[GRASS-SVN] r44406 - in grass/branches/develbranch_6: . raster/r.li
raster/r.li/r.li.daemon raster/r.li/r.li.pielou
raster/r.li/r.li.renyi
svn_grass at osgeo.org
svn_grass at osgeo.org
Wed Nov 24 11:43:46 EST 2010
Author: neteler
Date: 2010-11-24 08:43:45 -0800 (Wed, 24 Nov 2010)
New Revision: 44406
Added:
grass/branches/develbranch_6/raster/r.li/r.li.pielou/
grass/branches/develbranch_6/raster/r.li/r.li.pielou/Makefile
grass/branches/develbranch_6/raster/r.li/r.li.pielou/description.html
grass/branches/develbranch_6/raster/r.li/r.li.pielou/pielou.c
grass/branches/develbranch_6/raster/r.li/r.li.pielou/r_li_pielou.png
grass/branches/develbranch_6/raster/r.li/r.li.renyi/
grass/branches/develbranch_6/raster/r.li/r.li.renyi/Makefile
grass/branches/develbranch_6/raster/r.li/r.li.renyi/description.html
grass/branches/develbranch_6/raster/r.li/r.li.renyi/r_li_renyi.png
grass/branches/develbranch_6/raster/r.li/r.li.renyi/renyi.c
Modified:
grass/branches/develbranch_6/contributors_extra.csv
grass/branches/develbranch_6/raster/r.li/Makefile
grass/branches/develbranch_6/raster/r.li/description.html
grass/branches/develbranch_6/raster/r.li/r.li.daemon/index.h
Log:
Luca Delucchi + Duccio Rocchini: two new indices
Modified: grass/branches/develbranch_6/contributors_extra.csv
===================================================================
--- grass/branches/develbranch_6/contributors_extra.csv 2010-11-24 16:19:56 UTC (rev 44405)
+++ grass/branches/develbranch_6/contributors_extra.csv 2010-11-24 16:43:45 UTC (rev 44406)
@@ -10,6 +10,7 @@
Carl Anderson,<candrsn mindspring.com>,-
Charles Ehlschlaeger,<cre111 wiu.edu>,-
Christoph Simon,<ciccio kiosknet.com.br>,-
+Duccio Rocchini,<ducciorocchini gmail.com>,-
Dylan Beaudette,<dylan.beaudette gmail.com>,yes
Eric Mitchell,<emitchell altaira.com>,-
Francesco Pirotti,<francesco.pirotti unipd.it>,-
@@ -20,6 +21,7 @@
Lars Ahlzen,<lars ahlzen.com>,-
Lorenzo Moretti,<lorenzo moretti bologna.enea.it>,-
Lubos Mitas,<lmitas ncsa uiuc.edu>,-
+Luca Delucchi,<lucadeluge gmail.com>,-
Malcolm Blue,<mblue nb sympatico.ca>,-
Maria Brovelli,<maria.brovelli polimi.it>,-
Michael Perdue,<michael_perdue yahoo.ca>,-
Modified: grass/branches/develbranch_6/raster/r.li/Makefile
===================================================================
--- grass/branches/develbranch_6/raster/r.li/Makefile 2010-11-24 16:19:56 UTC (rev 44405)
+++ grass/branches/develbranch_6/raster/r.li/Makefile 2010-11-24 16:43:45 UTC (rev 44406)
@@ -13,6 +13,8 @@
r.li.padsd \
r.li.patchdensity \
r.li.patchnum \
+ r.li.pielou \
+ r.li.renyi \
r.li.richness \
r.li.setup \
r.li.shannon \
Modified: grass/branches/develbranch_6/raster/r.li/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/description.html 2010-11-24 16:19:56 UTC (rev 44405)
+++ grass/branches/develbranch_6/raster/r.li/description.html 2010-11-24 16:43:45 UTC (rev 44406)
@@ -154,10 +154,12 @@
<b>Diversity indices</b>:
<ul>
- <li> <a href="r.li.dominance.html">r.li.dominance</a>: Calculates dominance's diversity index on a raster map</li>
- <li> <a href="r.li.richness.html">r.li.richness</a>: Calculates dominance's diversity index on a raster map</li>
- <li> <a href="r.li.shannon.html">r.li.shannon</a>: Calculates Shannon's diversity index on a raster map</li>
- <li> <a href="r.li.simpson.html">r.li.simpson</a>: Calculates Simpson's diversity index on a raster map</li>
+ <li> <a href="r.li.dominance.html">r.li.dominance</a>: Calculates dominance diversity index on a raster map</li>
+ <li> <a href="r.li.pielou.html">r.li.pielou</a>: Calculates Pielou eveness index on a raster map</li>
+ <li> <a href="r.li.renyi.html">r.li.renyi</a>: Calculates Renyi entropy on a raster map</li>
+ <li> <a href="r.li.richness.html">r.li.richness</a>: Calculates richness diversity index on a raster map</li>
+ <li> <a href="r.li.shannon.html">r.li.shannon</a>: Calculates Shannon diversity index on a raster map</li>
+ <li> <a href="r.li.simpson.html">r.li.simpson</a>: Calculates Simpson diversity index on a raster map</li>
</ul>
<h2>ADDING NEW INDICES</h2>
Modified: grass/branches/develbranch_6/raster/r.li/r.li.daemon/index.h
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.daemon/index.h 2010-11-24 16:19:56 UTC (rev 44405)
+++ grass/branches/develbranch_6/raster/r.li/r.li.daemon/index.h 2010-11-24 16:43:45 UTC (rev 44406)
@@ -5,6 +5,7 @@
*
* \author Claudio Porta, Lucio Davide Spano, Serena Pallecchi students of Computer Science University of Pisa (Italy)
* Commission from Faunalia Pontedera (PI) www.faunalia.it
+ * Luca Delucchi and Duccio Rocchini, Fondazione Edmund Mach, Italy: r.li.pielou, r.li.renyi
*
*
* This program is free software under the GPL (>=v2)
@@ -12,7 +13,6 @@
*
* \version 1.1
*
- * BUGS: please send bugs reports to spano at cli.di.unipi.it porta at cli.di.unipi.it pallecch at cli.di.unipi.it
*/
@@ -31,6 +31,10 @@
int patch_number(int fd, char **par, area_des ad, double *result);
int shape_index(int fd, char **par, area_des ad, double *result);
int shannon(int fd, char **par, area_des ad, double *result);
+
+int pielou(int fd, char **par, area_des ad, double *result);
+int renyi(int fd, char **par, area_des ad, double *result);
+
int simpson(int fd, char **par, area_des ad, double *result);
int meanPatchSize(int fd, char **par, area_des ad, double *result);
int meanPixelAttribute(int fd, char **par, area_des ad, double *result);
Added: grass/branches/develbranch_6/raster/r.li/r.li.pielou/Makefile
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.pielou/Makefile (rev 0)
+++ grass/branches/develbranch_6/raster/r.li/r.li.pielou/Makefile 2010-11-24 16:43:45 UTC (rev 44406)
@@ -0,0 +1,18 @@
+MODULE_TOPDIR = ../../..
