From 8e2f2f44f46c18f7bd621a2ef9a3d0aa813d76d9 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Mon, 20 Jan 2014 17:20:10 +0100
Subject: pattern_sim: Overhaul and add SASE spectrum simulation

---
 libcrystfel/src/hdf5-file.c | 61 +++++++++++++++++++++++++++++++++++++++++----
 libcrystfel/src/image.h     | 15 +++++++++++
 2 files changed, 71 insertions(+), 5 deletions(-)

(limited to 'libcrystfel/src')

diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index 95ceb9c1..ad9495b5 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -295,6 +295,8 @@ int hdf5_write_image(const char *filename, struct image *image)
 	herr_t r;
 	hsize_t size[2];
 	double lambda, eV;
+	double *arr;
+	int i;
 
 	fh = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
 	if ( fh < 0 ) {
@@ -362,11 +364,7 @@ int hdf5_write_image(const char *filename, struct image *image)
 	eV = ph_lambda_to_eV(image->lambda);
 	r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
 	             H5S_ALL, H5P_DEFAULT, &eV);
-	if ( r < 0 ) {
-		H5Dclose(dh);
-		H5Fclose(fh);
-		return 1;
-	}
+
 	H5Dclose(dh);
 
 	dh = H5Dcreate2(fh, "/LCLS/photon_wavelength_A", H5T_NATIVE_DOUBLE, sh,
@@ -383,6 +381,59 @@ int hdf5_write_image(const char *filename, struct image *image)
 		H5Fclose(fh);
 		return 1;
 	}
+
+	H5Dclose(dh);
+
+	arr = malloc(image->spectrum_size*sizeof(double));
+	if ( arr == NULL ) {
+		H5Fclose(fh);
+		return 1;
+	}
+	for ( i=0; i<image->spectrum_size; i++ ) {
+		arr[i] = 1.0e10/image->spectrum[i].k;
+	}
+
+	size[0] = image->spectrum_size;
+	sh = H5Screate_simple(1, size, NULL);
+
+	dh = H5Dcreate2(gh, "spectrum_wavelengths_A", H5T_NATIVE_DOUBLE, sh,
+	                H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
+	if ( dh < 0 ) {
+		H5Fclose(fh);
+		return 1;
+	}
+	r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
+	             H5S_ALL, H5P_DEFAULT, arr);
+	H5Dclose(dh);
+
+	for ( i=0; i<image->spectrum_size; i++ ) {
+		arr[i] = image->spectrum[i].weight;
+	}
+	dh = H5Dcreate2(gh, "spectrum_weights", H5T_NATIVE_DOUBLE, sh,
+	                H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
+	if ( dh < 0 ) {
+		H5Fclose(fh);
+		return 1;
+	}
+	r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
+	             H5S_ALL, H5P_DEFAULT, arr);
+
+	H5Dclose(dh);
+	free(arr);
+
+	size[0] = 1;
+	sh = H5Screate_simple(1, size, NULL);
+
+	dh = H5Dcreate2(gh, "number_of_samples", H5T_NATIVE_INT, sh,
+	                H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
+	if ( dh < 0 ) {
+		H5Fclose(fh);
+		return 1;
+	}
+
+	r = H5Dwrite(dh, H5T_NATIVE_INT, H5S_ALL,
+	             H5S_ALL, H5P_DEFAULT, &image->nsamples);
+
 	H5Dclose(dh);
 
 	H5Gclose(gh);
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index a1ac75a3..0c189cad 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -44,6 +44,10 @@
 #include "crystal.h"
 #include "index.h"
 
+typedef enum {
+	SPECTRUM_TOPHAT,
+	SPECTRUM_SASE
+} SpectrumType;
 
 /* Structure describing a feature in an image */
 struct imagefeature {
@@ -67,6 +71,13 @@ struct imagefeature {
 /* An opaque type representing a list of image features */
 typedef struct _imagefeaturelist ImageFeatureList;
 
+/* Structure describing a wavelength sample from a spectrum */
+struct sample
+{
+	double k;
+	double weight;
+};
+
 
 /**
  * image:
@@ -144,6 +155,10 @@ struct image {
 	int                     id;   /* ID number of the thread
 	                               * handling this image */
 
+	struct sample           *spectrum;
+	int                     nsamples; /* Number of wavelengths */
+	int                     spectrum_size;  /* Size of "spectrum" */
+
 	/* Per-shot radiation values */
 	double                  lambda;        /* Wavelength in m */
 	double                  div;           /* Divergence in radians */
-- 
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