Move stream handling functions to a separate module

9 files changed, 153 insertions, 169 deletions

diff --git a/Makefile.am b/Makefile.am
index daa4e174..111ec48d 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -9,5 +9,6 @@ EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h \
              src/povray.h src/index-priv.h src/geometry.h src/templates.h \
              data/sfac/Ca.nff data/sfac/C.nff data/sfac/Fe.nff data/sfac/H.nff \
              data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff data/sfac/P.nff \
-             data/sfac/S.nff data/sfac/f0_WaasKirf.dat src/render_hkl.h
+             data/sfac/S.nff data/sfac/f0_WaasKirf.dat src/render_hkl.h \
+             src/stream.h
 SUBDIRS = src data doc scripts
diff --git a/Makefile.in b/Makefile.in
index e9f28d3e..154245aa 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -207,7 +207,8 @@ EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h \
              src/povray.h src/index-priv.h src/geometry.h src/templates.h \
              data/sfac/Ca.nff data/sfac/C.nff data/sfac/Fe.nff data/sfac/H.nff \
              data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff data/sfac/P.nff \
-             data/sfac/S.nff data/sfac/f0_WaasKirf.dat src/render_hkl.h
+             data/sfac/S.nff data/sfac/f0_WaasKirf.dat src/render_hkl.h \
+             src/stream.h
 
 SUBDIRS = src data doc scripts
 all: config.h
diff --git a/src/Makefile.am b/src/Makefile.am
index fa6a6f41..09ee5062 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -18,7 +18,7 @@ endif
 pattern_sim_LDADD = @LIBS@
 
 process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
-                      reflections.c symmetry.c
+                      reflections.c symmetry.c stream.c
 process_hkl_LDADD = @LIBS@
 
 indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
@@ -62,11 +62,11 @@ facetron_SOURCES = facetron.c cell.c hdf5-file.c utils.c detector.c peaks.c \
 facetron_LDADD = @LIBS@
 
 cubeit_SOURCES = cubeit.c cell.c hdf5-file.c utils.c detector.c diffraction.c \
-                 sfac.c render.c filters.c image.c symmetry.c
+                 sfac.c render.c filters.c image.c symmetry.c stream.c
 cubeit_LDADD = @LIBS@
 
 reintegrate_SOURCES = reintegrate.c cell.c hdf5-file.c utils.c detector.c \
-                      peaks.c image.c diffraction.c sfac.c geometry.c
+                      peaks.c image.c diffraction.c sfac.c geometry.c stream.c
 reintegrate_LDADD = @LIBS@
 
 INCLUDES = "-I$(top_srcdir)/data"
diff --git a/src/Makefile.in b/src/Makefile.in
index 81a5c34e..8c8e93e0 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -67,7 +67,8 @@ compare_hkl_DEPENDENCIES =
 am_cubeit_OBJECTS = cubeit.$(OBJEXT) cell.$(OBJEXT) \
 	hdf5-file.$(OBJEXT) utils.$(OBJEXT) detector.$(OBJEXT) \
 	diffraction.$(OBJEXT) sfac.$(OBJEXT) render.$(OBJEXT) \
-	filters.$(OBJEXT) image.$(OBJEXT) symmetry.$(OBJEXT)
+	filters.$(OBJEXT) image.$(OBJEXT) symmetry.$(OBJEXT) \
+	stream.$(OBJEXT)
 cubeit_OBJECTS = $(am_cubeit_OBJECTS)
 cubeit_DEPENDENCIES =
 am_facetron_OBJECTS = facetron.$(OBJEXT) cell.$(OBJEXT) \
@@ -118,13 +119,13 @@ powder_plot_OBJECTS = $(am_powder_plot_OBJECTS)
 powder_plot_DEPENDENCIES =
 am_process_hkl_OBJECTS = process_hkl.$(OBJEXT) sfac.$(OBJEXT) \
 	statistics.$(OBJEXT) cell.$(OBJEXT) utils.$(OBJEXT) \
-	reflections.$(OBJEXT) symmetry.$(OBJEXT)
+	reflections.$(OBJEXT) symmetry.$(OBJEXT) stream.$(OBJEXT)
 process_hkl_OBJECTS = $(am_process_hkl_OBJECTS)
 process_hkl_DEPENDENCIES =
 am_reintegrate_OBJECTS = reintegrate.$(OBJEXT) cell.$(OBJEXT) \
 	hdf5-file.$(OBJEXT) utils.$(OBJEXT) detector.$(OBJEXT) \
 	peaks.$(OBJEXT) image.$(OBJEXT) diffraction.$(OBJEXT) \
-	sfac.$(OBJEXT) geometry.$(OBJEXT)
+	sfac.$(OBJEXT) geometry.$(OBJEXT) stream.$(OBJEXT)
 reintegrate_OBJECTS = $(am_reintegrate_OBJECTS)
 reintegrate_DEPENDENCIES =
 am_render_hkl_OBJECTS = render_hkl.$(OBJEXT) cell.$(OBJEXT) \
@@ -265,7 +266,7 @@ pattern_sim_SOURCES = pattern_sim.c diffraction.c utils.c image.c \
 	$(am__append_2)
 pattern_sim_LDADD = @LIBS@
 process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
-                      reflections.c symmetry.c
+                      reflections.c symmetry.c stream.c
 
