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r.univar_main.c
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r.univar_main.c
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/*
* r.univar
*
* Calculates univariate statistics from the non-null cells of a GRASS raster
* map
*
* Copyright (C) 2004-2006, 2012 by the GRASS Development Team
* Author(s): Hamish Bowman, University of Otago, New Zealand
* Extended stats: Martin Landa
* Zonal stats: Markus Metz
*
* This program is free software under the GNU General Public
* License (>=v2). Read the file COPYING that comes with GRASS
* for details.
*
* This program is a replacement for the r.univar shell script
*/
#if defined(_OPENMP)
#include <omp.h>
#endif
#include <assert.h>
#include <string.h>
#include <float.h>
#include "globals.h"
param_type param;
zone_type zone_info;
/* Parallelization
* Only raster statistics reduction in process_raster() is parallelized.
* print_stats*() where sorting takes place for percentile computation are not.
* We may try parallel sorting algorithms in the future for further speedup.
*/
typedef struct zone_bucket {
size_t n;
size_t n_alloc;
void *nextp;
CELL *cells;
FCELL *fcells;
DCELL *dcells;
} zone_bucket;
typedef struct zone_workspace {
double sum;
double sumsq;
double sum_abs;
size_t size;
double min;
double max;
zone_bucket bucket;
} zone_workspace;
typedef struct thread_workspace {
int fd;
int fdz;
void *raster_row;
CELL *zoneraster_row;
} thread_workspace;
/* ************************************************************************* */
/* Set up the arguments we are expecting ********************************** */
/* ************************************************************************* */
void set_params(void)
{
param.inputfile = G_define_standard_option(G_OPT_R_MAPS);
param.zonefile = G_define_standard_option(G_OPT_R_MAP);
param.zonefile->key = "zones";
param.zonefile->required = NO;
param.zonefile->description =
_("Raster map used for zoning, must be of type CELL");
param.output_file = G_define_standard_option(G_OPT_F_OUTPUT);
param.output_file->required = NO;
param.output_file->description =
_("Name for output file (if omitted or \"-\" output to stdout)");
param.output_file->guisection = _("Output settings");
param.percentile = G_define_option();
param.percentile->key = "percentile";
param.percentile->type = TYPE_DOUBLE;
param.percentile->required = NO;
param.percentile->multiple = YES;
param.percentile->options = "0-100";
param.percentile->answer = "90";
param.percentile->description =
_("Percentile to calculate (requires extended statistics flag)");
param.percentile->guisection = _("Extended");
param.nprocs = G_define_standard_option(G_OPT_M_NPROCS);
param.separator = G_define_standard_option(G_OPT_F_SEP);
param.separator->guisection = _("Formatting");
param.shell_style = G_define_flag();
param.shell_style->key = 'g';
param.shell_style->description = _("Print the stats in shell script style");
param.shell_style->guisection = _("Formatting");
param.extended = G_define_flag();
param.extended->key = 'e';
param.extended->description = _("Calculate extended statistics");
param.extended->guisection = _("Extended");
param.table = G_define_flag();
param.table->key = 't';
param.table->description =
_("Table output format instead of standard output format");
param.table->guisection = _("Formatting");
param.use_rast_region = G_define_flag();
param.use_rast_region->key = 'r';
param.use_rast_region->description =
_("Use the native resolution and extent of the raster map, instead of "
"the current region");
return;
}
static int open_raster(const char *infile);
static univar_stat *univar_stat_with_percentiles(int map_type);
static void process_raster(univar_stat *stats, thread_workspace *tw,
const struct Cell_head *region, int nprocs);
/* *************************************************************** */
/* **** the main functions for r.univar ************************** */
/* *************************************************************** */
int main(int argc, char *argv[])
{
int rasters;
struct Cell_head region;
