/* * Copyright (C) 1998-2001 NCSA * All rights reserved. * * Programmer: Quincey Koziol * Friday, May 29, 1998 * * Purpose: Dataspace functions. */ #define H5S_PACKAGE /*suppress error about including H5Spkg */ #include "H5private.h" /* Generic Functions */ #include "H5Dprivate.h" /* Datasets (for their properties) */ #include "H5Eprivate.h" /* Error handling */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* ID Functions */ #include "H5Spkg.h" /* Dataspace functions */ #include "H5Vprivate.h" /* Vector functions */ /* Interface initialization */ #define PABLO_MASK H5Sselect_mask #define INTERFACE_INIT NULL static int interface_initialize_g = 0; /* Declare external the free list for hssize_t arrays */ H5FL_ARR_EXTERN(hssize_t); /* Declare a free list to manage arrays of size_t */ H5FL_ARR_DEFINE_STATIC(size_t,-1); /* Declare a free list to manage arrays of hsize_t */ H5FL_ARR_DEFINE_STATIC(hsize_t,-1); /* Declare a free list to manage the H5S_sel_iter_t struct */ H5FL_DEFINE_STATIC(H5S_sel_iter_t); /* Declare a free list to manage blocks of single datatype element data */ H5FL_BLK_EXTERN(type_elem); /*-------------------------------------------------------------------------- NAME H5S_select_copy PURPOSE Copy a selection from one dataspace to another USAGE herr_t H5S_select_copy(dst, src) H5S_t *dst; OUT: Pointer to the destination dataspace H5S_t *src; IN: Pointer to the source dataspace RETURNS Non-negative on success/Negative on failure DESCRIPTION Copies all the selection information (include offset) from the source dataspace to the destination dataspace. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ herr_t H5S_select_copy (H5S_t *dst, const H5S_t *src) { herr_t ret_value=SUCCEED; /* return value */ FUNC_ENTER_NOAPI(H5S_select_copy, FAIL); /* Check args */ assert(dst); assert(src); /* Copy regular fields */ dst->select=src->select; /* Need to copy order information still */ /* Copy offset information */ if (NULL==(dst->select.offset = H5FL_ARR_ALLOC(hssize_t,src->extent.u.simple.rank,1))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed"); if(src->select.offset!=NULL) HDmemcpy(dst->select.offset,src->select.offset,(src->extent.u.simple.rank*sizeof(hssize_t))); /* Perform correct type of copy based on the type of selection */ switch (src->extent.type) { case H5S_SCALAR: /*nothing needed */ break; case H5S_SIMPLE: /* Deep copy extra stuff */ switch(src->select.type) { case H5S_SEL_NONE: case H5S_SEL_ALL: /*nothing needed */ break; case H5S_SEL_POINTS: ret_value=H5S_point_copy(dst,src); break; case H5S_SEL_HYPERSLABS: ret_value=H5S_hyper_copy(dst,src); break; default: assert("unknown selection type" && 0); break; } /* end switch */ break; case H5S_COMPLEX: /*void */ break; default: assert("unknown data space type" && 0); break; } /* end switch */ done: FUNC_LEAVE (ret_value); } /* H5S_select_copy() */ /*-------------------------------------------------------------------------- NAME H5Sget_select_npoints PURPOSE Get the number of elements in current selection USAGE hssize_t H5Sget_select_npoints(dsid) hid_t dsid; IN: Dataspace ID of selection to query RETURNS The number of elements in selection on success, 0 on failure DESCRIPTION Returns the number of elements in current selection for dataspace. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ hssize_t H5Sget_select_npoints(hid_t spaceid) { H5S_t *space = NULL; /* Dataspace to modify selection of */ hssize_t ret_value; /* return value */ FUNC_ENTER_API(H5Sget_select_npoints, 0); H5TRACE1("Hs","i",spaceid); /* Check args */ if (NULL == (space=H5I_object_verify(spaceid, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a data space"); ret_value = (*space->select.get_npoints)(space); done: FUNC_LEAVE (ret_value); } /* H5Sget_select_npoints() */ /*-------------------------------------------------------------------------- NAME H5Sselect_valid PURPOSE Check whether the selection fits within the extent, with the current offset defined. USAGE htri_t H5Sselect_void(dsid) hid_t dsid; IN: Dataspace ID to query RETURNS TRUE if the selection fits within the extent, FALSE if it does not and Negative on an error. DESCRIPTION Determines if the current selection at the current offet fits within the extent for the dataspace. