aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--Makefile.am8
-rw-r--r--Makefile.in24
-rw-r--r--README7
-rw-r--r--src/hdf5-file.c18
-rw-r--r--src/image.h4
-rw-r--r--src/indexamajig.c37
-rw-r--r--src/pattern_sim.c4
-rw-r--r--src/reflist.c1
-rw-r--r--src/stream.c152
-rw-r--r--src/stream.h14
10 files changed, 197 insertions, 72 deletions
diff --git a/Makefile.am b/Makefile.am
index 5a309f76..ce2d06d7 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -45,7 +45,7 @@ src_process_hkl_SOURCES = src/process_hkl.c src/sfac.c src/statistics.c \
src/cell.c src/utils.c src/reflections.c \
src/symmetry.c src/stream.c src/beam-parameters.c \
src/thread-pool.c src/image.c src/detector.c \
- src/hdf5-file.c
+ src/hdf5-file.c src/reflist.c
src_indexamajig_SOURCES = src/indexamajig.c src/hdf5-file.c src/utils.c \
src/cell.c src/image.c src/peaks.c src/index.c \
@@ -104,11 +104,13 @@ src_partialator_SOURCES = src/partialator.c src/cell.c src/hdf5-file.c \
if BUILD_CUBEIT
src_cubeit_SOURCES = src/cubeit.c src/cell.c src/hdf5-file.c src/utils.c \
src/detector.c src/render.c src/filters.c src/image.c \
- src/symmetry.c src/stream.c src/thread-pool.c
+ src/symmetry.c src/stream.c src/thread-pool.c src/reflist.c
endif
src_estimate_background_SOURCES = src/estimate_background.c src/stream.c \
- src/utils.c src/cell.c src/thread-pool.c
+ src/utils.c src/cell.c src/thread-pool.c \
+ src/image.c src/detector.c src/hdf5-file.c \
+ src/reflist.c
tests_list_check_SOURCES = tests/list_check.c src/reflist.c src/thread-pool.c \
src/utils.c
diff --git a/Makefile.in b/Makefile.in
index b76f0796..b65b60a3 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -106,21 +106,25 @@ src_compare_hkl_LDADD = $(LDADD)
src_compare_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
am__src_cubeit_SOURCES_DIST = src/cubeit.c src/cell.c src/hdf5-file.c \
src/utils.c src/detector.c src/render.c src/filters.c \
- src/image.c src/symmetry.c src/stream.c src/thread-pool.c
+ src/image.c src/symmetry.c src/stream.c src/thread-pool.c \
+ src/reflist.c
@BUILD_CUBEIT_TRUE@am_src_cubeit_OBJECTS = src/cubeit.$(OBJEXT) \
@BUILD_CUBEIT_TRUE@ src/cell.$(OBJEXT) src/hdf5-file.$(OBJEXT) \
@BUILD_CUBEIT_TRUE@ src/utils.$(OBJEXT) src/detector.$(OBJEXT) \
@BUILD_CUBEIT_TRUE@ src/render.$(OBJEXT) src/filters.$(OBJEXT) \
@BUILD_CUBEIT_TRUE@ src/image.$(OBJEXT) src/symmetry.$(OBJEXT) \
@BUILD_CUBEIT_TRUE@ src/stream.$(OBJEXT) \
-@BUILD_CUBEIT_TRUE@ src/thread-pool.$(OBJEXT)
+@BUILD_CUBEIT_TRUE@ src/thread-pool.$(OBJEXT) \
+@BUILD_CUBEIT_TRUE@ src/reflist.$(OBJEXT)
src_cubeit_OBJECTS = $(am_src_cubeit_OBJECTS)
src_cubeit_LDADD = $(LDADD)
src_cubeit_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
am_src_estimate_background_OBJECTS = \
src/estimate_background.$(OBJEXT) src/stream.$(OBJEXT) \
src/utils.$(OBJEXT) src/cell.$(OBJEXT) \
- src/thread-pool.$(OBJEXT)
+ src/thread-pool.$(OBJEXT) src/image.$(OBJEXT) \
+ src/detector.$(OBJEXT) src/hdf5-file.$(OBJEXT) \
+ src/reflist.$(OBJEXT)
