[svn-r12437] Purpose:

new feature. h5dump output of binary data

Description:
a new switch -b FILE_NAME that dumps the contents of memory data to file FILE_NAME in binary form

new program binread.c that reads the contents of this file and outputs it to stdout

added a test for the h5dump shell script that does a run of -b
the binread.c program reads the data used in this run, usage is ./binread FILE_NAME


Solution:

Platforms tested:
linux
solaris
AIX

Misc. update:

5 files changed, 165 insertions, 22 deletions

diff --git a/tools/h5dump/Makefile.am b/tools/h5dump/Makefile.am
index 0cdc47b..94a6d73 100644
--- a/tools/h5dump/Makefile.am
+++ b/tools/h5dump/Makefile.am
@@ -26,7 +26,7 @@ INCLUDES=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 TEST_PROG=h5dumpgentest
 TEST_SCRIPT=testh5dump.sh testh5dumpxml.sh
 
-check_PROGRAMS=$(TEST_PROG)
+check_PROGRAMS=$(TEST_PROG) binread
 check_SCRIPTS=$(TEST_SCRIPT)
 SCRIPT_DEPEND=h5dump$(EXEEXT)
 
diff --git a/tools/h5dump/Makefile.in b/tools/h5dump/Makefile.in
index 897ad53..3c78e7e 100644
--- a/tools/h5dump/Makefile.in
+++ b/tools/h5dump/Makefile.in
@@ -30,7 +30,7 @@
 # HDF5 Library Makefile(.in)
 #
 
-SOURCES = h5dump.c h5dumpgentest.c
+SOURCES = binread.c h5dump.c h5dumpgentest.c
 
 srcdir = @srcdir@
 top_srcdir = @top_srcdir@
@@ -58,7 +58,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(srcdir)/testh5dump.sh.in $(srcdir)/testh5dumpxml.sh.in \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am
-check_PROGRAMS = $(am__EXEEXT_1)
+check_PROGRAMS = $(am__EXEEXT_1) binread$(EXEEXT)
 bin_PROGRAMS = h5dump$(EXEEXT)
 subdir = tools/h5dump
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
@@ -72,11 +72,15 @@ am__installdirs = "$(DESTDIR)$(bindir)"
 binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
 am__EXEEXT_1 = h5dumpgentest$(EXEEXT)
 PROGRAMS = $(bin_PROGRAMS)
+binread_SOURCES = binread.c
+binread_OBJECTS = binread.$(OBJEXT)
+binread_LDADD = $(LDADD)
+am__DEPENDENCIES_1 = $(top_builddir)/tools/lib/libh5tools.la
+am__DEPENDENCIES_2 = $(top_builddir)/src/libhdf5.la
+binread_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_2)
 h5dump_SOURCES = h5dump.c
 h5dump_OBJECTS = h5dump.$(OBJEXT)
 h5dump_LDADD = $(LDADD)
-am__DEPENDENCIES_1 = $(top_builddir)/tools/lib/libh5tools.la
-am__DEPENDENCIES_2 = $(top_builddir)/src/libhdf5.la
 h5dump_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_2)
 h5dumpgentest_SOURCES = h5dumpgentest.c
 h5dumpgentest_OBJECTS = h5dumpgentest.$(OBJEXT)
@@ -94,8 +98,8 @@ LTCOMPILE = $(LIBTOOL) --tag=CC --mode=compile $(CC) $(DEFS) \
 CCLD = $(CC)
 LINK = $(LIBTOOL) --tag=CC --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
 	$(AM_LDFLAGS) $(LDFLAGS) -o $@
-SOURCES = h5dump.c h5dumpgentest.c
-DIST_SOURCES = h5dump.c h5dumpgentest.c
+SOURCES = binread.c h5dump.c h5dumpgentest.c
+DIST_SOURCES = binread.c h5dump.c h5dumpgentest.c
 ETAGS = etags
 CTAGS = ctags
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
@@ -434,6 +438,9 @@ clean-checkPROGRAMS:
 	  echo " rm -f $$p $$f"; \
 	  rm -f $$p $$f ; \
 	done
+binread$(EXEEXT): $(binread_OBJECTS) $(binread_DEPENDENCIES) 
+	@rm -f binread$(EXEEXT)
+	$(LINK) $(binread_LDFLAGS) $(binread_OBJECTS) $(binread_LDADD) $(LIBS)
 h5dump$(EXEEXT): $(h5dump_OBJECTS) $(h5dump_DEPENDENCIES) 
 	@rm -f h5dump$(EXEEXT)
 	$(LINK) $(h5dump_LDFLAGS) $(h5dump_OBJECTS) $(h5dump_LDADD) $(LIBS)
@@ -447,6 +454,7 @@ mostlyclean-compile:
 distclean-compile:
 	-rm -f *.tab.c
 