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ htri_t H5Sselect_valid(hid_t spaceid) { H5S_t *space = NULL; /* Dataspace to modify selection of */ htri_t ret_value; /* return value */ FUNC_ENTER_API(H5Sselect_valid, 0); H5TRACE1("b","i",spaceid); /* Check args */ if (NULL == (space=H5I_object_verify(spaceid, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a data space"); ret_value = (*space->select.is_valid)(space); done: FUNC_LEAVE (ret_value); } /* H5Sselect_valid() */ /*-------------------------------------------------------------------------- NAME H5S_select_deserialize PURPOSE Deserialize the current selection from a user-provided buffer into a real selection in the dataspace. USAGE herr_t H5S_select_deserialize(space, buf) H5S_t *space; IN/OUT: Dataspace pointer to place selection into uint8 *buf; IN: Buffer to retrieve serialized selection from RETURNS Non-negative on success/Negative on failure DESCRIPTION Deserializes the current selection into a buffer. (Primarily for retrieving from disk). This routine just hands off to the appropriate routine for each type of selection. The format of the serialized information is shown in the H5S_select_serialize() header. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ herr_t H5S_select_deserialize (H5S_t *space, const uint8_t *buf) { const uint8_t *tbuf; /* Temporary pointer to the selection type */ uint32_t sel_type; /* Pointer to the selection type */ herr_t ret_value=FAIL; /* return value */ FUNC_ENTER_NOAPI(H5S_select_deserialize, FAIL); assert(space); tbuf=buf; UINT32DECODE(tbuf, sel_type); switch(sel_type) { case H5S_SEL_POINTS: /* Sequence of points selected */ ret_value=H5S_point_deserialize(space,buf); break; case H5S_SEL_HYPERSLABS: /* Hyperslab selection defined */ ret_value=H5S_hyper_deserialize(space,buf); break; case H5S_SEL_ALL: /* Entire extent selected */ ret_value=H5S_all_deserialize(space,buf); break; case H5S_SEL_NONE: /* Nothing selected */ ret_value=H5S_none_deserialize(space,buf); break; default: break; } done: FUNC_LEAVE (ret_value); } /* H5S_select_deserialize() */ /*-------------------------------------------------------------------------- NAME H5Sget_select_bounds PURPOSE Gets the bounding box containing the selection. USAGE herr_t H5S_get_select_bounds(space, start, end) hid_t dsid; IN: Dataspace ID of selection to query hsize_t *start; OUT: Starting coordinate of bounding box hsize_t *end; OUT: Opposite coordinate of bounding box RETURNS Non-negative on success, negative on failure DESCRIPTION Retrieves the bounding box containing the current selection and places it into the user's buffers. The start and end buffers must be large enough to hold the dataspace rank number of coordinates. The bounding box exactly contains the selection, ie. if a 2-D element selection is currently defined with the following points: (4,5), (6,8) (10,7), the bounding box with be (4, 5), (10, 8). Calling this function on a "none" selection returns fail. The bounding box calculations _does_ include the current offset of the selection within the dataspace extent. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ herr_t H5Sget_select_bounds(hid_t spaceid, hsize_t *start, hsize_t *end) { H5S_t *space = NULL; /* Dataspace to modify selection of */ herr_t ret_value; /* return value */ FUNC_ENTER_API(H5Sget_select_bounds, FAIL); H5TRACE3("e","i*h*h",spaceid,start,end); /* Check args */ if(start==NULL || end==NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid pointer"); if (NULL == (space=H5I_object_verify(spaceid, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); ret_value = (*space->select.bounds)(space,start,end); done: FUNC_LEAVE (ret_value); } /* H5Sget_select_bounds() */ /*-------------------------------------------------------------------------- NAME H5S_select_iterate PURPOSE Iterate over the selected elements in a memory buffer. USAGE herr_t H5S_select_iterate(buf, type_id, space, operator, operator_data) void *buf; IN/OUT: Buffer containing elements to iterate over hid_t type_id; IN: Datatype ID of BUF array. H5S_t *space; IN: Dataspace object containing selection to iterate over H5D_operator_t op; IN: Function pointer to the routine to be called for each element in BUF iterated over. void *operator_data; IN/OUT: Pointer to any user-defined data associated with the operation. RETURNS Returns the return value of the last operator if it was non-zero, or zero if all elements were processed. Otherwise returns a negative value. DESCRIPTION Iterates over the selected elements in a memory buffer, calling the user's callback function for each element. The selection in the dataspace is modified so that any elements already iterated over are removed from the selection if the iteration is interrupted (by the H5D_operator_t function returning non-zero) in the "middle" of the iteration and may be re-started by the user where it left off. NOTE: Until "subtracting" elements from a selection is implemented, the selection is not modified. --------------------------------------------------------------------------*/ herr_t H5S_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op, void *operator_data) { H5T_t *dt; /* Datatype structure */ H5P_genplist_t *dx_plist; /* Dataset transfer property