rf: update method of version handling (freesurfer#758)

* rf: update method of version handling

* added doc

.gitignore

@@ -10,7 +10,9 @@ ld_map.txt
 # generated help files
 *.help.xml.h
 .idea/**/*.xml
-# generated cxx files
+
+# generated source files
+utils/version_info.h
 qdec/QdecLibInit.cxx
 qdec/vtkKWQdecAppTcl.cxx
 qdec/vtkKWQdecViewTcl.cxx

AntsDenoiseImageFs/AntsDenoiseImageFs.cpp

@@ -24,7 +24,7 @@
 #include "AntsDenoiseImageFs.help.xml.h"
 
 
-int main(int argc, char const *argv[])
+int main(int argc, char **argv)
 {
   // parse args
   ArgumentParser parser;

AntsN4BiasFieldCorrectionFs/AntsN4BiasFieldCorrectionFs.cpp

@@ -25,7 +25,7 @@
 #include "AntsN4BiasFieldCorrectionFs.help.xml.h"
 
 
-int main(int argc, char const *argv[])
+int main(int argc, char **argv)
 {
   // parse args
   ArgumentParser parser;

CMakeLists.txt

@@ -38,9 +38,12 @@ if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
   endif()
 endif()
 
-# create build stamp during install
+# version stamp
+set(FS_VERSION "$ENV{USER}-local" CACHE STRING "Distribution version")
+
+# build stamp
 string(TIMESTAMP TODAY "%Y%m%d")
-set(BUILD_STAMP "freesurfer-local-build-dev-${TODAY}" CACHE STRING "Distribution build stamp")
+set(BUILD_STAMP "freesurfer-local-build-${TODAY}" CACHE STRING "Distribution build stamp")
 install(CODE "file(WRITE ${CMAKE_INSTALL_PREFIX}/build-stamp.txt ${BUILD_STAMP}\\n)")
 
 # set the default build type to 'Release' for optimization purposes
@@ -287,6 +290,7 @@ add_subdirectory(distribution)
 # the top-level include dir contain the most commonly included freesurfer header files
 set(FS_INCLUDE_DIRS
   ${CMAKE_SOURCE_DIR}/include
+  ${CMAKE_BINARY_DIR}/include
   ${CMAKE_SOURCE_DIR}/packages/minc
   ${CMAKE_SOURCE_DIR}/packages/netcdf
   ${CMAKE_SOURCE_DIR}/packages/nifti

attic/check_siemens_dir/check_siemens_dir.cpp

@@ -61,11 +61,7 @@ int main(int argc, char *argv[]) {
   DIR *dp;
   int nargs;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option 
-    (argc, argv, 
-     "$Id: check_siemens_dir.c,v 1.10 2011/03/02 00:04:01 nicks Exp $", 
-     "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "check_siemens_dir");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/dmri_tensoreig/dmri_tensoreig.cpp

@@ -103,8 +103,7 @@ int main(int argc, char *argv[]) {
   char outfile[1024];
   const double minexp = exp(-10^35);
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, vcid, "$Name$");
+  nargs = handleVersionOption(argc, argv, "dmri_tensoreig");
   if (nargs && argc - nargs == 1) exit (0);
   argc -= nargs;
   cmdline = argv2cmdline(argc,argv);

attic/histo_fix_topology/histo_fix_topology.cpp

@@ -67,8 +67,7 @@ main(int argc, char *argv[]) {
   MRI_SEGMENT       *ms ;
   MRI_SEGMENT_VOXEL *msv ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: histo_fix_topology.c,v 1.3 2011/03/02 00:04:09 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "histo_fix_topology");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/histo_segment/histo_segment.cpp

@@ -69,8 +69,7 @@ main(int argc, char *argv[]) {
   double      thresh, min_neuron_area ;
 
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: histo_segment.c,v 1.2 2011/03/02 00:04:09 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "histo_segment");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/label_area/label_area.cpp

@@ -64,8 +64,7 @@ main(int argc, char *argv[]) {
   MRI_SURFACE  *mris ;
   float        area ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: label_area.c,v 1.9 2012/04/25 13:37:44 fischl Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "label_area");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/label_border/label_border.cpp

@@ -62,8 +62,7 @@ main(int argc, char *argv[]) {
   MRI_SURFACE  *mris ;
   LABEL        *area ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: label_border.c,v 1.2 2011/03/02 00:04:11 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "label_border");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_apply_inu_correction/mri_apply_inu_correction.cpp

@@ -68,7 +68,7 @@ int main(int argc, char *argv[]) {
 
   Progname = argv[0];
 
