[GRASS-SVN] r51925 - grass-addons/grass7/imagery/i.segment
svn_grass at osgeo.org
svn_grass at osgeo.org
Fri Jun 1 21:58:33 PDT 2012
Author: momsen
Date: 2012-06-01 21:58:33 -0700 (Fri, 01 Jun 2012)
New Revision: 51925
Modified:
grass-addons/grass7/imagery/i.segment/get_input.c
grass-addons/grass7/imagery/i.segment/main.c
Log:
some bug(s?) remain. I/O with segmentation library and groups written
Modified: grass-addons/grass7/imagery/i.segment/get_input.c
===================================================================
--- grass-addons/grass7/imagery/i.segment/get_input.c 2012-06-01 23:13:31 UTC (rev 51924)
+++ grass-addons/grass7/imagery/i.segment/get_input.c 2012-06-02 04:58:33 UTC (rev 51925)
@@ -1,269 +1,273 @@
/* PURPOSE: Parse and validate the input, including opening input rasters and creating segmentation files */
#include <stdlib.h>
-#include <fcntl.h> /* needed for creat and open for the segmentation files.
- used those functions per the programmer's manual, correct usage? */
+#include <string.h>
+#include <fcntl.h> /* needed for creat and open for the segmentation files.
+ used those functions per the programmer's manual, correct usage? */
#include <grass/gis.h>
#include <grass/glocale.h>
#include <grass/imagery.h>
-#include <grass/segment.h> /* segmentation library */
+#include <grass/segment.h> /* segmentation library */
#include "iseg.h"
-int parse_args(int argc, char *argv[], struct files *files, struct functions *functions)
+int parse_args(int argc, char *argv[], struct files *files,
+ struct functions *functions)
{
- /* reference: http://grass.osgeo.org/programming7/gislib.html#Command_Line_Parsing */
-
- struct Option *group, *subgroup, *seeds, *output, *method, *threshold; /* Establish an Option pointer for each option */
- struct Flag *diagonal; /* Establish a Flag pointer for each option */
+ /* reference: http://grass.osgeo.org/programming7/gislib.html#Command_Line_Parsing */
- group = G_define_standard_option(G_OPT_I_GROUP);
-
- subgroup = G_define_standard_option(G_OPT_I_SUBGROUP);
-
- /* OK to require the user to create a group? Otherwise later add an either/or option to give just a single raster map... */
-
- //~ input = G_define_standard_option(G_OPT_R_INPUT); /* Request a pointer to memory for each option */
- //~ input->key = "input"; /* TODO: update to allow groups. Maybe this needs a group/subgroup variables, or we can check if the input is group/subgroup/raster */
- //~ input->type = TYPE_STRING;
- //~ input->required = YES;
- //~ input->description = _("Raster map to be segmented.");
-
- /* Using raster for seeds, maybe consider allowing vector points/centroids later. */
- seeds = G_define_standard_option(G_OPT_R_INPUT);
- seeds->key = "seeds";
- seeds->type = TYPE_STRING;
- seeds->required = NO;
- seeds->description = _("Optional raster map with starting seeds.");
-
- output = G_define_standard_option(G_OPT_R_OUTPUT);
-//seems API handles this part ?
- //~ output->key = "output";
- //~ output->type = TYPE_STRING;
- //~ output->required = YES;
- //~ output->description = _("Name of output raster map.");
+ struct Option *group, *subgroup, *seeds, *output, *method, *threshold; /* Establish an Option pointer for each option */
+ struct Flag *diagonal; /* Establish a Flag pointer for each option */
-//TODO: when put in a new raster map, error message:
-//~ Command 'd.rast map=testing at samples' failed
-//~ Details: Raster map <testing at samples> not found
+ group = G_define_standard_option(G_OPT_I_GROUP);
-//Also, that error seems to be accumulated, putting in a new output map names results in:
-//~ Command 'd.rast map=testing at samples' failed
-//~ Details: Raster map <testing at samples> not found
-//~ Command 'd.rast map=test2 at samples' failed
-//~ Details: Raster map <test2 at samples> not found
-
- method = G_define_option();
- method->key = "method";
- method->type = TYPE_STRING;
- method->required = NO;
- method->answer = _("region_growing");
- method->options = "region_growing, mean_shift";
- method->description = _("Segmentation method.");
-
- threshold = G_define_option();
- threshold->key = "threshold";
- threshold->type = TYPE_DOUBLE;
- threshold->required = YES;
- threshold->description = _("Similarity threshold.");
-
- diagonal = G_define_flag();
+ subgroup = G_define_standard_option(G_OPT_I_SUBGROUP);
+
+ /* OK to require the user to create a group? Otherwise later add an either/or option to give just a single raster map... */
+
+ //~ input = G_define_standard_option(G_OPT_R_INPUT); /* Request a pointer to memory for each option */
+ //~ input->key = "input"; /* TODO: update to allow groups. Maybe this needs a group/subgroup variables, or we can check if the input is group/subgroup/raster */
+ //~ input->type = TYPE_STRING;
+ //~ input->required = YES;
+ //~ input->description = _("Raster map to be segmented.");
+
+ /* Using raster for seeds, maybe consider allowing vector points/centroids later. */
+ seeds = G_define_standard_option(G_OPT_R_INPUT);
+ seeds->key = "seeds";
+ seeds->type = TYPE_STRING;
+ seeds->required = NO;
+ seeds->description = _("Optional raster map with starting seeds.");
+
+ output = G_define_standard_option(G_OPT_R_OUTPUT);
+ //seems API handles this part ?
