Move contents of intensities.{c,h} to peaks.{c,h}

10 files changed, 147 insertions, 196 deletions

diff --git a/Makefile.am b/Makefile.am
index 22f39ce1..cca1fbe9 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,6 +1,6 @@
 EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h src/relrod.h \
              src/utils.h src/diffraction.h src/detector.h src/ewald.h \
-             src/sfac.h src/intensities.h src/reflections.h src/list_tmp.h \
+             src/sfac.h src/reflections.h src/list_tmp.h \
              src/statistics.h src/displaywindow.h src/render.h src/hdfsee.h \
              data/displaywindow.ui src/dirax.h src/peaks.h src/index.h \
              src/filters.h src/diffraction-gpu.h src/cl-utils.h
diff --git a/Makefile.in b/Makefile.in
index 2244ddbf..47bcef1a 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -197,7 +197,7 @@ top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h src/relrod.h \
              src/utils.h src/diffraction.h src/detector.h src/ewald.h \
-             src/sfac.h src/intensities.h src/reflections.h src/list_tmp.h \
+             src/sfac.h src/reflections.h src/list_tmp.h \
              src/statistics.h src/displaywindow.h src/render.h src/hdfsee.h \
              data/displaywindow.ui src/dirax.h src/peaks.h src/index.h \
              src/filters.h src/diffraction-gpu.h src/cl-utils.h
diff --git a/src/Makefile.am b/src/Makefile.am
index ef9338c5..4041e1e2 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -9,8 +9,7 @@ AM_CFLAGS = -Wall
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\"
 
 pattern_sim_SOURCES = pattern_sim.c diffraction.c utils.c image.c cell.c \
-                      hdf5-file.c detector.c sfac.c intensities.c \
-                      reflections.c
+                      hdf5-file.c detector.c sfac.c peaks.c reflections.c
 if HAVE_OPENCL
 pattern_sim_SOURCES += diffraction-gpu.c cl-utils.c
 endif
@@ -22,8 +21,8 @@ process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
 process_hkl_LDADD = @LIBS@
 
 indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
-                      intensities.c peaks.c index.c filters.c \
-                      diffraction.c detector.c sfac.c dirax.c reflections.c
+                      peaks.c index.c filters.c diffraction.c detector.c \
+                      sfac.c dirax.c reflections.c
 indexamajig_LDADD = @LIBS@
 if HAVE_OPENCL
 indexamajig_SOURCES += diffraction-gpu.c cl-utils.c
diff --git a/src/Makefile.in b/src/Makefile.in
