int main(int argc, char **argv)
{
char *mapname, /* ptr to name of output layer */
*setname, /* ptr to name of input mapset */
*ipolname; /* name of interpolation method */
int fdi, /* input map file descriptor */
fdo, /* output map file descriptor */
method, /* position of method in table */
permissions, /* mapset permissions */
cell_type, /* output celltype */
cell_size, /* size of a cell in bytes */
row, col, /* counters */
irows, icols, /* original rows, cols */
orows, ocols, have_colors, /* Input map has a colour table */
overwrite, /* Overwrite */
curr_proj; /* output projection (see gis.h) */
void *obuffer, /* buffer that holds one output row */
*obufptr; /* column ptr in output buffer */
struct cache *ibuffer; /* buffer that holds the input map */
func interpolate; /* interpolation routine */
double xcoord1, xcoord2, /* temporary x coordinates */
ycoord1, ycoord2, /* temporary y coordinates */
col_idx, /* column index in input matrix */
row_idx, /* row index in input matrix */
onorth, osouth, /* save original border coords */
oeast, owest, inorth, isouth, ieast, iwest;
char north_str[30], south_str[30], east_str[30], west_str[30];
struct Colors colr; /* Input map colour table */
struct History history;
struct pj_info iproj, /* input map proj parameters */
oproj; /* output map proj parameters */
struct Key_Value *in_proj_info, /* projection information of */
*in_unit_info, /* input and output mapsets */
*out_proj_info, *out_unit_info;
struct GModule *module;
struct Flag *list, /* list files in source location */
*nocrop, /* don't crop output map */
*print_bounds, /* print output bounds and exit */
*gprint_bounds; /* same but print shell style */
struct Option *imapset, /* name of input mapset */
*inmap, /* name of input layer */
*inlocation, /* name of input location */
*outmap, /* name of output layer */
*indbase, /* name of input database */
*interpol, /* interpolation method:
nearest neighbor, bilinear, cubic */
*memory, /* amount of memory for cache */
*res; /* resolution of target map */
struct Cell_head incellhd, /* cell header of input map */
outcellhd; /* and output map */
G_gisinit(argv[0]);
module = G_define_module();
G_add_keyword(_("raster"));
G_add_keyword(_("projection"));
G_add_keyword(_("transformation"));
module->description =
_("Re-projects a raster map from given location to the current location.");
inmap = G_define_standard_option(G_OPT_R_INPUT);
inmap->description = _("Name of input raster map to re-project");
inmap->required = NO;
inmap->guisection = _("Source");
inlocation = G_define_option();
inlocation->key = "location";
inlocation->type = TYPE_STRING;
inlocation->required = YES;
inlocation->description = _("Location containing input raster map");
inlocation->gisprompt = "old,location,location";
inlocation->key_desc = "name";
imapset = G_define_standard_option(G_OPT_M_MAPSET);
imapset->label = _("Mapset containing input raster map");
imapset->description = _("default: name of current mapset");
imapset->guisection = _("Source");
indbase = G_define_option();
indbase->key = "dbase";
indbase->type = TYPE_STRING;
indbase->required = NO;
indbase->description = _("Path to GRASS database of input location");
indbase->gisprompt = "old,dbase,dbase";
indbase->key_desc = "path";
indbase->guisection = _("Source");
outmap = G_define_standard_option(G_OPT_R_OUTPUT);
outmap->required = NO;
outmap->description = _("Name for output raster map (default: same as 'input')");
outmap->guisection = _("Target");
ipolname = make_ipol_list();
interpol = G_define_option();
interpol->key = "method";
interpol->type = TYPE_STRING;
interpol->required = NO;
interpol->answer = "nearest";
interpol->options = ipolname;
