First bit of Crystal

4 files changed, 160 insertions, 29 deletions

diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index 1c35e03f..da7e8f64 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -8,7 +8,7 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
                          src/symmetry.c src/stream.c src/peaks.c \
                          src/reflist-utils.c src/filters.c \
                          src/render.c src/index.c src/dirax.c src/mosflm.c \
-                         src/cell-utils.c src/integer_matrix.c
+                         src/cell-utils.c src/integer_matrix.c src/crystal.c
 
 if HAVE_FFTW
 libcrystfel_la_SOURCES += src/reax.c
@@ -24,7 +24,7 @@ libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
                                  src/render.h src/index.h src/image.h \
                                  src/filters.h src/dirax.h src/mosflm.h \
                                  src/index-priv.h src/reax.h src/cell-utils.h \
-                                 src/integer_matrix.h
+                                 src/integer_matrix.h src/crystal.h
 
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -Wall
 AM_CPPFLAGS += -I$(top_srcdir)/lib @LIBCRYSTFEL_CFLAGS@
diff --git a/libcrystfel/src/crystal.c b/libcrystfel/src/crystal.c
new file mode 100644
index 00000000..85430b6f
--- /dev/null
+++ b/libcrystfel/src/crystal.c
@@ -0,0 +1,104 @@
+/*
+ * crystal.c
+ *
+ * A class representing a single crystal
+ *
+ * Copyright © 2013 Deutsches Elektronen-Synchrotron DESY,
+ *                  a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ *   2013 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "crystal.h"
+#include "utils.h"
+
+
+/**
+ * SECTION:crystal
+ * @short_description: Crystal
+ * @title: Crystal
+ * @section_id:
+ * @see_also:
+ * @include: "crystal.h"
+ * @Image:
+ *
+ * This structure represents a single crystal.
+ */
+
+
+struct _crystal
+{
+	/* Information about the crystal */
+	UnitCell                *indexed_cell;
+	UnitCell                *candidate_cells[MAX_CELL_CANDIDATES];
+	int                     ncells;
+	double                  m;  /* Mosaicity in radians */
+	double                  osf;
+	double                  profile_radius;
+	int                     pr_dud;
+	double                  diffracting_resolution;
+
+	/* Integrated (or about-to-be-integrated) reflections */
+	RefList                 *reflections;
+	long long int           n_saturated;  /* Number of overloads */
+};
+
+
+/************************** Setters and Constructors **************************/
+
+
+/**
+ * crystal_new:
+ *
+ * Create a new %Crystal.
+ *
+ * Returns: the new unit cell, or NULL on failure.
+ *
+ */
+Crystal *crystal_new()
+{
+	Crystal *cryst;
+
+	cryst = malloc(sizeof(Crystal));
+	if ( cryst == NULL ) return NULL;
+
+	return cryst;
+}
+
+
+/**
+ * crystal_free:
+ * @cryst: A %Crystal to free.
+ *
+ * Frees a %Crystal, and all internal resources concerning that crystal.
+ *
+ */
+void crystal_free(UnitCell *cryst)
+{
+	if ( cryst == NULL ) return;
+	free(crysta);
+}
+
+
+/********************************** Getters ***********************************/
diff --git a/libcrystfel/src/crystal.h b/libcrystfel/src/crystal.h
new file mode 100644
index 00000000..4f53eead
--- /dev/null
+++ b/libcrystfel/src/crystal.h
@@ -0,0 +1,48 @@
+/*
+ * crystal.h
+ *
+ * A class representing a single crystal
+ *
+ * Copyright © 2013 Deutsches Elektronen-Synchrotron DESY,
+ *                  a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ *   2013 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifndef CRYSTAL_H
+#define CRYSTAL_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+/**
+ * Crystal:
+ *
+ * This data structure is opaque.  You must use the available accessor functions
+ * to read and write its contents.
+ **/
+typedef struct _crystal Crystal;
+
+
+extern Crystal *crystal_new(void);
+extern void crystal_free(Crystal *cryst);
+
+#endif	/* CRYSTAL_H */
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index afa9e4a7..bd90a920 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -41,6 +41,7 @@
 #include "cell.h"
 #include "detector.h"
 #include "reflist.h"
+#include "crystal.h"
 
 
 #define MAX_CELL_CANDIDATES (32)
@@ -79,10 +80,9 @@ typedef struct _imagefeaturelist ImageFeatureList;
  *    uint16_t                *flags;
  *    double                  *twotheta;
  *
- *    UnitCell                *indexed_cell;
- *    UnitCell                *candidate_cells[MAX_CELL_CANDIDATES];
- *    int                     ncells;
-
+ *    Crystal                 **crystals;
+ *    int                     n_crystals;
+ *
  *    struct detector         *det;
  *    struct beam_params      *beam;
  *    char                    *filename;
@@ -90,22 +90,13 @@ typedef struct _imagefeaturelist ImageFeatureList;
  *
  *    int                     id;
  *
- *    double                  m;
- *
  *    double                  lambda;
  *    double                  div;
  *    double                  bw;
- *    double                  osf;
- *    double                  profile_radius;
- *    int                     pr_dud;
- *    double                  diffracting_resolution;
  *
  *    int                     width;
  *    int                     height;
  *
- *    RefList                 *reflections;
- *    long long unsigned int  n_saturated;
- *
  *    ImageFeatureList        *features;
  * };
  * </programlisting>
@@ -141,9 +132,8 @@ struct image {
 	uint16_t                *flags;
 	double                  *twotheta;
 
-	UnitCell                *indexed_cell;
-	UnitCell                *candidate_cells[MAX_CELL_CANDIDATES];
-	int                     ncells;
+	struct crystal          **crystals;
+	int                     n_crystals;
 
 	struct detector         *det;
 	struct beam_params      *beam;  /* The nominal beam parameters */
@@ -153,25 +143,14 @@ struct image {
 	int                     id;   /* ID number of the thread
 	                               * handling this image */
 
-	/* Information about the crystal */
-	double                  m;  /* Mosaicity in radians */
-
 	/* Per-shot radiation values */
 	double                  lambda;        /* Wavelength in m */
 	double                  div;           /* Divergence in radians */
 	double                  bw;            /* Bandwidth as a fraction */
-	double                  osf;           /* Overall scaling factor */
-	double                  profile_radius; /* Radius of reflection */
-	int                     pr_dud;        /* Post refinement failed */
-	double                  diffracting_resolution;  /* Max 1/d in m^-1 */
 
 	int                     width;
 	int                     height;
 
-	/* Integrated (or about-to-be-integrated) reflections */
-	RefList                 *reflections;
-	long long int           n_saturated;  /* Number of overloads */
-
 	/* Detected peaks */
 	ImageFeatureList        *features;