[svn-r605] Added in h5dump tools created by Ruey-Hsia.

Renamed what was called h5dump.c to h5tools.c.
Changed Makefile.in to reflect all the changes.
(Make dependence is to be processed later.)

Tested in Solaris 2.5

1 files changed, 523 insertions, 0 deletions

diff --git a/tools/h5dumputil.c b/tools/h5dumputil.c
new file mode 100644
index 0000000..d0b3847
--- /dev/null
+++ b/tools/h5dumputil.c
@@ -0,0 +1,523 @@
+/*
+ *  Note: this program is a modification of h5dump.c by Robb Matzke.
+ */
+#include <assert.h>
+#include <ctype.h>
+#include <h5dump.h>
+#include <hdf5.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+/*
+ * The output functions need a temporary buffer to hold a piece of the
+ * dataset while it's being printed.  This constant sets the limit on the
+ * size of that temporary buffer in bytes.  For efficiency's sake, choose the
+ * largest value suitable for your machine (for testing use a small value).
+ */
+#define H5DUMP_BUFSIZE	1024
+
+#define OPT(X,S)	((X)?(X):(S))
+#define MIN(X,Y)	((X)<(Y)?(X):(Y))
+#define NELMTS(X)	(sizeof(X)/sizeof(*X))
+#define ALIGN(A,Z)	((((A)+(Z)-1)/(Z))*(Z))
+
+#define DATASET_DATA 	1
+
+/*-------------------------------------------------------------------------
+ * Function:	h5dump_prefix
+ *
+ * Purpose:	Prints the prefix to show up at the begining of the line.
+ *
+ * Return:	void
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, July 23, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+h5dump_prefix(char *s/*out*/, const h5dump_t *info, hsize_t elmtno, int ndims,
+	      hsize_t min_idx[], hsize_t max_idx[])
+{
+    hsize_t	p_prod[8], p_idx[8];
+    hsize_t	n, i;
+    char	temp[1024];
+
+    /*
+     * Calculate the number of elements represented by a unit change in a
+     * certain index position.
+     */
+    for (i=ndims-1, p_prod[ndims-1]=1; i>0; --i) {
+	p_prod[i-1] = (max_idx[i]-min_idx[i]) * p_prod[i];
+    }
+
+    /*
+     * Calculate the index values from the element number.
+     */
+    for (i=0, n=elmtno; i<(hsize_t)ndims; i++) {
+	p_idx[i] = n / p_prod[i] + min_idx[i];
+	n %= p_prod[i];
+    }
+
+    /*
+     * Print the index values.
+     */
+    *temp = '\0';
+    for (i=0; i<(hsize_t)ndims; i++) {
+	if (i) strcat(temp, OPT(info->idx_sep, ","));
+	sprintf(temp+strlen(temp), OPT(info->idx_n_fmt, "%lu"),
+		(unsigned long)p_idx[i]);
+    }
+
+    /*
+     * Add prefix and suffix to the index.
+     */
+    sprintf(s, OPT(info->idx_fmt, "%s: "), temp);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	h5dump_sprint
+ *
+ * Purpose:	Prints the value pointed to by VP into the string S assuming
+ *		the data type of VP is TYPE.
+ *
+ * Return:	void
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, July 23, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+h5dump_sprint(char *s/*out*/, const h5dump_t *info, hid_t type, void *vp)
+{
+    size_t	i, n, offset;
+    char	temp[1024], *name;
+    hid_t	memb;
+    int		nmembs, j;
+    
+    if (H5Tequal(type, H5T_NATIVE_DOUBLE)) {
+	sprintf(temp, "%g", *((double*)vp));
+    } else if (H5Tequal(type, H5T_NATIVE_FLOAT)) {
+	sprintf(temp, "%g", *((float*)vp));
+    } else if (H5Tequal(type, H5T_NATIVE_CHAR) ||
+	       H5Tequal(type, H5T_NATIVE_UCHAR)) {
+	switch (*((char*)vp)) {
+	case '\\':
+	    strcpy(temp, "\\\\");
+	    break;
+	case '\b':
+	    strcpy(temp, "\\b");
+	    break;
+	case '\f':
+	    strcpy(temp, "\\f");
+	    break;
+	case '\n':
+	    strcpy(temp, "\\n");
+	    break;
+	case '\r':
+	    strcpy(temp, "\\r");
+	    break;
+	case '\t':
+	    strcpy(temp, "\\t");
+	    break;
+	default:
+	    if (isprint(*((char*)vp))) sprintf(temp, "%c", *((char*)vp));
+	    else sprintf(temp, "\\%03o", *((unsigned char*)vp));
+	    break;
+	}
+    } else if (H5Tequal(type, H5T_NATIVE_SHORT)) {