list */ H5S_sel_iter_t *iter=NULL; /* Selection iteration info */ uint8_t *loc; /* Current element location in buffer */ hssize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of element in dataspace */ hssize_t nelmts; /* Number of elements in selection */ hsize_t space_size[H5O_LAYOUT_NDIMS]; /* Dataspace size */ hsize_t *off=NULL; /* Array to store sequence offsets */ hsize_t curr_off; /* Current offset within sequence */ hsize_t tmp_off; /* Temporary offset within sequence */ size_t *len=NULL; /* Array to store sequence lengths */ size_t curr_len; /* Length of bytes left to process in sequence */ size_t vector_size; /* Value for vector size */ size_t nseq; /* Number of sequences generated */ size_t curr_seq; /* Current sequnce being worked on */ size_t nbytes; /* Number of bytes used in sequences */ size_t max_bytes; /* Maximum number of bytes allowed in sequences */ size_t elmt_size; /* Datatype size */ int ndims; /* Number of dimensions in dataspace */ int i; /* Local Index variable */ herr_t user_ret=0; /* User's return value */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5S_select_iterate, FAIL); /* Check args */ assert(buf); assert(H5I_DATATYPE == H5I_get_type(type_id)); assert(space); assert(op); /* Get the hyperslab vector size */ /* (from the default data transfer property list, for now) */ dx_plist = H5I_object(H5P_DATASET_XFER_DEFAULT); assert(dx_plist); if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value"); /* Allocate the vector I/O arrays */ if((len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); if((off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); /* Get the datatype size */ if (NULL==(dt=H5I_object_verify(type_id,H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype"); if((elmt_size=H5T_get_size(dt))==0) HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid"); /* Allocate iterator */ if((iter = H5FL_ALLOC(H5S_sel_iter_t,1))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate selection iterator"); /* Initialize iterator */ if ((*space->select.iter_init)(space, elmt_size, iter)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); /* Get the number of elements in selection */ if((nelmts = (*space->select.get_npoints)(space))<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't get number of elements selected"); /* Get the rank of the dataspace */ ndims=space->extent.u.simple.rank; /* Copy the size of the space */ assert(space->extent.u.simple.size); assert(ndims>0); HDmemcpy(space_size, space->extent.u.simple.size, ndims*sizeof(hsize_t)); space_size[ndims]=elmt_size; /* Compute the maximum number of bytes required */ H5_ASSIGN_OVERFLOW(max_bytes,nelmts*elmt_size,hsize_t,size_t); /* Loop, while elements left in selection */ while(max_bytes>0 && user_ret==0) { /* Get the sequences of bytes */ if((*space->select.get_seq_list)(space,0,iter,elmt_size,vector_size,max_bytes,&nseq,&nbytes,off,len)<0) HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); /* Loop, while sequences left to process */ for(curr_seq=0; curr_seq0 && user_ret==0) { /* Compute the coordinate from the offset */ for(i=ndims, tmp_off=curr_off; i>=0; i--) { coords[i]=tmp_off%space_size[i]; tmp_off/=space_size[i]; } /* end for */ /* Get the location within the user's buffer */ loc=(unsigned char *)buf+curr_off; /* Call user's callback routine */ user_ret=(*op)(loc,type_id,(hsize_t)ndims,coords,operator_data); /* Increment offset in dataspace */ curr_off+=elmt_size; /* Decrement number of bytes left in sequence */ curr_len-=elmt_size; } /* end while */ } /* end for */ /* Decrement number of elements left to process */ assert((nbytes%elmt_size)==0); max_bytes-=nbytes; } /* end while */ /* Set return value */ ret_value=user_ret; done: /* Release selection iterator */ if(iter!=NULL) { if ((*space->select.iter_release)(iter)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); H5FL_FREE(H5S_sel_iter_t,iter); } /* end if */ /* Release length & offset vectors */ if(len!=NULL) H5FL_ARR_FREE(size_t,len); if(off!=NULL) H5FL_ARR_FREE(hsize_t,off); FUNC_LEAVE(ret_value); } /* end H5S_select_iterate() */ /*-------------------------------------------------------------------------- NAME H5Sget_select_type PURPOSE Retrieve the type of selection in a dataspace USAGE H5S_sel_type H5Sget_select_type(space_id) hid_t space_id; IN: Dataspace object to reset RETURNS Non-negative on success/Negative on failure. Return value is from the set of values in the H5S_sel_type enumerated type. DESCRIPTION This function retrieves the type of selection currently defined for a dataspace. --------------------------------------------------------------------------*/ H5S_sel_type H5Sget_select_type(hid_t space_id) { H5S_t *space = NULL; /* dataspace to modify */ H5S_sel_type