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-rw-r--r--src/dirax.c33
-rw-r--r--src/index.c149
-rw-r--r--src/indexamajig.c22
-rw-r--r--src/mosflm.c121
4 files changed, 158 insertions, 167 deletions
diff --git a/src/dirax.c b/src/dirax.c
index 0930f8f9..ebb53f25 100644
--- a/src/dirax.c
+++ b/src/dirax.c
@@ -385,12 +385,45 @@ static int dirax_readable(struct image *image)
}
+static void write_drx(struct image *image)
+{
+ FILE *fh;
+ int i;
+ char filename[1024];
+
+ snprintf(filename, 1023, "xfel-%i.drx", image->id);
+
+ fh = fopen(filename, "w");
+ if ( !fh ) {
+ ERROR("Couldn't open temporary file xfel.drx\n");
+ return;
+ }
+ fprintf(fh, "%f\n", 0.5); /* Lie about the wavelength. */
+
+ for ( i=0; i<image_feature_count(image->features); i++ ) {
+
+ struct imagefeature *f;
+
+ f = image_get_feature(image->features, i);
+ if ( f == NULL ) continue;
+
+ fprintf(fh, "%10f %10f %10f %8f\n",
+ f->rx/1e10, f->ry/1e10, f->rz/1e10, 1.0);
+
+ }
+ fclose(fh);
+}
+
+
+
void run_dirax(struct image *image)
{
unsigned int opts;
int status;
int rval;
+ write_drx(image);
+
image->dirax_pid = forkpty(&image->dirax_pty, NULL, NULL, NULL);
if ( image->dirax_pid == -1 ) {
ERROR("Failed to fork for DirAx\n");
diff --git a/src/index.c b/src/index.c
index 4d2a158f..69711b42 100644
--- a/src/index.c
+++ b/src/index.c
@@ -108,152 +108,6 @@ void cleanup_indexing(IndexingPrivate **priv)
}
-static void write_drx(struct image *image)
-{
- FILE *fh;
- int i;
- char filename[1024];
-
- snprintf(filename, 1023, "xfel-%i.drx", image->id);
-
- fh = fopen(filename, "w");
- if ( !fh ) {
- ERROR("Couldn't open temporary file xfel.drx\n");
- return;
- }
- fprintf(fh, "%f\n", 0.5); /* Lie about the wavelength. */
-
- for ( i=0; i<image_feature_count(image->features); i++ ) {
-
- struct imagefeature *f;
-
- f = image_get_feature(image->features, i);
- if ( f == NULL ) continue;
-
- fprintf(fh, "%10f %10f %10f %8f\n",
- f->rx/1e10, f->ry/1e10, f->rz/1e10, 1.0);
-
- }
- fclose(fh);
-}
-
-
-/* write .spt file for mosflm */
-/* need to sort mosflm peaks by intensity... */
-struct sptline {
- double x; /* x coordinate of peak */
- double y; /* y coordinate of peak */
- double h; /* height of peak */
- double s; /* sigma of peak */
-};
-
-
-static int compare_vals(const void *ap, const void *bp)
-{
- const struct sptline a = *(struct sptline *)ap;
- const struct sptline b = *(struct sptline *)bp;
-
- if ( a.h < b.h ) return 1;
- if ( a.h > b.h ) return -1;
- return 0;
-}
-
-
-static void write_spt(struct image *image)
-{
- FILE *fh;
- int i;
- char filename[1024];
- double fclen=67.8; /* fake camera length in mm */
- double fpix=0.075; /* fake pixel size in mm */
- double pix;
- double height=100;
- double sigma=1;
- int nPeaks = image_feature_count(image->features);
-
- snprintf(filename, 1023, "xfel-%i.spt", image->id);
-
- fh = fopen(filename, "w");
- if ( !fh ) {
- ERROR("Couldn't open temporary file xfel.spt\n");
- return;
- }
-
- fprintf(fh, "%10d %10d %10.8f %10.6f %10.6f\n", 1, 1, fpix, 1.0, 0.0);
- fprintf(fh, "%10d %10d\n", 1, 1);
- fprintf(fh, "%10.5f %10.5f\n", 0.0, 0.0);
-
- struct sptline *sptlines;
- sptlines = malloc(sizeof(struct sptline)*nPeaks);
-
- for ( i=0; i<nPeaks; i++ ) {
-
- struct imagefeature *f;
-
- f = image_get_feature(image->features, i);
- if ( f == NULL ) continue;
-
- struct panel *pan;
- pan = find_panel(image->det,f->x,f->y);
- if ( pan == NULL ) continue;
-
- pix = 1000/pan->res; /* pixel size in mm */
- height = f->intensity;
-
- sptlines[i].x = (f->y - pan->cy)*pix*fclen/pan->clen/1000;
- sptlines[i].y = -(f->x - pan->cx)*pix*fclen/pan->clen/1000;
- sptlines[i].h = height;
- sptlines[i].s = sigma;
-
- }
-
- qsort(sptlines, nPeaks, sizeof(struct sptline), compare_vals);
-
- for ( i=0; i<nPeaks; i++ ) {
-
- fprintf(fh, "%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
- sptlines[i].x, sptlines[i].y,
- 0.0, 0.0,
- sptlines[i].h, sptlines[i].s);
-
- }
-
