commit 2ca056b9efdda62c487a2e6aec1e444d4b1d683c
parent 7b5b0d50f6859aa72f7f73b2bd6e3b7ed7fe97d5
Author: Vincent Forest <vincent.forest@meso-star.com>
Date: Fri, 10 Aug 2018 14:21:20 +0200
Store the grid layout wrt morton order
Diffstat:
3 files changed, 101 insertions(+), 39 deletions(-)
diff --git a/src/htrdr_c.h b/src/htrdr_c.h
@@ -33,6 +33,49 @@ wavelength_to_wavenumber(const double lambda/*In nanometer*/)
return wavenumber_to_wavelength(lambda);
}
+static INLINE uint64_t
+morton3D_encode_u21(const uint32_t u21)
+{
+ uint64_t u64 = u21 & ((1<<21) - 1);
+ ASSERT(u21 <= ((1 << 21) - 1));
+ u64 = (u64 | (u64 << 32)) & 0xFFFF00000000FFFF;
+ u64 = (u64 | (u64 << 16)) & 0x00FF0000FF0000FF;
+ u64 = (u64 | (u64 << 8)) & 0xF00F00F00F00F00F;
+ u64 = (u64 | (u64 << 4)) & 0x30C30C30C30C30C3;
+ u64 = (u64 | (u64 << 2)) & 0x9249249249249249;
+ return u64;
+}
+
+static INLINE uint32_t
+morton3D_decode_u21(const uint64_t u64)
+{
+ uint64_t tmp = (u64 & 0x9249249249249249);
+ tmp = (tmp | (tmp >> 2)) & 0x30C30C30C30C30C3;
+ tmp = (tmp | (tmp >> 4)) & 0xF00F00F00F00F00F;
+ tmp = (tmp | (tmp >> 8)) & 0x00FF0000FF0000FF;
+ tmp = (tmp | (tmp >> 16)) & 0xFFFF00000000FFFF;
+ tmp = (tmp | (tmp >> 32)) & 0x00000000FFFFFFFF;
+ ASSERT(tmp <= ((1<<21)-1));
+ return (uint32_t)tmp;
+}
+
+static INLINE uint64_t
+morton_xyz_encode_u21(const uint32_t xyz[3])
+{
+ return (morton3D_encode_u21(xyz[0]) << 2)
+ | (morton3D_encode_u21(xyz[1]) << 1)
+ | (morton3D_encode_u21(xyz[2]) << 0);
+}
+
+static INLINE void
+morton_xyz_decode_u21(const uint64_t code, uint32_t xyz[3])
+{
+ ASSERT(xyz && code < ((1ull << 63)-1));
+ xyz[0] = (uint32_t)morton3D_decode_u21(code >> 2);
+ xyz[1] = (uint32_t)morton3D_decode_u21(code >> 1);
+ xyz[2] = (uint32_t)morton3D_decode_u21(code >> 0);
+}
+
extern LOCAL_SYM res_T
open_output_stream
(struct htrdr* htrdr,
diff --git a/src/htrdr_grid.c b/src/htrdr_grid.c
@@ -28,12 +28,17 @@
#include <fcntl.h>
#include <unistd.h> /* sysconf */
+const int32_t GRID_VERSION = 0;
+const int32_t GRID_VERSION_NONE = -1;
+
struct htrdr_grid {
FILE* fp;
char* data;
- size_t definition[3];
+ size_t definition[3]; /* Submitted definition */
+ size_t def_adjusted; /* Adjusted definition along the 3 dimensions */
size_t cell_sz;
size_t pagesize;
+ size_t data_sz; /* Size in bytes of the overall grid data + padding */
ref_T ref;
struct htrdr* htrdr;
@@ -49,19 +54,12 @@ grid_release(ref_T* ref)
ASSERT(ref);
grid = CONTAINER_OF(ref, struct htrdr_grid, ref);
if(grid->fp) {
- const int is_finalized = 1;
- CHK(fwrite(&is_finalized, sizeof(int), 1, grid->fp) == 1);
+ rewind(grid->fp);
+ CHK(fwrite(&GRID_VERSION, sizeof(int), 1, grid->fp) == 1);