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/binread.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5dump.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5dumpgentest.Po@am__quote@
 
diff --git a/tools/h5dump/binread.c b/tools/h5dump/binread.c
new file mode 100644
index 0000000..d3b43a9
--- /dev/null
+++ b/tools/h5dump/binread.c
@@ -0,0 +1,100 @@
+
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html.  If you do not have     *
+ * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+/* 
+ This program reads binary output from h5dump (-b option).
+ To use change the following 3 symbols accordingly.
+ For example, to read 6 elements of a float type from a file "out.dat", define
+
+  #define NELMTS     6
+  #define TYPE       float
+  #define FORMAT     "%f "
+
+*/
+
+#define NELMTS     2
+#define TYPE       int
+#define FORMAT     "%d "
+
+/*-------------------------------------------------------------------------
+ * Function: usage
+ *
+ * Purpose: Prints a usage message on stderr and then returns.
+ *
+ * Return: void
+ *
+ * Programmer:	Pedro Vicente Nunes
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+usage (void)
+{
+ fprintf(stderr, "\
+ usage: binread FILE_NAME\n");
+}
+
+/*-------------------------------------------------------------------------
+ * Function: main
+ *
+ * Purpose: main program.
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int
+main (int argc, const char *argv[])
+{
+ FILE  *stream;
+ int    numread;
+ TYPE   buf[NELMTS];
+ size_t i, nelmts = NELMTS;
+ char  *fname=NULL;
+
+ if (argc != 2)
+ {
+  usage();
+  exit(1);
+ }
+
+ fname = strdup(argv[1]);
+
+ if( (stream = fopen(fname, "rb" )) != NULL )
+ {
+  numread = fread( buf, sizeof( TYPE ), nelmts, stream );
+  printf( "Number of items read = %d\n", numread );
+  
+  for (i = 0; i < nelmts; i++)
+  {
+   printf(FORMAT,buf[i]);
+  }
+  printf("\n");
+
+  fclose( stream );
+ }
+ else
+  printf( "File %s could not be opened\n",fname );
+
+ free(fname);
+
+ return 0;
+}
+
diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c
index 2a6b33a..c2bc761 100644
--- a/tools/h5dump/h5dump.c
+++ b/tools/h5dump/h5dump.c
@@ -351,7 +351,7 @@ struct handler_t {
  * parameters. The long-named ones can be partially spelled. When
  * adding more, make sure that they don't clash with each other.
  */
-static const char *s_opts = "hnpeyBHirVa:c:d:f:g:k:l:t:w:xD:uX:o:s:S:A";
+static const char *s_opts = "hnpeyBHirVa:c:d:f:g:k:l:t:w:xD:uX:o:b:s:S:A";
 static struct long_options l_opts[] = {
     { "help", no_arg, 'h' },
     { "hel", no_arg, 'h' },
@@ -600,6 +600,7 @@ usage(const char *prog)
     fprintf(stdout, "     -g P, --group=P      Print the specified group and all members\n");
     fprintf(stdout, "     -l P, --soft-link=P  Print the value(s) of the specified soft link\n");
     fprintf(stdout, "     -o F, --output=F     Output raw data into file F\n");
+    fprintf(stdout, "     -b F                 Output raw data into file F in binary form (use with -d)\n");
     fprintf(stdout, "     -t P, --datatype=P   Print the specified named data type\n");
     fprintf(stdout, "     -w N, --width=N      Set the number of columns of output\n");
     fprintf(stdout, "     -x, --xml            Output in XML using Schema\n");
@@ -1952,7 +1953,7 @@ dump_subsetting_header(struct subset_t *sset, int dims)
  *-------------------------------------------------------------------------
  */
 static void
-dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int pindex)
+dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int display_ai)
 {
     h5tool_format_t   *outputformat = &dataformat;
     int         status = -1;
@@ -1967,7 +1968,7 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int pindex)
     outputformat->line_ncols = nCols;
     outputformat->do_escape=display_escape;
     /* print the matrix indices */
-    outputformat->pindex=pindex;
+    outputformat->pindex=display_ai;
     if (outputformat->pindex) {
         outputformat->idx_fmt   = "(%s): ";
         outputformat->idx_n_fmt = "%lu";
@@ -2001,7 +2002,7 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int pindex)
 
