i.pca: change output back to DCELL for no rescaling, update manual, copy color table from input band for filtering

git-svn-id: https://svn.osgeo.org/grass/grass/trunk@53388 15284696-431f-4ddb-bdfa-cd5b030d7da7

imagery/i.pca/i.pca.html

@@ -12,41 +12,23 @@ reading the input raster map layers. When the rescale
 option is used, the output files are rescaled to fit the
 min,max range.
 
-<h2>OPTIONS</h2>
-
-<h3>Parameters:</h3>
-<dl>
-<dt><b>input=</b><em>name,name</em>[<em>,name,name</em>,...] 
-<dd>Name of two or more input raster map layers.
-
-<dt><b>output=</b><em>name</em> 
-<dd>The output raster map layer name to which suffixes are
-added.  Each output raster map layer is assigned this
-user-specified <em>name</em> with a numerical (.1, .2, ...
-.n) suffix.
-
-<dt><b>rescale=</b><em>min,max</em> 
-<dd>The optional output category range. (Default: 0,255) If
-rescale=0,0,  no rescaling is performed on output files.
-
-<dd>If output is rescaled, the output raster will be of type CELL. If 
-the output is not rescaled, the output raster will be of type DCELL.
+<p>
+If the output is not rescaled (<em>rescale=0,0</em>, the output raster 
+maps will be of type DCELL, otherwise the output raster maps will be of 
+type CELL.
 
-<dt><b>-n</b> <em>normalize input raster maps</em> 
-<dd>By default, the values of the input raster maps are centered for each 
+<p>By default, the values of the input raster maps are centered for each 
 map separately with <em>x - mean</em>. With <em>-n</em>, the input raster 
 maps are normalized for each map separately with <em>(x - mean) / stddev</em>. 
 Normalizing is highly recommended when the input raster maps have different
 units, e.g. represent different environmental parameters. 
 
-<dt><b>-f</b> <em>output will be filtered input bands</em> 
-<dd>This option, together with the <em>percent</em> option, can be used 
-to remove noise from input bands. Input bands will be recalculated from 
-a subset of the principal components. The subset is selected by using 
-only the most important (highest eigenvalue) principal components which 
-explain together <em>percent</em> percent variance observed in the 
-input bands.
-</dl>
+<p>The <em>-f</em> flag, together with the <em>percent</em> option, can 
+be used to remove noise from input bands. Input bands will be 
+recalculated from a subset of the principal components (inverse PCA). 
+The subset is selected by using only the most important (highest 
+eigenvalue) principal components which explain together <em>percent</em> 
+percent variance observed in the input bands.
 
 
 <h2>NOTES</h2>
@@ -60,16 +42,20 @@ history files. View with <em>r.info</em>.
 
 <h2>EXAMPLE</h2>
 
-Using the Spearfish Imagery sample dataset
+Using Landsat imagery in the North Carolina sample dataset:
 
 <div class="code"><pre>
-i.pca in=spot.ms.1,spot.ms.2,spot.ms.3 out=spot_pca
+i.pca in=lsat7_2002_10,lsat7_2002_20,lsat7_2002_30,lsat7_2002_40,lsat7_2002_50,lsat7_2002_70 \
+    out=lsat7_2002_pca
 
-r.info -h spot_pca.1
+r.info -h lsat7_2002_pca.1
    Eigen values, (vectors), and [percent importance]:
-   PC1   1159.75 ( 0.6237, 0.6503, 0.4337) [88.38%]
-   PC2    146.50 ( 0.2403, 0.3685,-0.8981) [11.16%]
-   PC3      5.97 (-0.7438, 0.6643, 0.0735) [ 0.45%]
+   PC1   4334.35 ( 0.2824, 0.3342, 0.5092,-0.0087, 0.5264, 0.5217) [83.04%]
+   PC2    588.31 ( 0.2541, 0.1885, 0.2923,-0.7428,-0.5110,-0.0403) [11.27%]
+   PC3    239.22 ( 0.3801, 0.3819, 0.2681, 0.6238,-0.4000,-0.2980) [ 4.58%]
+   PC4     32.85 ( 0.1752,-0.0191,-0.4053, 0.1593,-0.4435, 0.7632) [ 0.63%]
+   PC5     20.73 (-0.6170,-0.2514, 0.6059, 0.1734,-0.3235, 0.2330) [ 0.40%]
+   PC6      4.08 (-0.5475, 0.8021,-0.2282,-0.0607,-0.0208, 0.0252) [ 0.08%]
 </pre></div>
 
