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-rw-r--r--MANIFEST5
-rw-r--r--tools/h5dump/CMakeLists.txt27
-rw-r--r--tools/h5dump/h5dump.c20
-rw-r--r--tools/h5jam/CMakeLists.txt35
-rw-r--r--tools/h5jam/h5jam.c440
-rw-r--r--tools/h5jam/h5unjam.c179
-rw-r--r--tools/h5jam/testfiles/h5jam-help.txt9
-rw-r--r--tools/h5jam/testfiles/h5unjam-help.txt7
-rw-r--r--tools/h5stat/CMakeLists.txt6
-rw-r--r--tools/h5stat/h5stat.c507
-rw-r--r--tools/lib/h5tools.c136
-rw-r--r--tools/lib/h5tools_str.c8
-rw-r--r--tools/testfiles/h5dump-help.txt94
13 files changed, 899 insertions, 574 deletions
diff --git a/MANIFEST b/MANIFEST
index d2a7b12..1be085e 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1173,6 +1173,7 @@
./tools/testfiles/packedbits.ddl
./tools/testfiles/file_space.h5
./tools/testfiles/file_space.ddl
+./tools/testfiles/h5dump-help.txt
./tools/testfiles/tall-1.ddl
./tools/testfiles/tall-2.ddl
./tools/testfiles/tall-3.ddl
@@ -1803,11 +1804,13 @@
# test files for jam
./tools/h5jam/testfiles/twithub.h5
+./tools/h5jam/testfiles/twithub513.h5
+./tools/h5jam/testfiles/h5jam-help.txt
+./tools/h5jam/testfiles/h5unjam-help.txt
./tools/h5jam/testfiles/u10.txt
./tools/h5jam/testfiles/tall.h5
./tools/h5jam/testfiles/u511.txt
./tools/h5jam/testfiles/u512.txt
-./tools/h5jam/testfiles/twithub513.h5
./tools/h5jam/testfiles/u513.txt
# test files for h5copy
diff --git a/tools/h5dump/CMakeLists.txt b/tools/h5dump/CMakeLists.txt
index 9da1203..a176ba0 100644
--- a/tools/h5dump/CMakeLists.txt
+++ b/tools/h5dump/CMakeLists.txt
@@ -216,6 +216,7 @@ IF (BUILD_TESTING)
tvlstr.h5.xml
)
SET (HDF5_REFERENCE_TEST_FILES
+ h5dump-help.txt
tbin1.ddl
tbin1.ddl
tbin2.ddl
@@ -475,6 +476,29 @@ IF (BUILD_TESTING)
##############################################################################
##############################################################################
+ MACRO (ADD_HELP_TEST testname resultcode)
+ # If using memchecker add tests without using scripts
+ IF (HDF5_ENABLE_USING_MEMCHECKER)
+ ADD_TEST (NAME H5DUMP-${testname} COMMAND $<TARGET_FILE:h5dump> ${ARGN})
+ ELSE (HDF5_ENABLE_USING_MEMCHECKER)
+ ADD_TEST (
+ NAME H5DUMP-${testname}
+ COMMAND "${CMAKE_COMMAND}"
+ -D "TEST_PROGRAM=$<TARGET_FILE:h5dump>"
+ -D "TEST_ARGS:STRING=${ARGN}"
+ -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
+ -D "TEST_OUTPUT=h5dump-${testname}.out"
+ -D "TEST_EXPECT=${resultcode}"
+ -D "TEST_REFERENCE=h5dump-${testname}.txt"
+ -P "${HDF5_RESOURCES_DIR}/runTest.cmake"
+ )
+ ENDIF (HDF5_ENABLE_USING_MEMCHECKER)
+ IF (NOT "${last_test}" STREQUAL "")
+ SET_TESTS_PROPERTIES (H5DUMP-${testname} PROPERTIES DEPENDS ${last_test})
+ ENDIF (NOT "${last_test}" STREQUAL "")
+ SET (last_test "H5DUMP-${testname}")
+ ENDMACRO (ADD_HELP_TEST)
+
MACRO (ADD_SKIP_H5_TEST skipresultfile skipresultcode testtype)
IF (${testtype} STREQUAL "SKIP")
IF (NOT HDF5_ENABLE_USING_MEMCHECKER)
@@ -616,6 +640,7 @@ IF (BUILD_TESTING)
NAME H5DUMP-clearall-objects
COMMAND ${CMAKE_COMMAND}
-E remove
+ h5dump-help.out
filter_fail.out
filter_fail.out.err
packedbits.out
@@ -854,6 +879,8 @@ IF (BUILD_TESTING)
ENDIF (NOT "${last_test}" STREQUAL "")
SET (last_test "H5DUMP-clearall-objects")
+ ADD_HELP_TEST(help 0 -h)
+
# test for signed/unsigned datasets
ADD_H5_TEST (packedbits 0 packedbits.h5)
# test for displaying groups
diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c
index 05ec369..cfeaaef 100644
--- a/tools/h5dump/h5dump.c
+++ b/tools/h5dump/h5dump.c
@@ -4560,7 +4560,7 @@ error:
if (hand) {
free_handler(hand, argc);
hand = NULL;
-}
+ }
h5tools_setstatus(EXIT_FAILURE);
return hand;
@@ -4630,7 +4630,6 @@ main(int argc, const char *argv[])
/* Initialize h5tools lib */
h5tools_init();
if((hand = parse_command_line(argc, argv))==NULL) {
- h5tools_setstatus(EXIT_FAILURE);
goto done;
}
@@ -4834,14 +4833,17 @@ done:
/* Free tables for objects */
table_list_free();
- if (H5Fclose(fid) < 0)
- h5tools_setstatus(EXIT_FAILURE);
-
- if(hand)
- free_handler(hand, argc);
+ if(hand)
+ free_handler(hand, argc);
- HDfree(prefix);
- HDfree(fname);
+ if(fid >=0)
+ if (H5Fclose(fid) < 0)
+ h5tools_setstatus(EXIT_FAILURE);
+
+ if(prefix)
+ HDfree(prefix);
+ if(fname)
+ HDfree(fname);
/* To Do: clean up XML table */
diff --git a/tools/h5jam/CMakeLists.txt b/tools/h5jam/CMakeLists.txt
index 979a1f3..0f63234 100644
--- a/tools/h5jam/CMakeLists.txt
+++ b/tools/h5jam/CMakeLists.txt
@@ -56,6 +56,8 @@ IF (BUILD_TESTING)
u511.txt
u512.txt
u513.txt
+ h5jam-help.txt
+ h5unjam-help.txt
)
SET (HDF5_REFERENCE_TEST_FILES
tall.h5
@@ -92,6 +94,37 @@ IF (BUILD_TESTING)
##############################################################################
##############################################################################
+ MACRO (ADD_HELP_TEST testname resultcode)
+ # If using memchecker add tests without using scripts
+ IF (HDF5_ENABLE_USING_MEMCHECKER)
+ ADD_TEST (NAME H5JAM-${testname} COMMAND $<TARGET_FILE:h5jam> ${ARGN})
+ ADD_TEST (NAME H5JAM-UNJAM-${testname} COMMAND $<TARGET_FILE:h5unjam> ${ARGN})
+ ELSE (HDF5_ENABLE_USING_MEMCHECKER)
+ ADD_TEST (
+ NAME H5JAM-${testname}
+ COMMAND "${CMAKE_COMMAND}"
+ -D "TEST_PROGRAM=$<TARGET_FILE:h5jam>"
+ -D "TEST_ARGS=${ARGN}"
+ -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
+ -D "TEST_OUTPUT=jam-${testname}.out"
+ -D "TEST_EXPECT=${resultcode}"
+ -D "TEST_REFERENCE=jam-${testname}.txt"
+ -P "${HDF5_RESOURCES_DIR}/runTest.cmake"
+ )
+ ADD_TEST (
+ NAME H5JAM-UNJAM-${testname}
+ COMMAND "${CMAKE_COMMAND}"
+ -D "TEST_PROGRAM=$<TARGET_FILE:h5unjam>"
+ -D "TEST_ARGS=${ARGN}"
+ -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
+ -D "TEST_OUTPUT=unjam-${testname}.out"
+ -D "TEST_EXPECT=${resultcode}"
+ -D "TEST_REFERENCE=unjam-${testname}.txt"
+ -P "${HDF5_RESOURCES_DIR}/runTest.cmake"
+ )
+ ENDIF (HDF5_ENABLE_USING_MEMCHECKER)
+ ENDMACRO (ADD_HELP_TEST)
+
MACRO (CLEANUP testname)
ADD_TEST (
NAME H5JAM-CLEANUP-${testname}-clear-objects
@@ -309,6 +342,8 @@ IF (BUILD_TESTING)
##############################################################################
##############################################################################
+ ADD_HELP_TEST(help 0 -h)
+
JAMTEST (tall_u10 u10.txt tall.h5 ta2.h5)
CHECKFILE (tall_u10 tall.h5 ta2.h5)
# CLEANUP (tall_u10 ta2.h5)
diff --git a/tools/h5jam/h5jam.c b/tools/h5jam/h5jam.c
index 5eaa26a..b300583 100644
--- a/tools/h5jam/h5jam.c
+++ b/tools/h5jam/h5jam.c
@@ -38,14 +38,14 @@ char *ub_file = NULL;
* 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 = "hi:u:o:c:V"; /* add more later ? */
+static const char *s_opts = "hi:u:o:c:V"; /* add more later ? */
static struct long_options l_opts[] = {
{"help", no_arg, 'h'},
{"hel", no_arg, 'h'},
- {"i", require_arg, 'i'}, /* input file */
- {"u", require_arg, 'u'}, /* user block file */
- {"o", require_arg, 'o'}, /* output file */
- {"clobber", no_arg, 'c'}, /* clobber existing UB */
+ {"i", require_arg, 'i'}, /* input file */
+ {"u", require_arg, 'u'}, /* user block file */
+ {"o", require_arg, 'o'}, /* output file */
+ {"clobber", no_arg, 'c'}, /* clobber existing UB */
{"clobbe", no_arg, 'c'},
{"clobb", no_arg, 'c'},
{"clob", no_arg, 'c'},
@@ -72,11 +72,11 @@ usage (const char *prog)
{
fflush (stdout);
fprintf (stdout,
- "usage: %s -u user_block_file -i h5_file [-o ofile | --clobber] \n",
- prog);
+ "usage: %s -u user_block_file -i h5_file [-o ofile | --clobber] \n",
+ prog);
fprintf (stdout, " Add 'user_block_file' to front of \n");
fprintf (stdout,
- " 'h5_file', pad so 'h5_file' starts on proper\n");
+ " 'h5_file', pad so 'h5_file' starts on proper\n");
fprintf (stdout, " byte.\n");
fprintf (stdout, "\n");
fprintf (stdout, " %s -h \n", prog);
@@ -86,6 +86,31 @@ usage (const char *prog)
}
+
+/*-------------------------------------------------------------------------
+ * Function: leave
+ *
+ * Purpose: Shutdown and call exit()
+ *
+ * Return: Does not return
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+leave(int ret)
+{
+ if (ub_file)
+ HDfree (ub_file);
+ if (input_file)
+ HDfree (input_file);
+ if (output_file)
+ HDfree (output_file);
+
+ h5tools_close();
+
+ exit(ret);
+}
+
/*-------------------------------------------------------------------------
* Function: parse_command_line
*
@@ -111,30 +136,30 @@ parse_command_line (int argc, const char *argv[])
while ((opt = get_option (argc, argv, s_opts, l_opts)) != EOF)
{
switch ((char) opt)
- {
- case 'o':
- output_file = HDstrdup (opt_arg);
- break;
- case 'i':
- input_file = HDstrdup (opt_arg);
- break;
- case 'u':
- ub_file = HDstrdup (opt_arg);
- break;
- case 'c':
