[svn-r14559] 2nd batch for h5repack 1.6 a la 1.8

1) make the command line syntax same as h5dump, add long switch names
2) percentage printing bug in the copy code

remove one unused source file 

tested: windows, linux, solaris

3 files changed, 297 insertions, 181 deletions

diff --git a/tools/h5repack/Makefile.in b/tools/h5repack/Makefile.in
index b7867de..30c22d2 100644
--- a/tools/h5repack/Makefile.in
+++ b/tools/h5repack/Makefile.in
@@ -54,9 +54,9 @@ DISTCLEAN=h5repack.sh
 
 ## Source and object files for programs...
 ##
-PROG_SRC=h5repack.c h5repack_copy.c h5repack_refs.c h5repack_filters.c  h5repack_list.c h5repack_main.c h5repack_opttable.c h5repack_parse.c h5repack_verify.c h5repacktst.c
-OBJS=h5repack.lo h5repack_filters.lo h5repack_copy.lo h5repack_refs.lo h5repack_list.lo h5repack_main.lo h5repack_opttable.lo h5repack_parse.lo h5repack_verify.lo	
-TEST_OBJS=h5repack.lo h5repack_filters.lo  h5repack_copy.lo h5repack_refs.lo h5repack_list.lo h5repack_opttable.lo h5repack_parse.lo h5repack_verify.lo h5repacktst.lo
+PROG_SRC=h5repack.c h5repack_copy.c h5repack_refs.c h5repack_filters.c  h5repack_main.c h5repack_opttable.c h5repack_parse.c h5repack_verify.c h5repacktst.c
+OBJS=h5repack.lo h5repack_filters.lo h5repack_copy.lo h5repack_refs.lo h5repack_main.lo h5repack_opttable.lo h5repack_parse.lo h5repack_verify.lo	
+TEST_OBJS=h5repack.lo h5repack_filters.lo  h5repack_copy.lo h5repack_refs.lo h5repack_opttable.lo h5repack_parse.lo h5repack_verify.lo h5repacktst.lo
 DETECT_OBJS=testh5repack_detect_szip.lo
 PROG_OBJ=$(PROG_SRC:.c=.lo) $(DETECT_OBJS)
 
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 562af8b..3fc2ea6 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -29,10 +29,7 @@ extern char  *progname;
  */
 #define FORMAT_OBJ      " %-27s %s\n"   /* obj type, name */
 #define FORMAT_OBJ_ATTR "  %-27s %s\n"  /* obj type, name */
-#define PER(A,B) { per = 0;                                            \
-                   if (A!=0)                                           \
-                    per = (double) fabs( (double)(B-A) / (double)A  ); \
-                 }
+
 
 /*-------------------------------------------------------------------------
  * local functions
@@ -225,7 +222,6 @@ int do_copy_objects(hid_t fidin,
     hsize_t  dsize_out;         /* output dataset size after filter */
     int      apply_s;           /* flag for apply filter to small dataset sizes */
     int      apply_f;           /* flag for apply filter to return error on H5Dcreate */
-    double   per;               /* percent utilization of storage */
     void     *buf=NULL;         /* buffer for raw data */
     void     *sm_buf=NULL;      /* buffer for raw data */
     int      has_filter;        /* current object has a filter */
@@ -490,7 +486,7 @@ int do_copy_objects(hid_t fidin,
                         } /* hyperslab read */
                      }/*nelmts*/
                         