+	sprintf(temp, "%d", *((short*)vp));
+    } else if (H5Tequal(type, H5T_NATIVE_USHORT)) {
+	sprintf(temp, "%u", *((unsigned short*)vp));
+    } else if (H5Tequal(type, H5T_NATIVE_INT)) {
+	sprintf(temp, "%d", *((int*)vp));
+    } else if (H5Tequal(type, H5T_NATIVE_UINT)) {
+	sprintf(temp, "%u", *((unsigned*)vp));
+    } else if (H5Tequal(type, H5T_NATIVE_LONG)) {
+	sprintf(temp, "%ld", *((long*)vp));
+    } else if (H5Tequal(type, H5T_NATIVE_ULONG)) {
+	sprintf(temp, "%lu", *((unsigned long*)vp));
+    } else if (H5T_COMPOUND==H5Tget_class(type)) {
+	nmembs = H5Tget_nmembers(type);
+	strcpy(temp, OPT(info->cmpd_pre, "{"));
+	for (j=0; j<nmembs; j++) {
+	    if (j) strcat(temp, OPT(info->cmpd_sep, ","));
+
+	    /* The name */
+	    name = H5Tget_member_name(type, j);
+	    sprintf(temp+strlen(temp), OPT(info->cmpd_name, ""), name);
+	    free(name);
+
+	    /* The value */
+	    offset = H5Tget_member_offset(type, j);
+	    memb = H5Tget_member_type(type, j);
+	    h5dump_sprint(temp+strlen(temp), info, memb, (char*)vp+offset);
+	    H5Tclose(memb);
+	}
+	strcat(temp, OPT(info->cmpd_suf, "}"));
+    } else {
+	strcpy(temp, "0x");
+	n = H5Tget_size(type);
+	for (i=0; i<n; i++) {
+	    sprintf(temp+strlen(temp), "%02x", ((unsigned char*)vp)[i]);
+	}
+    }
+
+    sprintf(s, OPT(info->elmt_fmt, "%s"), temp);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	h5dump_simple
+ *
+ * Purpose:	Print some values from a dataset with a simple data space.
+ *		This is a special case of h5dump().
+ *
+ * Return:	Success:	0
+ *
+ *		Failure:	-1
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, July 23, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+h5dump_simple(FILE *stream, const h5dump_t *info, hid_t dset, hid_t p_type, int obj_data)
+{
+    hid_t		f_space;		/*file data space	*/
+    int			ndims;			/*dimensionality	*/
+    hsize_t		elmtno, i;		/*counters		*/
+    int			carry;			/*counter carry value	*/
+    hssize_t		zero[8];		/*vector of zeros	*/
+    int			need_prefix=1;		/*indices need printing	*/
+
+    /* Print info */
+    hsize_t		p_min_idx[8];		/*min selected index	*/
+    hsize_t		p_max_idx[8];		/*max selected index	*/
+    size_t		p_type_nbytes;		/*size of memory type	*/
+    hsize_t		p_nelmts;		/*total selected elmts	*/
+    char		p_buf[256];		/*output string		*/
+    size_t		p_column=0;		/*output column		*/
+    size_t		p_ncolumns=80;		/*default num columns	*/
+    char 		p_prefix[1024];		/*line prefix string	*/
+
+    /* Stripmine info */
+    hsize_t		sm_size[8];		/*stripmine size	*/
+    hsize_t		sm_nbytes;		/*bytes per stripmine	*/
+    hsize_t		sm_nelmts;		/*elements per stripmine*/
+    unsigned char	*sm_buf;		/*buffer for raw data	*/
+    hid_t		sm_space;		/*stripmine data space	*/
+
+    /* Hyperslab info */
+    hssize_t		hs_offset[8];		/*starting offset	*/
+    hsize_t		hs_size[8];		/*size this pass	*/
+    hsize_t		hs_nelmts;		/*elements in request	*/
+
+    /*
+     * Check that everything looks okay.  The dimensionality must not be too
+     * great and the dimensionality of the items selected for printing must
+     * match the dimensionality of the dataset.
+     */
+    if (obj_data == DATASET_DATA)
+         f_space = H5Dget_space(dset);
+    else
+         f_space = H5Aget_space(dset);
+   
+    ndims = H5Sextent_ndims(f_space);
+    if ((size_t)ndims>NELMTS(sm_size)) return -1;
+
+    /* Assume entire data space to be printed */
+    for (i=0; i<(hsize_t)ndims; i++) p_min_idx[i] = 0;
+    H5Sextent_dims(f_space, p_max_idx, NULL); 
+    for (i=0, p_nelmts=1; i<(hsize_t)ndims; i++) {
+	p_nelmts *= p_max_idx[i]-p_min_idx[i];
+    }
+
+    /*
+     * Determine the strip mine size and allocate a buffer.  The strip mine is
+     * a hyperslab whose size is manageable.