- do_clobber = TRUE;
- break;
- case 'h':
- usage (h5tools_getprogname());
- exit (EXIT_SUCCESS);
- case 'V':
- print_version (h5tools_getprogname());
- exit (EXIT_SUCCESS);
- case '?':
- default:
- usage (h5tools_getprogname());
- exit (EXIT_FAILURE);
- }
+ {
+ case 'o':
+ output_file = HDstrdup (opt_arg);
+ break;
+ case 'i':
+ input_file = HDstrdup (opt_arg);
+ break;
+ case 'u':
+ ub_file = HDstrdup (opt_arg);
+ break;
+ case 'c':
+ do_clobber = TRUE;
+ break;
+ case 'h':
+ usage (h5tools_getprogname());
+ leave (EXIT_SUCCESS);
+ case 'V':
+ print_version (h5tools_getprogname());
+ leave (EXIT_SUCCESS);
+ case '?':
+ default:
+ usage (h5tools_getprogname());
+ leave (EXIT_FAILURE);
+ }
}
}
@@ -155,204 +180,197 @@ parse_command_line (int argc, const char *argv[])
int
main (int argc, const char *argv[])
{
- int ufid;
- int h5fid;
- int ofid;
- void *edata;
- H5E_auto2_t func;
- hid_t ifile;
- hid_t plist;
- herr_t status;
- htri_t testval;
- hsize_t usize;
- hsize_t h5fsize;
- hsize_t startub;
- hsize_t where;
- hsize_t newubsize;
- off_t fsize;
- h5_stat_t sbuf;
- h5_stat_t sbuf2;
- int res;
-
- h5tools_setprogname(PROGRAMNAME);
- h5tools_setstatus(EXIT_SUCCESS);
-
- /* Disable error reporting */
- H5Eget_auto2(H5E_DEFAULT, &func, &edata);
- H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
-
- parse_command_line (argc, argv);
-
- if (ub_file == NULL)
- {
- /* no user block */
- error_msg("no user block file name\n");
- usage (h5tools_getprogname());
- exit (EXIT_FAILURE);
+ int ufid = -1;
+ int h5fid = -1;
+ int ofid = -1;
+ void *edata;
+ H5E_auto2_t func;
+ hid_t ifile = -1;
+ hid_t plist = -1;
+ herr_t status;
+ htri_t testval;
+ hsize_t usize;
+ hsize_t h5fsize;
+ hsize_t startub;
+ hsize_t where;
+ hsize_t newubsize;
+ off_t fsize;
+ h5_stat_t sbuf;
+ h5_stat_t sbuf2;
+ int res;
+
+ h5tools_setprogname(PROGRAMNAME);
+ h5tools_setstatus(EXIT_SUCCESS);
+
+ /* Disable error reporting */
+ H5Eget_auto2(H5E_DEFAULT, &func, &edata);
+ H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+
+ parse_command_line (argc, argv);
+
+ if (ub_file == NULL) {
+ /* no user block */
+ error_msg("no user block file name\n");
+ usage (h5tools_getprogname());
+ leave (EXIT_FAILURE);
}
- if (input_file == NULL)
- {
- /* no user block */
- error_msg("no HDF5 file\n");
- usage (h5tools_getprogname());
- exit (EXIT_FAILURE);
+ if (input_file == NULL) {
+ /* no user block */
+ error_msg("no HDF5 file\n");
+ usage (h5tools_getprogname());
+ leave (EXIT_FAILURE);
}
- testval = H5Fis_hdf5 (input_file);
+ testval = H5Fis_hdf5 (input_file);
- if (testval <= 0)
- {
- error_msg("Input HDF5 file is not HDF \"%s\"\n", input_file);
- exit (EXIT_FAILURE);
+ if (testval <= 0) {
+ error_msg("Input HDF5 file is not HDF \"%s\"\n", input_file);
+ leave (EXIT_FAILURE);
}
- ifile = H5Fopen (input_file, H5F_ACC_RDONLY, H5P_DEFAULT);
+ ifile = H5Fopen (input_file, H5F_ACC_RDONLY, H5P_DEFAULT);
- if (ifile < 0)
- {
- error_msg("Can't open input HDF5 file \"%s\"\n", input_file);
- exit (EXIT_FAILURE);
+ if (ifile < 0) {
+ error_msg("Can't open input HDF5 file \"%s\"\n", input_file);
+ leave (EXIT_FAILURE);
}
- plist = H5Fget_create_plist (ifile);
- if (plist < 0)
- {
- error_msg("Can't get file creation plist for file \"%s\"\n",
- input_file);
- exit (EXIT_FAILURE);
+ plist = H5Fget_create_plist (ifile);
+ if (plist < 0) {
+ error_msg("Can't get file creation plist for file \"%s\"\n", input_file);
+ H5Fclose(ifile);
+ leave (EXIT_FAILURE);
}
- status = H5Pget_userblock (plist, &usize);
- if (status < 0)
- {
- error_msg("Can't get user block for file \"%s\"\n",
- input_file);
- exit (EXIT_FAILURE);
+ status = H5Pget_userblock (plist, &usize);
+ if (status < 0) {
+ error_msg("Can't get user block for file \"%s\"\n", input_file);
+ H5Pclose(plist);
+ H5Fclose(ifile);
+ leave (EXIT_FAILURE);
}
- H5Pclose(plist);
- H5Fclose(ifile);
+ H5Pclose(plist);
+ H5Fclose(ifile);
- ufid = HDopen(ub_file, O_RDONLY, 0);
- if(ufid < 0) {
- error_msg("unable to open user block file \"%s\"\n",
- ub_file);
- exit (EXIT_FAILURE);
+ ufid = HDopen(ub_file, O_RDONLY, 0);
+ if(ufid < 0) {
+ error_msg("unable to open user block file \"%s\"\n", ub_file);
+ leave (EXIT_FAILURE);
}
- res = HDfstat(ufid, &sbuf);
- if(res < 0) {
- error_msg("Can't stat file \"%s\"\n", ub_file);
- exit (EXIT_FAILURE);
+ res = HDfstat(ufid, &sbuf);
+ if(res < 0) {
+ error_msg("Can't stat file \"%s\"\n", ub_file);
+ HDclose (ufid);
+ leave (EXIT_FAILURE);
}
- fsize = sbuf.st_size;
+ fsize = sbuf.st_size;
- h5fid = HDopen(input_file, O_RDONLY, 0);
- if(h5fid < 0) {
- error_msg("unable to open HDF5 file for read \"%s\"\n",
- input_file);
- exit (EXIT_FAILURE);
+ h5fid = HDopen(input_file, O_RDONLY, 0);
+ if(h5fid < 0) {
+ error_msg("unable to open HDF5 file for read \"%s\"\n", input_file);
+ HDclose (ufid);
+ leave (EXIT_FAILURE);
}
- res = HDfstat(h5fid, &sbuf2);
- if(res < 0) {
- error_msg("Can't stat file \"%s\"\n", input_file);
- exit (EXIT_FAILURE);
+ res = HDfstat(h5fid, &sbuf2);
+ if(res < 0) {
+ error_msg("Can't stat file \"%s\"\n", input_file);
+ HDclose (h5fid);
+ HDclose (ufid);
+ leave (EXIT_FAILURE);
}
- h5fsize = sbuf2.st_size;
+ h5fsize = sbuf2.st_size;
- if (output_file == NULL)
- {
- ofid = HDopen (input_file, O_WRONLY, 0);
-
- if (ofid < 0)
- {
- error_msg("unable to open output file \"%s\"\n",
- output_file);
- exit (EXIT_FAILURE);
- }
+ if (output_file == NULL) {
+ ofid = HDopen (input_file, O_WRONLY, 0);
+
+ if (ofid < 0) {
+ error_msg("unable to open output file \"%s\"\n", output_file);
+ HDclose (h5fid);
+ HDclose (ufid);
+ leave (EXIT_FAILURE);
+ }
}
- else
- {
- ofid = HDopen (output_file, O_WRONLY | O_CREAT | O_TRUNC, 0644);
-
- if (ofid < 0)
- {
- error_msg("unable to create output file \"%s\"\n",
- output_file);
- exit (EXIT_FAILURE);
- }
+ else {
+ ofid = HDopen (output_file, O_WRONLY | O_CREAT | O_TRUNC, 0644);
+
+ if (ofid < 0) {
+ error_msg("unable to create output file \"%s\"\n", output_file);
+ HDclose (h5fid);
+ HDclose (ufid);
+ leave (EXIT_FAILURE);
+ }
}
- newubsize = compute_user_block_size ((hsize_t) fsize);
-
- startub = usize;
-
- if (usize > 0)
- {
- if (do_clobber == TRUE)
- {
- /* where is max of the current size or the new UB */
- if (usize > newubsize)
- {
- newubsize = usize;
- }
- startub = 0; /*blast the old */
- }
- else
- {
- /* add new ub to current ublock, pad to new offset */
- newubsize += usize;
- newubsize = compute_user_block_size ((hsize_t) newubsize);
- }
+ newubsize = compute_user_block_size ((hsize_t) fsize);
+
+ startub = usize;
+
+ if (usize > 0) {
+ if (do_clobber == TRUE) {
+ /* where is max of the current size or the new UB */
+ if (usize > newubsize) {
+ newubsize = usize;
+ }
+ startub = 0; /*blast the old */
+ }
+ else {
+ /* add new ub to current ublock, pad to new offset */
+ newubsize += usize;
+ newubsize = compute_user_block_size ((hsize_t) newubsize);
+ }
}
- /* copy the HDF5 from starting at usize to starting at newubsize:
- * makes room at 'from' for new ub */
- /* if no current ub, usize is 0 */
- copy_some_to_file (h5fid, ofid, usize, newubsize,
- (ssize_t) (h5fsize - usize));
+ /* copy the HDF5 from starting at usize to starting at newubsize:
+ * makes room at 'from' for new ub */
+ /* if no current ub, usize is 0 */
+ copy_some_to_file (h5fid, ofid, usize, newubsize, (ssize_t) (h5fsize - usize));
- /* copy the old ub to the beginning of the new file */
- if (!do_clobber)
- {
- where =
- copy_some_to_file (h5fid, ofid, (hsize_t) 0, (hsize_t) 0,
- (ssize_t) usize);
+ /* copy the old ub to the beginning of the new file */
+ if (!do_clobber) {
+ where = copy_some_to_file (h5fid, ofid, (hsize_t) 0, (hsize_t) 0, (ssize_t) usize);
}
- /* copy the new ub to the end of the ub */
- where = copy_some_to_file (ufid, ofid, (hsize_t) 0, startub, (ssize_t) - 1);
-
- /* pad the ub */
- where = write_pad (ofid, where);
+ /* copy the new ub to the end of the ub */
+ where = copy_some_to_file (ufid, ofid, (hsize_t) 0, startub, (ssize_t) - 1);
+ /* pad the ub */
+ where = write_pad (ofid, where);
- HDclose (ufid);
- HDclose (h5fid);
- HDclose (ofid);
+ if (ub_file)
+ HDfree (ub_file);
+ if (input_file)
+ HDfree (input_file);
+ if (output_file)
+ HDfree (output_file);
+
+ if (ufid >= 0) HDclose (ufid);
+ if (h5fid >= 0) HDclose (h5fid);
+ if (ofid >= 0) HDclose (ofid);
- return h5tools_getstatus();
+ return h5tools_getstatus();
}
/*-------------------------------------------------------------------------
* Function: copy_some_to_file
*
* Purpose: Copy part of the input file to output.
