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Oleksii Turkot
CrystFEL
Commits
d21f2eb6
Commit
d21f2eb6
authored
Mar 06, 2012
by
Thomas White
Browse files
Don't include 1/d in reflection lists, because it's pointless
parent
3710defb
Changes
9
Hide whitespace changes
Inline
Side-by-side
libcrystfel/src/reflist-utils.c
View file @
d21f2eb6
...
...
@@ -152,23 +152,20 @@ int find_equiv_in_list(RefList *list, signed int h, signed int k,
* write_reflections_to_file:
* @fh: File handle to write to
* @list: The reflection list to write
* @cell: Unit cell to use for generating 1/d values, or NULL.
*
* This function writes the contents of @list to @fh, using @cell to generate
* 1/d values to ease later processing. If @cell is NULL, 1/d values will not
* be included ('-' will be written in their place).
* This function writes the contents of @list to @fh,
*
* Reflections which have a redundancy of zero will not be written.
*
* The resulting list can be read back with read_reflections_from_file().
**/
void
write_reflections_to_file
(
FILE
*
fh
,
RefList
*
list
,
UnitCell
*
cell
)
void
write_reflections_to_file
(
FILE
*
fh
,
RefList
*
list
)
{
Reflection
*
refl
;
RefListIterator
*
iter
;
fprintf
(
fh
,
" h k l I phase sigma(I) "
"
1/d(nm^-1)
counts fs/px ss/px
\n
"
);
" counts fs/px ss/px
\n
"
);
for
(
refl
=
first_refl
(
list
,
&
iter
);
refl
!=
NULL
;
...
...
@@ -193,13 +190,6 @@ void write_reflections_to_file(FILE *fh, RefList *list, UnitCell *cell)
/* Reflections with redundancy = 0 are not written */
if
(
red
==
0
)
continue
;
if
(
cell
!=
NULL
)
{
s
=
2
.
0
*
resolution
(
cell
,
h
,
k
,
l
);
snprintf
(
res
,
16
,
"%10.2f"
,
s
/
1e9
);
}
else
{
strcpy
(
res
,
" -"
);
}
if
(
have_phase
)
{
snprintf
(
phs
,
16
,
"%8.2f"
,
rad2deg
(
ph
));
}
else
{
...
...
@@ -207,9 +197,8 @@ void write_reflections_to_file(FILE *fh, RefList *list, UnitCell *cell)
}
fprintf
(
fh
,
"%3i %3i %3i %10.2f %s %10.2f %s %7i %6.1f %6.1f
\n
"
,
h
,
k
,
l
,
intensity
,
phs
,
esd_i
,
res
,
red
,
fs
,
ss
);
"%3i %3i %3i %10.2f %s %10.2f %7i %6.1f %6.1f
\n
"
,
h
,
k
,
l
,
intensity
,
phs
,
esd_i
,
red
,
fs
,
ss
);
}
}
...
...
@@ -219,11 +208,8 @@ void write_reflections_to_file(FILE *fh, RefList *list, UnitCell *cell)
* write_reflist:
* @filename: Filename
* @list: The reflection list to write
* @cell: Unit cell to use for generating 1/d values, or NULL.
*
* This function writes the contents of @list to @file, using @cell to generate
* 1/d values to ease later processing. If @cell is NULL, 1/d values will not
* be included ('-' will be written in their place).
* This function writes the contents of @list to @file,
*
* Reflections which have a redundancy of zero will not be written.
*
...
...
@@ -235,7 +221,7 @@ void write_reflections_to_file(FILE *fh, RefList *list, UnitCell *cell)
*
* Returns: zero on success, non-zero on failure.
**/
int
write_reflist
(
const
char
*
filename
,
RefList
*
list
,
UnitCell
*
cell
)
int
write_reflist
(
const
char
*
filename
,
RefList
*
list
)
{
FILE
*
fh
;
...
...
@@ -250,7 +236,7 @@ int write_reflist(const char *filename, RefList *list, UnitCell *cell)
return
1
;
}
write_reflections_to_file
(
fh
,
list
,
cell
);
write_reflections_to_file
(
fh
,
list
);
fprintf
(
fh
,
REFLECTION_END_MARKER
"
\n
"
);
fclose
(
fh
);
...
