ENH: Make the 64-to-32 bit truncations explicit

cifti/afni_xml.c

@@ -196,7 +196,7 @@ afni_xml_list axml_read_file(const char * fname, int read_data)
    {
       if( reset_xml_buf(xd, &buf, &bsize) ) break;
 
-      blen = fread(buf, 1, (size_t)bsize, fp);
+      blen = (unsigned)fread(buf, 1, (size_t)bsize, fp);
 
       /* check for early termination */
       bshort = loc_strnlen(buf, blen);
@@ -285,7 +285,7 @@ afni_xml_list axml_read_buf(const char * buf_in, int64_t bin_len)
 
         /* decide how much to copy and copy */
         if( bin_remain >= bsize ) blen = (unsigned)bsize;
-        else                      blen = bin_remain;
+        else                      blen = (unsigned)bin_remain;
 
         if(blen > 0 && blen <= (unsigned)bsize) {
            memcpy(buf, bin_ptr, blen);
@@ -900,7 +900,7 @@ static char * strip_whitespace(const char * str, int slen)
    /* if string is long, forget it */
    if( !str || slen > 1024 ) return (char *)str;
 
-   len = strlen(str);
+   len = (int)strlen(str);
    if( slen > 0 && slen < len ) len = slen;
    if( len <= 0 ) return (char *)str;
 
@@ -994,7 +994,7 @@ static int disp_gen_text(afni_xml_control * xd, const char * header,
 
    if( len == wlen ) {
        str = "whitespace";     /* just note the whitespace */
-       len = strlen(str);
+       len = (int)strlen(str);
    }
 
    show_depth(xd, 1);

cifti/afni_xml_io.c

@@ -136,7 +136,7 @@ int axio_num_tokens(const char * str, int64_t maxlen)
       }
    }
 
-   return ntok;
+   return (int)ntok;
 }
 
 
@@ -165,7 +165,7 @@ int axio_show_attrs(FILE * fp, afni_xml_t * ax, int indent)
    if( !ax ) return 1;
 
    for( ind = 0, maxl = 1; ind < ax->attrs.length; ind++ ) {
-      slen = strlen(ax->attrs.name[ind]);
+      slen = (int)strlen(ax->attrs.name[ind]);
       if( slen > maxl ) maxl = slen;
    }
 

fsliolib/fslio.c

@@ -207,7 +207,7 @@ static int FslFileType(const char* fname)
   int flen;
   int retval=-1;
   if (fname==NULL) return retval;
-  flen = strlen(fname);
+  flen = (int)strlen(fname);
   /* debian@onerussian.com had to group conditions to avoid possible
    * illegal memory read-ins */
   if (flen<5) return retval;  /* smallest name + extension is a.nii */
@@ -301,7 +301,7 @@ char *FslMakeBaseName(const char *fname)
   char *basename;
   int blen;
   basename = nifti_makebasename(fname);
-  blen = strlen(basename);
+  blen = (int)strlen(basename);
 #ifdef HAVE_ZLIB
   if ((blen>7) && (strcmp(basename + blen-7,".mnc.gz") == 0))
     { basename[blen-7]='\0'; return basename; }
@@ -841,13 +841,13 @@ void* FslReadAllVolumes(FSLIO* fslio, char* filename)
  */
 size_t FslReadVolumes(FSLIO *fslio, void *buffer, size_t nvols)
 {
-  int volbytes;
+  size_t volbytes;
   size_t retval=0;
   if (fslio==NULL)  FSLIOERR("FslReadVolumes: Null pointer passed for FSLIO");
   if (znz_isnull(fslio->fileptr))  FSLIOERR("FslReadVolumes: Null file pointer");
   if (fslio->niftiptr!=NULL) {
     fslio->niftiptr->data = buffer;
-    volbytes = FslGetVolSize(fslio)  * fslio->niftiptr->nbyper;
+    volbytes = FslGetVolSize(fslio) * (size_t)fslio->niftiptr->nbyper;
     retval = nifti_read_buffer(fslio->fileptr,fslio->niftiptr->data,nvols*volbytes,fslio->niftiptr);
     retval /= volbytes;
   }
@@ -1167,13 +1167,14 @@ size_t FslReadTimeSeries(FSLIO *fslio, void *buffer, short xVox, short yVox, sho
 