interpol->description = _("Interpolation method to use");
interpol->guisection = _("Target");
interpol->descriptions = make_ipol_desc();
memory = G_define_option();
memory->key = "memory";
memory->type = TYPE_INTEGER;
memory->required = NO;
memory->description = _("Cache size (MiB)");
res = G_define_option();
res->key = "resolution";
res->type = TYPE_DOUBLE;
res->required = NO;
res->description = _("Resolution of output raster map");
res->guisection = _("Target");
list = G_define_flag();
list->key = 'l';
list->description = _("List raster maps in input location and exit");
nocrop = G_define_flag();
nocrop->key = 'n';
nocrop->description = _("Do not perform region cropping optimization");
print_bounds = G_define_flag();
print_bounds->key = 'p';
print_bounds->description =
_("Print input map's bounds in the current projection and exit");
print_bounds->guisection = _("Target");
gprint_bounds = G_define_flag();
gprint_bounds->key = 'g';
gprint_bounds->description =
_("Print input map's bounds in the current projection and exit (shell style)");
gprint_bounds->guisection = _("Target");
/* The parser checks if the map already exists in current mapset,
we switch out the check and do it
in the module after the parser */
overwrite = G_check_overwrite(argc, argv);
if (G_parser(argc, argv))
exit(EXIT_FAILURE);
/* get the method */
for (method = 0; (ipolname = menu[method].name); method++)
if (strcmp(ipolname, interpol->answer) == 0)
break;
if (!ipolname)
G_fatal_error(_("<%s=%s> unknown %s"),
interpol->key, interpol->answer, interpol->key);
interpolate = menu[method].method;
mapname = outmap->answer ? outmap->answer : inmap->answer;
if (mapname && !list->answer && !overwrite &&
G_find_raster(mapname, G_mapset()))
G_fatal_error(_("option <%s>: <%s> exists."), "output", mapname);
setname = imapset->answer ? imapset->answer : G_store(G_mapset());
if (strcmp(inlocation->answer, G_location()) == 0 &&
(!indbase->answer || strcmp(indbase->answer, G_gisdbase()) == 0))
#if 0
G_fatal_error(_("Input and output locations can not be the same"));
#else
G_warning(_("Input and output locations are the same"));
#endif
G_get_window(&outcellhd);
if(gprint_bounds->answer && !print_bounds->answer)
print_bounds->answer = gprint_bounds->answer;
curr_proj = G_projection();
/* Get projection info for output mapset */
if ((out_proj_info = G_get_projinfo()) == NULL)
G_fatal_error(_("Unable to get projection info of output raster map"));
if ((out_unit_info = G_get_projunits()) == NULL)
G_fatal_error(_("Unable to get projection units of output raster map"));
if (pj_get_kv(&oproj, out_proj_info, out_unit_info) < 0)
G_fatal_error(_("Unable to get projection key values of output raster map"));
/* Change the location */
G__create_alt_env();
G__setenv("GISDBASE", indbase->answer ? indbase->answer : G_gisdbase());
G__setenv("LOCATION_NAME", inlocation->answer);
permissions = G__mapset_permissions(setname);
if (permissions < 0) /* can't access mapset */
G_fatal_error(_("Mapset <%s> in input location <%s> - %s"),
setname, inlocation->answer,
permissions == 0 ? _("permission denied")
: _("not found"));
/* if requested, list the raster maps in source location - MN 5/2001 */
if (list->answer) {
int i;
char **list;
G_verbose_message(_("Checking location <%s> mapset <%s>"),
inlocation->answer, setname);
list = G_list(G_ELEMENT_RASTER, G__getenv("GISDBASE"),
G__getenv("LOCATION_NAME"), setname);
for (i = 0; list[i]; i++) {
fprintf(stdout, "%s\n", list[i]);
}
fflush(stdout);
exit(EXIT_SUCCESS); /* leave r.proj after listing */
}
if (!inmap->answer)
G_fatal_error(_("Required parameter <%s> not set"), inmap->key);
if (!G_find_raster(inmap->answer, setname))