+
+PGM = r.li.pielou
+
+EXTRA_CLEAN_DIRS=doxygenhtml
+
+LIB_NAME = grass_rli
+
+RLI_LIB = -l$(LIB_NAME)
+
+LIBES = $(GISLIB) $(RLI_LIB)
+
+DEPENDENCIES = $(GISDEP) $(LIB_NAME )
+
+include $(MODULE_TOPDIR)/include/Make/Module.make
+
+default: cmd
+
Property changes on: grass/branches/develbranch_6/raster/r.li/r.li.pielou/Makefile
___________________________________________________________________
Added: svn:mime-type
+ text/x-makefile
Added: svn:eol-style
+ native
Added: grass/branches/develbranch_6/raster/r.li/r.li.pielou/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.pielou/description.html (rev 0)
+++ grass/branches/develbranch_6/raster/r.li/r.li.pielou/description.html 2010-11-24 16:43:45 UTC (rev 44406)
@@ -0,0 +1,51 @@
+<h2>DESCRIPTION</h2>
+
+<em>r.li.pielou</em> calculates the "pielou's diversity index" as: <br>
+<img src="r_li_pielou.png"><br>
+with:
+<ul>
+ <li><b>J</b>: Pielou eveness index</li>
+ <li><b>H'</b>: Shannon index</li>
+ <li><b>S</b>: number of classes</li>
+</ul>
+
+<h2>NOTES</h2>
+Do not use absolute path names for output files. They are raster if
+moving window disposition was selected, otherwise they are in
+<tt>~/.r.li/output/</tt> folder.
+<br>
+If the input raster contains NULL value cells, <em>r.li.pielou</em>
+returns -1 for these cells. <br>
+If you want to keep NULL values instead, run subsequently on the resulting map:
+<br>
+<div class="code"><pre>
+r.null setnull=-1 map=my_map
+</pre></div>
+
+<h2>EXAMPLES</h2>
+To calculate Pielou's diversity index on the map "my_map", using the
+previously created "my_conf" configuration file (<em>r.li.setup</em>)
+and saving results in "my_out" raster map, run:<br>
+<div class="code"><pre>
+r.li.pielou map=my_map conf=my_conf output=my_out
+</pre></div>
+
+
+<h2>REFERENCES</h2>
+McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
+analysis program for quantifying landscape structure. USDA For. Serv.
+Gen. Tech. Rep. PNW-351. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</a>)
+
+
+<h2>SEE ALSO</h2>
+<em>
+<a href="r.li.html">r.li</a>,
+<a href="r.li.setup.html">r.li.setup</a>
+</em>
+
+<h2>AUTHORS</h2>
+Luca Delucchi and Duccio Rocchini, Fondazione E. Mach (Italy), based on the <em>r.li.shannon</em> code
+developed by Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
+
+<p><i>Last changed: $Date$</i>
+
Property changes on: grass/branches/develbranch_6/raster/r.li/r.li.pielou/description.html
___________________________________________________________________
Added: svn:mime-type
+ text/html
Added: svn:keywords
+ Author Date Id
Added: svn:eol-style
+ native
Added: grass/branches/develbranch_6/raster/r.li/r.li.pielou/pielou.c
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.pielou/pielou.c (rev 0)
+++ grass/branches/develbranch_6/raster/r.li/r.li.pielou/pielou.c 2010-11-24 16:43:45 UTC (rev 44406)
@@ -0,0 +1,802 @@
+
+/****************************************************************************
+ *
+ * MODULE: r.li.pielou
+ *
+ * PURPOSE: brief calculates pielou's diversity index
+ *
+ * AUTHOR(S): Luca Delucchi, Fondazione Edmund Mach
+ * Serena Pallecchi student of Computer Science University of Pisa (Italy)
+ *
+ * COPYRIGHT:
+ * This program is free software under the GPL (>=v2)
+ * Read the COPYING file that comes with GRASS for details.
+ *
+ ***************************************************************************/
+
+#include <stdlib.h>
+#include <fcntl.h>
+#include <math.h>
+
+#include <grass/gis.h>
+#include <grass/glocale.h>
+
+#include "../r.li.daemon/defs.h"
+#include "../r.li.daemon/avlDefs.h"
+#include "../r.li.daemon/avl.h"
+#include "../r.li.daemon/daemon.h"
+
+int calculate(int fd, area_des ad, double *result);
+
+int calculateD(int fd, area_des ad, double *result);
+
+int calculateF(int fd, area_des ad, double *result);
+
+/*This function is used to sort the values in the moving window */
+static int cmp(const void *pa, const void *pb)
+{
+ int *p1 = (int *)pa;
+ int *p2 = (int *)pb;
+
+ if (*p1 < *p2)
+ return -1;
+ if (*p1 > *p2)
+ return 1;
+ return 0;
+}
+
+int main(int argc, char *argv[])
+{
+ struct Option *raster, *conf, *output;
+
+ struct GModule *module;
+
+ G_gisinit(argv[0]);
+ module = G_define_module();
+ module->description =
+ _("Calculates Pielou's diversity index on a raster map");
+ module->keywords =
+ _("raster, landscape structure analysis, diversity index");
+
+ /* define options */
+
+ raster = G_define_standard_option(G_OPT_R_MAP);
+
+ conf = G_define_option();
+ conf->key = "conf";
+ conf->description = _("Configuration file");
+ conf->type = TYPE_STRING;
+ conf->gisprompt = "old_file,file,input";
+ conf->required = YES;
+
+ output = G_define_standard_option(G_OPT_R_OUTPUT);
+
+ if (G_parser(argc, argv))
+ exit(EXIT_FAILURE);
+
+ return calculateIndex(conf->answer, pielou, NULL, raster->answer,
+ output->answer);
+
+}
+
+int pielou(int fd, char **par, area_des ad, double *result)
+{
+
+ char *mapset;
+ int ris = RLI_OK;
+ double indice = 0;
+ struct Cell_head hd;
+
+