- * infid: fd of file to read
- * outfid: fd of file to write
- * startin: offset of where to read from infid
- * startout: offset of where to write to outfid
- * limit: bytes to read/write
+ * infid: fd of file to read
+ * outfid: fd of file to write
+ * startin: offset of where to read from infid
+ * startout: offset of where to write to outfid
+ * limit: bytes to read/write
*
- * If limit is < 0, the entire input file is copied.
+ * If limit is < 0, the entire input file is copied.
*
- * Note: this routine can be used to copy within
- * the same file, i.e., infid and outfid can be the
- * same file.
+ * Note: this routine can be used to copy within
+ * the same file, i.e., infid and outfid can be the
+ * same file.
*
* Return: Success: last byte written in the output.
* Failure: Exits program with EXIT_FAILURE value.
@@ -365,7 +383,7 @@ main (int argc, const char *argv[])
*/
hsize_t
copy_some_to_file (int infid, int outfid, hsize_t startin, hsize_t startout,
- ssize_t limit)
+ ssize_t limit)
{
char buf[1024];
h5_stat_t sbuf;
@@ -390,9 +408,9 @@ copy_some_to_file (int infid, int outfid, hsize_t startin, hsize_t startout,
if(limit < 0) {
res = HDfstat(infid, &sbuf);
if(res < 0) {
- error_msg("Can't stat file \n");
- exit (EXIT_FAILURE);
- }
+ error_msg("Can't stat file \n");
+ exit (EXIT_FAILURE);
+ }
howmuch = sbuf.st_size;
}
@@ -424,19 +442,19 @@ copy_some_to_file (int infid, int outfid, hsize_t startin, hsize_t startout,
HDlseek (infid, (off_t) from, SEEK_SET);
if (howmuch > 512)
- {
- nchars = HDread (infid, buf, (unsigned) 512);
- }
+ {
+ nchars = HDread (infid, buf, (unsigned) 512);
+ }
else
- {
- nchars = HDread (infid, buf, (unsigned)howmuch);
- }
+ {
+ nchars = HDread (infid, buf, (unsigned)howmuch);
+ }
if (nchars <= 0)
- {
- printf ("huh? \n");
- exit (EXIT_FAILURE);
- }
+ {
+ printf ("huh? \n");
+ exit (EXIT_FAILURE);
+ }
/*ncw = */ HDwrite (outfid, buf, (unsigned) nchars);
/* assert (ncw == nchars) */
@@ -444,15 +462,15 @@ copy_some_to_file (int infid, int outfid, hsize_t startin, hsize_t startout,
tot += nchars;
howmuch -= nchars;
if (howmuch > 512)
- {
- to -= nchars;
- from -= nchars;
- }
+ {
+ to -= nchars;
+ from -= nchars;
+ }
else
- {
- to -= howmuch;
- from -= howmuch;
- }
+ {
+ to -= howmuch;
+ from -= howmuch;
+ }
}
/* assert howmuch == 0 */
@@ -467,10 +485,10 @@ copy_some_to_file (int infid, int outfid, hsize_t startin, hsize_t startout,
*
* Purpose: Find the offset of the HDF5 header after the user block:
* align at 0, 512, 1024, etc.
- * ublock_size: the size of the user block (bytes).
+ * ublock_size: the size of the user block (bytes).
*
* Return: Success: the location of the header == the size of the
- * padded user block.
+ * padded user block.
* Failure: none
*
* Return: Success: last byte written in the output.
@@ -520,6 +538,6 @@ write_pad(int ofile, hsize_t where)
for(i = 0; i < psize; i++)
HDwrite (ofile, buf, 1);
- return(where + psize); /* the new size of the file. */
+ return(where + psize); /* the new size of the file. */
}
diff --git a/tools/h5jam/h5unjam.c b/tools/h5jam/h5unjam.c
index bfebc6c..d3b36a9 100644
--- a/tools/h5jam/h5unjam.c
+++ b/tools/h5jam/h5unjam.c
@@ -42,10 +42,10 @@ static const char *s_opts = "hu:i:o:d:V";
static struct long_options l_opts[] = {
{ "help", no_arg, 'h' },
{ "hel", no_arg, 'h' },
- {"i", require_arg, 'i'}, /* input file */
- {"u", require_arg, 'u'}, /* user block file */
- {"o", require_arg, 'o'}, /* output file */
- {"delete", no_arg, 'd'}, /* delete ub */
+ {"i", require_arg, 'i'}, /* input file */
+ {"u", require_arg, 'u'}, /* user block file */
+ {"o", require_arg, 'o'}, /* output file */
+ {"delete", no_arg, 'd'}, /* delete ub */
{"delet", no_arg, 'd'},
{"dele", no_arg, 'd'},
{"del", no_arg, 'd'},
@@ -81,6 +81,30 @@ usage(const char *prog)
}
/*-------------------------------------------------------------------------
+ * Function: leave
+ *
+ * Purpose: Shutdown and call exit()
+ *
+ * Return: Does not return
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+leave(int ret)
+{
+ if (ub_file)
+ HDfree (ub_file);
+ if (input_file)
+ HDfree (input_file);
+ if (output_file)
+ HDfree (output_file);
+
+ h5tools_close();
+
+ exit(ret);
+}
+
+/*-------------------------------------------------------------------------
* Function: parse_command_line
*
* Purpose: Parse the command line for the h5dumper.
@@ -99,33 +123,33 @@ usage(const char *prog)
static void
parse_command_line(int argc, const char *argv[])
{
- int opt = FALSE;
+ int opt = FALSE;
/* parse command line options */
while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
- switch ((char)opt) {
- case 'o':
- output_file = HDstrdup (opt_arg);
- break;
- case 'i':
- input_file = HDstrdup (opt_arg);
- break;
- case 'u':
- ub_file = HDstrdup (opt_arg);
- break;
- case 'd':
- do_delete = TRUE;
- break;
- case 'h':
- usage(h5tools_getprogname());
- exit(EXIT_SUCCESS);
- case 'V':
- print_version (h5tools_getprogname());
- exit (EXIT_SUCCESS);
- case '?':
- default:
- usage(h5tools_getprogname());
- exit(EXIT_FAILURE);
+ switch ((char) opt) {
+ case 'o':
+ output_file = HDstrdup (opt_arg);
+ break;
+ case 'i':
+ input_file = HDstrdup (opt_arg);
+ break;
+ case 'u':
+ ub_file = HDstrdup (opt_arg);
+ break;
+ case 'd':
+ do_delete = TRUE;
+ break;
+ case 'h':
+ usage(h5tools_getprogname());
+ leave(EXIT_SUCCESS);
+ case 'V':
+ print_version(h5tools_getprogname());
+ leave(EXIT_SUCCESS);
+ case '?':
+ default:
+ usage(h5tools_getprogname());
+ leave(EXIT_FAILURE);
}
}
@@ -156,19 +180,19 @@ parse_command_line(int argc, const char *argv[])
int
main(int argc, const char *argv[])
{
- int ifid;
- int ufid;
- int h5fid;
+ int ifid = -1;
+ int ufid = -1;
+ int h5fid = -1;
void *edata;
- H5E_auto2_t func;
- hid_t ifile;
- off_t fsize;
- hsize_t usize;
- htri_t testval;
- herr_t status;
- hid_t plist;
- int res;
- h5_stat_t sbuf;
+ H5E_auto2_t func;
+ hid_t ifile = -1;
+ hid_t plist = -1;
+ off_t fsize;
+ hsize_t usize;
+ htri_t testval;
+ herr_t status;
+ int res;
+ h5_stat_t sbuf;
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
@@ -183,63 +207,75 @@ main(int argc, const char *argv[])
if (testval <= 0) {
error_msg("Input HDF5 file is not HDF \"%s\"\n", input_file);
- exit(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
ifile = H5Fopen(input_file, H5F_ACC_RDONLY , H5P_DEFAULT);
if (ifile < 0) {
error_msg("Can't open input HDF5 file \"%s\"\n", input_file);
- exit(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
plist = H5Fget_create_plist(ifile);
if (plist < 0) {
error_msg("Can't get file creation plist for file \"%s\"\n", input_file);
- exit(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
- status = H5Pget_userblock(plist, & usize );
+ status = H5Pget_userblock(plist, & usize);
if (status < 0) {
error_msg("Can't get user block for file \"%s\"\n", input_file);
- exit(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
+ H5Pclose(plist);
+ H5Fclose(ifile);
+
if (usize == 0) {
- /* no user block to remove: message? */
+ /* no user block to remove: message? */
error_msg("\"%s\" has no user block: no change to file\n", input_file);
- exit(EXIT_SUCCESS);
-
+ h5tools_setstatus(EXIT_SUCCESS);
+ goto done;
}
ifid = HDopen(input_file,O_RDONLY,0);
if(ifid < 0) {
error_msg("unable to open input HDF5 file \"%s\"\n", input_file);
- exit(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
res = HDfstat(ifid, &sbuf);
if(res < 0) {
error_msg("Can't stat file \"%s\"\n", input_file);
- exit(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
fsize = sbuf.st_size;
if (do_delete && (ub_file != NULL)) {
- error_msg("??\"%s\"\n", ub_file);
- exit(EXIT_FAILURE);
+ error_msg("??\"%s\"\n", ub_file);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
if (ub_file == NULL) {
- /* write to sdtout */
- ufid = HDdup(1);
- } else {
+ /* write to sdtout */
+ ufid = HDdup(1);
+ }
+ else {
ufid = HDopen(ub_file,O_WRONLY|O_CREAT|O_TRUNC, 0644 );
if (ufid < 0) {
error_msg("unable to open user block file for output\"%s\"\n", ub_file);
- exit(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
}
@@ -248,23 +284,27 @@ main(int argc, const char *argv[])
if (h5fid < 0) {
error_msg("unable to open output HDF5 file \"%s\"\n", input_file);
- exit(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
- } else {
+ }
+ else {
h5fid = HDopen(output_file,O_WRONLY|O_CREAT|O_TRUNC, 0644 );
if (h5fid < 0) {
error_msg("unable to open output HDF5 file \"%s\"\n", output_file);
- exit(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
}
/* copy from 0 to 'usize - 1' into ufid */
if (!do_delete) {
- if(copy_to_file(ifid, ufid, 0, (ssize_t) usize) < 0) {
+ if(copy_to_file(ifid, ufid, 0, (ssize_t) usize) < 0) {
error_msg("unable to copy user block to output file \"%s\"\n", ub_file);
- exit(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
}
@@ -273,13 +313,22 @@ main(int argc, const char *argv[])
*/
if(copy_to_file(ifid, h5fid, (ssize_t) usize, (ssize_t)(fsize - (ssize_t)usize)) < 0) {
error_msg("unable to copy hdf5 data to output file \"%s\"\n", output_file);
- exit(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
+done:
+ if (ub_file) {
+ HDfree (ub_file);
+ if (ufid >= 0) HDclose(ufid);
+ }
+ if (input_file)
+ HDfree (input_file);
+ if (output_file)
+ HDfree (output_file);
- HDclose(ufid);
- HDclose(h5fid);
- HDclose(ifid);
+ if (h5fid >= 0) HDclose(h5fid);
+ if (ifid >= 0) HDclose(ifid);
return h5tools_getstatus();
}
diff --git a/tools/h5jam/testfiles/h5jam-help.txt b/tools/h5jam/testfiles/h5jam-help.txt
new file mode 100644
index 0000000..f5d1f19
--- /dev/null
+++ b/tools/h5jam/testfiles/h5jam-help.txt
@@ -0,0 +1,9 @@
+usage: h5jam -u user_block_file -i h5_file [-o ofile | --clobber]
+ Add 'user_block_file' to front of
+ 'h5_file', pad so 'h5_file' starts on proper
+ byte.