 process_hkl_LDADD = @LIBS@
 indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
@@ -301,11 +302,11 @@ facetron_SOURCES = facetron.c cell.c hdf5-file.c utils.c detector.c peaks.c \
 
 facetron_LDADD = @LIBS@
 cubeit_SOURCES = cubeit.c cell.c hdf5-file.c utils.c detector.c diffraction.c \
-                 sfac.c render.c filters.c image.c symmetry.c
+                 sfac.c render.c filters.c image.c symmetry.c stream.c
 
 cubeit_LDADD = @LIBS@
 reintegrate_SOURCES = reintegrate.c cell.c hdf5-file.c utils.c detector.c \
-                      peaks.c image.c diffraction.c sfac.c geometry.c
+                      peaks.c image.c diffraction.c sfac.c geometry.c stream.c
 
 reintegrate_LDADD = @LIBS@
 INCLUDES = "-I$(top_srcdir)/data"
@@ -453,6 +454,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/render_hkl.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/sfac.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/statistics.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stream.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/symmetry.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/templates.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/utils.Po@am__quote@
diff --git a/src/cubeit.c b/src/cubeit.c
index f6ff2c67..4bc466a6 100644
--- a/src/cubeit.c
+++ b/src/cubeit.c
@@ -31,6 +31,7 @@
 #include "diffraction.h"
 #include "render.h"
 #include "symmetry.h"
+#include "stream.h"
 
 
 #define MAX_THREADS (256)
@@ -383,75 +384,6 @@ static void write_slice(const char *filename, double *vals, int z,
 }
 
 
-static UnitCell *read_orientation_matrix(FILE *fh)
-{
-	float u, v, w;
-	struct rvec as, bs, cs;
-	UnitCell *cell;
-	char line[1024];
-
-	if ( fgets(line, 1023, fh) == NULL ) return NULL;
-	if ( sscanf(line, "astar = %f %f %f", &u, &v, &w) != 3 ) {
-		ERROR("Couldn't read a-star\n");
-		return NULL;
-	}
-	as.u = u*1e9;  as.v = v*1e9;  as.w = w*1e9;
-	if ( fgets(line, 1023, fh) == NULL ) return NULL;
-	if ( sscanf(line, "bstar = %f %f %f", &u, &v, &w) != 3 ) {
-		ERROR("Couldn't read b-star\n");
-		return NULL;
-	}
-	bs.u = u*1e9;  bs.v = v*1e9;  bs.w = w*1e9;
-	if ( fgets(line, 1023, fh) == NULL ) return NULL;
-	if ( sscanf(line, "cstar = %f %f %f", &u, &v, &w) != 3 ) {
-		ERROR("Couldn't read c-star\n");
-		return NULL;
-	}
-	cs.u = u*1e9;  cs.v = v*1e9;  cs.w = w*1e9;
-	cell = cell_new_from_axes(as, bs, cs);
-
-	return cell;
-}
-
-
-static int find_chunk(FILE *fh, UnitCell **cell, char **filename)
-{
-	char line[1024];
-	char *rval = NULL;
-
-	do {
-
-		rval = fgets(line, 1023, fh);
-		if ( rval == NULL ) continue;
-
-		chomp(line);
-
-		if ( strncmp(line, "Reflections from indexing", 25) != 0 ) {
-			continue;
-		}
-
-		*filename = strdup(line+29);
-
-		/* Skip two lines (while checking for errors) */
-		rval = fgets(line, 1023, fh);
-		if ( rval == NULL ) continue;
-		rval = fgets(line, 1023, fh);
-		if ( rval == NULL ) continue;
-
-		*cell = read_orientation_matrix(fh);
-		if ( *cell == NULL ) {
-			STATUS("Got filename but no cell for %s\n", *filename);
-			continue;
-		}
-
-		return 0;
-
-	} while ( rval != NULL );
-
-	return 1;
-}
-
-
 static void add_to_mean(UnitCell *cell, double *ast, double *bst, double *cst,
                         double *alst, double *best, double *gast)
 {
diff --git a/src/process_hkl.c b/src/process_hkl.c
index 0df12e75..7bc04846 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -26,6 +26,7 @@
 #include "sfac.h"
 #include "reflections.h"
 #include "symmetry.h"
+#include "stream.h"
 
