indexamajig: Reformat --help

src/indexamajig.c

@@ -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\nWith just the above options, this program does not do much of practical "
-"use.\nYou should also enable some of the following:\n\n"
+"\n"
+"\nWith just the above options, this program does not do much of practical use."
+"\nYou 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"
+"\nFor 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\nOptions for greater performance or verbosity:\n\n"
+"\n"
+"\nOptions 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\nControl of model and data input:\n\n"
+"\n"
+"\nControl 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"