fclose(grid->fp);
}
if(grid->data) {
- size_t grid_sz;
- grid_sz =
- grid->definition[0]
- * grid->definition[1]
- * grid->definition[2]
- * grid->cell_sz;
- grid_sz = ALIGN_SIZE(grid_sz, grid->pagesize);
- if(munmap(grid->data, grid_sz)) {
+ if(munmap(grid->data, grid->data_sz)) {
htrdr_log_err(grid->htrdr, "error unmapping the grid data -- %s.\n",
strerror(errno));
ASSERT(0);
@@ -84,9 +82,8 @@ htrdr_grid_create
{
const char byte = 0;
struct htrdr_grid* grid = NULL;
- size_t grid_sz;
+ size_t mcode_max;
long grid_offset;
- int is_finalized = 0;
int n;
res_T res = RES_OK;
ASSERT(htrdr && out_grid && filename && definition);
@@ -131,8 +128,7 @@ htrdr_grid_create
goto error; \
} \
} (void)0
- is_finalized = 0;
- WRITE(&is_finalized, 1, "is_finalized");
+ WRITE(&GRID_VERSION_NONE, 1, "version");
WRITE(&grid->pagesize, 1, "pagesize");
WRITE(&grid->cell_sz, 1, "cell_sz");
WRITE(grid->definition, 3, "definition");
@@ -149,15 +145,19 @@ htrdr_grid_create
goto error;
}
+ grid->def_adjusted = MMAX(MMAX(definition[0], definition[1]), definition[2]);
+ grid->def_adjusted = round_up_pow2(grid->def_adjusted);
+ mcode_max = grid->def_adjusted*grid->def_adjusted*grid->def_adjusted;
+
/* Define the grid size */
- grid_sz = definition[0] * definition[1] * definition[2] * sizeof_cell;
- grid_sz = ALIGN_SIZE(grid_sz, grid->pagesize);
+ grid->data_sz = mcode_max * sizeof_cell;
+ grid->data_sz = ALIGN_SIZE(grid->data_sz, grid->pagesize);
/* Save the position of the grid data into the file */
grid_offset = ftell(grid->fp);
/* Reserve the space for the grid data */
- n = fseek(grid->fp, (long)grid_sz, SEEK_CUR);
+ n = fseek(grid->fp, (long)grid->data_sz, SEEK_CUR);
if(n < 0) {
htrdr_log_err(htrdr,
"%s:%s: could reserve the space to store the grid -- %s.\n", FUNC_NAME,
@@ -174,7 +174,7 @@ htrdr_grid_create
/* Avoid to be positionned on the EOF */
rewind(grid->fp);
- grid->data = mmap(NULL, grid_sz, PROT_READ|PROT_WRITE,
+ grid->data = mmap(NULL, grid->data_sz, PROT_READ|PROT_WRITE,
MAP_SHARED|MAP_POPULATE, fileno(grid->fp), grid_offset);
if(grid->data == MAP_FAILED) {
htrdr_log_err(htrdr, "%s:%s: could not map the grid data -- %s.\n",
@@ -201,11 +201,11 @@ htrdr_grid_open
struct htrdr_grid** out_grid)
{
struct htrdr_grid* grid = NULL;
- size_t grid_sz;
size_t grid_offset;
size_t pagesize;
+ size_t mcode_max;
+ int32_t version;
int fd = -1;
- int is_finalized = 0;
res_T res = RES_OK;
ASSERT(htrdr && filename && out_grid);
@@ -235,9 +235,11 @@ htrdr_grid_open
goto error; \
} \
} (void)0
- READ(&is_finalized, 1, "is_finalized");
- if(!is_finalized) {
- htrdr_log_err(htrdr, "%s:%s: invalid grid.\n", FUNC_NAME, filename);
