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blockmedian.c
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blockmedian.c
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/*--------------------------------------------------------------------
*
* Copyright (c) 1991-2024 by the GMT Team (https://www.generic-mapping-tools.org/team.html)
* See LICENSE.TXT file for copying and redistribution conditions.
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation; version 3 or any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* Contact info: www.generic-mapping-tools.org
*--------------------------------------------------------------------*/
/*
* API functions to support the blockmedian application.
*
* Author: Walter H.F. Smith
* Date: 1-JAN-2010
* Version: 6 API
*
* Brief synopsis: reads records of x, y, data, [weight] and writes out median
* value per cell, where cellular region is bounded by West East South North
* and cell dimensions are delta_x, delta_y.
*/
#define BLOCKMEDIAN /* Since mean, median, mode share near-similar macros we require this setting */
#include "gmt_dev.h"
#include "longopt/blockmedian_inc.h"
#define THIS_MODULE_CLASSIC_NAME "blockmedian"
#define THIS_MODULE_MODERN_NAME "blockmedian"
#define THIS_MODULE_LIB "core"
#define THIS_MODULE_PURPOSE "Block average (x,y,z) data tables by median estimation"
#define THIS_MODULE_KEYS "<D{,>D},GG),A->"
#define THIS_MODULE_NEEDS "R"
#define THIS_MODULE_OPTIONS "-:>RVabdefhioqrw" GMT_OPT("FH")
#include "block_subs.h"
/* Note: For external calls to block* we do not allow explicit -G options; these should be added by examining -A which
* is required for external calls to make grids, even if just z is requested. This differs from the command line where
* -Az is the default and -G is required to set file name format. */
static int usage (struct GMTAPI_CTRL *API, int level) {
const char *name = gmt_show_name_and_purpose (API, THIS_MODULE_LIB, THIS_MODULE_CLASSIC_NAME, THIS_MODULE_PURPOSE);
const char *extra1[2] = {" [-G<grdfile>]", ""}, *extra2[2] = {" (requires -G)", ""};
if (level == GMT_MODULE_PURPOSE) return (GMT_NOERROR);
GMT_Usage (API, 0, "usage: %s [<table>] %s %s [-A<fields>] [-C] [-E[b|r|s[+l|h]]]%s [-Q] [-T<q>] [%s] "
"[-W[i|o][+s|w]] [%s] [%s] [%s] [%s] [%s] [%s] [%s] [%s] [%s] [%s] [%s] [%s] [%s]\n",
name, GMT_I_OPT, GMT_Rgeo_OPT, extra1[API->external], GMT_V_OPT, GMT_a_OPT, GMT_b_OPT, GMT_d_OPT,
GMT_e_OPT, GMT_f_OPT, GMT_h_OPT, GMT_i_OPT, GMT_o_OPT, GMT_q_OPT, GMT_r_OPT, GMT_w_OPT, GMT_colon_OPT, GMT_PAR_OPT);
if (level == GMT_SYNOPSIS) return (GMT_MODULE_SYNOPSIS);
GMT_Message (API, GMT_TIME_NONE, " REQUIRED ARGUMENTS:\n");
GMT_Option (API, "<");
GMT_Option (API, "I,R");
GMT_Message (API, GMT_TIME_NONE, "\n OPTIONAL ARGUMENTS:\n");
GMT_Usage (API, 1, "\n-A<fields>");
GMT_Usage (API, -2, "List of fields to be written as individual grids%s. Choose from "
"z, s, l, q25, q75, h, and w. s|l|h requires -E; l|q25|q75|h requires -Eb, w requires -W[o]. "
"Cannot be used with -Er|s [Default is z only].", extra2[API->external]);
GMT_Usage (API, 1, "\n-C Output center of block as location [Default is (median x, median y), but see -Q].");
GMT_Usage (API, 1, "\n-E[b|r|s[+l|h]]");
GMT_Usage (API, -2, "Extend output with L1 scale (s=MAD), low (l), and high (h) value per block, i.e., "
"output (x,y,z,s,l,h[,w]) [Default outputs (x,y,z[,w])]; see -W regarding w. Alternatively, append a directive:");
GMT_Usage (API, 3, "b: Write box-and-whisker output (x,y,z,l,25%%q,75%%q,h[,w]).");
GMT_Usage (API, 3, "r: Write record number of the median value per block.");
GMT_Usage (API, 3, "s: Write an unsigned integer source id (sid) taken from the x,y,z[,w],sid input. "
"For ties, report record number (or sid) of highest value (+h) or append +l for lowest [highest].");
if (!API->external) {
GMT_Usage (API, 1, "\n-G<grdfile>");
GMT_Usage (API, -2, "Specify output grid file name; no table results will be written to standard output. "
"If more than one field is set via -A then <grdfile> must contain %%s to format field code. Options -C and -Q are not allowed.");
}
GMT_Usage (API, 1, "\n-Q Quicker; get median z and x,y at that z [Default gets median x, median y, median z].");
GMT_Usage (API, 1, "\n-T<q>");
GMT_Usage (API, -2, "Set quantile (0 < q < 1) to report [Default is 0.5 which is the median of z].");
GMT_Option (API, "V");
GMT_Usage (API, 1, "\n-W[i|o][+s|w]");
GMT_Usage (API, -2, "Perform weighted calculations [no weights]. Optionally set weight directive:");
GMT_Usage (API, 3, "i: Read 4 cols (x,y,z,w) but skip w on output.");
GMT_Usage (API, 3, "o: Read 3 cols (x,y,z) but include weight sum (i.e., counts) on output.");
GMT_Usage (API, -2, "Default selects both weighted input and output. Optionally, append one modifier:");
GMT_Usage (API, 3, "+s Read/write standard deviations instead, using conversion w = 1/s.");
GMT_Usage (API, 3, "+w Read/write weights as is [Default].");
GMT_Option (API, "a,bi");
if (gmt_M_showusage (API)) GMT_Usage (API, -2, "Default is 3 columns (or 4 if -W is set).");
GMT_Option (API, "bo,d,e,f,h,i,o,q,r,w,:,.");
return (GMT_MODULE_USAGE);
}
static int parse (struct GMT_CTRL *GMT, struct BLOCKMEDIAN_CTRL *Ctrl, struct GMT_OPTION *options) {
/* This parses the options provided to blockmedian and sets parameters in CTRL.