- fprintf(fh,"%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
- -999.0,-999.0,-999.0,-999.0,-999.0,-999.0);
- fclose(fh);
-}
-
-/* write a dummy 1x1 pixel image file for mosflm. Without post refinement,
- mosflm will ignore this, but it must be present.*/
-void write_img(struct image *image)
-{
- FILE *fh;
- char filename[1024];
- unsigned short int * intimage;
-
- intimage = malloc(sizeof(unsigned short int));
- intimage[0] = 1;
-
- snprintf(filename, 1023, "xfel-%i_001.img", image->id);
-
- fh = fopen(filename, "w");
- if ( !fh ) {
- ERROR("Couldn't open temporary file xfel.spt\n");
- return;
- }
-
- fprintf(fh,"{\nHEADER_BYTES=512;\n");
- fprintf(fh,"BYTE_ORDER=little_endian;\n");
- fprintf(fh,"TYPE=unsigned_short;\n");
- fprintf(fh,"DIM=2;\n");
- fprintf(fh,"SIZE1=1;\n");
- fprintf(fh,"SIZE2=1;\n");
- fprintf(fh,"}\n");
- while ( ftell(fh) < 512 ) { fprintf(fh," "); };
- fwrite(intimage,sizeof(unsigned short int),1,fh);
- fclose(fh);
-}
-
void map_all_peaks(struct image *image)
{
int i;
@@ -292,13 +146,10 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
return;
case INDEXING_DIRAX :
STATUS("Running DirAx...\n");
- write_drx(image);
run_dirax(image);
break;
case INDEXING_MOSFLM :
STATUS("Running MOSFLM...\n");
- write_spt(image);
- write_img(image); /* dummy image */
run_mosflm(image, cell);
break;
case INDEXING_TEMPLATE :
diff --git a/src/indexamajig.c b/src/indexamajig.c
index de50383c..83eee4d1 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -53,7 +53,6 @@ struct static_index_args
UnitCell *cell;
int config_cmfilter;
int config_noisefilter;
- int config_writedrx;
int config_dumpfound;
int config_verbose;
int config_alternate;
@@ -161,10 +160,6 @@ static void show_help(const char *s)
" as \"simulated.h5\". You can TRY to combine this\n"
" with \"-j <n>\" with n greater than 1, but it's\n"
" not a good idea.\n"
-" --write-drx Write 'xfel.drx' for visualisation of reciprocal\n"
-" space. Implied by any indexing method other than\n"
-" 'none'. Beware: the units in this file are\n"
-" reciprocal Angstroms.\n"
" --dump-peaks Write the results of the peak search to stdout.\n"
" The intensities in this list are from the\n"
" centroid/integration procedure.\n"
@@ -318,7 +313,6 @@ static void process_image(void *pp, int cookie)
UnitCell *cell = pargs->static_args.cell;
int config_cmfilter = pargs->static_args.config_cmfilter;
int config_noisefilter = pargs->static_args.config_noisefilter;
- int config_writedrx = pargs->static_args.config_writedrx;
int config_dumpfound = pargs->static_args.config_dumpfound;
int config_verbose = pargs->static_args.config_verbose;
int config_alternate = pargs->static_args.config_alternate;
@@ -397,17 +391,12 @@ static void process_image(void *pp, int cookie)
pargs->static_args.output_mutex);
}
- /* Not indexing nor writing xfel.drx?
- * Then there's nothing left to do. */
- if ( (!config_writedrx) && (indm == INDEXING_NONE) ) {
- goto done;
- }
+ /* Not indexing? Then there's nothing left to do. */
+ if ( indm == NULL ) goto done;
/* Calculate orientation matrix (by magic) */
- if ( config_writedrx || (indm != INDEXING_NONE) ) {
- index_pattern(&image, cell, indm, pargs->static_args.cellr,
- config_verbose, pargs->static_args.ipriv);
- }
+ index_pattern(&image, cell, indm, pargs->static_args.cellr,
+ config_verbose, pargs->static_args.ipriv);
/* No cell at this point? Then we're done. */
if ( image.indexed_cell == NULL ) goto done;
@@ -527,7 +516,6 @@ int main(int argc, char *argv[])
int config_noindex = 0;
int config_dumpfound = 0;
int config_nearbragg = 0;
- int config_writedrx = 0;
int config_simulate = 0;
int config_cmfilter = 0;
int config_noisefilter = 0;
@@ -582,7 +570,6 @@ int main(int argc, char *argv[])
{"peaks", 1, NULL, 2},
{"cell-reduction", 1, NULL, 3},
{"near-bragg", 0, &config_nearbragg, 1},
- {"write-drx", 0, &config_writedrx, 1},
{"indexing", 1, NULL, 'z'},
{"geometry", 1, NULL, 'g'},
{"beam", 1, NULL, 'b'},