+ READ(&version, 1, "version");
+ if(version != GRID_VERSION) {
+ htrdr_log_err(htrdr, "%s:%s: incompatible grid version. Loaded version is "
+ "'%i' while the current version is '%i'.\n",
+ FUNC_NAME, filename, version, GRID_VERSION);
res = RES_BAD_ARG;
goto error;
}
@@ -271,14 +273,16 @@ htrdr_grid_open
#undef READ
grid_offset = ALIGN_SIZE((size_t)ftell(grid->fp), grid->pagesize);
- grid_sz =
- grid->definition[0]
- * grid->definition[1]
- * grid->definition[2]
- * grid->cell_sz;
- grid_sz = ALIGN_SIZE(grid_sz, grid->pagesize);
-
- grid->data = mmap(NULL, grid_sz, PROT_READ|PROT_WRITE,
+ grid->def_adjusted = MMAX(grid->definition[0], grid->definition[1]);
+ grid->def_adjusted = MMAX(grid->definition[2], grid->def_adjusted);
+ grid->def_adjusted = round_up_pow2(grid->def_adjusted);
+ mcode_max = grid->def_adjusted*grid->def_adjusted*grid->def_adjusted;
+
+ /* Define the grid size */
+ grid->data_sz = mcode_max * grid->cell_sz;
+ grid->data_sz = ALIGN_SIZE(grid->data_sz, grid->pagesize);
+
+ grid->data = mmap(NULL, grid->data_sz, PROT_READ|PROT_WRITE,
MAP_SHARED|MAP_POPULATE, fileno(grid->fp), (off_t)grid_offset);
if(grid->data == MAP_FAILED) {
@@ -289,8 +293,7 @@ htrdr_grid_open
}
rewind(grid->fp);
- is_finalized = 0;
- CHK(fwrite(&is_finalized, sizeof(int), 1, grid->fp) == 1);
+ CHK(fwrite(&GRID_VERSION_NONE, sizeof(int), 1, grid->fp) == 1);
exit:
*out_grid = grid;
@@ -320,15 +323,25 @@ htrdr_grid_ref_put(struct htrdr_grid* grid)
void*
htrdr_grid_at(struct htrdr_grid* grid, const size_t xyz[3])
{
- size_t slice;
- size_t pitch;
+ uint32_t coords[3];
+ uint64_t mcode;
ASSERT(grid && xyz);
ASSERT(xyz[0] < grid->definition[0]);
ASSERT(xyz[1] < grid->definition[1]);
ASSERT(xyz[2] < grid->definition[2]);
- pitch = grid->definition[0] * grid->cell_sz;
- slice = grid->definition[1] * pitch;
- return grid->data + xyz[2]*slice + xyz[1]*pitch + xyz[0]*grid->cell_sz;
+ coords[0] = (uint32_t)xyz[0];
+ coords[1] = (uint32_t)xyz[1];
+ coords[2] = (uint32_t)xyz[2];
+ mcode = morton_xyz_encode_u21(coords);
+ return htrdr_grid_at_mcode(grid, mcode);
+}
+
+void*
+htrdr_grid_at_mcode(struct htrdr_grid* grid, const uint64_t mcode)
+{
+ ASSERT(grid);
+ ASSERT(mcode < grid->def_adjusted*grid->def_adjusted*grid->def_adjusted);
+ return grid->data + mcode*grid->cell_sz;
}
void
diff --git a/src/htrdr_grid.h b/src/htrdr_grid.h
@@ -50,6 +50,12 @@ htrdr_grid_at
(struct htrdr_grid* grid,
const size_t xyz[3]);
+/* Follow the convention of the morton_xyz_encode_u21 function. */
+extern LOCAL_SYM void*
+htrdr_grid_at_mcode
+ (struct htrdr_grid* grid,
+ const uint64_t mcode);
+
extern LOCAL_SYM void
htrdr_grid_get_definition
(struct htrdr_grid* grid,