ret_value; /* Return value */ FUNC_ENTER_API(H5Sget_select_type, H5S_SEL_ERROR); H5TRACE1("St","i",space_id); /* Check args */ if (NULL == (space = H5I_object_verify(space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, H5S_SEL_ERROR, "not a data space"); /* Set return value */ ret_value=space->select.type; done: FUNC_LEAVE(ret_value); } /* end H5Sget_select_type() */ /*-------------------------------------------------------------------------- NAME H5S_select_shape_same PURPOSE Check if two selections are the same shape USAGE htri_t H5S_select_shape_same(space1, space2) const H5S_t *space1; IN: 1st Dataspace pointer to compare const H5S_t *space2; IN: 2nd Dataspace pointer to compare RETURNS TRUE/FALSE/FAIL DESCRIPTION Checks to see if the current selection in the dataspaces are the same dimensionality and shape. This is primarily used for reading the entire selection in one swoop. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS Assumes that there is only a single "block" for hyperslab selections. EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ htri_t H5S_select_shape_same(const H5S_t *space1, const H5S_t *space2) { H5S_hyper_span_t *span1=NULL,*span2=NULL; /* Hyperslab span node */ hsize_t elmts1=0,elmts2=0; /* Number of elements in each dimension of selection */ unsigned u; /* Index variable */ htri_t ret_value=TRUE; /* return value */ FUNC_ENTER_NOAPI(H5S_select_shape_same, FAIL); /* Check args */ assert(space1); assert(space2); if (space1->extent.u.simple.rank!=space2->extent.u.simple.rank) HGOTO_DONE(FALSE); /* Get information about memory and file */ for (u=0; uextent.u.simple.rank; u++) { switch(space1->select.type) { case H5S_SEL_HYPERSLABS: /* Check size hyperslab selection in this dimension */ if(space1->select.sel_info.hslab.diminfo != NULL) { elmts1=space1->select.sel_info.hslab.diminfo[u].block; } /* end if */ else { /* Check for the first dimension */ if(span1==NULL) span1=space1->select.sel_info.hslab.span_lst->head; /* Get the number of elements in the span */ elmts1=(span1->high-span1->low)+1; /* Advance to the next dimension */ span1=span1->down->head; } /* end else */ break; case H5S_SEL_ALL: elmts1=space1->extent.u.simple.size[u]; break; case H5S_SEL_POINTS: elmts1=1; break; case H5S_SEL_NONE: elmts1=0; break; default: assert(0 && "Invalid selection type!"); } /* end switch */ switch(space2->select.type) { case H5S_SEL_HYPERSLABS: /* Check size hyperslab selection in this dimension */ if(space2->select.sel_info.hslab.diminfo != NULL) { elmts2=space2->select.sel_info.hslab.diminfo[u].block; } /* end if */ else { /* Check for the first dimension */ if(span2==NULL) span2=space2->select.sel_info.hslab.span_lst->head; /* Get the number of elements in the span */ elmts2=(span2->high-span2->low)+1; /* Advance to the next dimension */ span2=span2->down->head; } /* end else */ break; case H5S_SEL_ALL: elmts2=space2->extent.u.simple.size[u]; break; case H5S_SEL_POINTS: elmts2=1; break; case H5S_SEL_NONE: elmts2=0; break; default: assert(0 && "Invalid selection type!"); } /* end switch */ /* Make certaint the selections have the same number of elements in this dimension */ if (elmts1!=elmts2) HGOTO_DONE(FALSE); } /* end for */ done: FUNC_LEAVE (ret_value); } /* H5S_select_shape_same() */ /*-------------------------------------------------------------------------- NAME H5S_select_fill PURPOSE Fill a selection in memory with a value USAGE herr_t H5S_select_fill(fill,fill_size,space,buf) const void *fill; IN: Pointer to fill value to use size_t fill_size; IN: Size of elements in memory buffer & size of fill value H5S_t *space; IN: Dataspace describing memory buffer & containing selection to use. void *buf; IN/OUT: Memory buffer to fill selection in RETURNS Non-negative on success/Negative on failure. DESCRIPTION Use the selection in the dataspace to fill elements in a memory buffer. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS The memory buffer elements are assumed to have the same datatype as the fill value being placed into them. EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ herr_t H5S_select_fill(void *_fill, size_t fill_size, const H5S_t *space, void *_buf) { H5P_genplist_t *dx_plist; /* Dataset transfer property list */ H5S_sel_iter_t *iter=NULL; /* Selection iteration info */ uint8_t *buf; /* Current location in buffer */ void *fill=_fill; /* Alias for fill-value buffer */ hssize_t nelmts; /* Number of elements in selection */ hsize_t *off=NULL; /* Array to store sequence offsets */ size_t *len=NULL; /* Array to store sequence lengths */ size_t vector_size; /* Value for vector size */ size_t nseq; /* Number of sequences generated */ size_t curr_seq; /* Current sequnce being worked on */ size_t nbytes; /* Number of