* Any GMT common options will override values set previously by other commands.
* It also replaces any file names specified as input or output with the data ID
* returned when registering these sources/destinations with the API.
*/
unsigned int n_errors = 0, k;
char arg[GMT_LEN16] = {""};
struct GMT_OPTION *opt = NULL;
struct GMTAPI_CTRL *API = GMT->parent;
for (opt = options; opt; opt = opt->next) {
switch (opt->option) {
case '<': /* Skip input files */
if (GMT_Get_FilePath (API, GMT_IS_DATASET, GMT_IN, GMT_FILE_REMOTE, &(opt->arg))) n_errors++;
break;
/* Processes program-specific parameters */
case 'A': /* Requires -G and selects which fields should be written as grids */
n_errors += gmt_M_repeated_module_option (API, Ctrl->A.active);
BLK_strip_commas (opt->arg, arg); /* Make local copy with any commas removed */
for (k = 0; arg[k] && Ctrl->A.n_selected < BLK_N_FIELDS; k++) {
switch (arg[k]) { /* z,s,l,q25,q75,h,w (without the commas) */
case 'z': Ctrl->A.selected[0] = true; break;
case 's': Ctrl->A.selected[1] = true; break;
case 'l': Ctrl->A.selected[2] = true; break;
case 'q':
if (!strncmp (&arg[k], "q25", 3U))
Ctrl->A.selected[3] = true;
else if (!strncmp (&arg[k], "q75", 3U))
Ctrl->A.selected[4] = true;
else {
GMT_Report (API, GMT_MSG_ERROR, "Unrecognized field argument %s in -A!\n", arg[k]);
n_errors++;
}
k += 2; /* Skip the quartile number (which is 25 or 75 or n_errors is already set */
break;
case 'h': Ctrl->A.selected[5] = true; break;
case 'w': Ctrl->A.selected[6] = true; break;
default:
GMT_Report (API, GMT_MSG_ERROR, "Unrecognized field argument %s in -A!\n", arg[k]);
n_errors++;
break;
}
Ctrl->A.n_selected++;
}
if (Ctrl->A.n_selected == 0) { /* No argument; let -Az be the default */
GMT_Report (API, GMT_MSG_DEBUG, "-A interpreted to mean -Az.\n");
Ctrl->A.selected[0] = true;
Ctrl->A.n_selected = 1;
}
break;
case 'C': /* Report center of block instead */
n_errors += gmt_M_repeated_module_option (API, Ctrl->C.active);
n_errors += gmt_get_no_argument (GMT, opt->arg, opt->option, 0);
break;
case 'E': /* Report extended statistics */
n_errors += gmt_M_repeated_module_option (API, Ctrl->E.active);
/* Report standard deviation, min, and max in cols 4-6 [Default] */
if (opt->arg[0] == 'b') /* Instead report min, 25%, 75% and max in cols 4-7 */
Ctrl->E.mode = BLK_DO_EXTEND4;
else if (opt->arg[0] == 'r' || opt->arg[0] == 's') { /* Report row number or sid of median */
switch (opt->arg[1]) { /* Look for modifiers */
case '+': /* New syntax with +h or +l to parse */
if (opt->arg[2] == 'l')
Ctrl->E.mode = BLK_DO_INDEX_LO;
else if (opt->arg[2] == 'h' || opt->arg[2] == '\0') /* E.g., let Er+ be thought of as -Er+h */
Ctrl->E.mode = BLK_DO_INDEX_HI;
else { /* Neither +l, +h, or just + is bad */
GMT_Report (API, GMT_MSG_ERROR, "Option -E: Unrecognized argument %s!\n", opt->arg);
n_errors++;
}
break;
case '-': /* Old syntax -Er- or -Es- for reporting index/source of lower value */
Ctrl->E.mode = BLK_DO_INDEX_LO;
break;
default: /* Default reports index/source of higher value */
Ctrl->E.mode = BLK_DO_INDEX_HI;
break;
}
if (opt->arg[0] == 's') /* report sid, add in flag */
Ctrl->E.mode |= BLK_DO_SRC_ID;
}
else if (opt->arg[0] == '\0') /* Plain -E : Report L1scale, low, high in cols 4-6 */
Ctrl->E.mode = BLK_DO_EXTEND3;
else { /* WTF? */
GMT_Report (API, GMT_MSG_ERROR, "Option -E: Unrecognized argument %s!\n", opt->arg);
n_errors++;
}
break;
case 'G': /* Write output grid(s) */
if (!API->external) n_errors += gmt_M_repeated_module_option (API, Ctrl->G.active);
if (!GMT->parent->external && Ctrl->G.n) { /* Command line interface */
GMT_Report (API, GMT_MSG_ERROR, "-G can only be set once!\n");
n_errors++;
}
else { /* From externals, or the first time (n == 0) from the command line */
if (Ctrl->G.n == BLK_N_FIELDS) {
