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Merged
PaulWessel merged 12 commits into from
Feb 28, 2021
Merged

Allow GMT_Put_Vector to convert other text items than datetime #4849

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aae7c2a
Allow GMT_Put_Vector to convert other text items than datetime
PaulWessel Feb 24, 2021
2b004b9
Update gmt_enum_dict.h
PaulWessel Feb 24, 2021
f2829cd
Update api.rst
PaulWessel Feb 24, 2021
e449d94
Update api.rst
PaulWessel Feb 24, 2021
5c8bd9c
Update api.rst
PaulWessel Feb 24, 2021
c285173
Simplify assignments and add comments
PaulWessel Feb 24, 2021
ea20f4f
Update gmt_api.c
PaulWessel Feb 24, 2021
bc4f157
Add test
PaulWessel Feb 24, 2021
861e9d0
Update gmt_api.c
PaulWessel Feb 24, 2021
ab85b6f
Update doc/rst/source/api.rst
PaulWessel Feb 28, 2021
d80ff6c
Update src/gmt_api.c
PaulWessel Feb 28, 2021
726ba48
Update src/gmt_api.c
PaulWessel Feb 28, 2021
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19 changes: 13 additions & 6 deletions doc/rst/source/api.rst
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Expand Up @@ -1360,12 +1360,19 @@ For vectors the same principles apply:
int GMT_Put_Vector (void *API, struct GMT_VECTOR *V, unsigned int col,
unsigned int type, void *vector);

where ``V`` is the :ref:`GMT_VECTOR <struct-vector>` created by GMT_Create_Data_, ``col`` is the vector
column in question, ``type`` is one of the
recognized data :ref:`types <tbl-types>` used for this vector, and ``vector`` is
a pointer to this custom vector. In addition, ``type`` may be also **GMT_DATETIME**, in which case
we expect an array of strings with ISO datetime strings and we do the conversion to internal
GMT time and allocate a vector to hold the result in the given ``col``.
where ``V`` is the :ref:`GMT_VECTOR <struct-vector>` created by GMT_Create_Data_,
``col`` is the vector column in question, ``type`` is one of the recognized data
:ref:`types <tbl-types>` used for this vector, and ``vector`` is a pointer to the
user's read-only custom vector. In addition, ``type`` may also be **GMT_TEXT**,
in which case we expect an array of strings with numbers, longitudes, latitudes,
or ISO datetime strings and we do the conversion to internal numerical values and
allocate a vector to hold the result in the given ``col``. By default that vector
will be assigned to type **GMT_DOUBLE** but you can add another primary data type
for the conversion if you prefer (e.g., **GMT_TEXT**\|\ **GMT_LONG** to get final
internal absolute time in integer seconds). For these four special data types GMT
allocates internal memory to hold the concerted data and ``vector`` is not used
any further.
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To extract a custom vector from an output :ref:`GMT_VECTOR <struct-vector>` you can use

.. _GMT_Get_Vector:
Expand Down
213 changes: 130 additions & 83 deletions src/gmt_api.c
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Expand Up @@ -252,6 +252,8 @@ static const char *GMT_geometry[] = {"Not Set", "Point", "Line", "Polygon", "Poi
static const char *GMT_class[] = {"QUIET", "NOTICE", "ERROR", "WARNING", "TIMING", "INFORMATION", "COMPATIBILITY", "DEBUG"};
static unsigned int GMT_no_pad[4] = {0, 0, 0, 0};
static const char *GMT_family_abbrev[] = {"D", "G", "I", "C", "X", "M", "V", "U", "-"};
static const char *GMT_type[GMT_N_TYPES] = {"byte", "byte", "integer", "integer", "integer", "integer",
"integer", "integer", "double", "double", "string", "datetime"};

/*! Two different i/o mode: GMT_Put|Get_Data vs GMT_Put|Get_Record */
enum GMT_enum_iomode {
Expand Down Expand Up @@ -6683,10 +6685,10 @@ GMT_LOCAL int gmtapi_write_vector (struct GMT_CTRL *GMT, void *dest, unsigned in
if (gmtapi_bin_input_memory (GMT, V->n_columns, V->n_columns) < 0) /* Segment header found, finish the segment we worked on and goto next */
gmt_write_segmentheader (GMT, fp, V->n_columns);
else { /* Format an ASCII record for output */
fprintf (fp, GMT->current.setting.format_float_out, GMT->current.io.curr_rec[0]);
gmt_ascii_output_col (GMT, fp, GMT->current.io.curr_rec[0], 0);
for (col = 1; col < V->n_columns; col++) {
fprintf (fp, "%s", GMT->current.setting.io_col_separator);
fprintf (fp, GMT->current.setting.format_float_out, GMT->current.io.curr_rec[col]);
gmt_ascii_output_col (GMT, fp, GMT->current.io.curr_rec[col], col);
}
if (V->text && V->text[row])
fprintf (fp, "%s%s", GMT->current.setting.io_col_separator, V->text[row]);
Expand Down Expand Up @@ -14466,56 +14468,139 @@ int GMT_Change_Layout_ (unsigned int *family, char *code, unsigned int *mode, vo

/* Deal with assignments of custom vectors and matrices to GMT containers */

GMT_LOCAL int gmtapi_insert_vector (struct GMTAPI_CTRL *API, union GMT_UNIVECTOR *V, unsigned int type, void *vector) {
/* Hook a vector to the correct union member given data type */
gmt_M_unused (API);
switch (type) {
case GMT_DOUBLE: V->f8 = vector; break;
case GMT_FLOAT: V->f4 = vector; break;
case GMT_ULONG: V->ui8 = vector; break;
case GMT_LONG: V->si8 = vector; break;
case GMT_UINT: V->ui4 = vector; break;
case GMT_INT: V->si4 = vector; break;
case GMT_USHORT: V->ui2 = vector; break;
case GMT_SHORT: V->si2 = vector; break;
case GMT_UCHAR: V->uc1 = vector; break;
case GMT_CHAR: V->sc1 = vector; break;
default:
return (GMT_NOT_A_VALID_TYPE);
break;
}
return (GMT_NOERROR);
}

GMT_LOCAL void * gmtapi_retrieve_vector (void *API, union GMT_UNIVECTOR *V, unsigned int type) {
void *vector = NULL;
gmt_M_unused (API);
switch (type) {
case GMT_DOUBLE: vector = V->f8; break;
case GMT_FLOAT: vector = V->f4; break;
case GMT_ULONG: vector = V->ui8; break;
case GMT_LONG: vector = V->si8; break;
case GMT_UINT: vector = V->ui4; break;
case GMT_INT: vector = V->si4; break;
case GMT_USHORT: vector = V->ui2; break;
case GMT_SHORT: vector = V->si2; break;
case GMT_UCHAR: vector = V->uc1; break;
case GMT_CHAR: vector = V->sc1; break;
default:
return NULL;
break;
}
return vector;
}

int GMT_Put_Vector (void *V_API, struct GMT_VECTOR *V, unsigned int col, unsigned int type, void *vector) {
/* Hooks a users custom vector onto V's column array and sets the type.
* It is the user's responsibility to pass correct type for the given vector.
* We also check that the number of rows have been set earlier. */
* We also check that the number of rows have been set earlier.
* We also allow special text-based arrays for longitude, latitude, datetime or Cartesian data to be passed
* which may be logically OR'ed with desired array type (e.g., GMT_LONG|GMT_TEXT.
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* Note: We do not check for data loss in the conversion (e..g, GMT_UCHAR|GMT_TEXT) */
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unsigned int special_type;
enum GMT_enum_alloc alloc_mode = GMT_ALLOC_EXTERNALLY; /* Default is to pass vectors in read-only */
struct GMTAPI_CTRL *API = NULL;
struct GMT_VECTOR_HIDDEN *VH = NULL;
char **dt = NULL;
double *t_vector = NULL;
uint64_t row, n_bad = 0;

API = gmtapi_get_api_ptr (V_API);
if (API == NULL) return_error (API, GMT_NOT_A_SESSION);
if (V == NULL) return_error (API, GMT_PTR_IS_NULL);
if (V->n_rows == 0) return_error (API, GMT_DIM_TOO_SMALL);
if (col >= V->n_columns) return_error (API, GMT_DIM_TOO_LARGE);
switch (type) {
case GMT_DOUBLE: V->type[col] = GMT_DOUBLE; V->data[col].f8 = vector; break;
case GMT_FLOAT: V->type[col] = GMT_FLOAT; V->data[col].f4 = vector; break;
case GMT_ULONG: V->type[col] = GMT_ULONG; V->data[col].ui8 = vector; break;
case GMT_LONG: V->type[col] = GMT_LONG; V->data[col].si8 = vector; break;
case GMT_UINT: V->type[col] = GMT_UINT; V->data[col].ui4 = vector; break;
case GMT_INT: V->type[col] = GMT_INT; V->data[col].si4 = vector; break;
case GMT_USHORT: V->type[col] = GMT_USHORT; V->data[col].ui2 = vector; break;
case GMT_SHORT: V->type[col] = GMT_SHORT; V->data[col].si2 = vector; break;
case GMT_UCHAR: V->type[col] = GMT_UCHAR; V->data[col].uc1 = vector; break;
case GMT_CHAR: V->type[col] = GMT_CHAR; V->data[col].sc1 = vector; break;
case GMT_DATETIME: /* Must convert from string-time to double */
if ((dt = gmtapi_get_char_char_ptr (vector)) == NULL) {
GMT_Report (API, GMT_MSG_ERROR, "Datetime string array is NULL\n");
return GMT_MEMORY_ERROR;
}
if ((t_vector = malloc (V->n_rows * sizeof(double))) == NULL) {
GMT_Report (API, GMT_MSG_ERROR, "Unable to allocate array of %" PRIu64 " doubles for converted datetime strings\n", V->n_rows);
return GMT_MEMORY_ERROR;
}
for (row = 0; row < V->n_rows; row++) {
if (gmt_scanf (API->GMT, dt[row], GMT_IS_ABSTIME, &(t_vector[row])) == GMT_IS_NAN) {
n_bad++;
t_vector[row] = API->GMT->session.d_NaN;
}
}
V->type[col] = GMT_DOUBLE; V->data[col].f8 = t_vector;
if (n_bad) GMT_Report (API, GMT_MSG_WARNING, "Unable to parse %" PRIu64 " datetime strings (ISO datetime format required)\n", n_bad);
break;
default:

special_type = type & (GMT_TEXT | GMT_DATETIME); /* Backwards compatible with just GMT_DATETIME */
if (special_type == 0) { /* Just passing in a numerical array directly via read-only pointer; hook it up */
if (gmtapi_insert_vector (API, &(V->data[col]), type, vector))
return_error (API, GMT_NOT_A_VALID_TYPE);
break;
V->type[col] = type; /* Set column type */
}
else { /* Convert text to something else */
bool no_T = false;
unsigned L_type = GMT_IS_UNKNOWN, got;
double value;
uint64_t row, n_bad = 0, L;
char **dt = NULL;
char text[GMT_LEN64] = {""};
GMT_putfunction api_put_val = NULL;