+ //~ output->key = "output";
+ //~ output->type = TYPE_STRING;
+ //~ output->required = YES;
+ //~ output->description = _("Name of output raster map.");
+
+ //TODO: when put in a new raster map, error message:
+ //~ Command 'd.rast map=testing at samples' failed
+ //~ Details: Raster map <testing at samples> not found
+
+ //Also, that error seems to be accumulated, putting in a new output map names results in:
+ //~ Command 'd.rast map=testing at samples' failed
+ //~ Details: Raster map <testing at samples> not found
+ //~ Command 'd.rast map=test2 at samples' failed
+ //~ Details: Raster map <test2 at samples> not found
+
+ method = G_define_option();
+ method->key = "method";
+ method->type = TYPE_STRING;
+ method->required = NO;
+ method->answer = _("region_growing");
+ method->options = "region_growing, mean_shift";
+ method->description = _("Segmentation method.");
+
+ threshold = G_define_option();
+ threshold->key = "threshold";
+ threshold->type = TYPE_DOUBLE;
+ threshold->required = YES;
+ threshold->description = _("Similarity threshold.");
+
+ diagonal = G_define_flag();
diagonal->key = 'd';
- diagonal->description = _("Use 8 neighbors (3x3 neighborhood) instead of the default 4 neighbors for each pixel.");
+ diagonal->description =
+ _
+ ("Use 8 neighbors (3x3 neighborhood) instead of the default 4 neighbors for each pixel.");
- //~ G_debug(1, "testing debug!");
- //~ When put this in, get an error (only when DEBUG is set, if not set, it runs fine)
- //~
- //~ Error box:
- //~ Unable to fetch interface description for command 'i.segment'.
- //~ Details: D1/1: testing debug!
-
- //~ G_debug(1, "For the option <%s> you chose: <%s>",
- //~ input->description, input->answer);
- //~
- //~ G_debug(1, "For the option <%s> you chose: <%s>",
- //~ seeds->description, seeds->answer);
- //~
- //~ G_debug(1, "For the option <%s> you chose: <%s>",
- //~ output->description, output->answer);
- //~
- //~ G_debug(1, "For the option <%s> you chose: <%s>",
- //~ method->description, method->answer);
- //~
- //~ G_debug(1, "For the option <%s> you chose: <%s>",
- //~ threshold->description, threshold->answer);
- //~
+ //~ G_debug(1, "testing debug!");
+ //~ When put this in, get an error (only when DEBUG is set, if not set, it runs fine)
+ //~
+ //~ Error box:
+ //~ Unable to fetch interface description for command 'i.segment'.
+ //~ Details: D1/1: testing debug!