GMT_Report (API, GMT_MSG_COMPAT, "Option -G: Too many output grids specified!\n");
n_errors++;
}
else /* We can add one more */
n_errors += gmt_get_required_file (GMT, opt->arg, opt->option, 0, GMT_IS_GRID, GMT_OUT, GMT_FILE_LOCAL, &(Ctrl->G.file[Ctrl->G.n]));
Ctrl->G.n++;
}
break;
case 'I': /* Get block dimensions */
n_errors += gmt_M_repeated_module_option (API, Ctrl->I.active);
n_errors += gmt_parse_inc_option (GMT, 'I', opt->arg);
break;
case 'Q': /* Quick mode for median z */
n_errors += gmt_M_repeated_module_option (API, Ctrl->Q.active);
/* Get median z and (x,y) of that point */
n_errors += gmt_get_no_argument (GMT, opt->arg, opt->option, 0);
break;
case 'T': /* Select a particular quantile [0.5 (median)] */
n_errors += gmt_M_repeated_module_option (API, Ctrl->T.active);
n_errors += gmt_get_required_double (GMT, opt->arg, opt->option, 0, &Ctrl->T.quantile);
break;
case 'W': /* Use in|out weights -W[i|o][+s|w] */
n_errors += gmt_M_repeated_module_option (API, Ctrl->W.active);
n_errors += BLK_parse_weight_opt (API, opt->arg, Ctrl->W.weighted, Ctrl->W.sigma);
break;
default: /* Report bad options */
n_errors += gmt_default_option_error (GMT, opt);
break;
}
}
if (Ctrl->G.active && !Ctrl->E.active) { /* See if we need to auto-supply -E or -Eb */
if (Ctrl->A.selected[1]) { /* s cannot go with the quantiles, so check */
if (Ctrl->A.selected[3] || Ctrl->A.selected[4]) {
GMT_Report (API, GMT_MSG_ERROR, "Cannot combine s with q25 or q75.\n");
n_errors++;
}
else { /* Plain -E is added */
GMT_Report (API, GMT_MSG_WARNING, "-E is required if -A specifies s, l, or h. -E was added.\n");
Ctrl->E.active = true;
Ctrl->E.mode = BLK_DO_EXTEND3; /* Report L1scale, low, high in cols 4-6 */
}
}
else if (Ctrl->A.selected[3] || Ctrl->A.selected[4]) { /* Need q25 or q75 and s not set, so add -Eb */
GMT_Report (API, GMT_MSG_WARNING, "-Eb is required if -A specifies q25 or q75. -Eb was added.\n");
Ctrl->E.active = true;
Ctrl->E.mode = BLK_DO_EXTEND4; /* Report low, 25%, 75% and high in cols 4-7 */
}
else if (Ctrl->A.selected[2] || Ctrl->A.selected[5]) { /* Plain -E is added */
GMT_Report (API, GMT_MSG_WARNING, "-E is required if -A specifies s, l, or h. -E was added.\n");
Ctrl->E.active = true;
Ctrl->E.mode = BLK_DO_EXTEND3; /* Report L1scale, low, high in cols 4-6 */
}
if (GMT->parent->external && !Ctrl->A.active) { /* From externals let -G equals -Az */
Ctrl->A.active = true;
Ctrl->A.selected[0] = true;
Ctrl->A.n_selected = 1;
}
}
n_errors += gmt_M_check_condition (GMT, !GMT->parent->external && Ctrl->A.active && !Ctrl->G.active, "Option -A requires -G\n");
n_errors += gmt_M_check_condition (GMT, GMT->parent->external && Ctrl->G.active && !Ctrl->A.active,
"Option -G requires -A\n");
n_errors += gmt_M_check_condition (GMT, Ctrl->G.active && (Ctrl->E.mode == BLK_DO_INDEX_LO ||
Ctrl->E.mode == BLK_DO_INDEX_HI),
"Option -Es|r are incompatible with -G\n");
if (Ctrl->G.active) { /* Make sure -A sets valid fields, some require -E */
if (Ctrl->A.active && Ctrl->A.n_selected > 1 && !GMT->parent->external && !strstr (Ctrl->G.file[0], "%s")) {
GMT_Report (API, GMT_MSG_ERROR, "Option -G: File format must contain a %%s for field type substitution.\n");
n_errors++;
}
else if (!Ctrl->A.active) /* Set default z output grid */
Ctrl->A.selected[0] = true, Ctrl->A.n_selected = 1;
else { /* Make sure -A choices are valid and that -E is set if extended fields are selected */
if (Ctrl->A.selected[6] && !Ctrl->W.weighted[GMT_OUT]) {
GMT_Report (API, GMT_MSG_ERROR, "-W or -Wo is required if -A specifies w.\n");
n_errors++;
}
}
n_errors += gmt_M_check_condition (GMT, Ctrl->C.active,
"Option -C: Cannot be combined with -G\n");
n_errors += gmt_M_check_condition (GMT, Ctrl->Q.active,
"Option -Q: Cannot be combined with -G\n");
Ctrl->C.active = true; /* But we set it under the hood to avoid computing modes of x and y */