-                     /*-------------------------------------------------------------------------
+                      /*-------------------------------------------------------------------------
                       * amount of compression used
                       *-------------------------------------------------------------------------
                       */
@@ -498,26 +494,36 @@ int do_copy_objects(hid_t fidin,
                       {
                           if (apply_s && apply_f)
                           {
+                              double per=0;
+                              hssize_t a, b;
+                              
                               /* get the storage size of the input dataset */
                               dsize_out=H5Dget_storage_size(dset_out);
-                              PER((hssize_t)dsize_in,(hssize_t)dsize_out);
-                              print_dataset_info(dcpl_out,travt->objs[i].name,per*100.0);
+                              
+                              a = dsize_in; b = dsize_out;
+                              if (a!=0)
+                                  per = (double) (b-a)/a;
+                              
+                              per = -per;
+                              per *=100;
+                              
+                              print_dataset_info(dcpl_out,travt->objs[i].name,per);
                           }
                           else
                               print_dataset_info(dcpl_id,travt->objs[i].name,0.0);
-                                          
-                      /* print a message that the filter was not applied 
-                         (in case there was a filter)
-                      */
-                      if ( has_filter && apply_s == 0 )
-                          printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
-                          travt->objs[i].name,
-                          (int)options->threshold);
-                      
-                      if ( has_filter && apply_f == 0 )
-                          printf(" <warning: could not apply the filter to %s>\n",
-                          travt->objs[i].name);
-                      
+                          
+                              /* print a message that the filter was not applied 
+                              (in case there was a filter)
+                          */
+                          if ( has_filter && apply_s == 0 )
+                              printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
+                              travt->objs[i].name,
+                              (int)options->threshold);
+                          
+                          if ( has_filter && apply_f == 0 )
+                              printf(" <warning: could not apply the filter to %s>\n",
+                              travt->objs[i].name);
+                          
                       } /* verbose */
                       
                      /*-------------------------------------------------------------------------
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index 6da0c55..4d45d56 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -15,17 +15,41 @@
 
 #include <stdlib.h>
 #include <string.h>
+#include <ctype.h>
 #include "h5tools_utils.h"
-#include "h5trav.h"
 #include "h5repack.h"
 
+
+static void usage(const char *prog);
+static int  parse_number(char *str);
+static void parse_command_line(int argc, const char* argv[], pack_opt_t* options);
+static void read_info(const char *filename,pack_opt_t *options);
+
+
 /* module-scoped variables */
 const char *progname = "h5repack";
 int d_status = EXIT_SUCCESS;
 
-/* local prototypes */
-static void usage(void);
-static void read_info(const char *filename,pack_opt_t *options);
+/*
+ * Command-line options: The user can specify short or long-named
+ * parameters.
+ */
+static const char *s_opts = "hVvf:l:m:e:nLc:i:s:";
+static struct long_options l_opts[] = {
+    { "help", no_arg, 'h' },
+    { "version", no_arg, 'V' },
+    { "verbose", no_arg, 'v' },
+    { "filter", require_arg, 'f' },
+    { "layout", require_arg, 'l' },
+    { "threshold", require_arg, 'm' },
+    { "file", require_arg, 'e' },
+    { "native", no_arg, 'n' },
+  
+    { NULL, 0, '\0' }
+};
+
+
+
 
 /*-------------------------------------------------------------------------
  * Function: main
@@ -45,113 +69,280 @@ static void read_info(const char *filename,pack_opt_t *options);
  *  October 2006: Added a new switch -n, that allows to write the dataset 
  *                using a native type. The default to write is the file type.
  *
+ * Modification:
+ *   PVN, November 19, 2007
+ *    adopted the syntax h5repack [OPTIONS]  file1 file2
+ *   PVN, November 28, 2007
+ *    added support for multiple global filters
  *-------------------------------------------------------------------------
  */
-
-
 int main(int argc, char **argv)
 {
     char          *infile  = NULL;
     char          *outfile = NULL;
     pack_opt_t    options;            /*the global options */
-    int           i, ret;
+    int           ret;
     
     /* initialize options  */
     h5repack_init (&options,0);
+
+    parse_command_line(argc, argv, &options);
     
-    if (argc<2)
+    if ( argv[ opt_ind ] != NULL && argv[ opt_ind + 1 ] != NULL ) 
     {
-        usage();
-        exit(1);
+        infile = argv[ opt_ind ];
+        outfile = argv[ opt_ind + 1 ];
+
+        if ( strcmp( infile, outfile ) == 0 )
+        {
+            error_msg(progname, "file names cannot be the same\n");
+            usage(progname);
+            exit(EXIT_FAILURE);
+            
+        }
     }
     
