| |
|
src_id | source image shared memory id> |
src_ext | source image file extension (default none) |
cor_id | shared memory id of corrected image |
cor_ext | corrected img. file extension (default none) |
dark_id | dark image shared memory
id |
dark_file | dark image file
name |
dark_const | value
subtract constant dark image value (default: no dark image subtraction
done) |
dark_ext | dark image file
extension (default none) |
do_dark | 0|1 if 0, suppress dark image
correction (default 1) |
save_dark | 0|1|2 save dark image memory
to file (default 2) |
inp_const | add
input image constant (default 0). |
inp_exp | apply
exponent to input image (default 1). |
inp_factor | value
multiply with input image factor (default 1). |
flood_id | flood field image
shared memory id |
flood_file | flood field image
file name (default: no floodfield used) |
bckg_id | scattering background
image shared memory id |
bckg_file | scattering background
image file name (default: no scattering background used) |
bckg_const | additive scattering
constant(default 0). |
bckg_fact | constant scattering
factor (default 1). |
header_id | shared memory id for
data header (default: not used) |
pass | 0|1 pass input file header to
output (default 0) |
header_min | minimum header length
for output file(default 0) |
header_ext | extension for header
output file (default none) |
distortion_file | file(default "spatial.dat") |
xfile | file (x distortion
read from edf file) |
yfile | file (y distortion
read from edf file)
|
xoutfile | file (x
distortion saved to edf file)
|
youtfile | file(y
distortion saved to edf file)
|
active_radius | value
(values outside will not be corrected)
|
psize_distort | 0|1|2 take image params
from distortion file 0: none, 1: pix, 2: pix, cen, dis, proj, rot (default 0)
|
cen_1 | xxx if set, defines Center_1
header value
|
cen_2 | xxx if set, defines Center_2
header value
|
i0 | xxx if set, defines Intensity0 header
value
|
i1 | xxx if set, defines Intensity1 header
value
|
off_1 | = xxx if set, defines Offset_1
header value
|
off_2 | xxx if set, defines Offset_2
header value
|
pix_1 | xxx if set, defines PSize_1 header
value
|
pix_2 | xxx if set, defines PSize_2 header
value
|
bis_1 | xxx if set, defines BSize_1 header
value
|
bis_2 | xxx if set, defines BSize_2 header
value
|
dis | xxx if set, defines SampleDistance
header value
|
ori | xxx if set, defines
RasterOrientation header value
|
tit | xxx if set, defines Title header
value
|
wvl | xxx if set, defines WaveLength
header value
|
pro | "Saxs"|"Waxs" projection type of
image (default Saxs)
|
rot_1 | angle (rad) for detector
rotation plane 1> (default 0.)
|
rot_2 | angle (rad) for detector
rotation plane 2> (default 0.)
|
rot_3 | angle (rad) for detector
rotation plane 3> (default 0.)
|
base_name | name(default
"image")
|
verbose | -1|0|1|2 message printing level
(default 1)
|
simul | 0|1 (default 0)
|
do_distortion | 0|1|2|3 distortion
correction (default 1)
(0: none, 1: after dark, 2: after flat, 3: after norm)
|
flat_distortion | 0|1 normalize to flat
image (default 0)
|
norm_int | 0|1 intensity normalization
(default 0 = no)
|
norm_factor | intensity
normalization factor> (default 1.)
|
overflow= | xxx (default 65535)
|
dummy | value (default 0.
= not set)
|
inp_min | (default
0. = not set)
|
inp_max | (default
0. = not set)
|
bin_1 | factor for
x-binning (default 1 = no binning)
|
bin_2 | value factor for
y-binning (default 1 = no binning)
|
azim_int | 0|1 azimuthal integration
(default 0 = no)
|
azim_pass | 0|1 pass full header to
azimuth. integr. (def. 1 = yes)
|
azim_id | shared memory id of
integrated image> (default -1)
|
azim_ext | azimuth image file
extension> (default none)
|
azim_r0 | minimum
integration radius (default 0.)
|
azim_r_num | radial
output size (default 0)
|
azim_a0 | 1st
integration start angle (default 0.)
|
azim_a1 | 2nd
integration start angle (default: not used)
|
azim_da | angular
integration interval (default 1.)
|
azim_a_num | angular
output size (default 0)
|
ave_id | shared memory id of
averaged image> (default -1)
|
ave_scf | constant averaging scale
factor> (default 1.)
|
mask_file | azimuthal integration
mask file name>
(default: not used)
|
clear | 0|1 reset all command options
(default 0)
|
dvo | Data value offset ; use it with type (see below).
