[svn-r29857] Description:

    Bring H5LD* routines from revise_chunks branch to trunk.

Tested on:
    MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
    (h5committest forthcoming)

1 files changed, 639 insertions, 0 deletions

diff --git a/hl/src/H5LD.c b/hl/src/H5LD.c
new file mode 100644
index 0000000..4abd740
--- /dev/null
+++ b/hl/src/H5LD.c
@@ -0,0 +1,639 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+* Copyright by The HDF Group.                                               *
+* 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://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+* access to either file, you may request a copy from help@hdfgroup.org.     *
+* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#include <string.h>
+#include <stdlib.h>
+#include <assert.h>
+#include <stdio.h>
+#include "H5LDprivate.h"
+
+/*-------------------------------------------------------------------------
+ *
+ * internal functions
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t H5LD_construct_info(H5LD_memb_t *memb, hid_t par_tid);
+static herr_t H5LD_get_dset_dims(hid_t did, hsize_t *cur_dims);
+static size_t H5LD_get_dset_type_size(hid_t did, const char *fields);
+static herr_t H5LD_get_dset_elmts(hid_t did, const hsize_t *prev_dims,
+    const hsize_t *cur_dims, const char *fields, void *buf);
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5LD_clean_vector
+ *
+ * Purpose: Process the vector of info:
+ *		1) free the array of pointers to member names in listv[n]
+ *		2) close the type id of the last member in listv[n]
+ *		3) free the H5LD_memb_t structure itself as pointed to by listv[n]
+ *
+ * Return: void
+ *
+ * Programmer:  Vailin Choi; Aug 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+void
+H5LD_clean_vector(H5LD_memb_t *listv[])
+{
+    unsigned n;		/* Local index variable */
+
+    HDassert(listv);
+
+    /* Go through info for each field stored in listv[] */
+    for(n = 0; listv[n] != NULL; n++) {
+	if(listv[n]->names) {
+	    HDfree(listv[n]->names);
+	    listv[n]->names = NULL;
+	} /* end if */
+
+	/* Close the type id of the last member in the field */
+	if(!(listv[n]->last_tid < 0)) {
+	    H5Tclose(listv[n]->last_tid);
+	    listv[n]->last_tid = -1;
+	} /* end if */
+
+	/* Free the H5LD_memb_t structure for the field */
+	HDfree(listv[n]);
+	listv[n] = NULL;
+    } /* end for */
+} /* H5LD_clean_vector() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5LD_construct_info()
+ *
+ * Purpose: Get the remaining info for a field:
+ *		1) Get the type id of the last member in the field
+ *		2) Get the total offset of all the members in the field
+ *		3) Get the type size of the last member in the field
+ *
+ * Return: Success: 0
+ *	   Failure: negative
+ *
+ * Programmer:  Vailin Choi; Aug 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5LD_construct_info(H5LD_memb_t *memb, hid_t par_tid)
+{
+    hid_t tmp_tid = -1;	/* Dataset type id */
+    unsigned i;		/* Local index variable */
+    herr_t ret_value = FAIL;	/* Return value */
+
+    /* Make a copy of the incoming datatype */
+    tmp_tid = H5Tcopy(par_tid);
+
+    /* Validate all the members in a field */
+    for(i = 0; memb->names[i] != NULL; i++) {
+        hid_t memb_tid;         /* Type id for a member in a field */
+        int idx;		/* Index # of a member in a compound datatype */
+
+        /* Get the member index and member type id */
+        if((idx = H5Tget_member_index(tmp_tid, memb->names[i])) < 0)
+            goto done;
+        if((memb_tid = H5Tget_member_type(tmp_tid, (unsigned)idx)) < 0)
+            goto done;
+
+	/* Sum up the offset of all the members in the field */
+        memb->tot_offset += H5Tget_member_offset(tmp_tid, (unsigned)idx);
+        if(H5Tclose(tmp_tid) < 0)
+            goto done;
+        tmp_tid = memb_tid;
+    } /* end for */
+
+    /* Get the type size of the last member in the field */
+    memb->last_tsize = H5Tget_size(tmp_tid);
+
+    /* Save the type id of the last member in the field */
