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Oleksii Turkot
CrystFEL
Commits
6e463f8b
Commit
6e463f8b
authored
Sep 07, 2010
by
Thomas White
Browse files
indexamajig: More fussing over --help
parent
fbb24f22
Changes
1
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src/indexamajig.c
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6e463f8b
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@@ -91,20 +91,22 @@ static void show_help(const char *s)
printf
(
"Process and index FEL diffraction images.
\n
"
"
\n
"
"
-h, --help Display this help message.
\n
"
" -h, --help
Display this help message.
\n
"
"
\n
"
"
-i, --input=<filename> Specify file containing list of images to process.
\n
"
" -i, --input=<filename>
Specify file containing list of images to process.
\n
"
" '-' means stdin, which is the default.
\n
"
"
\n
"
"
--indexing=<method> Use 'method' for indexing. Choose from:
\n
"
" --indexing=<method>
Use 'method' for indexing. Choose from:
\n
"
" none : no indexing
\n
"
" dirax : invoke DirAx
\n
"
" template : index by template matching
\n
"
" -g. --geometry=<file> Get detector geometry from file.
\n
"
" -g. --geometry=<file> Get detector geometry from file.
\n
"
" -p, --pdb=<file> PDB file from which to get the unit cell to match.
\n
"
" -x, --prefix=<p> Prefix filenames from input file with <p>.
\n
"
"
\n
"
"
\n
With just the above options, this program does not do much of practical use."
"
\n
You should also enable some of the following:
\n\n
"
"
--near-bragg Output a list of reflection intensities to stdout.
\n
"
" --near-bragg
Output a list of reflection intensities to stdout.
\n
"
" When pixels with fractional indices within 0.1 of
\n
"
" integer values (the Bragg condition) are found,
\n
"
" the integral of pixels within a ten pixel radius
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"
...
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@@ -115,49 +117,47 @@ static void show_help(const char *s)
" was located by the initial peak search close to
\n
"
" the
\"
near Bragg
\"
location, its coordinates will
\n
"
" be taken as the centre instead.
\n
"
"
--simulate Simulate the diffraction pattern using the indexed
\n
"
" --simulate
Simulate the diffraction pattern using the indexed
\n
"
" unit cell. The simulated pattern will be saved
\n
"
" as
\"
simulated.h5
\"
. You can TRY to combine this
\n
"
" with
\"
-j <n>
\"
with n greater than 1, but it's
\n
"
" not a good idea.
\n
"
"
--write-drx Write 'xfel.drx' for visualisation of reciprocal
\n
"
" --write-drx
Write 'xfel.drx' for visualisation of reciprocal
\n
"
" space. Implied by any indexing method other than
\n
"
" 'none'. Beware: the units in this file are
\n
"
" reciprocal Angstroms.
\n
"
"
--dump-peaks Write the results of the peak search to stdout.
\n
"
" --dump-peaks
Write the results of the peak search to stdout.
\n
"
" The intensities in this list are from the
\n
"
" centroid/integration procedure.
\n
"
"
\n
"
"
\n
For more control over the process, you might need:
\n\n
"
"
--no-match Don't attempt to match the indexed cell to the
\n
"
" --no-match
Don't attempt to match the indexed cell to the
\n
"
" model, just proceed with the one generated by the
\n
"
" auto-indexing procedure.
\n
"
"
--check-sanity Check that indexed locations approximately correspond
\n
"
" --check-sanity
Check that indexed locations approximately correspond
\n
"
" with detected peaks.
\n
"
"
--filter-cm Perform common-mode noise subtraction on images
\n
"
" --filter-cm
Perform common-mode noise subtraction on images
\n
"
" before proceeding. Intensities will be extracted
\n
"
" from the image as it is after this processing.
\n
"
"
--filter-noise Apply an aggressive noise filter which sets all
\n
"
" --filter-noise
Apply an aggressive noise filter which sets all
\n
"
" pixels in each 3x3 region to zero if any of them
\n
"
" have negative values. Intensity measurement will
\n
"
" be performed on the image as it was before this.
\n
"
"
--unpolarized Don't correct for the polarisation of the X-rays.
\n
"
"
--sat-corr Correct values of saturated peaks using a table
\n
"
" --unpolarized
Don't correct for the polarisation of the X-rays.
\n
"
" --sat-corr
Correct values of saturated peaks using a table
\n
"
" included in the HDF5 file.
\n
"
"
--no-sa Don't correct for the differing solid angles of
\n
"
" --no-sa
Don't correct for the differing solid angles of
\n
"
" the pixels.
\n
"
" --threshold=<n> Only accept peaks above <n> ADU. Default: 800.
\n
"
"
\n
"
"
\n
Options for greater performance or verbosity:
\n\n
"
" --verbose Be verbose about indexing.
\n
"
" --gpu Use the GPU to speed up the simulation.
\n
"
" -j <n> Run <n> analyses in parallel. Default 1.
\n
"
" --threshold=<n> Only accept peaks above <n> ADU. Default: 800.
\n
"
"
\n
"
"
\n
Control of model and data inpu
t:
\n\n
"
"
\n
If you used --simulate, you may also wan
t:
\n\n
"
" --intensities=<file> Specify file containing reflection intensities
\n
"
" to use when simulating.
\n
"
" -p, --pdb=<file> PDB file from which to get the unit cell to match.
\n
"
" -x, --prefix=<p> Prefix filenames from input file with 'p'.
\n
"
"
\n
"
"
\n
Options for greater performance or verbosity:
\n\n
"
" --verbose Be verbose about indexing.
\n
"
" --gpu Use the GPU to speed up the simulation.
\n
"
" -j <n> Run <n> analyses in parallel. Default 1.
\n
"
);
}
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