Available for linux64 bits only. SPDVERSION must be set to new.
|
type | Values are : Unsigned16 or FloatIEEE32. Available for linux64 bits only. SPDVERSION must be set to new.
|
| |
active_radius | defines a circular
"active area" in the image. No spatial distortion corrections are done for pixels outside this area
(default: 0., i.e. no "active area" used)
|
ave_id |
shared memory segment identifier for the azimuthal averaged
output image (default: -1, i.e. no identifier specified)
|
ave_scf | scale factor for the averaged values of the azimuthal image (default: 1.)
|
azim_a0 |
start angle for 1st azimuthal integration (default: 0.0)
|
azim_a1 |
start angle for 2nd azimuthal integration (default: not used)
|
azim_a_num | angular dimension of output buffer for azimuthal integration(default: 0)
|
azim_da |
angle interval for azimuthal integration (default: 1.0)
|
azim_ext |
filename extension for the azimuthal integrated output image
file (default: empty string, i.e. no output file written).
The base of the filename is in "base_name"
|
azim_id |
shared memory segment identifier for the azimuthal integrated
output image (default: -1, i.e. no identifier specified)
The two options azim_ext and azim_id specify the output for
the azimuthal integrated image. This can be:
- azim_ext: a output image file;
- azim_id: a shared memory segment.
The default values are that no output for the azimuthal
integrated image will be produced (no shared memory segment
and no filename extension specified).
|
azim_int |
if set, integrate the image along the azimuth angle
(default: 0, i.e. no integration)
|
azim_pass |
if set, all header values of the corrected image are passed
to the azimuthal integrated image (default: 1, i.e. set)
|
azim_r0 |
minimum radius for azimuthal integration (default: 0.0)
|
azim_r_num | radial
dimension of output buffer for azimuthal integration
(default: 0)
|
base_name |
contains the "file name base" from which all other file names
are derived (default: "image")
|
bckg_const | constant
to be added to the value of all scattering
background image pixels (default: 0.)
|
bckg_fact |
multiplication factor for the value of all scattering
background image pixels (default: 1.)
|
bckg_const | and bckg_fact are applied to the scattering
background image as given in the following formula:
scattering bckg_fact + bckg_const
|
bckg_file |
name of the file with the scattering background image
(default: no file, i.e. NULL pointer)
|
bckg_id |
shared memory segment identifier for the scattering
background image (default: -1, i.e. no identifier specified)
The two options bckg_id and bckg_file specify the input
source for the scattering background image. This can be:
- bckg_id: a shared memory segment;
- bckg_file: a scattering background image file.
Default is no scattering background correction (no shared
memory segment nor scattering background file defined).
Note that only one scattering background image input source
can be specified; if more than one is specified in the input
arguments, then only the last one will be taken into account.
|
bin_1 |
number of pixels to bin together in x-direction (default: 1,
i.e. no binning to be performed)
|
bin_2 |
number of pixels to bin together in y-direction (default: 1,
i.e. no binning to be performed)
|
bis_1 |
if set, defines value for "BSize_1" header keyword.
|
bis_2 |
if set, defines value for "BSize_2" header keyword.
|
bkg_const |
old name of "dark_const" parameter (do not use)
|
bkg_file |
old name of "dark_file" parameter (do not use)
|
bkg_id |
old name of "dark_id" parameter (do not use)
|
cen_1 |
if set, defines value for "Center_1" header keyword.
|
cen_2 |
if set, defines value for "Center_2" header keyword.
|
clear |
reset all previously given options to their default values
(default: 0, i.e. the previously given options are not reset)
|
cor_ext |
filename extension for the corrected output image file
(default: empty string, i.e. no output file written). The
base of the filename is in "base_name"
|
cor_file |
name of the output file for the corrected image (default: no
file, i.e. NULL pointer). This option is obsolete and should
be replaced by "cor_ext" with "base_name".
|
cor_id |
shared memory segment identifier for the corrected output
image (default: -1, i.e. no identifier specified)
The two options cor_id and cor_file specify the output for
the corrected image. This can be:
- cor_id: a shared memory segment;
- cor_file: a output image file.
Default is no output location (no shared memory segment nor
output file defined).
|
dark_const | : constant
for overall dark image subtraction (default: 0.)
For more details, see "dark_id" below.
|
dark_ext |
filename extension for the file with the dark (background)
image. This is mainly used to save an online dark image to a
file. (default: empty string, i.e. no output file written).
