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-rw-r--r--src/Makefile.am2
-rw-r--r--src/Makefile.in9
-rw-r--r--src/cell.c42
-rw-r--r--src/cell.h2
-rw-r--r--src/diffraction-gpu.c6
-rw-r--r--src/diffraction-gpu.h4
-rw-r--r--src/diffraction.c8
-rw-r--r--src/diffraction.h2
-rw-r--r--src/get_hkl.c2
-rw-r--r--src/image.h1
-rw-r--r--src/index.c7
-rw-r--r--src/index.h7
-rw-r--r--src/indexamajig.c53
-rw-r--r--src/pattern_sim.c19
14 files changed, 104 insertions, 60 deletions
diff --git a/src/Makefile.am b/src/Makefile.am
index e696fcbf..ef9338c5 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -23,7 +23,7 @@ process_hkl_LDADD = @LIBS@
indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
intensities.c peaks.c index.c filters.c \
- diffraction.c detector.c sfac.c dirax.c
+ diffraction.c detector.c sfac.c dirax.c reflections.c
indexamajig_LDADD = @LIBS@
if HAVE_OPENCL
indexamajig_SOURCES += diffraction-gpu.c cl-utils.c
diff --git a/src/Makefile.in b/src/Makefile.in
index 87fb7e4c..4b59a13d 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -69,15 +69,16 @@ hdfsee_OBJECTS = $(am_hdfsee_OBJECTS)
hdfsee_DEPENDENCIES =
am__indexamajig_SOURCES_DIST = indexamajig.c hdf5-file.c utils.c \
cell.c image.c intensities.c peaks.c index.c filters.c \
- diffraction.c detector.c sfac.c dirax.c diffraction-gpu.c \
- cl-utils.c
+ diffraction.c detector.c sfac.c dirax.c reflections.c \
+ diffraction-gpu.c cl-utils.c
@HAVE_OPENCL_TRUE@am__objects_1 = diffraction-gpu.$(OBJEXT) \
@HAVE_OPENCL_TRUE@ cl-utils.$(OBJEXT)
am_indexamajig_OBJECTS = indexamajig.$(OBJEXT) hdf5-file.$(OBJEXT) \
utils.$(OBJEXT) cell.$(OBJEXT) image.$(OBJEXT) \
intensities.$(OBJEXT) peaks.$(OBJEXT) index.$(OBJEXT) \
filters.$(OBJEXT) diffraction.$(OBJEXT) detector.$(OBJEXT) \
- sfac.$(OBJEXT) dirax.$(OBJEXT) $(am__objects_1)
+ sfac.$(OBJEXT) dirax.$(OBJEXT) reflections.$(OBJEXT) \
+ $(am__objects_1)
indexamajig_OBJECTS = $(am_indexamajig_OBJECTS)
indexamajig_DEPENDENCIES =
am__pattern_sim_SOURCES_DIST = pattern_sim.c diffraction.c utils.c \
@@ -231,7 +232,7 @@ process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
process_hkl_LDADD = @LIBS@
indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
intensities.c peaks.c index.c filters.c diffraction.c \
- detector.c sfac.c dirax.c $(am__append_3)
+ detector.c sfac.c dirax.c reflections.c $(am__append_3)
indexamajig_LDADD = @LIBS@
@HAVE_GTK_TRUE@hdfsee_SOURCES = hdfsee.c displaywindow.c render.c hdf5-file.c utils.c image.c \
@HAVE_GTK_TRUE@ filters.c
diff --git a/src/cell.c b/src/cell.c
index 721756c9..42f34dfa 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -615,3 +615,45 @@ double resolution(UnitCell *cell, signed int h, signed int k, signed int l)
return oneoverd / 2;
}
+
+
+UnitCell *load_cell_from_pdb(const char *filename)
+{
+ FILE *fh;
+ char *rval;
+ UnitCell *cell = NULL;
+
+ fh = fopen(filename, "r");
+
+ do {
+
+ char line[1024];
+
+ rval = fgets(line, 1023, fh);
+
+ if ( strncmp(line, "CRYST1", 6) == 0 ) {
+
+ float a, b, c, al, be, ga;
+ int r;
+
+ r = sscanf(line+7, "%f %f %f %f %f %f",
+ &a, &b, &c, &al, &be, &ga);
+ if ( r != 6 ) {
+ ERROR("Couldn't understand CRYST1 line\n");
+ return NULL;
+ }
+
+ cell = cell_new_from_parameters(a*1e-10,
+ b*1e-10, c*1e-10,
+ deg2rad(al),
+ deg2rad(be),
+ deg2rad(ga));
+
+ }
+
+ } while ( rval != NULL );
+
+ fclose(fh);
+
+ return cell;
+}
diff --git a/src/cell.h b/src/cell.h
index 5a534268..924cb0ef 100644
--- a/src/cell.h
+++ b/src/cell.h
@@ -77,4 +77,6 @@ extern void cell_print(UnitCell *cell);
extern UnitCell *match_cell(UnitCell *cell, UnitCell *template, int verbose);
