Add -b option to powder_plot, make hdf5_read() not use nominal energy

12 files changed, 53 insertions, 24 deletions

diff --git a/Makefile.am b/Makefile.am
index 5c1be076..052b9e62 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -68,7 +68,8 @@ src_check_hkl_SOURCES = src/check_hkl.c src/sfac.c src/cell.c src/utils.c \
                         src/thread-pool.c
 
 src_powder_plot_SOURCES = src/powder_plot.c src/cell.c src/utils.c src/image.c \
-                          src/hdf5-file.c src/detector.c src/thread-pool.c
+                          src/hdf5-file.c src/detector.c src/thread-pool.c \
+                          src/beam-parameters.c
 
 src_render_hkl_SOURCES = src/render_hkl.c src/cell.c src/reflections.c \
                          src/utils.c  src/povray.c src/symmetry.c src/render.c \
diff --git a/Makefile.in b/Makefile.in
index adddfa87..3e8f1851 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -192,7 +192,7 @@ src_pattern_sim_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
 am_src_powder_plot_OBJECTS = src/powder_plot.$(OBJEXT) \
 	src/cell.$(OBJEXT) src/utils.$(OBJEXT) src/image.$(OBJEXT) \
 	src/hdf5-file.$(OBJEXT) src/detector.$(OBJEXT) \
-	src/thread-pool.$(OBJEXT)
+	src/thread-pool.$(OBJEXT) src/beam-parameters.$(OBJEXT)
 src_powder_plot_OBJECTS = $(am_src_powder_plot_OBJECTS)
 src_powder_plot_LDADD = $(LDADD)
 src_powder_plot_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
@@ -617,7 +617,8 @@ src_check_hkl_SOURCES = src/check_hkl.c src/sfac.c src/cell.c src/utils.c \
                         src/thread-pool.c
 
 src_powder_plot_SOURCES = src/powder_plot.c src/cell.c src/utils.c src/image.c \
-                          src/hdf5-file.c src/detector.c src/thread-pool.c
+                          src/hdf5-file.c src/detector.c src/thread-pool.c \
+                          src/beam-parameters.c
 
 src_render_hkl_SOURCES = src/render_hkl.c src/cell.c src/reflections.c \
                          src/utils.c  src/povray.c src/symmetry.c src/render.c \
diff --git a/src/calibrate_detector.c b/src/calibrate_detector.c
index ab8b3ecb..e8b5ed37 100644
--- a/src/calibrate_detector.c
+++ b/src/calibrate_detector.c
@@ -151,7 +151,7 @@ int main(int argc, char *argv[])
 
 	hdfile = hdfile_open(filename);
 	hdfile_set_image(hdfile, "/data/data");
-	hdf5_read(hdfile, &image, 1, 2000.0);
+	hdf5_read(hdfile, &image, 1);
 
 	if ( split ) {
 		split_image(&image);
diff --git a/src/cubeit.c b/src/cubeit.c
index e412c2c1..608f0e48 100644
--- a/src/cubeit.c
+++ b/src/cubeit.c
@@ -231,8 +231,7 @@ static void sum_image(void *pg, int cookie)
 		return;
 	}
 
-	/* FIXME: Nominal photon energy */
-	hdf5_read(hdfile, &image, 1, 2000.0);
+	hdf5_read(hdfile, &image, 1);
 
 	cell_get_cartesian(apargs->cell, &ax, &ay, &az, &bx, &by,
 	                                &bz, &cx, &cy, &cz);
diff --git a/src/dw-hdfsee.c b/src/dw-hdfsee.c
index 1a3f6b7b..abf81e8f 100644
--- a/src/dw-hdfsee.c
+++ b/src/dw-hdfsee.c
@@ -1245,7 +1245,7 @@ static gint displaywindow_newhdf(GtkMenuItem *item, struct newhdf *nh)
 	if ( nh->dw->not_ready_yet ) return 0;
 
 	hdfile_set_image(nh->dw->hdfile, nh->name);
-	hdf5_read(nh->dw->hdfile, nh->dw->image, 0, 0.0);
+	hdf5_read(nh->dw->hdfile, nh->dw->image, 0);
 
