indexamajig: More fussing over --help

src/indexamajig.c

@@ -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"
 "\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"
+"     --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\n"
@@ -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"
 "\nFor 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"
-"\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"
+"     --threshold=<n>      Only accept peaks above <n> ADU.  Default: 800.\n"
 "\n"
-"\nControl of model and data input:\n\n"
+"\nIf you used --simulate, you may also want:\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"
+"\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"
 );
 }