+    memb->last_tid = H5Tcopy(tmp_tid);
+
+    /* Indicate success */
+    ret_value = SUCCEED;
+
+done:
+    H5E_BEGIN_TRY
+	H5Tclose(tmp_tid);
+    H5E_END_TRY
+
+    return(ret_value);
+} /* H5LD_construct_info() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5LD_construct_vector
+ *
+ * Purpose: Process the comma-separated list of fields in "fields" as follows:
+ * 	Example:
+ *		"fields": "a.b.c,d"
+ *		listv[0]->tot_offset = total offset of "a" & "b" & "c"
+ *		listv[0]->last_tid = type id of "c"
+ *		listv[0]->last_tsize = type size of "c"
+ *		listv[0]->names[0] = "a"
+ *		listv[0]->names[1] = "b"
+ *		listv[0]->names[2] = "c"
+ *		listv[0]->names[3] = NULL
+ *
+ *		listv[1]->tot_offset = offset of "d"
+ *		listv[1]->last_tid = type id of "d"
+ *		listv[1]->last_tsize = type size of "d"
+ *		listv[1]->names[0] = "d"
+ *		listv[1]->names[1] = NULL
+ *
+ * Return: Success: # of comma-separated fields in "fields"
+ *	   Failure: negative value
+ *
+ * Programmer:  Vailin Choi; Aug 2010
+ *
+*-------------------------------------------------------------------------
+*/
+int
+H5LD_construct_vector(char *fields, H5LD_memb_t *listv[]/*OUT*/, hid_t par_tid)
+{
+    int nfields;	                /* The # of comma-separated fields in "fields" */
+    hbool_t end_of_fields = FALSE;	/* end of "fields" */
+    char *fields_ptr;	                /* Pointer to "fields" */
+    int ret_value = FAIL;		/* Return value */
+
+    HDassert(listv);
+    HDassert(fields);
+
+    fields_ptr = fields;
+    nfields = 0;
+
+    /* Process till end of "fields" */
+    while(!end_of_fields) {
+	H5LD_memb_t *memb = NULL; 	/* Pointer to structure for storing a field's info */
+        char *cur;	                /* Pointer to a member in a field */
+	size_t len;			/* Estimated # of members in a field */
+	hbool_t gotcomma = FALSE;	/* A comma encountered */
+	hbool_t gotmember = FALSE;	/* Getting member in a field */
+        hbool_t valid = TRUE;           /* Whether a field being processed is valid or not */
+	int j = 0;			/* The # of members in a field */
+
+	len = (HDstrlen(fields_ptr) / 2) + 2;
+
+	/* Allocate memory for an H5LD_memb_t for storing a field's info */
+	if(NULL == (memb = (H5LD_memb_t *)HDcalloc((size_t)1, sizeof(H5LD_memb_t))))
+	    goto done;
+
+	/* Allocate memory for an array of pointers to member names */
+	if(NULL == (memb->names = (char **)HDcalloc(len, sizeof(char *))))
+	    goto done;
+
+	memb->names[j] = fields_ptr;
+	memb->last_tid = -1;
+	cur = fields_ptr;
+
+	/* Continue processing till: not valid or comma encountered or "fields" ended */
+	while(valid && !gotcomma && !end_of_fields) {
+	    switch(*fields_ptr) {
+                case '\0':	/* end of list */
+                    if(gotmember) { /* getting something and end of "fields" */
+                        *cur++ = '\0';;
+                        memb->names[++j] = NULL;
+                    } /* end if */
+                    else /* getting nothing but end of list */
+                        valid = FALSE;
+                    end_of_fields = TRUE;
+                    break;
+	
+                case '\\': /* escape character */
+                    ++fields_ptr; /* skip it */
+                    if(*fields_ptr == '\0')
+                        valid = FALSE;
+                    else {
+                        *cur++ = *fields_ptr++;
+                        gotmember = TRUE;
+                    } /* end else */
+                    break;
+
+                case '.': /* nested field separator */
+                    *fields_ptr++ = *cur++ = '\0';;
+                    if(gotmember) {
+                        memb->names[++j] = cur;
+                        gotmember = FALSE;
+                    } /* end if */
+                    else
+                        valid = FALSE;
+                    break;
+
+                case ',': /* field separator */
+                    *fields_ptr++ = *cur++ = '\0';;
+                    if(gotmember) {