+ mapset = G_find_cell(ad->raster, "");
+ if (G_get_cellhd(ad->raster, mapset, &hd) == -1)
+ return RLI_ERRORE;
+
+
+ switch (ad->data_type) {
+ case CELL_TYPE:
+ {
+ calculate(fd, ad, &indice);
+ break;
+ }
+ case DCELL_TYPE:
+ {
+ calculateD(fd, ad, &indice);
+ break;
+ }
+ case FCELL_TYPE:
+ {
+ calculateF(fd, ad, &indice);
+ break;
+ }
+ default:
+ {
+ G_fatal_error("data type unknown");
+ return RLI_ERRORE;
+ }
+ }
+
+ if (ris != RLI_OK) {
+ return RLI_ERRORE;
+ }
+
+ *result = indice;
+
+ return RLI_OK;
+
+}
+
+
+int calculate(int fd, area_des ad, double *result)
+{
+
+ CELL *buf;
+ CELL corrCell;
+ CELL precCell;
+ int i, j;
+ int mask_fd = -1, *mask_buf;
+ int ris = 0;
+ int masked = FALSE;
+ int a = 0; /* a=0 if all cells are null */
+ long m = 0;
+ long tot = 0;
+ long zero = 0;
+ long totCorr = 0;
+ double indice = 0;
+ double somma = 0;
+ double percentuale = 0;
+ double area = 0;
+ double t;
+ double logaritmo;
+
+ /* add to compute the number of class */
+ long *array_copy;
+ int totNumClass = 1;
+ double logTotNumClass;
+
+ generic_cell cc;
+
+ generic_cell cc_passage; /*add to compute the number of class */
+
+ avl_tree albero = NULL;
+
+ AVL_table *array;
+
+ cc.t = CELL_TYPE;
+
+ /* open mask if needed */
+ if (ad->mask == 1) {
+ if ((mask_fd = open(ad->mask_name, O_RDONLY, 0755)) < 0)
+ return RLI_ERRORE;
+ mask_buf = G_malloc(ad->cl * sizeof(int));
+ if (mask_buf == NULL) {
+ G_fatal_error("malloc mask_buf failed");
+ return RLI_ERRORE;
+ }
+ masked = TRUE;
+ }
+
+
+ G_set_c_null_value(&precCell, 1);
+
+
+ /*for each row */
+ for (j = 0; j < ad->rl; j++) {
+ buf = RLI_get_cell_raster_row(fd, j + ad->y, ad);
+
+
+ if (masked) {
+ if (read(mask_fd, mask_buf, (ad->cl * sizeof(int))) < 0) {
+ G_fatal_error("mask read failed");
+ return RLI_ERRORE;
+ }
+ }
+
+
+ for (i = 0; i < ad->cl; i++) { /* for each cell in the row */
+ area++;
+ corrCell = buf[i + ad->x];
+
+ if (masked && mask_buf[i + ad->x] == 0) {
+ G_set_c_null_value(&corrCell, 1);
+ area--;
+ }
+
+ if (!(G_is_null_value(&corrCell, cc.t))) {
+ a = 1;
+ if (G_is_null_value(&precCell, cc.t)) {
+ precCell = corrCell;
+ }
+
+ if (corrCell != precCell) {
+ if (albero == NULL) {
+ cc.val.c = precCell;
+ albero = avl_make(cc, totCorr);
+
+ if (albero == NULL) {
+ G_fatal_error("avl_make error");
+ return RLI_ERRORE;
+ }
+ else
+ m++;
+ }
+ else {
+ cc.val.c = precCell;
+ ris = avl_add(&albero, cc, totCorr);
+ switch (ris) {
+ case AVL_ERR:
+ {
+ G_fatal_error("avl_add error");
+ return RLI_ERRORE;
+ }
+ case AVL_ADD:
+ {
+ m++;
+ break;
+ }
+ case AVL_PRES:
+ {
+ break;
+ }
+ default:
+ {
+ G_fatal_error("avl_add unknown error");
+ return RLI_ERRORE;
+ }
+ }
+ }
+ totCorr = 1;
+ }
+ else {
+ totCorr++;
+ }
+ precCell = corrCell;
+ }
+
+ } /* end for */
+ } /* end for */
+
+
+ /*last closing */
+ if (a != 0) {
+ if (albero == NULL) {
+ cc.val.c = precCell;
+ albero = avl_make(cc, totCorr);
+
+ if (albero == NULL) {
+ G_fatal_error("avl_make error");
+ return RLI_ERRORE;
+ }
+ m++;
+ }
+ else {
+ cc.val.c = precCell;
+ ris = avl_add(&albero, cc, totCorr);
+ switch (ris) {
+ case AVL_ERR:
+ {
+ G_fatal_error("avl_add error");
+ return RLI_ERRORE;
+ }
+ case AVL_ADD:
+ {
+ m++;
+ break;
+ }
+ case AVL_PRES:
+ {
+ break;
+ }
+ default:
+ {
+ G_fatal_error("avl_add unknown error");
+ return RLI_ERRORE;
+ }
+ }
+ }
+ }
+
+ array = G_malloc(m * sizeof(AVL_tableRow));
+ if (array == NULL) {
+ G_fatal_error("malloc array failed");
+ return RLI_ERRORE;
+ }
+ tot = avl_to_array(albero, zero, array);
+
+ if (tot != m) {
+ G_warning("avl_to_array unaspected value. the result could be wrong");
+ return RLI_ERRORE;
+ }
+
+ array_copy = G_malloc(m * sizeof(AVL_tableRow));
+ for (i = 0; i < m; i++) {
+ cc_passage = array[i]->k;
+ array_copy[i] = cc_passage.val.c;
+ }
+
+ qsort(array_copy, m, sizeof(int), cmp);
+
+ for (i = 1; i < m; i++) {
+ if (array_copy[i - 1] != array_copy[i]) {
+ totNumClass++;
+ }
+ }
+
+ /* calculate summary */
+ for (i = 0; i < m; i++) {
+ t = (double)array[i]->tot;
+ percentuale = (double)(t / area);
+ logaritmo = (double)log(percentuale);
+ somma = somma + (percentuale * logaritmo);
+ }
+
+ logTotNumClass = (double)log(totNumClass);
+ /*if a is 0, that is all cell are null, i put index=-1 */
+ if (a != 0) {
+ indice = ((-1) * somma) / logTotNumClass;
+ }
+ else {
+ indice = (double)(-1);
+ }
+
+ if (isnan(indice) || isinf(indice)) {
+ indice = -1;
+ }
+ G_debug(1, "somma: %g, number of logTotNumClass: %g, valore finale: %g",
+ somma, logTotNumClass, indice);
+
+ *result = indice;
+
+ G_free(array);
+ if (masked) {
+ G_free(mask_buf);
+ }
+
+ return RLI_OK;
+}
+
+
+
+int calculateD(int fd, area_des ad, double *result)
+{
+
+ DCELL *buf;
+ DCELL corrCell;
+ DCELL precCell;
+
+ int i, j;
+ int mask_fd = -1, *mask_buf;
+ int ris = 0;
+ int masked = FALSE;
+
+ int a = 0; /* a=0 if all cells are null */
+ long m = 0;
+ long tot = 0;
+ long zero = 0;
+ long totCorr = 0;
+ double indice = 0;
+ double somma = 0;
+ double percentuale = 0;
+ double area = 0;
+ double t;
