MINC 2023-11-14 (15d994de)

Code extracted from: https://github.com/BIC-MNI/libminc.git at commit 15d994def83274b715711afffa73268167ec2cc6 (develop).
InsightSoftwareConsortium · Nov 16, 2023 · c3952a8 · c3952a8
1 parent 8a13bf6
commit c3952a8
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Showing 49 changed files with 106 additions and 95 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -7,12 +7,12 @@ PROJECT(LIBMINC)
 
 SET(LIBMINC_PACKAGE_VERSION_MAJOR 2)
 SET(LIBMINC_PACKAGE_VERSION_MINOR 4)
-SET(LIBMINC_PACKAGE_VERSION_PATCH 05)
+SET(LIBMINC_PACKAGE_VERSION_PATCH 06)
 
 SET(LIBMINC_SOVERSION "5.3.0")
 
 SET(LIBMINC_PACKAGE "libminc")
-SET(LIBMINC_PACKAGE_BUGREPORT "a.janke@gmail.com")
+SET(LIBMINC_PACKAGE_BUGREPORT "vladimir.fonov@gmail.com")
 
 SET(LIBMINC_PACKAGE_NAME    "libminc")
 SET(LIBMINC_PACKAGE_VERSION "${LIBMINC_PACKAGE_VERSION_MAJOR}.${LIBMINC_PACKAGE_VERSION_MINOR}.${LIBMINC_PACKAGE_VERSION_PATCH}")
@@ -54,6 +54,8 @@ IF(NOT LIBMINC_EXTERNALLY_CONFIGURED)
   OPTION(LIBMINC_USE_NIFTI               "Build with NIfTI support" OFF)
   OPTION(LIBMINC_USE_SYSTEM_NIFTI        "Use system NIfTI-1 library" OFF)
 
+  OPTION(LIBMINC_USE_ASAN                "Build with Address Sanitizer" OFF)
+
   SET (LIBMINC_EXPORTED_TARGETS "LIBMINC-targets")
   SET (LIBMINC_INSTALL_BIN_DIR bin)
   SET (LIBMINC_INSTALL_LIB_DIR lib${LIB_SUFFIX})
@@ -109,6 +111,13 @@ IF(UNIX)
   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
 ENDIF(UNIX)
 
+
+IF(LIBMINC_USE_ASAN)
+  add_compile_options(-fno-omit-frame-pointer -fsanitize=address)
+  add_link_options(-fno-omit-frame-pointer -fsanitize=address)
+ENDIF(LIBMINC_USE_ASAN)
+
+
 # check for prereqs
 INCLUDE(CheckFunctionExists)
 INCLUDE(CheckSymbolExists)

diff --git a/libcommon/ParseArgv.c b/libcommon/ParseArgv.c
@@ -82,7 +82,7 @@ static void PrintVersion(ArgvInfo *argTable);
  *
  * Quick replacement for strtol which eliminates the undesirable property
  * of interpreting numbers with leading '0' characters as octal, while
- * retaining "0x" as indicating a hexidecimal number.
+ * retaining "0x" as indicating a hexadecimal number.
  */
 long int
 ParseLong(const char *argPtr, char **endPtr)
@@ -173,7 +173,7 @@ ParseArgv(argcPtr, argv, argTable, flags)
       length = strlen(curArg);
 
       /*
-       * Loop throught the argument descriptors searching for one with
+       * Loop through the argument descriptors searching for one with
        * the matching key string.  If found, leave a pointer to it in
        * matchPtr.
        */

diff --git a/libcommon/minc2_error.c b/libcommon/minc2_error.c
@@ -46,7 +46,7 @@
  * A few fixes to the configure script.
  *
  * Revision 6.1  1999/10/19 14:45:09  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6

diff --git a/libcommon/minc2_error.h b/libcommon/minc2_error.h
@@ -3,7 +3,7 @@
 @DESCRIPTION: File containing error codes for libminc package.
 @GLOBALS    : 
 @CALLS      : 
-@CREATED    : 17 Feburary, 2004 (Robert Vincent)
+@CREATED    : 17 February, 2004 (Robert Vincent)
 @MODIFIED   : 
  *
  * $Log: minc_error.h,v $

diff --git a/libcommon/minc_error.c b/libcommon/minc_error.c
@@ -46,7 +46,7 @@
  * A few fixes to the configure script.
  *
  * Revision 6.1  1999/10/19 14:45:09  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6