+
+ h5jam -h
+ Print a usage message and exit
+ h5jam -V
+ Print HDF5 library version and exit
diff --git a/tools/h5jam/testfiles/h5unjam-help.txt b/tools/h5jam/testfiles/h5unjam-help.txt
new file mode 100644
index 0000000..3eb73c5
--- /dev/null
+++ b/tools/h5jam/testfiles/h5unjam-help.txt
@@ -0,0 +1,7 @@
+usage: h5unjam -i h5_file -o user_block_file_out -o h5_file_out [-d | --delete]
+ Extract user block from 'h5_file' into 'user_block_file'
+ and HDF5 file into 'h5_file_out'
+ h5unjam -h
+ Print a usage message and exit
+ h5unjam -V
+ Print HDF5 library version and exit
diff --git a/tools/h5stat/CMakeLists.txt b/tools/h5stat/CMakeLists.txt
index 86ad3ad..89f2ba0 100644
--- a/tools/h5stat/CMakeLists.txt
+++ b/tools/h5stat/CMakeLists.txt
@@ -155,12 +155,6 @@ IF (BUILD_TESTING)
ENDIF (NOT "${last_test}" STREQUAL "")
SET (last_test "H5STAT-clearall-objects")
- # If using memchecker add tests without using scripts
- IF (HDF5_ENABLE_USING_MEMCHECKER)
- ADD_TEST (NAME H5STAT-help COMMAND h5stat -h)
- ADD_TEST (NAME H5STAT-filters COMMAND h5stat h5stat_filters.h5)
- ENDIF (HDF5_ENABLE_USING_MEMCHECKER)
-
# Test for help flag
ADD_H5_TEST (h5stat_help1 0 -h)
ADD_H5_TEST (h5stat_help2 0 --help)
diff --git a/tools/h5stat/h5stat.c b/tools/h5stat/h5stat.c
index fd21266..b7026cc 100644
--- a/tools/h5stat/h5stat.c
+++ b/tools/h5stat/h5stat.c
@@ -15,7 +15,7 @@
#include <stdlib.h>
#include <string.h>
-#include "H5private.h" /* Generic Functions */
+#include "H5private.h" /* Generic Functions */
#include "h5tools.h"
#include "h5tools_utils.h"
#include "h5tools_ref.h"
@@ -27,7 +27,7 @@
/* Parameters to control statistics gathered */
#define SIZE_SMALL_GROUPS 10
-#define SIZE_SMALL_ATTRS 10
+#define SIZE_SMALL_ATTRS 10
#define SIZE_SMALL_DSETS 10
#define SIZE_SMALL_SECTS 10
@@ -60,7 +60,7 @@ typedef struct ohdr_info_t {
/* Info to pass to the iteration functions */
typedef struct iter_t {
hid_t fid; /* File ID */
- hsize_t filesize; /* Size of the file */
+ hsize_t filesize; /* Size of the file */
unsigned long uniq_groups; /* Number of unique groups */
unsigned long uniq_dsets; /* Number of unique datasets */
unsigned long uniq_dtypes; /* Number of unique named datatypes */
@@ -74,7 +74,7 @@ typedef struct iter_t {
unsigned long *group_bins; /* Pointer to array of bins for group counts */
ohdr_info_t group_ohdr_info; /* Object header information for groups */
- hsize_t max_attrs; /* Maximum attributes from a group */
+ hsize_t max_attrs; /* Maximum attributes from a group */
unsigned long num_small_attrs[SIZE_SMALL_ATTRS]; /* Size of small attributes tracked */
unsigned attr_nbins; /* Number of bins for attribute counts */
unsigned long *attr_bins; /* Pointer to array of bins for attribute counts */
@@ -99,14 +99,14 @@ typedef struct iter_t {
hsize_t attrs_heap_storage_size; /* fractal heap size for attributes (1.8) */
hsize_t SM_hdr_storage_size; /* header size for SOHM table (1.8) */
hsize_t SM_index_storage_size; /* index (btree & list) size for SOHM table (1.8) */
- hsize_t SM_heap_storage_size; /* fractal heap size for SOHM table (1.8) */
- hsize_t super_size; /* superblock size */
- hsize_t super_ext_size; /* superblock extension size */
- hsize_t ublk_size; /* user block size (if exists) */
- H5F_file_space_type_t fs_strategy; /* File space management strategy */
- hsize_t fs_threshold; /* Free-space section threshold */
- hsize_t free_space; /* amount of freespace in the file */
- hsize_t free_hdr; /* size of free space manager metadata in the file */
+ hsize_t SM_heap_storage_size; /* fractal heap size for SOHM table (1.8) */
+ hsize_t super_size; /* superblock size */
+ hsize_t super_ext_size; /* superblock extension size */
+ hsize_t ublk_size; /* user block size (if exists) */
+ H5F_file_space_type_t fs_strategy; /* File space management strategy */
+ hsize_t fs_threshold; /* Free-space section threshold */
+ hsize_t free_space; /* amount of freespace in the file */
+ hsize_t free_hdr; /* size of free space manager metadata in the file */
unsigned long num_small_sects[SIZE_SMALL_SECTS]; /* Size of small free-space sections */
unsigned sect_nbins; /* Number of bins for free-space section sizes */
unsigned long *sect_bins; /* Pointer to array of bins for free-space section sizes */
@@ -120,19 +120,19 @@ typedef struct iter_t {
static int display_all = TRUE;
/* Enable the printing of selected statistics */
-static int display_file = FALSE; /* display file information */
-static int display_group = FALSE; /* display groups information */
-static int display_dset = FALSE; /* display datasets information */
+static int display_file = FALSE; /* display file information */
+static int display_group = FALSE; /* display groups information */
+static int display_dset = FALSE; /* display datasets information */
static int display_dset_dtype_meta = FALSE; /* display datasets' datatype information */
-static int display_attr = FALSE; /* display attributes information */
+static int display_attr = FALSE; /* display attributes information */
static int display_free_sections = FALSE; /* display free space information */
-static int display_summary = FALSE; /* display summary of file space information */
+static int display_summary = FALSE; /* display summary of file space information */
static int display_file_metadata = FALSE; /* display file space info for file's metadata */
static int display_group_metadata = FALSE; /* display file space info for groups' metadata */
static int display_dset_metadata = FALSE; /* display file space info for datasets' metadata */
-static int display_object = FALSE; /* not implemented yet */
+static int display_object = FALSE; /* not implemented yet */
/* a structure for handling the order command-line parameters come in */
struct handler_t {
@@ -303,7 +303,7 @@ ceil_log10(unsigned long x)
static herr_t
attribute_stats(iter_t *iter, const H5O_info_t *oi)
{
- unsigned bin; /* "bin" the number of objects falls in */
+ unsigned bin; /* "bin" the number of objects falls in */
/* Update dataset & attribute metadata info */
iter->attrs_btree_storage_size += oi->meta_size.attr.index_size;
@@ -318,12 +318,12 @@ attribute_stats(iter_t *iter, const H5O_info_t *oi)
/* Add attribute count to proper bin */
bin = ceil_log10((unsigned long)oi->num_attrs);
if((bin + 1) > iter->attr_nbins) {
- iter->attr_bins = (unsigned long *)realloc(iter->attr_bins, (bin + 1) * sizeof(unsigned long));
+ iter->attr_bins = (unsigned long *)realloc(iter->attr_bins, (bin + 1) * sizeof(unsigned long));
assert(iter->attr_bins);
- /* Initialize counts for intermediate bins */
+ /* Initialize counts for intermediate bins */
while(iter->attr_nbins < bin)
- iter->attr_bins[iter->attr_nbins++] = 0;
+ iter->attr_bins[iter->attr_nbins++] = 0;
iter->attr_nbins++;
/* Initialize count for new bin */
@@ -351,23 +351,23 @@ attribute_stats(iter_t *iter, const H5O_info_t *oi)
* Modifications: Refactored code from the walk_function
* EIP, Wednesday, August 16, 2006
*
- * Vailin Choi 12 July 2007
- * 1. Gathered storage info for btree and heap
- * (groups and attributes)
- * 2. Gathered info for attributes
+ * Vailin Choi 12 July 2007
+ * 1. Gathered storage info for btree and heap
+ * (groups and attributes)
+ * 2. Gathered info for attributes
*
- * Vailin Choi 14 July 2007
- * Cast "num_objs" and "num_attrs" to size_t
- * Due to the -Mbounds problem for the pgi-32 bit compiler on indexing
+ * Vailin Choi 14 July 2007
+ * Cast "num_objs" and "num_attrs" to size_t
+ * Due to the -Mbounds problem for the pgi-32 bit compiler on indexing
*
*-------------------------------------------------------------------------
*/
static herr_t
group_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
{
- H5G_info_t ginfo; /* Group information */
- unsigned bin; /* "bin" the number of objects falls in */
- herr_t ret;
+ H5G_info_t ginfo; /* Group information */
+ unsigned bin; /* "bin" the number of objects falls in */
+ herr_t ret;
/* Gather statistics about this type of object */
iter->uniq_groups++;
@@ -393,7 +393,7 @@ group_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
