Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Oleksii Turkot
CrystFEL
Commits
58149b59
Commit
58149b59
authored
Sep 07, 2010
by
Thomas White
Browse files
indexamajig: Reformat --help
parent
ccfe7416
Changes
1
Hide whitespace changes
Inline
Side-by-side
src/indexamajig.c
View file @
58149b59
...
...
@@ -100,8 +100,9 @@ static void show_help(const char *s)
" dirax : invoke DirAx
\n
"
" template : index by template matching
\n
"
" -g. --geometry=<file> Get detector geometry from file.
\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
"
"
\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
"
" When pixels with fractional indices within 0.1 of
\n
"
" integer values (the Bragg condition) are found,
\n
"
...
...
@@ -118,13 +119,6 @@ static void show_help(const char *s)
" 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
"
" --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
"
" 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
"
" --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
"
...
...
@@ -132,21 +126,32 @@ static void show_help(const char *s)
" --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
"
" model, just proceed with the one generated by the
\n
"
" auto-indexing procedure.
\n
"
" --unpolarized Don't correct for the polarisation of the X-rays.
\n
"
" --check-sanity Check that indexed locations approximately correspond
\n
"
" with detected peaks.
\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
"
" 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
"
" included in the HDF5 file.
\n
"
" --no-sa Don't correct for the differing solid angles of
\n
"
" the pixels.
\n
"
"
\n\n
Options for greater performance or verbosity:
\n\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
"
"
\n\n
Control of model and data input:
\n\n
"
"
\n
"
"
\n
Control of model and data input:
\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
"
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment