Skip to content

Commit

Permalink
Make sure create_table sets allocation mode (#5953)
Browse files Browse the repository at this point in the history 
* Make sure create_table sets allocation mode

I noticed that gmtmath were unable to free datasets it had allocated because the tables never had their alloc_mode set to GMT_ALLOC_INTERNALLY.

* Update gmt_io.c

* Improve alloc_levels etc

* A few fixes

* Track allocation mode per column

Since GMT_Put_Vector adds individual vectors we really need to track allocation mode accordingly.

* Update gmt_io.c

* Update grdview.c

Fix bad grdview usage.

* Update grdview.c

* Cleaner freeing
  • Loading branch information
@PaulWessel
PaulWessel authored Nov 9, 2021
1 parent fd54c73 commit c25e954
Show file tree
Hide file tree
Showing 13 changed files with 170 additions and 105 deletions.
36 changes: 25 additions & 11 deletions src/gmt_api.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3632,9 +3632,11 @@ GMT_LOCAL struct GMT_DATASET * gmtapi_import_dataset (struct GMTAPI_CTRL *API, i
struct GMT_DATASEGMENT *S = NULL;
struct GMT_MATRIX *M_obj = NULL;
struct GMT_VECTOR *V_obj = NULL;
struct GMT_DATASET_HIDDEN *DH = NULL;
struct GMT_DATASET_HIDDEN *DH = NULL, *DHi = NULL;
struct GMT_DATATABLE_HIDDEN *TH = NULL;
struct GMT_DATASEGMENT_HIDDEN *SH = NULL;
struct GMT_MATRIX_HIDDEN *MH = NULL;
struct GMT_VECTOR_HIDDEN *VH = NULL;
struct GMTAPI_DATA_OBJECT *S_obj = NULL;
struct GMT_CTRL *GMT = API->GMT;

Expand Down Expand Up @@ -3757,19 +3759,25 @@ GMT_LOCAL struct GMT_DATASET * gmtapi_import_dataset (struct GMTAPI_CTRL *API, i
if (GMT->common.q.mode == GMT_RANGE_ROW_IN || GMT->common.q.mode == GMT_RANGE_DATA_IN)
GMT_Report (API, GMT_MSG_WARNING, "Row-selection via -qi is not implemented for GMT_IS_REFERENCE with GMT_IS_DATASET external memory objects\n");
GMT_Report (API, GMT_MSG_INFORMATION, "Referencing data table from GMT_DATASET memory location\n");
DHi = gmt_get_DD_hidden (Din_obj);
if ((tbl + Din_obj->n_tables) >= n_alloc) { /* Need more space to hold these new tables */
n_alloc += Din_obj->n_tables;
D_obj->table = gmt_M_memory (GMT, D_obj->table, n_alloc, struct GMT_DATATABLE *);
}
for (tbl_in = 0; tbl_in < Din_obj->n_tables; tbl_in++, tbl++) /* Pass over the pointers only */
for (tbl_in = 0; tbl_in < Din_obj->n_tables; tbl_in++, tbl++) { /* Pass over the pointers only */
D_obj->table[tbl] = Din_obj->table[tbl_in];
Din_obj->table[tbl_in] = NULL; /* Since passed to D_obj */
}
Din_obj->n_tables = 0; /* Only the husk remains of this fruit */
D_obj->n_tables = tbl;
D_obj->geometry = S_obj->geometry; /* Since provided when registered */
DH->alloc_mode = DHi->alloc_mode; /* Must use whatever alloc_mode the input reference had */
DH->alloc_level = DHi->alloc_level; /* Must use whatever alloc_level the input reference had */
check_col_switch = true;
update = regit = via = true; /* Have reason to update min/max as well as registering D_obj when done */
break;

