Use ADU per eV in geometry file, rather than ADU per photon in beam file

Conflicts:

	src/get_hkl.c
	tests/morphology_check.c

17 files changed, 43 insertions, 61 deletions

diff --git a/doc/examples/cspad-feb2011.geom b/doc/examples/cspad-feb2011.geom
index 7eaedda0..9ef79077 100644
--- a/doc/examples/cspad-feb2011.geom
+++ b/doc/examples/cspad-feb2011.geom
@@ -1,3 +1,5 @@
+adu_per_eV = 1.0
+
 q0a0/min_fs =    0
 q0a0/min_ss =    0
 q0a0/max_fs =  193
diff --git a/doc/examples/lcls-cxi-9keV.beam b/doc/examples/lcls-cxi-9keV.beam
index fb1f94bb..bf4a32bd 100644
--- a/doc/examples/lcls-cxi-9keV.beam
+++ b/doc/examples/lcls-cxi-9keV.beam
@@ -14,10 +14,3 @@ beam/bandwidth = 0.001
 
 ; Beam divergence in radians
 beam/divergence = 0.008
-
-
-; Detector's quantum efficiency
-detector/dqe = 1.0
-
-; Number of detector ADU per photon
-detector/adu_per_photon = 1.0
diff --git a/doc/examples/lcls-dec.beam b/doc/examples/lcls-dec.beam
index b52f30e1..f277b729 100644
--- a/doc/examples/lcls-dec.beam
+++ b/doc/examples/lcls-dec.beam
@@ -14,10 +14,3 @@ beam/bandwidth = 0.001
 
 ; Beam divergence in radians
 beam/divergence = 0.001
-
-
-; Detector's quantum efficiency
-detector/dqe = 0.9
-
-; Number of detector ADU per photon
-detector/adu_per_photon = 167.0
diff --git a/doc/examples/lcls-dec.geom b/doc/examples/lcls-dec.geom
index f98b42fd..ef6bcbb7 100644
--- a/doc/examples/lcls-dec.geom
+++ b/doc/examples/lcls-dec.geom
@@ -5,6 +5,7 @@ mask_bad = 0x00
 ; These default values will be used unless overridden by the per-panel values
 peak_sep = 50.0
 integr_radius = 10.0
+adu_per_eV = 0.0835
 
 upper/min_fs = 0
 upper/max_fs = 1023
diff --git a/doc/examples/lcls-june-r0013-r0128.geom b/doc/examples/lcls-june-r0013-r0128.geom
index 7e4be71c..ff1fab87 100644
--- a/doc/examples/lcls-june-r0013-r0128.geom
+++ b/doc/examples/lcls-june-r0013-r0128.geom
@@ -5,6 +5,7 @@ mask_bad = 0x00
 ; These default values will be used unless overridden by the per-panel values
 peak_sep = 50.0
 integr_radius = 10.0
+adu_per_eV = 0.01045
 
 ; Upper panel (nearest the beam)
 0/min_fs = 0
diff --git a/doc/examples/lcls-june.beam b/doc/examples/lcls-june.beam
index 8a263024..30f05813 100644
--- a/doc/examples/lcls-june.beam
+++ b/doc/examples/lcls-june.beam
@@ -14,10 +14,3 @@ beam/bandwidth = 0.01
 
 ; Beam divergence in radians
 beam/divergence = 0.0087
-
-
-; Detector's quantum efficiency
-detector/dqe = 0.9
-
-; Number of detector ADU per photon
-detector/adu_per_photon = 20.9
diff --git a/doc/examples/lcls-xpp-estimate.beam b/doc/examples/lcls-xpp-estimate.beam
index af9bb6ec..23ad560d 100644
--- a/doc/examples/lcls-xpp-estimate.beam
+++ b/doc/examples/lcls-xpp-estimate.beam
@@ -14,10 +14,3 @@ beam/bandwidth = 0.001
 