bytes used in sequences */ size_t max_bytes; /* Total number of bytes in selection */ herr_t ret_value=SUCCEED; /* return value */ FUNC_ENTER_NOAPI(H5S_select_fill, FAIL); /* Check args */ assert(fill_size>0); assert(space); assert(_buf); /* Check if we need a temporary fill value buffer */ if(fill==NULL) { if (NULL==(fill = H5FL_BLK_ALLOC(type_elem,fill_size,1))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "fill value buffer allocation failed"); } /* end if */ /* Get the hyperslab vector size */ /* (from the default data transfer property list, for now) */ dx_plist = H5I_object(H5P_DATASET_XFER_DEFAULT); assert(dx_plist); if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value"); /* Allocate the vector I/O arrays */ if((len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); if((off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); /* Allocate iterator */ if((iter = H5FL_ALLOC(H5S_sel_iter_t,1))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate selection iterator"); /* Initialize iterator */ if ((*space->select.iter_init)(space, fill_size, iter)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); /* Get the number of elements in selection */ if((nelmts = (*space->select.get_npoints)(space))<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't get number of elements selected"); /* Compute the number of bytes to process */ H5_CHECK_OVERFLOW(nelmts,hssize_t,size_t); max_bytes=(size_t)nelmts*fill_size; /* Loop, while elements left in selection */ while(max_bytes>0) { /* Get the sequences of bytes */ if((*space->select.get_seq_list)(space,0,iter,fill_size,vector_size,max_bytes,&nseq,&nbytes,off,len)<0) HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); /* Loop over sequences */ for(curr_seq=0; curr_seqselect.iter_release)(iter)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); H5FL_FREE(H5S_sel_iter_t,iter); } /* end if */ /* Release length & offset vectors */ if(len!=NULL) H5FL_ARR_FREE(size_t,len); if(off!=NULL) H5FL_ARR_FREE(hsize_t,off); /* Release fill value, if allocated */ if(_fill==NULL && fill) H5FL_BLK_FREE(type_elem,fill); FUNC_LEAVE (ret_value); } /* H5S_select_fill() */ /*------------------------------------------------------------------------- * Function: H5S_select_fscat * * Purpose: Scatters dataset elements from the type conversion buffer BUF * to the file F where the data points are arranged according to * the file data space FILE_SPACE and stored according to * LAYOUT and EFL. Each element is ELMT_SIZE bytes. * The caller is requesting that NELMTS elements are copied. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, June 20, 2002 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5S_select_fscat (H5F_t *f, const struct H5O_layout_t *layout, H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *space, H5S_sel_iter_t *iter, hsize_t nelmts, hid_t dxpl_id, const void *_buf) { const uint8_t *buf=_buf; /* Alias for pointer arithmetic */ hsize_t *off=NULL; /* Array to store sequence offsets */ size_t *len=NULL; /* Array to store sequence lengths */ size_t vector_size; /* Value for vector size */ size_t maxbytes; /* Number of bytes in the buffer */ size_t nseq; /* Number of sequences generated */ size_t nbytes; /* Number of bytes used in sequences */ H5P_genplist_t *dx_plist; /* Dataset transfer property list */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5S_select_fscat, FAIL); /* Check args */ assert (f); assert (layout); assert (elmt_size>0); assert (space); assert (iter); assert (nelmts>0); assert (_buf); /* Get the hyperslab vector size */ if(NULL == (dx_plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file access property list"); if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value"); /* Allocate the vector I/O arrays */ if((len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); if((off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); /* Compute the number of bytes available in buffer */ H5_ASSIGN_OVERFLOW(maxbytes,nelmts*elmt_size,hsize_t,size_t); /* Loop until all elements are written */ while(maxbytes>0) { /* Get list of sequences for selection to write */ if((*space->select.get_seq_list)(space,H5S_GET_SEQ_LIST_SORTED,iter,elmt_size,vector_size,maxbytes,&nseq,&nbytes,off,len)<0) HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); /* Write sequence list out */ if (H5F_seq_writev(f, dxpl_id, layout, dc_plist, space, elmt_size, nseq, len, off, buf)<0) HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); /* Update buffer */ buf += nbytes; /* Decrement number of elements left to process */ assert(nbytes%elmt_size==0); maxbytes -= nbytes; } /* end while */ done: if(len!=NULL) H5FL_ARR_FREE(size_t,len); if(off!