}
n_errors += gmt_M_check_condition (GMT, !GMT->common.R.active[RSET], "Must specify -R option\n");
n_errors += gmt_M_check_condition (GMT, Ctrl->T.quantile <= 0.0 || Ctrl->T.quantile >= 1.0,
"Option -T: Select 0 < q < 1 for quantile [0.5]\n");
n_errors += gmt_M_check_condition (GMT, GMT->common.R.inc[GMT_X] <= 0.0 || GMT->common.R.inc[GMT_Y] <= 0.0,
"Option -I: Must specify positive increment(s)\n");
n_errors += gmt_check_binary_io (GMT, (Ctrl->W.weighted[GMT_IN]) ? 4 : 3);
return (n_errors ? GMT_PARSE_ERROR : GMT_NOERROR);
}
GMT_LOCAL void blockmedian_output_record (struct GMT_CTRL *GMT, struct GMT_GRID_HEADER *h, uint64_t first_in_cell, uint64_t first_in_new_cell, double weight_sum, double *out, double *extra, unsigned int go_quickly, unsigned int emode, double *quantile, unsigned int n_quantiles, struct BLK_DATA *data) {
double weight_half, weight_count;
uint64_t node, n_in_cell, node1;
unsigned int k, k_for_xy;
int way;
gmt_M_unused(GMT);
/* Remember: Data are already sorted on z for each cell */
/* Step 1: Find the n_quantiles requested (typically only one unless -Eb was used) */
n_in_cell = first_in_new_cell - first_in_cell;
node = first_in_cell;
weight_count = data[first_in_cell].a[BLK_W];
k_for_xy = (n_quantiles == 3) ? 1 : 0; /* If -Eb is set get get median location, else same as for z (unless -Q) */
for (k = 0; k < n_quantiles; k++) {
weight_half = quantile[k] * weight_sum; /* Normally, quantile will be 0.5 (i.e., median), hence the name of the variable */
/* Determine the point where we hit the desired quantile */
while (weight_count < weight_half) weight_count += data[++node].a[BLK_W]; /* Wind up until weight_count hits the mark */
if (weight_count == weight_half) {
node1 = node + 1;
extra[k] = 0.5 * (data[node].a[BLK_Z] + data[node1].a[BLK_Z]);
if (k == k_for_xy && go_quickly == 1) { /* Only get x,y at the z-quantile if requested [-Q] */
out[GMT_X] = 0.5 * (data[node].a[GMT_X] + data[node1].a[GMT_X]);
out[GMT_Y] = 0.5 * (data[node].a[GMT_Y] + data[node1].a[GMT_Y]);
}
if (k == 0 && emode) { /* Return record number of median, selecting the high or the low value since it is a tie */
way = (data[node].a[BLK_Z] >= data[node1].a[BLK_Z]) ? +1 : -1;
if (emode & BLK_DO_INDEX_HI) extra[3] = (way == +1) ? (double)data[node].src_id : (double)data[node1].src_id;
else extra[3] = (way == +1) ? (double)data[node1].src_id : (double)data[node].src_id;
}
}
else {
extra[k] = data[node].a[BLK_Z];
if (k == k_for_xy && go_quickly == 1) { /* Only get x,y at the z-quantile if requested [-Q] */
out[GMT_X] = data[node].a[GMT_X];
out[GMT_Y] = data[node].a[GMT_Y];
}
if (k == 0 && emode) extra[3] = (double)data[node].src_id; /* Return record number of median */
}
}
out[GMT_Z] = extra[k_for_xy]; /* The desired quantile is passed via z */
if (go_quickly == 1) return; /* Already have everything requested so we return */
if (go_quickly == 2) { /* Return center of block instead of computing a representative location */
uint64_t row, col;
row = gmt_M_row (h, data[node].ij);
col = gmt_M_col (h, data[node].ij);
out[GMT_X] = gmt_M_grd_col_to_x (GMT, col, h);
out[GMT_Y] = gmt_M_grd_row_to_y (GMT, row, h);
return;
}
/* We get here when we need separate quantile calculations for both x and y locations */
weight_half = quantile[k_for_xy] * weight_sum; /* We want the same quantile for locations as was used for z */
if (n_in_cell > 2) qsort(&data[first_in_cell], n_in_cell, sizeof (struct BLK_DATA), BLK_compare_x);
node = first_in_cell;
weight_count = data[first_in_cell].a[BLK_W];
while (weight_count < weight_half) weight_count += data[++node].a[BLK_W];
out[GMT_X] = (weight_count == weight_half) ? 0.5 * (data[node].a[GMT_X] + data[node + 1].a[GMT_X]) : data[node].a[GMT_X];
if (n_in_cell > 2) qsort (&data[first_in_cell], n_in_cell, sizeof (struct BLK_DATA), BLK_compare_y);