src_estimate_background_OBJECTS = \
$(am_src_estimate_background_OBJECTS)
src_estimate_background_LDADD = $(LDADD)
@@ -205,7 +209,7 @@ am_src_process_hkl_OBJECTS = src/process_hkl.$(OBJEXT) \
src/symmetry.$(OBJEXT) src/stream.$(OBJEXT) \
src/beam-parameters.$(OBJEXT) src/thread-pool.$(OBJEXT) \
src/image.$(OBJEXT) src/detector.$(OBJEXT) \
- src/hdf5-file.$(OBJEXT)
+ src/hdf5-file.$(OBJEXT) src/reflist.$(OBJEXT)
src_process_hkl_OBJECTS = $(am_src_process_hkl_OBJECTS)
src_process_hkl_LDADD = $(LDADD)
src_process_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
@@ -611,7 +615,7 @@ src_process_hkl_SOURCES = src/process_hkl.c src/sfac.c src/statistics.c \
src/cell.c src/utils.c src/reflections.c \
src/symmetry.c src/stream.c src/beam-parameters.c \
src/thread-pool.c src/image.c src/detector.c \
- src/hdf5-file.c
+ src/hdf5-file.c src/reflist.c
src_indexamajig_SOURCES = src/indexamajig.c src/hdf5-file.c \
src/utils.c src/cell.c src/image.c src/peaks.c src/index.c \
@@ -661,10 +665,12 @@ src_partialator_SOURCES = src/partialator.c src/cell.c src/hdf5-file.c \
@BUILD_CUBEIT_TRUE@src_cubeit_SOURCES = src/cubeit.c src/cell.c src/hdf5-file.c src/utils.c \
@BUILD_CUBEIT_TRUE@ src/detector.c src/render.c src/filters.c src/image.c \
-@BUILD_CUBEIT_TRUE@ src/symmetry.c src/stream.c src/thread-pool.c
+@BUILD_CUBEIT_TRUE@ src/symmetry.c src/stream.c src/thread-pool.c src/reflist.c
src_estimate_background_SOURCES = src/estimate_background.c src/stream.c \
- src/utils.c src/cell.c src/thread-pool.c
+ src/utils.c src/cell.c src/thread-pool.c \
+ src/image.c src/detector.c src/hdf5-file.c \
+ src/reflist.c
tests_list_check_SOURCES = tests/list_check.c src/reflist.c src/thread-pool.c \
src/utils.c
@@ -843,6 +849,8 @@ src/filters.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/stream.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/reflist.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/cubeit$(EXEEXT): $(src_cubeit_OBJECTS) $(src_cubeit_DEPENDENCIES) src/$(am__dirstamp)
@rm -f src/cubeit$(EXEEXT)
$(AM_V_CCLD)$(LINK) $(src_cubeit_OBJECTS) $(src_cubeit_LDADD) $(LIBS)
@@ -876,8 +884,6 @@ src/mosflm.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/geometry.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-src/reflist.$(OBJEXT): src/$(am__dirstamp) \
- src/$(DEPDIR)/$(am__dirstamp)
src/diffraction-gpu.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/cl-utils.$(OBJEXT): src/$(am__dirstamp) \
diff --git a/README b/README
index 0f3ddbb7..5a59eea7 100644
--- a/README
+++ b/README
@@ -61,12 +61,7 @@ In addition, there is also:
- estimate_background, for calculating signal to noise ratios from
the indexed peaks.
- - calibrate_detector, which splits
-
- - reintegrate, which is like "indexamajig" but without the indexing
- step, instead getting the orientation matrix from the
- output of a previous run of either "indexamajig" or
- "reintegrate".
+ - calibrate_detector, which does nothing useful at the moment.
