Move unit cell utility stuff to separate module

libcrystfel/Makefile.am

@@ -7,7 +7,8 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
                          src/beam-parameters.c src/geometry.c src/statistics.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/render.c src/index.c src/dirax.c src/mosflm.c \
+                         src/cell-utils.c
 
 if HAVE_FFTW
 libcrystfel_la_SOURCES += src/reax.c
@@ -22,7 +23,7 @@ libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
                                  src/geometry.h src/peaks.h src/stream.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/index-priv.h src/reax.h src/cell-utils.h
 
 INCLUDES = "-I$(top_srcdir)/data"
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -Wall

libcrystfel/src/cell-utils.h

+/*
+ * cell-utils.h
+ *
+ * Unit Cell utility functions
+ *
+ * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
+ *                  a research centre of the Helmholtz Association.
+ * Copyright © 2012 Lorenzo Galli
+ *
+ * Authors:
+ *   2009-2012 Thomas White <taw@physics.org>
+ *   2012      Lorenzo Galli
+ *
+ * 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 CELL_UTILS_H
+#define CELL_UTILS_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+extern double resolution(UnitCell *cell,
+                         signed int h, signed int k, signed int l);
+
+extern UnitCell *cell_rotate(UnitCell *in, struct quaternion quat);
+extern UnitCell *rotate_cell(UnitCell *in, double omega, double phi,
+                             double rot);
+
+extern void cell_print(UnitCell *cell);
+
+extern UnitCell *match_cell(UnitCell *cell, UnitCell *tempcell, int verbose,
+                            const float *ltl, int reduce);
+
+extern UnitCell *match_cell_ab(UnitCell *cell, UnitCell *tempcell);
+
+extern UnitCell *load_cell_from_pdb(const char *filename);
+
+extern int cell_is_sensible(UnitCell *cell);
+
+extern void validate_cell(UnitCell *cell);
+
+#endif	/* CELL_UTILS_H */

libcrystfel/src/cell.h

 /*
  * cell.h
  *
- * Unit Cell Calculations
+ * A class representing a unit cell
  *
  * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
  *                  a research centre of the Helmholtz Association.
@@ -128,24 +128,6 @@ extern void cell_set_centering(UnitCell *cell, char centering);
 extern char cell_get_unique_axis(UnitCell *cell);
 extern void cell_set_unique_axis(UnitCell *cell, char unique_axis);
 
-extern double resolution(UnitCell *cell,
-                         signed int h, signed int k, signed int l);
-
-extern UnitCell *cell_rotate(UnitCell *in, struct quaternion quat);
-extern UnitCell *rotate_cell(UnitCell *in, double omega, double phi,
-                             double rot);
-
-extern void cell_print(UnitCell *cell);
-
-extern UnitCell *match_cell(UnitCell *cell, UnitCell *tempcell, int verbose,
-                            const float *ltl, int reduce);
-
-extern UnitCell *match_cell_ab(UnitCell *cell, UnitCell *tempcell);
-
-extern UnitCell *load_cell_from_pdb(const char *filename);
-
-extern int cell_is_sensible(UnitCell *cell);
-
-extern void validate_cell(UnitCell *cell);
+extern const char *cell_rep(UnitCell *cell);
 
 #endif	/* CELL_H */

libcrystfel/src/geometry.c

@@ -36,6 +36,7 @@
 
 #include "utils.h"
 #include "cell.h"
+#include "cell-utils.h"
 #include "image.h"
 #include "peaks.h"
 #include "beam-parameters.h"

libcrystfel/src/index.c

@@ -49,6 +49,7 @@
 #include "index-priv.h"
 #include "reax.h"
 #include "geometry.h"
+#include "cell-utils.h"
 
 
 /* Base class constructor for unspecialised indexing private data */

libcrystfel/src/peaks.c

@@ -51,6 +51,7 @@
 #include "filters.h"
 #include "reflist-utils.h"
 #include "beam-parameters.h"
+#include "cell-utils.h"
 
 
 /* Degree of polarisation of X-ray beam */

libcrystfel/src/reax.c

@@ -47,6 +47,7 @@
 #include "utils.h"
 #include "peaks.h"
 #include "cell.h"
+#include "cell-utils.h"
 #include "index.h"
 #include "index-priv.h"
 

libcrystfel/src/reflist-utils.c

@@ -35,6 +35,7 @@
 
 #include "reflist.h"
 #include "cell.h"
+#include "cell-utils.h"
 #include "utils.h"
 #include "reflist-utils.h"
 #include "symmetry.h"

src/check_hkl.c

@@ -43,6 +43,7 @@
 #include "symmetry.h"
 #include "reflist.h"
 #include "reflist-utils.h"
+#include "cell-utils.h"
 
 
 /* Number of bins for plot of resolution shells */

src/compare_hkl.c

@@ -44,6 +44,7 @@
 #include "statistics.h"
 #include "symmetry.h"
 #include "reflist-utils.h"
+#include "cell-utils.h"
 
 
 /* Number of bins for plot of resolution shells */

src/indexamajig.c

@@ -62,6 +62,7 @@
 #include "geometry.h"
 #include "stream.h"
 #include "reflist-utils.h"
+#include "cell-utils.h"
 
 #include "im-sandbox.h"
 

src/partial_sim.c

@@ -40,14 +40,15 @@
 #include <assert.h>
 #include <pthread.h>
 
-#include <utils.h>
-#include <reflist-utils.h>
-#include <symmetry.h>
-#include <beam-parameters.h>
-#include <detector.h>
-#include <geometry.h>
-#include <stream.h>
-#include <thread-pool.h>
+#include "image.h"
+#include "utils.h"
+#include "reflist-utils.h"
+#include "symmetry.h"
+#include "beam-parameters.h"
+#include "geometry.h"
+#include "stream.h"
+#include "thread-pool.h"
+#include "cell-utils.h"
 
 /* Number of bins for partiality graph */
 #define NBINS 50

src/pattern_sim.c

@@ -42,6 +42,7 @@
 #include "diffraction.h"
 #include "diffraction-gpu.h"
 #include "cell.h"
+#include "cell-utils.h"
 #include "utils.h"
 #include "hdf5-file.h"
 #include "detector.h"

src/post-refinement.c

@@ -45,6 +45,7 @@
 #include "symmetry.h"
 #include "geometry.h"
 #include "cell.h"
+#include "cell-utils.h"
 
 
 /* Maximum number of iterations of NLSq to do for each image per macrocycle. */

src/powder_plot.c

@@ -51,6 +51,7 @@
 #include "beam-parameters.h"
 #include "reflist-utils.h"
 #include "symmetry.h"
+#include "cell-utils.h"
 
 
 struct bin_stats {

src/render_hkl.c

@@ -48,6 +48,7 @@
 #include "render_hkl.h"
 #include "reflist.h"
 #include "reflist-utils.h"
+#include "cell-utils.h"
 
 
 #define KEY_FILENAME "key.pdf"

tests/gpu_sim_check.c

@@ -36,6 +36,7 @@
 #include <beam-parameters.h>
 #include <utils.h>
 #include <symmetry.h>
+#include <cell-utils.h>
 
 
 #ifdef HAVE_CLOCK_GETTIME

tests/pr_gradient_check.c

@@ -32,6 +32,7 @@
 
 #include <image.h>
 #include <cell.h>
+#include <cell-utils.h>
 #include <geometry.h>
 #include <reflist.h>
 #include "../src/post-refinement.h"