+extern UnitCell *load_cell_from_pdb(const char *filename);
+
#endif /* CELL_H */
diff --git a/src/diffraction-gpu.c b/src/diffraction-gpu.c
index cc7b9e5b..741f7b69 100644
--- a/src/diffraction-gpu.c
+++ b/src/diffraction-gpu.c
@@ -107,7 +107,7 @@ static void check_sinc_lut(struct gpu_context *gctx, int n)
void get_diffraction_gpu(struct gpu_context *gctx, struct image *image,
- int na, int nb, int nc, int no_sfac)
+ int na, int nb, int nc, UnitCell *ucell)
{
cl_int err;
double ax, ay, az;
@@ -130,9 +130,7 @@ void get_diffraction_gpu(struct gpu_context *gctx, struct image *image,
return;
}
- cell_get_cartesian(image->molecule->cell, &ax, &ay, &az,
- &bx, &by, &bz,
- &cx, &cy, &cz);
+ cell_get_cartesian(ucell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
cell[0] = ax; cell[1] = ay; cell[2] = az;
cell[3] = bx; cell[4] = by; cell[5] = bz;
cell[6] = cx; cell[7] = cy; cell[8] = cz;
diff --git a/src/diffraction-gpu.h b/src/diffraction-gpu.h
index b23dab63..a9e46b66 100644
--- a/src/diffraction-gpu.h
+++ b/src/diffraction-gpu.h
@@ -24,7 +24,7 @@ struct gpu_context;
#if HAVE_OPENCL
extern void get_diffraction_gpu(struct gpu_context *gctx, struct image *image,
- int na, int nb, int nc);
+ int na, int nb, int nc, UnitCell *ucell);
extern struct gpu_context *setup_gpu(int no_sfac, struct image *image,
double *intensities);
extern void cleanup_gpu(struct gpu_context *gctx);
@@ -32,7 +32,7 @@ extern void cleanup_gpu(struct gpu_context *gctx);
#else
static void get_diffraction_gpu(struct gpu_context *gctx, struct image *image,
- int na, int nb, int nc)
+ int na, int nb, int nc, UnitCell *ucell)
{
/* Do nothing */
ERROR("This copy of CrystFEL was not compiled with OpenCL support.\n");
diff --git a/src/diffraction.c b/src/diffraction.c
index 01624be8..c47920f5 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -171,7 +171,7 @@ struct rvec get_q(struct image *image, unsigned int xs, unsigned int ys,
void get_diffraction(struct image *image, int na, int nb, int nc,
- double *intensities, int do_water)
+ double *intensities, UnitCell *cell, int do_water)
{
unsigned int xs, ys;
double ax, ay, az;
@@ -179,11 +179,7 @@ void get_diffraction(struct image *image, int na, int nb, int nc,
double cx, cy, cz;
float k, klow, bwstep;
- if ( image->molecule == NULL ) return;
-
- cell_get_cartesian(image->molecule->cell, &ax, &ay, &az,
- &bx, &by, &bz,
- &cx, &cy, &cz);
+ cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
/* Allocate (and zero) the "diffraction array" */
image->data = calloc(image->width * image->height, sizeof(float));
diff --git a/src/diffraction.h b/src/diffraction.h
index dd0795fb..58ae10c3 100644
--- a/src/diffraction.h
+++ b/src/diffraction.h
@@ -20,7 +20,7 @@
#include "cell.h"
extern void get_diffraction(struct image *image, int na, int nb, int nc,
- double *intensities, int do_water);
+ double *intensities, UnitCell *cell, int do_water);
extern struct rvec get_q(struct image *image, unsigned int xs, unsigned int ys,
unsigned int sampling, float *ttp, float k);
diff --git a/src/get_hkl.c b/src/get_hkl.c
index 29ff0786..5e5331b4 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -110,8 +110,6 @@ int main(int argc, char *argv[])
char *output = NULL;
unsigned int *counts;
signed int h, k, l;
- FILE *fh;
- char *rval;
/* Long options */
const struct option longopts[] = {
diff --git a/src/image.h b/src/image.h
index 5f2cf3d0..2885b734 100644
--- a/src/image.h
+++ b/src/image.h
@@ -72,7 +72,6 @@ struct image {
float *data;
double *twotheta;
- struct molecule *molecule;
UnitCell *indexed_cell;