struct GModule *module;
univar_stat *stats;
char **p, *z;
int cell_type, min, max;
struct Range zone_range;
const char *mapset, *name;
int t;
G_gisinit(argv[0]);
module = G_define_module();
G_add_keyword(_("raster"));
G_add_keyword(_("statistics"));
G_add_keyword(_("univariate statistics"));
G_add_keyword(_("zonal statistics"));
G_add_keyword(_("parallel"));
module->label = _("Calculates univariate statistics from the non-null "
"cells of a raster map.");
module->description =
_("Statistics include number of cells counted, minimum and maximum cell"
" values, range, arithmetic mean, population variance, standard "
"deviation,"
" coefficient of variation, and sum.");
/* Define the different options */
set_params();
if (G_parser(argc, argv))
exit(EXIT_FAILURE);
if (param.zonefile->answer && param.use_rast_region->answer) {
G_fatal_error(
_("zones option and region flag -r are mutually exclusive"));
}
name = param.output_file->answer;
if (name != NULL && strcmp(name, "-") != 0) {
if (NULL == freopen(name, "w", stdout)) {
G_fatal_error(_("Unable to open file <%s> for writing"), name);
}
}
/* set nprocs parameter */
int nprocs;
sscanf(param.nprocs->answer, "%d", &nprocs);
if (nprocs < 1)
G_fatal_error(_("<%d> is not valid number of nprocs."), nprocs);
#if defined(_OPENMP)
omp_set_num_threads(nprocs);
#else
if (nprocs != 1)
G_warning(_("GRASS is compiled without OpenMP support. Ignoring "
"threads setting."));
nprocs = 1;
#endif
if (nprocs > 1 && G_find_raster("MASK", G_mapset()) != NULL) {
G_warning(_("Parallel processing disabled due to active MASK."));
nprocs = 1;
}
/* table field separator */
zone_info.sep = G_option_to_separator(param.separator);
zone_info.min = 0;
zone_info.max = 0;
zone_info.n_zones = 0;
/* setting up thread workspace */
thread_workspace *tw = G_malloc(nprocs * sizeof *tw);
/* open zoning raster */
if ((z = param.zonefile->answer)) {
mapset = G_find_raster2(z, "");
for (t = 0; t < nprocs; ++t)
tw[t].fdz = open_raster(z);
cell_type = Rast_get_map_type(tw->fdz);
if (cell_type != CELL_TYPE)
G_fatal_error("Zoning raster must be of type CELL");
if (Rast_read_range(z, mapset, &zone_range) == -1)
G_fatal_error("Can not read range for zoning raster");
Rast_get_range_min_max(&zone_range, &min, &max);
if (Rast_read_cats(z, mapset, &(zone_info.cats)))
G_warning("no category support for zoning raster");
zone_info.min = min;
zone_info.max = max;
zone_info.n_zones = max - min + 1;
}
/* count the input rasters given */
for (p = (char **)param.inputfile->answers, rasters = 0; *p; p++, rasters++)
;
/* process all input rasters */
int map_type = param.extended->answer ? -2 : -1;
stats = ((map_type == -1) ? create_univar_stat_struct(-1, 0) : 0);
for (p = param.inputfile->answers; *p; p++) {
/* Check if the native extent and resolution
of the input map should be used */
if (param.use_rast_region->answer) {
mapset = G_find_raster2(*p, "");
Rast_get_cellhd(*p, mapset, ®ion);
/* Set the computational region */
Rast_set_window(®ion);
}
else {
G_get_window(®ion);
}
for (t = 0; t < nprocs; t++)
tw[t].fd = open_raster(*p);
if (map_type != -1) {
/* NB: map_type must match when doing extended stats */
int this_type = Rast_get_map_type(tw->fd);
assert(this_type > -1);
if (map_type < -1) {
/* extended stats */
assert(stats == 0);
map_type = this_type;
stats = univar_stat_with_percentiles(map_type);
}
else if (this_type != map_type) {
G_fatal_error(_("Raster <%s> type mismatch"), *p);
}
}
process_raster(stats, tw, ®ion, nprocs);
/* close input raster */
for (t = 0; t < nprocs; t++)
Rast_close(tw[t].fd);
}
/* close zoning raster */
if (z) {
for (t = 0; t < nprocs; t++)
Rast_close(tw[t].fdz);
}
/* create the output */
if (param.table->answer)
print_stats_table(stats);
else
print_stats(stats);
/* release memory */
free_univar_stat_struct(stats);
exit(EXIT_SUCCESS);
}
static int open_raster(const char *infile)
{
const char *mapset;
int fd;
mapset = G_find_raster2(infile, "");
if (mapset == NULL) {
G_fatal_error(_("Raster map <%s> not found"), infile);
}
fd = Rast_open_old(infile, mapset);
G_free((void *)mapset);
return fd;
}