Included at no extra cost are:
diff --git a/src/hdf5-file.c b/src/hdf5-file.c
index 20141522..eef85591 100644
--- a/src/hdf5-file.c
+++ b/src/hdf5-file.c
@@ -292,21 +292,21 @@ static double get_wavelength(struct hdfile *f)
}
-static double get_f0(struct hdfile *f)
+static double get_i0(struct hdfile *f)
{
herr_t r;
hid_t dh;
- double f0;
+ double i0;
dh = H5Dopen2(f->fh, "/LCLS/f_11_ENRC", H5P_DEFAULT);
if ( dh < 0 ) return -1.0;
r = H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, &f0);
+ H5P_DEFAULT, &i0);
H5Dclose(dh);
if ( r < 0 ) return -1.0;
- return f0;
+ return i0;
}
@@ -434,13 +434,13 @@ int hdf5_read(struct hdfile *f, struct image *image, int satcorr)
/* Read wavelength from file */
image->lambda = get_wavelength(f);
- image->f0 = get_f0(f);
- if ( image->f0 < 0.0 ) {
+ image->i0 = get_i0(f);
+ if ( image->i0 < 0.0 ) {
ERROR("Couldn't read incident intensity - using 1.0.\n");
- image->f0 = 1.0;
- image->f0_available = 0;
+ image->i0 = 1.0;
+ image->i0_available = 0;
} else {
- image->f0_available = 1;
+ image->i0_available = 1;
}
if ( satcorr ) debodge_saturation(f, image);
diff --git a/src/image.h b/src/image.h
index 69c36de8..692ef7f8 100644
--- a/src/image.h
+++ b/src/image.h
@@ -76,8 +76,8 @@ struct image {
double lambda; /* Wavelength in m */
double div; /* Divergence in radians */
double bw; /* Bandwidth as a fraction */
- double f0; /* Incident intensity */
- int f0_available; /* 0 if f0 wasn't available
+ double i0; /* Incident intensity */
+ int i0_available; /* 0 if f0 wasn't available
* from the input. */
double osf; /* Overall scaling factor */
double profile_radius; /* Radius of reflection */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 72491450..320439b3 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -52,7 +52,7 @@ struct static_index_args
int config_cmfilter;
int config_noisefilter;
int config_verbose;
- int stream_flags;
+ int stream_flags; /* What goes into the output? */
int config_polar;
int config_satcorr;
int config_closer;
@@ -62,7 +62,7 @@ struct static_index_args
struct detector *det;
IndexingMethod *indm;
IndexingPrivate **ipriv;
- int peaks;
+ int peaks; /* Peak detection method */
int cellr;
struct beam_params *beam;
const char *element;
@@ -132,15 +132,20 @@ static void show_help(const char *s)
" in the HDF5 file.\n"
"\n\n"
"You can control what information is included in the output stream using\n"
-"' --record=<flags>'. Possible flags are:\n"
-"pixels Include a list of sums of pixel values within the\n"
-" integration domain, correcting for individual pixel\n"
-" solid angles.\n"
-"integrated Include a list of reflection intensities, produced by\n"
-" integrating around predicted peak locations.\n"
-" The flags 'pixels' and 'integrated' are mutually exclusive.\n"
-"peaks Include peak locations and intensities from the peak search.\n"
-"peaksifindexed Include peak locations only if the pattern could be indexed.\n"
+"' --record=<flags>'. Possible flags are:\n\n"
+" pixels Include a list of sums of pixel values within the\n"
+" integration domain, correcting for individual pixel\n"
+" solid angles.\n"
+"\n"
+" integrated Include a list of reflection intensities, produced by\n"
+" integrating around predicted peak locations.\n"
+"\n"
+" peaks Include peak locations and intensities from the peak search.\n"
+"\n"
+" peaksifindexed As 'peaks', but only if the pattern could be indexed.\n\n"
+"\n"
+"The default is '--record=integrated'. The flags 'pixels' and 'integrated'\n"
+"are mutually exclusive, as are the flags 'peaks' and 'peaksifindexed'.\n"
"\n\n"
"For more control over the process, you might need:\n\n"
" --cell-reduction=<m> Use <m> as the cell reduction method. Choose from:\n"
@@ -162,7 +167,7 @@ static void show_help(const char *s)
" --min-gradient=<n> Minimum gradient for Zaefferer peak search.\n"
" Default: 100,000.\n"
" -e, --image=<element> Use this image from the HDF5 file.\n"
-" Example: /data/data0."
