matthew Webster, FMRIB Image Analysis Group
-    
+
     Copyright (C) 2001-2009 University of Oxford  */
 
 /*  CCOPYRIGHT */
@@ -17,12 +17,13 @@
 #include <vector>
 
 #include "miscmaths/optimise.h"
-#include "newmatap.h"
-#include "newmatio.h"
+#include "armawrap/newmat.h"
+#include "armawrap/newmat.h"
 #include "newimage/newimageall.h"
 #include "utils/options.h"
 #include "miscmaths/kernel.h"
 
+using namespace std;
 using namespace MISCMATHS;
 using namespace NEWMAT;
 using namespace NEWIMAGE;
@@ -34,14 +35,14 @@ string examples="slicetimer -i <timeseries> [-o <corrected_timeseries>] [options
 Option<bool> help(string("-h,--help"), false,
 		  string("display this message"),
 		  false, no_argument);
-Option<bool> verbose(string("-v,--verbose"), false, 
-		     string("switch on diagnostic messages"), 
+Option<bool> verbose(string("-v,--verbose"), false,
+		     string("switch on diagnostic messages"),
 		     false, no_argument);
-Option<bool> odd(string("--odd"), false, 
-		     string("use interleaved acquisition"), 
+Option<bool> odd(string("--odd"), false,
+		     string("use interleaved acquisition"),
 		     false, no_argument);
-Option<bool> down(string("--down"), false, 
-		     string("reverse slice indexing (default is: slices were acquired bottom-up)"), 
+Option<bool> down(string("--down"), false,
+		     string("reverse slice indexing (default is: slices were acquired bottom-up)"),
 		     false, no_argument);
 Option<string> inputname(string("-i,--in"), string(""),
 			 string("filename of input timeseries"),
@@ -69,7 +70,7 @@ int do_slice_correction()
 {
   volume4D<float> timeseries;
   Matrix timings;
-  
+
   int no_volumes, no_slices;
   float repeat_time, offset=0, slice_spacing;
 
@@ -79,7 +80,7 @@ int do_slice_correction()
     if (!outputname.set())
       outputname.set_value(inputname.value() + "_st");
   } else if (outputname.set()) {
-    cerr << "Must specify an input volume (-i or --in) to generate corrected data." 
+    cerr << "Must specify an input volume (-i or --in) to generate corrected data."
 	 << endl;
     return -1;
   }
@@ -108,20 +109,20 @@ int do_slice_correction()
   // for(int i=1; i<=1201; i++) cout << i << " " << userkernel(i) << endl;
 
   float recenter = (((float) no_slices)/2 - 0.5)/ no_slices; // only valid for slice-count-based corrections
-  
+
   for (int slice=1; slice<=no_slices; slice++) {
 
     if (tglobal.set()) {
       offset = tglobal.value();
     } else if (tcustom.set()) {
       offset = timings(slice, 1);
-    } else if (ocustom.set()) { 
+    } else if (ocustom.set()) {
       int local_count=1;
       while (local_count <= no_slices) {
 	if (timings(local_count, 1) == slice) {
 	  offset = recenter -(local_count -1)* (slice_spacing / repeat_time);
 	  local_count = no_slices + 1;
-	} else 
+	} else
 	  local_count++;
       }
     } else if (odd.value()) { // acquisition order: 1,3,5, ..., 2,4,6 ...
@@ -131,7 +132,7 @@ int do_slice_correction()
 	offset = recenter - ((slice -1) / 2) * (slice_spacing / repeat_time);
     } else if (down.value()) {
       offset = recenter - (no_slices - slice) * (slice_spacing / repeat_time);
-    } else { 
+    } else {
       offset = recenter - (slice -1) * (slice_spacing / repeat_time);
     }
 
@@ -145,11 +146,11 @@ int do_slice_correction()
 	}
 	timeseries.setvoxelts(interpseries,x_pos,y_pos,slice-1);
       }
-    
+
     if (verbose.value())
       cerr << "Slice " << slice << " offset " << offset << endl;
   }
-  
+
   if (direction.value() == 1) timeseries.swapdimensions(3,2,1); // reverse Flip z and x
   if (direction.value() == 2) timeseries.swapdimensions(1,3,2); // reverse Flip z and y
 
@@ -160,7 +161,7 @@ int do_slice_correction()
 int main (int argc,char** argv)
 {
   Tracer tr("main");
-  
+
   OptionParser options(title, examples);
 
   try {
@@ -183,30 +184,29 @@ int main (int argc,char** argv)
 	options.usage();
 	exit(EXIT_FAILURE);
       }
-        
-    if ( inputname.unset()) 
+
+    if ( inputname.unset())
       {
 	options.usage();
-	cerr << endl 
-	     << "--in or -i MUST be used." 
+	cerr << endl
+	     << "--in or -i MUST be used."
 	     << endl;
 	exit(EXIT_FAILURE);
       }
-    
+
   }  catch(X_OptionError& e) {
     options.usage();
     cerr << endl << e.what() << endl;
     exit(EXIT_FAILURE);
   } catch(std::exception &e) {
     cerr << e.what() << endl;
-  } 
+  }
 
   int retval = do_slice_correction();
-  
+
   if (retval!=0) {
     cerr << endl << endl << "Error detected: try -h for help" << endl;
   }
 
   return retval;
 }
-