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/*
# This file is part of libkd.
# Licensed under a 3-clause BSD style license - see LICENSE
*/
#ifndef KDTREE_NO_FITS
#include "kdtree_fits_io.h"
#include "kdtree.h"
#include "fitsioutils.h"
#include "ioutils.h"
#include "errors.h"
#define KDTREE_FITS_VERSION 1
static char* get_table_name(const char* treename, const char* tabname) {
char* rtn;
if (!treename) {
return strdup_safe(tabname);
}
asprintf_safe(&rtn, "%s_%s", tabname, treename);
return rtn;
}
int MANGLE(kdtree_read_fits)(kdtree_fits_t* io, kdtree_t* kd) {
fitsbin_chunk_t chunk;
fitsbin_chunk_init(&chunk);
// kd->lr
chunk.tablename = get_table_name(kd->name, KD_STR_LR);
chunk.itemsize = sizeof(u32);
chunk.nrows = kd->nbottom;
chunk.required = FALSE;
if (kdtree_fits_read_chunk(io, &chunk) == 0) {
kd->lr = chunk.data;
}
free(chunk.tablename);
// kd->perm
chunk.tablename = get_table_name(kd->name, KD_STR_PERM);
chunk.itemsize = sizeof(u32);
chunk.nrows = kd->ndata;
chunk.required = FALSE;
if (kdtree_fits_read_chunk(io, &chunk) == 0) {
kd->perm = chunk.data;
}
free(chunk.tablename);
// kd->bb
chunk.tablename = get_table_name(kd->name, KD_STR_BB);
chunk.itemsize = sizeof(ttype) * kd->ndim * 2;
chunk.nrows = 0;
chunk.required = FALSE;
if (kdtree_fits_read_chunk(io, &chunk) == 0) {
int nbb_old = (kd->nnodes + 1) / 2 - 1;
int nbb_new = kd->nnodes;
// accept (but warn about) old-school buggy BB extension.
if (chunk.nrows == nbb_new) {
} else if (chunk.nrows == nbb_old) {
ERROR("Warning: this file contains an old, buggy, %s "
"extension; it has %i rather than %i items. Proceeding "
"anyway, but this is probably going to cause problems!",
chunk.tablename, nbb_old, nbb_new);
} else {
// error?
ERROR("Bounding-box table %s should contain either %i (new) or "
"%i (old) bounding-boxes, but it has %i.",
chunk.tablename, nbb_new, nbb_old, chunk.nrows);
free(chunk.tablename);
return -1;
}
kd->bb.any = chunk.data;
kd->n_bb = chunk.nrows;
}
free(chunk.tablename);
// kd->split
chunk.tablename = get_table_name(kd->name, KD_STR_SPLIT);
chunk.itemsize = sizeof(ttype);
chunk.nrows = kd->ninterior;
chunk.required = FALSE;
if (kdtree_fits_read_chunk(io, &chunk) == 0) {
kd->split.any = chunk.data;
}
free(chunk.tablename);
// kd->splitdim
chunk.tablename = get_table_name(kd->name, KD_STR_SPLITDIM);
chunk.itemsize = sizeof(u8);
chunk.nrows = kd->ninterior;
chunk.required = FALSE;
if (kdtree_fits_read_chunk(io, &chunk) == 0) {
kd->splitdim = chunk.data;
}
free(chunk.tablename);
// kd->data
chunk.tablename = get_table_name(kd->name, KD_STR_DATA);
chunk.itemsize = sizeof(dtype) * kd->ndim;
chunk.nrows = kd->ndata;
chunk.required = TRUE;
if (kdtree_fits_read_chunk(io, &chunk) == 0) {
kd->data.any = chunk.data;
}
free(chunk.tablename);
// kd->minval/kd->maxval/kd->scale
chunk.tablename = get_table_name(kd->name, KD_STR_RANGE);
chunk.itemsize = sizeof(double);
chunk.nrows = (kd->ndim * 2 + 1);
chunk.required = FALSE;
if (kdtree_fits_read_chunk(io, &chunk) == 0) {
double* r;
r = chunk.data;
kd->minval = r;
kd->maxval = r + kd->ndim;
kd->scale = r[kd->ndim * 2];
kd->invscale = 1.0 / kd->scale;
}
free(chunk.tablename);
if (!(kd->bb.any ||
(kd->split.any && (TTYPE_INTEGER || kd->splitdim)))) {
ERROR("kdtree contains neither bounding boxes nor split+dim data");
return -1;
}
if ((TTYPE_INTEGER && !ETYPE_INTEGER) &&
!(kd->minval && kd->maxval)) {
ERROR("treee does not contain required range information");
return -1;
}
if (kd->split.any) {
if (kd->splitdim)
kd->splitmask = UINT32_MAX;
else
compute_splitbits(kd);
}
return 0;
}
#define WRITE_CHUNK() \
do { \
if (flip_endian) { \
if (fitsbin_write_chunk_flipped(fb, &chunk, wordsize)) { \
ERROR("Failed to write (flipped) kdtree chunk"); \
fitsbin_chunk_clean(&chunk); \
return -1; \
} \
} else { \
if (fid ? \
fitsbin_write_chunk_to(fb, &chunk, fid) : \
fitsbin_write_chunk(fb, &chunk)) { \
ERROR("Failed to write kdtree chunk"); \
fitsbin_chunk_clean(&chunk); \
return -1; \
} \
} \
} while (0)
int MANGLE(kdtree_write_fits)(kdtree_fits_t* io, const kdtree_t* kd,
const qfits_header* inhdr, anbool flip_endian,
FILE* fid) {
fitsbin_chunk_t chunk;
fitsbin_t* fb = kdtree_fits_get_fitsbin(io);
qfits_header* hdr;
int wordsize = 0;
// haven't bothered to support this.