node = first_in_cell;
weight_count = data[first_in_cell].a[BLK_W];
while (weight_count < weight_half) weight_count += data[++node].a[BLK_W];
out[GMT_Y] = (weight_count == weight_half) ? 0.5 * (data[node].a[GMT_Y] + data[node + 1].a[GMT_Y]) : data[node].a[GMT_Y];
}
/* Must free allocated memory before returning */
#define bailout(code) {gmt_M_free_options (mode); return (code);}
#define Return(code) {GMT_Destroy_Data (API, &Grid); gmt_M_free (GMT, Out); Free_Ctrl (GMT, Ctrl); gmt_end_module (GMT, GMT_cpy); bailout (code);}
EXTERN_MSC int GMT_blockmedian (void *V_API, int mode, void *args) {
int error = 0;
bool do_extra = false, duplicate_col, bail = false;
uint64_t n_lost, node, first_in_cell, first_in_new_cell;
uint64_t n_read, nz, n_pitched, n_cells_filled, w_col, i_col = 0, sid_col;
size_t n_alloc = 0, nz_alloc = 0;
openmp_int row, col;
unsigned int emode = 0, n_input, n_output, n_quantiles = 1, go_quickly = 0;
unsigned int k, kk, NF = 0, fcol[BLK_N_FIELDS] = {2,3,4,5,6,7,0,0}, field[BLK_N_FIELDS];
double out[8], wesn[4], quantile[3] = {0.25, 0.5, 0.75}, extra[8], weight, half_dx, *in = NULL, *z_tmp = NULL;
char format[GMT_LEN512] = {""}, *old_format = NULL, *fcode[BLK_N_FIELDS] = {"z", "s", "l", "q25", "q75", "h", "w", ""}, *code[BLK_N_FIELDS];
char file[PATH_MAX] = {""};
struct GMT_OPTION *options = NULL;
struct GMT_GRID *Grid = NULL, *G = NULL, *GridOut[BLK_N_FIELDS];
struct GMT_RECORD *In = NULL, *Out = NULL;
struct BLK_DATA *data = NULL;
struct BLOCKMEDIAN_CTRL *Ctrl = NULL;
struct GMT_CTRL *GMT = NULL, *GMT_cpy = NULL;
struct GMTAPI_CTRL *API = gmt_get_api_ptr (V_API); /* Cast from void to GMTAPI_CTRL pointer */
/*----------------------- Standard module initialization and parsing ----------------------*/
if (API == NULL) return (GMT_NOT_A_SESSION);
if (mode == GMT_MODULE_PURPOSE) return (usage (API, GMT_MODULE_PURPOSE)); /* Return the purpose of program */
options = GMT_Create_Options (API, mode, args); if (API->error) return (API->error); /* Set or get option list */
if ((error = gmt_report_usage (API, options, 0, usage)) != GMT_NOERROR) bailout (error); /* Give usage if requested */
/* Parse the command-line arguments */
if ((GMT = gmt_init_module (API, THIS_MODULE_LIB, THIS_MODULE_CLASSIC_NAME, THIS_MODULE_KEYS, THIS_MODULE_NEEDS, module_kw, &options, &GMT_cpy)) == NULL) bailout (API->error); /* Save current state */
if (GMT_Parse_Common (API, THIS_MODULE_OPTIONS, options)) Return (API->error);
Ctrl = New_Ctrl (GMT); /* Allocate and initialize a new control structure */
if ((error = parse (GMT, Ctrl, options)) != 0) Return (error);
/*---------------------------- This is the blockmedian main code ----------------------------*/
gmt_M_memset (GridOut, BLK_N_FIELDS, struct GMT_GRID *); /* Initialize all pointers to NULL */
GMT_Report (API, GMT_MSG_INFORMATION, "Processing input table data\n");
if ((Grid = GMT_Create_Data (API, GMT_IS_GRID, GMT_IS_SURFACE, GMT_CONTAINER_ONLY, NULL, NULL, NULL, \
GMT_GRID_DEFAULT_REG, GMT_NOTSET, NULL)) == NULL) Return (API->error);
duplicate_col = (gmt_M_360_range (Grid->header->wesn[XLO], Grid->header->wesn[XHI]) && Grid->header->registration == GMT_GRID_NODE_REG); /* E.g., lon = 0 column should match lon = 360 column */
half_dx = 0.5 * Grid->header->inc[GMT_X];
go_quickly = (Ctrl->Q.active) ? 1 : 0;
if (!Ctrl->G.active && Ctrl->C.active && go_quickly == 1) {
GMT_Report (API, GMT_MSG_WARNING, "-C overrides -Q\n");
go_quickly = 0;
}
if (Ctrl->C.active) go_quickly = 2; /* Flag used in output calculation */
n_input = 3 + Ctrl->W.weighted[GMT_IN] + ((Ctrl->E.mode & BLK_DO_SRC_ID) ? 1 : 0); /* 3 columns on output, plus 1 extra if -W and another if -Es */
n_output = (Ctrl->W.weighted[GMT_OUT]) ? 4 : 3; /* 3 columns on output, plus 1 extra if -W */
if (Ctrl->E.active) { /* One or more -E settings */