iter->group_bins = (unsigned long *)realloc(iter->group_bins, (bin + 1) * sizeof(unsigned long));
assert(iter->group_bins);
- /* Initialize counts for intermediate bins */
+ /* Initialize counts for intermediate bins */
while(iter->group_nbins < bin)
iter->group_bins[iter->group_nbins++] = 0;
iter->group_nbins++;
@@ -433,22 +433,22 @@ group_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
static herr_t
dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
{
- unsigned bin; /* "bin" the number of objects falls in */
- hid_t did; /* Dataset ID */
- hid_t sid; /* Dataspace ID */
- hid_t tid; /* Datatype ID */
- hid_t dcpl; /* Dataset creation property list ID */
- hsize_t dims[H5S_MAX_RANK];/* Dimensions of dataset */
- H5D_layout_t lout; /* Layout of dataset */
- unsigned type_found; /* Whether the dataset's datatype was */
- /* already found */
- int ndims; /* Number of dimensions of dataset */
- hsize_t storage; /* Size of dataset storage */
- unsigned u; /* Local index variable */
- int num_ext; /* Number of external files for a dataset */
- int nfltr; /* Number of filters for a dataset */
- H5Z_filter_t fltr; /* Filter identifier */
- herr_t ret;
+ unsigned bin; /* "bin" the number of objects falls in */
+ hid_t did; /* Dataset ID */
+ hid_t sid; /* Dataspace ID */
+ hid_t tid; /* Datatype ID */
+ hid_t dcpl; /* Dataset creation property list ID */
+ hsize_t dims[H5S_MAX_RANK];/* Dimensions of dataset */
+ H5D_layout_t lout; /* Layout of dataset */
+ unsigned type_found; /* Whether the dataset's datatype was */
+ /* already found */
+ int ndims; /* Number of dimensions of dataset */
+ hsize_t storage; /* Size of dataset storage */
+ unsigned u; /* Local index variable */
+ int num_ext; /* Number of external files for a dataset */
+ int nfltr; /* Number of filters for a dataset */
+ H5Z_filter_t fltr; /* Filter identifier */
+ herr_t ret;
/* Gather statistics about this type of object */
iter->uniq_dsets++;
@@ -481,7 +481,7 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
/* Object header's total size for H5D_COMPACT layout includes raw data size */
/* "storage" also includes H5D_COMPACT raw data size */
if(lout == H5D_COMPACT)
- iter->dset_ohdr_info.total_size -= storage;
+ iter->dset_ohdr_info.total_size -= storage;
/* Track the layout type for dataset */
(iter->dset_layouts[lout])++;
@@ -495,7 +495,7 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
iter->nexternal += (unsigned long)num_ext;
iter->dset_external_storage_size += (unsigned long)storage;
} else
- iter->dset_storage_size += storage;
+ iter->dset_storage_size += storage;
/* Gather dataspace statistics */
sid = H5Dget_space(did);
@@ -640,7 +640,7 @@ datatype_stats(iter_t *iter, const H5O_info_t *oi)
* Purpose: Gather statistics about an object
*
* Return: Success: 0
- * Failure: -1
+ * Failure: -1
*
* Programmer: Quincey Koziol
* Tuesday, November 6, 2007
@@ -669,7 +669,7 @@ obj_stats(const char *path, const H5O_info_t *oi, const char *already_visited,
break;
case H5O_TYPE_NAMED_DATATYPE:
- datatype_stats(iter, oi);
+ datatype_stats(iter, oi);
break;
default:
@@ -724,7 +724,7 @@ lnk_stats(const char UNUSED *path, const H5L_info_t *li, void *_iter)
* Purpose: Gather statistics for free space sections in the file
*
* Return: Success: 0
- * Failure: -1
+ * Failure: -1
*
* Programmer: Vailin Choi; July 7th, 2009
*
@@ -734,24 +734,24 @@ static herr_t
freespace_stats(hid_t fid, iter_t *iter)
{
H5F_sect_info_t *sect_info = NULL; /* Free space sections */
- ssize_t nsects; /* Number of free space sections */
- size_t u; /* Local index variable */
+ ssize_t nsects; /* Number of free space sections */
+ size_t u; /* Local index variable */
/* Query section information */
if((nsects = H5Fget_free_sections(fid, H5FD_MEM_DEFAULT, 0, NULL)) < 0)
- return(FAIL);
+ return(FAIL);
else if(nsects) {
- if(NULL == (sect_info = (H5F_sect_info_t *)calloc((size_t)nsects, sizeof(H5F_sect_info_t))))
- return(FAIL);
- nsects = H5Fget_free_sections(fid, H5FD_MEM_DEFAULT, (size_t)nsects, sect_info);
- assert(nsects);
+ if(NULL == (sect_info = (H5F_sect_info_t *)calloc((size_t)nsects, sizeof(H5F_sect_info_t))))
+ return(FAIL);
+ nsects = H5Fget_free_sections(fid, H5FD_MEM_DEFAULT, (size_t)nsects, sect_info);
+ assert(nsects);
} /* end else-if */
for(u = 0; u < (size_t)nsects; u++) {
- unsigned bin; /* "bin" the number of objects falls in */
+ unsigned bin; /* "bin" the number of objects falls in */
- if(sect_info[u].size < SIZE_SMALL_SECTS)
- (iter->num_small_sects[(size_t)sect_info[u].size])++;
+ if(sect_info[u].size < SIZE_SMALL_SECTS)
+ (iter->num_small_sects[(size_t)sect_info[u].size])++;
/* Add section size to proper bin */
bin = ceil_log10((unsigned long)sect_info[u].size);
@@ -792,9 +792,9 @@ freespace_stats(hid_t fid, iter_t *iter)
* Saturday, August 12, 2006
*
* Modifications:
- * Vailin Choi; October 2009
- * Turn on display_group_metadata, display_dset_metadata
- * Add 'S' & 's' for printing free space info (previous checkin)
+ * Vailin Choi; October 2009
+ * Turn on display_group_metadata, display_dset_metadata
+ * Add 'S' & 's' for printing free space info (previous checkin)
*
*-------------------------------------------------------------------------
*/
@@ -802,86 +802,113 @@ static struct handler_t *
parse_command_line(int argc, const char *argv[])
{
int opt, i;
- struct handler_t *hand;
+ struct handler_t *hand = NULL;
/* Allocate space to hold the command line info */
- hand = (struct handler_t *)calloc((size_t)argc, sizeof(struct handler_t));
+ if((hand = (struct handler_t *)calloc((size_t)argc, sizeof(struct handler_t)))==NULL) {
+ error_msg("unable to parse command line arguments \n");
+ goto error;
+ }
/* parse command line options */
while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
- switch ((char)opt) {
- case 'h':
- usage(h5tools_getprogname());
- leave(EXIT_SUCCESS);
-
- case 'V':
- print_version(h5tools_getprogname());
- leave(EXIT_SUCCESS);
- break;
+ switch ((char) opt) {
+ case 'h':
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_SUCCESS);
+ if (hand) {
+ for (i = 0; i < argc; i++)
+ if(hand[i].obj) {
+ free(hand[i].obj);
+ hand[i].obj=NULL;
+ }
+
+ free(hand);
+ hand = NULL;
+ }
+ goto done;
+ break;
- case 'F':
- display_all = FALSE;
- display_file_metadata = TRUE;
- break;
+ case 'V':
+ print_version(h5tools_getprogname());
+ h5tools_setstatus(EXIT_SUCCESS);
+ if (hand) {
+ for (i = 0; i < argc; i++)
+ if(hand[i].obj) {
+ free(hand[i].obj);
+ hand[i].obj=NULL;
+ }
+
+ free(hand);
+ hand = NULL;
+ }
+ goto done;
+ break;
- case 'f':
- display_all = FALSE;
- display_file = TRUE;
- break;
+ case 'F':
+ display_all = FALSE;
+ display_file_metadata = TRUE;
+ break;
- case 'G':
- display_all = FALSE;
- display_group_metadata = TRUE;
- break;
+ case 'f':
+ display_all = FALSE;
+ display_file = TRUE;
+ break;
- case 'g':
- display_all = FALSE;
- display_group = TRUE;
- break;
+ case 'G':
+ display_all = FALSE;
+ display_group_metadata = TRUE;
+ break;
- case 'D':
- display_all = FALSE;
- display_dset_metadata = TRUE;
- break;
+ case 'g':
+ display_all = FALSE;
+ display_group = TRUE;
+ break;
- case 'd':
- display_all = FALSE;
- display_dset = TRUE;
- break;
+ case 'D':
+ display_all = FALSE;
+ display_dset_metadata = TRUE;
+ break;
- case 'T':
- display_all = FALSE;
- display_dset_dtype_meta = TRUE;
- break;
+ case 'd':
+ display_all = FALSE;
+ display_dset = TRUE;
+ break;
- case 'A':
- display_all = FALSE;
- display_attr = TRUE;
- break;
+ case 'T':
+ display_all = FALSE;
+ display_dset_dtype_meta = TRUE;
+ break;
- case 's':
- display_all = FALSE;
- display_free_sections = TRUE;
- break;
+ case 'A':
+ display_all = FALSE;
+ display_attr = TRUE;
+ break;
- case 'S':
- display_all = FALSE;
- display_summary = TRUE;
- break;
+ case 's':
+ display_all = FALSE;
+ display_free_sections = TRUE;
+ break;
- case 'O':
- display_all = FALSE;
- display_object = TRUE;
- for(i = 0; i < argc; i++)
- if(!hand[i].obj) {
- hand[i].obj = HDstrdup(opt_arg);
- break;
- } /* end if */
- break;
+ case 'S':
+ display_all = FALSE;