+     */
+    p_type_nbytes = H5Tget_size(p_type);
+    for (i=ndims, sm_nbytes=p_type_nbytes; i>0; --i) {
+	sm_size[i-1] = MIN (p_max_idx[i-1]-p_min_idx[i-1],
+			    H5DUMP_BUFSIZE/sm_nbytes);
+	sm_nbytes *= sm_size[i-1];
+	assert(sm_nbytes>0);
+    }
+    sm_buf = malloc(sm_nbytes);
+    sm_nelmts = sm_nbytes/p_type_nbytes;
+    sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
+
+    /* Local things */
+    if (info->line_ncols>0) p_ncolumns = info->line_ncols;
+
+    /* The stripmine loop */
+    memset(hs_offset, 0, sizeof hs_offset);
+    memset(zero, 0, sizeof zero);
+    for (elmtno=0; elmtno<p_nelmts; elmtno+=hs_nelmts) {
+
+	/* Calculate the hyperslab size */
+	for (i=0, hs_nelmts=1; i<(hsize_t)ndims; i++) {
+	    hs_size[i] = MIN(sm_size[i], p_max_idx[i]-hs_offset[i]);
+	    hs_nelmts *= hs_size[i];
+	}
+	
+	/* Read the data */
+	H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL,
+			    hs_size, NULL);
+	H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL,
+			    &hs_nelmts, NULL);
+
+
+	if (obj_data == DATASET_DATA)
+            H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf);
+        else
+            H5Aread(dset, p_type, sm_buf);
+
+	/* Print the data */
+	for (i=0; i<hs_nelmts; i++) {
+	    /* Render the element */
+	    h5dump_sprint(p_buf, info, p_type, sm_buf+i*p_type_nbytes);
+	    if (elmtno+i+1<p_nelmts) {
+		strcat(p_buf, OPT(info->elmt_suf1, ","));
+	    }
+
+	    /* Print the prefix */
+/* 
+	    if ((p_column +
+		 strlen(p_buf) +
+		 strlen(OPT(info->elmt_suf2, " ")) +
+		 strlen(OPT(info->line_suf, ""))) > p_ncolumns) {
+		need_prefix = 1;
+	    }
+
+	    if (need_prefix) {
+		h5dump_prefix(p_prefix, info, elmtno+i, ndims,
+			      p_min_idx, p_max_idx);
+		if (p_column) {
+		    fputs(OPT(info->line_suf, ""), stream);
+		    putc('\n', stream);
+		    fputs(OPT(info->line_sep, ""), stream);
+		}
+		fputs(p_prefix, stream);
+		p_column = strlen(p_prefix);
+		need_prefix = 0;
+	    } else {
+		fputs(OPT(info->elmt_suf2, " "), stream);
+		p_column += strlen(OPT(info->elmt_suf2, " "));
+
+	    }
+	    
+ */
+
+	    fputs(p_buf, stream);
+/* 
+	    p_column += strlen(p_buf);
+ */
+	}
+	
+	/* Calculate the next hyperslab offset */
+	for (i=ndims, carry=1; i>0 && carry; --i) {
+	    hs_offset[i-1] += hs_size[i-1];
+	    if (hs_offset[i-1]==(hssize_t)p_max_idx[i-1]) {
+		hs_offset[i-1] = p_min_idx[i-1];
+	    } else {
+		carry = 0;
+	    }
+	}
+    }
+/* 
+
+    if (p_column) {
+	fputs(OPT(info->line_suf, ""), stream);
+	putc('\n', stream);
+	fputs(OPT(info->line_sep, ""), stream);
+    }
+ */
+    H5Sclose(sm_space);
+    H5Sclose(f_space);
+    return 0;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	h5dump_fixtype
+ *
+ * Purpose:	Given a file data type choose a memory data type which is
+ *		appropriate for printing the data.
+ *
+ * Return:	Success:	Memory data type
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, July 23, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static hid_t
+h5dump_fixtype(hid_t f_type)
+{
+    hid_t	m_type=-1, f_memb;
+    hid_t	*memb=NULL;
+    char	**name=NULL;
+    int		nmembs, i;
+    size_t	size;
+
+    size = H5Tget_size(f_type);
+    switch (H5Tget_class(f_type)) {
+
+    case H5T_INTEGER:
+	/*
+	 * Use the smallest native integer type of the same sign as the file
+	 * such that the memory type is at least as large as the file type.