G_fatal_error(_("Raster map <%s> in location <%s> in mapset <%s> not found"),
inmap->answer, inlocation->answer, setname);
/* Read input map colour table */
have_colors = Rast_read_colors(inmap->answer, setname, &colr);
/* Get projection info for input mapset */
if ((in_proj_info = G_get_projinfo()) == NULL)
G_fatal_error(_("Unable to get projection info of input map"));
if ((in_unit_info = G_get_projunits()) == NULL)
G_fatal_error(_("Unable to get projection units of input map"));
if (pj_get_kv(&iproj, in_proj_info, in_unit_info) < 0)
G_fatal_error(_("Unable to get projection key values of input map"));
G_free_key_value(in_proj_info);
G_free_key_value(in_unit_info);
G_free_key_value(out_proj_info);
G_free_key_value(out_unit_info);
if (G_verbose() > G_verbose_std())
pj_print_proj_params(&iproj, &oproj);
/* this call causes r.proj to read the entire map into memeory */
Rast_get_cellhd(inmap->answer, setname, &incellhd);
Rast_set_input_window(&incellhd);
if (G_projection() == PROJECTION_XY)
G_fatal_error(_("Unable to work with unprojected data (xy location)"));
/* Save default borders so we can show them later */
inorth = incellhd.north;
isouth = incellhd.south;
ieast = incellhd.east;
iwest = incellhd.west;
irows = incellhd.rows;
icols = incellhd.cols;
onorth = outcellhd.north;
osouth = outcellhd.south;
oeast = outcellhd.east;
owest = outcellhd.west;
orows = outcellhd.rows;
ocols = outcellhd.cols;
if (print_bounds->answer) {
G_message(_("Input map <%s@%s> in location <%s>:"),
inmap->answer, setname, inlocation->answer);
if (pj_do_proj(&iwest, &isouth, &iproj, &oproj) < 0)
G_fatal_error(_("Error in pj_do_proj (projection of input coordinate pair)"));
if (pj_do_proj(&ieast, &inorth, &iproj, &oproj) < 0)
G_fatal_error(_("Error in pj_do_proj (projection of input coordinate pair)"));
G_format_northing(inorth, north_str, curr_proj);
G_format_northing(isouth, south_str, curr_proj);
G_format_easting(ieast, east_str, curr_proj);
G_format_easting(iwest, west_str, curr_proj);
if(gprint_bounds->answer) {
fprintf(stdout, "n=%s s=%s w=%s e=%s rows=%d cols=%d\n",
north_str, south_str, west_str, east_str, irows, icols);
}
else {
fprintf(stdout, "Source cols: %d\n", icols);
fprintf(stdout, "Source rows: %d\n", irows);
fprintf(stdout, "Local north: %s\n", north_str);
fprintf(stdout, "Local south: %s\n", south_str);
fprintf(stdout, "Local west: %s\n", west_str);
fprintf(stdout, "Local east: %s\n", east_str);
}
/* somehow approximate local ewres, nsres ?? (use 'g.region -m' on lat/lon side) */
exit(EXIT_SUCCESS);
}
/* Cut non-overlapping parts of input map */
if (!nocrop->answer)
bordwalk(&outcellhd, &incellhd, &oproj, &iproj);
/* Add 2 cells on each side for bilinear/cubic & future interpolation methods */
/* (should probably be a factor based on input and output resolution) */
incellhd.north += 2 * incellhd.ns_res;
incellhd.east += 2 * incellhd.ew_res;
incellhd.south -= 2 * incellhd.ns_res;
incellhd.west -= 2 * incellhd.ew_res;
if (incellhd.north > inorth)
incellhd.north = inorth;
if (incellhd.east > ieast)
incellhd.east = ieast;
if (incellhd.south < isouth)
incellhd.south = isouth;
if (incellhd.west < iwest)
incellhd.west = iwest;
Rast_set_input_window(&incellhd);
/* And switch back to original location */
G__switch_env();
/* Adjust borders of output map */
if (!nocrop->answer)
bordwalk(&incellhd, &outcellhd, &iproj, &oproj);
#if 0
outcellhd.west = outcellhd.south = HUGE_VAL;
outcellhd.east = outcellhd.north = -HUGE_VAL;
for (row = 0; row < incellhd.rows; row++) {
ycoord1 = Rast_row_to_northing((double)(row + 0.5), &incellhd);
for (col = 0; col < incellhd.cols; col++) {
xcoord1 = Rast_col_to_easting((double)(col + 0.5), &incellhd);
pj_do_proj(&xcoord1, &ycoord1, &iproj, &oproj);