-  nargs = handle_version_option (argc, argv, "$Id: mri_apply_inu_correction.c,v 1.3 2011/03/02 00:04:13 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_apply_inu_correction");
   argc -= nargs ;
 
   ac = argc ;

attic/mri_aseg_edit_reclassify/mri_aseg_edit_reclassify.cpp

@@ -87,8 +87,7 @@ main(int argc, char *argv[]) {
   VOXEL_LIST   *vl_border ;
   float        *svm_inputs = NULL, svm_out ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_aseg_edit_reclassify.c,v 1.5 2011/03/02 00:04:13 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_aseg_edit_reclassify");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_aseg_edit_train/mri_aseg_edit_train.cpp

@@ -227,8 +227,7 @@ main(int argc, char *argv[]) {
   }
 #endif
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_aseg_edit_train.c,v 1.3 2011/03/02 00:04:13 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_aseg_edit_train");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_auto_fill/mri_auto_fill.cpp

@@ -87,11 +87,7 @@ main(int argc, char *argv[])
   GCAM   *gcam;
   int     msec ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option
-          (argc, argv,
-           "$Id: mri_auto_fill.c,v 1.14 2011/03/02 00:04:13 nicks Exp $",
-           "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_auto_fill");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_bc_sc_bias_correct/mri_bc_sc_bias_correct.cpp

@@ -62,9 +62,8 @@ main(int argc, char *argv[]) {
   HISTOGRAM        *histo ;
   MRI_SEGMENTATION *mriseg ;
 
-  /* rkt: check for and handle version tag */
   Progname = argv[0] ;
-  nargs = handle_version_option (argc, argv, "$Id: mri_bc_sc_bias_correct.c,v 1.5 2011/03/02 00:04:13 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_bc_sc_bias_correct");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_build_priors/mri_build_priors.cpp

@@ -56,8 +56,7 @@ main(int argc, char *argv[]) {
   int    fno, nfiles ;
   MRI    *mri_src, *mri_target, *mri_wm, *mri_priors = NULL ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_build_priors.c,v 1.8 2011/03/02 00:04:13 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_build_priors");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_classify/mri_classify.cpp

@@ -70,8 +70,7 @@ main(int argc, char *argv[]) {
   char    *training_file_name, *output_file_name ;
   int     nargs, error, i ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_classify.c,v 1.2 2012/05/23 19:24:37 fischl Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_classify");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_compute_structure_transforms/mri_compute_structure_transforms.cpp

@@ -67,8 +67,7 @@ main(int argc, char *argv[]) {
   MRI            *mri_aseg ;
   float          xa, ya, za ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_compute_structure_transforms.c,v 1.3 2011/03/02 00:04:14 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_compute_structure_transforms");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_convert_mdh/mri_convert_mdh.cpp

@@ -254,8 +254,7 @@ int main(int argc, char **argv) {
   //DumpMDH_VB13(argv[1]);
   return(0);
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_convert_mdh.c,v 1.27 2011/03/02 00:04:14 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_convert_mdh");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_divide_segmentation/mri_divide_segmentation.cpp

@@ -66,7 +66,7 @@ main(int argc, char *argv[]) {
   MATRIX       *m_obs, *m_obs_T, *m_cov, *m_eig ;
 
   setRandomSeed(-1L) ;
-  nargs = handle_version_option (argc, argv, "$Id: mri_divide_segmentation.c,v 1.3 2014/05/28 20:27:57 fischl Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_divide_segmentation");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_elastic_energy/mri_elastic_energy.cpp

@@ -60,8 +60,7 @@ main(int argc, char *argv[]) {
   GCA_MORPH    *gcam ;
   MRI          *mri_lame ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_elastic_energy.c,v 1.2 2011/10/16 17:00:35 fischl Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_elastic_energy");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_estimate_tissue_parms/mri_estimate_tissue_parms.cpp

@@ -109,8 +109,7 @@ main(int argc, char *argv[]) {
   int          msec, minutes, seconds, nvolumes ;
   Timer start ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_estimate_tissue_parms.c,v 1.10 2015/03/12 20:24:06 zkaufman Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_estimate_tissue_parms");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_extract_conditions/mri_extract_conditions.cpp

@@ -63,8 +63,7 @@ main(int argc, char *argv[]) {
   MRI         *mri_in, *mri_out ;
   FILE        *fp ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_extract_conditions.c,v 1.5 2011/03/02 00:04:15 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_extract_conditions");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_fcili/mri_fcili.cpp

@@ -96,7 +96,7 @@ int main(int argc, char *argv[]) {
   int c,f, nrois, roi1, roi2, nframes;
   double v,ss, v1,v2,den,num, LL, LR, RL, RR;
 