diff --git a/libcommon/minc_error.h b/libcommon/minc_error.h
@@ -3,7 +3,7 @@
 @DESCRIPTION: File containing error codes for minc package.
 @GLOBALS    : 
 @CALLS      : 
-@CREATED    : 17 Feburary, 2004 (Robert Vincent)
+@CREATED    : 17 February, 2004 (Robert Vincent)
 @MODIFIED   : 
  *
  * $Log: minc_error.h,v $

diff --git a/libcommon/time_stamp.c b/libcommon/time_stamp.c
@@ -24,7 +24,7 @@
  * Fixed log message containing log substitution
  *
  * Revision 6.1  1999/10/19 14:45:14  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:23:41  neelin
  * Release of minc version 0.6

diff --git a/libcommon/time_stamp.h b/libcommon/time_stamp.h
@@ -16,7 +16,7 @@
  * Fixed log message containing log substitution
  *
  * Revision 6.1  1999/10/19 14:45:14  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:23:41  neelin
  * Release of minc version 0.6

diff --git a/libsrc/dim_conversion.c b/libsrc/dim_conversion.c
@@ -36,7 +36,7 @@
  * Use standard labs() and fabs() instead of our private macros
  *
  * Revision 6.1  1999/10/19 14:45:07  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6
@@ -537,7 +537,7 @@ PRIVATE int MI_get_dim_bufsize_step(mi_icv_type *icvp, int subsc[])
                  dimensions
 @OUTPUT     : (none)
 @RETURNS    : MI_ERROR if an error occurs
-@DESCRIPTION: Sets the variables for dimensions converions
+@DESCRIPTION: Sets the variables for dimensions conversions
 @METHOD     : 
 @GLOBALS    : 
 @CALLS      : NetCDF routines

diff --git a/libsrc/hdf_convenience.c b/libsrc/hdf_convenience.c
@@ -309,12 +309,12 @@ hdf_is_dimension_name(struct m2_file *file, const char *varnm)
  * may not yet exist in the file.
  */
 static hid_t
-hdf_path_from_name(struct m2_file *file, const char *varnm, char *varpath)
+hdf_path_from_name(struct m2_file *file, const char *varnm, char *varpath, size_t varpathlength)
 {
     if (!strcmp(varnm, MIimage) ||
       !strcmp(varnm, MIimagemax) ||
       !strcmp(varnm, MIimagemin)) {
-      sprintf(varpath, "/minc-2.0/image/%d/", file->resolution);
+      snprintf(varpath, varpathlength, "/minc-2.0/image/%d/", file->resolution);
     }
     else if (hdf_is_dimension_name(file, varnm)) {
       strcpy(varpath, "/minc-2.0/dimensions/");
@@ -1102,7 +1102,7 @@ hdf_attput(int fd, int varid, const char *attnm, nc_type val_typ,
             char temp[128];
             unsigned int i;
 
-            sprintf(temp, "junkXXXX");
+            snprintf(temp, sizeof(temp), "junkXXXX");
 
             new_type_id = H5Tcopy(var->ftyp_id);
             if (new_type_id < 0) {
@@ -1295,7 +1295,7 @@ hdf_vardef(int fd, const char *varnm, nc_type vartype, int ndims,
       return (MI_ERROR);
     }
 
-    if (hdf_path_from_name(file, varnm, varpath) < 0) {
+    if (hdf_path_from_name(file, varnm, varpath, sizeof(varpath)) < 0) {
       return (MI_ERROR);
     }
 
@@ -2221,7 +2221,7 @@ hdf_open(const char *path, int mode)
 
     /*Set cachine parameters*/
     fpid=H5Pcreate( H5P_FILE_ACCESS );
-    /* Limit file compatability to 1.8.x */
+    /* Limit file compatibility to 1.8.x */
     H5Pset_libver_bounds (fpid, H5F_LIBVER_V18, H5F_LIBVER_V18);
 
     /*setup a bigger cache to work with typical chunking ( MI_MAX_VAR_BUFFER_SIZE )*/
@@ -2332,7 +2332,7 @@ hdf_create(const char *path, int cmode, struct mi2opts *opts_ptr)
 