+ double logaritmo;
+
+ /*add to compute the number of class */
+ long *array_copy;
+ int totNumClass = 1;
+ double logTotNumClass;
+
+ avl_tree albero = NULL;
+ AVL_table *array;
+ generic_cell cc;
+ generic_cell cc_passage; /*add to compute the number of class */
+ cc.t = DCELL_TYPE;
+
+ /* open mask if needed */
+ if (ad->mask == 1) {
+ if ((mask_fd = open(ad->mask_name, O_RDONLY, 0755)) < 0)
+ return RLI_ERRORE;
+ mask_buf = G_malloc(ad->cl * sizeof(int));
+ if (mask_buf == NULL) {
+ G_fatal_error("malloc mask_buf failed");
+ return RLI_ERRORE;
+ }
+ masked = TRUE;
+ }
+
+
+ G_set_d_null_value(&precCell, 1);
+
+ /*for each row */
+ for (j = 0; j < ad->rl; j++) {
+ buf = RLI_get_dcell_raster_row(fd, j + ad->y, ad);
+
+
+ if (masked) {
+ if (read(mask_fd, mask_buf, (ad->cl * sizeof(int))) < 0) {
+ G_fatal_error("mask read failed");
+ return RLI_ERRORE;
+ }
+ }
+
+
+ for (i = 0; i < ad->cl; i++) { /* for each dcell in the row */
+ area++;
+ corrCell = buf[i + ad->x];
+
+ if (masked && mask_buf[i + ad->x] == 0) {
+ G_set_d_null_value(&corrCell, 1);
+ area--;
+ }
+
+ if (!(G_is_null_value(&corrCell, DCELL_TYPE))) {
+ a = 1;
+ if (G_is_null_value(&precCell, DCELL_TYPE)) {
+ precCell = corrCell;
+ }
+ if (corrCell != precCell) {
+ if (albero == NULL) {
+ cc.val.dc = precCell;
+ albero = avl_make(cc, totCorr);
+ if (albero == NULL) {
+ G_fatal_error("avl_make error");
+ return RLI_ERRORE;
+ }
+ m++;
+ }
+ else {
+ cc.val.dc = precCell;
+ ris = avl_add(&albero, cc, totCorr);
+ switch (ris) {
+ case AVL_ERR:
+ {
+ G_fatal_error("avl_add error");
+ return RLI_ERRORE;
+ }
+ case AVL_ADD:
+ {
+ m++;
+ break;
+ }
+ case AVL_PRES:
+ {
+ break;
+ }
+ default:
+ {
+ G_fatal_error("avl_add unknown error");
+ return RLI_ERRORE;
+ }
+ }
+ }
+ totCorr = 1;
+ }
+ else {
+ totCorr++;
+ }
+ precCell = corrCell;
+ }
+
+ } /*close for */
+ } /*close for */
+
+ if (masked) {
+ G_free(mask_buf);
+ }
+
+ /*last closing */
+ if (a != 0) {
+ if (albero == NULL) {
+ cc.val.dc = precCell;
+ albero = avl_make(cc, totCorr);
+ if (albero == NULL) {
+ G_fatal_error("avl_make error");
+ return RLI_ERRORE;
+ }
+ m++;
+ }
+ else {
+ cc.val.fc = precCell;
+ ris = avl_add(&albero, cc, totCorr);
+ switch (ris) {
+ case AVL_ERR:
+ {
+ G_fatal_error("avl_add error");
+ return RLI_ERRORE;
+ }
+ case AVL_ADD:
+ {
+ m++;
+ break;
+ }
+ case AVL_PRES:
+ {
+ break;
+ }
+ default:
+ {
+ G_fatal_error("avl_add unknown error");
+ return RLI_ERRORE;
+ }
+ }
+ }
+
+
+ array = G_malloc(m * sizeof(AVL_tableRow));
+ if (array == NULL) {
+ G_fatal_error("malloc array failed");
+ return RLI_ERRORE;
+ }
+ tot = avl_to_array(albero, zero, array);
+
+ if (tot != m) {
+ G_warning
+ ("avl_to_array unaspected value. the result could be wrong");
+ return RLI_ERRORE;
+ }
+
+ array_copy = G_malloc(m * sizeof(AVL_tableRow));
+
+ for (i = 0; i < m; i++) {
+ cc_passage = array[i]->k;
+ array_copy[i] = cc_passage.val.c;
+ }
+
+ qsort(array_copy, m, sizeof(int), cmp);
+
+ for (i = 1; i < m; i++) {
+ if (array_copy[i - 1] != array_copy[i]) {
+ totNumClass++;
+ }
+ }
+
+
+ /* calculate summary */
+ for (i = 0; i < m; i++) {
+ t = (double)array[i]->tot;
+ percentuale = (double)(t / area);
+ logaritmo = (double)log(percentuale);
+ somma = somma + (percentuale * logaritmo);
+ }
+
+ G_free(array);
+
+ logTotNumClass = (double)log(totNumClass);
+
+ indice = (-1) * somma / logTotNumClass;
+ }
+ else {
+ /*if a is 0, that is all cell are null, i put index=-1 */
+ indice = ((double)(-1));
+ }
+
+ if (isnan(indice) || isinf(indice)) {
+ indice = -1;
+ }
+ G_debug(1, "somma: %g, number of logTotNumClass: %g, valore finale: %g",
+ somma, logTotNumClass, indice);
+
+ *result = indice;
+
+ return RLI_OK;
+}
+
+
+int calculateF(int fd, area_des ad, double *result)
+{
+
+ FCELL *buf;
+ FCELL corrCell;
+ FCELL precCell;
+
+ int i, j;
+ int mask_fd = -1, *mask_buf;
+ int ris = 0;
+ int masked = FALSE;
+ int a = 0; /* a=0 if all cells are null */
+ long m = 0;
+ long tot = 0;
+ long zero = 0;
+ long totCorr = 0;
+ double indice = 0;
+ double somma = 0;
+ double percentuale = 0;
+ double area = 0;
+ double t;
+ double logaritmo;
+ long *array_copy;
+ int totNumClass = 1;
+ double logTotNumClass;
+
+ avl_tree albero = NULL;
+ AVL_table *array;
+ generic_cell cc;
+ generic_cell cc_passage;
+ cc.t = FCELL_TYPE;
+
+ /* open mask if needed */
+ if (ad->mask == 1) {
+ if ((mask_fd = open(ad->mask_name, O_RDONLY, 0755)) < 0)
+ return RLI_ERRORE;
+ mask_buf = G_malloc(ad->cl * sizeof(int));
+ if (mask_buf == NULL) {
+ G_fatal_error("malloc mask_buf failed");
+ return RLI_ERRORE;
+ }
+ masked = TRUE;
+ }
+
+
+ G_set_f_null_value(&precCell, 1);
+
+
+ /*for each row */
+ for (j = 0; j < ad->rl; j++) {
+ buf = RLI_get_fcell_raster_row(fd, j + ad->y, ad);
+
+
+ if (masked) {
+ if (read(mask_fd, mask_buf, (ad->cl * sizeof(int))) < 0) {
+ G_fatal_error("mask read failed");
+ return RLI_ERRORE;
+ }
+ }
+
+ for (i = 0; i < ad->cl; i++) { /* for each fcell in the row */
+ area++;
+ corrCell = buf[i + ad->x];
+ if (masked && mask_buf[i + ad->x] == 0) {
