Fill in photon energy, clen and adu for CBFs

This needed a bit of reorganisation and clarification of who is
repsonsible for loading what.  The low-level file loaders, e.g.
hdf5_read and hdf5_read2 in hdf5-file.c or cbf_read in image.c, are
responsible.  There is a helper function adjust_centering_for_rail in
detector.h which they can use.

It seems like this could be done more cleanly at the imagefile layer.
However, we need to make sure that the "old" hdfile API still works on
its own, even when not accessed via the new imagefile API.

4 files changed, 100 insertions, 40 deletions

diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index b2e3cc58..e3b351ff 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -528,37 +528,15 @@ int panel_number(struct detector *det, struct panel *p)
 }
 
 
-void fill_in_values(struct detector *det, struct hdfile *f, struct event* ev)
+void adjust_centering_for_rail(struct panel *p)
 {
-	int i;
-
-	for ( i=0; i<det->n_panels; i++ ) {
-
-		double offs;
-		struct panel *p = &det->panels[i];
+	double offs;
 
-		if ( p->clen_from != NULL ) {
-
-			double val;
-			int r;
-
-			r = hdfile_get_value(f, p->clen_from, ev, &val,
-			                     H5T_NATIVE_DOUBLE);
-			if ( r ) {
-				ERROR("Failed to read '%s'\n", p->clen_from);
-			} else {
-				p->clen = val * 1.0e-3;
-			}
-
-		}
-
-                /* Offset in +z direction from calibrated clen to actual */
-		offs = p->clen - p->clen_for_centering;
-		p->cnx += p->rail_x * offs;
-		p->cny += p->rail_y * offs;
-		p->clen = p->clen_for_centering + p->coffset + p->rail_z * offs;
-
-	}
+	/* Offset in +z direction from calibrated clen to actual */
+	offs = p->clen - p->clen_for_centering;
+	p->cnx += p->rail_x * offs;
+	p->cny += p->rail_y * offs;
+	p->clen = p->clen_for_centering + p->coffset + p->rail_z * offs;
 }
 
 
@@ -1076,10 +1054,8 @@ static void parse_toplevel(struct detector *det, struct beam_params *beam,
 
 	} else if ( strcmp(key, "photon_energy") == 0 ) {
 		if ( beam != NULL ) {
-
 			double v;
 			char *end;
-
 			v = strtod(val, &end);
 			if ( (val[0] != '\0') && (end[0] == '\0') ) {
 				beam->photon_energy = v;
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index 04e3c1ec..e9dd1154 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -224,9 +224,8 @@ extern void get_pixel_extents(struct detector *det,
                               double *min_x, double *min_y,
                               double *max_x, double *max_y);
 
-extern void fill_in_values(struct detector *det, struct hdfile *f,
-                           struct event* ev);
 extern void fill_in_adu(struct image *image);
+extern void adjust_centering_for_rail(struct panel *p);
 
 extern int panel_is_in_rigid_group(const struct rigid_group *rg,
                                    struct panel *p);
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index 9a52fd4d..dc86d641 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -1390,8 +1390,10 @@ int hdfile_get_value(struct hdfile *f, const char *name,
 }
 
 
-void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f,
-                             struct event *ev, struct image *image)
+static void hdfile_fill_in_beam_parameters(struct beam_params *beam,
+                                           struct hdfile *f,
+                                           struct event *ev,
+                                           struct image *image)
 {
 	double eV;
 
@@ -1404,8 +1406,8 @@ void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f,
 
 		int r;
 
-		r = hdfile_get_value(f, beam->photon_energy_from, ev, &eV,
-		                     H5T_NATIVE_DOUBLE);
+		r = hdfile_get_value(f, beam->photon_energy_from,
+		                     ev, &eV, H5T_NATIVE_DOUBLE);
 		if ( r ) {
 			ERROR("Failed to read '%s'\n",
 			      beam->photon_energy_from);
@@ -1417,6 +1419,36 @@ void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f,
 }
 