     /*Set cachine parameters*/
     fpid = H5Pcreate (H5P_FILE_ACCESS);
-    /* Limit file compatability to 1.8.x */
+    /* Limit file compatibility to 1.8.x */
     H5Pset_libver_bounds (fpid, H5F_LIBVER_V18, H5F_LIBVER_V18);
 
     /*setup a bigger cache to work with typical chunking ( MI_MAX_VAR_BUFFER_SIZE )*/

diff --git a/libsrc/image_conversion.c b/libsrc/image_conversion.c
@@ -100,7 +100,7 @@
  * A few fixes to the configure script.
  *
  * Revision 6.1  1999/10/19 14:45:07  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6

diff --git a/libsrc/minc.h b/libsrc/minc.h
@@ -95,7 +95,7 @@
  * Start of modifications to get minc working with netcdf 3.5.
  *
  * Revision 6.1  1999/10/19 14:45:08  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6

diff --git a/libsrc/minc_basic.h b/libsrc/minc_basic.h
@@ -40,7 +40,7 @@
  * A few fixes to the configure script.
  *
  * Revision 6.1  1999/10/19 14:45:08  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6

diff --git a/libsrc/minc_convenience.c b/libsrc/minc_convenience.c
@@ -111,7 +111,7 @@
  * A few fixes to the configure script.
  *
  * Revision 6.1  1999/10/19 14:45:09  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6
@@ -1342,7 +1342,7 @@ MNCAPI int micreate_group_variable(int cdfid, const char *name)
 @INPUT      : id - cdf file id
               tm_stamp  - timestamp as returned by time_stamp() function.
 @OUTPUT     : (none)
-@RETURNS    : MI_NOERROR if successfuly
+@RETURNS    : MI_NOERROR if successful
 @DESCRIPTION: Appends the string (which should be in the format returned
               by the time_stamp() function) to the global "history" 
               attribute.

diff --git a/libsrc/minc_private.h b/libsrc/minc_private.h
@@ -23,7 +23,7 @@
  * #include minc_config.h and minc_error.h
  *
  * Revision 6.1  1999/10/19 14:45:09  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6

diff --git a/libsrc/minc_routines.h b/libsrc/minc_routines.h
@@ -23,7 +23,7 @@
  * Minor changes for Windows compatibility
  *
  * Revision 6.1  1999/10/19 14:45:10  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6

diff --git a/libsrc/minc_simple.c b/libsrc/minc_simple.c
@@ -529,7 +529,7 @@ minc_save_start(char *path,     /* Path to the file */
     int var_ndims;              /* Number of dimensions per variable */
     int var_dims[MI_S_NDIMS];   /* Dimension ID's per variable */
     int i, j;                   /* Generic loop counters */
-    int old_ncopts;             /* For supressing fatal error messages */
+    int old_ncopts;             /* For suppressing fatal error messages */
     struct file_info *p_file;   /* For accessing the file structure */
     struct var_info *p_var;
     struct att_info *p_att;

diff --git a/libsrc/minc_structures.h b/libsrc/minc_structures.h
@@ -14,7 +14,7 @@
 @MODIFIED   : 
  * $Log: minc_structures.h,v $
  * Revision 6.1  1999-10-19 14:45:10  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6

diff --git a/libsrc/minc_useful.h b/libsrc/minc_useful.h
@@ -18,7 +18,7 @@
  * Minor changes for Windows compatibility
  *
  * Revision 6.1  1999/10/19 14:45:10  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6

diff --git a/libsrc/minc_varlists.h b/libsrc/minc_varlists.h
@@ -7,7 +7,7 @@
 @MODIFIED   : 
  * $Log: minc_varlists.h,v $
  * Revision 6.1  1999-10-19 14:45:11  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6

diff --git a/libsrc/nd_loop.c b/libsrc/nd_loop.c
@@ -22,7 +22,7 @@
  * in order to include them in the main minc library.
  *
  * Revision 6.1  1999/10/19 14:45:13  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:23:41  neelin
  * Release of minc version 0.6

diff --git a/libsrc/nd_loop.h b/libsrc/nd_loop.h
@@ -27,7 +27,7 @@
  * in order to include them in the main minc library.
  *
  * Revision 6.1  1999/10/19 14:45:14  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:23:41  neelin
  * Release of minc version 0.6