case GMT_IS_DUPLICATE|GMT_VIA_MATRIX:
case GMT_IS_DUPLICATE|GMT_VIA_MATRIX: /* There is no difference since in both cases we must allocate dataset arrays */
case GMT_IS_REFERENCE|GMT_VIA_MATRIX:
/* Each matrix source becomes a separate table with a single segment unless there are NaN-records as segment headers */
if ((M_obj = S_obj->resource) == NULL) {
Expand Down Expand Up @@ -3916,8 +3924,10 @@ GMT_LOCAL struct GMT_DATASET * gmtapi_import_dataset (struct GMTAPI_CTRL *API, i
gmt_M_free (GMT, D_obj); return_null (API, GMT_PTR_IS_NULL);
}
if (V_obj->type[0] != GMT_DOUBLE) {
GMT_Report (API, GMT_MSG_ERROR, "Only double-precision vectors can be passed via reference to datasets\n");
gmt_M_free (GMT, D_obj); return_null (API, GMT_NOT_A_VALID_TYPE);
}
VH = gmt_get_V_hidden (V_obj);
if (GMT->common.q.mode == GMT_RANGE_ROW_IN || GMT->common.q.mode == GMT_RANGE_DATA_IN)
GMT_Report (API, GMT_MSG_WARNING, "Row-selection via -qi is not implemented for GMT_IS_REFERENCE|GMT_VIA_VECTOR external memory objects\n");
/* Each column double array source becomes preallocated column arrays in a separate table with a single segment */
Expand All @@ -3928,18 +3938,20 @@ GMT_LOCAL struct GMT_DATASET * gmtapi_import_dataset (struct GMTAPI_CTRL *API, i
V_obj->n_columns, V_obj->n_rows);
D_obj->table[D_obj->n_tables] = gmt_get_table (GMT);
D_obj->table[D_obj->n_tables]->segment = gmt_M_memory (GMT, NULL, 1, struct GMT_DATASEGMENT *);
D_obj->table[D_obj->n_tables]->segment[0] = GMT_Alloc_Segment (API, smode, 0, n_columns, NULL, NULL);
S = D_obj->table[D_obj->n_tables]->segment[0] = GMT_Alloc_Segment (API, smode, 0, n_columns, NULL, NULL);
SH = gmt_get_DS_hidden (S);
for (col = 0; col < V_obj->n_columns; col++) {
if (GMT->common.i.select) /* -i has selected some columns */
col_pos = GMT->current.io.col[GMT_IN][col].col; /* Which data column to pick */
else if (GMT->current.setting.io_lonlat_toggle[GMT_IN] && col < GMT_Z) /* Worry about -: for lon,lat */
col_pos = 1 - col; /* Read lat/lon instead of lon/lat */
else
col_pos = col; /* Just goto that column */
D_obj->table[D_obj->n_tables]->segment[0]->data[col] = V_obj->data[col_pos].f8;
S->data[col] = V_obj->data[col_pos].f8;
SH->alloc_mode[col] = VH->alloc_mode[col]; /* Inherit from what we got */
}
DH = gmt_get_DD_hidden (D_obj);
if (smode) D_obj->table[D_obj->n_tables]->segment[0]->text = V_obj->text;
if (smode) S->text = V_obj->text;
gmtapi_increment_d (D_obj, V_obj->n_rows, n_columns, 1U); /* Update counters for D_obj with 1 segment */
DH->alloc_mode = GMT_ALLOC_EXTERNALLY; /* Since we just hooked on the arrays */
new_ID = GMT_Register_IO (API, GMT_IS_DATASET, GMT_IS_REFERENCE, geometry, GMT_IN, NULL, D_obj); /* Register a new resource to hold D_obj */
Expand Down Expand Up @@ -3994,6 +4006,8 @@ GMT_LOCAL struct GMT_DATASET * gmtapi_import_dataset (struct GMTAPI_CTRL *API, i
return_null (API, GMT_OBJECT_NOT_FOUND); /* Some internal error... */
API->object[new_item]->resource = D_obj;
API->object[new_item]->status = GMT_IS_USED; /* Mark as read */
API->object[new_item]->alloc_mode = DH->alloc_mode; /* Clarify allocation mode for this object */
API->object[new_item]->alloc_level = DH->alloc_level;
}
if (D_obj->n_tables == 0) { /* Only found empty files (e.g., /dev/null) and we have nothing to show for our efforts. Return an single empty table with no segments. */
D_obj->table = gmt_M_memory (GMT, D_obj->table, 1, struct GMT_DATATABLE *);
Expand Down Expand Up @@ -4321,6 +4335,7 @@ GMT_LOCAL int gmtapi_export_dataset (struct GMTAPI_CTRL *API, int object_ID, uns
V_obj->type[col] = S_obj->type; /* Set same data type for all columns */
V_obj->data[col].f8 = S->data[col]; /* Set pointer only */
VH->alloc_mode[col] = GMT_ALLOC_EXTERNALLY; /* Since not duplicated, just pointed to */
SH->alloc_mode[col] = GMT_ALLOC_EXTERNALLY; /* To prevent freeing in D_obj */
}
if (S->text) {
V_obj->text = S->text;
Expand All @@ -4329,7 +4344,6 @@ GMT_LOCAL int gmtapi_export_dataset (struct GMTAPI_CTRL *API, int object_ID, uns
V_obj->n_rows = n_rows;
VH->alloc_level = S_obj->alloc_level; /* Otherwise D_obj will be freed before we get to use data */
S_obj->alloc_mode = DH->alloc_mode; /* Otherwise D_obj will be freed before we get to use data */
SH->alloc_mode = GMT_ALLOC_EXTERNALLY; /* To prevent freeing in D_obj */
}
else { /* Got a preallocated container */