+	 * If there is no memory type large enough then use the largest
+	 * memory type available.
+	 */
+	if (size<=sizeof(char)) {
+	    m_type = H5Tcopy(H5T_NATIVE_CHAR);
+	} else if (size<=sizeof(short)) {
+	    m_type = H5Tcopy(H5T_NATIVE_SHORT);
+	} else if (size<=sizeof(int)) {
+	    m_type = H5Tcopy(H5T_NATIVE_INT);
+	} else if (size<=sizeof(long)) {
+	    m_type = H5Tcopy(H5T_NATIVE_LONG);
+	} else {
+	    m_type = H5Tcopy(H5T_NATIVE_LLONG);
+	}
+	H5Tset_sign(m_type, H5Tget_size(f_type));
+	break;
+	
+    case H5T_FLOAT:
+	/*
+	 * Use the smallest native floating point type available such that
+	 * its size is at least as large as the file type.  If there is not
+	 * native type large enough then use the largest native type.
+	 */
+	if (size<=sizeof(float)) {
+	    m_type = H5Tcopy(H5T_NATIVE_FLOAT);
+	} else if (size<=sizeof(double)) {
+	    m_type = H5Tcopy(H5T_NATIVE_DOUBLE);
+	} else {
+	    m_type = H5Tcopy(H5T_NATIVE_LDOUBLE);
+	}
+	break;
+
+    case H5T_COMPOUND:
+	nmembs = H5Tget_nmembers(f_type);
+	memb = calloc(nmembs, sizeof(hid_t));
+	name = calloc(nmembs, sizeof(char*));
+	
+	for (i=0, size=0; i<nmembs; i++) {
+	    f_memb = H5Tget_member_type(f_type, i);
+	    memb[i] = h5dump_fixtype(f_memb);
+	    size = ALIGN(size, H5Tget_size(memb[i])) + H5Tget_size(memb[i]);
+	    H5Tclose(f_memb);
+	    name[i] = H5Tget_member_name(f_type, i);
+	    if (memb[i]<0 || NULL==name[i]) goto done;
+	}
+
+	m_type = H5Tcreate(H5T_COMPOUND, size);
+	for (i=0, size=0; i<nmembs; i++) {
+	    H5Tinsert(m_type, name[i], size, memb[i]);
+	    size = ALIGN(size, H5Tget_size(memb[i])) + H5Tget_size(memb[i]);
+	}
+	break;
+
+    case H5T_TIME:
+    case H5T_STRING:
+    case H5T_BITFIELD:
+    case H5T_OPAQUE:
+	/*
+	 * These type classes are not implemented yet.
+	 */
+	break;
+
+    default:
+	/* What the heck? */
+	break;
+    }
+
+ done:
+    /* Clean up temp buffers */
+    if (memb && name) {
+	for (i=0; i<nmembs; i++) {
+	    if (memb[i]>=0) H5Tclose(memb[i]);
+	    if (name[i]) free(name[i]);
+	}
+	free(memb);
+	free(name);
+    }
+    
+    return m_type;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	h5dump
+ *
+ * Purpose:	Print some values from a dataset.  The values to print are
+ *		determined by the P_SPACE argument and the format to use to
+ *		print them is determined by the P_TYPE argument.
+ *
+ * Return:	Success:	0
+ *
+ *		Failure:	-1
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, July 23, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+h5dump1(FILE *stream, const h5dump_t *info, hid_t dset, hid_t _p_type, int obj_data)
+{
+    hid_t	f_space;
+    hid_t	p_type = _p_type;
+    hid_t	f_type;
+    int		status;
+
+    /* Check the data space */
+    if (obj_data == DATASET_DATA) 
+        f_space = H5Dget_space(dset);
+    else
+        f_space = H5Aget_space(dset);
+
+    if (H5Sis_simple(f_space)<=0) return -1;
+    H5Sclose(f_space);
+
+    /*
+     * Check the data type.  If the caller didn't supply a data type then
+     * use an appropriate native data type.
+     */
+
+     if (obj_data == DATASET_DATA) 
+         f_type = H5Dget_type(dset);
+     else
+         f_type = H5Aget_type(dset);
+
+    if (p_type<0) {
+	p_type = h5dump_fixtype(f_type);
+	H5Tclose(f_type);
+	if (p_type<0) return -1;
+    }
+
+    /* Print the data */
+    status = h5dump_simple(stream, info, dset, p_type, obj_data);
+    if (p_type!=_p_type) H5Tclose(p_type);
+    return status;
+}