=NULL) H5FL_ARR_FREE(hsize_t,off); FUNC_LEAVE (ret_value); } /* H5S_select_fscat() */ /*------------------------------------------------------------------------- * Function: H5S_select_fgath * * Purpose: Gathers data points from file F and accumulates them in the * type conversion buffer BUF. The LAYOUT argument describes * how the data is stored on disk and EFL describes how the data * is organized in external files. ELMT_SIZE is the size in * bytes of a datum which this function treats as opaque. * FILE_SPACE describes the data space of the dataset on disk * and the elements that have been selected for reading (via * hyperslab, etc). This function will copy at most NELMTS * elements. * * Return: Success: Number of elements copied. * Failure: 0 * * Programmer: Quincey Koziol * Monday, June 24, 2002 * * Modifications: * *------------------------------------------------------------------------- */ hsize_t H5S_select_fgath (H5F_t *f, const struct H5O_layout_t *layout, H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *space, H5S_sel_iter_t *iter, hsize_t nelmts, hid_t dxpl_id, void *_buf/*out*/) { uint8_t *buf=_buf; /* Alias for pointer arithmetic */ hsize_t *off=NULL; /* Array to store sequence offsets */ size_t *len=NULL; /* Array to store sequence lengths */ size_t vector_size; /* Value for vector size */ size_t maxbytes; /* Number of bytes in the buffer */ size_t nseq; /* Number of sequences generated */ size_t nbytes; /* Number of bytes used in sequences */ H5P_genplist_t *dx_plist; /* Dataset transfer property list */ hsize_t ret_value=nelmts; /* Return value */ FUNC_ENTER_NOAPI(H5S_select_fgath, 0); /* Check args */ assert (f); assert (layout); assert (elmt_size>0); assert (space); assert (iter); assert (nelmts>0); assert (_buf); /* Get the hyperslab vector size */ if(NULL == (dx_plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a file access property list"); if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, 0, "unable to get value"); /* Allocate the vector I/O arrays */ if((len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O length vector array"); if((off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O offset vector array"); /* Compute the number of bytes available in buffer */ H5_ASSIGN_OVERFLOW(maxbytes,nelmts*elmt_size,hsize_t,size_t); /* Loop until all elements are written */ while(maxbytes>0) { /* Get list of sequences for selection to write */ if((*space->select.get_seq_list)(space,H5S_GET_SEQ_LIST_SORTED,iter,elmt_size,vector_size,maxbytes,&nseq,&nbytes,off,len)<0) HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed"); /* Read sequence list in */ if (H5F_seq_readv(f, dxpl_id, layout, dc_plist, space, elmt_size, nseq, len, off, buf)<0) HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); /* Update buffer */ buf += nbytes; /* Decrement number of elements left to process */ assert(nbytes%elmt_size==0); maxbytes -= nbytes; } /* end while */ done: if(len!=NULL) H5FL_ARR_FREE(size_t,len); if(off!=NULL) H5FL_ARR_FREE(hsize_t,off); FUNC_LEAVE (ret_value); } /* H5S_select_fgath() */ /*------------------------------------------------------------------------- * Function: H5S_select_mscat * * Purpose: Scatters NELMTS data points from the scatter buffer * TSCAT_BUF to the application buffer BUF. Each element is * ELMT_SIZE bytes and they are organized in application memory * according to SPACE. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Monday, July 8, 2002 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5S_select_mscat (const void *_tscat_buf, size_t elmt_size, const H5S_t *space, H5S_sel_iter_t *iter, hsize_t nelmts, hid_t dxpl_id, void *_buf/*out*/) { H5P_genplist_t *dx_plist; /* Dataset transfer property list */ uint8_t *buf=(uint8_t *)_buf; /* Get local copies for address arithmetic */ const uint8_t *tscat_buf=(const uint8_t *)_tscat_buf; hsize_t *off=NULL; /* Array to store sequence offsets */ size_t vector_size; /* Value for vector size */ size_t *len=NULL; /* Array to store sequence lengths */ size_t curr_len; /* Length of bytes left to process in sequence */ size_t maxbytes; /* Number of bytes in the buffer */ size_t nseq; /* Number of sequences generated */ size_t curr_seq; /* Current sequence being processed */ size_t nbytes; /* Number of bytes used in sequences */ herr_t ret_value=SUCCEED; /* Number of elements scattered */ FUNC_ENTER_NOAPI(H5S_select_mscat, FAIL); /* Check args */ assert (tscat_buf); assert (elmt_size>0); assert (space); assert (iter); assert (nelmts>0); assert (buf); /* Get the hyperslab vector size */ if(NULL == (dx_plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list"); if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value"); /* Allocate the vector I/O arrays */ if((len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); if((off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); /* Compute