Added biomass growth module

git-svn-id: https://svn.osgeo.org/grass/grass/trunk@38036 15284696-431f-4ddb-bdfa-cd5b030d7da7

gui/wxpython/xml/menudata.xml

@@ -2258,6 +2258,13 @@
               <handler>self.OnMenuCmd</handler>
 	      <command>i.vi</command>
 	    </menuitem>
+	    <menuitem>
+	      <label>Biomass Growth</label>
+	      <help>Calculates the growth of biomass for a day.</help>
+	      <keywords>imagery,biomass growth,vegetation index,biophysical parameters</keywords>
+              <handler>self.OnMenuCmd</handler>
+	      <command>i.biomass</command>
+	    </menuitem>
 	    <separator />
 	    <menuitem>
 	      <label>Emissivity</label>

imagery/Makefile

@@ -3,6 +3,7 @@ MODULE_TOPDIR = ..
 SUBDIRS = \
 	i.albedo \
 	i.atcorr \
+	i.biomass \
 	i.cca \
 	i.cluster \
 	i.eb.evapfr \

imagery/i.biomass/Makefile

@@ -0,0 +1,14 @@
+MODULE_TOPDIR = ../..
+
+PGM = i.biomass
+
+LIBES = $(GISLIB) $(RASTERLIB)
+DEPENDENCIES = $(GISDEP) $(RASTERDEP)
+
+include $(MODULE_TOPDIR)/include/Make/Module.make
+
+ifneq ($(USE_LARGEFILES),)
+	EXTRA_CFLAGS = -D_FILE_OFFSET_BITS=64
+endif
+
+default: cmd

imagery/i.biomass/biomass.c

@@ -0,0 +1,21 @@
+#include<stdio.h>
+#include<math.h>
+#include<stdlib.h>
+ double biomass(double fpar, double solar_day, double evap_fr,
+		 double light_use_ef) 
+{
+    double result, apar, conversion_coefs;
+
+    
+	/*fPAR in Bastiaassen and Ali = a (= 1.257) * NDVI + b (= -0.161); */ 
+	/*light use efficiency is variable for each crop! */ 
+	/* Cotton light_use_ef in Uzbekistan is 1.9 */ 
+	
+	/*      apar                    = (b+a*ndvi); */ 
+	conversion_coefs = 0.0864 * 10;
+    apar = fpar * (0.48 * solar_day);
+    result = apar * light_use_ef * evap_fr * conversion_coefs;
+    return result;
+}
+
+

imagery/i.biomass/i.biomass.html

@@ -0,0 +1,40 @@
+<H2>DESCRIPTION</H2>
+
+<EM>i.biomass</EM> Calculates the biomass growth for a day after [1][2]. 
+
+Input:
+<ul>
+ <li>fPAR, the modified Photosynthetic Active Radiation for crops.
+ <li>Light Use Efficiency [0.0-1.0], in Uzbekistan cotton is at 1.9 most of the time.
+ <li>Latitude [0.0-90.0], from i.latlong.
+ <li>DOY [1-366].
+ <li>Transmissivity of the Atmosphere single-way [0.0-1.0], mostly around 0.7+ in clear sky.
+ <li>Water availability [0.0-1.0], possibly using direct output from i.eb.evapfr.
+</ul>
+
+<H2>NOTES</H2>
+It can use the output of i.eb.evapfr directly as water availability input.
+
+<H2>TODO</H2>
+remove Latitude, DOY and Tsw from input and replace with a raster input compatible with r.sun output.
+
+<H2>SEE ALSO</H2>
+
+<em>
+<A HREF="i.eb.evapfr">i.eb.evapfr</A><br>
+</em>
+
+<H2>REFERENCES</H2>
+
+  <p>[1] Bastiaanssen, W.G.M., Ali, S., 2002. A new crop yield forecasting model based on satellite measurements applied across the Indus Basin, Pakistan. Agriculture, Ecosystems and Environment, 94(3):321-340. 
+
+  <p>[2] Chemin, Y., Platonov, A., Abdullaev, I., Ul-Hassan, M. 2005. Supplementing farm level water productivity assessment by remote sensing in transition economies. Water International. 30(4):513-521.
+
+
+<H2>AUTHORS</H2>
+
+Yann Chemin, Bec de Mortagne, France<BR>
+
+
+<p>
+<i>Last changed: $Date:$</i>