if (gmtapi_retrieve_vector (API, &(V->data[col]), type)) { /* Refuse to overwrite existing pointer unless NULL */
GMT_Report (API, GMT_MSG_ERROR, "Array already exist for column %d\n", col);
return_error (API, GMT_PTR_NOT_NULL);
}
type -= special_type; /* Remove the higher bit flag(s) */
if (type == 0) type = GMT_DOUBLE; /* Default is double precision if a type was not specified */
if ((dt = gmtapi_get_char_char_ptr (vector)) == NULL) {
GMT_Report (API, GMT_MSG_ERROR, "Given string array is NULL\n");
return_error (API, GMT_MEMORY_ERROR);
}
strncpy (text, dt[0], GMT_LEN64); /* Since gmt_scanf may try to temporarily change the string... */
if ((L = strlen (text)) == 0) {
GMT_Report (API, GMT_MSG_ERROR, "Given blank string in array\n");
return_error (API, GMT_MEMORY_ERROR);
}
if (special_type == GMT_DATETIME || gmtlib_maybe_abstime (API->GMT, text, &no_T)) /* Honor backwards compatibility for GMT_DATETIME */
L_type = GMT_IS_ABSTIME;
else if (strchr ("WE", text[L]))
L_type = GMT_IS_LON;
else if (strchr ("SN", text[L]))
L_type = GMT_IS_LAT;
else if (strchr (text, ':'))
L_type = GMT_IS_GEO;
if ((api_put_val = gmtapi_select_put_function (API, type)) == NULL)
return_error (API, GMT_NOT_A_VALID_TYPE);
/* Here we know the type is valid */
if (gmtlib_alloc_univector (API->GMT, &V->data[col], type, V->n_rows) != GMT_NOERROR) {
GMT_Report (API, GMT_MSG_ERROR, "Unable to allocate array of %" PRIu64 " %s-values for converted strings\n", V->n_rows, GMT_type[type]);
return_error (API, GMT_MEMORY_ERROR);
}
/* Do the conversion to double precision */
for (row = 0; row < V->n_rows; row++) {
strncpy (text, dt[row], GMT_LEN64);
if ((got = gmt_scanf (API->GMT, text, L_type, &value)) == GMT_IS_NAN) {
n_bad++; /* Check for bad conversions */
value = API->GMT->session.d_NaN;
}
else if (got != GMT_IS_FLOAT && L_type == GMT_IS_UNKNOWN) /* Got something other than plain float, use that from now on */
L_type = got;
api_put_val (&(V->data[col]), row, value); /* Place value in vector of selected type */
}
V->type[col] = type; /* Flag as the new type after conversion */
if (L_type == GMT_IS_UNKNOWN) L_type = GMT_IS_FLOAT; /* We held out this long but now must default to it */
gmt_set_column_type (API->GMT, GMT_IO, col, L_type);
if (n_bad) { /* Report on values that could not be converted */
if (L_type == GMT_IS_LON)
GMT_Report (API, GMT_MSG_WARNING, "Unable to parse %" PRIu64 " longitude strings\n", n_bad);
else if (L_type == GMT_IS_LAT)
GMT_Report (API, GMT_MSG_WARNING, "Unable to parse %" PRIu64 " latitude strings\n", n_bad);
else if (L_type == GMT_IS_ABSTIME)
GMT_Report (API, GMT_MSG_WARNING, "Unable to parse %" PRIu64 " datetime strings (ISO datetime format required)\n", n_bad);
}
alloc_mode = GMT_ALLOC_INTERNALLY;
}

VH = gmt_get_V_hidden (V);
VH->alloc_mode[col] = (type == GMT_DATETIME) ? GMT_ALLOC_INTERNALLY : GMT_ALLOC_EXTERNALLY;
VH->alloc_mode[col] = alloc_mode;

return GMT_NOERROR;
}

Expand All @@ -14533,21 +14618,8 @@ void * GMT_Get_Vector (void *API, struct GMT_VECTOR *V, unsigned int col) {
if (API == NULL) return_null (API, GMT_NOT_A_SESSION);
if (V == NULL) return_null (API, GMT_PTR_IS_NULL);
if (col >= V->n_columns) return_null (API, GMT_DIM_TOO_LARGE);
switch (V->type[col]) {
case GMT_DOUBLE: vector = V->data[col].f8; break;
case GMT_FLOAT: vector = V->data[col].f4; break;
case GMT_ULONG: vector = V->data[col].ui8; break;
case GMT_LONG: vector = V->data[col].si8; break;
case GMT_UINT: vector = V->data[col].ui4; break;
case GMT_INT: vector = V->data[col].si4; break;
case GMT_USHORT: vector = V->data[col].ui2; break;
case GMT_SHORT: vector = V->data[col].si2; break;
case GMT_UCHAR: vector = V->data[col].uc1; break;
case GMT_CHAR: vector = V->data[col].sc1; break;
default:
return_null (API, GMT_NOT_A_VALID_TYPE);
break;
}
if ((vector = gmtapi_retrieve_vector (API, &(V->data[col]), V->type[col])) == NULL)
return_null (API, GMT_NOT_A_VALID_TYPE);
return vector;
}