The base of the filename is in "base_name"
|
dark_file |
name of the file with the dark image (default: no file, i.e. NULL pointer)
If dark_file contains a string value with a leading and a
trailing square bracket (e.g. dark_file = [char_string]), then
the name of the dark image file is to be read from the
keyword "char_string" in header of the source image file.
Add option verbose = 2 to get dark file name while processing.
|
dark_id |
shared memory segment identifier for the dark image
(default: -1, i.e. no identifier specified)
The three options dark_const, dark_id and dark_file specify
the input source for the dark image correction. This can be:
- dark_id: a shared memory segment;
- dark_file: a dark image file;
- dark_const: an overall constant to be applied to all pixels
of the image data.
Default is no shared memory segment nor dark image file
defined and the overall dark image constant 0. That also
implies that by default there is no dark image correction
performed.
If a source for the dark image correction is specified, then
normally the dark image correction is performed. However,
this can be prevented by setting "do_dark = 0" (see below).
Note that in principle only either a shared memory segment or
an image file can be specified; if both are specified in the
input arguments, then the one specified last will be used.
The overall constant can be specified in addition to either
of the two other options.
|
distortion_file | name of the file with the distortion
correction parameters
(default: "spatial.dat"). Note: if "xfile" and "yfile" are
specified, "distortion_file" is ignored.
|
dis |
if set, defines value for "SampleDistance" header keyword.
|
do_dark |
if set to 0, no dark image correction is performed, even if
there is a source for it (dark image buffer, file or constant
- see "dark_id", "dark_file" and "dark_const" above). The
purpose of this is to allow a saving of the online dark image
buffer for a later processing.
If set to 1 (default), then the dark image correction is
performed if there is a source for it.
|
do_distortion | controls the distortion
correction:
0: no distortion correction is performed
>0: distortion correction is performed as follows:
1: after the dark image subtraction (default)
2: after the flatfield division
3: after the normalization.
|
dummy |
value that is used to ignore a pixel. Pixels with this value
are not processed in the analysis (default: 0., i.e. not set)
|
flat_after | flag
indicating whether the floodfield correction is to be
done before or after the distortion correction. If the flag
is set, then floodfield will be done after distortion
(default: 1, i.e. set). This is obsolete, use "do_distortion"
instead.
|
flat_distortion | if set, the target image is normalized to a
flat image
(default: 0, i.e. not set)
|
flood_file | name of
the file with the floodfield image (default: no file,
i.e. NULL pointer)
|
flood_id |
shared memory segment identifier for the floodfield image
(default: -1, i.e. no identifier specified)
The two options flood_id and flood_file specify the input
source for the floodfile image. This can be:
- flood_id: a shared memory segment;
- flood_file: a floodfile image file.
Default is no floodfield correction (no shared memory segment
nor floodfield file defined).
Note that only one floodfield image input source can
be specified; if more than one is specified in the input
arguments, then only the last one will be taken into account.
|
from_ext |
filename extension for the input image file (default: ".edf")
|
header_ext | filename
extension for the file with the header of the input
source image. This is mainly used to save the online header
to a file when the input source image itself is not saved.
(default: empty string, i.e. no header file written). The
base of the filename is in "base_name"
|
header_id |
shared memory segment identifier where additional header
information for the output image is available (default: -1,
i.e. no identifier specified)
|
header_min | set
minimum header length for output files (default: 0, i.e.
take default value from EDF routines)
|
i0 |
if set, defines value for "Intensity0" header keyword.
|
i1 |
if set, defines value for "Intensity1" header keyword.
|
inp_const |
constant to be added to the value of all source image pixels
(default: 0.)
|
inp_exp |
exponent applied to the value of all source and dark image
pixels (default: 1.)
|
inp_factor |
multiplication factor for the value of all source image
pixels (default: 1.)
|
inp_const | , inp_exp and inp_factor are applied to the source
and dark image as given in the following formula:
corrected = (source ^ inp_exp - dark ^ inp_exp)
inp_factor + inp_const
|
inp_max |
maximum allowed value for a pixel. Pixels with bigger values
are not processed in the analysis (default: 0., i.e. not set)
|
inp_min |
minimum allowed value for a pixel. Pixels with smaller values
are not processed in the analysis (default: 0., i.e. not set)
|
mask_file |
name of the file with a mask image of pixels to ignore for
azimuthal integration (default: no file, i.e. NULL pointer)
|
norm_factor |
multiplication factor for the value of all scattering
intensity normalized image pixels (default: 1.). Used only if
"norm_int" is set
|
norm_int |
if set, normalize image to absolute scattering intensities
(default: 0, i.e. no normalization)
|
overflow |
pixel value used to mark an overflow (default: 0xffff)
|
off_1 |
if set, defines value for "Offset_1" header keyword.