+
+ //~ G_debug(1, "For the option <%s> you chose: <%s>",
+ //~ input->description, input->answer);
+ //~
+ //~ G_debug(1, "For the option <%s> you chose: <%s>",
+ //~ seeds->description, seeds->answer);
+ //~
+ //~ G_debug(1, "For the option <%s> you chose: <%s>",
+ //~ output->description, output->answer);
+ //~
+ //~ G_debug(1, "For the option <%s> you chose: <%s>",
+ //~ method->description, method->answer);
+ //~
+ //~ G_debug(1, "For the option <%s> you chose: <%s>",
+ //~ threshold->description, threshold->answer);
+ //~
//~ G_debug(1, "The value of the diagonal flag is: %d", diagonal->answer);
-
- if (G_parser(argc, argv))
- exit (EXIT_FAILURE);
-/* Validation */
+ if (G_parser(argc, argv))
+ exit(EXIT_FAILURE);
- /* use checker for any of the data validation steps!? */
-
- /* ToDo The most important things to check are if the
-input and output raster maps can be opened (non-negative file
-descriptor). */
+ /* Validation */
+ /* use checker for any of the data validation steps!? */
-/* Check and save parameters */
+ /* ToDo The most important things to check are if the
+ input and output raster maps can be opened (non-negative file
+ descriptor). */
- sscanf(threshold->answer, "%f", &functions->threshold);
-
- /* I'm assuming it is already validated as a number. Is this OK, or is there a better way to cast the input? */
- /* r.cost line 313
- if (sscanf(opt5->answer, "%d", &maxcost) != 1 || maxcost < 0)
- G_fatal_error(_("Inappropriate maximum cost: %d"), maxcost); */
-
- /* TODO: The following routines create a new raster map in the current mapset and open it for writing. G_legal_filename() should be called first to make sure that raster map name is a valid name. */
-
- files->out_name = output->answer; /* name of output raster map */
-
-/* Open Files (file segmentation) */
+ /* Check and save parameters */
-/* references: i.cost and http://grass.osgeo.org/programming7/segmentlib.html */
+ sscanf(threshold->answer, "%f", &functions->threshold);
- struct Ref Ref; /* subgroup reference list */
- int *in_fd, *seg_in_fd, seg_out_fd;
- RASTER_MAP_TYPE data_type;
- int n, row, nrows, ncols, srows, scols, seg_in_mem;
- void *inbuf;
- const char *in_file[7], *out_file;
- /*TODO put const 7 for now, need to dynamically get size based on number of input rasters, commented out "new" statement later on */
-
+ /* I'm assuming it is already validated as a number. Is this OK, or is there a better way to cast the input? */
+ /* r.cost line 313
+ if (sscanf(opt5->answer, "%d", &maxcost) != 1 || maxcost < 0)
+ G_fatal_error(_("Inappropriate maximum cost: %d"), maxcost); */
+
+ /* TODO: The following routines create a new raster map in the current mapset and open it for writing. G_legal_filename() should be called first to make sure that raster map name is a valid name. */
+
+ files->out_name = output->answer; /* name of output raster map */
+
+
+ /* Open Files (file segmentation) */
+ G_verbose_message("Checking image (sub)group...");
+ /* references: i.cost and http://grass.osgeo.org/programming7/segmentlib.html */
+
+
+ struct Ref Ref; /* subgroup reference list */
+ int *in_fd, *seg_in_fd, seg_out_fd;
+ RASTER_MAP_TYPE data_type;
+ int n, row, nrows, ncols, srows, scols, seg_in_mem;
+ void *inbuf;
+ const char *in_file[10], *out_file; /* max 10 rasters in imagery group, until figure out how to do this dynamically */
+
/* int buf[NCOLS]; */
- /* c question... will using void data type be the right way, until I know what the data type is? */
- /* that was in the developer's manual... but would void *buf also work? */
- /* void *buf; */ /* for copying from raster into segmentation file */
-
-
+ /* c question... will using void data type be the right way, until I know what the data type is? */
+ /* that was in the developer's manual... but would void *buf also work? */
+ /* void *buf; *//* for copying from raster into segmentation file */
+
+
/* ****** open the input rasters ******* */
-
+
/* i.smap/openfiles.c lines 17-23 checked if subgroup had maps, does API handles the checks?
