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Oleksii Turkot
CrystFEL
Commits
483e3d58
Commit
483e3d58
authored
Nov 28, 2012
by
Thomas White
Browse files
indexamajig: Add --integrate-saturated
parent
1d7ab964
Changes
5
Hide whitespace changes
Inline
Side-by-side
libcrystfel/src/peaks.c
View file @
483e3d58
...
...
@@ -293,10 +293,9 @@ static int integrate_peak(struct image *image, int cfs, int css,
val
=
image
->
data
[
idx
];
/*
Veto pea
k if
it
contains saturation in bg region */
/*
Chec
k if
peak
contains saturation in bg region */
if
(
use_max_adu
&&
(
val
>
p
->
max_adu
)
)
{
if
(
saturated
!=
NULL
)
*
saturated
=
1
;
return
1
;
}
bg_tot
+=
val
;
...
...
@@ -353,10 +352,9 @@ static int integrate_peak(struct image *image, int cfs, int css,
val
=
image
->
data
[
idx
]
-
bg_mean
;
/*
Veto pea
k if
it
contains saturation */
/*
Chec
k if
peak
contains saturation */
if
(
use_max_adu
&&
(
val
>
p
->
max_adu
)
)
{
if
(
saturated
!=
NULL
)
*
saturated
=
1
;
return
1
;
}
pk_counts
++
;
...
...
@@ -697,7 +695,8 @@ static struct integr_ind *sort_reflections(RefList *list, UnitCell *cell,
/* Integrate the list of predicted reflections in "image" */
void
integrate_reflections
(
struct
image
*
image
,
int
use_closer
,
int
bgsub
,
double
min_snr
,
double
ir_inn
,
double
ir_mid
,
double
ir_out
)
double
ir_inn
,
double
ir_mid
,
double
ir_out
,
int
integrate_saturated
)
{
struct
integr_ind
*
il
;
int
n
,
i
;
...
...
@@ -794,7 +793,10 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
&
intensity
,
&
sigma
,
ir_inn
,
ir_mid
,
ir_out
,
1
,
bgMasks
[
pnum
],
&
saturated
);
if
(
saturated
)
image
->
n_saturated
++
;
if
(
saturated
)
{
image
->
n_saturated
++
;
if
(
!
integrate_saturated
)
r
=
1
;
}
/* I/sigma(I) cutoff */
if
(
intensity
/
sigma
<
min_snr
)
r
=
1
;
...
...
libcrystfel/src/peaks.h
View file @
483e3d58
...
...
@@ -43,7 +43,8 @@ extern void search_peaks(struct image *image, float threshold,
extern
void
integrate_reflections
(
struct
image
*
image
,
int
use_closer
,
int
bgsub
,
double
min_snr
,
double
ir_inn
,
double
ir_mid
,
double
ir_out
);
double
ir_inn
,
double
ir_mid
,
double
ir_out
,
int
integrate_saturated
);
extern
double
peak_lattice_agreement
(
struct
image
*
image
,
UnitCell
*
cell
,
double
*
pst
);
...
...
src/im-sandbox.c
View file @
483e3d58
...
...
@@ -328,7 +328,8 @@ static void process_image(const struct index_args *iargs,
iargs
->
min_int_snr
,
iargs
->
ir_inn
,
iargs
->
ir_mid
,
iargs
->
ir_out
);
iargs
->
ir_out
,
iargs
->
integrate_saturated
);
}
}
else
{
image
.
reflections
=
NULL
;
...
...
src/im-sandbox.h
View file @
483e3d58
...
...
@@ -66,6 +66,7 @@ struct index_args
double
ir_mid
;
double
ir_out
;
struct
copy_hdf5_field
*
copyme
;
int
integrate_saturated
;
};
...
...
src/indexamajig.c
View file @
483e3d58
...
...
@@ -161,6 +161,8 @@ static void show_help(const char *s)
" least 10%% of the located peaks.
\n
"
" --no-bg-sub Don't subtract local background estimates from
\n
"
" integrated intensities.
\n
"
" --integrate-saturated During the final integration stage, don't reject
\n
"
" peaks which contain pixels above max_adu.
\n
"
);
}
...
...
@@ -242,6 +244,7 @@ int main(int argc, char *argv[])
float
ir_inn
=
4
.
0
;
float
ir_mid
=
5
.
0
;
float
ir_out
=
7
.
0
;
int
integrate_saturated
=
0
;
copyme
=
new_copy_hdf5_field_list
();
if
(
copyme
==
NULL
)
{
...
...
@@ -288,6 +291,7 @@ int main(int argc, char *argv[])
{
"min-integration-snr"
,
1
,
NULL
,
12
},
{
"tolerance"
,
1
,
NULL
,
13
},
{
"int-radius"
,
1
,
NULL
,
14
},
{
"integrate-saturated"
,
0
,
&
integrate_saturated
,
1
},
{
0
,
0
,
NULL
,
0
}
};
...
...
@@ -634,6 +638,7 @@ int main(int argc, char *argv[])
iargs
.
ir_inn
=
ir_inn
;
iargs
.
ir_mid
=
ir_mid
;
iargs
.
ir_out
=
ir_out
;
iargs
.
integrate_saturated
=
integrate_saturated
;
create_sandbox
(
&
iargs
,
n_proc
,
prefix
,
config_basename
,
fh
,
use_this_one_instead
,
ofh
);
...
...
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