 	/* Check that the geometry still fits */
 	if ( !geometry_fits(nh->dw->image, nh->dw->simple_geom) ) {
@@ -1530,7 +1530,7 @@ DisplayWindow *displaywindow_open(const char *filename, const char *peaks,
 
 			if ( !fail ) {
 				dw->image = calloc(1, sizeof(struct image));
-				hdf5_read(dw->hdfile, dw->image, 0, 0.0);
+				hdf5_read(dw->hdfile, dw->image, 0);
 			} else {
 				ERROR("Couldn't select path\n");
 				free(dw);
diff --git a/src/hdf5-file.c b/src/hdf5-file.c
index 313489e4..6db904d4 100644
--- a/src/hdf5-file.c
+++ b/src/hdf5-file.c
@@ -390,8 +390,7 @@ static void debodge_saturation(struct hdfile *f, struct image *image)
 }
 
 
-int hdf5_read(struct hdfile *f, struct image *image, int satcorr,
-              double nominal_photon_energy)
+int hdf5_read(struct hdfile *f, struct image *image, int satcorr)
 {
 	herr_t r;
 	float *buf;
@@ -434,10 +433,6 @@ int hdf5_read(struct hdfile *f, struct image *image, int satcorr,
 
 	/* Read wavelength from file */
 	image->lambda = get_wavelength(f);
-	if ( image->lambda < 0.0 ) {
-		ERROR("Couldn't read wavelength - using nominal value.\n");
-		image->lambda = ph_en_to_lambda(eV_to_J(nominal_photon_energy));
-	}
 
 	image->f0 = get_f0(f);
 	if ( image->f0 < 0.0 ) {
diff --git a/src/hdf5-file.h b/src/hdf5-file.h
index 7a0d4382..f5ee71b3 100644
--- a/src/hdf5-file.h
+++ b/src/hdf5-file.h
@@ -27,8 +27,7 @@ struct hdfile;
 extern int hdf5_write(const char *filename, const void *data,
                       int width, int height, int type);
 
-extern int hdf5_read(struct hdfile *f, struct image *image, int satcorr,
-                     double nominal_photon_energy);
+extern int hdf5_read(struct hdfile *f, struct image *image, int satcorr);
 
 extern struct hdfile *hdfile_open(const char *filename);
 extern int hdfile_set_image(struct hdfile *f, const char *path);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 987d026f..1e5fc47a 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -241,8 +241,17 @@ static void process_image(void *pp, int cookie)
 
 	}
 
-	hdf5_read(hdfile, &image, pargs->static_args.config_satcorr,
-	          beam->photon_energy);
+	hdf5_read(hdfile, &image, pargs->static_args.config_satcorr);
+	if ( image.lambda < 0.0 ) {
+		if ( beam != NULL ) {
+			image.lambda = beam->photon_energy;
+		} else {
+			ERROR("No wavelength in file, so you need to give "
+			      "a beam parameters file with -b.\n");
+			hdfile_close(hdfile);
+			return;
+		}
+	}
 
 	if ( config_cmfilter ) {
 		filter_cm(&image);
diff --git a/src/powder_plot.c b/src/powder_plot.c
index b1beb414..c6d2f045 100644
--- a/src/powder_plot.c
+++ b/src/powder_plot.c
@@ -26,6 +26,7 @@
 #include "detector.h"
 #include "index.h"
 #include "hdf5-file.h"
+#include "beam-parameters.h"
 
 
 static void show_help(const char *s)
@@ -37,6 +38,8 @@ static void show_help(const char *s)
 "  -h, --help                 Display this help message.\n"
 "  -g. --geometry=<file>      Get detector geometry from file.\n"
 "  -i, --input=<file>         Input filename.\n"
+"  -b, --beam=<file>          Get beam parameters (specifically, wavelength)"
+"                              from file if non present in the HDF5 file.\n"
 "\n");
 }
 