-  nargs = handle_version_option (argc, argv, vcid, "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_fcili");
   if (nargs && argc - nargs == 1) exit (0);
   argc -= nargs;
   cmdline = argv2cmdline(argc,argv);

attic/mri_gcab_train/mri_gcab_train.cpp

@@ -115,11 +115,7 @@ main(int argc, char *argv[]) {
   parms.use_gradient = 0 ;
   spacing = 8 ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option
-    (argc, argv,
-     "$Id: mri_gcab_train.c,v 1.4 2011/03/16 20:23:33 fischl Exp $",
-     "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_gcab_train");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_gdfglm/mri_gdfglm.cpp

@@ -152,8 +152,7 @@ int main(int argc, char **argv) {
   char OutGDFile[2000];
   int nargs;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_gdfglm.c,v 1.9 2011/05/05 15:28:03 greve Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_gdfglm");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_histo_normalize/mri_histo_normalize.cpp

@@ -66,11 +66,7 @@ main(int argc, char *argv[]) {
   HISTOGRAM    *histos[MAX_SUBJECTS], *htemplate ;
   double       rms, rms_avg ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option 
-    (argc, argv, 
-     "$Id: mri_histo_normalize.c,v 1.3 2011/03/02 00:04:19 nicks Exp $", 
-     "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_histo_normalize");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_ibmc/mri_ibmc.cpp

@@ -712,7 +712,7 @@ int main(int argc, char *argv[])
   ibmc = (IBMC *) calloc(sizeof(IBMC),1);
   ibmc->DoSmooth = 0;
 
-  nargs = handle_version_option (argc, argv, vcid, "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_ibmc");
   if (nargs && argc - nargs == 1) exit (0);
   argc -= nargs;
   cmdline = argv2cmdline(argc,argv);

attic/mri_interpolate/mri_interpolate.cpp

@@ -63,13 +63,15 @@ main(int argc, char *argv[]) {
   char         *in_fname, *out_fname, **av ;
   MRI          *mri_in, *mri_ctrl, *mri_out;
   int          ac, nargs=0, x, y, z ;
-  char         cmdline[CMD_LINE_LEN] ;
   double       val;
 
   make_cmd_version_string
     (argc, argv,
      "$Id: mri_interpolate.c,v 1.5 2011/10/06 01:18:12 fischl Exp $",
      "$Name:  $",cmdline);
+  make_cmd_version_string
+  std::string cmdline = getAllInfo(argc, argv, "mri_interpolate");
+
   setRandomSeed(-1L) ;
   Progname = argv[0] ;
 

attic/mri_label_accuracy/mri_label_accuracy.cpp

@@ -71,8 +71,7 @@ main(int argc, char *argv[]) {
   double accuracy ;
   MRI_REGION box ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_label_accuracy.c,v 1.2 2011/03/02 00:04:22 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_label_accuracy");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_make_bem_surfaces/mri_make_bem_surfaces.cpp

@@ -184,8 +184,7 @@ main(int argc,char *argv[])
   /* struct stat buf; */
   int nargs;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_make_bem_surfaces.c,v 1.13 2011/03/29 16:37:02 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_make_bem_surfaces");
   if (nargs && argc - nargs == 1)
   {
     exit (0);

attic/mri_make_density_map/mri_make_density_map.cpp

@@ -77,8 +77,7 @@ main(int argc, char *argv[]) {
   GCA_MORPH   *gcam ;
 
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_make_density_map.c,v 1.8 2011/03/02 00:04:22 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_make_density_map");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_make_register/mri_make_register.cpp

@@ -89,8 +89,7 @@ int main(int argc, char *argv[]) {
   int i;
   int nargs;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_make_register.c,v 1.9 2011/03/02 00:04:22 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_make_register");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_make_template/mri_make_template.cpp

@@ -121,8 +121,7 @@ main(int argc, char *argv[]) {
   /*  LTA    *lta;*/
   MRI *mri_tmp=0 ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_make_template.c,v 1.26 2011/03/02 00:04:22 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_make_template");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_map_atrophy/mri_map_atrophy.c

@@ -84,8 +84,7 @@ main(int argc, char *argv[]) {
   MRI         *mri_time1, *mri_time2, *mri_tmp, *mri_atrophy ;
   TRANSFORM   *transform1, *transform2 ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_map_atrophy.c,v 1.4 2011/03/02 00:04:22 nicks Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_map_atrophy");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;

attic/mri_mosaic/mri_mosaic.cpp

@@ -61,8 +61,7 @@ main(int argc, char *argv[]) {
   Timer start ;
   MRI          *mri[MAX_INPUT_IMAGES], *mri_mosaic ;
 
-  /* rkt: check for and handle version tag */
-  nargs = handle_version_option (argc, argv, "$Id: mri_mosaic.c,v 1.1 2015/09/25 16:05:20 fischl Exp $", "$Name:  $");
+  nargs = handleVersionOption(argc, argv, "mri_mosaic");
   if (nargs && argc - nargs == 1)
     exit (0);
   argc -= nargs;