index 4b59a13d..1d7547a0 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -68,26 +68,25 @@ am__hdfsee_SOURCES_DIST = hdfsee.c displaywindow.c render.c \
 hdfsee_OBJECTS = $(am_hdfsee_OBJECTS)
 hdfsee_DEPENDENCIES =
 am__indexamajig_SOURCES_DIST = indexamajig.c hdf5-file.c utils.c \
-	cell.c image.c intensities.c peaks.c index.c filters.c \
-	diffraction.c detector.c sfac.c dirax.c reflections.c \
-	diffraction-gpu.c cl-utils.c
+	cell.c image.c peaks.c index.c filters.c diffraction.c \
+	detector.c sfac.c dirax.c reflections.c diffraction-gpu.c \
+	cl-utils.c
 @HAVE_OPENCL_TRUE@am__objects_1 = diffraction-gpu.$(OBJEXT) \
 @HAVE_OPENCL_TRUE@	cl-utils.$(OBJEXT)
 am_indexamajig_OBJECTS = indexamajig.$(OBJEXT) hdf5-file.$(OBJEXT) \
-	utils.$(OBJEXT) cell.$(OBJEXT) image.$(OBJEXT) \
-	intensities.$(OBJEXT) peaks.$(OBJEXT) index.$(OBJEXT) \
-	filters.$(OBJEXT) diffraction.$(OBJEXT) detector.$(OBJEXT) \
-	sfac.$(OBJEXT) dirax.$(OBJEXT) reflections.$(OBJEXT) \
-	$(am__objects_1)
+	utils.$(OBJEXT) cell.$(OBJEXT) image.$(OBJEXT) peaks.$(OBJEXT) \
+	index.$(OBJEXT) filters.$(OBJEXT) diffraction.$(OBJEXT) \
+	detector.$(OBJEXT) sfac.$(OBJEXT) dirax.$(OBJEXT) \
+	reflections.$(OBJEXT) $(am__objects_1)
 indexamajig_OBJECTS = $(am_indexamajig_OBJECTS)
 indexamajig_DEPENDENCIES =
 am__pattern_sim_SOURCES_DIST = pattern_sim.c diffraction.c utils.c \
-	image.c cell.c hdf5-file.c detector.c sfac.c intensities.c \
+	image.c cell.c hdf5-file.c detector.c sfac.c peaks.c \
 	reflections.c diffraction-gpu.c cl-utils.c
 am_pattern_sim_OBJECTS = pattern_sim.$(OBJEXT) diffraction.$(OBJEXT) \
 	utils.$(OBJEXT) image.$(OBJEXT) cell.$(OBJEXT) \
 	hdf5-file.$(OBJEXT) detector.$(OBJEXT) sfac.$(OBJEXT) \
-	intensities.$(OBJEXT) reflections.$(OBJEXT) $(am__objects_1)
+	peaks.$(OBJEXT) reflections.$(OBJEXT) $(am__objects_1)
 pattern_sim_OBJECTS = $(am_pattern_sim_OBJECTS)
 pattern_sim_DEPENDENCIES =
 am_powder_plot_OBJECTS = powder_plot.$(OBJEXT) cell.$(OBJEXT) \
@@ -223,16 +222,16 @@ top_srcdir = @top_srcdir@
 AM_CFLAGS = -Wall
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\"
 pattern_sim_SOURCES = pattern_sim.c diffraction.c utils.c image.c \
-	cell.c hdf5-file.c detector.c sfac.c intensities.c \
-	reflections.c $(am__append_2)
+	cell.c hdf5-file.c detector.c sfac.c peaks.c reflections.c \
+	$(am__append_2)
 pattern_sim_LDADD = @LIBS@
 process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
                       reflections.c
 
