Let -d set starting column via modifier (#5966)

* Let -d set starting column via modifier

See #5630 for background discussion.  The best solution is to add an optional modifier to override the default settings for the starting column, which for backwards compatible reasons shall remain 2 for input and 0 for output.

* Update opt list

Author: PaulWessel

doc/rst/source/common_SYN_OPTs.rst_

@@ -28,11 +28,11 @@
 
 .. |SYN_OPT-c| replace:: **-c**\ :ref:`row,col|index <-c_full>`
 
-.. |SYN_OPT-d| replace:: **-d**\ :ref:`nodata <-d_full>`
+.. |SYN_OPT-d| replace:: **-d**\ [**+c**\ *col*]\ :ref:`nodata <-d_full>`
 
-.. |SYN_OPT-di| replace:: **-di**\ :ref:`nodata <-di_full>`
+.. |SYN_OPT-di| replace:: **-di**\ [**+c**\ *col*]\ :ref:`nodata <-di_full>`
 
-.. |SYN_OPT-do| replace:: **-do**\ :ref:`nodata <-do_full>`
+.. |SYN_OPT-do| replace:: **-do**\ [**+c**\ *col*]\ :ref:`nodata <-do_full>`
 
 .. |SYN_OPT-e| replace:: **-e**\ :ref:`regexp <-e_full>`
 

doc/rst/source/explain_-d.rst_

@@ -1,2 +1,2 @@
-**-d**\ [**i**\|\ **o**]\ *nodata* :ref:`(more ...) <-d_full>`
+**-d**\ [**i**\|\ **o**]\ [**+c**\ *col*]\ *nodata* :ref:`(more ...) <-d_full>`
     Replace input columns that equal *nodata* with NaN and do the reverse on output. |Add_-d|

doc/rst/source/explain_-d_full.rst_

@@ -3,7 +3,7 @@ The **-d** option
 
 **Syntax**
 
-**-di**\|\ **o**\ *nodata*
+**-di**\|\ **o**\ *nodata*\ [**+c**\ *col*]
     Substitute specific values with NaN.
 
 **Description**
@@ -14,8 +14,10 @@ an unlikely value (e.g., -99999). Since GMT cannot guess this special missing da
 option to have such values replaced with NaNs. Similarly, the **-d** option can replace all NaNs with the chosed
 *nodata* value should the GMT output need to conform to such a requirement.
 
-For input only, use **-di**\ *nodata* to examine all input columns. If any item equals *nodata*, the value is
-interpreted as a missing data item and is substituted with the value NaN.
+For input only, use **-di**\ *nodata* to examine all input columns after the first two. If any item equals *nodata*,
+the value is interpreted as a missing data item and is substituted with the value NaN.
 
 For output only, use **-do**\ *nodata* to examine all output columns. If any item equals NaN, the NaN value is
 substituted with the chosen missing data value *nodata*.
+
+Use the **+c** modifier to override the starting column used for the examinations [2 for input, 0 for output].

doc/rst/source/explain_-di.rst_

@@ -1,2 +1,2 @@
-**-di**\ *nodata* :ref:`(more ...) <-di_full>`
+**-di**\ *nodata*\ [**+c**\ *col*] :ref:`(more ...) <-di_full>`
     Replace input columns that equal *nodata* with NaN. |Add_-di|

doc/rst/source/explain_-do.rst_

@@ -1,2 +1,2 @@
-**-do**\ *nodata* :ref:`(more ...) <-do_full>`
+**-do**\ *nodata*\ [**+c**\ *col*] :ref:`(more ...) <-do_full>`
     Replace output columns that equal NaN with *nodata*. |Add_-do|

