Separate CM subtraction and noise filter

7 files changed, 45 insertions, 20 deletions

diff --git a/src/displaywindow.c b/src/displaywindow.c
index 2501f38b..0fc71254 100644
--- a/src/displaywindow.c
+++ b/src/displaywindow.c
@@ -982,7 +982,8 @@ static gint displaywindow_press(GtkWidget *widget, GdkEventButton *event,
 
 
 DisplayWindow *displaywindow_open(const char *filename, const char *peaks,
-                                  int boost, int binning, int clean)
+                                  int boost, int binning, int cmfilter,
+                                  int noisefilter)
 {
 	DisplayWindow *dw;
 	char *title;
@@ -1048,7 +1049,8 @@ DisplayWindow *displaywindow_open(const char *filename, const char *peaks,
 
 	dw->binning = binning;
 	dw->boostint = boost;
-	dw->clean = clean;
+	dw->cmfilter = cmfilter;
+	dw->noisefilter = noisefilter;
 	displaywindow_update(dw);
 
 	/* Peak list provided at startup? */
diff --git a/src/displaywindow.h b/src/displaywindow.h
index 0ca59933..ee34dab9 100644
--- a/src/displaywindow.h
+++ b/src/displaywindow.h
@@ -63,7 +63,8 @@ typedef struct {
 	int		height;		/* Size of the drawing area */
 	int		binning;
 	int		boostint;
-	int		clean;		/* Whether or not to clean the image */
+	int		cmfilter;	/* Use CM subtraction */
+	int		noisefilter;	/* Use aggressive noise filter */
 
 	int		show_col_scale;
 	int		scale;
@@ -74,7 +75,8 @@ typedef struct {
 /* Open an image display window showing the given filename, or NULL */
 extern DisplayWindow *displaywindow_open(const char *filename,
                                          const char *peaks, int boost,
-                                         int binning, int clean);
+                                         int binning, int cmfilter,
+                                         int noisefilter);
 
 
 #endif	/* DISPLAYWINDOW_H */
diff --git a/src/filters.c b/src/filters.c
index f6f5e0b8..172be222 100644
--- a/src/filters.c
+++ b/src/filters.c
@@ -97,7 +97,7 @@ static void noise_filter(struct image *image)
 
 
 /* Pre-processing to make life easier */
-void clean_image(struct image *image)
+void filter_cm(struct image *image)
 {
 	int px, py;
 
@@ -111,5 +111,10 @@ void clean_image(struct image *image)
 	}
 	}
 
+}
+
+
+void filter_noise(struct image *image)
+{
 	noise_filter(image);
 }
diff --git a/src/filters.h b/src/filters.h
index b28cb908..97bcf5a2 100644
--- a/src/filters.h
+++ b/src/filters.h
@@ -18,6 +18,8 @@
 #endif
 
 
-extern void clean_image(struct image *image);
+extern void filter_cm(struct image *image);
+extern void filter_noise(struct image *image);
+
 
 #endif	/* FILTERS_H */
diff --git a/src/hdfsee.c b/src/hdfsee.c
index a1d16b56..ff74ead6 100644
--- a/src/hdfsee.c
+++ b/src/hdfsee.c
@@ -38,9 +38,11 @@ static void show_help(const char *s)
 "  -p, --peak-overlay=<filename>    Draw circles in positions listed in file.\n"
 "  -i, --int-boost=<n>              Multiply intensity by <n>.\n"
 "  -b, --binning=<n>                Set display binning to <n>.\n"
-"      --clean-image                Perform common-mode noise subtraction and\n"
-"                                    background removal on images before\n"
-"                                    proceeding.\n"
+"      --filter-cm                  Perform common-mode noise subtraction.\n"
+"      --filter-noise               Apply an aggressive noise filter which\n"
+"                                    sets all pixels in each 3x3 region to\n"
+"                                    zero if any of them have negative\n"
+"                                    values.\n"
 "\n");
 }
 
@@ -79,7 +81,8 @@ int main(int argc, char *argv[])
 	char *peaks = NULL;
 	int boost = 1;
 	int binning = 2;
-	int config_clean = 0;
+	int config_cmfilter = 0;
+	int config_noisefilter = 0;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -87,7 +90,8 @@ int main(int argc, char *argv[])
 		{"peak-overlay",       1, NULL,               'p'},
 		{"int-boost",          1, NULL,               'i'},
 		{"binning",            1, NULL,               'b'},
-		{"clean-image",        0, &config_clean,       1},
+		{"filter-cm",          0, &config_cmfilter,    1},
+		{"filter-noise",       0, &config_noisefilter, 1},
 		{0, 0, NULL, 0}
 	};
 