 process_hkl_LDADD = @LIBS@
 indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
-	intensities.c peaks.c index.c filters.c diffraction.c \
-	detector.c sfac.c dirax.c reflections.c $(am__append_3)
+	peaks.c index.c filters.c diffraction.c detector.c sfac.c \
+	dirax.c reflections.c $(am__append_3)
 indexamajig_LDADD = @LIBS@
 @HAVE_GTK_TRUE@hdfsee_SOURCES = hdfsee.c displaywindow.c render.c hdf5-file.c utils.c image.c \
 @HAVE_GTK_TRUE@                 filters.c
@@ -361,7 +360,6 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/image.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/index.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/indexamajig.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/intensities.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pattern_sim.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/peaks.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/powder_plot.Po@am__quote@
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 1ffae789..03711d56 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -25,7 +25,6 @@
 #include "utils.h"
 #include "hdf5-file.h"
 #include "index.h"
-#include "intensities.h"
 #include "peaks.h"
 #include "diffraction.h"
 #include "diffraction-gpu.h"
diff --git a/src/intensities.c b/src/intensities.c
deleted file mode 100644
index b0eef542..00000000
--- a/src/intensities.c
+++ /dev/null
@@ -1,149 +0,0 @@
-/*
- * intensities.c
- *
- * Extract intensities from patterns
- *
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#include <stdlib.h>
-#include <math.h>
-#include <stdio.h>
-#include <assert.h>
-
-#include "image.h"
-#include "intensities.h"
-#include "cell.h"
-#include "sfac.h"
-#include "diffraction.h"
-
-
-#define MAX_HITS (1024)
-
-
-struct reflhit {
-	signed int h;
-	signed int k;
-	signed int l;
-	double min_distance;
-	int x;
-	int y;
-};
-
-
-static double sum_nearby_points(float *data, int width, int x, int y)
-{
-	int dx, dy;
-	double intensity = 0;
-
-	for ( dx=-3; dx<=3; dx++ ) {
-	for ( dy=-3; dy<=3; dy++ ) {
-		intensity += data[(x+dx) + width*(y+dy)];
-	}
-	}
-
-	return intensity;
-}
-
-
-void output_intensities(struct image *image, UnitCell *cell)
-{
-	int x, y;
-	double ax, ay, az;
-	double bx, by, bz;
-	double cx, cy, cz;
-	struct reflhit hits[MAX_HITS];
-	int n_hits = 0;
-	int i;
-
-	cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
-
-	for ( x=0; x<image->width; x++ ) {
-	for ( y=0; y<image->height; y++ ) {
-
-		double hd, kd, ld;  /* Indices with decimal places */
-		double dh, dk, dl;  /* Distances in h,k,l directions */
-		signed int h, k, l;
-		struct rvec q;
-		double dist;
-		int found = 0;
-		int j;
-
-		q = get_q(image, x, y, 1, NULL, 1.0/image->lambda);
-
-		hd = q.u * ax + q.v * ay + q.w * az;
-		kd = q.u * bx + q.v * by + q.w * bz;
-		ld = q.u * cx + q.v * cy + q.w * cz;
-
-		h = (signed int)rint(hd);
-		k = (signed int)rint(kd);
-		l = (signed int)rint(ld);
-
-		dh = hd - h;
-		dk = kd - k;
-		dl = ld - l;
-		dist = sqrt(pow(dh, 2.0) + pow(dk, 2.0) + pow(dl, 2.0));
-		if ( dist > 0.1 ) continue;
-
-		for ( j=0; j<n_hits; j++ ) {
-			if ( (hits[j].h == h) && (hits[j].k == k)
-			                      && (hits[j].l == l) ) {
-
-				if ( dist < hits[j].min_distance ) {
-					hits[j].min_distance = dist;
-					hits[j].x = x;
-					hits[j].y = y;
-				}
-
-				found = 1;
-
-			}
-		}
-
-		if ( !found ) {
-			hits[n_hits].min_distance = dist;
-			hits[n_hits].x = x;
-			hits[n_hits].y = y;
-			hits[n_hits].h = h;
-			hits[n_hits].k = k;
-			hits[n_hits].l = l;
-			n_hits++;
-			assert(n_hits < MAX_HITS);
-		}
-
-	}
-	}
-
-	STATUS("Found %i reflections\n", n_hits);
-
-	/* Explicit printf() used here (not normally allowed) because
-	 * we really want to output to stdout */
-	printf("New pattern: %7.5f %7.5f %7.5f %7.5f\n",
-	       image->orientation.w, image->orientation.x,
-	       image->orientation.y, image->orientation.z);
-	for ( i=0; i<n_hits; i++ ) {
-
-		double intensity;
-
-		/* Bounds check */
-		if ( hits[i].x + 3 >= image->width ) continue;
-		if ( hits[i].x - 3 < 0 ) continue;
-		if ( hits[i].y + 3 >= image->height ) continue;
-		if ( hits[i].y - 3 < 0 ) continue;
-
-		intensity = sum_nearby_points(image->data, image->width,
-		                              hits[i].x, hits[i].y);
-
-		printf("%3i %3i %3i %6f (at %i,%i)\n",
-		       hits[i].h, hits[i].k, hits[i].l, intensity,
-		       hits[i].x, hits[i].y);
-
-	}
-
-	/* Blank line at end */
-	printf("\n");
-}
diff --git a/src/intensities.h b/src/intensities.h
deleted file mode 100644
index 10664ab2..00000000
--- a/src/intensities.h
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * intensities.h
- *
- * Extract intensities from patterns
- *
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#ifndef INTENSITIES_H
-#define INTENSITIES_H
-
-#include "image.h"
-#include "cell.h"
-
-extern void output_intensities(struct image *image, UnitCell *cell);
-
-#endif	/* INTENSITIES_H */
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 3593e4b4..0e8c60e2 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -28,7 +28,7 @@
 #include "utils.h"
 #include "hdf5-file.h"
 #include "detector.h"
-#include "intensities.h"
+#include "peaks.h"
 #include "sfac.h"
 #include "reflections.h"
 