if (V_obj->n_rows < n_rows || V_obj->n_columns < n_columns)
Expand Down Expand Up @@ -8633,7 +8647,7 @@ GMT_LOCAL int gmtapi_end_io_dataset (struct GMTAPI_CTRL *API, struct GMTAPI_DATA
DH = gmt_get_DD_hidden (D);
TH = gmt_get_DT_hidden (T);
if (count[GMT_SEG] >= 0) { /* Finalize segment allocations */
if (!T->segment[count[GMT_SEG]]) T->segment[count[GMT_SEG]] = gmt_get_segment (API->GMT);
if (!T->segment[count[GMT_SEG]]) T->segment[count[GMT_SEG]] = gmt_get_segment (API->GMT, T->n_columns);
gmtlib_assign_segment (API->GMT, GMT_OUT, T->segment[count[GMT_SEG]], count[GMT_ROW], T->n_columns); /* Allocate and place arrays into segment */
count[GMT_SEG]++; /* Set final number of segments */
T->n_segments++;
Expand Down Expand Up @@ -10143,7 +10157,7 @@ GMT_LOCAL int gmtapi_put_record_dataset (struct GMTAPI_CTRL *API, unsigned int m
case GMT_WRITE_SEGMENT_HEADER: /* Export a segment header record; write NaNs if binary */
count[GMT_SEG]++; /* Start of new segment */
if (count[GMT_SEG]) { /* Must first copy over records for the previous segments; last (or only) segment will be done by GMT_End_IO */
if (!T->segment[count[GMT_SEG]-1]) T->segment[count[GMT_SEG]-1] = gmt_get_segment (API->GMT);
if (!T->segment[count[GMT_SEG]-1]) T->segment[count[GMT_SEG]-1] = gmt_get_segment (API->GMT, T->n_columns);
gmtlib_assign_segment (GMT, GMT_OUT, T->segment[count[GMT_SEG]-1], count[GMT_ROW], T->n_columns); /* Allocate and place arrays into previous segment */
count[GMT_ROW] = 0; /* Reset for next segment */
T->n_segments++;
Expand All @@ -10153,7 +10167,7 @@ GMT_LOCAL int gmtapi_put_record_dataset (struct GMTAPI_CTRL *API, unsigned int m
T->segment = gmt_M_malloc (GMT, T->segment, count[GMT_SEG], &TH->n_alloc, struct GMT_DATASEGMENT *);
gmt_M_memset (&T->segment[was], TH->n_alloc - was, struct GMT_DATASEGMENT *);
}
if (!T->segment[count[GMT_SEG]]) T->segment[count[GMT_SEG]] = gmt_get_segment (GMT);
if (!T->segment[count[GMT_SEG]]) T->segment[count[GMT_SEG]] = gmt_get_segment (GMT, T->n_columns);
s = (record) ? (char *)record : GMT->current.io.segment_header; /* Default to last segment header record if NULL */
if (s && strlen(s)) { /* Found a segment header */
if (T->segment[count[GMT_SEG]]->header) gmt_M_str_free (T->segment[count[GMT_SEG]]->header); /* Hm, better free the old guy before strdup'ing a new one */
Expand Down Expand Up @@ -14718,7 +14732,7 @@ void * GMT_Alloc_Segment (void *V_API, unsigned int mode, uint64_t n_rows, uint6
API->error = GMT_NOERROR;
if ((Snew = S) != NULL) /* Existing segment given */
first = false;
else if ((Snew = gmt_get_segment (API->GMT)) == NULL) /* Something went wrong */
else if ((Snew = gmt_get_segment (API->GMT, n_columns)) == NULL) /* Something went wrong */
return_null (V_API, GMT_MEMORY_ERROR);
/* Only reallocate if desired n_rows differ from current n_rows */
alloc = (first || (n_rows && n_rows != Snew->n_rows)); /* Alloc first time or reallocate later if necessary */
Expand Down
2 changes: 1 addition & 1 deletion src/gmt_dcw.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -631,7 +631,7 @@ struct GMT_DATASET * gmt_DCW_operation (struct GMT_CTRL *GMT, struct GMT_DCW_SEL
gmt_M_malloc2 (GMT, S->data[GMT_X], S->data[GMT_Y], S->n_rows, NULL, double);
gmt_M_memcpy (S->data[GMT_X], P->data[GMT_X], S->n_rows, double);
gmt_M_memcpy (S->data[GMT_Y], P->data[GMT_Y], S->n_rows, double);
SH->alloc_mode = GMT_ALLOC_INTERNALLY; /* Allocated in GMT */
SH->alloc_mode[GMT_X] = SH->alloc_mode[GMT_Y] = GMT_ALLOC_INTERNALLY; /* Allocated in GMT */
seg++;
}
}
Expand Down
2 changes: 1 addition & 1 deletion src/gmt_hidden.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ struct GMT_DATASEGMENT_HIDDEN { /* Supporting information hidden from the API
double lat_limit; /* For polar caps: the latitude of the point closest to the pole */
struct GMT_OGR_SEG *ogr; /* NULL unless OGR/GMT metadata exist for this segment */
struct GMT_DATASEGMENT *next; /* NULL unless polygon and has holes and pointing to next hole */
enum GMT_enum_alloc alloc_mode; /* Allocation mode [GMT_ALLOC_INTERNALLY] */
enum GMT_enum_alloc *alloc_mode; /* Allocation mode per column [GMT_ALLOC_INTERNALLY] */
char *file[2]; /* Name of file or source [0 = in, 1 = out] */
};

Expand Down
Loading

0 comments on commit c25e954

Please sign in to comment.