assert(!(flip_endian && fid));
fitsbin_chunk_init(&chunk);
// kdtree header is an empty fitsbin_chunk.
chunk.tablename = get_table_name(kd->name, KD_STR_HEADER);
hdr = fitsbin_get_chunk_header(fb, &chunk);
if (inhdr)
fits_copy_all_headers(inhdr, hdr, NULL);
if (flip_endian)
fits_add_reverse_endian(hdr);
else
fits_add_endian(hdr);
fits_header_addf (hdr, "KDT_NAME", "kdtree: name of this tree", "'%s'", kd->name ? kd->name : "");
fits_header_add_int(hdr, "KDT_NDAT", kd->ndata, "kdtree: number of data points");
fits_header_add_int(hdr, "KDT_NDIM", kd->ndim, "kdtree: number of dimensions");
fits_header_add_int(hdr, "KDT_NNOD", kd->nnodes, "kdtree: number of nodes");
fits_header_add_int(hdr, "KDT_VER", KDTREE_FITS_VERSION, "kdtree: version number");
qfits_header_add(hdr, "KDT_EXT", (char*)kdtree_kdtype_to_string(kdtree_exttype(kd)), "kdtree: external type", NULL);
qfits_header_add(hdr, "KDT_INT", (char*)kdtree_kdtype_to_string(kdtree_treetype(kd)), "kdtree: type of the tree's structures", NULL);
qfits_header_add(hdr, "KDT_DATA", (char*)kdtree_kdtype_to_string(kdtree_datatype(kd)), "kdtree: type of the data", NULL);
qfits_header_add(hdr, "KDT_LINL", (kd->has_linear_lr ? "T" : "F"), "kdtree: has_linear_lr", NULL);
WRITE_CHUNK();
free(chunk.tablename);
fitsbin_chunk_reset(&chunk);
if (kd->lr) {
chunk.tablename = get_table_name(kd->name, KD_STR_LR);
chunk.itemsize = sizeof(u32);
chunk.nrows = kd->nbottom;
chunk.data = kd->lr;
if (flip_endian)
wordsize = sizeof(u32);
hdr = fitsbin_get_chunk_header(fb, &chunk);
fits_add_long_comment
(hdr, "The \"%s\" table contains the kdtree \"LR\" array. "
"This array has one %u-byte, native-endian unsigned int for each "
"leaf node in the tree. For each node, it gives the index of the "
"rightmost data point owned by the node.",
chunk.tablename, chunk.itemsize);
WRITE_CHUNK();
free(chunk.tablename);
fitsbin_chunk_reset(&chunk);
}
if (kd->perm) {
chunk.tablename = get_table_name(kd->name, KD_STR_PERM);
chunk.itemsize = sizeof(u32);
chunk.nrows = kd->ndata;
chunk.data = kd->perm;
if (flip_endian)
wordsize = sizeof(u32);
hdr = fitsbin_get_chunk_header(fb, &chunk);
fits_add_long_comment
(hdr, "The \"%s\" table contains the kdtree permutation array. "
"This array contains one %u-byte, native-endian unsigned int for "
"each data point in the tree. For each data point, it gives the "
"index that the data point had in the original array on which the "
"kdtree was built.", chunk.tablename, chunk.itemsize);
WRITE_CHUNK();
free(chunk.tablename);
fitsbin_chunk_reset(&chunk);
}
if (kd->bb.any) {
chunk.tablename = get_table_name(kd->name, KD_STR_BB);
chunk.itemsize = sizeof(ttype) * kd->ndim * 2;
chunk.nrows = kd->nnodes;
chunk.data = kd->bb.any;
if (flip_endian)
wordsize = sizeof(ttype);
hdr = fitsbin_get_chunk_header(fb, &chunk);
fits_add_long_comment
(hdr, "The \"%s\" table contains the kdtree bounding-box array. "
"This array contains two %u-dimensional points, stored as %u-byte, "
"native-endian %ss, for each node in the tree. Each data "
"point owned by a node is contained within its bounding box.",
chunk.tablename, (unsigned int)kd->ndim,
(unsigned int)sizeof(ttype),
kdtree_kdtype_to_string(kdtree_treetype(kd)));
WRITE_CHUNK();
free(chunk.tablename);
fitsbin_chunk_reset(&chunk);
}
if (kd->split.any) {
chunk.tablename = get_table_name(kd->name, KD_STR_SPLIT);
chunk.itemsize = sizeof(ttype);
chunk.nrows = kd->ninterior;
chunk.data = kd->split.any;
if (flip_endian)
wordsize = sizeof(ttype);
hdr = fitsbin_get_chunk_header(fb, &chunk);
if (!kd->splitdim) {
fits_add_long_comment
(hdr, "The \"%s\" table contains the kdtree splitting-plane "
"boundaries, and also the splitting dimension, packed into "
"a %u-byte, native-endian %s, for each interior node in the tree. "
"The splitting dimension is packed into the low %u bit%s, and the "