@@ -886,7 +873,6 @@ int main(int argc, char *argv[])
qargs.static_args.cell = cell;
qargs.static_args.config_cmfilter = config_cmfilter;
qargs.static_args.config_noisefilter = config_noisefilter;
- qargs.static_args.config_writedrx = config_writedrx;
qargs.static_args.config_dumpfound = config_dumpfound;
qargs.static_args.config_verbose = config_verbose;
qargs.static_args.config_alternate = config_alternate;
diff --git a/src/mosflm.c b/src/mosflm.c
index 40780451..974b82c5 100644
--- a/src/mosflm.c
+++ b/src/mosflm.c
@@ -102,6 +102,124 @@ static int read_newmat(const char * filename, struct image *image)
}
+/* write .spt file for mosflm */
+/* need to sort mosflm peaks by intensity... */
+struct sptline {
+ double x; /* x coordinate of peak */
+ double y; /* y coordinate of peak */
+ double h; /* height of peak */
+ double s; /* sigma of peak */
+};
+
+
+static int compare_vals(const void *ap, const void *bp)
+{
+ const struct sptline a = *(struct sptline *)ap;
+ const struct sptline b = *(struct sptline *)bp;
+
+ if ( a.h < b.h ) return 1;
+ if ( a.h > b.h ) return -1;
+ return 0;
+}
+
+
+static void write_spt(struct image *image)
+{
+ FILE *fh;
+ int i;
+ char filename[1024];
+ double fclen=67.8; /* fake camera length in mm */
+ double fpix=0.075; /* fake pixel size in mm */
+ double pix;
+ double height=100;
+ double sigma=1;
+ int nPeaks = image_feature_count(image->features);
+
+ snprintf(filename, 1023, "xfel-%i.spt", image->id);
+
+ fh = fopen(filename, "w");
+ if ( !fh ) {
+ ERROR("Couldn't open temporary file xfel.spt\n");
+ return;
+ }
+
+ fprintf(fh, "%10d %10d %10.8f %10.6f %10.6f\n", 1, 1, fpix, 1.0, 0.0);
+ fprintf(fh, "%10d %10d\n", 1, 1);
+ fprintf(fh, "%10.5f %10.5f\n", 0.0, 0.0);
+
+ struct sptline *sptlines;
+ sptlines = malloc(sizeof(struct sptline)*nPeaks);
+
+ for ( i=0; i<nPeaks; i++ ) {
+
+ struct imagefeature *f;
+
+ f = image_get_feature(image->features, i);
+ if ( f == NULL ) continue;
+
+ struct panel *pan;
+ pan = find_panel(image->det,f->x,f->y);
+ if ( pan == NULL ) continue;
+
+ pix = 1000/pan->res; /* pixel size in mm */
+ height = f->intensity;
+
+ sptlines[i].x = (f->y - pan->cy)*pix*fclen/pan->clen/1000;
+ sptlines[i].y = -(f->x - pan->cx)*pix*fclen/pan->clen/1000;
+ sptlines[i].h = height;
+ sptlines[i].s = sigma;
+
+ }
+
+ qsort(sptlines, nPeaks, sizeof(struct sptline), compare_vals);
+
+ for ( i=0; i<nPeaks; i++ ) {
+
+ fprintf(fh, "%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
+ sptlines[i].x, sptlines[i].y,
+ 0.0, 0.0,
+ sptlines[i].h, sptlines[i].s);
+
+ }
+
+ fprintf(fh,"%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
+ -999.0,-999.0,-999.0,-999.0,-999.0,-999.0);
+ fclose(fh);
+}
+
+
+/* Write a dummy 1x1 pixel image file for mosflm. Without post refinement,
+ * mosflm will ignore this, but it must be present. */
+static void write_img(struct image *image)
+{
+ FILE *fh;
+ char filename[1024];
+ unsigned short int * intimage;
+
+ intimage = malloc(sizeof(unsigned short int));
+ intimage[0] = 1;
+
+ snprintf(filename, 1023, "xfel-%i_001.img", image->id);
+
+ fh = fopen(filename, "w");
+ if ( !fh ) {
+ ERROR("Couldn't open temporary file xfel.spt\n");
+ return;
+ }
+
+ fprintf(fh,"{\nHEADER_BYTES=512;\n");
+ fprintf(fh,"BYTE_ORDER=little_endian;\n");
+ fprintf(fh,"TYPE=unsigned_short;\n");
+ fprintf(fh,"DIM=2;\n");
+ fprintf(fh,"SIZE1=1;\n");
+ fprintf(fh,"SIZE2=1;\n");
+ fprintf(fh,"}\n");
+ while ( ftell(fh) < 512 ) { fprintf(fh," "); };
+ fwrite(intimage,sizeof(unsigned short int),1,fh);
+ fclose(fh);
+}
+
+
void run_mosflm(struct image *image, UnitCell *cell)
{
int i,j;
@@ -113,6 +231,9 @@ void run_mosflm(struct image *image, UnitCell *cell)
char newmatfile[128];
int fail;
+ write_spt(image);
+ write_img(image); /* dummy image */
+
wavelength = image->lambda*1e10;
cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
sg = cell_get_spacegroup(cell);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-08 16:02:49 +0000