...
@@ -284,10 +270,9 @@ RefList *read_reflections_from_file(FILE *fh)
if
(
strcmp
(
line
,
REFLECTION_END_MARKER
)
==
0
)
return
out
;
r
=
sscanf
(
line
,
"%i %i %i %f %s %f %s %i %f %f"
,
&
h
,
&
k
,
&
l
,
&
intensity
,
phs
,
&
sigma
,
ress
,
&
cts
,
&
fs
,
&
ss
);
if
(
(
r
!=
10
)
&&
(
!
first
)
)
{
r
=
sscanf
(
line
,
"%i %i %i %f %s %f %i %f %f"
,
&
h
,
&
k
,
&
l
,
&
intensity
,
phs
,
&
sigma
,
&
cts
,
&
fs
,
&
ss
);
if
(
(
r
!=
9
)
&&
(
!
first
)
)
{
reflist_free
(
out
);
return
NULL
;
}
...
...
libcrystfel/src/reflist-utils.h
View file @
d21f2eb6
...
...
@@ -38,9 +38,9 @@
#define REFLECTION_END_MARKER "End of reflections"
extern
void
write_reflections_to_file
(
FILE
*
fh
,
RefList
*
list
,
UnitCell
*
cell
);
extern
void
write_reflections_to_file
(
FILE
*
fh
,
RefList
*
list
);
extern
int
write_reflist
(
const
char
*
filename
,
RefList
*
list
,
UnitCell
*
cell
);
extern
int
write_reflist
(
const
char
*
filename
,
RefList
*
list
);
extern
RefList
*
read_reflections_from_file
(
FILE
*
fh
);
...
...
libcrystfel/src/stream.c
View file @
d21f2eb6
...
...
@@ -285,8 +285,7 @@ void write_chunk(FILE *ofh, struct image *i, struct hdfile *hdfile, int f)
if
(
i
->
reflections
!=
NULL
)
{
fprintf
(
ofh
,
REFLECTION_START_MARKER
"
\n
"
);
write_reflections_to_file
(
ofh
,
i
->
reflections
,
i
->
indexed_cell
);
write_reflections_to_file
(
ofh
,
i
->
reflections
);
fprintf
(
ofh
,
REFLECTION_END_MARKER
"
\n
"
);
}
else
{
...
...
scripts/gen-sfs
View file @
d21f2eb6
...
...
@@ -50,8 +50,7 @@ use strict;
my
\$
line;
open(FILE, "
${
PDB
}
-temp.hkl");
printf(" h k l I phase sigma(I) 1/d(nm^-1) ".
"counts fs/px ss/px
\\
n");
printf(" h k l I phase sigma(I) counts fs/px ss/px
\\
n");
while (
\$
line = <FILE> ) {
...
...
@@ -63,9 +62,8 @@ while ( \$line = <FILE> ) {
my
\$
intensity =
\$
4*
\$
4; # Square to convert F->I
my
\$
phase =
\$
5;
printf("%3i %3i %3i %10.2f %8.2f %10.2f %s %7i %6.1f %6.1f
\n
",
\$
h,
\$
k,
\$
l,
\$
intensity,
\$
phase, 0.0,
" -", 1, 0.0, 0.0);
printf("%3i %3i %3i %10.2f %8.2f %10.2f %7i %6.1f %6.1f
\n
",
\$
h,
\$
k,
\$
l,
\$
intensity,
\$
phase, 0.0, 1, 0.0, 0.0);
} else {
printf(STDERR "Couldn't understand line '%s'
\n
",
\$
line);
...
...
scripts/gen-sfs-ano
View file @
d21f2eb6
...
...
@@ -48,8 +48,7 @@ use strict;
my
\$
line;
open(FILE, "
${
PDB
}
-temp1.hkl");
printf(" h k l I phase sigma(I) 1/d(nm^-1) ".
"counts fs/px ss/px
\\
n");
printf(" h k l I phase sigma(I) counts fs/px ss/px
\\
n");
while (
\$
line = <FILE> ) {
...
...