-    for ( i = 1; i < argc; i++)
+    else
     {
-        if (strcmp(argv[i], "-h") == 0) {
-            usage();
-            exit(0);
-        }
-        if (strcmp(argv[i], "-i") == 0) {
-            infile = argv[++i];
-        }
-        else if (strcmp(argv[i], "-o") == 0) {
-            outfile = argv[++i];
-        }
-        else if (strcmp(argv[i], "-v") == 0) {
-            options.verbose = 1;
-        }
-        else if (strcmp(argv[i], "-f") == 0) {
+        error_msg(progname, "file names missing\n");
+        usage(progname);
+        exit(EXIT_FAILURE);
+    }
+
+  
+    /* pack it */
+    ret=h5repack(infile,outfile,&options);
+    
+    /* free tables */
+    h5repack_end(&options);
+    
+    if (ret==-1)
+        return 1;
+    else
+        return 0;
+}
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: usage
+ *
+ * Purpose: print usage
+ *
+ * Return: void
+ *
+ *-------------------------------------------------------------------------
+ */
+static void usage(const char *prog)
+{
+ printf("usage: %s [OPTIONS] file1 file2\n", prog);
+ printf("  file1                    Input HDF5 File\n");
+ printf("  file2                    Output HDF5 File\n");
+ printf("  OPTIONS\n");
+ printf("   -h, --help              Print a usage message and exit\n");
+ printf("   -v, --verbose           Verbose mode, print object information\n");
+ printf("   -V, --version           Print version number and exit\n");
+ printf("   -n, --native            Use a native HDF5 type when repacking\n");
+ 
+ printf("   -m T, --threshold=T     Do not apply the filter to datasets smaller than T\n");
+ printf("   -e M, --file=M          Name of file M with the -f and -l options\n");
+ printf("   -f FILT, --filter=FILT  Filter type\n");
+ printf("   -l LAYT, --layout=LAYT  Layout type\n");
+ 
+ printf("\n");
+
+ printf("  T - is an integer greater than 1, size of dataset in bytes \n");
+ printf("  M - is a filename.\n");
+ 
+ printf("\n");
+
+ printf("  FILT - is a string with the format:\n");
+ printf("\n");
+ printf("    <list of objects>:<name of filter>=<filter parameters>\n");
+ printf("\n");
+ printf("    <list of objects> is a comma separated list of object names, meaning apply\n");
+ printf("      compression only to those objects. If no names are specified, the filter\n");
+ printf("      is applied to all objects\n");
+ printf("    <name of filter> can be:\n");
+ printf("      GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n");
+ printf("      SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n");
+ printf("      SHUF, to apply the HDF5 shuffle filter\n");
+ printf("      FLET, to apply the HDF5 checksum filter\n");
+ printf("      NONE, to remove all filters\n");
+ printf("    <filter parameters> is optional filter parameter information\n");
+ printf("      GZIP=<deflation level> from 1-9\n");
+ printf("      SZIP=<pixels per block,coding> pixels per block is a even number in\n");
+ printf("            2-32 and coding method is either EC or NN\n");
+ printf("      SHUF (no parameter)\n");
+ printf("      FLET (no parameter)\n");
+
+ printf("      NONE (no parameter)\n");
+ printf("\n");
+ printf("  LAYT - is a string with the format:\n");
+ printf("\n");
+ printf("    <list of objects>:<layout type>=<layout parameters>\n");
+ printf("\n");
+ printf("    <list of objects> is a comma separated list of object names, meaning that\n");
+ printf("      layout information is supplied for those objects. If no names are\n");
+ printf("      specified, the layout type is applied to all objects\n");
+ printf("    <layout type> can be:\n");
+ printf("      CHUNK, to apply chunking layout\n");
+ printf("      COMPA, to apply compact layout\n");
+ printf("      CONTI, to apply continuous layout\n");
+ printf("    <layout parameters> is optional layout information\n");
+ printf("      CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n");
+ printf("      COMPA (no parameter)\n");
+ printf("      CONTI (no parameter)\n");
+ printf("\n");
+ printf("Examples of use:\n");
+ printf("\n");
+ printf("1) h5repack -v -f GZIP=1 file1 file2\n");
+ printf("\n");
+ printf("   GZIP compression with level 1 to all objects\n");
+ printf("\n");
+ printf("2) h5repack -v -f A:SZIP=8,NN file1 file2\n");
+ printf("\n");
+ printf("   SZIP compression with 8 pixels per block and NN coding method to object A\n");
+ printf("\n");
+ printf("3) h5repack -v -l A,B:CHUNK=20x10 -f C,D,F:NONE file1 file2\n");
+ printf("\n");
+ printf("   Chunked layout, with a layout size of 20x10, to objects A and B\n");
+ printf("   and remove filters to objects C, D, F\n");
+ printf("\n");
+
+ printf("4) h5repack -f SHUF -f GZIP=1 file1 file2 \n");
+ printf("\n");
+ printf("   Add both filters SHUF and GZIP in this order to all datasets\n");
+ printf("\n");
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: parse_command_line
+ *
+ * Purpose: parse command line input
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static void parse_command_line(int argc, const char* argv[], pack_opt_t* options)
+{
+    
+    int opt;
+   
+    /* parse command line options */
+    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) 
+    {
+        switch ((char)opt) 
+        {
+        case 'h':
+            usage(progname);
+            exit(EXIT_SUCCESS);
+        case 'V':
+            print_version(progname);
+            exit(EXIT_SUCCESS);
+        case 'v':
+            options->verbose = 1;
+            break;
+        case 'f':
             