 int FslSeekVolume(FSLIO *fslio, size_t vols)
 {
-  int offset;
+  znz_off_t offset;
   if (fslio==NULL)  FSLIOERR("FslSeekVolume: Null pointer passed for FSLIO");
   if (fslio->niftiptr!=NULL) {
-    offset = fslio->niftiptr->iname_offset +
-      vols * FslGetVolSize(fslio) * fslio->niftiptr->nbyper;
+    offset = (znz_off_t)fslio->niftiptr->iname_offset
+      + (znz_off_t)vols * (znz_off_t)FslGetVolSize(fslio) * fslio->niftiptr->nbyper;
     if (znz_isnull(fslio->fileptr)) FSLIOERR("FslSeekVolume: Null file pointer");
-    return znzseek(fslio->fileptr,offset,SEEK_SET);
+    /* The int return cannot represent an offset beyond 2GB. */
+    return (int)znzseek(fslio->fileptr,offset,SEEK_SET);
   }
   if (fslio->mincptr!=NULL) {
     fprintf(stderr,"Warning:: Minc is not yet supported\n");
@@ -1257,8 +1258,8 @@ void FslSetDimensionality(FSLIO *fslio, size_t dim)
 {
   if (fslio==NULL)  FSLIOERR("FslSetDimensionality: Null pointer passed for FSLIO");
   if (fslio->niftiptr!=NULL) {
-    fslio->niftiptr->ndim = dim;
-    fslio->niftiptr->dim[0] = dim;
+    fslio->niftiptr->ndim = (int)dim;
+    fslio->niftiptr->dim[0] = (int)dim;
   }
   if (fslio->mincptr!=NULL) {
     fprintf(stderr,"Warning:: Minc is not yet supported\n");
@@ -2044,7 +2045,7 @@ int FslReadRawHeader(void *buffer, const char* filename)
     fprintf(stderr,"Could not open header %s\n",filename);
     return 0;
   }
-  retval = znzread(buffer,1,348,fp);
+  retval = (int)znzread(buffer,1,348,fp);
   znzclose(fp);
   if (retval != 348) {
     fprintf(stderr,"Could not read header %s\n",filename);
@@ -2148,9 +2149,9 @@ double ***FslGetVolumeAsScaledDouble(FSLIO *fslio, int vol)
         if ((fslio->niftiptr->dim[0] < 3) || (fslio->niftiptr->dim[0] > 4))
                 FSLIOERR("FslGetVolumeAsScaledDouble: Incorrect dataset dimension, 3D-4D needed");
 
-        xx = (fslio->niftiptr->nx == 0 ? 1 : (long)fslio->niftiptr->nx);
-        yy = (fslio->niftiptr->ny == 0 ? 1 : (long)fslio->niftiptr->ny);
-        zz = (fslio->niftiptr->nz == 0 ? 1 : (long)fslio->niftiptr->nz);
+        xx = (fslio->niftiptr->nx == 0 ? 1 : fslio->niftiptr->nx);
+        yy = (fslio->niftiptr->ny == 0 ? 1 : fslio->niftiptr->ny);
+        zz = (fslio->niftiptr->nz == 0 ? 1 : fslio->niftiptr->nz);
 
         if (fslio->niftiptr->scl_slope == 0) {
                 slope = 1.0;
@@ -2232,10 +2233,10 @@ double ****FslGetBufferAsScaledDouble(FSLIO *fslio)
         if ((fslio->niftiptr->dim[0] <= 0) || (fslio->niftiptr->dim[0] > 4))
                 FSLIOERR("FslGetBufferAsScaledDouble: Incorrect dataset dimension, 1-4D needed");
 
-        xx = (fslio->niftiptr->nx == 0 ? 1 : (long)fslio->niftiptr->nx);
-        yy = (fslio->niftiptr->ny == 0 ? 1 : (long)fslio->niftiptr->ny);
-        zz = (fslio->niftiptr->nz == 0 ? 1 : (long)fslio->niftiptr->nz);
-        tt = (fslio->niftiptr->nt == 0 ? 1 : (long)fslio->niftiptr->nt);
+        xx = (fslio->niftiptr->nx == 0 ? 1 : fslio->niftiptr->nx);
+        yy = (fslio->niftiptr->ny == 0 ? 1 : fslio->niftiptr->ny);
+        zz = (fslio->niftiptr->nz == 0 ? 1 : fslio->niftiptr->nz);
+        tt = (fslio->niftiptr->nt == 0 ? 1 : fslio->niftiptr->nt);
 
         if (fslio->niftiptr->scl_slope == 0) {
                 slope = 1.0;

nifti2/nifti2_io.c

@@ -478,9 +478,9 @@ int nifti_fileexists(const char* fname);
 /* prototypes for internal functions - not part of exported library          */
 