 ; Beam divergence in radians
 beam/divergence = 0.001
-
-
-; Detector's quantum efficiency
-detector/dqe = 1.0
-
-; Number of detector ADU per photon
-detector/adu_per_photon = 1.0
diff --git a/doc/examples/lcls-xpp-estimate.geom b/doc/examples/lcls-xpp-estimate.geom
index c64c985a..7c4d21a8 100644
--- a/doc/examples/lcls-xpp-estimate.geom
+++ b/doc/examples/lcls-xpp-estimate.geom
@@ -10,3 +10,4 @@
 0/res = 9090  ; 110 micron pixel size
 0/badrow_direction = x
 0/peak_sep = 4
+0/adu_per_eV = 1.0
diff --git a/doc/examples/simple.geom b/doc/examples/simple.geom
index 62ee53db..65769883 100644
--- a/doc/examples/simple.geom
+++ b/doc/examples/simple.geom
@@ -1,3 +1,5 @@
+adu_per_eV = 1.0
+
 ; Upper panel
 0/min_fs = 0
 0/max_fs = 1023
diff --git a/libcrystfel/src/beam-parameters.c b/libcrystfel/src/beam-parameters.c
index 082e9651..654d7550 100644
--- a/libcrystfel/src/beam-parameters.c
+++ b/libcrystfel/src/beam-parameters.c
@@ -51,8 +51,6 @@ struct beam_params *get_beam_parameters(const char *filename)
 	b->photon_energy = -1.0;
 	b->bandwidth = -1.0;
 	b->divergence = -1.0;
-	b->dqe = -1.0;
-	b->adu_per_photon = -1.0;
 
 	do {
 
@@ -88,10 +86,6 @@ struct beam_params *get_beam_parameters(const char *filename)
 			b->bandwidth = atof(bits[2]);
 		} else if ( strcmp(bits[0], "beam/divergence") == 0 ) {
 			b->divergence = atof(bits[2]);
-		} else if ( strcmp(bits[0], "detector/dqe") == 0 ) {
-			b->dqe = atof(bits[2]);
-		} else if ( strcmp(bits[0], "detector/adu_per_photon") == 0 ) {
-			b->adu_per_photon = atof(bits[2]);
 		} else {
 			ERROR("Unrecognised field '%s'\n", bits[0]);
 		}
@@ -125,15 +119,6 @@ struct beam_params *get_beam_parameters(const char *filename)
 		ERROR("Invalid or unspecified value for 'beam/divergence'.\n");
 		reject = 1;
 	}
-	if ( b->dqe < 0.0 ) {
-		ERROR("Invalid or unspecified value for 'detector/dqe'.\n");
-		reject = 1;
-	}
-	if ( b->adu_per_photon < 0.0 ) {
-		ERROR("Invalid or unspecified value for"
-		      " 'detector/adu_per_photon'.\n");
-		reject = 1;
-	}
 
 	if ( reject ) {
 		ERROR("Please fix the above problems with the beam"
diff --git a/libcrystfel/src/beam-parameters.h b/libcrystfel/src/beam-parameters.h
index 6f5d8a75..2cf1bf39 100644
--- a/libcrystfel/src/beam-parameters.h
+++ b/libcrystfel/src/beam-parameters.h
@@ -40,9 +40,6 @@ struct beam_params
 	                        *        a rectangular distribution with this as
 	                        *        its (full) width. */
 	double divergence;     /* divergence (radians) */
-
-	double dqe;            /* Detector DQE (fraction) */
-	double adu_per_photon; /* Detector "gain" */
 };
 
 
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index ee09eb73..6c4dcbb6 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -365,15 +365,14 @@ void record_image(struct image *image, int do_poisson)
 		sa = proj_area / (dsq + Lsq);
 
 		if ( do_poisson ) {
-			counts = poisson_noise(intensity * ph_per_e
-			                              * sa * image->beam->dqe );
+			counts = poisson_noise(intensity * ph_per_e * sa);
 		} else {
-			cf = intensity * ph_per_e * sa * image->beam->dqe;
+			cf = intensity * ph_per_e * sa;
 			counts = cf;
 		}
 