if (xcoord1 > outcellhd.east)
outcellhd.east = xcoord1;
if (ycoord1 > outcellhd.north)
outcellhd.north = ycoord1;
if (xcoord1 < outcellhd.west)
outcellhd.west = xcoord1;
if (ycoord1 < outcellhd.south)
outcellhd.south = ycoord1;
}
}
#endif
if (res->answer != NULL) /* set user defined resolution */
outcellhd.ns_res = outcellhd.ew_res = atof(res->answer);
G_adjust_Cell_head(&outcellhd, 0, 0);
Rast_set_output_window(&outcellhd);
G_message(" ");
G_message(_("Input:"));
G_message(_("Cols: %d (%d)"), incellhd.cols, icols);
G_message(_("Rows: %d (%d)"), incellhd.rows, irows);
G_message(_("North: %f (%f)"), incellhd.north, inorth);
G_message(_("South: %f (%f)"), incellhd.south, isouth);
G_message(_("West: %f (%f)"), incellhd.west, iwest);
G_message(_("East: %f (%f)"), incellhd.east, ieast);
G_message(_("EW-res: %f"), incellhd.ew_res);
G_message(_("NS-res: %f"), incellhd.ns_res);
G_message(" ");
G_message(_("Output:"));
G_message(_("Cols: %d (%d)"), outcellhd.cols, ocols);
G_message(_("Rows: %d (%d)"), outcellhd.rows, orows);
G_message(_("North: %f (%f)"), outcellhd.north, onorth);
G_message(_("South: %f (%f)"), outcellhd.south, osouth);
G_message(_("West: %f (%f)"), outcellhd.west, owest);
G_message(_("East: %f (%f)"), outcellhd.east, oeast);
G_message(_("EW-res: %f"), outcellhd.ew_res);
G_message(_("NS-res: %f"), outcellhd.ns_res);
G_message(" ");
/* open and read the relevant parts of the input map and close it */
G__switch_env();
Rast_set_input_window(&incellhd);
fdi = Rast_open_old(inmap->answer, setname);
cell_type = Rast_get_map_type(fdi);
ibuffer = readcell(fdi, memory->answer);
Rast_close(fdi);
G__switch_env();
Rast_set_output_window(&outcellhd);
if (strcmp(interpol->answer, "nearest") == 0) {
fdo = Rast_open_new(mapname, cell_type);
obuffer = (CELL *) Rast_allocate_output_buf(cell_type);
}
else {
fdo = Rast_open_fp_new(mapname);
cell_type = FCELL_TYPE;
obuffer = (FCELL *) Rast_allocate_output_buf(cell_type);
}
cell_size = Rast_cell_size(cell_type);
xcoord1 = xcoord2 = outcellhd.west + (outcellhd.ew_res / 2);
/**/ ycoord1 = ycoord2 = outcellhd.north - (outcellhd.ns_res / 2);
/**/ G_important_message(_("Projecting..."));
G_percent(0, outcellhd.rows, 2);
for (row = 0; row < outcellhd.rows; row++) {
obufptr = obuffer;
for (col = 0; col < outcellhd.cols; col++) {
/* project coordinates in output matrix to */
/* coordinates in input matrix */
if (pj_do_proj(&xcoord1, &ycoord1, &oproj, &iproj) < 0)
Rast_set_null_value(obufptr, 1, cell_type);
else {
/* convert to row/column indices of input matrix */
col_idx = (xcoord1 - incellhd.west) / incellhd.ew_res;
row_idx = (incellhd.north - ycoord1) / incellhd.ns_res;
/* and resample data point */
interpolate(ibuffer, obufptr, cell_type,
&col_idx, &row_idx, &incellhd);
}
obufptr = G_incr_void_ptr(obufptr, cell_size);
xcoord2 += outcellhd.ew_res;
xcoord1 = xcoord2;
ycoord1 = ycoord2;
}
Rast_put_row(fdo, obuffer, cell_type);
xcoord1 = xcoord2 = outcellhd.west + (outcellhd.ew_res / 2);
ycoord2 -= outcellhd.ns_res;
ycoord1 = ycoord2;
G_percent(row, outcellhd.rows - 1, 2);
}
Rast_close(fdo);
if (have_colors > 0) {
Rast_write_colors(mapname, G_mapset(), &colr);
Rast_free_colors(&colr);
}
Rast_short_history(mapname, "raster", &history);
Rast_command_history(&history);
Rast_write_history(mapname, &history);
G_done_msg(NULL);
exit(EXIT_SUCCESS);
}
int rectify(char *name, char *mapset, struct cache *ebuffer,
double aver_z, char *result, char *interp_method)
{
struct Cell_head cellhd;
int ncols, nrows;
int row, col;
double row_idx, col_idx;
int infd, outfd;
RASTER_MAP_TYPE map_type;
int cell_size;
void *trast, *tptr;
double n1, e1, z1;
double nx, ex, nx1, ex1, zx1;
struct cache *ibuffer;