 /* extension routines */
-static int  nifti_read_extensions(nifti_image *nim, znzFile fp, int64_t remain);
-static int  nifti_read_next_extension( nifti1_extension * nex, nifti_image *nim,                                       int remain, znzFile fp );
-static int  nifti_check_extension(nifti_image *nim, int size,int code, int rem);
+static int64_t  nifti_read_extensions(nifti_image *nim, znzFile fp, int64_t remain);
+static int  nifti_read_next_extension( nifti1_extension * nex, nifti_image *nim,                                       int64_t remain, znzFile fp );
+static int  nifti_check_extension(nifti_image *nim, int size,int code, int64_t rem);
 static void update_nifti_image_for_brick_list(nifti_image * nim,
                                               int64_t nbricks);
 static int  nifti_add_exten_to_list(nifti1_extension *  new_ext,
@@ -503,7 +503,7 @@ static int  nifti_NBL_matches_nim(const nifti_image *nim,
 static int  rci_read_data(nifti_image *nim, int64_t *pivots, int64_t *prods,
                           int nprods, const int64_t dims[], char *data,
                           znzFile fp, int64_t base_offset);
-static int rci_alloc_mem(void **data, const int64_t prods[8], int nprods, int nbyper);
+static int64_t rci_alloc_mem(void **data, const int64_t prods[8], int nprods, int nbyper);
 static int  make_pivot_list(nifti_image * nim, const int64_t dims[8],
                             int64_t pivots[8], int64_t prods[8], int * nprods );
 
@@ -886,7 +886,8 @@ int nifti_image_load_bricks( nifti_image * nim , int64_t nbricks,
 
    znzclose(fp);
 
-   return NBL->nbricks;
+   /* the count came from the caller, who passed it as this many bricks */
+   return (int)NBL->nbricks;
 }
 
 
@@ -5983,7 +5984,7 @@ nifti_image *nifti_image_read( const char *hname , int read_data )
       return NULL;
    }
    else if ( rv == 1 ) { /* process special file type */
-      nim = nifti_read_ascii_image( fp, hfile, filesize, read_data );
+      nim = nifti_read_ascii_image( fp, hfile, (int)filesize, read_data );
       znzclose(fp);
       free(hfile);
       return nim;
@@ -6251,7 +6252,7 @@ nifti_image * nifti_read_ascii_image(znzFile fp, const char *fname, int flen,
  *
  * return the number of extensions read in, or < 0 on error
  *----------------------------------------------------------------------*/
-static int nifti_read_extensions( nifti_image *nim, znzFile fp, int64_t remain )
+static int64_t nifti_read_extensions( nifti_image *nim, znzFile fp, int64_t remain )
 {
    nifti1_extender    extdr;      /* defines extension existence  */
    nifti1_extension   extn;       /* single extension to process  */
@@ -6479,7 +6480,7 @@ static int nifti_fill_extension( nifti1_extension *ext, const char * data,
  *     error        : -1
  *----------------------------------------------------------------------*/
 static int nifti_read_next_extension( nifti1_extension * nex, nifti_image *nim,
-                                      int remain, znzFile fp )
+                                      int64_t remain, znzFile fp )
 {
    int swap = nim->byteorder != nifti_short_order();
    int count, size, code = -1;
@@ -6490,7 +6491,7 @@ static int nifti_read_next_extension( nifti1_extension * nex, nifti_image *nim,
 
    if( remain < 16 ){
       if( g_opts.debug > 2 )
-         fprintf(stderr,"-d only %d bytes remain, so no extension\n", remain);
+         fprintf(stderr,"-d only %" PRId64 " bytes remain, so no extension\n", remain);
       return 0;
    }
 