@@ -145,7 +149,8 @@ int main(int argc, char *argv[])
 	for ( i=0; i<nfiles; i++ ) {
 		main_window_list[i] = displaywindow_open(argv[optind+i], peaks,
 		                                         boost, binning,
-		                                         config_clean);
+		                                         config_cmfilter,
+		                                         config_noisefilter);
 		if ( main_window_list[i] == NULL ) {
 			ERROR("Couldn't open display window\n");
 		} else {
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 7c227cb1..ac5fb0ae 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -49,6 +49,8 @@ static void show_help(const char *s)
 "                           dirax    : invoke DirAx\n"
 "\n"
 "      --verbose           Be verbose about indexing.\n"
+"      --gpu               Use the GPU to speed up the simulation.\n"
+"\n"
 "      --write-drx         Write 'xfel.drx' for visualisation of reciprocal\n"
 "                           space.  Implied by any indexing method other than\n"
 "                           'none'.  Beware: the units in this file are\n"
@@ -57,9 +59,13 @@ static void show_help(const char *s)
 "      --near-bragg        Output a list of reflection intensities to stdout.\n"
 "      --simulate          Simulate the diffraction pattern using the indexed\n"
 "                           unit cell.\n"
-"      --gpu               Use the GPU to speed up the simulation.\n"
-"      --clean-image       Perform common-mode noise subtraction and\n"
-"                           background removal on images before proceeding.\n"
+"      --filter-cm         Perform common-mode noise subtraction on images\n"
+"                           before proceeding.  Intensities will be extracted\n"
+"                           from the image as it is after this processing.\n"
+"      --filter-noise      Apply an aggressive noise filter which sets all\n"
+"                           pixels in each 3x3 region to zero if any of them\n"
+"                           have negative values.  Intensity measurement will\n"
+"                           be performed on the image as it was before this.\n"
 "      --no-match          Don't attempt to match the indexed cell to the\n"
 "                           model, just proceed with the one generated by the\n"
 "                           auto-indexing procedure.\n"
@@ -170,7 +176,8 @@ int main(int argc, char *argv[])
 	int config_nearbragg = 0;
 	int config_writedrx = 0;
 	int config_simulate = 0;
-	int config_clean = 0;
+	int config_cmfilter = 0;
+	int config_noisefilter = 0;
 	int config_nomatch = 0;
 	int config_gpu = 0;
 	int config_verbose = 0;
@@ -190,7 +197,8 @@ int main(int argc, char *argv[])
 		{"write-drx",          0, &config_writedrx,    1},
 		{"indexing",           1, NULL,               'z'},
 		{"simulate",           0, &config_simulate,    1},
-		{"clean-image",        0, &config_clean,       1},
+		{"filter-cm",          0, &config_cmfilter,    1},
+		{"filter-noise",       0, &config_noisefilter, 1},
 		{"no-match",           0, &config_nomatch,     1},
 		{"verbose",            0, &config_verbose,     1},
 		{"alternate",          0, &config_alternate,   1},
@@ -296,8 +304,8 @@ int main(int argc, char *argv[])
 
 		hdf5_read(hdfile, &image);
 
-		if ( config_clean ) {
-			clean_image(&image);
+		if ( config_cmfilter ) {
+			filter_cm(&image);
 		}
 
 		/* Perform 'fine' peak search */
diff --git a/src/render.c b/src/render.c
index 432b81ab..a4be5a14 100644
--- a/src/render.c
+++ b/src/render.c
@@ -77,7 +77,8 @@ float *render_get_image_binned(DisplayWindow *dw, int binning, float *max)
 
 		hdf5_read(dw->hdfile, image);
 		dw->image_dirty = 0;
-		if ( dw->clean ) clean_image(image);
+		if ( dw->cmfilter ) filter_cm(image);
+		if ( dw->noisefilter ) filter_noise(image);
 
 		/* Deal with the old image, if existing */
 		if ( dw->image != NULL ) {