the number of bytes available in buffer */ H5_ASSIGN_OVERFLOW(maxbytes,nelmts*elmt_size,hsize_t,size_t); /* Loop until all elements are written */ while(maxbytes>0) { /* Get list of sequences for selection to write */ if((*space->select.get_seq_list)(space,0,iter,elmt_size,vector_size,maxbytes,&nseq,&nbytes,off,len)<0) HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed"); /* Loop, while sequences left to process */ for(curr_seq=0; curr_seq0); assert (space); assert (iter); assert (nelmts>0); assert (tgath_buf); /* Get the hyperslab vector size */ if(NULL == (dx_plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset transfer property list"); if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, 0, "unable to get value"); /* Allocate the vector I/O arrays */ if((len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O length vector array"); if((off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "can't allocate I/O offset vector array"); /* Compute the number of bytes available in buffer */ H5_ASSIGN_OVERFLOW(maxbytes,nelmts*elmt_size,hsize_t,size_t); /* Loop until all elements are written */ while(maxbytes>0) { /* Get list of sequences for selection to write */ if((*space->select.get_seq_list)(space,0,iter,elmt_size,vector_size,maxbytes,&nseq,&nbytes,off,len)<0) HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed"); /* Loop, while sequences left to process */ for(curr_seq=0; curr_seqselect.iter_init)(file_space, elmt_size, file_iter)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); /* Allocate memory iterator */ if((mem_iter = H5FL_ALLOC(H5S_sel_iter_t,1))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate selection iterator"); /* Initialize memory iterator */ if ((*mem_space->select.iter_init)(mem_space, elmt_size, mem_iter)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); /* Get number of bytes in selection */ maxbytes=(*file_space->select.get_npoints)(file_space)*elmt_size; /* Initialize sequence counts */ curr_mem_seq=curr_file_seq=0; mem_nseq=file_nseq=0; /* Loop, until all bytes are processed */ while(maxbytes>0) { /* Check if more file sequences are needed */ if(curr_file_seq>=file_nseq) { /* Get sequences for file selection */ if((*file_space->select.get_seq_list)(file_space,H5S_GET_SEQ_LIST_SORTED,file_iter,elmt_size,vector_size,maxbytes,&file_nseq,&file_nbytes,file_off,file_len)<0) HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); /* Start at the beginning of the sequences again */ curr_file_seq=0; } /* end if */ /* Check if more memory sequences are needed */ if(curr_mem_seq>=mem_nseq) { /* Get sequences for memory selection */ if((*mem_space->select.get_seq_list)(mem_space,0,mem_iter,elmt_size,vector_size,maxbytes,&mem_nseq,&mem_nbytes,mem_off,mem_len)<0) HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); /* Start at the beginning of the sequences again */ curr_mem_seq=0; /* Set the buffer pointer using the first sequence */ H5_CHECK_OVERFLOW(mem_off[0],hsize_t,size_t); buf=(uint8_t *)_buf+(size_t)mem_off[0]; } /* end if */ /* Check if current file sequence will fit into current memory sequence */ if(mem_len[curr_mem_seq]>=file_len[curr_file_seq]) { /* Save the current number file sequence */ orig_file_seq=curr_file_seq; /* Determine how many file sequences will fit into current memory sequence */ tmp_file_len=0; tot_file_seq=0; while((tmp_file_len+file_len[curr_file_seq])<=mem_len[curr_mem_seq] && curr_file_seqselect.iter_release)(file_iter)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); H5FL_FREE(H5S_sel_iter_t,file_iter); } /* end if */ /* Release memory selection iterator */ if(mem_iter!=NULL) { if ((*mem_space->select.iter_release)(mem_iter)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); H5FL_FREE(H5S_sel_iter_t,mem_iter); } /* end if */ /* Free vector arrays */ if(file_len!=NULL) H5FL_ARR_FREE(size_t,file_len); if(file_off!=NULL) H5FL_ARR_FREE(hsize_t,file_off); if(mem_len!=NULL) H5FL_ARR_FREE(size_t,mem_len); if(mem_off!=NULL) H5FL_ARR_FREE(hsize_t,mem_off); FUNC_LEAVE(ret_value); } /* end H5S_select_read() */ /*------------------------------------------------------------------------- * Function: H5S_select_write * * Purpose: Writes directly from application memory into a file * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Tuesday, July 23, 2002 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5S_select_write(H5F_t *f, const H5O_layout_t *layout, H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, const void *_buf/*out*/) { H5P_genplist_t *dx_plist; /* Dataset transfer property list */ H5S_sel_iter_t *mem_iter=NULL; /* Memory selection iteration info */ H5S_sel_iter_t *file_iter=NULL; /* File selection iteration