select_current_env();
Rast_get_cellhd(name, mapset, &cellhd);
/* open the file to be rectified
* set window to cellhd first to be able to read file exactly
*/
Rast_set_input_window(&cellhd);
infd = Rast_open_old(name, mapset);
map_type = Rast_get_map_type(infd);
cell_size = Rast_cell_size(map_type);
ibuffer = readcell(infd, seg_mb_img, 0);
Rast_close(infd); /* (pmx) 17 april 2000 */
G_message(_("Rectify <%s@%s> (location <%s>)"),
name, mapset, G_location());
select_target_env();
G_set_window(&target_window);
G_message(_("into <%s@%s> (location <%s>) ..."),
result, G_mapset(), G_location());
nrows = target_window.rows;
ncols = target_window.cols;
if (strcmp(interp_method, "nearest") != 0) {
map_type = DCELL_TYPE;
cell_size = Rast_cell_size(map_type);
}
/* open the result file into target window
* this open must be first since we change the window later
* raster maps open for writing are not affected by window changes
* but those open for reading are
*/
outfd = Rast_open_new(result, map_type);
trast = Rast_allocate_output_buf(map_type);
for (row = 0; row < nrows; row++) {
n1 = target_window.north - (row + 0.5) * target_window.ns_res;
G_percent(row, nrows, 2);
Rast_set_null_value(trast, ncols, map_type);
tptr = trast;
for (col = 0; col < ncols; col++) {
DCELL *zp = CPTR(ebuffer, row, col);
e1 = target_window.west + (col + 0.5) * target_window.ew_res;
/* if target cell has no elevation, set to aver_z */
if (Rast_is_d_null_value(zp)) {
G_warning(_("No elevation available at row = %d, col = %d"), row, col);
z1 = aver_z;
}
else
z1 = *zp;
/* target coordinates e1, n1 to photo coordinates ex1, nx1 */
I_ortho_ref(e1, n1, z1, &ex1, &nx1, &zx1, &group.camera_ref,
group.XC, group.YC, group.ZC, group.M);
G_debug(5, "\t\tAfter ortho ref (photo cords): ex = %f \t nx = %f",
ex1, nx1);
/* photo coordinates ex1, nx1 to image coordinates ex, nx */
I_georef(ex1, nx1, &ex, &nx, group.E21, group.N21, 1);
G_debug(5, "\t\tAfter geo ref: ex = %f \t nx = %f", ex, nx);
/* convert to row/column indices of source raster */
row_idx = (cellhd.north - nx) / cellhd.ns_res;
col_idx = (ex - cellhd.west) / cellhd.ew_res;
/* resample data point */
interpolate(ibuffer, tptr, map_type, &row_idx, &col_idx, &cellhd);
tptr = G_incr_void_ptr(tptr, cell_size);
}
Rast_put_row(outfd, trast, map_type);
}
G_percent(1, 1, 1);
Rast_close(outfd); /* (pmx) 17 april 2000 */
G_free(trast);
close(ibuffer->fd);
release_cache(ibuffer);
Rast_get_cellhd(result, G_mapset(), &cellhd);
if (cellhd.proj == 0) { /* x,y imagery */
cellhd.proj = target_window.proj;
cellhd.zone = target_window.zone;
}
if (target_window.proj != cellhd.proj) {
cellhd.proj = target_window.proj;
G_warning(_("Raster map <%s@%s>: projection don't match current settings"),
name, mapset);
}
if (target_window.zone != cellhd.zone) {
cellhd.zone = target_window.zone;
G_warning(_("Raster map <%s@%s>: zone don't match current settings"),
name, mapset);
}
select_current_env();
return 1;
}
int main(int argc, char *argv[])
{
char *p;
int method;
int in_fd;
int selection_fd;
int out_fd;
DCELL *result;
char *selection;
RASTER_MAP_TYPE map_type;
int row, col;
int readrow;
int nrows, ncols;
int n;
int copycolr;
int half;
stat_func *newvalue;
stat_func_w *newvalue_w;
ifunc cat_names;
double quantile;
const void *closure;
struct Colors colr;
struct Cell_head cellhd;
struct Cell_head window;
struct History history;
struct GModule *module;
struct
{
struct Option *input, *output, *selection;
struct Option *method, *size;
struct Option *title;
struct Option *weight;
struct Option *gauss;
struct Option *quantile;
} parm;
struct
{
struct Flag *align, *circle;
} flag;
DCELL *values; /* list of neighborhood values */