"splitting location uses the remaining bits. "
"The left child of a node contains data points that lie on the "
"low side of the splitting plane, and the right child contains "
"data points on the high side of the plane.",
chunk.tablename, chunk.itemsize,
kdtree_kdtype_to_string(kdtree_treetype(kd)),
kd->dimbits, (kd->dimbits > 1 ? "s" : ""));
} else {
fits_add_long_comment
(hdr, "The \"%s\" table contains the kdtree splitting-plane "
"boundaries as %u-byte, native-endian %s, for each interior node in the tree. "
"The dimension along which the splitting-plane splits is stored in "
"a separate array. "
"The left child of a node contains data points that lie on the "
"low side of the splitting plane, and the right child contains "
"data points on the high side of the plane.",
chunk.tablename, chunk.itemsize,
kdtree_kdtype_to_string(kdtree_treetype(kd)));
}
WRITE_CHUNK();
free(chunk.tablename);
fitsbin_chunk_reset(&chunk);
}
if (kd->splitdim) {
chunk.tablename = get_table_name(kd->name, KD_STR_SPLITDIM);
chunk.itemsize = sizeof(u8);
chunk.nrows = kd->ninterior;
chunk.data = kd->splitdim;
if (flip_endian)
wordsize = sizeof(u8);
hdr = fitsbin_get_chunk_header(fb, &chunk);
fits_add_long_comment
(hdr, "The \"%s\" table contains the kdtree splitting-plane "
"dimensions as %u-byte unsigned ints, for each interior node in the tree. "
"The location of the splitting-plane along that dimension is stored "
"in a separate array. "
"The left child of a node contains data points that lie on the "
"low side of the splitting plane, and the right child contains "
"data points on the high side of the plane.",
chunk.tablename, chunk.itemsize);
WRITE_CHUNK();
free(chunk.tablename);
fitsbin_chunk_reset(&chunk);
}
if (kd->minval && kd->maxval) {
double tempranges[kd->ndim * 2 + 1];
int d;
memcpy(tempranges, kd->minval, kd->ndim * sizeof(double));
memcpy(tempranges + kd->ndim, kd->maxval, kd->ndim * sizeof(double));
tempranges[kd->ndim*2] = kd->scale;
chunk.tablename = get_table_name(kd->name, KD_STR_RANGE);
chunk.itemsize = sizeof(double);
chunk.nrows = (kd->ndim * 2 + 1);
chunk.data = tempranges;
if (flip_endian)
wordsize = sizeof(double);
hdr = fitsbin_get_chunk_header(fb, &chunk);
fits_add_long_comment
(hdr, "The \"%s\" table contains the scaling parameters of the "
"kdtree. This tells how to convert from the format of the data "
"to the internal format of the tree (and vice versa). "
"It is stored as an array "
"of %u-byte, native-endian doubles. The first %u elements are "
"the lower bound of the data, the next %u elements are the upper "
"bound, and the final element is the scale, which says how many "
"tree units there are per data unit.",
chunk.tablename, chunk.itemsize, (unsigned int)kd->ndim, (unsigned int)kd->ndim);
fits_add_long_comment
(hdr, "For reference, here are the ranges of the data. Note that "
"this is not used by the libkd software, it's just for human readers.");
for (d=0; d<kd->ndim; d++)
fits_add_long_comment
(hdr, " dim %i: [%g, %g]", d, kd->minval[d], kd->maxval[d]);
fits_add_long_comment(hdr, "scale: %g", kd->scale);
fits_add_long_comment(hdr, "1/scale: %g", kd->invscale);
free(chunk.tablename);
WRITE_CHUNK();
fitsbin_chunk_reset(&chunk);
}
if (kd->data.any) {
chunk.tablename = get_table_name(kd->name, KD_STR_DATA);
chunk.itemsize = sizeof(dtype) * kd->ndim;
chunk.nrows = kd->ndata;
chunk.data = kd->data.any;
if (flip_endian)
wordsize = sizeof(dtype);
hdr = fitsbin_get_chunk_header(fb, &chunk);
fits_add_long_comment
(hdr, "The \"%s\" table contains the kdtree data. "
"It is stored as %u-dimensional, %u-byte native-endian %ss.",
chunk.tablename, (unsigned int)kd->ndim, (unsigned int)sizeof(dtype),
kdtree_kdtype_to_string(kdtree_datatype(kd)));
free(chunk.tablename);
WRITE_CHUNK();
fitsbin_chunk_reset(&chunk);
}
return 0;
}
#undef WRITE_CHUNK
#endif
|
