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authorThomas White <taw@physics.org>2013-05-30 10:17:22 -0700
committerThomas White <taw@physics.org>2013-05-30 10:17:22 -0700
commit06d18d4fe84ea1c28ba6e0a40b230a454f1852f0 (patch)
tree8c5b72c09534c6997e14da7c71a4933d6559d52a /libcrystfel/src
parentb6c871b70cae2fd6359b8066bdfade29f62d7fe5 (diff)
indexamajig: Get rid of --min-integration-snr
This functionality belongs in process_hkl.
Diffstat (limited to 'libcrystfel/src')
-rw-r--r--libcrystfel/src/integration.c20
-rw-r--r--libcrystfel/src/integration.h1
2 files changed, 6 insertions, 15 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);