@@ -49,12 +52,15 @@ int main(int argc, char *argv[])
 	struct hdfile *hdfile;
 	char *filename = NULL;
 	char *geometry = NULL;
+	char *beamf = NULL;
+	struct beam_params *beam = NULL;
 
 	/* Long options */
 	const struct option longopts[] = {
 		{"help",               0, NULL,               'h'},
 		{"input",              1, NULL,               'i'},
 		{"geometry",           1, NULL,               'g'},
+		{"beam",               1, NULL,               'b'},
 		{0, 0, NULL, 0}
 	};
 
@@ -77,6 +83,10 @@ int main(int argc, char *argv[])
 			geometry = strdup(optarg);
 			break;
 
+		case 'b' :
+			beamf = strdup(optarg);
+			break;
+
 		default :
 			return 1;
 		}
@@ -93,6 +103,11 @@ int main(int argc, char *argv[])
 		return 1;
 	}
 
+	if ( beamf != NULL ) {
+		beam = get_beam_parameters(beamf);
+		free(beamf);
+	}
+
 	image.det = get_detector_geometry(geometry);
 	if ( image.det == NULL ) {
 		ERROR("Failed to read detector geometry from '%s'\n", geometry);
@@ -102,7 +117,16 @@ int main(int argc, char *argv[])
 
 	hdfile = hdfile_open(filename);
 	hdfile_set_image(hdfile, "/data/data");
-	hdf5_read(hdfile, &image, 1, 2000.0); /* FIXME: Hardcoded */
+	hdf5_read(hdfile, &image, 1);
+	if ( image.lambda < 0.0 ) {
+		if ( beam != NULL ) {
+			image.lambda = beam->photon_energy;
+		} else {
+			ERROR("No wavelength in file, so you need to give "
+			      "a beam parameters file with -b.\n");
+			return 1;
+		}
+	}
 
 	for ( x=0; x<image.width; x++ ) {
 	for ( y=0; y<image.height; y++ ) {
@@ -121,5 +145,7 @@ int main(int argc, char *argv[])
 	}
 	}
 
+	free(beamf);
+
 	return 0;
 }
diff --git a/src/reintegrate.c b/src/reintegrate.c
index 8450eaab..67e7b347 100644
--- a/src/reintegrate.c
+++ b/src/reintegrate.c
@@ -123,8 +123,7 @@ static void process_image(void *pg, int cookie)
 		return;
 	}
 
-	/* FIXME: Nominal photon energy */
-	hdf5_read(hdfile, &image, pargs->config_satcorr, 2000.0);
+	hdf5_read(hdfile, &image, pargs->config_satcorr);
 
 	map_all_peaks(&image);
 
diff --git a/src/sum_stack.c b/src/sum_stack.c
index 3d2388ab..c25a79aa 100644
--- a/src/sum_stack.c
+++ b/src/sum_stack.c
@@ -185,8 +185,7 @@ static void add_image(void *args, int cookie)
 		return;
 	}
 
-	/* FIXME: Nominal photon energy */
-	hdf5_read(hdfile, &image, 1, 2000.0);
+	hdf5_read(hdfile, &image, 1);
 
 	if ( pargs->config_cmfilter ) {
 		filter_cm(&image);
diff --git a/src/templates.c b/src/templates.c
index 37188145..ed557afa 100644
--- a/src/templates.c
+++ b/src/templates.c
@@ -70,9 +70,10 @@ IndexingPrivate *generate_templates(UnitCell *cell, const char *filename,
 		ERROR("Couldn't select path\n");
 		return NULL;
 	}
-	hdf5_read(hdfile, &image, 0, nominal_photon_energy);
+	hdf5_read(hdfile, &image, 0);
 	hdfile_close(hdfile);
 	image.det = det;
+	if ( image.lambda < 0.0 ) image.lambda = nominal_photon_energy;
 
 	priv = calloc(1, sizeof(struct _indexingprivate_template));
 	priv->base.indm = INDEXING_TEMPLATE;