-		image->data[x + image->width*y] = counts
-		                                  * image->beam->adu_per_photon;
+		image->data[x + image->width*y] = counts * p->adu_per_eV
+		                               * ph_lambda_to_eV(image->lambda);
 
 		/* Sanity checks */
 		if ( isinf(image->data[x+image->width*y]) ) n_inf2++;
@@ -577,6 +576,8 @@ static int parse_field_for_panel(struct panel *panel, const char *key,
 		panel->cnx = atof(val);
 	} else if ( strcmp(key, "corner_y") == 0 ) {
 		panel->cny = atof(val);
+	} else if ( strcmp(key, "adu_per_eV") == 0 ) {
+		panel->adu_per_eV = atof(val);
 	} else if ( strcmp(key, "rigid_group") == 0 ) {
 		panel->rigid_group = find_or_add_rg(det, val);
 	} else if ( strcmp(key, "clen") == 0 ) {
@@ -737,6 +738,7 @@ struct detector *get_detector_geometry(const char *filename)
 	det->defaults.ssx = 0.0;
 	det->defaults.ssy = 1.0;
 	det->defaults.rigid_group = NULL;
+	det->defaults.adu_per_eV = NAN;
 	strncpy(det->defaults.name, "", 1023);
 
 	do {
@@ -871,6 +873,11 @@ struct detector *get_detector_geometry(const char *filename)
 			      " panel %s\n", det->panels[i].name);
 			reject = 1;
 		}
+		if ( isnan(det->panels[i].adu_per_eV) ) {
+			ERROR("Please specify the number of ADU per eV for"
+			      " panel %s\n", det->panels[i].name);
+			reject = 1;
+		}
 		/* It's OK if the badrow direction is '0' */
 		/* It's not a problem if "no_index" is still zero */
 		/* The default peak_sep is OK (maybe) */
@@ -1242,6 +1249,7 @@ int write_detector_geometry(const char *filename, struct detector *det)
 		fprintf(fh, "%s/ss = %+fx %+fy\n", p->name, p->ssx, p->ssy);
 		fprintf(fh, "%s/corner_x = %g\n", p->name, p->cnx);
 		fprintf(fh, "%s/corner_y = %g\n", p->name, p->cny);
+		fprintf(fh, "%s/adu_per_eV = %g\n", p->name, p->adu_per_eV);
 
 		if ( p->no_index ) {
 			fprintf(fh, "%s/no_index = 1\n", p->name);
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index 53aca93d..b3743935 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -59,6 +59,7 @@ struct panel
 	double   peak_sep; /* Characteristic peak separation */
 	double   integr_radius;  /* Peak integration radius */
 	char    *rigid_group;  /* Rigid group, or -1 for none */
+	double   adu_per_eV;   /* Number of ADU per eV */
 
 	double fsx;
 	double fsy;
diff --git a/libcrystfel/src/utils.h b/libcrystfel/src/utils.h
index 8d5ee479..8c11abd6 100644
--- a/libcrystfel/src/utils.h
+++ b/libcrystfel/src/utils.h
@@ -186,6 +186,12 @@ static inline int within_tolerance(double a, double b, double percent)
 /* Joules to eV */
 #define J_to_eV(a) ((a)/ELECTRON_CHARGE)
 
+/* Photon wavelength (m) to energy (eV) */
+#define ph_lambda_to_eV(a) J_to_eV(ph_lambda_to_en(a))
+
+/* Photon energy (eV) to wavelength (m) */
+#define ph_eV_to_lambda(a) ph_en_to_lambda(eV_to_J(a))
+
 #define UNUSED __attribute__((unused))
 