 
+static void hdfile_fill_in_clen(struct detector *det, struct hdfile *f,
+                                struct event *ev)
+{
+	int i;
+
+	for ( i=0; i<det->n_panels; i++ ) {
+
+		struct panel *p = &det->panels[i];
+
+		if ( p->clen_from != NULL ) {
+
+			double val;
+			int r;
+
+			r = hdfile_get_value(f, p->clen_from, ev, &val,
+			                     H5T_NATIVE_DOUBLE);
+			if ( r ) {
+				ERROR("Failed to read '%s'\n", p->clen_from);
+			} else {
+				p->clen = val * 1.0e-3;
+			}
+
+		}
+
+		adjust_centering_for_rail(p);
+
+	}
+}
+
+
 int hdf5_read(struct hdfile *f, struct image *image, const char *element,
               int satcorr)
 {
@@ -1481,7 +1513,7 @@ int hdf5_read(struct hdfile *f, struct image *image, const char *element,
 
 	if ( image->beam != NULL ) {
 
-		fill_in_beam_parameters(image->beam, f, NULL, image);
+		hdfile_fill_in_beam_parameters(image->beam, f, NULL, image);
 
 		if ( image->lambda > 1000 ) {
 			/* Error message covers a silly value in the beam file
@@ -1885,13 +1917,13 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev,
 
 	H5Dclose(f->dh);
 	f->data_open = 0;
-	fill_in_values(image->det, f, ev);
+	hdfile_fill_in_clen(image->det, f, ev);
 
 	if ( satcorr ) debodge_saturation(f, image);
 
 	if ( image->beam != NULL ) {
 
-		fill_in_beam_parameters(image->beam, f, ev, image);
+		hdfile_fill_in_beam_parameters(image->beam, f, ev, image);
 
 		if ( (image->lambda > 1.0) || (image->lambda < 1e-20) ) {
 
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index a8c278fc..849d95bf 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -521,6 +521,48 @@ static int unpack_panels(struct image *image, signed int *data, int data_width)
 }
 
 
+static void cbf_fill_in_beam_parameters(struct beam_params *beam,
+                                        struct imagefile *f,
+                                        struct image *image)
+{
+	double eV;
+
+	if ( beam->photon_energy_from == NULL ) {
+
+		/* Explicit value given */
+		eV = beam->photon_energy;
+
+	} else {
+
+		ERROR("Can't get photon energy from CBF yet.\n");
+		eV = 0.0;
+
+	}
+
+	image->lambda = ph_en_to_lambda(eV_to_J(eV))*beam->photon_energy_scale;
+}
+
+
+static void cbf_fill_in_clen(struct detector *det, struct imagefile *f)
+{
+	int i;
+
+	for ( i=0; i<det->n_panels; i++ ) {
+
+		struct panel *p = &det->panels[i];
+
+		if ( p->clen_from != NULL ) {
+
+			ERROR("Can't get clen from CBF yet.\n");
+
+		}
+
+		adjust_centering_for_rail(p);
+
+	}
+}
+
+
 static int read_cbf(struct imagefile *f, struct image *image)
 {
 	cbf_handle cbfh;
@@ -617,6 +659,17 @@ static int read_cbf(struct imagefile *f, struct image *image)
 	unpack_panels(image, data, dimfast);
 	free(data);
 
+	if ( image->beam != NULL ) {
+		cbf_fill_in_beam_parameters(image->beam, f, image);
+		if ( image->lambda > 1000 ) {
+			ERROR("WARNING: Missing or nonsensical wavelength "
+			      "(%e m) for %s.\n",
+			      image->lambda, image->filename);
+		}
+	}
+	cbf_fill_in_clen(image->det, f);
+	fill_in_adu(image);
+
 	cbf_free_handle(cbfh);
 	return 0;
 }