+ display_summary = TRUE;
+ break;
- default:
- usage(h5tools_getprogname());
- leave(EXIT_FAILURE);
+ case 'O':
+ display_all = FALSE;
+ display_object = TRUE;
+ for (i = 0; i < argc; i++)
+ if (!hand[i].obj) {
+ hand[i].obj = HDstrdup(opt_arg);
+ break;
+ } /* end if */
+ break;
+
+ default:
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_FAILURE);
+ goto error;
} /* end switch */
} /* end while */
@@ -889,9 +916,26 @@ parse_command_line(int argc, const char *argv[])
if (argc <= opt_ind) {
error_msg("missing file name\n");
usage(h5tools_getprogname());
- leave(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto error;
} /* end if */
+done:
+ return hand;
+
+error:
+ if (hand) {
+ for (i = 0; i < argc; i++)
+ if(hand[i].obj) {
+ free(hand[i].obj);
+ hand[i].obj=NULL;
+ }
+
+ free(hand);
+ hand = NULL;
+ }
+ h5tools_setstatus(EXIT_FAILURE);
+
return hand;
}
@@ -968,9 +1012,9 @@ print_file_info(const iter_t *iter)
* Saturday, August 12, 2006
*
* Modifications:
- * bug #1253; Oct 6th 2008; Vailin Choi
- * Fixed segmentation fault: print iter->group_bins[0] when
- * there is iter->group_nbins
+ * bug #1253; Oct 6th 2008; Vailin Choi
+ * Fixed segmentation fault: print iter->group_bins[0] when
+ * there is iter->group_nbins
*
*-------------------------------------------------------------------------
*/
@@ -1165,8 +1209,8 @@ print_dataset_info(const iter_t *iter)
* Programmer:
*
* Modifications:
- * Vailin Choi; October 2009
- * Moved from print_dataset_info()
+ * Vailin Choi; October 2009
+ * Moved from print_dataset_info()
*
*-------------------------------------------------------------------------
*/
@@ -1178,20 +1222,20 @@ print_dset_dtype_meta(const iter_t *iter)
unsigned u; /* Local index variable */
if(iter->dset_ntypes) {
- printf("Dataset datatype information:\n");
- printf("\t# of unique datatypes used by datasets: %lu\n", iter->dset_ntypes);
- total = 0;
- for(u = 0; u < iter->dset_ntypes; u++) {
- H5Tencode(iter->dset_type_info[u].tid, NULL, &dtype_size);
- printf("\tDataset datatype #%u:\n", u);
- printf("\t\tCount (total/named) = (%lu/%lu)\n",
- iter->dset_type_info[u].count, iter->dset_type_info[u].named);
- printf("\t\tSize (desc./elmt) = (%lu/%lu)\n", (unsigned long)dtype_size,
- (unsigned long)H5Tget_size(iter->dset_type_info[u].tid));
- H5Tclose(iter->dset_type_info[u].tid);
- total += iter->dset_type_info[u].count;
- } /* end for */
- printf("\tTotal dataset datatype count: %lu\n", total);
+ printf("Dataset datatype information:\n");
+ printf("\t# of unique datatypes used by datasets: %lu\n", iter->dset_ntypes);
+ total = 0;
+ for(u = 0; u < iter->dset_ntypes; u++) {
+ H5Tencode(iter->dset_type_info[u].tid, NULL, &dtype_size);
+ printf("\tDataset datatype #%u:\n", u);
+ printf("\t\tCount (total/named) = (%lu/%lu)\n",
+ iter->dset_type_info[u].count, iter->dset_type_info[u].named);
+ printf("\t\tSize (desc./elmt) = (%lu/%lu)\n", (unsigned long)dtype_size,
+ (unsigned long)H5Tget_size(iter->dset_type_info[u].tid));
+ H5Tclose(iter->dset_type_info[u].tid);
+ total += iter->dset_type_info[u].count;
+ } /* end for */
+ printf("\tTotal dataset datatype count: %lu\n", total);
}
return 0;
@@ -1270,42 +1314,41 @@ print_storage_summary(const iter_t *iter)
HDfprintf(stdout, "File space management strategy: %s\n", FS_STRATEGY_NAME[iter->fs_strategy]);
printf("Summary of file space information:\n");
total_meta =
- iter->super_size + iter->super_ext_size + iter->ublk_size +
- iter->group_ohdr_info.total_size +
- iter->dset_ohdr_info.total_size +
- iter->dtype_ohdr_info.total_size +
- iter->groups_btree_storage_size +
- iter->groups_heap_storage_size +
- iter->attrs_btree_storage_size +
- iter->attrs_heap_storage_size +
- iter->datasets_index_storage_size +
- iter->datasets_heap_storage_size +
- iter->SM_hdr_storage_size +
- iter->SM_index_storage_size +
- iter->SM_heap_storage_size +
- iter->free_hdr;
+ iter->super_size + iter->super_ext_size + iter->ublk_size +
+ iter->group_ohdr_info.total_size +
+ iter->dset_ohdr_info.total_size +
+ iter->dtype_ohdr_info.total_size +
+ iter->groups_btree_storage_size +
+ iter->groups_heap_storage_size +
+ iter->attrs_btree_storage_size +
+ iter->attrs_heap_storage_size +
+ iter->datasets_index_storage_size +
+ iter->datasets_heap_storage_size +
+ iter->SM_hdr_storage_size +
+ iter->SM_index_storage_size +
+ iter->SM_heap_storage_size +
+ iter->free_hdr;
HDfprintf(stdout, " File metadata: %Hu bytes\n", total_meta);
HDfprintf(stdout, " Raw data: %Hu bytes\n", iter->dset_storage_size);
percent = ((float)iter->free_space / (float)iter->filesize) * 100;
HDfprintf(stdout, " Amount/Percent of tracked free space: %Hu bytes/%3.1f%\n",
- iter->free_space, percent);
+ iter->free_space, percent);
if(iter->filesize < (total_meta+iter->dset_storage_size+iter->free_space)) {
- unaccount = (total_meta + iter->dset_storage_size + iter->free_space) - iter->filesize;
- HDfprintf(stdout, " ??? File has %Hu more bytes accounted for than its size! ???\n", unaccount);
+ unaccount = (total_meta + iter->dset_storage_size + iter->free_space) - iter->filesize;
+ HDfprintf(stdout, " ??? File has %Hu more bytes accounted for than its size! ???\n", unaccount);
}
else {
- unaccount = iter->filesize - (total_meta + iter->dset_storage_size + iter->free_space);
- HDfprintf(stdout, " Unaccounted space: %Hu bytes\n", unaccount);
+ unaccount = iter->filesize - (total_meta + iter->dset_storage_size + iter->free_space);
+ HDfprintf(stdout, " Unaccounted space: %Hu bytes\n", unaccount);
}
- HDfprintf(stdout, "Total space: %Hu bytes\n",
- total_meta+iter->dset_storage_size+iter->free_space+unaccount);
+ HDfprintf(stdout, "Total space: %Hu bytes\n", total_meta+iter->dset_storage_size+iter->free_space+unaccount);
if(iter->nexternal)
- HDfprintf(stdout, "External raw data: %Hu bytes\n", iter->dset_external_storage_size);
+ HDfprintf(stdout, "External raw data: %Hu bytes\n", iter->dset_external_storage_size);
return 0;
@@ -1337,13 +1380,13 @@ print_file_metadata(const iter_t *iter)
HDfprintf(stdout, "\tObject headers: (total/unused)\n");
HDfprintf(stdout, "\t\tGroups: %Hu/%Hu\n",
iter->group_ohdr_info.total_size,
- iter->group_ohdr_info.free_size);
+ iter->group_ohdr_info.free_size);
HDfprintf(stdout, "\t\tDatasets(exclude compact data): %Hu/%Hu\n",
- iter->dset_ohdr_info.total_size,
- iter->dset_ohdr_info.free_size);
+ iter->dset_ohdr_info.total_size,
+ iter->dset_ohdr_info.free_size);
HDfprintf(stdout, "\t\tDatatypes: %Hu/%Hu\n",
iter->dtype_ohdr_info.total_size,
- iter->dtype_ohdr_info.free_size);
+ iter->dtype_ohdr_info.free_size);
HDfprintf(stdout, "\tGroups:\n");
HDfprintf(stdout, "\t\tB-tree/List: %Hu\n", iter->groups_btree_storage_size);
@@ -1391,7 +1434,7 @@ print_group_metadata(const iter_t *iter)
printf("File space information for groups' metadata (in bytes):\n");
HDfprintf(stdout, "\tObject headers (total/unused): %Hu/%Hu\n",
- iter->group_ohdr_info.total_size, iter->group_ohdr_info.free_size);
+ iter->group_ohdr_info.total_size, iter->group_ohdr_info.free_size);
HDfprintf(stdout, "\tB-tree/List: %Hu\n", iter->groups_btree_storage_size);
HDfprintf(stdout, "\tHeap: %Hu\n", iter->groups_heap_storage_size);
@@ -1419,10 +1462,10 @@ print_dset_metadata(const iter_t *iter)
printf("File space information for datasets' metadata (in bytes):\n");
HDfprintf(stdout, "\tObject headers (total/unused): %Hu/%Hu\n",
- iter->dset_ohdr_info.total_size, iter->dset_ohdr_info.free_size);
+ iter->dset_ohdr_info.total_size, iter->dset_ohdr_info.free_size);
HDfprintf(stdout, "\tIndex for Chunked datasets: %Hu\n",
- iter->datasets_index_storage_size);
+ iter->datasets_index_storage_size);
HDfprintf(stdout, "\tHeap: %Hu\n", iter->datasets_heap_storage_size);
return 0;
@@ -1442,9 +1485,9 @@ print_dset_metadata(const iter_t *iter)
* Saturday, August 12, 2006
*
* Modifications:
- * Vailin Choi; October 2009
- * Activate "display_group_metadata", "dislay_dset_metadata" and
- * "display_dset_dtype_info".
+ * Vailin Choi; October 2009
+ * Activate "display_group_metadata", "dislay_dset_metadata" and
+ * "display_dset_dtype_info".