imagery/i.biomass/main.c

@@ -0,0 +1,203 @@
+
+/****************************************************************************
+ *
+ * MODULE:       i.biomass
+ * AUTHOR(S):    Yann Chemin - yann.chemin@gmail.com
+ * PURPOSE:      Creates a map of biomass growth
+ *               
+ *
+ * COPYRIGHT:    (C) 2002-2009 by the GRASS Development Team
+ *
+ *               This program is free software under the GNU General Public
+ *   	    	 License (>=v2). Read the file COPYING that comes with GRASS
+ *   	    	 for details.
+ *
+ *****************************************************************************/
+   
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <grass/gis.h>
+#include <grass/raster.h>
+#include <grass/glocale.h>
+
+double solar_day(double lat, double doy, double tsw);
+double biomass(double apar, double solar_day, double evap_fr,
+        double light_use_ef);
+
+int main(int argc, char *argv[]) 
+{
+    int nrows, ncols;
+    int row, col;
+    struct GModule *module;
+    struct Option *input1, *input2, *input3, *input4, *input5, *input6;
+    struct Option *output1;
+    struct History history;	/*metadata */
+    struct Colors colors;
+    char *result1;	/*output raster name */
+    int infd_fpar, infd_luf, infd_lat;
+    int infd_doy, infd_tsw, infd_wa;
+    int outfd1;
+    char *fpar, *luf, *lat, *doy, *tsw, *wa;
+    void *inrast_fpar, *inrast_luf, *inrast_lat;
+    void *inrast_doy, *inrast_tsw, *inrast_wa;
+    DCELL * outrast1;
+    /************************************/ 
+    G_gisinit(argv[0]);
+    module = G_define_module();
+    module->keywords = _("biomass, fpar, yield");
+    module->description =
+	_("biomass growth calculation, precursor of crop yield calculation");
+    
+    /* Define the different options */ 
+    input1 = G_define_standard_option(G_OPT_R_INPUT);
+    input1->key = "fpar";
+    input1->description = _("Name of the fPAR map");
+
+    input2 = G_define_standard_option(G_OPT_R_INPUT);
+    input2->key = "luf";
+    input2->description =
+	_("Name of the light use efficiency map (UZB:cotton=1.9)");
+
+    input3 = G_define_standard_option(G_OPT_R_INPUT);
+    input3->key = "lat";
+    input3->description = _("Name of the degree latitude map [dd.ddd]");
+
+    input4 = G_define_standard_option(G_OPT_R_INPUT);
+    input4->key = "doy";
+    input4->description = _("Name of the Day of Year map [1-366]");
+
+    input5 = G_define_standard_option(G_OPT_R_INPUT);
+    input5->key = "tsw";
+    input5->description =
+	_("Name of the single-way transmissivity map [0.0-1.0]");
+
+    input6 = G_define_standard_option(G_OPT_R_INPUT);
+    input6->key = "wa";
+    input6->description =
+	_("Value of the water availability map [0.0-1.0]");
+
+    output1 = G_define_standard_option(G_OPT_R_INPUT);
+    output1->description =
+	_("Name of the output daily biomass growth layer [kg/ha/d]");
+    
+    /********************/ 
+    if (G_parser(argc, argv))
+	exit(EXIT_FAILURE);
+    fpar = input1->answer;
+    luf = input2->answer;
+    lat = input3->answer;
+    doy = input4->answer;
+    tsw = input5->answer;
+    wa = input6->answer;
+    result1 = output1->answer;
+    
+    /***************************************************/ 
+    if ((infd_fpar = Rast_open_cell_old(fpar, "")) < 0)
+	G_fatal_error(_("Unable to open raster map <%s>"), fpar);
+    inrast_fpar = Rast_allocate_d_raster_buf();
+
+    if ((infd_luf = Rast_open_cell_old(luf, "")) < 0)
+	G_fatal_error(_("Unable to open raster map <%s>"), luf);
+    inrast_luf = Rast_allocate_d_raster_buf();
+    
+    if ((infd_lat = Rast_open_cell_old(lat, "")) < 0)
+	G_fatal_error(_("Unable to open raster map <%s>"), lat);
+    inrast_lat = Rast_allocate_d_raster_buf();
+    
+    if ((infd_doy = Rast_open_cell_old(doy, "")) < 0)
+	G_fatal_error(_("Unable to open raster map <%s>"), doy);
+    inrast_doy = Rast_allocate_d_raster_buf();
+    
+    if ((infd_tsw = Rast_open_cell_old(tsw, "")) < 0)