- can no subgroup be entered, just a group? */
-
- if (!I_get_subgroup_ref(group->answer,subgroup->answer, &Ref))
- G_fatal_error(_("Unable to read REF file for subgroup <%s> in group <%s>"),
- subgroup->answer, group->answer);
-
- if (Ref.nfiles <= 0)
- G_fatal_error(_("Subgroup <%s> in group <%s> contains no raster maps"),
- subgroup->answer, group->answer);
-
- /* open input group maps for reading */
-
- /* TODO ? compiler warning, in_fd was not initialized */
-
- for(n = 0; n < Ref.nfiles; n++)
- {
- in_fd[n] = Rast_open_old(Ref.file[n].name, Ref.file[n].mapset);
- }
+ can no subgroup be entered, just a group? */
-
+ if (!I_get_subgroup_ref(group->answer, subgroup->answer, &Ref))
+ G_fatal_error(_
+ ("Unable to read REF file for subgroup <%s> in group <%s>"),
+ subgroup->answer, group->answer);
+
+ if (Ref.nfiles <= 0)
+ G_fatal_error(_
+ ("Subgroup <%s> in group <%s> contains no raster maps"),
+ subgroup->answer, group->answer);
+
+ /* open input group maps for reading */
+
+ in_fd = G_malloc(Ref.nfiles * sizeof(seg_out_fd)); /* need sizeof( integer ) */
+
+ G_verbose_message("Opening input rasters...");
+ for (n = 0; n < Ref.nfiles; n++) {
+ in_fd[n] = Rast_open_old(Ref.file[n].name, Ref.file[n].mapset);
+ }
+
+
/* ********** find out file segmentation size ************ */
+ G_verbose_message("Calculate temp file sizes...");
/*loop again... need to get largest option
- //for today assume all are the same
- //data_type = Rast_get_map_type(in_fd[n]); */
- files->nbands = Ref.nfiles;
-
- data_type = Rast_get_map_type(in_fd[0]);
+ //for today assume all are the same
+ //data_type = Rast_get_map_type(in_fd[n]); */
+ files->nbands = Ref.nfiles;
+
+ data_type = Rast_get_map_type(in_fd[0]);
files->data_type = data_type;
-
+
nrows = Rast_window_rows();
ncols = Rast_window_cols();
-
- /*TODO: i.cost and i.watershed take different approaches...
- //hardcode for now */
- srows = nrows / 8;
- scols = ncols / 8;
- /* TODO: make calculations for this */
- seg_in_mem = 4;
+ /*TODO: i.cost and i.watershed take different approaches...
+ //hardcode for now */
+ srows = nrows / 8;
+ scols = ncols / 8;
-/* G_debug(1, " %d rows, %d cols", nrows, ncols); ... never tried this, just copied from other module */
-
-
+ /* TODO: make calculations for this */
+ seg_in_mem = 4;
+
+ /* G_debug(1, " %d rows, %d cols", nrows, ncols); ... never tried this, just copied from other module */
+
+
/* ******* create temporary segmentation files ********* */
-
+ G_verbose_message("Getting temp file names...");
/* Initalize access to database and create temporary files */
-
- /* in_file = new char[Ref.nfiles]; Need G_allocate or something here? */
-
- for(n = 0; n < Ref.nfiles; n++)
- {
- in_file[n] = G_tempfile();
- }
-
- out_file = G_tempfile();
-
+
+
+ for (n = 0; n < Ref.nfiles; n++) {
+ in_file[n] = G_tempfile();
+ }
+ out_file = G_tempfile();
+
/* Format segmented files */
-
- /* TODO ? compiler warning, in_fd was not initialized */
-
- for(n = 0; n < Ref.nfiles; n++)
- {
- seg_in_fd[n] = creat(in_file[n], 0666);
- if (segment_format(seg_in_fd[n], nrows, ncols, srows, scols, sizeof(data_type)) != 1) /* TODO: this data_type should be from each map */
- G_fatal_error("can not create temporary file");
- close(seg_in_fd[n]); /* why close when we just reopen again? Different access mode between creat and open ? */
+
+ seg_in_fd = G_malloc(Ref.nfiles * sizeof(seg_out_fd)); /* need sizeof( integer ) */
+ G_verbose_message("Creating temporary data files...");
+ for (n = 0; n < Ref.nfiles; n++) {
+ seg_in_fd[n] = creat(&in_file[n], 0666);
+ if (segment_format(seg_in_fd[n], nrows, ncols, srows, scols, sizeof(data_type)) != 1) /* TODO: this data_type should be from each map */
+ G_fatal_error("can not create temporary file");
+ close(seg_in_fd[n]); /* why close when we just reopen again? Different access mode between creat and open ? */
}
- seg_out_fd = creat(out_file, 0666);
- if (segment_format(seg_out_fd, nrows, ncols, srows, scols, sizeof(data_type)) != 1)
+ seg_out_fd = creat(out_file, 0666);
+ if (segment_format
+ (seg_out_fd, nrows, ncols, srows, scols, sizeof(data_type)) != 1)