diff --git a/src/peaks.c b/src/peaks.c
index d146ce24..a76ed78f 100644
--- a/src/peaks.c
+++ b/src/peaks.c
@@ -27,6 +27,19 @@
 #include "peaks.h"
 #include "detector.h"
 #include "filters.h"
+#include "diffraction.h"
+
+
+#define MAX_HITS (1024)
+
+struct reflhit {
+	signed int h;
+	signed int k;
+	signed int l;
+	double min_distance;
+	int x;
+	int y;
+};
 
 
 #define PEAK_WINDOW_SIZE (10)
@@ -461,3 +474,117 @@ void dump_peaks(struct image *image)
 
 	}
 }
+
+
+static double sum_nearby_points(float *data, int width, int x, int y)
+{
+	int dx, dy;
+	double intensity = 0;
+
+	for ( dx=-3; dx<=3; dx++ ) {
+	for ( dy=-3; dy<=3; dy++ ) {
+		intensity += data[(x+dx) + width*(y+dy)];
+	}
+	}
+
+	return intensity;
+}
+
+
+void output_intensities(struct image *image, UnitCell *cell)
+{
+	int x, y;
+	double ax, ay, az;
+	double bx, by, bz;
+	double cx, cy, cz;
+	struct reflhit hits[MAX_HITS];
+	int n_hits = 0;
+	int i;
+
+	cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
+
+	for ( x=0; x<image->width; x++ ) {
+	for ( y=0; y<image->height; y++ ) {
+
+		double hd, kd, ld;  /* Indices with decimal places */
+		double dh, dk, dl;  /* Distances in h,k,l directions */
+		signed int h, k, l;
+		struct rvec q;
+		double dist;
+		int found = 0;
+		int j;
+
+		q = get_q(image, x, y, 1, NULL, 1.0/image->lambda);
+
+		hd = q.u * ax + q.v * ay + q.w * az;
+		kd = q.u * bx + q.v * by + q.w * bz;
+		ld = q.u * cx + q.v * cy + q.w * cz;
+
+		h = (signed int)rint(hd);
+		k = (signed int)rint(kd);
+		l = (signed int)rint(ld);
+
+		dh = hd - h;
+		dk = kd - k;
+		dl = ld - l;
+		dist = sqrt(pow(dh, 2.0) + pow(dk, 2.0) + pow(dl, 2.0));
+		if ( dist > 0.1 ) continue;
+
+		for ( j=0; j<n_hits; j++ ) {
+			if ( (hits[j].h == h) && (hits[j].k == k)
+			                      && (hits[j].l == l) ) {
+
+				if ( dist < hits[j].min_distance ) {
+					hits[j].min_distance = dist;
+					hits[j].x = x;
+					hits[j].y = y;
+				}
+
+				found = 1;
+
+			}
+		}
+
+		if ( !found ) {
+			hits[n_hits].min_distance = dist;
+			hits[n_hits].x = x;
+			hits[n_hits].y = y;
+			hits[n_hits].h = h;
+			hits[n_hits].k = k;
+			hits[n_hits].l = l;
+			n_hits++;
+			assert(n_hits < MAX_HITS);
+		}
+
+	}
+	}
+
+	STATUS("Found %i reflections\n", n_hits);
+
+	/* Explicit printf() used here (not normally allowed) because
+	 * we really want to output to stdout */
+	printf("New pattern: %7.5f %7.5f %7.5f %7.5f\n",
+	       image->orientation.w, image->orientation.x,
+	       image->orientation.y, image->orientation.z);
+	for ( i=0; i<n_hits; i++ ) {
+
+		double intensity;
+
+		/* Bounds check */
+		if ( hits[i].x + 3 >= image->width ) continue;
+		if ( hits[i].x - 3 < 0 ) continue;
+		if ( hits[i].y + 3 >= image->height ) continue;
+		if ( hits[i].y - 3 < 0 ) continue;
+
+		intensity = sum_nearby_points(image->data, image->width,
+		                              hits[i].x, hits[i].y);
+
+		printf("%3i %3i %3i %6f (at %i,%i)\n",
+		       hits[i].h, hits[i].k, hits[i].l, intensity,
+		       hits[i].x, hits[i].y);
+
+	}
+
+	/* Blank line at end */
+	printf("\n");
+}
diff --git a/src/peaks.h b/src/peaks.h
index 2e868342..ba85f0f5 100644
--- a/src/peaks.h
+++ b/src/peaks.h
@@ -21,5 +21,6 @@
 extern int image_fom(struct image *image);
 extern void search_peaks(struct image *image);
 extern void dump_peaks(struct image *image);
+extern void output_intensities(struct image *image, UnitCell *cell);
 
 #endif	/* PEAKS_H */