if (Ctrl->E.mode & BLK_DO_EXTEND3) { /* Add s,l,h cols */
n_output += 3;
do_extra = true;
fcol[5] = 5; /* Since no q25,75 */
}
else if (Ctrl->E.mode & BLK_DO_EXTEND4) { /* Add l, 25%, 75%, h cols */
n_output += 4;
n_quantiles = 3;
do_extra = true;
fcol[2] = 3; fcol[3] = 4; fcol[4] = 5; fcol[5] = 6;
}
if (Ctrl->E.mode & BLK_DO_INDEX_LO || Ctrl->E.mode & BLK_DO_INDEX_HI) { /* Add index */
n_output++;
emode = Ctrl->E.mode & (BLK_DO_INDEX_LO + BLK_DO_INDEX_HI);
}
}
if (!(Ctrl->E.mode & BLK_DO_EXTEND4)) quantile[0] = Ctrl->T.quantile; /* Just get the single quantile [median] */
if (gmt_M_is_verbose (GMT, GMT_MSG_INFORMATION)) {
snprintf (format, GMT_LEN512, "W: %s E: %s S: %s N: %s n_columns: %%d n_rows: %%d\n", GMT->current.setting.format_float_out, GMT->current.setting.format_float_out, GMT->current.setting.format_float_out, GMT->current.setting.format_float_out);
GMT_Report (API, GMT_MSG_INFORMATION, format, Grid->header->wesn[XLO], Grid->header->wesn[XHI], Grid->header->wesn[YLO], Grid->header->wesn[YHI], Grid->header->n_columns, Grid->header->n_rows);
}
gmt_set_xy_domain (GMT, wesn, Grid->header); /* May include some padding if gridline-registered */
/* Specify input and output expected columns */
if ((error = GMT_Set_Columns (API, GMT_IN, n_input, GMT_COL_FIX)) != GMT_NOERROR) {
Return (error);
}
if (!Ctrl->G.active && (error = GMT_Set_Columns (API, GMT_OUT, n_output, GMT_COL_FIX)) != GMT_NOERROR) {
Return (error);
}
/* Register likely data sources unless the caller has already done so */
if (GMT_Init_IO (API, GMT_IS_DATASET, GMT_IS_POINT, GMT_IN, GMT_ADD_DEFAULT, 0, options) != GMT_NOERROR) { /* Registers default input sources, unless already set */
Return (API->error);
}
if (!Ctrl->G.active && GMT_Init_IO (API, GMT_IS_DATASET, GMT_IS_POINT, GMT_OUT, GMT_ADD_DEFAULT, 0, options) != GMT_NOERROR) { /* Registers default output destination, unless already set */
Return (API->error);
}
/* Initialize the i/o for doing record-by-record reading/writing */
if (GMT_Begin_IO (API, GMT_IS_DATASET, GMT_IN, GMT_HEADER_ON) != GMT_NOERROR) { /* Enables data input and sets access mode */
Return (API->error);
}
sid_col = (Ctrl->W.weighted[GMT_IN]) ? 4 : 3; /* Column with integer source id [if -Es is set] */
n_read = n_pitched = 0; /* Initialize counters */
GMT->session.min_meminc = GMT_INITIAL_MEM_ROW_ALLOC; /* Start by allocating a 32 MB chunk */
/* Read the input data */
do { /* Keep returning records until we reach EOF */
if ((In = GMT_Get_Record (API, GMT_READ_DATA, NULL)) == NULL) { /* Read next record, get NULL if special case */
if (gmt_M_rec_is_error (GMT)) { /* Bail if there are any read errors */
Return (GMT_RUNTIME_ERROR);
}
else if (gmt_M_rec_is_eof (GMT)) /* Reached end of file */
break;
continue; /* Go back and read the next record */
}
if (In->data == NULL) {
gmt_quit_bad_record (API, In);
Return (API->error);
}
in = In->data; /* Only need to process numerical part here */
if (gmt_M_is_dnan (in[GMT_Z])) /* Skip if z = NaN */
continue;
/* Clean data record to process */
n_read++; /* Number of records read */
if (gmt_M_y_is_outside (GMT, in[GMT_Y], wesn[YLO], wesn[YHI])) continue; /* Outside y-range */
if (gmt_x_is_outside (GMT, &in[GMT_X], wesn[XLO], wesn[XHI])) continue; /* Outside x-range (or longitude) */
/* We appear to be inside: Get row and col indices of this block */
if (gmt_row_col_out_of_bounds (GMT, in, Grid->header, &row, &col)) continue; /* Sorry, outside after all */
if (duplicate_col && (wesn[XHI]-in[GMT_X] < half_dx)) { /* Only compute median values for the west column and not the repeating east column with lon += 360 */
in[GMT_X] -= 360.0; /* Make this point be considered for the western block mean value */
col = 0;
}
/* OK, this point is definitively inside and will be used */
