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-rw-r--r--libcrystfel/src/integration.c20
-rw-r--r--libcrystfel/src/integration.h1
-rw-r--r--src/indexamajig.c8
-rw-r--r--src/process_image.c2
-rw-r--r--src/process_image.h1
5 files changed, 6 insertions, 26 deletions
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 315c8a33..e874d5c6 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1394,7 +1394,7 @@ static void estimate_resolution(RefList *reflections, Crystal *cr,
static void integrate_prof2d(IntegrationMethod meth, Crystal *cr,
- struct image *image, double min_snr,
+ struct image *image,
double ir_inn, double ir_mid, double ir_out)
{
RefList *reflections;
@@ -1498,7 +1498,7 @@ static void integrate_box(struct intcontext *ic, struct peak_box *bx,
static void integrate_rings(IntegrationMethod meth, Crystal *cr,
- struct image *image, double min_snr,
+ struct image *image,
double ir_inn, double ir_mid, double ir_out)
{
RefList *list;
@@ -1542,7 +1542,7 @@ static void integrate_rings(IntegrationMethod meth, Crystal *cr,
* in overall data block */
int cfs, css; /* Corner coordinates */
double intensity;
- double sigma, snr;
+ double sigma;
int saturated;
double one_over_d;
int r;
@@ -1597,14 +1597,7 @@ static void integrate_rings(IntegrationMethod meth, Crystal *cr,
integrate_box(&ic, bx, &intensity, &sigma);
- /* I/sigma(I) cutoff
- * Rejects reflections below --min-integration-snr, or if the
- * SNR is clearly silly. Silly indicates that the intensity
- * was zero. */
- snr = fabs(intensity)/sigma;
- if ( (isnan(snr) || (snr < min_snr)) ) continue;
-
- /* Record intensity and set redundancy to 1 on success */
+ /* Record intensity and set redundancy to 1 */
set_intensity(refl, intensity);
set_esd_intensity(refl, sigma);
set_redundancy(refl, 1);
@@ -1623,7 +1616,6 @@ static void integrate_rings(IntegrationMethod meth, Crystal *cr,
void integrate_all(struct image *image, IntegrationMethod meth,
- int use_closer, double min_snr,
double ir_inn, double ir_mid, double ir_out,
int integrate_saturated)
{
@@ -1638,12 +1630,12 @@ void integrate_all(struct image *image, IntegrationMethod meth,
case INTEGRATION_RINGS :
integrate_rings(meth, image->crystals[i], image,
- min_snr, ir_inn, ir_mid, ir_out);
+ ir_inn, ir_mid, ir_out);
return;
case INTEGRATION_PROF2D :
integrate_prof2d(meth, image->crystals[i], image,
- min_snr, ir_inn, ir_mid, ir_out);
+ ir_inn, ir_mid, ir_out);
return;
default :
diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h
index 913297fa..8edcb91f 100644
--- a/libcrystfel/src/integration.h
+++ b/libcrystfel/src/integration.h
@@ -68,7 +68,6 @@ typedef enum {
extern IntegrationMethod integration_method(const char *t, int *err);
extern void integrate_all(struct image *image, IntegrationMethod meth,
- int use_closer, double min_snr,
double ir_inn, double ir_mid, double ir_out,
int integrate_saturated);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 84a372cb..dc244866 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -121,8 +121,6 @@ static void show_help(const char *s)
" Default: 100,000.\n"
" --min-snr=<n> Minimum signal-to-noise ratio for peaks.\n"
" Default: 5.\n"
-" --min-integration-snr=<n> Minimum signal-to-noise ratio for peaks\n"
-" during integration. Default: -infinity.\n"
" --int-radius=<r> Set the integration radii. Default: 4,5,7.\n"
"-e, --image=<element> Use this image from the HDF5 file.\n"
" Example: /data/data0.\n"
@@ -191,7 +189,6 @@ int main(int argc, char *argv[])
iargs.threshold = 800.0;
iargs.min_gradient = 100000.0;
iargs.min_snr = 5.0;
- iargs.min_int_snr = -INFINITY;
iargs.det = NULL;
iargs.peaks = PEAK_ZAEF;
iargs.beam = NULL;
@@ -255,7 +252,6 @@ int main(int argc, char *argv[])
{"hdf5-peaks", 1, NULL, 9},
{"copy-hdf5-field", 1, NULL, 10},
{"min-snr", 1, NULL, 11},
- {"min-integration-snr",1, NULL, 12},
{"tolerance", 1, NULL, 13},
{"int-radius", 1, NULL, 14},
{"median-filter", 1, NULL, 15},
@@ -368,10 +364,6 @@ int main(int argc, char *argv[])
iargs.min_snr = strtof(optarg, NULL);
break;
- case 12 :
- iargs.min_int_snr = strtof(optarg, NULL);
- break;
-
case 13 :
toler = strdup(optarg);
break;
diff --git a/src/process_image.c b/src/process_image.c
index f432f8eb..6bddae50 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -174,8 +174,6 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
/* Integrate all the crystals at once - need all the crystals so that
* overlaps can be detected. */
integrate_all(&image, iargs->int_meth,
- iargs->closer,
- iargs->min_int_snr,
iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
iargs->integrate_saturated);
diff --git a/src/process_image.h b/src/process_image.h
index 03041562..ac197927 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -55,7 +55,6 @@ struct index_args
float threshold;
float min_gradient;
float min_snr;
- double min_int_snr;
struct detector *det;
IndexingMethod *indm;
IndexingPrivate **ipriv;