more user options for beam photon energy

libcrystfel/src/beam-parameters.c

@@ -8,6 +8,7 @@
  *
  * Authors:
  *   2010,2012 Thomas White <taw@physics.org>
+ *   2012      Chunhong Yoon
  *
  * This file is part of CrystFEL.
  *
@@ -35,6 +36,7 @@
 
 #include "beam-parameters.h"
 #include "utils.h"
+#include "hdf5-file.h"
 
 
 struct beam_params *get_beam_parameters(const char *filename)
@@ -86,7 +88,12 @@ struct beam_params *get_beam_parameters(const char *filename)
 		} else if ( strcmp(bits[0], "beam/radius") == 0 ) {
 			b->beam_radius = atof(bits[2]);
 		} else if ( strcmp(bits[0], "beam/photon_energy") == 0 ) {
-			b->photon_energy = atof(bits[2]);
+			if ( strncmp(bits[2], "/", 1) == 0 ) {
+				b->photon_energy = 0; // 0 means special case
+				b->photon_energy_from = strdup(bits[2]);	
+			} else {
+				b->photon_energy = atof(bits[2]);
+			}
 		} else if ( strcmp(bits[0], "beam/bandwidth") == 0 ) {
 			b->bandwidth = atof(bits[2]);
 		} else if ( strcmp(bits[0], "beam/divergence") == 0 ) {
@@ -113,7 +120,7 @@ struct beam_params *get_beam_parameters(const char *filename)
 		ERROR("Invalid or unspecified value for 'beam/radius'.\n");
 		reject = 1;
 	}
-	if ( b->photon_energy < 0.0 ) {
+	if ( b->photon_energy < 0.0 ) { // 0 is ok
 		ERROR("Invalid or unspecified value for"
 		      " 'beam/photon_energy'.\n");
 		reject = 1;
@@ -141,3 +148,12 @@ struct beam_params *get_beam_parameters(const char *filename)
 
 	return b;
 }
+
+void fill_in_beamParam(struct beam_params *beam, struct hdfile *f)
+{
+	if ( beam->photon_energy_from != NULL ) {
+		beam->photon_energy = get_value(f, beam->photon_energy_from );
+		free(beam->photon_energy_from);
+		beam->photon_energy_from = NULL;
+	}
+}

libcrystfel/src/beam-parameters.h

@@ -8,6 +8,7 @@
  *
  * Authors:
  *   2010,2012 Thomas White <taw@physics.org>
+ *   2012      Chunhong Yoon
  *
  * This file is part of CrystFEL.
  *
@@ -33,6 +34,7 @@
 #include <config.h>
 #endif
 
+#include "hdf5-file.h"
 
 struct beam_params
 {
@@ -46,10 +48,13 @@ struct beam_params
 	double divergence;     /* divergence (radians) */
 
 	double profile_radius; /* Reciprocal space size of a reflection */
+	
+	char *photon_energy_from; /* hdf5 group name */
 };
 
 
 extern struct beam_params *get_beam_parameters(const char *filename);
 
+extern void fill_in_beamParam(struct beam_params *beam, struct hdfile *f);
 
 #endif	/* BEAM_PARAMETERS_H */

src/im-sandbox.c

@@ -235,6 +235,11 @@ static void process_image(const struct index_args *iargs,
 		return;
 	}
 
+	if (beam->photon_energy == 0) { // read from existing hdf5
+		fill_in_beamParam(beam, hdfile);
+	}
+	image.lambda = ph_en_to_lambda(eV_to_J(beam->photon_energy));
+	
 	if ( image.lambda < 0.0 ) {
 		if ( beam != NULL ) {
 			ERROR("Using nominal photon energy of %.2f eV\n",

src/pattern_sim.c

@@ -498,7 +498,12 @@ int main(int argc, char *argv[])
 	/* Define image parameters */
 	image.width = image.det->max_fs + 1;
 	image.height = image.det->max_ss + 1;
-	image.lambda = ph_en_to_lambda(eV_to_J(image.beam->photon_energy));
+	if (image.beam->photon_energy == 0) {
+		ERROR("Invalid photon_energy format in beam file\n")
+		return 1;
+	} else {
+		image.lambda = ph_en_to_lambda(eV_to_J(image.beam->photon_energy));
+	}
 	image.bw = image.beam->bandwidth;
 	image.div = image.beam->divergence;