+" Example: /data/data0.\n"
" Default: The first one found.\n"
"\n"
"\nOptions for greater performance or verbosity:\n\n"
@@ -431,6 +436,7 @@ int main(int argc, char *argv[])
struct beam_params *beam = NULL;
char *element = NULL;
double nominal_photon_energy;
+ int stream_flags = STREAM_INTEGRATED;
/* Long options */
const struct option longopts[] = {
@@ -460,6 +466,7 @@ int main(int argc, char *argv[])
{"insane", 0, &config_insane, 1},
{"image", 1, NULL, 'e'},
{"basename", 0, &config_basename, 1},
+ {"record", 1, NULL, 5},
{0, 0, NULL, 0}
};
@@ -529,6 +536,11 @@ int main(int argc, char *argv[])
element = strdup(optarg);
break;
+ case 5 :
+ stream_flags = parse_stream_flags(optarg);
+ if ( stream_flags < 0 ) return 1;
+ break;
+
case 0 :
break;
@@ -673,6 +685,7 @@ int main(int argc, char *argv[])
free(pdb);
/* Start by writing the entire command line to stdout */
+ fprintf(ofh, "CrystFEL stream format 2.0\n");
fprintf(ofh, "Command line:");
for ( i=0; i<argc; i++ ) {
fprintf(ofh, " %s", argv[i]);
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 948458bc..c0318176 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -472,8 +472,8 @@ int main(int argc, char *argv[])
image.filename = NULL;
image.features = NULL;
image.flags = NULL;
- image.f0 = 1.0;
- image.f0_available = 1;
+ image.i0 = 1.0;
+ image.i0_available = 1;
powder = calloc(image.width*image.height, sizeof(*powder));
diff --git a/src/reflist.c b/src/reflist.c
index e7d072c0..3a53330c 100644
--- a/src/reflist.c
+++ b/src/reflist.c
@@ -44,6 +44,7 @@ struct _refldata {
/* Intensity */
double intensity;
+ double esd_i;
};
diff --git a/src/stream.c b/src/stream.c
index fbe0abad..4e34a48c 100644
--- a/src/stream.c
+++ b/src/stream.c
@@ -21,6 +21,63 @@
#include "cell.h"
#include "utils.h"
#include "image.h"
+#include "stream.h"
+
+
+static void exclusive(const char *a, const char *b)
+{
+ ERROR("The stream options '%s' and '%s' are mutually exclusive.\n",
+ a, b);
+}
+
+
+int parse_stream_flags(const char *a)
+{
+ int n, i;
+ int ret = STREAM_NONE;
+ char **flags;
+
+ n = assplode(a, ",", &flags, ASSPLODE_NONE);
+
+ for ( i=0; i<n; i++ ) {
+
+ if ( strcmp(flags[i], "pixels") == 0) {
+ if ( ret & STREAM_INTEGRATED ) {
+ exclusive("pixels", "integrated");
+ return -1;
+ }
+ ret |= STREAM_PIXELS;
+ } else if ( strcmp(flags[i], "integrated") == 0) {
+ if ( ret & STREAM_PIXELS ) {
+ exclusive("pixels", "integrated");
+ return -1;
+ }
+ ret |= STREAM_INTEGRATED;
+ } else if ( strcmp(flags[i], "peaks") == 0) {
+ if ( ret & STREAM_PEAKS_IF_INDEXED ) {
+ exclusive("peaks", "peaksifindexed");
+ return -1;
+ }
+ ret |= STREAM_PEAKS;
+ } else if ( strcmp(flags[i], "peaksifindexed") == 0) {
+ if ( ret & STREAM_PEAKS ) {
+ exclusive("peaks", "peaksifindexed");
+ return -1;
+ }
+ ret |= STREAM_PEAKS_IF_INDEXED;
+ } else {
+ ERROR("Unrecognised stream flag '%s'\n", flags[i]);
+ return 0;
+ }
+
+ free(flags[i]);
+
+ }
+ free(flags);
+
+ return ret;
+
+}
int count_patterns(FILE *fh)
@@ -76,6 +133,31 @@ static UnitCell *read_orientation_matrix(FILE *fh)
static void write_reflections(struct image *image, FILE *ofh)
{
+ Reflection *refl;
+ RefListIterator *iter;
+
+ fprintf(ofh, "Reflections measured after indexing\n");
+ /* FIXME: Unify this with write_reflections() over in reflections.c */
+ fprintf(ofh, " h k l I phase sigma(I) "
+ " 1/d(nm^-1) counts\n");
+
+ for ( refl = first_refl(image->reflections, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) ) {
+
+ signed int h, k, l;
+ double intensity, esd_i, s;
+
+ get_indices(refl, &h, &k, &l);
+ intensity = get_intensity(refl);
+ esd_i = 0.0; /* FIXME! */
+ s = 0.0; /* FIXME! */
+
+ /* h, k, l, I, sigma(I), s */