+ G_set_f_null_value(&corrCell, 1);
+ area--;
+ }
+
+ if (!(G_is_null_value(&corrCell, cc.t))) {
+ a = 1;
+ if (G_is_null_value(&precCell, cc.t)) {
+ precCell = corrCell;
+ }
+ if (corrCell != precCell) {
+ if (albero == NULL) {
+ cc.val.fc = precCell;
+ albero = avl_make(cc, totCorr);
+ if (albero == NULL) {
+ G_fatal_error("avl_make error");
+ return RLI_ERRORE;
+ }
+ m++;
+ }
+ else {
+ cc.val.fc = precCell;
+ ris = avl_add(&albero, cc, totCorr);
+ switch (ris) {
+ case AVL_ERR:
+ {
+ G_fatal_error("avl_add error");
+ return RLI_ERRORE;
+ }
+ case AVL_ADD:
+ {
+ m++;
+ break;
+ }
+ case AVL_PRES:
+ {
+ break;
+ }
+ default:
+ {
+ G_fatal_error("avl_add unknown error");
+ return RLI_ERRORE;
+ }
+ }
+ }
+ totCorr = 1;
+ }
+ else {
+ totCorr++;
+ }
+
+ precCell = corrCell;
+ }
+
+ }
+ }
+
+ /*last closing */
+ if (a != 0) {
+ if (albero == NULL) {
+ cc.val.fc = precCell;
+ albero = avl_make(cc, totCorr);
+ if (albero == NULL) {
+ G_fatal_error("avl_make error");
+ return RLI_ERRORE;
+ }
+ m++;
+ }
+ else {
+ cc.val.fc = precCell;
+ ris = avl_add(&albero, cc, totCorr);
+ switch (ris) {
+ case AVL_ERR:
+ {
+ G_fatal_error("avl_add error");
+ return RLI_ERRORE;
+ }
+ case AVL_ADD:
+ {
+ m++;
+ break;
+ }
+ case AVL_PRES:
+ {
+ break;
+ }
+ default:
+ {
+ G_fatal_error("avl_add unknown error");
+ return RLI_ERRORE;
+ }
+ }
+ }
+ }
+
+ array = G_malloc(m * sizeof(AVL_tableRow));
+ if (array == NULL) {
+ G_fatal_error("malloc array failed");
+ return RLI_ERRORE;
+ }
+ tot = avl_to_array(albero, zero, array);
+
+ if (tot != m) {
+ G_warning("avl_to_array unaspected value. the result could be wrong");
+ return RLI_ERRORE;
+ }
+
+ array_copy = G_malloc(m * sizeof(AVL_tableRow));
+
+ for (i = 0; i < m; i++) {
+ cc_passage = array[i]->k;
+ array_copy[i] = cc_passage.val.c;
+ }
+
+ qsort(array_copy, m, sizeof(int), cmp);
+
+ for (i = 1; i < m; i++) {
+ if (array_copy[i - 1] != array_copy[i]) {
+ totNumClass++;
+ }
+ }
+
+ /* calculate summary */
+ for (i = 0; i < m; i++) {
+ t = (double)array[i]->tot;
+ percentuale = (double)(t / area);
+ logaritmo = (double)log(percentuale);
+ somma = somma + (percentuale * logaritmo);
+ }
+
+ logTotNumClass = (double)log(totNumClass);
+
+
+ /*if a is 0, that is all cell are null, i put index=-1 */
+ if (a != 0) {
+ indice = ((-1) * somma) / logTotNumClass;
+ }
+ else {
+ indice = (double)(-1);
+ }
+
+ if (isnan(indice) || isinf(indice)) {
+ indice = -1;
+ }
+ G_debug(1, "somma: %g, number of logTotNumClass: %g, valore finale: %g",
+ somma, logTotNumClass, indice);
+
+ *result = indice;
+
+ G_free(array);
+ if (masked) {
+ G_free(mask_buf);
+ }
+ return RLI_OK;
+}
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--- grass/branches/develbranch_6/raster/r.li/r.li.renyi/Makefile (rev 0)
+++ grass/branches/develbranch_6/raster/r.li/r.li.renyi/Makefile 2010-11-24 16:43:45 UTC (rev 44406)
@@ -0,0 +1,18 @@
+MODULE_TOPDIR = ../../..
+
+PGM = r.li.renyi
+
+EXTRA_CLEAN_DIRS=doxygenhtml
+
+LIB_NAME = grass_rli
+
+RLI_LIB = -l$(LIB_NAME)
+
+LIBES = $(GISLIB) $(RLI_LIB)
+
+DEPENDENCIES = $(GISDEP) $(LIB_NAME )
+
+include $(MODULE_TOPDIR)/include/Make/Module.make
+
+default: cmd
+
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===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.renyi/description.html (rev 0)
+++ grass/branches/develbranch_6/raster/r.li/r.li.renyi/description.html 2010-11-24 16:43:45 UTC (rev 44406)
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+<h2>DESCRIPTION</h2>
+<em>r.li.renyi</em>
+calculates the "renyi's diversity index" as:<br>
+<img src="r_li_renyi.png"> <br>
+with: <br>
+<ul>
+ <li><b>H</b>: Renyi entropy</li>
+ <li><b>alpha</b>: order of the generalized entropy</li>
+ <li><b>i</b>: ith class</li>
+ <li><b>S</b>: number of classes</li>
+ <li><b>p<small>i</small></b>: proportion of the landscape occupied by class i</li>
+</ul>
+
+<h2>NOTES</h2>
+Do not use absolute path names for output files. They are raster if
+moving window disposition was selected, otherwise they are in
+<tt>~/.r.li/output/</tt> folder.
+<br>
+If the input raster contains NULL value cells, <em>r.li.renyi</em>
+returns -1 for these cells. <br>
+If you want to keep NULL values instead, run subsequently on the resulting map:
+<br>
+<div class="code"><pre>
+r.null setnull=-1 map=my_map
+</pre></div>
+
+<h2>EXAMPLES</h2>
+To calculate Renyi's diversity index on map "my_map", using the
+previously created "my_conf" configuration file (<em>r.li.setup</em>)
+and saving results in "my_out" raster map, run:<br>
+<div class="code"><pre>
+r.li.renyi map=my_map conf=my_conf output=my_out alpha=0.6
+</pre></div>
+
+<h2>NOTES</h2>
+Do not use absolute path names for output files. They are raster if
+moving window disposition was selected, otherwise they are in
+~/.r.li/output folder. <br>
+
+If input raster is full of null values <em>r.li.renyi</em> returns -1.<br>
+If you want to have null values instead run <br>
+<div class="code"><pre>
+r.null setnull=-1 map=my_map
+</pre></div>
+after index calculation.