node = gmt_M_ijp (Grid->header, row, col); /* Bin node */
if (n_pitched == n_alloc) data = gmt_M_malloc (GMT, data, n_pitched, &n_alloc, struct BLK_DATA);
data[n_pitched].ij = node;
data[n_pitched].src_id = (Ctrl->E.mode & BLK_DO_SRC_ID) ? (uint64_t)lrint (in[sid_col]) : n_read;
data[n_pitched].a[BLK_W] = ((Ctrl->W.weighted[GMT_IN]) ? ((Ctrl->W.sigma[GMT_IN]) ? 1.0 / in[3] : in[3]) : 1.0);
if (!Ctrl->C.active) { /* Need to store (x,y) so we can compute median location later */
data[n_pitched].a[GMT_X] = in[GMT_X];
data[n_pitched].a[GMT_Y] = in[GMT_Y];
}
data[n_pitched].a[BLK_Z] = in[GMT_Z];
n_pitched++;
} while (true);
GMT->session.min_meminc = GMT_MIN_MEMINC; /* Reset to the default value */
if (GMT_End_IO (API, GMT_IN, 0) != GMT_NOERROR) { /* Disables further data input */
Return (API->error);
}
if (n_read == 0) { /* Blank/empty input files */
GMT_Report (API, GMT_MSG_WARNING, "No data records found; no output produced\n");
if (!(API->external && Ctrl->G.active))
bail = true;
}
else if (n_pitched == 0) { /* No points inside region */
GMT_Report (API, GMT_MSG_WARNING, "No data points found inside the region; no output produced\n");
if (!(API->external && Ctrl->G.active))
bail = true;
}
if (bail) { /* Time to quit */
Return (GMT_NOERROR);
}
if (n_pitched < n_alloc) {
n_alloc = n_pitched;
data = gmt_M_malloc (GMT, data, 0, &n_alloc, struct BLK_DATA);
}
w_col = gmt_get_cols (GMT, GMT_OUT) - 1; /* Weights always reported in last output column */
fcol[6] = (unsigned int)w_col; /* Since we don't know what it is until parsed */
/* Ready to go. */
if (Ctrl->G.active) { /* Create the grid(s) */
char *remarks[BLK_N_FIELDS] = {"Median value per bin", "L1 scale per bin", "Lowest value per bin", "25% quartile", "75% quartile", "Highest value per bin", "Weight per bin"};
for (k = kk = 0; k < BLK_N_FIELDS; k++) {
if (!Ctrl->A.selected[k]) continue;
field[NF] = fcol[k]; /* Just keep record of which fields we are actually using */
code[NF] = fcode[k];
if ((GridOut[NF] = GMT_Create_Data (API, GMT_IS_GRID, GMT_IS_SURFACE, GMT_CONTAINER_AND_DATA, NULL, Grid->header->wesn, Grid->header->inc, \
Grid->header->registration, GMT_NOTSET, NULL)) == NULL) Return (API->error);
if (GMT_Set_Comment (API, GMT_IS_GRID, GMT_COMMENT_IS_TITLE, "Grid produced by blockmedian", GridOut[NF]) != GMT_NOERROR) Return (API->error);
if (GMT_Set_Comment (API, GMT_IS_GRID, GMT_COMMENT_IS_OPTION | GMT_COMMENT_IS_COMMAND, options, GridOut[NF]) != GMT_NOERROR) Return (API->error);
if (GMT_Set_Comment (API, GMT_IS_GRID, GMT_COMMENT_IS_REMARK, remarks[k], GridOut[NF])) Return (API->error);
if (G == NULL) G = GridOut[NF]; /* First grid header used to get node later */
for (node = 0; node < G->header->size; node++)
GridOut[NF]->data[node] = GMT->session.f_NaN;
if (API->external && n_read == 0) { /* Write the empty grids back to the external caller */
if (strstr (Ctrl->G.file[kk], "%s"))
sprintf (file, Ctrl->G.file[kk], code[k]);
else
strncpy (file, Ctrl->G.file[kk], PATH_MAX-1);
if (GMT_Write_Data (API, GMT_IS_GRID, GMT_IS_FILE, GMT_IS_SURFACE, GMT_CONTAINER_AND_DATA, NULL, file, GridOut[k]) != GMT_NOERROR) {
Return (API->error);
}
}
if (Ctrl->G.n > 1) kk++; /* Only true for APIs */
NF++; /* Number of actual field grids */
}
if (API->external && n_read == 0) { /* Delayed return */
Return (GMT_NOERROR);
}
}
else { /* Get ready for rec-by-rec output */
if (GMT_Begin_IO (API, GMT_IS_DATASET, GMT_OUT, GMT_HEADER_ON) != GMT_NOERROR) { /* Enables data output and sets access mode */
gmt_M_free (GMT, data);
Return (API->error);
}
if (GMT_Set_Geometry (API, GMT_OUT, GMT_IS_POINT) != GMT_NOERROR) { /* Sets output geometry */
gmt_M_free (GMT, data);
Return (API->error);
}
}
GMT_Report (API, GMT_MSG_INFORMATION, "Calculating block medians\n");
if (emode) { /* Index column last, with weight col just before */