doc/rst/source/std-opts-classic.rst

@@ -34,7 +34,7 @@ Common Options (Classic Mode)
      - :ref:`Select binary input <-bi_full>`
    * - **-bo**\ *record*\ [**+b**\|\ **l**]
      - :ref:`Select binary output <-bo_full>`
-   * - **-d**\ [**i**\|\ **o**]\ *nodata*
+   * - **-d**\ [**i**\|\ **o**]\ *nodata*\ [**+c**\ *col*]
      - :ref:`Replace columns with nodata with NaN <-d_full>`
    * - **-e**\ [**~**]\ *"pattern"* \| **-e**\ [**~**]/\ *regexp*/[**i**]
      - :ref:`Filter data records that match the given pattern <-e_full>`

doc/rst/source/std-opts.rst

@@ -30,7 +30,7 @@ Common Options
      - :ref:`Select binary output <-bo_full>`
    * - **-c**\ [*row*\ ,\ *col*\|\ *index*]
      - :ref:`Advance plot focus to selected (or next) subplot panel <-c_full>`
-   * - **-d**\ [**i**\|\ **o**]\ *nodata*
+   * - **-d**\ [**i**\|\ **o**]\ *nodata*\ [**+c**\ *col*]
      - :ref:`Replace columns with nodata with NaN <-d_full>`
    * - **-e**\ [**~**]\ *"pattern"* \| **-e**\ [**~**]/\ *regexp*/[**i**]
      - :ref:`Filter data records that match the given pattern <-e_full>`

src/gmt_common.h

@@ -162,6 +162,7 @@ struct GMT_COMMON {
 	struct d {	/* -d[i][o]<nan_proxy> */
 		bool active[2];
 		bool is_zero[2];
+		unsigned int first_col[2];	/* Only apply from this column onward */
 		double nan_proxy[2];
 		char string[GMT_LEN64];
 	} d;

src/gmt_init.c

@@ -7645,6 +7645,7 @@ void gmtlib_explain_options (struct GMT_CTRL *GMT, char *options) {
 		case 'k':	/* -di option to tell GMT the relationship between NaN and a nan-proxy for input */
 
 			GMT_Usage (API, 1, "\n%s Replace any <nodata> values in input data with NaN.", GMT_di_OPT);
+			GMT_Usage (API, 3, "+c Append first column to be affected [2].");
 			break;
 
 		case 'l':	/* -l option to set up auto-legend items*/
@@ -7671,6 +7672,7 @@ void gmtlib_explain_options (struct GMT_CTRL *GMT, char *options) {
 
 			GMT_Usage (API, 1, "\n%s", GMT_do_OPT);
 			GMT_Usage (API, -2, "Replace any NaNs in output data with <nodata>.");
+			GMT_Usage (API, 3, "+c Append first column to be affected [0].");
 			break;
 
 		case 'f':	/* -f option to tell GMT which columns are time (and optionally geographical) */
@@ -9064,29 +9066,38 @@ GMT_LOCAL int gmtinit_parse_data_range (struct GMT_CTRL *GMT, char *arg, unsigne
 
 /*! . */
 unsigned int gmt_parse_d_option (struct GMT_CTRL *GMT, char *arg) {
-	unsigned int dir, first, last;
-	char *c = NULL;
+	unsigned int dir, first, last, col, def_col[2] = {GMT_Z, GMT_X};
+	char *c = NULL, *q = NULL;
 
 	if (!arg || !arg[0]) return (GMT_PARSE_ERROR);	/* -d requires an argument */
+	if ((q = strstr (arg, "+c"))) {	/* Want to override start columns */
+		col = atoi (&q[2]);
+		q[0] = '\0';	/* Chop off for now */
+	}
 	if (arg[0] == 'i') {
 		first = last = GMT_IN;
 		c = &arg[1];
+		if (q) def_col[GMT_IN] = col;
 	}
 	else if (arg[0] == 'o') {
 		first = last = GMT_OUT;
 		c = &arg[1];
+		if (q) def_col[GMT_OUT] = col;
 	}
 	else {
 		first = GMT_IN;	last = GMT_OUT;
 		c = arg;
+		if (q) def_col[GMT_IN] = def_col[GMT_OUT] = col;
 	}
 