UnitCell *candidate_cells[MAX_CELL_CANDIDATES];
int ncells;
diff --git a/src/index.c b/src/index.c
index daa16b27..f2b8ffb9 100644
--- a/src/index.c
+++ b/src/index.c
@@ -57,8 +57,8 @@ static void write_drx(struct image *image)
}
-void index_pattern(struct image *image, IndexingMethod indm, int no_match,
- int verbose)
+void index_pattern(struct image *image, UnitCell *cell, IndexingMethod indm,
+ int no_match, int verbose)
{
int i;
int nc = 0;
@@ -115,8 +115,7 @@ void index_pattern(struct image *image, IndexingMethod indm, int no_match,
STATUS("--------------------\n");
}
- new_cell = match_cell(image->candidate_cells[i],
- image->molecule->cell, verbose);
+ new_cell = match_cell(image->candidate_cells[i], cell, verbose);
image->indexed_cell = new_cell;
if ( new_cell != NULL ) {
STATUS("Matched on attempt %i.\n", i);
diff --git a/src/index.h b/src/index.h
index 26ce1c44..b30db837 100644
--- a/src/index.h
+++ b/src/index.h
@@ -18,6 +18,9 @@
#endif
+#include "cell.h"
+
+
typedef enum {
INDEXING_NONE,
INDEXING_DIRAX,
@@ -25,7 +28,7 @@ typedef enum {
} IndexingMethod;
-extern void index_pattern(struct image *image, IndexingMethod indm,
- int no_match, int verbose);
+extern void index_pattern(struct image *image, UnitCell *cell,
+ IndexingMethod indm, int no_match, int verbose);
#endif /* INDEX_H */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 5a47254f..e0871fe7 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -32,6 +32,7 @@
#include "detector.h"
#include "sfac.h"
#include "filters.h"
+#include "reflections.h"
static void show_help(const char *s)
@@ -77,6 +78,8 @@ static void show_help(const char *s)
" --no-match Don't attempt to match the indexed cell to the\n"
" model, just proceed with the one generated by the\n"
" auto-indexing procedure.\n"
+" --intensities=<file> Specify file containing reflection intensities\n"
+" to use.\n"
);
}
@@ -138,30 +141,22 @@ static struct image *get_simage(struct image *template, int alternate)
image->lambda = ph_en_to_lambda(eV_to_J(1.8e3));
- image->molecule = copy_molecule(template->molecule);
- free(image->molecule->cell);
- image->molecule->cell = cell_new_from_cell(template->indexed_cell);
-
return image;
}
-static void simulate_and_write(struct image *simage,
- struct gpu_context **gctx)
+static void simulate_and_write(struct image *simage, struct gpu_context **gctx,
+ double *intensities, UnitCell *cell)
{
/* Set up GPU if necessary */
if ( (gctx != NULL) && (*gctx == NULL) ) {
- *gctx = setup_gpu(0, simage, simage->molecule);
+ *gctx = setup_gpu(0, simage, intensities);
}
if ( (gctx != NULL) && (*gctx != NULL) ) {
- get_diffraction_gpu(*gctx, simage, 24, 24, 40);
+ get_diffraction_gpu(*gctx, simage, 24, 24, 40, cell);
} else {
- get_diffraction(simage, 24, 24, 40, 0, 0);
- }
- if ( simage->molecule == NULL ) {
- ERROR("Couldn't open molecule.pdb\n");
- return;
+ get_diffraction(simage, 24, 24, 40, intensities, cell, 0);
}
record_image(simage, 0);
@@ -193,6 +188,9 @@ int main(int argc, char *argv[])
IndexingMethod indm;
char *indm_str = NULL;
struct image image;
+ UnitCell *cell;
+ double *intensities = NULL;
+ char *intfile = NULL;
/* Long options */
const struct option longopts[] = {
@@ -210,6 +208,7 @@ int main(int argc, char *argv[])
{"no-match", 0, &config_nomatch, 1},
{"verbose", 0, &config_verbose, 1},
{"alternate", 0, &config_alternate, 1},
+ {"intensities", 0, NULL, 'q'},
{0, 0, NULL, 0}
};
@@ -232,6 +231,11 @@ int main(int argc, char *argv[])
break;
}
+ case 'q' : {
+ intfile = strdup(optarg);
+ break;
+ }
+
case 0 : {
break;
}
@@ -257,6 +261,12 @@ int main(int argc, char *argv[])