G_fatal_error("can not create temporary file");
- close(seg_out_fd);
+ close(seg_out_fd);
-
- /* Open and initialize all segment files */
- for(n = 0; n < Ref.nfiles; n++)
- {
- seg_in_fd[n] = open(in_file[n], 2); /* TODO: second parameter here is different in many places... */
- if (segment_init(&files->bands_seg[n], seg_in_fd[n], seg_in_mem) != 1)
- G_fatal_error("can not initialize temporary file");
- }
- seg_out_fd = open(out_file, 2);
- if (segment_init(&files->out_seg, seg_out_fd, seg_in_mem) != 1)
- G_fatal_error("can not initialize temporary file");
+ /* Open and initialize all segment files */
+ G_debug(1, "Initializing temporary data files..."); /* program dies sometime after this point, and before line 234 */
+ for (n = 0; n < Ref.nfiles; n++) {
+ seg_in_fd[n] = open(&in_file[n], 2); /* TODO: second parameter here is different in many places... */
+ if (segment_init(&files->bands_seg[n], seg_in_fd[n], seg_in_mem) != 1)
+ G_fatal_error("can not initialize temporary file");
+ }
+ seg_out_fd = open(out_file, 2);
+ if (segment_init(&files->out_seg, seg_out_fd, seg_in_mem) != 1)
+ G_fatal_error("can not initialize temporary file");
+
/* convert flat files to segmented files */
- inbuf = Rast_allocate_buf(data_type); /* buffer from the raster file */
-
- /* buf = new data_type [ncols] */ /* buffer to read data into, cell by cell. But can I just write inbuf directly to the segmentation file??? */
-
- for (n = 0; n < Ref.nfiles; n++)
- {
- for (row = 0; row < nrows; row++)
- {
- Rast_get_row(in_fd[n], inbuf, row, data_type);
- //~ for (col = 0; col < ncols; col++)
- //~ {
- //~ /*fill buf */
- //~ // G_incr_void_ptr
- //~ }
-
- segment_put_row (&files->bands_seg[n], inbuf, row);
- }
+ G_verbose_message("Read input rasters into temporary data files...");
+ inbuf = Rast_allocate_buf(data_type); /* buffer from the raster file */
+
+ /* buf = new data_type [ncols] *//* buffer to read data into, cell by cell. But can I just write inbuf directly to the segmentation file??? */
+
+ for (n = 0; n < Ref.nfiles; n++) {
+ for (row = 0; row < nrows; row++) {
+ Rast_get_row(in_fd[n], inbuf, row, data_type);
+ //~ for (col = 0; col < ncols; col++)
+ //~ {
+ //~ /*fill buf */
+ //~ // G_incr_void_ptr
+ //~ }
+
+ segment_put_row(&files->bands_seg[n], inbuf, row);
}
+ }
- /* Don't need to do anything else for the output segmentation file? It is initialized to zeros and will be written to later... */
+ /* Don't need to do anything else for the output segmentation file? It is initialized to zeros and will be written to later... */
- /* Free memory */
-
- for(n = 0; n < Ref.nfiles; n++)
- {
- Rast_close(in_fd[n]);
- }
-
- G_free(inbuf);
-
- /* Need to clean up anything else? Need to close segmentation files? Or they should be open still since they will be used later? Close after all processing is done? */
-
- /*
- from r.cost
- unlink(in_file);*/ /* remove submatrix files */
-
- return 0;
+ /* Free memory */
+
+ for (n = 0; n < Ref.nfiles; n++) {
+ Rast_close(in_fd[n]);
+ }
+
+ G_free(inbuf);
+ G_free(in_fd);
+ G_free(seg_in_fd);
+
+ /* Need to clean up anything else? Need to close segmentation files? Or they should be open still since they will be used later? Close after all processing is done? */
+
+ /*
+ from r.cost
+ unlink(in_file); *//* remove submatrix files */
+
+ return 0;
}
Modified: grass-addons/grass7/imagery/i.segment/main.c
===================================================================
--- grass-addons/grass7/imagery/i.segment/main.c 2012-06-01 23:13:31 UTC (rev 51924)
+++ grass-addons/grass7/imagery/i.segment/main.c 2012-06-02 04:58:33 UTC (rev 51925)
@@ -35,8 +35,12 @@
G_add_keyword(_("segmentation"));
module->description = _("Segments an image.");
+// G_debug(1, "Starting parse_args...");
parse_args(argc, argv, &files, &functions);
/* Write Segmentation Function Next Week !!! */
+
+ G_debug(1, "starting write_output...");
+ G_verbose_message("Main: starting write_output...");
write_output(&files);
G_done_msg("Number of segments created: ");
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