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Oleksii Turkot
CrystFEL
Commits
385cd10c
Commit
385cd10c
authored
Mar 09, 2012
by
Thomas White
Browse files
Formatting
parent
2d37463b
Changes
1
Hide whitespace changes
Inline
Side-by-side
src/indexamajig.c
View file @
385cd10c
...
...
@@ -600,9 +600,6 @@ int main(int argc, char *argv[])
{
"input"
,
1
,
NULL
,
'i'
},
{
"output"
,
1
,
NULL
,
'o'
},
{
"no-index"
,
0
,
&
config_noindex
,
1
},
{
"peaks"
,
1
,
NULL
,
2
},
{
"cell-reduction"
,
1
,
NULL
,
3
},
{
"tolerance"
,
1
,
NULL
,
13
},
{
"indexing"
,
1
,
NULL
,
'z'
},
{
"geometry"
,
1
,
NULL
,
'g'
},
{
"beam"
,
1
,
NULL
,
'b'
},
...
...
@@ -614,67 +611,72 @@ int main(int argc, char *argv[])
{
"no-sat-corr"
,
0
,
&
config_satcorr
,
0
},
{
"sat-corr"
,
0
,
&
config_satcorr
,
1
},
/* Compat */
{
"threshold"
,
1
,
NULL
,
't'
},
{
"min-gradient"
,
1
,
NULL
,
4
},
{
"min-snr"
,
1
,
NULL
,
11
},
{
"min-integration-snr"
,
1
,
NULL
,
12
},
{
"no-check-prefix"
,
0
,
&
config_checkprefix
,
0
},
{
"no-closer-peak"
,
0
,
&
config_closer
,
0
},
{
"insane"
,
0
,
&
config_insane
,
1
},
{
"image"
,
1
,
NULL
,
'e'
},
{
"basename"
,
0
,
&
config_basename
,
1
},
{
"bg-sub"
,
0
,
&
config_bgsub
,
1
},
/* Compat */
{
"no-bg-sub"
,
0
,
&
config_bgsub
,
0
},
{
"peaks"
,
1
,
NULL
,
2
},
{
"cell-reduction"
,
1
,
NULL
,
3
},
{
"min-gradient"
,
1
,
NULL
,
4
},
{
"record"
,
1
,
NULL
,
5
},
{
"cpus"
,
1
,
NULL
,
6
},
{
"cpugroup"
,
1
,
NULL
,
7
},
{
"cpuoffset"
,
1
,
NULL
,
8
},
{
"bg-sub"
,
0
,
&
config_bgsub
,
1
},
/* Compat */
{
"no-bg-sub"
,
0
,
&
config_bgsub
,
0
},
{
"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
},
{
0
,
0
,
NULL
,
0
}
};
/* Short options */
while
((
c
=
getopt_long
(
argc
,
argv
,
"hi:wp:j:x:g:t:o:b:e:"
,
longopts
,
NULL
))
!=
-
1
)
{
longopts
,
NULL
))
!=
-
1
)
{
switch
(
c
)
{
case
'h'
:
case
'h'
:
show_help
(
argv
[
0
]);
return
0
;
case
'i'
:
case
'i'
:
filename
=
strdup
(
optarg
);
break
;
case
'o'
:
case
'o'
:
outfile
=
strdup
(
optarg
);
break
;
case
'z'
:
case
'z'
:
indm_str
=
strdup
(
optarg
);
break
;
case
'p'
:
case
'p'
:
pdb
=
strdup
(
optarg
);
break
;
case
'x'
:
case
'x'
:
prefix
=
strdup
(
optarg
);
break
;
case
'j'
:
case
'j'
:
nthreads
=
atoi
(
optarg
);
break
;
case
'g'
:
case
'g'
:
geometry
=
strdup
(
optarg
);
break
;
case
't'
:
case
't'
:
threshold
=
strtof
(
optarg
,
NULL
);
break
;
case
'b'
:
case
'b'
:
beam
=
get_beam_parameters
(
optarg
);
if
(
beam
==
NULL
)
{
ERROR
(
"Failed to load beam parameters"
...
...
@@ -683,40 +685,28 @@ int main(int argc, char *argv[])
}
break
;
case
2
:
speaks
=
strdup
(
optarg
);
case
'e'
:
element
=
strdup
(
optarg
);
break
;
case
3
:
s
cellr
=
strdup
(
optarg
);
case
2
:
s
peaks
=
strdup
(
optarg
);
break
;
case
1
3
:
tole
r
=
strdup
(
optarg
);
case
3
:
scell
r
=
strdup
(
optarg
);
break
;
case
4
:
case
4
:
min_gradient
=
strtof
(
optarg
,
NULL
);
break
;
case
11
:
min_snr
=
strtof
(
optarg
,
NULL
);
break
;
case
12
:
min_int_snr
=
strtof
(
optarg
,
NULL
);
break
;
case
'e'
:
element
=
strdup
(
optarg
);
break
;
case
5
:
case
5
:
stream_flags
=
parse_stream_flags
(
optarg
);
if
(
stream_flags
<
0
)
return
1
;
break
;
case
6
:
case
6
:
cpu_num
=
strtol
(
optarg
,
&
endptr
,
10
);
if
(
!
(
(
optarg
[
0
]
!=
'\0'
)
&&
(
endptr
[
0
]
==
'\0'
)
)
)
{
ERROR
(
"Invalid number of CPUs ('%s')
\n
"
,
...
...
@@ -725,7 +715,7 @@ int main(int argc, char *argv[])
}
break
;
case
7
:
case
7
:
cpu_groupsize
=
strtol
(
optarg
,
&
endptr
,
10
);
if
(
!
(
(
optarg
[
0
]
!=
'\0'
)
&&
(
endptr
[
0
]
==
'\0'
)
)
)
{
ERROR
(
"Invalid CPU group size ('%s')
\n
"
,
...
...
@@ -739,7 +729,7 @@ int main(int argc, char *argv[])
}
break
;
case
8
:
case
8
:
cpu_offset
=
strtol
(
optarg
,
&
endptr
,
10
);
if
(
!
(
(
optarg
[
0
]
!=
'\0'
)
&&
(
endptr
[
0
]
==
'\0'
)
)
)
{
ERROR
(
"Invalid CPU offset ('%s')
\n
"
,
...
...
@@ -752,19 +742,32 @@ int main(int argc, char *argv[])
}
break
;
case
9
:
case
9
:
hdf5_peak_path
=
strdup
(
optarg
);
break
;
case
10
:
case
10
:
add_copy_hdf5_field
(
copyme
,
optarg
);
break
;
case
0
:
case
11
:
min_snr
=
strtof
(
optarg
,
NULL
);
break
;
case
12
:
min_int_snr
=
strtof
(
optarg
,
NULL
);
break
;
default
:
case
13
:
toler
=
strdup
(
optarg
);
break
;
case
0
:
break
;
default
:
return
1
;
}
}
...
...
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