*
*-------------------------------------------------------------------------
*/
@@ -1455,29 +1498,29 @@ print_file_statistics(const iter_t *iter)
display_file = TRUE;
display_group = TRUE;
display_dset = TRUE;
- display_dset_dtype_meta = TRUE;
+ display_dset_dtype_meta = TRUE;
display_attr = TRUE;
- display_free_sections = TRUE;
- display_summary = TRUE;
+ display_free_sections = TRUE;
+ display_summary = TRUE;
display_file_metadata = TRUE;
display_group_metadata = TRUE;
display_dset_metadata = TRUE;
}
- if(display_file) print_file_info(iter);
- if(display_file_metadata) print_file_metadata(iter);
+ if(display_file) print_file_info(iter);
+ if(display_file_metadata) print_file_metadata(iter);
- if(display_group) print_group_info(iter);
- if(!display_all && display_group_metadata) print_group_metadata(iter);
+ if(display_group) print_group_info(iter);
+ if(!display_all && display_group_metadata) print_group_metadata(iter);
- if(display_dset) print_dataset_info(iter);
+ if(display_dset) print_dataset_info(iter);
if(display_dset_dtype_meta) print_dset_dtype_meta(iter);
- if(!display_all && display_dset_metadata) print_dset_metadata(iter);
+ if(!display_all && display_dset_metadata) print_dset_metadata(iter);
- if(display_attr) print_attr_info(iter);
- if(display_free_sections) print_freespace_info(iter);
- if(display_summary) print_storage_summary(iter);
+ if(display_attr) print_attr_info(iter);
+ if(display_free_sections) print_freespace_info(iter);
+ if(display_summary) print_storage_summary(iter);
}
@@ -1533,12 +1576,13 @@ print_statistics(const char *name, const iter_t *iter)
int
main(int argc, const char *argv[])
{
- iter_t iter;
- const char *fname = NULL;
- hid_t fid;
- hid_t fcpl;
- struct handler_t *hand;
- H5F_info2_t finfo;
+ iter_t iter;
+ const char *fname = NULL;
+ hid_t fid;
+ hid_t fcpl;
+ struct handler_t *hand = NULL;
+ H5F_info2_t finfo;
+ int i;
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
@@ -1548,11 +1592,9 @@ main(int argc, const char *argv[])
/* Initialize h5tools lib */
h5tools_init();
- hand = parse_command_line (argc, argv);
- if(!hand) {
- error_msg("unable to parse command line arguments \n");
- leave(EXIT_FAILURE);
- } /* end if */
+ if((hand = parse_command_line(argc, argv))==NULL) {
+ goto done;
+ }
fname = argv[opt_ind];
@@ -1561,27 +1603,28 @@ main(int argc, const char *argv[])
fid = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
if(fid < 0) {
error_msg("unable to open file \"%s\"\n", fname);
- leave(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
} /* end if */
/* Initialize iter structure */
iter_init(&iter, fid);
if(H5Fget_filesize(fid, &iter.filesize) < 0)
- warn_msg("Unable to retrieve file size\n");
+ warn_msg("Unable to retrieve file size\n");
assert(iter.filesize != 0);
/* Get storge info for file-level structures */
if(H5Fget_info2(fid, &finfo) < 0)
- warn_msg("Unable to retrieve file info\n");
+ warn_msg("Unable to retrieve file info\n");
else {
- iter.super_size = finfo.super.super_size;
- iter.super_ext_size = finfo.super.super_ext_size;
- iter.SM_hdr_storage_size = finfo.sohm.hdr_size;
- iter.SM_index_storage_size = finfo.sohm.msgs_info.index_size;
- iter.SM_heap_storage_size = finfo.sohm.msgs_info.heap_size;
- iter.free_space = finfo.free.tot_space;
- iter.free_hdr = finfo.free.meta_size;
+ iter.super_size = finfo.super.super_size;
+ iter.super_ext_size = finfo.super.super_ext_size;
+ iter.SM_hdr_storage_size = finfo.sohm.hdr_size;
+ iter.SM_index_storage_size = finfo.sohm.msgs_info.index_size;
+ iter.SM_heap_storage_size = finfo.sohm.msgs_info.heap_size;
+ iter.free_space = finfo.free.tot_space;
+ iter.free_hdr = finfo.free.meta_size;
} /* end else */
if((fcpl = H5Fget_create_plist(fid)) < 0)
@@ -1605,26 +1648,36 @@ main(int argc, const char *argv[])
u = 0;
while(hand[u].obj) {
if (h5trav_visit(fid, hand[u].obj, TRUE, TRUE, obj_stats, lnk_stats, &iter) < 0)
- warn_msg("Unable to traverse object \"%s\"\n", hand[u].obj);
- else
- print_statistics(hand[u].obj, &iter);
+ warn_msg("Unable to traverse object \"%s\"\n", hand[u].obj);
+ else
+ print_statistics(hand[u].obj, &iter);
u++;
} /* end while */
} /* end if */
else {
if (h5trav_visit(fid, "/", TRUE, TRUE, obj_stats, lnk_stats, &iter) < 0)
- warn_msg("Unable to traverse objects/links in file \"%s\"\n", fname);
- else
- print_statistics("/", &iter);
+ warn_msg("Unable to traverse objects/links in file \"%s\"\n", fname);
+ else
+ print_statistics("/", &iter);
} /* end else */
- if (hand) free(hand);
-
- if(H5Fclose(fid) < 0) {
- error_msg("unable to close file \"%s\"\n", fname);
- leave(EXIT_FAILURE);
+done:
+ if(hand) {
+ for (i = 0; i < argc; i++)
+ if(hand[i].obj) {
+ free(hand[i].obj);
+ hand[i].obj=NULL;
+ }
+
+ free(hand);
+ hand = NULL;
+
+ if(H5Fclose(fid) < 0) {
+ error_msg("unable to close file \"%s\"\n", fname);
+ h5tools_setstatus(EXIT_FAILURE);
+ }
}
- leave(EXIT_SUCCESS);
+ leave(h5tools_getstatus());
}
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index bb951a0..2ed13d0 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -226,7 +226,7 @@ hbool_t h5tools_render_region_element(FILE *stream, const h5tool_format_t *info,
hsize_t elmt_counter);
static int h5tools_print_region_data_blocks(hid_t region_id,
- FILE *stream, const h5tool_format_t *info, h5tools_context_t ctx,
+ FILE *stream, const h5tool_format_t *info, h5tools_context_t *cur_ctx,
h5tools_str_t *buffer/*string into which to render */, size_t ncols,
int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata);
@@ -239,7 +239,7 @@ hbool_t h5tools_dump_region_data_points(hid_t region_space, hid_t region_id,
hsize_t elmt_counter);
int h5tools_print_region_data_points(hid_t region_space, hid_t region_id,
- FILE *stream, const h5tool_format_t *info, h5tools_context_t ctx,
+ FILE *stream, const h5tool_format_t *info, h5tools_context_t *cur_ctx,
h5tools_str_t *buffer, size_t ncols,
int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata);
@@ -851,8 +851,7 @@ h5tools_region_simple_prefix(FILE *stream, const h5tool_format_t *info,
}
/* Calculate new prefix */
- h5tools_str_region_prefix(&prefix, info, elmtno, ptdata, ctx->ndims,
- ctx->p_max_idx, ctx);
+ h5tools_str_region_prefix(&prefix, info, elmtno, ptdata, ctx->ndims, ctx->p_max_idx, ctx);
/* Write new prefix to output */
if (ctx->indent_level >= 0) {
@@ -1388,7 +1387,7 @@ h5tools_render_region_element(FILE *stream, const h5tool_format_t *info,
*/
static int
h5tools_print_region_data_blocks(hid_t region_id,
- FILE *stream, const h5tool_format_t *info, h5tools_context_t ctx,
+ FILE *stream, const h5tool_format_t *info, h5tools_context_t *cur_ctx,
h5tools_str_t *buffer/*string into which to render */, size_t ncols,
int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata)
{
@@ -1401,15 +1400,22 @@ h5tools_print_region_data_blocks(hid_t region_id,
hsize_t elmtno; /* elemnt index */
unsigned int region_flags; /* buffer extent flags */
hsize_t curr_pos;
- int jndx;
- size_t indx;
+ size_t jndx;
+ int indx;
int type_size;
hid_t mem_space = -1;
void *region_buf = NULL;
- int blkndx;
+ hsize_t blkndx;
hid_t sid1 = -1;
int ret_value = SUCCEED;
+ h5tools_context_t ctx;
+ assert(info);
+ assert(cur_ctx);
+ assert(buffer);
+ assert(ptdata);
+
+ memset(&ctx, 0, sizeof(ctx));
/* Get the dataspace of the dataset */
if((sid1 = H5Dget_space(region_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
@@ -1444,13 +1450,16 @@ h5tools_print_region_data_blocks(hid_t region_id,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for count");
curr_pos = 0;
+ ctx.indent_level = cur_ctx->indent_level;
+ ctx.cur_column = cur_ctx->cur_column;
+ ctx.prev_multiline = cur_ctx->prev_multiline;
+ ctx.ndims = ndims;
for (blkndx = 0; blkndx < nblocks; blkndx++) {
- ctx.ndims = ndims;
ctx.need_prefix = TRUE;
ctx.cur_elmt = 0;
- for (jndx = 0; jndx < ndims; jndx++) {
- start[jndx] = ptdata[jndx + blkndx * ndims * 2];
- count[jndx] = dims1[jndx];
+ for (indx = 0; indx < ndims; indx++) {
+ start[indx] = ptdata[indx + blkndx * ndims * 2];
+ count[indx] = dims1[indx];
}
if(H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) < 0)
@@ -1483,24 +1492,24 @@ h5tools_print_region_data_blocks(hid_t region_id,
h5tools_region_simple_prefix(stream, info, &ctx, curr_pos, ptdata, 0);
elmtno = 0;
- for (indx = 0; indx < numelem; indx++, elmtno++, ctx.cur_elmt++) {
+ for (jndx = 0; jndx < numelem; jndx++, elmtno++, ctx.cur_elmt++) {
/* Render the region data element begin */
h5tools_str_reset(buffer);
- h5tools_str_append(buffer, "%s", indx ? OPTIONAL_LINE_BREAK "" : "");
+ h5tools_str_append(buffer, "%s", jndx ? OPTIONAL_LINE_BREAK "" : "");
h5tools_str_sprint(buffer, info, region_id, type_id,
- ((char*)region_buf + indx * type_size), &ctx);
+ ((char*)region_buf + jndx * type_size), &ctx);
- if (indx + 1 < numelem || (region_flags & END_OF_DATA) == 0)
+ if (jndx + 1 < numelem || (region_flags & END_OF_DATA) == 0)
h5tools_str_append(buffer, "%s", OPT(info->elmt_suf1, ","));
dimension_break = h5tools_render_region_element(stream, info, &ctx, buffer, &curr_pos,
- ncols, ptdata, indx, elmtno);
+ ncols, ptdata, jndx, elmtno);
/* Render the region data element end */
if(FALSE == dimension_break)
elmtno = 0;
- } /* end for (indx = 0; indx < numelem; indx++, region_elmtno++, ctx.cur_elmt++) */
+ } /* end for (jndx = 0; jndx < numelem; jndx++, region_elmtno++, ctx.cur_elmt++) */
ctx.indent_level--;
} /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */
@@ -1561,6 +1570,10 @@ h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id,
hid_t type_id;
int i;
+ assert(info);
+ assert(ctx);
+ assert(buffer);
+
if((nblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0)
H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_select_hyper_nblocks failed");
@@ -1673,7 +1686,7 @@ h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id,
ctx->need_prefix = TRUE;
- h5tools_print_region_data_blocks(region_id, rawdatastream, info, *ctx,
+ h5tools_print_region_data_blocks(region_id, rawdatastream, info, ctx,
buffer, ncols, ndims, type_id, nblocks, ptdata);
done:
@@ -1732,7 +1745,7 @@ h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id,
*/
int
h5tools_print_region_data_points(hid_t region_space, hid_t region_id,
- FILE *stream, const h5tool_format_t *info, h5tools_context_t ctx,