info */ const uint8_t *buf=NULL; /* Local buffer pointer, for address arithmetic */ hsize_t *mem_off=NULL; /* Array to store sequence offsets in memory */ hsize_t *file_off=NULL; /* Array to store sequence offsets in the file */ size_t vector_size; /* Value for vector size */ size_t *mem_len=NULL; /* Array to store sequence lengths in memory */ size_t *file_len=NULL; /* Array to store sequence lengths in the file */ size_t maxbytes; /* Number of bytes in selection */ size_t mem_nseq; /* Number of sequences generated in the file */ size_t file_nseq; /* Number of sequences generated in memory */ size_t mem_nbytes; /* Number of bytes used in memory sequences */ size_t file_nbytes; /* Number of bytes used in file sequences */ size_t curr_mem_seq; /* Current memory sequence to operate on */ size_t curr_file_seq; /* Current file sequence to operate on */ size_t tmp_file_len; /* Temporary number of bytes in file sequence */ unsigned partial_file; /* Whether a partial file sequence was accessed */ size_t orig_file_len=0; /* Original file sequence length for partial file access */ size_t orig_file_seq; /* Original file sequence to operate on */ size_t tot_file_seq; /* Number of file sequences to access */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5S_select_write, FAIL); /* Get the hyperslab vector size */ if(NULL == (dx_plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list"); if (H5P_get(dx_plist,H5D_XFER_HYPER_VECTOR_SIZE_NAME,&vector_size)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value"); /* Allocate the vector I/O arrays */ if((mem_len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); if((mem_off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); if((file_len = H5FL_ARR_ALLOC(size_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); if((file_off = H5FL_ARR_ALLOC(hsize_t,vector_size,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); /* Allocate file iterator */ if((file_iter = H5FL_ALLOC(H5S_sel_iter_t,1))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate selection iterator"); /* Initialize file iterator */ if ((*file_space->select.iter_init)(file_space, elmt_size, file_iter)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); /* Allocate memory iterator */ if((mem_iter = H5FL_ALLOC(H5S_sel_iter_t,1))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate selection iterator"); /* Initialize memory iterator */ if ((*mem_space->select.iter_init)(mem_space, elmt_size, mem_iter)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); /* Get number of bytes in selection */ maxbytes=(*file_space->select.get_npoints)(file_space)*elmt_size; /* Initialize sequence counts */ curr_mem_seq=curr_file_seq=0; mem_nseq=file_nseq=0; /* Loop, until all bytes are processed */ while(maxbytes>0) { /* Check if more file sequences are needed */ if(curr_file_seq>=file_nseq) { /* Get sequences for file selection */ if((*file_space->select.get_seq_list)(file_space,H5S_GET_SEQ_LIST_SORTED,file_iter,elmt_size,vector_size,maxbytes,&file_nseq,&file_nbytes,file_off,file_len)<0) HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); /* Start at the beginning of the sequences again */ curr_file_seq=0; } /* end if */ /* Check if more memory sequences are needed */ if(curr_mem_seq>=mem_nseq) { /* Get sequences for memory selection */ if((*mem_space->select.get_seq_list)(mem_space,0,mem_iter,elmt_size,vector_size,maxbytes,&mem_nseq,&mem_nbytes,mem_off,mem_len)<0) HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); /* Start at the beginning of the sequences again */ curr_mem_seq=0; /* Set the buffer pointer using the first sequence */ H5_CHECK_OVERFLOW(mem_off[0],hsize_t,size_t); buf=(const uint8_t *)_buf+(size_t)mem_off[0]; } /* end if */ /* Check if current file sequence will fit into current memory sequence */ if(mem_len[curr_mem_seq]>=file_len[curr_file_seq]) { /* Save the current number file sequence */ orig_file_seq=curr_file_seq; /* Determine how many file sequences will fit into current memory sequence */ tmp_file_len=0; tot_file_seq=0; while((tmp_file_len+file_len[curr_file_seq])<=mem_len[curr_mem_seq] && curr_file_seqselect.iter_release)(file_iter)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); H5FL_FREE(H5S_sel_iter_t,file_iter); } /* end if */ /* Release memory selection iterator */ if(mem_iter!=NULL) { if ((*mem_space->select.iter_release)(mem_iter)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); H5FL_FREE(H5S_sel_iter_t,mem_iter); } /* end if */ /* Free vector arrays */ if(file_len!=NULL) H5FL_ARR_FREE(size_t,file_len); if(file_off!=NULL) H5FL_ARR_FREE(hsize_t,file_off); if(mem_len!=NULL) H5FL_ARR_FREE(size_t,mem_len); if(mem_off!=NULL) H5FL_ARR_FREE(hsize_t,mem_off); FUNC_LEAVE(ret_value); } /* end H5S_select_write() */