Get rid of "--filter-cm"

This was completely specific to pnCCDs, and not even properly general to the
different configurations there.

5 files changed, 7 insertions, 22 deletions

diff --git a/src/dw-hdfsee.c b/src/dw-hdfsee.c
index 8ad12a2a..ec90b87e 100644
--- a/src/dw-hdfsee.c
+++ b/src/dw-hdfsee.c
@@ -1529,8 +1529,6 @@ static int geometry_fits(struct image *image, struct detector *geom)
 
 static void do_filters(DisplayWindow *dw)
 {
-	if ( dw->cmfilter ) filter_cm(dw->image);
-
 	if ( dw->median_filter > 0 ) {
 		filter_median(dw->image, dw->median_filter);
 	}
@@ -1795,7 +1793,7 @@ static gint displaywindow_press(GtkWidget *widget, GdkEventButton *event,
 
 
 DisplayWindow *displaywindow_open(const char *filename, const char *peaks,
-                                  double boost, int binning, int cmfilter,
+                                  double boost, int binning,
                                   int noisefilter, int colscale,
                                   const char *element, const char *geometry,
                                   int show_rings, double *ring_radii,
@@ -1824,7 +1822,6 @@ DisplayWindow *displaywindow_open(const char *filename, const char *peaks,
 	dw->scale = colscale;
 	dw->binning = binning;
 	dw->boostint = boost;
-	dw->cmfilter = cmfilter;
 	dw->noisefilter = noisefilter;
 	dw->not_ready_yet = 1;
 	dw->surf = NULL;
diff --git a/src/dw-hdfsee.h b/src/dw-hdfsee.h
index 6bc2ae12..3e908947 100644
--- a/src/dw-hdfsee.h
+++ b/src/dw-hdfsee.h
@@ -100,7 +100,6 @@ typedef struct {
 
 	int		binning;
 	double		boostint;
-	int		cmfilter;	/* Use CM subtraction */
 	int		noisefilter;	/* Use aggressive noise filter */
 	int             median_filter;
 	int             use_geom;
@@ -119,7 +118,7 @@ typedef struct {
 /* Open an image display window showing the given filename, or NULL */
 extern DisplayWindow *displaywindow_open(const char *filename,
                                          const char *peaks, double boost,
-                                         int binning, int cmfilter,
+                                         int binning,
                                          int noisefilter, int colscale,
                                          const char *element,
                                          const char *geometry, int show_rings,
diff --git a/src/hdfsee.c b/src/hdfsee.c
index 2db58f41..24d6d9cc 100644
--- a/src/hdfsee.c
+++ b/src/hdfsee.c
@@ -58,11 +58,10 @@ static void show_help(const char *s)
 "      --ring-size=<n>              Set the size for those circles.\n"
 "  -i, --int-boost=<n>              Multiply intensity by <n>.\n"
 "  -b, --binning=<n>                Set display binning to <n>.\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"
+"      --filter-noise               Apply an aggressive noise filter to the\n"
+"                                    image data.\n"
+"      --median-filter=<n>          Apply a median filter to the image data.\n"
+
 "      --show-rings                 Overlay rings that indicate resolution.\n"
 "      --simple-rings=XX,YY,...     Overlay rings at specified radii XX, YY, ...\n"
 "                                    in pixel units.\n"
@@ -113,7 +112,6 @@ int main(int argc, char *argv[])
 	char *peaks = NULL;
 	double boost = 1.0;
 	int binning = 2;
-	int config_cmfilter = 0;
 	int config_noisefilter = 0;
 	int config_showrings = 0;
 	int colscale = SCALE_COLOUR;
@@ -132,7 +130,6 @@ int main(int argc, char *argv[])
 		{"peak-overlay",       1, NULL,               'p'},
 		{"int-boost",          1, NULL,               'i'},
 		{"binning",            1, NULL,               'b'},
-		{"filter-cm",          0, &config_cmfilter,    1},
 		{"filter-noise",       0, &config_noisefilter, 1},
 		{"colscale",           1, NULL,               'c'},
 		{"image",              1, NULL,               'e'},
@@ -264,7 +261,6 @@ 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_cmfilter,
 		                                         config_noisefilter,
 		                                         colscale, element,
 		                                         geometry,
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 27ec31fc..208c0ed0 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -104,9 +104,6 @@ static void show_help(const char *s)
 "For more control over the process, you might need:\n\n"
 "    --tolerance=<tol>   Set the tolerances for cell comparison.\n"
 "                          Default: 5,5,5,1.5.\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"
@@ -114,7 +111,7 @@ static void show_help(const char *s)
 "    --median-filter=<n> Apply a median filter to the image data.  Intensity\n"
 "                         measurement will be performed on the image as it\n"
 "                         was before this.  The side length of the median\n"
-"                         filter box will be <n>.  Default: 0 (no filter).\n"
+"                         filter box will be 2<n>+1.  Default: 0 (no filter).\n"
 "    --no-sat-corr       Don't correct values of saturated peaks using a\n"
 "                         table included in the HDF5 file.\n"
 "    --threshold=<n>     Only accept peaks above <n> ADU.  Default: 800.\n"
@@ -185,7 +182,6 @@ int main(int argc, char *argv[])
 
 	/* Defaults */
 	iargs.cell = NULL;
-	iargs.cmfilter = 0;
 	iargs.noisefilter = 0;
 	iargs.median_filter = 0;
 	iargs.satcorr = 1;
@@ -239,7 +235,6 @@ int main(int argc, char *argv[])
 		{"image",              1, NULL,               'e'},
 
 		/* Long-only options with no arguments */
-		{"filter-cm",          0, &iargs.cmfilter,           1},
 		{"filter-noise",       0, &iargs.noisefilter,        1},
 		{"no-sat-corr",        0, &iargs.satcorr,            0},
 		{"sat-corr",           0, &iargs.satcorr,            1},
diff --git a/src/process_image.c b/src/process_image.c
index a8eeb663..ef673c84 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -134,8 +134,6 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		return;
 	}
 
-	if ( iargs->cmfilter ) filter_cm(&image);
-
 	/* Take snapshot of image after CM subtraction but before applying
 	 * horrible noise filters to it */
 	data_size = image.width * image.height * sizeof(float);