static univar_stat *univar_stat_with_percentiles(int map_type)
{
univar_stat *stats;
unsigned int i, j;
unsigned int n_zones = zone_info.n_zones;
if (n_zones == 0)
n_zones = 1;
i = 0;
while (param.percentile->answers[i])
i++;
stats = create_univar_stat_struct(map_type, i);
for (i = 0; i < n_zones; i++) {
for (j = 0; j < stats[i].n_perc; j++) {
sscanf(param.percentile->answers[j], "%lf", &(stats[i].perc[j]));
}
}
return stats;
}
static void process_raster(univar_stat *stats, thread_workspace *tw,
const struct Cell_head *region, int nprocs)
{
/* use G_window_rows(), G_window_cols() here? */
const int rows = region->rows;
const int cols = region->cols;
const RASTER_MAP_TYPE map_type = Rast_get_map_type(tw->fd);
const size_t value_sz = Rast_cell_size(map_type);
const int n_zones = zone_info.n_zones;
const int n_alloc = n_zones ? n_zones : 1;
for (int t = 0; t < nprocs; t++) {
tw[t].raster_row = Rast_allocate_buf(map_type);
if (n_zones) {
tw[t].zoneraster_row = Rast_allocate_c_buf();
}
}
#if defined(_OPENMP)
omp_lock_t *minmax = G_malloc(n_alloc * sizeof *minmax);
for (int z = 0; z < n_alloc; z++) {
omp_init_lock(&minmax[z]);
}
#endif
int computed = 0;
#pragma omp parallel
{
int t_id = 0;
#if defined(_OPENMP)
t_id = omp_get_thread_num();
#endif
zone_workspace *zw = G_malloc(n_alloc * sizeof *zw);
for (int z = 0; z < n_alloc; z++) {
zone_workspace *zd = &zw[z];
zd->sum = 0;
zd->sumsq = 0;
zd->sum_abs = 0;
zd->size = 0;
zd->min = DBL_MAX;
zd->max = -DBL_MAX;
zd->bucket.n = 0;
zd->bucket.n_alloc = 0;
zd->bucket.nextp = NULL;
zd->bucket.cells = NULL;
zd->bucket.fcells = NULL;
zd->bucket.dcells = NULL;
}
#pragma omp for
for (int row = 0; row < rows; row++) {
thread_workspace *w = &tw[t_id];
Rast_get_row(w->fd, w->raster_row, row, map_type);
void *ptr = w->raster_row;
CELL *zptr = NULL;
if (n_zones) {
Rast_get_c_row(w->fdz, w->zoneraster_row, row);
zptr = w->zoneraster_row;
}
for (int col = 0; col < cols; col++) {
int zone = 0;
if (n_zones) {
/* skip NULL cells in zone map */
if (Rast_is_c_null_value(zptr)) {
ptr = G_incr_void_ptr(ptr, value_sz);
zptr++;
continue;
}
zone = *zptr - zone_info.min;
}
zone_workspace *zd = &zw[zone];
/* count all including NULL cells in input map */
zd->size++;
/* can't do stats with NULL cells in input map */
if (Rast_is_null_value(ptr, map_type)) {
ptr = G_incr_void_ptr(ptr, value_sz);
if (n_zones)
zptr++;
continue;
}
if (param.extended->answer) {
zone_bucket *bucket = &zd->bucket;
/* check allocated memory */
if (bucket->n >= bucket->n_alloc) {
bucket->n_alloc += 1000;
size_t msize;
switch (map_type) {
case DCELL_TYPE:
msize = bucket->n_alloc * sizeof(DCELL);
bucket->dcells = (DCELL *)G_realloc(
(void *)bucket->dcells, msize);
bucket->nextp =
(void *)&(bucket->dcells[bucket->n]);
break;
case FCELL_TYPE:
msize = bucket->n_alloc * sizeof(FCELL);
bucket->fcells = (FCELL *)G_realloc(
(void *)bucket->fcells, msize);
bucket->nextp =
(void *)&(bucket->fcells[bucket->n]);
break;
case CELL_TYPE:
msize = bucket->n_alloc * sizeof(CELL);
bucket->cells =
(CELL *)G_realloc((void *)bucket->cells, msize);
bucket->nextp = (void *)&(bucket->cells[bucket->n]);
break;
}
}
/* put the value into stats->XXXcell_array */
memcpy(bucket->nextp, ptr, value_sz);
bucket->nextp = G_incr_void_ptr(bucket->nextp, value_sz);
}
double val = ((map_type == DCELL_TYPE) ? *((DCELL *)ptr)
: (map_type == FCELL_TYPE) ? *((FCELL *)ptr)
: *((CELL *)ptr));
zd->sum += val;
zd->sumsq += val * val;
zd->sum_abs += fabs(val);
if (val > zd->max)
zd->max = val;
if (val < zd->min)
zd->min = val;
ptr = G_incr_void_ptr(ptr, value_sz);
if (n_zones)
zptr++;
zd->bucket.n++;
} /* end column loop */
if (!(param.shell_style->answer)) {
#pragma omp atomic update
computed++;
G_percent(computed, rows, 2);
}
} /* end row loop */
for (int z = 0; z < n_alloc; z++) {
zone_workspace *zd = &zw[z];
if (param.extended->answer) {
#pragma omp critical
{
/*
Transfers for each thread from local bucket to global
buffer. Case 1: first transfer, skip reallocation and
point to the buffer. Case 2: other transfers, reallocate
exactly if there is any non-empty bucket.