 
 /* Number of divisions for intensity histograms */
@@ -535,26 +536,6 @@ static void merge_all(FILE *fh, double **pmodel, ReflItemList **pobserved,
 }
 
 
-static int count_patterns(FILE *fh)
-{
-	char *rval;
-
-	int n_total_patterns = 0;
-	do {
-		char line[1024];
-
-		rval = fgets(line, 1023, fh);
-		if ( rval == NULL ) continue;
-		if ( (strncmp(line, "Reflections from indexing", 25) == 0)
-		    || (strncmp(line, "New pattern", 11) == 0) ) {
-		    n_total_patterns++;
-		}
-	} while ( rval != NULL );
-
-	return n_total_patterns;
-}
-
-
 int main(int argc, char *argv[])
 {
 	int c;
diff --git a/src/reintegrate.c b/src/reintegrate.c
index af5f9e7a..3261ba72 100644
--- a/src/reintegrate.c
+++ b/src/reintegrate.c
@@ -28,6 +28,7 @@
 #include "hdf5-file.h"
 #include "symmetry.h"
 #include "peaks.h"
+#include "stream.h"
 
 
 #define MAX_THREADS (256)
@@ -147,75 +148,6 @@ static void *worker_thread(void *pargsv)
 }
 
 
-static UnitCell *read_orientation_matrix(FILE *fh)
-{
-	float u, v, w;
-	struct rvec as, bs, cs;
-	UnitCell *cell;
-	char line[1024];
-
-	if ( fgets(line, 1023, fh) == NULL ) return NULL;
-	if ( sscanf(line, "astar = %f %f %f", &u, &v, &w) != 3 ) {
-		ERROR("Couldn't read a-star\n");
-		return NULL;
-	}
-	as.u = u*1e9;  as.v = v*1e9;  as.w = w*1e9;
-	if ( fgets(line, 1023, fh) == NULL ) return NULL;
-	if ( sscanf(line, "bstar = %f %f %f", &u, &v, &w) != 3 ) {
-		ERROR("Couldn't read b-star\n");
-		return NULL;
-	}
-	bs.u = u*1e9;  bs.v = v*1e9;  bs.w = w*1e9;
-	if ( fgets(line, 1023, fh) == NULL ) return NULL;
-	if ( sscanf(line, "cstar = %f %f %f", &u, &v, &w) != 3 ) {
-		ERROR("Couldn't read c-star\n");
-		return NULL;
-	}
-	cs.u = u*1e9;  cs.v = v*1e9;  cs.w = w*1e9;
-	cell = cell_new_from_axes(as, bs, cs);
-
-	return cell;
-}
-
-
-static int find_chunk(FILE *fh, UnitCell **cell, char **filename)
-{
-	char line[1024];
-	char *rval = NULL;
-
-	do {
-
-		rval = fgets(line, 1023, fh);
-		if ( rval == NULL ) continue;
-
-		chomp(line);
-
-		if ( strncmp(line, "Reflections from indexing", 25) != 0 ) {
-			continue;
-		}
-
-		*filename = strdup(line+29);
-
-		/* Skip two lines (while checking for errors) */
-		rval = fgets(line, 1023, fh);
-		if ( rval == NULL ) continue;
-		rval = fgets(line, 1023, fh);
-		if ( rval == NULL ) continue;
-
-		*cell = read_orientation_matrix(fh);
-		if ( *cell == NULL ) {
-			STATUS("Got filename but no cell for %s\n", *filename);
-			continue;
-		}
-
-		return 0;
-
-	} while ( rval != NULL );
-
-	return 1;
-}
-
-
 static void integrate_all(int nthreads, struct detector *det, FILE *fh,
                           int config_basename, const char *prefix)
 {
diff --git a/src/stream.c b/src/stream.c