DCELL(*values_w)[2]; /* list of neighborhood values and weights */
G_gisinit(argv[0]);
module = G_define_module();
G_add_keyword(_("raster"));
G_add_keyword(_("algebra"));
G_add_keyword(_("statistics"));
module->description =
_("Makes each cell category value a "
"function of the category values assigned to the cells "
"around it, and stores new cell values in an output raster "
"map layer.");
parm.input = G_define_standard_option(G_OPT_R_INPUT);
parm.selection = G_define_standard_option(G_OPT_R_INPUT);
parm.selection->key = "selection";
parm.selection->required = NO;
parm.selection->description = _("Name of an input raster map to select the cells which should be processed");
parm.output = G_define_standard_option(G_OPT_R_OUTPUT);
parm.method = G_define_option();
parm.method->key = "method";
parm.method->type = TYPE_STRING;
parm.method->required = NO;
parm.method->answer = "average";
p = G_malloc(1024);
for (n = 0; menu[n].name; n++) {
if (n)
strcat(p, ",");
else
*p = 0;
strcat(p, menu[n].name);
}
parm.method->options = p;
parm.method->description = _("Neighborhood operation");
parm.method->guisection = _("Neighborhood");
parm.size = G_define_option();
parm.size->key = "size";
parm.size->type = TYPE_INTEGER;
parm.size->required = NO;
parm.size->description = _("Neighborhood size");
parm.size->answer = "3";
parm.size->guisection = _("Neighborhood");
parm.title = G_define_option();
parm.title->key = "title";
parm.title->key_desc = "phrase";
parm.title->type = TYPE_STRING;
parm.title->required = NO;
parm.title->description = _("Title of the output raster map");
parm.weight = G_define_standard_option(G_OPT_F_INPUT);
parm.weight->key = "weight";
parm.weight->required = NO;
parm.weight->description = _("Text file containing weights");
parm.gauss = G_define_option();
parm.gauss->key = "gauss";
parm.gauss->type = TYPE_DOUBLE;
parm.gauss->required = NO;
parm.gauss->description = _("Sigma (in cells) for Gaussian filter");
parm.quantile = G_define_option();
parm.quantile->key = "quantile";
parm.quantile->type = TYPE_DOUBLE;
parm.quantile->required = NO;
parm.quantile->description = _("Quantile to calculate for method=quantile");
parm.quantile->options = "0.0-1.0";
parm.quantile->answer = "0.5";
flag.align = G_define_flag();
flag.align->key = 'a';
flag.align->description = _("Do not align output with the input");
flag.circle = G_define_flag();
flag.circle->key = 'c';
flag.circle->description = _("Use circular neighborhood");
flag.circle->guisection = _("Neighborhood");
if (G_parser(argc, argv))
exit(EXIT_FAILURE);
sscanf(parm.size->answer, "%d", &ncb.nsize);
if (ncb.nsize <= 0)
G_fatal_error(_("Neighborhood size must be positive"));
if (ncb.nsize % 2 == 0)
G_fatal_error(_("Neighborhood size must be odd"));
ncb.dist = ncb.nsize / 2;
if (parm.weight->answer && flag.circle->answer)
G_fatal_error(_("weight= and -c are mutually exclusive"));
if (parm.weight->answer && parm.gauss->answer)
G_fatal_error(_("weight= and gauss= are mutually exclusive"));
ncb.oldcell = parm.input->answer;
ncb.newcell = parm.output->answer;
if (!flag.align->answer) {
Rast_get_cellhd(ncb.oldcell, "", &cellhd);
G_get_window(&window);
Rast_align_window(&window, &cellhd);
Rast_set_window(&window);
}
nrows = Rast_window_rows();
ncols = Rast_window_cols();
/* open raster maps */
in_fd = Rast_open_old(ncb.oldcell, "");
map_type = Rast_get_map_type(in_fd);
/* get the method */
for (method = 0; (p = menu[method].name); method++)
if ((strcmp(p, parm.method->answer) == 0))
break;
if (!p) {
G_warning(_("<%s=%s> unknown %s"),
parm.method->key, parm.method->answer, parm.method->key);
G_usage();
exit(EXIT_FAILURE);
}
if (menu[method].method == c_quant) {
quantile = atoi(parm.quantile->answer);