@@ -62,10 +61,10 @@ while ( \$line = <FILE> ) {
my
\$
iminus =
\$
5*
\$
5;
printf("%3i %3i %3i %10.2f - 0.0 %s %7i %6.1f %6.1f
\n
",
\$
h,
\$
k,
\$
l,
\$
iplus,
" -",
1, 0.0, 0.0);
\$
h,
\$
k,
\$
l,
\$
iplus, 1, 0.0, 0.0);
printf("%3i %3i %3i %10.2f - 0.0 %s %7i %6.1f %6.1f
\n
",
-
\$
h, -
\$
k, -
\$
l,
\$
iminus,
" -",
1, 0.0, 0.0);
-
\$
h, -
\$
k, -
\$
l,
\$
iminus, 1, 0.0, 0.0);
} else {
printf(STDERR "Couldn't understand line '%s'
\n
",
\$
line);
...
...
src/get_hkl.c
View file @
d21f2eb6
...
...
@@ -77,8 +77,6 @@ static void show_help(const char *s)
"
\n
"
"Don't forget to specify the output filename:
\n
"
" -o, --output=<filename> Output filename (default: stdout).
\n
"
" -p, --pdb=<filename> Use unit cell parameters from this PDB file to
\n
"
" generate resolution values in the output file.
\n
"
);
}
...
...
@@ -364,7 +362,6 @@ int main(int argc, char *argv[])
char
*
beamfile
=
NULL
;
struct
beam_params
*
beam
=
NULL
;
RefList
*
input
;
UnitCell
*
cell
=
NULL
;
/* Long options */
const
struct
option
longopts
[]
=
{
...
...
@@ -379,7 +376,6 @@ int main(int argc, char *argv[])
{
"intensities"
,
1
,
NULL
,
'i'
},
{
"multiplicity"
,
0
,
&
config_multi
,
1
},
{
"beam"
,
1
,
NULL
,
'b'
},
{
"pdb"
,
1
,
NULL
,
'p'
},
{
"trim-centrics"
,
0
,
&
config_trimc
,
1
},
{
0
,
0
,
NULL
,
0
}
};
...
...
@@ -421,14 +417,6 @@ int main(int argc, char *argv[])
beamfile
=
strdup
(
optarg
);
break
;
case
'p'
:
cell
=
load_cell_from_pdb
(
optarg
);
if
(
cell
==
NULL
)
{
ERROR
(
"Failed to get cell from '%s'
\n
"
,
optarg
);
return
1
;
}
break
;
case
0
:
break
;
...
...
@@ -453,11 +441,6 @@ int main(int argc, char *argv[])
}
}
if
(
cell
==
NULL
)
{
ERROR
(
"You need to give a PDB file with the unit cell.
\n
"
);
return
1
;
}
if
(
holo_str
!=
NULL
)
{
holo
=
get_pointgroup
(
holo_str
);
free
(
holo_str
);
...
...
@@ -583,7 +566,7 @@ int main(int argc, char *argv[])
}
write_reflist
(
output
,
input
,
cell
);
write_reflist
(
output
,
input
);
reflist_free
(
input
);
...
...
src/partial_sim.c
View file @
d21f2eb6
...
...
@@ -525,7 +525,7 @@ int main(int argc, char *argv[])
if
(
random_intensities
)
{
STATUS
(
"Writing full intensities to %s
\n
"
,
save_file
);
write_reflist
(
save_file
,
full
,
cell
);
write_reflist
(
save_file
,
full
);
}
if
(
phist_file
!=
NULL
)
{
...
...
src/partialator.c
View file @
d21f2eb6
...
...
@@ -556,7 +556,7 @@ int main(int argc, char *argv[])
STATUS
(
"%i images could not be refined on the last cycle.
\n
"
,
n_dud
);
/* Output results */
write_reflist
(
outfile
,
full
,
images
[
0
].
indexed_cell
);
write_reflist
(
outfile
,
full
);
/* Clean up */
for
(
i
=
0
;
i
<
n_usable_patterns
;
i
++
)
{
...
...
src/process_hkl.c
View file @
d21f2eb6
...
...
@@ -617,7 +617,7 @@ int main(int argc, char *argv[])
hist_nbins
);
}
write_reflist
(
output
,
model
,
NULL
);
write_reflist
(
output
,
model
);
fclose
(
fh
);
...
...
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