+                        memb->names[++j] = NULL;
+                        gotmember = FALSE;
+                    } /* end if */
+                    else
+                        valid = FALSE;
+                    gotcomma = TRUE;
+                    break;
+
+                default: 
+                    *cur++ = *fields_ptr++;
+                    gotmember = TRUE;
+                    break;
+	    } /* end switch */
+	} /* while (valid && !gotcomma && !end_of_fields) */
+
+	/* If valid, put into listv and continue processing further info */
+	if(valid) {
+	    listv[nfields++] = memb;
+	    if(H5LD_construct_info(memb, par_tid) < 0)
+		goto done;
+	} /* end if */
+        else {
+	    if(memb)
+                HDfree(memb);
+	    goto done;
+	} /* end else */
+    } /* while !end_of_fields */
+
+    /* Indicate success */
+    ret_value = nfields;
+
+done:
+    listv[nfields] = NULL;
+    if(ret_value == FAIL)
+	H5LD_clean_vector(listv);
+
+    return(ret_value);
+}  /* H5LD_construct_vector() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5LD_get_dset_dims
+ *
+ * Purpose: To return the current size for each dimension of the
+ *	    dataset's dataspace
+ *
+ * Return: Success: 0
+ *	   Failure: negative value
+ *
+ * Programmer:  Vailin Choi; March 2010
+ *
+*-------------------------------------------------------------------------
+*/
+static herr_t
+H5LD_get_dset_dims(hid_t did, hsize_t *cur_dims)
+{
+    hid_t sid = -1;             /* Dataspace ID */
+    herr_t ret_value = FAIL;    /* Return Value */
+
+    /* Verify parameter */
+    if(cur_dims == NULL)
+        goto done;
+
+    /* Get the dataset's dataspace */
+    if((sid = H5Dget_space(did)) < 0)
+        goto done;
+
+    /* Get the current dimension size */
+    if(H5Sget_simple_extent_dims(sid, cur_dims, NULL) < 0)
+        goto done;
+
+    /* Indicate success */
+    ret_value = SUCCEED;
+
+done:
+    H5E_BEGIN_TRY {
+        H5Sclose(sid);
+    } H5E_END_TRY;
+
+    return(ret_value);
+} /* H5LD_get_dset_dims() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5LD_get_dset_type_size
+ *
+ * Purpose: To return the size of the dataset's datatype in bytes
+ *	null "fields": return the size of the dataset's datatype
+ *	non-null "fields": return the size of the dataset's datatype
+ *			   with respect to the selection in "fields"
+ *
+ * Return: Success: size of the dataset's datatype
+ *	   Failure: 0 (valid datatypes are never zero size)
+ *
+ * Programmer:  Vailin Choi; March 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static size_t
+H5LD_get_dset_type_size(hid_t did, const char *fields)
+{
+    hid_t dset_tid = -1;	/* Dataset's type identifier */
+    hid_t tid = -1;		/* Native Type identifier */
+    H5LD_memb_t **listv = NULL;	/* Vector for storing information in "fields" */
+    char *dup_fields = NULL;	/* A copy of "fields" */
+    size_t ret_value = 0;       /* Return value */
+
+    /* Get the datatype of the dataset */
+    if((dset_tid = H5Dget_type(did)) < 0)
+        goto done;
+    if((tid = H5Tget_native_type(dset_tid, H5T_DIR_DEFAULT)) < 0)
+        goto done;
+
+    if(fields == NULL) /* If no "fields" is specified */
+        ret_value = H5Tget_size(tid);
+    else { /* "fields" are specified */
+        size_t len;			/* Estimate the number of comma-separated fields in "fields" */
+        size_t tot = 0;			/* Data type size of all the fields in "fields" */
+        int n = 0, num = 0;		/* Local index variables */
+
+        HDassert(fields && *fields);
+
+        /* Should be a compound datatype if "fields" exists */
+        if(H5Tget_class(dset_tid) != H5T_COMPOUND)
+            goto done;
+
+	/* Get a copy of "fields" */
+        if(NULL == (dup_fields = HDstrdup(fields)))
+            goto done;
+
+	/* Allocate memory for a list of H5LD_memb_t pointers to store "fields" info */
+	len = (HDstrlen(fields) / 2) + 2;
+	if(NULL == (listv = (H5LD_memb_t **)HDcalloc(len, sizeof(H5LD_memb_t *))))
+            goto done;
+