closure = &quantile;
}
half = (map_type == CELL_TYPE) ? menu[method].half : 0;
/* establish the newvalue routine */
newvalue = menu[method].method;
newvalue_w = menu[method].method_w;
/* copy color table? */
copycolr = menu[method].copycolr;
if (copycolr) {
G_suppress_warnings(1);
copycolr =
(Rast_read_colors(ncb.oldcell, "", &colr) > 0);
G_suppress_warnings(0);
}
/* read the weights */
if (parm.weight->answer) {
read_weights(parm.weight->answer);
if (!newvalue_w)
weights_mask();
}
else if (parm.gauss->answer) {
if (!newvalue_w)
G_fatal_error(_("Method %s not compatible with Gaussian filter"), parm.method->answer);
gaussian_weights(atof(parm.gauss->answer));
}
else
newvalue_w = NULL;
/* allocate the cell buffers */
allocate_bufs();
result = Rast_allocate_d_buf();
/* get title, initialize the category and stat info */
if (parm.title->answer)
strcpy(ncb.title, parm.title->answer);
else
sprintf(ncb.title, "%dx%d neighborhood: %s of %s",
ncb.nsize, ncb.nsize, menu[method].name, ncb.oldcell);
/* initialize the cell bufs with 'dist' rows of the old cellfile */
readrow = 0;
for (row = 0; row < ncb.dist; row++)
readcell(in_fd, readrow++, nrows, ncols);
/* open the selection raster map */
if (parm.selection->answer) {
G_message(_("Opening selection map <%s>"), parm.selection->answer);
selection_fd = Rast_open_old(parm.selection->answer, "");
selection = Rast_allocate_null_buf();
} else {
selection_fd = -1;
selection = NULL;
}
/*open the new raster map */
out_fd = Rast_open_new(ncb.newcell, map_type);
if (flag.circle->answer)
circle_mask();
if (newvalue_w)
values_w =
(DCELL(*)[2]) G_malloc(ncb.nsize * ncb.nsize * 2 * sizeof(DCELL));
else
values = (DCELL *) G_malloc(ncb.nsize * ncb.nsize * sizeof(DCELL));
for (row = 0; row < nrows; row++) {
G_percent(row, nrows, 2);
readcell(in_fd, readrow++, nrows, ncols);
if (selection)
Rast_get_null_value_row(selection_fd, selection, row);
for (col = 0; col < ncols; col++) {
DCELL *rp = &result[col];
if (selection && selection[col]) {
*rp = ncb.buf[ncb.dist][col];
continue;
}
if (newvalue_w)
n = gather_w(values_w, col);
else
n = gather(values, col);
if (n < 0)
Rast_set_d_null_value(rp, 1);
else {
if (newvalue_w)
newvalue_w(rp, values_w, n, closure);
else
newvalue(rp, values, n, closure);
if (half && !Rast_is_d_null_value(rp))
*rp += 0.5;
}
}
Rast_put_d_row(out_fd, result);
}
G_percent(row, nrows, 2);
Rast_close(out_fd);
Rast_close(in_fd);
if (selection)
Rast_close(selection_fd);
/* put out category info */
null_cats();
if ((cat_names = menu[method].cat_names))
cat_names();
Rast_write_cats(ncb.newcell, &ncb.cats);
if (copycolr)
Rast_write_colors(ncb.newcell, G_mapset(), &colr);
Rast_short_history(ncb.newcell, "raster", &history);
Rast_command_history(&history);
Rast_write_history(ncb.newcell, &history);
exit(EXIT_SUCCESS);
}
int main(int argc, char *argv[]) {
// initialize new seed for random number generator
srand((unsigned) time(NULL));
// allocate memory to store data loaded for each neuron
double celldirs[40], cellspks[40];
// number of cell files to read
int ncells = 100;
if (argc > 1) ncells = atoi(argv[1]);
// number of bootstrap iterations
int nboot = 100000;
// allocate strings to construct filenames
char fnum[4];
char fname[128];
// allocate memory to store various things
double PD[ncells], PDboot[ncells], PDr[ncells], PDr_boot,
boot_spks[40], plate_out[9];
// allocate and initialize vector of indices
int boot_ind[40];
for (int i=0; i<40; i++) boot_ind[i]=i;
// loop through each cell
int i, j, k, bootcount;
for (i=1; i<=ncells; i++) {
// construct the filename
if (i<10) sprintf(fnum, "00%d", i);
else if (i<100) sprintf(fnum, "0%d", i);
else sprintf(fnum, "%d", i);