-            /* add the -f filter option */
-            if (h5repack_addfilter(argv[i+1],&options)<0)
+            /* parse the -f filter option */
+            if (h5repack_addfilter( opt_arg, options)<0)
             {
                 error_msg(progname, "in parsing filter\n");
-                exit(1);
+                exit(EXIT_FAILURE);
             }
-            
-            /* jump to next */
-            ++i;
-        }
-        else if (strcmp(argv[i], "-l") == 0) {
+            break;
+        case 'l':
             
             /* parse the -l layout option */
-            if (h5repack_addlayout(argv[i+1],&options)<0)
+            if (h5repack_addlayout( opt_arg, options)<0)
             {
                 error_msg(progname, "in parsing layout\n");
-                exit(1);
+                exit(EXIT_FAILURE);
             }
+            break;
             
-            /* jump to next */
-            ++i;
-        }
-        
-        else if (strcmp(argv[i], "-m") == 0) {
-            options.threshold = parse_number(argv[i+1]);
-            if ((int)options.threshold==-1) {
-                error_msg(progname, "invalid treshold size <%s>\n",argv[i+1]);
-                exit(1);
+
+        case 'm':
+
+            options->threshold = parse_number( opt_arg );
+            if ((int)options->threshold==-1) 
+            {
+                error_msg(progname, "invalid treshold size <%s>\n", opt_arg );
+                exit(EXIT_FAILURE);
             }
-            ++i;
-        }
+            break;
         
-        else if (strcmp(argv[i], "-e") == 0) {
-            read_info(argv[++i],&options);
-        }
-        else if (strcmp(argv[i], "-n") == 0) {
-            options.use_native = 1;
-        }
+        case 'e':
+            read_info( opt_arg, options);
+            break;
+
+        case 'n':
+            options->use_native = 1;
+            break;
         
-        else if (argv[i][0] == '-') {
-            error_msg(progname, " - is not a valid argument\n");
-            usage();
-            exit(1);
-        }
-    }
+     
+
+       
+
+        } /* switch */
+        
+        
+    } /* while */
     
-    if (infile == NULL || outfile == NULL)
+    /* check for file names to be processed */
+    if (argc <= opt_ind || argv[ opt_ind + 1 ] == NULL) 
     {
-        error_msg(progname, "file names missing\n");
-        usage();
-        exit(1);
+        error_msg(progname, "missing file names\n");
+        usage(progname);
+        exit(EXIT_FAILURE);
     }
+      
+
+ 
+ 
+}
+
+/*-------------------------------------------------------------------------
+ * Function: parse_number
+ *
+ * Purpose: read a number from command line argument
+ *
+ * Return: number, -1 for FAIL
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 23, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+
+int parse_number(char *str)
+{
+    unsigned    i;
+    int         n;
+    char        c;
+    size_t      len=strlen(str);
     
-    /* pack it */
-    ret=h5repack(infile,outfile,&options);
-    
-    /* free tables */
-    h5repack_end(&options);
-    
-    if (ret==-1)
-        return 1;
-    else
-        return 0;
+    for ( i=0; i<len; i++)
+    {
+        c = str[i];
+        if (!isdigit(c)){
+            return -1;
+        }
+    }
+    str[i]='\0';
+    n=atoi(str);
+    return n;
 }
 
 
 /*-------------------------------------------------------------------------
  * Function: read_info
  *
- * Purpose: read comp and chunk options from file
+ * Purpose: read comp and chunk options from a file
  *
  * Return: void, exit on error
  *
@@ -162,7 +353,7 @@ int main(int argc, char **argv)
  *-------------------------------------------------------------------------
  */
 