diff --git a/libsrc/netcdf_convenience.c b/libsrc/netcdf_convenience.c
@@ -107,7 +107,7 @@
  * For newer versions of glibc, this would cause a seg fault.
  *
  * Revision 6.2  1999/10/19 14:45:11  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.1  1997/10/06 12:54:08  neelin
  * Changed call to tmpnam to tempnam so that TMPDIR variable is checked when
@@ -257,7 +257,7 @@ PRIVATE int execute_decompress_command(char *command, const char *infile,
    /* we now ignore header_only and always uncompress the whole
     * file as the previous "header only" hack that used to work
     * on MINC1 files doesn't work reliably with MINC2 */
-   (void) sprintf(whole_command, "exec %s %s > %s 2> /dev/null", 
+   (void) snprintf(whole_command, sizeof(whole_command), "exec %s %s > %s 2> /dev/null", 
                   command, infile, outfile);
    status = system(whole_command);
 

diff --git a/libsrc/strdup.c b/libsrc/strdup.c
@@ -14,7 +14,7 @@
 @MODIFIED   : 
  * $Log: strdup.c,v $
  * Revision 6.1  1999-10-19 14:45:11  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6

diff --git a/libsrc/type_limits.h b/libsrc/type_limits.h
@@ -7,7 +7,7 @@
 @MODIFIED   : 
  * $Log: type_limits.h,v $
  * Revision 6.1  1999-10-19 14:45:12  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6

diff --git a/libsrc/value_conversion.c b/libsrc/value_conversion.c
@@ -41,7 +41,7 @@
  * A few fixes to the configure script.
  *
  * Revision 6.1  1999/10/19 14:45:12  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:24:54  neelin
  * Release of minc version 0.6

diff --git a/libsrc/voxel_loop.c b/libsrc/voxel_loop.c
@@ -99,7 +99,7 @@
  * in their own way.
  *
  * Revision 6.1  1999/10/19 14:45:15  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:23:41  neelin
  * Release of minc version 0.6

diff --git a/libsrc/voxel_loop.h b/libsrc/voxel_loop.h
@@ -30,7 +30,7 @@
  * in their own way.
  *
  * Revision 6.1  1999/10/19 14:45:16  neelin
- * Fixed Log subsitutions for CVS
+ * Fixed Log substitutions for CVS
  *
  * Revision 6.0  1997/09/12 13:23:41  neelin
  * Release of minc version 0.6

diff --git a/libsrc2/datatype.c b/libsrc2/datatype.c
@@ -23,7 +23,7 @@ int miget_data_type ( mihandle_t volume, mitype_t *data_type )
   return ( MI_NOERROR );
 }
 
-/** Return the byte size of the voxel datatytpe
+/** Return the byte size of the voxel datatype
  */
 int miget_data_type_size ( mihandle_t volume, misize_t *voxel_size )
 {

diff --git a/libsrc2/dimension.c b/libsrc2/dimension.c
@@ -184,7 +184,7 @@ int micopy_dimension ( midimhandle_t dim_ptr, midimhandle_t *new_dim_ptr )
   * enough range to represent detail on the order of 10 Angstroms in
   * typical medical imaging applications.
   *
-  * For the detailed defintion of \a class and \a type refer to the MINC 2.0 API
+  * For the detailed definition of \a class and \a type refer to the MINC 2.0 API
   * definition.
   * \ingroup mi2Dim
   */
@@ -1217,7 +1217,7 @@ int miset_dimension_separation ( midimhandle_t dimension, double separation )
   * Get the sampling interval (STEP) for a list of dimensions.
   * \param dimensions An array of dimension handles.
   * \param voxel_order The order in which the voxel indices increase/decrease.
-  * \param array_length The number of dimensions in the dimesions array.
+  * \param array_length The number of dimensions in the dimensions array.
   * \param separations An array of dimensions sampling intervals (step) values.
   *
   * Get or Set the scalar separation (sampling interval)
@@ -1245,7 +1245,7 @@ int miget_dimension_separations ( const midimhandle_t dimensions[],
 /**
   * Set the sampling interval (STEP) for a list of dimensions.
   * \param dimensions An array of dimension handles.
-  * \param array_length The number of dimensions in the dimesions array.
+  * \param array_length The number of dimensions in the dimensions array.
   * \param separations An array of dimensions sampling intervals (step) values.
   *
   * Refer to miget_dimension_separations().