+	/* Process and store info for "fields" */
+	if((num = H5LD_construct_vector(dup_fields, listv/*OUT*/, tid)) < 0)
+            goto done;
+
+	/* Sum up the size of all the datatypes in "fields" */
+	for(n = 0; n < num; n++)
+	    tot += listv[n]->last_tsize;
+
+	/* Clean up the vector of H5LD_memb_t structures */
+	H5LD_clean_vector(listv);
+
+	/* Return the total size */
+	ret_value = tot;
+    } /* end else */
+
+done:
+    H5E_BEGIN_TRY
+        H5Tclose(tid);
+        H5Tclose(dset_tid);
+    H5E_END_TRY
+
+    /* Free the array of H5LD_memb_t pointers */
+    if(listv)
+        HDfree(listv);
+
+    /* Free memory */
+    if(dup_fields)
+        HDfree(dup_fields);
+
+    return(ret_value);
+} /* H5LD_get_dset_type_size() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5LD_get_dset_elmts
+ *
+ * Purpose: To retrieve selected data from the dataset
+ *
+ * Return: Success: 0
+ *	   Failure: negative
+ *
+ * Programmer:  Vailin Choi; August 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5LD_get_dset_elmts(hid_t did, const hsize_t *prev_dims, const hsize_t *cur_dims,
+    const char *fields, void *buf)
+{
+    hid_t dtid = -1, tid = -1;	/* Dataset type id */
+    hid_t sid = -1, mid = -1;	/* Dataspace and memory space id */
+    hssize_t snum_elmts;        /* Number of dataset elements in the selection (signed) */
+    hsize_t num_elmts;          /* Number of dataset elements in the selection */
+    hsize_t start[H5S_MAX_RANK];/* Starting offset */
+    hsize_t count[H5S_MAX_RANK];/* ??offset */
+    H5LD_memb_t **listv = NULL;	/* Vector for storing information in "fields" */
+    char *dup_fields = NULL;	/* A copy of "fields" */
+    char *sav_buf = NULL;	/* Saved pointer temporary buffer */
+    unsigned ctr;	        /* Counter for # of curr_dims > prev_dims */
+    int ndims;		        /* Number of dimensions for the dataset */
+    int i; 		        /* Local index variable */
+    herr_t ret_value = FAIL;	/* Return value */
+
+    /* Verify parameters */
+    if(prev_dims == NULL || cur_dims == NULL || buf == NULL)
+	goto done;
+
+    /* Get dataset's dataspace */
+    if((sid = H5Dget_space(did)) < 0)
+	goto done;
+    
+    /* Get the number of dimensions */
+    if((ndims = H5Sget_simple_extent_ndims(sid)) < 0)
+	goto done;
+
+    /* Verify that cur_dims must have one dimension whose size is greater than prev_dims */
+    HDmemset(start, 0, sizeof start);
+    HDmemset(count, 0, sizeof count);
+    ctr = 0;
+    for(i = 0; i < ndims; i++)
+	if(cur_dims[i] > prev_dims[i]) {
+	    ++ctr;
+	    count[i] = cur_dims[i] - prev_dims[i];
+	    start[i] = prev_dims[i];
+	} /* end if */
+        else { /* < or = */
+	    start[i] = 0;
+	    count[i] = MIN(prev_dims[i], cur_dims[i]);
+	} /* end else */
+    if(!ctr)
+	goto done;
+
+    if(ctr == 1) { /* changes for only one dimension */
+	/* Make the selection in the dataset based on "cur_dims" and "prev_dims" */
+	if(H5Sselect_hyperslab(sid, H5S_SELECT_SET, start, NULL, count, NULL) < 0)
+	    goto done;
+    } /* end if */
+    else { /* changes for more than one dimensions */
+	HDmemset(start, 0, sizeof start);
+
+	/* Make the selection in the dataset based on "cur_dims" and "prev_dims" */
+	if(H5Sselect_hyperslab(sid, H5S_SELECT_SET, start, NULL, cur_dims, NULL) < 0)
+	    goto done;
+	if(H5Sselect_hyperslab(sid, H5S_SELECT_NOTB, start, NULL, prev_dims, NULL) < 0)
+	    goto done;
+    } /* end else */
+
+    /* Get the number of elements in the selection */
+    if(0 == (snum_elmts = H5Sget_select_npoints(sid)))
+        goto done;
+    num_elmts = (hsize_t)snum_elmts;
+
+    /* Create the memory space for the selection */
+    if((mid = H5Screate_simple(1, &num_elmts, NULL)) < 0)
+	goto done;
+
+    /* Get the native datatype size */
+    if((dtid = H5Dget_type(did)) < 0)
+        goto done;
+    if((tid = H5Tget_native_type(dtid, H5T_DIR_DEFAULT)) < 0)
+        goto done;
+
+    if(fields == NULL) { /* nothing in "fields" */
+	/* Read and store all the elements in "buf" */