-static 
+static
 void read_info(const char *filename,
                pack_opt_t *options)
 {
@@ -225,7 +416,7 @@ void read_info(const char *filename,
                 exit(1);
             }
         }
-       /*-------------------------------------------------------------------------
+        /*-------------------------------------------------------------------------
         * layout
         *-------------------------------------------------------------------------
         */
@@ -255,7 +446,7 @@ void read_info(const char *filename,
                 exit(1);
             }
         }
-       /*-------------------------------------------------------------------------
+        /*-------------------------------------------------------------------------
         * not valid
         *-------------------------------------------------------------------------
         */
@@ -270,84 +461,3 @@ void read_info(const char *filename,
 }
 
 
-
-/*-------------------------------------------------------------------------
- * Function: usage
- *
- * Purpose: print usage
- *
- * Return: void
- *
- *-------------------------------------------------------------------------
- */
-
-static
-void usage(void)
-{
-    printf("usage: h5repack -i input -o output [-h] [-v] [-f FILTER] [-l LAYOUT] [-n] [-m size] [-e file]\n");
-    printf("\n");
-    printf("-i input       Input HDF5 File\n");
-    printf("-o output      Output HDF5 File\n");
-    printf("[-h]           Print this message\n");
-    printf("[-v]           Verbose mode\n");
-    printf("[-n]           Use a native HDF5 type when repacking. Default is the file type\n");
-    printf("[-m size]      Do not apply the filter to objects smaller than size\n");
-    printf("[-e file]      Name of file with the -f and -l options\n");
-    printf("[-f FILTER]    Filter type\n");
-    printf("[-l LAYOUT]    Layout type\n");
-    printf("\n");
-    printf("FILTER is a string with the format:\n");
-    printf("\n");
-    printf("    <list of objects>:<name of filter>=<filter parameters>\n");
-    printf("\n");
-    printf("    <list of objects> is a comma separated list of object names, meaning apply\n");
-    printf("      compression only to those objects. If no names are specified, the filter\n");
-    printf("      is applied to all objects\n");
-    printf("    <name of filter> can be:\n");
-    printf("      GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n");
-    printf("      SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n");
-    printf("      SHUF, to apply the HDF5 shuffle filter\n");
-    printf("      FLET, to apply the HDF5 checksum filter\n");
-    printf("      NONE, to remove all filters\n");
-    printf("    <filter parameters> is optional filter parameter information\n");
-    printf("      GZIP=<deflation level> from 1-9\n");
-    printf("      SZIP=<pixels per block,coding> pixels per block is a even number in\n");
-    printf("            2-32 and coding method is either EC or NN\n");
-    printf("      SHUF (no parameter)\n");
-    printf("      FLET (no parameter)\n");
-    printf("      NONE (no parameter)\n");
-    printf("\n");
-    printf("LAYOUT is a string with the format:\n");
-    printf("\n");
-    printf("    <list of objects>:<layout type>=<layout parameters>\n");
-    printf("\n");
-    printf("    <list of objects> is a comma separated list of object names, meaning that\n");
-    printf("      layout information is supplied for those objects. If no names are\n");
-    printf("      specified, the layout type is applied to all objects\n");
-    printf("    <layout type> can be:\n");
-    printf("      CHUNK, to apply chunking layout\n");
-    printf("      COMPA, to apply compact layout\n");
-    printf("      CONTI, to apply continuous layout\n");
-    printf("    <layout parameters> is optional layout information\n");
-    printf("      CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n");
-    printf("      COMPA (no parameter)\n");
-    printf("      CONTI (no parameter)\n");
-    printf("\n");
-    printf("Examples of use:\n");
-    printf("\n");
-    printf("1) h5repack -v -i file1 -o file2 -f GZIP=1\n");
-    printf("\n");
-    printf("   GZIP compression with level 1 to all objects\n");
-    printf("\n");
-    printf("2) h5repack -v -i file1 -o file2 -f A:SZIP=8,NN\n");
-    printf("\n");
-    printf("   SZIP compression with 8 pixels per block and NN coding method to object A\n");
-    printf("\n");
-    printf("3) h5repack -v -i file1 -o file2 -l A,B:CHUNK=20x10 -f C,D,F:NONE\n");
-    printf("\n");
-    printf("   Chunked layout, with a layout size of 20x10, to objects A and B\n");
-    printf("   and remove filters to objects C, D, F\n");
-    printf("\n");
-}
-
-