 	for (dir = first; dir <= last; dir++) {
 		GMT->common.d.active[dir] = true;
 		GMT->common.d.nan_proxy[dir] = atof (c);
 		/* Need to know if 0 is used as NaN proxy since we must use a different comparison macro later */
 		GMT->common.d.is_zero[dir] = doubleAlmostEqualZero (0.0, GMT->common.d.nan_proxy[dir]);
+		GMT->common.d.first_col[dir] = def_col[dir];
 	}
+	if (q) q[0] = '+';	/* Restore modifier */
 	if (first == GMT_IN) strncpy (GMT->common.d.string, arg, GMT_LEN64-1);	/* Verbatim copy */
 	return (GMT_NOERROR);
 }

src/gmt_io.c

@@ -3661,8 +3661,7 @@ GMT_LOCAL void *gmtio_ascii_input (struct GMT_CTRL *GMT, FILE *fp, uint64_t *n,
 			else				/* Default column order */
 				col_pos = col_no;
 			n_convert = gmt_scanf (GMT, token, gmt_M_type (GMT, GMT_IN, col_pos), &val);
-			//n_convert = gmt_scanf (GMT, token, gmt_M_type (GMT, GMT_IN, in_col), &val);
-			if (n_convert != GMT_IS_NAN && col_pos > GMT_Y && gmt_input_is_nan_proxy (GMT, val))	/* Input matched no-data setting, so change to NaN */
+			if (n_convert != GMT_IS_NAN && gmt_input_is_nan_proxy (GMT, val, col_pos))	/* Input matched no-data setting, so change to NaN */
 				n_convert = GMT_IS_NAN;
 			if (n_convert == GMT_IS_NAN) {	/* Got a NaN or it failed to decode the string */
 				if (GMT->current.setting.io_nan_records || !GMT->current.io.skip_if_NaN[col_pos]) {	/* This field (or all fields) can be NaN so we pass it on */
@@ -4322,8 +4321,9 @@ void gmt_set_cartesian (struct GMT_CTRL *GMT, unsigned int dir) {
 /*! Handles non-proxy checking for input z values.  If the input value equals
  * the non_proxy then we return true so the value can be replaced by a NaN.
  */
-bool gmt_input_is_nan_proxy (struct GMT_CTRL *GMT, double value) {
+bool gmt_input_is_nan_proxy (struct GMT_CTRL *GMT, double value, unsigned int col) {
 	if (!GMT->common.d.active[GMT_IN]) return false;	/* Not active */
+	if (col < GMT->common.d.first_col[GMT_IN]) return false;	/* Not in column range */
 
 	if (GMT->common.d.is_zero[GMT_IN]) return doubleAlmostEqualZero (0.0, value);	/* Change to NaN if proxy value is ~zero */
 	return doubleAlmostEqual (GMT->common.d.nan_proxy[GMT_IN], value);		/* Change to NaN if value ~nan_proxy for a non-zero proxy */
@@ -4613,7 +4613,7 @@ int gmtlib_process_binary_input (struct GMT_CTRL *GMT, uint64_t n_read) {
 	/* Determine if this was a segment header, and if so return */
 	for (col_no = n_NaN = 0; col_no < n_read; col_no++) {
 		if (!gmt_M_is_dnan (GMT->current.io.curr_rec[col_no])) {	/* Clean data */
-			if (col_no > GMT_Y && gmt_input_is_nan_proxy (GMT, GMT->current.io.curr_rec[col_no]))	/* Input matched no-data setting, so change to NaN */
+			if (gmt_input_is_nan_proxy (GMT, GMT->current.io.curr_rec[col_no], col_no))	/* Input matched no-data setting, so change to NaN */
 				GMT->current.io.curr_rec[col_no] = GMT->session.d_NaN;
 			else if (GMT->common.i.select)	/* Cannot check here, done in gmtio_bin_colselect instead when order is set */
 				continue;