Beam file removal, part I

1 files changed, 78 insertions, 32 deletions

diff --git a/src/partial_sim.c b/src/partial_sim.c
index 47d8766e..32c5bb01 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -47,7 +47,6 @@
 #include "utils.h"
 #include "reflist-utils.h"
 #include "symmetry.h"
-#include "beam-parameters.h"
 #include "geometry.h"
 #include "stream.h"
 #include "thread-pool.h"
@@ -225,7 +224,6 @@ static void show_help(const char *s)
 " -o, --output=<file>      Write partials in stream format to <file>.\n"
 "     --images=<prefix>    Write images to <prefix>NNN.h5.\n"
 " -g. --geometry=<file>    Get detector geometry from file.\n"
-" -b, --beam=<file>        Get beam parameters from file\n"
 " -p, --pdb=<file>         PDB file from which to get the unit cell.\n"
 "\n"
 " -y, --symmetry=<sym>     Symmetry of the input reflection list.\n"
@@ -238,6 +236,11 @@ static void show_help(const char *s)
 "                           generated full intensities, if not using -i.\n"
 "     --noise-stddev=<val> Set the standard deviation of the noise.\n"
 "     --background=<val>   Background level in photons.  Default 3000.\n"
+"     --beam-divergence    Beam divergence in radians. Default 1 mrad.\n"
+"     --beam-bandwidth     Beam bandwidth as a fraction. Default 1%%.\n"
+"     --profile-radius     Reciprocal space reflection profile radius in m^-1.\n"
+"                           Default 0.001e9 m^-1\n"
+"     --photon-energy      Photon energy in eV.  Default 9000.\n"
 "\n"
 );
 }
@@ -411,11 +414,10 @@ int main(int argc, char *argv[])
 	int c;
 	char *input_file = NULL;
 	char *output_file = NULL;
-	char *beamfile = NULL;
 	char *geomfile = NULL;
 	char *cellfile = NULL;
 	struct detector *det = NULL;
-	struct beam_params *beam = NULL;
+	struct beam_params beam;
 	RefList *full = NULL;
 	char *sym_str = NULL;
 	SymOpList *sym;
@@ -440,13 +442,23 @@ int main(int argc, char *argv[])
 	int config_random = 0;
 	char *image_prefix = NULL;
 
+	/* Default beam parameters */
+	beam.divergence = 0.001;
+	beam.bandwidth = 0.01;
+	beam.profile_radius = 0.001e9;
+	beam.photon_energy = 9000.0;
+
+	/* Beam parameters which it doesn't make sense to use here */
+	beam.fluence = -1.0;
+	beam.beam_radius = -1.0;
+	beam.photon_energy_scale = 1.0;
+
 	/* Long options */
 	const struct option longopts[] = {
 		{"help",               0, NULL,               'h'},
-		{"version",            0, NULL,                8 },
+		{"version",            0, NULL,               'v'},
 		{"output",             1, NULL,               'o'},
 		{"input",              1, NULL,               'i'},
-		{"beam",               1, NULL,               'b'},
 		{"pdb",                1, NULL,               'p'},
 		{"geometry",           1, NULL,               'g'},
 		{"symmetry",           1, NULL,               'y'},
@@ -459,6 +471,10 @@ int main(int argc, char *argv[])
 		{"noise-stddev",       1, NULL,                5},
 		{"images",             1, NULL,                6},
 		{"background",         1, NULL,                7},
+		{"beam-divergence",    1, NULL,                8},
+		{"beam-bandwidth",     1, NULL,                9},
+		{"profile-radius",     1, NULL,               10},
+		{"photon-energy",      1, NULL,               11},
 
 		{"really-random",      0, &config_random,      1},
 
@@ -466,7 +482,7 @@ int main(int argc, char *argv[])
 	};
 
 	/* Short options */
-	while ((c = getopt_long(argc, argv, "hi:o:b:p:g:y:n:r:j:c:",
+	while ((c = getopt_long(argc, argv, "hi:o:p:g:y:n:r:j:c:v",
 	                        longopts, NULL)) != -1)
 	{
 		switch (c) {
@@ -475,7 +491,7 @@ int main(int argc, char *argv[])
 			show_help(argv[0]);
 			return 0;
 