+	if(H5Dread(did, tid, mid, sid, H5P_DEFAULT, buf) < 0)
+	    goto done;
+    } /* end if */
+    else { /* "fields" is specified */
+	unsigned char *buf_p = (unsigned char *)buf;   /* Pointer to the destination buffer */
+        char *tmp_buf;          /* Temporary buffer for data read */
+        size_t tot_tsize;	/* Total datatype size */
+        size_t len;		/* Estimate the number of comma-separated fields in "fields" */
+
+	/* should be a compound datatype if "fields" exists */
+	if(H5Tget_class(tid) != H5T_COMPOUND)
+	    goto done;
+
+	/* Get the total size of the dataset's datatypes */
+	if(0 == (tot_tsize = H5LD_get_dset_type_size(did, NULL)))
+	    goto done;
+	
+	/* Allocate memory for reading in the elements in the dataset selection */
+	if(NULL == (sav_buf = tmp_buf = (char *)HDcalloc((size_t)num_elmts, tot_tsize)))
+	    goto done;
+
+	/* Read the dataset elements in the selection */
+	if(H5Dread(did, tid, mid, sid, H5P_DEFAULT, tmp_buf) < 0)
+	    goto done;
+
+	/* Make a copy of "fields" */
+	if(NULL == (dup_fields = HDstrdup(fields)))
+	    goto done;
+
+	/* Allocate memory for the vector of H5LD_memb_t pointers */
+	len = (HDstrlen(fields) / 2) + 2;
+        if(NULL == (listv = (H5LD_memb_t **)HDcalloc(len, sizeof(H5LD_memb_t *))))
+	    goto done;
+
+	/* Process and store information for "fields" */
+        if(H5LD_construct_vector(dup_fields, listv, tid) < 0)
+            goto done;
+
+	/* Copy data for each dataset element in the selection */
+	for(i = 0; i < (int)num_elmts; i++) {
+            int j; 		/* Local index variable */
+
+	    /* Copy data for "fields" to the input buffer */
+	    for(j = 0; listv[j] != NULL; j++) {
+		HDmemcpy(buf_p, tmp_buf + listv[j]->tot_offset, listv[j]->last_tsize);
+		buf_p += listv[j]->last_tsize;
+	    } /* end for */
+	    tmp_buf += tot_tsize;
+	} /* end for */
+
+	/* Clean up the vector of H5LD_memb_t structures */
+	H5LD_clean_vector(listv);
+    } /* end else */
+
+    /* Indicate success */
+    ret_value = SUCCEED;
+
+done:
+    H5E_BEGIN_TRY
+	H5Tclose(dtid);
+	H5Tclose(tid);
+	H5Sclose(sid);
+	H5Sclose(mid);
+    H5E_END_TRY
+
+    /* Free the array of H5LD_memb_t pointers */
+    if(listv)
+        HDfree(listv);
+
+    /* Free memory */
+    if(dup_fields)
+        HDfree(dup_fields);
+    if(sav_buf)
+        HDfree(sav_buf);
+
+    return(ret_value);
+} /* H5LD_get_dset_elmts() */
+
+/*-------------------------------------------------------------------------
+ *
+ * Public functions
+ *
+ *-------------------------------------------------------------------------
+ */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5LDget_dset_dims
+ *
+ * Purpose: To retrieve the current dimension sizes for a dataset
+ *
+ * Return: Success: 0
+ *	   Failure: negative value
+ *
+ * Programmer:  Vailin Choi; March 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5LDget_dset_dims(hid_t did, hsize_t *cur_dims)
+{
+    return(H5LD_get_dset_dims(did, cur_dims));
+} /* H5LDget_dset_dims() */
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5LDget_dset_type_size
+ *
+ * Purpose:  To return the size in bytes of the datatype for the dataset
+ *
+ * Return: Success: size in bytes of the dataset's datatype
+ *	   Failure: 0 (valid datatypes are never zero size)
+ *
+ * Programmer:  Vailin Choi; March 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+size_t
+H5LDget_dset_type_size(hid_t did, const char *fields)
+{
+    return(H5LD_get_dset_type_size(did, fields));
+} /* H5LDget_dset_type_size() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5LDget_dset_elmts
+ *
+ * Purpose: To retrieve selected data from the dataset
+ *
+ * Return: Success: 0
+ *	   Failure: negative value
+ *
+ * Programmer:  Vailin Choi; March 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5LDget_dset_elmts(hid_t did, const hsize_t *prev_dims, const hsize_t *cur_dims, const char *fields, void *buf)
+{
+    return(H5LD_get_dset_elmts(did, prev_dims, cur_dims, fields, buf) );
+} /* H5LDget_dset_elmts() */
+