diff options
| -rw-r--r-- | libcrystfel/src/integration.c | 20 | ||||
| -rw-r--r-- | libcrystfel/src/integration.h | 1 | ||||
| -rw-r--r-- | src/indexamajig.c | 8 | ||||
| -rw-r--r-- | src/process_image.c | 2 | ||||
| -rw-r--r-- | src/process_image.h | 1 |
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; |