new file mode 100644
index 00000000..75a80c72
--- /dev/null
+++ b/src/stream.c
@@ -0,0 +1,111 @@
+/*
+ * stream.c
+ *
+ * Indexed stream tools
+ *
+ * (c) 2006-2010 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+
+#include "cell.h"
+#include "utils.h"
+
+
+int count_patterns(FILE *fh)
+{
+	char *rval;
+
+	int n_total_patterns = 0;
+	do {
+		char line[1024];
+
+		rval = fgets(line, 1023, fh);
+		if ( rval == NULL ) continue;
+		if ( (strncmp(line, "Reflections from indexing", 25) == 0)
+		    || (strncmp(line, "New pattern", 11) == 0) ) {
+		    n_total_patterns++;
+		}
+	} while ( rval != NULL );
+
+	return n_total_patterns;
+}
+
+
+static UnitCell *read_orientation_matrix(FILE *fh)
+{
+	float u, v, w;
+	struct rvec as, bs, cs;
+	UnitCell *cell;
+	char line[1024];
+
+	if ( fgets(line, 1023, fh) == NULL ) return NULL;
+	if ( sscanf(line, "astar = %f %f %f", &u, &v, &w) != 3 ) {
+		ERROR("Couldn't read a-star\n");
+		return NULL;
+	}
+	as.u = u*1e9;  as.v = v*1e9;  as.w = w*1e9;
+	if ( fgets(line, 1023, fh) == NULL ) return NULL;
+	if ( sscanf(line, "bstar = %f %f %f", &u, &v, &w) != 3 ) {
+		ERROR("Couldn't read b-star\n");
+		return NULL;
+	}
+	bs.u = u*1e9;  bs.v = v*1e9;  bs.w = w*1e9;
+	if ( fgets(line, 1023, fh) == NULL ) return NULL;
+	if ( sscanf(line, "cstar = %f %f %f", &u, &v, &w) != 3 ) {
+		ERROR("Couldn't read c-star\n");
+		return NULL;
+	}
+	cs.u = u*1e9;  cs.v = v*1e9;  cs.w = w*1e9;
+	cell = cell_new_from_axes(as, bs, cs);
+
+	return cell;
+}
+
+
+int find_chunk(FILE *fh, UnitCell **cell, char **filename)
+{
+	char line[1024];
+	char *rval = NULL;
+
+	do {
+
+		rval = fgets(line, 1023, fh);
+		if ( rval == NULL ) continue;
+
+		chomp(line);
+
+		if ( strncmp(line, "Reflections from indexing", 25) != 0 ) {
+			continue;
+		}
+
+		*filename = strdup(line+29);
+
+		/* Skip two lines (while checking for errors) */
+		rval = fgets(line, 1023, fh);
+		if ( rval == NULL ) continue;
+		rval = fgets(line, 1023, fh);
+		if ( rval == NULL ) continue;
+
+		*cell = read_orientation_matrix(fh);
+		if ( *cell == NULL ) {
+			STATUS("Got filename but no cell for %s\n", *filename);
+			continue;
+		}
+
+		return 0;
+
+	} while ( rval != NULL );
+
+	return 1;
+}
diff --git a/src/stream.h b/src/stream.h
new file mode 100644
index 00000000..b21b5e4d
--- /dev/null
+++ b/src/stream.h
@@ -0,0 +1,24 @@
+/*
+ * stream.h
+ *
+ * Indexed stream tools
+ *
+ * (c) 2006-2010 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+#ifndef STREAM_H
+#define STREAM_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+extern int count_patterns(FILE *fh);
+extern int find_chunk(FILE *fh, UnitCell **cell, char **filename);
+
+
+#endif	/* STREAM_H */