+ fprintf(ofh, "%3i %3i %3i %10.2f %s %10.2f %10.2f %7i\n",
+ h, k, l, intensity, " -", esd_i, s/1.0e9, 1);
+
+ }
}
@@ -83,7 +165,7 @@ static void write_peaks(struct image *image, FILE *ofh)
{
int i;
- fprintf(ofh, "Peaks from peak search in %s\n", image->filename);
+ fprintf(ofh, "Peaks from peak search\n");
fprintf(ofh, " x/px y/px (1/d)/nm^-1 Intensity\n");
for ( i=0; i<image_feature_count(image->features); i++ ) {
@@ -102,13 +184,10 @@ static void write_peaks(struct image *image, FILE *ofh)
f->x, f->y, q/1.0e9, f->intensity);
}
-
- fprintf(ofh, "\n");
}
-
-void write_chunk(FILE *ofh, struct image *image, int flags)
+void write_chunk(FILE *ofh, struct image *i, int f)
{
double asx, asy, asz;
double bsx, bsy, bsz;
@@ -117,36 +196,51 @@ void write_chunk(FILE *ofh, struct image *image, int flags)
fprintf(ofh, "----- Begin chunk -----\n");
- fprintf(ofh, "Image filename: %s\n", image->filename);
-
- cell_get_parameters(image->indexed_cell, &a, &b, &c, &al, &be, &ga);
- fprintf(ofh, "Cell parameters %7.5f %7.5f %7.5f nm,"
- " %7.5f %7.5f %7.5f deg\n",
- a*1.0e9, b*1.0e9, c*1.0e9,
- rad2deg(al), rad2deg(be), rad2deg(ga));
-
- cell_get_reciprocal(image->indexed_cell, &asx, &asy, &asz,
- &bsx, &bsy, &bsz,
- &csx, &csy, &csz);
- fprintf(ofh, "astar = %+9.7f %+9.7f %+9.7f nm^-1\n",
- asx/1e9, asy/1e9, asz/1e9);
- fprintf(ofh, "bstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
- bsx/1e9, bsy/1e9, bsz/1e9);
- fprintf(ofh, "cstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
- csx/1e9, csy/1e9, csz/1e9);
-
- if ( image->f0_available ) {
- fprintf(ofh, "I0 = %7.5f (arbitrary gas detector units)\n",
- image->f0);
+ fprintf(ofh, "Image filename: %s\n", i->filename);
+
+ if ( i->indexed_cell != NULL ) {
+ cell_get_parameters(i->indexed_cell, &a, &b, &c,
+ &al, &be, &ga);
+ fprintf(ofh, "Cell parameters %7.5f %7.5f %7.5f nm,"
+ " %7.5f %7.5f %7.5f deg\n",
+ a*1.0e9, b*1.0e9, c*1.0e9,
+ rad2deg(al), rad2deg(be), rad2deg(ga));
+
+ cell_get_reciprocal(i->indexed_cell, &asx, &asy, &asz,
+ &bsx, &bsy, &bsz,
+ &csx, &csy, &csz);
+ fprintf(ofh, "astar = %+9.7f %+9.7f %+9.7f nm^-1\n",
+ asx/1e9, asy/1e9, asz/1e9);
+ fprintf(ofh, "bstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
+ bsx/1e9, bsy/1e9, bsz/1e9);
+ fprintf(ofh, "cstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
+ csx/1e9, csy/1e9, csz/1e9);
+
+ } else {
+
+ fprintf(ofh, "No unit cell from indexing.\n");
+
+ }
+
+ if ( i->i0_available ) {
+ fprintf(ofh, "I0 = %7.5f (arbitrary units)\n", i->i0);
} else {
fprintf(ofh, "I0 = invalid\n");
}
fprintf(ofh, "photon_energy_eV = %f\n",
- J_to_eV(ph_lambda_to_en(image->lambda)));
+ J_to_eV(ph_lambda_to_en(i->lambda)));
+
+ if ( (f & STREAM_PEAKS)
+ || ((f & STREAM_PEAKS_IF_INDEXED) && (i->indexed_cell != NULL)) ) {
+ fprintf(ofh, "\n");
+ write_peaks(i, ofh);
+ }
- write_peaks(image, ofh);
- write_reflections(image, ofh);
+ if ( (f & STREAM_PIXELS) || (f & STREAM_INTEGRATED) ) {
+ fprintf(ofh, "\n");
+ write_reflections(i, ofh);
+ }
fprintf(ofh, "----- End chunk -----\n\n");
}
diff --git a/src/stream.h b/src/stream.h
index b5f05b19..71ab4b79 100644
--- a/src/stream.h
+++ b/src/stream.h
@@ -19,9 +19,23 @@
struct image;
+/* Possible options dictating what goes into the output stream */
+enum
+{
+ STREAM_NONE = 0,
+ STREAM_INTEGRATED = 1<<0,
+ STREAM_PIXELS = 1<<1,
+ STREAM_PEAKS = 1<<2,
+ STREAM_PEAKS_IF_INDEXED = 1<<3,
+};
+
+
extern int count_patterns(FILE *fh);
+
extern int find_chunk(FILE *fh, UnitCell **cell, char **filename, double *ev);
+
extern void write_chunk(FILE *ofh, struct image *image, int flags);
+extern int parse_stream_flags(const char *a);
#endif /* STREAM_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-17 19:29:55 +0000