// read in the dirs file
sprintf(fname, "data/cell_dirs_%s.txt", fnum);
readcell(fname, celldirs, 40, 0);
// read in the spks file
sprintf(fname, "data/cell_spks_%s.txt", fnum);
readcell(fname, cellspks, 40, 1);
// compute overall PD and PDr
platemethod(celldirs, cellspks, 40, plate_out);
PD[i-1] = plate_out[0];
PDr[i-1] = compute_PDr(celldirs, cellspks, 5, 8);
// bootstrap to compute prob(PDr_boot >= PDr) given shuffled data
bootcount = 0;
#pragma omp parallel for private(j,k,boot_spks,PDr_boot) reduction(+: bootcount)
for (j=0; j<nboot; j++) {
// randomly sample from cellspks into boot_spks with replacement
for (k=0; k<40; k++) boot_spks[k]=cellspks[rand()%40];
// compute PDr_boot for shuffled spike data
PDr_boot = compute_PDr(celldirs, boot_spks, 5, 8);
// if PDr_boot is greater than observed PDr then increment counter
if (PDr_boot >= PDr[i-1]) bootcount = bootcount + 1;
}
// compute proportion of times we simulated PDr_boot >= PDr observed
PDboot[i-1] = (double) bootcount / nboot;
}
// show vector of PDs and PDboot values
show_double_vec(PD, ncells);
show_double_vec(PDboot, ncells);
write_double_vec(PD, ncells, "PD.txt");
write_double_vec(PDboot, ncells, "PDboot.txt");
return 0;
}
int exec_rectify(char *extension, char *interp_method, char *angle_map)
{
char *name;
char *mapset;
char *result;
char *type = "raster";
int n;
struct Colors colr;
struct Categories cats;
struct History hist;
int colr_ok, cats_ok;
long start_time, rectify_time;
double aver_z;
int elevfd;
struct cache *ebuffer;
G_debug(1, "Open elevation raster: ");
/* open elevation raster */
select_target_env();
G_set_window(&target_window);
G_debug(1, "target window: rs=%d cs=%d n=%f s=%f w=%f e=%f\n",
target_window.rows, target_window.cols, target_window.north,
target_window.south, target_window.west, target_window.east);
elevfd = Rast_open_old(elev_name, elev_mapset);
if (elevfd < 0) {
G_fatal_error(_("Could not open elevation raster"));
return 1;
}
ebuffer = readcell(elevfd, seg_mb_elev, 1);
select_target_env();
Rast_close(elevfd);
/* get an average elevation of the control points */
/* this is used only if target cells have no elevation */
get_aver_elev(&group.control_points, &aver_z);
G_message("-----------------------------------------------");
/* rectify each file */
for (n = 0; n < group.group_ref.nfiles; n++) {
if (!ref_list[n])
continue;
name = group.group_ref.file[n].name;
mapset = group.group_ref.file[n].mapset;
result =
G_malloc(strlen(group.group_ref.file[n].name) + strlen(extension) + 1);
strcpy(result, group.group_ref.file[n].name);
strcat(result, extension);
G_debug(2, "ORTHO RECTIFYING:");
G_debug(2, "NAME %s", name);
G_debug(2, "MAPSET %s", mapset);
G_debug(2, "RESULT %s", result);
G_debug(2, "select_current_env...");
select_current_env();
cats_ok = Rast_read_cats(name, mapset, &cats) >= 0;
colr_ok = Rast_read_colors(name, mapset, &colr) > 0;
/* Initialze History */
if (Rast_read_history(name, mapset, &hist) < 0)
Rast_short_history(result, type, &hist);
G_debug(2, "reading was fine...");
time(&start_time);
G_debug(2, "Starting the rectification...");
if (rectify(name, mapset, ebuffer, aver_z, result, interp_method)) {
G_debug(2, "Done. Writing results...");
select_target_env();
if (cats_ok) {
Rast_write_cats(result, &cats);
Rast_free_cats(&cats);
}
if (colr_ok) {
Rast_write_colors(result, G_mapset(), &colr);
Rast_free_colors(&colr);
}
/* Write out History */
Rast_command_history(&hist);
Rast_write_history(result, &hist);
select_current_env();
time(&rectify_time);
report(rectify_time - start_time, 1);
}
else
report((long)0, 0);
G_free(result);
}
close(ebuffer->fd);
release_cache(ebuffer);
if (angle_map) {
camera_angle(angle_map);
}
return 0;
}