@@ -6696,7 +6697,7 @@ int nifti_is_valid_ecode( int ecode )
 /*----------------------------------------------------------------------
  * check for valid size and code, as well as can be done
  *----------------------------------------------------------------------*/
-static int nifti_check_extension(nifti_image *nim, int size, int code, int rem)
+static int nifti_check_extension(nifti_image *nim, int size, int code, int64_t rem)
 {
    /* check for bad code before bad size */
    if( ! nifti_is_valid_ecode(code) ) {
@@ -6713,7 +6714,7 @@ static int nifti_check_extension(nifti_image *nim, int size, int code, int rem)
 
    if( size > rem ){
       if( g_opts.debug > 2 )
-         fprintf(stderr,"-d ext size %d, space %d, no extension\n", size, rem);
+         fprintf(stderr,"-d ext size %d, space %" PRId64 ", no extension\n", size, rem);
       return 0;
    }
 
@@ -9525,7 +9526,7 @@ static int rci_read_data(nifti_image * nim, int64_t * pivots, int64_t * prods,
 
    return total size on success, and < 0 on failure
 */
-static int rci_alloc_mem(void **data, const int64_t prods[8], int nprods, int nbyper )
+static int64_t rci_alloc_mem(void **data, const int64_t prods[8], int nprods, int nbyper )
 {
    int64_t size;
    int     memindex;

nifti2/nifti_tool.c

@@ -6771,7 +6771,7 @@ int act_disp_ci( nt_opts * opts )
       }
 
       /* should we change disp_raw_data to allow for 64-bit nvalues? */
-      disp_raw_data(data, nim->datatype, len64 / nim->nbyper, space, 1);
+      disp_raw_data(data, nim->datatype, (int)(len64 / nim->nbyper), space, 1);
 
       nifti_image_free(nim);
    }
@@ -7575,7 +7575,7 @@ void * nt_read_header(const char * fname, int * nver, int * swapped, int check,
  *
  * the returned object is a (max 4-D) nifti_image
  *----------------------------------------------------------------------*/
-nifti_image * nt_read_bricks(nt_opts * opts, char * fname, int len,
+nifti_image * nt_read_bricks(nt_opts * opts, char * fname, int64_t len,
                              int64_t * list, nifti_brick_list * NBL)
 {
     nifti_image * nim;
@@ -7621,8 +7621,8 @@ nifti_image * nt_read_bricks(nt_opts * opts, char * fname, int len,
             disp_raw_data(opts->new_dim, DT_INT64, 8, ' ', 1);
             printf("   new_datatype = %d\n", opts->new_datatype);
             if( list && len > 0 ) {
-                printf("   brick_list[%d] = ", len);
-                disp_raw_data(list, DT_INT64, len, ' ', 1);
+                printf("   brick_list[%" PRId64 "] = ", len);
+                disp_raw_data(list, DT_INT64, (int)len, ' ', 1);
             }
             fflush(stdout);  /* disp_raw_data uses stdout */
         }

nifti2/nifti_tool.h

@@ -320,7 +320,7 @@ NI2_API int write_hdr2_to_file(nifti_2_header * nhdr, const char * fname);
 /* wrappers for nifti reading functions (allow MAKE_IM) */
 NI2_API nifti_image    * nt_image_read (nt_opts * opts, const char * fname,
                                         int read_data, int make_ver);
-NI2_API nifti_image    * nt_read_bricks(nt_opts * opts, char * fname, int len,
+NI2_API nifti_image    * nt_read_bricks(nt_opts * opts, char * fname, int64_t len,
                                         int64_t * list, nifti_brick_list * NBL);
 NI2_API void * nt_read_header(const char * fname, int * nver, int * swapped, int check,
                               int new_datatype, int64_t new_dim[8]);

niftilib/nifti1_io.c

@@ -7096,7 +7096,9 @@ int nifti_read_collapsed_image( nifti_image * nim, const int dims [8],
       fprintf(stderr,"+d read %d bytes of collapsed image from %s\n",
               bytes, nim->fname);
 
-   return bytes;
+   /* nifti_read_subregion_image() is declared to return int; a subregion
+      larger than 2GB cannot be requested through its int region_size. */
+   return (int)bytes;
 }
 
 
@@ -7320,7 +7322,9 @@ int nifti_read_subregion_image( nifti_image * nim,
     }
   }
   znzclose(fp);
-  return bytes;
+  /* nifti_read_subregion_image() is declared to return int; a subregion
+     larger than 2GB cannot be requested through its int region_size. */
+  return (int)bytes;
 }