return 1;
}
+ if ( intfile != NULL ) {
+ intensities = read_reflections(intfile);
+ } else {
+ intensities = NULL;
+ }
+
if ( indm_str == NULL ) {
STATUS("You didn't specify an indexing method, so I won't"
" try to index anything.\n"
@@ -273,10 +283,9 @@ int main(int argc, char *argv[])
}
free(indm_str);
- image.molecule = load_molecule();
- if ( image.molecule == NULL ) {
- ERROR("You must provide molecule.pdb in the working "
- "directory.\n");
+ cell = load_cell_from_pdb("molecule.pdb");
+ if ( cell == NULL ) {
+ ERROR("Couldn't read unit cell (from molecule.pdb)\n");
return 1;
}
@@ -354,7 +363,7 @@ int main(int argc, char *argv[])
/* Calculate orientation matrix (by magic) */
if ( config_writedrx || (indm != INDEXING_NONE) ) {
- index_pattern(&image, indm, config_nomatch,
+ index_pattern(&image, cell, indm, config_nomatch,
config_verbose);
}
@@ -376,16 +385,17 @@ int main(int argc, char *argv[])
/* Simulate if requested */
if ( config_simulate ) {
if ( config_gpu ) {
- simulate_and_write(simage, &gctx);
+ simulate_and_write(simage, &gctx, intensities,
+ cell);
} else {
- simulate_and_write(simage, NULL);
+ simulate_and_write(simage, NULL, intensities,
+ cell);
}
}
/* Finished with alternate image */
if ( simage->twotheta != NULL ) free(simage->twotheta);
if ( simage->data != NULL ) free(simage->data);
- free_molecule(simage->molecule);
free(simage);
/* Only free cell if found */
@@ -402,7 +412,6 @@ done:
} while ( rval != NULL );
fclose(fh);
- free_molecule(image.molecule);
STATUS("There were %i images.\n", n_images);
STATUS("%i hits were found.\n", n_hits);
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 4fd7da66..2ff12226 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -162,6 +162,7 @@ int main(int argc, char *argv[])
int number = 1; /* Number used for filename of image */
int n_images = 1; /* Generate one image by default */
int done = 0;
+ UnitCell *cell;
/* Long options */
const struct option longopts[] = {
@@ -240,7 +241,7 @@ int main(int argc, char *argv[])
image.width = 1024;
image.height = 1024;
image.lambda = ph_en_to_lambda(eV_to_J(1790.0)); /* Wavelength */
- image.molecule = load_molecule();
+ cell = load_cell_from_pdb("molecule.pdb");
#include "geometry-lcls.tmp"
@@ -281,7 +282,7 @@ int main(int argc, char *argv[])
image.data = NULL;
image.twotheta = NULL;
- cell_get_parameters(image.molecule->cell, &a, &b, &c, &d, &d, &d);
+ cell_get_parameters(cell, &a, &b, &c, &d, &d, &d);
STATUS("Particle size = %i x %i x %i (=%5.2f x %5.2f x %5.2f nm)\n",
na, nb, nc, na*a/1.0e-9, nb*b/1.0e-9, nc*c/1.0e-9);
@@ -290,15 +291,11 @@ int main(int argc, char *argv[])
gctx = setup_gpu(config_nosfac, &image,
intensities);
}
- get_diffraction_gpu(gctx, &image, na, nb, nc);
+ get_diffraction_gpu(gctx, &image, na, nb, nc, cell);
} else {
- get_diffraction(&image, na, nb, nc, intensities,
+ get_diffraction(&image, na, nb, nc, intensities, cell,
!config_nowater);
}
- if ( image.molecule == NULL ) {
- ERROR("Couldn't open molecule.pdb\n");
- return 1;
- }
if ( image.data == NULL ) {
ERROR("Diffraction calculation failed.\n");
goto skip;
@@ -307,7 +304,7 @@ int main(int argc, char *argv[])
record_image(&image, !config_nonoise);
if ( config_nearbragg ) {
- output_intensities(&image, image.molecule->cell);
+ output_intensities(&image, cell);
}
if ( config_powder ) {
@@ -359,8 +356,8 @@ skip:
free(image.det.panels);
free(powder);
- free(image.molecule->reflections);
- free(image.molecule);
+ free(cell);
+ free(intensities);
return 0;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-14 23:56:03 +0000