     /* Print all the values. */
     if (obj_data == DATASET_DATA) {
-        hid_t       f_type = H5Dget_type(obj_id);
+        hid_t       f_type = H5Dget_type(obj_id); 
         char        string_prefix[64];
         h5tool_format_t    string_dataformat;
 
@@ -2665,21 +2666,40 @@ static void dump_fcontents(hid_t fid)
  * Programmer:  Albert Cheng, 2000/09/30
  *
  * Modifications:
+ *  pvn June, 1, 2006. Add a switch for binary output
  *
  *-------------------------------------------------------------------------
  */
 static int
-set_output_file(const char *fname)
+set_output_file(const char *fname, int is_bin)
 {
-    FILE    *f;	/* temporary holding place for the stream pointer
-                 * so that rawdatastream is changed only when succeeded */
-
-    if ((f = fopen(fname, "w")) != NULL) {
-	rawdatastream = f;
-	return 0;
-    }
-
-    return -1;
+ FILE    *f;	/* temporary holding place for the stream pointer
+* so that rawdatastream is changed only when succeeded */
+
+ if (rawdatastream && rawdatastream != stdout) {
+  if (fclose(rawdatastream))
+   perror("closing rawdatastream");
+  else
+   rawdatastream = NULL;
+ }
+ 
+ /* binary output */
+ if (is_bin)
+ {
+  if ((f = fopen(fname, "wb")) != NULL) {
+   rawdatastream = f;
+   return 0;
+  }
+ }
+ else
+ {
+  if ((f = fopen(fname, "w")) != NULL) {
+   rawdatastream = f;
+   return 0;
+  }
+ }
+ 
+ return -1;
 }
 
 /*-------------------------------------------------------------------------
@@ -3110,6 +3130,7 @@ handle_datatypes(hid_t fid, char *type, void UNUSED * data)
  *              Tuesday, 20. February 2001
  *
  * Modifications:
+ *  pvn June, 1, 2006. Add a switch for binary output
  *
  *-------------------------------------------------------------------------
  */
@@ -3234,7 +3255,7 @@ parse_start:
             last_was_dset = FALSE;
             break;
         case 'o':
-            if (set_output_file(opt_arg) < 0){
+            if (set_output_file(opt_arg, 0) < 0){
                 /* failed to set output file */
                 usage(progname);
                 leave(EXIT_FAILURE);
@@ -3244,6 +3265,17 @@ parse_start:
             last_was_dset = FALSE;
             break;
 
+       case 'b':
+            if (set_output_file(opt_arg, 1) < 0){
+                /* failed to set output file */
+                usage(progname);
+                leave(EXIT_FAILURE);
+            }
+
+            bin_output = TRUE;
+            last_was_dset = FALSE;
+            break;
+
         /** begin XML parameters **/
         case 'x':
             /* select XML output */
diff --git a/tools/h5dump/testh5dump.sh.in b/tools/h5dump/testh5dump.sh.in
index c23651b..f390110 100644
--- a/tools/h5dump/testh5dump.sh.in
+++ b/tools/h5dump/testh5dump.sh.in
@@ -320,6 +320,9 @@ TOOLTEST tlonglinks.ddl tlonglinks.h5
 # test for vms
 TOOLTEST tvms.ddl tvms.h5
 
+# test for binary output
+TOOLTEST tbin.ddl -d integer -b out.bin test1.h5
+
 if test $nerrors -eq 0 ; then
    echo "All $DUMPER tests passed."
 fi