+
+<h2>REFERENCES</h2>
+McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
+analysis program for quantifying landscape structure. USDA For. Serv.
+Gen. Tech. Rep. PNW-351. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</a>)
+
+<h2>SEE ALSO</h2>
+<em>
+<a href="r.li.html">r.li</a>,
+<a href="r.li.setup.html">r.li.setup</a>
+</em>
+
+<h2>AUTHORS</h2>
+Luca Delucchi and Duccio Rocchini, Fondazione E. Mach (Italy), based on the <em>r.li.shannon</em> code
+developed by Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
+
+<p><i>Last changed: $Date$</i>
+
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===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.renyi/renyi.c (rev 0)
+++ grass/branches/develbranch_6/raster/r.li/r.li.renyi/renyi.c 2010-11-24 16:43:45 UTC (rev 44406)
@@ -0,0 +1,714 @@
+
+/****************************************************************************
+ *
+ * MODULE: r.li.renyi
+ *
+ * PURPOSE: brief calculates renyi's diversity index
+ *
+ * AUTHOR(S): Luca Delucchi, Fondazione Edmund Mach
+ * Serena Pallecchi student of Computer Science University of Pisa (Italy)
+ *
+ * COPYRIGHT:
+ * This program is free software under the GPL (>=v2)
+ * Read the COPYING file that comes with GRASS for details.
+ *
+ ***************************************************************************/
+
+#include <stdlib.h>
+#include <fcntl.h>
+#include <math.h>
+
+#include <grass/gis.h>
+#include <grass/glocale.h>
+
+#include "../r.li.daemon/defs.h"
+#include "../r.li.daemon/avlDefs.h"
+#include "../r.li.daemon/avl.h"
+#include "../r.li.daemon/daemon.h"
+
+double calculate(area_des ad, int fd, char **par, double *result);
+
+double calculateD(area_des ad, int fd, char **par, double *result);
+
+double calculateF(area_des ad, int fd, char **par, double *result);
+
+int main(int argc, char *argv[])
+{
+ struct Option *raster, *conf, *output, *alpha;
+ struct GModule *module;
+ char **par = NULL;
+
+ G_gisinit(argv[0]);
+ module = G_define_module();
+ module->description =
+ _("Calculates Renyi's diversity index on a raster map");
+ module->keywords =
+ _("raster, landscape structure analysis, diversity index");
+
+ /* define options */
+
+ raster = G_define_standard_option(G_OPT_R_MAP);
+
+ conf = G_define_option();
+ conf->key = "conf";
+ conf->description = _("Configuration file");
+ conf->type = TYPE_STRING;
+ conf->gisprompt = "old_file,file,input";
+ conf->required = YES;
+
+ alpha = G_define_option();
+ alpha->key = "alpha";
+ alpha->description =
+ _("Alpha value is the order of the generalized entropy");
+ alpha->type = TYPE_STRING;
+ alpha->required = YES;
+
+ output = G_define_standard_option(G_OPT_R_OUTPUT);
+
+ if (G_parser(argc, argv))
+ exit(EXIT_FAILURE);
+
+ if (atoi(alpha->answer) == 1) {
+ G_fatal_error
+ ("If alpha = 1 Renyi index is not defined. (Ricotta et al., 2003, Environ. Model. Softw.)");
+ exit(RLI_ERRORE);
+ }
+ else if (atof(alpha->answer) < 0.) {
+ G_fatal_error
+ ("Alpha must be > 0 otherwise Renyi index is not defined. (Ricotta et al., 2003, Environ. Model. Softw.)");
+ exit(RLI_ERRORE);
+ }
+ else {
+ par = &alpha->answer;
+ }
+ return calculateIndex(conf->answer, renyi, par, raster->answer,
+ output->answer);
+
+}
+
+int renyi(int fd, char **par, area_des ad, double *result)
+{
+ char *mapset;
+ int ris = RLI_OK;
+ double indice = 0;
+ struct Cell_head hd;
+
+ mapset = G_find_cell(ad->raster, "");
+ if (G_get_cellhd(ad->raster, mapset, &hd) == -1)
+ return RLI_ERRORE;
+
+ switch (ad->data_type) {
+ case CELL_TYPE:
+ {
+ ris = calculate(ad, fd, par, &indice);
+ break;
+ }
+ case DCELL_TYPE:
+ {
+ ris = calculateD(ad, fd, par, &indice);
+ break;
+ }
+ case FCELL_TYPE:
+ {
+ ris = calculateF(ad, fd, par, &indice);
+ break;
+ }
+ default:
+ {
+ G_fatal_error("data type unknown");
+ return RLI_ERRORE;
+ }
+
+ }
+
+ if (ris != RLI_OK)
+ return RLI_ERRORE;
+
+ *result = indice;
+
+ return RLI_OK;
+
+}
+
+
+
+double calculate(area_des ad, int fd, char **par, double *result)
+{
+ CELL *buf;
+ CELL corrCell;
+ CELL precCell;
+
+ int i, j;
+ int mask_fd = -1, *mask_buf;
+ int ris = 0;
+ int masked = FALSE;
+ int a = 0; /* a=0 if all cells are null */
+ long m = 0;
+ long tot = 0;
+ long zero = 0;
+ long totCorr = 0;
+ double indice = 0;
+ double somma = 0;
+ double p = 0;
+ double area = 0;
+ double t;
+
+ avl_tree albero = NULL;
+ AVL_table *array;
+ generic_cell uc;
+ uc.t = CELL_TYPE;
+
+ /* open mask if needed */
+ if (ad->mask == 1) {
+ if ((mask_fd = open(ad->mask_name, O_RDONLY, 0755)) < 0)
+ return RLI_ERRORE;
+ mask_buf = G_malloc(ad->cl * sizeof(int));
+ if (mask_buf == NULL) {
+ G_fatal_error("malloc mask_buf failed");
+ return RLI_ERRORE;
+ }
+ masked = TRUE;
+ }
+
+ G_set_c_null_value(&precCell, 1);
+
+
+ for (j = 0; j < ad->rl; j++) { /* for each row */
+ if (masked) {
+ if (read(mask_fd, mask_buf, (ad->cl * sizeof(int))) < 0) {
+ G_fatal_error("mask read failed");