Expand All @@ -14566,21 +14638,9 @@ int GMT_Put_Matrix (void *API, struct GMT_MATRIX *M, unsigned int type, int pad,
if (API == NULL) return_error (API, GMT_NOT_A_SESSION);
if (M == NULL) return_error (API, GMT_PTR_IS_NULL);
if (M->n_columns == 0 || M->n_rows == 0) return_error (API, GMT_DIM_TOO_SMALL);
switch (type) {
case GMT_DOUBLE: M->type = GMT_DOUBLE; M->data.f8 = matrix; break;
case GMT_FLOAT: M->type = GMT_FLOAT; M->data.f4 = matrix; break;
case GMT_ULONG: M->type = GMT_ULONG; M->data.ui8 = matrix; break;
case GMT_LONG: M->type = GMT_LONG; M->data.si8 = matrix; break;
case GMT_UINT: M->type = GMT_UINT; M->data.ui4 = matrix; break;
case GMT_INT: M->type = GMT_INT; M->data.si4 = matrix; break;
case GMT_USHORT: M->type = GMT_USHORT; M->data.ui2 = matrix; break;
case GMT_SHORT: M->type = GMT_SHORT; M->data.si2 = matrix; break;
case GMT_UCHAR: M->type = GMT_UCHAR; M->data.uc1 = matrix; break;
case GMT_CHAR: M->type = GMT_CHAR; M->data.sc1 = matrix; break;
default:
return_error (API, GMT_NOT_A_VALID_TYPE);
break;
}
if (gmtapi_insert_vector (API, &(M->data), type, matrix))
return_error (API, GMT_NOT_A_VALID_TYPE);
M->type = type;
MH = gmt_get_M_hidden (M);
MH->alloc_mode = GMT_ALLOC_EXTERNALLY; /* Since it clearly is a user array */
MH->pad = pad; /* Placing the pad argument here */
Expand All @@ -14600,21 +14660,8 @@ void * GMT_Get_Matrix (void *API, struct GMT_MATRIX *M) {
void *matrix = NULL;
if (API == NULL) return_null (API, GMT_NOT_A_SESSION);
if (M == NULL) return_null (API, GMT_PTR_IS_NULL);
switch (M->type) {
case GMT_DOUBLE: matrix = M->data.f8; break;
case GMT_FLOAT: matrix = M->data.f4; break;
case GMT_ULONG: matrix = M->data.ui8; break;
case GMT_LONG: matrix = M->data.si8; break;
case GMT_UINT: matrix = M->data.ui4; break;
case GMT_INT: matrix = M->data.si4; break;
case GMT_USHORT: matrix = M->data.ui2; break;
case GMT_SHORT: matrix = M->data.si2; break;
case GMT_UCHAR: matrix = M->data.uc1; break;
case GMT_CHAR: matrix = M->data.sc1; break;
default:
return_null (API, GMT_NOT_A_VALID_TYPE);
break;
}
if ((matrix = gmtapi_retrieve_vector (API, &(M->data), M->type)) == NULL)
return_null (API, GMT_NOT_A_VALID_TYPE);
return matrix;
}

Expand Down
4 changes: 2 additions & 2 deletions src/gmt_enum_dict.h
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Expand Up @@ -76,7 +76,7 @@ static struct GMT_API_DICT gmt_api_enums[GMT_N_API_ENUMS] = {
{"GMT_CPT_TIME", 16},
{"GMT_CUBE_IS_STACK", 64},
{"GMT_DATA_ONLY", 2},
{"GMT_DATETIME", 11},
{"GMT_DATETIME", 32},
{"GMT_DOUBLE", 9},
{"GMT_DUPLICATE_ALLOC", 1},
{"GMT_DUPLICATE_DATA", 2},
Expand Down Expand Up @@ -234,7 +234,7 @@ static struct GMT_API_DICT gmt_api_enums[GMT_N_API_ENUMS] = {
{"GMT_STRICT_CONVERSION", 1024},
{"GMT_SYNOPSIS", 1},
{"GMT_TBL", 0},
{"GMT_TEXT", 10},
{"GMT_TEXT", 16},
{"GMT_TIME_CLOCK", 1},
{"GMT_TIME_ELAPSED", 2},
{"GMT_TIME_NONE", 0},
Expand Down
20 changes: 16 additions & 4 deletions src/gmt_io.c
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Expand Up @@ -925,12 +925,20 @@ GMT_LOCAL unsigned int gmtio_assign_aspatial_cols (struct GMT_CTRL *GMT) {
return (n); /* Only numerical columns add to the count */
}

