diff options
| -rw-r--r-- | doc/man/indexamajig.1 | 2 | ||||
| -rw-r--r-- | libcrystfel/src/integration.c | 21 | ||||
| -rw-r--r-- | libcrystfel/src/integration.h | 3 | ||||
| -rw-r--r-- | src/indexamajig.c | 4 |
4 files changed, 17 insertions, 13 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index 351a2e45..25bc1cd6 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -330,7 +330,7 @@ Do not record integrated reflections in the stream. The resulting output won't .PD 0 .IP \fB--int-diag=\fIcondition\fR\fR .PD -Show detailed information about reflection integration when \fIcondition\fR is met. The \fIcondition\fR can be \fBall\fR, \fBnone\fR, a set of Miller indices separated by commas, or \fBrandom\fR. The default is \fB--int-diag=none\fR, and \fBrandom\fR means to show information about a random 1% of the peaks. +Show detailed information about reflection integration when \fIcondition\fR is met. The \fIcondition\fR can be \fBall\fR, \fBnone\fR, a set of Miller indices separated by commas, \fBrandom\fR or \fBnegative\fR. \fBrandom\fR means to show information about a random 1% of the peaks. \fBnegative\fR means to show peaks with intensities which are negative my more than 3 sigma. The default is \fB--int-diag=none\fR. .SH BUGS ReAx indexing is experimental. It works very nicely for some people, and crashes for others. In a future version, it will be improved and fully supported. diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c index 63495c43..3746d3a8 100644 --- a/libcrystfel/src/integration.c +++ b/libcrystfel/src/integration.c @@ -223,8 +223,6 @@ struct peak_box int rp; /* Reference profile number */ Reflection *refl; - - int verbose; }; @@ -598,7 +596,6 @@ static struct peak_box *add_box(struct intcontext *ic) ic->boxes[idx].J = 0.0; ic->boxes[idx].rp = -1; ic->boxes[idx].refl = NULL; - ic->boxes[idx].verbose = 0; ic->boxes[idx].bgm = gsl_matrix_calloc(3, 3); if ( ic->boxes[idx].bgm == NULL ) { @@ -1295,6 +1292,13 @@ static int get_int_diag(struct intcontext *ic, Reflection *refl) return random() < RAND_MAX/100; } + if ( ic->int_diag == INTDIAG_NEGATIVE ) { + double i, sigi; + i = get_intensity(refl); + sigi = get_esd_intensity(refl); + return i < -3.0*sigi; + } + if ( ic->int_diag == INTDIAG_INDICES ) { signed int h, k, l; get_indices(refl, &h, &k, &l); @@ -1349,7 +1353,6 @@ static void integrate_prof2d(IntegrationMethod meth, Crystal *cr, refl = next_refl(refl, iter) ) { double pfs, pss; - signed int h, k, l; struct peak_box *bx; int pn; struct panel *p; @@ -1384,9 +1387,6 @@ static void integrate_prof2d(IntegrationMethod meth, Crystal *cr, bx->p = p; bx->pn = pn; - get_indices(refl, &h, &k, &l); - bx->verbose = get_int_diag(&ic, refl); - /* Which reference profile? */ bx->rp = 0;//bx->pn; @@ -1462,7 +1462,7 @@ static void integrate_prof2d(IntegrationMethod meth, Crystal *cr, pss += bx->offs_ss; set_detector_pos(bx->refl, 0.0, pfs, pss); - if ( bx->verbose ) show_peak_box(&ic, bx); + if ( get_int_diag(&ic, refl) ) show_peak_box(&ic, bx); } @@ -1520,8 +1520,6 @@ static void integrate_rings_once(Reflection *refl, struct image *image, bx->css = css; bx->p = p; bx->pn = pn; - get_indices(refl, &h, &k, &l); - bx->verbose = get_int_diag(ic, refl); if ( ic->meth & INTEGRATION_CENTER ) { r = center_and_check_box(ic, bx, &saturated); @@ -1579,6 +1577,7 @@ static void integrate_rings_once(Reflection *refl, struct image *image, set_esd_intensity(refl, sigma); set_redundancy(refl, 1); + get_indices(refl, &h, &k, &l); one_over_d = resolution(cell, h, k, l); if ( one_over_d > ic->limit ) ic->limit = one_over_d; @@ -1587,7 +1586,7 @@ static void integrate_rings_once(Reflection *refl, struct image *image, pss += bx->offs_ss; set_detector_pos(refl, 0.0, pfs, pss); - if ( bx->verbose ) show_peak_box(ic, bx); + if ( get_int_diag(ic, refl) ) show_peak_box(ic, bx); } diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h index 68ce91ec..38cb8163 100644 --- a/libcrystfel/src/integration.h +++ b/libcrystfel/src/integration.h @@ -39,7 +39,8 @@ typedef enum { INTDIAG_NONE, INTDIAG_RANDOM, INTDIAG_ALL, - INTDIAG_INDICES + INTDIAG_INDICES, + INTDIAG_NEGATIVE } IntDiag; diff --git a/src/indexamajig.c b/src/indexamajig.c index c450fd83..b769d303 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -548,6 +548,10 @@ int main(int argc, char *argv[]) iargs.int_diag = INTDIAG_ALL; } + if ( strcmp(int_diag, "negative") == 0 ) { + iargs.int_diag = INTDIAG_NEGATIVE; + } + r = sscanf(int_diag, "%i,%i,%i", &h, &k, &l); if ( r == 3 ) { iargs.int_diag = INTDIAG_INDICES; |