+	G_fatal_error(_("Unable to open raster map <%s>"), tsw);
+    inrast_tsw = Rast_allocate_d_raster_buf();
+    
+    if ((infd_wa = Rast_open_cell_old(wa, "")) < 0)
+	G_fatal_error(_("Unable to open raster map <%s>"), wa);
+    inrast_wa = Rast_allocate_d_raster_buf();
+    
+    nrows = G_window_rows();
+    ncols = G_window_cols();
+    outrast1 = Rast_allocate_d_raster_buf();
+    
+    /* Create New raster files */ 
+    if ((outfd1 = Rast_open_raster_new(result1, DCELL_TYPE)) < 0)
+	G_fatal_error(_("Unable to create raster map <%s>"), result1);
+     
+    /* Process pixels */ 
+    for (row = 0; row < nrows; row++)
+    {
+	DCELL d;
+	DCELL d_fpar;
+	DCELL d_luf;
+	DCELL d_lat;
+	DCELL d_doy;
+	DCELL d_tsw;
+	DCELL d_solar;
+	DCELL d_wa;
+	G_percent(row, nrows, 2);
+	
+        /* read input maps */ 
+        if (Rast_get_d_raster_row(infd_fpar, inrast_fpar, row)< 0)
+	    G_fatal_error(_("Unable to read from <%s> row %d"),fpar,row);
+	if (Rast_get_d_raster_row(infd_luf,inrast_luf,row)<0)
+	    G_fatal_error(_("Unable to read from <%s> row %d"),luf,row);
+	if (Rast_get_d_raster_row(infd_lat, inrast_lat, row) < 0)
+	    G_fatal_error(_("Unable to read from <%s> row %d"),lat,row);
+	if (Rast_get_d_raster_row(infd_doy, inrast_doy, row) < 0)
+	    G_fatal_error(_("Unable to read from <%s> row %d"),doy,row);
+	if (Rast_get_d_raster_row(infd_tsw, inrast_tsw, row) < 0)
+	    G_fatal_error(_("Unable to read from <%s> row %d"),tsw,row);
+	if (Rast_get_d_raster_row(infd_wa,inrast_wa,row)<0)
+	    G_fatal_error(_("Unable to read from <%s> row %d"),wa,row); 
+        /*process the data */ 
+        for (col = 0; col < ncols; col++)
+        {
+            d_fpar = ((DCELL *) inrast_fpar)[col];
+            d_luf = ((DCELL *) inrast_luf)[col];
+            d_lat = ((DCELL *) inrast_lat)[col];
+            d_doy = ((DCELL *) inrast_doy)[col];
+            d_tsw = ((DCELL *) inrast_tsw)[col];
+            d_wa = ((DCELL *) inrast_wa)[col];
+	    if (Rast_is_d_null_value(&d_fpar) ||
+		 Rast_is_d_null_value(&d_luf) ||
+		 Rast_is_d_null_value(&d_lat) || 
+                 Rast_is_d_null_value(&d_doy) ||
+		 Rast_is_d_null_value(&d_tsw) ||
+		 Rast_is_d_null_value(&d_wa)) 
+		Rast_set_d_null_value(&outrast1[col], 1);
+	    else {
+		d_solar = solar_day(d_lat, d_doy, d_tsw);
+		d = biomass(d_fpar,d_solar,d_wa,d_luf);
+		outrast1[col] = d;
+	    }
+        }
+	if (Rast_put_d_raster_row(outfd1, outrast1) < 0)
+	    G_fatal_error(_("Failed writing raster map <%s>"), result1);
+    }
+    
+    /* Color table for biomass */ 
+    Rast_init_colors(&colors);
+    Rast_add_color_rule(0, 0, 0, 0, 1, 255, 255, 255, &colors);
+    G_free(inrast_fpar);
+    G_free(inrast_luf);
+    G_free(inrast_lat);
+    G_free(inrast_doy);
+    G_free(inrast_tsw);
+    G_free(inrast_wa);
+    G_free(outrast1);
+    Rast_close_cell(infd_fpar);
+    Rast_close_cell(infd_luf);
+    Rast_close_cell(infd_lat);
+    Rast_close_cell(infd_doy);
+    Rast_close_cell(infd_tsw);
+    Rast_close_cell(infd_wa);
+    Rast_close_cell(outfd1);
+    Rast_short_history(result1, "raster", &history);
+    Rast_command_history(&history);
+    Rast_write_history(result1, &history);
+    exit(EXIT_SUCCESS);
+}
+
+

imagery/i.biomass/solar_day.c

@@ -0,0 +1,25 @@
+#include<stdio.h>
+#include<math.h>
+#include<stdlib.h>
+
+    /*
+     * Average Solar Diurnal Radiation after Bastiaanssen (1995) 
+     */
+    
+#define PI 3.1415927
+double solar_day(double lat, double doy, double tsw) 
+{
+    double ws, cosun, n10_temp, delta, ds, result;
+
+    ds = 1.0 + 0.01672 * sin(2 * PI * (doy - 93.5) / 365.0);
+    delta = 0.4093 * sin((2 * PI * doy / 365) - 1.39);
+    n10_temp = lat * PI / 180.0;
+    ws = acos(-tan(n10_temp) * tan(delta * PI / 180.0));
+    cosun =
+	ws * sin(delta * PI / 180.0) * sin(n10_temp) +
+	cos(delta * PI / 180.0) * cos(n10_temp) * sin(ws);
+    result = (cosun * 1367 * tsw) / (PI * ds * ds);
+    return result;
+}
+
+