+ FILE *stream, const h5tool_format_t *info, h5tools_context_t *cur_ctx,
h5tools_str_t *buffer, size_t ncols,
int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata)
{
@@ -1741,82 +1754,96 @@ h5tools_print_region_data_points(hid_t region_space, hid_t region_id,
hsize_t elmtno; /* elemnt index */
unsigned int region_flags; /* buffer extent flags */
hsize_t curr_pos;
- size_t indx;
- int jndx;
+ hsize_t total_size[H5S_MAX_RANK];
+ int indx;
+ size_t jndx;
int type_size;
hid_t mem_space = -1;
void *region_buf = NULL;
int ret_value = SUCCEED;
+ h5tools_context_t ctx;
- if((type_size = H5Tget_size(type_id)) == 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
-
- if((region_buf = HDmalloc(type_size * npoints)) == NULL)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for region");
+ assert(info);
+ assert(cur_ctx);
+ assert(buffer);
+ assert(ptdata);
+ memset(&ctx, 0, sizeof(ctx));
/* Allocate space for the dimension array */
if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for dims");
dims1[0] = npoints;
+
+ /* Create dataspace for reading buffer */
if((mem_space = H5Screate_simple(1, dims1, NULL)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Screate_simple failed");
+ if((type_size = H5Tget_size(type_id)) == 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
+
+ if((region_buf = HDmalloc(type_size * npoints)) == NULL)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for region");
+
+ curr_pos = 0;
+ ctx.indent_level = cur_ctx->indent_level;
+ ctx.cur_column = cur_ctx->cur_column;
+ ctx.prev_multiline = cur_ctx->prev_multiline;
+ ctx.ndims = ndims;
+
if(H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
elmtno = 0;
- curr_pos = 0;
for (jndx = 0; jndx < npoints; jndx++, elmtno++) {
- ctx.ndims = ndims;
ctx.need_prefix = TRUE;
ctx.cur_elmt = 0; /* points are always 0 */
- /* Render the point element begin */
- h5tools_str_reset(buffer);
-
ctx.indent_level++;
+ if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) < 0)
+ HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
/* assume entire data space to be printed */
for (indx = 0; indx < (size_t) ctx.ndims; indx++)
ctx.p_min_idx[indx] = 0;
- if(H5Sget_simple_extent_dims(region_space, ctx.p_max_idx, NULL) < 0)
- HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
-
- if (ctx.ndims > 0) {
- ctx.size_last_dim = (int) (ctx.p_max_idx[ctx.ndims - 1]);
- }
- else
- ctx.size_last_dim = 0;
-
- if (ctx.ndims > 0)
- init_acc_pos(&ctx, ctx.p_max_idx);
+ init_acc_pos(&ctx, total_size);
/* print the data */
region_flags = START_OF_DATA;
if (jndx == npoints - 1)
region_flags |= END_OF_DATA;
- curr_pos = 0; /* points requires constant 0 */
+ for (indx = 0; indx < (size_t)ctx.ndims; indx++)
+ ctx.p_max_idx[indx] = cur_ctx->p_max_idx[indx];
+
ctx.sm_pos = jndx * ndims;
+ if (ctx.ndims > 0) {
+ ctx.size_last_dim = (int) (ctx.p_max_idx[ctx.ndims - 1]);
+ }
+ else
+ ctx.size_last_dim = 0;
+ curr_pos = 0; /* points requires constant 0 */
h5tools_region_simple_prefix(stream, info, &ctx, curr_pos, ptdata, 0);
+ /* Render the point element begin */
+ h5tools_str_reset(buffer);
+
+ h5tools_str_append(buffer, "%s", jndx ? OPTIONAL_LINE_BREAK "" : "");
h5tools_str_sprint(buffer, info, region_id, type_id,
((char*)region_buf + jndx * type_size), &ctx);
if (jndx + 1 < npoints || (region_flags & END_OF_DATA) == 0)
h5tools_str_append(buffer, "%s", OPT(info->elmt_suf1, ","));
- dimension_break =
- h5tools_render_region_element(stream, info, &ctx, buffer, &curr_pos,
- ncols, ptdata, (hsize_t)0, elmtno);
+ dimension_break = h5tools_render_region_element(stream, info, &ctx, buffer, &curr_pos,
+ ncols, ptdata, (hsize_t)0, elmtno);
/* Render the point element end */
-
- ctx.indent_level--;
if(FALSE == dimension_break)
elmtno = 0;
- } /* end for (jndx = 0; jndx < npoints; jndx++, region_elmtno++) */
+
+ ctx.indent_level--;
+ } /* end for (jndx = 0; jndx < npoints; jndx++, elmtno++) */
done:
HDfree(region_buf);
@@ -1866,6 +1893,10 @@ h5tools_dump_region_data_points(hid_t region_space, hid_t region_id,
hid_t dtype;
hid_t type_id;
+ assert(info);
+ assert(ctx);
+ assert(buffer);
+
if((npoints = H5Sget_select_elem_npoints(region_space)) <= 0)
H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_select_elem_npoints failed");
@@ -1975,7 +2006,7 @@ h5tools_dump_region_data_points(hid_t region_space, hid_t region_id,
ctx->need_prefix = TRUE;
h5tools_print_region_data_points(region_space, region_id,
- rawdatastream, info, *ctx, buffer, ncols, ndims, type_id, npoints, ptdata);
+ rawdatastream, info, ctx, buffer, ncols, ndims, type_id, npoints, ptdata);
done:
free(ptdata);
@@ -4233,8 +4264,7 @@ render_bin_output_region_data_points(hid_t region_space, hid_t region_id,
if(H5Sget_simple_extent_dims(region_space, dims1, NULL) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
- render_bin_output(stream, container, type_id,
- ((char*)region_buf + jndx * type_size));
+ render_bin_output(stream, container, type_id, ((char*)region_buf + jndx * type_size));
} /* end for (jndx = 0; jndx < npoints; jndx++) */
done:
diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
index 9b7e8f2..54e2584 100644
--- a/tools/lib/h5tools_str.c
+++ b/tools/lib/h5tools_str.c
@@ -390,8 +390,12 @@ h5tools_str_region_prefix(h5tools_str_t *str, const h5tool_format_t *info,
p_prod[i - 1] = (max_idx[i]) * p_prod[i];
for (i = 0; i < (size_t) ndims; i++) {
- ctx->pos[i] = curr_pos / p_prod[i];
- curr_pos -= p_prod[i] * ctx->pos[i];
+ if(curr_pos > 0) {
+ ctx->pos[i] = curr_pos / p_prod[i];
+ curr_pos -= p_prod[i] * ctx->pos[i];
+ }
+ else
+ ctx->pos[i] = 0;
ctx->pos[i] += (unsigned long) ptdata[ctx->sm_pos+i];
}
diff --git a/tools/testfiles/h5dump-help.txt b/tools/testfiles/h5dump-help.txt
new file mode 100644
index 0000000..9083782
--- /dev/null
+++ b/tools/testfiles/h5dump-help.txt
@@ -0,0 +1,94 @@
+usage: h5dump [OPTIONS] file
+ OPTIONS
+ -h, --help Print a usage message and exit
+ -n, --contents Print a list of the file contents and exit
+ -B, --superblock Print the content of the super block
+ -H, --header Print the header only; no data is displayed
+ -A, --onlyattr Print the header and value of attributes
+ -i, --object-ids Print the object ids
+ -r, --string Print 1-byte integer datasets as ASCII
+ -e, --escape Escape non printing characters
+ -V, --version Print version number and exit
+ -a P, --attribute=P Print the specified attribute
+ -d P, --dataset=P Print the specified dataset
+ -y, --noindex Do not print array indices with the data
+ -p, --properties Print dataset filters, storage layout and fill value
+ -f D, --filedriver=D Specify which driver to open the file with
+ -g P, --group=P Print the specified group and all members
+ -l P, --soft-link=P Print the value(s) of the specified soft link
+ -o F, --output=F Output raw data into file F
+ -b B, --binary=B Binary file output, of form B
+ -t P, --datatype=P Print the specified named datatype
+ -w N, --width=N Set the number of columns of output. A value of 0 (zero)
+ sets the number of columns to the maximum (65535).
+ Default width is 80 columns.
+ -m T, --format=T Set the floating point output format
+ -q Q, --sort_by=Q Sort groups and attributes by index Q
+ -z Z, --sort_order=Z Sort groups and attributes by order Z
+ -M L, --packedbits=L Print packed bits as unsigned integers, using mask
+ format L for an integer dataset specified with
+ option -d. L is a list of offset,length values,
+ separated by commas. Offset is the beginning bit in
+ the data value and length is the number of bits of
+ the mask.
+ -R, --region Print dataset pointed by region references
+ -x, --xml Output in XML using Schema
+ -u, --use-dtd Output in XML using DTD
+ -D U, --xml-dtd=U Use the DTD or schema at U
+ -X S, --xml-ns=S (XML Schema) Use qualified names n the XML
+ ":": no namespace, default: "hdf5:"
+ E.g., to dump a file called `-f', use h5dump -- -f
+ --enable-error-stack Prints messages from the HDF5 error stack as they
+ occur.
+
+ Subsetting is available by using the following options with a dataset
+ attribute. Subsetting is done by selecting a hyperslab from the data.
+ Thus, the options mirror those for performing a hyperslab selection.
+ One of the START, COUNT, STRIDE, or BLOCK parameters are mandatory if you do subsetting.
+ The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+ each dimension. START is optional and will default to 0 in each dimension.
+
+ -s START, --start=START Offset of start of subsetting selection
+ -S STRIDE, --stride=STRIDE Hyperslab stride
+ -c COUNT, --count=COUNT Number of blocks to include in selection
+ -k BLOCK, --block=BLOCK Size of block in hyperslab
+ START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the
+ number of dimensions in the dataspace being queried
+
+ D - is the file driver to use in opening the file. Acceptable values
+ are "sec2", "family", "split", "multi", "direct", and "stream". Without
+ the file driver flag, the file will be opened with each driver in
+ turn and in the order specified above until one driver succeeds
+ in opening the file.
+ F - is a filename.
+ P - is the full path from the root group to the object.
+ N - is an integer greater than 1.
+ T - is a string containing the floating point format, e.g '%.3f'
+ U - is a URI reference (as defined in [IETF RFC 2396],
+ updated by [IETF RFC 2732])
+ B - is the form of binary output: NATIVE for a memory type, FILE for the
+ file type, LE or BE for pre-existing little or big endian types.
+ Must be used with -o (output file) and it is recommended that
+ -d (dataset) is used. B is an optional argument, defaults to NATIVE
+ Q - is the sort index type. It can be "creation_order" or "name" (default)
+ Z - is the sort order type. It can be "descending" or "ascending" (default)
+
+ Examples:
+
+ 1) Attribute foo of the group /bar_none in file quux.h5
+
+ h5dump -a /bar_none/foo quux.h5
+
+ 2) Selecting a subset from dataset /foo in file quux.h5
+
+ h5dump -d /foo -s "0,1" -S "1,1" -c "2,3" -k "2,2" quux.h5
+
+ 3) Saving dataset 'dset' in file quux.h5 to binary file 'out.bin'
+ using a little-endian type
+
+ h5dump -d /dset -b LE -o out.bin quux.h5
+
+ 4) Display two packed bits (bits 0-1 and bits 4-6) in the dataset /dset
+
+ h5dump -d /dset -M 0,1,4,3 quux.h5
+
generated by cgit v0.12 at 2024-09-01 21:31:52 (GMT)