diff options
Diffstat (limited to 'src/indexamajig.c')
| -rw-r--r-- | src/indexamajig.c | 53 |
1 files changed, 23 insertions, 30 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index 5d57d336..8b0f5206 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -3,13 +3,13 @@ * * Index patterns, output hkl+intensity etc. * - * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, - * a research centre of the Helmholtz Association. + * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. * Copyright © 2012 Richard Kirian * Copyright © 2012 Lorenzo Galli * * Authors: - * 2010-2012 Thomas White <taw@physics.org> + * 2010-2013 Thomas White <taw@physics.org> * 2011 Richard Kirian * 2012 Lorenzo Galli * 2012 Chunhong Yoon @@ -81,11 +81,7 @@ static void show_help(const char *s) " Default: indexamajig.stream\n" "\n" " --indexing=<methods> Use 'methods' for indexing. Provide one or more\n" -" methods separated by commas. Choose from:\n" -" none : no indexing (default)\n" -" dirax : invoke DirAx\n" -" mosflm : invoke MOSFLM (DPS)\n" -" reax : DPS algorithm with known unit cell\n" +" methods separated by commas. See below.\n" " -g. --geometry=<file> Get detector geometry from file.\n" " -b, --beam=<file> Get beam parameters from file (provides nominal\n" " wavelength value if no per-shot value is found in\n" @@ -101,27 +97,7 @@ static void show_help(const char *s) " --hdf5-peaks=<p> Find peaks table in HDF5 file here.\n" " Default: /processing/hitfinder/peakinfo\n" "\n\n" -"You can control what information is included in the output stream using\n" -"' --record=<flag1>,<flag2>,<flag3>' and so on. Possible flags are:\n\n" -" integrated Include a list of reflection intensities, produced by\n" -" integrating around predicted peak locations.\n" -"\n" -" peaks Include peak locations and intensities from the peak\n" -" search.\n" -"\n" -" peaksifindexed As 'peaks', but only if the pattern could be indexed.\n" -"\n" -" peaksifnotindexed As 'peaks', but only if the pattern could NOT be indexed.\n" -"\n\n" -"The default is '--record=integrated'.\n" -"\n\n" "For more control over the process, you might need:\n\n" -" --cell-reduction=<m> Use <m> as the cell reduction method. Choose from:\n" -" none : no matching, just use the raw cell.\n" -" reduce : full cell reduction.\n" -" compare : match by at most changing the order of\n" -" the indices.\n" -" compare_ab : compare 'a' and 'b' lengths only.\n" " --tolerance=<tol> Set the tolerances for cell reduction.\n" " Default: 5,5,5,1.5.\n" " --filter-cm Perform common-mode noise subtraction on images\n" @@ -157,8 +133,6 @@ static void show_help(const char *s) " --no-check-prefix Don't attempt to correct the --prefix.\n" " --closer-peak Don't integrate from the location of a nearby peak\n" " instead of the predicted spot. Don't use.\n" -" --insane Don't check that the reduced cell accounts for at\n" -" least 10%% of the located peaks.\n" " --no-bg-sub Don't subtract local background estimates from\n" " integrated intensities.\n" " --use-saturated During the initial peak search, don't reject\n" @@ -170,6 +144,25 @@ static void show_help(const char *s) " --integrate-found Skip the spot prediction step, and just integrate\n" " the intensities of the spots found by the initial\n" " peak search.\n" +"\n" +"Indexing methods:\n\n" +" dirax Invoke DirAx, check linear combinations of the resulting cell\n" +" axes for agreement with your cell, and then check that the cell\n" +" accounts for at least half of the peaks from the peak search.\n" +" mosflm As 'dirax', but invoke MOSFLM instead.\n" +" reax Run the DPS algorithm, looking for the axes of your cell.\n" +"\n" +"You can add the following to the above indexing methods:\n" +" -raw Do not check the resulting unit cell\n" +" (Only for 'dirax' and 'mosflm').\n" +" -axes Check permutations of the axes for correspondence with your cell,\n" +" but do not check linear combinations.\n" +" (Only for 'dirax' and 'mosflm').\n" +" -bad Do not check that the cell accounts for any of the peaks.\n" +"\n" +"The default indexing method is 'none', which means no indexing will be done.\n" +"\n" +"Examples: 'dirax,mosflm,reax', 'dirax-raw,mosflm-raw', 'dirax-raw-bad'\n" ); } |