GMT_LOCAL unsigned int gmtio_type_index (unsigned int type) {
if (type == GMT_TEXT) return GMT_N_TYPES-2;
if (type == GMT_DATETIME) return GMT_N_TYPES-1;
return type;
}

/*! Fill a string with the aspatial columns */
void gmt_list_aspatials (struct GMT_CTRL *GMT, char buffer[]) {
char item[GMT_LEN64] = {""};
unsigned int type;
sprintf (buffer, "Aspatial columns:");
for (unsigned int k = 0; k < GMT->common.a.n_aspatial; k++) {
sprintf (item, " %s[%s]", GMT->common.a.name[k], GMT_type[GMT->common.a.type[k]]);
type = gmtio_type_index (GMT->common.a.type[k]);
sprintf (item, " %s[%s]", GMT->common.a.name[k], GMT_type[type]);
strcat (buffer, item);
}
}
Expand Down Expand Up @@ -4320,7 +4328,7 @@ int gmtlib_append_ogr_item (struct GMT_CTRL *GMT, char *name, enum GMT_enum_type
//*! . */
void gmtlib_write_ogr_header (FILE *fp, struct GMT_OGR *G) {
/* Write out table-level OGR/GMT header metadata */
unsigned int k, col;
unsigned int k, col, type;
char *flavor = "egpw";

fprintf (fp, "# @VGMT1.0 @G");
Expand All @@ -4335,8 +4343,12 @@ void gmtlib_write_ogr_header (FILE *fp, struct GMT_OGR *G) {
if (G->n_aspatial) {
fprintf (fp, "# @N%s", G->name[0]);
for (col = 1; col < G->n_aspatial; col++) fprintf (fp, "|%s", G->name[col]);
fprintf (fp, "\n# @T%s", GMT_type[G->type[0]]);
for (col = 1; col < G->n_aspatial; col++) fprintf (fp, "|%s", GMT_type[G->type[col]]);
type = gmtio_type_index (G->type[0]);
fprintf (fp, "\n# @T%s", GMT_type[type]);
for (col = 1; col < G->n_aspatial; col++) {
type = gmtio_type_index (G->type[col]);
fprintf (fp, "|%s", GMT_type[type]);
}
fprintf (fp, "\n");
}
fprintf (fp, "# FEATURE_DATA\n");
Expand Down
4 changes: 2 additions & 2 deletions src/gmt_resources.h
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Expand Up @@ -90,8 +90,8 @@ enum GMT_enum_type {
GMT_ULONG = 7, /* uint64_t, 8-byte unsigned integer type */
GMT_FLOAT = 8, /* 4-byte data float type */
GMT_DOUBLE = 9, /* 8-byte data float type */
GMT_TEXT = 10, /* Arbitrarily long text string [OGR/GMT use only] */
GMT_DATETIME = 11, /* string with date/time info [OGR/GMT use only] */
GMT_TEXT = 16, /* Arbitrarily long text string [OGR/GMT use only and GMT_Put_Vector only] */
GMT_DATETIME = 32, /* string with date/time info [OGR/GMT use and GMT_Put_Vector only] */
GMT_N_TYPES = 12, /* The number of supported data types above */
GMT_VIA_CHAR = 100, /* int8_t, 1-byte signed integer type */
GMT_VIA_UCHAR = 200, /* uint8_t, 1-byte unsigned integer type */
Expand Down
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