 

imagery/i.pca/local_proto.h

@@ -2,6 +2,6 @@
 #define __LOCAL_PROTO_H__
 
 /* support.c */
-void write_support(int, char *, double **, double *);
+void write_support(int, char *, char *, double **, double *);
 
 #endif

imagery/i.pca/main.c

@@ -171,7 +171,7 @@ int main(int argc, char *argv[])
     if (!calc_mu_cov(inp_fd, covar, mu, stddev, bands))
 	G_fatal_error(_("No non-null values"));
 
-    G_math_d_copy(covar[0], eigmat[0], bands*bands);
+    G_math_d_copy(covar[0], eigmat[0], bands * bands);
     G_debug(1, "Calculating eigenvalues and eigenvectors...");
     G_math_eigen(eigmat, eigval, bands);
 
@@ -217,15 +217,18 @@ int main(int argc, char *argv[])
 
     /* write colors and history to output */
     for (i = 0; i < bands; i++) {
-	char outname[80];
+	char outname[GNAME_MAX];
+
+	/* close input files */
+	Rast_unopen(inp_fd[i]);
 
 	sprintf(outname, "%s.%d", opt_out->answer, i + 1);
 
 	/* write colors and history to file */
-	write_support(bands, outname, eigmat, eigval);
-
-	/* close input files */
-	Rast_unopen(inp_fd[i]);
+	if (flag_filt->answer)
+	    write_support(bands, opt_in->answers[i], outname, eigmat, eigval);
+	else
+	    write_support(bands, NULL, outname, eigmat, eigval);
     }
     
     /* free memory */
@@ -395,7 +398,7 @@ write_pca(double **eigmat, double *mu, double *stddev,
     int rows = Rast_window_rows();
     int cols = Rast_window_cols();
     /* why CELL_TYPE when scaling output ? */
-    int outmap_type = (scale) ? CELL_TYPE : FCELL_TYPE;
+    int outmap_type = (scale) ? CELL_TYPE : DCELL_TYPE;
     int outcell_mapsiz = Rast_cell_size(outmap_type);
     int *out_fd = (int *) G_malloc(bands * sizeof(int));
     DCELL **inbuf = (DCELL **) G_malloc(bands * sizeof(DCELL *));
@@ -500,7 +503,6 @@ write_pca(double **eigmat, double *mu, double *stddev,
 			}
 		    }
 
-
 		    /* the cell entry is complete */
 		    if (scale && (pass == 1)) {
 			if (first)

imagery/i.pca/support.c

@@ -8,18 +8,24 @@
 static void write_history(int, char *, double **, double *);
 
 
-void write_support(int bands, char *outname, double **eigmat, double *eigval)
+void write_support(int bands, char *inname, char *outname, double **eigmat, double *eigval)
 {
     const char *mapset = G_mapset();
     struct Colors colors;
     struct FPRange range;
     DCELL min, max;
 
-    /* make grey scale color table */
-    Rast_read_fp_range(outname, mapset, &range);
-    Rast_get_fp_range_min_max(&range, &min, &max);
+    if (inname) {
+	Rast_read_colors(inname, "", &colors);
+    }
+    else {
+	/* make grey scale color table */
+	Rast_read_fp_range(outname, mapset, &range);
+	Rast_get_fp_range_min_max(&range, &min, &max);
+
+	Rast_make_grey_scale_fp_colors(&colors, min, max);
 
-    Rast_make_grey_scale_fp_colors(&colors, min, max);
+    }
 
     if (Rast_map_is_fp(outname, mapset))
 	Rast_mark_colors_as_fp(&colors);
@@ -66,14 +72,13 @@ static void write_history(int bands, char *outname, double **eigmat, double *eig
 	Rast_append_history(&hist, tmpeigen);
 
 	/* write eigen values to screen */
-	if(first_map)
+	if (first_map)
 	    fprintf(stdout, "%s\n", tmpeigen);
     }
 
-    Rast_command_history(&hist);
-
     /* only write to stderr the first time (this fn runs for every output map) */
     first_map = FALSE;
 
+    Rast_command_history(&hist);
     Rast_write_history(outname, &hist);
 }