 
diff --git a/src/get_hkl.c b/src/get_hkl.c
index 905da569..cec55495 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -56,7 +56,7 @@ static void show_help(const char *s)
 "      --noise                Add 10%% random noise.\n"
 "\n"
 "To calculate Poisson samples accurately, you must also give:\n"
-"  -b, --beam=<file>          Get beam parameters from file.\n"
+"      --adu-per-photon=<n>   Number of ADU per photon.\n"
 "\n"
 "You can artificially 'twin' the reflections, or expand them out.\n"
 "  -w, --twin=<sym>           Generate twinned data according to the given\n"
@@ -362,6 +362,8 @@ int main(int argc, char *argv[])
 	char *beamfile = NULL;
 	struct beam_params *beam = NULL;
 	RefList *input;
+	double adu_per_photon = 0.0;
+	int have_adu_per_photon = 0;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -375,8 +377,8 @@ int main(int argc, char *argv[])
 		{"expand",             1, NULL,               'e'},
 		{"intensities",        1, NULL,               'i'},
 		{"multiplicity",       0, &config_multi,       1},
-		{"beam",               1, NULL,               'b'},
 		{"trim-centrics",      0, &config_trimc,       1},
+		{"adu-per-photon",     1, NULL,                2},
 		{0, 0, NULL, 0}
 	};
 
@@ -413,8 +415,9 @@ int main(int argc, char *argv[])
 			expand_str = strdup(optarg);
 			break;
 
-		case 'b' :
-			beamfile = strdup(optarg);
+		case 2 :
+			adu_per_photon = strtof(optarg, NULL);
+			have_adu_per_photon = 1;
 			break;
 
 		case 0 :
@@ -476,11 +479,11 @@ int main(int argc, char *argv[])
 	}
 
 	if ( config_poisson ) {
-		if ( beam != NULL ) {
-			poisson_reflections(input, beam->adu_per_photon);
+		if ( have_adu_per_photon ) {
+			poisson_reflections(input, adu_per_photon);
 		} else {
-			ERROR("You must give a beam parameters file in order"
-			      " to calculate Poisson noise.\n");
+			ERROR("You must give the number of ADU per photon to "
+			      "use --poisson.\n");
 			return 1;
 		}
 	}
diff --git a/tests/gpu_sim_check.c b/tests/gpu_sim_check.c
index 4557b551..5b6f6da7 100644
--- a/tests/gpu_sim_check.c
+++ b/tests/gpu_sim_check.c
@@ -115,6 +115,7 @@ int main(int argc, char *argv[])
 	det->panels[0].cny = -512.0-sep;
 	det->panels[0].clen = 100.0e-3;
 	det->panels[0].res = 9090.91;
+	det->panels[0].adu_per_eV = 1.0;
 
 	det->panels[1].min_fs = 0;
 	det->panels[1].max_fs = 1023;
@@ -132,6 +133,7 @@ int main(int argc, char *argv[])
 	det->panels[1].cny = sep;
 	det->panels[1].clen = 100.0e-3;
 	det->panels[1].res = 9090.91;
+	det->panels[0].adu_per_eV = 1.0;
 
 	cpu_image.det = det;
 	gpu_image.det = det;
@@ -142,8 +144,6 @@ int main(int argc, char *argv[])
 	beam->photon_energy = 9000.0;
 	beam->bandwidth = 0.1 / 100.0;
 	beam->divergence = 0.0;
-	beam->dqe = 1.0;
-	beam->adu_per_photon = 1.0;
 	cpu_image.beam = beam;
 	gpu_image.beam = beam;
 
diff --git a/tests/integration_check.c b/tests/integration_check.c
index 1e439611..80a214d1 100644
--- a/tests/integration_check.c
+++ b/tests/integration_check.c
@@ -291,6 +291,8 @@ int main(int argc, char *argv[])
 
 	image.data = malloc(128*128*sizeof(float));
 	image.flags = NULL;
+	image.beam = NULL;
+	image.lambda = ph_eV_to_lambda(1000.0);
 
 	image.det = calloc(1, sizeof(struct detector));
 	image.det->n_panels = 1;
@@ -313,6 +315,7 @@ int main(int argc, char *argv[])
 	image.det->panels[0].clen = 1.0;
 	image.det->panels[0].res = 1.0;
 	image.det->panels[0].integr_radius = 10.0;
+	image.det->panels[0].adu_per_eV = 1.0;
 
 	image.width = 128;
 	image.height = 128;