+ return RLI_ERRORE;
+ }
+ }
+
+ buf = RLI_get_cell_raster_row(fd, j + ad->y, ad);
+ for (i = 0; i < ad->cl; i++) { /* for each cell in the row */
+ area++;
+ corrCell = buf[i + ad->x];
+
+ if ((masked) && (mask_buf[i + ad->x] == 0)) {
+ G_set_c_null_value(&corrCell, 1);
+ area--;
+ }
+
+ if (!(G_is_null_value(&corrCell, uc.t))) {
+ a = 1;
+ if (G_is_null_value(&precCell, uc.t)) {
+ precCell = corrCell;
+ }
+ if (corrCell != precCell) {
+ if (albero == NULL) {
+ uc.val.c = precCell;
+ albero = avl_make(uc, totCorr);
+ if (albero == NULL) {
+ G_fatal_error("avl_make error");
+ return RLI_ERRORE;
+ }
+ else
+ m++;
+ }
+ else {
+ uc.val.c = precCell;
+ ris = avl_add(&albero, uc, totCorr);
+ switch (ris) {
+ case AVL_ERR:
+ {
+ G_fatal_error("avl_add error");
+ return RLI_ERRORE;
+ }
+ case AVL_ADD:
+ {
+ m++;
+ break;
+ }
+ case AVL_PRES:
+ {
+ break;
+ }
+ default:
+ {
+ G_fatal_error("avl_make unknown error");
+ return RLI_ERRORE;
+ }
+ }
+ }
+ totCorr = 1;
+ } /* endif not equal cells */
+ else { /*equal cells */
+
+ totCorr++;
+ }
+ precCell = corrCell;
+ }
+
+ }
+ }
+
+ /*last closing */
+ if (a != 0) {
+ if (albero == NULL) {
+ uc.val.c = precCell;
+ albero = avl_make(uc, totCorr);
+ if (albero == NULL) {
+ G_fatal_error("avl_make error");
+ return RLI_ERRORE;
+ }
+ m++;
+ }
+ else {
+ uc.val.c = precCell;
+ ris = avl_add(&albero, uc, totCorr);
+ switch (ris) {
+ case AVL_ERR:
+ {
+ G_fatal_error("avl_add error");
+ return RLI_ERRORE;
+ }
+ case AVL_ADD:
+ {
+ m++;
+ break;
+ }
+ case AVL_PRES:
+ {
+ break;
+ }
+ default:
+ {
+ G_fatal_error("avl_add unknown error");
+ return RLI_ERRORE;
+ }
+ }
+ }
+ }
+ array = G_malloc(m * sizeof(AVL_tableRow));
+ if (array == NULL) {
+ G_fatal_error("malloc array failed");
+ return RLI_ERRORE;
+ }
+ tot = avl_to_array(albero, zero, array);
+ if (tot != m) {
+ G_warning("avl_to_array unaspected value. the result could be wrong");
+ return RLI_ERRORE;
+ }
+
+ char *sval;
+
+ sval = par[0];
+ double alpha_double;
+
+ alpha_double = (double)atof(sval);
+ /* claculate index summary */
+ for (i = 0; i < m; i++) {
+ t = (double)(array[i]->tot);
+ p = t / area;
+ G_debug(1,"Valore p: %g, valore pow: %g",p,pow(p,alpha_double));
+ somma = somma + pow(p, alpha_double);
+ }
+
+ indice = (1 / (1 - alpha_double)) * log(somma);
+ if (isnan(indice) || isinf(indice)) {
+ indice = -1;
+ }
+ G_debug(1, "Valore somma: %g Valore indice: %g", somma, indice);
+
+ *result = indice;
+
+
+ G_free(array);
+ if (masked)
+ G_free(mask_buf);
+
+ return RLI_OK;
+}
+
+
+double calculateD(area_des ad, int fd, char **par, double *result)
+{
+ DCELL *buf;
+ DCELL corrCell;
+ DCELL precCell;
+
+ int i, j;
+ int mask_fd = -1, *mask_buf;
+ int ris = 0;
+ int masked = FALSE;
+ int a = 0; /* a=0 if all cells are null */
+ long m = 0;
+ long tot = 0;
+ long zero = 0;
+ long totCorr = 0;
+ double indice = 0;
+ double somma = 0;
+ double p = 0;
+ double area = 0;
+ double t;
+
+ avl_tree albero = NULL;
+ AVL_table *array;
+ generic_cell uc;
+ uc.t = DCELL_TYPE;
+
+ /* open mask if needed */
+ if (ad->mask == 1) {
+ if ((mask_fd = open(ad->mask_name, O_RDONLY, 0755)) < 0)
+ return RLI_ERRORE;
+ mask_buf = G_malloc(ad->cl * sizeof(int));
+ if (mask_buf == NULL) {
+ G_fatal_error("malloc mask_buffailed");
+ return RLI_ERRORE;
+ }
+ masked = TRUE;
+ }
+
+ G_set_d_null_value(&precCell, 1);
+
+ for (j = 0; j < ad->rl; j++) { /* for each row */
+ if (masked) {
+ if (read(mask_fd, mask_buf, (ad->cl * sizeof(int))) < 0) {
+ G_fatal_error("mask read failed");
+ return RLI_ERRORE;
+ }
+ }
+
+ buf = RLI_get_dcell_raster_row(fd, j + ad->y, ad);
+
+ for (i = 0; i < ad->cl; i++) { /* for each dcell in the row */
+ area++;
+ corrCell = buf[i + ad->x];
+
+ if (masked && mask_buf[i + ad->x] == 0) {
+ G_set_d_null_value(&corrCell, 1);
+ area--;
+ }
+
+ if (!(G_is_null_value(&corrCell, uc.t))) {
+ a = 1;
+
+ if (G_is_null_value(&precCell, uc.t)) {
+ precCell = corrCell;
+ }
+ if (corrCell != precCell) {
+ if (albero == NULL) {
+ uc.val.dc = precCell;
+ albero = avl_make(uc, totCorr);
+ if (albero == NULL) {
+ G_fatal_error("avl_make error");
+ return RLI_ERRORE;
+ }
+ m++;
+ }
+ else {
+ uc.val.dc = precCell;
+ ris = avl_add(&albero, uc, totCorr);
+ switch (ris) {
+ case AVL_ERR:
+ {
+ G_fatal_error("avl_add error");
+ return RLI_ERRORE;
+ }
+ case AVL_ADD:
+ {
+ m++;
+ break;
+ }
+ case AVL_PRES:
+ {
+ break;
+ }
+ default:
+ {
+ G_fatal_error("avl_make unknown error");
+ return RLI_ERRORE;
+ }
+ }
+ }
+ totCorr = 1;
+ } /* endif not equal dcells */
+ else { /*equal dcells */
+
+ totCorr++;
+ }
+ precCell = corrCell;
+ }
+
+
+ }
+ }
+
+ /*last closing */
+ if (a != 0) {
+ if (albero == NULL) {
+ uc.val.dc = precCell;
+ albero = avl_make(uc, totCorr);
+ if (albero == NULL) {
+ G_fatal_error("avl_make error");
+ return RLI_ERRORE;
+ }
+ m++;
+ }
+ else {
+ uc.val.dc = precCell;
+ ris = avl_add(&albero, uc, totCorr);
+ switch (ris) {
+ case AVL_ERR:
+ {
+ G_fatal_error("avl_add error");
+ return RLI_ERRORE;
+ }
+ case AVL_ADD:
+ {
+ m++;
+ break;
+ }
+ case AVL_PRES:
+ {
+ break;
+ }
+ default:
+ {
+ G_fatal_error("avl_add unknown error");
+ return RLI_ERRORE;
+ }
+ }
+ }
+ }
+ array = G_malloc(m * sizeof(AVL_tableRow));
+ if (array == NULL) {
+ G_fatal_error("malloc array failed");
+ return RLI_ERRORE;
+ }
+ tot = avl_to_array(albero, zero, array);
+ if (tot != m) {
+ G_warning("avl_to_array unaspected value. the result could be wrong");
+ return RLI_ERRORE;
+ }
+
+ char *sval;
+
+ sval = par[0];
+ double alpha_double;
+
+ alpha_double = (double)atof(sval);
+ /* claculate index summary */
+ for (i = 0; i < m; i++) {
+ t = (double)(array[i]->tot);
+ p = t / area;
+ G_debug(1,"Valore p: %g, valore pow: %g",p,pow(p,alpha_double));
+ somma = somma + pow(p, alpha_double);
+ }
+
+ indice = (1 / (1 - alpha_double)) * log(somma);
+
+ if (isnan(indice) || isinf(indice)) {
+ indice = -1;
+ }
+
+ G_debug(1, "Valore somma: %g Valore indice: %g", somma, indice);
+
+ *result = indice;
+
+ G_free(array);
+ if (masked)
+ G_free(mask_buf);
+
+ return RLI_OK;
+}
+
+
+
+double calculateF(area_des ad, int fd, char **par, double *result)
+{
+ FCELL *buf;
+ FCELL corrCell;
+ FCELL precCell;
+
+ int i, j;
+ int mask_fd = -1, *mask_buf;
+ int ris = 0;
+ int masked = FALSE;
+ int a = 0; /* a=0 if all cells are null */
+ long m = 0;
+ long tot = 0;
+ long zero = 0;
+ long totCorr = 0;
+ double indice = 0;
+ double somma = 0;
+ double p = 0;
+ double area = 0;
+ double t;
+
+ avl_tree albero = NULL;
+ AVL_table *array;
+ generic_cell uc;
+ uc.t = FCELL_TYPE;
+
+ /* open mask if needed */
+ if (ad->mask == 1) {
+ if ((mask_fd = open(ad->mask_name, O_RDONLY, 0755)) < 0)
+ return RLI_ERRORE;
+ mask_buf = G_malloc(ad->cl * sizeof(int));
+ if (mask_buf == NULL) {
+ G_fatal_error("malloc mask_buf failed");
+ return RLI_ERRORE;
+ }
+ masked = TRUE;
+ }
+
+ G_set_f_null_value(&precCell, 1);
+
+
+ for (j = 0; j < ad->rl; j++) { /* for each row */
+ if (masked) {
+ if (read(mask_fd, mask_buf, (ad->cl * sizeof(int))) < 0) {
+ G_fatal_error("mask read failed");
+ return RLI_ERRORE;
+ }
+ }
+
+ buf = RLI_get_fcell_raster_row(fd, j + ad->y, ad);
+
+
+ for (i = 0; i < ad->cl; i++) { /* for each fcell in the row */
+
+ area++;
+ corrCell = buf[i + ad->x];
+
+ if (masked && mask_buf[i + ad->x] == 0) {
+ G_set_f_null_value(&corrCell, 1);
+ area--;
+ }
+
+ if (!(G_is_null_value(&corrCell, uc.t))) {
+ a = 1;
+ if (G_is_null_value(&precCell, uc.t)) {
+ precCell = corrCell;
+ }
+ if (corrCell != precCell) {
+ if (albero == NULL) {
+ uc.val.fc = precCell;
+ albero = avl_make(uc, totCorr);
+ if (albero == NULL) {
+ G_fatal_error("avl_make error");
+ return RLI_ERRORE;
+ }
+ m++;
+ }
+ else {
+ uc.val.fc = precCell;
+ ris = avl_add(&albero, uc, totCorr);
+ switch (ris) {
+ case AVL_ERR:
+ {
+ G_fatal_error("avl_add error");
+ return RLI_ERRORE;
+ }
+ case AVL_ADD:
+ {
+ m++;
+ break;
+ }
+ case AVL_PRES:
+ {
+ break;
+ }
+ default:
+ {
+ G_fatal_error("avl_make unknown error");
+ return RLI_ERRORE;
+ }
+ }
+ }
+ totCorr = 1;
+ } /* endif not equal fcells */
+ else { /*equal fcells */
+
+ totCorr++;
+ }
+ precCell = corrCell;
+ }
+
+
+ }
+ }
+
+ /*last closing */
+ if (a != 0) {
+ if (albero == NULL) {
+ uc.val.fc = precCell;
+ albero = avl_make(uc, totCorr);
+ if (albero == NULL) {
+ G_fatal_error("avl_make error");
+ return RLI_ERRORE;
+ }
+ m++;
+ }
+ else {
+ uc.val.fc = precCell;
+ ris = avl_add(&albero, uc, totCorr);
+ switch (ris) {
+ case AVL_ERR:
+ {
+ G_fatal_error("avl_add error");
+ return RLI_ERRORE;
+ }
+ case AVL_ADD:
+ {
+ m++;
+ break;
+ }
+ case AVL_PRES:
+ {
+ break;
+ }
+ default:
+ {
+ G_fatal_error("avl_add unknown error");
+ return RLI_ERRORE;
+ }
+ }
+ }
+ }
+
+ array = G_malloc(m * sizeof(AVL_tableRow));
+ if (array == NULL) {
+ G_fatal_error("malloc array failed");
+ return RLI_ERRORE;
+ }
+ tot = avl_to_array(albero, zero, array);
+ if (tot != m) {
+ G_warning("avl_to_array unaspected value. the result could be wrong");
+ return RLI_ERRORE;
+ }
+
+ char *sval;
+
+ sval = par[0];
+ double alpha_double;
+
+ alpha_double = (double)atof(sval);
+ /* calculate index summary */
+ for (i = 0; i < m; i++) {
+ t = (double)(array[i]->tot);
+ p = t / area;
+ G_debug(1,"Valore p: %g, valore pow: %g",p,pow(p,alpha_double));
+ somma = somma + pow(p, alpha_double);
+ }
+
+ indice = (1 / (1 - alpha_double)) * log(somma);
+
+ if (isnan(indice) || isinf(indice)) {
+ indice = -1;
+ }
+
+ G_debug(1, "Valore somma: %g Valore indice: %g", somma, indice);
+
+ *result = indice;
+
+ G_free(array);
+ if (masked)
+ G_free(mask_buf);
+
+ return RLI_OK;
+
+}
Property changes on: grass/branches/develbranch_6/raster/r.li/r.li.renyi/renyi.c
___________________________________________________________________
Added: svn:mime-type
+ text/x-csrc
Added: svn:eol-style
+ native
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