*/
zone_bucket *bucket = &zd->bucket;
univar_stat *g_bfr = &stats[z];
size_t old_size;
size_t add_size;
switch (map_type) {
case DCELL_TYPE:
if (NULL == g_bfr->dcell_array) {
g_bfr->dcell_array = bucket->dcells;
bucket->dcells = NULL;
}
else if (bucket->n != 0) {
old_size = g_bfr->n * sizeof(DCELL);
add_size = bucket->n * sizeof(DCELL);
g_bfr->dcell_array =
(DCELL *)G_realloc((void *)g_bfr->dcell_array,
old_size + add_size);
memcpy(&g_bfr->dcell_array[g_bfr->n],
bucket->dcells, add_size);
}
break;
case FCELL_TYPE:
if (NULL == g_bfr->fcell_array) {
g_bfr->fcell_array = bucket->fcells;
bucket->fcells = NULL;
}
else if (bucket->n != 0) {
old_size = g_bfr->n * sizeof(FCELL);
add_size = bucket->n * sizeof(FCELL);
g_bfr->fcell_array =
(FCELL *)G_realloc((void *)g_bfr->fcell_array,
old_size + add_size);
memcpy(&g_bfr->fcell_array[g_bfr->n],
bucket->fcells, add_size);
}
break;
case CELL_TYPE:
if (NULL == g_bfr->cell_array) {
g_bfr->cell_array = bucket->cells;
bucket->cells = NULL;
}
else if (bucket->n != 0) {
old_size = g_bfr->n * sizeof(CELL);
add_size = bucket->n * sizeof(CELL);
g_bfr->cell_array = (CELL *)G_realloc(
(void *)g_bfr->cell_array, old_size + add_size);
memcpy(&g_bfr->cell_array[g_bfr->n], bucket->cells,
add_size);
}
break;
}
g_bfr->n += bucket->n;
}
}
else {
#pragma omp atomic update
stats[z].n += zd->bucket.n;
}
#pragma omp atomic update
stats[z].size += zd->size;
#pragma omp atomic update
stats[z].sum += zd->sum;
#pragma omp atomic update
stats[z].sumsq += zd->sumsq;
#pragma omp atomic update
stats[z].sum_abs += zd->sum_abs;
#if defined(_OPENMP)
omp_set_lock(&minmax[z]);
#endif
if (stats[z].max < zd->max ||
(stats[z].max != stats[z].max && zd->max != DBL_MIN)) {
stats[z].max = zd->max;
}
if (stats[z].min > zd->min ||
(stats[z].min != stats[z].min && zd->min != DBL_MAX)) {
stats[z].min = zd->min;
}
#if defined(_OPENMP)
omp_unset_lock(&minmax[z]);
#endif
}
/* Free per-thread variables */
for (int z = 0; z < n_alloc; z++) {
zone_workspace *zd = &zw[z];
if (zd->bucket.cells)
G_free(zd->bucket.cells);
if (zd->bucket.fcells)
G_free(zd->bucket.fcells);
if (zd->bucket.dcells)
G_free(zd->bucket.dcells);
}
} /* end parallel region */
#if defined(_OPENMP)
for (int z = 0; z < n_alloc; z++) {
omp_destroy_lock(&minmax[z]);
}
G_free(minmax);
#endif
for (int t = 0; t < nprocs; t++) {
G_free(tw[t].raster_row);
}
if (n_zones) {
for (int t = 0; t < nprocs; t++) {
G_free(tw[t].zoneraster_row);
}
}
if (!(param.shell_style->answer))
G_percent(rows, rows, 2);
}