i_col = w_col--;
old_format = GMT->current.io.o_format[i_col]; /* Need to restore this at end */
GMT->current.io.o_format[i_col] = strdup ("%.0f"); /* Integer format for src_id */
}
/* Sort on node and Z value */
qsort (data, n_pitched, sizeof (struct BLK_DATA), BLK_compare_index_z);
Out = gmt_new_record (GMT, out, NULL); /* Since we only need to worry about numerics in this module */
/* Find n_in_cell and write appropriate output */
first_in_cell = n_cells_filled = nz = 0;
while (first_in_cell < n_pitched) {
weight = data[first_in_cell].a[BLK_W];
if (do_extra) {
if (nz == nz_alloc) z_tmp = gmt_M_malloc (GMT, z_tmp, nz, &nz_alloc, double);
z_tmp[0] = data[first_in_cell].a[BLK_Z];
nz = 1;
}
first_in_new_cell = first_in_cell + 1;
while ((first_in_new_cell < n_pitched) && (data[first_in_new_cell].ij == data[first_in_cell].ij)) {
weight += data[first_in_new_cell].a[BLK_W];
if (do_extra) { /* Must get a temporary copy of the sorted z array */
if (nz == nz_alloc) z_tmp = gmt_M_malloc (GMT, z_tmp, nz, &nz_alloc, double);
z_tmp[nz++] = data[first_in_new_cell].a[BLK_Z];
}
first_in_new_cell++;
}
/* Now we have weight sum [and copy of z in case of -E]; now calculate the quantile(s): */
blockmedian_output_record (GMT, Grid->header, first_in_cell, first_in_new_cell, weight, out, extra, go_quickly, emode, quantile, n_quantiles, data);
/* Here, x,y,z are loaded into out */
if (Ctrl->E.mode & BLK_DO_EXTEND4) { /* Need 7 items: x, y, median, min, 25%, 75%, max [,weight] */
out[3] = z_tmp[0]; /* 0% quantile (min value) */
out[4] = extra[0]; /* 25% quantile */
out[5] = extra[2]; /* 75% quantile */
out[6] = z_tmp[nz-1]; /* 100% quantile (max value) */
}
else if (Ctrl->E.mode & BLK_DO_EXTEND3) { /* Need 6 items: x, y, median, MAD, min, max [,weight] */
out[4] = z_tmp[0]; /* Low value */
out[5] = z_tmp[nz-1]; /* High value */
/* Turn z_tmp into absolute deviations from the median (out[GMT_Z]) */
if (nz > 1) {
for (node = 0; node < nz; node++) z_tmp[node] = fabs (z_tmp[node] - out[GMT_Z]);
gmt_sort_array (GMT, z_tmp, nz, GMT_DOUBLE);
out[3] = (nz%2) ? z_tmp[nz/2] : 0.5 * (z_tmp[(nz-1)/2] + z_tmp[nz/2]);
out[3] *= MAD_NORMALIZE; /* This will be L1 MAD-based scale */
}
else
out[3] = GMT->session.d_NaN;
}
if (Ctrl->W.weighted[GMT_OUT]) out[w_col] = (Ctrl->W.sigma[GMT_OUT]) ? 1.0 / weight : weight;
if (emode) out[i_col] = extra[3];
if (Ctrl->G.active) {
row = gmt_M_grd_y_to_row (GMT, out[GMT_Y], Grid->header);
col = gmt_M_grd_x_to_col (GMT, out[GMT_X], Grid->header);
node = gmt_M_ijp (Grid->header, row, col); /* Bin node */
for (k = 0; k < NF; k++)
GridOut[k]->data[node] = (gmt_grdfloat)out[field[k]];
}
else
GMT_Put_Record (API, GMT_WRITE_DATA, Out); /* Write this to output */
n_cells_filled++;
first_in_cell = first_in_new_cell;
}
gmt_M_free (GMT, data);
if (do_extra) gmt_M_free (GMT, z_tmp);
if (Ctrl->G.active) { /* Writes the grid(s) */
for (k = kk = 0; k < NF; k++) {
if (strstr (Ctrl->G.file[kk], "%s"))
sprintf (file, Ctrl->G.file[kk], code[k]);
else
strncpy (file, Ctrl->G.file[kk], PATH_MAX-1);
if (GMT_Write_Data (API, GMT_IS_GRID, GMT_IS_FILE, GMT_IS_SURFACE, GMT_CONTAINER_AND_DATA, NULL, file, GridOut[k]) != GMT_NOERROR) {
Return (API->error);
}
if (Ctrl->G.n > 1) kk++; /* Only true for APIs */
}
}
else if (GMT_End_IO (API, GMT_OUT, 0) != GMT_NOERROR) { /* Disables further data output */
Return (API->error);
}
n_lost = n_read - n_pitched; /* Number of points that did not get used */
GMT_Report (API, GMT_MSG_INFORMATION, "N read: %" PRIu64 " N used: %" PRIu64 " outside_area: %" PRIu64 " N cells filled: %" PRIu64 "\n", n_read, n_pitched, n_lost, n_cells_filled);
if (emode) {
gmt_M_str_free (GMT->current.io.o_format[i_col]); /* Free the temporary integer format */
GMT->current.io.o_format[i_col] = old_format; /* Restore previous format */
}
Return (GMT_NOERROR);
}