|
off_2 |
if set, defines value for "Offset_2" header keyword.
|
ori |
if set, defines value for "RasterOrientation" header keyword.
|
pass |
if set, all header values of the input source file are read
and written to the corrected output file (default: 0 not set)
|
pix_1 |
if set, defines value for "PSize_1" header keyword.
|
pix_2 |
if set, defines value for "PSize_2" header keyword.
|
pro |
string defining projection type to calculate the scattering
vectors for the azimuthal integration (default: "Saxs"):
"Saxs" normal SAXS images
"Waxs" images that have been projected to the Ewald sphere
|
psize_distort | if set, certain image
parameters for the corrected image are
taken from the distortion files (default: 0, i.e. not set).
If psize_distort = 1, only the pixel size for the corrected
image is taken from the distortion files.
If psize_distort = 2, the pixel size, center, offset, sample
distance, binning size, projection and rotation for the
corrected image are taken from the distortion file.
If psize_distort is set and any of the input arguments
pix_1, pix_2, cen_1, cen_2, off_1, off_2, bis_1, bis_2, dis,
pro, rot_1, rot_2 or rot_3, ori, wvl are set as well, then the value
given in the input arguments has precedence over the value in
the distortion files.
|
rot_1 |
angle (in radian) for the detector rotation in plane 1
|
rot_2 |
angle (in radian) for the detector rotation in plane 2
|
rot_3 |
angle (in radian) for the detector rotation in plane 3
(default: 0. for all 3 angles)
|
save_dark |
if set, the SPEC shared memory segment for the dark current
( = background) image is saved to a file with extension
".dark".
Possible values: 0 = not set,
1 = save always,
2 = save if new image (default).
Saving will only happen if the input source image is also
saved (i.e. "src_ext" is not empty)
|
scat_const | old name
of "bckg_const" parameter (do not use)
|
scat_fact |
old name of "bckg_fact" parameter (do not use)
|
scat_file |
old name of "bckg_file" parameter (do not use)
|
scat_id |
old name of "bckg_id" parameter (do not use)
|
simul_id |
if set, the routine only produces a simulated grid with
Gaussian peaks and puts it to the output destination; no
image processing is done (default: 0, i.e. not set)
|
src_ext |
filename extension for the file with the input source image.
This is mainly used to save an online input data to a file.
(default: empty string, i.e. no output file written). The
base of the filename is in "base_name"
|
src_id |
shared memory segment identifier for the input image data
(default: -1, i.e. no identifier specified)
Note that if there is both a shared memory segment and
filename(s) specified for the input image data, only the
filename(s) will be used.
|
tit |
if set, defines string value for "Title" header keyword.
|
to_ext |
filename extension for the corrected image file (default:
".cor"). This is obsolete, use "cor_ext" instead
|
verbose |
controls the level of message printing from the program:
-1: nothing is printed;
0: print only the message with types ERROR or FATAL;
1: (default) print all messages except those of type DMSG
(debug);
2: print all messages including debugging messages.
|
wvl |
if set, defines value for "WaveLength" header keyword.
|
xfile |
name of the input file with the values of the distortion
corrections for the x coordinate (default: no file, i.e. NULL
pointer). Needs to be specified simultaneously with "yfile".
See also remark at "distortion_file" above.
|
xoutfile |
name of the output file for the values of the distortion
corrections for the x coordinate (default: no file, i.e. NULL
pointer)
|
yfile |
name of the input file with the values of the distortion
corrections for the y coordinate (default: no file, i.e. NULL
pointer). Needs to be specified simultaneously with "xfile".
See also remark at "distortion_file" above.
|
youtfile |
name of the output file for the values of the distortion
corrections for the y coordinate (default: no file, i.e. NULL
pointer)
|
dvo and type |
These options are available for linux64 for instance.
Use these options to write output file as float or as unsigned integer, and you need to export SPDVERSION=new.
To write output files with 16-bit unsigned integers and to offset the data values by 10 the call is
spd dvo=-10 type=Unsigned16 dark_file=gc14_0_0034bccddark gc14_0_0034bccdraw
dvo must be added later to the stored data values to retrieve the correct values. The dvo value is written as an integer value after the header key DataValueOffset (default 0). The back-conversion is done automatically when the data are read by spd or one of the saxs-programs. Attention, DataValueOffset must always be added, independent of the data type.
Currently, only Unsigned16 and FloatIEEE32 are available as type-values.
|