-			case 8 :
+			case 'v' :
 			printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n");
 			printf(CRYSTFEL_BOILERPLATE"\n");
 			return 0;
@@ -488,10 +504,6 @@ int main(int argc, char *argv[])
 			output_file = strdup(optarg);
 			break;
 
-			case 'b' :
-			beamfile = strdup(optarg);
-			break;
-
 			case 'p' :
 			cellfile = strdup(optarg);
 			break;
@@ -578,8 +590,55 @@ int main(int argc, char *argv[])
 				return 1;
 			}
 			if ( background < 0.0 ) {
-				ERROR("Invalid background level.");
-				ERROR(" (must be positive).\n");
+				ERROR("Background level must be positive.\n");
+				return 1;
+			}
+			break;
+
+			case 8 :
+			beam.divergence = strtod(optarg, &rval);
+			if ( *rval != '\0' ) {
+				ERROR("Invalid beam divergence.\n");
+				return 1;
+			}
+			if ( beam.divergence < 0.0 ) {
+				ERROR("Beam divergence must be positive.\n");
+				return 1;
+			}
+			break;
+
+			case 9 :
+			beam.bandwidth = strtod(optarg, &rval);
+			if ( *rval != '\0' ) {
+				ERROR("Invalid beam bandwidth.\n");
+				return 1;
+			}
+			if ( beam.bandwidth < 0.0 ) {
+				ERROR("Beam bandwidth must be positive.\n");
+				return 1;
+			}
+			break;
+
+			case 10 :
+			beam.profile_radius = strtod(optarg, &rval);
+			if ( *rval != '\0' ) {
+				ERROR("Invalid profile radius.\n");
+				return 1;
+			}
+			if ( beam.divergence < 0.0 ) {
+				ERROR("Profile radius must be positive.\n");
+				return 1;
+			}
+			break;
+
+			case 11 :
+			beam.photon_energy = strtod(optarg, &rval);
+			if ( *rval != '\0' ) {
+				ERROR("Invalid photon energy.\n");
+				return 1;
+			}
+			if ( beam.photon_energy < 0.0 ) {
+				ERROR("Photon energy must be positive.\n");
 				return 1;
 			}
 			break;
@@ -607,18 +666,6 @@ int main(int argc, char *argv[])
 		return 1;
 	}
 
-	/* Load beam */
-	if ( beamfile == NULL ) {
-		ERROR("You need to provide a beam parameters file.\n");
-		return 1;
-	}
-	beam = get_beam_parameters(beamfile);
-	if ( beam == NULL ) {
-		ERROR("Failed to load beam parameters from '%s'\n", beamfile);
-		return 1;
-	}
-	free(beamfile);
-
 	/* Load cell */
 	if ( cellfile == NULL ) {
 		ERROR("You need to give a PDB file with the unit cell.\n");
@@ -642,7 +689,7 @@ int main(int argc, char *argv[])
 		ERROR("You need to give a geometry file.\n");
 		return 1;
 	}
-	det = get_detector_geometry(geomfile);
+	det = get_detector_geometry(geomfile, &beam);
 	if ( det == NULL ) {
 		ERROR("Failed to read geometry from '%s'\n", geomfile);
 		return 1;
@@ -700,10 +747,10 @@ int main(int argc, char *argv[])
 	image.width = det->max_fs + 1;
 	image.height = det->max_ss + 1;
 
-	image.lambda = ph_en_to_lambda(eV_to_J(beam->photon_energy));
-	image.div = beam->divergence;
-	image.bw = beam->bandwidth;
-	image.beam = beam;
+	image.lambda = ph_en_to_lambda(eV_to_J(beam.photon_energy));
+	image.div = beam.divergence;
+	image.bw = beam.bandwidth;
+	image.beam = &beam;
 	image.filename = "dummy.h5";
 	image.copyme = NULL;
 	image.crystals = NULL;
@@ -842,7 +889,6 @@ int main(int argc, char *argv[])
 	close_stream(stream);
 	cell_free(cell);
 	free_detector_geometry(det);
-	free(beam);
 	free_symoplist(sym);
 	reflist_free(full);
 	free(save_file);